New research center in Madagascar opens today

Mireya Mayor and Patricia Wright

Mireya Mayor and Patricia Wright

Today, renowned primatologist Dr. Patricia Wright, and the Prime Minister and the Minister of Higher Education of Madagascar will unveil and open NamanaBe Hall (which translates as Friendship Hall) – a new research, arts and community outreach building in Ranomafana, Madagascar.

The 1,440 square meter building is as ‘green’ as can be – built out of local materials (locally-sourced granite, brick, and eucalyptus flooring), with work by local artisans and craftsmen, it has gardens and solar panels on the roof, gray water recycling, solar hot water, natural cooling, and enhanced use of daylight. Apart from it being sustainable, it is also hoped to provide an example to local (and global) populations on how to employ “green” techniques in building design and construction.

Centre Valbio by Dede Randrianarista

Centre Valbio by Dede Randrianarista

NamanaBe Hall is the newest addition to Stony Brook University’s research center – Centre ValBio – built in 2003 to help indigenous people and the international community with conservation in Madagascar. It is a center of research in biodiversity, and also a community center for arts, environmental outreach, conservation education, and economic development of the region of the Ranomafana National Park. With the addition of NamanaBe Hall, Centre ValBio will become the largest, most modern, and most important research hub in Madagascar.

Construction of Namanabe Hall by Noel Rowe.

Construction of Namanabe Hall by Noel Rowe.

The new hall will have a conference room for 80 people, a computer training lab and library, an audiovisual office, dormitories, and a modern, sophisticated scientific laboratory equipped to study biodiversity (genetics, hormones and parasites) and infectious diseases. The whole campus will be equipped with high speed internet. In one word – perfect setting for a ScienceOnlineMadagascar 😉

During the opening ceremony, the founder of the Centre ValBio, Dr. Patricia Wright will receive a Commander National Medal of Honor.

Pat Wright with the villagers. Photo by Mitch Irwin.

Pat Wright with the villagers. Photo by Mitch Irwin.

A world-renowned primatologist, Dr. Wright is a McArthur Genius Fellow and will now be the first recepient of all three major medals that Malagasy government can give. The first is the Chevalier Medal of Honor. To get this high honor one must have done exceptional deeds in one’s field. If one accomplishes a second exceptional deed or work one can receive the Officier Medal eight to ten years after the Chevaliar. The third medal, the Commander, can only be awarded five years after the Officier and denotes a person who has done honorable and exceptional work throughout their careers.

The Medals of Honor are awarded to person’s of high achievement, who are creative and have contributed exceptionally to the country of Madagascar. Dr. Wright will now be the first recipient of all three, for her 26 years of conservation work to advance Malagasy biodiversity. Grammy-award winning Malagasy brand Tarika Be (voted by Time Magazine as one of the “10 Best Bands in the World” alongside U2 and Radiohead) will perform at the inauguration.

Thanks to Mireya Mayor and Stony Brook University for heads-up and information.

 

ScienceOnline2012 – interview with Trevor Owens

Every year I ask some of the attendees of the ScienceOnline conferences to tell me (and my readers) more about themselves, their careers, current projects and their views on the use of the Web in science, science education or science communication. So now we continue with the participants of ScienceOnline2012. See all the interviews in this series here.

Today my guest is Trevor Owens (blog, Twitter).

Welcome to A Blog Around The Clock. Would you, please, tell my readers a little bit more about yourself? Where are you coming from (both geographically and philosophically)? What is your background? Any scientific education?

I’m a digital archivist at the Library of Congress, I teach a very open and public digital history graduate seminar at American university and I am finishing my doctoral work in social science research methods in the College of Education and Human development at George Mason University.

I come to science from a historical bent; my BA is in the history of science. More specifically, I started out working on the history of science education. I wrote my thesis on the history of children’s books about Einstein and Curie. More recently I have been doing research on science communication and public understanding of science in places like gaming communities, or in discussions of statues on Yelp.

What aspect of science communication and/or particular use of the Web in science interests you the most?

Coming from a history/library/archives background I’m fascinated in the transformation going on in science communication are changing about the nature and discourse of the scientific enterprise and public understanding of science. When historians look back on late 20th and early 21st century science they will undoubtedly be interested in understanding how the web has facilitated, altered and otherwise shifted scientific inquiry and the dissemination of scientific knowledge. If we want to be able to reflect back on the science of our times I think we need to be thinking about collecting and preserving science and science communication that is happening on the web.

So I would say that I am interested in doing what I can to help document and explore what is changing and what is staying the same around the nature and practices of science and science communication.

Tell us a little more about your career trajectory so far: interesting projects past and present?

I worked on a few projects at the Center for History and New Media at George Mason University for about five years. In that time i was primarily focused on Zotero, a free and open source research management tool. Before that I worked on the games+learning+society conference for a few years. I’ve been at the Library of Congress for the last two years. In all of those roles I end up gravitating toward thinking about the role, nature, and place of science in society.

I can give a few examples of how these things all end up coming together in some of my recent publications. Each of these explore different subjects but they are all really about getting at ways we can go about understanding science in our world as documented in a range of digital modes.

Teaching intelligent design or sparking interest in science? What players do with Will Wright’s Spore. This article, forthcomming in Cultural Studies of Science is about figuring out how we should go about assessing the impact of a game like Spore on public understanding of science. My goal here was to think through how we could work from something like the Sporum, the games online forums, as a way to explore the ways that people are thinking about the game. In the end, this offers some initial evidence to suggest that a lot of the games players get past the problematic way the game presents evolution and use the game as a catalyst to get into some really interesting and fun thinking and discussion of science.

Tripadvisor rates Einstein: Using the social web to unpack the public meanings of a cultural heritage site. Near the US Capitol, in front of the National Academy of Sciences sits a gigantic bronze statue of Albert Einstein. The monument was created to celebrate Einstein and the sense of awe and wonder his work represents. This article explores the extent to which perspectives of the monument’s public supporters and critics can be seen in how people interact with it as evidenced in reviews and images of the monument posted online. I looked at how folks appropriate and discuss the monument on sites like  Fickr, Yelp, Tripadvisor, and Yahoo Travel, to explore how the broader public co-creates the meaning of this particular memorial.

Modding the history of science: Values and habits of mind in modder discussions of Sid Meier’s Civilization This article explores the issues involved in interpreting a game through analysis of the ways modders (gamers who modify the game) have approached the history of science, technology, and knowledge embodied in the game. Interestingly looking at online discussions of the game suggests that Civilization III cultivates an audience of modders who spend their time reimagining how the history of science and technology could work in the game.

What was the best aspect of ScienceOnline2012 for you? Any suggestions for next year?

It’s all about the people. I’ve been to ScienceOnline twice, in 2012 and in 2010 and found both experiences to be very enlightening and invigorating. To begin with, I am a big fan of unconferences, there is a good bit more excitement in the air at them. Beyond that, there are a lot of conferences out there that people have to go to for professional reasons, this remains an event that people go to because they want to go. Everybody is there powered primarily because of how much they care about science and science communication and while it can be physically and mentally exhausting it is really great at recharging your drive for the work.

Thank you! Hope to see you again in January.

Best of June at A Blog Around The Clock

I posted only 11 times in June. That is, on A Blog Around The Clock only (not counting the posts on The Network Central, The SA Incubator, Video of the Week, Image of the Week, or editing Guest Blog and Expeditions).

Brand new posts:

Why do we blog? To change the world
New and exciting kid on the block: PeerJ

Updates, News and Announcements:

Live chat today at noon about science blogging, circadian rhythms, sleep, metabolism and evolution
ScienceOnline2013 – be a part of the program!

ScienceOnline interviews:

ScienceOnline2012 – interview with Kathryn Bowers

Posts republished from the old archives:

New Journalistic Workflow

Best-of-the-Web linkfests:

The Scienceblogging Weekly (June 1st, 2012)
The Scienceblogging Weekly (June 8th, 2012)
The Scienceblogging Weekly (June 22nd, 2012)
The Scienceblogging Weekly (June 29th, 2012)

Previously in the “Best of…” series:

2012

May
April
March
February
January

2011

December
November
October
September
August
July
June
May
April
March
February
January

2010

December
November
October
September
August
July
June
May
April
March
February
January

2009

December
November
October
September
August
July
June
May
April
March
February
January

The Scienceblogging Weekly (June 29th, 2012)

Blog of the Week:

This week’s choice was easy – March of the Fossil Penguins, written by Dr. Daniel Ksepka. What is there not to like? Penguins! Fossils! Straight from the keyboard of the leading world expert on the topic. Enjoy!

 

Top 10:

How presidential elections are impacted by a 100 million year old coastline by Craig McClain:

Hale County in west central Alabama and Bamberg County in southern South Carolina are 450 miles apart. Both counties have a population of 16,000 of which around 60% are African American. The median households and per capita incomes are well below their respective state’s median, in Hale nearly $10,000 less. Both were named after confederate officers–Stephen Fowler Hale and Francis Marion Bamberg. And although Hale’s county seat is the self-proclaimed Catfish Capitol, pulling catfish out of the Edisto River in Bamberg County is a favorite past time. These two counties share another unique feature. Amidst a blanket of Republican red both Hale and Bamberg voted primarily Democratic in the 2000, 2004, and again in the 2008 presidential elections. Indeed, Hale and Bamberg belong to a belt of counties cutting through the deep south–Mississippi, Alabama, Georgia, South Carolina, and North Carolina–that have voted over 50% Democratic in recent presidential elections. Why? A 100 million year old coastline….

The Curious Case of the Poisoned Cows by Deborah Blum:

On a bright morning in early June, a Texas rancher named Jerry Abel turned his small herd of cattle out to graze. The 18 cows moved hungrily into that field of fresh grass. Within a few hours, only three were still alive. Abel’s 80 acre ranch sits just a little east of Austin and the story was strange enough that on Sunday a local CBS affiliate picked it up. “There was nothing you could do,” Abel told KEYE about his desperate efforts to save the animals. “Obviously, they were dying.”…

In the Steps of a Hungry Acrocanthosaurus by Brian Switek:

Compared to mounted dinosaur skeletons, fossil footprints might seem like mundane objects. They only record one small part of a fantastic creature, and it is harder to envision a whole dinosaur from the ground up than the wrap flesh around a skeletal frame. But we should not forget that dinosaur footprints are fossilized behavior—stone snapshots of an animal’s life. And sometimes, trackways record dramatic moments in dinosaur lives….

When It Comes to Numbers, We’re All Late Bloomers by Elizabeth Preston:

Good news for aspiring jelly-bean jar estimators who are under 30! Your intuitive grasp of numbers may not have peaked yet. Unlike other cognitive skills, the ability to approximate keeps improving well into adulthood. Since the skill is tied to mathematical smarts, this news might bring hope to struggling students….

Summer of Smoke by Christie Aschwanden:

June 8, 2012, Cedaredge Colorado—It was an ordinary Friday afternoon. I was at my desk writing when I looked out the window and saw an enormous plume of smoke billowing from the back of our property. It was the kind of moment when you’re supposed to remain calm and remember all the wise things you learned in first aid class or girl scouts. (Stop! Drop! Roll!) Instead, I panicked.

Plague at the Siege of Caffa, 1346 by Michelle Ziegler:

The first stage of the Black Death among Europeans was said to begin with the whoosh of a Mongol trebuchet. Gabriele De’ Mussi, a lawyer from near Genoa writing in about 1348, is believed to have recorded the account of the earliest use of plague as weapon of war at Caffa in 1346….

New flu gene found hiding in plain sight, and affects severity of infections by Ed Yong:

I could write the entire genome of a flu virus in around 100 tweets. It is just 14,000 letters long; for comparison, our genome has over 3 billion letters. This tiny collection of genetic material is enough to kill millions of people. Even though it has been sequenced time and time again, there is still a lot we don’t know about it….

‘Man-sheep-dog’: inter-species social skills by Paul Keil and Greg Downey:

Paul, the lead author, interviewed sheepdog trialer Damian Wilson about his interactions with his dog, a border collie named Yandarra Whiskey. Damian and Whiskey gave Paul a demonstration of the techniques used in sheepdog competitions as they together tried to move a mob of three sheep. In a competition in New South Wales, a trainer and dog have to move three sheep who have never been herded through a difficult obstacle course, and the trainer loses points if he (or, less frequently, she) breaks from a slow, measured pace walking the course. The rules mean that the dog itself must be trained until it anticipates the sheep’s reactions, and understands, on some level, what dog and trainer, together, are trying to accomplish. Although the trialer may give commands, the dog, too, is a kind of expert….

Preview: 3-D Space Shuttle Movie Will Bring the Launch Pad to Your Living Room by Tanya Lewis:

If you missed the final launch of the Space Shuttle, or the first private spacecraft rendezvous with the International Space Station, fear not. A new documentary to be released late this year promises you a fiery, 3-D, launch-pad view of these historic flights…

A Wartime Medical Dispenser by Jaipreet Virdi:

The Napoleonic Wars brought John Harrison Curtis’ studies to a standstill, as he became one of thousands of young men conscripted to fight against Napoleonic advances towards Britain. With his medical learning in hand, Curtis enlisted in the Royal Navy in 1808, to obtain his qualifications as surgeon and extend his medical skills. Since 1745, the Royal College of Surgeons in London, Edinburgh and Dublin, and the Navy held close associations with each other as the College was responsible for examining naval surgeons for active service. To be admitted as surgeon in the navy, candidates had to obtain a certificate of competence from the College and then be subjected to a two-hour oral examination at Somerset House….

 

Special topic #1: Getting young journalists and scientists to become savvy on the Web:

#Realtalk for the j-school graduate on the first five years of your career by Ann Friedman

Young journalists don’t seem to care about the Web: Why not? by Phillip Smith

Few Tweet successes as Generation Y fails to use blog-standard tools by Elizabeth Gibney

British Ph.D. Students Don’t Tweet by Elizabeth Gibney

 

Special topic #2: Wicked Problems:

Covering Wicked Problems by Jay Rosen

Overcoming Wicked Problems by Michael Shellenberger and Ted Nordhaus

Andrew Revkin on the Super Wicked Problem of Climate Change by Amanda Frank

David Roberts on the Simple Climate Problem by Andrew Revkin

Wicked Problems by UpLook

 

Best Images:

Global Distribution of Nobel Prizes Reflects Great Shifts in Modern History [Infographic] by Scientific American Magazine

 

Best Videos:

Mathematically Correct Breakfast by George Hart

A Song About A Circle Constant by Vi Hart

Oldest Sound Recording Resurrected from Paper by Eric Olson

A Glass Act — Harry Potter Theme Played on Wine Glasses by murayu74

What does traffic have to do with fluid dynamics? by FY! Fluid Dynamics

Milestone for WINS by The Academy of Natural Sciences of Drexel University

Beautiful Black Art by Tony Barnhart

Making the Invisible Visible in Video by MITNewsOffice

How Many Men Does it Take to Pull an Astronaut Out of the Ocean? by Amy Shira Teitel

Scraps to soil: New Yorkers carry compost to Greenmarkets instead of tossing it in the trash by Laura Geggel and Virat Markandeya

Instant Egghead – Do Cosmic Rays Spark Lightning? by Phil Yam

 

Science:

Beware Stimulus Effects in Psychology by Neuroskeptic

Do cephalopods dream of aquatic sheep? and Big in Japan by Zen Faulkes

TGIPF: The Weird World of Banana Slug Sex by Cassandra Willyard

How to Spot Pseudoneuroscience and Biobunk by APS

Bad science not about same-sex parenting by Andrew Perrin

Adrenaline Junkies Look to the Moon for Great New Fix by Amy Shira Teitel

Snakes that chew their food by Andrew Durso

The Anthropocene, and the tech that might save humans by Christie Nicholson

Far out in North Carolina by Stefan Rahmstorf

Ostrich! Get your ostrich here! The man behind the Greenmarket ostrich stand by Taylor Kubota

S.O.S. Save Our Seagrass by Whitney Campbell

What does the way you count on your fingers say about your brain? by Corrinne Burns

Size and evolution by Anthony King

Madness over sea level rise in North Carolina by John Bruno

How Will Global Warming Affect Lizards? A Detailed Physiological Study On Puerto Rican Anoles by Jonathan Losos

Seven sins of scientists part 5: snobbery by Paul Knoepfler

Tidal massaging reveals a hidden ocean on Saturn’s moon, Titan by Matthew Francis

How did the remote control get so awful and confusing? by Daniel Engber

Thoughts on Obamacare by Pal MD

Why supermarket tomatoes look great but taste bland and Exposed: the severe ethical breaches of superhero journalists and Mystery of the flatfish head solved *cough* four years ago *cough* and Why a new case of misconduct in psychology heralds interesting times for the field and Californian condor not extinct yet, but still regularly poisoned by lead by Ed Yong

Shiny! Top 10 reasons why seafarers love Joss Whedon’s Firefly by Miriam Goldstein and Craig McClain

Mysterious Fairy Circles Are ‘Alive’ by Rachel Nuwer

The Dolomite Problem – Peeking Under The Hood by Suvrat Kher

The Curse of the Lead Bullet by Deborah Blum

Should Linus Pauling’s erroneous 1953 model of DNA be retracted? by Jeff Perkel

How to trick people into eating dog food and H*MPING: Why do they do it? by Julie Hecht

The New ExxonMobil: Has the Tiger Changed Its Stripes? and A Court’s Scientific Smackdown: The D.C. Circuit Trashes Science Deniers on Global Warming and the EPA by Chris Mooney

America’s Other Audubon: A Victorian Woman’s Radical Journey of Art, Science & Entrepreneurship by Maria Popova

CDC proposes testing baby boomers for hepatitis C by Jessica M. Morrison

Climate-Studying Seals Bring Back Happy News by Elizabeth Preston

Brave New Worlds by Cameron Walker

Your Color Red Really Could Be My Blue by Natalie Wolchover

Science Denied by Phil Primack

A New Satellite Tool Tracks Deforestation by Rachel Nuwer

Sleeper Sharks Slurp Snoozing Seals by Brian Switek

The Lessons (and Echoes) of Silent Spring by Keith Kloor

The curse of the gingers by PZ Myers

The Higgs Boson is a Liberal Conspiracy To Get The Government More Involved In Mass* by Tom Levenson

Poland’s wolves trot across key wildlife overpasses by DeLene Beeland

In defense of pink microscopes by TheCellularScale

In Defense of #sciencegirlthing by Ben Young Landis

Social Justice in Animals and Animals in Visual Media by Marc Bekoff

Of wanton plants and prudish immune systems: late-night thoughts for National Pollinator Week by Leafwarbler

 

Media, Publishing, Technology and Society:

SciWriteLabs 8.1: The Lehrer affair, consequence-free plagiarism, and rules for blogging and SciWriteLabs 8.2: Is it kosher to re-use wording from Facebook updates in your journalism? And: do we need a Son of Sam law for media miscreants? by Seth Mnookin

Disrupting journalism education, too by Jeff Jarvis and Disrupting education by Dave Winer

Open Notebook Series: What is an Open Notebook? by Anthony Salvagno

Genius writing – or can a good lab journal help you become smarter? by Eric-Wubbo Lameijer

On Blogging, Direction And Ben Radford’s “Still Skeptical of Blogs” by Kylie Sturgess

Launching version 2.2: Twitter Integration by ScienceSeeker

A bad bad week for access by Richard Smith

Social Networking Concept May Have Emerged During Renaissance, Researchers Say by Tara Kelly

Wellcome Trust will penalise scientists who don’t embrace open access by Alok Jha

Shaking Up Israel’s National Archives: A conversation with Israel’s new chief archivist by Yair Rosenberg

Google’s One-Gender-Fits-All T-Shirts Don’t Fit by Ryan Tate

Library of Congress Acquires Carl Sagan Papers by Audrey Fischer

Putting People at the Center of Journalism by Josh Stearns

How do you tell when the news is biased? It depends on how you see yourself by Jonathan Stray

All A’Twitter: How Social Media Aids in Science Outreach – Discussion and Conclusions by Caitlyn
Zimmerman

Did you just tell me to go fuck myself? by Ian Mulvany

Scientists On Twitter: 30 Biologists And Chemists To Follow by Rebecca Searles

Measuring and Visualizing Interdisciplinarity by Samuel Arbesman

Why Porn and Journalism Have the Same Big Problem by Jordan Weissmann

Can you go on the press release diet? A 12-step program by Denise Graveline

How the New York Times technology blog, Bits, perpetuated the myth of a mental illness due to mobile phone use: Or, Follow the money by Les Posen

The Scienceblogging Weekly (June 22nd, 2012)

Blog of the Week:

Like clockwork, almost every day for more than two years, Tommy Leung and Susan Perkins bring you Parasite of the Day. Sometimes gross, but always fascinating. And considering how most of us don’t pay much attention to parasites these days, there is something cool to learn every single day.

 

Top 10:

The only good abortion is my abortion by Maggie Koerth-Baker:

…Of course, we don’t call it an abortion. We call it “a procedure” or a D&C. See, my potential abortion is one of the good abortions. I’m 31 years old. I’m married. These days, I’m pretty well off. I would very much like to stay pregnant right now. In fact, I have just spent the last year—following an earlier miscarriage—trying rather desperately to get pregnant…

Defending Jonah Lehrer by Bradley Voytek (about criticisim of neuroscience, not “self-plagiarism”):

Cognitive neuroscience grew out of experimental psychology, which has decades of amazing observations to link psychology and behavior. But with this legacy comes a lot of baggage. Experimental psychologists observed that we have the capacity for memory, attention, emotion, etc. and they sought to piece those phenomena apart. With the advent of neuroimaging techniques, psychologists put people in brain scanners to see where in the brain behaviors “were”. But this is the wrong way of thinking about these concepts.

The genius myth by Zen Faulkes:

…This myth of destiny and inevitable triumph of genius is, to me, completely the opposite of what science is. The scientific method leveled the playing field for discovering truth. Anyone could follow the methods and get to the bottom of things, so truth was no longer subject to tricky things like personal revelation….

Climate change is simple: We do something or we’re screwed by David Roberts:

…The challenge I took on was to convey the gist of my “brutal logic of climate change” post in a reasonably short amount of time, using as little scientific jargon as possible. Just: there is a problem that calls for urgent action. Business-as-usual means disaster. This is all gloom and doom — not even much humor. I know that turns people off or shuts them down. I know people need to feel a sense of hope and efficacy. I know — indeed, have recently been writing — that we need a vision of a sustainable future. But I needed to do my own version of “Danger Will Robinson!” Just to get it on the record…

Tunes without composers: music naturally evolves on DarwinTunes by Ed Yong:

…The tunes embedded above weren’t written by a composer, but fashioned through natural selection. They are the offspring of DarwinTunes, a program which creates bursts of noise that gradually evolve based on the preferences of thousands of human listeners. After hundreds of generations, tracks that are boring and grating soon morph into tunes that are really quite rhythmic and pleasant (even if they won’t be topping charts any time soon)….

Snake-eating beetles by Andrew Durso:

So little is known about the parasites of snakes that we tend to discount them all together, but the ecological and evolutionary interactions between hosts and their parasites can be very strong. This is a story about how two enterprising snake biologists solved a mystery that had been puzzling entomologists for decades…

Test-Tube Piggies: How did the guinea pig become a symbol of science? by Daniel Engber:

…To call someone or something a guinea pig may suggest a mere experiment (“Joe Biden was put out as a guinea pig for the White House”), or it can invoke the specter of exploitation (the U.S. Army wanted “to use young men as guinea pigs and throw them away”). The image either describes the scientific process or condemns it. It’s a totem or a scarecrow. What makes this wording more curious is the fact that guinea pigs, real ones, don’t mean much to working scientists. For all their rhetorical importance, the animals scarcely register in the lab…

What’s changed in evolution and ecology since I started my Ph.D. by Jeremy Yoder:

Last month, I filed my PhD dissertation, bringing to an end an intellectual and personal journey that began seven years ago in the summer of 2005. I know a lot more now than I did then, and I know a lot more about the boundaries of what I don’t know, too. But not only has my knowledge changed—evolution and ecology looks a lot different now than it did seven years ago when I was planning my dissertation research. At some point, and often multiple points, in the process of getting a PhD, everybody wonders whether what they’re doing is already out of date. Some of the transformations in the field I think I could see coming. For instance, it was clear in 2005 that computational power would keep increasing, phylogenetics would be used more and more to ask interesting questions, more and more genomes would be available for analysis, and evolutionary developmental biology was on the rise. It was unfortunately also predictable that it would be possible to study climate change in real time over PhD-length timescales. And although the 2008 global financial crisis didn’t help, it was clear that funding and jobs were going to be more competitive than they had been for our predecessors….

Drawing sharp boundaries in a fuzzy world by Chris Rowan:

Humans are natural splitters. We have an innate tendency to look at the world and mentally sort everything into different categories, and grades, and entities: this is one thing, that is another; it was this, now it’s that. Our perception of colour is a good example of how our brains automatically split a continuum into discrete boxes. We’ve incorporated our love of classification deep into science, trying to formalise and quantify the dividing lines we want to draw on everything: it’s this when conditions A and B are met, it’s that when we see Y and Z. But nature doesn’t often make it easy for us to draw our sharp dividing lines….

Why the Scientist Stereotype Is Bad for Everyone, Especially Kids by Michael Brooks:

To many – too many – science is something like North Korea. Not only is it impossible to read or understand anything that comes out of that place, there are so many cultural differences that it’s barely worth trying. It’s easier just to let them get on with their lives while you get on with yours; as long as they don’t take our jobs or attack our way of life, we’ll leave them in peace…

 

Special topic #1: Science: It’s a Girl Thing

“Science: It’s a Girl Thing”: Lab Barbie, Extra Lipstick by Maryn McKenna

Hey girl! Science wants YOU – but don’t forget the lipstick by Gozde Zorlu

Girls! Be A Scientist! You too Can Dance in the Lab in High Heels! by Deborah Blum

Friday Sprog Blogging: You’ve made it clear “it’s a girl thing,” but is “it” science? and Science For Princesses and How do we make room for pink microscopes? (More thoughts on gendered science kits.) by Janet D. Stemwedel

#sciencegirlthing: the PR guy’s take by David Wescott

E.U.’s ‘Science, it’s a girl thing’ campaign sparks a backlash by Olga Khazan

Science – It’s a Girl Thing (Insert Facepalm Here) by Carin Bondar and Joanne Manaster

Why “Pinkifying” Science Does More Harm Than Good by Noisy Astronomer

Hey Science, “How YOU doin’?” by Summer Ash

 

Special topic #2: Turtles

Turtle Anatomy, in Stunning Images from 1820 by Maria Popova

Galápagos Monday: Lynn’s Tortoises by Galápagos Monday: Lynn’s Tortoises

Terrifying sex organs of male turtles by Darren Naish

Turtles Have Horrifying Penises by Erin Gloria Ryan

Sex locked in stone: Fossil turtle pairs provide first direct evidence of prehistoric vertebrate mating. by Brian Switek

What Remains in the Rock by Brian Switek

Friday Weird Science: Why, you DIRTY LITTLE HERPS! by Scicurious

Preserved in the Act and Fossilized Turtle Whoopie by Craig McClain

 

Best Videos:

Eating on a Green Roof: New York’s Buildings Provide Food, Habitat for Wildlife by Rachel Nuwer, Chris New and Brennan Kelley

How do Spaceships Landing in Water Not Hit Boats? by Amy Shira Teitel

Must-watch video on rip currents by Miriam Goldstein

Whale Rainbow by rsean9000

Charged Gold Nanoparticles “Unzip” DNA by N.C.State

World Science Festival Fascinates With Robotic Animals, World’s Lightest Material, Quantum Levitation by Cara Santa Maria

 

Best Images:

Human Microbiome Project by Perrin Ireland

Greek octopus forms coalition with dolphin’s genitals by Rowan Hooper

 

Science:

The Difference Between Science ‘Skills’ and ‘Knowledge’ by Emily Richmond

How To Stop Science Alienation Syndrome by Deborah Blum

How to Determine If A Controversial Statement Is Scientifically True by Alan Henry

Numeric Pareidolia and Vortex Math by MarkCC

Tech-Based Dollhouse Inspires Future Girl Scientists by Kellie Foxx-Gonzalez

Med Student Rescues Body Part From Airport Security by Robert Krulwich

Things I Learnt from my (Unscientific) Experiences with Crowdsourcing. by David Ng

In Defense of Genetically Modified Crops by Sarah Zhang

When Did Americans Lose Their British Accents? and Why Do People Feel Phantom Cellphone Vibrations? by Matt Soniak

NASA Astronauts Brought Playmates to the Moon and Valentina Tereshkova Was the First Woman in Space and NASA and FAA Agree on the Future of Spaceflight and Vintage Space Fun Fact: NASA’s Canadian Contingent and Mars Rover Curiosity’s Retro Parachute by Amy Shira Teitel

Brains are Different on Macs by Neuroskeptic

Putting Fear In Your Ears: What Makes Music Sound Scary by Jessica Stoller-Conrad

Former Quantitative Trader Spurns Wall Street to Explore the Final Frontier by Patrick Clark

Can Anoles With Differently Shaped Genitals Interbreed? and Territorial And Thermoregulatory Behavior Of Sri Lankan Otocryptis Lizards by Jonathan Losos

How can scientists communicate to the public if they can’t even explain their work to each other? by Maggie

On this Father’s Day, let’s remember the allofathers, too by Emily Willingham

Are Fathers an Endangered Species? by Paul Raeburn

A shot to the head by Vaughan Bell

Get Ready, Because Voyager I Is *This Close* to Leaving Our Solar System by Rebecca J. Rosen

Does All Wine Taste the Same? by Jonah Lehrer

The Blind Spot: A Requiem by Megan Garber and Driving without a Blind Spot May Be Closer Than It Appears by Rachel Ewing

Notebooks Shed Light on an Antibiotic’s Contested Discovery by Peter Pringle

10-year-old solves science riddle and co-authors paper by Jon White

Keeping strong during a long winter nap by Zen Faulkes

What did Galileo ever do to you? by Ken Perrott

End the macho culture that turns women off science by Athene Donald

What’s in a (Gene) Name? by Hillary Rosner

Darwin, Worm Grunters, and Menacing Moles by Anthony Martin

Growing Up on Zoloft – Talking Drugs, Depression, and Identity With Katherine Sharpe by David Dobbs

ANAL CONES! Diadematid sea urchin mysteries! and Follow up on the Anal Cone! (thanks to the New Scientist) by Christopher Mah

How to find good sperm by Kristian Sjøgren

It has long been a mystery why flamingos in captivity suffer foot lesions. A Danish study now claims to have solved a part of this mystery. by Jeppe Wojcik

Black bears show counting skills on computers by Matt Bardo

DIY biology by Laura H. Kahn

Same Old Story: Too Many Graduate Students by Rob Knop

Scientists Find Weak Evidence That Unhealthy Lifestyles Lead to Weak Sperm by Allie Wilkinson

Sound Scholarly Communication by David De Roure

Sports doping, Victorian style by Vanessa Heggie

Welcome to the Anthropocene by David Biello

Goat Moms Recognize Their Kids Saying “Ma!” and The Shambulance: Ionic Foot Detox Baths by Elizabeth Preston

Thoughts on Tarbosaurus, Part 1. and Part 2 by Victoria Arbour

An Abstemious Home by Jessa Gamble

Crowdfunding: It’s not a grant … or is it? by Rebecca Rashid Achterman

The monthly ring: Expanding HIV prevention options for women by Dr. Zeda Rosenberg

Experiments hint at a new type of electronics: valleytronics and Quantum fluctuations may uncover a clue to high-temperature superconductivity by Matthew Francis

Reinventing the Wheel by Meagan Phelan

When Mammals Ate Dinosaurs by Brian Switek

The Rise of the Fork: Knives and spoons are ancient. But we’ve only been eating with forks for a few centuries. by Sara Goldsmith

‘Silent Spring’ is 50. The Credit, and the Blame, It Deserves. by David Ropeik

As America grows more polarized, conservatives increasingly reject science and rational thought by Amanda Marcotte

In the year 2023, and humans are on Mars for all to see by Kevin Orrman-Rossiter

Scalia’s Republican Brain: Why He’ll Come Up With a Reason to Overturn the Healthcare Mandate by Dylan Otto Krider

Does art-from-science really add anything? by Jon Butterworth

Prairie Ridge Ecostation by Christine L. Goforth

Let’s not get carried away by Markus Pössel

 

Media, Publishing, Technology and Society:

The Slow Web by Jack Cheng

Using Storytelling in Blogs by Maximilian Majewski

I’ll ask the questions here! by M.S.

Lawyer attacking The Oatmeal shocked by big mean Internet’s reaction and Lawyer tries and fails to shut down The Oatmeal’s charitable fundraiser by Casey Johnston and The Oatmeal v. FunnyJunk, Part IV: Charles Carreon Sues Everybody by Ken and The Guy Continues to Mess With The Oatmeal by Kevin Underhill and Funnyjunk’s Lawyer Charles Carreon Just Keeps Digging: Promises He’ll Find Some Law To Go After Oatmeal’s Matt Inman by Mike Masnick

Journalism education cannot teach its way to the future by Howard Finberg and Why Professors Value Journalism Degrees More Than Professionals (Beyond the Obvious) by Carrie Brown-Smith

How would you engage the community in a vagina discussion? by Steve Buttry

Socialising Research: How to get your research results noticed and used. by Jo Hawkins

All A’Twitter: How Social Media Aids in Science Outreach – Chapter 11: Set of Best Practices for Social Media Use by Caitlyn Zimmerman

Teachers and Administrators, Don’t Be Scared of Technology: It Won’t Replace the Classroom by Jody Passanisi and Shara Peters

Is it ok to get paid to promote Open Access? by John Dupuis

Pay attention to what Nick Denton is doing with comments by Clay Shirky

Watergate mythology invites pushback, ignores journalism’s messy nature by Andrew Beaujon

Why Women Still Can’t Have It All by Anne-Marie Slaughter and No One ‘Has It All,’ Because ‘Having It All’ Doesn’t Exist by Lindy West

When Twitter Stumbles, Sites Across the Web Go Down With It by Alexander Furnas

Open Access and Science Communication. Reflections on the need for a more open communication environment by Alessandro Delfanti

A step-by-step approach for science communication practitioners: a design perspective by Maarten C.A. van der Sanden and Frans J. Meijman

Does the technical staff at the World Health Organization (WHO) tweet? by Nina Bjerglund

An Open Letter To Conference Organizers and Panel Moderators by Sean Bonner

Twitterror by Oliver Reichenstein

To create a new social network or not to? Scientists weigh in. by Upwell

The Perfect Technocracy: Facebook’s Attempt to Create Good Government for 900 Million People and Inside Google’s Plan to Build a Catalog of Every Single Thing, Ever by Alexis Madrigal

Why Pen Names Might Be a Bad Idea for Most Bloggers by Ryan Matthew Pierson

Blogging relieves stress on new mothers by Victoria M Indivero

Should We (And Can We) Regulate What We Do Not Understand? by Kathleen Wisneski

Scholars are quickly moving toward a universe of web-native communication by Jason Priem, Judit Bar-Ilan, Stefanie Haustein, Isabella Peters, Hadas Shema, and Jens Terliesner

Bill Marriott: Chairman of the Blog by Michael S. Rosenwald

Apps I Want to Go Away by Sam Grobart

Some Thoughts on Peer Review and Altmetrics by Ian Mulvany

 

Extra: On the Finch report on Open Access:

Open access is the future of academic publishing, says Finch report by Alok Jha

The Finch Report on open access: it’s complicated by Stephen Curry

First thoughts on the Finch Report: Good steps but missed opportunities by Cameron Neylon

U.K. Panel Backs Open Access for All Publicly Funded Research Papers by Kai Kupferschmidt

Finch Report, a Trojan Horse, Serves Publishing Industry Interests Instead of UK Research Interests by Stevan Harnad

 

Extra: On the “self-plagiarism” saga:

On science blogs this week: Jonah Lehrer by Tabitha M. Powledge

Jonah Lehrer: The issues are simple by Paul Raeburn

This Week in Review: The potential of Microsoft’s Surface, and keeping blogging ideas fresh by Mark Coddington

Jonah Lehrer, Hypertext Author by Dorian Taylor

Jonah Lehrer “Self-Plagiarism” Brouhaha is Crap by Matthew E May

New Journalistic Workflow by Bora Zivkovic

Blogging and recycling: thoughts on the ethics of reuse. by Janet D. Stemwedel

How Jonah Lehrer should blog by Felix Salmon

The ethics of recycling content: Jonah Lehrer accused of self-plagiarism by Jonathan M. Gitlin

A (Partial) Defense of Jonah Lehrer by Robert Wright

The Tyranny of Novelty by Matthew Francis

Jonah Lehrer, self-borrowing and the problem with “big ideas” by Laura Hazard Owen

New Journalistic Workflow

This post is a slightly modified/updated version of the post originally published on April 5, 2009:

Jay Rosen tweets:

New method: slow blogging at PressThink, daily mindcasting at Twitter, work room at FriendFeed. Example: post in gestation http://is.gd/okca

This is how I understand that:

Step 1 is mindcasting on Twitter (often misunderstood for time-wasting lifecasting, e.g., this).

Step 2 is aggregation of a number of imported tweets and digestion of them on a platform like GooglePlus, Facebook or FriendFeed.

Step 3 is aggregation of several G+/FB/FF threads into a more coherent blog post.

The next step, Step 4, could potentially be to aggregate the ideas and knowledge from several blog posts and publish as an article in the traditional media outlets.

I can think of even Step 5 – aggregating a number of media articles into a book.

Traditional journalists would call only Step 4 and Step 5 ‘journalism’. New journalists would call all of these steps ‘journalism’.

Differences between traditional and new media, if looking at the process in this way?

1) all steps are transparent and visible to all (instead of privately jotted notes in a moleskin or post-it notes).

2) all steps involve other people who provide continuous feedback and provide additional sources, documents or expertise.

3) depending on the topic or personal proclivities, one can stop at any step, 1,2,3,4 or 5, and whatever is done so far is still journalism.

Web provides sufficient time, space and communication technologies to do it this way, while paper/radio/TV restrict how much one can be transparent, public, collaborative, responsive to feedback and what is deemed worthy of the word “journalism”. Half-baked articles cannot count in such an expensive and restricted system, but can – and can be very useful – in the new medium.

Also, these steps are platform-neutral:

Step 1 is easily done on Twitter, but other Twitter-like platforms can do the same thing. One can do the same even on places like Delicious, Stumbleupon, Digg, Reddit, Fark, Slashdot or Metafilter. Or even on a blog – this is what bloggers have been doing – quick links and one-liners many times a day – for years before any of those other platforms were invented. One can also do it on Facebook since it introduced the relevant functionalities. Also worth noting is that having this service on one’s mobile device allows for reporting from the scene, i.e., for “breaking news” as I defined here (see all the responses to that post aggregated – Step 2 – on FriendFeed).

Step 2 also can be done elsewhere, though FriendFeed was really suitable for it – aggregating and getting feedback. Google Plus seems to be the best for it now, though Facebook is fine as well. One’s blog is a perfectly good place for it, too.

Step 3 is usually done on a blog, but I can see how it can be done on any other platform that allows for longer pieces.

If one wants to go on to Step 4 or Step 5, one needs to pitch the work to a corporate media entity, probably all online in the future, and get an editorial approval as well as the services of a professional editor for spelling, punctuation, grammar and style. The editor, an expert on the process but not as expert as you are, not even close, on the topic of the piece, should not have a say on the content, but may choose to have it evaluated by other experts (‘peer-review’ of sorts) before accepting the piece.

Why do we blog? To change the world

Croatian newspaper Jutarnji List published a special 5000th issue on Tuesday. I am not sure when it will go online, but I have a text in it. Interestingly, it was easier for me to write it in English and let them translate into Croatian, than to try myself to write in Serbian – none of the terms, like “blog” existed at the time I was still living in the former Yugoslavia.

Thank you Tanja Rudez for editing, and Hela Jug for translating. Reading it now, I see that the translation is much better than the original! Here, with permission, is the original English text I sent in.

==================

Blog is software. It is a platform that is very easy and fast to use even by people with no technical skills. It is not surprising that scientists and mathematicians, people who do have some technical skills, were one of the first to adopt blogging platforms to discuss science.

As the technology, and the world as a whole, evolved over the last 15 years since the first blogs appeared, so did the science blogosopehere evolve with it. The first science and math bloggers emerged either out of technological or political blogospheres. Some, especially mathematicians, used blogs to talk to each other and crowdsource solutions to old math problems, most notably as a part of the Polymath Project. Some scientists started to use blogs for Open Notebook Science – putting their daily lab notes online for all to see. Popular science writers started discussing the beauties of space (Phil Plait), evolution (Carl Zimmer), physics (Sean Carroll), or the anti-science activities of the American political Right (Chris Mooney). Other early science bloggers emerged from old Usenet newsgroups dedicated to fighting against Creationism (Pandas Thumb, Pharyngula, Sandwalk) or Climate Change Denialism (Real Climate, Deltoid).

Political activism is not something the early science bloggers shied away from. Nick Anthis, a science blogger, discovered that George Deutch, censor appointed by G.W.Bush to NASA, faked his CV. Nick’s investigative reporting in 2006, relentlessly spread around the Web by other science bloggers, forced the mainstream media to start paying attention, which led to forced resignation of Deutch several months later. Likewise, science bloggers led the daily push for corporate media and diplomatic entities to pay attention to the case of six medics imprisoned in Libya, which eventually led to their release. PRISM, the astroturf organization designed to lobby the U.S. Senate against the NIH Open Access bill was exposed by science bloggers, leading to hundreds of thousands of people calling their senators urging them to pass the bill – and the bill passed easily. More recently, the #arseniclife affair put into perspective the tremendous power of Web-savvy blogging scientists to instantly peer-review, critique and place on the garbage heap of history a very bad NASA-funded study published in Science magazine.

As the years passed by, the science blogosphere both grew tremendously in size, and somewhat changed its focus. Apart from Nobel Prize and Field Medal Prize winners joining in, many others – junior faculty, postdocs, graduate and undergraduate students, and even highschoolers and kids – started using blogs to discuss science. Blogging software started getting used in the science classrooms. Brief posts, links and personal updates moved from blogs to emerging social networks like Twitter, Facebook, Tumblr, YouTube, Flickr, Instagram, Pinterest and the such, leaving the blogging platforms mainly for longer, deeply-researched pieces of writing. This made blogs more serious and respectable as the signal emerged out of the noise. Nobel Prize winners were joined by Pulitzer Prize winners – reputable science writers and journalists in large numbers joined the scientists in the science blogosphere, bringing with them both the higher standards of good writing and the high standards of journalistic ethics – linking to sources, interviewing additional sources, crediting the authors of art and photography used in blog posts, and transparency of potential conflicts of interest. This resulted in a shift in tone as well – instead of pushing against pseudoscience and medical quackery, the dominant topic of the early years, most of today’s science blogging is targeting lay audience in bringing the beauty and excitement of science to as broad population as possible.

Another development placed science blogs ahead of other nodes of the blogosphere – congregation of science blogs into blogging networks. Nature Network (hosted by Nature Publishing Group) and Scienceblogs.com (run by Seed Media Group, now under National Geographic) collected science bloggers and gave them an imprimatur of mainstream media. Bloggers on such networks were vetted, thus trusted to be correct and ethical in their work. Over the past couple of years, this process accelarated, with highly reputable science blogging networks now being hosted by a variety of media organizations, science publishers and scientific societies, including Scientific American, Discover, Wired, PLoS, Guardian, Cosmos (Australia), American Geophysical Union, American Chemical Society and more. Self-organized blogging collectives that carefully choose which science bloggers can join them (Lab Spaces, Scientopia, Field of Science, etc), are also treated with the same amount of respect both by the mainstream media and by the scientific community.

Finally, the science bloggers are probably the best self-organized population of bloggers. Realizing the need to filter out blogs that do not cover science well, including blogs that push an anti-science agenda, science bloggers built specialized aggregators that can include only those science bloggers that have passed a type of “peer-review” by the other science bloggers. Researchblogging.org, Scienceblogging.org and especially now ScienceSeeker.org are “stamps of approval” for science bloggers that allow them, on occasion, to be treated as press by conference organizers, to be added to press lists of journals, and generally to be treated with respect as professionals, as opposed to the early stereotypes of bloggers being untrustworthy kids writing in their pyjamas in their parents’ basements. Somehow, I don’t think that description fits the bloggers whose books are on NYTime bestseller lists, or who are invited to give Keynote addresses at big scientific meetings. Blog is just software, but scientists and science writers are using that software in serious ways, making the world a better place.

ScienceOnline2013 – be a part of the program!

As the ScienceOnline world is growing, we have been busily preparing for ScienceOnline2013, our flagship meeting in Raleigh NC (January 31 – February 2, 2013) for a few months now. The organizing wiki was set up while ScienceOnline2012 was still in session, and it’s time to start putting together the program.

There are already many good ideas on the Program Suggestions page of the wiki. If you intend to come to the event and you want to do something there – moderate a session, present a brief demo, etc., volunteer by editing that page and adding your ideas there.

How is the program made? Read this account for hints.

We will close the Program Suggestions page on July 1st, so hurry up.

As we are closing the wiki unusually early this year, we will also leave a couple of time-slots in the program for topics that arise later, perhaps even for topics decided during the meeting itself. Stay tuned.

The Scienceblogging Weekly (June 15th, 2012)

Blog of the Week:

Russ Williams is the Director of the North Carolina Zoological Society and, as far as I know, the only “director of a zoo” who blogs. And does he ever – Russ has been blogging up a storm ever since 2005 when Ed Cone taught him how (you may call me The Blogfather, but Ed Cone is the blogfather for many of us in North Carolina). On his blog Russlings, Russ covers plenty – what is new at the N.C.Zoo in Asheboro, what is new in other zoos around the country and the world, what is new in policy and politics of animal conservation, plus cool pictures and videos of wildlife. But where the value really comes up is at the times of natural disasters – Russ is “in the know” and often the first and/or the only person to blog about the status of zoos and aquaria, as well as farm animals, wildlife preserves etc, in the affected areas. During disasters, Russlings is the Go-To place for such coverage.

 

Top 10:

How Our Disinterest in ‘The Environment’ Signals the End of Nature by Christopher Mims:

No one reading this has the slightest fucking clue what “nature” is, and in 1995 fisheries scientist Daniel Pauly proved it. In the paper that introduced the term “shifting baselines,” Pauly described how experts who determined how many fish should be caught often started with whatever the baseline state of the ecosystem was when they started their careers, instead of considering what a fishery might have looked like in the past, when it wasn’t nearly as degraded….

Getting used to being in charge of the planet by David Roberts:

…Nonetheless, like evolution, the dominance of human beings on Spaceship Earth is a profound and terrifying threat to all sorts of traditional worldviews. If Darwin showed us that God is not our author, the Anthropocene shows that He is not our caretaker. There’s no parent to supply us with endless resources and endless room to dispose of our waste. There’s no one to protect us or prevent us from screwing it all up….

Walking the Line: How to Identify Safe Limits for Human Impacts on the Planet by David Biello:

Is preserving the general environmental conditions that allowed civilization to flourish—a moderate climate, a rich array of species, rivers that reach the sea—necessary to ensure humanity endures? Or is minimizing alterations to the global environment introduced by human activity—rising levels of CO2 from fossil-fuel burning, widespread extinction, dams that impound water—more important to our success? Choosing the right approach is vital as the scale of human impact on the planet becomes so large that scientists are calling this new epoch in Earth’s history the Anthropocene (when human activity alters global climate and ecosystems)…

#GMOFAQ: Transferring genes from one species to another is neither unnatural nor dangerous by Michael Eisen:

Last week I wrote about the anti-science campaign being waged by opponents of the use of genetically modified organisms in agriculture. In that post, I promised to address a series of questions/fears about GMOs that seem to underly peoples’ objections to the technology. I’m not going to try to make this a comprehensive reference site about GMOs and the literature on their use and safety (I’m compiling some good general resources here.) I want to say a few things about myself too…

Sea level rise 101 by John Bruno:

Based on the NC legislature’s decree about the science of sea level rise projections and some of the related propaganda we have seen from climate change deniers, I get the sense there is a lot of confusion about sea level rise. So here is a primer on what we know about sea level and climate change…

Dirty soil and diabetes: Anniston’s toxic legacy by Brett Israel:

The Rev. Thomas Long doesn’t have neighbors on Montrose Avenue anymore. Everyone is gone. Widespread chemical contamination from a Monsanto plant was discovered in this quiet city in the Appalachian foothills back in the 1990s. In West Anniston, behind Long’s home, a church was fenced off, and men in “moon suits” cleaned the site for weeks. Nearby, boarded windows and sunken porches hang from abandoned shotgun houses. Stray dogs roam the narrow streets. A red “nuisance” sign peeks above the un-mowed lawn of one empty house. Bulldozers will be here soon…

Pollution, Poverty, People of Color: No beba el agua. Don’t drink the water. by Liza Gross

Jessica Sanchez sits on the edge of her seat in her mother’s kitchen, hands resting on her bulging belly. Eight months pregnant, she’s excited about the imminent birth of her son. But she’s scared too. A few feet away, her mother, Bertha Dias, scrubs potatoes with water she bought from a vending machine. She won’t use the tap water because it’s contaminated with nitrates…

The crayola-fication of the world: How we gave colors names, and it messed with our brains (part II) by Aatish Bhatia:

Lately, I’ve got colors on the brain. In part I of this post I talked about the common roads that different cultures travel down as they name the colors in their world. And I came across the idea that color names are, in some sense, culturally universal. The way that languages carve up the visual spectrum isn’t arbitrary. Different cultures with independent histories often end up with the same colors in their vocabulary. Of course, the word that they use for red might be quite different – red, rouge, laal, whatever. Yet the concept of redness, that vivid region of the visual spectrum that we associate with fire, strawberries, blood or ketchup, is something that most cultures share….

How the Chicken Conquered the World by Jerry Adler and Andrew Lawler:

The chickens that saved Western civilization were discovered, according to legend, by the side of a road in Greece in the first decade of the fifth century B.C. The Athenian general Themistocles, on his way to confront the invading Persian forces, stopped to watch two cocks fighting and summoned his troops, saying: “Behold, these do not fight for their household gods, for the monuments of their ancestors, for glory, for liberty or the safety of their children, but only because one will not give way to the other.” The tale does not describe what happened to the loser, nor explain why the soldiers found this display of instinctive aggression inspirational rather than pointless and depressing. But history records that the Greeks, thus heartened, went on to repel the invaders, preserving the civilization that today honors those same creatures by breading, frying and dipping them into one’s choice of sauce. The descendants of those roosters might well think—if they were capable of such profound thought—that their ancient forebears have a lot to answer for….

‘Sexual depravity’ of penguins that Antarctic scientist dared not reveal by Robin McKie:

It was the sight of a young male Adélie penguin attempting to have sex with a dead female that particularly unnerved George Murray Levick, a scientist with the 1910-13 Scott Antarctic Expedition. No such observation had ever been recorded before, as far as he knew, and Levick, a typical Edwardian Englishman, was horrified. Blizzards and freezing cold were one thing. Penguin perversion was another….

 

Special topic #1: stimulants in school:

The Questions About ADHD Drugs The New York Times Didn’t Ask by Matthew Herper

The labels change, the game remains the same by Vaughan Bell

The NY Times: When Stimulants Are Bad by Robert Whitaker

The Horror of Drug-Boosted Grades and SAT Scores by Jacob Sullum

Should Ritalin Be Distributed To Everyone Taking the SATs? by Gary Stix.

 

Special topic #2: Prometheus and science in the movies:

The biology of Prometheus by Zen Faulkes

The Science of Prometheus – a review, containing a lot of spoilers by Frank Swain

Prometheus: an archaeological perspective (sort of). by Henry Rothwell

Ridley Scott’s Prometheus Examines the Roots of Alien’s Mythology by Larry Greenemeier

‘Prometheus’ Offers a Creationist Indulgence for Science Geeks by James Gorman

Prometheus: what was that about? Ten key questions by Ben Walters

Stealing fire by Zen Faulkes

Space: The Science of Prometheus by Discovery News

What’s Wrong With Prometheus (a Partial List) by Julian Sanchez


Best Videos:

Instant Egghead – What Causes Brain Freeze? by Ferris Jabr and Eric Olson

The Fabulab’s Flame Challenge by Jeanne Garbarino, Perrin Ireland and Deborah Berebichez

Curly Haired Mafia – Prometheus SPOILERS!!! (video) by Lali DeRosier, DNLee and Dr.Rhubidium


Best Image:

UCD worker wins award for rare photo of bee sting in action by Andrea Gallo


Science:

Sensory Ecology of the Third Eye by Ashli Moore

Lovely Lysenko by Dominic Berry

Assuming the Doctor’s a ‘He’ by Danielle Ofri, M.D.

