Darwin

I like the idea of book reviews for really old books. It eliminates the risk that you'll get stuck writing a review of a really bad book, because, well, everybody already knows the bad ones. Of course, there's a risk that you're just writing a hagiogram about a book that everybody holds sacred.

Steve Jones' recent Wall Street Journal review of Darwin's Voyage of the Beagle is sort of like that. He emphasizes the book's strong points, especially when compared to the earthworm monograph and barnacle series:

"The Voyage of the Beagle," in contrast, sings. Its language is that of a young man intoxicated by the tropics ("To a person fond of natural history, such a day as this brings with it a deeper pleasure than he can ever hope to experience again") and careless of the risks ("Upon landing I found that I was to a certain degree a prisoner . . . a traveller has no protection beside his fire-arms"). The youthful Darwin was a master of unadorned English. He took with him more than geology textbooks: "Milton's Paradise Lost had been my chief favourite, and in my excursions during the voyage of the Beagle, when I could take only a single small volume, I always chose Milton."

In this, Jones tactfully avoids the parts of the book that detail the backwardness of "dark-coloured natives." I think many of today's reviewers would have given the book a more critical treatment. In my thinking, the book gains by being an honest portrait of its time, clearly by an extraordinary thinker -- but one whose weaknesses are displayed as well as his strengths.

Jones does a bit of retrospective analysis that deepens the current interest, focusing on Darwin's description of St. Helena. By Darwin's time, it already was home to many introduced species, mainly from England. Now, the native flora and fauna are disappearing:

Now things on St. Helena have gotten worse. The island has 49 unique species of flowering plant, and 13 of fern, all found only there. At least seven have been driven out since the arrival of men five centuries ago, two survive only in cultivation, and many more are on the edge. The last St. Helena Olive died of mold in 1994, and of the ebony thickets only two small bushes remain. Its giant earwig (at three inches, the world's largest), giant ground beetle and St. Helena dragonfly, all common in Darwin's time, have not been seen for many years. The snail seen by Darwin is now reduced to a population of about 600. The St. Helena Petrel is extinct, and just one endemic winged creature, the Wire Bird, is left, and that too is threatened.

That's the magic of revisiting naturalists' works -- things really have changed. Being able to observe those changes puts us in the position of Hipparchus, who -- comparing notes with observers hundreds of years earlier -- noticed that Spica had moved relative to the equinox. Sometimes the long-scale comparison gives us insight into processes that are not obvious from year to year.

The New Yorker has a fascinating article about Irene Pepperberg and the way people are grieving over her deceased parrot, Alex:

In Wheaton, she quietly worked the crowd into a pleasurable state of shared outrage. At one point, she said that colleagues had admonished her, "Birds can't do what you say he can do. They just don't have the brainpower." Linnea Faris, a woman from Michigan who was wearing a "Remember Alex" T-shirt, shook her head in disbelief. Faris told me, "My husband doesn't really understand it. I can't fully explain it myself. But I've spent hours crying over that damn bird." She went on, "People used to think birds weren't intelligent. Well, they used to think women weren't intelligent, either. They talked about the smaller circumference of our skulls as though it made us inferior to men! You know what? They were wrong on both counts."

The article gives a bit of historical background to studies of intelligence in animals, from Descartes and Darwin through C. Lloyd Morgan and B. F. Skinner. Oh, and the obligatory "Clever Hans" story.

Also, a lot of more current research on animal intelligence, including crows. I liked this part about a smart crow named Betty, which seems to solve problems that other crows have trouble with:

Though some crows, like Betty, cracked the challenge quickly, others took many tries; still others never mastered it. Watching videos of Betty on Kacelnik's Web site, I noticed that she seemed to have a particularly focussed and alert way about her. Even Kacelnik, who is loath to anthropomorphize, confessed to me, "An element of our finding that still puzzles me is that while Betty was not chosen or treated in any special way, she was different. She showed a readiness to coöperate and solve problems that none of the other animals in our study have replicated. We have no idea why."

