For shame

Andrew Sullivan points to a deeply troubling poll result: 54 percent of Americans who attend church more often say that torturing suspected terrorists is acceptable, compared to 42 percent of those who "seldom or never" go to services. Have these people even read the Gospel? Even heard it preached? In the most literal sense, this is a damning discovery about American Christians.

DFW in a nutshell

Tom Bissell discusses the commencement speech David Foster Wallace gave at the 2005 Kenyon College Commencement, on the occasion of said speech's publication as a stand-alone book. Bissell is right that it's a fantastic essay -- simpler and clearer than much of Wallace's writing, yet containing all of the over-self-consciousness and humanity that marked the best of his fiction.

The capital-T Truth is about life before death. It is about making it to thirty, or maybe even fifty, without wanting to shoot yourself in the head. It is about the real value of a real education, which has nothing to do with grades or degrees and everything to do with simple awareness -- awareness of what is so real and essential, so hidden in plain sight all around us, that we have to keep reminding ourselves "This is water, this is water; these Eskimos might be much more than they seem."

But Bissell's wrong to say that the speech wasn't available in print before this: I discovered it in my copy of The Best American Non-required Reading 2006, which (with all due respect to the publishers of the new volume) is probably a better value.

Happy Birthday Strunk & White: You suck!

For the 50th anniversary of The Elements of Style, the little writing guide by William Strunk, Jr. and E.B. White, the New York Times "Room for debate" feature invites linguists and grammar geeks to discuss the book's impact. The only "debate" however, seems to be over whether S&W is merely outdated and worthless, or actively harmful. Here's Geoffrey Pullman, professor of linguistics at the University of Edinburgh:

Again and again, Strunk and White recommend the stuffy and unidiomatic, and warn against what sounds effective and natural. Even their beliefs about English as it used to be are wrong; but foisting their prejudices on today’s students is much more so.

And here's professor of English Ben Yagoda, from the University of Delaware:

White purports to be talking about “style” but is really advocating a particular style. It is a style of absence: absence of grammatical mistakes, breeziness, opinions, jargon, clichés, mixed metaphors, wordiness and, indeed, anything that could cloud the transparency of the prose and remind readers that a real person composed it.

Clearly none of the contributors have recently read through a pile of undergraduate writing assignments. S&W, and the "stuffy and unidiomatic" style they advocate, is the only antidote for the sort of dreadful writing undergraduates learn to produce over twelve years of assignments based on filling up a given amount of space. Beginning writers don't have an ear for what is "effective and natural" -- they need training wheels.

Photo by JKim1.

I've benefited from those training wheels myself. As both a writer and reader of scientific prose, I have nothing but respect for S&W's knee-jerk reaction against the passive voice, and their repeated exhortations to write clearly and simply. Sometimes the passive voice is indeed better (as S&W freely concede), but without great care it can reduce an already technical passage to an unreadable tangle. Likewise, it is sometimes necessary to use specialized vocabulary and twisty verbiage to communicate complex ideas; but more often these get in the way of communicating scientific results.

The little book never pretends to be the last word, but it is a vital starting point. As White wrote in the introduction:

It is an old observation that the best writers sometimes disregard the rules of rhetoric. When they do, however, the reader will usually find in the sentence some compensating merit, attained at the cost of the violation. Unless he is certain of doing as well, he will probably do best to follow the rules. After he has learned, by their guidance, to write plain English adequate for everyday uses, let him look, for the secrets of style, to the study of the masters of literature.

"No exceptional circumstances whatsoever"

Jesse Lava runs through the actual, on-the-books, law of the land regarding torture. Bottom line: torture, and even "acts of cruel, inhuman or degrading treatment or punishment which do not amount to torture" are illegal, regardless of how useful it is, or how scared we are, or what we saw Jack Bauer do in last week's episode. (It's impressive, and sad, the degree to which the language of the Geneva Conventions actually anticipates the justifications being bandied about in the media right now.) You'd think all this would go without saying. And, apparently you'd be wrong.

Female birds stop singing when they move north

A study in this week's Proceedings of the Royal Society B suggests that the sexually dimorphic pattern of birdsong we're used to in temperate latitudes -- with males singing elaborately and females usually not -- evolves because female birds stop singing when their species move to more northerly latitudes [$-a]. Why this is, however, remains an open question.

