Monthly Archives: September 2008

Alphistia: A project in geofiction

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Alphistia is a fictional nation conceived in Tolkienian detail by Tony Skaggs. I discovered it when Tony emailed me yesterday on an unrelated topic, and I clicked the URL in his signature.

“Alphistia is mostly a ‘me, myself, and I’ project,” Tony wrote when I asked him about it, “although I’ve been surprised that since I put up a couple of youtube videos, I’ve had contacts from several language geeks (I use that word as a high honor) who have gone to the trouble to learn it a bit and write me in pretty fluent Alphistian.”

That’s right. Alphistian is a well-elaborated language, from grammar to syntax. I’m enough of a geek to use a word like “Tolkienian” advisedly, but I’d say it fits here. (I’ll confess up front that I haven’t made it through the video language lessons on YouTube.) Alphistia also has a draft constitution, a detailed geography, and an epic mythology. There’s also a manifesto that reads like a declaration of independence for left-leaning pioneers:

Alphistia would be modeled on the best ideals of the Western Englightenment: a secular society with a respect for human rights and the dignity of the individual. Politically, Alphistia would be a constitutional republic, with a democratically elected government, using a form of proportional representation. Economically, it would encourage small businesses and profit-making cooperatives. The economic system would be a sustainable, humane, and regulated capitalism.

Utopian, maybe, but if we didn’t have utopias, how would we know what we want our society to look like? Vanderse hoiven (friendly greetings), Tony.

DNA barcoding: A glitch in the system?

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ResearchBlogging.orgFollowing up on last week’s post about uncovering hidden species using DNA diversity (or “DNA barcoding”), an open-access paper in this week’s issue of PNAS demonstrates a potentially significant glitch in the system: mitochondrial pseudogenes.

The original DNA barcoding concept is straightforward, if not uncontroversial – use a standard DNA sequence marker to identify (“barcode”) species that might be challenging to ID otherwise, or previously not known as separate species. The proposed standard marker is a mitochondrial gene that codes for the protein cytochrome oxidase I (COI), which varies quite a bit between animal species (though it wouldn’t work for plants, whose mitochondrial DNA mutates very rarely). The lab where I work has used COI for a lot of studies in yucca moths, though not barcoding per se.


Photo by fabbio.

One potential problem with barcoding is that sequencing any gene in one species using procedures derived from another species is always a bit risky. DNA sequencing relies on primers, short snippets of DNA that bind to a region near the target gene as part of the reaction that makes lots of copies of that gene for analysis (this is called PCR, for polymerase chain reaction). The easiest way to get sequence data for a new species is to try and use primers from a close relative – if there aren’t any mutations at the primer site, they should carry over. But mutation happens, and it can definitely happen at primer sites.

Primer site mutations are a minor problem compared to pseudogenes, the focus of the new paper by Song et al. Pseudogenes are a result of gene duplication, a mutation in which an extra copy of a gene is accidentally created during DNA replication. Because it’s redundant, the extra copy can absorb mutations that destroy its function without harming individuals who carry it. The duplicate is then “junk DNA,” free to accumulate mutations – a pseudogene. (Gene duplication is also one way that new proteins and gene functions can evolve – but that’s beyond the scope of the present post.) A primer site mutation just means that primers from one species won’t work on another, but a pseudogene might still bind to primers. And then you can get sequence data from the pseudogene instead of the target gene.

DNA barcoding identifies species based on how many mutations have accumulated since they split from a common ancestor; a pseudogene, which mutates faster, can make two samples look further apart then than they are. So barcoding studies that accidentally use pseudogenes may identify two species where only one exists. Song et al. use data on mitochondrial pseudogenes in insects and crustaceans to argue that pseudogenes are both common and unpredictable. They also perform barcoding on grasshoppers and crustaceans using data “contaminated” with pseudogenes and data without – unsurprisingly, pseudogenes inflated the number of species detected by barcoding. Although Song et al. suggest a few ways to reduce the odds of interference from pseudogenes, they conclude that there is no way to completely eliminate this problem.

Last week’s paper by Smith and colleagues showed the importance of species identification for conservationists, ecologists, and evolutionary biologists. This new result suggests that DNA barcoding may not be the best way to identify species.

References

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

H. Song, J.E. Buhay, M.F. Whiting, K.A. Crandall (2008). Many species in one: DNA barcoding overestimates the number of species when nuclear mitochondrial pseudogenes are coamplified PNAS, 105 (36), 13486-91 DOI: 10.1073/pnas.0803076105

It has come to my attention

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… that some readers are attempting to post comments, but experiencing some sort of glitch with the commenting system, in at least one case having to do with the “word verification” anti-spam device. I’m not sure what’s going on – I’ve successfully posted a nonsense comment myself (logged out of Blogger, to approximate the experience of a reader). I’m going to try and dig a bit more, and see what I can do to fix it. I’m reluctant to disable the word verification, but I also want readers to be able to comment!

Update 2008.09.14 – There’s a known issue for Blogger in Beta that sounds like what’s been described to me, though it’s supposed to have been fixed as of 2006. I’ve posted a note in Blogger’s support forum. Until I have an answer I’m switching comment submission back to the old Blogger system, where you’ll be taken to a separate page to post a comment. It’s clunky, but it used to work.

Welcome to the blogosphere

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Resistance is futile: Michael “MJ” Sharp, with whom I spent many a sleepless night editing the EMU campus newspaper WeatherVane, has started a blog. MJ’s currently in Germany, where he’s worked with a project that counsels U.S. soldiers seeking conscientious objector status, and he’s done quite a bit of traveling besides, including to Iraq. Which naturally leads one to wonder, why isn’t he running for Vice President?

Blogging research

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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

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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

Sarah Vowell on John McCain

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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

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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

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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.