Why We (Accidentally) Name Babies for Hurricanes by Elizabeth Preston

What is a vagina? by Emily Willingham

Imaginary Numbers are Real by Matthew Francis

Curious Experiments by Archbishop Marsh’s Library. “‘Curious Experiments’ for ‘The Amusement and Entertainment of Ladies, as well as Gentlemen’ which took place before a paying audience in Dublin in 1743.” recreated by high school students 270 years later.

Crowdfunding: A New Opportunity for Science and Innovation by John R. Platt

Old Books that Guided Science by Samuel Arbesman

Why you probably won’t experience your own traumatic death by George Dvorsky

June Gloom by Cameron Walker

Dear Slate: America Needs More Artists by See Arr Oh

Negative results and dodgy papers: keep quiet or publish? by Tom W. Phillips

Our Animal Natures by Barbara Natterson-Horowitz and Kathryn Bowers

‘I’m Not Your Wife!’ A New Study Points to a Hidden Form of Sexism by Gayle Tzemach Lemmon

Achtman on Plague Evolution by Michelle Ziegler

Would You Call Me A Scientist? by Sheril Kirshenbaum

Visiting “Brains. The Mind as Matter” at the Wellcome Collection by The curious neuron

Food Trade Too Complex to Track Food Safety by Maryn McKenna

The Johannes Kepler Defense by Romeo Vitelli

Taking the colour out of light. by Thony C. “The man who didn’t invent the achromatic lens” John Dollond born 9 June 1706.

Carnivorous plants respond to increased soil nitrogen, eco-news websites completely miss the point by Andrew Thaler

Virginia Lawmaker Says ‘Sea Level Rise’ Is A ‘Left Wing Term,’ Excises It From State Report On Coastal Flooding by Rebecca Leber

Teaching Neuroanatomy With A Showercap by Neuroskeptic

Fungus Inside Us: A New Health Frontier? by Brandon Keim

The Top Ten Strangest Self-Experiments Ever by Alex Boese

G r e a t e r / l e t t e r / s p a c i n g / helps reading in dyslexia by The Neurocritic

Dangerous Interventions: MMS and Autism by Emily Willingham

Cholera vaccine deployed to control African outbreak by Gozde Zorlu

Bath salts and… zombies? by Donna

You Don’t Have What it Takes by Lucy E. Hornstein MD

What they didn’t tell you about the transit of Venus by Rebekah Higgitt

Science Outreach: What Do You Need? by Matt Shipman

Double Xpression: Liz Neeley, Science Communicator Extraordinaire by Jeanne Garbarino

Overeating Makes Flies Obese, Diabetic, Dead by Elizabeth Preston

Creationism Uses Dinosaurs to Lure Kids Into Radical Ideas, But Scientists Should Not Care Too Much by Cameron English

No, America Does NOT Need More Scientists and Engineers by Derek Lowe

Plant uses chemical weapons to make mice spit out its seeds and To control cannibal toads, you just need the right bait and Fear of spiders changes bodies of grasshoppers and makes plants decay more slowly and Microbial Menagerie and Male spider castrates himself and gets more stamina by Ed Yong

Where have I been? Or, science outreach’s place in science. by Lauren Meyer

The culinary adventures of a cuttlefish by Jonas

Science Communication: A sort-of-kind-of Carnival, and some more thoughts of mine by Scicurious

Scientists map ‘Facebook for birds’ by Alan Boyle

Double Xpression: Debbie Berebichez, PhD Physicist by Jeanne Garbarino

The anthropologist and the kurgans by John Hawks

Scientists Tackle The Geography Of Nature Vs. Nurture In Maps Of U.K. by Ted Burnham

Does Acceptance of Evolution Matter? by Ed Brayton

Did Neanderthals Produce Cave Paintings? by Sarah Everts


Media, Publishing, Technology and Society:

Sorry, Young Man, You’re Not the Most Important Demographic in Tech by Alexis Madrigal

Online Seniors: Tech-Savvier Than You Think by Frederic Lardinois

Open access to research is inevitable, says Nature editor-in-chief by Alok Jha

A Serious Look at Funny Faces by Henry Adams – on the history of cartoons.

An Anarchist Constitution for Twitter by Rebecca Greenfield

Why Twitter Matters: Tomorrow’s Knowledge Network by Nigel Cameron

Learning To Write From Chopin by Murr Brewster

An alternative to the college degree? by Amy Scott

From scrubbing floors to Ivy League: Homeless student to go to dream college by Vivian Kuo

11 dreams for the publishing debate — #1 fewer papers and 11 dreams for the publishing debate — #2 get real credit for surveys and exposition and 11 dreams for the publishing debate — #3 get real credit for refereeing and #4 get real credit for communicating and
#5 sharing all our work every way we can by Peter Krautzberger

All A’Twitter: How Social Media Aids in Science Outreach – Chapter 8: Talking with the Social Media Experts and Chapter 9: Gathering Survey Results, and Chapter 10: Coming to Conclusions by Caitlyn Zimmerman

Why the World’s Most Perfect News Tweet Is Kind of Boring by Megan Garber

Do Journo Watchers Ignore Environmental Beat? by Keith Kloor

Exhausted With The Same by Erika Napoletano

Why you should be excited about vector-based maps in iOS 6 by Tim De Chant

Pitch Perfect – a primer for scientists reaching out to journalists by Liz Neeley

Social media and Google Analytics – who’s interested in botany? by Alun Salt

Paying for information versus *access* to information: A key distinction for news publishers by Robert Niles

Please RT by n+1 editors

New and exciting kid on the block: PeerJ

As many of you know, before accepting a job at Scientific American, I worked at PLoS for three years (and became a vocal Open Access Evangelist even before that). While there, I worked closely with Pete Binfield who replaced Chris Surridge as managing editor of PLoS ONE shortly after my arrival there. Pete and I became friends, bumped into each other at meetings, he came to ScienceOnline at least a couple of times, and we remained in frequent contact after my move.

I am sure I was just one of many who was taken completely by surprise by the announcement that Pete is leaving PLoS to start a new project. His partner in this project is Jason Hoyt, up till now Chief Scientist and VP of R&D of Mendeley, also a ScienceOnline veteran.

If these two people, some of the best in the business, decide to leave cushy jobs in respected organization to start something new, one sits up and pays attention! This is not one of your run-of-the mill start-ups that come and go. So, I talked to Pete soon afterward, and today the cat is out of the bag – press release and all the details are now public.

So, what is it?

PeerJ is a new Open Access journal, as well as a new Open Access PrePrint service (see their blog for updates). PeerJ will open for submissions in Summer 2012, and will publish its first articles in December 2012.

Peer Review

Just like at PLoS ONE, reviewers will not be distracted by the superficial question of “is this sexy, earthshaking, Nobel-worthy, paradigm-shifting stuff” and will be forced to actually dig in and review the paper for the quality of science in the manuscript.

Where does money come from?

Its source of start-up funding is Tim O’Reilly with an initial infusion of $950,000. After that, the journal will support itself from membership fees. What are membership fees? They replace publication fees that many TA and OA journals currently charge authors for the publication of their manuscripts. Instead of paying for publication of each paper, authors pay only once and have a lifetime to keep publishing with PeerJ.

There are three levels of membership, suitable for people in different institutions, countries, scientific fields, or career stages. The basic $99 plan allows for publication of one paper per year, the $169 price-tag applies to those who expect to publish twice per year, and $259 membership fee is designed for more frequent authors. Each of the three levels also includes unlimited publication on the PrePrint server. If you are confused, yes, those are not annual fees, but once-only lifetime fees (as someone quipped: Publish ’till you Perish)

What’s the catch?

Very wisely, PeerJ is starting out by targeting the (bio)medical community first. It is this area of research in which the frequency of publication has reached levels best described as ‘madness’. Pressure is enormous to publish, publish often, and then publish some more. Can you imagine paleontologists being under the same pressure – poor Earth would be dug up three times over by now!

Think for a moment – how many papers is one, on average, an author on? While PIs of big labs in big institutions in big countries rake in many publications per year, one can imagine quite a steep slope on that curve with most of the authors residing in the very long tail of the “one-hit-wonder” authors. How many postdocs, technicians, graduate, undergraduate and high school students will publish more than one or two papers in their lifetimes? How many will 8-year old kids who happened to be in that class which published the famous bumblebee paper? How many citizen scientists will co-author a paper more than once? How many PI’s cats (yes, those were authors in the past) will write more than one paper?

Yet, each one of them will have to pay membership dues if a paper is to be published in PeerJ (there is an exception and a limit – papers with more than twelve authors will only have to have twelve paying authors, so PI’s cat may be off the hook if enough students and technicians sign on).

Cost of publishing a few papers by over-producers will be offset by thousands of single-paper authors who will also pay the fee. And even the hyper-frequent authors will not publish all of their stuff in PeerJ – they tend to like to spread their seed around, publishing some stuff in GlamourMagz for reputation, some in the Society journal to appease the friend the editor, some in PLoS ONE for speed when in fear of scooping, and perhaps one or two per year in PeerJ. Not that much work and cost typesetting PDFs for PeerJ after all, right?

Now imagine a person who starts publishing as an MS student, moves to a different lab for PhD, another one or two labs for postdocs, then gets hired for a temp job, then finally gets a tenure-track position somewhere else. At each one of those steps, this person persuades collaborators, students and others (including cats) to also sign on in order to publish together. Thus the circle spreads until every scientist on the planet, professional or amateur, old or new, is in the system. And new people keep coming into the system all the time. After all, $99 is a reasonable sum that most can afford to pay and will not resist too hard.

Oh, and think about the above paragraph again – does not this process require building and having a, gasp, community? And being able to sell the concept to one’s friends and collaborators? And the pre-print part is open to experimentation – not everything in there needs to look like a traditional paper from the time of print, opening up a possibility that creative people will use the platform to come up with novel ways of reporting their findings, more suited for the 21st century.

Brilliant, right? Now let’s hope it works! Time will tell…

There has already been quite a lot of coverage of PeerJ in various places, some content to summarize the press release, but others speculating about the future developments. See Scientific American, ScienceInsider, Confessions of a Science Librarian (part 1), Confessions of a Science Librarian (part 2), Gavia Libraria, The Library Journal, csid, Publishers Weekly, Reciprocal Space, Ars Technica, Huffington Post Science, Uncommon Ground, PandoDaily, Reuters, Mendeley and Nature.com for early examples.

It also shows how their usual focus on money and a strangely elitist view of “what good science is” led the Scholarly Kitchen guys on a totally random walk away from what this is all about into wild speculation. Heh.

The Scienceblogging Weekly (June 8th, 2012)

Wow – this was hard! I could have had at least Top 20 instead of Top 10 (but you’ll find them all listed down there anyway)…

 

Blog of the Week:

Tanya Khovanova’s Math Blog is a blog by Tanya Khovanova, a Visiting Scholar and Research Affiliate at MIT, a 1976 gold medalist (and 1975 silver medalist) at the International Mathematics Olympiad. What she does the most (though there is occasionally other stuff there) is to pose difficult (and some not to so difficult) mathematical problems and puzzles for her readers to try to solve in the comments. Go ahead and give it a try yourself!

 

Top 10:

Sea Level Rise Is Tied to Prevalence of Homosexuality by Craig McClain:

Although only two years old and previously unrecognized by the scientific establishment, Global Draining (GD) has now become a widely accepted theory. GD states that sea level is falling not rising (Southern Fried Science, 2010a). Current rates of GD indicate the entire world’s ocean will be empty by 2026 (Southern Fried Science, 2010a). Local-scale observation of in situ draining combined with a robust theoretical model firmly place the rate of draining at 40 Gigatons of water per year (Dr. M, 2010). It has been argued that both one and multiple holes occur in the ocean floor that allow for GD (i.e. the monoclavis versus polyclavis hypotheses via McCay, 2010; Southern Fried Science, 2010b). However, the impacts and causes of GD are not clearly understood. Despite this, GD is a fundamental tenet of nearly every facet of science and likely correlated with many aspects of biology, economics, sociology, religion, and politics. For example, GD is likely to lead to massive die offs of sharks and reduce global atmospheric oxygen levels (Shark Diver, 2010)…

The crayola-fication of the world: How we gave colors names, and it messed with our brains (part I) by Aatish Bhatia:

In Japan, people often refer to traffic lights as being blue in color. And this is a bit odd, because the traffic signal indicating ‘go’ in Japan is just as green as it is anywhere else in the world. So why is the color getting lost in translation? This visual conundrum has its roots in the history of language…

Arsenic Life Wrap-Up: The Good, the ‘Not-So-Good’ by See Arr Oh:

“Arsenic Life,” a hot-button issue for much of the past year, reemerged this week with two new papers, one propitious, and one, well…not so much….

In defense of frivolities and open-ended experiments by Bradley Voytek:

My first child was born just about nine months ago. From the hospital window on that memorable day, I could see that it was surprisingly sunny for a Berkeley autumn afternoon. At the time, I’d only slept about three of the last 38 hours. My mind was making up for the missing haze that usually fills the Berkeley sky. Despite my cloudy state, I can easily recall those moments following my first afternoon laying with my newborn son. In those minutes, he cleared my mind better than the sun had cleared the Berkeley skies…

Women’s Work by Virginia Hughes:

I write mostly about neuroscience, genetics and biotechnology. That means I spend most of my time talking to and writing about men.

In May of 2011 (chosen arbitrarily just because it was a year ago and I’m pretty sure I wasn’t thinking about this gender gap then), 89 percent of my phone interviews were with men.

I can think of a few reasons for this…

The Mechanics and Meaning of That Ol’ Dial-Up Modem Sound by Alexis Madrigal:

Of all the noises that my children will not understand, the one that is nearest to my heart is not from a song or a television show or a jingle. It’s the sound of a modem connecting with another modem across the repurposed telephone infrastructure. It was the noise of being part of the beginning of the Internet…

I’m not a speciesist, but… by Jack Scanlan:

Is it a paradox to hate your own species? Is such a feeling the product of a broken and conflicted mind? Or could it perhaps be the signature of psychopathy? Every day these questions run through my mind and I feel guilty. Why? Well, because I do hate my own species. Homo sapiens is terrible, and I’m surprised more people don’t recognise this…

The science and ethics of voluntary amputation by Mo Costandi:

…In January 2000, the mass media ran several stories about Robert Smith, a surgeon at the Falkirk and District Royal Infirmary who had amputated the legs of two patients at their own request and was planning a third amputation. The news stories incorrectly described the patients as suffering from Body Dysmorphic Disorder. They further stated that the director of NHS trust running the hospital at which Smith works described the amputation of healthy limbs as “inappropriate”; since then, no British hospital has performed a voluntary amputation…

In Defense of Mickey Mouse Science by Byron Jennings:

…I suppose one could hook up the computers directly to the experiments and have them generate models, test the models against new observations and then modify the experimental apparatus without any human intervention. However, I am not sure that would be science. Science is ultimately a human activity and the models we produce are products of the human mind. It is not enough that the computer knows the answer. We want to have some feeling for the results, to understand them. Without the simple models, Mickey Mouse science, that would not be possible: the big news made ever so small…

From plaster to programming: How borrowed technologies are changing paleontology by Justine E. Hausheer:

In popular culture, paleontologists are like Indiana Jones. Rugged men wandering through rocky deserts, wearing wide-brimmed leather hats and multi-pocketed khaki vests. Rock-hammers hang nonchalantly from their belt-loops, maps and note-pads protrude from pockets. On a whim, they brush aside some sand to reveal a ferocious skull and massive vertebrae, and then they puzzle out the mysteries of dinosaurs just by staring at the rocks. But in contemporary science, paleontologists are biologists, computer programmers, and engineers…

 

Special topic: Scientists, Journalism and Outreach

Eh, the whole week started with The Unwritten Rules of Journalism by Adam Ruben and then the blogosphere exploded – see for yourself:

Make Me Feel Something, Please by Soren Wheeler

Will Scientists Ever Get Science Writing? by Deborah Blum

Science Careers Magazine: A platform for a funny guy who says he really hates science journalism by Charlie Petit

Keep Cool Science Journalists by Khalil A. Cassimally

Congratulations! You’re Dumb! by Matthew Francis

Science is more than freaks and circuses by Paul Livingston

A KISS for communicating science by biochembelle

Scientists Engaging With The Public: Let’s Get Started and Talking About Science: Why Do You Do What You Do? by Matt Shipman

Summary of the #ReachingOutSci Series by nature.com Communities Team

On Outreach: something’s got to give by scicurious

A Call To Arms For Young Science Journalists by Khalil A. Cassimally

Which came first, rewarding outreach or doing it? On chickens, eggs, and overworked scientists by Kate Clancy

The root of problems by Zen Faulkes

Quick thoughts on the what and why of science outreach by Cedar Riener

Where Have All the Scientists Gone? by Magdeline Lum

Why are scientists trapped in the ivory tower and what can be done to escape? by Jeanne Garbarino

Speak Up, Scientists! by Tom Bartlett

So You Want To Communicate Science Online: The Flowchart by Miriam Goldstein

Some Scattered Thoughts on Outreach Work by Eight Crayon Science

One Venus transit – but many kinds of scientific outreach by Chris Rowan

 

Best Videos:

A Wildlife Rescue Center for New York City by Rachel Nuwer, video by Kelly Slivka and Kate Yandell.

The Curious Sex Lives Of Animals (VIDEO) by Cara Santa Maria and Carin Bondar

What we didn’t know about penis anatomy (video) by Diane Kelly

CreatureCast – Ginko (video) by Casey Dunn

Fruitfly Development, Cell by Cell (video) by Joe Hanson

 

Science:

How Our Disinterest in ‘The Environment’ Signals the End of Nature by Christopher Mims

Dramatic impacts on beach microbial communities following the Deepwater Horizon oil spill by Holy Bik

I Point To TED Talks and I Point to Kim Kardashian. That Is All. by Carl Zimmer

NASA’s Manned Venus Orbital Mission and This Is What Happens When Galaxies Collide and The X-15′s First Glide by Amy Shira Teitel

North Carolina’s attempted ban on sea level rise is a boon for Global Draining researchers by Southern Fried Scientist

How Intuition and the Imagination Fuel Scientific Discovery and Creativity: A 1957 Guide by Maria Popova

Battleship Earth: Does the Pentagon have the right weapons to fight off an alien invasion? by Cara Parks and Joshua E. Keating

Is Arsenic the Worst Chemical in the World? and The Arsenic Diet by Deborah Blum

Bad Reaction: The Toxicity of Chemical-Free Claims by Sharon Hill

Peptide shows potential to reverse skin fibrosis and Turning down the heat revs up brown fat by Kathleen Raven

Mermaids Embodies the Rotting Carcass of Science TV and Time for a Dinosaur Attack? by Brian Switek

David Dobbs and science storytelling: Lost in your brain. by Paul Raeburn

Piscine Geriatrics and Update on the iFish by whizbang

“HULK SMASH GM” – mixing angry Greens with bad science by Martin Robbins

For an Isolated Tribe, Time Follows the Terrain, and the Future is Uphill by Valerie Ross

Turning Scientific Perplexity into Ordinary Statistical Uncertainty by Cosma Shalizi

Credible Amelia Earhart Signals Were Ignored by Rossella Lorenzi and More Amelia Earhart Nonsense by Brian Dunning

“How do you feel about Evidence-Based Medicine?” by Harriet Hall

Wind-aided birds on their way north by Liz O’Connell

Transit of Venus through the ages by Jonathan Nally

Attempts to predict earthquakes may do more harm than good by David Petley

Reporting Preliminary Findings by Steven Novella

What makes sea-level rise? by Stefan Rahmstorf

Detectable but not hazardous: radioactive marine life of Fukushima by Miriam Goldstein

Elaine Fuchs: “There’s no comfortable route for a scientist” by Rachel Zwick

Why the GOP distrusts science and Conservatives Attack Scientific Findings About Why They Hate Science (Helping to Confirm the Science) by Chris Mooney

Jumping Vampire Spiders Choose Victims by Headwear and Why You Can’t Kill a Mosquito with a Raindrop and Rare Blooms by Elizabeth Preston

To study vampire spiders, build Frankenstein mosquitoes and Cockroaches and geckos disappear by swinging under ledges… and inspire robots and Giant insects disappeared thanks to falling oxygen levels and agile birds and Bacteria turn themselves into living electric grids by sending currents down mineral wires and How to weigh dinosaurs with lasers and Will we ever… clone a mammoth? by Ed Yong

New species are found all the time, even in Europe. by Tim Parshall

Sunday morning musings by PalMD

Winning the climate culture war and The top five things voters need to know about conservatives and climate change by David Roberts

Genetic Modification – What’s the big deal? by Donna

Cancer on the Brain by David Ropeik

Learning by Making: American kids should be building rockets and robots, not taking standardized tests. by Dale Dougherty

“Arsenic bacteria”: If you hadn’t nailed ‘im to the perch ‘e’d be pushing up the daisies by Ashutosh Jogalekar

BP Demands Scientist Emails in Gulf Oil Spill Lawsuit by Brandon Keim

Will Lex Luthor save North Carolina from climate change? by Michael Yudell

Coordinated Hunting in Red Devils by Craig McClain

Use it or lose it? by Levi Morran

Natural voyeurism: Animal webcams make peeping Toms of us all by Kelly Slivka

Why We Don’t Believe In Science by Jonah Lehrer

Mermaids do not exist, and five other important things people should, but do not, know about the ocean by WhySharksMatter

Transits of Earth from Other Planets by John Rennie

Bend me, shape me: flexible electronics perform under punishing conditions by Matthew Francis

The Invasivore’s Dilemma by Michelle Nijhuis

Beware Of The Branches: The Impacts Of Habitat Structure On Locomotion And Path Choice by Timothy Higham

Science Hubris, or Shame on You, Mayim Bialik by Lucy E. Hornstein MD

Your guide to zombie parasite journalism by Carl Zimmer

Science Gallery Pushes Art With A Social Conscience by Lucas Kavner

This Is Your Quail on Drugs, Behaving Badly by Neda Semnani

Making neuroscience public: Neurohype, neuroscepticism and neuroblogging by Brigitte Nerlich

Dictators Turn Strangely Benevolent in Online Game by Dave Mosher

The Platypus Fallacy. by T. Ryan Gregory

What You Know About the Difference in Dolphins and Porpoises is Wrong by SoundingTheSea

Has the public’s understanding of science devolved into a perverse worship of uncertainty? by Pamela Ronald

Darwin’s ‘clumsy’ prose by Angelique Richardson

Life and science challenges: flames, Hawkeye, the needle and the damage done by Jeanne Garbarino

Mars One: The Martian Chronicles or Big Brother Live on Mars? by Danica Radovanovic

Driving without a Blind Spot May Be Closer Than It Appears by Rachel Ewing

I love waking up to bad science in the morning paper by Rachel Felt

Interloper of the Venus Transit by Phil Plait

Brian: The Typographical Error that Brought Early Career Neuroscientists and Artists Together by Megan J. Dowie, Erin Forsyth and Leah Forsyth

How can I stop…… stammering? by Stuart Farrimond

Identical Twins, Different Lives by Neuroskeptic

That Antidepressants In Water Cause Autism Study by Neuroskeptic, and Fish, Antidepressants, Autism and a Problematic Research Premise by Dorothy Bishop, and Taking the Bait: A Fish (and autism) Story by Deborah Blum

Zombies are not a health problem (for us). Should they be a solution? by Jonathan Purtle

Portrait of the Archaeologist as Young Artist by Heather Pringle

Building a Shadow CV by Jacquelyn Gill

WHO adopts global vaccine action plan by Gozde Zorlu

The Republican Brain: The perils and promise of taking a stand. by Paul Raeburn

N. Carolina Senate decides to include science in sea level projections after all by John Timmer

 

Media, Publishing and Technology:

Lessons in blogging (and tweeting) from Samuel Pepys by Justin Ellis

Social Networks Over Time and the Invariants of Interaction by Samuel Arbesman

This I believe about journalism, newspapers and the future of media by Tim J. McGuire

Beyond citations: Scholars’ visibility on the social Web by Judit Bar-Ilan, Stefanie Haustein, Isabella Peters, Jason Priem, Hadas Shema and Jens Terliesner

Wi-Fi and Amtrak: Missed Connections by Ron Nixon – obviously written by someone who’s never boarded anything but Acela, which is notorious for bad wifi. I find wifi perfectly usable on the Carolinian route of Amtrak.

The North West London Blues by Zadie Smith

SPARC Open Access Newsletter, issue #164 by Peter Suber

Facebook will sell me to you, and you to me by Scott Rosenberg

A brief history of Car Talk: “They’ve changed the way people see public radio in America” by Andrew Phelps

Ebook revolution can kindle a passion for publishing by Ed Victor

My Gettysburg oration: A vision for journalism that can long endure by Steve Buttry

All A’Twitter: How Social Media Aids in Science Outreach – Chapter 6: Struggles of Facebook for the Multipurpose Marine Cadastre and Chapter 7: Survey Design by Caitlyn Zimmerman

Not a fan of the big Bitly revamp? Here are 9 alternatives by Nancy Messieh and A little free advice for Bitly by Dave Winer

Added Value: I do not think those words mean what you think they mean and 25,000 signatures and still rolling: Implications of the White House petition by Cameron Neylon

Sustainable quality by Dan Conover

Revisiting the View from Nowhere by John L. Robinson

How Writing A Science Blog Saved My PhD and 3 Mandatory Tools For Digital Scientists by Julio Peironcely

How the Internet Became Boring by Christopher Mims

“Dear Author” by Ted C. MacRae

What Is a Blog Post? by Rob Jenkins

Startup Culture: Values vs. Vibe by Chris Moody

Ask TON: Organizing notes by Jeanne Erdmann and Siri Carpenter

Why Reporting Is Ripe For Innovation by Vadim Lavrusik

Guys! I Have the Next Big Thing: A Social Network for Hermit Crabs by Alexis Madrigal

Arianna Huffington says HuffPo’s ‘sideboob’ news page is meant as a joke by Ruth Spencer

Does your newsroom have a smart-refrigerator strategy? by Adrienne LaFrance

How to improve environmental coverage? by Curtis Brainard

10 Timeframes by Paul Ford

It’s a Googly World: A Map of the Planet’s Most Visited Websites by Country by Rebecca J. Rosen

Twitter Gives you the Bird by Armin and Twitter’s new bird logo by Dave Winer

The great newspaper liquidation by Jack Shafer

ScienceOnline2012 – interview with Kathryn Bowers

Every year I ask some of the attendees of the ScienceOnline conferences to tell me (and my readers) more about themselves, their careers, current projects and their views on the use of the Web in science, science education or science communication. So now we continue with the participants of ScienceOnline2012. See all the interviews in this series here.

Today my guest is Kathryn Bowers (blog, Twitter).

Welcome to A Blog Around The Clock. Would you, please, tell my readers a little bit more about yourself?

I’m a writer and editor and have just finished a book, called Zoobiquity. It explores a simple but provocative question: how would our health improve if human doctors talked with animal doctors? After all, animals and humans get many of the same diseases—from cancer, heart disease, and obesity to mental health conditions like anxiety, depression, and eating issues. Yet physicians and veterinarians almost never consult one another. Exploring comparative medicine quickly brings up issues of shared physiology, shared biology, and shared genetics. And so the book also is informed by a healthy dose of evolutionary biology and behavioral ecology.

I co-wrote it with Barbara Natterson-Horowitz, who’s a cardiologist and psychiatrist at the UCLA Medical Center. A few years ago she began volunteering her time at the Los Angeles Zoo. Mornings she can be found performing heart procedures on human patients at UCLA hospital; on some afternoons, she might be examining a chimpanzee, sea lion, condor, or python. She was telling me about the many crossovers she was seeing between human and animal patients, and we were both surprised by how surprised we were. Obviously humans are animals, and intellectually we understand that we share not just many “raw materials”—bones, blood, hearts, nerves—but also environments (and in some cases behaviors that evolved to respond to those environments). The fascinating ubiquity of the overlap between human and animal health spurred us to research and write the book, and also gave us the idea for our title, which combines the Latinate “ubiquity” with the Greek root for animal, “zo.”

Where are you coming from (both geographically and philosophically)? What is your background? Any scientific education?

I grew up in a scientific household. My father, Arthur Sylvester, is a geologist (now emeritus) at UC Santa Barbara. Some of my earliest memories are set against the backdrop of his second floor office on campus: relief maps covered the walls, nearly every available surface held rock samples, fossils, minerals, and stacks of books and papers. Downstairs a special room housed an object of wonder and magnificence: a seismograph. I sometimes accompanied him on weekends to change the long scrolls of paper, and he’d show me the jagged lines indicating all the mini-earthquakes that had happened that week—which I hadn’t felt. I realized that the Earth had secrets. On family vacations along California’s remote back highways, no USGS benchmark went un-hiked-to, no roadcut unphotographed (roadcuts, those vertical slices cut through hills to facilitate new highways, are the joy of every geologist because the strata reveal themselves in naked, unvegetated splendor.) Our house was often filled with geologists, paleobotanists, geochemists, physicists, seismologists, and hydrologists…and of course, trilobites, granite slabs, academic journals and maps.

Most field scientists are—or become—ardent naturalists. My father was always interested in conservation and the interdependence of the plants and animals he encountered. In the Mojave Desert, Death Valley, the Sierra, and many of his overseas field sites, he taught me to peer closely at rock crystals, fossils, and wildlife. But he also made sure I never lost sight of the big picture—entire geologic formations, mountains, continents. It’s impossible to grow up with a geologist and not absorb a deep appreciation for time—and by extension, evolution. There’s a wonderful description of architecture as being like “frozen music.” I’ve always preferred the grander idea that geology is frozen time. Once you know that all of Yellowstone National Park is a giant volcanic crater or that the peaks of the Himalayas used to be at the bottom of a sea, or that the solid granite cliffs of Norway’s fjords are rising at infinitesimally slow speeds we can’t perceive, you develop a profound appreciation for your personal (and our species’) position on Earth. In Zoobiquity, we urge readers to keeping looking “farther left” on the evolutionary timeline – beyond early hominids and even primates —for the shared links that connect human health to everything that came before it.

If my dad was the scientist, my mom was the communicator. She’s a teacher, a writer, and a born investigator. Resourceful, endlessly creative, always up for an adventure, she’s one of the best researchers I know. She was also the true techie of my family, so any interest I have in electronic communication comes straight from her. And she let me do things like join 4-H and raise rabbits in our back yard.

So although my degree is a B.A., not a B.S., and although I’ve worked in journalism and editing rather than as a scientist, I did have an informal training in science that prepared me well to co-author a book that attempts to bring together human medicine, veterinary medicine and evolutionary biology.

Tell us a little more about your career trajectory so far: interesting projects past and present?

I graduated from Stanford and went straight to Boston, to intern at the Atlantic Monthly. I became an assistant and worked my way up to staff editor. Under the tutelage of the Atlantic’s brilliant editors, I learned the importance of checking sources, facts, and back-stories.

In Boston, I met my husband, Andy Bowers. When he became the London Bureau Chief for NPR, we moved to London for three years, and after that, to Moscow. In London, I worked as a writer-producer for CNN-International; in Moscow, I served as an assistant press attaché for the American Embassy. Andy is now a senior editor at Slate, where he pioneered and oversees all their podcasts. He’s an amazing writer and editor and plays a huge role in helping me shape and polish my own thinking and writing. After we returned to the United States I spent many years as a freelance book editor before starting work on Zoobiquity. Currently, I’ve been teaching a course on medical narrative at UCLA. I designed it with the specific goal of teaching future physicians how to communicate their science better—through personal non-fiction stories that use the tools of the fiction writer but are scrupulously reported and sourced.

And I’ve recently become the associate editor of the biology section of Evolution: This View of Life.

What is taking up the most of your time and passion these days? What are your goals?

At the moment, launching Zoobiquity takes up most of my time. But here’s something that surprises me: after nearly five years of starting many sentences with “did you know that animals….[fill in the blank here]…get shingles; engage in foreplay; seek out intoxicating substances, die of stress-induced heart attacks…” I’m still fascinated by the subject. You’d think at some point I’d start getting blasé about, if not bored by, our many overlaps with our animal cousins. But our deep connection to all living things—even plants—is endlessly fascinating to me.

If you’re a scientist (or hang out with them all the time) you might not quite realize the extent to which even important news from your field doesn’t trickle into the general consciousness. This is useful for both scientists and science communicators to remember: no one can be an expert on every topic, so a reader’s lack of knowledge about your field doesn’t indicate ignorance or disinterest. And it also doesn’t imply an inability to understand your work. It’s just a matter of choosing your material carefully and presenting it in non-jargony ways.

What aspect of science communication and/or particular use of the Web in science interests you the most?

I am by nature a synthesizer. I love working with other people. My idea of a good time is a big brainstorming session, with white boards, lots of colored pens, and smart people who are inclined to say, “yes, and what about…?” The Web’s ability to connect people seems especially suited to science, which thrives on a special combination of personal vision and group collaboration. Journalism shares that. I’d like to inspire more “humanities types” to geek out a little. C’mon, English majors, learn a little bit about genetics, why don’t you? Historians: maybe epigenetics has some role in the rise and fall of human civilizations? Dancers, musicians and art historians: could there possibly be some underlying animal behaviors that make human artistic endeavors less a pure product of culture and more a trait we share with many living beings?

I also love how the Web allows scientists to learn how to communicate with non-scientists. Blogs like this one, which fill an important niche between the peer-reviewed journals and the sometimes-fatuous coverage of science in the mainstream media, are connecting smart readers with researchers and clinicians who want their work to be more widely understood.

How does (if it does) blogging figure in your work? How about social networks, e.g., Twitter, Google Plus and Facebook? Do you find all this online activity to be a net positive (or even a necessity) in what you do?

Our Zoobiquity website is built on a Tumblr, which I really like. But my favorite social media outlet is Twitter (more on that below). I tweet as @kathrynsbowers and @Zoobiquity.

When and how did you first discover science blogs? What are some of your favourites? Have you discovered any cool science blogs by the participants at the Conference?

This will sound like transparent flattery, Bora, but believe me that it’s true: In the early stages of researching Zoobiquity, I came across “A Blog Around the Clock” and it became the first entry on my RSS reader.

Months later, when I finally got on Twitter, I almost entirely stopped reading RSS feeds. The satisfying cacophony of voices and dazzling array of topics that Twitter provided eclipsed the slower scouring of blog posts I used to do. (I grant that I lost some depth in favor of breadth.)

I was somewhat late to Twitter, but I had the good fortune to time my plunge into it very well: my first day on Twitter was literally the Monday after ScienceOnline2011 wrapped up. As the participants traveled home, my shiny, newly hatched Twitter feed crackled with excitement, connection, hilarity, camaraderie. “Who ARE these people?” I thought, frantically adding follow after follow. For weeks I sat quietly listening, working up the nerve to enter the conversation.

I was determined to find a way to join the exchange…and ecstatic when I secured a spot for Scio2012.

More adulation, but again it’s perfectly true: I value Twitter for one simple reason, the ScienceOnline community. I think that people who don’t “get” Twitter simply haven’t found a community like ScienceOnline. (I’m not a leading voice in the community. I just really appreciate the conversations and multiple entry portals it provides.)

As for blogs and tweeters: I love Jason Goldman’s topics and sensibility; I wasn’t able to meet her at Scio2012, but Kate Clancy’s intelligence rings loud and true through her writing; Jennifer Frazer has a gorgeous tone to her writing—delicate and descriptive, also funny and philosophical. I’m half terrified of, half in love with Emily Willingham. They’re usual suspects, but Steve Silberman, Deborah Blum, Christopher Mims, Maryn McKenna, Sci Curious, David Dobbs and Ed Yong are must-follows.

What was the best aspect of ScienceOnline2012 for you? Any suggestions for next year? Is there anything that happened at this Conference – a session, something someone said or did or wrote – that will change the way you think about science communication, or something that you will take with you to your job, blog-reading and blog-writing?

The whole conference was fulfilling, but a few things stand out:

Creative Buzz: I was driving out to the Duke Lemur Center. I was stuffed in the very back row of the van, in a seat far from the door. I was just about to succumb to a serious case of claustrophobia when the woman sitting next to me pulled out her notebook. It was full of the MOST memorable, witty images. She had just been to Perrin Ireland’s graphic-note taking seminar. I thought, “wow, this is a whole new way of communicating that I’ve never seen before.” It changed the way I thought of how to interact with a lecture-style seminar. And it kept me from having to ask the driver to stop the van.

Openness/Access: It was very exciting to see luminaries just strolling around like normal people. And to a person they were willing to talk. Is it too name-droppy to say that meeting Diane Kelly was a thrill? Ed Yong? Carl Zimmer and Jonathan Eisen? Deborah Blum and Joanne Manaster were unbelievably welcoming. So were Sarah Chow, Holly Bik, and Jeffrey Perkel. And that down-to-earth quality was evident in just about everyone I approached, from seat-mates on the shuttle to fellow caffeine-addicts at breakfast.

Humor: The stories at the banquet—every one of which was publishable or broadcast-able—were striking. They were so funny and honest. On individual levels, I found a similar degree of playfulness among the people I met. I appreciated being with a group of really smart, hard-working people who also love having a good time, unpretentiously.

Thank you, Bora, for the spirit of community you’ve fostered and led. And thanks for the opportunity to appear on your blog!

Thank you! Hope to see you again in January.

The Scienceblogging Weekly (June 1st, 2012)

Blog of the Week:

Vintage Space is a blog by Amy Shira Teitel, science writer and historian of space exploration living in Arizona. She has been busy lately, contributing articles to Discovery News, Motherboard, Spaceflight Observer podcasts, Scientific American Guest Blog, Soapbox Science blog, Timeline Magazine, AmericaSpace and Universe Today, among else. Vintage Space is her writing laboratory, where she first explores topics she may subsequently expand into longer pieces for other venues. And she links to all of her articles as they go live in various places so you can keep up with her prolific output. Those of you regular readers of Scientific American blogs may remember her guest posts, and for those of you not familiar, those can give you the taste of her fascinating forays into the history of space: Sky Crane – how to land Curiosity on the surface of Mars and Apollo 1: The Fire That Shocked NASA and John Glenn: The Man Behind the Hero.

Top 10:

Nicotine and the Chemistry of Murder by Deborah Blum:

The 1850 murder of Gustave Fougnies in Belgium is not famous because of the cleverness of his killers. Not at all. They – his sister and brother-in-law – practically set off signal flares announcing their parts in a suspicious death.

It’s not famous because it was such a classic high society murder. The killers were the dashing, expensive, and deeply indebted Comte and Countess de Bocarmé. The death occurred during a dangerously intimate dinner at their chateau, a 18th century mansion on an estate in southern Belgium.

Nor it is remembered because the Comte died by guillotine in 1851 – so many did after all.

No, this is a famous murder because of its use of a notably lethal poison. And because the solving of this particular murder changed the history of toxicology, helped lay the foundation for modern forensic science. The poison, by the way, was the plant alkaloid nicotine….

Richard Dawkins, Edward O. Wilson, and the Consensus of the Many by David Sloan Wilson:

…I mean Dawkins and Wilson no disrespect by calling them two among many. I trust that they would agree and would defer to others especially when it comes to mathematical models, which is not their area of expertise. If the public is going to become literate on the issues at stake—as well they should, because they are fundamental to the study of human sociality—then they will need to realize that both Wilson and Dawkins get some things right and other things wrong. Moreover, the entire community of scientists is in more agreement than the infamous exchange in Nature seems to indicate. Taking the argument from authority seriously can lead to a breakthrough in the public’s understanding of social evolution. …

The protein makes the poison: Dancing fruit flies and terfenadine by Ashutosh Jogalekar:

…Dose-specific toxicity is indeed of paramount importance in medicine, but if you delve deeper, the common mechanism underlying the toxicity of many drugs often has less to do with the specific drugs themselves and more to do with the other major player in the interaction of drugs with the human body – proteins. Unwarranted dosages of drugs are certainly dangerous, but even in these cases the effect is often mediated by specific proteins. Thus in this post, I want to take a slightly different tack and want to reinforce the idea that when it comes to drugs it’s often wise to remember that “the protein makes the poison”. I want to reinforce the fact that toxicity is often a function of multiple entities and not just one. In fact this concept underlies most of the side-effects of drugs, manifested in all those ominous sounding warnings delivered in rapid fire intonations in otherwise soothing drug commercials…

The trouble with brain scans by Vaughan Bell:

Neuroscientists have long been banging their heads on their desks over exaggerated reports of brain scanning studies. Media stories illustrated with coloured scans, supposedly showing how the brain works, are now a standard part of the science pages and some people find them so convincing that they are touted as ways of designing education for our children, evaluating the effectiveness of marketing campaigns and testing potential recruits…

Cloaking the rainbow by Rose Eveleth:

Invisibility cloaks aren’t just for Harry Potter anymore. Last year, researchers made one that cloaked things in time. Now they’ve made thousands of tiny invisibility cloaks that trap a rainbow. That’s right, 25,000 invisibility cloaks trapping a rainbow. The first question you might be asking is: why? Why does it take 25,000 invisibility cloaks to trap a rainbow? Or maybe, why trap a rainbow in the first place?

An Analysis of Blaster Fire in Star Wars by Rhett Allain:

You have no idea how long I have been planning to look at the blasters in Star Wars. No idea. Finally, the 35th Anniversary of Star Wars has motivated me to complete my study (which I haven’t actually started). Here is the deal: What are these blasters? How fast are the blaster bolts? Do the blasters from the spacecraft travel at about the same speed as the handheld blasters? Why do people still think these are lasers?…

Don’t worry so much about being the right type of science role model by Marie-Claire Shanahan:

What does it mean to be a good role? Am I a good role model? Playing around with kids at home or in the middle of a science classroom, adults often ask themselves these questions, especially when it comes to girls and science. But despite having asked them many times myself, I don’t think they’re the right questions…

Evolutionary psychology: A dialogue by Jeremy Yoder:

A Biologist went down to the coffee shop one day, because the walk out to the edge of the University campus provided some brief respite from the laboratory. Along the way the Biologist encountered an Evolutionary Psychologist, who was also going to the coffee shop, and they fell to walking together…

How I Stopped Worrying (about science accuracy) And Learned to Love The Story by Phil Plait:

When I was a kid – and who am I kidding; when I was an adult too – I made fun of the science in movies. “That’s so fakey!” I would cry out loud when a spaceship roared past, or a slimy alien stalked our heroes. Eventually, my verbal exclamations evolved into written ones. Not long after creating my first website (back in the Dark Internet Ages of 1997) I decided it would be fun to critique the science of movies, and I dove in with both glee and fervor. No movie was safe, from Armageddon to Austin Powers…

The Fantastic Gliding Stegosaurus by Brian Switek:

Stegosaurus is undoubtedly one of the most perplexing dinosaurs. What was all that iconic armor for? (And how did amorous stegosaurs get around that complication?) Paleontologists have been investigating and debating the function of Stegosaurus ornamentation for decades, but without much consensus. The dinosaur’s spectacular plates were certainly prominent visual signals, but could they also have been used for regulating body temperature? Or might there be some evolutionary impetus we’re not thinking of?

 

Science:

The Anatomy of a Videogame-Scare Story by Brian Fung

My Favorite Toxic Chemical by John Spevacek:

Urban trees reveal income inequality and Home Income inequality, as seen from space by Tim De Chant

Neuroscientists should study Zombie Ants by TheCellularScale

Octopuses Host a Masterclass on Hiding by Elizabeth Preston

Toxic Carnival: Day Three and Toxic Carnival: Day Four and Toxic Carnival: Day Five by Matthew Hartings

Social Sauropods? by Brian Switek

Birds Have Juvenile Dinosaur Skulls by Brian Switek

Ecological complexity breeds evolutionary complication by Jeremy Yoder:

Fire-chasing beetles sense infrared radiation from fires hundreds of kilometres away by Ed Yong:

Crowdfunding as the future of science funding? by Anthony Salvagno

Revisiting why incompetents think they’re awesome by Chris Lee. “Dunning-Kruger study today: The uninformed aren’t as doomed as the Web suggests.”

Lost in your brain by David Dobbs – “When science writer David Dobbs is suddenly unable to remember how to drive his kids to school, he sets off on a quest to understand his own brain, and makes a shocking discovery.”

Earth took ten million years to recover from Permian-Triassic extinction by Duncan Geere

Of Darwin, Earthworms, and Backyard Science by Anthony Martin

The great Pacific garbage reality by Usha Lee McFarling – “The great Pacific garbage reality. It’s not tsunami debris we should fear; it’s the trash clogging our oceans.”

The snakes that eat caviar by Andrew Durso

On the humanity (or lack thereof) of the X-Men by Megan M. McCullen

Tuatara reptile slices food with ‘steak-knife teeth’ by Victoria Gill

Traumatized animal radically changes diet and behavior in an unhealthy way: the real story of the “vegetarian shark” by David Shiffman

Reaching Out: Why are scientists trapped in the ivory tower and what can be done to escape? by Jeanne Garbarino

Keep shouting. You never know who is listening. by Emily Finke


Media, Publishing and Technology:

We need to reinvent the article by Sean Blanda

Blogonomics, ten years on by Henry Copeland

The 10 Biggest Social Media Lies by Mike Elgan

The Floppy Disk means Save, and 14 other old people Icons that don’t make sense anymore by Scott Hanselman

Wikipedia as an explainer by Dave Winer

Libre redistribution – a key facet of Open Access by Ross Mounce

Amid Tweets and Slide Shows, the Longform Still Thrives: How the form survives in this digital era by Emma Bazilian

Making More Scientists by John Wilbanks

What is it that journalists do? It can’t be reduced to just one thing by Jonathan Stray

Why “We the People” should support open access by Bill Hooker

Live chat today at noon about science blogging, circadian rhythms, sleep, metabolism and evolution

Join Robin Lloyd and myself today at 12 noon EDT for the first edition of the Scientific American Fast Chat. Log in and ask questions, and we’ll try to answer. The whole thing will last about 30 minutes.

Best of May at A Blog Around The Clock

I posted 22 times in May. That is, on A Blog Around The Clock only (not counting the posts on The Network Central, The SA Incubator, Video of the Week, Image of the Week, or editing Guest Blog and Expeditions).

Brand new posts:

Clocks, metabolism, evolution – toward an integrative chronobiology
The SA Incubator, or, why promote young science writers?
When Should Schools Start in the morning?
3 Science Questions to Ask U.S. Presidential Candidates
How barley domesticated its clock
Under construction – ITER in LEGO
Shaq and the Mini-Shaq, the extreme primates.

Best-of-the-Web linkfests:

The Scienceblogging Weekly (May 11, 2012)
The Scienceblogging Weekly (May 18, 2012)
The Scienceblogging Weekly (May 25th, 2012)
Today at The Browser

Updates, News and Announcements:

Open Laboratory…getting closer!
Upcoming science/sci-comm events

Several new ScienceOnline interviews:

ScienceOnline2012 – interview with Lali Derosier
ScienceOnline2012 – interview with Joe Kraus
ScienceOnline2012 – interview with Sarah Chow
ScienceOnline2012 – interview with Mark Henderson
ScienceOnline2012 – interview with Adam Regelmann

Some posts republished from the old archives:

Why social insects do not suffer from ill effects of rotating and night shift work?
Domestication – it’s a matter of time (always is for me, that’s my ‘hammer’ for all nails)
(Non) Adaptive Function of Sleep
Chossat’s Effect in humans and other animals

Previously in the “Best of…” series:

2012

April
March
February
January

2011

December
November
October
September
August
July
June
May
April
March
February
January

2010

December
November
October
September
August
July
June
May
April
March
February
January

2009

December
November
October
September
August
July
June
May
April
March
February
January

Clocks, metabolism, evolution – toward an integrative chronobiology

The biannual meeting of the Society for Research on Biological Rhythms happened last week. Unfortunately, I could not attend, so will have to wait another two years for the next opportunity.

I am not sure how this stuff happens, but there was a flurry of new papers in the circadian field just preceding the event. Several of them have already received quite a lot of attention in both old and new media, and rightfully so, but I decided not to cover them one at a time just as the embargo lifted for each one of them.

Instead, I will just very briefly describe and explain the main take-home messages of each one of them, link to the best coverage for those who want more detail (“Cover what you do best. Link to the rest.“), and then try to come up with more of a ‘big picture’ summary of the current state of the field.

I apologize in advance for covering and linking to some of the papers that are not published in Open Access journals. I am not as strict about this policy as some other bloggers are (“if my readers cannot access it, they cannot fact-check me”), and will occasionally cover non-OA papers. Even if most of my readers cannot access them, I gather that a miniscule proportion can access and, if I got something wrong, can alert the other readers in the comments. And speaking of Open Access, I am not one to sign many online petitions, but this one is worth it so please sign if you have not done it already.

So, let’s see what new and exciting in chronobiology these days…

~~~

BRAIN

Article: Ben Collins, Elizabeth A. Kane, David C. Reeves, Myles H. Akabas, Justin Blau, Balance of Activity between LNvs and Glutamatergic Dorsal Clock Neurons Promotes Robust Circadian Rhythms in Drosophila, Neuron, Volume 74, Issue 4, 706-718, 24 May 2012

What is it about: Robustness of daily rhythms and their flexible, adaptive responses to the environment, require a feedback loop between a cluster of clock cells in the brain and another cluster of non-clock cells in the brain of Drosophila melanogaster.

What is new: Feedback loops between two or more brain centers (or tissues, or organs) as necessary for either existence of some circadian rhythms, or for the rhythms’ robustness and fine-tuned response to the environment, have been studied mostly in vertebrates, especially birds and lizards, and to some extent mammals. Such feedback loops have been found in the fruitfly as well. This paper finds out a lot of detail about this feedback loop, including the use of glutamate as a neurotransmitter in one half of the loop. As Drosophila is still the lab organism with the most developed techniques for precise genetic manipulations, this is an important advance.

Take-home message: How core clock genes turn each other on and off within a cell over 24 hours is just the beginning, a small part of the story. To work properly, to be adaptive, and to respond well to environmental cues, circadian rhythms require organization at a higher level, with fine-tuned communication among clock-cells and between clock and non-clock tissues.

Some more thoughts: This is a technical tour-de-force. Fruitfly genetics techniques today are so powerful and this paper appears to use them all: inserting, deleting, downregulating and upregulating genes of choice in precisely targeted cells in the brain. As every behavioral biologist knows, once introduced into an experiment animals do whatever the heck they please. The behavior measured in this paper was a simple light-avoidance test – fruitfly larvae (and in the last experiment, also adults) are placed in a petri dish that is half in light, half in darkness, and the movement and position of the larvae is monitored. Considering how messy such behavioral data tend to be, the results in this paper are quite impressive.

The Abstract/Summary, the Introduction, and the (far too short) Discussion are very clear, straighforward and easy to read and understand. They are also upfront and direct about their main take-home message. The many pages in-between, though, are clearly meant to be read only by Drosophila clock geneticists who can actually wade through the essentially endless litany of acronyms in hope of replicating or following up on this study. Clocks are my field, but I am not a geneticist or drosophilist, so much of the Materials & Methods and Results sections in this paper are over my head. Maddeningly, some of the most important stuff is hidden in the Supplemental Materials, including this model for how the whole thing works (shouldn’t this image be up front, on the top of the whole thing?):

Drosophila neuron model

Drosophila neuron model

Note: If I remained in research, I would have done something like this, not necessarily in fruitflies, but definitely looking at neural networks, feedback loops and higher-level organization of the circadian system, within ecological and evolutionary contexts. This may bias me toward liking this paper as much as I do.

Good coverage elsewhere: None that I can find. Only a warmed-up (and not that good) press release at Futurity and ScienceDaily.

~~~

EVOLUTION

Article: Rachel S. Edgar et al., Peroxiredoxins are conserved markers of circadian rhythms, Nature, Published online 16 May 2012, doi:10.1038/nature11088

What is it about: A protein (peroxiredoxin) that is found in almost all living organisms has two states/conformations that cycle at approximately 24 hours. Presence and proper function of core circadian clock genes is not necessary for the cycling of this protein. An Archea species that does not live on the surface does not have the clock and does not have this protein.

What is new: This finding in human red blood cells and a Protist (O.tauri) was published last year. This paper adds similar data for a whole bunch of other organisms: cyanobacteria, archaea, fungi, plants, insects and vertebrates.

Take-home message: There are really two take-home messages, one physiological, one evolutionary. First, this demonstrates that circadian clocks are properties of the entire cells (or assemblages of cells in case of multicellular organisms), not just the transcription/translation loops of core clock genes.

