Monthly Archives: October 2008

Security theater

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Photo by nedrichards.

Under the guidance of security expert Bruce Schneier, Jeffrey Goldberg goes on a quest to see what he can and can’t take through airport security. It’s simultaneously funny, sad, and worrying:

… because I have a fair amount of experience reporting on terrorists … I’ve amassed an inspiring collection of al-Qaeda T-shirts, Islamic Jihad flags, Hezbollah videotapes, and inflatable Yasir Arafat dolls (really). All these things I’ve carried with me through airports across the country. I’ve also carried, at various times: pocketknives, matches from hotels in Beirut and Peshawar, dust masks, lengths of rope, cigarette lighters, nail clippers, eight-ounce tubes of toothpaste (in my front pocket), bottles of Fiji Water (which is foreign), and, of course, box cutters. I was selected for secondary screening four times—out of dozens of passages through security checkpoints—during this extended experiment. At one screening, I was relieved of a pair of nail clippers; during another, a can of shaving cream.

The piece is a perfect encapsulation of how absurd airport security has become – all about making passengers feel like they’ve had a hard time getting to the plane, so we know terrorists would have to take their shoes off. Which would totally stop me, were I a terrorist.

via kottke.org

Old vials of chemical residue published in Science

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ResearchBlogging.orgThe chief lesson from a new article in this week’s Science is, never, ever throw out out your samples. Most people are probably familiar with Stanley Miller’s classic biochemistry experiment, in which he produced amino acids in a simulation of Earth’s early atmosphere [PDF]. That experiment was groundbreaking, but since it was published in 1953 geochemsists have questioned whether it accurately reflected conditions on ancient Earth. But another of Miller’s experimental results, which went unpublished until now, may be the response to that criticism.


Volcanic steam: the origin of
life on Earth?
Photo by vtveen.

After Miller’s death in 2007, one of his former graduate students inherited a bunch of boxes full of Miller’s experimental products. The box included products from an experiment simulating steamy conditions around a volcanic vent. The student, Jeffrey Bada, decided to re-analyze the preserved product using (among other approaches) high-performance liquid chromatography, a method of identifying organic compounds that wasn’t available when Miller did his original work in the 1950s. It turns out that the volcano experiment produced an even richer array of amino acids than Miller knew [$-a]. Enough, maybe, to lay the groundwork for life. That’s what Bada and his coauthors argue:

Reduced gases and lightning associated with volcanic eruptions in hot spots or island arc–type systems could have been prevalent on the early Earth before extensive continents formed. … Amino acids formed in volcanic island systems could have accumulated in tidal areas, where they could be polymerized by carbonyl sulfide, a simple volcanic gas that has been shown to form peptides under mild conditions.

Naturally, this is only a jumping-off point for further work, starting with replication of Miller’s original experiment. But it’s a useful discovery, and a cautionary tale to any grad student who’s careless about record-keeping – you never know when that throwaway result will turn out to be useful.

References

A.P. Johnson, H.J. Cleaves, J.P. Dworkin, D.P. Glavin, A. Lazcano, J.L. Bada (2008). The Miller volcanic spark discharge experiment Science, 322 (5900), 404-404 DOI: 10.1126/science.1161527

S.L. Miller (1953). A production of amino acids under possible primitive Earth conditions Science, 117, 528-9 Full text (PDF)

Sympatric skepticism

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ResearchBlogging.orgThe new issue of The Journal of Evolutionary Biology has a great article on a question that dates back to Darwin: sympatric speciation[$-a].

Sympatric speciation is simply speciation that occurs when a species splits into two reproductively isolated groups without any physical barrier arising between those groups. It’s often treated as the opposite of allopatric speciation, in which a species is split by some external barrier (a new mountain range, a river, &c) and the separated populations evolve on different trajectories until they’re unable to exchange genes even if the barrier is removed. There are a number of ways biologists think this can happen – for instance, a population of insects using two different, co-occurring host plants, might split into two species on the different hosts – but not many good cases where we’re pretty sure that it has happened.

