Endless forms most beautiful

Via Unreasonable faith, from Life in the Undergrowth, which I may have to rent.

Milkweed's bitter arms race against herbivores

Plants are locked in a long twilight struggle with herbivores, particularly insects - sometimes they evolve a new defensive mechanism, "escaping" to diversify into new groups [$-a], but mostly natural selection works with the traits they already have. That means arms races - plants evolving greater concentrations of defense chemicals, and herbivores evolving greater tolerance of those chemicals. In this month's Evolution, a new study of defensive chemistry evolution in milkweed [$-a] documents exactly this process.

Asclepias viridis, a milkweed
Photo by gravitywave.

The study by Agrawal et al. follows up on earlier work in the same group, which established the evolutionary relationships between the members of the milkweed genus, Asclepias. Milkweeds are named for their defense against insect herbivores, a milky sap full of nasty chemicals - coumaric acids, caffeic acids, cardenolides, and flavonoids. The authors raised a large sample of milkweed species in a controlled environment, then measured the levels of these chemicals in each species. By mapping the chemical profiles onto the previously-developed phylogeny of Asclepias, they could estimate how milkweeds' chemistry has evolved since the genus first arose.

Aphids on Asclepias
Photo by aroid.

This analysis revealed that milkweeds have gotten nastier over their evolutionary history. But it's not that clear-cut: the diversity of defensive chemicals present in Asclepias decreased, even as the total production increased - so the plants seemed to be paring down an initial diversity of defenses into a few chemicals that worked especially well. Coumaric and caffeic acids, which are produced from the same biochemical precursors, forced a trade-off so that as one increased, the other decreased. On the other hand, cardenolides and flavonoids, which are both produced in another biochemical pathway, were positively associated.

If this sounds complicated, that's because it is. As Agrawal and his coauthors point out, we actually don't have a good sense at what timescale an arms race should manifest - that is, are we talking about plants evolving greater defenses over a few generations, or over millions of years, as this study? Natural selection can appear to be moving a population strongly in one direction for a year or two - and then turn out to be fluctuating all over the place [$-a] if you watch for decades. How year-to-year selection acting on multiple traits translates into the grand trends of evolution - whether the explosive diversification of flowering plants or the emergence of human intelligence - remains one of the big puzzles for those of us who study the living world.

Reference

A.A. Agrawal, J.-P. Salminen, M. Fishbein (2009). Phylogenetic trends in phenolic metabolism of milkweeds (Asclepias): Evidence for escalation. Evolution, 63 (3), 663-73 DOI: 10.1111/j.1558-5646.2008.00573.x

P.R. Ehrlich, P.H. Raven (1964). Butterflies and plants: a study in coevolution Evolution, 18, 586-608 DOI: http://www.jstor.org/pss/2406212

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

File under "wish I'd thought of that"

Charles Darwin's diary from his time as ship's naturalist aboard the H.M.S. Beagle, now in convenient blog form. Chuck is also twittering intermittently, presumably by some kind of steampunk Victorian iPhone.

Cooperation from selfishness?

This week's PNAS has another (open access!) paper taking a crack at the problem of how cooperation can evolve. The authors create a world where cooperation arises spontaneously in a population of selfish individuals by modeling a fundamental human drive: the desire for a good neighborhood.

Helbing and Yu set up a model world ruled by the Prisoner's Dilemma, a common game theory scenario in which pairs of interacting individuals can choose to cooperate or not cooperate with each other. If both refuse to cooperate, neither gets anything; if one cooperates and the other doesn't, the cheater gets a reward, but the cooperator pays a cost; if both cooperate, then they both get a smaller reward. If neither interactor can predict the other's choice, the most sensible strategy is to just never cooperate - you make out pretty well when the other guy is silly enough to cooperate with you, and you're no worse off than you started out if you both refuse to cooperate.

Previous models have made cooperation work in Prisoner's Dilemma situations a few different ways. One way is to allow individuals to remember how they have treated each other over multiple iterations of the PD interaction, so that cheaters can be punished [$-a]; another is to let the game play out across space in such a way that cooperators can cluster together, so that they are more likely to interact with other cooperators [$-a].

Helbing and Yu's model is a variation on the "spatial" flavor - individuals occupy cells in a grid, and interact with those in adjacent cells. Strictly speaking, it isn't an evolutionary model (even though the authors describe it as such), because there doesn't seem to be any inheritance of behavior from one generation to another; instead, individuals "learn" from their neighbors, imitating the ones who are most successful in terms of interaction rewards. There's a random element to individual behavior, to approximate trial and error strategies. Perhaps most importantly, individuals can migrate across the grid, moving to adjacent unoccupied cells where they expect to find a greater reward.