Second, the protein in question, the peroxiredoxin, could be akin to “scaffolding”, something that allows a cell to keep cycling while genes come and go, mutate and change and duplicate, while being fine-tuned by natural selection. Over billions of years, this can result in major groups of organisms (e.g., animals vs. plants vs. fungi vs. bacteria, vs. several different groups of protists) having entirely different circadian genes, yet all of them using the same “logic” (transcription/translation feedback loops).

Both the peroxiredoxins and the circadian clocks are thought to have originated as defense from UV radiation of the early oceanic surfaces (Pittendrigh, C.S., 1967. Circadian rhythms, space research, and manned space flight. In: Life Sciences and Space Research 5:122-134. North-Holland, Amsterdam.), or defense against other kinds of demage, including that from oxidation, so it makes sense that they co-originated and co-evolved only once in the history of the planet, perhaps around 2.5 million years ago when photosynthetis bacteria introduced lots of molecular oxygen into the Earth’s atmosphere. It also makes sense that they both are missing in organisms that have never lived close to the oceanic or terrestrial surface (e.g., many Archaea).

Essential reading: When the two papers (on red blood cells and the protists) came out last year, I wrote a very comprehensive post that places this research direction into historical, philosophical, methodological and even media context. There is not much in that post that would change with the publication of this new paper apart from additional confirmation in several new species. So just go and read it again.

Some more thoughts: Peroxiredoxins cycle in all kinds of different cells with an approximately 24 hour period. This makes them, almost by definition, circadian clocks. Last year’s papers also show that the peroxiredoxin clock dominates its phase over the clock driven by core circadian genes. But there is something still to find out, and it is important: can the peroxiredoxin clock drive any other rhythms? For it to work as a biological pacemaker, it is not sufficient for it to cycle itself, it also need to drive timing of other events in the cell (and the entire organism). I am assuming that this research group will look at this problem next.

Mammals have six peroxiredoxin genes. In an experiment (Zhang et al., Cell , 2009), human cell lines were engineered in such a way that each culture had a different peroxiredoxin gene knocked out. None of the knock-outs had any effect on the regular circadian expression of the core clock gene Bmal1. Of course, having six genes indicates redundancy in function. One would need to knock out all six simultaneously in order to see an effect on other rhythms in the cell, but there is a question if cells with all peroxiredoxins knocked out can survive at all. Someone should try this.

Also, that experiment was done in mammalian cells. Mammals are probably the worst model system for studying this question. Vertebrates have undergone several events of gene (and genome) duplication, and mammals got at least another one. If you look at mammals, every clock gene exists in multiples (e.g,. Per1, Per2, Per3). Poor peroxiredoxin probably cannot do much in such a massively genetically determined system.

Gene duplication allows for evolutionary experimentation. As long as one copy of the gene keeps working, the others are free to mutate. Some mutations will be selected against (e.g., if they mess up the clock function) and others will be selected for (e.g., if they fine-tune the circadian function, making it more flexible and adaptable, or start performing some other valuable function instead). This means that functions formerly in the domain of higher-level organization or the domain of phenotypic plasticity, are now under control of genes. This process is called Genetic assimilation (and sometimes Baldwin effect, though that term is usually reserved for genetic assimilation of learned behaviors). So it is quite possible that the clock in mammals is over-determined by genes, making it useless for the study of peroxiredoxins as scaffolding for circadian evolution.

If I was doing this research, I would stay away from these vertebrate oddballs for at least the next five or ten years, and focus my time, funds and energy on the study of bacteria, archaea, protists, fungi and perhaps some plants – smaller the genome the better.

Good coverage elsewhere: Great coverage by Ed Yong, Megan Scudellari and Ewen Callaway. Was also covered by Debora MacKenzie.

Additional reading: Whence Clocks? and Clock Evolution

~~~

Article: Faure, S., Turner, A.S., Gruszka, D., Christodoulou, V., Davis, S.J., von Korff, M. & Laurie, D.A. Mutation at the circadian clock gene EARLY MATURITY 8 adapts domesticated barley (Hordeum vulgare) to short growing seasons, Proceedings of the National Academy of Sciences, DOI: 10.1073/pnas.1120496109

What is it about: In barley cultivars from Northern Europe a mutation in a gene responsible for flowering feeds back on the circadian clock genes, greatly reducing the amplitude of the gene cycling, effectively shutting down the clock. Without proper clock function, barley does not use the clock to measure seasonal changes in daylength (photoperiodism) but instead matures at the fastest rate its development permits. This allows barley to mature and flower early in the season, as well as to photosynthetise throughout the long days of summer in the North.

What is new: Yet another organism in which some of the clock function is temporarily or permanently eliminated. Good news: unlike the other such organisms which tend to be not-well-studied inhabitants of extreme environments, barley is a domesticated plant, well researched and easy to use in the lab.

Take-home message: one has to be careful with interpreting studies like these – just because an organism does not show a couple of well-studied rhythms in physiology and behavior, and does not show cycling in expression of core clock genes does not mean that all circadian function is gone. Ensembles of cells, or feedback loops between tissues, or cytoplasmic factors like peroxiredoxin may still be working in the organism, it’s just that this cannot be detected with the techniques used in the study.

Good coverage elsewhere: As far as I know, I am the only one who covered this paper.

~~~

REPRODUCTION

Article: Summa KC, Vitaterna MH, Turek FW (2012) Environmental Perturbation of the Circadian Clock Disrupts Pregnancy in the Mouse. PLoS ONE 7(5): e37668. doi:10.1371/journal.pone.0037668 (Open Access)

What is it about: Female mice kept in 24 cycles get and remain pregnant easily. Female mice kept in rotating shifts (either advances or delays of the 24 hour cycle by 6 hours every several days) do not. Difference is striking!

What is new: Interactions between circadian rhythms and reproductive cycles have been studied for decades in many different organisms. Last year, a study with already pregnant mice moved to rotating shifts did not result in spontaneous losses of pregnancy. This study suggests that rotating shifts prevent pregnancy to begin in the first place, probably by interfering with implantation of the egg in the uterus.

Take-home message: Another example how clock is not just about timing of downstream events, but also plays part in them more directly. While this study was done in rodents, it works well together with epidemiological data from humans working on rotating shifts. As the light-dark cycle is shifted, the brain clock resets itself pretty quickly, over a period of a couple of days. But peripheral clocks in all the other organs will reset slower, each at its own rate. This include the ovaries, uterus etc, which may not be ready for egg implantation at the time of day when the brain send the relevant signal. In essence, internal desynchronization of clocks prevents all the parts of the system to work in synchrony – this is the main negative effect of jet-lag, and it applies to reproduction as much as it does to digestion and other functions.

circadian phaseshift pregnancy

Effect of entrainment on success of pregnancy

Some more thoughts: Both the paper and the media coverage are clear, straightforward and readable. But if one wanted to explain these data by building a formal/conceptual or mathematical model this could easily get mind-bogglingly complicated: one would have to take into account multiple feedback loops between repeatedly desynchronized oscillators, plus potential effects of photoperiodism.

Good coverage elsewhere: Sarah Fecht did a great job. Most of the rest of the media just regurgitated the press release. Oh, this was even covered by Daily Mail 😉

See also: Oxytocin and Childbirth. Or not.

~~~

CANCER

Article: Johnni Hansen, Christina F Lassen, Nested case–control study of night shift work and breast cancer risk among women in the Danish military. Occup Environ Med doi:10.1136/oemed-2011-100240

What is it about: A large-scale study of Danish female soldiers found a higher incidence of breast cancer in those who had to work night shifts. Longer the period of night-shift work, greater the incidence. Also, early risers were more susceptible to this negative effect of night shift work.

What is new: Earlier studies were mostly done in nurses in the USA. This provides a much larger data-set of women followed over a long period of time in a different profession in a different country. Military environment also controls for many other aspects of life (food, quality of medical care, physical fitness, etc.) which tends to be more uniform than in the general population.

Take-home message: Prolonged night shift work, especially if you are an early bird, may be bad for your health.

Some more thoughts: Internal desynchronization between various body clocks, especially long-term, is bound to have negative consequences. Suffering from jet lag occasionally when traveling is fine. But getting jet-lagged every day for years is seriously impairing all sorts of body functions (see reproduction above).

Good coverage elsewhere: Steven Reinberg

~~~

METABOLISM

Article: Yuta Fuse, Akiko Hirao, Hiroaki Kuroda, Makiko Otsuka, Yu Tahara and Shigenobu Shibata, Differential roles of breakfast only (one meal per day) and a bigger breakfast with a small dinner (two meals per day) in mice fed a high-fat diet with regard to induced obesity and lipid metabolism. Journal of Circadian Rhythms 2012, 10:4 doi:10.1186/1740-3391-10-4 (Open Access)

What is it about: Three groups of mice were fed a high-fat diet, each group getting exactly the same amount of food each day (and eating it all up each day). One group had free access to food at all times (and ate all the time). The second group was given food in a limited time regimen: a large breakfast and a small dinner. The third group was given all the food to gobble up in one large brekfast. The group that got only a large breakfast got obese, had other metabolic problems and had a disrupted expression of circadian genes.

What is new: Another interesting paper showing that timing of meals determines how the food is processed by the body.

Take-home message: Eating one big meal per day is bad for your health – spread it out a little.

Some more thoughts: The paper is interesting as the data suggest something different from most of the other papers in this line of research (see the next two papers below).

Good coverage elsewhere: I could not find any.

~~~

Article: Megumi Hatori, Christopher Vollmers, Amir Zarrinpar, Luciano DiTacchio, Eric A. Bushong, Shubhroz Gill, Mathias Leblanc, Amandine Chaix, Matthew Joens, James A.J. Fitzpatrick, Mark H. Ellisman, Satchidananda Panda, Time-Restricted Feeding without Reducing Caloric Intake Prevents Metabolic Diseases in Mice Fed a High-Fat Diet. Cell Metabolism, 17 May 2012 doi:10.1016/j.cmet.2012.04.019

What is it about: Groups of mice were fed either normal or high-fat diet either with continuous free access to food or with feeding time limited to 8 hours during the night (remember that mice are nocturnal – this is their active period, i.e., their “day”). The results appear to be opposite from the paper above (by Fuse at al.) – it is the mice with unlimited feeding that got obese and developed metabolic problems, as well as reduced amplitude of the circadian gene expression.

What is new: Hmmm, which one of the two papers is “more right” than the other? The devil is in the details, so we’ll have to look there.

There are two obvious differences between the two papers. The Hatori paper gave full volume of the normal daily intake of food, while the Fuse paper gave mice only 80% of the normal food quantities per day – which is calory restriction in itself. This may explain why the free-feeding mice in Hatori paper got obese and developed problems, while the mice in the Fuse paper did not.

Second, there is a difference in timing of meals in time-restricted groups. There is “time-restricted feeding” and then there is “time-restricted feeding”! The Hatori paper restricted feeding to an 8-hour period starting one hour after lights-off and ending three hours before lights-on. The Fuse group gave breakfast at the moment of lights-off (the paper does not say for how long – presumably with reduced diet the hungry mice just ate it all very fast) and a smaller “dinner” at the moment of lights-on. These are very different timing schedules!

In many ways, the two-meal schedule of the Fuse paper is similar to the time-restricted schedule of the Hatori paper. Note that these two schedules did the best in regard to obesity and metabolism. Both the free-feeding (especially with the full diet in the Hatori paper) and extremely restricted feeding (brief but huge breakfast in the Fuse paper) resulted in bad metabolic effects. One can perhaps conclude that extremes are bad – one huge meal is bad as is continuous grazing, but that the spread of feeding over two or more smaller meals does better.

Take-home message: The perennial “more research is needed”….until then it is wise to eat your meals at normal times, more than once per day, no grazing in-between, and no midnight snacks…

Hatori image

Effect of feeding regimen on body weight and metabolism

Some more thoughts: Hatori paper is….overwhelming! There is so much work done. As I was reading it all, my thought was that ten pages in the middle of the paper could be completely cut out of the paper and the result would still remain exactly the same – just weigh the mice! All sorts of things were measured in a variety of ways, from gene expression patterns, to standard metabolic tests to histology. All that work strengthens the notion that obesity and metabolic problems are correlated, so the work is definitely not for nothing, and is very impressive. It certainly adds a lot of information to the notion that circadian clock is not just a timer, but intimately involved in regulation of metabolism.

Good coverage elsewhere: Peter Janiszewski, Ph.D. and Garth Sundem. Also see Michael Coston. There was plenty of coverage in mainstream media, mostly OK, some bad…

~~~

Article: Till Roenneberg, Karla V. Allebrandt, Martha Merrow, Céline Vetter, Social Jetlag and Obesity. Current Biology, Volume 22, Issue 10, 939-943, 10 May 2012. doi: 10.1016/j.cub.2012.03.038

What is it about: A huge number of Europeans from various ages, latitudes and longitudes were assessed for a variety of circadian, sleep and health parameters. It turns out that most suffer from “social jet-lag” – an internal desynchronization between various body clocks as a result of continuous mismatch between the natural body rhythms and societally and culturally imposed wake-up, school, work and bed-time schedules. During the school/work week, people are massively sleep deprived. They then make up for it, “paying off the sleep debt”, over the weekends. The difference between the amount of sleep one gets on work/school nights and the amount of sleep one gets during the weekend is especially stunning in adolescents, whose internal clocks are naturally phase-delayed and thus most dramatically out of sync of what the society is forcing them to do:

roenneberg image

Average sleep time by age and gender (top) and discrepancy between workday and weekend sleep (bottom)

One of the most remarkable results is that people with the largest workday/weekend discrepancy, the most socially jet-lagged individuals, are also most prone to smoking, drinking, obesity and other health problems. Naturally thin people (B) did not get obese if they were more sleep deprived, but those somewhat prone to obesity became obese if they were also sleep deprived due to social jet-lag:

roenneberg image2

Effect of social jetlag on obesity in obesity-prone people (top) and thin people (bottom)

What is new: Bits and pieces of this were known for a while. But nobody has ever done such a tremendous study on such a large number of people, controlling for so many factors and measuring so many parameters and so many outcomes. This is definitely a tour-de-force paper of the year in this field and is appropriately matched with a brand new book by the lead author – Internal Time: Chronotypes, Social Jet Lag, and Why You’re So Tired – which I am currently reading.

Take-home message: Socially imposed school and work schedules are messing with our health. Political will is needed to change the mindset, change the culture, and change the way we use time in the society.

Some more thoughts: This paper goes together well with the several papers described above – living a life outside of synchrony with the light-dark cycle of the natural environment (and no, artificial indoor light cannot match it) has serious health consequences, leading to metabolic, physiological, reproductive and psychological problems that negatively affect billions of people on Earth, and cost the society billions of dollars of lost productivity, unnecessary medical care, and loss of educational potential in teenage students. Watch the video:

Note: Again, and infuriatingly so, most of the interesting stuff is in the Supplemental Materials.

Good coverage elsewhere: Maria Popova, Jamie Condliffe, Robert T. Gonzalez, Allison Aubrey, Kate Southam and many others.

Additional readings: When Should Schools Start in the morning? and Everything You Always Wanted To Know About Sleep (But Were Too Afraid To Ask) and Sun Time is the Real Time.

~~~

SUMMARY

Genes are, for the most part, invisible to natural (and sexual) selection.

What evolution can work on are phenotypes – composites of anatomical, physiological and behavioral traits as they change during the development and lifetime of an organism. Genes are selected for, indirectly, inasmuch as they contribute to the phenotype. While in different organisms and in different cases selection may act on a number of different levels – genes, embryos, cells, organs, organisms, groups, species – usually the most important unit of selection is the individual organism.

How a gene contributes to the phenotype is affected by many factors – multiples ways of splicing it, multiple ways of post-translational modification, which other genes are present, where and when is it expressed during development, interactions between cells, tissues and organs, and interactions between the organism and its environment. As genes, chromosomes and genomes sometimes get duplicated, this provides more opportunities for traits, previously resulting from higher-level interactions, to get incorporated into the genetic instructions via the process of genetic assimilation.

The basic unit of life is the cell. A single-celled organism has to have all of its internal processes coordinated in order to display adaptive responses to the environment in order to survive and reproduce. In multi-celled organisms, each cell type has to behave properly, communicate properly with the other cells, and coordinate its activities with all the other cells in the body for the organism to display adaptive responses to the environment in order to survive and reproduce.

Molecules that do all, or almost all of the work are proteins. They build structures, they catalyze reactions, break down food, store and use energy, control communication between cells, regulate the expression of the genes, and more.

But proteins are hard to study! Nucleic acids are much easier – they are stable, inert, the 3D conformation does not matter, and laboratory techniques have been developed to discover, sequence and study snippets of DNA and RNA in ways that today can be done by middle-schoolers or in DIY science projects. When you have the hammer, everything is a nail. When you have genetic tools, your graduate students are instructed to use them. And then sometimes they forget why they are doing this in the first place…

We study nucleic acids because they are markers, or proxies, for proteins. We locate genes and hope that the processes of transcription, splicing and translation do not confound too much what the resulting proteins are and what they do. This means that study of genes – their sequences and patterns of expression – is a reasonable first step in studying a biological phenomenon as it provides us with tools and information needed to study proteins, cells and higher-order phenomena that are evolutionarily relevant.

Of the Big Four – anatomy, biochemistry, physiology, behavior – it is behavioral traits that are the furthest removed from the underlying genes. It is really difficult to find genes directly involved in behavior. Big screens for genes for behaviors usually come up with genes for kinases, neurotransmitter receptors, neuronal development factors and other generalized components of the nervous system.

Circadian clock is an exception. While one may argue that the clock is not actually a behavior but a physiological mechanism that regulates many other behaviors, it is still the closest to a behavioral trait we ever got in discovering underlying genetics. Most people in the field agree that all major genes involved in clock function have been discovered (mostly during the 1990s) and that it is not productive to search for more.

Sure, the Abstract book of last week’s SRBR meeting still contains some posters and blitz-sessions by students with a detailed genetics work (well, the students need to learn the techniques, right?), but most of the Big Honchos of the field have moved on – to properties of the entire cells, neural networks, properties of multi-clock systems, and interactions with the environment. In a sense, after a detour of the 1990s when all the focus and energy was placed into gene discovery (“opening the black box”), the field of chronobiology is going back to its roots – a historically incredibly comparative and integrative subdiscipline of biology.

For a long time we have thought of circadian clocks as simply timers – something that determines when other downstream functions happen. But evidence over the last couple of decades has accumulated that clocks are much more intimately involved in some of those functions, beyond just timing.

Ten years ago, when I was exiting the field, the interaction between clocks and metabolism was just starting to be explored. We learned that fruitfly clock-gene timeless is involved in cocaine addiction. We learned that mutations in clock genes that change circadian period also change other aspects of timing, from frequencies of fruitfly courtship songs, to developmental timing in nematodes, to photoperiodic responses, to reproductive cycles.

Today, involvement of the circadian clock in many aspects of metabolism is probably the most exciting and most heavily studied area in the field. And this is shown by all the papers I highlighted today. The focus away from identification of genes and moving on to proteins, cells, neural networks, multi-oscillatory systems, and interactions with the environment are making the field as exciting as ever, and in vanguard of much of the rest of biology which is still overly focused on DNA. And the findings have obvious and stark implications not just for our better understanding of Life, but also for understanding of adaptation of organisms to the changing climate, and for understanding the consequences on human health.

ScienceOnline2012 – interview with Adam Regelmann

Every year I ask some of the attendees of the ScienceOnline conferences to tell me (and my readers) more about themselves, their careers, current projects and their views on the use of the Web in science, science education or science communication. So now we continue with the participants of ScienceOnline2012. See all the interviews in this series here.

Today my guest is Adam Regelmann (Quartzy, LinkedIn, Twitter).

Welcome to A Blog Around The Clock. Would you, please, tell my readers a little bit more about yourself? Where are you coming from (both geographically and philosophically)? What is your background? Any scientific education?

Geographically: Minneapolis -> New York City (College, MD, PhD at Columbia) -> St. Louis (Residency at Wash U) -> Palo Alto (co-founder at Quartzy)

Philosophically: After working for many years in biomedical research labs, I became resolved to make science move faster. I believe one of the big problems in science, in both academia and industry, is a lack of a standardized lab infrastructure. We use the scientific method to think about how to test our observations, but there is no “laboratory method” for actually doing science.

Tell us a little more about your career trajectory so far: interesting projects past and present?

I have taken a somewhat circuitous route to my current life. I started my foray into Science as a 9th grader when I told my dad “I want to work with white blood cells this summer”. He was a professor at the University of Minnesota Medical School. He asked one of his colleagues if I could work in her lab. She said yes, and I began my first research project – examining the protease activity of of bronchial washings from patients with cystic fibrosis (CF). I found that better nourished CF patients had less proteolytic activity in their lungs than those with poorer nutrition. I was hooked, and, I spent the remainder of my high-school summers in the lab.

After high school, I attended Columbia University in New York and continued this summer tradition, working first for a chemistry professor, and then for a microbiologist. I published my first first-author paper with the microbiologist (biochemical analysis of a divalent cation sensor protein in E. coli and Salmonella), which was a wonderful feeling. I went on to complete an MD/PhD at Columbia, and during my research years I became increasingly aware and increasingly frustrated by the inefficiencies that plague scientific research.

I couldn’t believe that it was the 21st century and one of the best institutions in the country still used excel, whiteboards, paper and fax machines to coordinate daily activities in the lab. I started working on a project to help my lab, and when other labs became interested I realized that there was an immense need here. The big idea of coordinating all aspects of scientific research through a standardized online platform thrilled me, so my programmer-friend and I launched the system, called Quartzy with the aim of advancing research by making labs more efficient.

What is taking up the most of your time and passion these days? What are your goals?

Quartzy is a 24/7 job. Just ask my wife. I imagine a world where the pace of science is no longer dragged down by the inability to find the resources to do experiments. I would like for Quartzy to serve that purpose, which is why it’s free for scientists. I strongly believe that keeping Quartzy free is the only way for it to become the standard method for lab management. I would like scientists to be able to spend every dollar they have on actual experiments, not on lab management software.

Quartzy makes money from vendors. They can either have Quartzy host their catalogs, or participate in our marketplace, so users can buy directly from them through Quartzy. We also do some contract customization work. Over 12,000 scientists are on Quartzy. The cool thing is that as this number grows, the efficiency increases exponentially. For example, when a grad student leaves one lab and joins another, if both labs are on Quartzy the time it takes for her to start her new project is significantly lower since she’ll know where everything is.

What aspect of science communication and/or particular use of the Web in science interests you the most?

The development of web-based tools to enhance communication in the sciences is probably the most profound advance in the last decade. It has always been odd to me that the internet started as an instrument to allow scientists to efficiently communicate, but all the cool developments sprung up in the consumer sector, leaving the sciences in the dust. Although these new science-focused tools are all still in their youth, they have the power to completely disrupt every aspect of the scientific process from actually doing experiments to publishing results to peer review. The noise to signal ratio is a little high right now, since we’re in the “Wild-west” days of this movement, but that’s also why it’s an extremely exciting time.

How does (if it does) blogging figure in your work? How about social networks, e.g., Twitter, Google Plus and Facebook? Do you find all this online activity to be a net positive (or even a necessity) in what you do?

Absolutely positive. These networks are vital to communicating with our users, but also vital to communication in general at this point in time. Science has never been done in a vacuum, and these networks allow people to rapidly discover information that could have taken months to learn about otherwise. At first, I was overwhelmed at the prospect of using these tools in science, but if used correctly they can be a huge asset. Twitter and Facebook are especially powerful because of the size of their respective networks. If you’re a scientist right now and you’re not using at least one of these tools, you are at a significant disadvantage.

When and how did you first discover science blogs? What are some of your favourites? Have you discovered any cool science blogs by the participants at the Conference?

I’m not sure when I discovered them. It was probably when doing research for my PhD. Two specific blogs that I was made aware of at Scio12 are The Artful Amoeba and The Mother Geek. Also, it was super cool to meet Jonathan Eisen at the conference, whose blog I’ve followed for a while.

What was the best aspect of ScienceOnline2012 for you? Any suggestions for next year? Is there anything that happened at this Conference – a session, something someone said or did or wrote – that will change the way you think about science communication, or something that you will take with you to your job, blog-reading and blog-writing?

Because of ScienceOnline2012, I will probably become more active on google+. A lot of people were talking it up there. As far as the conference itself goes: much of the conference focused on navigating the intersection of science and writing, or how to improve your writing, which was great, but I was thinking it might be cool to invite some scientists to actually present some of their new data and see how all the science writers in the room cover the same presentations.

Thank you! Hope to see you again in January.

Upcoming science/sci-comm events

World Science Festival

World Science Festival will be in New York City on May 30th – June 3rd. Some events are sold out, but some still have tickets and some are free. I’ll try to go to a couple of events myself if I can.

Tweetups

Tweetups are very informal and open events – food and drinks only, not formal program – people interested in science, science communication, science policy, science journalism/writing/media, science blogging and social media, science education, scientific publishing, etc.

#DCSciTweetUp: If you are in Washington DC on May 31st, try to show up at the Pre-thirst #DCSciTweetUp – Dr. Matthew Francis is going to be in town to speak at Thirst DC and will come to chat with local scientists and science communicators at the Science Club, starting at 5:30pm.

Next #NYCSciTweetUp will be in New York City during the World Science Festival when guests are in town and locals are excited about science. We’ll meet on June 2nd. I’ll be there. Come by if you can.

Next #TriSciTweetup will be at The Looking Glass Cafe in Carrboro, NC on June 12th at 6pm.

#soNYC

The next #soNYC is on June 7, 2012 from 7:00 PM to 9:00 PM – the topic: Reaching out of the ivory tower.

The Story Collider

Next event, “I’m Not Science” will be at 8pm at Union Hall, Brooklyn, NY, on June 20th, 2012.

ScienceOnlineSeattle

Next ScienceOnlineSeattle (Facebook, Twitter, blog, hashtag #soSEA) event will be announced soon The first event, “Shared Science” – was storified here and recorded here. The second event, “Dances with Data” was storified here and the video recording is here.

ScienceOnlineVancouver

Next ScienceOnlineVancouver (Facebook, Twitter, blog, hashtag #soVAN) event will be on 12th June, 2012 from 19:00 to 21:00 Pacific time, at Science World at TELUS World of Science 1455 Quebec Street, Vancouver, BC Canada V6A 3Z7. The topic is: “Naked Science: Excuse me your science is showing” Livestream will be here.

You can find the video recording, Storify of tweets, and slideshows of presentations from the first event – “Where do you get your science?” – here. The second event, “Making contact” was recorded and storified here.

ScienceOnlineBayArea

Next ScienceOnlineBayArea (Twitter, Facebook, blog, hashtag #soBAY) event will be about Science Crowdfunding, on June 21st.

The Storify of tweets of the first event – “Data Visualization and Data Journalism in Science” – is here. Second event, “Social Media for Science Outreach”, was on May 24th – Storify to come soon.

Science Writers 2012

Science Writers 2012, the NASW/CASW annual meeting, will be on October 26-30, 2012 in Raleigh, NC. Registration opens on August 15th.

ScienceOnline2013

ScienceOnline2013, the flagship event of the ScienceOnline community, will be in Raleigh, NC on January 31st – February 2nd. You can add your suggestions for the program on the planning wiki. Registration opens in fall.

ScienceOnlineTeen

ScienceOnlineTeen, focused on science education, will be on Saturday, April 13, 2013 in New York City. Registration is now open, and the deadline for the Logo Contest is August 1, 2012.

The Scienceblogging Weekly (May 25th, 2012)

Blog of the Week:

Over the years, Better Posters blog has become the “Go To” place to send students when they start preparing posters for their first scientific meetings. Updated weekly, on Thursdays, this blog by Dr. Zen Faulkes (who also blogs at his other two awesome blogs NeuroDojo and Marmorkrebs, as well as on the #SciFund blog) provides ideas, suggestions, underlying theory, and thorough, fair critiques of poster design for scientific conferences. It is a link I (and I am sure many others) send whenever asked what is the best resource for preparing a good poster. Zen Faulkes also has a broader category of posts about presentations in general, both oral and poster, under the Zen of Presentations tag on his other blog.

Top 10:

Phineas Gage’s connectome by Mo Costandi:

Anyone who has studied psychology or neuroscience will be familiar with the incredible case of Phineas Gage, the railroad worker who had a metre-long iron rod propelled straight through his head at high speed in an explosion. Gage famously survived this horrific accident, but underwent dramatic personality changes afterwards. In recent years researchers reconstructed his skull and the passage of the rod through it, to try to understand how these changes were related to his brain damage. Now, neuroscientists from the University of California, Los Angeles have produced Gage’s connectome – a detailed wiring diagram of his brain, showing how its long-range connections were altered by the injury.

Replication studies: Bad copy by Ed Yong:

Positive results in psychology can behave like rumours: easy to release but hard to dispel. They dominate most journals, which strive to present new, exciting research. Meanwhile, attempts to replicate those studies, especially when the findings are negative, go unpublished, languishing in personal file drawers or circulating in conversations around the water cooler. “There are some experiments that everyone knows don’t replicate, but this knowledge doesn’t get into the literature,” says Wagenmakers. The publication barrier can be chilling, he adds. “I’ve seen students spending their entire PhD period trying to replicate a phenomenon, failing, and quitting academia because they had nothing to show for their time.” These problems occur throughout the sciences, but psychology has a number of deeply entrenched cultural norms that exacerbate them. It has become common practice, for example, to tweak experimental designs in ways that practically guarantee positive results. And once positive results are published, few researchers replicate the experiment exactly, instead carrying out ‘conceptual replications’ that test similar hypotheses using different methods. This practice, say critics, builds a house of cards on potentially shaky foundations…

Plan X; or, Planning White’s Small Step by Amy Shira Teitel:

In 1964, the launch schedule for the Gemini program was set and it was tight. Missions with new objectives would launch every eight to ten weeks taking NASA a step closer to the Moon each time. But hardware setbacks and some surprising feats by Soviet cosmonauts took a toll on the schedule. In the first half of 1965, NASA developed a plan that would see Gemini match and begin to overtake the Soviet Union in space. It was done largely in secret and known internally as Plan X….

Against the Infantilization of the Natural History Museum by Justin Erik Halldór Smith (and related: Relics With Much to Tell About Bird Diets May Be Lost to Time by Sarah Fecht):

…The project of exhaustively collecting and describing the basic kinds of large animal, and analyzing and displaying these animals’ bodily parts and systems, is a project that gained momentum in the late Renaissance and that was largely completed by the end of the 19th century. Like, say, realist painting in the Western tradition, it is a project that has a bounded history (indeed the two histories fairly closely overlap one another). This means that an alpaca intestine displayed in formaldehyde is a sample of a part of a South American camelid; but it is also an artefact of a modern European knowledge project. In this respect a proper natural history museum, that is to say an unreconstructed adult natural history museum, is really two museums at once: it is a museum of nature, but also a museum of the history of a very singular attempt to know nature quite literally inside-out….

What a Physics Student Can Teach Us About How Visitors Walk Through a Museum by Henry Adams:

….To devise a good layout requires some understanding of what museum visitors do, and there’s surprisingly little literature on this topic. Most of the studies of museum-goers that I’ve seen rely on questionnaires. They ask people what they did, what they learned, and what they liked and didn’t like. No doubt there are virtues to this technique, but it assumes that people are aware of what they’re doing. It doesn’t take into account how much looking depends on parts of the brain that are largely instinctive and intuitive and often not easily accessible to our rational consciousness. Was there another mode of investigation and description that would illuminate what was actually taking place?…

Lies You’ve Been Told About the Pacific Garbage Patch by Annalee Newitz:

You’ve probably heard of the “Pacific garbage patch,” also called the “trash vortex.” It’s a region of the North Pacific ocean where the northern jet stream and the southern trade winds, moving opposite directions, create a vast, gently circling region of water called the North Pacific Gyre — and at its center, there are tons of plastic garbage. You may even have seen this picture of the garbage patch, above — right? Wrong….

The (misunderstood) language of DNA by Genegeek:

I love analogies and use them often to get people to think about scientific concepts in new ways. I’ll share some of my favourite ones on the blog but today, I want to talk about Analogies Gone Bad….There is a lovely analogy to help people understand DNA code: DNA can be seen as a language…

Killers that sux by DrRubidium:

You might notice the sting of the injection. Within seconds you’d realize you’re having trouble moving your eyes and fingers, followed by your arms and legs. If you were standing, you’d collapse. In a heap on the floor, you’d realize nearly every muscle in your body was paralyzed. Being fully conscious, your sense of panic would be rising as rapidly as the paralysis was spreading. Swallowing and breathing has become more and more difficult. Slipping into unconsciousness, your last conscious thought may well be “I am going to die.”…

What Is the “Bible of Psychiatry” Supposed to Do? The Peculiar Challenges of an Uncertain Science by Vaughan Bell:

The American Psychiatric Association have just published the latest update of the draft DSM-5 psychiatric diagnosis manual, which is due to be completed in 2013. The changes have provoked much comment, criticism, and heated debate, and many have used the opportunity to attack psychiatric diagnosis and the perceived failure to find “biological tests” to replace descriptions of mental phenomena. But to understand the strengths and weaknesses of psychiatric diagnosis, it’s important to know where the challenges lie….

Do Plants Smell Other Plants? This One Does, Then Strangles What It Smells by Robert Krulwich:

“Plants smell,” says botanist David Chamovitz. Yes, they give off odors, but that’s not what Chamovitz means. He means plants can smell other plants. “Plants know when their fruit is ripe, when their [plant] neighbor has been cut by a gardener’s shears, or when their neighbor is being eaten by a ravenous bug; they smell it,” he writes in his new book, What a Plant Knows. They don’t have noses or a nervous system, but they still have an olfactory sense, and they can differentiate. He says there’s a vine that can smell the difference between a tomato and a stalk of wheat. It will choose one over the other, based on…smell! In a moment I’ll show you how….

Special topic: pigeons

Why Aren’t Cities Littered With Dead Pigeons? by John Metcalfe:

Any fair-sized city in the United States is lousy with pigeons, hoovering up bread crumbs from public squares and head-bobbing so much they look like little Jay Zs groovin’ to some fresh beats. The favorite rumpus room of the pigeon, New York City, is thought to contain anywhere between 1 and 7 million of the flapping rats of the sky. So where are all the dead ones?

Big Bird: Are New York’s pigeons getting fatter? An investigation into animal obesity. by David Merritt Johns

Pigeon GPS Identified by Megan Scudellari: “A population of neurons in pigeon brains encodes direction, intensity, and polarity of the Earth’s magnetic field.”

Pigeons have tiny compasses in their heads by Greg Laden.

Speaking pigeon by Kelly Slivka: Keeping up with New York City’s feathered underdogs.

Science:

The Zebra Neuron by TheCellularScale – Von Economo Neurons discovered in more and more species, lose the “human specialness” role.

Is the Purpose of Sleep to Let Our Brains “Defragment,” Like a Hard Drive? by Neuroskeptic. Or is it “Disk Cleaner”, or “Reboot”?

Gaming and Exercise: Will Diablo III Derail Your Discipline? by Melanie Tannenbaum – from the horse’s mouth – this research was done in her lab.

It’s supposed to hurt to think about it! by Ethan Siegel: “One of the most fundamental questions about the Universe that anyone can ask is, “Why is there anything here at all?””

Legal highs making the drug war obsolete by Vaughan Bell:

The Drachma and the Euro as a Cybernetic Question by Michael Tobis:

Life Traces as Cover Art and The Ichnology of Peeps by Tony Martin.

Copulatory vocalizations of chacma baboons (Papio ursinus), gibbons (Hylobates hoolock), and humans. by NCBI ROFL. Sonograms, thus it is science!

Putting the ‘Fear’ in Climate Change by Paige Brown – “Do scientists and climate communicators really need the ‘scary’ headlines and alarming facts to get media coverage?”

Energy Drinks: What’s the Big Deal? by Dirk Hanson: “The sons of Red Bull are sporting record concentrations of caffeine.”

Failure – what doesn’t get published in Psychology (for good reason?) by Åse Kvist Innes-Ker.

Uncertainty overdone by Bryan Walker: “As a concerned human being I don’t want scientists to soft-pedal on that evidence.”

A Sensitive Subject, on quantifying uncertainties in modeling climate change and its impacts, by Tamsin Edwards:

Could Angry Birds lead to mass murder? by Martin Robbins: “Attempts to link last year’s Norway shootings to Call of Duty are spectacularly misguided. Moral panic about violent video games is based on prejudice, ignorance and the selective use of flawed research.”

Chemistry at the hairdresser by JessTheChemist.

Our Favorite Toxic Chemicals and Toxic Carnival: Day One and Toxic Carnival: Day Two and Pain, Undoubtedly, Comes with the Cure by Matthew Hartings.

Neurons are like equations by TheCellularScale .

Persuasion and the Brain by David R. Gruber:

New sense organ helps giant whales to coordinate the world’s biggest mouthfuls by Ed Yong

In The Beginning Was the Mudskipper? by Carl Zimmer

Virtual resurrection shows that early four-legged animal couldn’t walk very well by Ed Yong

The Positively Biased Life by Matthew Chew on non-publication of negative data, and on ecology as a discipline.

Will you explain the differences (and similarities) between endemic and epidemic diseases? by Emily Willingham. Eeeek – imagine a pandemic of iguanas!

It is a mistake to eliminate government science. Part I and Part II by Simon Goring

Carpenter versus Aurora 7 by Amy Shira Teitel

You scientist, we want you to get ahead….but not too FAR ahead! by Anne Buchanan

Birding from parking level five: Suburban ospreys in Florida by Justine E. Hausheer

The smokeless stove: A partnership between academics and designers in New York City has produced a stove that could reduce child deaths in Africa by Emma Bryce

Media, Publishing and Technology:

Your 5-minute, 5-day orientation to Twitter by Anton Zuiker

Web Design Manifesto 2012 by Jeffrey Zeldman

The teacher I hated who changed my life by General Tso:

How to Deal with Information Overload by Walter Jessen and Simon Franz.

Can Blogs Be Used to Resolve Conflicts? by Greg Laden:

Data journalism research at Columbia aims to close data science skills gap by Emily Bell and Alex Howard

The Facebook Fallacy by Michael Wolff: “For all its valuation, the social network is just another ad-supported site. Without an earth-changing idea, it will collapse and take down the Web.”

How Amy O’Leary live-tweeted her own speech — and won the #backchannel by Andrew Phelps

The verdict: is blogging or tweeting about research papers worth it? and When was the last time you asked how your published research was doing? by Melissa Terras

Who gives a tweet? After 24 hours and 860 downloads, we think quite a few actually do by Kaisa Puustinen and Rosalind Edwards

Why newspapers need to lose the ‘view from nowhere’ by Mathew Ingram

Buzz Bissinger: Newspaper editors are “very cautious — too cautious” by Adrienne LaFrance

How obsession can fuel science blogging: The story of Retraction Watch by Ivan Oransky

Text mining: what do publishers have against this hi-tech research tool? by Alok Jha

Copy editing: It’s taught me a lot, but it has to change by Steve Buttry

3 Science Questions to Ask U.S. Presidential Candidates

As you may already be aware from my previous posts, The Guardian U.S. and NYU’s Studio 20 journalism lab have teamed up to push a project called The Citizens’ Agenda into the media discourse surrounding the U.S. presidential 2012 election. The idea: find out what you–the citizens–want the candidates to be discussing over the next four months – usually meaning questions of substance about policy rather than horserace and gotcha questions so pervasive in mainstream media.

A couple of weeks ago, I posted a call for the Scientific American community to provide us with the three most important science-related questions that they would like to see the candidates asked by the media or during presidential debates in the fall. The Scientific American community is one (actually the first to have this finished) of a number of topical communities providing questions. Naturally, our readers are interested in science, so we are focused on  the science topics here.

Our Facebook page post soliciting question received over 120 comments (as well as 104 Likes and 61 Shares). The blog post itself got an additional 18 comments. We asked you “What three science questions do you think the U.S. presidential candidates should answer before we vote on November 6?” and since some comments included multiple questions, we got a grand total of 246 questions!

I am extremely happy with the quality and quantity of the submitted questions. You took this seriously and came up with a number of excellent questions.

An informal scan of the questions leads me to categorize questions by focus. There are: questions that ask for candidates to state science facts; questions that ask candidates’ stances on hot and politicized science issues; questions that ask about the role of science in governing; and fun/silly/provocative questions

There is value in all four types of questions. Each one of them is multi-layered and is actually trying to examine the following:

– are candidates reasonably educated in basic science?
– are candidates well informed about current understanding of various aspects of the world?
– to what extent will candidates apply scientific knowledge and advice by scientists in shaping policy, as opposed to interest groups that may or may not adhere to empirical knowledge in their agendas?
– to what extent will candidate’s style of governing resemble scientific method: observing and studying the world as it really is (as opposed to what one wishes it to be), collecting and analyzing data, and applying best available remedies to the problems?

In short, all the questions are trying to get at this core issue: are the candidates reality-based?

But for purposes of our effort, we also had to classify the questions by topic.

Interestingly, the topic of greatest interest, judging from your responses (23 questions clearly and solely in this category), is Science Education – its value, its role in society, the role of federal government in regulating it, and the need for its reform and funding. Interestingly, Role of Government in Science (22 questions) is also mostly about science education, so we fused the two categories into one.

This question, by our reader Cherry Kersey probably captures it the best:

How important do you feel science and science related education is in young children and how would you affect change so that U.S. students are competitive with the rest of the western world in these key subjects?

Some other examples are:

Do you think that promotion of critical thinking is a primary goal of education?

What role does the federal government play in supporting scientific education, infrastructure and research?

From media reports, it seems the U.S.  lags behind many other developed countries in protecting the populace from harmful chemicals and substances. Our laws and regulations seem to be designed to protect business interests first and foremost, and only to protect the populace or environment when it has been clearly proven (for example, from a lot of people/animals dying or being sickened by something that has been on the market for a number of years) and there is public outrage. What would you do to address this?

How will you help the USA recapture its #1 place in the STEM sciences, and how is education part of this important agenda?

Do you support evidence based education? If not, how are we to improve education? If so, how soon can we get rid of No Child Left Behind, which had no pilot?

What is the cost of American college education relative to its value to students and to the nation at large? Please describe that cost/benefit ratio in terms of its distribution throughout the current population of students who are in college or who are about to attend. Is that ratio favorable or unfavorable? If less than favorable, what actions would you recommend as President to make it more favorable?

What role does the federal government play in supporting scientific education, infrastructure and research?

Can the decline in U.S. ranking in science be directly attributed to the anti-science policies of today’s conservatives, and what affects will the continuation of these policies have on the standing of the U.S. as a leader in science in the future?

Do you believe the federal government should place more emphasis on increasing the number of young Americans who pursue careers in science, technology, engineering or mathematics, or not?

Are you going to seriously fund scientific research? How will science help you develop policy? What are you going to do to make the benefits of scientific research benefit the American people?

In your opinion, who gets to decide the truth of a scientific concept? The people, the experts, or the well-funded?

What are you going to do to increase the number of scientists in office, ensuring the people making scientific decisions are in fact qualified to do so?

Will you support reestablishment of the Office of Technology Assessment to aid officials in proper evaluation of complex scientific issues? If not, why?

How will science help you develop policy?

What government body do we have to thank for the most inventions applicable to modern daily life in the last 50 years? (Answer is NASA)

~~~

The second topic, with 18 questions focusing entirely on it, is Evolution, still a hot topic in this country. Our chosen question is by our reader Joseph Yaroch:

Explain why you think voters should care about your stance on evolution.

Here is a sampling of some other related questions:

Do you understand the role natural selection has played in the development of complex life over the last several billion years?

What is your opinion on the debate of evolutionary theory vs creationism?

Do you accept the theory of evolution? If so, do you accept that simply saying so is counter-intuitive to our current legal financial subsidies binding church & state?

Do humans and apes have a common ancestor?

What actions will be taken on school boards across the country that are eliminating scientific evidence of evolution from the curriculum?

Are you willing to defend separation of church and state and support the teaching of evolution in schools?

~~~

The third most exciting topic to our readers, with 17 questions clearly and solely in this category, is Climate Change. The most representative question comes from our reader Eli Hernandez is:

Is global warming and climate change significantly and negatively affected by human industrial and fossil fuel consumption activity and if so what is our Government’s Role and Responsibility in mediating a solution?

Some more examples:

What should the US role be in controlling climate change and what would you do to advance it?

Even the most devout global warming advocates grudgingly admit that proposed regulations would only delay the inevitable (if global warming is in fact occurring), while the political/economic costs of such regulation would be devastating to the United States. Are you factoring the cost vs. the benefits of global warming regulation in your policy decisions? Will you publish this analysis?

How does the greenhouse effect work, and do you think that humans are interfering with its proper function?

Do you accept the scientific consensus on climate change and what policies do you propose to prevent and mitigate its effects.

Do you agree with over 90% of the world’s climate scientists that humans are at least CONTRIBUTING to global warming?

~~~

The topics that follow are Space Exploration, Energy, Science Funding, Environment+Sustainability, Economics, GMOs, and general science questions (of the “what is an electron?” type), as well as a number of other categories with just 1-2 questions.

Finally, there was a “Silly” category, with only 12 questions (yes, guys, you were serious about this project!). Our favorite in the Silly category is this one, by nouseforaname.

Was Jar-Jar [Binks] possible through evolution?