In the new article, Kirkpatrick and his coauthors argue that the problem is one of definition. Sympatic speciation, as a concept, is set up to be impossible to test conclusively: Although it’s easy to show that two closely-related species occupy the same territory in the present, it’s rarely possible to show that they became different species while they were occupying the same territory at some point in the past, much less that they were “panmictic,” or freely interbreeding.

The problem for empiricists is that biogeographical sympatry is relatively straightforward to diagnose, but the initial condition of panmixia specified by population genetic models is virtually impossible to test.

As an alternative, the authors suggest ignoring the Platonic ideals of “allopatric” versus “sympatric” speciation, and instead concentrating on the interaction between divergent natural selection and gene flow in causing or preventing speciation. Not only is this sensible, it’s what most evolutionary ecologists are doing right now, anyway.

Reference

B.M. Fitzpatrick, J.A. Fordyce, S. Gavrilets (2008). What, if anything, is sympatric speciation? Journal of Evolutionary Biology, 1452-9 DOI: 10.1111/j.1420-9101.2008.01611.x

Paper trail

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The Washington Post has copies of two secret memos in which the Bush Administration officially endorsed waterboarding. What forced the Administration to go on-record? The CIA wanted cover:

The repeated requests for a paper trail reflected growing worries within the CIA that the administration might later distance itself from key decisions about the handling of captured al-Qaeda leaders, former intelligence officials said. The concerns grew more pronounced after the revelations of mistreatment of detainees at the Abu Ghraib prison in Iraq, and further still as tensions grew between the administration and its intelligence advisers over the conduct of the Iraq war.

Prosecution, alas, remains an open question.

Via the Daily Beast.

Pacifism in the age of the professional military

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It’s a little weird being a pacifist in the modern United States. Sure, we don’t pick fistfights, and we vote for anti-war (or at least less pro-war) politicians, but even in wartime we don’t face the hard choice of a military draft, as my grandfathers did during World War II. The military is an all-volunteer organization these days, and pacifists are free not to volunteer.

Is that all there is to peaceful living? The new issue of The Mennonite has an excellent essay by M.J. Sharp, in which he reminds his readers that pacifism means more than omitting to participate in war – it means actively helping to oppose it. M.J. recounts the story of Robert Weiss, a serviceman who came to be a conscientious objector while in the Army, and argues that those of us for whom pacifism is easy should stand up to help those for whom it is still a tough choice:

I have had many opportunities to tell the stories of our forbears, and I know from experience that those stories inspire others. But let’s make it more than our history. God is moving among some service members today as vibrantly as God moved among the early disciples and early Anabaptists. Our task is to help meld our historical understanding of Jesus’ call to peace with the fresh awakenings among those who once wielded weapons of war.

Nowhere to go but uphill

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ResearchBlogging.orgHistorical data sets are invaluable in assessing the impact of climate change on natural systems. Case in point: in today’s issue of Science, a new paper uses a century-old survey of small mammals in Yosemite National Park to see how the park’s community has shifted as climate warmed [$-a].


Belding’s ground squirrels contracted their
high-altitude range as climate warmed.
Photo by infinite wilderness.

Moritz et al. repeated a survey of small mammals – chipmunks, shrews, ground squirrels, and the like – originally conducted by the biologist Joseph Grinnell between 1914 and 1920. Since that time, average minimum monthly temperatures in the Yosemite area have increased approximately three degrees Centigrade (five and a half degrees Fahrenheit), and Moritz et al. found significant changes in the distributions of small mammals associated with that warming.

In the face of warming temperatures, the easiest thing for animals to do is move up to the cooler climes at higher elevations, and this is what many species did. Those at lower elevations expanded their ranges uphill. But small mammals already living at high elevations, like the aptly named Alpine Chipmunk (Tamias alpinus) have nowhere cooler to go – so their ranges contracted over the last century. As the globe warms up, this pattern is likely being repeated in ecosystems everywhere – not a happy prospect for critters that live at high elevations.

