Category Archives: Ecology

Science Cafe Raleigh: Rain Forests – Going, Going, Gone?

Happy New Year! We are excited to be starting a new year of science cafes. Our January Science Café (description below) will be held on Tuesday 1/18 at Tir Na Nog on South Blount Street. Our speaker for the evening will be Dr. Meg Lowman, Director of the Nature Research Center (a new wing of the Museum of Natural Sciences currently under construction). Dr. Lowman is a world famous canopy researcher. To learn more about her and her work please see the information listed below (be sure to look at her website). We will have a fun and informative discussion about the amazing (and sometimes strange) diversity of life that can be found in the earth’s rainforests as well as how researchers have figured out ways to study sometimes elusive plants and animals. We will talk about the importance of what is being discovered in the rainforests and how these discoveries can affect our way of life. I hope that many of you can come.

Tuesday, January 18, 2011

6:30-8:30 p.m. with discussion beginning at 7:00 followed by Q&A
Tir Na Nog, 218 South Blount Street, Raleigh, 833-7795

Every child grows up with a sense of awe about tropical forests — extraordinary creatures including poison dart frogs, sloths, orchids and jaguars representing a veritable treasure-trove of biodiversity. But scientists estimate that more than half of Africa’s rain forests are gone, with at least 40 percent losses in Asia and Latin America and 95 percent in Madagascar. Even with new technologies, measuring tropical deforestation is not easy, and illegal logging is epidemic in many parts of the world. What is the prognosis for the future of tropical rain forests? And how will human beings fare if these vital ecosystems disappear? What essential services do tropical forests provide for the planet, and how can we conserve them for our children?

About our speaker:

Dr. Meg Lowman (www.canopymeg.com) is Director of the Nature Research Center, North Carolina Museum of Natural Sciences and a research professor at NC State University. Over the past three decades, “Canopy Meg” has earned an international reputation as a pioneer in forest canopy ecology, tropical rain forest conservation, and for designing canopy access tools including ropes, hot-air balloons, walkways and construction cranes. Equipped with degrees in biology, ecology and botany, Lowman developed her childhood interest of building tree forts into mapping canopy biodiversity worldwide and spearheading the construction of canopy walkways in tropical forests for conservation. She uses science education to influence government policy and encourage environmental stewardship. Her book, “Life in the Treetops,” earned a cover review in the New York Times Sunday Book Review.

Guest Blog at Scientific American – first guest post: Apple, meet Orange

Building the new science blogging network at Scientific American will take some time. But there are already seven blogs on the site, mostly written by Scientific American editors, writers and correspondents. One blog that is written by others – scientists and bloggers – is the Guest Blog that has been around for several years now.

Starting today, I will be in charge of the Guest Blog, and have invited a number of interesting people to contribute guest posts for it (Interested? Pitch me a story at: Bora@sciam.com).

The first contributor is Dr.Carin Bondar (Twitter) with a post about conservation – the dueling approaches to species preservation: saving one species at a time, or saving entire ecosystems and ecological communities. Carin reviews recent studies from both ‘schools’ and makes her own decision as to which approach makes more sense. Go read it here!

Look Up! The Billion-Bug Highway You Can’t See (video)

How Do Underwater Oil Plumes Form? (video)

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

Follow me under the fold:

Continue reading

At the Museum: bonobos and bioluminescence

Two great lectures at the North Carolina Museum of Natural Sciences:

1. Museum hosts presentation on ‘Bioluminescence Below the Bahamas’

RALEIGH ― Join Duke University biologist Sonke Johnsen for a detailed look into the world of marine bioluminescence and its use as an adaptation to help organisms hide, hunt and communicate. Johnsen’s multimedia presentation, “Deep Light: Bioluminescence and Vision 2,000 Feet below the Bahamas,” takes place at the North Carolina Museum of Natural Sciences on Thursday, August 12 at 7pm. Free.

Johnsen is associate professor of biology and director of The Johnsen Lab at Duke, which studies bioluminescence ― an organism’s ability to produce its own light ― and other aspects of visual ecology. He recently participated in an inaugural survey of deep-sea floor bioluminescence and continues to collaborate with Edith Widder, bioluminescence expert and a former curator of GLOW: Living Lights, the first-ever museum exhibit to explore the phenomenon of bioluminescence. Now showing at the Museum of Natural Sciences, this exhibit reveals the world of light-producing terrestrial organisms, from fireflies to foxfire fungus, before traveling to the mid-ocean, where an estimated 90 percent of animals produce light. GLOW runs through September 12.

Adult tickets to GLOW are available at a discounted rate on these evenings, with tickets sold from 5 to 6:30pm. For more information, visit www.naturalsciences.org.

=====

2. Vanessa Woods to discuss “Bonobo Handshake” at Museum of Natural Sciences

In the midst of the war-torn Congo, there exists a peaceful society in which females are in charge, war is nonexistent, and sex is as common and friendly as a handshake. Welcome to the world of bonobos, a rare ape with whom we share 98.7 percent of our DNA. On Thursday, August 19 at 6:30pm, join author and Duke University scientist Vanessa Woods for a detailed discussion of her new book, “Bonobo Handshake,” at the NC Museum of Natural Sciences in downtown Raleigh. Free.

“For thousands of years, we have wondered what makes us human,” says Woods. “To find the answer, we study our closest living relatives, chimpanzees and more recently, bonobos. Neither species is easy to study, but bonobos are particularly difficult, being the world’s most endangered ape in the world’s most dangerous country. But this makes them all the more important, and bonobos could not only unlock the secret of what makes us human, but also teach us how being a little less human could go a long way.” Woods will be signing copies of her book in the Museum Store prior to her lecture.

Woods is an internationally published author and journalist and is the main Australian/ New Zealand feature writer for the Discovery Channel. She graduated with a Masters of Science Communication from the Centre for the Public Awareness of Science at the Australian National University and has written for various publications including BBC Wildlife, New Scientist, and Travel Africa. In 2003, Woods won the Australasian Science award for journalism. In 2007, her children’s book on space was named an Acclaimed Book by the UK Royal Society and shortlisted for the Royal Society’s Junior Science Book Prize.

Deepwater Horizon oil spill interrupted bluefin tuna spawning

According to a new paper showing temporal and spatial patterns of migratory routes and spawning grounds of bluefin tuna, they were in the Gulf of Mexico spawning at the moment the oil well exploded and all that oil started gushing out (and then dispersed with toxic chemicals).
Nobody is fishing there now, and no professional media or amateur reporting or photography are allowed, but I am assuming some of the radiotransmitters in some of the individuals may still be operational and that data from the area, during the spill, will become available in the future.

Amateur Video Of Gulf Oil Slick – Worse Than BP Admits

[Source]

When the dinner bell rings for seafloor scavengers, larger animals get first dibs (video)

News from NESCentCraig MccLain of the Deep Sea News fame just had a paper published. This is the video that explains what that is all about:

Also read the press release. And the reference is:
McClain, C. and J. P. Barry (2010). “Habitat heterogeneity, biogenic disturbance, and resource availability work in concert to regulate biodiversity in deep submarine canyons.” Ecology.
Related:
Deep sea paradox: little food, tons of life
Craig McClain talk at Sigma Xi

Four things everyone needs to know about sharks (video)


A shark conservation documentary and lesson plan, made by David Shiffman of Southern Fried Science.

The Ecological and Economic Importance of Sharks, Threats They Face, and How You Can Help (CANCELLED)

From the NC Museum of Life Sciences:

Program Type: Science Talk
Date: Mar. 9, 7 pm – Mar. 9, 8 pm
Location: Museum of Natural Sciences – Auditorium
Fee: $6 General Public, $4 Members, $3 Students
The Ecological and Economic Importance of Sharks, Threats They Face, and How You Can Help
Lecture, slide show & video presentation by marine biologist David Shiffman
David Shiffman and friendShiffman graduated with distinction in Biology from Duke and is now a Masters in Marine Biology candidate at the College of Charleston in South Carolina. His research focuses on the feeding behavior and conservation of sandbar sharks. Shiffman is also a prolific writer for Southern Fried Science, one of the most widely read marine biology blogs on the internet.
Seating is limited. Reserve your seat now for this multimedia presentation by visiting or calling the Museum Box Office at 919.733.7450 x212. Fee: $6 for general public (discounts for Museum Members and Students).
The Museum’s current special exhibit, “Megalodon: Largest Shark that Ever Lived,” will be open from 5 to 7pm prior to the presentation. At 60 feet long and weighing nearly 100 tons, Carcharodon megalodon was the most powerful fish that ever lived and a dominant marine predator. While the Megalodon vanished 2 million years ago, its fascinating story continues to inspire lessons for contemporary science and shark conservation. “Megalodon” runs through May 9, 2010. Fee: $7 Adults; $5 Seniors/Students; $4 Children (5-11); free to Members.

Megalodon and other sharks at Darwin Day

Last night, braving horrible traffic on the way there, and snow on the way back, I made my way to the N.C. Museum of Natural Sciences for the Darwin Day shark lecture co-organized by NESCent and the sneak preview of the Megalodon exhibit which officially opens today.
megalodon 001.jpg
I have to say that the trip was very much worth making – the exhibit is excellent! I like the way the exhibit is making good use of the space – so many exhibits feel cluttered and an all-out assault on all of one’s senses. Upon entering the room, it looks quite sparse. Yet, once I started going around I saw how much it actually covers, how well organized the exhibit layout is, how much information (including a lot of new-to-me information) is included and presented so very clearly and tastefully, and how much it has something for everyone independent of age, background or interest. And of course – the fossils! Absolutely amazing and stunning fossils! From the magnificent Megalodon jaws, to some of the strangest teeth arrangements one has ever seen in any jaw of any animal.
megalodon 002.jpg
Then, exhausted and a little faintly from the lack of food yesterday (yes, it was a busy day), I entered the lecture hall afraid I’d fall asleep or pass out in the middle of the talk. I need not have worried – Adam Summers is an amazing speaker. I was able not just to pay attention throughout, I was excited throughout the talk. For a jaded biologist and blogger, when many public lectures tend to present stuff already well known to me, it was refreshing to keep learning new stuff every couple of minutes or so. And not just new factoids, but new questions and new ways of thinking about them – why are sharks larger than bony fish, why sharks have no bone, how do sharks swim, how do sharks and bony fish manage to swim very fast, etc. Questions I never asked myself before.
There were things in there that are outside my realm of expertise, for which I am essentially a layman: engineering principles, a formula I am unfamiliar with, a couple of graphs….yet all of that was made very clear on an intuitive level. How? Because Adam is really good at using analogies (“think of this as…”) and metaphors (snuck into the description without any warning). Be it water-filters, armor, stacks of coins, or houses made of sponges, it all becomes vivid and immediately makes sense.
It is also obvious that a lot of research went into this, yet very few actual data were shown – only the key data that are essential to make the point. This is a public lecture – there is no need to drown the audience in gazillions of graphs and discussions of statistics. The slides, including the images and brief video clips were both beautiful and essential for grasping the point he is making. And then there was quite a lot of humor, mainly of the self-deprecating kind making fun of himself and his students in the context of scientist stereotypes – how they look, talk, think and behave.
All in all – well done. Who ever said that scientists don’t know how to communicate to lay audience, eh?