Now I really wish someone would ask that question in the debate!

~~~

Now that the questions are out, watch the The Guardian U.S. site for updates. Spread the word. Let’s all try to push for these questions to actually get asked of the candidates in the debates, or in other media outlets.

Chossat’s Effect in humans and other animals

This post was originally published on April 09, 2006.

This April 09, 2006 post places another paper from my old lab (Reference #17) within a broader context of physiology, behavior, ecology and evolution. The paper was a result of a “communal” experiment in the lab, i.e., it was not included in anyone’s Thesis. My advisor designed it and started the experiment with the first couple of birds. When I joined the lab, I did the experiment in an additional number of animals. When Chris Steele joined the lab, he took over the project and did the rest of the lab work, including bringing in the idea for an additional experiment that was included, and some of the analysis. We all talked about it in our lab meetings for a long time. In the end, the boss did most of the analysis and all of the writing, so the order of authors faithfully reflects the relative contributions to the work.

What is not mentioned in the post below is an additional observation – that return of the food after the fasting period induced a phase-shift of the circadian system, so we also generated a Phase-Response Curve, suggesting that food-entrainable pacemaker in quail is, unlike in mammals, not separate from the light-entrainable system.

Finally, at the end of the post, I show some unpublished data – a rare event in science blogging.

If you know what Chossat’s Effect is, I guess you are a) a physiologist, b) expert in thermoregulation, and c) old. This is term that got expunged from the scientific lexicon a few decades ago, in an effort – correct me if I am wrong on this – spearheaded by the U.S. textbook companies, to replace scientific terminology named after the discoverers (and sometimes even Latin and Greek terms) with bland English neologisms.

But I love Schwann’s Cells, Fallopian Tubes (or Mullerian Ducts), Purkinje Fibers, Brocca’s Area and the amazing Bundle of His! Those terms are memorable, make it easy to sneak in some historical context into teaching science, and have an emotional effect of bringing forth images of ancient scientists working under candlelight, sacrificing their eyesight and health, their social standing and sometimes even their lives, in the feverish hunger for knowledge.

So, what is Chossat’s Effect? It comes from a 19th century French scientist who was studying the physiology of starvation [1]. The ‘modern’ term for this effect is “fasting-induced nocturnal hypothermia” (doesn’t that sound like something that would prompt the students in the classroom to immediatelly stop paying attention to the teacher and instead pick-up their cell-phones and start text-messaging their friends?).

Actually, this is a very interesting area of research that is very tightly connected to circadian biology. This post is likely to be long, so feel free to skim and just focus on the first part if you are into birds, second part if you are interested in mammals, and the last part if you are into humans.

Birds

All warm-blooded animals (and yes, that includes at least some reptiles, not to mention a few heat-producing plants like stink-cabbage) exhibit a daily rhythm of body temperature. If an animal is active during the day (diurnal) and sleeps during the night, reducing the metabolic rate during the night is a good way to save energy.

Some of the smallest birds, like swifts and hummingbirds, need to feed continuously in order to stay alive. At night, when they are not able to forage (flowers are closed, it’s hard to see, and owls are hunting at the time), they drop their metabolic rate, and thus body temperature, quite dramatically. The body temperature gets down as low as the environmental temperature, sometimes daringly close to the freezing point. The total drop can be as large as 40 degrees Celsius in some instances! This is called daily torpor (yup, click on that link – it is an excellent blog post) and the metabolic rate drops as much as 95% [2, 3]. This is like full-scale winter hibernation EVERY DAY!

Chossat’s effect does not refer to daily torpor, though. It describes a drop in temperature during the night that is larger than the usual circadian fluctuation, in animals undergoing fasting, e.g., during spells of very bad weather (e.g., hurricanes).

Normal amplitude (daily maximum minus nightly minimum) of body temperature in birds with normal access to food ranges between about 1 and 2 degrees Celsius. For instance, a daily maximum may be 41 degrees and the nightly minimum may be 39 degrees (yes, the birds are much warmer than mammals, which makes them inhospitable to microbes that cause many mammalian diseases), which calculates to 2 degrees of amplitude.

During fasting (or food deprivation in the laboratory), the nightly minima drop down to lower levels than in fed birds. The minimum gets lower and lower with each additional night. Importantly, the daily maxima do not change at all. It is thought that it is advantageous for birds to retain their normal metabolic rates during the day so they can immediately resume foraging once the bad weather subsides. Also, if the bad weather persists for too long, the birds need the daytime metabolic rates in order to fly away [4].

According to John Wingfield’s “Emergency Life-History Stage” hypothesis [5], an individual’s perception of inclement weather directly affect the levels of stress hormones (e.g., corticosterone). An individual who does not perceive the bad weather to be “too bad”, will reduce daytime activity and reduce night-time temperature in order to save energy – this individual has made a decision to sit it out.

On the other hand, an individual who perceives bad weather to be “really bad” (or if it lasts too long) will have higher levels of stress hormones and will attempt to fly away during the day. This is not the same mechanism as the seasonal migration, which is usually a nocturnal flight, i.e., they do not experience Zugunruhe, just stress. Stressed birds do not attempt to escape at night, at which time they have allowed their body temperature to drop by several degrees.

Nocturnal hypothermia has been studied in a large number of species of birds (see, for examples, references # 6-12), but most of the work was performed on pigeons [13-15] and quail [16]. Not all avian species exhibit this response. Laurilla at al. [18] write:

“On the other hand, many large birds that are adapted to long fasting periods as a part of their life histories, e.g. penguins and geese (Cherel et al., 1988; Castellini andRea, 1992), owls (Hohtola et al., 1994) and some raptors (McKechnie andLovegrove, 1999) do not show marked hypothermia during fasting. Some species enter hypothermia upon food restriction only when isolated from conspecifics in a laboratory environment, while in the field they remain normothermic by huddling. These observations have even led some authors to question the usefulness of the concept of hypothermia (Lovegrove and Smith, 2003).”[8]

Here is a graphic example of a fasting-induced nocturnal hypothermia in quail (from[17]). The period between the two triangles is the time (3 days) during which the birds had water but no food. Before and after, birds were fed ad libitum. Below is a graph that shows the difference between the temperature minima during the first, second and third day (top) and night (bottom) of food deprivation in comparison to the last three days and nights of normal feeding prior to the fasting treatment:


Much of the more recent research is looking at other environmental cues that can modify the Chossat’s effect, as well as the involvement of the circadian clock in this time-specific form of thermoreguluation.

For instance, some of the ambient cues that affect the response include ambient temperature [16, 20], ambient light [17], photoperiod [18, 19], single vs. repeated fasting [18, 19], caloric food restriction vs. complete food deprivation [13], social situation, e.g., opportunity for huddling [8] and presence of stationary vs. flying predators [19, 20]. Here is an example of an effect of ambient temperature on nocturnal hypothermia in fasted pigeons (from [20]). Lower the ambient temperature, deepeer the Chossat’s effect:

Here is the effect of the presence of a predator (from [2]). In the presence of a perched hawk (P), nocturnal hypothermia reached normally low levels. In the presence of the flying hawk (F), temperature did not drop as much. Presumably, the pigeons kept the metabolic rate high enough to be able to fly fast if needed:

As stated above, hypothermia occurs only during the night while the temperature during the days remains normal. However, all the studies are performed either in natural conditions of day and night or in light-dark cycles in the laboratory. In constant darkness, the circadian rhythm of temperature persists and hypothermia is apparent. Moreover, the temperature drops both at the minima during the ‘subjective night’ and at the maxima during the ‘subjective day’ (from [17]):


This suggests that light has a direct (or “masking“) effect on body temperature during the light-phase of the cycle. But is this effect acting directly on the thermoregulatory centers in the hypothalamus or is it mediated by the circadian clock that drives the rhythm of body temperature? In Japanese quail, the circadian pacemakers are located in the eyes. When the eyes are removed [17], both the daily maxima in the light-phase and the nightly minima during the dark phase drop, suggesting that the effect is mediated via the circadian clock, as the light perceived by the photoreceptors in the pineal gland and in the deep brain is incapable of keeping the daily maxima from dropping:


Mammals

Some small mammals, such as smallest rodents and shrews, exhibit a full-blown daily torpor either normally [21] or in response to fasting [22]. Here is an example of a daily torpor of a mouse-opposum:

In nocturnal animals, which many mammals are, body temperature is high at night when the animals are active and it drops during the day when the animals are sleeping. In rats, fasting induces diurnal hypothermia, i.e., drop of the daily minimum during the day (black circles, compared to pre- and post- treatment values in white symbols) while the nightly maxima remain unaffected [23]:

Chronic caloric food restriction leads to the drop in both the daily minima and nightly maxima of temperature [24]. All the studies until recently have studied responses in relatively small animals (both birds and mammals) with high metabolic rates and high energy needs.

But do larger animals, like humans, also exhibit Chossat’s effect? After all, the first documented case, that by Chossat himself, was in a dog. This was repeated recently [25]. But even dogs are pretty small compared to humans.

Recently, researchers have addressed this question in a number of species of large mammals, including sheep, goats, horses and yaks [26-29]. Some additional environmental cues were also studied, including the effects of shearing on the circadian temperature rhythm in sheep [30]. Here is a record from a goat:

Notice that, unlike in birds, both the maxima and minima gradually go down.

But, as far as I could find by digging through the literature, nobody has ever performed a similar study in humans. I am assuming that it has been noticed if body temperature drops in fasted humans, but I am not aware of a study systematically addressing this question.

Humans

More than a decade ago I was teaching one of many sections of an Animal Anatomy and Physiology Course. This course requires students to perform a research project. One group of students studied the effects of fasting on body temperature and blood pressure in humans.

They found 8 subjects, all healthy, athletic, non-drinking, non-smoking students ages 19-23. They were instructed to eat normally during the Day1 of the experiment. They subsequently spent 36 hours in a house drinking only water and eating nothing. Every four hours, temperature and pressure were measured. By using kids’ digital ear thermometers and manual sphigmomanometers they managed, for the most part, not to awaken the subjects during the night. Here are examples of body temperature of three of the subjects – Night1, followed by Day2 and Night 2:



Here are the pooled data for all eight subjects, starting with Day2 and followed by Night1 and Night2 plotted on top of each other for comparison:

Obviously, body temperature of Night2, after a day of fasting, was lower than that of Night1, after the day of normal feeding. I do not have their raw data any more, but if I remember correctly, the data for blood pressure looked very similar. I heard they had a huge breakfast, courtesy of the young researchers, at the end of the experiment.

So, Chossat’s Effect appears to be operating in humans as well. Now, this is cool in itself, and I sure hope that someone with access to good clinical lab repeats this study, but there is something else about these data that really excites me. This finding can be used as a tool for studying something entirely different!

The Hypothesis

One of the first demonstrations that humans have daily rhythms involved the time-of-day dependence of time perception. In other words, our subjective “feel” of the speed of passage of time changes systematically with the time of day. At the same time, it has been known for a couple of centuries now that the subjective time perception is also altered during fever. And we know that circadian clock governs daily rhtyhms of body temperature.

So, what affects the time perception: time of day or body temperature? If the time passes faster in the evening than at dawn, is it because of the circadian clock acting on the time-perception brain-centers directly, or because we are warmer at the time (which is also driven by the circadian clock)?

This question has haunted circadian researchers for decades and they have devised ever more elaborate experiments to tease the two hypotheses apart, with no avail – we still do not know. But, if by depriving the subjects of food, we can dissociate clock-time from temperature, perhaps we can address this question after all. If the subjective perception of 1 minute (do not use 1 second or 1 hour – those are durations unsuited for this experiment) is similar between the night after a fed day and the night after the fasting day, then the perception is directly driven by the circadian clock.

If, on the other hand, perception of a minute changes systematically between the two nights, then we conclude that it is body temperature that affects subjective time perception. Please, someone do this! And if you do, or even if you just want to replicate the Chossat’s Effect in humans, I would appreciate it if you would properly cite this post:

Bora Zivkovic, Chossat’s Effect in humans and other animals (2006), A Blog Around The Clock, http://blogs.scientificamerican.com/a-blog-around-the-clock/2012/05/22/chossats-effect-in-humans-and-other-animals

REFERENCES:

[1] M. Chossat, Sur l’inanition, Paris, 1843
[2] Hiebert, S.M. 1990. Energy costs and temporal organization of torpor in the rufous hummingbird (Selasphorus rufus). Physiological Zoology . 63:1082-1097.
[3] Hiebert, S.M. 1991. Seasonal differences in the response of rufous hummingbirds to food restriction: body mass and the use of torpor. Condor 93:526-537.
[4] Tobias Wang, Carrie C.Y. Hung, David J. Randall, THE COMPARATIVE PHYSIOLOGY OF FOOD DEPRIVATION: From Feast to Famine, Annual Review of Physiology, January 2006, Vol. 68, Pages 223-251
[5] Wingfield, JC; Maney, DL; Breuner, CW; Jacobs, JD; Lynn, S; Ramenofsky, M; Richardson, RD, Ecological bases of hormone-behavior interactions: The “emergency life history stage”, American Zoologist [Am. Zool.]. Vol. 38, no. 1, pp. 191-206. 1998.
[6] Tracy A. Maddocks, Fritz Geiser, Energetics, Thermoregulation and Nocturnal Hypothermia in Australian Silvereyes, Condor, Vol. 99, No. 1 (Feb., 1997) , pp. 104-112
[7] Randi Eidsmo Reinertsen and Svein Haftorn, The effect of short-time fasting on metabolism and nocturnal hypothermia in the Willow Tit Parus montanus, Journal of Comparative Physiology B: Biochemical, Systemic, and Environmental Physiology, Volume 154, Number 1 (January 1984): 23 – 28
[8] Barry G. Lovegrove and Gary A. Smith, Is ‘nocturnal hypothermia’ a valid physiological concept in small birds?: a study on Bronze Mannikins Spermestes cucullatus, Ibis, Volume 145, Issue 4, Page 547 – October 2003
[9] MacMillen RE, Trost CH., Nocturnal hypothermia in the Inca dove, Scardafella inca, Comp Biochem Physiol. 1967 Oct;23(1):243-53.
[10] Colleen T. Downs, Mark Brown, NOCTURNAL HETEROTHERMY AND TORPOR IN THE MALACHITE SUNBIRD (NECTARINIA FAMOSA).
[11] Waite, TA, Nocturnal hypothermia in gray jays Perisoreus canadensis wintering in interior Alaska, ORNIS SCAND. Vol. 22, no. 2, pp. 107-110. 1991.
[12] Cécile Thouzeau, Claude Duchamp, and Yves Handrich, Energy Metabolism and Body Temperature of Barn Owls Fasting in the Cold, Physiological and Biochemical Zoology, volume 72 (1999), pages 170-178
[13] Rashotte ME, Henderson D., Coping with rising food costs in a closed economy: feeding behavior and nocturnal hypothermia in pigeons, J Exp Anal Behav. 1988 Nov;50(3):441-56.
[14] R. Graf, S. Krishna and H. C. Heller, Regulated nocturnal hypothermia induced in pigeons by food deprivation, Am J Physiol Regul Integr Comp Physiol 256: R733-R738, 1989
[15] Michael E. Rashotte, Iuri F. Pastukhov, Eugene L. Poliakov, and Ross P. Henderson, Vigilance states and body temperature during the circadian cycle in fed and fasted pigeons (Columba livia), Am J Physiol Regul Integr Comp Physiol 275: R1690-R1702, 1998
[16] Hohtola E, Hissa R, Pyornila A, Rintamaki H, Saarela S., Nocturnal hypothermia in fasting Japanese quail: the effect of ambient temperature, Physiol Behav. 1991 Mar;49(3):563-7.
[17] Herbert Underwood, Christopher T. Steele and Bora Zivkovic, Effects of Fasting on the Circadian Body Temperature Rhythm of Japanese Quail, Physiology & Behavior, Vol. 66, No. 1, pp. 137-143, 1999
[18] Mirja Laurila, Tiina Pilto, Esa Hohtola, Testing the flexibility of fasting-induced hypometabolism in birds: effect of photoperiod and repeated food deprivations, Journal of Thermal Biology 30 (2005) 131-138
[19] MIRJA LAURILA, THERMOREGULATORY CONSEQUENCES OF STARVATION AND DIGESTION IN BIRDS, PhD Dissertation, Faculty of Science, Department of Biology, University of Oulu, 2005 (http://herkules.oulu.fi/isbn9514277147/isbn9514277147.pdf)
[20] Mirja Laurila, Esa Hohtola, The effect of ambient temperature and simulated predation risk on fasting-induced nocturnal hypothermia of pigeons in outdoor conditions, Journal of Thermal Biology 30 (2005) 392-399
[21] Francisco Bozinovic, Gricelda RuÍz, Arturo CortÉs & Mario Rosenmann, Energetics, thermoregulation and torpor in the Chilean mouse-opossum Thylamys elegans (Didelphidae), Revista Chilena de Historia Natural 78: 199-206, 2005
[22] Lovegrove BG, Raman J, Perrin MR., Daily torpor in elephant shrews (Macroscelidea: Elephantulus spp.) in response to food deprivation, J Comp Physiol [B]. 2001 Feb;171(1):11-21.
[23] Kei Nagashima, Sadamu Nakai, Kenta Matsue, Masahiro Konishi, Mutsumi Tanaka, and Kazuyuki Kanosue, Effects of fasting on thermoregulatory processes and the daily oscillations in rats, Am J Physiol Regul Integr Comp Physiol 284: R1486-R1493, 2003.
[24] Yoda T, Crawshaw LI, Yoshida K, Su L, Hosono T, Shido O, Sakudara S, Fukuda Y & Kanosue K (2000) Effects of food deprivation on daily changes in body temperature and behavioural thermoregulation in rats. Am J Physiol 278: R134-R139.
[25] G. Piccione, G. Caola and R. Refinetti, Daily Rhythms of Blood Pressure, Heart Rate, and Body Temperature in Fed and Fasted Male Dogs, J. Vet. Med. A 52, 377-381 (2005)
[26] Giuseppe Piccione, Giovanni Caola, Roberto Refinetti, Circadian rhythms of body temperature and liver function in fed and food-deprived goats, Comparative Biochemistry and Physiology Part A 134 (2003) 563-572
[27] Piccione, G., Caola, G., Refinetti, R., 2002a. Circadian modulation of starvation-induced hypothermia in sheep and goats. Chronobiol. Int. 19, 531-541.
[28] Piccione, G., Caola, G., Refinetti, R., 2002b. The circadian rhythm of body temperature of the horse. Biol. Rhythm Res. 33, 113-119.
[29] Xing-Tai Han, Ao-Yun Xie, Xi-Chao Bi, Shu-Jie Liu and Ling-Hao Hu, Effects of high altitude and season on fasting heat production in the yak Bos grunniens or Poephagus grunniens, British Journal of Nutrition (2002), 88, 189-197
[30] Giuseppe Piccione, Giovanni Caola, and Roberto Refinetti, Effect of shearing on the core body temperature of three breeds of Mediterranean sheep, Small Ruminant Research 46 (2002) 211-215

ScienceOnline2012 – interview with Mark Henderson

Every year I ask some of the attendees of the ScienceOnline conferences to tell me (and my readers) more about themselves, their careers, current projects and their views on the use of the Web in science, science education or science communication. So now we continue with the participants of ScienceOnline2012. See all the interviews in this series here.

Today my guest is Mark Henderson (personal blog, work blog, Twitter).

Welcome to A Blog Around The Clock. Would you, please, tell my readers a little bit more about yourself? Where are you coming from (both geographically and philosophically)? What is your background? Any scientific education?

I’m now Head of Communications at the Wellcome Trust, the UK based biomedical research charity. Before that I was Science Editor of The Times in London for 11 years. And before that I really had very little to do with science at all. I did a history degree, and got into science writing serendipitously when I was asked/told to take the brief by an editor. It was a perfect move for me.

What I’d never really appreciated before starting to write about science was that it isn’t, as Carl Sagan put it, just a body of knowledge. It’s also a way of thinking.

Tell us a little more about your career trajectory so far: interesting projects past and present?

I’ve just published a book called The Geek Manifesto, which explores the often difficult relationship between science and politics. It argues that too few politicians and civil servants grasp that Sagan maxim, and as a result tend to let science down, and fail to use its methods as they could to deliver better policy. And that’s partly the fault of those of us who do love and appreciate science — we don’t make ourselves felt as a political voice.

What is taking up the most of your time and passion these days? What are your goals?

One of the big ideas of the book is that it’s up to geeks, bloggers, skeptics, rationalists, scientists to turn the value we place on scientific thinking into a stronger political force. So my talks, blogging and campaigning are very much aimed at encouraging people who care about these issues to lobby their political representatives and to complain constructively, about both politics and the media.

In my day job at the Wellcome Trust, I’m particularly interested in learning how best to exploit the disruptive technology of the web to promote both the Trust and the fields of science it supports, and to engage the public and opinion-formers more successfully. It used to be that “source” organisations like the Trust generally had to communicate through third parties. That’s not really true any more.

What aspect of science communication and/or particular use of the Web in science interests you the most?

It’s that ability to reach audiences directly, and to build communities that discuss science and the issues that surround it. The wonderful thing about blogs and Twitter is the ability to interact with scientists, writers and others all over the world — it was a remarkable feeling at ScienceOnline this year to meet so many people I felt I knew through blogs and Twitter, but who I’d not yet met in the flesh.

How does (if it does) blogging figure in your work? How about social networks, e.g., Twitter, Google Plus and Facebook? Do you find all this online activity to be a net positive (or even a necessity) in what you do?

I have a personal blog around the book. The Wellcome Trust also has a blog for which I’m ultimately responsible. I principally use Twitter for science purposes — Facebook is mostly for friends, though I’m trying to use it better for science communication and engagement too.

I can’t actually imagine professional or personal life without online activity now. When I was at The Times, I found the introduction of the paywall very difficult. I found ways to keep going on Twitter, but it did cut my work off from people I thought might otherwise be interested in it.

When and how did you first discover science blogs? What are some of your favourites? Have you discovered any cool science blogs by the participants at the Conference?

I suppose I really started getting into science blogs around 2007 to 2008. I have too many favourites to list many, but I always particularly valued Daniel MacArthur’s Genetic Future blog. Good to see he’s been back at Genomes Unzipped recently.

What was the best aspect of ScienceOnline2012 for you? Any suggestions for next year? Is there anything that happened at this Conference – a session, something someone said or did or wrote – that will change the way you think about science communication, or something that you will take with you to your job, blog-reading and blog-writing?

I loved meeting people I knew online for the first time — people like Misha Angrist and Maryn McKenna whose work I really enjoy and admire. The sessions on the politics of science were really lively. And as I’d literally just started at the Wellcome Trust then, it was especially interesting to explore some of what an organisation like us could do in this space. I hope to be able to announce some exciting developments that will be informed by what I learnt at ScienceOnline very soon…

Thank you! Hope to see you again in January.

When Should Schools Start in the morning?

This is not really a new post. But it is not exactly a re-publishing of an old post either. It is a lightly edited mashup or compilation of excerpts from several old posts – I hope it all makes sense this way, all in one place. The sources of material are these old posts:

Sleep Schedules in Adolescents (March 26, 2006)
ClockNews – Adolescent Sleep (March 28, 2006)
More on sleep in adolescents (April 01, 2006)
When Should Schools Start in the morning? (April 02, 2006)
All Politics Is Local (June 29, 2006)
Adolescent Sleep Schedule (September 10, 2006)
Books: “Snooze…Or Lose! – 10 “No-War” Ways To Improve Your Teen’s Sleep Habits” by Helene A. Emsellem, MD (May 15, 2008)

==========

I am glad to see that there is more and more interest in and awareness of sleep research. Just watch Sanjay Gupta on CNN or listen to the recent segment on Weekend America on NPR.

At the same time, I am often alarmed at the levels of ignorance still rampant in the general population, and even more the negative social connotations of sleep as an indicator of laziness.

Nothing pains me more than when I see educators (in comments) revealing such biases in regards to their student in the adolescent years. Why do teachers think that their charges are lazy, irresponsible bums, and persist in such belief even when confronted with clear scientific data demonstrating that sleep phase in adolescents is markedly delayed in comparison to younger and older people?

In short, presumably under the influence of the sudden surge of sex steroid hormones (and my own research gently touched on this), the circadian clock phase-advances in teen years. It persists in this state until one is almost 30 years old. After that, it settles into its adult pattern. Of course, we are talking about human populations, not individuals – you can surely give me an anecdote about someone who does not follow this pattern. That’s fine. Of course there are exceptions, as there is vast genetic (and thus phenotypic) variation in human populations. This does not in any way diminish the findings of population studies.

Everyone, from little children, through teens and young adults to elderly, belongs to one of the ‘chronotypes’. You can be a more or less extreme lark (phase-advanced, tend to wake up and fall asleep early), a more or less extreme owl (phase-delayed, tend to wake up and fall asleep late). You can be something in between – some kind of “median” (I don’t want to call this normal, because the whole spectrum is normal) chronotype.

Along a different continuum, one can be very rigid (usually the extreme larks find it really difficult to adjust to work schedules that do not fit their clocks), or quite flexible (people who find it easy to work night-shifts or rotating shifts and tend to remain in such jobs long after their colleagues with less flexible clocks have quit).

No matter where you are on these continua, once you hit puberty your clock will phase-delay. If you were an owl to begin with, you will become a more extreme owl for about a dozen years. If you are an extreme lark, you’ll be a less extreme lark. In the late 20s, your clock will gradually go back to your baseline chronotype and retain it for the rest of your life.

The important thing to remember is that chronotypes are not social constructs (although work-hours and school-hours are). No amount of bribing or threatening can make an adolescent fall asleep early. Don’t blame video games or TV. Even if you take all of these away (and you should that late at night, and replace them with books) and switch off the lights, the poor teen will toss and turn and not fall asleep until midnight or later, thus getting only about 4-6 hours of sleep until it is time to get up and go to school again.

More and more school districts around the country, especially in more enlightened and progressive areas, are heeding the science and making a rational decision to follow the science and adjust the school-start times accordingly. Instead of forcing teenagers to wake up at their biological midnight (circa 6am) to go to school, where invariably they sleep through the first two morning classes, more and more schools are adopting the reverse busing schedule: elementary schools first (around 7:50am), middle schools next (around 8:20am) and high schools last (around 8:50am). I hope all schools around the country eventually adopt this schedule and quit torturing the teens and then blaming the teens for sleeping in class and making bad grades.

No matter how much you may wish to think that everything in human behavior originates in culture, biology will trump you every now and then, and then you should better pay attention, especially if the life, health, happiness and educational quality of other people depends on your decisions.

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Recently, Lance Mannion wrote an interesting post on the topic, which reminded me also of an older post by Ezra Klein in which the commenters voiced all the usual arguments heard in this debate.

There are a couple of more details that I have not touched upon in the previous posts.

First, lack of sleep can lead to obesity and even diabetes, as the circadian clock is tightly connected to the ghrelin/leptin system of hormonal control of hunger, feeding and fat-deposition.

Second, lack of sleep discourages exercise. Put these two pieces of data together, and you get a national epidemic of obesity, not just a bunch of sleep-deprived children.

Third, lack of sleep has a well-documented effect on mood. No, teenagers are not naturally that moody – at least not all of them. They are just barely “functional” (instead of “optimal”) and walk through life like zombies because they are operating on 4-8 hours of sleep instead of 9 hours (optimal for teens, it goes down to about 8 for adults). Of course they are moody.

Fourth, chronic sleep deprivation can have long-term consequences, ranging from psychiatric diseases to cancer. Remember that teens in high-school (and college students are faring worse!) are constantly jet-lagged!

There is even a hypothesis floating around that sleep-delay in adolescence may affect the onset of picking up smoking.

Fifth – and I did not think of this although it is obvious – teenagers above a certain age, still in high school, are allowed to drive. If they are driving themselves to school at 6 or 7am, when their circadian clocks think is it 3 or 4am, it is as if they are driving drunk. There is actually a scale devised by one of the sleep researchers that tells which time of the night corresponds to what number of bottles of beer. Driving at 4am (or driving a ship, like Exxon Valdez, or operating a power-plant, like one in Chernobyl) is the equivalent of driving drunk – way over the legal limits. Teenagers driving at 7am are equally “drunk”.

One of the reasons for the resistance to healthy initiatives to change school-start schedules stems from the fact that the world is organized by adults and adults want to have the world run according to schedules that fit their moods and are unwilling to change it – they may not know that teens feel differently, or they defend their preferences nonetheless.

A large proportion of adults in this country still subscribe to barbaric notions that sleep is a shameful activity, a sign of laziness, and that teens need to be tortured in order to “steel” them to grow into “real men”. This has roots all the way back to the Puritan so-called “work-ethic” which is really a “no fun for anyone” punitive ethic long ago shown to be physically and emotionally debilitating.

When I was a kid, back in old now-non-existent Yugoslavia, most schools in big urban areas worked in two shifts. All the kids started school at 8am and ended at 1:15pm for one week, then started at 2pm and ended at 7:15pm the next week, and so on…

If a school had, let’s say, twelve classes of the seventh grade, six of those would be in the A-shift and the other six in the B-shift. Each shift had its own complete set of teachers, assistants, nurses…everything except the one shared Principal and the school psychologist.

The time between 1:15pm and 2pm was for supplementary classes (either for those who needed extra help, or for those preparing for Math Olympics and such) and clubs. That was also time for kids from two shifts to meet and get to know each other (it is amazing how many kids from opposite shifts started dating each other after the year-end Big Trip to the Coast). There was no such thing as the American hype for high-school competitive sports, which I still find strange and curious after 15 [now 20] years in this country.

Thus, you get to sleep in for a week (but miss out on afternoon activities), then have to get up relatively early for a week but have the afternoon free to gallivant around town. Nobody there understands what’s the American fuss over kids being home alone – of course they are home alone, cleaning the house, fixing meals, doing homework and BETTER be getting to school on time!

Teachers were pretty understanding about sleeping types. I do not recall ever having a big test, quiz or exam being given at the extremes of the day (around 8am or around 7pm). As an owl myself, I was much more likely to raise my hand, participate in discussions, or volunteer for oral examinations during the week when I was in school in the afternoon, and that was fine with most of my teachers.

Transportation was not an issue. Most kids lived close enough to their neighborhood school to walk. For those who lived a little farther away – hey, no problem, that’s Europe, so Belgrade has a huge and pretty efficient public transportation system. I do not remember ever seeing any of my friends ever being dropped off to school by a parent driving a car! Or being brought to or picked up from school by a parent beyond fourth grade at all – period. And the minimum driving age being 18, nobody drove themselves to school either.

In rural areas, there was no need for two shifts – something like 9am-2:15pm was good enough to accommodate all of the kids.

I do not think that this kind of system can be implemented in the USA. It relies on an efficient public transportation which, with exception of a few oldest East Coast cities, is practically non-existent. American cities have been built for cars.

But some things can be done.

First, swap the starting times so elementary kids go to school first, middle school next and high school last (e.g., around 8am, 8:30am and 9am respectively). Studies show that teens do not go to sleep later if their school starts later. Some cynics claim that is what teens will do. But they do not. Actually, they fall asleep at the same time, thus gaining an additional hour of sleep.

Teens are almost adults. The current generation of teens, perhaps because of a closer and tighter contact with their parents than any generation before, is the most serious, mature and responsible generation I have seen. Give them a benefit of the doubt. Just because you were into mischief and hated your parents when you were their age does not mean that today’s kids are the same.

Second, start the school day – for all kids every day – with PE (or some kind of exercise), preferably outdoors, as both exposure to daylight and the exercise have been shown to aid in phase-shifting the circadian clock.

Third, let them eat breakfast afterwards (sticking to a meal schedule also helps entrain the clock). Follow up with the electives which kids may be most interested in.

By the time they hit math, science and English classes around 11 or so, their bodies are finally fully awake and they can understand what the teacher is saying, and do the tests with a clear mind instead of in a sleepy haze.

Do not permit any caffeine to be sold in schools. Advise parents not to allow TV or any other electronics to be in kids’ bedrooms. Let them enjoy those activities in the living room. Bedroom is for sleeping, and sleeping alone. A book before bed is fine, but screens just keep them awake even longer.

Finally, rethink all those extra activities you are forcing the teens to do: sports, art, music, etc. In teen’s minds, the day does not start with the beginning of school in the morning. We may think that we are at work most of our day. Teens do not – they consider their day to begin at the time school-day is over. Their day begins in the afternoon. School is something they have to deal with before they can have their day. Realize this and give them time and space to do with their day what they want. Do not push them to do things that you think they’ll need to get into Harvard. Let them be – leave them alone. Then they’ll go to sleep at a normal time.

Concern for our kids’ physical and mental health HAS to trump all other concerns, including economic costs, cultural traditions and adult preferences. We have a problem and we need to do something, informed by science, to fix the problem. Blaming the messenger, proposing to do nothing, and, the worst, blaming the kids, is unacceptable.

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All of this targets high-schoolers. However, there is barely any mention of college students who are, chronobiologically, in the same age-group as high-school students, i.e., their sleep cycles are phase-delayed compared to both little kids and to adults.

In a way, this may be because there is not much adults can do about college students. They are supposedly adults themselves and capable of taking care of themselves. Nobody forces (at least in theory) them to take 8am classes. Nobody forces them to spend nights partying either.

They are on their own, away from their parents’ direct supervision, so nobody can tell them to remove TVs and electronic games out of their bedrooms. The college administrators cannot deal with this because it is an invasion of students’ privacy.

Forward-looking school systems in reality-based communities around the country have, over the last several years, implemented a policy that is based on science – sending elementary school kids to school first in the morning, middle-schoolers next, and high-schoolers last. This is based on the effects of puberty on the performance of the human circadian clock.

For teenagers, 6am is practically midnight – their bodies have barely begun to sleep. Although there have been some irrational (or on-the-surface-economics-based) voices of opposition – based on outdated notions of laziness – they were not reasonable enough, especially not in comparison to the scientific and medical information at hand, for school boards to reject these changes.

I am very happy that my kids are going to school in such an enlightened environment, and I am also happy to note that every year more school systems adopt the reasonable starting schedules based on current scientific knowledge.

Yet, college students are, from what I heard, in much worse shape than high-schoolers. Both groups should sleep around 9 hours per day (adults over thirty are good with about 8 hours). High-schoolers get on average 6.9 hours. College students are down to about five! The continuous insomnia of college students even has its own name in chronobiology: Student Lag (like jet-lag without travelling to cool places). Is there anything we, as a society, can do to alleviate student lag? Should we?

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This kind of ignorant bleating makes me froth at the mouth every time – I guess it is because this is my own blogging “turf”.

One of the recurring themes of my blog is the disdain I have for people who equate sleep with laziness out of their Puritan core of understanding of the world, their “work ethic” which is a smokescreen for power-play, their vicious disrespect for everyone who is not like them, and the nasty feeling of superiority they have towards the teenagers just because they are older, bigger, stronger and more powerful than the kids. Not to forget the idiotic notions that kids need to be “hardened”, or that, just because they managed to survive some hardships when they were teens, all the future generations have to be sentenced to the same types of hardships, just to make it even. This is bullying behavior, and disregarding and/or twisting science in the search for personal triumphalism irks me to no end.

I hated getting up early, too. I still hate it, and I’m so far beyond growth hormones that I don’t even remember how they felt. But I do remember that in middle and high school, I dragged myself out of the house at 5 a.m. every day of the week to deliver papers before I caught the 6:45 a.m. bus to school. I never fell asleep in class. Neither did anybody else. And something caused me to grow 6 inches and add 35 pounds between sophomore and junior year. At the end of that kind of day, complete with cross-country, basketball or track, I had no trouble falling asleep at 10 p.m.

He said that he grew up in height and weight when he was in high school. Who knows how much more he would have grown if he was not so sleep deprived (if his self-congatulatory stories are to be believed and he did not slack off every chance he had). Perhaps he would not grow up to be so grouchy and mean-spirited if he had a more normal adolescence.

I don’t know where he got the idea that growth hormone is a cause of the phase-delay of circadian rhythms in adolescence. It could be, but it is unlikely – we just don’t know yet. But, if a hormone is a cause, than it is much more likely to be sex steroids. Perhaps his sleep-deprived and testosterone-deprived youth turned him into a sissy with male anxiety he channels into lashing at those weaker than him?

In previous centuries, adolescents in an agrarian society got up at 4:30 or 5a.m. with their parents to milk the cows or do any other of a long list of chores. Did growth hormones pass them by? Where were the “studies” that showed they really needed to go to bed after midnight and sleep until 10? And why weren’t their parents all being reported to the DSS? Oh, that’s right, there was no DSS. How did that generation survive?

He assumes that in times before electricity, teenagers used to wake up and fall asleep at the same time adults did. Well, they did not. Studies of sleep patterns in primitive tribes show that adolescents are the last ones to wake up (and nobody bashes them for it – it is the New Primitives with access to the media that do that) and the last ones to fall asleep – they serve as first-shift sentries during the night watch.

Even in this, the 21st century, kids who enter the military at 17 find that they can fall asleep easily at 9:30 or 10, because they know they’re going to be getting up at 4:30 or 5. Apparently the Army hasn’t read the study on circadian rhythms.

Actually, the military being the most worried by this problem is funding a lot of research on circadian rhythms and sleep and has been for decades. Because they know, first hand, how big a problem it is and that yelling sargeants do not alert soldiers make.

Kids, if you need more sleep, my study shows there’s a simple way to get it. Turn off – I mean “power down” – the cell phone, the iPod and the computer sometime before 11 p.m. Turn off the TV. Turn off the light. Lie down in bed and close your eyes.

…and sit in the dark for the next four hours, heh?

What especially drives me crazy is that so many teachers, people who work with adolescents every day, succumb to this indulgence in personal power over the children. It is easier to get into a self-righteous ‘high’ than to study the science and do something about the problem. It is easier to blame the kids than to admit personal impotence and try to do something about it by studying the issue.

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My regular readers are probably aware that the topic of adolescent sleep and the issue of starting times of schools are some of my favourite subjects for a variety of reasons: I am a chronobiologist, I am an extreme “owl” (hence the name of this blog), I am a parent of developing extreme “owls”, I have a particular distaste for Puritanical equation of sleep with laziness which always raises its ugly head in discussions of adolescent sleep, and much of my own past research was somewhat related to this topic.

So, I was particularly pleased when Jessica of the excellent Bee Policy blog informed me of the recent publication of a book devoted entirely to this topic. Snooze…or Lose! by Helen Emsellem was published by National Academies and Jessica managed to get me an advanced reading copy to review.

You can also read the book online (or buy the PDF). Much more information on the topic can be found on the book webpage, on the National Slep Foundation website, on Dr.Emsellem’s homepage and the Start Later for Excellence in Education Proposal (S.L.E.E.P.) website. I strongly encourage you to look around those webpages.

Her daughter Elyssa wrote one of the chapters in the book and is promoting the book and the information relevant to teenagers at the place where teenagers are most likely to see it – on MySpace (you see – it’s not just music bands who caught onto this trick – serious information can be promoted at MySpace as well).

The main audience for this book are teenagers themselves and their parents – I think in this order although officially the order is reversed. Secondarily, the audience are teachers, administrators and officials in charge of school policy. Who this book is not targeted to are scientists and book reviewers because there are no end notes!

Anyway, considering that the main audience are teens, their parents and teachers (i.e., laypeople), the book is admirably clear and readable. The book starts out with presenting the problem – the chronic sleep deprivation of adolescents in modern society – and provides ample evidence that this is indeed a wide-spread problem. It continues with a simple primer on physiology of sleep and circadian rhythms, followed by a review of the current knowledge of the negative consequences of chronic sleep deprivation: from susceptibility to diseases, through psychological and behavioral problems, to problems of physical and mental performance.

A whole chapter – the one I found most interesting – is devoted to the role of sleep in various kinds of memory and the negative effects of sleep deprivation on learning – both declarative and episodic memory, as well as kinesthetic memory needed for athletic performance and safe driving. This is where I missed the end notes the most.

Throughout the book, Dr.Emsellem makes statements of fact about sleep that are obviously derived from research. I’d like to see the references to that research so I can evaluate for myself how strong each such statement is. Although my specialty is chronobiology (physiology, development, reproduction, behavior, ecology and evolution) of birds, and secondarily that of mammals, reptiles, invertebrates and microorganisms (I could never quite get excited about clocks in fish, fungi and plants, or molecular aspects of circadian rhythms, or medical aspects of human rhythms), I am quite familiar with the literature on sleep, including in humans.

Thus, I know that the statements in the book reflect scientific consensus but that the meaning of “consensus” is quite elastic. In some cases, it means “there is a mountain of evidence for this statement and no evidence against it, so it is highly unlikely that this will change any time soon”. In other cases it means “there are a few studies suggesting this, but they are not perfect and there are some studies with differing results, and this can stand for now but is likely to me modified or completely overturned by future research”.

Having end notes would help the expert reader see how weak or strong each one of these findings is, and would also be suggestive to lay readers that the statements in the book are supported by actual research and are not just the author’s invention as seen in so many self-help books. End notes and references add to the believability of the text even if one does not bother to check the papers out.

The book then turns to variety of factors, both biological and social, that conspire to deprive our teens of sleep, both from the perspective of a sleep researcher and from the perspective of teenagers. Little snippets of teenagers’ thoughts on the topic are included throughout the book and add an important perspective as well as make the book more fun to read. Otherwise, the “case studies”, the bane of so many psychology books, are kept to the minimum, discussed very briefly, and used wisely..

In the next section, Dr.Emsellem turns to solutions. First, she present several tests of sleep deprivation that readers can administer themselves in order to self-diagnose the problem. She then describes ten different strategies that parents and teens can work on together in order to solve the problem of sleep deprivation and all the concomittant negative effects (and Alyssa adds her own chapter on the teen perspective on how those can work). If that does not work, she describes additional methods that a sleep doctor may prescribe to help solve the problem. There is also a short chapter describing a couple of other sleep disorders, e.g., sleep apnea, that also contribute to sleep deprivation in affected individuals.

The last portion of the book addresses the social aspects of sleep deprivation and changes that parents and teens can make in their homes, as well as broader community, towards solving the problem. For adults, being a role model for the child is important and this requires paying attention to one’s own sleep hygiene.

The very last portion is really the raison d’etre of the book – how to make one’s community change the school starting times. The author presents a couple of examples of school districts in which such change was enacted, the strategies parents used to force such changes and the incredible positive results of such changes. The whole book is really designed to provide information to parents and teens who are working on changing their local attitudes toward school starting times.

The schools used to start about 9am for most of the century (and before). Then, due to the pressure from business and economic (read “busing”) woes of school districts, the school starting times started creeping earlier and earlier starting back in 1970s until they reach the horribly early times seen today in many places, requiring kids to get up as early as 5am in order to catch the school bus on time. As a result, high schoolers (and to some extent middle schoolers and college students) sleep through the first two periods in school, feel weak and groggy all day long, more easily succumb to diseases, have trouble learning and performing well in school and the athletic field, and are in too bad mood to be pleasant at home – this is not the natural state of things as much as the stereotype of the “grouchy teen” is prevalent in the society, it is mainly due to sleep deprivation and the biggest factor causing sleep deprivation are early school starting times.

In places in which enlightened and progressive school boards succumbed to the wishes of parents and students, i.e., in places in which parents and students used smart diplomatic tactics to engender such change, the positive results are astounding. The grades went up. The test scores went up. The students are happy. The parents are happy. The teachers are happy. The coaches are happy because their teams are winning all the state championships. There is a decrease in tardiness and absences. There is a decrease in sick days and even in numbers of diagnoses of ADD and depression in teens. There is a drop in teen crime. There is a drop in car accidents involving teens (by 15% in one place!). The whole county feels upbeat about it!

While the book makes me – a scientist – thirsty for end notes and references, it does remarkably well what it was designed to do – arm the parent and kids with knowledge needed to make a positive change in their communities – a change that is necessary in order to raise new generations to be healthy and successful, something we owe to our children.

We should do this no matter how much it costs, but the experiences from places in which the changes were made, contrary to doomsayers, is that there was no additional cost to this at all. The changes were implemented slowly and with everyone involved pitching in their opinion and their expertise until the best possible system was arrived at, adapted to the local community situation. No new buses were needed to be rented. No unexpected new costs appeared. And having a safe, happy community saved money elsewhere (e.g., accidents and crime rate decline). And it worked wonderfully everywhere.

So, get the book and let your child read it, you read it, give a copy to other people in your community: the teachers, the school principal, the pediatrician, the child psychologist, the school board members, the superintendent of education and the governor. This is something that is easy to do, there are no good reasons against it and the health and the future of our kids is at stake. It is something worth fighting for and this book is your first weapon.

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Related:

Everything You Always Wanted To Know About Sleep (But Were Too Afraid To Ask)
Sun Time is the Real Time
What is a ‘natural’ sleep pattern?
Lesson of the Day: Circadian Clocks are HARD to shift!
Circadian Rhythms in Human Mating
Seasonal Affective Disorder – The Basics
Data for #drunksci: Daily rhythm of alcohol tolerance
Basics: Biological Clock
Spring Forward, Fall Back – should you watch out tomorrow morning?
(Non) Adaptive Function of Sleep

(Non) Adaptive Function of Sleep

This was first published on November 01, 2005.

Here is a nice article in Washington Post – Ecological Niche May Dictate Sleep Habits – about the adaptive function of sleep.

It addresses some of the themes I am interested in.

First, the unfortunate fact is that sleep was initially defined by researchers of humans, i.e., medical researchers. Inevitably, the (electrophysiological) definition of sleep was thus saddled with unnecessary anthropocentric elements that for decades hampered the study of evolution of sleep.

I was present at the meeting (here in Biotechnology Center in RTP) several years ago when the bigwigs of the sleep research community were first exposed to some very new ideas via not one but two talks about sleep in fruitflies (by Marcia Belvin and Joan Hendricks). That was quite an earthshaking event as the definition of sleep was substantially changed right then and there. Interestingly, the new (behavioral) definition was received not with resistance but with enthusiasm. Everyone in the room understood the potential of the new way of thinking to break off the shackles that sleep research had to suffer in for so long.

Since then, the marriage of circadian and sleep research has resulted in sleep research taking off at a breathtaking speed. As a result, many old assumptions and dogmas had to be discarded. For many years sleep researchers shunned evolutionary explanations and focused on physiological and medical aspects of the phenomenon. However, progress in sleep medicine depends on a better understanding of what sleep is for – a decidedly evolutionary question.

Another theme is the old battle between adaptationism and the more sophisticated view of evolution that incorporates the phenomena of developmental and phylogenetic constraints, as well as the concept of exaptation. Just because a mechanism currently serves a particular function does not mean that this function is what the mechanism originally evolved for. In other words, current function is not necessarily the original function (bird wings were initially adaptations for thermoregulation and later got exapted for flight). Here is the adaptationist statement:

The theorists have long disagreed about one another’s ideas, but most agree on one thing: If nature makes people sleep away so much of their lives, the reason has to be something crucial. That seemed to be the only way to explain why sleep-deprived people crave sleep so badly that they doze off behind the wheel of a car going 60 mph, and why rats deprived of sleep die sooner than rats deprived of food.

The article then trots out a couple of currently favoured hypotheses about the adaptive function of sleep:

Yet a wealth of sleep research has regularly produced baffling paradoxes and conflicting lines of evidence about the uses, role and need for sleep. If sleep is primarily about providing mental rest, why do people’s brains remain so active during sleep, as research in recent decades has found?

If sleep is about providing the body with rest, why do couch potatoes need as much sleep as Olympic athletes? Moreover, animals such as horses, which perform far more physical labor than humans, need much less sleep than people do.

If sleep primarily hones cognitive functions, why do the intellectually lazy need as much sleep as Nobel Prize-winning physicists? Also, why do humans — who are a lot smarter than rats — sleep less than rodents?

Finally, while much conventional thinking suggests that Americans should be sleeping more, a very large 2002 study found that people who sleep eight hours or more a night are likely to die younger than those who sleep seven. (Don’t touch that alarm clock; the study did not find that deliberately sleeping less increases life span.)

Considering that a vast majority of sleep researchers are MDs, not neccessarily up to speed in evolutionary theory, such sentiments are not surprising. It takes an evolutionary biologist to move the ball forward:

Jerome Siegel, a psychiatrist at the University of California at Los Angeles who described these discordant findings in acomprehensive review of the available research, published in the journal Nature last week, said he began to question the notion that sleep performs some essential function after noting that species that sleep less than others do not sleep any deeper — as they would if they were making up for the shorter time. Animals that sleep fewer hours generally sleep less deeply, while animals that sleep longer usually sleep more deeply.

Siegel, a respected sleep researcher who is also affiliated with the Department of Veterans Affairs, said he came to the conclusion there was only one explanation that could explain the paradoxes: in a word, evolution.

Rather than being designed to perform some critical function, Siegel wrote in his paper, sleep may be the way various species, humans included, have adapted to their ecological niches. While many valuable functions probably take place during sleep, Siegel suggested that it is possible that those functions are not the reason for sleep.

“There is this huge variation in sleep across species, and it fits with this huge variation in the niches that animals occupy,” Siegel said in an interview.

“The analogy I make is between hibernation and sleep,” he said. “No one says, ‘What is hibernation for? It is a great mystery.’ . . . It’s obvious that animals hibernate because there is no food, and by shutting down the brain and body they save energy.”

Sleep, Siegel suggested, may play much the same role. As evidence, he cited research that has found systematic differences in the way carnivores, omnivores and herbivores sleep: Carnivores sleep longer; herbivores, shorter; and omnivores, including humans, are somewhere in the middle.

“If animals have to eat grass all day, they can’t sleep a lot, but if they eat meat and are successful at killing an antelope, why bother to stay awake?” he asked.

On the other hand, mammals at greater risk of being eaten — such as newborns — spend large amounts of time asleep, presumably safe in hiding places devised by their parents. Supporting the evolutionary explanation, Siegel’s own research has shown that when the luxury of safe hiding places is unavailable — in the ocean, for instance — baby dolphins and baby killer whales reverse the pattern found among terrestrial mammals. These marine mammals sleep little or never as newborns and gradually increase the amount they sleep as they mature.

Let me put it simply: sleep makes you sit still and be quiet at times when it is dangerous to move around and there is nothing else important to do. All the other functions were added later due to either timing (some things are better done at certain times of day that coincide with either sleep-time or wake-time and the two processes get linked) or particular brain states (i.e., some functions, for instance the consolidation of memory, are easier to perform at times when the brain is NOT receiving much input from the outside environment):

The theory does not so much contradict other theories about the role of sleep as much as place them in context: “What I am saying is that it is not that sleep has been adapted to allow some vital function to be fulfilled, but the core function of sleep is to adapt animals to their ecological niche,” Siegel said. “Given the animal is inactive for a certain period of the day, certain functions will migrate to that period because it is more efficient” to perform them at that time.

Interestingly, this hypothesis does not conflict with an old (and frankly quite unpopular) notion that mammals and birds did not evolve sleep as a new process (after all, insects sleep, we now know), but that they evolved wakefulness as a novel state of the mind.

Insects, fish, amphibians, reptiles etc., have periods of activity and periods of slumber. The period of slumber corresponds to mammalian/avian state of sleep. But, the active state in cold-blooded animals is more similar to sleep-walking than real wakefulness.

Did birds and mammals independently evolve wakefulness or was there a whole suit of (now extinct) reptilian and dinosaurian lineages who were also wide awake? Did evolution of wakefulness provide a substrate for the evolution of consciousness? Interesting speculations, but nothing close to an answer to date. At least, provocative hypotheses by Jerome Siegel and some others are prompting the sleep scientists to reconsider everything they hold dear and therein lies progress.

Siegel’s paper is available online (unfortunately, behind a paywall). Carl Zimmer has an article on this in New York Times.

Today at The Browser

I am today’s guest editor at The Browser. The Browser curates and aggregates the best reads from around the Web, in several categories. It is a great honor to be asked to serve as a day editor there.

The only difficulty is the limit – I had to choose six articles or blog posts from the past month. Only six!?!

I am used to compiling many more links – per day, let alone month!

I collect all the #SciAmBlogs posts every work-day evening. I collect the best of the Web weekly. Khalil and I take turns collecting all the young science writers’ work every Friday. Not to mention all the links I tweet that never make it into any of those linkfests!

How to reduce an entire month to only six? Yikes – that was hard. So many excellent posts and articles had to be, one by one, eliminated from my list. And my list started out huge. But in the end, late last night, I had my six and I sent them in.

Which six?

You’ll have to see for yourself!

Shaq and the Mini-Shaq, the extreme primates.

The world’s smallest primate in his hand measures only five inches and weighs two ounces, clearly dwarfed by the 7’1” 325-pound Shaq.

The world’s smallest primate in his hand measures only five inches and weighs two ounces, clearly dwarfed by the 7’1” 325-pound Shaq.

Shaquille O’Neil, one of the world’s most recognizable professional basketball players has used his stature to highlight one of the world’s smallest primates: the mouse lemur from Madagascar.

Shaq, an NBA legend who retired last year and earned a doctorate degree in education from Barry University in 2012, posed with a mouse lemur at Zoo Miami in March to advocate for Centre ValBio, a non-profit conservation organization based in the rainforests of Madagascar. Under the direction of primatologist Dr. Patricia Wright, Centre ValBio aims to better understand and protect the island’s endangered wildlife and habitats.

National Geographic Explorer and TV Host Mireya Mayor & Shaq

National Geographic Explorer and TV Host Mireya Mayor & Shaq

Fuggles the lemur was on loan from the Duke Lemur Center in North Carolina, traveling down to Florida with two handlers and copious supplies of mealworms. Both institutions – Centre ValBio and Duke Lemur Center – are doing excellent work with the people of Madagascar to preserve endangered species habitat through education and economic development. CVB has also built a research facility there.

Shaq was joined by Dr. Mireya Mayor, an author and National Geographic Explorer & TV Host who focuses on primates.

Mireya Mayor and <em>Microcebus mittermier</em> in 2000

Mireya Mayor and Microcebus mittermier in 2000

Mayor has been working in Madagascar since 1997 and has been involved in primate conservation for over 15 years. The idea to photograph one of the world’s largest primates (Shaq) with the world’s smallest came to her when she looked at a National Geographic photograph taken of her and a mouse lemur she co-discovered in northern Madagascar in 2000 (Microcebus mittermieri).

Shaq flexes his muscle for Centre ValBio & the wildlife of Madagascar.

Shaq flexes his muscle for Centre ValBio & the wildlife of Madagascar.

All photos by Ron Magill.

The Scienceblogging Weekly (May 18, 2012)

Blog of the Week:

For the greatest portion of the history of biology, every organism was a “model organism”. One would pick a problem and then choose which organism would be most suited for answering those particular questions. Then, in the 1990s, everyone jumped onto the bandwagon of studying just a handful of organisms that could be genetically modified at the time: mouse, fruitfly, thale cress, zebrafish, African clawed frog, bread mold, brewer’s yeast, or E.coli. All the other organisms were all but abandoned, only studied by a small number of die-hard researchers and, increasingly, amateurs. Now that technology allows us to investigate (and to some extent manipulate) entire genomes of almost any species we’d like, researchers are going back and rediscovering the abandoned model organisms once again. One of these is Anolis, a large group of species of lizards, noted for their dewlaps, and known especially for their fast adaptive radiation on tropical islands.

And now there is a blog that covers everything about these lizards – Anole Annals. Posts are written both by veteran researchers and their students, from several laboratories, as well as other contributors. They cover both recent and historical papers on evolution, ecology, biogeography, behavior, physiology, biomechanics and genetics of this diverse group of reptiles. They also describe their own research, including anecdotes and adventures from field work, equipment they use in the lab, and successes in discovery. On top of that, they help people ID the species from pictures, pay attention to the appearance of anoles in art and in the popular culture and generally have a lot of fun doing all of this. A blog entirely devoted to just one group of animals sounds very ‘niche’, but what they did was build a blog that has something for everyone and is a great fun (as well as insightful and educational) read for everyone.

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Top 10:

The secret molecular life of soap bubbles (1913) by Greg Gbur:

…Today we take for granted that all material objects in the universe are comprised of discrete “bits” of matter, which we call atoms; however, even up until the early 20th century there were still proponents of the continuum hypothesis, in which all matter is assumed to be infinitely divisible…

Motherhood, war, and attachment: what does it all mean? by Emily Willingham:

I’m sure many mothers can attest to the following: You have friends who also are mothers. I bet that for most of us, those friends represent a spectrum of attitudes about parenting, education, religion, Fifty Shades of Grey, recycling, diet, discipline, Oprah, and more. They also probably don’t all dress just like you, talk just like you, have the same level of education as you, same employment, same ambitions, same hair, or same toothpaste. And I bet that for many of us, in our interactions with our friends, we have found ourselves judging everything from why she insists on wearing those shoes to why she lets little Timmy eat Pop Tarts. Yet, despite all of this mental observation and, yes, judging, we still manage to get along, go out to dinner together, meet at one another’s homes, and gab our heads off during play dates. That’s not a war. That’s life….

As oxygen filled the world, life’s universal clock began to tick by Ed Yong:

The Earth’s earliest days were largely free of oxygen. Then, around 2.5 billion years ago, primitive bacteria started to flood the atmosphere with this vital gas. They produced it in the process of harnessing the sun’s energy to make their own nutrients, just as plants do today. The building oxygen levels reddened the planet, as black iron minerals oxidised into rusty hues. They also killed off most of the world’s microbes, which were unable to cope with this new destructive gas. And in the survivors of this planetary upheaval, life’s first clock began to tick and tock….

Poisoning the Dalai Lama. Or Not by Deborah Blum:

Earlier this week, the Tibetan Buddhist leader, the Dalai Lama, told British journalists that he’d been warned of an ingenious Chinese plot to assassinate him with poison. Very ingenious, according to the plot he laid out for the Sunday Telegraph. He’d learned, he said, of a plan to send out a squad of women, pretending to be followers, who would have poison spread through either their hair or headscarves. When he laid his hands on their heads for a blessing, a lethal dose could be absorbed through his skin…

The Brain Hidden Epidemic: Tapeworms Living Inside People’s Brains by Carl Zimmer:

….But sometimes tapeworms take a wrong turn. Instead of going into a pig, the eggs end up in a human. This can occur if someone shedding tapeworm eggs contaminates food that other people then eat. When the egg hatches, the confused larva does not develop into an adult in the human’s intestines. Instead, it acts as it would inside a pig. It burrows into the person’s bloodstream and gets swept through the body. Often those parasites end up in the brain, where they form cysts….

Why Octopuses Should Run Our National Security Infrastructure by Annalee Newitz:

Next time the government wants new ideas about how to protect our nation’s security, it should consult an octopus. That’s the unusual proposition of marine biologist Rafe Sagarin, a pioneer in the infant field of “natural security,” where experts use models from nature to help them come up with emergency responses to everything from terrorist attacks to pandemics. Sagarin has just published a book about his work called Learning from the Octopus: How Secrets from Nature Can Help Us Fight Terrorist Attacks, Natural Disasters, and Disease. Any scientific theory that involves the superiority of cephalopods is automatically intriguing, so I called up Sagarin to talk about it.

Solving the Mystery of the Placental Jellyfish by Craig McClain:

Yesterday the DSN crew first saw the video above. What is this large floating sheet of goo? Is it alive? Was it once alive? The two leading contenders seems to be that it is A) an old whale placenta or B) a rare and enigmatic deep-sea jellyfish. And the answer is…. B)

Physics’s PR problem: Moving beyond string theory and multiple universes by Ashutosh Jogalekar:

….The problem is that most of the popular physics that the public enjoys constitutes perhaps 10% of the research that physicists worldwide are engaged in. Again, count the number of physics books in your local bookstore, and you will notice that about 90% of them cover quantum mechanics, cosmology, particle physics and “theories of everything”. You would be hard-pressed to find volumes on condensed matter physics, biophysics, the physics of “soft” matter like liquids and non-linear dynamics. And yes, these are bonafide fields of physics that have engaged physics’s best minds for decades and which are as exciting as any other field of science. Yet if you ask physics-friendly laymen what cutting-edge physics is about, the answers will typically span the Big Bang, Higgs boson, black holes, dark matter, string theory and even time-travel. There will be scant mention if any of say spectroscopy, optics, polymers, magnetic resonance, lasers or even superconductivity….

Dear Media, Leave My Dinosaurs Alone by Brian Switek:

I wish I could take dinosaurs away from the media for a while. Someone certainly should. Lazy journalists and unscrupulous documentary creators have amply demonstrated that they just can’t play nice with Tyrannosaurus, Triceratops and kin…

Do Bonobos And Chimpanzees Offer A Path To Understanding Human Behavior? by Sheril Kirshenbaum:

What leads people to acts of violence and genocide? What triggers empathy and altruism? Duke evolutionary biologist Brian Hare and research scientist Vanessa Woods believe the answer may be found in the great ape known as the bonobo….

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Special topic: snakes:

And the Cascabel will Fall Quiet… by John F Taylor. Rattlesnakes may actually be learning and they may become more dangerous if their roundups aren’t stopped.

Spore Dispersal by Snakes by Jessica M. Budke

The Secret to Success Is Giant-Jawed Snake Babies by Elizabeth Preston

Identifying snake sheds, part II by Andrew Durso

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Science:

Pacific plastic, sea skaters, and the media: behind the scenes of my recent paper by Miriam Goldstein. Once you are featured in The Onion, your career has reached the peak. What more can one do after that?

In the wake of high-profile controversies, psychologists are facing up to problems with replication. by Ed Yong. Psychology example, applicable at least to some extent to other fields.

The Flavor of Neutrinos by Matthew Francis

Confusing messages about sugar are stupid by David Despain

Two Earths would be needed to sustain human activity by 2030, report finds by Meghan Neal

Science vs. PR by Robert McHenry. How a scientific paper about chemistry turned into mass media articles about alien dinosaurs.

Who hates cilantro? Study aims to find out by Cari Nierenberg

Microbiology at Sea: A tale of ballast, vomit, and cockroaches by Holly Bik

Is the U.S. Ready for Home HIV Tests? by Benjamin Plackett

Lessons from the Lab: How to Make Group Projects Successful by Annie Murphy Paul. “Megacollaboration is becoming the norm in science. Here’s what we can learn about what works when working together.”

Sometimes scientists have a duty to swap the pipette for the placard by Adam Smith

Academics on archosaurs: Jerry Harris by Dave Hone

Whistle Recognition in Bottlenose Dolphins by Tara Thean

The regulation of nonsense by Jann Bellamy on medical quackery and CAM.

What Happens to All That Volcanic Ash? by Erik Klemetti

Cannibalism? by Mark Crislip

Science Standards: The Next Generation by Rhett Allain

Is the holocaust denial/climate change denial comparison apt? by Mark Hoofnagle

The Coming Beepocalypse, It’s hard out there for a bee, and Bees and STDs by Bug Girl

Huge Turtle Was Titanoboa’s Neighbor by Brian Switek

De-caffeinating pills? Say it ain’t so, Think Geek by David Kroll

Human morality is evolving by Ken Perrott

5 Things the Science Doesn’t Say About the Conservative Brain by Chris Mooney

The Republican Brain by Chris Mooney by Chad Orzel

Turning Wolves into Hounds by Heather Pringle

Dendrites of Direction by TheCellularScale

LA smog: more cows than cars? by Scott K. Johnson

The New Atheism and Evolutionary Religious Studies: Clarifying Their Relationship by David Sloan Wilson

Opinion: Academia Suppresses Creativity by Fred Southwick

Methods for Studying Coincidences by Samuel Arbesman

Is misconduct more likely in drug trials than in other biomedical research? by Ivan Oransky

A rising tide of willful ignorance by Rob Schofield. Lobbyists pushing to dictate which data scientists are allowed to use.

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Media, Publishing and Technology:

All A’Twitter: How Social Media Aids in Science Outreach a Master’s Thesis by Caitlyn Zimmerman about the pros & cons and strategies in using social media in Marine Conservation outreach.

Guest Editorial: It’s Time To e-Volve: Taking Responsibility for Science Communication in a Digital Age by Christie Wilcox

Young scientists ask: Is there room out there for one more science communicator? by Denise Graveline

The SA Incubator: Helping Hatch Science Writers Since July 2011 by Erin Podolak

Research Blogs and the Discussion of Scholarly Information by Hadas Shema, Judit Bar-Ilan and Mike Thelwall, a research paper about science blogs using the ResearchBlogging.org aggregator. Responses by Scicurious, Neurocritic, Jonathan Eisen, Caroline Tucker, Misha Angrist and Invader Xan.

Beyond a Trend: How Scientists Use Social Media by Jessica Rohde

Twitter is like… by dorkymum. A beautiful metaphor to try on n00bs.

Do I Write? Or Do I Tweet? by Geoff Brumfiel

Mom, this is how twitter works by Jessica Hische

Printed books existed nearly 600 years before Gutenberg’s Bible by Annalee Newitz

Digital Pagination by Nate Barham. The page-flip is just another in a long line of “unnecessary” features to help us poor humans understand the content.

My personal take: 3 reasons I don’t like newspaper paywalls by Mathew Ingram and a response to it, Paywalls are backward-looking by Dave Winer.

Commenting, Moderation, and Provocation by Marc Bousquet

Aggregation guidelines: Link, attribute, add value by Steve Buttry – a definitive guide.

Please Don’t Learn to Code by Jeff Atwood, and Should you learn to code? by Dave Winer, and Don’t tell me not to learn! by Eva Amsen.

The newsonomics of News U.: Journalism and education are both about knowledge. Could their post-disruption business models start to blur? by Ken Doctor.

See, this is why publishers irritate me so much and Publishers versus everyone by Mike Taylor

The government spends billions on research. Should we have to pay $20,000 more to see the results? by Suzy Khimm

The Tao of Shutterstock: What Makes a Stock Photo a Stock Photo? by Megan Garber

How Facebook Saved Us from Suburbia by Christopher Mims and Does Facebook Turn People Into Narcissists? by Tara Parker-Pope

The tip of the iceberg- what digital photography really costs by Brendan Moyle

A Brief History and Proposed Definition for ‘Attention Economics’ by Adrian J. Ebsary

Under construction – ITER in LEGO

If you just received your new issue of Scientific American, you saw the article The Problems with ITER and the Fading Dream of Fusion Energy by Geoff Brumfiel. Accompanying image (a little small online, but nice and big in print) is a photograph by Hironobu Maeda of a sculpture by Sachiko Akinaga. It is a LEGO model of the ITER fusion reactor which has been under construction for many years now, and apparently will keep being under construction for many years to come.

You may think that the image is a photoshop, or a drawing, or that perhaps the LEGO model does exist somewhere, perhaps in some studio in Japan, or at ITER construction site itself.

But no. The model is in the middle of the Scientific American newsroom! A couple of weeks ago when I went to our New York City office, I took these photos of the model. Now that the embargo has lifted, I can show you some more details of the model:

The SA Incubator, or, why promote young science writers?

Erin Podolak (blog, Twitter) was interviewed at The SA Incubator a few weeks ago. Then she decided to turn the tables on me and interview me about The SA Incubator – why and how did I conceive of that blog, what is it for and how it works.

You can read the article she wrote from that interview on her blog (also re-published on The SA Incubator itself).

Below is the full “transcript” of what I told Erin – I thought some of you may find it interesting:

1. Scientific American’s blog network is extensive. Why have a blog dedicated specifically to the work of young science journalists?

There are several reasons for it. Let me try to cover all the main points.

Limit on the network size.

Scientific American’s blog network is relatively big as networks go, but still limited in size for a number of reasons. There is a limited budget, for starters.

Second, a network any larger than this would be a strain on time and effort for me and developers to manage. At this point, it is at least possible for an interested reader to read all the posts on the network (I do!). If it gets any bigger, this becomes impossible and the readers’ habits change: instead of at least occasionally checking out all the bloggers they only focus on their favorites (some readers always will, but at least some don’t) – thus the ‘network effect’ for bloggers is diminished.

Finally, a blog network is not a simple, additive collection of writers – it is a community of people who work together, write together, read each other, comment on each other’s posts, coordinate their blogging, socialize in the backforums (and in real life when opportunities arise through travel), help each other as needed, etc. If the network gets too big, this feeling of belonging to a “family” evaporates, and there is even a danger of the community splitting into warring factions.

It is important for a network to have a mix of seasoned bloggers and fresh voices on the network, for a variety of reasons (for example, veterans serve as role-models, cheerleaders, advisers and troll-beaters for the newbies). While it is important for the network to have as much diversity as possible, so each blogger can tap into and bring in a different audience, it is also important for the community to be coherent and friendly so one blogger’s audience also checks out the other bloggers.

As a natural rotation occurs – some bloggers leave and new ones get invited in their place – both the diversity and coherence need to stay in place. That would be impossible to pull off if the network was too large. We have space for perhaps 2-3 more blogs to reach that maximum.

Being left out.

When there is a limit on the network’s size, this means new people cannot easily get in. And there may be many of them and quite deserving of spotlight. Many of the youngest writers are still in school, too busy with class assignments, or are in internships, or are too busy breaking into freelancing to be able to blog with regular frequency. Some of them do most or all of their writing in more traditional venues, for pay, and do not have blogging experience at all. Some may want to write but do not want to blog. I don’t want to force them to do what they cannot or will not do, yet feel I should highlight their work elsewhere anyway.

Thus SA Incubator interviews and linkfests. And thus open invitation to young writers to submit pitches for the Guest Blog.

Push vs pull media.

Writers and journalists who specialize in science, health and envirionmental reporting tend to write for specialized news outlets – science magazines, New York Times Science every Tuesday, NPR Science Friday, science cable channels, science blogs – places that are easy to avoid if one is not interested in science. They have the requisite background (often in science as well as journalism), training and knowledge to do it right. But they tend to be hired to write for outlets mostly visited by audiences who actively seek science content – that is the “pull” method. Readers pulled into specialized science media tend to already have sufficient background and interest in science.

How do we reach the unsuspecting audiences, those that do not actively seek science content? How do we grab and bring in people who don’t even know that science is fun? They may be looking for politics, or celebrity gossip, or sports, not science. How do we “push” science on them, show them it is fun, important and relevant for them?

One way is for each one of us to push the science stories to our non-sciency friends on social networks (Twitter, Facebook, Google Plus, etc). But even better method is by having cool science stories appear in outlets where they congregate – the “mass” media outlets, from New York Times to Huffington Post, to public radio, to cable TV, to Hollywood.

Specialized vs. mass media.

Unfortunately, science stories in the mass media tend not to be written by specialized science writers, and are thus often wrong. I do not intend to pick specifically on Larry Moran but this link to his blog I have handy and is fresh in my mind – his is just a recent example of a very frequently seen category error – blaming bad mass media reporting on science journalists. Larry saw a really bad science story on the cover of USA Today and blamed it on science journalists. The problem is: that story was not written by a science journalist! There is nothing science journalists (e.g., NASW members) can do about it – it is not in their power to “police” people who are not part of their cohort.

Vast proportion of science stories in mass media are not written by science journalists. They are written by beat reporters who are required to turn in, let’s say, 7 articles per day (that is an hour of research and writing for each) only tiny proportion of which have anything to do with science. They do not have the background, expertise and experience in science reporting to get it right. They are not given sufficient time to do the research necessary to get it right. They are incapable of accessing, reading and understanding a jargony scientific paper (or even know they are supposed to at least try to read it) in order to get it right. So they submit bad copy. And their editors, not knowing anything about science reporting either, run with it.

Shaming the MSM (Main-Stream Media).

Much of what science bloggers do – and do very well – is critique the science coverage by the mass media. They fisk the bad articles, often several per day, sometimes as systematically as going line by line to show where the articles got the science wrong. This is actually a great educational method – by showing how and why each sentence is wrong, it allows the science blogger to teach the readers the correct version of science in question, as well as how to think critically about science coverage.

Believe me – the authors of these articles and their editors know when this happens to them. Their knee-jerk response is to get very defensive and dismissive (“dirty, hippy bloggers covered by cheeto dust, blogging in their pyjamas in their parents’ basements” is the stereotype they may use or imply), but they get burned and subconsciously learn the lesson to be more careful and at least not repeat the same mistakes in the future.

If a particular mass media outlet (Daily Mail comes to mind) consistently publishes bad science articles, and gets snarkily yet devastatingly criticized for it by knowledgeable expert bloggers almost every day, there is only so long they can remain dismissive of those criticisms. They may not publicly say anything, but they will think, and they will have internal meetings discussing what to do to improve their science coverage as to avoid future criticism.

If this happens, and if they have sufficient budget, the obvious solution is to hire a specialist science reporter. Where do you find one? Google it. What do you find? Hopefully, Scientific American, its articles written by freelancers, its blogs, its weekly Scienceblogging linkfests, or ScienceOnline interviews, or amazing posts on the Guest Blog, or the interviews and weekly linkfests on The SA Incubator. Hire away! Let the good young writers infiltrate the media giants and transform them from within.

Friends in Low Places.

I tell all the young, upcoming science writers to carefully read every word of the transcript of the commencement speech to Berkeley Journalism School’s Class of 2011 given by Robert Krulwich after his mind-blowing experience at ScienceOnline2011. Friends in Low Places. Helping each other. Going Places. Becoming a New Paradigm.

I am one of those. I started blogging on a whim, back in 2004. I got invited to a blog network early on – in 2006. I got a job in the comments section of my blog post in 2007. I got my current job in 2010 because of my blogging. This is a success story.

I never had the Impostor Syndrome when I was doing research. I still have Impostor Syndrome as a writer. English is my second language. I was not trained to write. I don’t know how to turn a pretty phrase. I know nothing about structure and composition of an article. I have difficulty writing on deadline. Why would anyone want to read what I write – my over-long, convoluted, stream-of-consciousness blog posts? I don’t know!

But obviously some people do. And they became my community, my second family. It is that community that helped me every step of the way. They cheered me on. They hit my PayPal button when I was jobless. They pushed for me to get hired. They keep coming to ScienceOnline, they hug me at tweetups, they submit posts to Open Laboratory, they say Yes when I invite them to join the SciAm blog network, they were there for me all along and helped me climb over that wall that Krulwich talks about.

It’s payback time. It is now my turn to help others climb that wall, too.

It was easier to get noticed back when I started. Veteran bloggers or veteran science writers do not need much promotion. But there are many great new voices in the science writing world. This world is now big and growing fast, so it is getting harder and harder to get heard over the din. I find it my duty to seek out and hear those voices, discover talent, promote them, help them climb over the wall.

I’ve been doing it all along – nothing makes me happier than when someone I discovered, encouraged and promoted “makes it” in the real world, gets recognition, hopefully a paid gig! That’s what I see as my main mission in life. I guess that’s why they call me the Blogfather.

Horizontal loyalty.

This is another phrase from the Krulwich’s talk:

So for this age, for your time, I want you to just think about this: Think about NOT waiting your turn.

Instead, think about getting together with friends that you admire, or envy. Think about entrepeneuring. Think about NOT waiting for a company to call you up. Think about not giving your heart to a bunch of adults you don’t know. Think about horizontal loyalty. Think about turning to people you already know, who are your friends, or friends of their friends and making something that makes sense to you together, that is as beautiful or as true as you can make it.

And when it comes to security, to protection, your friends may take better care of you than CBS took care of Charles Kuralt in the end. In every career, your job is to make and tell stories, of course. You will build a body of work, but you will also build a body of affection, with the people you’ve helped who’ve helped you back.

This is really the key reason why I started The SA Incubator. And why I invite young writers to write for the Guest Blog. And why we always try to get ample travel grants for students to attend ScienceOnline. And why I always (not successfully yet) submit a “young writers” panel for the NASW and WCSJ and AAAS meetings.

It is not so much about helping new writers get jobs in old media companies (though that helps pay bills for a little while). It is about helping them find each other, build relationships, build friendships, build start-ups, build a whole new science writing ecosystem that will automatically do both “push” and “pull” and reach everyone and displace bad science reporting from the most visible areas of the media, while providing them with a living. This requires a lot of them, but they need to know each other and work together toward that goal. The SA Incubator is one of those “meeting places” for them. And Khalil and I are planning some features in the future that will make this aspect even more visible.

2. In general, how does the blog do in terms of activity (comments, hits, etc) compared to others in the Scientific American network?

Unlike most of the other blogs on the network, The SA Incubator had to start from zero. No old subscribers to bring on over from “the old blog”. No fascinating blogger author to lure his or her fans. And no clear and obvious clue at the outset what the blog was going to be about. It also did not get all of the needed attention at the beginning as I had to focus on bigger priorities in getting the network built, launched, started and promoted.

It took some time to figure out how the blog should really look like – and certainly to make it clearer to the readers what to expect there if they keep coming back. But over the last few weeks, as the frequency of posting has increased, as Khalil Cassimally joined me as a co-blogger, and already profiled writers spread the links to the interviews around their own networks, I can see that the traffic is starting to grow quite nicely. Too early to tell, though.

What is more important than the immediate traffic to each post is the longevity – Scientific American has, as you can expect, quite a lot of “google juice”, so future searches for the names of writers should bring one to the Incubator interviews. I see it more as a lasting repository than as a source of daily hits gone viral.

3. When deciding to profile a journalist or include their work in the Incubator, what qualities or characteristics are you looking for? If someone wanted to be included how should they go about that?

This first period of interviews is, naturally, populated by people whose work I am already very familiar with. I may have even met them in person, e.g., at Science Writers or ScienceOnline conferences, local tweetups etc. I have followed their work for a year or two and I like what they do. Perhaps they pitched me a story or two for the Guest Blog. Or I may be a regular reader of their personal science blogs.

As a Visiting Faculty at the NYU program for science, health and environmental reporting, and a member of the advisory board of the equivalent UNC program, I am familiar with students from these two schools. And I also try to familarize myself with the work of students at other schools as much as I can.

As the series progresses, Khalil and I will need to get familiar with the work of others, perhaps new people just coming into the field.

There are many ways to do that – follow/subscribe/friend us on Twitter, Facebook, Google Plus and elsewhere. Become a regular commenter on our network’s blogs (yes, I read all the comments). Pitch me a story for the Guest Blog. Email us a little introduction to yourself. When you write a good blog post, or make a video, podcast or infographic, or have an article published somewhere, let me know – just DM me the link on Twitter. If I like it, I will promote it. If I like your stuff in general, I am likely to ask you for a SA Incubator interview as well.

How barley domesticated its clock

barleyMost organisms that live on or near the surface of the Earth or its oceans have evolved a circadian clock – a daily timer of all biochemical, physiological and behavioral functions.

Daily cycle of light and darkness in the environment is a selective factor – having an internal clock is an adaptation that allows organisms to predict and prepare for instead of passively react to cyclical changes in the environment. The regularity of the light-dark cycle is usually a good predictor for other (perhaps not as precise) cycles of temperature, availability of food, or activity of predators.

ResearchBlogging.orgIt gets trickier for organisms that live in places where the light-dark cycle may be missing for big chunks of the year (the polar regions), or where light-dark cycle is not a good predictor of other relevant events in the environment (e.g,. cannot predict rain in very arid regions), or where light cannot penetrate at all (deep ocean, caves, underground burrows). In such organisms the clock may get uncoupled from some of its functions, e.g., it may still time biochemical but not behavioral events. Or the clock may be temporarily or permanently turned off.

Even animals that constantly live in caves still tend to have functioning circadian clocks even if they are not used by these animals to drive rhythms in behavior. In animals that regularly travel into and out of the caves, like bats, the clock is robust.

A number of organisms have been studied in which the clock may temporarily be turned off. In the chestnut tree , circadian clock stops in winter. In reindeer in the high Northern latitudes, behavioral rhythms (and underlying clock) work only during the short springs and autumns, not during the long polar winters and summers. In social insects, castes that spend their time inside the hive and need to work around the clock also do not have a functioning circadian clock.

The organisms that live in extreme environments tend to be difficult to study. It may be a harsh environment for the human researchers to spend long periods of time in. The organisms may not be easy to bring into the lab to study under controlled conditions. Most of such organisms are far from being standard “laboratory models” which means that little is known about their genetics, biochemistry, physiology and behavior.

Thus, one is limited in choices as to which rhythms to study and what conclusions one can take from such studies. A limited number of overt rhythms can be easily monitored in a standardized manner even in the laboratory. A record of overall physical activity and movement is usually made. Additional measured rhythms may be daily fluctuations in hormones, e.g., melatonin. And tissue samples may be taken over a 24-hour period for analysis of patterns of expression of core clock genes.

This approach may miss stuff. For example, even if there is no cycling of clock genes or overt behavioral rhythms, this does not mean that the clock may not be working anyway – cytoplasmatic cellular clocks, or ensembles of neural cells producing weak rhythms, or hormonal feedback loops between endocrine glands could still be producing daily cycles in some aspects of metabolism not identified by the researchers. The adaptive function of the clock is so strong, if nothing else for coordinating internal events, that is is difficult to persuasively and definitively demonstrate that absolutely nothing in the body cycles around a 24-hours cycle.

An important function of the clock is also in measuring changes in daylength – days get longer in spring and shorter during fall. Even environments that have no daily cycles for a while, or no utility in using light-dark cycles, may have strong seasonality, and seasons are another important aspect of the environment related to time. Most organisms use their circadian clocks to measure the changes in daylength through a mechanism called photoperiodism. So even organisms that have no use for daily clocks, may still retain them for their higher-level function of fine-tuning the annual calendar of events.

Domestication also has an effect on circadian clock as one can argue that the lab and the farm are “extreme environments” in some sense. It is well known that many domesticated strains of laboratory mice, rats and nematodes have lost seasonality. Most of our domesticated animals have vastly prolonged breeding seasons – sometimes spanning the entire year, or adding a Fall season to the existing Spring one  – compared to their wild relatives. Domestication may be a strong selective force for abandoning seasonality, which reduces the need for a functional circadian clock as well, especially if human care – feeding, defense, etc. – replace the need for the organism to fend for itself in sync with the cycles of nature.

Now a new player is entering this line of research – barley (Hordeum vulgare). Last week, Faure et al, published an open access paper in PNAS showing that strains of barley from Northern Europe have mutations in one of their photoperiodic genes – EARLY MATURITY8 (EAM8) – and that this gene greatly reduces the amplitude of expression of the core circadian clock genes.

As a result, northern varieties of barley can start flowering early and fast in the season, completely ignoring daylength, just following the normal developmental program. At the same time the disrupted clock allows for much longer daily activity of photosynthesis during long summer days, as it does not shut it down before darkness arrives in the evening.

One can imagine how such mutants were prized in the earlier history of the domestication. As humans moved more and more north, only the barley that could be harvested early and produced large yields was valuable. Late harvest may have been too late: humans may have already moved on, driven by hunger, and left the field to be harvested by birds. Or the harvest, being so small and late, would have been used only for consumption (winter is coming – time to brew some beer!) and not for seed for the next year.

Plant circadian clocks are very complex at the molecular level, involving several different feedback loops in expression, some operating in the morning, others in the evening, etc. Importantly, some of the genes involved in photoperiodism and flowering are intricately connected to the clock and may be a part of some of the clock feedback loops. Most of the past research focused on the way clock genes regulate flowering genes. This is an unusual paper in that it discovers the opposite direction – how a gene involved in flowering feeds back on the clock genes and regulates the way the clock works.

What is exciting about this work is that barley is not a difficult organism to do research on. One does not need heroic efforts or expensive Arctic or speleological gear to study it – it is a domesticated plant, easily grown in fields, glasshouses and labs. Furthermore, much of its biology is already well known, including the similarity between its genes and those of Arabidopsis thaliana, the standard model for plant research.

As a number of strains of barley exist, some southern some northern, there is plenty of material to do comparative studies to figure out exactly which genes and processes were involved in the process of domestication – what was selected for as the humans took their crops with them on their northward migrations. This makes barley potentially a useful standard laboratory model for the general studies of evolution under domestication.

Reference:

Faure, S., Turner, A.S., Gruszka, D., Christodoulou, V., Davis, S.J., von Korff, M. & Laurie, D.A. Mutation at the circadian clock gene EARLY MATURITY 8 adapts domesticated barley (Hordeum vulgare) to short growing seasons, Proceedings of the National Academy of Sciences, DOI: 10.1073/pnas.1120496109

Related at Scientific American:

Chestnut Tree Circadian Clock Stops In Winter
Evolutionary Medicine: Does reindeer have a circadian stop-watch instead of a clock?
Domestication – it’s a matter of time (always is for me, that’s my ‘hammer’ for all nails)
Why social insects do not suffer from ill effects of rotating and night shift work?
Clock Evolution
Whence Clocks?
Circadian clock without DNA–History and the power of metaphor
Basics: Biological Clock
Clock Classics: It All Started with the Plants

Image: Wikimedia Commons, public domain.

Domestication – it’s a matter of time (always is for me, that’s my ‘hammer’ for all nails)

I originally published this post on August 6, 2008.

Since this article came out in The American Scientist in early 1999 (you can read the entire thing here (pdf)) I have read it many times, I used it in teaching, I discussed it in Journal Clubs, and it is a never-ending fascination for me.

Back in the 1950s, Dmitri Konstantinovich Belyaev started an experiment in which he selectively bred Silver Foxes, very carefully, ONLY for their tameness (and “tameness” was defined very rigorously in terms of type and speed of response, distance that triggers aggression, etc.).

What happened really fast in this experiment is that many other traits showed up, seemingly out of nowhere, in the subsequent generations. They started having splotched and piebald coloration of their coats, floppy ears, white tips of their tails and paws. Their body proportions changed. They started barking. They improved on their performance in cognitive experiments. They started breeding earlier in spring, and many of them started breeding twice a year.

Most of the people reacting to this experiment invoked pleiotropy, i.e., how changes in one gene affect expression of many other genes. See this NYT article for instance. However, even while I was reading it for the first time, my mind screamed – development!

And not just development, but more specifically, heterochrony – change in timing of developmental event.

If you alter the expression of one of the genes that affects developmental timing, you affect all sorts of things.

For instance, when the neural crest cells migrate they become melanocytes in the skin – if due to changes in timing they are late to arrive to some distal parts, e.g., paws and tail-tips, those part will be white. Neural crest cells also migrate to become the adrenal medulla – that little part of the body that releases (nor)epinephrine (adrenaline). If fewer of those cells arrive there on time, less the animal will show stress-response later in life.

There appears to be tight correlation between timers that act on different scales, e.g., developmental and circadian timing, circadian and fast behavioral timing, circadian and seasonal timing, etc.

I always wished I could get a lab, some foxes, an IACUC approval and some money to run these animals through a battery of standard experiments comparing dogs, wild foxes and domesticated foxes on all sorts of parameters of circadian rhythms, photoperiodism (they did change their seasonality patterns of breeding, after all), etc.

The bottom line is that a subtle change in timing of expression of a single developmental gene, something one can select for by choosing one of the traits (in this case a behavioral trait), will affect the change in timing of expression in many other genes. The difference between wild and domesticated foxes may not be in any DNA sequence at all – it could presumably be all epigenetic (see also). Sequence differences would arise later, as the two populations are not inter-mixing any more (for over 60 years now).

When you put together development, genetics and evolution, you can see that big changes (or, really, any changes at the very beginning of the evolutionary change) in DNA sequence are not necessary for big changes in entire suites of phenotypic traits. But in the 1950s, the bean-bag deterministic genetics was the norm, so the Belyaev experiment was a big jolt to the scientific community in the West (not so much for the Russian evolutionary biologists, though), so we need to look at this experiment through a decent grasp of history.

Now, I’d like to know what is the state of the experiment today. Ten years ago, the project appeared doomed – they had to sell foxes for fur in order to keep going at a small scale. Has this been fixed? Has anyone from the West help finance the continuation of the project? Has anyone in the West acquired some of the foxes and continued with the project? What are the recent developments?

Related at Scientific American:

Man’s new best friend? A forgotten Russian experiment in fox domestication by Jason G. Goldman

Learning from Domesticated Foxes by The Dog Zombie

The Russian Fox Study by Jason G. Goldman

Why social insects do not suffer from ill effects of rotating and night shift work?

This post was first published on May 10, 2009

ResearchBlogging.orgMost people are aware that social insects, like honeybees, have three “sexes”: queens, drones and workers.

Drones are males. Their only job is to fly out and mate with the queen after which they drop dead.

Female larvae fed ‘royal jelly’ emerge as queens. After mating, the young queen takes a bunch of workers with her and sets up a new colony. She lives much longer than other bees and spends her life laying gazillions of eggs continuously around the clock, while being fed by workers.

Female larvae not fed the ‘royal jelly’ emerge as workers.

Workers perform a variety of jobs in the hive. Some are hive-cleaners, some are ‘nurses’ (they feed the larvae), some are queen’s chaperones (they feed the queen), some are guards (they defend the hive and attack potential enemies) and some are foragers (they collect nectar and pollen from flowers and bring it back to the hive).

What most people are not aware of, though, is that there is a regular progression of ‘jobs’ that each worker bee goes through. The workers rotate through the jobs in an orderly fashion. They all start out doing generalized jobs, e.g., cleaning the hive. Then they move up to doing a more specialized job, for instance being a nurse or taking care of the queen. Later, they become guards, and in the end, when they are older, they become foragers – the terminal phase.

This pattern of behavioral development is called “age polyethism” (poly = many, ethism = expression of behavior), or sometimes “temporal polyethism” (image from BeeSpotter):

This developmental progression in behavior is accompanied by changes in brain structure, patterns of neurotransmitter and hormone synthesis and secretion, and patterns of gene expression in the central nervous system.

Some years ago (as in “more than ten years ago”) Gene Robinson and his students started looking at daily patterns of activity in honeybees. The workers in their early stages are doing jobs inside the hive, where it is always dark. They clean the hive, take care of the eggs and pupae, and feed the larvae and the queen around the clock. Each individual bee sometimes works and sometimes sleeps, without any semblance of a 24-hour pattern. Different individuals work and sleep at different, apparently random times. The hive as a whole is thus constantly busy – there is always a large subset of workers performing their duties, day and night.

As they get older, they start doing the jobs, like being guards, that expose them to the outside of the hive, thus to the light-dark and temperature cycles of the outside world.

Finally, the foragers only go out during the daytime and have clear and distinct daily rhythms. Furthermore, the foragers have to consult an internal clock in order to orient towards the Sun in their travels, as well as to be able to communicate the distance and location of flowers to their mates in the hive using the ‘waggle dance’. As bees are social insects, it is difficult to keep individuals in isolation for longer periods of time, but it has been done successfully and, in such studies, foragers exhibit both freerunning (in constant darkness) and entrained (in light-dark cycles) circadian rhythms, while younger workers do not.

In the Robinson lab, then PhD student Dan Toma and postdoc Guy Bloch did much of the early and exciting work on figuring out how the rhythmicity develops in individual worker bees as they pass through the procession of ‘jobs’.

In an early study, they measured levels of expression of mRNA of the core clock gene Period (Per). The gene was expressed at low levels and no visible daily rhythm in early-stage workers, but at much higher levels and in a circadian fashion in foragers.

As the levels of expression were measured crudely – in entire bee brains – it was impossible at the time to be sure which of the two potential mechanisms were operating: 1) the cellular clock did not work until the bee became a forager, or 2) the cellular clocks were working, but different cells were not synchronized with each other, producing a collectively arrhythmic output: both as measured by gene expression of the entire brain and as measured by behavior of the live bee.

Either way, the study showed correlation: the appearance of the functional circadian clock coincided with other changes in the brain structure, brain chemistry and bee behavior. They could not say at the time what causes what, or even if the synchronicity of changes was purely coincidental. They needed to go beyond correlation and for that they needed to experimentally change the timing to see if various processes can be dissociated or if they are tightly bound to each other.

And there is a clever way to do this!

First, they took some hives and removed all the foragers from it. This disrupted the harmony of the division of labor in the hive – too many cleaners and nurses, but nobody is bringing the food home. When that happens, the behavioral development of other workers speeds up dramatically – in almost no time, some nurses and guards develop into foragers. And, lo and behold, the moment they became foragers, they developed rhythms in behavior and rhythms of the Per gene expression in the brain. So, as the development is accelerated, everything about it is accelerated at the same rate: gene expression, brain structure, neurochemistry, and behavioral rhythmicity.

Nice, but then they did something even better. They removed most of the cleaners and nurses from some hives. Again, the balance of the division of labor was disrupted – plenty of food is arriving into the hive but there is not enough bees inside to take care of that food, process it, feed the larvae, etc. What happened then?

Well, some of the foragers went back into the hive and started performing the house-keeping duties instead of flying out and about. And, interestingly, their brain structure and chemistry reverted its development to resemble that of cleaners and nurses. They lost behavioral rhythmicity and started working randomly around the clock. And the rhythm of clock-gene expression disappeared as well.

So, genetic, neural, endocrine, circadian and behavioral changes all go together at all times. Social structure of the colony, through the patterns of pheromones present in the hive, affects the gene expression, brain development and function, and behavior of individual bees. Just like the gene expression and behavioral patterns, the patterns of melatonin synthesis and secretion in honeybee brains is low and arrhythmic in young workers and becomes greater and rhythmic in foragers. With the recent sequencing of the honeybee genome, the potential for future research in honeybee chronobiology looks promising and exciting.

But are these findings generalizable or are they specific to honeybees? How about other species of bees or other social insects, like wasps, ants and termites? Are they the same?

Other species of socials insects have been studied in terms of age polyethism as well. The earliest study I am aware of (let me know if there is an older one) studying behavioral rhythmicity in relation to behavioral development was a 2004 Naturwissenschaften paper by Sharma et al. on harvester ants. In that study, different castes of worker ants exhibited different patterns – some were strongly diurnal, some nocturnal, some had strange shifts in period, and some were arrhythmic. Those with rhythms could entrain to light-dark cycles as well as display freerunning rhythms in constant darkness.

Just last month [April 2009], a new paper on harvester ants came out in BMC Ecology (Open Access). In it, Ingram et al. show that foragers have circadian rhythms (both in constant darkness and entrained to LD cycles) in expression of Period gene (as well as behavioral rhythms), while ants working on tasks inside the hive do not exhibit any rhythms either in clock-gene expression or in behavior, suggesting that the connection between age polyethism and the development of the circadian clock may be a universal property of all social insects.

We know that in humans, night-shift and rotating-shift schedules are bad for health as the body is in the perpetual state of jet-lag: the numerous clocks in our bodies are not synchronized with each other. We have evolved to be diurnal animals, entrained to environmental light cycles and not traveling over many time zones within hours, or working around the clock. Social insects have evolved a different strategy to deal with the potentially ill effects of shift-work: switch off the clock entirely until one develops far enough that time-keeping becomes a requirement.

References:

Yang, L., Qin, Y., Li, X., Song, D., & Qi, M. (2007). Brain melatonin content and polyethism in adult workers of Apis mellifera and Apis cerana (Hym., Apidae) Journal of Applied Entomology, 131 (9-10), 734-739 DOI: 10.1111/j.1439-0418.2007.01229.x

Sharma, V., Lone, S., Goel, A., & Chandrashekaran, M. (2004). Circadian consequences of social organization in the ant species Camponotus compressus. Naturwissenschaften, 91 (8) DOI: 10.1007/s00114-004-0544-6

Ingram, K., Krummey, S., & LeRoux, M. (2009). Expression patterns of a circadian clock gene are associated with age-related polyethism in harvester ants, Pogonomyrmex occidentalis. BMC Ecology, 9 (1) DOI: 10.1186/1472-6785-9-7


The Scienceblogging Weekly (May 11, 2012)

In the flood of information, filters are invaluable – people you trust to pick the best so you can focus on that, only that, and ignore the less important stuff.

Editors (including Jason here at the network) at ScienceSeeker.org and editors (including Krystal here at the network) at ResearchBlogging.org filter the best science blog posts each week.

Ed Yong’s weekly linkfests (like this one) and monthly Top 10 choices he’d pay for (see this for an example) are must-bookmark resources.

Some other bloggers are occasional or regular sources of links I pay attention to, e.g., John Dupuis on academia, publishing, libraries and books, Chad Orzel on academia and science – especially physics, Mike the Mad Biologist on science and politics, and the crew at the Knight Science Journalism Tracker for the media coverage of science. And at the NASW site, Tabitha Powledge has a must-read On science blogs this week summary every Friday.

Most of the articles and blog posts I read every day are brought to my attention by my friends on Twitter, Google Plus and Facebook, I get some through email notifications, as well as gleaned from ScienceBlogging.org and ScienceSeeker.org science blog aggregators. I then share a LOT of those links to my followers on Twitter, Facebook and Google Plus every day.

Every workday around midnight I post a linkfest on The Network Central to make it easier to see our network posts if you missed them during the day. Khalil and I take turns highlighting the best work by up-and-coming science writers on The SA Incubator blog. Weekly posting of the ever-growing list of posts submitted for the Open Laboratory is another resource. SciAm homepage is also set as a collection of filters – we decide what goes into “Blogs” box, what in the “Latest News” feed, what in the “Science Agenda” on top of the page, and what to collect into “In-Depth Reports” over time.

Now I will also start a weekly collection of links that are “best of the best” of everything I read over a period of a week – not the posts from #SciAmBlogs, but the rest of the Web: other blogs and other media sites. That means a lot of cutting! I mean, I tweet TONS of links every day! Choosing the best will not come easy to me, so this is a good exercise for me as well, and I hope will become a useful resource to you.

I’ll try to do this every Friday, time of day dependent on travel, work, life etc. Let me know in the comments if you have suggestions for formatting, timing, etc.

Blog of the Week:

Academic Panhandling: The art of granting for your supper. Everything you ever needed to know about writing grant proposals, written by a professional grant writer.

Top 10:

The Moscow Rules – Science Edition: Part 1, Part 2, Part 3, Part 4, Part 5, Part 6, Part 7, Part 8, Part 9 and Part 10 by Zen Faulkes, guest-blogging at Scientopia:

The Moscow Rules were directives that undercover American intelligence agents allegedly used in the Cold War. The rules were there to increase agent’s chances of making it out safely.

Sometimes, being in academic science can feel like being enemy territory in a cold war. You are often in strange territory (new lab), with many unfamiliar people (other grad students, post-docs, faculty) whose motivations are unclear. You might not trust them completely (especially administrators). There might not be the risk of attempted assassination by having poison injected into you with a specially built umbrella, but there’s enough similarity that the Moscow Rules can still apply…

If You Want A Lizard To Run Fast, Yell At It by Jonathan Losos:

…“As you well know, some days things just don’t seem to go well when testing whole animal performance. On one of those days out of frustration, fatigue, etc., we simply yelled at an apparent “slacker” lizard in jest. Much to our surprise this seemed to make a difference. We were also aware of the two recent papers for other species of lizards in which sound appeared relevant to behaviors associated with detecting threats. So, we figured what the heck, why not test for such effects systematically. Unlike many of the studies that you and others have performed with anoles, unless we simply can’t get a lizards to run along the racetrack or they appear unhealthy, we include data from all of the individuals rather than subjectively rating the trials for their quantity. Perhaps, some of the gains in speed associated with our yelling were greatest for those individuals that otherwise might have been discarded after receiving a poor subjective quality rating. Of course, we lack a simple way of determining this. Similarly, we have not yet methodically tested for whether expletives are more effective that milder language.”…

Invisible aliens: they’re not life as we know it — yet by John Rennie:

Both publications posit that life, at its most abstract, involves a thermodynamic disequilibrium. That is, life involves physical structures that can only maintain their integrity with inputs of energy. These physical structures will require covalent bonds between atoms (to allow nontrivial chemical reactions), so the environment in which life appears must allow such chemistry to occur. Some kind of liquid, but not necessarily water, would therefore also be necessary to enable those reactions. Finally, some molecules in the living system would need to be capable of Darwinian evolution for the life to arise. (Take note, creationist doubters of evolution: it is now a useful part of the definition of life!)

From theory and experiments, both papers argue that life with these traits could evolve under a wide (but definitely limited) range of environments. Carbon-based life on worlds with liquid water might represent a particularly versatile and common set of solutions, but biochemistry could go in many directions even on Earthlike worlds. And on planets and moons where terrestrial life would perish instantly, life based on silicon instead of carbon or liquid hydrocarbons instead of water might thrive…

Plastic Lessons by Shara Yurkiewicz:

I always feel awkward when I talk to plastic patients. The simulation mannequins are impressive: their eyes blink, their chests expand as they breathe, they have pulses, they bleed, they burn. A screen monitors vital signs: I administer a pressor and a dipping blood pressure perks up, or I order a beta blocker and a racing heart rate slows. A physician in the next room lends her voice to play the patient, responding to what I do and say. A physician in the same room becomes a tech, relying results of my tests and nudging me through the next steps when I veer off course….

Twilight of the giants in taxonomy by Emmett Duffy:

In an important sense, nothing exists until it’s given a name. And in the living world of organisms, names—official, scientific names—are assigned by unique creatures called taxonomists, experts in the minutiae of structure and biology of particular groups of organisms, working according to a strict and arcane body of rules of biological nomenclature. These individuals tend to be specialists—sages of whales, anglerfishes, microscopic worms that live only between the grains of sand on beaches, microscopic algae, purple sulfur bacteria, and everything in between…

Is Technology Destroying Your Relationships? by A.V.Flox:

Social networks put a number on those weak ties, but we all have weak ties in our meatspace lives. Marche bemoans how we use machines to check out at the grocery store instead of waiting in line with other people to have our purchases rung up by an actual human. But I wonder — even if you were to speak to the woman giving you dirty looks because you were buying a product with a big carbon footprint, can you actually call that a meaningful relationship?

I talk to people all the time — cab drivers, waiters, flight attendants, the guy at the post office, my manicurist, my barista, the boys at the convenience store where I buy my cigarettes, the guy at the newsstand. I am there, in the flesh. Does this mean our connections are any more meaningful than a like or a plus on social media?

Weak ties exist. They’re everywhere. All we have to do to make them meaningful is take the chance to go deeper. This is as true online as it is offline.

What does it mean to say that something causes 16% of cancers? by Ed Yong:

…executives and policy-makers love PAFs, and they especially love comparing them across different risk factors. They are nice, solid numbers that make for strong bullet points and eye-grabbing Powerpoint slides. They have a nasty habit of becoming influential well beyond their actual scientific value. I have seen them used as the arbitrators of decisions, lined up on a single graphic that supposedly illustrates the magnitude of different problems. But of course, they do no such thing…

The Mysterious Case of the Vanishing Genius by Mike Martin:

Margie Profet was always a study in sharp contradictions. A maverick thinker remembered for her innocent demeanor, she was a woman who paired running shorts with heavy sweaters year-round, and had a professional pedigree as eccentric as her clothing choices: Profet had multiple academic degrees but no true perch in academe. In the late 1980s and early 1990s, Profet published original theories about female reproduction that pushed the boundaries of evolutionary biology, forcing an entire field to take note. Indeed, back then it was hard not to notice Margie Profet, a vibrant young woman who made a “forever impression” on grade school chums and Harvard Ph.D.s alike. Today, the most salient fact about Profet is her absence. Neither friends, former advisers, publishers, nor ex-lovers has any idea what happened to her or where she is today. Sometime between 2002 and 2005, Profet, who was then in her mid-40s, vanished without a trace…

Fear fans flames for chemical makers by Patricia Callahan and Sam Roe (see also Part 2 Big Tobacco wins fire marshals as allies in flame retardant push and Part 3 Distorting science):

Manufacturers of fire retardants rely on questionable testimony, front groups to push standards that boost demand for their toxic — and ineffective — products

Asymmetrical snakes by Andrew Durso:

Animals have a long tradition of being bilaterally symmetrical – that is, of the left side and the right being nearly identical. Sure, there are a few exceptions – the human heart is nearly always farther to the left side, for instance. Snakes and other elongate, limbless animals sometimes stagger their paired organs (gonads, kidneys) so that one is in front of the other, to better fit in their cylindrical bodies. Most snakes have even done away with one of their two lungs. But the basic external body plan, the bones and muscles on the left and the right, are always mirror-images of one another, right?

Enter the pareatid snakes…

Science:

Drop the base to make bagels more delectable by Raychelle Burks:

Sometimes, just hearing that certain chemicals are in food just puts people off. “I think that a lot of people would be really surprised about the precise chemicals that are used to make their favorite foods,” said Dr. Hartings. Take Cool Whip for example. One of its ingredients is polysorbate-60, a chemical that helps give Cool Whip its puffy appearance. Polysorbate-60 moonlights as an ingredient in sexual lubricants like K-Y YOURS+MINE. Our foods contain all kinds of chemicals that have more than one job. Thankfully, one of those jobs is making food delicious.

Insects that skate on the ocean benefit from plastic junk by Ed Yong:

Imagine a world of two dimensions, a world with no up or down… just across. No climbing, falling, jumping, or ducking… just shimmying and sidling. Welcome to the world of the sea skater.

Sea skaters, or ocean striders, are small bugs. They’re relatives of the pond skaters or water striders that zip spread-eagled across the surface of ponds and lakes. Except they skate over the open ocean, eating plankton at the surface…

Problems in the neurozone by Pete Etchells:

Having a scan of your brain is a uniquely odd experience. I had one done once. I was loaded, torpedo-like, into a claustrophobia-inducing, cocoon-like chamber for nearly an hour, the first few terrifying minutes of which I spent desperately trying to recall whether I had actually passed that metal ball-bearing I swallowed when I was a kid. The machines themselves are pretty damn loud, but something about repetitive clunking noises seems to lull me into a state of relaxation, so I spent the majority of my time in the launch chamber trying not to snooze. Honestly, it was all quite enjoyable…

Abandoment issues by Dr. Al Dove, guest-blogging at NeuroDojo:

There exists on my hard drive a folder into which I loathe copying files, but only slightly less than I would loathe deleting them all together. It is a folder called “Aborted Manuscripts” and it is this folder which is the source of my shame. It is a graveyard of stupid ideas and of great ones poorly executed, of unfinished cogitations, of journal rejections, of unresponsive colleagues and of frustrating students. It’s a roadmap documenting 15 years of science (read: “me”) not doing what science (read: “me”) is supposed to do – get published…

Put Away The Bell Curve: Most Of Us Aren’t ‘Average’ by Shankar Vedantam:

The bell curve powerfully shapes how we think of human performance: If lots of students or employees happen to show up as extreme outliers — they’re either very good or very bad — we assume they must represent a skewed sample, because only a few people in a truly random sample are supposed to be outliers.

New research suggests, however, that rather than describe how humans perform, the bell curve may actually be constraining how people perform. Minus such constraints, a new paper argues, lots of people are actually outliers.

Human performance, by this account, does not often fit the bell curve or what scientists call a normal distribution. Rather, it is more likely to fit what scientists call a power distribution…

The real CSI: what happens at a crime scene? by Craig Taylor:

From the diver who finds the body parts, to the forensic specialist who identifies flecks of paint on the victim and the handwriting expert who examines the killer’s notes… What happens behind the yellow tape of one crime scene

Of mice and Marmaduke (and dinosaur farts) by Mike Argento:

EDITOR’S NOTE: The following column contains sophomoric humor and references to the bodily functions of dinosaurs and the size of certain anatomical features of mice, all in the name of science. If this kind of thing offends you, please skip this and go right to Marmaduke. That dog, he cracks us up…

Spacesuit In A Cave by Sarah Everts:

Most visitors to the million-year-old Dachstein Giant Ice Cave prefer to wear standard winter coats during visits to its freezing, icy interior. But for five days the Dachstein cave systems were a temporary lab for a squad of space scientists. Some 50 scientists assembled from three continents to use the UNESCO World Heritage site as a proxy for Mars—a first for the cave system, which normally hosts jazz concerts, modern art exhibits, laser shows, and a steady stream of tourists….

Experimental Biology Blogging: Self-promotion and ‘self-promotion’ by Scicurious:

But of course, this is because academics have two different kinds of self-promotion. One is ok, and one is not. One takes place in the ivory tower, and one involves the dreaded public…

1859’s “Great Auroral Storm”—the week the Sun touched the earth by Matthew Lasar:

Noon approached on September 1, 1859, and British astronomer Richard Christopher Carrington was busy with his favorite pastime: tracking sunspots, those huge regions of the star darkened by shifts in its magnetic field. He projected the Sun’s image from his viewing device onto a plate of glass stained a “pale straw colour,” which gave him a picture of the fiery globe one inch shy of a foot in diameter…

The Physics of Spilled Coffee by Jon Cartwright:

…Krechetnikov and his graduate student Hans Mayer decided to investigate coffee spilling at a fluid dynamics conference last year when they watched overburdened participants trying to carry their drinks to and fro. They quickly realized that the physics wasn’t simple. Aside from the mechanics of human walking, which depends on a person’s age, health, and gender, there is the highly involved science of liquid sloshing, which depends on a complex interplay of accelerations, torques, and forces. …

Why Do Conference Talks Suck, and How Can We Change That? by Matthew R. Francis:

…Yes, some speakers are better than others, and a few of the 42 talks I heard were very good. Also, I know I used to commit many of the same sins I witnessed in talks yesterday and the day before, so as I list the problems, I’ll flag my own bad habits (current and former). Based on conversations with my friends, this is not a problem limited to particle physics conferences, much less to physics conferences in general: it’s endemic in science, and perhaps most academic fields…