Reference

C Moritz, JL Patton, CJ Conroy, JL Parra, GC White, SR Beissinger (2008). Impact of a Century of Climate Change on Small-Mammal Communities in Yosemite National Park, USA. Science, 322, 261-4 DOI: 10.1126/science.1163428

Joshua tree genetics suggest coevolutionary divergence

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ResearchBlogging.orgThe latest results from the Pellmyr Lab’s ongoing study of Joshua tree and its pollinators are online as part of the new October issue of Evolution. It’s the cover article, no less. The study, whose lead author is Chris Smith (now on the faculty at Willamette University) compares patterns in the population genetics of Joshua trees and the moths that pollinate them, and shows that although the moths have become two separate species, the trees may not have followed suit [PDF].

Evolution cover
Photo by Chris Smith.

Female yucca moths carry pollen between Joshua tree flowers in special mouthparts. When she arrives at a new flower, the female moth lays her eggs inside it, then deliberately applies pollen to the flower’s receptive surface. When the fertilized flower develops into a fruit, the moth eggs hatch, and the larvae eat some of the seeds inside the fruit.

Among the yuccas, Joshua trees are unique because they’re pollinated by two species of moths, which are each other’s closest evolutionary relative. One species is found in the eastern part of Joshua tree’s range, the other in the west. Joshua trees from the east and west have differently-shaped flowers [PDF], which is consistent with the hypothesis that coevolution between moths and trees has driven both toward an evolutionary split.

“Western” Joshua trees at Joshua Tree National Park. Photo by me.

The new study goes deeper to look at genetic relationships between different populations of the moths and the trees, and what it finds isn’t as tidy as the earlier work might suggest: While Joshua trees’ morphology corresponds nicely to the split in the pollinators, the patterns visible in their chloroplast DNA does not. In some populations, trees look “eastern,” but have chloroplast DNA more closely related to “western” populations. This suggests that, although the moths have become separate species, they’re still moving between the two kinds of Joshua tree frequently enough that the trees haven’t quite split. Why do the two tree types look different, then? One possibility is coevolution with the two moth species, which might exert selection the trees in different ways.

There’s still a lot of work to do before we fully understand what’s going on here. Will Godsoe, the other doctoral student in our lab, is doing some intensive niche modeling to see how much environmental differences might be contributing to the patterns we see here. My own dissertation will look at whether the same incongruities turn up in nuclear DNA, which can have a different evolutionary history than that in the chloroplast.

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

C.I. Smith, W.K.W. Godsoe, S. Tank, J.B. Yoder, O. Pellmyr (2008). Distinguishing coevolution from covicariance in an obligate pollination mutualism: asynchronous divergence in Joshua tree and its pollinators. Evolution, 62 (10), 2676-87 DOI: 10.1111/j.1558-5646.2008.00500.x

Utopian lepidoptery

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This month’s issue of Wired reports on DNA barcoding, with extensive interviews of barcoding masterminds Dan Janzen and Paul Hebert. In spite of myself, I’m charmed by the article’s description of Janzen as a “utopian lepidopterist.”


Photo by fabbio.

I’ve posted about one recent Janzen-Hebert barcoding paper, and about a subsequently-released study that suggests a major problem for the usefulness of the preferred “barcode” gene, COI. I’d say the Wired coverage is actually pretty OK for a popular treatment – it acknowledges criticism of barcoding, even though, in typical Wired fashion, the piece is obviously most interested in the whiz-bang ideas like a “species tricorder” handheld device for field I.D. of organisms. Good geek that I am, I would have liked to see more discussion of the actual technical issues – what about the difficulties of using mitochondrial DNA for plant I.D.?

Update: No one is proposing using mitochondrial DNA for barcoding plants. Which is good, because it would be silly – DNA in the plant mitochondrion mutates extremely slowly, so it doesn’t build up much difference between closely-related species. Instead, Kress and coauthors proposed using both a nuclear gene and a segment of chloroplast DNA in a 2005 paper.