Can Genetically Engineered Crops Help Feed the World?

A new forum at World Science is up. As always, listen to the podcast first, then ask questions in the forum:

This week, India rejected what would have been the country’s first a genetically modified food crop, a transgenic eggplant.
The company that developed it, an Indian subsidiary of Monsanto, claims the crop would reduce pesticide use and boost yields. But the Indian government has decided to do independent assessments of the crop’s potential impacts on consumer health and the environment.
What does this mean for the future of GM crops in India and elsewhere? And does this technology have a role to play in feeding the world’s hungry?
We put these questions to Dr. Lisa Weasel. She’s a professor of biology at Portland State University, and the author of Food Fray: Inside the controversy of genetically modified food. She writes that GM crops are more of “a condiment than a main course” in solving the world’s food shortage.
Now it’s your turn to chat with Lisa Weasel. Join the conversation — it’s just to the right.
* Human beings have been altering plants ever since the beginning of agriculture. Why is genetic engineering any different from the older, more traditional ways of tinkering with crop varieties?
* Is there any scientific evidence of harm to human health from eating GM food?
* Why are small farmers in developing countries especially concerned about GM crops?

My latest scientific paper: Extended Laying Interval of Ultimate Eggs of the Eastern Bluebird

ResearchBlogging.orgYes, years after I left the lab, I published a scientific paper. How did that happen?
Back in 2000, I published a paper on the way circadian clock controls the time of day when the eggs are laid in Japanese quail. Several years later, I wrote a blog post about that paper, trying to explain in lay terms what I did, why I did it, what I found, and how it fits into the broader context of this line of research. The paper was a physiology paper, and my blog post also focused on the physiological aspects of it.
But then, I wrote (back in March 2006 – eons ago in Web-time) an additional blog post on one of my old blogs (reposted on this one here, here and here) in which I followed further, thinking about the data in more ecological and evolutionary terms, and proposing hypotheses following from the data that can only be tested in other species out in the wild. As you can see if you click on the links, this post did not receive much commentary.
Then, about a year ago, I received an e-mail out of the blue, from a researcher at the Cornell Ornithology Lab, essentially offering to test one of the hypotheses I outlined in that post. My first reaction was “sure, go ahead, I am happy someone wants to do this, but please cite the blog post as the origin of the hypothesis”… The response was along the lines of “no, no, no – we are thinking about working WITH you on testing this hypothesis”. Wow! Sure, of course, I’m game!
They already had preliminary data which they sent to me to take a look. They are coming from an ecological tradition and are very familiar with the ecological literature, some of which they sent to me to read. On the other hand, I am coming from a physiological tradition and am very familiar with that literature, some of which I sent to them to read.
A month or so later, one of them, Caren Cooper, came down to Chapel Hill. We met and, over coffee, spent a couple of hours staring at the data and discussed what it all means. Then we got started at writing the paper.
And now, the paper is out: Caren B. Cooper, Margaret A. Voss, and Bora Zivkovic, Extended Laying Interval of Ultimate Eggs of the Eastern Bluebird, The Condor Nov 2009: Vol. 111, Issue 4, pg(s) 752-755 doi: 10.1525/cond.2009.090061
In this paper – which is really a preliminary pilot study (who knows, we may yet get a grant to do more) – Caren and Margaret set up video cameras on a bunch of nests of Eastern Bluebirds (Sialia sialis). From the tapes they got times when the eggs were laid. The times were approximate. But the analysis gave us exactly the same result when we used the times when the nest was obviously empty before the bird sat on it to lay the egg, the times when the bird first got up to reveal the egg to the camera, and the mid-point between those two times.
I am not aware of anyone ever looking at timing of egg-laying in wild birds out in the field. There is a huge literature on timing of laying in quail and chicken (and some in turkeys) in the laboratory, but none I am aware of in wild birds. Most researchers, when asked when their species lays eggs are surprised at the question and answer something along the lines of “no idea, but we find the eggs when we come to check the nests in the morning, so perhaps over night, or at dawn?” So, this paper is a first in this domain.
What we have shown is that bluebirds, just like chicken and quail, have an S-shaped pattern of egg-laying patterns (see my older post for theory and graphic visualization).
The question is: how does a bird “know” when to stop laying? When is enough enough? When is the clutch (all of the eggs laid in one breeding attempt) complete? Most of ecological literature is focused on energetics: are birds getting hungry, have they depleted some important source of energy, etc.
But the circadian field looks for internal mechanisms. Running a circadian clock takes very little energy. Even when the animals are extremely hungry, the clock keeps ticking with no changes in frequency (if anything, the amplitude gets bigger, implying even more work!). Even when an animal gets very sick and is dying, at the time when many bodily functions start ceasing, the clock works until the very end. Being produced by a molecular feedback loop in which some reactions use and others release energy, and all of this happening in just a small number of brain cells, the clock is very energy efficient and does not require the organism to be healthy and well fed.
What is important in regard to circadian regulation of egg-laying is to understand that female birds have not one, but two circadian clocks. Let’s call one of them A and the other one B. Clock A is located in the brain (or retinae or pineal or some combination, depending on the species) and is sensitive to light: it readily entrains to a light-dark cycle. No matter what the intrinsic frequency of the clock may be (as uncovered in constant darkness conditions), it is forced to a frequency of exactly 24 hours by the entraining power of the day/night cycle.
Clock B, on the other hand, is intimately tied to reproduction. It is a result of an interplay between the clock in the brain and neuro-endocrine signals between the brain and the ovary (which may itself house its own part of the clock). Brain clock sends hormonal signals to the ovary. Those signals entrain the ovarian rhythms AND result in ovulation. Ovulation itself produces hormones that signal to the brain clock and entrain it. This feedback loop is in itself The Clock. This clock is light-blind and its intrinsic frequency is not 24 hours – it is around 26-27 hours in both quail and chicken, and almost two days long in turkeys.
These two clocks, A and B, interact with each other. Let’s imagine a hypothetical scenario in which clocks A and B are very tightly coupled. The external light-dark cycles that all the birds in the wild are constantly exposed to entrain the clock A to the exactly 24 hours period. Clock B, being tightly coupled to Clock A is then also forced to oscillate with a period of exactly 24 hours. What would that mean to the bird? She would be laying one egg per day, always at exactly the same time of day, every single day of her life: in spring, summer, fall and winter. She’d spend all her resources on making big yolky eggs every day. She would be sitting on a huge pile of eggs throughout her life. She would not be able even to move short-distance to a better nesting ground, let alone prepare and undergo a long-distance migration. Her eggs would be also hatching at the rate of one per day. Thus, she would have progeny of a variety of ages at all times, each age having different requirements for care or abilities to follow the mother around. Some hatchlings would freeze to death in winter, or starve to death at time when the food is scarce. Others would die from predation at times when they are highly visible (in the snow) or just because there are so many of them they cannot all hide under a bush.
An opposite scenario: clocks A and B do not interact with each other at all. In this case, A would be entrained to the 24 hour cycle of night and day. Clock B, being light-blind, would freerun with its own endogenous frequency, i.e., with a period of roughly 26-27 hours. Again, the poor bird would be laying one egg per day all of her life. The only difference is that the eggs would not be laid always at the same time of day, but scattered all over the 24-hour cycle. Both scenarios are obviously maladaptive to the bird.
But, oscillator theory provides a third scenario in which clocks A and B are only loosely coupled. There are phase-relationships between the two clocks when they are coupled: A entrains B. There are phase-relationships when the two are at odds: A inhibits B (and thus no ovulation happens). The phase-relationships are dependent on daylength: when the days are short in winter A inhibits B and no eggs are laid. When the days are very long in the middle of the summer (or in constant light) all phases are permissive to ovulation and the clock B can freerun with its own period of 26-27 hours.
But the interesting phenomenon happens in-between, once the length of the day gets just a little bit longer in spring, in normal breeding season. There is only a narrow zone of phase-relationships in which the two clocks are coupled – outside of that zone, ovulation is inhibited. Thus the clock A starts ticking at the beginning of that zone (e.g., at dawn in some species, at around noon in quail) and starts freerunning through it until it “phase-locks” with the clock A and, for a while, appears to be running with the period of 24 hours. But underneath, the pulses of hormones are gradually shifting later and later, just a little bit each day. Finally, these hormonal influences allow the clock B to again break free from the clock A, freerun some more until it gets out of the permissive phase – the feedback loop is broken and the ovulations stops. The clutch is over.
a3%20OVI%20-%20medium%20PP.jpg
The resulting pattern is S-shaped: early in the clutch eggs are laid a little bit later each day, the middle of the clutch appears entrained to the 24-hour cycle, and the last egg or two again are laid later until the egg-laying stops completely. In quail, which was bred for centuries for egg-production, the selection affected the strength of coupling between the two clocks. Thus, in photoperiods (daylengths) that are just barely longer than the ‘critical photoperiod’ (the minimal daylength needed to provide any permissive phases at all, thus the first daylength in spring at which the bird can start laying), quail will have S-shaped patterns but the middle portion, the “straight one” that is entrained, is artificially long – I have seen clutches lasting for two months and consisting of 60 eggs!
Birds out in the wild, where natural selection is likely to produce an optimal clutch-size (not a maximal one that humans prefer), may or may not use the same mechanism to determine how and when the clutch starts and ends. So, what we did was see if Bluebirds also show the S-shaped pattern that would suggest they do. And they do:
Condor image.JPG
The first egg in the clutch is laid earlier than the subsequent eggs. All the eggs in the middle (1-6 of them, not 30 – we collapsed them all into one “time-point” in the graph) are laid at about the same time, indicating entrainment of B by A (i.e., to the light-dark cycle). The second-to-last egg may be laid a little later, and the very last egg is laid much later. These results suggest that quail is not a weird unique animal, or that Galliformes (chicken-like birds) are different from other kinds, e.g.., Passeriformes (songbirds). The mechanism is likely the same – not dependent on external factors like food and energy, but a result of a fine-honed system of interactions between two circadian clocks.
Of course, this is just a first observational study, but the results are encouraging. Next steps would be to: a) improve the temporal precision of measurements by, perhaps, installing thermo-couples in the nests (there is a huge but short-lasting body temperature spike exactly at the time of lay), b) increase the sample size, c) compare the bluebirds living in three very different latitudes where both the weather conditions and photoperiodic changes are different to see how the natural selection shaped their responses, and d) do a comparative study of a few more species belonging to other groups. We’ll see if we’ll try to submit a grant proposal in the future.
Unfortunately, this paper is not Open Access. I wanted to send it to PLoS ONE, which I think is the best journal in the world and IS the future of publishing. But it was important for Caren and Margaret to publish in a journal that their peers consider important, and Condor is a fine little journal for this. So I agreed to go along with it.
Also, the listing of the original blog post in the List Of References, to my dismay, disappeared between the Provisional PDF and Final PDF versions. It is now linked to inline in the text, placing it down to the level of the dreaded “personal communication”, once again foiling our attempts to give serious science blogging some respect. Ah well….
Interestingly, I did not know when the paper came out. Apparently, it was published back in November. I learned about it a couple of days ago when I got a first reprint request from a researcher in Russia!
But hey, I am happy. I got a paper published. And now I am using my blog and social networks to promote it… ;-)
Cooper, C., Voss, M., & Zivkovic, B. (2009). Extended Laying Interval of Ultimate Eggs of the Eastern Bluebird The Condor, 111 (4), 752-755 DOI: 10.1525/cond.2009.090061

Ecology, conservation, and restoration of oyster reefs in North Carolina

On Tuesday I went to the monthly pizza lunch at Sigma Xi, featuring a guest lecture by Dr. David B. Eggleston, Professor of Marine, Earth and Atmospheric Science at North Carolina State University and the Director of Center for Marine Sciences and Technology (CMAST).
I posted a brief summary of the talk on the Science In The Triangle blog.

