Archive for the ‘Science research’ Category

Think of the children… work on Drosophila

Monday, March 2nd, 2009
bolducfly3-1small.jpgFigure 1 from Bolduc and Tully’s recent paper in Fly. It shows that many genes characterized for memory function in animal models affect mental retardation in humans. Click to enlarge.

Way back in October, politics were stressful and Sarah Palin (and others) were confused about fruit fly research. But now, even politicians should understand that there is no conflict of interest between basic science research on fruit flies and saving the children: in a special issue of the journal Fly, a new review paper describes the utility of Drosophila in studying the biology of intellectual disabilities.

Many forms of mental retardation have genetic determinants, and science research into the biological basis of these disabilities is an obvious avenue to improving lives. As the paper by François Bolduc and Tim Tully describes, Drosophila is a valuable animal model for investigating the genetic basis of intellectual disabilities. About 87% of the genes identified in humans to cause mental retardation have orthologs in Drosophila.

It turns out that Drosophila is an especially good model for studying mental retardation. Genes for learning and memory are more well-conserved between humans and flies than other classes of genes, and flies are well-developed as a model system for conditioning and memory assays. Because they are small and breed quickly, flies are also a useful resource for testing pharmaceutical treatment. This paper describes a number of mental disabilities that are caused by mutation at single genes, and the insights gained by evaluating the Drosophila orthologs. And as more genetic determinants are identified, research on model systems like fruit flies will reveal valuable information on how these genes are expressed and whether medical interventions are safe and effective.

Baboon Metaphysics

Monday, February 23rd, 2009

baboonmetaphysics1.jpegDorothy Cheney and Robert Seyfarth‘s recent book on baboon social behavior, Baboon Metaphysics, has been nominated for… oddest title of the year!

The title echos Charles Darwin’s own comment about the fascinating behavior of baboons, made over 170 years ago: “He who understands baboon would do more towards metaphysics than Locke.”

You can vote (as many times as you like) for Cheney and Seyfarth’s book here.

They’ve got some tough competition, though, including Curbsite Consultation of the Colon and—current frontrunner—The 2009-2014 World Outlook for 60-milligram Containers of Fromage Frais. Vote early, vote often.

Dance dance… evolution?

Saturday, November 22nd, 2008

Some things are really hard to understand. Like, how to resolve pathways of functional coupling in human hemoglobin—even if using quantitative low temperature isoelectric focusing of asymmetric mutant hybrids. So hard!

Fortunately, Dr. Vince LiCata, a researcher at Louisiana State University, has performed an interpretive dance on this very topic. In fact, Dr. LiCata has recently won the 2009 AAAS/Science “Dance Your PhD” Contest in the “professor” category. (There are also grad student, post-doc, and most-popular-on-YouTube categories.) Watch Dr. LiCata and his team perform the winning dance:

This is an extraordinary contest. Previous winners received a year’s subscription to Science. But this year the winners get something more:

Each [winner] will be paired with a professional choreographer. (A team of 4 choreographers in Chicago are ready and waiting.) Over the next couple of weeks (via email and telephone) you must help your choreographer understand your article, its aims, the hypotheses it tests, and its big-picture context. With that knowledge, the choreographers will collaborate with a group of professional dancers to create a 4-part dance based on the science behind the 4 winning research articles.

You will be honored guests at the 2009 AAAS Annual Meeting in Chicago in February, [where] you will have front row seats to the world debut of “THIS IS SCIENCE”—the professional dance interpretation of your scientific research.

The mission of this contest is to bring scientists and artists together, and to engage the public with science. I’ve never heard of anything quite like it, at least not anything that is being developed from such grassroots origins—the intent is to produce a full theatrical run and world tour! Winners are expected to participate as “science diplomats,” bridging that perilous gap between basic science research and public interest and understanding. How fantastic! You can watch other dances, like creator John Bohannon’s interpretation of the role of the WSS operon in the adaptive evolution of experimental populations of Pseudomonas fluorescens SBW25, on the contest site or on YouTube.

Palin not for fruit fly research

Saturday, October 25th, 2008

As you may have heard, Sarah Palin had something to say about science in her recent policy speech in Pittsburg. The woman may be all about seal DNA research, but she thinks fruit fly research is absurd. I kid you not! A quote, from her speech promoting investment of federal research dollars towards childhood disabilities like autism:

For many parents of children with disabilities, the most valuable thing of all is information. Early identification of a cognitive or other disorder, especially autism, can make a life-changing difference. […] We’ve got a three trillion dollar budget, and Congress spends some 18 billion dollars a year on earmarks for political pet projects. That’s more than the shortfall to fully fund the IDEA. Where does a lot of that earmark money end up anyway? […] You’ve heard about some of these pet projects they really don’t make a whole lot of sense and sometimes these dollars go to projects that have little or nothing to do with the public good. Things like fruit fly research in Paris, France. I kid you not.