And to my mind, the saddest statement in the whole article, which echoes a conversation I was having yesterday:

"Irene's work could not really have been planned ahead, as nobody knew what was possible. . . . Alex's development as a unique animal accompanied Irene's as a unique scientist. Hers is not a career trajectory one would advise to young scientists--it's too risky."

It shouldn't have been viewed as risky at all! The worst that could happen is a confirmation of the previous biases against significant learning capacity. But there was nothing in theory that didn't permit what turned out to be the case, and plenty of anecdotal evidence in support. When Darwin cited correspondences with animal breeders in support of the idea of heritable variation, that's good science, reaching out to the edges of what people knew about heredity. Pepperberg began to reach out to the edges of what people know about animal learning.

Frankly, I admire her (and her assistants) the most for their ability to run through the incredible degree of repetition necessary to test these kinds of learning with the parrots. One passage in the article notes that Pepperberg collaborated with an autism researcher on the effects of similar teaching methods (with some success). It's a good comparison in terms of the required patience, also. I think that few researchers are really cut out for the kind of work that Pepperberg does, and that may contribute to some lack of understanding of the results and their limits.

The NY Times reports on evolution and education in Texas:

Starting this summer, the state education board will determine the curriculum for the next decade and decide whether the "strengths and weaknesses" of evolution should be taught. The benign-sounding phrase, some argue, is a reasonable effort at balance. But critics say it is a new strategy taking shape across the nation to undermine the teaching of evolution, a way for students to hear religious objections under the heading of scientific discourse.

Already, legislators in a half-dozen states -- Alabama, Florida, Louisiana, Michigan, Missouri and South Carolina -- have tried to require that classrooms be open to "views about the scientific strengths and weaknesses of Darwinian theory," according to a petition from the Discovery Institute, the Seattle-based strategic center of the intelligent design movement.

The story mainly covers the local Texas aspects of the story, with quotes from the state education board chairman ("I believe a lot of incredible things") and some pro-evolution opponents.

I looked at the website where the Texans for Better Science Education lay out examples of the "weaknesses" that should be taught. They're pretty weak, all right. I think that most of these could be included in a science course as "common myths about evolutionary theory."

Consider these:

The Cambrian explosion quickly produced all of the basically different body structures, and some of these have since become extinct. This is very different from the evolutionary tree of life, which suggests a slow and gradual increase in body structures.

No, no it doesn't. Evolutionary theory provides no reason to think that body structures should change at a slow constant rate. The synthetic theory emphasizes why bursts of adaptive change should happen episodically.

Many life forms persist through large expanses of geologic time with essentially no change. Evolution theory suggests that mutations occur randomly over time and are selected to produce continuing change as the environment continually changes.

No, no it doesn't. Some organisms may well have relatively constant environments for millions of years.

Selective breeding has produced only very limited change with no new structures occurring over thousands of years and multitudes of generations of selection.

Umm... teosinte? I think that biology texts should devote a lot more attention to selective breeding, as the best concrete examples of evolution in action.

So, that reflects on the basic problem with the idea of teaching evolution's "weaknesses": A real weakness is not a matter of ignorance, but a matter of evidence weighing in favor of some alternative hypothesis. We don't have that here.

The June Scientific American (no link available) has an article on page 32 about the "therapeutic value of blogging." That's some relief, after the stories a couple of months ago about blogging being potentially deadly.

And it's no small irony, considering that the article I found on the previous two pages had great potential to give me therapeutic opportunities here.

In the article, titled, "Need for speed?" David Biello wrote up some of the human genetics results of the past 6 months, placing them as a point-counterpoint presentation of our acceleration result.