Neither imitation nor migration alone allow cooperation to survive in this model world, but some interaction between the two does. This result holds, apparently, for a wide range of possible combinations of payoff conditions. For some conditions, the model will even allow cooperators to "invade" a world full of non-cooperators. The speed with which individuals can move across the grid - cooperators seeking other cooperators, and avoiding cheaters - is critical, say the authors. They call this "success-driven migration" - and it does seem to allow cooperation - though not altruism - to arise out of selfishness.

See also Wired Science's coverage.

Reference

M. Doebeli, C. Hauert (2005). Models of cooperation based on the Prisoner's Dilemma and the Snowdrift game Ecology Letters, 8 (7), 748-66 DOI: 10.1111/j.1461-0248.2005.00773.x

D. Helbing, W. Yu (2009). The outbreak of cooperation among success-driven individuals under noisy conditions PNAS DOI: 10.1073/pnas.0811503106

M.A. Nowak, R.M. May (1992). Evolutionary games and spatial chaos Nature, 359 (6398), 826-829 DOI: 10.1038/359826a0

R.L. Trivers (1971). The evolution of reciprocal altruism Quarterly Rev. Biol., 46, 35-57

Mad as hell, and entertaining

Via Twitter/BillCorbett: Back in 2002, John Scalzi pretty much nailed the three major strains of American political thought:

Liberals: The stupidest and weakest members of the political triumvirate, they allowed conservatives to turn their name into a slur against them, exposing them as the political equivalent of the kid who lets the school bully pummel him with his own fists (Stop hitting yourself. Stop hitting yourself. Stop hitting yourself).
...
Conservatives: Self-hating moral relativists, unless you can convince me that an intellectual class that publicly praises family values but privately engages in sodomy, coke and trophy wives is more aptly described in some other way.
...
Libertarians: Never got over the fact they weren’t the illegitimate children of Robert Heinlein and Ayn Rand; currently punishing the rest of us for it. Unusually smug for a political philosophy that’s never gotten anyone elected for anything above the local water board.

Prefiguring, it turns out, the best entry in the 50 most loathsome people in America in 2008, #43: You.

You’re hopping mad about an auto industry bailout that cost a squirt of piss compared to a Wall Street heist of galactic dimensions, due to a housing crash you somehow have blamed on minorities. It took you six years to figure out what a tool Bush is, but you think Obama will make it all better. You deem it hunky dory that we conduct national policy debates via 8-second clips from “The View.” You think God zapped humans into existence a few thousand years ago, although your appendix and wisdom teeth disagree.

Perspective

Via Twitter/@Frauenfelder

Wikipedia in simplified English: Double plus good?

I have just learned about the simplified English version of Wikipedia from xkcd. It is Wikipedia, written for beginning English readers. That means the writers use simple words and short sentences. This makes them sound like Ernest Hemmingway. Simple English Wikipedia does not have an entry for Ernest Hemmingway. A search for "Ernest Hemmingway" on Simple English Wikipedia finds only a reference to Fall Out Boy and an article about Aleister Crowley.

There is one word I always look up when I want to try a new reference source.

Evolution
In the study of life and living things, evolution is the term used to describe the way a type of living thing changes over a long period of time. "Evolution" is a scientific theory (an explanation) that is used by scientists to explain why different creatures and plants are the way that they are, and act the way that they do.

That is pretty good.

A horse has a single hoof on each foot, a cow has two, a bird has its whole arm changed into a wing, and a human has a hand. But if we look at fossils - made when very old dead things got squashed between clay or sand, which hardened into rocks, we can see all these animals were once one type of animal: Fishes.

That is not as good. I am not sure why this is.

I lied. There are two words I always look up to try new reference sources. Can you guess the other one?

Mennonites
The Mennonites are a group of Christian Anabaptists named after Menno Simons (1496–1561). His teachings were a relatively minor influence on the group,though. They are of the historic peace churches. Mennonites are committed to nonviolence, nonviolent resistance/reconciliation, and pacifism.

That is double plus not as good. I am afraid that if I write like this much longer, I will forget how to write long sentences.

Feedburning, bookmarking, and tag cloud-ing

Compulsive additions to the blog: syndication is now by Feedburner (apologies if this mucks with anyone's existing subscriptions), social bookmarking links for every post courtesy AddThis, and - as you'll note in the right-hand column - an attractive new label cloud by phydeaux3.

A second chance for Last Chance to See

Just discovered: Stephen Fry joins Mark Carwardine in returning to the places and creatures visited by Carawardine and chronicled by Douglas Adams in the excellent little book Last Chance to See, a travelogue of desperately endangered animals. The second Last Chance, like the first, is principally a BBC documentary project - we shall have to see if a book grows out of Fry's new journey. Regrettably, none of the video seems to be viewable this side of the Atlantic.

AV Club on Eyes Wide Shut

Via kottke.org: The Onion AV Club rehabilitates Eyes Wide Shut. I don't remember much of the critical panning that accompanied the movie's original release, and I didn't see it till some grad-student friends and I committed to watch Stanley Kubrick's major films in chronological order a couple years ago. But I agree with the review that it's up to Kubrick's usual high standards.