So here’s the thing. Fruit fly research is valuable because it contributes to our knowledge of things like… autism. Here’s a list of recent basic science research findings using Drosophila melanogaster, my model organism of choice, that have contributed to understanding autism.

September 2007: Research on Drosophila describes the function of neurexin, a protein encoded by a gene for autism. This gene is currently being developed for autism screening in children. Popular press. Scientific article.

April 2008: Drug screening in Drosophila reveals that some pharmaceuticals have the potential to reverse the effects of fragile X syndrome, a leading cause of autism. Popular press. Scientific article.

October 2008: Research on Drosophila shows that mutations at the gene that causes fragile X syndrome affect the transport of mRNA molecules, and suggests a new mechanism for how the disease works. Scientific article.

In progress: A research group in Belgium (not the same as France, but close!) is investigating a gene thought to cause autism, neurobeachin, using Drosophila. Project announcement.

And I am not a genius. These were the first few hits on Google for “drosophila autism.” Furthermore, a quick Pubmed search for “drosophila autism” generates 114 hits (that’s 114 published scientific papers, Palin) and a search for “drosophila ‘mental retardation'” generates 826 hits. That’s research that has an awful lot to do with the public good.

Making an example of couch potatoes

Tuesday, October 21st, 2008
cpo.jpgIllustration by Beto Alvarez, Inquirer Staff Artist

Yesterday the Philadelphia Inquirer profiled an article just published by my lab, which demonstrates the role of a gene called couch potato in determining reproductive diapause in fruit flies. Genes in flies are named after their mutant phenotype; when this gene is disrupted, the animals lie around like lazy couch potatoes.

The nifty thing about this new work is that it demonstrates how a single gene—and more specifically, a single nucleotide site within that gene—affects a major phenotype under strong selection in natural populations. Diapause is a physiological state which permits flies to withstand long periods of stress. Flies are more likely to survive winter if they are in diapause, but not all flies are capable of entering diapause. This paper demonstrates that a single nucleotide polymorphism, which is located within the couch potato gene, determines whether flies are diapause-capable or not. From Florida to Maine, natural populations of fruit flies have gradually increasing frequencies of the nucleotide that confers diapause capability—almost all Maine flies, which must survive long winters, carry the diapause allele. Evidence suggests that this polymorphism affects other traits, like lifespan and reproduction, as well. So it’s likely that this single mutation has significant effects on the evolution of many traits. A tidy example of evolution at work (for those keeping track).

The article was published yesterday in PNAS.

Palin for seal DNA research

Thursday, September 11th, 2008

seal1.jpgYesterday Talking Points Memo pointed out that several of Alaska Governor Palin’s earmark requests were for… science. Specifically:

Palin’s office requested $2 million in federal monies to study crab mating habits; $494,900 for the recreational halibut harvest and $3.2 million for seal genetics research.

Most of the blogospheric attention on this has been focused on the scandal of Palin’s love of earmarks or the inconsistency of her positions. But there has also been some implicit criticism of spending so much money on something as preposterous as research on seal DNA. Josh Marshall of TPM redirected the discussion by addressing the issue head-on, explaining, along with the fact that his father was a marine biologist, that he did not mean to imply that spending money on such research is wasteful just because it sounds funny. This point was motivated by several substantive comments, which included the declaration that while spending taxpayer dollars on ecologically important issues is good, doing so through pork barrel initiatives is not. For example:

good science is funded through peer review, not via earmarks and lobbying.

we don’t want science funded this way, it leads to croneyism and misuse. give the money to NIH and NSF and don’t do by congressman trading favors.

earmarks are lousy way to fund science, bad, bad, bad.

More on PLoS One

Monday, August 18th, 2008
starlingbycoen.jpgA photo of a starling by Coen Elemans, lead author in a new PLoS One paper about superfast songbird muscles.

There’s another point about PLoS One that I wish I’d made in my earlier post: it’s the only journal publishing scientific articles on a broad range of topics that doesn’t have the extremely competitive acceptance rate of Science or Nature. An author submitting a manuscript chooses a journal based on more than just impact factor, of course. A well-respected subject-specific journal is often the best place to send work, especially if you’ve published related results there before and it’s regularly read by colleagues in your discipline. But what if your manuscript characterizes something that crosses multiple fields? Something of unusual or quirky significance? Maybe it’s not earth-shattering enough for Nature, but it would be a shame to leave it underexposed in a subject-specific journal.

Suddenly, PLoS One is perfect.

