Monthly Archives: August 2010

Evolutionary and Developmental Precursors for the Human Mathematical Mind

Now that summer is starting to fade, here is something else to look forward to: The 2010-2011 American Scientist Pizza Lunch speaker series returns next month.

Join us at noon, Tuesday, Sept. 21 here at Sigma Xi to hear Duke University cognitive psychologist Elizabeth Brannon give a talk entitled: “Evolutionary and Developmental Precursors for the Human Mathematical Mind.” In other words, Brannon studies what we all take for granted: our ability to do the numbers. She does it, in part, with studies of human babies and other primates.

Thanks to a grant from the N.C. Biotechnology Center, American Scientist Pizza Lunch is free and open to science journalists and science communicators of all stripes. Feel free to forward this message to anyone who might want to attend. RSVPs are required (for the slice count) to cclabby@amsci.org

Directions to Sigma Xi, the Scientific Research Society in RTP, are here: http://www.sigmaxi.org/about/center/directions.shtml

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Lots of great stuff today – here is a sampling:
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Hydrogen Bonding (video)

Grand Rounds Vol. 6 No. 49 – a conference in a tropical island resort

The summer is almost over, but we can try to remain in the summery mood just a little bit longer. Perhaps we can go to a medical conference held at a luscious tropical island resort, listen to presentations, chat in the hallways, and then have great fun at the bar in the evenings. And call it Grand Rounds. No coats and ties allowed – this meeting is supposed to be fun!

Day 1 – Morning session: Biomedical Science

Let’s start with controversy! Laika’s MedLibLog digs into the XMRV controversy with another comprehensive treatment prompted by the newest paper in the field – Does the NHI/FDA Paper Confirm XMRV in CFS? Well, Ditch the MR and Scratch the X… and… you’ve got MLV. And Abbie at ERV covers the same paper without mincing her words – ouch! – in XMRV and chronic fatigue syndrome: Scientific Blue Balls.

Diane Meier at The John A. Hartford Foundation blog wrote a review and summary of a blockbuster study on palliative care and quality (and length!) of life: Palliative Care: We Still Have a Lot to Learn.

Day 1 – afternoon session: The Brain and The Mind

SharpBrains contributors have two entries this week. The first one is by Jo Ellen Roseman and Mary Koppel at AAAS: The Brain in Science Education: What Should Everyone Learn? The second one is Why working memory matters in the knowledge age: study by Dr. Tracy Alloway.

How to Cope with Pain reviews exciting, new, non-invasive and non-medication treatments for pain, in Brain Re-training To Decrease Pain.

Will Meek, PhD is working through human psychology, one post at a time. The latest installment is Romantic vs Committed Love.

Dinah at Shrink Rap, differentiating normal moods from those associated with mental illness: Emotion versus Mental Illness.

Day 1 – hallway conversations: Practice, Patients, Nursing and Cases

Katrina Racial Violence is a poignant recollection of treating a Katrina survivor, who had been threatened with violence, by Toni Brayer, MD at EverythingHealth.

‘Nancy Nurse, RN, MD’ on the Muse, RN is a post motivated by the phrase “If she’s so smart, why isn’t she a doctor?”. Its a little dicey…but Nurses need some dice every once in a while.

Medical Resident, from A Medical Resident’s Journey responds to a recent blog post in the New York Times by Pauline Chen on medical errors: On Medical Mistakes…. And another post on the same topic, at Supporting Safer HealthcareI Care For You; I Am Your Doctor – focuses on the fact that, unfortunately, communication can break down at this most crucial time.

Physician Quality Report Cards, Part II on Kent Bottles Private Views is a post about a physician’s resistance to administrative review and patient feedback. Doctor report cards, NFL football, teachers, controversy, and nasty comments. What more could you want in a blog post?

Fizzy, last week’s host of Grand Rounds over on Mothers in Medicine, starts with a cartoon and writes about looking too young to be a doctor: Get confident, stupid!

Waterworks at Other things amanzi is a great story by Bongi about a joke he played on a not-so-hard-working urologist.

From Kimberly Manning, FACP at ACP Hospitalist, Life at Grady: Black and white, a story about a patient questioning his doctor’s race.

When do medical students start learning to practice medicine defensively? It didn’t take long for this one to encounter the opening lesson: Defensive Medicine 101… it starts now, at The Notwithstanding Blog.

And a little comparative medicine from Dog Zombie: Comparative medicine: what is a wallaby?

Greg Friese at Everyday EMS Tips: Paramedic that Knows Everything Declines Additional Learning

Day 2 – morning session: Medicine and Technology

Livetweeting surgery is becoming all the rage these days. Ramona of Suture for a Living writes about the latest case: Double Hand Transplant on Twitter.

Physicians are a group that greatly adopted the use of smartphones in theor work. Ryan DuBosar at ACP Internist comments in QD: News Every Day–What smartphone are you using?

In Doctors Not Using Email Like It’s 2010 It’s 2010, Elaine Schattner, MD at Medical Lessons considers physicians’ selective use of email, a no-longer-new technology that might, if embraced, facilitate communication between doctors and patients.

Michelle R. Wood of Occam Practice Management looks at some Famous Last Words in regard to technology, and how those words turned out…including the worries about the “paperless” Health Information Technology.

Day 2 – afternoon session: History of Medicine

Delia O’Hara at Birth Story introduces us to a historical figure of Alexis Carrel, who pioneered vascular surgery and transplant surgery.

At From the Hands of Quacks, Jaipreet Virdi gives us a glimpse of quirky medicine from the past, in How to Avoid Deafness and for those who want to know more, there is a Reading List.

Day 2 – hallway conversations: Healthcare policy

Louise at Colorado Health Insurance Insider discusses Amendment 63 On The Ballot In Colorado which will determine who can purchase health insurance.

Day 2 – evening at the bar: The Fun Stuff

The Happy Hospitalist tried something new – to draw a cartoon: Parkinson’s Cruise Cartoon (The Happy Hospitalist Original)

The Poetry Contest at The Examining Room of Dr.Charles ends tonight. Many great health/medical poems were submitted and some of them were posted there. Here is Thirteen Ways of Seeing, a poem (in 13 parts) by Aidel Moodnick.

And with this, the tropical island resort conference ends. Have a great trip home! We’ll see you all again next week at the Grand Rounds hosted by Musings of a Dinosaur.

Introducing The Guardian Science Blogging Network

Early this morning, The Guardian launched their brand new science blogging network, adding another shiny new island to the growing archipelago of the science blogging universe.

Alok Jha introduces the network:

You would not know it from general media coverage but, on the web, science is alive with remarkable debate. According to the Pew Research Centre, science accounts for 10% of all stories on blogs but only 1% of the stories in mainstream media coverage. (The Pew Research Center’s Project for Excellence in Journalism looked at a year’s news coverage starting from January 2009.)

