Archive for July, 2008

It keeps coming back

Thursday, July 10th, 2008

snapper.jpgMy friends from college and I have a reunion vacation every year in a cabin in the Adirondacks, and there is this turtle that lives in the pond on the property that keeps joining us. It is a massive snapping turtle. It looks just like the picture and it is terrifying.

Two years ago we tried to catch it. The reptile specialist in my department recommended a reinforced cardboard box and some sort of lasso on a very long stick. The advice was imparted reluctantly; he actually recommended staying away from it altogether and showed incredulity when I explained about the skinny dipping. As a somewhat fearsome individual himself, this was a shock, and it justified the alarmist attitude that was already preventing the boys from lounging in the inner tubes. Some impatient internet research had convinced me that snappers, while vicious and aggressive and sure to snap off your digits if you disturb them on land, are of a diffident and temperate personality underwater. Our empirical evidence only partially supported this claim: it did bite one of us on the foot; the foot, like the turtle, was in the water; the leg and all the rest was on land. (Amputation was avoided, and no one died of Salmonella poisoning.) This was, if I recall correctly, our introduction, and that first impression may have instilled an unreasonable level of antagonism between us.

Anyway the year we brought the relocation equipment, we couldn’t find the turtle. This year, with short memories and fresh enthusiasm for a splash in the lake, we saw it again. It likes hanging around the dock, and provides plenty of opportunity for ogling. So grotesquely prehistoric! I love it, but it scares me. It’s quite the summer thrill.

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.

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Love letter to The Origin

Wednesday, July 9th, 2008

minidarwin.jpgToday on Hullabaloo, tristero writes an affectionate post about the marvelousness of Darwin’s On the Origin of Species. It’s cool to see interest and enthusiasm for this work outside of science media. The inspiration came from Olivia Judson’s piece in the The Times, which confesses that lots of biologists haven’t actually read it. Both posts are appeals to correct that. I’d like to add another argument to theirs: the most impressive thing about The Origin is Darwin’s staggering amount of observation and inference, and its explanatory power is a delight to non-scientists and a thrill for modern biologists.

The Origin is one of the most important theoretical accomplishments in science, yet it is entirely accessible to lay readers. This simply doesn’t happen anymore. In fact, Darwin’s entire process would be unusual today. Although he did some tinkering, particularly by breeding animals, Darwin was not really an experimentalist. Mostly he was a naturalist: he kept his eyes open, recorded everything, and synthesized it all to produce his cohesive—and largely correct—theory of natural selection. Now, experiments, often complicated and expensive experiments, test hypotheses. (This is called the scientific method.) Even observational studies are formally executed, with carefully circumscribed parameters—and certainly they are published that way, unlike Darwin’s creative assemblage of facts, insights and conjectures. But even as hypotheses are carefully chosen and experiments painstakingly designed, the ultimate synthesis still takes place in the brain. Darwin’s beloved book will always be relevant, because it is an inspirational reminder to keep the breadth of observation as wide as possible.

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.

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Words of wisdom

Tuesday, July 1st, 2008

jenny-graves.jpgOver on evolgen, RPM notes that biologist Jenny Graves gives a compelling interview in PLoS Genetics. And she does: she makes a couple insightful points about science and popular culture, and describes her work with enthusiasm and charm. RPM pulled a quote about the importance of good science education for little kids; Graves doesn’t equivocate over her distress that some children are brought up to “believe in utter nonsense.” But my favorite comment from her interview has to do with the fundamental and inextricable importance of evolution in biology:

“[S]ometimes, when you ask a functional question, you get an evolutionary answer.”

To me, this is such an elegant way to impart the importance of being broad-minded, and broadly trained. It conveys the uncertainty of science, of how you never know just where the research will take you.

Graves explains that she was trained as a molecular geneticist, and admits she didn’t see the relevance of evolutionary biology to her work at first. (She says she thought evolutionary biologists belonged on another planet.) Her interview reveals how good science can be enlightening. When her work on gene mapping in marsupials led her to make inferences about the evolution of mammalian chromosomes, her perspective changed. She’s interested now in science education, to reverse the trend she sees in the current “credulous generation.” I look forward to the launch of her “dumb design” website, which will explain functional anomalies in evolutionary terms and, I’m sure, antagonize the intelligent design people. She also reveals why the anti-science culture is waging an ultimately futile campaign. It’s not a battle of beliefs, but a battle against common sense and, well… self-actualization:

“It’s so dangerous to encourage people to believe what they are told rather than what they observe.”