Craig McClain talk at Sigma Xi

Although I’ve known Craig McClain for a few years now, both online and offline, I only had some vague ideas about what kind of research he is doing. I knew it has something to do with the Deep Sea and with the evolution of body size, but I did not know the details. So, when the opportunity arose to hear him give a talk summarizing his work, I jumped to it and went to see him on Tuesday at Sigma Xi as a part of their pizza lunch series.
Craig1.jpg
First I have to say that Craig is a great speaker (if you are looking for one for a seminar series, this is useful information for you) – it was fun and very clear. And thought-provoking. And fascinating. I am still thinking about it, what it all means, etc.
Craig2.jpg
But Delene was there as well and she took copious notes and wrote a great blog post about the talk so there is no need for me to duplicate that effort. So if you want to know more about the substance of the talk, just go and read her take either on her own blog Wild Muse or the same post on the ScienceInTheTriangle blog.
Craig3.jpg

The Astonishing Existence of Life on the Deep Sea Floor

Next Sigma Xi pizza lunch science talk:

Pizza lunch returns at noon, Tuesday, Dec. 15 with a talk by marine biologist Craig R. McClain, assistant director of science for the National Evolutionary Synthesis Center in Durham. McClain conducts deep-sea research and has participated in expeditions to the Antarctic and to remote regions of the Pacific and Atlantic. Expect him to dive into puzzling realms with his talk: An Empire Lacking Food: The Astonishing Existence of Life on the Deep Sea Floor.
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 a reliable slice count) to cclabby@amsci.org
Directions to Sigma Xi: http://www.sigmaxi.org/about/center/directions.shtml