Given the choice, though, I tend to prefer 2001: A Space Odyssey and Dr. Strangelove, which between the two of them account for my interests in evolution, hard science fiction, conscientious objection to war, and Peter Sellers.

Why liberal Christians should fight Creationism

Slacktivist Fred Clark bounces off that depressing, depressing poll result on American's acceptance of the historical fact of evolution in a series of posts that beautifully encapsulate the liberal Christian frustration with YEC's and what he quite correctly characterizes as the relatively recent, highly non-conservative Biblical "literalist" movement. First, there's exasperation at the sheer perversity of it:

It's hard to know what that means, exactly, to "believe in" or "not believe in" evolution. It's like not believing in Missouri, or not believing in thermal conduction. Those two examples are a bit different from one another, but they both get at aspects of what this odd sort of disbelief entails.

"Not believing in Missouri" doesn't affect the Show-Me State one way or another. To say that you don't "believe in" Missouri is really to say that you deny it exists -- that its existence is a fact you refuse to accept. ...

On the other hand, if someone tells you that they "don't believe in" thermal conduction, it's likely that they're not so much saying they deny its existence as that they don't understand what you mean when you say "thermal conduction." For all their supposed disbelief, after all, they still avoid sitting on metal park benches in the winter. [Italics sic.]

Then, there's vexation that people who subscribe to such nonsense claim to do it in defense of the value of Scripture:

[Literalism's children, YECism and "Left Behind"-style apocalypticism] are new and radically innovative ideas introduced or adopted by people who had set out, initially, to uphold "the authority of the scriptures" (to use one of their favorite phrases). That this effort to defend the Bible's "traditional" meaning has resulted in their introducing replacement meanings that override and disregard its traditional meaning is bitterly ironic, but this irony is lost on them.

And, finally, there's anger over the very real consequences of literalism for faith:

House-of-cards fundamentalism allows for no distinctions between babies and bathwater, between the central tenets of the faith and the adiophora and error. So once one part of this belief system begins to collapse -- as it inevitably will since young-earth creationism is disprovable -- then it all has to go. ...

The second reason that creationism or "creation science" is a pet-peeve of mine is that I spent many years working on behalf of the Evangelical Environmental Network to try to persuade evangelicals that "creation care" was not just permissible, but a responsibility. This is made much more difficult when the audience you are addressing -- as was sometimes, but not always, the case -- regards the first 11 chapters of the Book of Genesis as a "literal" journalistic account and only as a literal journalistic account. [Italics sic.]

Biblical literalism is bad theology, and that's bad for the Church. If the Church is the expression of Jesus' example and teaching in the world (Christ's body, you might say), then Biblical literalism is literally preventing the expression of Jesus in the world.

-------
Edit, 19 Feb: fixed broken link to that depressing, depressing poll result.

Want to speciate? Stay home.

I've said it before, and I'll say it again: the formation of new species is almost always an accident. There you are, adapting to changes in your obligate pollinator, or the local environment - and suddenly, you can't mate with the folks on the other side of the mountain. That's the lesson I take from an article in last week's PNAS, which suggests that a diverse group of birds got that way by being homebodies [$-a]

Oriental white-eye
(Zosterops palpebrosus)
Photo by Lip Kee.

The authors (including Jared Diamond, who communicated the paper to PNAS), set out to determine why there are so many species of white-eyes, a group of songbirds distributed across Africa, Southeast Asia, and the southern Pacific. They built a phylogeny for the group, calibrated it to real time using the geological dates of origin for Pacific islands occupied by white-eyes, and then estimated the rate at which the group produced new species. They found, as reported by Wired.com, that the largest group of white-eyes have one of the fastest species-accumulation rates recorded in vertebrates, about 1.6 new species every million years.

That's a weird result, when you think about it - we're talking about birds, and widely-distributed birds, here. All things being equal, speciation is facilitated by lack of movement - Appalachian salamanders, for instance, diversified largely because they're too gimpy to move between stream drainages very often [$-a]. Furthermore, the authors say, white-eyes don't display a lot of ecological differences that might contribute to isolation. So how did they speciate at a record-setting pace?

The solution? The authors propose that white-eyes are prone to rapid changes in their dispersal ability. As evidence, they cite numerous cases in which white-eyes must have crossed great distances to colonize one island, then failed to make it across much smaller distances to colonize others nearby. Nodding to Diamond's groundbreaking work on human history and cultural evolution, they compare this to the colonization of Polynesia, in which people stopped traveling long distances as the chance of discovering an uninhabited island decreased.