On the web, thousands of scientists, journalists, hobbyists and numerous other interested folk write about and create lively discussions around palaeontology, astronomy, viruses and other bugs, chemistry, pharmaceuticals, evolutionary biology, extraterrestrial life or bad science. For regular swimmers in this fast-flowing river of words, it can be a rewarding (and sometimes maddening) experience. For the uninitiated, it can be overwhelming.

The Guardian’s science blogs network is an attempt to bring some of the expertise and these discussions to our readers. Our four bloggers will bring you their untrammeled thoughts on the the latest in evolution and ecology, politics and campaigns, skepticism (with a dollop of righteous anger) and particle physics (I’ll let them make their own introductions).

The four initial bloggers (apart from Alok who will continue blogging on the already well-known Guardian ScienceBlog) are Martin Robbins, Jon Butterworth, Evan Harris and my old friend and SciBling GrrlScientist.

So, subscribe to their RSS feed and their Twitter list and their official Twitter account, then go and post Hello comments on their blogs.

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I am back, after a 10-hr drive from NJ to NC, and preparing Grand Round for tomorrow morning. In the meantime, read these:

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Open Laboratory 2010 – submissions so far

Note: if you have recently moved your blog, please e-mail me the corrected URLs for your entries

The list is growing fast – check the submissions to date and get inspired to submit something of your own – an essay, a poem, a cartoon or original art.

The Submission form is here so you can get started. Under the fold are entries so far, as well as buttons and the bookmarklet. The instructions for submitting are here.

You can buy the last four annual collections here. You can read Prefaces and Introductions to older editions here.

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What’s Your STEM? and What do science bloggers blog about? My study of the Wikio Top 100

Why was a bear following an anteater through Peru’s mountains?

Goat breath causes aphids to drop to the ground

Does it matter to your P.I. what you did this weekend?

Kangaroo testicle? Chefs in Serbia say, ‘Yes!’ (Related: Offal is Good)

Obama Signs Sweeping Student Loan Reform Bill Into Law

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Still far from home, but you can read these in the meantime:
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While I am gone, you can read these:
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Here, while I’m gone to a wedding, a few links for you:
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Call for submissions for Grand Rounds, medical blog carnival

The next edition (Vol. 6 No. 49) of Grand Rounds, the medical blog carnival, will be hosted by me, right here at A Blog Around the Clock. I have hosted it a couple of times early on, but have not done so in a few years. Time to get back to it!

So send me all your posts that have something to do with medicine: fun and quirky stuff, personal stuff, biomedical science, healthcare policy, nursing, patients and cases and medical practice and Medicine2.0 and everything you can think of that is related to medicine and health.

The deadline for submission is August 30th by midnight Eastern time. The carnival will be posted some time in the morning of August 31st.

Send you entries to: nick AT blogborygmi DOT com (though it would be nice if you could also CC it to me at Coturnix AT gmail DOT com if you can remember).

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Wealth of great stuff today!

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BIO101 – Physiology: Coordinated Response

This is the third of three parts of the lecture on physiology and the end of the course. Please fact-check, make it better.

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Lots of good reading today:

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Just a few….but good ones!

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Terra Sigillata has moved!

My friend David Kroll, better known online as Abel PharmBoy, has found a new home for his blog Terra Sigillata after leaving scienceblogs.com a few weeks ago.

He joined the excellent CENtral Science network, hosted by American Chemical Society.

Change your bookmarks, subscriptions and feeds to the new URL of Terra Sigillata and go say Hello in the comments of the Welcome post.

BIO101 – Physiology: Regulation and Control

This is the second of three parts of a lecture on this topic. Please fact-check, make it better.

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Off the grid yesterday, but managed to collect a few good links:

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BIO101 – Introduction to Anatomy and Physiology

This is the first of three parts of a lecture on this topic. Please fact-check, make it better.

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Open Laboratory 2010 – submissions so far

Note: if you have recently moved your blog, please e-mail me the corrected URLs for your entries

The list is growing fast – check the submissions to date and get inspired to submit something of your own – an essay, a poem, a cartoon or original art.

The Submission form is here so you can get started. Under the fold are entries so far, as well as buttons and the bookmarklet. The instructions for submitting are here.

You can buy the last four annual collections here. You can read Prefaces and Introductions to older editions here.

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Briefly:

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Just a few….

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BIO101 – Current Biological Diversity

In this lecture, as well as in the previous two, I tackle areas of Biology where I am really weak: origin of life, diversity of life, and taxonomy/systematics. The course is (somewhat intentionally) anthropo- and mammalo-centric, for adult non-science majors, but they do have to give talks about the biology of a plant and an animal later in the course. These are also areas where there has been a lot of change recently (often not yet incorporated into textbooks), and I am unlikely to be up-to-date, so please help me bring these lectures up to standards….

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Do Big Cats like catnip? (video)

BIO101 – Evolution of Biological Diversity

In this lecture, as well as in the previous one and the next one, I tackle areas of Biology where I am really weak: origin of life, diversity of life, and taxonomy/systematics. These are also areas where there has been a lot of change recently (often not yet incorporated into textbooks), and I am unlikely to be up-to-date, so please help me bring these lectures up to standards….

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A Data-driven Look at the Real-time Web Ecosystem (video)

Hillary Mason @hmason

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A few miscellaneous links for the weekend:

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BIO101 – Origin of Biological Diversity

Today, and in the following two lectures, I tackle areas of Biology where I am really weak: origin of life, diversity of life, and taxonomy/systematics. These are also areas where there has been a lot of change recently (often not yet incorporated into textbooks), and I am unlikely to be up-to-date, so please help me bring these lectures up to standards….

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Drumroll, please! Introducing: Scienceblogging.org

What? Yet another science blogging network? No, no, no! This is even better. Let me explain.

For four years, Scienceblogs.com was the biggest, most popular, most visible and most high-trafficked science blogging network in the world. A couple of other networks existed, known mostly to the connoisseurs. And thousands of independent bloggers, with a couple of early-adopter exceptions, were almost invisible except for the most devout readers.

For many people, The Last 24 Hours page at Scienceblogs.com was their browser’s homepage. They would start their day by checking the page out, to see what is new in the world of science. That page was a one-stop-shopping page for all things science-bloggy.

But over the last month or two, the world of science blogging changed. Scienceblogs.com is there, big and good, but not as dominant as it once was. Other existing networks suddenly became more interesting and more visible. They started growing. New networks got started and are still being built at an alarming rate of approximately one per week. This is a good thing – many more blogs are now enjoying increased visibility, traffic and influence.

