Blogging research

ResearchBlogging.orgWondering what’s with these check-mark icons that have started popping up on my posts? They’re part of my new membership in the Research Blogging community, which aggregates ‘blog posts about peer-reviewed scientific literature.

Members use the Research Blogging online tool to create citations for papers they’re blogging about, and they copy the citation code into the relevant post to create a stylish reference list. The citation code includes tags that are picked up by Research Blogging’s web crawler, which then links the page containing the citation to Research Blogging’s relevant topic pages (such as biology) and RSS feed. Posts that I submit to Research Blogging will also be marked with the aggregator’s icon, so someone arriving directly at Denim & Tweed can quickly scan for posts about peer-reviewed papers. It’s a great way to find out what other science bloggers are reading, and it’s boosted my traffic to values that are statistically distinguishable from zero. If you like reading about science, or if you blog about it, Research Blogging is extremely useful.

Birds converge on flightlessness

ResearchBlogging.orgWhen two organisms evolve in similar ways independently, we call it convergent evolution. Classical examples include the fish-like shape of whales and the separate evolution of flight by both bats and birds. Now, in this week’s PNAS, a (huge) group of scientists report that ratites, the group of flightless birds including emus, ostriches, rheas, cassowaries, and kiwis, lost the ability to fly at least three separate times in their evolutionary history [$-a].


Photo by Morti Riuuallon.

The key question this paper addresses is whether ratites are all the descendants of a single common ancestor (a “monophyletic” grouping) – if they are, then chances are that flightlessness only evolved once, and in that ancestor. The new paper’s authors use a large DNA sequence data set to show that that tinamous, the group of flying birds most closely related to ratites, actually arose within the monophyletic group of the ratites. This makes the ratites polyphyletic, not monophyletic. Since the next-most-closely related birds fly, and it’s probably easier to lose the ability to fly than it is to regain it, this suggests that the common ancestor of the ratite-tinamou group could fly, and that ratites probably lost the ability to fly multiple times.

Reference

J. Harshman, E.L. Braun, M.J. Braun, C.J. Huddleston, R.C.K. Bowie, J.L. Chojnowski, S.J. Hackett, K.-L. Han, R.T. Kimball, B.D. Marks, K.J. Miglia, W.S. Moore, S. Reddy, F.H. Sheldon, D.W. Steadman, S.J. Steppan, C.C. Witt, T. Yuri (2008). Phylogenomic evidence for multiple losses of flight in ratite birds PNAS, 105 (36), 13462-7 DOI: 10.1073/pnas.0803242105

Well, it made me laugh.

What’s truly funny is that there’s so much footage of McCain looking confused, irritated, and/or flabbergasted from his own acceptance speech.

Sarah Vowell on John McCain


Photo by tammylo.

Best New York Times op-ed ever: Sarah Vowell turns her wry historical perspective on the Republican presidential ticket.

Senator McCain has been both lauded and derided as a “gambler” for choosing the obscure governor of Alaska, Sarah Palin, as his running mate. That’s nothing compared to the sucker bet the American people are forced to make every four years. For instance, who knew that Herbert Hoover, who had been such a heroic do-gooder for the Belgians during their food crisis of 1914, would turn out to be a president blatantly blasé about Americans who were starving during the Great Depression? And what was it like to turn on the radio in Kansas City on Aug. 6, 1945, to hear the news about Hiroshima and realize that the commander in chief who gave the order to unleash the most terrifying weapon in the history of the world was the guy who used to sell you your hats? Follow-up: How did Harry Truman draw on his executive experience as the proprietor of a haberdashery to decide whether to vaporize a town?

Christ Church as it is: Creationist Credentials

A couple of weeks ago, I introduced Christ Church, Moscow, Idaho’s friendly neighborhood theocracy-in-embryo, which weds garden-variety Christian Right hypocrisy with creepy, racist Neo-Confederate overtones. Today, I’m going to have a look at the Christ Church-affiliated New Saint Andrews College.