First, he cites Gregory Cochran, who does as good a job explaining our result in one sentence as I've seen:

"We found very many human genes undergoing selection" ... "We believe that this can be explained by an increase in the strength of selection as people became agriculturalists, a major ecological change, and a vast increase in the number of favorable mutations as agriculture led to increased population size."

In that form, it is hard to see how anyone could disagree. Clearly, agriculture was a major ecological shift for humans, and it imposed new selection pressures associated with diet, disease, social organization and other ecological factors. At the same time, the population grew and more people meant more mutations. That's the story; the rest is detail filled in by anthropology, genomics, and math.

Biello then cites another recent study that partially confirms our results. That study, by Lluis Quintana-Murci and colleagues, found a much smaller number of selected genes (55), but what is important is that every one of these genes has an F_ST greater than 0.65. In other words, in every one of these cases, an allele that is vanishingly rare in most of the world has reached a frequency over 80 percent in one population. As allele frequencies go, these are extreme differences -- much, much larger than the average genetic difference between populations, characterized by an F_ST around 0.1. We also found a few such alleles in our survey of selected genes, but the vast majority of genes have not generated such extreme differences in frequency -- mainly because they haven't been around long enough. In other words, the Quintana-Murci study confirms the distribution of positively selected alleles, across the range where it overlaps with other studies, including ours.

Then Biello turns to the doubters. Noah Rosenberg coauthored a study earlier this year that reported polymorphism data from a sample of populations around the world.

"We are a young species," remarks geneticist Noah Rosenberg of the University of Michigan at Ann Arbor, who participated in a comprehensive study of genetic variation that appeared in Nature in February. "Different human populations have not been separated for long enough periods of time to develop their own new alleles."

Now, I never hold quotes in the press against people, because they represent a very small portion of what they may have said to a writer, and there are many opportunities for miscommunication. Still, I have to write about this, because it's about my work! So I'll try to describe the misconceptions illustrated by the article.

I am pretty sure that Rosenberg must know that his statement in the article is false. For one thing, "developing" a new allele is simply mutation, and mutation occurs continuously. All human populations have rare alleles that have originated recently and remain distributed only across small areas. Rosenberg's surveys of gene variation have identified many such alleles.

But more important to the current question, positive selection carries an allele to high frequency very rapidly -- much more quickly than the 50,000-year or longer span of time we are talking about. An allele with a five percent fitness edge can go from zero to fixation in several hundred generations -- in humans, they can make very large frequency changes in a thousand years.

If we took the quote at face value, Rosenberg would be saying that human evolution is impossible -- and that new selected alleles like lactase persistence and sickle cell simply cannot exist. We may be a young species (although I would argue the point), but that doesn't mean that we have stopped evolving!

Two prominent geneticists quoted in the article suggest that a bottleneck may explain the pattern of human genetic variation. Here also, I have to be cautious interpreting their quotes -- because even though they may seem relevant, they are referring to their own research papers, which don't actually address the question of linkage disequilibrium and positive selection.

Marcus Feldman suggests that a series of bottlenecks are a likely explanation for the pattern of human genetic variation, in particular, the decreasing gradient of genetic diversity with increasing distance from Africa. This is the "serial founder effect" scenario that I have written about before. I criticized Feldman's and other papers on this subject this spring, referring to "the Stanford school of genetic orthodoxy." My basic point is that all of the results are assumed to support the idea of bottlenecks: no one has yet tested the hypothesis. Even simulations that show the credibility of the concept do not test the hypothesis, because they do not examine credible alternatives, either demographic or selective.

More important, bottlenecks during the dispersal from Africa 50,000 years ago cannot possibly explain linkage blocks concentrated in coding genes with a mean age of 5500 years!

Why is there such difficulty understanding natural selection? I find it quite incredible that many of the scientists who would rail against ignoring Darwin in public schools at the same time actively root out Darwin's theory from their graduate students. Still, there it is. One prominent geneticist (I won't give the name) recently asked me, "You don't really think that lactase was selected, do you?" Many really believe that natural selection has stopped and that recent human evolution reflects nothing more than the cumulative effects of bottlenecks.