References

K.H. Kozak, D.W. Weisrock, A. Larson (2006). Rapid lineage accumulation in a non-adaptive radiation: phylogenetic analysis of diversification rates in eastern North American woodland salamanders (Plethodontidae: Plethodon) Proceedings of the Royal Society B: Biological Sciences, 273 (1586), 539-46 DOI: 10.1098/rspb.2005.3326

R.G. Moyle, C.E. Filardi, C.E. Smith, J. Diamond (2009). Explosive Pleistocene diversification and hemispheric expansion of a "great speciator" Proceedings of the National Academy of Sciences, 106 (6), 1863-8 DOI: 10.1073/pnas.0809861105

Isn't dating Darwinian enough already?

Sent to me by Roxy Allen, who seems to be out to wave public misperceptions about evolution in my face (on Darwin Day, she pointed me to that depressing, depressing poll result): Darwin Dating is your go-to for eugenic relationship-building, or so it claims.

Sick of dating websites filled with ugly, unattractive, desperate fatsos? We are.

Darwin Dating was created exclusively for beautiful, desirable people. Our strict rules and natural selection process ensures all our members have winning looks. Will you make the cut?

Obvious issues: (1) members are actually self-selected, as long as they send in a reasonably good photo; (2) since when are photos on Internet dating sites honest indicators? (3) do you really want to go looking for a mate amongst attractive/dishonest people who self-selected for a pretend-exclusive fringe dating site? Bio-nerd issue: attractiveness may have little relation to true Darwinian fitness (i.e., ability to successfully raise lots of offspring).

Boycotting Louisiana over creationist law

In the wake of Louisiana's passage of a back-door Creationism "education" law, the Society of Integrative and Comparative Biology is canceling plans to hold an upcoming conference in New Orleans. Good for them. The new location? Salt Lake City.

Edge essayists on religion vs. science

Bouncing off Jerry Coyne's essay on the (in)compatibility between science and religion (which occasioned a rant from me), Edge asked a long list of big names - including the authors of the two books to which Coyne was responding - to comment on the question. It spans the full range from conciliatory to cutting, and all of it is well worth reading.

Via Open Culture

The historical Jesus on iTunes

Via Open Culture: iTunes U, the collection of free university lectures in podcast format, has Thomas Sheehan's Stanford Continuing Studies course on the historical Jesus. I'm a couple lectures deep and loving it.

"25 things" infection dynamics

Slate's survey of its readers determines that spread of the Facebook meme followed a pattern analogous to emergent disease evolution - a long period of low density, during which various mutants ("16 things," "17 things," &c) competed; then a rapid spread when one variant hit the big time.

Darwin's 200th: Coverage highlights

I shall update this post as the day goes on.

Olivia Judson writes that Darwin "makes an easy hero":

His achievements were prodigious; his science, meticulous. His work transformed our understanding of the planet and of ourselves.

At the same time, he was a humane, gentle, decent man, a loving husband and father, and a loyal friend. Judging by his letters, he was also sometimes quite funny. He was, in other words, one of those rare beings, as likeable as he was impressive.

Boingboing harshes everyone's buzz with depressing poll numbers.

It's Alive makes snarky hay of Darwin's Victorian approach to conservation.

On Deep Thoughts and Silliness, Bob O'Hara uses Darwin's ignorance of the mechanism of inheritance as a jumping-off point for a nice thought about the collaborative nature of science.

Propterdoc worries about whether over-promotion of Darwin's 200th is bad for biology's image.

The Daily Mammal discusses Darwin's speculations about land-to-aquatic transitions in mammals.

ScienceBlogs, as usual, has more going on than I can follow and still do my work. But it looks great.

On Morning Edition, the inimitable Robert Krulwich considers how Darwin's work was shaped by his wife's faith and the death of their eldest daughter.

Susan Brooks connects progressive theology and politics to acceptance of evolution

... progressive Christian theology ... has long emphasized the continuity of the human with the rest of creation. Progressive Christians by and large oppose regarding human nature as fixed and static and a unique "lord of creation." The inescapable learning from evolutionary biology is that human beings are deeply creatures. We share 90% of our genes with mice. If that doesn't take the "lords of creation" down a peg, I fail to see what will!

Sally Steenland suggests that the big day should prompt religion and science to kiss.

The other big 200th today

I'd be deeply remiss if I neglected to mention that today is also the 200th anniversary of the birth of Abraham Lincoln.

Library of Congress.

Sarah Vowell, Lincoln's leading hipster advocate, says it best in The Partly Cloudy Patriot:

How many of us drew his beard in crayon? We built models of his boyhood cabin with Elmer's glue and toothpicks. We memorized the Gettysburg Address, reciting its ten sentences in stovepipe hats stapled out of black construction paper. The teachers taught us to like Washington and to respect Jefferson. But Lincoln - him they taught us to love.