Photo by Vicki & Chuck Rogers.

The study's authors reconstruct the evolution of home range (temperate versus tropical) and sexual song dimorphism (both sexes singing versus only males singing) in the New World blackbirds, the family that includes orioles, cowbirds, and red-winged blackbirds (pictured). The reconstruction reveals a strongly significant association between the evolution of male-only singing and transitions from tropical to temperate breeding ranges. The authors discuss this transition in a few key groups, including North American red-winged blackbirds (Agelaius phoeniceus) and their sister species, the Cuban red-shouldered blackbird (A. assimilis):

Females of A. assimilis are nearly indistinguishable from conspecific males in song structure and song rate and are also similar in plumage and body size ... whereas females of A. phoeniceus differ considerably from conspeicific males in these traits .... it is clear that the changes in female song and plumage must have occurred quite rapidly. [In-text citations omitted.]

As clear as the observed pattern is, however, there doesn't seem to be a good general explanation for it. The authors point to cases where female singing is lost within tropical-breeding lineages, which might help disentangle the effects of latitude and other evolutionary forces generating the observed pattern. In these cases, loss of female song is associated with colonial nesting and polygynous breeding, whereas singing by both sexes is associated with year-round pairing.

The temperate-breeding blackbirds tend to be migratory, with males often arriving at the breeding range ahead of females to establish nest sites and territories. In these cases singing by the males serves to attract females and to announce ownership of territory. Could that migration-induced division of labor lead females to give up singing? I'm just an amateur birder, but it sounds plausible to me.

Reference

Price, J., Lanyon, S., & Omland, K. (2009). Losses of female song with changes from tropical to temperate breeding in the New World blackbirds Proceedings of the Royal Society B: Biological Sciences, 276 (1664), 1971-80 DOI: 10.1098/rspb.2008.1626

Talking systematics

Over at dechronization, Luke Harmon has started a series of interviews with leading systematic biologists. The first two are with Jack Sullivan, the editor-in-chief of Systematic Biology, and Joe Felsenstein, widely considered the godfather of modern phylogenetics. They're both well worth reading, and excellent examples of why scientists should blog: in what other venue would you see personal interviews with either of these guys?

(Full disclosure: Jack is on my doctoral committee, and I've audited his systematics class, which uses Felsenstein's authoritative textbook.)

Earth Day 2009

Un-bear-able (ha) predation creates variable natural selection

Natural selection is a fact of life. As Steven Jay Gould put it, it's an "inescapable conclusion" arising from the "undeniable facts" that (1) populations of living things have inheritable variation in many traits; and (2) produce a surplus of offspring. But populations often experience selection from multiple sources, and in conflicting directions. The cover article for this month's issue of Evolution suggests that bears may be creating ongoing selection in wild salmon populations, but the strength, and outcome, of that selection varies from stream to stream [$-a].

Selective agent at work
Photo by Dr.DeNo.

Salmon are famously anadromous -- they hatch in freshwater streams and swim out to sea, only to return to the stream of their birth to spawn before they die. Male salmon are generally better off if they're bigger, both to maximize stored energy for the return to their spawning site, and to better compete for mates when they arrive. Natural selection for larger bodies, however, is checked by bears, who preferentially target large, fatty fish. Yet bear predation varies from stream to stream: in narrower streams, where salmon are easier to catch, bears can fill up on big, newly-arrived fish; but in wide streams, bigger fish can more easily evade bears, so bears tend to target older, weaker fish instead.

In the new study, Carlson et al. show that this variation in the ease with which bears can catch big, newly arrived salmon results in variable natural selection among different streams. In three streams of different widths, they estimated the reproductive success of male salmon by measuring the gonads -- which shrink with each mating -- of males dead from old age or killed by bears. They then compared the relative reproductive success of these males with measurements of their body size. They found that the fitness of male salmon in the three study populations was a result of the compromise between the practical need to be larger, and the danger of predation by bears. More intense bear predation resulted in selection for smaller males; less intense predation favored larger males. What's more, the analysis found directional selection, but not stabilizing selection -- if this is correct, then the three salmon populations have not reached an evolutionary equilibrium yet.