NSA cultivates a reputation as the ivory tower’s ivory tower – the curriculum includes lots of Classical studies, including Greek and Latin; the school’s vision statement puts much emphasis on the supremacy of Western Culture (or “Traditio occidentalis“). Zombie C.S. Lewis could totally be a member of the faculty, if he were into theocratic fundamentalism. Said faculty are all wearing Scholarly Robes in the group photo.


The original ivory tower is at the
University of Pittsburgh

Photo by Jeremy B. Yoder.

There’s nothing wrong with focusing on classical studies. NSA’s air of musty erudition has attracted a mostly positive profile by the New York Times Magazine and a favorable rating from the conservative Intercollegiate Studies Institute. (Full disclosure: my alma mater, Eastern Mennonite University, was also recognized by ISI.)

But, basically by their own admission, Christ Church’s theology is strongly right-wing. Is NSA’s ivory tower secure against the ideology of the church that founded it? The evidence is, not so much. NSA’s Code of Conduct sounds all sorts of alarm bells:

“The College seeks to recover true academic freedom, that is, submission to God’s Word in all our actions and attitudes in and out of the classroom.

As does the NSA Students’ Pledge:

I pledge to maintain sound Christian doctrine, to regularly attend an orthodox church, and to maintain a teachable spirit. I pledge to abstain from actively promoting doctrines contrary to the mission and goals of the College.

Who decides what is “God’s Word” and “sound Christian doctrine?” Conveniently, Doug Wilson, the pastor of Christ Church, is both a Board of Trustees member and a “Senior Fellow” at NSA. In fact, of seventeen faculty members, three are Wilsons. That’s DW, his son (if I’m not mistaken) Nathan, and brother Gordon.

Gordon L. Wilson, the “Senior Fellow of Natural Philosophy,” is actually my closest contact to NSA. Last fall I attended a debate on the topic of intelligent design between GLW and Washington State University biologist Mike Webster. It wasn’t pretty. GLW, who is basically miles to the right of Michael Behe, didn’t make a very good impression on behalf of NSA’s high-minded curriculum in rhetoric and philosophy – he dodged questions, failed to support his assertions, and generally displayed an inability (or unwillingness) to comprehend the logical underpinnings of the Scientific Method. In a particularly telling moment, he asserted that the reason ID/Creationists haven’t developed any testable hypotheses is because biased funding agencies won’t give them money.

That, of course, is laughable to anyone who does science for a living (i.e., a sizable chunk of GLW’s audience), because no one gets grant funding to develop hypotheses. Funding requests are descriptions of how you will test a hypothesis through a specific program of experiments or data collection. In other words, scientists receive funding after they develop hypotheses and convince funding agencies that they have a good way to test them.


The Eastern Box Turtle,
Terrapene carolina

Photo by West Virgina Blue.

It’s entirely possible that Gordon Wilson doesn’t actually know how scientific funding works. Which is consistent with the hypothesis that he’s more interested in adhering to his concept of “sound Christian doctrine” than doing science. The only published peer-reviewed research NSA’s Senior Fellow of Natural Philosophy has produced is a 2005 paper on the breeding ecology of box turtles [$-a]. (GLW’s NSA profile also mentions published “research, field notes, and abstracts,” but this is the only paper that comes up in a Google Scholar search.) It’s basically a census, although there are some t-tests. And it was funded not by an outside grant, but by what seems to be a donation from the biology department where GLW was an instructor when he did the study. Here’s the only mention of funding in the Acknowledgments section:

We would like to thank Paul Sattler (Chair) for allocating Liberty University Biology funds for the purchase of much of the field equipment necessary for this study.

To put this in perspective: I’m now a fourth-year doctoral student, and I’m not nearly to the point of having enough published work on my CV to say I’ve earned my doctorate yet, much less apply for a faculty position at a good university. I’ve personally written (as near as I can recall) four major grant requests, and contributed to a fifth; I’m a coauthor on a review article, one published original research article [$-a], and a third in press; I’m a coauthor on two more articles that are submitted for review, and I’m waiting for my first first-authored paper to go out to reviewers. And (what the heck) I’ve been published in the letters column of Science. Let me repeat: my pubs list is piddly. But it’s bigger than Gordon Wilson’s, and he’s somehow on the faculty at NSA. With the word “senior” in his title.