Sleek, Smart Spacesuits Are on the Horizon by Amy Shira Teitel:

Spacesuits are poised to go the way of the cell phone – once bulky and cumbersome, researchers are working on making them slim and smart. In the future, astronauts might be wearing specially engineered garments that combine the life-preserving features of a spacesuit with augmented reality technology that could intuit the wearer’s needs…

How and Why Neuroscience should be taught in School by TheCellularScale:

…Neuroscience is sort of where genetics was 20-30 years ago: The scientific frontier, fascinating to the public, changing the general worldview, raising ethical questions, science fiction’s closest reflection in reality. This has its benefits and its downfalls. There is currently strong general enthusiasm for neuroscience for just these reasons, but because everything ‘neuro’ is so exciting, the risk of media misrepresentation is high and the misuse of neuroscience concepts and terms by pseudo-science is common. …

Fetal Attraction by Robert Krulwich:

…Dr. Johnson says cells from fetal boys and girls have been found in mothers “four to five decades following the last pregnancy.” That fetus may have grown into a middle aged pharmacist, and still his cells are inside his mother. Cells wouldn’t persist in foreign body for NO reason. They must be doing something, but what?…

On Biocultural Anthropology by Daniel Lende:

…what brings many students into anthropology, and still impassions me about the field, is that it does approach the question of “What does it mean to be human?” in the broadest, most interdisciplinary way. And it strikes me that we have some core analytical approaches to that question that matter, and that this style of thinking is what really makes up the holism of anthropology, rather than a particular commitment to four-fields and working across the different sub-disciplines. This human lens includes a comparative approach, an attention to variation across time and space, a recognition that we as researchers inevitably bias our own data, and, yes, a commitment to drawing on multiple strands of research…

94 Elements by The 94 Elements team:

There are 94 naturally occurring elements, from Hydrogen to Plutonium, and together they make up everything in the world. The stories of the elements are the stories of our own lives, revealing the details of our personal lives, the patterns of our economies, and our relationships with our natural resources.

94 Elements is a new global filmmaking project, exploring our lives through the lens of the elements. The project is producing a collection of stories by different filmmakers about the endless ways the elements touch our daily lives. Each filmmaker takes one element as the basis for a film around how it’s used. The films are surprising and moving human stories – this is not about science, but about our human relationships with our mineral resources.

How Does the FDA Monitor Your Medical Implants? It Doesn’t, Really by Lena Groeger:

Each prescription drug you take has a unique code that the government can use to track problems. But artificial hips and pacemakers? They are implanted without identification, along with many other medical devices. In fact, the FDA doesn’t know how many devices are implanted into patients each year – it simply doesn’t track that data.

The past decade has seen numerous high profile cases of malfunctioning medical devices, which have led to injury or even death. Critics say the FDA’s minimal monitoring of devices contributes to these problems….

Leptin: Linking Malnutrition and Vulnerability to Infection by Michelle Ziegler:

As long as leptin levels stay within normal levels, all of the functions displayed above function normally. As the leptin levels drop, many of these functions are adversely effected. It is a wide-spread trigger for a starvation response. Why cripple the immune response during starvation? My best guess would be because of the huge energy expenditure required to keep the immune response running normally, especially in cellular proliferation.

Experts debate what makes a healthy vagina by Anna Salleh:

New US findings suggest our accepted definition of a healthy vagina could be ethnically biased, say some researchers, but others caution against over-interpreting the data.

A new study published today in Science Translational Medicine found, what an accompanying commentary describes as, an “unexpected and astonishing” variability over time in the vaginal bacterial communities of apparently healthy women….

The Ph.D. Now Comes With Food Stamps by Stacey Patton:

…A record number of people are depending on federally financed food assistance. Food-stamp use increased from an average monthly caseload of 17 million in 2000 to 44 million people in 2011, according to the U.S. Department of Agriculture’s Web site. Last year, one in six people—almost 50 million Americans, or 15 percent of the population—received food stamps.

Ms. Bruninga-Matteau is part of an often overlooked, and growing, subgroup of Ph.D. recipients, adjunct professors, and other Americans with advanced degrees who have had to apply for food stamps or some other form of government aid since late 2007….

Nicholas Kristof and the Bad, Bad Chemical World by Deborah Blum:

…Because his secondary crusade of the last few years, you know, the one against evil industrial chemicals, is really starting to annoy me. This is not saying that he’s entirely wrong – there are evil industrial chemicals out there. And, in many cases, they aren’t as well researched or as well regulated as they should be.

But if we, as journalists, are going to demand meticulous standards for the study and oversight of chemical compounds then we should try to be meticulous ourselves in making the case. And much as I would like it to be otherwise, I don’t see enough of that in Kristof’s chemical columns. They tend instead to be sloppy in their use of language, less than thorough, and chemophobic enough to undermine his legitimate points….

How Academic Biologists and Physicists View Science Outreach by Elaine Howard Ecklund, Sarah A. James and Anne E. Lincoln:

Scholars and pundits alike argue that U.S. scientists could do more to reach out to the general public. Yet, to date, there have been few systematic studies that examine how scientists understand the barriers that impede such outreach. Through analysis of 97 semi-structured interviews with academic biologists and physicists at top research universities in the United States, we classify the type and target audiences of scientists’ outreach activities. Finally, we explore the narratives academic scientists have about outreach and its reception in the academy, in particular what they perceive as impediments to these activities. We find that scientists’ outreach activities are stratified by gender and that university and disciplinary rewards as well as scientists’ perceptions of their own skills have an impact on science outreach. Research contributions and recommendations for university policy follow.

Blue-eyed-people-are-all-related zombie news by Jon Wilkins:

…So, to recap, 1) Cool paper. 2) Sex between blue-eyed people is not incest. 3) We have no idea when or where this mutation came from, but it is now conceivable that we could ask the question. 4) Embarrassingly bad science reporting spontaneously rises from the grave four years later and tries to eat your brain.

Conceptual Replication by Dave Nussbaum:

There is no substitute for direct replication – if you cannot reproduce the same result using the same methods then you cannot have a cumulative science. But conceptual replication also has a very important role to play in psychological science. What is conceptual replication? It’s when instead of replicating the exact same experiment in exactly the same way, we test the experiment’s underlying hypothesis using different methods…

Replicating Dissonance by Dave Nussbaum:

Another reason conceptual replication is so important is that if the field relies exclusively on direct replication then they risk replicating the same mistakes as well. Today I wanted to illustrate this risk by looking back at the history of one of social psychology’s most influential theories: cognitive dissonance. The richness and depth of Cognitive Dissonance Theory is a result of dozens of conceptual replications. I suggest that, had it not been for conceptual replication – had dissonance only been tested and re-tested in the original paradigm (Brehm’s Free Choice Paradigm) – the theory may not have stood up to recent criticisms directed at that particular paradigm…

Chimp acts like jerk, gets praised by scientists by Eoin O’Carroll:

A chimpanzee at Furuvik Zoo in Sweden has been lauded for his ‘innovation’ and ‘sophisticated cognitive skills,’ after behaving like a complete schmuck.

What is Peru’s dolphin and pelican die-off telling us? by Al Dove:

As many as 900 dolphins and over 4,000 pelicans have washed up dead on the beaches of northern Peru in the last couple of months, (see news coverage here, here and here), leading to a flurry of activity as various authorities and other interested parties move to find out what is going on. Experts cited in the news coverage suggest that unusually warm surface waters (10F higher than the season average) are changing the swimming patterns of the huge anchovetta schools off the coast of Peru, driving them deeper and out of the diving range of pelicans. In other words, the pelicans appear to be starving. The dolphins on the other hand, have shown a high prevalence of infection with morbilivirus, which is an infectious disease…

Why a Sperm Cell Is Like a Roomba by Elizabeth Preston:

A sperm cell, much like an expensive robotic vacuum cleaner, is a minimally intelligent body on a mission. Both the Roomba and the male gamete have to navigate a walled space without much idea where they’re going or why. And although it won’t clean your floors on the way, the sperm cell uses some of the same strategy as the robot vacuum…

In the Spring, Bat Moms Choose Girls by Elizabeth Preston:

Naturally a mother bat is happy to welcome into the world a bouncing baby whatever, as long as it has all its fingers and toe-claws. But she also wants her little one to have every advantage she can give it. So when spring comes early, big brown bats prefer to keep their female embryos. Unwanted males are reabsorbed into their mothers’ bodies as if they never existed…

Media, Publishing and Technology:

Science and Truth: We’re All in It Together by Jack Hitt:

…By now, readers understand that the definitive “copy” of any article is no longer the one on paper but the online copy, precisely because it’s the version that’s been read and mauled and annotated by readers. (If a book isn’t read until it’s written in — as I was always told — then maybe an article is not published until it’s been commented upon.) Writers know this already. The print edition of any article is little more than a trophy version, the equivalent of a diploma or certificate of merit — suitable for framing, not much else.

We call the fallout to any article the “comments,” but since they are often filled with solid arguments, smart corrections and new facts, the thing needs a nobler name. Maybe “gloss.” In the Middle Ages, students often wrote notes in the margins of well-regarded manuscripts. These glosses, along with other forms of marginalia, took on a life of their own, becoming their own form of knowledge, as important as, say, midrash is to Jewish scriptures. The best glosses were compiled into, of course, glossaries and later published — serving as some of the very first dictionaries in Europe.

Any article, journalistic or scientific, that sparks a debate typically winds up looking more like a good manuscript 700 years ago than a magazine piece only 10 years ago. The truth is that every decent article now aspires to become the wiki of its own headline. …

Neuroscience: Bloggers rule? by Paul Raeburn:

..We might be hard put to find any area of science coverage that hasn’t been subject to those kinds of distortions. Coverage of Lipitor and its ilk was certainly as likely to contain dramatic headlines, and particular agendas, including those of pharmaceutical companies. And ideological arguments? It depends upon what the meaning of “ideological” is…

Brain waves by Curtis Brainard:

From advice about “exercising your mind” to treatises on “the gay brain,” media coverage of neuroscience in the UK often pushes “thinly disguised ideological arguments” and reinforces artificial divisions between social groups, according to a new study….

What Will Become of the Paper Book? by Michael Agresta:

…In the past several years, we’ve all heard readers mourn the passing of the printed word. The elegy is familiar: I crave the smell of a well-worn book, the weight of it in my hands; all of my favorite books I discovered through loans from a friend, that minor but still-significant ritual of trust; I need to see it on my shelf after I’ve read it (and I don’t mind if others see it too); and what is a classic if not a book where I’m forced to rediscover my own embarrassing college-age marginalia?

Luddites can take comfort in the persistence of vinyl records, postcards, and photographic film. The paper book will likewise survive, but its place in the culture will change significantly. As it loses its traditional value as an efficient vessel for text, the paper book’s other qualities—from its role in literary history to its inimitable design possibilities to its potential for physical beauty—will take on more importance. The future is yet to be written, but a few possibilities for the fate of the paper book are already on display on bookshelves near you…

Abraham Lincoln Did Not Invent Facebook: How a Guy and His Blog Fooled the Whole Wide Internet by Megan Garber:

…He expected — and banked on — the web’s virality, he says; he didn’t anticipate, though, how eagerly that web’s self-defined news sources would pass along his “discovery.” And he assumed people would figure out the story’s hoaxiness much more quickly than they actually did — and, then, that the corrective powers of the social web would make that joke clear within the first hour or so after the story went live…

WWW inventor warns against call for comment sections to be placed under Data Rentention Act by Kristine Lowe:

…Berners-Lee said he was concerned about how increased demands for monitoring the web, both from governments looking for greater powers to track down terrorists and companies looking to trade our personal web data for commercial purposes, threatens the very infrastructure of the web.

He described his worry that people in the end will no longer trust and use the web for e.g. researching sensitive things like depression if they fear everything they do online is being monitored…

7 New Educational Startups Founded By Minorities in Tech by Wayne Sutton:

One of today’s most challenging yet promising markets is the educational system. If you want to see startups hungry to disrupt an industry, look no further. Founders are trying to solve the problems plaguing our education system: including reconciling student debt, providing students with the skills required to land a job both before and after graduation, and offering the best course material online regardless of age, location and educational level…

5 things med students can do to engage in social media and medicine by Josh Herigon:

One topic we neglected, however, was what current medical students can do right now to get their foot in the door and begin engaging in the social media and medicine conversation. I had hoped to get to this topic during my panel discussion, but there just weren’t enough hours to cover everything. Below is my attempt to remedy this omission. Here are a few simple things you can do:

Blinding us with science journals by Peter McKnight:

A competitive university culture that discourages the sharing of knowledge has led to the publication of many flawed and fraudulent studies…

The Arrogance of Publishers vs. Academic Culture – Why the Outcome Is Virtually Certain a scholarly kitchen metaphor by Mark Carrigan:

Imagine a situation where homes had no kitchens and utensils were unavailable. We would all be dependent on cafes and restaurants to eat and, it follows, our idea of what it is to prepare food would be exhausted by those working in such a capacity within these establishments. Now introduce kitchens into homes and affordable utensils into shops. Suddenly we can cook meals at home. Obviously the quality of the infrastructure is lower and there’s less expertise. For the sake of the thought-experiment, assume kitchens and utensils appeared suddenly, to an extent profoundly disruptive of established practices of going out for every meal. The meals cooked at home would be of poor quality, probably pragmatically orientated and often imitating (poorly) the meals available in restaurants and cafes.

The Science of Obituaries: Dead Pools, Obits in the Can and More by Arthur S. Brisbane:

Mr. McDonald said The Times currently has 1,500 advance obits in the can – “and we’re adding about 250 a year. Even if you subtract the number of those we’ll publish in a given year – say, 50 – the archive is growing significantly.”…

The Psychological Prerequisites of Punditry by Julian Sanchez (also see response by Andrew Sullivan):

….The nice way to say this is that selects for pundits who have a thick skin—or forces them to quickly develop one. The less nice way to say it is that it forces you to stop giving a shit what other people think. Maybe not universally——you’ll pick out a domain of people whose criticisms are allowed to slip through the armor—but by default….

Four perspectives on communicating your research, and then one more. #EB2012 by William Gunn:

…The most popular sentence of the whole session was “Don’t underestimate your audience’s intelligence, but do underestimate their vocabulary.” In other words, drop the jargon if you want the public to get what you’re saying. …

Filter-then-publish vs. publish-then-filter by Mike Taylor:

…In the face of such a flood of information, no-one can read everything that’s made it through the filters into all their favourite journals. So in practice what actually happens is that each of us filters again – finding relevant publications in a huge range of journals by the social web we’re in: mailing lists, blogs, Twitter, and so on. I believe some people even use FaceBook….

10 Commandments of Twitter for Academics by Katrina Gulliver:

…Twitter is what you make of it, and its flexibility is one of its greatest strengths. I’m going to explain why I have found it useful, professionally and personally, and lay out some guidelines for academics who don’t know where to start….

Fungible by Stijn Debrouwere:

A treatise on fungibility, or, a framework for understanding the mess the news industry is in and the opportunities that lie ahead.

Why Publishers Don’t Like Apps by Jason Pontin:

…But the real problem with apps was more profound. When people read news and features on electronic media, they expect stories to possess the linky-ness of the Web, but stories in apps didn’t really link. The apps were, in the jargon of information technology, “walled gardens,” and although sometimes beautiful, they were small, stifling gardens. For readers, none of that beauty overcame the weirdness and frustration of reading digital media closed off from other digital media. …

The brilliant Joe Weisenthal by Felix Salmon:

Appelbaum is absolutely right that Weisenthal stands apart by starting earlier, writing more, publishing faster. That’s who Joe is. But he’s absolutely wrong that there’s an “intensely competitive world of financial blogging, dominated by young men who work long hours and comment on every new development”. Go on — name a single other financial blogger who fits that description. I’m waiting. There’s the anonymous group blog ZeroHedge, perhaps. But the fact is that Henry Blodget, in hiring and promoting Joe, has succeeded in identifying and harnessing and leveraging a nervous energy which has been there all along. He didn’t start with some kind of inhuman job description and then hire Joe to fill it; he found Joe and then basked in the fruits of encouraging him to simply be his natural self.

River of News — FTW! by Dave Winer:

…I don’t think that fancy layout trumps newness. The name “news” tells you what’s important about news. Newness. So if you follow that clue, it leads you to the obvious conclusion that news should present first the newest bits we have. What’s next? The second newest bits. And third, fourth and so on. permalink
News is one of those things that is that simple. But it takes people a while to get there if they don’t allocate the time to take walks in the park and think about this stuff in an organized way….

Blogging and Kickstarter go together by Dave Winer:

…But once the users can communicate with each other, we will be able to pool our experience, and given enough time, smart users will learn the technology well enough to make the products that (key point here) they know there is demand for. Because they are the ones demanding it….

The Pernicious Myth That Slideshows Drive ‘Traffic’ by Alexis Madrigal:

…If you’re trying to juice page views, your staff will ineluctably be forced to make galleries. Where else can they get a 10x or 20x multiplier on their work? I can guarantee you that will not help you break the kinds of stories or do the kinds of analysis that will keep people coming back. Not only that, but it’s demoralizing to your best people, the ones who want to be out there producing their best work.

Worse, readers may click through your slideshow, but they’ll hate you a liiitttle bit more than they did when they got to the site. And I bet they’ll feel the same way about whatever advertiser was unlucky enough to get stuck on the page with some stupid thing that a reporter did with a little bit of hate in his heart and fingertips. ….

ScienceOnline2012 – interview with Sarah Chow

Every year I ask some of the attendees of the ScienceOnline conferences to tell me (and my readers) more about themselves, their careers, current projects and their views on the use of the Web in science, science education or science communication. So now we continue with the participants of ScienceOnline2012. See all the interviews in this series here.

Today my guest is Sarah Chow (blog, Twitter).

Welcome to A Blog Around The Clock. Would you please tell my readers a little bit more about yourself?

sarah chowCurrently, I am a PhD student at the University of British Columbia studying Pacemaker proteins. These are proteins that help make your heart beat. The main goal is to understand how these proteins are regulated by a molecule called cAMP, by measuring the thermodynamic properties of the reaction between cAMP and the Pacemaker protein.

Although my current research focuses on very small microscopic things, my undergraduate degree is in Kinesiology, which focuses on macroscopic portions of the body. I also have a certificate in health and fitness studies.

Understanding how the body functions macroscopically and connecting it microscopically is what brought me do my PhD research today.

Tell us a little more about your career trajectory so far?

Out of high school, I wanted to be a Physical Education teacher as well as a track and field coach, because I had such great mentors in those fields. After doing a work study semester at the local science centre teaching children, it didn’t feel like the right fit for me.

I fell into research serendipitously. I casually mentioned to my anatomy teaching assistant I was interested in doing scientific research. She immediately introduced me to a professor within the department of kinesiology. Seven years later, that professor, is now, and still, my supervisor.

How did you first start becoming interested in Science Communication?

I have always been interested in communicating science, in fact, before switching from my masters degree to a PhD, I seriously considered applying to a Masters in Journalism Program. But, my research project was doing so well at the time, I decided to stick with it.

In August 2011, I attended the Banff Science Communication Program in Banff, Alberta, Canada and it changed my life. My classmates were a mixture of graduate students, science writers, science filmmakers, and science journalists. The faculty was comprised of veterans in their fields: two television directors from the Discovery Channel, four science communicators who have written books, worked as editors for Scientific American, created podcasts, blogs, and even hosted their own science television show. I ate, slept and breathed science communication for two-weeks. And within this short period of time, I created a podcast, a short science film, wrote a science article for the general public, and a website.

At the end of those two weeks, I was a science communicator convert. My heart told me, Sarah, this is who you are.

Why is science communication important to you?

I believe we have the power to govern our own path in life by making informed choices. Understanding how science is the basis of everything that surrounds us can help that process. The reason why I do research is not only to understand how the heart works, but in the bigger scheme of things, we all have this pacemaker protein in common. If that protein fails, not only is your life affected, but your surrounding loved ones lives, your community and your world is now changed because of this one little protein dictating the rhythm of your heart. Having people understand how and why science is so important and the global impact it can have on ones life is why I believe science communication is important.

What is taking up the most of your time and passion these days? What are your goals?

My main goal is to finish my PhD degree by finishing up experiments and writing my thesis.

However, a lot of my time right now is dedicated to improving my science communication skills. I’ve been blogging regularly on my website, which is a mixture of podcasts, video, and writing. My website is more of an “online laboratory” where I can experiment with different styles of communication. I also podcast for Experimental Podcast, am editor for Science Seeker News, TV show co-host for UBCevents on campus and taking improv and acting lessons to improve my presentation skills.

I am also one of the co-organizer of ScienceOnlineVancouver, a monthly discussion series focusing on issues and topics surrounding science communication.

What aspect of science communication and/or particular use of the Web in science interests you the most?

I am most interested in communication science via “transmedia”, using podcasting, video blogging and combining photos with audio clips to tell an engaging science story to the public. I really like to immerse my readers into my stories by engaging their sense by using sounds and visuals.

The web is useful because I can use sound, photos, words, movies, to create a three-dimensional story, which can be difficult via more traditional forms of science communication such as print.

How does (if it does) blogging figure in your work? How about social networks, e.g., Twitter, Google Plus and Facebook? Do you find all this online activity to be a net positive (or even a necessity) in what you do?

Blogging and tweeting about my work helps me to better understand my research and break it down into easier bits for me to digest and drill into my brain.

In general, blogging, twitter, google plus and facebook are all different avenues to give me a voice and showcase my interest. Now is my voice being heard? That’s a different question. But it allows me to interact and connect with people who are interested and passionate about science and science communication. It helps me broaden my community, which would not be possible without social media.

What was the best aspect of ScienceOnline2012 for you? Any suggestions for next year? Is there anything that happened at this Conference – a session, something someone said or did or wrote – that will change the way you think about science communication, or something that you will take with you to your job, blog-reading and blog-writing?

Being at Scio12 reminds me of the TV show series Cheers theme song:

Makin’ your way in the world today takes everything you’ve got.
Takin’ a break from all your worries, sure would help a lot.
Wouldn’t you like to get away?

Sometimes you want to go, where everybody knows your name,
and they’re always glad you came.
You wanna be where you can see, our troubles are all the same,
You wanna be where everybody knows your name.

It’s a safe, encouraging and inspiring place to be to share ideas. It’s a community.

The best advice I got from Scio12 was from @DrRubidium and @davidmanly’s session. Just hit the damn submit button and don’t look back. (That may be paraphrased a bit, but that’s how I remember it.)

What do you do in your spare time? If you have any.

I enjoy running, biking, hiking and volleyball. Basically anything that keeps me outdoors and active. I also like baking and reading a good book.

Thank you! Hope to see you again in January.

Open Laboratory…getting closer!

Yesterday, in the NYC offices of Scientific American, I was given a sweet present – three copies of the galleys of the new edition of the “Open Laboratory”, aka, ‘The Best Science Writing Online 2012’:

Looks great, inside and outside!

Also yesterday, we discovered that the book is now listed on Amazon.com so you can start pre-ordering it. Just click right over here!

ScienceOnline2012 – interview with Joe Kraus

Every year I ask some of the attendees of the ScienceOnline conferences to tell me (and my readers) more about themselves, their careers, current projects and their views on the use of the Web in science, science education or science communication. So now we continue with the participants of ScienceOnline2012. See all the interviews in this series here.

Today my guest is Joe Kraus (blog, Twitter).

Welcome to A Blog Around The Clock. Would you, please, tell my readers a little bit more about yourself? Where are you coming from (both geographically and philosophically)? What is your background? Any scientific education?

I was born and raised in Southern Wisconsin in the late 1960s and 1970s. I went to Beloit College from 1985-1989 (with a short stint of engineering education in 1988) where I got my BS in Physics. Once I graduated college, my interests turned to astronomy for a time when I worked for a high end amateur telescope manufacturing company. My wife got her Masters in Statistics, and we ended up moving to Maryland just outside of Washington DC in 1991. There was a small recession going on, and I had a hard time finding a professional job with only a BS.

I always liked computers and libraries, and in the early 1990s I learned more about this new/old thing called the Internet. In 1993, I started the second phase of my life by attending graduate school at the University of Maryland, College Park in Library & Information Science. After I got my MLS in 1995, we moved to northern Virginia for a little while where I was the engineering librarian at George Mason University. By 1997, we were still feeling a little claustrophobic in the Washington DC metro area. We were able to move out to Denver, Colorado in early 1998, and I have been at the University of Denver as the Science & Engineering Librarian since then.

Tell us a little more about your career trajectory so far: interesting projects past and present?

I have been involved in the Special Libraries Association (SLA) since 1995. I was the Chair of the Physics-Astronomy-Mathematics Division in 2007, and I was the Chair of the Sci-Tech Division in 2011. As chair of those two divisions, I provided program planning for two different annual SLA Conferences. With the rise of the social web, I have gotten more involved with other organizations, such as the Library Society of the World (LSW. With the help of several other LSW participants, we organized a library Unconference in 2008. In 2009, I joined the editorial staff and helped launch the Open Access journal Collaborative Librarianship. I also post items to the Collaborative Librarianship News blog. In 2010, I helped organize another unconference, but this one was targeted to science and engineering librarians. We are organizing the 2nd STELLA Unconference later this year in New York City.

What is taking up the most of your time and passion these days? What are your goals?

As the Science & Engineering Librarian at DU, I help a lot of students and faculty learn about and use scientific databases and journals. I have also been writing and reading about scholarly communications issues. I have a passion for blogging and telling people about the wonderful world of science.

What aspect of science communication and/or particular use of the Web in science interests you the most?

The Internet is such an awesome way for people to share information and connect with one another. I am particularly interested in advocating for Open Access (and other cost-effective methods) to journal articles and Open Data proposals.

How does (if it does) blogging figure in your work? How about social networks, e.g., Twitter, Google Plus and Facebook? Do you find all this online activity to be a net positive (or even a necessity) in what you do?

I am on a lot of social networks, but the ones I find the most useful are Friendfeed, Twitter, and Diigo for tagging articles. My two main blogs are http://www.nuthingbut.net and http://www.sciencelibrary.org. Most of the social networks I use are marked at http://about.me/jokrausdu.

When and how did you first discover science blogs? What are some of your favorites? Have you discovered any cool science blogs by the participants at the Conference?

First off, I would like to thank Christina Pikas for introducing me to you and to many other science bloggers. Of the Science Online Librarian group, I highly recommend others follow Stephanie Willen Brown, John Dupuis, Bonnie Swoger, and Kiyomi Deards.

What was the best aspect of ScienceOnline2012 for you? Any suggestions for next year? Is there anything that happened at this Conference – a session, something someone said or did or wrote – that will change the way you think about science communication?

This is the best conference concerning the scientific communication industry. It has a great mix of people from science journalism, science publishers, science book authors, scientists, science bloggers, and science librarians. Concerning next year, I would like to see the topic of Open Access and Open Data addressed. We should have an update session concerning the “Declaration of Independence” from Elsevier.

I have two take-aways from the 2012 conference. 1) I enjoyed using the electrical outlets that were available in the middle of the seating sections. The person who duck taped all of the extension cords and 6 outlet power strips deserves a raise. This allowed people to live tweet and live blog the conference without fear of draining a battery. 2) I found the discussion of the conflict between science journalists (who paraphrase scientists for a lay audience) and the scientists (who write for narrow specialized audiences) to be productive. Both sides now have a better understanding of the views of the other.

Overall, I find this conference to be essential in my quest to better understand the scientific communication process. I am looking forward to coming back to North Carolina again in 2013. Many thanks go to Bora (and Anton and Karyn and many others) for putting together such a great conference.

Thank you! Hope to see you again in January.

ScienceOnline2012 – interview with Lali Derosier

Every year I ask some of the attendees of the ScienceOnline conferences to tell me (and my readers) more about themselves, their careers, current projects and their views on the use of the Web in science, science education or science communication. So now we continue with the participants of ScienceOnline2012. See all the interviews in this series here.

Today my guest is Lali Derosier (blog, Twitter).

Welcome to A Blog Around The Clock. Would you, please, tell my readers a little bit more about yourself? Where are you coming from?

Lali picThat’s never a short answer for me.  I was born in South America and educated in the States.  We moved around quite a bit.  Now that I am raising two American children, I am discovering odd gaps in my cultural education that I never realized were there. It does make for some occasionally hilarious family moments.  I came to the Orlando, FL area right out of college and I’ve been living and working here ever since.  It’s the longest amount of time I’ve stayed anywhere, so I guess this is where I am from.  At least, until the next time we move.  

What is your background? Any scientific education?

My focus on science began fairly early.  I went to the MAST Academy for high school (a maritime science magnet school), where I had a concentration in Oceanic and Atmospheric Sciences.  I went on to major in Biological Sciences at Smith College.  After teaching for about 10 years, I decided to pursue a Master’s in Science Education.  That experience was very eye-opening for me, in terms of how other educators teach and perceive science.  It was sobering.

Tell us a little more about your career trajectory so far: interesting projects past and present?

Thirteen years into teaching, I am only now beginning to feel like an expert in my field.  I used to think of myself as a “science teacher” but now I realize that I’m actually a “high school teacher.”  The fact that I teach science is almost incidental to how important it is to understand the developmental challenges of the adolescent age group.  Doing my Master’s program after teaching for a long time helped to crystalize some thoughts that I have had on changes that need to happen in teacher-training and curriculum development. The PhD bug has bitten me hard, but I am waiting a few months to see if the urge passes.

At my own school, I have been given the opportunity to develop a program for high school students to engage in authentic research in sciences.  I am open to anything from local science competitions to lab-based research internships to national science fairs.  It is pretty open ended, so the challenge for me has been to define the scope of the project so that it suits the needs of the students here.

It is easy to over-reach, and I’d rather start small and build it up over time.  I’m finding that I have to constantly curb my enthusiasm.  I am also excited to be working with Stacy Baker on her ScienceOnlineTeen event next year.  My focus for her unconference will be to address needs of teachers who are looking to use blogging as a learning tool, so that they can better support their students.

What is taking up the most of your time and passion these days? What are your goals?

Apart from the full time work and full time parenting, I’ve been thinking a lot about curriculum development.  Anti-science legislation makes it clear that science curriculum needs to be developed by teachers.  Specifically, by experienced teachers with science training.  I can’t imagine ever leaving the classroom, but I think if I did it would be to work with science education policy writing and curriculum development.  There is so much to learn in classroom teaching.  There will never be a time when I’ll feel I’ve mastered everything there is to learn.  That’s the fun of teaching.  Even if I give the same course for 50 years, each cohort has its own challenges and personality.  No two years are ever the same.

What aspect of science communication and/or particular use of the Web in science interests you the most?

The interactivity of the Web is incredibly appealing.  The internet has dramatically changed access to current research, scientists, and science writing.  The combination of journal publications, professional and personal blogs, and science journalism means that readers (students, in my case) can engage the research on multiple levels and in a combination of ways.  The immediacy with which scientific findings can be reported, dissected, commented on, and defended is wholly attributable to the internet.   

I get frustrated when I see educators trying to make the Web conform to traditional classroom styles of communication. Didactic, front-loaded teaching styles don’t mesh well with effective internet communication.  The internet is dynamic. That’s what makes it valuable. In order for teachers to be able to use Web 2.0 tools effectively, they’re going to need to loosen the reins quite a bit.  As technology becomes more accessible, more integrated into our daily lives, I am interested to see how educational practices will change.  The generational change of teachers will be very important too.  We’re in a transition right now, where some teachers consider themselves digital natives and others don’t.

How does (if it does) blogging figure in your work? How about social networks, e.g., Twitter, Google Plus and Facebook? Do you find all this online activity to be a net positive (or even a necessity) in what you do?

I am connected absolutely everywhere, and I wouldn’t have it any other way!  Blogging (as a writer) is new to me, but I use Twitter for microblogging, bookmarking, compiling to-be-read lists… you name it.  I don’t deny that some people take to connectivity better than others, but all of our students need to become proficient with it.  Schools can’t wait until they have to accept digital communication to get along.  They have to seek it out and innovate.  In many cases, our students know better than we do, and we should let them show us what works.

When and how did you first discover science blogs?

I stumbled on to the Deep Sea News crew early on in 2011.  Through them, I became aware of the main ScienceOnline event and my network just branched out from there.  I mainly use Twitter to keep up with blog posts from SciO12 attendees.  I find that I don’t read specific blogs so much as I sift through my twitter feed and click on titles that interest me.

Is there anything that happened at this Conference – a session, something someone said or did or wrote – that will change the way you think about science communication, or something that you will take with you to your job, blog-reading and blog-writing?

I’ll confess that I arrived at #Scio12 feeling like a bit of an impostor.  I was there on an information-gathering mission, hoping to bring back ideas that I could pitch to my administration for how we might integrate the Web into classrooms and curriculum.  As I have written elsewhere, what I found at #Scio12 was nothing short of inspirational.  I met people who, despite busy schedules and demanding work, find time to blog and engage online.

In my own work, I am always conscious of the fact that I have so much to learn.  I love asking questions and watching other teachers work.  I left with a “can-do” attitude and a lot of confidence in my own abilities to become a teacher for other teachers.  It isn’t such a large leap from how I already engage information online to doing my own writing and curating in a formal way.  This is what I most want to communicate to my fellow teachers.

Blogging for learning isn’t really an “add-on” to other things.  It is an extension of a skill that young people are developing naturally as they interact on the Web.  I also realised that people at every level of education, from grade school to post-professional, are encountering the same kinds of difficulties in how young people communicate.  I think blogs can be exploited to bridge the gap between informal and formal science writing.

Thank you!

Best of April at A Blog Around The Clock

I posted 13 times in April. That is, on A Blog Around The Clock or on Observations (not counting the much more frequent posts on The Network Central, The SA Incubator, Video of the Week, Image of the Week, or editing Guest Blog and Expeditions).

New stuff:

What 3 Science Questions Do You Think the Presidential Candidates Need to Answer before November 6th?

Anthropologists love Scientific American

Events and updates:

A week in Edmonton

Sciencey events over the next few weeks

New ScienceOnline interviews:

ScienceOnline2012 – interview with Rebecca Guenard

ScienceOnline2012 – interview with Tanya Lewis

ScienceOnline2012 – interview with Kate Prengaman

ScienceOnline2012 – interview with Tracy Vence

And I republished a few posts from the old archives:

Flirting under Moonlight on a Hot Summer Night, or, The Secret Night-Life of Fruitflies

Some hypotheses about a possible connection between malaria and jet-lag

Whence Clocks?

Clock Evolution

Previously in the “Best of…” series:

2012

March
February
January

2011

December
November
October
September
August
July
June
May
April
March
February
January

2010

December
November
October
September
August
July
June
May
April
March
February
January

2009

December
November
October
September
August
July
June
May
April
March
February
January

What 3 Science Questions Do You Think the Presidential Candidates Need to Answer before November 6th?

 

As you may remember from back in February, the Guardian U.S. and NYU’s Studio 20 journalism lab teamed up to learn what all citizens think about the upcoming election, not just those who care about politics with a capital P.

Back then, the questions were posed to the candidates in the GOP primary race. Now that this race is effectively over, it is time to shift focus to the general election.

Now we want to ask the science-loving Scientific American community to voice their questions, ideas and concerns with what’s been missing from the national conversation so far. What do you want to know before you cast your vote this November?

Other (media) organizations will tap into their own communities to identify questions relevant to their interests. We want to her you, the STEM community, as to which science, engineering, technology, medicine, environment and technology-related questions you want to see asked of the two major party candidates.

So tell us: if you could pose a question to both Barack Obama and Mitt Romney, what would it be?

Give us your own question and “like” your favorites from fellow Scientific Americans on our Facebook page, and we’ll publish the top three both on our site and The Guardian’s Citizens Agenda.

Add your three suggestions to our Facebook page by Tuesday at noon.

—-
Image Source

ScienceOnline2012 – interview with Tracy Vence

Every year I ask some of the attendees of the ScienceOnline conferences to tell me (and my readers) more about themselves, their careers, current projects and their views on the use of the Web in science, science education or science communication. So now we continue with the participants of ScienceOnline2012. See all the interviews in this series here.

Today my guest is Tracy Vence (LinkedIn, Twitter).

Welcome to A Blog Around The Clock. Would you, please, tell my readers a little bit more about yourself? Where are you coming from (both geographically and philosophically)? What is your background? Any scientific education?

Thanks for having me! It’s truly an honor. I am a scientist-turned-journalist in the sense that I studied biology as an undergraduate and journalism in graduate school. I’m now at GenomeWeb in New York, where I cover genomics research and related news for a monthly magazine called Genome Technology, and also curate life science-related stories of interest from around the Web for The Daily Scan and GenomeWeb Careers blogs.

I grew up a kid obsessed with science — entering robotics competitions after school, attending microbiology camp each summer, and taking apart just about everything I could get my hands on to figure out how it worked.

Naturally, I spent plenty of time in the lab as an undergrad, where I did independent research on aggressive behaviors in the water strider Aquarius remigis. I was fortunate to have linked up with two very supportive advisers, one of whom guided my A. remigis project (and gave me unrestricted access to all the gadgets, reagents, and Drosophila cultures in his lab), and the other who invited me to join his inaugural graduate-level science writing seminar. It was in that class I first learned about science writing: The Career. Before then I’d never considered the prospect of reading and writing about science for a living. Soon enough, I was sending off applications to J-schools.

Today, I’m still a kid obsessed with science. I still want to know how everything works.

Tell us a little more about your career trajectory so far: interesting projects past and present? What is taking up the most of your time and passion these days? What are your goals?

After a hard news-intensive graduate program and a couple of internships with local newspapers, I was ready to dive back into science once I had earned my master’s degree. Post-grad school, I worked as a Web intern for the journal BioTechniques, where I covered a variety of life science news and got my first experience writing long-form features on topics like open science, database annotation, and federal funding trends.

Now, at GenomeWeb, I produce both hard news and more in-depth features on genomics research, policy, intellectual property, and more. One of the greatest perks of the job is traveling to conferences to soak in the newest research, attempting to digest all of the advances in a fast-paced field. It’s an exciting time in genomics, to be sure. There’s never a shortage of great science to bring up at the dinner table, nor of great science that should probably never be brought up at the dinner table (here I more or less refer to fecal microbiota transplants, which by the way, I find fascinating).

Speaking of gut flora, microbiome research is a current interest of mine. I look forward to putting my academic studies in clinical nutrition to use for future reporting endeavors on advances in that field.

What aspect of science communication and/or particular use of the Web in science interests you the most?

It has been great to track what the ‘net has done for things like DIYbio and citizen science, and it will be interesting to see what it does for those and similar projects in the future. I’m also really interested in online education and outreach — specifically, how to engage children and foster an early interest in science.

How does (if it does) blogging figure in your work? How about social networks, e.g., Twitter, Google Plus and Facebook? When and how did you first discover science blogs? What are some of your favourites?

Blogging is now part of my day job, but reading blogs has always been indispensable to me as a science writer. Increasingly, social networking is becoming a critical part of my job, as well — primarily through Twitter (I’m new, but have been tweeting on behalf of GenomeWeb, here, here, and here for some time).

Before I began blogging, myself, I followed several science blogs, many of which I still check daily. I’ve also had the privilege of meeting the talented scientists and journalists behind some of those blogs through events like Science Online, society meetings, scientific conferences, and the like.

As a journalist, I also like to keep a close eye on projects that focus on the future of media — scientific and otherwise. The Knight Science Journalism Tracker, the Nieman Lab, and Jay Rosen’s Twitter feed are representative of my go-to sources for such.

What was the best aspect of ScienceOnline2012 for you? Any suggestions for next year? Is there anything that happened at this Conference – a session, something someone said or did or wrote – that will change the way you think about science communication, or something that you will take with you to your job, blog-reading and blog-writing?

I have to say, it took me a few days to fully deconstruct all that I’d heard and experienced at #Scio12, both in and out of the sessions. And then David Wescott came out with this post, describing his “conflicted take,” which really resonated with me.

That some scientists face a lack of support when it comes to communicating their work was not necessarily news, just something I had never really given much thought before.

There was some talk about how to support scientists who wish to communicate their work in the comments at David’s post and in parallel discussions on Twitter, and several pitches at the Scio13 planning wiki appear to accommodate that need. I look forward to participating in those discussions in person come January, online in the meantime.

With that said, it never ceases to amaze me how much time truly smart people are willing to give me to explain their science and the issues surrounding it. Chatting with remarkably talented researchers is, by far, the greatest part of my job, and I could not be more thankful for it.

Thank you for the interview. Hope to see you next year!

ScienceOnline2012 – interview with Kate Prengaman

Every year I ask some of the attendees of the ScienceOnline conferences to tell me (and my readers) more about themselves, their careers, current projects and their views on the use of the Web in science, science education or science communication. So now we continue with the participants of ScienceOnline2012. See all the interviews in this series here.

Today my guest is Kate Prengaman (homepage/blog, Twitter).

Welcome to A Blog Around The Clock. Would you, please, tell my readers a little bit more about yourself? Where are you coming from (both geographically and philosophically)? What is your background? Any scientific education?

Hi! Thanks for having me! Right now, I’m writing to you from Madison, Wisconsin, where I am working on my MA in science journalism. Although I’ve been interested in a science writing career for awhile, last year was the year I finally decided to put my goals into action, come back to school, start blogging, making connections, and figuring out where I want my future to take me.

Tell us a little more about your career trajectory so far: interesting projects past and present?

Well, I have a BS in Biology and Environmental Science, and I worked for a few years as a field botanist on a bunch of different projects; from endangered species demography in Florida to vegetation mapping of national parks in Alaska and the Mojave desert. Since I returned to school, I’ve been writing about ecology and conservation (my passions) but also about technology, energy, mental health, and food. I’m really fortunate to be working as a research assistant for Deborah Blum as well.

Currently, my coolest project is working with cartography and data visualizations. I used to do a lot of data management and technical mapping (GIS) for my previous job, and I was excited to discover that those skills carry over into science communication. So, I am teaching myself to use Tableau (a data visualization software program) and build maps that tell stories. It’s really fun.

What is taking up the most of your time and passion these days? What are your goals?

Right now, my primary goal is navigating though the world of science writing to figure out where I want to take my career. There are so many more options and opportunities in this field that I had imagined, and attending ScienceOnline2012 and talking to people about their work played a huge part in opening my eyes to the possibilities. Beyond that, my goal is to find a way to make a living talking to interesting people about fascinating science, and then telling those stories.

What aspect of science communication and/or particular use of the Web in science interests you the most?

The best part of of the online science communication community is that it’s truly a community. I’m very new, but it’s inspiring to see so many smart and funny people discussing all kinds of science and its implications across the web. Personally, I am especially excited at the moment to be learning how to use the interactive potential of the web to create ways for people to truly experience information, like the Tableau program I mentioned earlier. I’m so excited, in fact, that I just moved to a self-hosted website so that I could incorporate these graphics I’m learning to make into my blog.

How does (if it does) blogging figure in your work? How about social networks, e.g., Twitter, Google Plus and Facebook? Do you find all this online activity to be a net positive (or even a necessity) in what you do?

As a beginning science journalist, I feel like blogging a great way to get my name out there and a great place to explore and develop my own writing. Although I was initially a skeptic, I must admit that I love twitter. I follow all of the journalists that I admire, and all day long, my twitter feed is full of excellent science writing, interesting news, and occasionally, cute baby penguins in sweaters. I try to limit my twitter access when I need to focus, but I check in throughout the day.

When and how did you first discover science blogs? What are some of your favourites? Have you discovered any cool science blogs by the participants at the Conference?

This is hard to admit, but I didn’t really follow any science blogs until I started graduate school last year. In my defense, I spent most of my time living in the desert with a tent and no cell reception, so I just didn’t have much time to read online. I would read the NYTimes every time I checked back into civilization, and that was it. I read a lot of science books, though. Now, I’ve done a 180, I have so many favorite science blogs that it’s hard to choose. I love the literary voice and strong story-telling at The Last Word on Nothing. I think Superbug is a great example of how many stories you can find, even on a relatively narrow topic. I’m a bit afraid of specialization, but I appreciate that example of how to do it so successfully.

What was the best aspect of ScienceOnline2012 for you? Any suggestions for next year? Is there anything that happened at this Conference – a session, something someone said or did or wrote – that will change the way you think about science communication, or something that you will take with you to your job, blog-reading and blog-writing?

For me, the best aspect of ScienceOnline2012 was how open everyone was to talking about their experiences, positives and negatives, as well as just the extreme amount of friendliness. I went only knowing my adviser and one classmate, and came home knowing so many amazing people. In some ways, it’s made my life harder, I have more blogs to read and more tweets is my feed sharing more awesome things to read, but overall, it’s just been so inspiring. It makes me want to be better at what I do, so I can be a better part of the ScienceOnline community in the future.

Thank you for the interview. Hope to see you next year!

Clock Evolution

This post, originally published on January 16, 2005, was modified from one of my written prelims questions from early 2000.

EVOLUTIONARY PHYSIOLOGY OF BIOLOGICAL CLOCKS

“Circadian clocks allow organisms to predict, instead of merely react to, cyclic (predictable) changes in the environment”. A sentence similar to this one is the opening phrase of many a paper in the field of chronobiology. Besides becoming a truth by virtue of frequent repetition, such a statement appeals to common sense. It is difficult to imagine a universe in which it was not true. Yet, the data supporting the above statement are few and far-between. Believe it or not, the data are not always supporting it either.

This post will attempt to briefly review the literature on evolutionary and adaptive aspects of biological rhythmicity. Also, using the perspectives and the methodology of evolutionary physiology, I will try to suggest some ways to test the hypothesis stated in the first sentence above.

REASONING BEHIND THE ARGUMENT FROM COMMON SENSE

For outside observers of the field of chronobiology and its recent successes in molecular, neural and medical aspects of biological rhythmicity, it may come as a surprise that the field was founded by ecologists, ethologists and evolutionary biologists. When the statements about adaptive function of clocks were initially made, the authors were much more careful than is usually seen today. It was meant as a hypothesis to be tested, and elaborate reasoning was often offered to persuade the reader why it might be true (Daan 1981, Pittendrigh 1967,1993, Enright 1970).

One of the most common arguments that a clock must be adaptive (for one reason or another) was its ubiquity – all plants, fungi, protista, invertebrates and vertebrates (more recently cyanobacteria, too) tested by the pioneers in the field showed circadian rhythmicity. The way those rhythms behaved in the laboratory in various experimental treatments was surprisingly similar over all species. Thus, the reasoning goes, if a physiological mechanism is found in every living thing, and it seems to work in the same way in all of them, then it must have originated early due to natural selection and was preserved over eons due to natural selection.

Some of the earliest experimental work was designed to test the genetic basis of biological rhythmicity. Many generations of laboratory organisms were raised and spent all their lives in aperiodic environments, yet the rhythms persist (Sheeba et al. 1999). Period of the rhythm was species -specific, highly heritable, and very amenable to artificial selection. So, if it is in the genes, the clock must have evolved due to some kind of selective pressure.

When reviewing evolutionary literature on biological rhythms, it is often difficult to distinguish between hypotheses of current utility from hypotheses of origin. It was often assumed that same selective pressures which keep the clocks ticking all over biosphere today, are the pressures responsible for the initial discovery of timing mechanisms by early forms of life.

The current adaptive functions of biological rhythms are often divided into two, mutually not exclusive categories. The Internal Synchronization hypothesis stresses the need for temporal separation of incompatible biochemical and physiological processes within a body (or cell), and for temporal synchronization of processes which need to coincide. An example of the former would be temporal separation of photosynthesis from nitrogen fixation. For the latter, surge of a hormone and availability of its receptor need to be synchronized for the generation of the endocrine effect. Evolution of such timing control mechanisms would presumably alleviate energetic costs of constant production of enzymes and their substrates.

The External Synchronization hypothesis supposes existence of temporal niches. For instance it would be adaptive for an animal to forage at the time when food is available, to hide when the predators are hungry, and to find an individual of the opposite sex at the time conducive to mating. Notably, it was never explicitly stated that possession of a clock is adaptive only if everyone else has a clock, too. So, who had it first?

The two hypotheses are easily meshed. A bird will sleep instead of foraging while its body temperature is low. It will wake up, raise its temperature and corticosterone levels and start to forage when the conditions outside are most conducive to it – when it’s warm, light and worms are crawling around. The old adage about the early bird getting the worm is often invoked (and, as R.A.Heinlein once quipped, “it just goes to say that the worm should have stayed in bed”).

Coupled to the second hypothesis is also the notion that circadian clock is involved in temporal memory (Enright 1975, Biebach et al. 1991). Thus every event which is committed to memory will, along with information about “what” and “where”, also have a time-stamp given by the clock – the “when” of memory. If doing something at one time of day yesterday resulted in survival it might be prudent to do it again today at the exactly same time (Daan 1995).

One important distinction between the origin of the first clock and its current use is in the size and complexity of the organisms in question. The first clock presumably appeared in a unicellular organism. Most of the research today focuses on multicellular organisms.

In the first case, we are talking about a single-cell clock, in the second about the circadian system, which may be composed of many clocks of different properties, all interacting with each other, with the environment, and with other functions of the body. There is only so much a single cell can do. A complex clockshop which exists at a higher level of organization can evolve complex new functions, e.g., photoperiodic time measurement, time-compensated sun-compass orientation, tidal, lunar and circannual rhythms.

In the study of evolution of biological rhythms, are we talking about evolution of the cellular building blocks or evolution of higher-order systems?

CHRONOBIOLOGY IN THE CONTEXT OF EVOLUTIONARY PHYSIOLOGY

The 2000 review of Evolutionary Physiology by Feder, Bennett and Huey currently serves as a manifesto of the field (Feder et al. 2000). In this section, I will follow the organization of their paper to explore how circadian physiology might fit into the framework of evolutionary physiology, as well as how evolutionary approaches may benefit the study of biological rhythms.

Evolutionary physiology is a relatively recent natural outgrowth of the field of comparative physiology, which, in turn, developed out of general mechanistic physiology. The evolutionary physiologists are direct intellectual (and often academic) descendants of traditional comparative physiologists, so the topics remain similar: scaling, symmorphosis, as well as studies of metabolism, respiration, osmoregulation, thermoregulation and locomotor performance. However, other aspects of physiology have been tackled by other groups of scientists, e.g., comparative endocrinology, neurobiology, sensory physiology, digestive physiology and reproductive physiology are vibrant fields of their own. Comparative chronobiology has a long tradition, too (Horton 2001). The importance of comparative studies to understanding of underlying mechanisms can be seen from examples of medically driven areas of physiology (e.g., sleep). Such areas fumbled in the dark for decades due to lack of basic understanding of what the process is all about, which in turn was due to lack of comparative studies of the phenomenon within an adaptive and evolutionary context.

It would be erroneous to state that evolutionary thinking was not a part of physiological thinking in the past, yet evolutionary physiology explicitly imports evolutionary theories, paradigms, concepts, models and techniques into the study of physiological adaptation. Feder et al. (2000) recognize four major developments which led to the rise of evolutionary physiology out of its general and comparative precursors.

First, the critique of adaptationist thinking (Gould and Lewontin1979) had an enormous ripple effect through all of biology, including physiology. The naive assumption that every trait is an adaptation forged by natural selection gave way to a more sophisticated view of evolution that includes non-adaptive forces like constraints and drift. Here, the ubiquity of biological clocks and the inability to imagine a clock-less universe led to the common view that not just the sheer existence of the clock, but every aspect of its mechanism must be an adaptation to the environment which evolved through the agency of natural selection. The non-adaptive evolutionary mechanisms are difficult to fathom in this context, and no explicit statements were made in the literature along these lines.