I suggest, as a sample of his speeches, the second inaugural, which concludes appropriately for our turbulent present:

With malice toward none; with charity for all; with firmness in the right, as God gives us to see the right, let us strive on to finish the work we are in; to bind up the nation's wounds; to care for him who shall have borne the battle, and for his widow, and his orphan – to do all which may achieve and cherish a just and lasting peace, among ourselves, and with all nations.

Blogs for Darwin

Happy Darwin Day! Check out Blog for Darwin for remarks on the great occasion across the science blogosphere.

Darwin's 200th: What evolution can teach Christianity

Today is the 200th anniversary of Charles Darwin's birth, and 150 years since he published his groundbreaking book, The Origin of Species. The Origin provided the first widely-accepted explanation for the evolution of life on Earth, and, although Darwin was wrong on some points (if only he had known about genes!), a century and a half of scientific work has shown that he was right about more.

That century and a half has not diffused the perception, especially in the United States and other highly religious countries, that acceptance of a scientific account for the history of life is antithetical to religion. As a Darwinian and a Christian, this is a topic with which I struggle, and about which I've written a great deal here. Although I'm not sure that science can coexist with a real belief in the supernatural, I do hold that science is both compatible with the moral questions at the heart of religion and essential to answering them.

Photo by rmcnicholas.

For Darwin's 200th, then, I'd like to briefly present three examples of evolutionary insights that complement the Christian moral perspective. I focus on Christianity here (and elsewhere in this blog) not because I think it has an exclusive hold on the truth, but because it is the tradition in which I was raised, and the one that shapes my own moral perspective. I think the following points are easily applicable to just about any other moral system, religious or non.

Our evolutionary past shapes us today.

Christianity (and, indeed, most other religions) starts from the fundamental problem of human behavior: We do things that we know are hurtful to those around us, often because we enjoy doing them. As the apostle wrote, "For what I do is not the good I want to do; no, the evil I do not want to do—this I keep on doing." (Romans 7:19)

The Christian tradition calls this original sin; the evolutionary perspective points to its origin in the remnants of past adaptations. We have two bones in each forearm because we evolved from ancestors with those two bones in their pectoral fins [$-a]; we may be hostile to outsiders because that parochialism helped early humans to form closer-knit societies [$-a]. Far from giving us an excuse to do whatever we feel like, these results can help us figure out how to overcome evolved behaviors that hurt others.

Christ calls us to transcend our past.

Just as it shapes our hurtful impulses, our evolutionary past has a hand in the better angels of our nature. We may care for our children and close relatives, for instance, in part because they carry many of our genes - so helping them helps our own evolutionary fitness [$-a]. Similarly, the need to live peacefully with our immediate neighbors may have shaped deep emotional aversions to murder [PDF].

In the Sermon on the Mount, though, Jesus lays out a moral model that calls us beyond what comes naturally:

"You have heard that it was said to the people long ago, 'Do not murder,' ... But I tell you that anyone who is angry with his brother will be subject to judgment." (Matt. 5:21-2)

And:

"You have heard that it was said, 'Love your neighbor and hate your enemy.' But I tell you: Love your enemies and pray for those who persecute you ... If you love those who love you, what reward will you get? (Matt. 5:43-6)

Evolutionary thinking can help us realize Christ's call.

When we understand the deep causes of hurtful behavior, we can figure out better how to overcome them. To pick just one example: Jesus proposes a moral solution to the problem of hostility to strangers mentioned above in the parable of the Good Samaritan (Luke 10:25-37) when he redefines the concept of "neighbor" to mean something bigger than "people of the same race/religion." But how do we overcome deep-seated biases against people who don't look like us? One new study suggests hacking the mental habits that create those biases in the first place, by making the effort to become familiar with people of other races - Caucasian volunteers trained to better differentiate between African American faces showed reduced evidence of bias against African Americans.

Like the Christian moral model, the evolutionary perspective understands that humans are imperfect - but suggests ways we can do better. This is why it pains me to hear other Christians dismiss evolutionary science out of hand (apart from my nerdy compulsions to correct factual error): Understanding evolution can help us in our ongoing struggle to live together, if only we're open to the data science provides. The current advances in our understanding of human behavior are only possible because today's researchers stand on the shoulders of a giant: Charles Darwin.

References

J.-K. Choi, S. Bowles (2007). The coevolution of parochial altruism and war Science, 318 (5850), 636-40 DOI: 10.1126/science.1144237

K. Foster, T. Wenseleers, F. Ratnieks (2006). Kin selection is the key to altruism Trends in Ecology & Evolution, 21 (2), 57-60 DOI: 10.1016/j.tree.2005.11.020

J.D. Greene (2001). An fMRI investigation of emotional engagement in moral judgment Science, 293 (5537), 2105-8 DOI: 10.1126/science.1062872

S. Lebrecht, L.J. Pierce, M.J. Tarr, J.W. Tanaka (2009). Perceptual other-race training reduces implicit racial bias PLoS ONE, 4 (1) DOI: 10.1371/journal.pone.0004215