What is amazing to me is that these same geneticists embrace hypotheses of population history that cannot possibly have happened. The other geneticists quoted in the article, Carlos Bustamante and his graduate student Kirk Lohmueller, wrote a paper earlier this spring arguing that deleterious mutations have reached high frequency in Europeans (moreso than Africans) because of a bottleneck during European history. The press reported this work as "Whites genetically weaker than blacks, study finds." The hypothesis in the paper is that protein-coding sites otherwise conserved in most mammals may differ among humans because of relaxed selection in a bottleneck.

Here's why they're wrong: their bottleneck is impossible. They propose that the European population was a small, isolated population of 5,700 effective individuals from 214,000 years ago up to the Last Glacial Maximum. I suppose I should take some encouragement that they believe Neandertals were European ancestors (because otherwise, where exactly would this small, isolated population of Europeans have lived). But it's still quite impossible -- it implies no gene flow between Africans and Europeans across that entire span. You see, that is the only way that genetic drift can lead to this kind of result -- large differences in frequencies between continents for hundreds of deleterious alleles. It takes a bottleneck of exceptional length, along with complete isolation.

In what has become a troubling trend, these details were hidden away in the online supplementary information of the paper. It is no surprise that most people read only the paper's conclusions, without critically evaluating the methods. But when the assumptions are hidden so that it takes an effort to look at them, you can understand that the paper does not receive the kind of scrutiny that it deserves. These are not obscure laboratory techniques; they are the basic evidence on which the conclusions were based.

Now, Bustamante knows that positive selection has been very important in recent human evolution, because he wrote an important paper on the subject in 2005. I wrote about the paper at the time -- it was one of the works that really got us thinking about acceleration in the first place. So why in the world did their more recent paper adopt such a ridiculous model of population history?

In any event, I don't think that either of these studies from earlier this year are relevant to our acceleration results. They address different aspects of genetic variation. However, acceleration may help to explain the high frequencies of some gene variants conserved in other mammals -- the results explained by Lohmueller and colleagues as relaxed selection under a bottleneck.

The acceleration of recent positive selection would predict that many otherwise conserved gene variants may be segregating in humans, because they are the targets of positive selection. These conserved sites are among those most likely to show a strong sign of recent selection, because adaptive changes on them are necessarily rare (we know they're rare, because they haven't happened very often among other species). Most such sites are still conserved in humans -- it's just not possible to change their function in adaptive ways. But the massive ecological changes of recent human history have created the opportunity for adaptive responses that are not present in other mammalian lineages. We shouldn't be surprised to see that some such changes are currently underway.

Now, that's a different interpretation of the same data, and it's a testable hypothesis. Are these conserved sites in regions that show other signs of positive selection? If they are, then acceleration explains the data. I'm looking into it now.

Yesterday I ran across a piece by Tim Radford from earlier this year in the Guardian, titled, "The book that changed the world." It's a short article about the reception of Darwin's Origin of Species, an "instant bestseller":

Origin was the book of the year - perhaps the book of the century - but it faced some stiff competition in 1859. Alfred Lord Tennyson printed the first Idylls of the King, his long cycle of Arthurian poems. John Stuart Mill wrote his mighty work On Liberty. Samuel Smiles delivered Self Help, a classic in a genre that has kept publishing houses alive ever since. George Eliot published Adam Bede and Charles Dickens produced A Tale of Two Cities.

It was the best of times and the worst of times for Charles Darwin.

The tidbits of historical context make it interesting to read, although there may not be much new for people who are familiar with Darwin's contemporaries and their reviews of the Origin.

One cruel review was published anonymously - by convention reviews were then unsigned - but the Darwin camp quickly identified the hand of Richard Owen, the titan of palaeontology. "Some of my relations say it cannot possibly be Owen's article, because the reviewer speaks so very highly of prof Owen. Poor, dear simple folk!" Darwin mused wryly afterwards, but he was hurt by attacks from scholars he had once respected.