But there is a problem for the reader – how to track all those networks and all those blogs? They are scattered all over the place. It takes time to go through all the bookmarks and feeds in order to catch everything.

So, Anton Zuiker, Dave Munger and myself decided to do something about it – make a one-stop-shopping place for all things science-bloggy.

The result is Scienceblogging.org (also automatically redirected from Scienceblogging.com). Anton was a smart guy and bought that URL years ago!

Now we hope that you will set Scienceblogging.org as your homepage in your browser and start your day there, checking out what’s new in the world of science.

You should also subscribe to the official Twitter account.

So, what is it all about?

The page will aggregate RSS feeds from all the major (and some minor) science blogging networks, group blogs, aggregators and services. As the site develops further, it will also encompass other online (and offline) science communication efforts, including Twitter feeds, links to major scientific journals and magazines, ScienceOnline annual conference, and the Open Laboratory annual anthology of the best writing on science, nature and medical blogs.

If you look around, you will see feeds for all the networks, several major group blogs, press services (like Futurity), aggregators (like ResearchBlogging.org), blog carnivals, etc.

If you are the owner/manager of one of these (or other) sites, and there is something you want to change, let us know – we want the community input as to how to improve the site.

Perhaps you have multiple blogs on your site/network but no common feed. We may have included only a feed for one of your blogs instead of all, or used FriendFeed as a temporary solution. You can fix that – make a common feed and send us the URL so we can switch it.

You may like the way a pretty logo appears next to the names of various networks, but do not like the ugly red Y of Yahoo next to yours. You can fix that as well – switch from Yahoo pipes to a better feed (RSS or Atom) and your logo will show up as well.

Is your network missing? Let us know. Are you building a new network? As soon as it goes live, let us know and send us your feed.

If you have (or intend to post) images on Flickr with science themes, please tag them with #scienceblogging and they will also appear on the site.

We need your help – we want to include independent bloggers as well. But how do we go about it? There are thousands of them! We cannot include all of those feeds. If we fuse them all into a single feed, that would be a firehose moving at the speed of light. There must be a better system!

Of course, indy bloggers will occasionally show up there – when they host carnivals, do guest-posts on networks, or have their posts aggregated on ResearchBlogging.org, but there must be other ways as well – let us know your ideas.

We also intend to include some Twitter feeds. For example, just before, during and after major conferences, like Science Online London, or ScienceOnline2011, we will put widgets on the sidebar showcasing tweets with the associated hashtags. But what other feeds? Twitter Lists are limited to 500 accounts – which 3-5 Lists combined cover pretty much all the important science twitterers? Let us know.

Likewise for FriendFeed rooms. Any other services we should include (YouTube, perhaps)?

What is missing from the Blogroll on the sidebar of the blog?

We are also putting together a common feed for all the sciencey blog carnivals and will try to keep the feed up to date. Are any carnivals missing from this list? If so, do they have RSS feeds? If not, can you make one?

Finally, check out the blog. For now, we have posts there like Welcome to Scienceblogging, Some thoughts about science blog aggregation, Blog Carnivals: what, how and why? and Just one way. We will use the blog to update you on the news about the site, as well as the news about the science blogging community and its endeavors, including meetings like ScienceOnline and the annual anthology – Open Laboratory. I will do a Q&A with founders, owners and managers of all the networks and other sites we cover so you can learn more about each one of them. We will try to highlight some of the independent bloggers who are not on any networks. And we will likely have some guest bloggers in the future. We appreciate all the other ideas you may have. And we welcome all kinds of feedback: criticisms, suggestions, praise.

Subscribe to the blog feed to keep up.

I hope you help us spread the word about Scienceblogging.org, link to it from your sites, save it as your browser’s homepage, bookmark it and visit it often. And help us make it better over time.

Update:

The reaction was overwhelming and overwhelmingly positive. Hundreds of tweets, several blog posts, several new suggestions/applications fo =r getting added to the site. etc. Thank you all so much!

See also posts by Dave Munger on ResearchBlogging.org and his own blog, and the comments there.

Also see blog posts by DrugMonkey, John Dupuis, PZ Myers, Jason G. Goldman, Zen Faulkes, Jeremy Yoder, Odyssey, Sandeep Gautam, Christina Pikas, Larry Moran (being his grouchy self and not having read our introductory posts, including this one, that specifically address his concern in advance of the launch of the site, eh…, Benjamin Brooks and UC San Diego’s Jacobs School of Engineering, and the comments on them – there is a bunch of interesting ideas for future improvement and development in several of those posts.

As our posts on Scienceblogging.org blog, including the latest – Adding more blogs to Scienceblogging.org – suggest, we are just getting started and are asking the community for helping out with ideas, and technical know-how for future development, especially considering the need to include independent bloggers without overhwelming the system with thousands of feeds (or a feed containing a thousand blogs).

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Just a few, to keep you busy for a little while…

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Carnal Carnival #1 – Essentials of Elimination

It is a good thing that transmission of smells over the Web has not been worked out yet, as this carnival would unlikely be smelling of roses… This month’s topic of the Carnal Carnival is, as you may already have heard, poop. Yes, excretion, defecation, elimination and the resulting products. All things colonic.

The response by the blogosphere was amazing so the carnival is quite big. So fix yourself some coffee (and you may learn how and if that will affect your stool once you read some of these posts), relax (that is also important for the process) and enjoy (yes, it is supposed to be pleasure)!

DeLene Beeland, of Wild Muse, knows how informative animal poop is to ecologists when they play nature detectives: Divining the secrets of scat.

While DeLene focuses on exctracting DNA from poop, Michelle, of C6-H12-O6, takes a look at another important piece of information that both field and lab biologists can get from the dark stuff that wildlife leaves around: On detecting stress endocrines in hamster poop.

And sometimes, the poop animals leave around is not just tiny little droppings…. Just ask Alistair Dove, of Deep Type Flow – he took this picture: If you have to go, go big!

Coprolites! The fossilized poop hard as a rock (fortunately, after deposition). David Bressan, of History of geology, gives us a history of the scientific study of coprolites: Geology history in caricatures: A Coprolitic Vision.

Joseph Calamia, of Discoblog, then provides an example of the kind of knowledge one can gain by studying coprilites: Look at the Size of That Chinchilla Poop–to Know How Much It Rained

And if that is not enough, can you imagine how much one can learn by combining the study of coprolites and coprophagy?! Brian Switek, of Laelaps, describes one case just like that: Unique Fossils Record the Dining Habits of Ancient Sharks

Brian Switek is not done yet. An obsession, if you may. Another cool coprolite story: Fossil feces from an Indiana sinkhole preserve traces of a meat-eater’s meal

And Chris Nedin, of Ediacaran, discovers The World’s Oldest Poo.