Recent Science-Related Events in the Triangle

Last couple of weeks months were awfully busy, on many fronts, not least finalizing the ScienceOnline2010 program, herding cats almost 100 moderators/presenters to do various stuff (e.g., respond to my e-mails) in a timely manner, and making sure that registration goes smoothly. This is also the time of year when activation energy for doing anything except going to bed to hide under the covers is very high for people suffering from SAD. Thus, you did not see many ‘original’ posts here lately, I know.
But, it’s not that I have been totally idle. Apart from teaching my BIO101 lab again, I also went to several science-related events in the Triangle over the past two months. I feel like I should blog about each one of them separately, at length and with nuance, as this hangs over my neck like the Sword of Damocles – I feel I should not blog about anything else until all of these event reports are out of the way.
So, in a compromise solution, instead of a bunch of long separate posts, I will collect all the brief reports from all the events here, in a single post, get that over with and mentally free myself to blog about other stuff soon.
Lisa Sanders at UNC
Lisa Sanders is a physician and a professor of medicine, but you probably heard of her in a different context: Lisa writes the Diagnosis column in The New York Times, has recently published a book Every Patient Tells a Story, and has inspired and acts as the medical adviser to the TV show House (of which I heard, not being a TV watcher, at the beginning of her talk).
Lisa Sanders came to the Triangle last month and gave talks at Duke and UNC. Bride of Coturnix and I went to the UNC talk which filled a large auditorium. Her book is being read by all the UNC medical students who will then discuss the book in smaller groups.
The process of diagnosis has three steps: interview, physical exam and laboratory tests.
Laboratory tests have become more and more dominant as the preferred part of the diagnosis process, for a number of (cultural) reasons:
First, they are the quickest, thus save the physician time (others do the work).
Second, unlike interviews that seem subjective, or physical exams that look medieval, lab tests look like ScienceTM! – there are numbers there. And you can’t argue against numbers, can you? This works great on the background of lack of statistical sophistication (or outright innumeracy) on the part of both physicians and patients. No arguing. No second opinions. The process moves on smoothly for everyone. Except, the numbers cannot be trusted as much they usually are.
Third, a number is not an opinion, thus it is a safeguard against lawsuits. It saves physician’s asses in such cases.
Both the frenzy and the (perceived) lack of time and the fear of lawsuits would be diminished if we had a real healthcare reform (not the compromise of a compromise of a compromise bill that is brewing in the US Senate right now, but an actual reform) in which the physicians could get their authority and trust back and be able to practice their art and craft and science with some degree of freedom. In a system in which insurance companies determine how care is done, physicians are just technicians and cannot earn authority and trust.
So, with everyone jumping onto lab tests, the art of interview and the art of physical examination are slowly dying out. They are not even taught in some medical schools any more. Where they are taught, as soon as newly minted physicans are on their own they join the medical culture that frowns upon these two steps of the diagnostic process.
Yet, Dr.Sanders showed data from two studies (done in different countries by different people in different years), both providing almost exactly the same results. In about 75-80% of the cases (physician encountering a new patient for the first time), the physician comes up with a correct diagnosis after the interview. In about 10-12% of the cases, the doctor has to correct her/himself after the physical exam in order to arrive at the correct diagnosis. And in only the remaining 10-12% or so cases did the lab tests provide information that forced the physician to change one’s mind and come up with the correct diagnosis. In 8 out of 10 cases, the interview was sufficient!
When asked why they are shunning the interviews, physicians respond that they have no time – the system is forcing them to see too many patients per day. A study shows that physicians interrupt patients’ stories abruptly, very soon, sometimes as early as 3 seconds into the interview. Yet, in another study, when doctors were asked specifically not to interrupt, the interviews lasted only one minute longer. Just one minute! Thus interruption does not really save any time – it’s an illusion.
But what is more important is that the interruption itself means something. First, it means that the physician is not really listening. Second, it tells the patient that the doctor is not listening. By relaxing for that extra minute and actively listening to the patient, not just fishing for diagnostically important information in the account but also listening to hear how the patient perceives him/herself, and how that perception is altered by the illness, the physician gains a better understanding of the patient, can probably come up with a better diagnosis and, most importantly, gains trust with the patient. That trust is very important later, when the physician needs to rely on the patients to be disciplined about the treatment. The interruption loses that trust, something that smooth-talking medical quacks are quick to jump on, offering to listen even if their treatments are completely bogus.
What a patient does during the interview is story-telling. A physician needs to be trained to listen to and understand such stories – to glean how the change in health status affects the self-confidence, self-view and self-worth of the patient, how it changes one’s life-plans and ambitions, what fears it brings, what difficult adjustments in lifestyle it requires. To see the patient as a person, not just a disease.
And then, the story-telling does not end with the interview. The physicians and nurses need to communicate with each other about the patient and that also entails, when done right, story-telling (which need not be spoken, it can be in the chart). Finally, the healthcare providers need to know how to tell the story back to the patient, both to convey the diagnosis and to gain the trust needed for the patient to accept and follow through with the treatment. Quick recitatiton of code-numbers and Latin words just won’t do.
So Lisa Sanders, with her book, her column, her advising of House MD and her speaking tour, tries to teach the importance of the interview and the physical exam, the art of listening and storytelling. I am glad that UNC is taking her seriously.
october 038.jpg
The next day, a bunch of us met with Dr.Sanders at the West End Wine Bar in Durham. It was great fun to talk to her in an informal setting and to ask questions that I did not dare ask at the public talk in front of hundreds of med school professors and students and something like the entire nursing school of UNC. After all, my only perspective on medicine is from the position of a patient (and a reader of some med-blogs) so I learned a lot, yet was aware how little I actually know about medical training and practice. Anton organized that meet-up with the local science communicators and wrote his summary of the week’s events on his blog:
october 039.jpg
Steven Churchill at Sigma Xi
Steven Churchill is a professor of Evolutionary Anthropology at Duke University. His focus is on the role of projectile weapons in the evolution of humans. Dr.Churchill gave a talk at Sigma Xi as a part of their Pizza Lunch monthly series.
November 001.jpgWhat is a projectile weapon? It is something that can be thrown far away – more than just a couple of meters – and with sufficient power to seriously injure or kill a large animal. A non-projectile weapon, even if it can be thrown with force to a shorter distance of a couple of meters, requires either ambush hunting or chasing the prey into a corner or a bog where it can be approached and stabbed from a close distance. A projectile weapon allows hunters to hunt out in the open, perhaps just hiding in the tall grass. Thus two types of weaponry target different kinds of prey.
But inventing projectile weapons requires refinement in technical skills of making them, technical skills in throwing them, and changes in anatomy to make projectile weapons effective. And once invented, projectile weapons have novel ecological impacts, including impacts on further cultural evolution of humans.
This is what Dr.Churchill is studying. He is focusing on Europe, the invention of projectile weapons by modern (“Cro-Magnon”) humans and lack of such invention in Neanderthals, how that impacted the ecological relationship between the two species, and how that contributed to Neanderthal extinction as well as extinction (through competitive exclusion, as well as direct competition by killing) of all the large European carnivores except wolves.
In the talk, Dr.Churchill surveyed several different aspects of his research. He is approaching the question from several different angles. One is the study of spear tips in the archaeological record – their shape and size, the weight, the aerodynamics of the shape, etc. all tell something about their use as either close-contact or projectile weapons. Some (rare) spear handles and spear-throwers tell their own stories.
Then there is the fossil record of humans, Neanderthals and other large carnivores that show numbers and geographical distributions, migrations and dates of extinctions.
Next, there are anatomical cues – skeleton is malleable during development and bones in the upper arm develop differently in cultures that use contact weapons versus those that use projectile weapons as the stabbing technique is different from the throwing technique – throwers have different torsion angles in the humerus and also the humerus of one arm gets thicker than that of the other arm – this pattern is found in humans, but not in Neanderthals.
Finally, the general shape of Neanderthals would make them strong stabbers but poor throwers, so even if they tried throwing (perhaps by seeing the spears used that way by modern humans) they would not have been effective hunters with that technique.
November 004.jpgThen, there are wounds in the bones of some fossil humans and Neanderthals. By conducting an experiment – throwing spears into pig carcasses at various speeds, powers and distances (yes, throwing done by a machine) and analyzing the effects on bones – Churchill and his students could conclude that the wounds in the fossil bones were indeed the result of projectile weapons thrown from a distance.
The talk was, as is usually the case on these occasions, a quick survey of various studies. I did not read all the papers by him or his competitors, so I cannot write anything from a position of my own expertise. But my feeling is this:
Each piece of evidence he showed is weak on its own, but put together they make a strong case. And the strength is not purely additive, i.e., in the sense that more data is stronger than fewer data. The strength comes from consilience. Let me try to explain how that works.
Let’s call his preferred hypothesis ‘Hypothesis A’. One piece of evidence he shows is consistent with Hypothesis A, and weakens (or eliminates) an alternative Hypothesis B, but is also strongly vulnerable to alternative Hypothesis C. Another piece of evidence is consistent with his Hypothesis A, and weakens an alternative Hypothesis C, but is also strongly vulnerable to alternative Hypothesis D. Yet another piece of evidence is consistent with his Hypothesis A, and weakens an alternative Hypothesis D, but is also strongly vulnerable to alternative Hypothesis B. When you look at all of his evidence together, all of it is consistent with Hypothesis A and all alternatives look weak. Thus with all pieces being individually weak, the whole edifice still looks very powerful.
Now, to make clear, Dr.Churchill pointed out several times that the research he focuses on, his Hypothesis A, is not the one and only explanation for the extinction of Neanderthals (and other large predators). He just asserts that it is an important component of the process that led to this result and perhaps a more important component than some other people in the field are ready to admit. Of course, that’s how science works: different people focus on different aspects of a problem, and the strength of each person’s data will determine how the whole picture is built in the end.
This was definitely an interesting talk on a topic I never thought about before. DeLene was also there and wrote her thoughts about the lecture on her blog Wild Muse as well as on the Science In The Triangle blog.
RTI Fellows Symposium: Integrating Basic and Applied Research
This was a two-day event at the University of North Carolina’s Friday Center in Chapel Hill. This was also the first time I saw the Friday Center from within and I was looking at it with the eyes of a conference organizer. It has a Goldilocks quality to it: not so pleasant, intimate and science-themed as Sigma Xi, and not as big, cold and corporate as the Raleigh Convention Center. Just the right size and feel. But expensive as hell – Sigma Xi has been good to us over the years, not sure if we could negotiate a similar deal with Friday…..though we have definitely grown and a 420-seat main conference room at Friday Center looks good.
I could attend only the Monday morning portion of the meeting, but Sabine Vollmer was at the Symposium for the whole thing and wrote two blogs posts about the rest of the program here and here with a lot of details.
There were four broad themes entertained by the symposium: Personalized Medicine, Behavioral Neuroscience of Alcoholism, Global Climate Change and Education Opportunity and Achievement. Each of the themes had its own breakout session later, but Monday morning was reserved for Keynote Speakers, one on each of the four topics, each of interest to me in one way or another.
Let me first dispose of the things I did not like about the conference before I get into things I liked.
Over the past few years, most of the conferences I go to are informal, unconference or unconference-like events: from Scifoo in Mountain View, to Science FEST in Trieste, to ConvergeSouth in Greensboro, to our own ScienceOnline meetings. Even the ‘real’ science meeting I like to go to, the SRBR meeting, is very relaxed and informal – shorts-and-Hawaiian-shirt-clad scientists giving funny and entertaining talks about their new findings in my own field, with internal jokes, calling out friends in the audience and occasional hackling joke from the room (OK, OK, I overstate – folks are mostly nice and polite, especially when the talk is given by someone younger, e.g, a properly dressed graduate student, waiting in attentive silence until the end and then asking proper questions afterwards, but still, the general atmosphere is friendly and relaxed).
I realize of course that different conferences require different setup and different levels of formality. Not everything is a Bar Camp. While I was personally uncomfortable wearing my suit-and-tie costume at the IASP meeting, I understood that this was a business meeting in a business venue with businessmen (and a handful of businesswomen) in business attire talking about business.
But this one, I think, was a mismatch. All (or almost all) speakers were scientists talking about science. Almost everyone in the audience were scientists. For this kind of meeting, the organization was far too formal. And not just in pomp and ceremony and dress-code. For example, if you look at the abstracts, they don’t really say anything about the topic of the talk – they go in great detail about the speaker, including all the past and present appointments, awards and honorary degrees. This indicates that the organizers were more interested in the power hierarchy (i.e., ‘look at VIPs we managed to get here to talk’) instead of the substance of what they are saying. It felt more like a big corporate show-off than a conference meant for an exchange of ideas.
Then, there was no time designated for Question & Answer periods after the talks. I wanted to ask questions, but there was just no mechanism for doing so. I understand there were panels afterwards, but even those were built strangely – with panelists, after each gave a separate talk, sitting at a table on a podium above the audience, physically looking down at the audience, thus psychologically inhibiting all but the bravest from actually speaking up. I do not know how it went, but I doubt it was a free-wheeling discussion.
Then, the talks. Two speakers actually read their talks. Arrrgh! Yawn (and I was FULL of caffeine).
Others were much better. Howard McLeod gave a good, clear introduction into personal genomics and personal medicine, its pros and cons. Robert Jackson from Duke provided a good summary of the current state of science of climate change.
Ronald Dahl talked about adolescent brain development (something I am very interested in, both professionally and as a father of two adolescents), especially the lengthening of the period between onset of puberty which arrives earlier and earlier (the timing of which is not matched by an earlier development of other brain functions, including self-control) and the delay of societally approved age for onset of sexual activity (including marriage). Thus the duration of the period during which adolescents are sexually mature (but not entirely emotionally mature) but discouraged from sexual activity is getting longer and longer – which is an obvious problem. Couple that with the tendency of adolescents to be unable to resist, despite personal fear, engaging in risky behaviors, problems like teen alcoholism and traffic accidents are on the rise.
Lunch Keynote Speaker, Ralph Tarter, was the biggest dissapointment. His talk about bridging the Two Cultures and lessons from Hollywood was surprising for its naivete easily detectable by anyone who’s been reading science blogs for more than a year or so (including Framing Wars, response to Sizzle and response to Unscientific America, along with bloggers who routinely write about history of science). It was infused with nostalgia for good old days when scientists and poets drank wine and talked together (ehm, scientists and poets at the time were the one and the same people – that was Victorian era when gentlemen of means could afford to indulge themselves in such pastimes as philosophy, natural history and poetry and meeting their like-minded buddies at the pub). Science today is a very different business, specialized, expensive, profesionalized and rightly so. That’s progress.
The worst part was the lunch talk was the last point – a very erroneous analogy between peer-review of grants and movie reviews. First error: grants are reviewed before they are funded – movies are reviewed after they are funded. Second, as much as the grant review is prone to error, it is still done by well-meaning teams of scientists who are at least trying to evaluate the proposals according to their merits. Yes, outlandish proposals have a harder time than bandwagon stuff or conservative approaches, but it is at least attempted to be done fairly. Which movie gets funded is totally up to whims of movie moguls and producers. I bet even smaller percentage of submitted movie scripts gets actually made into movies than a proportion of grant proposals that gets funded. And while grant reviewers may look at the past publishing records of the grant submitters, the movie magnates are not in any way swayed by the statistics of positive or negative views of particular actors by movie critics in the media.
The highlight of the day was the talk by James Evans. I know Jim well, but I have never seen him speak before. And he blew me away. He knew that all the other speakers on the Personalized Medicine topics will be over-optimistic, so he took it on himself to provide a counter-view, a summary of cautionary notes backed up by data and a nice dose of humor. It was a very energetic and fun talk that explained very clearly what claims by personal genomics companies really mean, why they are so seductive if you don’t stop to think about them, and how they stack up against reality.
NESCent panel on intersection of public policy, economics, & evolution
NESCent Catalysis Meeting, coorganized by the Evolution Institute was on November 13-15, 2009 and several of the participants remained another day and came to NESCent on the 16th to report on the meeting in a form of a panel. The meeting and the panel were organized by David Sloan Wilson, professor of evolution at Binghamton University and one of my newest SciBlings. The other panelists were Dennis Embry, John Gowdy, Douglas Kenrick, Joel Peck, Harvey Whitehouse and Peter Turchin.
The main idea of the meeting is that evolutionary theory has something to offer in the realm of understanding human societies and thus shaping policies governing aspects of human activity. In the domain of economics, for example, it appears that the classical economics (i.e., the Chicago School) is unbeatable in the corridors of power. Yet, it is essentially faulty and this has been shown many times, including by numerous Nobel Prize winners in Economics. The idea that humans are rational (and perfectly informed) economic players is just plain wrong. Yet our economic policy is built upon that error. Perhaps developing and using models from evolutionary theory can finally bring the well-past-due overturn of the faulty economics and become the basis for smart, modern economic policies. The work is just beginning.
Perhaps the insights from the study of social and eusocial animals, mainly insects, can inform the discussion about social behavior of humans. How do simple rules for simple brains result in complex behaviors of, for example, bee swarms? Perhaps if we used such simple rules, instead of relying on every individual human being highly intelligent, impartial and rational, we can devise policies that will actually work, in various domains of human activity.
Taking into account multi-level selection models of evolution one can start understanding the differences between small-group societies (e.g, in rural areas) and large-group societies (e.g., in large cities), why those result in diefferent behaviors of individual humans living there, and why the differences between the two types of groups often lead to civil wars (often wars we usually do not see or describe as civil wars due to our own myopia, not realizing that a war between two adjacent regions may, in fact, be a war between the city and the country “mentality” – something quite obviously applicable to the US red vs. blue states, really small-town conservatism vs. big-city liberalism). Why imposing large-group organization (i.e., a President and a Parliament, i.e., a ‘centralized government’ of a unified country) may not work in a country like Afghanistan in which the society was always organized via local kin-and-friend networks – evolutionary theory can open our eyes on such questions.
This group of people, coming from a variety of backgrounds including history, anthropology, ecology, economics, psychology, political science, ethology and evolutionary biology, will try to tackle these and similar questions over the years to come.
Interestingly, the meeting was apparently an Unconference (though they have never heard of the term before), with discussions starting some months before the event (I presume online), leading to the choices of topics actually discussed in sessions which were free-style discussions, not speeches. One of the panelists noted that interdisciplinary meetings are usually excercises in misunderstanding, as each participant brings in different language and different axioms, but not this meeting – people actually made an effort, in advance, to study and learn other people’s perspectives before encountering them in the sessions in real life. This made the meeting, judging from the enthusiasm of all panelists, a resounding success.
This was the first time I ever visited NESCent (though I was excited when I first heard about its founding five years ago) and it was really nice to see Craig McClain and Robin Ann Smith again, as well as to meet, for the first time in real life, John Logsdon who blogs on Sex, Genes and Evolution and has come to NESCent for a nine-year sabbatical.
November 005.jpg
Solid Waste Management Vendor Fair at the RTP Headquarters
I got to see this almost by accident. I was going to the RTP headquarters to talk to them about their new blog and, for the price of free pizza, wondered around the exhibit and saw a brief talk about the ways North Carolina is doing recycling solid waste, why that is a good thing, and what are the prospect for the future. But I will let Cara Rousseau give you more details, in a post on the new RTP blog.
SCONC celebration of the Origin of Species 150-year anniversary at NESCent
Just a couple of days after my first ever visit to NESCent, I found myself there again. The occasion, the anniversary of the publication of the Origin Of Species (though officially today), was a good excuse for SCONC to have its monthly meeting at NESCent.
Robin Smith welcomed us all with a piece of great news – the funding for NESCent was extended for another five years! Then, while we were enjoying some delicious food, we were treated to three interesting presentations by current NESCent post-docs: Julie Meachen-Samuels talking about Smilodon, how it hunted differently than modern Big Cats and what it means for our understanding of palaeo-ecology and evolution, Trina Roberts about the diversity and biogeography of tree shrews (and how to get DNA from museum skeletal specimens!), and Eric Schuettpelz about the way ferns radiated into many species with the appearance of forests of (flowering) trees by occupying a new niche – living on the tree trunks as epiphytes, in the shade.
I found myself thinking about parallels between the Smilodon presentation and the one on projectile weapons I heard a couple of weeks before. Neanderthals uses stabbing close-contact weapons (and are now extinct) while modern humans used projectile weapons, thus being able to hunt different kinds of prey (and are now extant). Similarly, most Big Cats today hunt by giving chase to their prey and then killing it with their long canine teeth, often having to hold the teeth clenched in the trachea for several minutes until the victim dies. But Smilodons (the saber-tooth cats) had to hunt differently – from an ambush, presumably in thick forests and not out in the open country. They overpowered their prey using the weight and strength of their forelimbs and only at the end finished the completely immobilized victim with a quick slice with their canines. If they tried to keep their teeth inside still struggling large animals for more than a moment, their long but thin canines would break. In some ways, the Smilodon hunting technique is analogous to using close-quarters weapons, while the techniques of modern Big Cats is more analogous to hunting with projectile weapons (with themselves being “projectiles”). With such a massive body, with hindquarters so much smaller than the front half of the animal, and with no tail they could use for balance, saber-tooth cats could not run fast enough and long enough to be “projectiles”. Perhaps that’s why they, like Neanderthals, are now all dead.
And yes, we had a Darwin birthday cake – Russ Campbell has the pictures.