NSA might have a bang-up program as far as Latin studies go, but its resident “biologist” is clearly more interested in ideology than biology. I can’t say that bodes well for the “intellectual rigor” of the rest of the curriculum.

Edit, 7 Sept. 2008:
Added a couple of links to the NSA faculty pages in references to Doug Wilson’s positions at NSA and the number of Wilsons on the faculty.

Correction, 9 Sept. 2008:
Corrected the relationships between the Wilsons on the NSA faculty.

References

W. Godsoe, J.B. Yoder, C.I. Smith, O. Pellmyr (2008). Coevolution and Divergence in the Joshua Tree/Yucca Moth Mutualism The American Naturalist, 171 (6), 816-23 DOI: 10.1086/587757

R. Gomulkiewicz, D.M. Drown, M.F. Dybdahl, W. Godsoe, S.L. Nuismer, K.M. Pepin, B.J. Ridenhour, C.I. Smith, J.B. Yoder (2007). Dos and don’ts of testing the geographic mosaic theory of coevolution Heredity, 98 (5), 249-58 DOI: 10.1038/sj.hdy.6800949

G.L. Wilson, C.H. Ernst (2005). Reproductive Ecology of the Terrapene carolina carolina (Eastern Box Turtle) in Central Virginia Southeastern Naturalist, 4 (4) DOI: 10.1656/1528-7092(2005)004[0689:REOTTC]2.0.CO;2

J.B. Yoder, B. Shneiderman (2008). Science 2.0: Not So New? Science, 320 (5881), 1290-1 DOI: 10.1126/science.320.5881.1290

Blessed be Darwin

The Onion reports: Evolutionists flock to Darwin-shaped wall stain.

Since witnesses first reported the unexplained marking—which appears to resemble a 19th-century male figure with a high forehead and large beard—this normally quiet town has become a hotbed of biological zealotry. Thousands of pilgrims from as far away as Berkeley’s paleoanthropology department have flocked to the site to lay wreaths of flowers, light devotional candles, read aloud from Darwin’s works, and otherwise pay homage to the mysterious blue-green stain.

School shooting defused peacefully

Yesterday, in Willoughby, Ohio, a student brought a gun to school – and, instead of calling in the SWAT team, the principal and assistant principal confronted him and talked him down.

“Our gut told us that the young man did not want to hurt us, but he may in fact be ready to hurt himself very soon,” Lyons told NPR’s “All Things Considered” in an interview broadcast this afternoon. “Panic mode did set in a bit, but we then said to ourselves, ‘what are we going to do to keep this young man safe?'” Lyons said that he and the principal drew on years of experience working with kids, and, when the student threatened suicide, Lyons actually told him about his memories of a high school friend who had killed himself.

Not only is this an example of incredible bravery, it demonstrates that a peaceful response to a violent situation takes more nerve and creativity than simply resorting to force. I have a t-shirt with that message, but Lyons and his fellow administrator lived it yesterday.

Species hiding in plain sight

ResearchBlogging.orgIt’s a truism that biologists have cataloged only a fraction of the living things on Earth. This is a major problem for conservationists, ecologists, and evolutionary biologists, because many of the questions we want to answer (“Which parcel of rain forest should we preserve?” or “How do species interactions play out over millions of years?”) hinge how we count species.

One solution is DNA barcoding, which uses the evolutionary divergence encoded in DNA sequences to tell species apart [$-a]. Barcoding is supposed to help researchers identify species without being experts in the fiddly business of taxonomy based on physical traits. It can also differentiate species that might never be recognized as separate without a DNA analysis.


Caterpillar with braconid pupae
Photo by Anita Gould.

An open-access article in last week’s PNAS does exactly that for a group of wasps in the family Braconidae. Braconid wasps are parasitoids, laying their eggs in live hosts. Eventually the eggs hatch and the larvae eat their host alive, then emerge to form pupae like those on the Hog Sphinx Moth caterpillar in the photo. (Insert obligatory reference to Alien here.)