And in the spirit of the thing, let me tell you about new research published in PLoS One. Coen Elemans, from the University of Utah, and colleagues at the University of Pennsylvania provide the first direct evidence of superfast muscles in songbirds. They found that the syringeal muscles in starlings can produce twitch contraction halftimes of 3.23±0.44 ms, the fastest isometric twitch kinematics ever measured in vertebrates. Superfast muscles are a special type of muscle and appear to have evolved multiple times in different vertebrate taxa (rattlesnakes shake their rattle with superfast muscles, for example). These findings have already earned mentions in The New York Times, National Geographic, and many newspapers both stateside and international. They’re relevant to multiple subdisciplines, and publishing them in, say, a muscle physiology journal would have left them overlooked by the birdsong community. Fortunately, PLoS One enjoys high exposure: in the New York Times alone, ten reports on PLoS One articles were published so far this year, almost a third of the number of reports on PNAS articles. Not bad for a journal with an entirely different editorial and publishing process.

What’s the deal with PLoS One?

Wednesday, July 9th, 2008

plosone1.jpgI am really interested to see how PLoS One, the multi-trick, lowborn pony in the open-access PLoS stable, turns out.

PLoS One was launched two years ago by the Public Library of Science, an organization that promotes open access science publishing. (Open access means the articles are totally free and accessible online, to any old person who wants to read them and may have paid tax dollars to fund them.) PLoS also publishes PLoS Biology and PLoS Medicine, two highly esteemed journals that rival the best long-established, limited access journals, and four other well regarded subject-specific publications. There are a couple things that make PLoS One different. It only publishes online, it publishes weekly, and it publishes on any topic in science or medicine—this makes it very high volume. It also permits blog-style reviews, comments, ratings and trackbacks. But most importantly, it doesn’t reject papers for lack of significance. Papers are reviewed for integrity, but not for “impact.” The articles of a diligent but uninspired graduate student who unwisely chose to study a boring and essentially irrelevant corner of science might find a home here, for example.


A unicorn in the garden

Monday, July 7th, 2008
rainbowdonkeycorn.jpgA donkeycorn in a water garden. Photograph by Mary Schwalm.

There’s been a lot of coverage of Richard Lenski’s citrate-metabolizing bacteria this summer, and it’s pretty entertaining. Lenski is a biologist at Michigan State and has been maintaining populations of E. coli bacteria in his lab for two decades. Bacteria rapidly divide, grow and die; they acquire random mutations, and lose them; it’s called evolution, and it happens. Over the years Lenski has published numerous papers on his experimental bacterial evolution project, all of which describe the populations, you know, changing over time.

Probably nothing would have happened if science writer Carl Zimmer hadn’t profiled Lenski’s work. Zimmer is one of the best science writers out there, transforming basic science research findings into fascinating tales of biological anomalies and unlikely plot twists, and he’s devoted a lot of attention to Lenski’s evolving bacteria. Last year he wrote about the work in The New York Times and he also described it in his book Microcosm, published this past May. Lenski was recently inducted in the National Academy of Sciences—a big honking deal: Congratulations, Dr. Lenski!—and his inaugural publication in the Academy’s scientific journal describes a discovery having to do with the bacteria evolving the ability to metabolize citrate. These results were also presented by graduate student Zachary Blount at the evolution conference in Minnesota this June, to an entertained audience who watched a video of what it took to analyze the 40 trillion cells in the experiment. Zimmer also wrote, eloquently, about this finding, and why it’s cool, in a June 2 post on his blog. (Recommended reading if you’re interested in the details of the actual science.) With an interested reception in the scientific community and national attention in the popular media, Lenski and his well-adapted cells were, obviously, ripe targets for an outraged rejection by the anti-evolution people.


I *heart* Uppsala and other comments about the 2007 ESEB meeting

Tuesday, August 28th, 2007

uppsala-cathedral.jpgI just returned from Uppsala, Sweden and the 2007 European Society for Evolutionary Biology conference. A few high points of the trip:

Fighting vertigo beneath the spires of Scandinavia’s tallest cathedral during the daily assemblage of evolutionary biologists on the front steps of Uppsala University’s main building.

Michael Majerus‘s plenary talk on the social history of the peppered moth, in which he excoriated fact-averse journalists (and Judith Hooper in particular) for destroying good science in the public consciousness, and which Nick Matzke has summarized nicely (and linked to the text of Majerus’s talk) on the Panda’s Thumb blog.

Sally Otto‘s plenary talk on the costs of sex, in which she argued that the ability of recombination to reintroduce variation lost by drift does more to explain the paradox of sex than any other hypothesis. Fantastic talk. I hope to blog more about this later.

Marlene Zuk‘s symposium talk on gender bias in science. Confession: I didn’t actually see this talk, but now wish I had. Another attendee told me about it afterwards, and I suspect it is pretty well represented by this lecture she presented last year. I hope to blog more about this later as well.