An essay by Michael Berkman and colleagues in the current PLoS Biology reviews the results of the National Survey of High School Biology Teachers as relevant to evolution and creationism. The study has gotten some press, for example this New Scientist article:

The researchers polled a random sample of nearly 2000 high-school science teachers across the US in 2007. Of the 939 who responded, 2% said they did not cover evolution at all, with the majority spending between 3 and 10 classroom hours on the subject.

However, a quarter of the teachers also reported spending at least some time teaching about creationism or intelligent design. Of these, 48% -- about 12.5% of the total survey -- said they taught it as a "valid, scientific alternative to Darwinian explanations for the origin of species".

The first paragraph of the essay's conclusion summarizes the reason for concern.

Our survey of biology teachers is the first nationally representative, scientific sample survey to examine evolution and creationism in the classroom. Three different survey questions all suggest that between 12% and 16% of the nation's biology teachers are creationist in orientation. Roughly one sixth of all teachers professed a "young earth" personal belief, and about one in eight reported that they teach creationism or intelligent design in a positive light. The number of hours devoted to these alternative theories is typically low -- but this nevertheless must surely convey to students that these theories should be accorded respect as scientific perspectives.

It does seem surprising to me that a sixth of biology teachers would express views consistent with young earth creationism -- I mean, what drew them to biology? But I don't think that the proportion by itself is alarming. I mean, it's a lower percentage than the general public. And I'm not persuaded by the idea that students will have "positive role models" for developing the idea that creationism is a scientific theory. They have plenty of positive role models already.

What really does concern me is the absolute minimal amount of time that high school biology courses spend on evolution. Without evolution, biology really lacks any mechanism to talk about cause and variation -- dissecting a fetal pig may help show you how the body works, but it can't show you why different individuals should vary, or why drugs should have different reactions in different people, why genetic disorders shouldn't happen very often, but why they sometimes happen anyway, why hybrid corn works but hybrid dairy cattle don't, and why oil just broke $130 a barrel and is still rising. In other words, important stuff -- the sort of basic consumer knowledge of biology that we want future citizens to know.

Here's what the study revealed about time spent on evolution:

We followed most previous studies in asking teachers to think about how they allocate time over the course of the school year. We went a step further in also asking whether evolution serves as a unifying theme for the content of the course. Over the entire year of high school biology we found substantial variation among America's high school teachers (see Table 1). Not surprisingly, we found that those who take most seriously the advice of NSES to make evolution a unifying theme spent the most time on evolution. Overall, teachers devoted an average of 13.7 hours to general evolutionary processes (including human evolution), with 59% allocating between three and 15 hours of class time (see Table S1). Only 2% excluded evolution entirely. But significantly fewer teachers covered human evolution, which is not included as an NSES benchmark. Of teachers surveyed, 17% did not cover human evolution at all in their biology class, while a majority of teachers (60%) spent between one and five hours of class time on it.

That's two and a half weeks of classroom time on evolution, out of a year-long course in biology.

What actually scares me is the number of practicing biologists -- especially geneticists -- who are working only on the knowledge of evolution they got in high school biology. Because university genetics, biochemistry, and biology curricula often require no coursework in evolutionary biology. They need no coursework at all in human evolution. So you wonder how they get to be practicing researchers while knowing nothing at all about the number of people who built the pyramids. Here it is. And high school biology teachers may have only a smattering of evolution in their collegiate biology training. It's no mistake that many teachers don't see it as a central issue -- neither training programs nor state standards tend to require any substantial knowledge about evolution.