What this means for these salmon populations over time is hard to say. Divergent natural selection has resulted in rapid evolution of reproductive isolation [$-a] in introduced salmon populations. However, the direction and intensity of natural selection can vary strongly over time [$-a] -- so the directional selection Carlson et al. document here, over two or three years in each stream, may look very different measured over a longer sampling period.

References

Carlson, S., Hilborn, R., Hendry, A., & Quinn, T. (2007). Predation by bears drives senescence in natural populations of salmon PLoS ONE, 2 (12) DOI: 10.1371/journal.pone.0001286

Carlson, S, Rich, HB, Jr., & Quinn, T (2009). Does variation in selection imposed by bears drive divergence among populations in the size and shape of sockeye salmon? Evolution, 63 (5), 1244-61 DOI: 10.1111/j.1558-5646.2009.00643.x

Grant, PR, & Grant, BR (2002). Unpredictable evolution in a 30-Year study of Darwin's finches Science, 296 (5568), 707-11 DOI: 10.1126/science.1070315

Hendry, A. (2000). Rapid evolution of reproductive isolation in the wild: Evidence from introduced salmon Science, 290 (5491), 516-8 DOI: 10.1126/science.290.5491.516

Wake me up when April ends

In the wake of shootings in Pittsburgh and Binghamton, NY (and Graham, WA and Charlotte, NC), Dahlia Lithwick wonders pointedly when Americans will stop treating gun violence like a force of nature and start thinking about the weapons that make it possible and the unbelievable right-wing vitriol that, in the wake of Barack Obama's election as President, may be helping to fuel it.

Nobody claims that Glenn Beck is responsible for killing people. Nobody thinks guns are inherently evil. But how can there be an honest national debate over gun violence if we cannot even acknowledge the connections between people who admonish us to become "armed and dangerous" and a citizen's decision to arm himself and kill?

The guns, and the anger, are symptoms of a sick culture. Certainly, you can treat alcoholism by banning booze, but you haven't cured it until the alcoholic knows why he cannot -- must not -- have a drink, and has the spiritual and mental resources to enforce that decision.

(Also on Slate: excerpts of a new book about the Columbine killings.)

Ants trim trees for more living space

In the natural world, cooperative interactions evolve not as expressions of altruism, but as careful "negotiations" between interacting species. Each player may benefit from the relationship, but each stands to benefit from trying to cheat the other. In this month's issue of The American Naturalist, we see a prime example: mutualistic ants sterilize their host plants [$-a] to get the most out of the interaction.

Cordia nodosa flowers (top)
and ant domatia (bottom)
Photos by Russian_in_Brazil.

The ant species Allomerus octoarticulatus is part of a classic protection mutualism with the tropical tree Cordia nodosa, in which the plant grows structures called domatia that provide shelter for a colony of ants, and nutrient rich "food bodies" for the ants to feed on. The ants, in turn, patrol the plant and drive off herbivores. This mutually beneficial relationship also sets up a conflict of interest. The tree must divide its resources between providing food and shelter for its resident ant colony -- growing new domatia and fruiting bodies -- and its own reproductive efforts -- growing flowers and fruit. The ants, naturally, would prefer for the host tree to spend as much energy as possible on them.

Indeed, Allomerus octoarticulatus has been observed killing the flowers of its host trees. This is what led the new paper's author, Megan Frederickson, to conduct a simple experiment on C. nodosa, asking whether such pruning prompts the tree to grow more domatia. She experimentally removed flowers from trees occupied by a species of ants that don't engage in flower pruning to see if pruned trees grew more domatia -- and pruned trees grew more domatia over the course of four months than trees that were allowed to flower and produce fruit.

Ant-hosting plants need not be totally subject to the whims of their protectors, however -- this kind of regulation works both ways. A study published last year in Science found that ant-hosting Acacia trees cut back on support for their resident ant colonies [$-a] when herbivores are removed and ant protection is no longer needed. (I wrote about this study back when it was released.) It seems likely that flower-pruning ants are exerting strong selection on Cordia nodosa to circumvent this behavior -- a new tree variant that can overcome pruning, or make life uncomfortable for pruning ants, should have a large selective advantage.

In the absence of such a mutation, as Frederickson points out, Allomerus octoarticulatus is creating a tragedy of the commons by reducing the long-term viability of its host tree's populations in exchange for the short-term benefit of more living space. As it stands, Cordia nodosa can only reproduce when it hosts non-pruning ant species, which are a minority in the populations Frederickson studied. Only time, and further study, can determine whether this mutualism might break down altogether.