[Giraffe droppings. Image from here]

Carla Davidson, of Mommiologist, asks: What’s in a baby poop? And then she answers her own question.

But what is in whose poop may differ with geography and diet. Mike the Mad Biologist explains why: Some Thoughts About the Statistics of the Human Microbiome

Some ingenuity, some clever bioengineering, and you can get your poop all colorful! Peggy Kolm, of Everyday Biology, explains how and why: E. chromi and The Scatalog

And sometimes, your poop needs to find a way back into you – The Lorax, of Angry By Choice, explains: Poop Transplants, Is Your Microbiota an Organ System.

And it is not just us – I (here at A Blog Around The Clock) remind you that Food goes through a rabbit twice. Think what that means!

It means some poo is soft and some poo is hard! Scicurious, of Neurotic Physiology, dissects a study that looked at various foods and drinks and how they affect the hardness (or liquidity) of one’s stool but got something very important wrong in their methodology: So, how would you say your poop FEELS today?

One can learn quite a lot about an animal, including about the physiology of its digestive system, by analyzing its poop. Zen Faulkes, of NeuroDojo, provides an excellent example: Nothing but the finest…feces.

Why do certain species of caterpillar fling their poop far and wide? I know you always wanted to know the answer to that question. The wait is over – Meera Lee Sethi, of Inkling Magazine, tells it all: Projectile Poop: Why Some Caterpillars Go Ballistic.

The Science Pundit starts out slowly, but builds up tension in a powerful crescendo of ever-increasing levels of disgust: More poop Mommy; I’m hungry!


[Koprolithen. Image from here]

Many people read books while sitting on the toilet. But some do the opposite! Christina Pikas, of Christina’s LIS Rant, collects librarians’ tall tales about their customers and what they do: Craptacular: stories of poop in the library!

And as books and toilets appear to have a deep historical connection, it is not surprising that there are also books about poop. And some bloggers decided to review them. Alice Bell reviews a few of them in Poo Books.

Todd Simmons, at Matter Daily, reviews Holy Shit: A Book Review.

Finally, John F. Ptak, of Ptak Science Books looks at Horse Poop and the Stars: Robert Hooke, 1673 (No, it Wasn’t Pegasus).

Whale poop made quite a splash a few months back, so it got covered by several bloggers:

First was Jason Goldman, of The Thoughtful Animal: Whale Poop

Next, Hilary Maybaum, at Wet: Save the Whale Poop

Finally, Smriti Rao, at Discoblog: A Novel Geoengineering Idea: Increase the Ocean’s Quotient of Whale Poop


[Tiger droppings. Image from here]

One animal’s poop may be food, or home, for another organism, for example a carnivorous plant. Grant Jacob, of Code of Life, describes one such case: Aww, crap.

Here at A Blog Around The Clock, I explain another case – how a fungus uses animal droppings as home, and the difficulties it has in leaving it: Postscript to Pittendrigh’s Pet Project – Phototaxis, Photoperiodism and Precise Projectile Parabolas of Pilobolus on Pasture Poop

And sometimes it is poop of one animal feeding another, as Hannah Waters, of Culturing Science, discovered: Marine Snow: dead organisms and poop as manna in the ocean.

Sanitation is a big problem in many parts of the world. Diseases are often spread via feces deposited in open pits. Liz Borkowski, of The Pump Handle, describes an effective strategy to help: In Praise of Toilets.

The comment thread on this old post by Brian Sack at Banterist is hilarious, but also very informative: China Dispatch: Using the Squat Toilet.

Human poo is not the only potential source of disease. Birds can also play their part, including at the beaches. S. E. Gould, of Lab Rat, thus decided to take a look at the Seagull Poo.

There is something fascinating about penguins and their poop. SamW, at From C to Carnivore had to spread the fascination to two posts: Tracking penguins in (& from) space and Tracking penguins in time.

The same story was also covered by TreeHugger: Ain’t Technology Amazing? Scientists Can Track Penguin Poop From Space!

And an old post by Shelley Batts, of Retrospectacle, explains the IgNobel Prize-winning research: Science Vault: Projectile Penguin Poop Pressures

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I also could not resist collecting some of the older posts I remember from some years ago…they were that memorable!

Revere, of Effect Measure: The future is always a crap shoot

Darren Neish, of Tetrapod Zoology: Getting the phrase ‘shit happens’ into the title of a technical publication

Miriam Goldstein, currently of Deep Sea News, formerly of the Oyster’s Garter: How poop is slowing climate change

Dahlia Rideout, at Divine Caroline: What Happens When You Go Number 2 in Space? (video)

Let’s finish on a musical note. Kevin Zelnio of Deep Sea News wrote and recorded a song: Everything Poops:

That’s it for this month. I hope you have enjoyed this and learned something and got inspired! Next edition of the Carnal Carnival will be in September 2010, hosted by Carin Bondar – Biologist With a Twist – the theme will be barf. Follow the carnival on Twitter for updates.

Food goes through a rabbit twice. Think what that means!

ResearchBlogging.orgRabbits are funny animals!

For one thing, rabbits eat grass. Usually animals that eat grass are large and have complex multi-chamber stomachs (think of cows) and very long intestines (sheep), or a very large cecum (horses). Cellulose is difficult to digest, and herbivores use some help from intestinal bacteria. The bacteria are slow, though, so the food usually remains in these large fermentation chambers for a long time.

But rabbits are small. They have a single small stomach, and as much intestines as they can pack into their small bodies, and as large a cecum as they can get. But that is not enough – the food, half digested, passes through them too fast. What a waste of energy!

So they have to do something that you and I may find distasteful, but rabbits apparently enjoy – coprophagy! Yes, they eat their own feces.

But there is a trick to it. Food goes through the rabbit twice. Not once, not three or four times, just twice. How do the rabbits accomplish that?

The droppings that passed through the rabbit only once – caecotrophs – are small and soft and clumped up like grapes. They are apparently yummy to rabbits and get eaten. Droppings that made the passage through the rabbit twice are larger, separate from each other, and dry.

Interestingly, they mostly defecate dry droppings in the morning, and soft droppings in the evening.

And the timing of excretion of these two types of feces is under the control of the circadian clock – the rhythm (and the separation between timing of soft and dry pellets) persists in constant darkness, can be entrained by light-dark cycles, and can be entrained by feeding cycles (Refs, 1, 4, 5, 6).

It is interesting to me that much of this research was done a long time ago – in the 1940s for the feces composition and the 1970s for the circadian rhythms (including comparative studies in other animals, e.g., rodents that have a similar system, Refs. 2-3). I guess it would be hard to get funding for this kind of research in today’s climate. Though, understanding that the food passes through the rabbits twice, and the temporal dynamics of the process, is important for studies like this one – monitoring the spread of radioactivity from a spill site by monitoring the radioactivity in rabbit pellets in the countryside.