Second, new awareness of non-independence of species as analytical units for comparative biology has resulted in development of new analytical tools, new approaches to comparative studies, and, most importantly, in the shift in emphasis to ancestor-descendant relationships. Comparative studies of biological clocks were the foundation on which the whole field of chronobiology was built. Yet, these studies were not explicitly phylogenetic. The clocks are so widespread that comparisons were rarely made between closely related species. It was, and still is, more common to compare representatives of plants to fungi to insects to mammals. On those rare occasions when a phylogenetic tree appears in chronobiological literature, it is most likely to be the Tree of Life and not just a tiny piece of it. Thus, the non-independence of species is a problem that did not have much impact on comparative work to date, but is one that will have to be tackled in the future when more analyses of closely related species are performed.

Third, incorporation of tools of evolutionary biology into physiology allows research to state evolutionary hypotheses a priori, instead of post hoc. Using these tools, one is able to monitor evolution in progress and predict future evolutionary trajectories, instead of just registering the results of past evolution. In chronobiology, a few studies have recently been performed along these lines, more concerned with photoperiodic than circadian time-measurement, though (Ben Saad and Maurel 2001, Heideman et al. 1999, Heideman and Bronson 1991).

Fourth, use of most recent tools of molecular biology allows one to escape from standard genetic laboratory models to many other species of interest to physiologists. Comparative molecular analyses of genes involved in circadian rhythmicity have been performed in Diptera and Lepidoptera, and work on other organisms is sure to follow in the near future (Piccin et al. 2000, Peixoto et al. 1998, Costa and Kyriacou 1998, Kyriacou et al. 1996, Saleem et al. 2001).

Evolutionary biology aims to answer two kinds of questions: about the process (“how evolution works”) and the pattern (“what has evolution wrought so far in the history of life on this particular planet”). Evolutionary physiology, as its subset, is likewise interested in both process and pattern. After all, one informs the other and vice versa. In the same vein, mechanistic and evolutionary data inform each other and vice versa, too. While traditional comparative physiology explained mechanistically how the organisms adapt to their environments and added adaptive explanations post hoc, the modern evolutionary physiology starts with evolutionary predictions and tests them with comparative studies in the laboratory and in the field.

Of particular interest is the question of optimality – is there a close match between requirements of the environments and the physiological answers to these, or are safety margins and overdesign the rule. It would be difficult to define what would safety margins and overdesign mean in the field of circadian clocks. The clock is at the very core of physiological function of an organism. It acts as a relay station which controls practically every other aspect of biochemistry, physiology and behavior. It is not expected that the cellular clock at the core will be much affected by the environment, but the outputs of the clock, the signals from the clock to all the other functions, are much more likely to be the target of selection. Plasticity of the circadian system and of its coupling to downstream functions is a trait that can be expected to correlate to environmental parameters, e.g., stability vs. variability of the environment.

EVOLUTIONARY CRONOPHYSIOLOGY TO DATE

Several approaches to study of evolutionary pattern and process have been employed by students of biological rhythms. These include studies of variation in natural populations, including latitudinal clines (Skopik and Takeda 1987, Sawyer et al. 1997), tests of correlated traits, e.g., circadian vs. photoperiodic (Majoy and Heideman 2000) or circadian vs. developmental timing (Bloch et al. 2001), and studies of responses to artificial selection.

Comparative studies have been performed on levels from molecular to organismal. However, the choice of species is questionable. If relevant environmental parameter is the light-dark cycle, then most species studied so far occupied the same environmental niche – the earth surface in a temperate region. For a comparative study to be able to discriminate between ecological specialization and phylogenetic inertia, one needs to compare organisms occupying different environments. In the case of clocks, such environments would include polar regions (light-dark cycle of LD 6mo:6mo), equator (constant LD12h:12h), and life below the surface (constant darkness, DD). Although many species have been studied in such conditions in the lab, the study of organisms that live in such conditions in the wild is rare. Recent studies on subterranean and cave animals are a welcome change to the comparative work in chronobiology (Lee 1969, Hoenen and Gnaspini 1999, Riccio and Goldman 2000a, b, Avivi et al. 2001, Koilraj et al. 2000, Trajano and Menna-Barreto 2000).

Most recent data on adaptive function of circadian clocks employed measurements of fitness in altered light environments, as well as comparisons of fitness between genetic mutants of clock function. However, the only measure of fitness used is longevity (Pittendrigh and Minis 1972, Klarsfeld and Rouyer 1998, Hurd and Ralph 1998), and only two papers look at the trade-off between longevity and the lifetime reproductive output (Sheeba et al. 2000, Beaver et al. 2002).

Phenotypic engineering is the hallmark of studies by Patricia DeCoursey, one of the pioneers of the field (DeCoursey et al. 1997, 2000, DeCoursey and Krulas 1998). She measures survival of various species of rodents in the wild after she has removed their circadian pacemakers in the suprachiasmatic nuclei of the hypothalamus. The data are not as straightforward as one might expect – the survival is dependent on how bad was the year in regard to abundance of predators. Masking effects of light on behavior, i.e., burrowing during the day due to bright light, can protect clockless animals from predation in some cases, dependent on the species of rodent and the species of predator. There are two main problems with these kinds of studies. First, the effect of removal of the clock is observed in only one generation. If some clock-less individuals managed to survive and reproduce every year, and if it was engineered (genetically?) in such a way that the progeny were also clock-less, would such a population manage to establish itself in the wild? What alternative mechanisms it would evolve to decrease risk from predation? Would other correlated aspects of timing (e.g., photoperiodism, developmental timing, ultradian rhythms) additionally reduce their fitness? If we are removing a mechanism that was inherited for billions of years, why would we expect that an alternative mechanism would exist to protect the animals in the absence of the clock?

FINDING THE CORRECT ECOLOGICAL CONTEXT FOR EVOLUTIONARY CHRONOPHYSIOLOGY

Earlier in this post I noted that most of the thinking about adaptive function of biological clocks concentrated on adaptation to physical environment – the daily rhythm of light and darkness. That is quite reasonable assumption when one is concerned with the original appearance of a biological clock in the primordial soup, and might still be valid in studies of some unicellular organisms (Dvornyk et al. 2002). Yet, in a world of today, in which it seems that everyone’s got a clock, it seems reasonable to assume that biotic aspects of the environment would be the key selective pressure for current uses of biological timing mechanisms. Thus, studies of temporal aspects of interactions between individuals, groups, populations and species can potentially provide important insights into the evolution of biological clocks. That kind of research would also be forced into further sophistication. Many biotic interactions are dependent on niche-constructing traits, as well as on traits that evolved due to simultaneous selective pressure at two or more levels of organization, e.g., genic, individual and group selection acting at the same time either in the same direction, the opposite direction, or at some angle between the vectors.

Several exciting research findings along these lines of thought have been reported recently. First, in 1998, the “resonance hypothesis” was tested in cyanobacteria by Carl Johnson’s group at Vanderbilt University. The notion that intrinsic (“freerunning”) period of the circadian clock needs to be similar to the period of the entraining cycle (24 hours in nature) was tested in period mutants of Synechococcus sp (Ouyang et a. 1998). Various mutants were exposed to different lengths of the light cycle. Two mutants were tested at the time in competitive assay protocols. In every case, the strain with intrinsic period more closely matching the entraining period won the competitive assay. Thus, being in sync with the environment confers fitness against conspecific competitors (Johnson et al. 1998).

A series of papers appeared recently on temporal niche exclusion between two con-generic species of golden spiny mice living in sympatry in Israel. Originally both nocturnal, in the area of sympatry one of the species adopted a diurnal lifestyle. Physiological adaptations to diurnality, including thermoregulation, osmoregulation and vision, were not altered. The circadian performance in the laboratory was not different either. The only difference was in the coupling between the clock and the behavioral output (sleep-wake cycle) in the field, i.e., detachment of the activity rhythm from circadian control under the ecological pressure of competitor’s presence (Kornfeld-Schor et al. 2001).

Fleury et al (2000) tested the hypothesis that the least competitive parasitoids of fruitflies would gain adaptive advantage from parasitizing their hosts earlier in the day than their competitors. Comparison of three species of parasitoids in the lab and field revealed that this indeed is the case, as well as that the time-of-day of parasitism was directly driven by the properties of the circadian clock in each of the three species (Fleury et al. 2000).

Bolas spiders use chemical mimicry to lure their moth prey to within the reach of the bolas – their weapon for capturing prey. Two species of moths that are the favorite prey of this spider are active at different times of night and also produce different blends of pheromones. Bolas spiders produce different pheromone blends to match their prey at correct times of the night (Cesar Gemeno, pers.comm.).

Finally, probably the most impressive example of multiple species involved in an arms race around the circadian clock is the case of malaria (Garcia et al. 2001). Mosquitoes are vectors carrying malarial plasmodia. Mosquitoes in tropical regions are nocturnal and, furthermore, restrict their activity to short periods of night. The exact time of night during which they are active is different for different species of mosquitoes in different geographic regions, presumably to avoid the times when the local bat species are most active hunting. Mosquitoes are attracted to heat, carbon-dioxide and certain odorant molecules. A human (or animal) in fever emits heat, carbon-dioxide and, as components of sweat, the same odorant compounds. Malarial patients (human or veterinary) exhibit fever only during a restricted time of night – the time of night when the local mosquitoes are most likely to bite. Fever is induced by billions of malarial plasmodia simultaneously bursting out of red blood cells into the plasma.

Apart from inducing fever, massive release of malarial particles also temporarily overwhelms the immune system, thus ensuring that sufficient numbers of plasmodia are present in the plasma at the time when the mosquitoes are likely to take a drink of blood. Since it lives in the constant darkness, how does the plasmodium know when to appear out of its hiding in the red blood cells? Hotta et al. (2000) discovered that the malarial plasmodium gets temporal information from its host. Appearance of melatonin in blood in the evening triggers a response through a Ca++-dependent transduction pathway. The clock of the plasmodium integrates this information to exactly time the emergence from the red blood cell. Thus circadian clocks of human (and animal) patients, plasmodia, mosquitoes and bats have been involved in arms-races around the circadian clock, with the resulting patterns of timing being different for different species of plasmodial parasites, mosquito vectors, bat predators and mammalian hosts. This is a kind of system that offers the greatest promise for future studies of evolution of circadian clocks and systems.

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DeCoursey, P.J. and Krulas J.R. (1998). Behavior of SCN-lesioned chipmunks in natural habitat: a pilot study. J.Biol.Rhythms 13:229-244.

DeCoursey, P.J., Walker, J.K. and Smith, S.A. (2000). A circadian pacemaker in free-living chipmunks: essential for survival? J.Comp.Physiol.A 186:169-180.

Dvornyk, V., Vinogradova, O. and Nevo, E. (2002). Long-term microclimatic stress causes rapid adaptive radiation of kaiABC clock gene family in a cyanobacterium, Nostoc linckia, from “Evolution Canyons” I and II, Israel. Proc.Natl.Acd.Sci.USA 99:2082-2987.

Enright, J.T. (1970). Ecological aspects of endogenous rhythmicity. Annu.Rev.Ecol.Syst.1:221-237.

Enright, J.T. (1975). The circadian tape recorder and its entrainment. In Physiological Adaptation to the Environment (ed. F.J.Vernberg), pp. 465-476. Intext Educational Publishers, Ney York.

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Fleury, F., Allemand, R., Vavre, F., Fouillet, P. and Bouletrau, M. (2000). Adaptive significance of a circadian clock: temporal segregation of activities reduces intrinsic competitive inferiority in Drosophila parasitoids. Proc.R.Soc.Lond.B 267:1005-1010.

Garcia, C.R.S., Markus, R.P., and Madeira, L. (2001). Tertian and Quartan Fevers: Temporal Regulation in Malarial Infection. J.Biol.Rhythms 16:436-443.

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Hoenen, S. and Gnaspini, P. (1999). Activity rhythms and behavioral characterization of two epigean and one cavernicolous harvestmen (Arachnida, Opiliones, Gonyleptidae). J.Arachnol. 27:159-164.

Horton, T.H. (2001). Conceptual issues in the ecology and evolution of circadian rhythms. In Handbook of Behavioral Neurobiology 12: Circadian clocks (ed. J.S.Takahashi, F.W.Turek and R.Y.Moore), pp.45-57. Kluwer Academic/Plenum Publishers, New York.

Hotta, C.T., Gazarini, M.L., Beraldo, F.H., Varotti, F.P., Lopes, C., Markus, R.P., Pozzan, T. and Garcia, C.R.S. (2000). Calcium-dependent modulation by melatonin of the circadian rhythm in malarial parasites. Nature Cell Bio. 2:466:468.

Hurd, M.W. and Ralph, M.R. (1998). The significance of circadian organization for longevity in the golden hamster. J.Biol.Rhythms 13:430-436.

Johnson, C.H., Golden, S.S., and Kondo, T. (1998). Adaptive significance of circadian programs in cyanobacteria. Trends in Microbiol. 6:407-410.

Klarsfeld, A. and Rouyer, F. (1998). Effects of circadian mutations and LD periodicity on the life span of Drosophila melanogaster. J.Biol.Rhythms 13:471-478.

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Lee, D.S. (1969). Possible circadian rhythm in the cave salamander Haideotriton wallacei. Bull.Maryland Herp.Soc. 5:85-88.

Majoy, S.B. and Heideman, P.D. (2000). Tau differences between short-day responsive and short-day nonresponsive white-footed mice (Peromyscus leucopus) do not affect reproductive photoresponsiveness. J.Biol.Rhythms 15:501-513.

Ouyang, Y., Andersson, C.R., Kondo, T., Golden, S.S. and Johnson, C.H. (1998). Resonating circadian clock enhance fitness in cyanobacteria. Proc.Natl.Acad.Sci.USA 95:8660-8664.

Peixoto, A.A., Hennessy, J.M., Townson, I., Hasan, G., Rosnash, M., Costa, R. and Kyriacou, C.P. (1998). Molecular coevolution within a Drosophila clock gene. Proc.Natl.Acad.Sci.USA 95:4475-4480.

Piccin A., Couchman, M., Clayton, J.D., Chalmers, D., Costa R. and Kyriacou, C.P. (2000). The clock gene period of the housefly, Musca domestica, rescues behavioral rhythmicity in Drosophila melanogaster: evidence for intermolecular coevolution? Genetics 154:747-758.

Pittendrigh, C.S. (1967). Circadian rhythms, space research and manned space flight. In Life Sciences and Space Research, pp.122-134. North Holland, Amsterdam.

Pittendrigh, C.S. (1993). Temporal organization: reflections of a Darwinian clock-watcher. A.Rev.Physiol.55:17-54.

Pittendrigh, C.S. and Minis, D.H. (1972). Circadian systems: longevity as a function of circadian resonance in Drosophila melanogaster. Proc.Natl.Acad.Sci.USA 69:1537-1539.

Riccio, A.P. and Goldman, B.D. (2000a). Circadian rhythms of locomotor activity in naked mole-rats (Heterocephalus glaber). Physiol&Behav.71:1-13.

Riccio, A.P. and Goldman, B.D. (2000b). Circadian rhythms of body temperature and metabolic rate in naked mole-rats. Physiol&Behav.71:15-22.

Saleem, Q., Anand, A., Jain, S. and Brahmachari, S.K. (2001). The polyglutamine motif is highly conserved at the Clock locus in various organisms and is not polymorphic in humans. Hum. Genet. 109:136-142.

Sawyer, L.A., Hennessy, J.M., Peixoto, A.A., Rosato, E., Parkinson, H., Costa, R. and Kyriacou, C.P. (1997). Natural variation in a Drosophila clock gene and temperature compensation. Science 278: 2117-2120.

Sheeba, V., Sharma, V.K., Chandrashekaran, M.K. and Joshi, A. (1999). Persistence of eclosion rhythm in Drosophila melanogaster after 600 generations in an aperiodic environment. Naturwissenshaften 86: 448-449.

Sheeba, V., Sharma, V.K., Shubha, K., Chandrashekaran, M.K. and Joshi, A. (2000). The effect of different light regimes on adult life span in Drosophila melanogaster is partly mediated through reproductive output. J.Biol.Rhythms 115:380-392.

Skopik, S.D. and Takeda, M. (1987). Diapause Induction and Termination: North-South Strain Differences in Ostrinia nubilalis. J.Biol.Rhythms 2:13-22.

Trajano, E. and Menna-Barreto, L. (2000). Locomotor activity rhythms in cave catfishes, genus Taunayia, from Eastern Brazil (Teleostei: Siluriformes: Heptapterinae). Biol.Rhythm Res. 31:469-480.

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Related:

Whence Clocks?
Circadian clock without DNA–History and the power of metaphor
Basics: Biological Clock
The Clock Metaphor
The New Meanings of How and Why in Biology?
Some hypotheses about a possible connection between malaria and jet-lag
Evolutionary Medicine: Does reindeer have a circadian stop-watch instead of a clock?
The Mighty Ant-Lion
Are Zombies nocturnal?
City Of Light: Insomniac Urban Animals
Me and the copperheads–or why we still don’t know if snakes secrete melatonin at night
Diversity of insect circadian clocks – the story of the Monarch butterfly
Biological Clocks in Protista
Do sponges have circadian clocks?
Daily Rhythms in Cnidaria
Carolus Linnaeus’s Floral Clocks
Clock Classics: It All Started with the Plants
Chestnut Tree Circadian Clock Stops In Winter
Flirting under Moonlight on a Hot Summer Night, or, The Secret Night-Life of Fruitflies
Too Hard for Science? Centuries to Solve the Secrets of Cicadas
Circadian Clocks in Microorganisms
Clocks in Bacteria I: Synechococcus elongatus
Clocks in Bacteria II: Adaptive Function of Clocks in Cyanobacteria
Clocks in Bacteria III: Evolution of Clocks in Cyanobacteria
Clocks in Bacteria IV: Clocks in other bacteria
Clocks in Bacteria V: How about E.coli?

Whence Clocks?

This post about the origin, evolution and adaptive function of biological clocks originated as a paper for a class, in 1999 I believe. I reprinted it here in December 2004, as a third part of a four-part post (the fourth part contains all the references). Later, I re-posted it here in 2005 and here in 2009. Thus, some of the information is out of date, the writing is still very ‘academic’, but main points still stand, I think/hope.

III. Whence Clocks?

Origin, Evolution, and Adaptive Function of Biological Clocks

The old saw about the early bird just goes to show that the worm should have stayed in bed. (Heinlein 1973)

Now darkness falls.
Quail chirps.
What use Hawk eyes?

(Basho)

Local/temporary and global/universal environments.

In the study of adaptive functions, usually the question is asked about a function A in the species X. This implies that the species X has evolved the function A as a response to recently and currently selective local environment a. One then studies the pertinent aspects of the environment a, the function A of X in the field and in the lab, and, perhaps, the similar function A2 of a similar species Y in the similar environment a2.

However, not all adaptive functions are adaptations to local environments. Some aspects of the environment are global. All organisms on Earth are adapted to its gravity. It can be safely assumed that even the first life form on the planet had this adaptation. Some environmental factors are global now but might not have been throughout the history of the planet, like the proportions of oxygen, nitrogen and other gases in the atmosphere. Some adaptations are very frequent although they do not seem to have a correlate in the external environment – for instance sexual reproduction. Such adaptations are result of the particularity of the mechanisms of evolutionary change on Earth, and might not have evolved if the life on Earth initially adopted different mechanisms of evolution. Other adaptations are correlated with an environmental factor which is global for a large number (but not all) of very diverse organisms, e.g., the properties of the marine environment.

Temporal structure of the environment.

Movements of the Earth, the Moon, and the Sun in relation to each other, and the rotation of Earth around its tilted axis, have tangible effects on all organisms inhabiting surface, or near-surface, habitats of the land and oceans of the planet. Only deep-soil Archaea, and the deep-oceanic organisms may conceivably escape from all the astronomically generated rhythms of the Earth’s surface: daily cycle of light and darkness, the phases of the moon, the tides, and the seasons of the year.

The common properties of all these cycles are their precision and regularity – they are highly predictable. Organisms cannot evolve adaptations to rare and unpredictable events (e.g., meteor impacts), but can easily adapt to predictable and rapid cyclic events in the environment (Bornemisza 1955).

Why would organisms need to adapt to the natural cycles? In short: because they need to adapt to their environments, and the effect of the cycles is that each organism needs to adapt to more than one environment. For a rabbit, a meadow is a single spatial environment. However, it comprises of a number of temporal environments. The meadow by day and the same meadow at night are two very different worlds. If we multiply that with four seasons (spring, summer, fall, and winter environments) and at least two extreme values of intensities of moonlight at night, we arrive at the conclusion that the rabbit needs to adapt to twelve different environments!

All these cycles have been quite stable throughout the history of Earth. The alteration of night and day affected even the simplest unicellular organisms which were the only inhabitants of the planet for most of its history, as they rely on sunlight as the source of energy for metabolism and replication. As the organisms grew bigger, lived longer, and invaded other environments, longer cycles gained in importance, too. Seasonal changes in daylength are substantial towards the poles, and the annual changes in weather conditions are quite dramatic around equator.

Adaptations to environmental cycles.

What are the possible ways an organism may adapt to temporal changes? Certainly, an organism may use its sensory mechanisms to behaviorally react to the changes as they happen. When the sun comes up in the morning, the animal perceives the light and the warmth, wakes up and goes out to forage (or goes into the burrow to sleep). When nice weather and plentiful food arrive in spring, the animal mates and raises its young. In principle, this arrangement could work, as each species would evolve its own time-table of stimulus-responses to cues.

However, the extremely predictable changes are a form of information, and information is an important resource as it creates opportunities which can be exploited. It can be advantageous to an organism to be able to predict the changes before they occur. If a bird lets its body temperature drop while sleeping at night, and starts warming up at the crack of dawn, it will take some time, perhaps an hour or two, before its temperature is optimally high for foraging and predator avoidance. Another bird which can predict the time of dawn can start raising the temperature while it is still dark outside. At dawn, it is ready to go – the early bird gets the worm! The early bird leaves progeny – the other one goes extinct.

Another avian example: One bird saves the energy by keeping its reproductive system regressed during the winter. When spring brings nice weather, this bird grows its gonads, a process which takes a couple of weeks (longer in mammals). When the reproductive system is ready, provided the potential mates have also reacted the same way, the bird mates, lays eggs and raises hatchlings.

Another bird predicts the coming of spring by measuring the lengthening of the daylength (photoperiod). On the first day of nice weather, the bird is ready to mate. This bird is not wasting the first couple of weeks of bountiful food and warm air. A few weeks later, her chicks are out foraging and outcompeting the younger, smaller chicks of the first bird. The second bird can also expand its range towards the poles, as it can perform the whole reproductive effort within a very short window of opportunity, while the first bird would lay the first egg at the time when the bad weather has already returned.

It is obvious I love birds, so let me indulge in another avian example. As the winter gets closer, but the weather is still nice and the food abundant, a bird measures the shortening of the photoperiod and anticipates that the weather will change. She stops her reproductive effort early, she puts on large fat reserves, shrinks many internal organs, drops her old tattered feathers and grows new, healthy, and not so sexually attractive plumage. She gets together with other conspecifics of the area who were, up till then, fiercely territorial. Together they undergo a period of a flying exercise and fitness program. At a particular day of the year, the whole flock heads south to the distant warm winter feeding grounds. On their way there, the birds use the position of the sun to orient. The position of the sun changes during the day, but as these birds have the sense of time, they can compensate for the sun’s movement across the sky, and will not get lost on the way. They will use the same methods to prepare for, accurately time, and precisely retrace the route on their flight back home in spring. Another bird which passively responds to the environment will stay at home until the first frost and will freeze together with her last clutch of newly-hatched chicks. If she attempts to migrate, she will have to do it alone, with no preparation, with insufficient energy stores, and with no idea how to navigate to the target environment and back.

Clocks as adaptations.

The competitive advantages of having an internal anticipatory system have played a role in the evolution of biological clocks (Pittendrigh 1965, 1967, 1993, DeCoursey 1990). Daily biological clocks, or circadian clocks, are endogenous, inherited timing devices which control rhythms of many physiological and behavioral functions. The clock can time changes in a variety of processes at any time of day that is advantageous to the organism, as well as translate the daily changes into rhythms with longer or shorter periods. The clocks, being organic structures, are not absolutely precise, so they have evolved the means by which external timing cues, like dawn and dusk, can entrain the phase of the clock to the local time.

The possession of the internal timing mechanism will also allow the organisms to invade novel ecological niches, e.g., polar regions, intertidal regions, migratory way of life, etc. As the predators and prey evolve biological clocks, the selective pressure on other organisms to do the same increases even more, as the biotic aspects of the environment get even more temporally complex in even more selectively meaningful ways. This may lead to coevolutionary arms-races around the circadian clock, as a predator tries to invade and the prey to escape a particular temporal niche. Unlike other arms-races, this kind will not lead to runaway selection of novel traits, as the clock is a closed loop (they may chase each other in circles forever). However, this may lead to an adaptive trend towards greater sophistication and flexibility of the timing mechanisms, including multi-oscillator systems, clocks modulated by the internal states, circannual clocks, etc.

The function of the clock in adaptation to the temporal changes in external environment is not its only function. Another hypothesis exists which states that one of the important roles of the timing mechanisms is the internal coordination of physiological and metabolic functions. Some cellular and organismal processes are incompatible with each other. If there is no possibility that two processes can be segregated spatially, then their temporal isolation is the only remaining solution. Theories differ in assigning relative importance to the two functions, and in stating which function arose in evolution first (Winfree 1990, pp.387-394, Edmunds 1988, pp.368-370, Pittendrigh 1961,1967, 1981, 1993, Enright 1970, 1975).

Another hypothesis is that the circadian clock is the organ of the sense of time (Daan 1995, Enright 1975). Unlike other sensory modalities, the clock does not respond to any form of energy from the environment. It measures the passage of time internally, and gives the non-directional physical time a direction (“arrow”) by virtue of being in a living organism (Frazer 1996). The clock is, thus, an internal representation of time, a cognitive temporal map analogous to the cognitive spatial maps. This allows the organism to perform interval time measurement, distinction between before and after, measurement of duration of events, and learning of the local time of day (Shettleworth 1998, pp.333-378.). Presumably, only this last function requires that the clock, indirectly via other sensory modalities, be entrained to the local time.

Origin of timing mechanisms.

There are three main lines of thought concerning the origin, evolution and adaptive function of biological clocks (Winfree 1990). The first view assumes that in the beginning the organisms were arrhythmic. The cyclic nature of energetic availability and cycles of potentially degrading effects of the sun’s ultraviolet rays on particular pigmented enzymes, provided the selective environment. A cell with a timer can predict the changes and adjust its metabolic activities to minimize energetic and material loss. This cell will outcompete the other cells in the Archeozoic sea (Pittendrigh 1967). The emergence of such a system so early in the evolution of life leads to prediction that the molecular mechanisms of circadian rhythmicity will be highly conserved among all organisms (Winfree 1990, p.389).

The second view assumes that the environment itself forces rhythmicity onto the early unicellular organisms (Goodwin 1966). To economize waste, the cell evolves modifier genes. Each of these gene products will have a role in facilitating a smooth transition from one to the next phase of the imposed cycle. As more and more such genes evolve, every state of the cycle comes under genetic control. Three billion years later “the cell might surprise itself to discover…when some scientist first puts it into constant conditions, that it shuffles its way spontaneously through almost the same cycle” (Winfree 1990, p.390). So, even though all the cogs and wheels were, the whole clock itself was never selected for.

The third view states that all biochemical processes are cyclic. Furthermore, this cyclicity is part of the definition of life. Some of the cycles are regular, and the periodicity of such oscillations can be modified by natural selection (Winfree 1990, pp.391-392). Flexibility in counteracting stabilizing homeostatic mechanisms can add another degree of freedom in which to search for optimization. The second and third views expect to see almost as many circadian mechanisms as there are species. If one speculates that the life originated in the shallow tidal pools, than the circatidal rhythms might have been the first to arise, either before or simultaneously with the circadian clocks.

There is nothing incompatible between the three views. They could have conceivably all contributed to the emergence of timing mechanisms. However, neither one of them explains why was it that a self-sustaining clock evolved. Why does a circadian rhythm persist in constant conditions for many days, months and years? The organisms were selected only for ability to cycle in a regularly cycling environment. Why is the clock not an hourglass mechanism which can be turned over by the environmental cues every day? Enright (1970, 1975) suggests that role of the clock in acquisition of temporal memories might have had an influence. Aschoff (cited in Enright 1970) suggested that an oscillator which is capable of a small number of cycles will be adaptive in times of weather catastrophes, during hiding and burrowing, and during hibernation. Such a timer, by virtue of capability for a few oscillations, inevitably can cycle indefinitely.

Comparative method in the study of clocks.

As temporal structure is a property of a global environment, the study of the mechanisms of time measurement will depend on our understanding of the origin, evolution and adaptive function of circadian clocks. Should we expect a mechanism as conserved as glycolysis, or use of ATP for energy, or mechanism of DNA transcription? Or should we expect that every narrow group of organisms has evolved a different mechanism? Or something in between? And how do we study the clocks in order to distinguish between phylogenetically conserved generalities and the ecologically determined novel particularities?

Comparative method is a “range of techniques that infer how one organism evolved by comparing what evolution produced in that case with what it produced in other cases…The comparative method… has three important applications… First, it enables us to directly test the historical assumptions tacit in adaptationist hypotheses. Second, it enables us to test the proposed link between environmental feature and adapted trait. Third, we can use it to make sense of the adaptationist claim about the explanatory priority of selection” (Sterelny and Griffiths 1999, pp.243-244).

An adaptationist hypothesis (e.g., about the adaptive function of the circadian clock) can be tested by checking the actual sequence of evolutionary changes to see if it is the one presumed by the hypothesis. A hypothesis may propose that a particular trait arose before another trait (e.g, hourglass before clock, circadian before circatidal rhythm, single before multi-oscillator systems, etc.). The hypothesis can be tested by comparing the traits in earlier and later representatives of a lineage (in the case of clocks as responses to a general feature of the environment – the entire tree of life).

Comparative method can also directly test the adaptationist hypothesis that adapted traits are responses to particular features of the environment by measuring if there is a tight correlation between a particular environment and a particular trait (e.g., are the deep-oceanic creatures, or cave and subterranean animals arrhythmic; is there a correlation between degrees of robustness of the circadian amplitude and the stationary vs. migratory habit, or burrowing vs. open field habitat).

Adaptationist extremist position is that convergent evolution illustrates the overwhelming power of natural selection over all other evolutionary mechanisms (genetic drift, sexual selection, etc.). But, convergence tells us nothing about the relative powers of selection and history unless we can somehow count all the possible convergences that have not happened – all the times history “won”. Is a presence of a trait in a number of organisms the result of convergent evolution? This can be answered only by extensive use of comparative method. One cannot know if something is a convergence without a phylogenetic tree. If analysis of the tree reveals that the trait appeared repeatedly de novo, than it is a convergence and the force of natural selection is a primary explanation. If analysis of the tree reveals that all members of a lineage posses the trait, than it is not a convergence. The trait was probably adaptive for the common ancestor, but it might not be adaptive at all today. It could still be an adaptation as it may serve many different adaptive (exaptive) functions in different species and exist merely as phylogenetic inertia in others.

The adaptive hypothesis requires that the clock be phase-shiftable by an environmental cue and that it be temperature compensated. These are the two absolute requirements for its proper function. Every timing system will satisfy these minimal requirements no matter what the underlying mechanism may be. So, these two properties cannot be informative about the mechanisms, and if “we are to test the proposition of a common mechanism and use only formal properties, these must be of such a nature that selection can reasonably be dismissed as the agent responsible for their universal association with cellular clock systems; in short, the properties must lack adaptive value” (Pittendrigh and Bruce 1959) and the “study of features which do not seem to have any survival value…may be indicative of the structural properties of the system” (Pavlidis 1971).

So, is the circadian clock a universal adaptation, a case of convergent evolution, or a generatively entrenched relic of history? Here, one needs to make a sharp distinction between the circadian clock which is the timekeeping molecular mechanism in a single cell, and the circadian system which includes all the cellular clocks, all the sensory input pathways to the clocks, and all the mechanisms of translating clock states into overt rhythms of a whole organism (Underwood et al. 1997a). A clock is a molecular mechanism, while a system uses the molecular mechanisms to produce overt rhythms.

Circadian systems.

Data so far indicate that all the biological rhythms studied to date possess the basic properties of entrainability and temperature compensation. I have collected literature on observations and experiments in hundreds if not thousands of species of unicells, plants, fungi and animals, but the limitations of time and space prevent me from presenting them all in this abstract, so I will have to leave them for a later publication. All timing systems can be brought to match the local time, and will do so in a precise manner over a range of temperatures (if they could not they would be thermometers, not clocks). Temperature compensation varies with latitude in fruit flies (Sawyer et al. 1997). Critical photoperiod for induction of reproduction in mammals and birds, as well as the number of eggs in a clutch in birds, both traits regulated by the circadian system, correlates with latitude in many species (Baker 1937, 1938a,b., Daan and Aschoff 1975, Bronson and Heideman 1994). This indicates that the circadian clock (and all other circa-rhythms) is an adaptation, as the trait tightly correlates with the environment.

It is interesting to note that many organisms which live in caves and under ground still have circadian rhythms. For instance, Mediterranean blind mole-rats have circadian rhythms entrainable by light (David-Gray et al. 1998), as do the natural or induced disperser phenotypes of the African naked mole-rats (Goldman 1999, contrary to Davis-Walton and Sherman 1994). Cave-dwelling crickets have circadian rhythms which are nor entrainable by light, but by noise/silence cycles (Marques and Hoenen 1999).

Cave-dwelling catfish are apparently arrhythmic, but a rhythm emerges if the fish are exposed to a light-dark cycle (Trajano and Menna-Barreto 1999). Overt behavioral rhythmicity is dependent on intensities of light and levels of temperature in Japanese Newts (Nagai and Oishi 1999) and Leopard Geckos (Chris Steele, unpublished data). These data suggest that circadian systems in these organisms are “rudimentary organs” which were not entirely lost during the course of evolution from their surface-dwelling ancestors. Alternatively, one can argue that the clocks persist in these organisms due to their utility in orchestrating myriads of physiological events within the body, and that the persistence of a behavioral output is just a left-over from the past.

Some emergent properties of circadian systems are lost only to reappear again and again when the need for them arises, presumably because it is relatively easy to re-invent them since all the clock parts are already present. For instance tidal rhythms have been found in birds and lizards (Daan and Koene 1981, Sawara et al. 1990, Wikelski and Hau 1995). Lunar cycles appear in some terrestrial species of plants, invertebrates, mammals, birds and reptiles (Abrami 1972, Skutelsky 1996, Brigham et al. 1999, Chris Steele, unpublished data).

Circadian rhythmicity does not disappear in artificially imposed relaxed selective environments. After 600 generations in constant conditions, fruit flies retain precise circadian rhythmicity in behavior and pupal eclosion (Sheeba et al. 1999) suggesting that rhythmicity is important in regulating cyclic biochemical processes within an individual fly, as much as in proper phasing to the environmental cycles. Similar conclusion can be drawn from the fact that it is easy, by experimental manipulation or by genetic selection, to eliminate behavioral but not physiological circadian rhythms in quail (Guyomarc’h’ et al. 1998, Zivkovic et al. 1999).

Interestingly, it took a long time to discover circadian rhythms in the laboratory Nematode C.elegans. In this animal, the so-called “clock-genes” are present, the ortholog of PER cycles with an ultradian rhythm with a period of about 6 hours and is thought to regulate timing of developmental events (Jeon et al. 1999). The circadian rhythmicity in this animal was not completely eliminated through many generations of laboratory rearing practices, yet the involvement of circadian clock genes in timing of development is apparently compatible with their use for circadian behavioral timing.

Archaea and most Eubacteria are arrhythmic. For Archaea, the explanation might lie in their ecology – they usually inhabit the most inhospitable regions of the planet including deep-oceanic hydrothermal vents, deep soil, rocks, salt deposits, polar regions, underground hot-water springs, where the rhythms of the planetary surface might not have any direct effect on their survival. Some Cyanobacteria have circadian rhythms as they need to temporaly separate incompatible reactions of photosynthesis and nitrogen fixation (Johnson and Golden 1999). Real Bacteria, being Prokaryotes, might just be capable of a rapid response to the direct environmental fluxes, and a timer might impose too rigid a control in, on their scale, essentially unpredictable environments.

Cellular clocks.

Molecular clocks are invisible to selection. Circadian systems, being in direct interaction with the environment, are more likely to show correlations with the environment and a faster rate of change over evolutionary time scales. It is perfectly safe to state that all mammalian systems are built basically the same way, which differs from the avian, reptilian, insect or plant systems. Some data also exists suggestive of correlations between some formal circadian properties and specific ecological niches.

All the circadian systems contain, as their parts, cellular circadian clocks. Nothing a priori dictates that the cellular clocks need to have, or not have, exactly the same molecular mechanisms of rhythmicity. It is conceivable that a cellular clock can be just a rudimentary timer, even an hourglass, and that the multicellular organization of the system provides temperature compensation, and entrainment properties. Also, even if the dynamics of the mechanism are the same, it is not necessary that the actual molecular players remain the same.

What do the actual molecular data show? Each circadian clock cell in all organisms is a self-sustaining circadian oscillator, resettable directly or indirectly by light, and it is temperature compensated (reviewed by Dunlap 1999). The dynamics of the mechanism are very similar in cyanobacteria, plants, fungi, insects and mammals. The molecular clock is a negative feedback transcription-translation-based oscillator in all of the studied organisms. Fungi, insects and mammals use PAS-domain-containing proteins as positive elements. Insects and mammals have pairs or families of negative elements. Several genes can be found both in the fruit fly and in the mouse., e.g., per, tim, clk and cyc in flies have homologs in per1, per2, per3, tim, clock and bmal in mice. Drosophila dbt is a sequence homolog to casein kinase 1.

These are the similarities. How about differences? All negative elements cycle (in expression) in fungi and insects, but only some in mouse. No positive element cycles in fungi, one in the fruit fly and a different one in the mouse. The phases at which elements act are shifted – fungi and mammals have a day-phase clock, while the fruit fly has a night-phase clock – a complete change in internal logic of resetting by light.

So it seems that nature is using some well-conserved themes but is mixing and matching the details. Is there a consensus today about the evolution of circadian function on Earth? Past five years have seen an avalanche of new molecular data. Every few weeks a paper is published, it seems, which leads to a change in one’s opinion on the evolutionary conservatism of the clock. A surprising finding of a similar gene or function in two very distinct organisms points to overall great similarity of mechanisms. Next paper discovers a seemingly unexplainable difference in mechanisms between relatively closely related organisms, and suggests that each species has freedom to tinker with the basic clock mechanism. The field as a whole is oscillating on this issue. If there is anything like a consensus, it is the idea that clock is always running and is full of redundant elements. As long as a wheel or a cog can be removed or replaced without stopping the clock, the overall mechanism will stay the same, although the individual players may, one by one, all be replaced over long periods of evolutionary time.

However, data exist which challenge the notion that transcription/translation loops of clock genes are mechanisms of all aspects of circadian rhythmicity (Hall 1996, Lakin-Thomas and Johnson 1999, Lakin-Thomas 2000). In an alga, Acetabularia, circadian rhythmicity persists in cells from which the nucleus was removed and the transcription of non-nuclear DNA was pharmacologicaly blocked. However, this rhythmicity damps out after several cycles, and re-introduction of the nucleus restarts the rhythm with the phase dictated by the nucleus (Edmunds 1988). These data suggest that the circadian clock in this organism consists of two parts – a nuclear (transcription/translation loop) and a cytoplasmic clock. These two clocks interact with each other. A computer model was developed (Roenneberg and Merrow 1998, 1999) which shows how such a feedback system of two oscillators can account for stability of period, persistence of rhythm in prolonged constant conditions, temperature compensation, resistance to environmental noise, and entrainment properties of the cellular clock.

There are also data suggestive that some of the circadian rhythms are and others are not controlled by the “clock genes”. Null mutations, deletions and continuous overexpression of per gene in fruitflies does not entirely abolish circadian rhythmicity. The behavioral activity rhythms of fruitflies are characterized by two peaks. Evening peak is assumed to be the time when the insects are foraging. The morning peak is the time when the insects are involved in reproductive activities: search, courtship and mating.

Elimination of cycling of PER protein eliminates the evening peak. However, the morning peak persists for several more cycles, then the period gets shorter (ultradian), and finally dissolves into arrhythmicity (Renn et al. 1999, Helfrich-Forster 2000, Gvakharia et al. 2000, Kaneko et al. 2000).

In the giant silkmoth, PER protein never enters the nucleus in the pacemaker cells responsible for overt behavioral rhythmicity. However, it does enter the nucleus in some peripheral tissues (Sauman and Reppert 1996), suggesting that a transcription/translation loop is part of some but not all cellular circadian clocks.

Two separate circadian systems can be observed in female birds of some species. One system, driving rhythms such as locomotor activity, feeding activity, body temperature, oxygen consumption and melatonin release is sensitive to light and melatonin and can be readily entrained to light-dark cycles. The other circadian system drives all the mentioned overt rhythms, but also the circadian rhythm of ovulation and oviposition. This rhythm is not directly entrained by light cycles. It tends to free-run through a portion of the day. As the two systems interact, and as they show two different periods (24h for the entrained system and some other value for the other system), the two rhythms continuously change mutual phase relationships. Some phase relationships are “permissive” and others are “forbidden”. As the ovulatory rhythm intrudes into the “forbidden zone”, its interaction with the other system makes it phase-jump back to the starting (default) phase from which it starts free-running again. Interaction between two clocks may be neural (e.g., between two hypothalamic pairs of nuclei) or hormonal (perhaps sex steroid hormones). The main system consists of the pineal gland, the retinae, and a pair of hypothalamic nuclei. The brain clocks are not self-sustained oscillators – they need a daily input from either the eyes or the pineal, depending on the species. It is not known if the retinal/pineal clocks are self-sustained oscillators in the long term. Their presence is necessary for circadian rhythmicity, but a feedback signal from the hypothalamus to these structures might be necessary, too. Data so far cannot distinguish between the hypothesis that cellular clocks in the retina or pineal are autonomous clocks which entrain other parts of the system, or that a feedback loop between damped oscillators in the center and the periphery are necessary for sustained circadian output. Likewise, the ovulatory circadian rhythm may involve an interaction between cellular circadian clocks in the brain and in the ovary, or a hormonal feedback loop which does not even utilize any clock-genes and in which no single cell acts as a clock.

The idea that circadian rhythm, or similar mechanisms are involved in other aspects of biological timing is strong and some links have been made, particularly, with the timing of developmental events. Mutations of the per gene affect the developmental time in fruitflies (Kyriacou et al. 1990). The so-called heterochronic genes in C. elegans turned out to be orthologs of per and tim (Jeon et al.1999), in an organism with no circadian rhythms. However, a 90 minute cycle of chairy, which times the formation of somites in the chick embryo does not involve protein synthesis (Palmeirim and Pourquie, cited in Pennisi 1997).

To summarize, the current view of circadian rhythm generating mechanism is that it is a transcription/translation feedback loop between clock-genes and their protein products. However, the challenges to this view are coming from within the field. Some circadian rhythms are probably generated by cellular clocks consisting of two interacting loops, one being nuclear, the other cytoplasmic. As these clock-cells are organized in tissues, the communication between individual cells in that tissue confers novel properties to the circadian system of which individual cells are not capable. As most organisms, even unicells, posses more than one circadian clock, interactions between different clock-tissues allows for evolution of more complex temporal phenomena, including photoperiodic time measurement, lunar, tidal and circannual rhythms, and continuously consulted clocks. Some circadian systems are perhaps not even utilizing the individual clock-cells, but may be properties of neuroendocrine feedback loops between two or more clock or non-clock tissues (Cassone and Menaker 1984).

It is difficult to glean from the published data if this is so, but one can hypothesize that the individual variation is far greater in the properties of the whole circadian systems than in the properties of molecular circadian clocks. Period of circadian rhythmicity of the individual cells might be very similar between individuals of the same population, but the periods of the overt rhythms vary greatly, as do the emergent properties, e.g., photoperiodic sensitivity, or the critical photoperiod (e.g., Heideman and Bronson 1991, Heideman et al. 2000) due to differences in development of the whole circadian systems and hormonal influences on their properties. If this hypothesis is true, than Natural Selection will have to operate on the mechanisms of integration of the whole systems to a greater degree than on the sequences of clock-genes themselves. If cellular clocks are viewed as Lego blocks, and the circadian systems as the structures built out of these blocks, then it becomes apparent that most evolutionary changes will be in the way the blocks are put together, rather than in the shapes, sizes and colors of the blocks themselves.

Inferring Rhythmic Behavior and Physiology from Vertebrate Fossils .

I recalled what he had said of the pineal gland, and wondered what he saw with this preternatural eye. (H.P.Lovecraft, From Beyond)

From the perspective of a paleontologist, a question arises if one can infer the type of rhythmicity displayed by an animal from the fossilized remains of its bones. One asks if the fossils can tell us if particular animals were diurnal or nocturnal, and if their reproduction and migration were seasonal.

Before one starts to hypothesize about dinosaurian sleeping habits, a study of living vertebrates is in order. In an oversimplified (and Eurocentric) scheme, most of the living mammals are nocturnal, birds are diurnal, an reptiles are bimodal (dawn and dusk). But a closer look at the exceptions might be more revealing. Reptiles in the tropics are more likely to develop nocturnal habit, while at higher latitudes and/altitudes diurnality might be more common. Many diurnal birds temporarily switch to nocturnality during migration, when the production of energy favors the cool of the night. In mammals, it is mostly the small animals that are nocturnal.

Large mammals of the polar regions, like seals and walruses are diurnal, while large mammals of the Serengeti are usually bimodal.
If diurnality is taken as the default condition, the question to ask is: what adaptation to nocturnal life can be seen in the skeleton of an animal. Adaptations to nighttime activity involve adaptations to cold and adaptations to dark.

If we assume that dinosaurs were ectothermic, virtually all of them should have been nocturnal because of their large size. A large body mass dissipates heat more slowly, and is more likely to overheat. Endotherms produce their own heat but are also thought to possess more sophisticated methods of getting rid of surplus thermal energy, so if some of the dinosaurs were endotherms, they might as well have been diurnal. Also, the largest tropical mammals, like elephants, keep their core body temperature much lower than the mammalian average (20-30 C, as opposed to 37). No dinosaur was small enough to exhibit daily torpor.

Adaptations to dark involve sensory systems. There are three possible ways to adapt to life in the dark:

– evolving very sensitive eyes,
– evolving very sensitive hearing and smell, perhaps even echolocation, at the expense of largely degenerated vision, and
– evolving both very sensitive vision and other sensory modalities.

Of the three cases, the first and the third are repeatedly observed in nocturnal vertebrates. Think of owls, lemurs and cats. The second solution is employed by animals that live in caves, hollow trees or in underground tunnels. Dinosaurs were too large for this kind of fossorial habitat.

In all of these senses, increase of acuity is likely to be associated with the relative increase of size of that organ. In a fossil skeleton, enlarged ears are unlikely to be identifiable. Also, importance of the auditory acuity might be small in a world where the movements of predators and prey alike produce minor earthquakes. Detection of the enemy at a large distance might be more important, so emitting and hearing infrasound (like elephants and giraffes) could have evolved in Dinosaurs. A strong sense of smell will result in enlarged olfactory bulbs which will leave their imprints on the interior of the skull. Large eyes require large sockets. Binocular vision would also translate into a more sophisticated central processing mechanisms of visual information. Large orbits with a big overlap of visual fields, as well as large olfactory bulbs were found in the skulls of T.rex. Most bird-like dinosaurs (eg.Troodon) also had disproportionately large eyes. Were they nocturnal? Who did they hunt at night? Was their prey sleeping at the time? Where would a Brachiosaur hide for an overnight sleep? Was one guardian always awake? A careful analysis of the ecology of a certain area at a certain time might shine some light on these questions, since both temporal niches are likely to have been filled.

As for annual rhythms, they might be preserved as growth rings in the bones, reflecting the seasonal changes in food or mineral availability, UV-radiation, disease or activity (Hermann and Danielmeyer 1994). Timing of seasonal reproduction and migration is likely to have been determined by photoperiodic response. Unfortunately, living vertebrates have variable anatomical organization of the photoperiodic system. While the pineal gland and its hormone melatonin seem to be necessary in mammals, in other vertebrates pineal, parapineal organ, eyes, hypothalamus and gonads may or may not be involved. In vertebrate evolution, however, there is a trend for the pineal and parapineal organs to gradually lose a photoreceptive function and gain a secretory role.

In fish, amphibians and reptiles, pineal is a fully developed photoreceptive organ. In birds it is still responsive to light, but the histology suggests a neuroendocrine organ instead of a photoreceptor. Mammalian pineal has completely lost ability to sense light.

Parapineal organ is a highly developed “third eye” with a lens in most fish, amphibians and some reptiles (lizards, Sphenodon). In other reptiles, as well as all birds and mammals, parapineal is gone. Even pineal itself is missing in some organisms like crocodile, dugong, armadillo, anteater, sloth and pangolin, or is very small as in elephants, rhinos, manatees, whales, monotremes, marsupials and bats. The existence and size of the pineal gland and/or parapineal organ seems to correlate well with the climate and latitude.

Global species, like horses, cows, sheep and rabbits have large pineals. Polar animals, like seals, sea lions and walruses tend to have the largest pineals. This fact, together with the hypothesis that the pineal is somehow involved in thermoregulation, prompted Roth and Roth (1980) to argue that dinosaurs were cold-blooded and restricted to tropical climates, since most Dinosaur skulls do not show evidence of the presence of the pineal-parapineal complex. In all vertebrates except primates, pineal gland leaves an imprint on the inside of the skull on the roof of the brain. Parapineal lies in a hole in the skull called the pineal foramen. Only in Diplodocids there was evidence for the existence of the parapineal organ, and only in some bird-like Dinosaurs for the pineal itself. In any case, existence of parapineal foramina is easily perceived in fossil skulls, and it is the study of living organisms’ roles of these organs that needs to be correlated with the daily and seasonal rhythms, as well with thermoregulation.

The circadian clock, of which pineal is a part, is also involved in orientation by sun compass, night-sky orientation and magnetoreception. These mechanisms, although useful for all animals, are particularly necessary for long distance migrants, as some Dinosaurs were shown to be. A wide variety of animals has deposits of magnetic ferri-oxide thought to be involved in magnetoreception (Wiltschko and Wiltschko 1995). In vertebrates these deposits are usually concentrated within the ethmoid bone where they are innervated by the ophthalmic branch of the trigeminal nerve. I t is likely that Dinosaurs possessed these deposits, and it would be very interesting to compare the species with respect to quantity, location, particle-size and orientation of biomagnetite. Unfortunately, study of this phenomenon in living animals is still in its pioneering stages, so any theorizing concerning Dinosaurs would still be pure speculation.

In summary, analysis of vertebrate fossil skulls in light of relative sizes of sensory organs including eyes, olfactory bulbs, pineal and parapineal organs and magnetite particles, can give us insights into spatio-temporal physiology, ecology and behavior of Dinosaurs and other extinct vertebrates.

Tests of Adaptive Function.

As there are two main hypotheses regarding adaptive function of biological rhythms, there are also two lines of research involved in testing these hypotheses. The hypothesis that the primary role of a circadian clock is to orchestrate physiological and biochemical functions and events within a body has usually been tested by looking at longevity of either normal or clock-altered organisms placed in unnatural light cycles. For instance, fruitflies kept in different periods of light-dark cycles, as well as various clock-mutants have been reported to have different lengths of lifespans (Pittendrigh and Minis 1972). Similar findings were obtained form a study of hamsters (Hurd and Ralph 1998). The fact that breeding 600 generations in constant darkness did not lead to the loss of any circadian function in fruitflies adds another argument in support of this hypothesis (Sheeba et al. 1999).

The hypothesis that behavioral adaptations to timing of environmental events, including the temporal organization of natural enemies, has also been recently addressed. In cyanobacteria, colonies of various period mutants were subjected to competition assays in various lengths of light-dark cycles (Ouyang et al. 1998). Invariably, the strain whose endogenous period more closely matched that of the environmental cycle won the competition.

In rodents, lesions of the suprachiasmatic nucleus renders these animal arrhythmic even in light-dark cycles. In field conditions, lesioned individuals were more susceptible to predation than their intact conspecifics in the same area. This effect was greater when the predator pressure was greater (DeCoursey et al. 1997, 2000). These data suggest that correct timing of activity is crucial for survival of prey species. However, these studies do not address the question if, in absence of the clock, organisms could have evolved alternative mechanisms of temporal control.

In my opinion, the best way to study adaptive function of circadian clocks is to study coevolution of temporal parameters in two or more species of natural enemies. For instance, one can study circadian rhythmicity in a venomous snake, e.g., rattlesnake and its venom-resistant prey, the ground squirrel. In areas of sympatry, at what times of day are the two species active, and does that differ from the populations in allopatry? Is there a circadian rhythm in snake’s venom production, venom composition and toxicity, amount of venom injected in a bite, inclination to bite in response to a stimulus? Likewise, is there a circadian rhythm of resistance to venom and in evasive behaviors in the squirrels? Are those rhythms different in allopatry? Who is “winning”: the predator or the prey?

The same kind of questions can be asked in other systems, e.g., resistant predator and poisonous prey (garter snake and tiger salamander); resistant predator and venomous prey (desert mouse and scorpion); venomous defender and non-resistant intruder (guard honeybee and Death’s Head Sphinx Moth); non-resistant host and venomous parasitoid (American cockroach and it’s wasp prey), etc. Collectively, results of these experiments would give insight into the dynamics of evolution of circadian clock properties in their adaptive contexts.

A more complex system, one involving more than two species, might be more difficult to study, but would be even more informative. For instance, there is a case (Sara Oppenheim, personal communication) where a single specialist wasp parasitoid (Cardiochiles nigriceps) lays its eggs in larvae of two closely related moth species Heliothis virescens (HV) and Heliothis subflexa (HS). The two moths inhabit two very different plant hosts: HV feeds on tobacco, tomato and cotton, HS only on a Physallis plant. The host plants synthesize their deterrent chemicals (e.g., nicotine) evenly throughout the day. However, they show a circadian rhythm in synthesis of volatile compounds induced by the insect herbivory. These volatiles attract the wasps to the plant which carries the moth larvae. Plants emit different quantities and compositions of volatiles dependent on the species of moth which is attacking them. Wasps, in turn, are active bi-modally during the day – morning and evening only. HV lives on the surface of the leaf and is very vulnerable to the attacks of the parasitoid. On the other hand, HS quickly bores its way into the seed lantern of the plant where the wasp cannot reach it. A tobacco plant has enough leaf surface to accommodate a very large number of HV, but the Physallis plant has only a limited number of lanterns available at any time. It is not known, but it would be very interesting to discover, if the two moth species have evolved different temporal aspects of their biology. For instance, do HV larvae all emerge simultaneously in large numbers and find safety in numbers, while HS emerge one at a time as each individual needs time to search for and find a lantern? At what time of day do the larvae emerge, climb, feed, drop on the ground and pupate? Is there a difference in the sensitivity to light in two species as the HS hidden in a lantern is more protected from environmental light than the HV which sits out in the open? If there are differences in clock properties do they also translate into differences in developmental timing, frequency of courtship song, photoperiodic time-measurement and the ability of one of the species to invade higher latitudes? How are the plants, the wasp, and the two moths tracking each other in time – who is “winning” the race around the circadian clock? Can the changes in circadian properties be considered a part of the mechanism by which the two moth species speciated from each other in relatively recent past? Answers to these and similar questions would provide great insights into evolution and adaptive function of circadian systems.