References

Frederickson, M. (2009). Conflict over reproduction in an ant-plant symbiosis: Why Allomerus octoarticulatus ants sterilize Cordia nodosa trees. The American Naturalist, 173 (5), 675-81 DOI: 10.1086/597608

Palmer, T., Stanton, M., Young, T., Goheen, J., Pringle, R., & Karban, R. (2008). Breakdown of an ant-plant mutualism follows the loss of large herbivores from an African savanna Science, 319 (5860), 192-5 DOI: 10.1126/science.1151579

Endless forms: The world's greatest mimic

Via Migrations.

The future of the newsmedia is already on my iPod

An article in Fast Company suggests that, with its booming online presence and willing-to-donate audience, National Public Radio may be the future of news in the U.S. The conflict between local affiliates -- who do most of the fundraising, and pay to broadcast NPR content -- and the push to make more shows available online is discussed, though it's not really anything I hadn't heard before. One thing I hadn't: from 1998 to 2008, while audiences for newspapers declined 11.4%, and network TV news dropped 28%, NPR's listenership grew 95.6%.

NPR's listenership has nearly doubled since 1999, even as newspaper circulation dropped off a cliff. Its programming now reaches 26.4 million listeners weekly -- far more than USA Today's 2.3 million daily circ or Fox News' 2.8 million prime-time audience. When newspapers were closing bureaus, NPR was opening them, and now runs 38 around the world, better than CNN.

Another point made in the article: NPR.org isn't able to provide good local news. This seems like an obvious niche for the local affiliates, many of whom produce their own original journalism (though with variable success). Seems like the ideal would be for my profile on NPR.org to know my zip code, and mix locally-produced content into my programming stream. When it was time for a new travel mug, the main site could direct my donation to the affiliate, maybe collecting a share for the national programming in the process.

Graduate degrees underwater

Emily Bazelon discusses how freshly-minted PhDs, Masters, and JDs say they're coping in the Great Downturn.

The studies that show [the economic benefit of an advanced degree] typically crunch broad swaths of data. They look at the census, or other large population samples, and show a positive correlation between income and years of education. This means that college and graduate school are generally a good bet. But it doesn't tell you that every single degree pays off financially at every single point in time.

And so there are lots of just-graduated grad students, many with debt from student loans, unable to do the work they're highly qualified to do.

I'm fortunate in multiple regards, here; I've probably got another two years to go, thanks to a just-received DDIG, so I'm not hitting the job market until the worst has (hopefully) passed. Because I've been lucky enough to be funded as either a teaching assistant or a research assistant (and can expect continued funding as one or the other), I don't have new debt related to grad school, even if I'm not exactly getting rich doing it. Being in a mostly NSF-funded field has been harrowing in recent years, but under the new administration things are looking better for funding in pure science - NSF did pretty well under the stimulus package, and should see better treatment in the regular budget, too. My only major worry is that when I graduate, I'll be competing for post-doctoral spots with an extra-large cohort of other folks who waited out the downturn as students.

Crucified agape

Tradition tells us to choose between respect for persons and participation in the movement of history; Jesus refuses because the movement of history is personal. Between the absolute agape which lets itself be crucified, and effectiveness (which it is assumed will usually need to be violent), the resurrection forbids us to choose, for in the light of resurrection crucified agape is not folly (as it seems to the Hellenizers to be) and weakness (as the Judaizers believe) but the wisdom and power of God (I Cor. 1:22-25).

John Howard Yoder, The Politics of Jesus (William B. Eerdmans Publishing Company, 1972)

Photo by jby.

Evolution-proof insecticide?

In this week's issue of PLoS Biology, an essay describes the perfect means for controlling malaria-carrying mosquitoes: an "evolution-proof insecticide." By taking advantage of the life history traits of both mosquitoes and the malaria parasite, Read et al. argue it should be possible to create an insecticide that will cut malaria transmission without selecting for resistance in the mosquitoes.

Malaria remains a major public health problem in much of the world - according the World Health Organization, a child dies of the disease every 30 seconds, and the cost of malaria may cut economic growth by as much as 1.3% in countries with high infection rates. In the absence of a vaccine, the best approach for malaria management is to control the mosquitoes that transmit the malaria parasite. This is usually done with insecticides, but these have a limited useful lifespan, as they create strong selective pressure for mosquito populations to evolve resistance.