References:

1. Bellier R, Gidenne T, Vernay M, & Colin M (1995). In vivo study of circadian variations of the cecal fermentation pattern in postweaned and adult rabbits. Journal of animal science, 73 (1), 128-35 PMID: 7601725

2. Kenagy, G., & Hoyt, D. (1979). Reingestion of feces in rodents and its daily rhythmicity Oecologia, 44 (3), 403-409 DOI: 10.1007/BF00545245

3. Kenagy GJ, Veloso C, & Bozinovic F (1999). Daily rhythms of food intake and feces reingestion in the degu, an herbivorous Chilean rodent: optimizing digestion through coprophagy. Physiological and biochemical zoology : PBZ, 72 (1), 78-86 PMID: 9882606

4. Hörnicke H, Ruoff G, Vogt B, Clauss W, & Ehrlein HJ (1984). Phase relationship of the circadian rhythms of feed intake, caecal motility and production of soft and hard faeces in domestic rabbits. Laboratory animals, 18 (2), 169-72 PMID: 6748594

5. Pairet M, Bouyssou T, & Ruckebusch Y (1986). Colonic formation of soft feces in rabbits: a role for endogenous prostaglandins. The American journal of physiology, 250 (3 Pt 1) PMID: 3456721

6. Hörnicke, H., Batsch, F., & Hornicke, H. (1977). Coecotrophy in Rabbits: A Circadian Function Journal of Mammalogy, 58 (2) DOI: 10.2307/1379586

Rebooting The News, on science blogging and media

Rebooting The News, the cannot-miss weekly podcast about the current state and the future of media, hosted by Dave Winer and Jay Rosen, will have special guests this coming Monday at 10am EDT – Arikia Millikan and myself. The topic will be the current state of science blogging and science journalism. I hope you tune in on Monday at 10, and if you miss it, the podcasts are recorded and will be available shortly after at the homepage.

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Another incredibly busy day…..though Carnal Carnival is on schedule for late tonight, a couple of hours after the midnight deadline….

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How Do Underwater Oil Plumes Form? (video)

UCLA’s Peter Narins’ lecture on frog communication (video)

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…eh, another busy day:

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BIO101 – Organisms In Time and Space: Ecology

As you may know, I have been teaching BIO101 (and also the BIO102 Lab) to non-traditional students in an adult education program for about twelve years now. Every now and then I muse about it publicly on the blog (see this, this, this, this, this, this and this for a few short posts about various aspects of it – from the use of videos, to the use of a classroom blog, to the importance of Open Access so students can read primary literature). The quality of students in this program has steadily risen over the years, but I am still highly constrained with time: I have eight 4-hour meetings with the students over eight weeks. In this period I have to teach them all of biology they need for their non-science majors, plus leave enough time for each student to give a presentation (on the science of their favourite plant and animal) and for two exams. Thus I have to strip the lectures to the bare bones, and hope that those bare bones are what non-science majors really need to know: concepts rather than factoids, relationship with the rest of their lives rather than relationship with the other sciences. Thus I follow my lectures with videos and classroom discussions, and their homework consists of finding cool biology videos or articles and posting the links on the classroom blog for all to see. A couple of times I used malaria as a thread that connected all the topics – from cell biology to ecology to physiology to evolution. I think that worked well but it is hard to do. They also write a final paper on some aspect of physiology.

Another new development is that the administration has realized that most of the faculty have been with the school for many years. We are experienced, and apparently we know what we are doing. Thus they recently gave us much more freedom to design our own syllabus instead of following a pre-defined one, as long as the ultimate goals of the class remain the same. I am not exactly sure when am I teaching the BIO101 lectures again (late Fall, Spring?) but I want to start rethinking my class early. I am also worried that, since I am not actively doing research in the lab and thus not following the literature as closely, that some of the things I teach are now out-dated. Not that anyone can possibly keep up with all the advances in all the areas of Biology which is so huge, but at least big updates that affect teaching of introductory courses are stuff I need to know.

I need to catch up and upgrade my lecture notes. And what better way than crowdsource! So, over the new few weeks, I will re-post my old lecture notes (note that they are just intros – discussions and videos etc. follow them in the classroom) and will ask you to fact-check me. If I got something wrong or something is out of date, let me know (but don’t push just your own preferred hypothesis if a question is not yet settled – give me the entire controversy explanation instead). If something is glaringly missing, let me know. If something can be said in a nicer language – edit my sentences. If you are aware of cool images, articles, blog-posts, videos, podcasts, visualizations, animations, games, etc. that can be used to explain these basic concepts, let me know. And at the end, once we do this with all the lectures, let’s discuss the overall syllabus – is there a better way to organize all this material for such a fast-paced class.

Today, we try to cover the vast field of ecology in just an hour, thus just a very basic survey of key terms and principles. Again, I do a lot of drawing on the whiteboard in this lecture, but have not reproduce any of that here.

See the previous lectures:

BIO101 – Biology and the Scientific Method
BIO101 – Cell Structure
BIO101 – Protein Synthesis: Transcription and Translation
BIO101 – Cell-Cell Interactions
BIO101 – Cell Division and DNA Replication
BIO101 – From Two Cells To Many: Cell Differentiation and Embryonic Development
BIO101 – From Genes To Traits: How Genotype Affects Phenotype
BIO101 – From Genes To Species: A Primer on Evolution
BIO101 – What Creatures Do: Animal Behavior

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BIO101 – What Creatures Do: Animal Behavior

As you may know, I have been teaching BIO101 (and also the BIO102 Lab) to non-traditional students in an adult education program for about twelve years now. Every now and then I muse about it publicly on the blog (see this, this, this, this, this, this and this for a few short posts about various aspects of it – from the use of videos, to the use of a classroom blog, to the importance of Open Access so students can read primary literature). The quality of students in this program has steadily risen over the years, but I am still highly constrained with time: I have eight 4-hour meetings with the students over eight weeks. In this period I have to teach them all of biology they need for their non-science majors, plus leave enough time for each student to give a presentation (on the science of their favourite plant and animal) and for two exams. Thus I have to strip the lectures to the bare bones, and hope that those bare bones are what non-science majors really need to know: concepts rather than factoids, relationship with the rest of their lives rather than relationship with the other sciences. Thus I follow my lectures with videos and classroom discussions, and their homework consists of finding cool biology videos or articles and posting the links on the classroom blog for all to see. A couple of times I used malaria as a thread that connected all the topics – from cell biology to ecology to physiology to evolution. I think that worked well but it is hard to do. They also write a final paper on some aspect of physiology.