T. Lewens. (2007). Darwin. New York: Routledge. Amazon.com.

M. Ruse. (2000). Can a Darwinian be a Christian? Cambridge University Press. Amazon.com.

N.H. Shubin, E.B. Daeschler, F.A. Jenkins (2006). The pectoral fin of Tiktaalik roseae and the origin of the tetrapod limb Nature, 440 (7085), 764-71 DOI: 10.1038/nature04637

Funding creative science

Stephen Quake laments the grant-approval process of most U.S. federal funding agencies, and suggests making room for risky proposals:

I wonder if this should also be the time to rethink the basic foundations of how science is funded. Could we stimulate more discovery and creativity if more scientists had the security of their own salary and a long-term commitment to a minimal level of research support? Would this encourage risk-taking and lead to an overall improvement in the quality of science?

The NIH model Quake describes - which sets aside specific funding sources for out-of-the-box proposals - seems sensible, given additional funds for such use.

The Times annotates the Origin

As part of its special coverage of Darwin's 200th, the New York Times has a very well put-together presentation of The Origin of Species, with annotation of key passages by working scientists. The complete text of the first edition is also offered for download [PDF], if you haven't got it already.

Reflective Christianity

Slacktivist Fred Clark(!), "a Baptist in the evangelical tradition" reacts to his inclusion on a list of the top Atheist/Agnostic/Skeptic blogs with a meditation on faith, certainty, and the value of listening to - and interacting with - opposing viewpoints:

Like most humans, I'm bound to be wrong about many things, and the things I'm likeliest to be wrong about are those things I'm least aware I might be wrong about. So it seems not just prudent, but necessary, to engage as many disparate views as possible.

------
(!) In the original version of this post, I inexplicably confused Fred Clark, a thoughtful, humane, and progressive Christian - whose blog I follow regularly - with Fred Phelps, a fundamentalist troglodyte. This mistake would, no doubt, have massively offended both of them, should either have seen it. My deepest, sincerest apologies to Clark.

Evolutionary merchandising, just in time for Darwin Day

Spreadshirt Market Place Product
Black Drift Happens tee


Spreadshirt Market Place Product
Natural Selection wringer tee

I've never quite found a t-shirt design that speaks to me as a bio-nerd. Sure, there are tees out there that promote evolution (usually in opposition to creationism), or science in general, and some are pretty awesome. But where's the evolutionary biology equivalent of the infinite in-jokes for computer programmers, say? I haven't seen 'em.

Here, then, are my first attempts to fill this minuscule hole in the market, two designs capturing the twin evolutionary forces of natural selection and genetic drift. Design by me, printing by Spreadshirt. I've ordered my own copies of the two pictured here, and they're great - stylish, comfortable American Apparel tees with clean, bright printing. More options are at my new Spreadshirt store Denim & Tees, or you can work up your own in Spreadshirt's nifty online designer.

Natural selection and speciation, 150 years later

Science kicks off the week of Darwin's 200th with a special section devoted to the latest on speciation [$-a], the literal origin of species. It includes a new review by Dolph Schluter, discussing the role of natural selection speciation [$-a], which suggests a new way to think about selection creating reproductive isolation.

Schluter contrasts ecological speciation, in which reproductive isolation arises in the course of adaptation to different environments, "mutation-order" speciation - isolation arising by the accumulation of different genetic and morphological changes in the course of adaptation to the same (or the same kind of) environment. That is, natural selection can cause a population to split into two species if different parts of population are "solving" different ecological problems, or if they arrive at different "answers" to the same problem.

The mutation-order scenario makes sense, though it's new to me. As an example, Schluter cites a recent study in Mimulus in which a mutation of the mitochondrial DNA in one population creates sterile males in hybridization with other populations [$-a]. He proposes that much mutation-order speciation occurs because of conflict between different levels of natural selection, as when "selfish genes" create reproductive incompatibilities in the course of spreading through a host population. This is a departure from what biologists usually consider speciation by natural selection, but Schluter makes an interesting point.

References

A.L. Case, J.H. Willis (2008). Hybrid male sterility in Mimulus (Phrymaceae) is associated with a geographically restricted mitochondrial rearrangement Evolution, 62 (5), 1026-39 DOI: 10.1111/j.1558-5646.2008.00360.x

D. Schluter (2009). Evidence for ecological speciation and its alternative Science, 323 (5915), 737-41 DOI: 10.1126/science.1160006

A. Sugden, C. Ash, B. Hanson, L. Zahn (2009). Happy birthday, Mr. Darwin Science, 323 (5915) DOI: 10.1126/science.323.5915.727

A limerick for Darwin's 200th

Thursday is, of course, the 200th anniversary of Charles Darwin's birth. To kick off a week of commemorations, symposia, and nerdy parties, I humbly submit a limerick:

The vicar, one Quite Reverend Darwin
Considered, whilst penning each sermon,
How he might have advanced,
Had he taken that chance
To go with the Beagle a-voyagin'.