Why does plastic accumulate in the North Pacific Gyre? (video)

Talkin’ Trash

I know everyone in the sci-blogosphere is swooning over Carl Sagan. But as a kid I never cared much about him – I usually fell asleep halfway through each episode of ‘Cosmos’. But I would not miss for anything an episode of ‘The Underwater Odyssey of Commander Cousteau’ with Jacques-Yves Cousteau. That was breathtaking. And what he and the crew of Calypso did was truly ground-breaking, both in terms of scientific discoveries and in terms of under-water filming. And those discoveries and breakthroughs were shared with us, the audience, in an intimate and immediate manner.
That was a long time ago. The techniques of under-water filming pioneered by the crew are now probably considered to be ‘nothing special’. And I bet half the crew of Calypso were cameramen and sound engineers and lighting engineers and video mixers and other TV and movie professionals.
Can’t do that any more. Or rarely, with a huge cost, only on a very limited number of voyages on very large ships.
But what one can do, even on vessels much smaller than Calypso, is to have an embedded reporter. Not an old-timey one, but a modern reporter: someone who can search the Web for information, who can write, and blog, and tweet, and take and post photographs, and record and post audio podcasts, and record and post videos, all without help from any professional engineers, using small portable digital equipment and, most importantly, doing it in nearly Real Time, not after the ship docks after the voyage.
One of those new-style embedded reporters on a research ship is Lindsey Hoshaw. I was alerted to her by a tweet by Jay Rosen on Saturday. How did she get to do that?
She is a Stanford graduate in environmental journalism who was interested in the Pacific Garbage Patch and she put her proposal on Spot.us and asked people to help her raise the necessary funds:

I’ve been offered a space aboard the ship as the only journalist to chronicle this voyage. My enthusiasm for this project is only surpassed by the amazing opportunity I’ve been offered by The New York Times to publish an article and accompanying photos of my journey.
The Times has never written extensively about the Garbage Patch and my multimedia slideshow and article will be the first of its kind for the newspaper’s website.
As a recent graduate of Stanford University’s communications program, I have a background in environmental journalism. I have produced podcasts, audio slideshows and videos about environmental issues in the Bay Area and I have been studying the Garbage Patch for the past three years.

From their side the New York Times did not promise they’ll carry the story, but appear quite inclined to do so if the quality of her work is good:

LINDSEY HOSHAW, a freelance journalist in Palo Alto, Calif., hopes to sell a multimedia slide show and maybe an article to The Times about the Great Pacific Garbage Patch, a mass of floating plastic trash caught in swirling currents in a stretch of ocean twice the size of Texas.
But first, she has to get there. To help finance a $10,000 reporting trip aboard a research vessel, Hoshaw has turned to Spot.Us, a Web site where reporters appeal for donations to pay for their projects. If she can raise $6,000 before the September departure date — so far, only about $1,600 has come in — she will take out a loan for the rest, she said.
The Times has told Hoshaw that it might pay about $700 for the pictures, more if it also buys a story.
To some, this is exploitation — the mighty New York Times forcing a struggling journalist to beg with a virtual tin cup. But Hoshaw does not think so. To her, it is an opportunity she cannot pass up — a story she has long dreamed of, and a chance for a byline in The Times. To David Cohn, the founder of the nonprofit Spot.Us, it is a way for the public to commission journalism that it wants. For The Times, it is another step into a new world unthinkable even a few years ago.

She got on the ship today! You can follow Lindsey Hoshaw’s trip on Twitter (which she wisely separated from her personal account) and on her brand new blog.
You can follow her voyage on the Facebook page as well, where she also wrote:

What does this all mean both for Spot.Us and for the potential future of journalism? We would never claim to have answers, but we do have theories.
Every pitch on Spot.Us is defacto a collaboration. At the very least it is between the reporter and the community of supporters.
But often news organizations get involved. Sometimes we get TWO news organizations involved. In the future – I hope we can get THREE news organizations to collaborate around a single pitch.
We are producing a custom CMS that is based around the idea that “collaboration is queen.” It is the acknowledgment that no single news organization can do everything and that it is okay to “link to the rest.” It requires a new level of transparency and honesty in our reporting.

On Rebooting the News #24 this morning (I am assuming that all my readers listen to the show religiously every Monday), Jay and Dave talked about her as well:

On September 8, Lindsey Hoshaw set sail for The Great Pacific Garbage Patch, a huge pool of debris out in the middle of the Pacific that’s been known about for a while but rarely reported on or photographed. Her trip has been funded by users who think it’s an important venture. That happened at spot.us, the crowd-funding site for investigative journalism created by David Cohn, who used to work with Jay on NewAssignment.Net. (Background: See Lindsey’s original pitch in July 2009 and Jay’s original post for NewAssignment.Net back in 2006.) The New York Times has agreed to run her account and photos if they are up to Times standards. Meanwhile you can follow along on Twitter by adding thegarbagegirl.
That’s the re-booted system of news at work, already at work!
Dave: we’ve had reporters there before. Anyone who sailed by the Garbage Patch could have been our correspondent on the scene. We just have to teach them to do it.
Jay: it’s unlikely we’d be able to fund a reporter and a photographer and a videographer, which is why it’s important for journalists to be able to do multiple things.

Now you may say “Hmmm, that sounds familiar….didn’t I hear something about this before?” And yes, you did.
Another research vessel just returned from the Pacific Gyre where the crew studied the Garbage Patch. That was the Seaplex expedition, led by Miriam Goldstein, a well-known ocean blogger from the Oyster’s Garter blog. Miriam too, separated her personal Twitter account from the expedition account (I don’t actually know who from the crew tweeted from the official account). And she also blogged about it on the official Seaplex blog. So that crew also had an ‘embedded reporter’ of sorts – Miriam herself.

But take another look at the crew. Notice something? Miriam was not the only experienced blogger there. Or even the most experienced as a reporter. There were three other people there whose main purpose was to record and report from the trip – the Project Kaisei people, who also used their own Twitter account. One of them is Annie Crawley, founder of DiveImagination who also tweeted from the voyage.

So it seems all these trips have young journalists embedded as reporters, or as parts of the scientific crew, using all the modern communication technologies to report from the voyages in real time as well as to prepare more robust reports afterwards.
Oh, did I say that’s all? No, Lindsey Hoshaw is not the only person with reporting and blogging experience on that ship. There is also Bonnie Monteleone on board. Bonnie is a blogger on The Plastic Ocean (associated with the organization of the same name (hat-tip to North Carolina Sierra Club Blog):

UNCW’s Bonnie Monteleone and Jennifer O’Keefe, Director of Keep America Beautiful- New Hanover County, will represent North Carolina’s passion for the ocean by going out into the Atlantic Gyre, followed by Monteleone joining Algalita Marine Research Foundation into the North Pacific Gyre. They will be taking samples to quantify pelagic plastics found on the oceans surface, collecting surface feeding fish to necropsy for ingested plastics and bringing national awareness to the issues of man made debris entering our oceans. Most of this research is personally funded and why they need your help.