Photo by LoreleiRanveig.

As Read et al. point out, it's not that we need to kill off mosquitoes as such; we just need to stop them from transmitting malaria. If this can be accomplished without strongly reducing the mosquitoes' fitness, it would reduce or eliminate selection for resistance. Malaria typically needs a long time to incubate inside a mosquito before it becomes transmissible to humans, and, in what Read et al. call "one of the great ironies of malaria," this incubation time is longer than most mosquitoes live. That is, the mosquitoes who successfully transmit malaria are the small proportion of the population who live long enough to incubate the parasite.

Here's where evolutionary biology interacts with the life history of malaria parasites in a highly convenient way: an insecticide that selectively targets older mosquitoes will have a smaller impact on the mosquito population's fitness. This is because most of a female mosquito's fitness - the total number of offspring she produces - is concentrated in her first one or two egg-laying cycles. Her fitness can increase if she survives to complete more cycles, but it's pretty rare that she does. From natural selection's point of view, that first of eggs counts much more than possible future batches, because they're not very likely.

For that hypothetical female mosquito to transmit malaria, she has to bite an infected human in the course of feeding to fuel one egg-laying cycle, then incubate the malaria parasites for an additional two to six cycles. Therefore, say Read et al., an insecticide that doesn't harm mosquitoes until they complete their first few egg-laying cycles is the "evolution-proof" solution - the only offspring it "steals" from the affected mosquitoes were pretty improbable anyway, and it prevents the malaria parasites from incubating long enough to successfully infect a new human host.

As it happens, the evolution-proof insecticide might not be a chemical agent, but a biological one. A paper I discussed back in January suggested that infecting malaria-carrying mosquitoes with the parasitic Wolbachia bacterium could control mosquito populations [$-a] by, yes, reducing their total lifespan to something less than the malaria parasite's incubation time. In short, it looks like the goal of a malaria-free world is not as improbable as it used to be.

References

McMeniman, C., Lane, R., Cass, B., Fong, A., Sidhu, M., Wang, Y., & O'Neill, S. (2009). Stable introduction of a life-shortening Wolbachia infection into the mosquito Aedes aegypti Science, 323 (5910), 141-144 DOI: 10.1126/science.1165326

Read, A., Lynch, P., & Thomas, M. (2009). How to make evolution-proof insecticides for malaria control PLoS Biology, 7 (4) DOI: 10.1371/journal.pbio.1000058

Why Jesus "suffered under Pontius Pilate"

Larry Hurtado discusses why the Roman government crucified Jesus (politics), as well as what Pilate's motives and the implications behind his chosen method of execution mean for Christianity.

Crucifixion was commonly regarded as not only frighteningly painful but also the most shameful of deaths. Essentially, it was reserved for those who were perceived as raising their hands against Roman rule or those who in some other way seemed to challenge the social order—for example, slaves who attacked their masters, and insurrectionists, such as the many Jews crucified by Roman Gen. Vespasian in the Jewish rebellion of 66-72.

The easter-egg hunt for scholarly PDFs

The Open Source Paleontologist has few good suggestions on digging up electronic copies of scholarly papers when you're outside the walled garden of institutional subscriptions. Google Scholar is getting better at identifying online PDF copies related to its results, but given that it doesn't seem to know about my doctoral advisor's considerable archive (he posts PDFs of all his pubs, as more and more academics do), I have to wonder what it's missing. I've started going there to check for PDFs before resorting to an [$-a] tag, though.

Primary sourcing

Via the Daily Dish: download the complete International Committee of the Red Cross report on torture of prisoners at Guantanamo Bay [PDF]. There needs to be an investigation, and prosecution of those responsible. If we let Spain do the job for us, it'll be a national shame on top of national shame.

Vocabulary for the day: "favorable enumeration"

Inspired by recent miseducational shenanigans in Texas, On the Media runs a great piece on the latest Creationist strategies for shoehorning fundamentalism into science class. NCSE's Eugenie Scott interviews well, and sparks fly when Bob Garfield talks to Casey Luskin, a "policy analyst" from the anti-science Discovery Institute:

BOB GARFIELD: What are the issues?