(It is widely considered that Darwin, had he not taken an interest in natural history, would've ended up as a clergyman; see David Quamman's excellent pocket biography, The Reluctant Mr. Darwin.)

Dear Senator, part II

Just found a follow-up email from Science Debate 2008, reporting that previously planned cuts to science funding in the still-under-debate economic stimulus bill have been reduced or withdrawn. Still no obvious coverage on ScienceDebate2008.com, which is frankly weird.

Tracking the elusive "25 Things"

Slate gets all empirical with the Facebook meme.

Dear Senator

Sheesh. Of course science is the first thing they try to cut from the pending stimulus bill. Text free for the taking to anyone who wants to pester their congresscritters - which you should, if you care about science in the U.S.

OK, so it gets a little melodramatic at the end there, but I'm trying for impact. Edit as you see fit - individualized letters are more likely to have an impact.

Dear Senator,

I'm a graduate student in biology at the University of Idaho, and I'm writing to ask that you support President Obama's stimulus plan, with full funding for basic scientific research.

Science and technology - the fruits of basic scientific research funded by the National Science Foundation, National Institutes of Health, and other government scientific agencies - are responsible for half of all U.S. economic growth since World War II. Yet today, after years of virtually no increases in basic research funding, laboratories across the country are at risk of shutting down, with untold consequences for our long-term competitiveness in the global economy.

Basic research makes economic sense over the short term, too - with the increase in funding proposed in the stimulus bill, granting agencies would immediately be able to fund more of the grant requests they're considering right now. That's money to pay lab staff, and buy reagents and equipment - most often from American companies like Thermo Fisher and Qiagen.

For these reasons, the stimulus bill before the Senate originally contained vital increases in basic scientific research funding. Now, however, a group of senators, including Susan Collins and Ben Nelson, are proposing cuts to the stimulus bill that would eliminate much - and in the case of NSF, all - funding for science. Considering what a tiny portion of the bill's proposed spending was already devoted to science funding, and the immediate and long-term value it would have brought our economy, this is a shortsighted idea at best.

So I hope you will give full support to President Obama's stimulus bill, and reject the Collins-Nelson cuts in science funding. The scientific and economic future of our nation depend on this.

regards,
Jeremy B. Yoder

[I should also note that the talking points above come from an email sent out by Shawn Otto over the ScienceDebate2008 e-mail list; I can't find coverage of this issue on the SD2008 site, however.]

Draft Neanderthal genome next week

Nature News reports that the first complete genome sequence for a Neanderthal will be released, appropriately enough, on next Thursday, the 12th of February, and the 200th anniversary of Charles Darwin's birth. It's the same group at the Max Planck Institute that released the first million bases of Neanderthal nuclear and mitochondrial DNA sequence [$-a] back in 2006. As in the earlier work, the new data were collected with a "454" next-generation DNA sequencer.

The earlier publication, which I just read this week as part of a reading group focused on next-generation sequencing technology, was more like a stunt than a groundbreaking result in evolutionary genetics. The actual results were two new estimates of the human/Neanderthal divergence times (basically confirming earlier estimates), and a coalescent estimate of the effective population size of the common ancestor, neither of which would be worth a whole paper, let alone a letter to Nature.

But it was pretty awesome just as a stunt - at every step of the analysis, the authors did some clever error checking by comparing the Neanderthal sequence to human and chimpanzee genomes, and they came up with actual nuclear sequence data from a freaking Neanderthal. Ahem. The collection of an entire Neanderthal genome is a big deal as a stunt, but I'll look forward to seeing what new insight into human evolution comes out of it.

Reference

R.E. Green, J.Krause, S.E. Ptak, A.W. Briggs, M.T. Ronan, J.F. Simons, L. Du, M. Egholm, J.M. Rothberg, M. Paunovic, S. Pääbo (2006). Analysis of one million base pairs of Neanderthal DNA Nature, 444 (7117), 330-6 DOI: 10.1038/nature05336

Darwin's Beagle diaries as audiobook

Darwin Online presents Charles Darwin's diaries from his historic voyage on the H.M.S. Beagle in audiobook format, five files totaling about an hour and a quarter.

Evolution 2009: Evolution will be blogged

An advantage of being in charge of the website for Evolution 2009, the joint annual convention of the American Society of Naturalists, Society of Systematic Biologists, and Society for the Study of Evolution: when I suggest that we ought to do something to involve science bloggers in the conference, I get to set it up. Or maybe that's actually a disadvantage.