So Bonnie, who is both a student at UNC-Wilmington and staff in the Department of Chemistry & Biochemistry there, will be able to do a direct comparison between the Atlantic and Pacific Garbage Patches. And write and post videos from both expeditions.
Ah, what a tangled web! And the distinctions are getting blurry – who is a scientist, who is crew, who is journalist? Everyone is a little bit of everything these days. The journalists are surrounded by scientists – a constant source of information – and scientists are surrounded by journalists – a constant source of questions. They both also help with the daily ship routines (there is no space on small ships for freeloaders – hoist the sails!). And they all report from the voyage, each in his or her own way, some focusing more on the science, others more on the human connection, both at least some on the personal experience.
Now, if you’ve ever been to one of the ScienceOnline conferences (e.g., last year, or the year before….), you know that Ocean Bloggers are a jolly bunch – they come to the conference and what do they do for three days non-stop? They sing Sea Shanties! But they also do the best, most creative and most informative sessions! They are totally at the cutting edge of the new online technologies and many of them are awesome writers.
Karen, Craig, Kevin, Miriam, Mark, Jennifer, Rick, Allie, Christie, James, Jason, Sheril, Andrew and David and many others are all amazing bloggers! And very active on Twitter, FriendFeed, Facebook and elsewhere online (it is entirely possible that Karen tweets more times per day than I do!).
And I know that most of them are planning to come to ScienceOnline2010. I have learned that the best thing to do with the Ocean Bloggers is to give them an one-hour time slot and let them loose. They don’t need no guidance from me – they are much more creative than I am and ‘get’ the spirit of the Unconference better than most. They’ll plot something in secret and surprise us all right there and then.
Also, what I did as soon as I saw Jay’s original tweet was start following Lindsey Hoshaw on Twitter. She followed me back so we could exchange Direct Messages….and, she’ll also try to come to ScienceOnline2010. Now I just need to catch Bonnie (she is in Wilmington, an hour’s drive from here – perhaps she can carpool with Anne-Marie) and Annie Crawley and all the ‘embedded reporters’ and bloggers from all of this summer’s Garbage Patch voyages will be there. So perhaps they can all get together and tell us all about it – compare notes. Each one of them came to this with a different background, with different skills and experiences, with different goals. What did they learn about modern journalism out at sea?
Or perhaps they can put all of their stuff together – all the tweets, blog posts, photographs, podcasts, videos and polished articles (or at least links to polished articles if they are published in corporate media, e.g., New York Times) can, perhaps, be placed in a single online spot which we can then all link to and boost the Google rank so people who search for the ‘Garbage Patch’ find it up high in their searches. Perhaps they can plot how to do it at their session. Or, knowing them, they can do it quicker and use the conference to unveil the site to the world.
Remember what Lindsey Hoshaw wrote (above):

What does this all mean both for Spot.Us and for the potential future of journalism? We would never claim to have answers, but we do have theories. Every pitch on Spot.Us is defacto a collaboration. At the very least it is between the reporter and the community of supporters. But often news organizations get involved. Sometimes we get TWO news organizations involved. In the future – I hope we can get THREE news organizations to collaborate around a single pitch. We are producing a custom CMS that is based around the idea that “collaboration is queen.” It is the acknowledgment that no single news organization can do everything and that it is okay to “link to the rest.” It requires a new level of transparency and honesty in our reporting.

Today, we are all Jacques-Yves Cousteau. And all of the filming crew.
Last year some of the ocean bloggers were involved in the session with the title “Hey! You Can’t Say That!”. Perhaps next year they can call the session “Oh, You Bet I Can Talk Trash!” or “Blogging Garbage” or, like this post, “Talking Trash”….
Whatever they decide to do, I am looking forward to the result, and to their session. And the Sea Shanties the evening after it.

Put down the duckie (at least don’t throw it into the ocean)!

Miriam Goldstein of the Oyster’s Garter and Double X blogs (follow her on Twitter) is embarking on a sea-faring expedition!
SEAPLEX is a Scripps Institution of Oceanography at UC San Diego project studying plastics – yes, including the rubber duckies – accumulating in the oceans, specifically in the North Pacific Gyre. Miriam is leading the team of PhD students and volunteers who will be studying various aspects of the plastics in the sea and their environmental impact.
Though the life at sea is hard and busy and they will not have much time (or access) to do so, they will try to keep us all updated via blog and Twitter, so start following them now.

An Innovative Use of Twitter: monitoring fish catch! Now published.

A few months ago, I posted about a very innovative way of using Twitter in science – monitoring fish catch by commercial fishermen.
The first phase of the study is now complete and the results are published in the journal Marine and Coastal Fisheries: Dynamics, Management, and Ecosystem Science 2009; 1: 143-154: Description and Initial Evaluation of a Text Message Based Reporting Method for Marine Recreational Anglers (PDF) by M. Scott Baker Jr. and Ian Oeschger. It is relatively short and easy to read, so I recommend you take a look.
The next phase will continue with the program, with refinements, and will also include records of fish catch from fishing tournaments. Also, I hope to see this study presented at ScienceOnline’10 next January as an example of the forward-looking use of modern online technologies for collection of scientific data by citizen scientists.

Waves of Ocean Literacy

Periodic Tables and the Museum of Life and Science Present:
April 14, 2009 | 7:00 P.M.
Waves of Ocean Literacy
Speaker: Cynthia Cudaback, NC State University
If the Earth is a body, the ocean is its blood, circulating over most of the surface, moderating temperature and sustaining life. Cynthia Cudaback provides college and high school students with the tools they need to be informed stewards of the ocean, and its importance to the long-term sustainability of our planet. Her talk will focus on the success of marine education efforts, and opportunities for improvement.
Join us tomorrow night for a discussion about conserving the planet’s liquid resources.
———–
Periodic Tables is a monthly gathering where curious adults can meet in a casual setting to discuss the latest science in plain English. At Periodic Tables, you will chat with your neighbors and local experts about interesting and relevant science happenings right here in the Triangle and beyond. No lengthy PowerPoint presentations, no drawn-out seminars, no confusing jargon. Simply smart and relevant science in a relaxed atmosphere. Eating and drinking is encouraged, and there is no such thing as a stupid question.
Come out and join us on the second Tuesday of every month for a lively conversation at Broad Street Café. Come early to enjoy the fantastic appetizers, wood-fired pizza, burgers and salads that complement their 15 beers on tap and full liquor bar.
Want instant reminders about Periodic Tables? Become our fan on Facebook (http://www.new.facebook.com/pages/Durham-NC/Periodic-Tables-Durhams-Science-Cafe/40756115791)
For more information on Periodic Tables and our future topics please visit our website at http://www.ncmls.org/periodictables

An Innovative Use of Twitter: monitoring fish catch!

From NC Sea Grant:

….At nearly every fisheries management meeting he attends, Baker hears the same complaint: North Carolina’s recreational fishermen don’t have to account for their catch. Two years ago, during a regional meeting about snapper and grouper, Baker looked down at his hands and finally saw a possible answer: his mobile phone.
“I wondered if you could send a text message to a computer database somewhere instead of just texting from phone to phone,” he says. “And if you could do that, maybe that was something recreational fishermen could do to track their catches and fishing effort.”
Commercial fishermen and seafood dealers must submit extensive paperwork tracking what they bring in on a daily basis. But there is no such requirement in the recreational industry.
———-snip————-
Baker first shared his text messaging idea with friend Ian Oeschger, a software developer. A self-described “nerdy person,” Oeschger was intrigued. He agreed to build a system to accept text messages from anglers and translate that information into data.
“When I think of an idea that seems juicy like that, I just can’t help myself,” Oeschger says.
With funding from a North Carolina Sea Grant minigrant, Baker and Oeschger designed a pilot project to test their idea. The pair asked six Wilmington-area charter boat captains to use pre-paid mobile phones to text their fishing reports to an online text messaging service called “Twitter” (www.twitter.com).
A free service, Twitter allows people to connect with each other through “micro-blogging,” or posting messages that are no more than 140 characters. Once used primarily by teenagers and Blackberry addicts, “tweeting” is entering the mainstream — NASA even has a Twitter account posting status updates for high profile projects like the Mars I-Rover.
For Baker and Oeschger, Twitter provided an ideal online “collection bin” for the anglers’ experimental texts. Oeschger then built a separate database to continually query Twitter for new updates and put data into useable form.
“Most of the work was figuring out, ‘What does the data need to do?’ and ‘What is the most concise way for fishermen to communicate?'” Oeschger explains.
To answer these questions, he and Baker designed a compact syntax for fishermen to text in their reports, thereby minimizing reporting time and allowing for more content to be submitted in a single text message. For example, N2 E4 FA8R BL3 WEx20 translates to: Two anglers fished (N2), They fished for four hours (E4), They released eight false albacore (FA8R), they kept three Bluefish (BL3), and they kept one 20-inch weakfish (WEx20).
During an 18-week period, the charter captains submitted 128 trip reports describing 1957 finfish catches – 1123 were kept, 834 released. The captains describe the system as convenient, cost efficient and timely.
———-snip—————
In addition to more accurate data, the immediacy of text-message based reporting systems may help all fishermen feel a greater sense of ownership when it comes to management decisions, Baker points out. Extensive paperwork for commercial fishermen and third person reports from the recreational industry’s MRIP can take several weeks or months to process. During that time, fisheries may be opened and closed based on old data, something that affects livelihoods on both sides.
“By having fishermen report data in a fast and efficient manner, you make them a greater part of the management process.”

Wow! Read the entire text for more details. This strikes me as a really innovative and useful application of Twitter. Hopefully it will spawn other copy-cats by people who can put microblogging platforms to a good use in scientific, medical or environmental fields.

Science crowdsourcing – ecology

Help scientists track plant and animal cycles:

The USA-National Phenology Network (USA-NPN) — a University of Arizona, Tucson-based group of scientists and citizens that monitors the seasonal cycles of plants and animals — is calling for volunteers to help track the effect of climate change on the environment.
The group is launching a national program encouraging citizen volunteers to observe seasonal changes among plants and animals, like flowering, migration and egg-laying. They can then log in and record their observations online at the USA-NPN website.
“The program is designed for people interested in participating in climate change science, not just reading about it,” said Jake Weltzin, executive director of the USA-NPN and a scientist at the U.S. Geological Survey.
Phenology is the study of the climate’s influence on animal and plant life cycles. Climate change can affect these cyclical patterns and put certain species of plants and animals in danger.
Having a large volunteer base to help track these changes enables researchers to predict the effects of global climate change on plants, animals and ecosystems, said Mark D. Schwartz, chair of the USA-NPN board of directors. The data can be used to predict wildfires, droughts and pollen production.

If interested, go to USA National Phenology Network to sign up and participate:

The USA National Phenology Network brings together citizen scientists, government agencies, non-profit groups, educators and students of all ages to monitor the impacts of climate change on plants and animals in the United States. The network harnesses the power of people and the Internet to collect and share information, providing researchers with far more data than they could collect alone.
—————
We are looking for volunteers to help us monitor some 200 plant species found across the United States. This effort will eventually expand to include animals and physical phenomena, such as bird migrations and ice out on ponds. Please explore our website to learn more about USA-NPN. Better yet, click “Participate” to join us!