Another new development is that the administration has realized that most of the faculty have been with the school for many years. We are experienced, and apparently we know what we are doing. Thus they recently gave us much more freedom to design our own syllabus instead of following a pre-defined one, as long as the ultimate goals of the class remain the same. I am not exactly sure when am I teaching the BIO101 lectures again (late Fall, Spring?) but I want to start rethinking my class early. I am also worried that, since I am not actively doing research in the lab and thus not following the literature as closely, that some of the things I teach are now out-dated. Not that anyone can possibly keep up with all the advances in all the areas of Biology which is so huge, but at least big updates that affect teaching of introductory courses are stuff I need to know.

I need to catch up and upgrade my lecture notes. And what better way than crowdsource! So, over the new few weeks, I will re-post my old lecture notes (note that they are just intros – discussions and videos etc. follow them in the classroom) and will ask you to fact-check me. If I got something wrong or something is out of date, let me know (but don’t push just your own preferred hypothesis if a question is not yet settled – give me the entire controversy explanation instead). If something is glaringly missing, let me know. If something can be said in a nicer language – edit my sentences. If you are aware of cool images, articles, blog-posts, videos, podcasts, visualizations, animations, games, etc. that can be used to explain these basic concepts, let me know. And at the end, once we do this with all the lectures, let’s discuss the overall syllabus – is there a better way to organize all this material for such a fast-paced class.

Today, we discuss animal behavior. Note that I tend to do a lot of drawing on the whiteboard in this lecture, which is not seen in these notes. I also show a lot of short YouTube videos that show examples of strange animal behaviors.

See the previous lectures:

BIO101 – Biology and the Scientific Method
BIO101 – Cell Structure
BIO101 – Protein Synthesis: Transcription and Translation
BIO101 – Cell-Cell Interactions
BIO101 – Cell Division and DNA Replication
BIO101 – From Two Cells To Many: Cell Differentiation and Embryonic Development
BIO101 – From Genes To Traits: How Genotype Affects Phenotype
BIO101 – From Genes To Species: A Primer on Evolution

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Some good stuff collected last night:

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Postscript to Pittendrigh’s Pet Project – Phototaxis, Photoperiodism and Precise Projectile Parabolas of Pilobolus on Pasture Poop

ResearchBlogging.orgPostscript to Pittendrigh's Pet Project - Phototaxis, Photoperiodism and Precise Projectile Parabolas of Pilobolus on Pasture PoopThis is an edited, expanded, updated, revised and (hopefully) improved version of an old post. You can see the original here (or click on the “From The Archives” icon as usual).

Have you ever been out in the country visiting a farm? If so, you must have seen piles of manure, either stashed somewhere or just lying around the paddocks. And if that manure was a little older and starting to dry out and decompose, you likely saw some fine, white fuzz on its surface. Have you seen that? That fuzz is Pilobolus (not the dance troupe, but the fungus), one of a number of species in the genus. If you had a strong magnifying glass with you, and you trained it at the fuzz, you would have seen something like this:

Pilobolus has a portion of its life-cycle in which it has to pass through the digestive tract of a large herbivorous mammal. Since large mammals roam far and wide, this is a great way for the fungus to disperse. There is one problem, though: once excreted out with the feces, how do fungal spores get back into a large mammal again?

Unlike rabbits and some rodents, large mammals do not tend to eat their own manure. Actually, if you observe a field with a properly kept cow herd – a relatively small number of animals in a relatively large area, and rotated regularly between fields – you will notice that all the cows poop in one spot and no cow ever comes close to that spot to graze. So, what is a poor Pilobolus to do?

It gets ready, it aims, and it shoots!

Ready

Pilobolus assumes the position, builds a weapon, fills it with ammunition, aims and shoots. The position is on top of the pile of manure. The ammunition are spores, packaged tightly at the very tip of the filament. The weapon is the sporangiophore, a large swelled organ right below the tip.

The sporangiophore fills up with sap – osmotically active compounds – which builds up pressure until it is about 7 kilograms per square centimeter (100 pounds per square inch). There is also a line of weakness where the cap – the spore package – joins the sporangiophore vesicle. In the end, the pressure causes the sporangiophore to explode which sends the package of spores far, far away – if the wind is in the right direction, as far as 12 feet.

The goo from the sporangiophore goes with the spore package. It is very sticky, so wherever the spores land they tend to stay put. Ideally, that is on a blade of grass which is far enough from the manure pile to have a chance of getting eaten by a cow.

Here is a pretty picture of Pilobolus and a photomicrograph of the spore mass (crushed by the slide and slipcover):


[images from BioImages]

This is very cool (though wait for more coolness below), but also has an economic and environmental impact. Pilobolus spores themselves do not cause harm to their mammalian hosts, but some parasitic worms have evolved a neat trick – hitchiking on the Pilobolus spores right into the digestive tracts of large mammals.

While domestic cattle is regularly dewormed, the real problem is with wild ruminants, especially in places in which they do not have large areas to roam in, as in the elk in the Yellowstone Park. Here is a photograph of a Pilobolus harboring the Dyctiocaulus larvae:

Aim

So, Pilobolus shoots its spores really far away, by exerting enormous pressure on the ‘cap’. But, anyone who’s been in an artillery unit in the military will tell you that the distance is determined by angle. Soldiers manning the cannons know that an approximately 45 degree angle of the cannon will result in the greatest distance for the projectile. But a cannon projectile is a large, heavy object (also smooth and aerodynamic), so air resistance plays almost no part in this calculation – the force of gravity is the only force that the projectile needs to overcome.

A fungal spore is a microscopic object. At the small scale (pdf), physics works a little differently – gravity effects are minimal and the air resistance (drag) is the main determinant of maximal distance. Thus, 45 degrees is not neccessarily the optimal angle for achieving the greatest distance.

Frances Trail and Iffa Gaffoor, working with Steven Vogel at Duke University, made some calculations (which I have not seen and I do not think they got published, but I heard them from Dr.Vogel some years ago), looking at the shape and size of spore-caps of several species of Pilobolus (they published data on some other shooting fungi, though – you can read the paper here if you have access, sorry – not OA). The optimal angle for maximal distance ranges, in different species, between 9 and 30 degrees, the most common fuzz found on cow dung requiring about 15 degrees. The maximal distance, without wind, is about 6-7 feet. Quite right. Six feet is about as close as cows will come to a cowpie in well managed cattle establishments.

But does Pilobolus really shoot at 15 degrees? Well, what it does is it shoots towards the Sun. The way Pilobolus aims is through positive phototaxis. Like a sunflower, it follows the Sun in the sky and shoots at the Sun in the morning.