In any event, we're experimenting with a blogswarm for this year's conference - if you're attending the conference and think you'd like to 'blog about it, or just want to help spread the word, head over to the just-posted blogging page, download a badge to put on your site (see my sidebar, and the inset on this post, for examples), and drop me an e-mail so I can add your URL to the list of participating science blogs. I'm also interested in suggestions, both conceptual and technical, for how to improve the resources at that page, which currently consist of a small selection of logo badges, and the list of participants - I'd particularly like to try aggregating relevant posts from participating blogs into a single RSS feed.

With blogging becoming more common as a way to educate the public and converse with other scientists, I hope this will improve Evolution's profile outside academic biology and facilitate conversation among attendees before, during, and after the conference. Also, as a colleague (who shall remain nameless) pointed out, this should make it easier to organize the kegger.

Reference

S.A. Batts, N.J. Anthis, T.C. Smith (2008). Advancing science through conversations: Bridging the gap between blogs and the academy. PLoS Biology, 6 (9) DOI: 10.1371/journal.pbio.0060240

Science, blogged

Another example of how blogging can be great for science, both as public education and as communication among scientists: The Open Source Paleontologist Andrew Farke first walks his readers through his nifty new study of skull injuries in Triceratops, which suggests that their horns were used for combat (as opposed to mere display), then follows up with a post detailing the open-source technologies behind the paper.

This is better, to my mind, than whatever coverage the New York Times science section can give Farke's result. Farke links directly to the PLoS-published paper - mainstream science coverage tells me the journal, at best, and leaves me to ferret out the paper myself. (It's not that much work, but I'm lazy.) I can read the author's own explanation of the result, and post comments to ask for clarification, which better approximates the experience at a conference. And, as a bonus, I learn about some ways I can improve my own, very non-paleontological, work: Zotero, for instance, looks well worth a try.

Arrested development, and reproductive incompatibility, from duplicate genes

Speciation isn't something that evolution sets out to do - it just sort of happens. One day, a species colonizes two sides of a river, say, migration across the river drops off, and then a few million years of genetic drift later, there are two species where once there was one. The question is, what's the final genetic change that makes the accident of speciation irrevocable?

A paper in this week's Science pinpoints exactly that change. Bikard and coauthors report that, in the little flowering plant Arabidopsis thaliana (the plant world's answer to white lab mice and Drosophila fruit flies), it only takes one duplicated gene to finalize speciation [$-a]. It's a clear-cut case of a classic speciation scenario, Bateson-Dobzhansky-Muller incompatibility.

Arabidopsis thaliana
Photo by tico bassie.

It all comes down to gene duplication, which I've discussed before in the context of the trouble it gives to genetic analysis. Making copies of an entire genome is an error-prone process, and sometimes a whole gene gets duplicated twice. If that extra copy is inherited, it means that the carrier has redundant coding for whatever the original gene does - so now one copy can mutate without affecting its carrier's fitness. Often this just results in loss of function for the mutating copy - sometimes it leads to new gene functions. In Arabidopsis, it's lead to reproductive incompatibility between two strains of the plant that took different evolutionary paths.

Bikard et al. noticed that, when they crossed two strains of Arabidopsis, the resulting seeds didn't include every possible combination of the parental strains' genes - and a few seeds grew short, not-quite-healthy looking roots when germinated. Some of the hybrid seeds just died in mid-development. With a lot more controlled crosses, the authors narrowed the candidate genes down to a pair that normally work together in synthesizing the essential amino acid histidine. Each of the two parental strains had working copies of the two genes - but when you crossed them, sometimes the seeds couldn't produce histidine, and so they snuffed it.

This looked like the above-mentioned (and awkwardly named) Bateson-Dobzhansky-Muller incompatibility [$-a], which is an old idea about how populations evolve reproductive incompatibilities to become separate species. Under B-D-M incompatibility, a new gene evolves in one population that doesn't work if it interacts with genes from the other. Imagine if Windows users didn't have to share documents with Mac users: as the two operating systems went through multiple redesigns and their respective versions of Microsoft Office(TM) were revised to keep up, it might no longer be possible to read a Mac-written Word document on a Windows machine.

Here, as Bikard et al. showed, one of the histidine-producing genes in Arabidopsis was accidentally duplicated - and one copy mutated into non-functionality. The catch is that, in the two partially incompatible strains, different copies went nonfunctional. So now, when the two lines are crossed, a small fraction of the seeds produced get nonfunctional copies of the duplicated gene. They die. And where once there were two strains of Arabidopsis thaliana, there's something a little more like two separate species, all because of what boils down to the flip of a coin.

References

D. Bikard, D. Patel, C. Le Mette, V. Giorgi, C. Camilleri, M.J. Bennett, O. Loudet (2009). Divergent evolution of duplicate genes leads to genetic incompatibilities within A. thaliana Science, 323 (5914), 623-6 DOI: 10.1126/science.1165917

K. Bomblies, D Weigel (2007). Arabidopsis — a model genus for speciation Current Op. Genet. & Dev., 17 (6), 500-4 DOI: 10.1016/j.gde.2007.09.006