Parasitoid wasps are thought to be hugely diverse, in part because coevolutionary interactions between larvae and their hosts’ immune systems might force each wasp species to specialize on one or a few hosts. Smith and coauthors use barcoding based on nuclear and mitochondrial DNA to determine the diversity of braconid wasps within a Costa Rican conservation area, comparing the results to those produced from a traditional taxonomic survey. Traditional methods found 171 potential species – and barcoding turned up another 142! These additional species were basically identical to the eye, but in many cases they’re actually collections of similar species using different hosts.

So not only are there more wasp species than traditional methods would detect – they’re more specialized than we’d know without barcoding. DNA Barcoding can make some biologists (including me) a little squeamish; it’s worrying to picture a world where no one really knows the organisms they study except through DNA sequence data. But Smith et al. are applying the method to find diversity that would probably not be detected in any other way, with results that bear directly on how we think about the interactions between parasitoids and their hosts. That’s unquestionably a good thing.

References

P.D.N. Hebert, A. Cywinska, S.L. Ball, J.R. deWaard (2003). Biological identifications through DNA barcodes Proc. Royal Soc. B., 270 (1512), 313-21 DOI: 10.1098/rspb.2002.2218

M.A. Smith, J.J. Rodriguez, J.B. Whitfield, A.R. Deans, D.H. Janzen, W. Hallwachs, P.D.N. Hebert (2008). Extreme diversity of tropical parasitoid wasps exposed by iterative integration of natural history, DNA barcoding, morphology, and collections PNAS, 105 (34), 12359-64 DOI: 10.1073/pnas.0805319105

Mennonite Weekly goes Web 2.0

Mennonite Weekly Review, an independent publication covering the news of what a taxonomist might call the Mennonite community sensu lato (Mennonite Church USA, Old Order, Amish, Brethren, and other flavors of Anabaptists), has a slick new website. The overall setup is far easier to navigate than the old site, which was frankly painful to dig through, and articles now have comment forums attached. I’ll definitely be keeping an eye on this new site, and very probably making a donation.

Big herbivores shape plant community response to global warming

ResearchBlogging.orgThe cover article from this week’s PNAS has important implications for how we plan for, and deal with, climate change. Post and Pedersen report that the way an arctic plant community changes in response to warming depends heavily on the presence of large herbivores [$-a], like muskoxen and caribou.


Photo by Giant Ginkgo.

Previously, it was thought that one effect of global climate change would be for woody shrubs and dwarf trees to become more common in arctic and subarctic plant communities. This increase in woody plants could trap more atmospheric carbon and increase the albedo of the land – meaning more heat could be reflected back into space. Both of which effects might help slow a warming global climate.

However, Post and Pedersen show that large herbivores can reduce this shift in community composition. In huge five-year study, they set up experimental plots from which caribou and muskoxen were either excluded by fencing, or not excluded. Within each class of plot, they also placed 1.5-m “open-topped chambers” (OTCs) made of fiberglass – basically, cylinders that help trap solar heat, warming the ground inside. In the fenced plots, the plant communities inside the OTCs shifted toward more woody species; but in the unfenced plots, where large herbivores could reach in and graze inside the warmed cylinders, plant communities didn’t develop greater cover by woody species.

Now, it’s not surprising that large herbivores can have a profound effect on the plant species that grow in their grazing land. Where I come from, in the northeast U.S., large swaths of forest have been dramatically altered [$-a] by a population explosion of white-tailed deer freed from their natural predators. But Post and Pedersen have drawn a connection between this effect and the ways in which natural communities may respond to the most dramatic environmental change in human history. It just goes to show what a massively complex system we humans are tinkering with, and how little we know about what that tinkering may ultimately do.

References

E. Post, C. Pedersen (2008). Opposing plant community responses to warming with and without herbivores PNAS, 105 (34), 12353-8 DOI: 10.1073/pnas.0802421105

F.L. Russell, D.B. Zippin, N.L. Fowler (2001). Effects of white-tailed deer (Odocoileus virginianus) on plants, plant populations and communities: A review The American Midland Naturalist, 146 (1), 1-26 DOI: 10.1674/0003-0031(2001)146[0001:EOWTDO]2.0.CO;2