If you place Pilobolus in a box with light coming in only through a pinhole, all the fungi will shoot their spores at the pinhole:

How does Pilobolus see the light? Beneath the sporangium is a lens-like subsporangial vesicle, with a light-sensitive `retina’. It controls the growth and shape of the sporangiophore quite precisely. Thus, the packet of spores is always aimed at a light source:

So, the Pilobolus spores are found 6-12 feet away from the manure and they reproduce quite nicely even in the best managed cattle herds. So, they are probably shot at their optimal 15-degree angle. But they shoot at the Sun. Ergo, they shoot at the Sun when the Sun is about 15 degrees above the horizon.

One can think of two possible ways this can be achieved. One would be a mechanical sensor that triggers the explosion when the angle between the stalk and the cap is 15 degrees. This would work only if each individual was always standing upright on a flat surface, which is not the case on the rough relief of a manure pile.

The other strategy is to time the release so it coincides with the time when the Sun is about 15 degrees above the horizon. But, the trajectory of the Sun differs at different times of year.
In the middle of the summer in a high latitude, when the daylength is, let’s say, 18 hours, the Sun shoots straight up from the East and reaches the zenith right above exactly at noon. Thus, the Sun is around 15 degrees above the horizon about 90 minutes after dawn.

In winter, when the day may be only 6 hours long, the Sun traverses the sky low above the horizon from East to South to West, and may reach 15 degrees much slower (some Earth scientist in the audience can make a quick calculation here), e.g., 2 or even 3 hours after dawn.

How does the Pilobolus adjust to seasonal differences in Sun’s trajectory? By using its circadian clock, which entrains to different photoperiods with a systematically different phase:

Actually, the Pilobolus was the first fungus in which a clock was discovered. The effects of daylength on timing of spore-release was discovered back in 1948. The endogenous rhythmicity – meaning that the spores get shot every day even if there is no light present (in continous darkness) – was discovered in 1951. The major breakthrough was provided by (pdf) Esther-Ruth Uebelmesser in her dissertation:

At the same time that Schmidle published his findings, Esther-Ruth Uebelmesser (1954) dedicated her thesis work to the same subject. Her thesis is remarkable in many ways. Many of her experiments anticipated circadian protocols, frequently used in later years (different T-cycles and photoperiods, reciprocity, night interruption experiments, entrainment by temperature cycles, etc.). Although she did not fully exploit the richness of her experimental approaches in her interpretations, she must be considered a pioneer of the field and has certainly inspired Colin Pittendrigh to use Pilobolus as a circadian model system (Bruce et al., 1960). Probably, Pittendrigh abandoned this model system because of the unbearable smell penetrating the laboratory when the bovine dung media was prepared (Michael Menaker and Gene Block, personal communication, December 2000).

—————————snip—————————-

While in Neurospora accumulation of conidia (conidial bands) appears to be driven in these protocols with a constant phase angle in reference to lights-off (Fig. 2A), the phase angle of the spore-shooting rhythm in Pilobolus was systematically different with changing cycle lengths (Fig. 2B), possibly reflecting circadian entrainment. Closer investigation, however, revealed that the Pilobolus sporulation rhythm is also driven by the LD cycle, but unlike in Neurospora, by lights-on. Sporulation in Pilobolus is triggered by light, and the spores mature for approximately 28 h before they are shot (see arrows in Fig. 2B and C). The maturation time represents a kind of memory capacity for prior events. This is seen in experiments in which the fungi were released to DD (e.g., from LD 4:4 shown in Fig. 2C). The rhythm, synchronized to a given light cycle, persists for another 28 h until the endogenous circadian control takes over. Thus, depending on conditions, the production of asexual spores in Pilobolus is controlled both by the clock (phase angle) and by light (a driven spore release once per LD cycle).

[images from Roenneberg and Merrow 2001]

What this all means is that a circadian clock in this fungus is entrained by the dawn (not dusk) and it integrates photoperiodic information in a manner that is consistent with the need to shoot spores towards the Sun at the time of the morning when the Sun first reaches 15 degrees (actually, the tracking movement of the spore lags the Sun by about 20 minutes – fungi are slow to move – but even that is probably compensated for by the circadian clock).

Moreover, Pittendrigh’s students discovered that the Pilobolus clock is extremely sensitive to light (both intensity and duration of light). Its clock requires only a millisecond of light to be completely reset.

Shoot

In a more recent paper, the explosive ejection of the spores was filmed with an ultra-high-speed video camera and in their subsequent calculations derived from the images, the “launch speeds ranged from 2 to 25 m s−1 and corresponding accelerations of 20,000 to 180,000 g propelled spores over distances of up to 2.5 meters.” You can see the video (turn on the volume – it is set to music) here:

What next?

This is where the story ends, for the time being. But there are still gaps.

For instance, I am not sure if it was ever tested in the laboratory that Pilobolus actually shoots at 15 degrees. This is, according to Dr.Vogel, relatively easy to do, by placing the fungi on a manure-based medium at the center of one of those transparent semi-spheres used by exhibitors at various product fairs (e.g., technology fairs). The ejected spores stick to the inside of the transparent plastic and can be seen from the outside. Measuring the length of the arc from the desk to the spore (and knowing the radius) is all one needs to calculate the angle.

Second, we still do not know for sure if the Pilobolus cues in to the season-specific photoperiod (more likely) or the season-specific Sun trajectory (less likely). One can, in the laboratory, dissociate these two factors by exposing groups of fungi to summer-specific photoperiod and winter-specific trajectory (using a strong flashlight attached to a string and mounted on an arc-shaped wire, attached to a little motor) or vice-versa, as well as season-specific photoperiod with diffuse (instead of focused) light source.

Finally, an evolutionary question. Horses are not as picky as cows concerning the distance from the manure at which they will graze. Pilobolus lives in our horses and shows up in the manure all the time. Is there relaxed selection for the populations (species?) that live in horses? Is their timing off? Is their angle-determination lousy? This would be an easy head-to-head test in the lab (and field) as well. And if there is such a difference between species, looking at molecules – dynamics of gene expression patterns and protein-protein interactions – can perhaps teach us something more about the ways simple parts can accomplish complex tasks in these organisms.

But, if you’d rather learn all of the above in a Dr.Seuss-like poem, go ahead, it’s right here.

References:

Bruce, V., Weight, F., & Pittendrigh, C. (1960). Resetting the Sporulation Rhythm in Pilobolus with Short Light Flashes of High Intensity Science, 131 (3402), 728-730 DOI: 10.1126/science.131.3402.728

TRAIL, F., GAFFOOR, I., & VOGEL, S. (2005). Ejection mechanics and trajectory of the ascospores of Gibberella zeae (anamorph Fuarium graminearum) Fungal Genetics and Biology, 42 (6), 528-533 DOI: 10.1016/j.fgb.2005.03.008

Fischer, M., Stolze-Rybczynski, J., Cui, Y., & Money, N. (2010). How far and how fast can mushroom spores fly? Physical limits on ballistospore size and discharge distance in the Basidiomycota Fungal Biology, 114 (8), 669-675 DOI: 10.1016/j.funbio.2010.06.002

Roenneberg, T., & Merrow, M. (2001). Seasonality and Photoperiodism in Fungi Journal of Biological Rhythms, 16 (4), 403-414 DOI: 10.1177/074873001129001999

Uebelmesser E-R (1954) Über den endogenen Tagesrhythmus der Sporangienbildung von Pilobolus. Arch Mikrobiol 20:1-33.