Effects of clocks on evolution.

We have so far seen that there is individual variation in timing mechanisms (Aschoff 1998); that this variation is heritable; that timing is an important adaptive function, hence that clocks are products of evolution by natural selection. Let us now see if the possession of a clock can, in turn, direct or restrict the possible paths of further evolutionary change.

As noted above, it seems that biological clock mechanisms, perhaps even the same as circadian ones, are involved in timing of developmental events (Saunders 1972, Kyriacou et al. 1990, Moore et al. 1998). From this one can predict that changes in circadian clock properties will also have an effect on embryonic development, and vice versa. Thus adaptive changes in behavioral timing may be constrained by the needs of normal development, and heterochronic mechanisms of evolution might effect a change of fitness of the adults due to the change in physiological or behavioral synchronization.

In insects, developmental events are controlled by hormonal communication involving prothoracic glands and gonads (Nijhout 1994, 1999). Prothoracic glands are sites of circadian clocks in some insects (Vafopolou and Steel 1991, 1998). In some systems, a wasp parasitoid injects a virus into its moth victim (egg or larva) resulting in gonadectomy. The result is a change of timing of developmental events and disruption of pupation in the end. Is it possible that the lack of gonadal hormones broke one part of the feedback loop of the timer responsible for development?

As we have noted several times so far, circadian clocks are also involved in time measurement at other temporal scales from hours to years. For instance, mutations in fruitfly per gene change not just the period of circadian rhythms of behavior but also ultradian frequencies of the courtship songs (Dowse et al. 1987, Kyriacou and Hall 1980, Kyriacou et al. 1993). Likewise, sensitivity to olfactory cues is under circadian control (Krishnan et al. 1999). Although these mutations might not alter the timing of courtship activity during the day (this morning peak of sexual activity does not seem to be controlled by the PER-based mechanism), the changes in song frequency, receptivity to the song frequency, and timing of sensitivity to pheromones might greatly reduce the chance of a wild type and a mutant actually recognizing each other as mates and mating in a mixed population setting, leading to sympatric speciation via behavioral and temporal isolation due to a single nucleotide change.

On the other end of the spectrum, it is possible to construct a model in which a two-oscillator system measuring photoperiod (Warman and Lewis 1997) and another three-oscillator system controlling a free-running circannual rhythm interact to control precise timing of emergence of 17- and 13-year periodic cicadas (Williams and Simon 1995).

Likewise, many changes which various animals underwent under domestication, e.g., albinism, temperament, loss of seasonality, change in developmental time and rate of maturation, etc., point to changes in the clock systems under artificial selection (e.g., Trut 1999).

Can we go further? Circadian clocks are ubiquitous in all multicellular and many unicellular organisms. They provide a whole range of adaptive mechanisms involving development, physiology and behavior. Is it possible to have life without clocks? In my opinion, and data are needed to disprove it, without multi-oscillator circadian systems there would be no possibility for Life to invade oceanic surface, intertidal and terrestrial environments. Some components may be secondarily lost, but the process of invasion necessitated the presence of functioning circadian, lunar, tidal and photoperiodic clocks. Back in depths of the ocean, some kind of clock, not necessarily circadian, would be necessary for internal synchronization of complex organisms, and without such a timer, there would be no complex Metazoa on Earth. This leaves the bottom-dwelling microorganisms as the only organisms which do not need a clock, but will still exhibit some kinds of biochemical cycles, as life itself is defined by cycles (Bonner 1993, Kauffman 1993, 1995, Goodwin 1963, Maynard-Smith and Szathmary 1999).

If we go to another planet and find something that might be alive, how can we decide if it really is. Does it take energy from the environment, stores it, cycles it, uses it and dissipates it? Does it grow and reproduce? Does the offspring resemble parents? Is there a diversity of organisms on the planet? One more question: Is its environment periodic and does it have innate cycles corresponding in period to the environmental cycle? If yes, it is alive, as it possesses an universal adaptation which non-life cannot acquire or evolve. Endogenous rhythmicity is a diagnostic property of Life, more so than the underlying chemistry, as even living forms which do not use DNA as hereditary material, or are even not carbon-based, will still cycle in sync with the star and the moon of their native planets.

Related:

Circadian clock without DNA–History and the power of metaphor
Basics: Biological Clock
The Clock Metaphor
The New Meanings of How and Why in Biology?
Some hypotheses about a possible connection between malaria and jet-lag
Evolutionary Medicine: Does reindeer have a circadian stop-watch instead of a clock?
The Mighty Ant-Lion
Are Zombies nocturnal?
City Of Light: Insomniac Urban Animals
Me and the copperheads–or why we still don’t know if snakes secrete melatonin at night
Diversity of insect circadian clocks – the story of the Monarch butterfly
Biological Clocks in Protista
Do sponges have circadian clocks?
Daily Rhythms in Cnidaria
Carolus Linnaeus’s Floral Clocks
Clock Classics: It All Started with the Plants
Chestnut Tree Circadian Clock Stops In Winter
Flirting under Moonlight on a Hot Summer Night, or, The Secret Night-Life of Fruitflies
Too Hard for Science? Centuries to Solve the Secrets of Cicadas
Circadian Clocks in Microorganisms
Clocks in Bacteria I: Synechococcus elongatus
Clocks in Bacteria II: Adaptive Function of Clocks in Cyanobacteria
Clocks in Bacteria III: Evolution of Clocks in Cyanobacteria
Clocks in Bacteria IV: Clocks in other bacteria
Clocks in Bacteria V: How about E.coli?

ScienceOnline2012 – interview with Tanya Lewis

Every year I ask some of the attendees of the ScienceOnline conferences to tell me (and my readers) more about themselves, their careers, current projects and their views on the use of the Web in science, science education or science communication. So now we continue with the participants of ScienceOnline2012. See all the interviews in this series here.

Today my guest is Tanya Lewis (homepage, blog, Twitter), a Graduate Student in Science Communication at the University of California, Santa Cruz.

Welcome to A Blog Around The Clock. Would you, please, tell my readers a little bit more about yourself? Where are you coming from (both geographically and philosophically)? What is your background? Any scientific education?

tanyalewisI guess I should start with where I spent ¾ of my life so far: Hawaii. I grew up on the Big Island, in a cowboy town (yes, these exist in paradise). I spent much of my childhood romping, or more often, running, around mountains like lofty Mauna Kea, sun-drenched beaches, and the gravel track at my high school.

But I couldn’t wait to get off the rock and explore “the Mainland” U.S. I attended Brown University, where I studied biomedical engineering. A fascination with the brain led me to work in a lab developing a brain-computer interface known as BrainGate . It’s an implantable chip that records brain signals and decodes them to enable people with paralysis to control prosthetic devices. After graduating, I knew I wanted to spend time abroad, so I applied for a research fellowship to go to Germany. I worked in a lab there studying how primates encode hand movements.

At some point, I realized I enjoyed explaining my work way more than the work itself. A little fairy spoke to me in the night and told me to become a science writer. So I did – I joined the Science Communication Program at the University of California at Santa Cruz, where I am currently. It’s been a moray ever since.

Tell us a little more about your career trajectory so far: interesting projects past and present?

In my brief but thrilling science journalism career, I’ve worked at a news office at Stanford, the local newspaper The Santa Cruz Sentinel, and now at the SETI radio show “Big Picture Science” – each an adventure of its own. This summer I’ll be venturing into the wonderful world of online science journalism, working for Wired.com in San Francisco.

In my classes at UCSC, I’ve done both news writing and long-form writing. Features are probably my favorite at this point, because of the freedom to choose a topic of interest and explore it in depth, creatively. Right now I’m working on a feature about underwater volcanoes, a subject near and dear to me, having grown up near a very active volcano (Hawaii’s Kilauea volcano). It’s fun getting to learn about volcanology, while vicariously experiencing the mysterious volcanic deep-sea landscape.

What is taking up the most of your time and passion these days? What are your goals?

In my graduate program, we just started a unit on investigative reporting and multimedia. So I’m splitting my time between hard-nosed Bob Woodward-esque reporting and peering through a camera lens. It’s a great mix, and looks to be a lot of fun. Meanwhile, I’m getting a taste of radio (to use a little synesthesia), working on the science radio show “Big Picture Science.” I’m kind of a closet filmmaking geek, and I enjoy the creative process of writing/producing/editing a project, so this will be a great adventure. Plus, the show’s hosts, Molly Bentley and Seth Shostak, are a bundle of fun to work with.

My career goal is to work in a collaborative journalism environment (such as at a science magazine or online site/blog), on stories or projects that allow me some creative freedom in the choice and handling of topics. At some point, I could see myself freelancing, for the flexibility of the lifestyle. But right now, the idea of doing it fulltime slightly terrifies me. I want enough job stability so I can realize the instability of my interests.

What aspect of science communication and/or particular use of the Web in science interests you the most?

Feature writing (online or in print) and documentary film both appeal to me, but online media is the way of the present (never mind the future). I find blogging a fun form of journalism, and one I’d like to explore more. As e-readers continue to improve, I foresee more interactivity in the act of reading. Remember those “Choose your own adventure” books? Maybe we’ll develop something akin to that, where you can easily navigate science content of your choosing, while retaining something of a narrative structure. Just a thought. I also think we’ll get better at integrating video and audio into written journalism, so it’s less distracting and more illustrative. I don’t think the written word will fall out of style anytime soon, but we will need to work hard to keep people invested in it. Hopefully I’ve kept you invested in reading this far!

How does (if it does) blogging figure in your work? How about social networks, e.g., Twitter, Google Plus and Facebook? Do you find all this online activity to be a net positive (or even a necessity) in what you do?

Right now, I’m ashamed to say my blogging presence has been somewhat lacking of late, ironically because I’ve been spending all my time studying journalism. But I contribute sporadically to our class blog, “The Crashing Edge: Current Waves of Central Coast Science”. I’ve also done some blogging at conferences, such as this year’s Science Online meeting and at last year’s American Geophysical Union Fall Meeting.

The social networks I primarily use are Twitter and Facebook. I tend to use Facebook more for personal communication, and Twitter strictly as a professional platform to share ideas in science and science journalism. I have found Twitter a useful place for keeping current with science news and immersing myself in the commentary of the science journalist community.

When and how did you first discover science blogs? What are some of your favourites? Have you discovered any cool science blogs by the participants at the Conference?

Blogs are a somewhat recent addition to my consumption of science literature. In high school and college, I tended to read scientific journal articles, popular science magazines (e.g. Scientific American, Popular Science), and The New York Times. The science blogs I read these days vary, though some of my favorites are Ed Yong’s Discover blog “Not Exactly Rocket Science” and the Scientific American Blog Network blogs (and I’m not just saying that for brownie points!). I tend to read individual blog posts (mentioned on Twitter or elsewhere) more than reading specific blogs every day, however. The Knight Science Journalism Tracker is one I try to read more regularly, though.

What was the best aspect of ScienceOnline2012 for you? Any suggestions for next year? Is there anything that happened at this Conference – a session, something someone said or did or wrote – that will change the way you think about science communication, or something that you will take with you to your job, blog-reading and blog-writing?

This being my first ScienceOnline, and having no baseline with which to compare it, I can confidently say it was a fantastic conference. Or unconference. I think the best aspect of it for me was the egalitarian and collaborative atmosphere, where you could sit in a room with a New York Times reporter or all-star blogger and feel free to converse as peers. Some of the sessions which stood out to me were Deborah Blum’s and David Dobbs’s session on shape and music in longform writing (see my Storify post), and the session on Women in Science Blogging (see here). The dinner banquet with storytelling by The Monti was good fun, too. I came away inspired by the many scintillating conversations I had with other journalists and scientists at the various social events, in the coffee room, or even on the bus. I liked the format, the only improvement I can think of is to get the word out to more journalists and scientists about this terrific event. I definitely hope to attend next year, if possible. Aloha, a hui ho!

Thank you for the interview. Hope to see you next year!

Some hypotheses about a possible connection between malaria and jet-lag

I originally published this post on March 19, 2006.

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In the (in)famous  journal called “Medical Hypotheses” Kumar and Sharma [1] propose that jet-lagged travellers may be more susceptible to getting infected with malaria. They write:

Rapid travel across several time zones leads to constellation of symptoms popularly known as “jet lag”, caused primarily due to mismatch between the timing of circadian clocks of the traveller and the external periodic environment. It is often seen that the jet-lagged individuals who visit their family and friends in areas endemic to malaria have an enhanced susceptibility to malarial infection than the local residents. It would therefore be interesting to explore whether increased susceptibility to malarial infection among the visitors has anything to do with their state of jetlagged.

Indeed an interesting hypothesis. Of course, the travelers may also be less resistant to malaria than the locals, or less likely to have a life-style and behavioral patterns conducive to avoiding the mosquito bites, something that may be “second nature” to the locals. They continue:

Individuals with moderate to severe skin response to mosquito bite are largely protected against mosquito borne malaria because itch alerts an individual to mosquito bite and prepares him/her to take necessary precautions to prevent mosquito bite. Itch in an individual follows a diurnal pattern, and it is about hundred folds higher during midnight than midday. A hundred fold increase in itch sensitivity is viewed as a crucial preventive measure against mosquito bites, as this coincides with the midnight flight activity peak of female Anopheles mosquitoes, when she sucks blood from the host after mating peaks in the evening to raise her progeny. Normally individuals residing in endemic areas have their daily peak of itch sensitivity overlapping with the peak – biting phase of female Anopheles mosquitoes. As a result, they are relatively well protected against malarial infection.

Interesting idea: if you are sensitive to bites at the time when no mosquitoes are flying and are not sensitive to bites at the time when mosquitoes are flying, you may not get to squash that mosquito in time to prevent the Plasmodia to be injected into your bloodstream. Additionally, a jet-lagged individual may experience a peak of body temperature at night. Mosquitoes, among else, home in on the warmth of their victims. Thus, jet-lagged individuals may be warmer than the surrounding locals at midnight and thus more attractive to mosquitoes at that time.

On the other hand individuals visiting endemic areas from different time zones, particularly during the first couple of days are under the state of jet lag, and their peak protective daily behavioural itch sensitivity lies out of phase with the biting peak of female mosquitoes. Therefore, such individuals are at a greater risk for sustaining malaria compared to the residents. Thus from chronobiological perspective one is of the opinion that a person can be protected against malaria by appropriately adjusting circadian clocks regulating itch sensitivity to the periodic environment. We hope that recent developments in circadian biology will help us predict extent of adjustments necessary in a new environment, which can then be of paramount importance for the protection of jet-lagged travelers to endemic regions against malaria. Some protection against malaria in the chronotherapeutic procedures such as melatonin administration, light therapy, scheduled physical exercise, maximum exposure to new environment during vector free times, social interactions, and appropriate food habits, are a few recommended preventive measures for travelers visiting a malaria endemic areas, in addition to malarial antibiotic prophylaxis.

Sounds like good advice, although the administration of melatonin is always an iffy question. However, this hypothesis got my mind all twirling and I came up with some hypotheses of my own. However, it is important to distinguish between different kinds of hypotheses regarding a putative link between jet-lag and malaria. They suggest that jet-lag may:

1) affect the rate/ease of infection with malaria,
2) affect the symptoms of malaria in an infected individual,
3) affect the ability of the body to fight off the infection,
4) affect the effectiveness of treatments, and
5) affect the likelihood that the infected individual will spread the disease to others.

The Kumar/Sharma hypothesis is clearly of the #1 type. I will look more at other types of hypotheses – those that apply to already infected individuals. For that, let’s first go quickly through the basic biology of malaria.

Plasmodium Falciparum

Plasmodium Falciparum (source unknown - let me know if you find out)

Malaria is caused by a protist in the genus Plasmodium. While Plasmodium falciparum is the most common species, three or four other species are also causes of malaria in humans, and dozens of other species cause malaria or malaria-like diseases in other animals, including mammals, birds and reptiles.

Plasmodium is transmitted through bites of several species of mosquito from the genus Anopheles. Once injected into the final host (e.g., human), the plasmodia remain in the skin for several hours, then migrate to lymph nodes, spleen and liver where they undergo several transformations. The final stage – the gametocyte – migrates into the red blood cells. Inside each red blood cell one can find a large number of plasmodia, hiding there from the immune system of the host. The whole life-cycle lasts several days, even weeks to complete.

Anopheles

Anopheles (source unknown)

All the plasmodia burst out of red blood cells simultaneously. Enormous number of plasmodia suddenly released into the blood overwhelms the immune system of the host, allowing the plasmodia to survive unscathed for quite a long time. This time is sufficient for them to invade blood vessels in the skin where, if they are lucky, a mosquito will bite and the plasmodia can invade the mosquito again and search for the next host.

The bursting of red blood cells triggers high fever and sweating. High temperature, high carbon-dioxide, as well as some odors [2] present in the sweat are all highly attractive to mosquitoes, rasing the probability that the host will get bitten. In some species of Plasmodium (like P.falciparum), the bursting of red blood cells occurs every night. In some species of Plasmodium, the resulting fever occurs every two nights and in some every four nights (rarely three), causing, respectively, tertian and quartan fevers. Tertian and quartan malaria are treated by chloroquine, while falciparum malaria is treated by quinine, mefloquine or halofantrine.

Plasmodium in a red cell

Plasmodium in a red cell (source unknown)

Obviously, from the perspective of a Plasmodium, timing is crucial. First, it is important to errupt in synchrony. Yet, hidden inside red blood cells, plasmodia cannot communicate with each other. Second, it is important to time the eruption in such a way as to maximize the probabilty that some of the gametocytes will be picked up by mosquitoes. Thus, it is important for the eruption to occur at the time of day when mosquitoes are most actively foraging for blood.

How do the Plasmodia solve the problem of timing? This is where circadian biology comes in [3,4,5]. Plasmodia residing inside red blood cells use the time-clues generated by the host. More specifically, they key onto the nightly release of melatonin by the pineal gland. Melatonin is practically undetectable in the blood during the day and the concentrations rise steeply in the evening remaining high for the duration of the night (exact patterns differ between vertebrate species), then dropping again at dawn.

plasmodium falciparum cycle

Plasmodium falciparum life cycle (source unknown)

Plasmodia have melatonin receptors [3]. Interestingly, unlike melatonin receptors in vertebrates which are nuclear receptors, the receptors in Plasmodia are membrane receptors. Membrane receptors are much faster than nuclear receptors which is important when a biological event has to be timed with precision.

However, the plasmodia do not destroy the red blood cell immediately after receiving the melatonin signal – that would be too early in the evening for the timing to be adaptive, as the mosquitoes are still too busy looking for mates and mating at that time. Instead, the plasmodia use their own circadian clocks to measure the exact timing of eruption.

In a way, it appears that the host melatonin signal entrains (synchronizes) the clocks in plasmodia, and then the Plasmodium clock determines the phase (exact timing) for the eruption out of red blood cells.

Different species of Anopheles and even geographically distinct populations of the same species have different times of peak foraging (biting) activity. In each geographical region, the local population (or species) of Plasmodium evolved the timing of eruption to match that of the local mosquitoes.

Let’s now introduce another player. Apart from the parasite (Plasmodium), the host (a vertebrate, e.g., a human), and the vector (mosquito), one should also consider the predator – insectivorous bats that hunt for mosquitoes. The way that the malaria literature tends to think about timing can schematically be presented like this:

Timing of activity: bat vs. mosquito vs. Plasmodium vs. human

Timing of activity: bat vs. mosquito vs. Plasmodium vs. human

There is an assumption that plasmodium eruption, human fever, mosquito foraging and bat hunting are all synchronous. We have already looked at this from the perspective of the Plasmodium – it is adaptive for the Plasmodium for the three bottom lines to be accurate, i.e, that the parasite, the host and the vector are in synchrony. This also means that this is maladaptive to humans. It is also maladaptive to mosquitoes whose fitness does suffer somewhat if they are loaded with parasites.

On the other hand, it is maladaptive for mosquitoes and plasmodia, and adaptive for humans and bats, if the peak hunting time for bats coincides with the peak foraging time of mosquitoes. More these two events are in sync, more mosquitoes will get eaten, thus less plasmodia will get into a new host and less humans will get infected.

The dynamics of the timing relationship between the four species can be described as an Evolutionary Arms-Race Around The Circadian Clock. While some of the players will try to maximize their fitness by achieving synchrony, the other players maximize their fitness by avoiding synchrony with each other. This can be depicted, for bats and mosquitoes, like this:

Anopheles vs. bat arms-race around the clock

Anopheles vs. bat arms-race around the clock

In this case, mosquitoes evolve to forage at later times of night, and bats evolve to track the mosquitoes by hunting later at night.

This can go on back and forth endlessly. But, and here is a big “but”. This model is quite oversimplified as it posits only four players and for each player an absolute loyalty to the other three. But is the real world that simple?

Plasmodium species are pretty host-specific. Species that thrive inside humans, may not thrive or even survive inside the bodies of other animals and vice versa. So, the parasite is pretty loyal to its host. It is also completely dependent on Anopheles – it will most likely not survive inside a different kind of mosquito.

The same mosquito that usually bites a human will happily take a blood meal from another animal. This is actually used as one of the prevention techniques: a village is surrounded by fields full of cattle, sheep, goats, horses, donkeys or camels. The mosquitoes coming out of the woods at night encounter these animals first and get satiated with blood before they ever encounter humans. The animals themselves do not get sick.

Bats are unlikely, in my opinion, to be specialized on Anopheles as their only prey. If there are no mosquitoes around, they will happily hunt other insects (and the tropical regions where malaria is common are swarming with many species of insects!). I think that involvement of bats in the arms-race is the weakest aspect of the hypothesis. Here are four basic types of bat hunting activity that are theoretically possible:

bat activity patterns

Bat activity patterns

The hypothesis suggests that bats mostly fly around midnight when the mosquitoes are most active, i.e., the bats are winners and mosquitoes loosers in the arms-race (A). If the peak is at some other point during the night, that would suggest that bats are involved in the arms-race but the mosquitoes are currently winning (B). This may also suggest that bats highly prefer some other type of prey. The bats may be active throughout the night (C) which seems most likely. Finally, the bats may have a bimodal distribution: a lot of hunting early and late at night with a siesta right around midnight (D).

This would suggest that mosquitoes have found their best temporal niche in that dangerous world, i.e, although the bats are not involved in the arms-race, the mosquitoes are and are thus winners, without making the bats “loosers” in the process.

What is the real story? I don’t know. Obviously, it is possible to monitor patterns of bat activity [6,7], yet it still needs to be done in regions in which malaria is common. Some of the bats studied in the USA follow predominantly pattern C from the figure above, and it is not too far-fetched to hypothesize that all bats everywhere have similar patterns:

bat activity

Bat activity

What are the Anopheles patterns? While they search for blood around midnight, that is not the only time they are flying around.

Most of the early part of night is spent looking for mates, mating and laying eggs [8]. Thus, they are easy pickings for bats at times when they are not actively seeking humans. It appears that becoming diurnal is not a good option for Anopheles in the tropics – perhaps there are more birds there than bats, or the birds are more dangerous? It is not impossible for a mosquito to become diurnal – the mosquito we are used to seeing around here – the Culex – is crepuscular (dawn and dusk) and the Asian tiger mosquito is fully diurnal.

Anopheles oviposition

Anopheles oviposition

How does jet-lag figure in here? Apart from the hypothesis stated by Kumar and Sharma that itch sensitivity to mosquito bites gets displaced (and what I added – that temperature rhythm is also displaced), jet-lag will have other effects, too. Let’s look at possible effects it may have on people who already have malaria (and you’ll see why I had to use so much space describing all of the details of the arms-race above!).

Will jet-lag affect the way our body copes with the infection? In a jet-lagged human, there is no clear and sharp rhythm of melatonin release. Some amounts of melatonin are synthetized and secreted at all times of day. This means that the Plasmodium has lost its temporal anchor – there is no signal to use for determination of timing for eruption out of red blood cells. Thus, the gametocytes will errupt at random times – one cell now, another in an hour, another tomorrow. There is no safety in numbers any more – the human immune system is now perfectly capable of dealing with all the plasmodia in the circulation. Of course, the immune system itself may be somewhat compromised in a jet-lagged person.

Will jet-lag affect the way malaria presents its symptoms? The asynchronous eruption of plasmodia also means that there will be no abrupt onset of high fever at midnight. Instead, one may expect a continous low-grade fever. Nightly episodes of high fever are an important symptom of malaria. Will a physician with a patient who exhibits continuous low-grade fever ever suspect malaria?

Especially a physician in a country in which there is no malaria and the patient has returned home from the tropical travels and is jet-lagged from a return trip.

Will jet-lag affect the effectiveness of drug treatments? I don’t know the details of the way anti-malarial drugs work, so make sure you tell me if I get this all wrong. If the number of plasmodia in the circulation at any time is relatively small, and if the enzymatic destruction of the drug by liver is operating at a constant low rate (instead of with a circadian rhythm of its own), then being jet-lagged should enhance the effectiveness of the drugs, or even allow for the dose to be lowered.

Will jet-lag affect the ability of the patient to be a source of transmittion of the disease to others? With plasmodia erupting at all times of day and with most plasmodia being destroyed by the immune system throughout the day, it is much less likely that any will be present in the skin capillaries at just the right time – at midnight. Also, without a high fever coupled with sweating, the patient is less attractive to the mosquitoes than a malarial patient in the neighboring house who is local and not jet-lagged. Thus, the likelihood of plasmodia being picked up by mosquitoes is even smaller.

To summarize: according to the Kumar/Sharma hypothesis, being jet-lagged increases the chances for contracting malaria. On the other hand, if you already have the disease, it may be good for you to get jet-lagged! As long as you tell your physician that malaria is a serious option so the symptoms are not misinterpreted, you should be better off jet-lagged, allowing your body to fight the disease one plasmodium at a time.

Finally, as a matter of public health policy, how does one get the whole population of malarial patients in one country jet-lagged so as to reduce the transmission rates? Should hospitals induce jet-lag in malaria patients by shifting light-cycles or administering melatonin? How do the pros and cons of such treatment balance? Ah, so many hypotheses, so little data! I hope someone studies this in the future.

One last thing – notice that much of the work described above was performed by researchers outside of USA – not that it is important, but it shows that millions of NIH dollars are not neccessary for great science. Apart from a little bit of cellular physiology, most of the information comes from ecological field-work, and ALL of it is inspired by and informed by evolutionary theory. Not a single gel was run.

Now, I am not dissing molecular biology. Malaria is the only complex parasitic disease in which all players (plasmodium, mosquito and human) have their complete genomes sequenced, and much will be gleaned from such data in terms of designing better anti-malarial drugs, etc. But, as the above research shows, Big (molecular) Biology is not neccessary for findings that have a potential to seriously affect the infection and transmission rates of the disease.

References:

[1] Jet lag and enhanced susceptibility to malaria, C. Jairaj Kumar and Vijay Kumar Sharma, Medical Hypotheses (2006) 66, 671-685

[2] Fooling Anopheles: Scientists Aim to Wipe Out Malaria by Outsmarting a Mosquito’s Sense of Smell

[3] Calcium-dependent modulation by melatonin of the circadian rhythm in malarial parasites, Carlos T. Hotta, Marcos L. Gazarini,Flávio H. Beraldo, Fernando P. Varotti, Cristiane Lopes, Regina P. Markus, Tullio Pozzan and Célia R. S. Garcia, NATURE CELL BIOLOGY , VOL 2, JULY 2000, p.468

[4] Melatonin and N-acetyl-serotonin cross the red blood cell membrane and evoke calcium mobilization in malarial parasites, C.T. Hotta, R.P. Markus and C.R.S. Garcia, Braz J Med Biol Res 36(11) 2003

[5] Tertian and Quartan Fevers: Temporal Regulation in Malarial Infection, Célia R. S. Garcia, Regina P. Markus, and Luciana Madeira, JOURNAL OF BIOLOGICAL RHYTHMS, Vol. 16 No. 5, October 2001 436-443

[6] Sampling bats for six or twelve hours in each night? Esberard CEL, Bergallo HG, REVISTA BRASILEIRA DE ZOOLOGIA 22 (4): 1095-1098 DEC 2005

[7] Nightly, seasonal, and yearly patterns of bat activity at night roosts in the Central Appalachians, Agosta SJ, Morton D, Marsh BD, Kuhn KM, JOURNAL OF MAMMALOGY 86 (6): 1210-1219 DEC 2005

[8] Daily oviposition patterns of the African malaria mosquito Anopheles gambiae Giles (Diptera: Culicidae) on different types of aqueous substrates, Leunita A Sumba, Kenneth Okoth, Arop L Deng, John Githure, Bart GJ Knols, John C Beier and Ahmed Hassanali, Journal of Circadian Rhythms 2004, 2:6

Sciencey events over the next few weeks

There is tons to do this month – wherever you may be, or may travel to, try to attend some of these:

#DCscitweetup in Washinton DC on April 12th.

ScienceOnlineSeattle, in Seattle on April 16th

The Story Collider, NYC, Wednesday April 18th

ScienceOnlineVancouver, in Vancouver on April 19th

ScienceOnlineBayArea, in San Francisco on April 19th

North Carolina Science Festival, April 13-29.

The Philadelphia Science Festival, April 20-29.

Grand Opening of the Nature Research Center, the new wing of the NC Museum of Natural Sciences, Raleigh NC, Apr. 20-21st.

#NYCSciTweetup, NYC, April 22nd (exact location TBA).

Science Online NYC, May 2nd.

A week in Edmonton

As you may already know, I spent a whole week last month in Edmonton, Alberta, Canada. I had a blast! And here is some coverage of the events of the week:

#BoraZUofA: A thought-provoking week with Bora Zivkovic by Marie-Claire Shanahan:

Just a few weeks ago I waved goodbye to Scientific American blogs editor Bora Zikovic and thanked him for a wonderful week of talks at the University of Alberta. Somehow in just a week we’d managed to chat about science teaching, science blogs, the history of academic publishing, open-access, post-publication peer review, science on Twitter and so much more. It was exciting and exhausting, and my ideas notebook is completely full.

As part of the University’s Distinguished Visitor program, a small group of faculty from cell biology (Joel Dacks), anthropology (Bora’s brother, Marko Zivkovic) and science education (me) brought Bora to town to speak with students and faculty. No matter what the topic, the theme seemed to be: keep an open mind. Be willing to consider new ways of doing things but also remember that they might not be as they first appear….

My Week with @BoraZ by Torah Kachur:

…..The fact is that the web has changed how science is done – and Bora is evidence of that. From bloggers being way more than just men in pyjamas in their parents basement to full lab books being completed open and online for the whole world to watch. The 21st century will be driven by bloggers being the peer reviewers, open access dominating publishing houses and science being done for all the public to follow and learn.

We, the bloggers, are the nerds behind the paradigm shift in the pursuit of science. Bora will continue to advocate for more Open Access journals so that the public can engage in science and it will become more accessible to everyone. And we, at Science in Seconds will continue to be geeky and super sarcastic.

This entire time I spent with Bora laughing at jokes only a scientist could love and discussing every topic under the sun, his brother Marco – a cultural anthropologist who is studying scientist culture – was sitting there….studying us….making us his guinea pigs….and occassionally throwing out a comment about just how different the dorks of the world really are…

#BoraZUofA Linkfest: A collection of the sites and posts referenced in Bora’s talks by Marie-Claire Shanahan:

Scientific American blog editor Bora Zivkovic‘s visit to the University of Alberta was a wonderful whirlwind of talks on science education, science communication, open science, peer review and the scientific publishing industry. I’ve summarized his talks in an overview of the week. If you’re interested in a more in-depth look, Bora has also shared a list of links to the sites, posts and people he mentioned or used in his talks (or intended to use in some cases). It’s a terrific guide to exploring these issues online…

Visiting editor talks technology in education by Rachel Singer:

The internet is changing science education and communication in a remarkable way, according to a Scientific American magazine editor visiting the U of A this week.

As part of the U of A’s Distinguished Visitor Program, Bora Zivkovic will be delivering various talks on implementing technology in science education, including how to communicate research through social media, and navigating the benefits and pitfalls of scientific interaction online.

Zivkovic says the focus of his trip is to get people to reconsider science education and to promote science online….

SOCIAL MEDIA IN EDUCATION by Katelyn Hoffart and Kaitlyn Grant:

The “blogfather” of Scientific American magazine’s blog network, Bora Zivkovic, discussed the use of social media in education and research at a University of Alberta talk last week.

Zivkovic ended a week-long speaking series with a drop-in discussion on communicating research through social media. Students and staff discussed with Zivkovic the ins and outs of using blogs as personal and professional tools for research.

Blogs have brought together people from different professions and interests, including Marie-Claire Shanahan, an associate professor in the Faculty of Education who shared her experience of blog-initiated partnership to the discussion….

Skeptically Speaking #156: Beyond 42:

This week, we’re experiencing the power of stories to communicate science. Join us for Beyond 42: How Science Can Use Stories to Explain Life, the Universe and Everything. This event, recorded live in Edmonton, features Scientific American Blog Editor Bora Zivkovic, and a fantastic cast of scientists telling moving stories that communicate the wonder of science and discovery….

Teaching and learning through online science: First Bora Zivkovic (@BoraZ) talk at University of Alberta in Edmonton, Alberta, Canada (Storify) by Tim Skellet.

Changing the nature of science literacy online: Second Zivkovic (@BoraZ) talk at University of Alberta in Edmonton, Alberta, Canada (Storify) by Tim Skellet.

Navigating the benefits and pitfalls of scientific interaction online: Third Bora Zivkovic (@BoraZ) talk at University of Alberta in Edmonton, Canada (Storify) by Tim Skellet.

And, only tangentially related to the events of the week – the #arseniclife saga and the nature of the current science media ecosystem – this new paper in which I was quoted (and I am happy with the quote – if you do not have access and are interested in the context of the quote I have a PDF I can send you, just ask): To hype, or not to(o) hype by Andrea Rinaldi:

…Of course, the media landscape is extremely varied, as science blogger and writer Bora Zivkovic pointed out. “There is no unified thing called ‘Media’. There are wonderful specialized science writers out there, and there are beat reporters who occasionally get assigned a science story as one of several they have to file every day,” he explained. “There are careful reporters, and there are those who tend to hype. There are media outlets that value accuracy above everything else; others that put beauty of language above all else; and there are outlets that value speed, sexy headlines and ad revenue above all.”…

ScienceOnline2012 – interview with Rebecca Guenard

Every year I ask some of the attendees of the ScienceOnline conferences to tell me (and my readers) more about themselves, their careers, current projects and their views on the use of the Web in science, science education or science communication. So now we continue with the participants of ScienceOnline2012. See all the interviews in this series here.

Today my guest is Rebecca Guenard (blog, Twitter).

Welcome to A Blog Around The Clock. Would you, please, tell my readers a little bit more about yourself? Where are you coming from (both geographically and philosophically)? What is your background? Any scientific education?

Hi, I’m Rebecca Guenard. I currently live outside of Philadelphia, PA with my husband and our two boys.

I have loved math and science for as long as I can remember. I have a B.S. and a Ph.D. in Chemistry.

I spent a year working for the chemical industry where I learned I was better suited for academia.

Tell us a little more about your career trajectory so far: interesting projects past and present?

I began my career in academia as an adjunct while we started our family. Then I took a permanent teaching position at Temple University. I worked at Temple for five years, teaching the large freshman lectures, as well as upper division courses for majors. At the same time I conducted research, sort of a nontraditional postdoc. My aim was to seek a tenure track position, but the needs of my family were such that I left Temple to work independently from home. Now I am part-time cruise director and part-time science writer.

The transition from academia was tough, I had been in hallowed halls since I was 17 years old. I had grown attached to the structure of the academic system. So I took a few years to concentrate on kids and figure out life outside that hierarchy. I kept my hand in chemistry while I privately tutored, but I opened myself up to new experiences. I volunteered for an organization that needed help improving communications. The experience taught me a lot and gave me the confidence to combine chemistry and communications, as I had originally intended when I left Temple.

Science writing is another form of teaching. A 50 minute lecture for a freshman class is a kind of performance; there is an entertainment factor associated with it. This is especially true for chemistry because students tend to be intimidated by the subject. A good chemistry professor pulls students in, settles their fears and while their attention is gripped shoves in as much curriculum as they can.

I have the same philosophy when I communicate science with the written word.

What is taking up the most of your time and passion these days? What are your goals?

Currently, most of my time is taken up with telling stories. I developed a blog called atomic-o-licious last summer which I am using to feel my way through science communications.

I am interested in accessibility. If you want to read science content you have hundreds of options. If you seek it out you will find it. But there are so many people who never seek out science. Maybe they are busy or intimidated, for whatever the reason science isn’t a priority. There is an extensive audience that needs to be offered different bait. It is that audience I seek with atomic-o-licious.

I would love for my blog to be like a Dave Barry column which attracts readers because it is entertaining, it makes them laugh. But there is a bonus, science is folded in among the humor.

Every day I can pull a story from my life and relate it to chemistry; I see the world through chemistry-colored glasses. And most days life just cracks me up. What a dream to have an outlet for combining the two!

Chemistry is a tough subject; readers are naturally drawn to life sciences, chemistry tends to drive people away. But I am going to draw them, gosh darnnit.

One of my goals is to expand my readership. It is creeping up slowly. I am grateful for the receptiveness of the science writing community, and I look forward to reaching a broader audience.

I am also continually pitching stories to mainstream publications to get my name in print and out to a non-science audience which might be enticed back to my blog (plus I wouldn’t mind getting paid).

What aspect of science communication and/or particular use of the Web in science interests you the most?

The Web is full of amazing science resources. Since I am most interested in creating a narrative, in telling a good story, I am focused on blogs right now. I also like blogs for aggregating information. Social media makes it so easy to share new, interesting research that is written about on blogs.

I also like the idea of having a YouTube channel, a place to create chem videos, but I need time to formulate the goals of such a channel.

How does (if it does) blogging figure in your work? How about social networks, e.g., Twitter, Google Plus and Facebook? Do you find all this online activity to be a net positive (or even a necessity) in what you do?

Aside from being a form of science communication, I view my blog as a portfolio. If you take the whole body of work hopefully you can see that I am growing and learning in the craft of science writing.

I would have zero readership without social networks. They are vital to expanding science communication. I like that social networks connect me to other science communicators.

I had a narrow view of science prior to social networks. There was the research I was doing and the research papers that I read that were close to what I was doing; who had time for anything else. With social networks I am connected to people with different backgrounds and interests and through our network they bring what they are studying to me. It is a process that still amazes me. I am exposed to so much more than I ever was before social networks.

When and how did you first discover science blogs? What are some of your favourites? Have you discovered any cool science blogs by the participants at the Conference?

The Loom is probably the first science blog I discovered, but I can’t remember how I came across it. Prior to that I mostly read science in print and on news sites. But until recently, when I came out from under my chem prof bell jar, I was oblivious to how much was available.

I ricochet throughout the web daily. I mostly visit blogs within science blog networks or stories that are brought to my attention on Twitter.

What was the best aspect of ScienceOnline2012 for you? Any suggestions for next year? Is there anything that happened at this Conference – a session, something someone said or did or wrote – that will change the way you think about science communication, or something that you will take with you to your job, blog-reading and blog-writing?

Every aspect of the conference changed the way I think about science communication. I was trained to hold on tight to information. Some of the research projects I was on were industry collaborations so the research results were proprietary, but also science is a competitive environment in which to be raised. Knowledge is power, you don’t relinquish it, that is the message that gets whispered in your ear.

There is a lesson to be learned from the difficulty the scientific community has had relaying the importance of climate change. We can’t just keep the general public out of scientific research and expect that they will suddenly snap into compliance when we discover something troublesome. Climate scientists have had to spend precious years explaining how they know what they know about climate change instead of taking steps to stop it.

This issue coupled with social media has developed a new breed of scientists who understand the need for the open communication of research. I am having to play catch-up and unlearn my training. This conference was an invaluable aid in taking those steps. All of the openness was weird at first, the twitter followers, the conference wikispace, the open access conference schedule. I felt exposed. But I met people I wouldn’t even have made eye contact with at another conference.

I had many interactions with people at scio12 that have influenced my work. I spoke with journalism veterans who gave me concrete advice on finding narratives, maintaining blogs and refining stories. I also talked to people who have been blogging longer than me and graciously extended their advice, encouragement, and support. It was a wonderful experience. I look forward to scio13!

Thank you for the interview. Hope to see you next year!

Flirting under Moonlight on a Hot Summer Night, or, The Secret Night-Life of Fruitflies

I originally published this post on May 19, 2007.

As we mentioned just the other day (May 2007), studying animal behavior is tough as “animals do whatever they darned please“. Thus, making sure that everything is controlled for in an experimental setup is of paramount importance. Furthermore, for the studies to be replicable in other labs, it is always a good idea for experimental setups to be standardized. Even that is often not enough. I do not have access to Science but you may all recall a paper from several years ago in which two labs tried to simultaneously perform exactly the same experiment in mice, using all the standard equipment, exactly the same protocols, the same strain bought from the same supplier on the same date, the same mouse-feed, perhaps even the same colors of technicians’ uniforms and yet, they got some very different data!

The circadian behavior is, fortunately, not chaotic, but quite predictable, robust and easily replicable between labs in a number of standard model organisms. Part of the success of the Drosophila research program in chronobiology comes from the fact that for decades all the labs used exactly the same experimental apparatus, this one, produced by Trikinetics (Waltham, Massachusetts) and Carolina Biologicals (Burlington, North Carolina):

This is a series of glass tubes, each containing a single insect. An infrared beam crosses the middle of each tube and each time the fly breaks the beam, by walking or flying up and down the tube, the computer registers one “pen deflection”. All of those are subsequently put together into a form of an actograph, which is the standard format for the visual presentation of chronobiological data, which can be further statistically analyzed.

The early fruitfly work was done mainly in Drosophila pseudoobscura. Most of the subsequent work on fruitfly genetics used D.melanogaster instead. Recently, some researchers started using the same setup to do comparative studies of other Drosophila species. Many fruitfly clock labs have hundreds, even thousands, of such setups, each contained inside a “black box” which is essentially an environmental chamber in which the temperature and pressure are kept constant, noise is kept low and constant (“white noise”), and the lights are carefully controlled – exact timing of lights-on and lights-off as well as the light intensity and spectrum.

In such a setup, with a square-wave profile of light (abrupt on and off switches), every decent D.melanogaster in the world shows this kind of activity profile:
2fruitfly crepuscular
The activity is bimodal: there is a morning peak (thought to be associated with foraging in the wild) and an evening peak (thought to be associated with courtship and mating in the wild).

The importance of standardization is difficult to overemphasize – without it we would not be able to detect many of the subtler mutants, and all the data would be considered less trustworthy. Yet, there is something about standardization that is a negative – it is highly artificial. By controlling absolutely everything and making the setup as simple as possible, it becomes very un-representative of the natural environment of the animal. Thus, the measured behavior is also likely to be quite un-natural.

Unlike in the lab, the fruitflies out in nature do not live alone – they congregate with other members of the species. Unlike in a ‘black box’, the temperature fluctuates during the day and night in the real world. Also unlike the lab, the intensity and spectrum of light change gradually during the duration of the day while the nights are not pitch-black: there are stars and the Moon providing some low-level illumination as well. Thus, after decades of standardized work, it is ripe time to start investigating how the recorded behaviors match up with the reality of natural behavior in fruitflies.

Three recent papers address these questions by modifying the experimental conditions in one way or another, introducing additional environmental cues that are usually missing in the standard apparatus.

Flirting

In the first paper, Nocturnal Male Sex Drive in Drosophila (Current Biology, Volume 17, Issue 3 , 6 February 2007, Pages 244-251), by Fujii, Krishnan, Hardin and Amrein, the problem of isolation was dealt with. In order to do this, a different apparatus had to be used, in this case a bunch of petri-dishes placed under the watchful eye of a video camera:

Two flies at a time were placed in each petri-dish: either two males, two females or one male and one female. Their general locomotor activity was compared to that of isolated insects of both sexes. In addition, some more concrete behaviors – “close-proximity” (i.e., two individuals approaching each other), courtship and mating were monitored as well.

So, what did they find? Putting two males or two females together did not change the activity patterns much. But putting one male and one female together provoked a large change of behavior – most of the approaches, courting and mating occured during the night!

Here are individual males:

And here are male-female pairs:

Additionally, they found that the flies revert back to their standard patterns if placed back into isolation (so being virgin vs. experienced does not matter and the shift in patterns of behavior is not permanent).

Also, by entraining males and females 11 hours out of phase with each other and then placing them together, they discovered that the males drove the couples’ behavioral patterns – the pair always assumed the phase of the male.

Finally, experiments with various genetic knock-outs and mutants (I’ll spare you the tedious details) revealed that a) the males drive the pattern due to their perception of the females’ smell and b) intact circadian pacemakers in both the brain and the antennae (the fly equivalent of the olfactory bulb in some sense) are necessary for the shift of behavior to a nocturnal pattern.

Moonlight

So, if the first paper suggests that the smell of virgin females can lure males to get active in pitch darkness, would a low-level light at night also encourage flies to stay up all night and party? The role of dim light during the nights was studied in the second paper, Moonlight shifts the endogenous clock of Drosophila melanogaster (PNAS, February 27, 2007, vol. 104, no. 9, pp. 3538-3543) by Wolfgang Bachleitner, Lena Kempinger, Corinna Wülbeck, Dirk Rieger, and Charlotte Helfrich-Förster.

In an earlier paper from the same lab, shutting down the activity in one of the clock genes eliminated the morning peak of activity, but the evening peak remained for quite a few days (even weeks) afterwards (does that mean that eating is less important than mating?), suggesting that the two peaks are driven by different clocks.

In this paper, the authors used an artificial light equivalent in intensity to a quarter-moon light. They compared activity patterns as well as patterns of clock-gene expression in standard light-dark cycles, in constant dark, in constant moonlight, and in a light-moonlight cycle.

Both the activity and the gene expression changed dramatically when moonlight was present. The morning peak started earlier, during the latter portion of the moonlit night, while the evening peak extended into the early portion of the next moonlit night:

The pattern of cycling of clock-proteins followed the same pattern as activity – advanced (and broadened) in the part of the brain thought to house the morning oscillator and delayed (and broadened) in parts of the brain thought to house the evening oscillator (though the literature is still not clear on their exact location).

Furthermore, deletion of an important photopigment (cryptochrome, which is not a clock gene in flies) only slightly raised the treshold of sensitivity to light – the activity patterns changed in the same way as in wildtype flies once the intensity of moonlight was raised to 0.5 lux. Being a blue-light pigment, cryptochrome may be imporant in detection of changing spectra during dawn and dusk and thus involved in the measurement of photoperiod (daylength).

But, deletion of a gene that results in lack of compound eyes (but not ocelli) made the flies blind to moonlight (not daylight, though). So, light detection by compound eyes is necessary for the changes in activity patterns in the presence of moonlight. Also, the peripheral clock in the compound eyes did not switch patterns of gene expression under moonlight in wildtype flies.

Hot Summer Nights

I initially intended to include another paper in this review – Integration of Light and Temperature in the Regulation of Circadian Gene Expression in Drosophila (PLoS Genet 3(4): e54 doi:10.1371/journal.pgen.0030054) by Boothroyd CE, Wijnen H, Naef F, Saez L, Young MW – but now that I have read it, I realize that it may be better to write about it on its own (and not just because it is huge, but also because it is conceptually complex) or together with another paper that recently saw some press and deserves some coverage by me as well. So, for now, yes, one can use temperature cycles to alter the patterns of fruitfly activities (and move it somewhat into the night) but that is not the main finding of the paper.

In summary, what a simple light-dark cycle in the laboratory does to isolated fruitflies is “box” their activity entirely within the light phase of the cycle. In other words, it exerts a strong masking effect of light on activity. Out in nature, presence of dim light, temperature cycles and conspecifics allows these insects to spread their activity into the night. While we still agree that the pattern, being bimodal, is that of a crepuscular animal, these new findings suggest that the fruitflies are not predominantly diurnal as thought to date, but flexible in their behavior and under some conditions even strongly nocturnal animals.

 

How to break into science writing using your blog and social media (#sci4hels)

Yesterday I skyped into Czerne Reid’s science journalism class at University of Florida to talk about breaking into science writing as a profession, and especially the use of blogs and social media as tools for accomplishing that goal.

Just a few days before that, as a part of our regular Question Time in preparation for our panel at WCSJ2013 in Helsinki, we tackled the same question:

What does a new science journalist do to get noticed? How do you get people to read your work, give you assignments, follow you on Twitter, and generally just know who you are?

Rose Eveleth collected and organized the responses we received on Twitter (using hashtag #sci4hels), but here I’d like to provide, all in one place, a bunch of links to resources, other people’s thoughts about it, and a few brief thoughts of my own.

Ways of becoming a science writer

There are two basic trajectories: one more traditional, which I like to call “vertical”, and the other one I call “horizontal” which, though it happened with individual writers for a long time, seems to be a much more frequent, if not dominant trajectory these days.

The vertical trajectory is the one taken by people who, perhaps from a very early age, knew they wanted to become writers or journalists, perhaps specifically science journalists. They major in journalism in college (perhaps double-major in a science as well), work on their school paper, start internships early in their local papers (or radio or TV stations), then go to a Master’s program in science journalism. By the time they graduate from that, they already have lots of experience, several internships, many clips, perhaps some local awards, and are ready to start making a living as staff writers or freelancers.

The horizontal trajectory describes people who start out in science, with every intention of making a career in research. But, as tenure track is now an alternative career in science, most science students need to find other options. Some of them – those who always liked to write, wrote diaries as kids, etc. – will explore the option of becoming science writers. The most direct horizontal trajectory involves starting a science blog while still doing research, becoming known for good writing there, then start pitching stories for online (and later print) magazines, and gradually leaving the lab bench and starting to make a living by writing alone. Brian Switek, John Timmer and Ed Yong are probably the best known examples of people who took this path. Heck, I am one of those examples, too. Many more are somewhere along that trajectory right now.

Of course, those are extremes, too neatly cut apart. Many people will do something in the middle, combining the two approaches in some way. For example, they may pursue a career in research while also taking summer internships at science magazines, or editing the science section of the college newspaper. Some may major in science, then go to j-school for Masters. Also, not all of the new entries into science writing are young. Sure, some make the switch after college or Masters in science, but others make the switch later, after getting a PhD, or finishing a postdoc, or after years of teaching as adjunct faculty with no hope of ever getting a tenure track position, or even after many years as full faculty, once grant money dries out and there are no more resources to keep running the lab.

Either way, there comes a time when one becomes a professional science writer/journalist and has to make a living that way. What does one need to do to succeed?

Understanding the new media ecosystem

It is important to be aware that 20th century media ecosystem is a very unusual aberration in the way people communicated throughout history. Means of production were expensive. Very few people could afford to own printing presses, radio and TV studios, etc. Running all that complicated equipment required technical expertise and professional training. Thus media became locked up in silos, hierarchical, broadcast-only with little-to-none (and then again centrally controlled) means for feedback. There was a wealthy, vocal minority that determined what was news, and how to frame it, and the vast majority was consuming the news in silence.

Today, all one needs is some source of electricity (e.g., a small battery in your smartphone) and some means of accessing the Internet. The act of publishing is reduced to clicking on the “Publish” button. Yes, this still leaves some people out of the media, especially in the developing countries, but compared to just twenty years ago, vastly larger numbers of people now have access to the means of production of news. The obstacles to access – money, technical skills for running the machinery – are now much, much lower, almost free.

This turns everything on its head! Silos are breaking down, economics of media are severely disrupted, former gatekeepers are squealing in distress, old hierarchies are broken down (and replaced by new hierarchies), and now everyone has to learn new “media hygiene” practices: who to trust, how to filter the information, how to organize it for one’s self. The new ecosystem now contains both the traditional outlets and the individuals, “people formerly known as the audience“, as equal players.

There is only so much time and energy anyone can invest into consumption of the media. In the flood of information coming out every second, how does one get science to the audience? Specialized science media outlets cannot see each other as competition any more – they are now collaborators, helping each other toward the same goal: trying to, at least occasionally, displace trivia, Hollywood gossip, and dangerous pseudoscience with good science news. Individual science writers, as equal participants in the media ecosystem, should do the same: replace the notion of competition with the idea of cooperation.

How does a new science writer succeed in this new ecosystem? In the 20th century, one would try to ingratiate oneself with the gatekeepers, the editors. As they are still part of the ecosystem and probably will be for some time in the future, this strategy is still valuable, but it is only one of many. More important, if anything, is to build support networks with your colleagues, peers and buddies. The concepts of ‘Friends in Low Places’ and ‘Horizontal Loyalty’ are not just theoretical – put them to practice.

You may think of two potential career routes: getting hired as a staff writer somewhere (getting harder with each passing year), or to freelance. But there is a third way now: start and build your own media empire.

Huffington Post, DailyKos, Talking Points Memo, BoingBoing started out as unknown person’s personal blogs – after turning into group blogs, then adding functionalities that let readers contribute, today they are media organizations that make money, hire and pay editors, and more. Perhaps your own blog can turn into something like this. But teaming up with your own Friends In Low Places may make such a start-up more successful.

First you have to write

People who want to become professional writers are, I assume, people who always liked to write. Childhood diaries. LiveJournals filled with teenage angst. Long Facebook updates. It’s time to take this seriously and do your writing in a more serious, organized, professional manner. Start a blog. This is your writing laboratory. Start blogging about science. Nobody will know about your blog until you start promoting it, so don’t worry that your early posts are clumsy (you can even delete the first few embarrassing posts later, once you are happy with your blog and start promoting it).

Practice the usual journalistic forms – the feature, the interview, the brief news story with inverted pyramid. You will need to demonstrate that you are capable of writing in such forms and styles. But don’t limit yourself to traditional form