Warm temperature affects sex ratio in mammals

Anne-Marie writes, in Hot Mommas Make Boys:

A study published in the latest edition of the Journal of Mammalogy reports the results of a 30 year study on a population of northern elephant seals (Mirounga angustirostris), which shows that the male:female pup ratio is significantly higher in years with warmer sea surface temperature and weaker atmospheric pressure differentials.
What is the mechanism behind this? Unlike reptiles, which actually have their biological sex determined by temperature, the sex of mammalian embryos is entirely dependent on their chromosomes. This is where the phenomenon differs between the two taxa: reptiles depend on environmental factors to determine sex, whereas in mammals it is the sex ratio of offspring that complete development that is affected. Sex ratios are adjusted by selectively resorbing or aborting embryos of a specific sex. But which sex gets the boot when times are hard?

Global warming? More and more male elephant seals fighting to death over fewer and fewer females? Yikes!

Wet or Dry, it’s our Earth

Carnival of the Arid #2, the blog carnival about deserts, is up on Coyote Crossing.
Related to lack of water is, well, lack of water and how it affects people, leads to wars over water, etc. So for the World Water Day on March 22, the blogosphere will write about transboundary water. Send your entries to Daniel for this one-off carnival (or is this more properly called Synchroblogging?).

Daniel, welcome back to the blogosphere

Those of you who have been following the science blogosphere for a while may remember that excellent old blog Down to Earth which, sadly, went dormant back in 2006.
I am happy to announce that Daniel Collins has now started a new blog, focused on water, hydrology and other All Things Wet, at Cr!key Creek (with the cool sub-heading: “Water cycle meet Media cycle”). One to check out and bookmark!

Meetings I’d like to go to….Part V

Genetic Manipulation of Pest Species: Ecological and Social Challenges:

In the past 10 years major advances have been made in our ability to build transgenic pest strains that are conditionally sterile, harbor selfish genetic elements, and express anti-pathogen genes. Strategies are being developed that involve release into the environment of transgenic pest strains with such characteristics. These releases could provide more environmentally benign pest management and save endangered species, but steps must be taken to insure that this is the case and that there are no significant health or environmental risks associated with releases. Our conference will foster discussion of risks and benefits of these technologies among scientists, policy makers, and citizens.

March 4-6, 2009
North Carolina State University, Raleigh, NC
This is very soon – I’ll try to go to some of it if I can….

Carnival of the Arid – call for submissions

Did you know that the largest desert on Earth is Antarctica? And the second largest is Arctic? And only then comes Sahara!
Well, I knew that because Hal Heathwole taught a Desert Ecology course that many of my buddies in grad school took. But if you don’t believe me, check out the Wikipedia page about deserts.
And then, don’t stop at that. Do you have a blog? If not, start one. If yes, sit down and write a post about a desert. Then send it to the very first edition of the Carnival of the Arid:

Submissions should have something to do with a desert somewhere in the world. (If you’re not sure whether your work is desert-related, check out this definition at Wikipedia, and if you’re still not sure, send it in anyway.) Submissions can be scientific in nature, or history, or travelog. Images are welcome, photographic or otherwise. Discussions of culture and politics are welcome if they’re desert-related. The one restriction, other than geographical, is that — at least when I’m compiling it — paeans to destroying the desert probably won’t make it. (Developers and ORVers take note.) Paeans to preserving or protecting the desert are fine, as are alerts of current pressing issues.

If you are not sure about participating in a carnival, read this first. Then tune in on Saturday for the session Blog carnivals: why you should participate at ScienceOnline’09 and you may change your mind.

Coral disease outbreaks and warming waters

The next Sigma Xi Pizza Lunch — noon, Wednesday, Dec. 17 — is a chance to learn more about climate change’s expected environmental toll. UNC-Chapel Hill marine biologist and ecologist John Bruno will discuss recent research on links between coral disease outbreaks and warming waters.
The Pizza Lunch speaker series is free and open to science journalists and science communicators of all stripes. Feel free to forward this invitation to anyone you would like to see included. RSVPs are required (so we can get a reliable slice count) to cclabby@amsci.org.
Directions to Sigma XI: http://www.sigmaxi.org/about/center/directions.shtml

Where are the acorns?

CNN reports: Scientists baffled by mysterious acorn shortage:

Up and down the East Coast, residents and naturalists alike have been scratching their heads this autumn over a simple question: Where are all the acorns? Oak trees have shed their leaves, but the usual carpet of acorns is not crunching underfoot. In far-flung pockets of northern Virginia, Maryland, Pennsylvania, West Virginia and other states, scientists have found no acorns whatsoever.

But closer reading reveals that it is lay people and amateur naturalists who are baffled, while scientists are not. Scientists are well aware that the oaks produce corn in cycles – bumper years followed by lean years. The cycles are quite regular, and can be used to predict outbreaks of Lyme Disease:

One of the notions put forward in the article was that abundance of acorns in one year leads to abundance of rodents (mostly white-footed mice and chipmunks) the next year, and abundance of ticks – thus Lyme Disease – the third year. Now, Ostfeld and collaborators have added several more years of data and performed a detailed analysis of a large (13 years) dataset that strongly suggests that their initial hunch was correct.

New journal: Ideas in Ecology and Evolution

Ideas in Ecology and Evolution is a new Open Access journals which is also experimenting with the review process.
Bob O’Hara and commenters go into details. I hope it does not end like Medical Hypotheses: a great source of blog-fodder for snarky bloggers and not much else. We’ll keep an eye….

The world that contains giant spherical bunnies and poisonous birds is worth living in

And blogging about! Obligatory readings of the day:
The Evolution of Poisonous Birds:

This research elegantly demonstrates that the evolution of just one character — in this case, toxicity — can profoundly affect the evolution of a suite of other characters, ranging from body size and behavioral traits to ecological niche.

Allen’s Rule, Phenotypic Plasticity, and The Nature of Evolution:

Within species … across clines or subspecies … this raises very significant (and addressable) questions regarding adaptation in the genetic vs. the ontogenetic realms. If Allen’s rule is primarily an ontogenetic effect in some species, one can still consider the possibility that it is adaptive, but the nature of adaptation becomes somewhat more nuanced. Which is appropriate, because adaptation is probably never as straight forward as the textbook version of it towards which we tend to gravitate.

Climate Change and the Neglected Majority

The next Sigma Xi lunch pizza in RTP will be noon MONDAY, Nov. 17. Come hear Rob Dunn, assistant professor of zoology at NC State, talk about “Climate Change and the Neglected Majority.” Dunn, among other things, is interested in insects and how changes in their distribution affect ecosystems.
Sigma Xi’s Pizza Lunch speaker series is free and open to science journalists and science communicators of all stripes (feel free to forward this message to anyone you would like to be included). RSVPs are required to cclabby@amsci.org.

27 Best Deep-Sea Species, take two

The list is now final. Here are the top 13:
#13 Deep-sea corals
#12: Yeti Crab
#11 Venus’s Flower Basket
#10: Echinothuriid Sea Urchins
#9: Bathynomus, the GIANT ISOPOD!!!!
#8 Red Lure Jellyfish
#7 Predatory Tunicates
#6: Giant Sea Spiders
#5 Barreleye Fish
#4 Gold-Footed or Scaly Foot Snail
#3 Flesh Eating Sponges
#2: Bone-Devouring Zombie Worms from Hell
#1 Vampire Squid

27 Best Deep-Sea Species

About half have already been posted:
#27: Brachiopods
#26: Pig Butt Worm
#25: Crawling Crinoids
#24: Tube Worms
#23: Dumbo Octopus
#22: Xenophyophores
#21: Phronima
#20: Swimming Sea Cucumbers
#19: Black Devil Anglerfish
#18: Venus Fly-trap Anemone
#17: Tripod fish, Bathypterois
#16: Chaunax, the red-eyed gaper
#15: Spookfish, Rhinochimaera pacifica
#14: Alviniconcha, the Hairy Vent Snail
Keep checking for others….

Bats eat birds – join the discussion

As the month of September is coming to a close, and the topic of the month in PLoS ONE is bats, we decided to end the focus with a Journal Club.
Starting today, and lasting a week, there will be a Journal Club on this PLoS ONE article – Bats’ Conquest of a Formidable Foraging Niche: The Myriads of Nocturnally Migrating Songbirds by Ana G. Popa-Lisseanu, Antonio Delgado-Huertas, Manuela G. Forero, Alicia Rodriguez, Raphael Arlettaz and Carlos Ibanez:

Along food chains, i.e., at different trophic levels, the most abundant taxa often represent exceptional food reservoirs, and are hence the main target of consumers and predators. The capacity of an individual consumer to opportunistically switch towards an abundant food source, for instance, a prey that suddenly becomes available in its environment, may offer such strong selective advantages that ecological innovations may appear and spread rapidly. New predator-prey relationships are likely to evolve even faster when a diet switch involves the exploitation of an unsaturated resource for which few or no other species compete. Using stable isotopes of carbon and nitrogen as dietary tracers, we provide here strong support to the controversial hypothesis that the giant noctule bat Nyctalus lasiopterus feeds on the wing upon the multitude of flying passerines during their nocturnal migratory journeys, a resource which, while showing a predictable distribution in space and time, is only seasonally available. So far, no predator had been reported to exploit this extraordinarily diverse and abundant food reservoir represented by nocturnally migrating passerines.

Folks in the The Kalcounis-Ruppell lab, Hershey lab and O’Brien lab in the Department of Biology at UNC Greensboro, have read and discussed the paper and posted their comments here.
You know what to do – go there, register/login and join the conversation.

iNaturalist rocks!

iNaturalist%20logo.gif
Thanks Bill for drawing my attention to iNaturalist which has the makings of an awesome site!
What is it?
It is essentially a Google Map where people can add pins every time they see an interesting critter: a plant, fungus, animal, etc. What is recorded is geographical coordinates and time when it was posted.
Moreover, people can link from the pins to pictures of the sighted critters if they upload them on Flickr (nice way to interlink existing social networking sites instead of reinventing the wheel). And they can put additional information, e.g., description of the habitat where they saw the creature. They can try to identify it and others can chime in agreeing or disagreeing on the ID. One can also view maps in various ways – by time, by broader groups (e.g., insects, birds…), or by the degree of agreement people have about the ID.
The site has, apparently, just started, thus the number of people and the number of sightings is still relatively small and limited to mainly a couple of geographic locations (mostly California and Washington state).
But, imagine a couple of years from now, with millions of people pinning millions of sightings, providing additional information and then having the community agree on the ID? How about ecologists putting in all their field survey data (at least after publication if not before)? How about everyone who participates in the Christmas bird hunt? What an incredible database that will be! Something that one can search with machines, build and test models, and use the results to test ideas about, for instance, effects of weather events (hurricanes, fires, floods, El Nino, etc.) or broader weather changes (e.g., Global Warming).
In order for this database to become useful, I hope that the developers, as soon as possible, make sure it is possible for all the info to be machine searchable. And also to provide, perhaps, various fields that will lure people to put in more information. Right now, there is a date when the pin is posted, but the date of actual sighting is much more important. Exact latitude and longitude. Perhaps altitude. Perhaps depth for aquatic organisms. Exact time of day of the sighting. Description of the habitat. Number of individuals. Measurements of different kinds (one often cannot infer from pictures if the critter is 3cm or 30cm long, for instance). Behavioral observations. And of course the ID.
Such a database would be biased of course. People will tend to record when they see something unusual, or cool, or charismatic megafauna, rather than grass or field of corn or a bunch of squirrels in a tree. Also, more critters will be found in urban areas, on farms, in parks and by the roadsides than in places where one needs climbing (or diving) gear, or an hour of work with a machete in order to get to the habitat. But ecological models using the database could be made to account for these biases anyway.
In any case, I urge you to bookmark this site, and to use it. And let’s see how it shapes up over time.