CASEY LUSKIN: Well, the issues are that there is a scientific controversy over evolution. And, of course, some scientists will tell you that there is no controversy, but the reality is that during the hearings of the Texas State Board of Education, we saw a number of Ph.D. biologists from top institutions come and testify about their scientific doubts about evolution.

BOB GARFIELD: Are you familiar with the fallacy of favorable enumeration? It says that you find a handful of examples that support your premise and you focus on them to the exclusion of the vast preponderance of circumstances that don't support your premise.

CASEY LUSKIN: Cherry picking is what you’re saying.

BOB GARFIELD: That’s called cherry picking.

CASEY LUSKIN: Okay, got it.

It's not the punch line, but you have to love "Well, the issues are that there is a scientific controversy over evolution. And, of course, some scientists will tell you that there is no controversy ..." That's right. You certainly can't trust us scientists to tell you about science. No sirree. We're biased.

Replanting the clear-cut

America's spiritual vocabulary--with its huge defining terms such as "God," "soul," "sacrifice," "mysticism," "faith," "salvation," "grace," "redemption"--has been enduring a series of abuses so constricting that the damage may last for centuries. Too many of us have tried to sidestep this damage by simply rejecting the terminology. The defamation of a religious vocabulary cannot be undone by turning away: the harm is undone when we work to reopen each word's true history, nuance, and depth. Holy words need stewardship as surely as do gardens, orchards, or ecosystems. When lovingly tended, such words surround us with spaciousness and mystery the way a sacred grove surrounds us with cathedral light, peace, and oxygenated air. When we merely abandon our holy words, and fail to replace them, we end up living in a spiritual clear-cut.

David James Duncan, "What fundamentalists need for their salvation." (God Laughs and Plays, Triad Books: 2006)

Photo by jby.

It has not been a quiet week in Lake Wobegon

The Onion goes for the low-hanging fruit with above-average results:

According to officials, the bodies were discovered when hundreds gathered to watch Mr. Berge's 1949 maroon Pontiac sink into the thawing lake as part of the annual Sons of Knute Ice Melt contest. As the car submerged, onlookers witnessed a number of purplish- looking corpses float to the surface, most of them decapitated.

A difficult adaptive landscape

Results of some free time to play around with Inkscape, which is looking to be a viable alternative to Illustrator. T-shirt worthy?

URL shortners = actually evil

Via Kottke.org: Joshua Schachter points out a few hazards of handing your links over to TinyURL and their ilk, and suggests some solutions.

The worst problem is that shortening services add another layer of indirection to an already creaky system. A regular hyperlink implicates a browser, its DNS resolver, the publisher's DNS server, and the publisher's website. With a shortening service, you're adding something that acts like a third DNS resolver, except one that is assembled out of unvetted PHP and MySQL, without the benevolent oversight of luminaries like Dan Kaminsky and St. Postel.

Since starting up on Twitter, it'd occurred to me that clicking a shortened URL is a pig in a poke at best. Yet somehow it doesn't feel as dangerous to accept a shortened URL from @apelad or @nprscottsimon as it would if I just found one in my email. Perhaps because, if they did post a hazardous link, I'd just un-follow?

Twitter = evil

PZ Meyers reaches the obvious conclusion:

Come on. You don't think a benign force would compel people to start using ridiculous terms like "tweet" and "twitter", do you? It's like "blog" — a monstrosity that can corrupt a whole language.

Naturally, he has an account.

Must be a deadline coming up

Traffic to the Evolution 2009 website has almost doubled in the last four days. The deadline for talk submission is Sunday, of course. I'd say something smug about how everyone else procrastinates, except that I'm blogging about website hits when I should be working on the project I'm planning to present.

Speciation changes ecosystem

We know that ecosystem processes can act on organisms to help create reproductive isolation and speciation - now, a new paper released online in advance of publication in Nature shows that speciation can change the ecosystem [$-a].

The study's authors are a group of University of British Columbia scientists, including Luke Harmon (who occasionally blogs at Dechronization) and Simone Des Roches, who have since come to my department at UI as a faculty member and doctoral student, respectively. They focus on the case of ecological speciation in sticklebacks (Gasterosteus aculeatus), which have repeatedly into evolved two reproductively isolated, ecologically different forms [$-a] after colonizing North American freshwater lakes from the ocean about 10,000 years ago. One of the two forms is "limnetic," living in open water near the surface and feeding on plankton; the other is "benthic," living on lake bottoms and feeding on invertebrates.