Yafetto, L., Carroll, L., Cui, Y., Davis, D., Fischer, M., Henterly, A., Kessler, J., Kilroy, H., Shidler, J., Stolze-Rybczynski, J., Sugawara, Z., & Money, N. (2008). The Fastest Flights in Nature: High-Speed Spore Discharge Mechanisms among Fungi PLoS ONE, 3 (9) DOI: 10.1371/journal.pone.0003237

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Ooops, forgot my blogiversary!

I posted my first post on my first blog on August 14th, 2004. In a previous life….

BIO101 – From Genes To Species: A Primer on Evolution

As you may know, I have been teaching BIO101 (and also the BIO102 Lab) to non-traditional students in an adult education program for about twelve years now. Every now and then I muse about it publicly on the blog (see this, this, this, this, this, this and this for a few short posts about various aspects of it – from the use of videos, to the use of a classroom blog, to the importance of Open Access so students can read primary literature). The quality of students in this program has steadily risen over the years, but I am still highly constrained with time: I have eight 4-hour meetings with the students over eight weeks. In this period I have to teach them all of biology they need for their non-science majors, plus leave enough time for each student to give a presentation (on the science of their favourite plant and animal) and for two exams. Thus I have to strip the lectures to the bare bones, and hope that those bare bones are what non-science majors really need to know: concepts rather than factoids, relationship with the rest of their lives rather than relationship with the other sciences. Thus I follow my lectures with videos and classroom discussions, and their homework consists of finding cool biology videos or articles and posting the links on the classroom blog for all to see. A couple of times I used malaria as a thread that connected all the topics – from cell biology to ecology to physiology to evolution. I think that worked well but it is hard to do. They also write a final paper on some aspect of physiology.

Another new development is that the administration has realized that most of the faculty have been with the school for many years. We are experienced, and apparently we know what we are doing. Thus they recently gave us much more freedom to design our own syllabus instead of following a pre-defined one, as long as the ultimate goals of the class remain the same. I am not exactly sure when am I teaching the BIO101 lectures again (late Fall, Spring?) but I want to start rethinking my class early. I am also worried that, since I am not actively doing research in the lab and thus not following the literature as closely, that some of the things I teach are now out-dated. Not that anyone can possibly keep up with all the advances in all the areas of Biology which is so huge, but at least big updates that affect teaching of introductory courses are stuff I need to know.

I need to catch up and upgrade my lecture notes. And what better way than crowdsource! So, over the new few weeks, I will re-post my old lecture notes (note that they are just intros – discussions and videos etc. follow them in the classroom) and will ask you to fact-check me. If I got something wrong or something is out of date, let me know (but don’t push just your own preferred hypothesis if a question is not yet settled – give me the entire controversy explanation instead). If something is glaringly missing, let me know. If something can be said in a nicer language – edit my sentences. If you are aware of cool images, articles, blog-posts, videos, podcasts, visualizations, animations, games, etc. that can be used to explain these basic concepts, let me know. And at the end, once we do this with all the lectures, let’s discuss the overall syllabus – is there a better way to organize all this material for such a fast-paced class.

Today, we introduce the concept of evolution, mainly via natural selection (sexual selection will come later in the course, and neutral selection etc. are too much for this level). Note that I tend to do a lot of drawing on the whiteboard in this lecture, which is not seen in these notes.

See the previous lectures:

BIO101 – Biology and the Scientific Method
BIO101 – Cell Structure
BIO101 – Protein Synthesis: Transcription and Translation
BIO101 – Cell-Cell Interactions
BIO101 – Cell Division and DNA Replication
BIO101 – From Two Cells To Many: Cell Differentiation and Embryonic Development
BIO101 – From Genes To Traits: How Genotype Affects Phenotype

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Reminder – Carnal Carnival entries due this Thursday at midnight

All the information you need is here.

Send entries to me at carnivalcarnal AT gmail DOT com (or, this month only, to Coturnix AT gmail DOT com) by Thursday, August 19th at midnight EST.

Open Laboratory 2010 – submissions so far

Note: if you have recently moved your blog, please e-mail me the corrected URLs for your entries

The list is growing fast – check the submissions to date and get inspired to submit something of your own – an essay, a poem, a cartoon or original art.

The Submission form is here so you can get started. Under the fold are entries so far, as well as buttons and the bookmarklet. The instructions for submitting are here.

You can buy the last four annual collections here. You can read Prefaces and Introductions to older editions here.

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Why republish an old blog post?

Republishing an old post is usually a way to feed the blog at the time when the blogger has no time to produce fresh content, e.g., during travels and vacations. Sometimes, it is a way to bring entire series of posts in front of new readers (I have done this with my BIO101 posts and Clock Tutorial posts, and more).

Sometimes, this is a way to bring up an old post that provides background context for a brand new post that comes right afterward. This way, readers are served two related posts in succession, instead of being asked to follow a link to get background, which is a more effective way to ensure that the readers of the new post actually read the old, background post.

But I rarely see re-posting done for another reason: editing, updating and improving old posts. Often I read an old post of mine and dislike the way I wrote it. I guess, like most chronic writers, I feel like my writing is improving over time. But I am too lazy to actually do something about it – I let the old posts linger in the archives the way they were originally written.

This week, I will try to do something more with two old posts of mine. The proximate reason is the impending Carnal Carnival. But the ultimate reason is that I want to give this idea a try – see if I can edit and improve on the old posts.

So, over the next few days, expect to see edited, updated, expanded and improved versions of these two posts:

First, Friday Weird Sex Blogging – Postscript to Pittendrigh’s Pet Project – Phototaxis, Photoperiodism and Precise Projectile Parabolas of Pilobolus on Pasture Poop. This post is already long and thorough, but it can use some editing. There was also a cool paper published in the meantime so a mention and citation are warranted. There is also a cool video now available that really should be a part of that post.

Second, How to use a Squat Toilet. This is essentially a picture, one sentence and a link. But it is one of my most frequently visited posts ever, usually from image searches for “squat toilet”. And the link provides a great entry into the topic which I should delve into in some more depth. So, this one is going to be not just mildly edited, but completely written anew.

Stay tuned….

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