Will the rich save the planet?

Save the planet? Buy it:

Millionaires are purchasing entire ecosystems around the world and turning them into conservation areas. Their goal? To stop environmental catastrophe.

But will they know how to do it well? Will they inject some of their own incorrect ideas into their projects? Who will they listen to when designing these? Will their kids continue?

Info about the way OA benefits conservation is itself not OA

How free access internet resources benefit biodiversity and conservation research: Trinidad and Tobago’s endemic plants and their conservation status:

Botanists have been urged to help assess the conservation status of all known plant species. For resource-poor and biodiversity-rich countries such assessments are scarce because of a lack of, and access to, information. However, the wide range of biodiversity and geographical resources that are now freely available on the internet, together with local herbarium data, can provide sufficient information to assess the conservation status of plants. Such resources were used to review the vascular plant species endemic to Trinidad and Tobago and to assess their conservation status. Fifty-nine species were found to be endemic, much lower than previously stated. Using the IUCN Red List criteria 18 endemic species were assessed as Critically Endangered, 16 as Endangered, 15 as Vulnerable, three as Near Threatened, and three as Data Deficient (i.e. insufficient data are available to assess their conservation status). Although such rapid assessments cannot replace in depth research, they provide essential baseline information to target research and conservation priorities and identify specific conservation actions.

Kevin Zelnio:

In a paper just out in the conservation journal Oryx, Van Den Eynden and colleagues discuss how they evaluated plant endemism, conservation status and reserve effectiveness utilizing only freely available online resources from the internet and local Herbaria. There were several conclusions drawn about plant conservation, but here is a tidbit about how free access to information helped in assessing conservation status.

“Research institutes that use information technology to catalogue and distribute information online promote the advancement of knowledge at a global scale. Using such free-access online resources, and advice offered freely by taxonomy experts, a review of the endemic vascular plant species of Trinidad and Tobago and an assessment of their conservation status was carried out in a relatively short time and without significant cost. This in turn has been made freely available online (Van den Eynden, 2006). Such rapid evaluation of conservation status cannot replace the need for in depth field-based monitoring and assessment but it provides valuable baseline information for the identification and targeting of specific conservation and research needs. The methods used can be applied by most countries for initial assessments of plant extinction risks. Lack of resources or research data is no longer an argument not to do so.”

Free information, it werks bitchez.
(Unfortunately their paper was NOT freely accessible, the irony of it all…)

The Machete Therapy

Anne-Marie is in Belize, doing some field-work, including chasing jaguars with specially trained dogs (scat-sniffers). Although electricity is rare and sporadic, she manages occasionally to post a quick dispatch on her blog. I wish I was there to see her (and those of you who have met her at the Science Blogging Conference may also have a hard time imagining the scene, as she is so nice and gentle) indulging herself in Machete Therapy:

I have discovered the wonders of Machete Therapy. If you have anything bothering you, stressing you out, weighing on your mind, just take on 100 m transects of jungle with a machete. It is astoundingly cathartic. Not sure what this says about me?

For us here back in the civilization, would hedge-trimming do?

Ecological succession: scientific theories succeeding each other?

Since I am not an ecologist, when I teach the ecology lecture I ‘go by the book’ and trust that the textbook will be reasonably accurate. But now, perhaps I should rethink the way I teach about ecological succession…What do my ecological readers think?

But, do elephants like to eat my hostas?

The wilding of the American West is definitely a controversial idea. Josh Donlan provides links to the details of the proposal and asks the readers to do a quick poll about it – go do it!

Viruses in the Oceans: join the latest Journal Club

Brendan Bohannan, Richard W. Castenholz, Jessica Green and their students and postdcos at the Center for Ecology and Evolutionary Biology at University of Oregon are currently doing a Journal Club on the PLoS ONE article The Sorcerer II Global Ocean Sampling Expedition: Metagenomic Characterization of Viruses within Aquatic Microbial Samples, which is part of the PLoS Global Ocean Sampling Collection. Please join in the discussion.

Food and Guilt – questions about some extraordinary claims

There is a lot of stuff one hears about food, sustainability, environment, etc., and it is sometimes hard to figure out what is true and what is not, what is based on science and what is emotion-based mythology.
For instance, some things I have heard over the years and have no means to evaluate if they are even close to plausible:
Claim #1: if we used every square inch of arable or potentially arable land, clearing the rainforest, turning deserts into fields, removing cities, malls and highways, killing all the animals, destroying all natural ecosystems, moving all humans to the Moon and planting all of the Earth’s landmass (except, perhaps Antarctica and Mt.Everest), there would still not be enough grain, fruits and vegetables to feed the entire current human population. True or False? Source?
Claim #2: if we used all the available technology to maximize the production of fish, shellfish, sea-weed, etc., the entire production on the oceans would still not be able to feed the entire current human population. True or False? Source?
Claim #3: if all of the suitable (and unsuitable but convertable, e.g,. cities, deserts) land was converted into small farms where chickens really freely roam and peck around the yard, there would not be enough chicken meat to feed the entire current human population. True or False? Source?
I guess if any or all of those are even close to true, the idea is that we have to trade-off and compromise: we cannot eat just plants, or just seafood, or just free-range chicken, but have to combine all (plus farm-raised animals of several species raised as humanely as possible, plus a little bit of game meat) of these in some way that can feed all of us without destroying the environment.
So, anyone know any answers, or at even educated guesses as to the veracity of any of the three above claims?

Now We Are Six*

Blogging on Peer-Reviewed Research

Is there any kid who does not love giraffes? They are just so amazing: tall, leggy, fast and graceful, with prehensile tongues and a need to go through complex calistehnics in order to drink. The favourites at zoos, in natural history museums and on TV nature shows.
Giraffes were also important players in the history of evolutionary thought and I bet you have all seen, and heard the criticisms of, the iconic comparison between Lamarck’s and Darwin’s notions of evolution using a comic strip featuring giraffes and how they got their long necks.
Giraffes sleep very little and mostly standing on their feet. They give birth while standing, with no apparent ill consequences to the newborn which, after falling from such a great height, gets up on its feet and is ready to walk and run with the herd within minutes.
Like almost any other mammalian species, a giraffe can sometimes be born albino, but in this case only the yellow background is white, while the brown splotches remain (similar to the “tuxedo” mutation in quail) suggesting that just one of the multiple “color” genes is malfunctioning.
The behavioral (sexual selection) hypothesis that the length of the giraffes’ necks has something to do with male-male fighting, co-called “necking”, is apparently going out of favor, while more ecological hypotheses are gaining in acceptance (again – this appears to be cyclical).
But, one thing that you think when you think of giraffes is the giraffe, i.e., one thing, one species. There have been inklings recently that this thinking may change, finally culminating in a very interesting paper published yesterday in Journal of Biology (free pdf of the paper is available):

A central question in the evolutionary diversification of large, widespread, mobile mammals is how substantial differentiation can arise, particularly in the absence of topographic or habitat barriers to dispersal. All extant giraffes (Giraffa camelopardalis) are currently considered to represent a single species classified into multiple subspecies. However, geographic variation in traits such as pelage pattern is clearly evident across the range in sub-Saharan Africa and abrupt transition zones
between different pelage types are typically not associated with extrinsic barriers to gene flow, suggesting reproductive isolation.
By analyzing mitochondrial DNA sequences and nuclear microsatellite loci, we show that there are at least six genealogically distinct lineages of giraffe in Africa, with little evidence of interbreeding between them. Some of these lineages appear to be maintained in the absence of contemporary barriers to gene flow, possibly by differences in reproductive timing or pelage-based assortative mating, suggesting that populations usually recognized as subspecies have a long history of reproductive isolation. Further, five of the six putative lineages also contain genetically discrete populations, yielding at least 11 genetically distinct populations.
Such extreme genetic subdivision within a large vertebrate with high dispersal capabilities is unprecedented and exceeds that of any other large African mammal. Our results have significant implications for giraffe conservation, and imply separate in situ and ex situ management, not only of pelage morphs, but also of local populations.

In other words, there appear to be more than one species of giraffes currently living in Africa – probably six species, and perhaps as many as eleven. And while the individuals of different giraffe species readily mate in captivity, it seems not to happen out in the wild.
Furthermore, two of those six new species belong to very small and shrinking populations. If the finding of this paper is accepted by the scientific community and the six populations receive official recognition as six species, this will turn the two smallest populations into endangered species, worthy of our protection.
An anonymous commenter on Grrrl’s blog has a great idea and I think we should start a contest: make a picture of Noah’s Ark with SIX pairs of giraffes towering over all the other pairs of animals instead of just one pair. Feel free to make it a LOLgiraffe picture. Post the links in the comments here or on Grrrl’s post and we’ll highlight them and pronounce the winners after the holidays.
* Apologies to A.A.Milne

RIP: George Folkerts (November 26, 1938 – December 14, 2007)

George Folkerts was one of those naturalists of the ‘old school’, interested in everything and excited about learning and sharing the knowledge throughout his life. He died on Friday, suddenly and unexpectedly, at the end of a typically busy day at Auburn University.
Anne-Marie was his student, one of thousands who had the privilege to learn from and with Folkerts, and one of those who now has to carry on his work. She wrote about him in two very touching posts: Huge loss on many levels and Classifying grief.

Tinamou’s Dilemma: Canines or Talons?

When I first read about a new paper about the behavior and ecology of maned wolves, I immediately thought of the blogger most uniquely qualified to write about it. Anne-Marie’s research is on maned wolves and in her latest post she describes an ecological love-hate triangle in which the maned wolves flush out birds, mostly tinamous, out of the bushes – just to have them preyed upon by hawks. Anne-Marie provides more details, the back-story and the cute pictures.

Don’t go near that empty beer bottle if your metabolism is fast!

That is, if you are a shrew and do not want to be just a dead data-point for some ingenious young ecologists….who at least clean up the tricky trash left by drunk drivers.