A stickleback
Photo by frequency.

Harmon et al. reasoned that the presence of these two different fish must have a substantial effect on lake food webs. To test this hypothesis, they set up mesocosms - big cattle tanks seeded with a standard mix of sediment, plankton, and invertebrates - and introduced either (1) sticklebacks of the "generalized" type ancestral to the benthic and limnetic types, (2) either the benthic or limnetic type alone, or (3) both the benthic and limnetic types together. They found that the fish species present in the mesocosm strongly affected the plankton species diversity - limnetic-type nearly eliminated one of their preferred prey species - and on measures of total ecosystem productivity and metabolic activity.

Perhaps the most important effect was on dissolved organic content (DOC) and light transmission in the water column. Mesocosms containing both fish types had about the same amount of (non-living) organic material as those containing the generalist ancestor, but the two-species treatment changed the DOC composition to make the water column more transparent to light. In a real lake, this effect could significantly change the productivity and composition of the aquatic plant community, which would in turn reshape the rest of the food web.

The buzzword for this phenomenon is "ecosystem engineering," which the ESA blog puts front-and-center in its discussion of this paper. I think Harmon et al.'s result is most interesting as the closing of a feedback loop between the ecosystem and a population undergoing speciation. It's evidence that a speciation event can actually alter the conditions that created it in the first place - which might prevent future speciation events, or create opportunities for new ones.

Reference

Harmon, L., B. Matthews, S. Des Roches, J. Chase, J. Shurin, & D. Schluter (2009). Evolutionary diversification in stickleback affects ecosystem functioning Nature DOI: 10.1038/nature07974

Vines, T., & D. Schluter (2006). Strong assortative mating between allopatric sticklebacks as a by-product of adaptation to different environments Proc. R. Soc. B, 273 (1589), 911-6 DOI: 10.1098/rspb.2005.3387

"There were a few flipper babies."

The AV Club gives the under-appreciated Brain Candy its dues.

The Kids In The Hall’s ill-fated debut feature is closer in conception, ambition, and scope to Monty Python movies like Life Of Brian and Monty Python And The Holy Grail than the Saturday Night Live movies being churned out at the time by SNL Studios. Like Idiocracy,it’s less about a character or a set of characters than society as a whole.

Comedy doesn't come much blacker than when one of your movie's most quotable laugh lines is a crack about birth defects.

Scientific methods in the genomic age

Nature Methods has a good editorial considering the issues around defining what science is in the age of exploratory genomics [$-a].

As schoolchildren we are taught that the scientific method involves a question and suggested explanation (hypothesis) based on observation, followed by the careful design and execution of controlled experiments, and finally validation, refinement or rejection of this hypothesis. ... Scientists' defense of this methodology has often been vigorous, likely owing to the historic success of predictive hypothesis-driven mechanistic theories in physics, the dangers inherent in 'fishing expeditions' and the likelihood of false correlations based on data from improperly designed experiments.

Their conclusion is that hypothesis-driven science will absorb the the current flood of genomic data as the basis for new hypotheses to direct future large-scale data collection:

But 'omics' data can provide information on the size and composition of biological entities and thus determine the boundaries of the problem at hand. Biologists can then proceed to investigate function using classical hypothesis-driven experiments. It is still unclear whether even this marriage of the two methods will deliver a complete understanding of biology, but it arguably has a better chance than either method on its own.

As I've said before, massive genomic datasets change science mainly through their quantity, not their quality. On the one hand, science has always involved undirected observation - Darwin didn't have any strong hypotheses in mind when he hopped aboard the Beagle. Classical natural history is a discipline devoted to almost nothing but undirected data collection, and it's been the grist for evolution and ecology research since the beginning of time. On the other, it seems to me that genomic "fishing expeditions" are more hypothesis-driven than we realize, even if the only hypothesis is "Neanderthal genomes will be different from modern humans."

Carnival of Evolution #10 at The Oyster's Garter

The tenth issue of the The Carnival of Evolution is now live at The Oyster's Garter, complete with a whimsical framing narrative. Topics range from the relationship between stress and testosterone levels to an essay on the species problem that complements my own contribution, to the suprising usefulness of half a wing.