Some teachers have a much better idea -- make evolution a central theme, and spend nearly four weeks on it. These are balanced by others who think that no evolution at all is necessary:

Those teachers who stressed evolution by making it the unifying theme of their course spent more time on it. Overall, only 23% strongly agreed that evolution served as the unifying theme for their biology or life sciences courses (Table S2); these teachers devoted 18.5 hours to evolution, 50% more class time than other teachers. When we asked whether an excellent biology course could exist without mentioning Darwin or evolutionary theory at all, 13% of teachers agreed or strongly agreed that such a course could exist.

This is a deep division, which also exists at the university level. There are a large group of "science-friendly" people who do not understand evolutionary biology, and who do not have a practical idea of its importance. These people are without a doubt against teaching creationism in science courses, but they cannot be for evolution except in the most nebulous sense, because they have no more than a nebulous idea of what evolution is. Unfortunately, some professional biologists, geneticists, and other scientists are among this group.

We're entering an age in which health decisions will be made based on genetic information -- when everyone may know their own gene sequences if they want to. New diseases are emerging, new crops are being developed, and new organisms are being transplanted from one continent to another. Decisions about the economic development of entire regions -- perhaps entire nations -- are now subject to the evaluation of biodiversity, including threatened and endangered species.

The people making these decisions ten to twenty years from now will have an average of 13.7 hours of education on evolution.

References:

Berkman MB, Pacheco JS, Plutzer E. 2008. Evolution and Creationism in America's Classrooms: A National Portrait. PLoS Biol 6(5): e124 doi:10.1371/journal.pbio.0060124

The University of Pennsylvania Museum of Archaeology and Anthropology has just opened a new exhibit on human evolution, titled "Surviving: The Body of Evidence." An online article by Janet Monge and Alan Mann explains the idea of the exhibit and its unique emphasis:

The genesis of the idea came from Alan Mann's realization that students seemed to understand the broad impact of evolutionary process if they could witness it for themselves in their own bodies and minds. In order to evoke this response in the context of the exhibit, we challenge visitors to try to understand and define what it means to be human -- to revel in the experience of humanness. We ask them to witness the evolutionary process and to contextualize the human experience. This part of the exhibit is peppered with over 200 touchable casts of both modern and extinct mammals and primates, including many of our human ancestors, our chimp relatives, and even comparisons to horses and whales.

Visitors are now ready to see evolutionary history in their own bodies. Using multimedia devices surrounding a massive model of a woman's body, they see themselves not as perfect or perfectible beings, but as animals dealing with the various medical dilemmas that characterize the shared human experience -- bad backs, difficult childbirths, teeth that do not fit in our jaws, as well as many other maladies that are best understood from an evolutionary perspective.

Janet very kindly sent me links to the exhibit's online components. This page discusses the "Year of Evolution," an observance involving many Philadelphia institutions leading up to Darwin's 200th birthday.

Meanwhile, the "Surviving" exhibit's online site provides an interactive overview of several of the exhibit's areas, short videos that present perspectives on human anatomy, and other multimedia compositions. A great introductory video starts with kids' perspectives on evolution and the future -- a nice way to contextualize the exhibit's importance for evolution education. Another multimedia piece presents four of the scientists crucial to building modern biology, and provides audio put into their own voices that describes some of their contributions. Educators may appreciate the inclusion of Rosalind Franklin and Mary Leakey along with the more stodgy-looking Linnaeus and Darwin.

I think it's a neat site to look at if you're thinking about planning projects for teaching evolutionary biology, or to share with students.

Cornelia Dean writes a long profile of Francisco Ayala in today's Science Times. The occasion is the publication of his new book, Darwin's Gift to Science and Religion.

Dr. Ayala gives about 50 talks a year, he said in a recent interview in New York, a day after he delivered the inaugural Louis Levine-Gabriella de Beer lecture in genetics at City College. (He had spoken the day before, at North Carolina State University, on the evolution of morality, and spoke two days later at McGill University in Toronto, where his subject was Darwinism and religion.)

Because of his eminence -- he is a member of the National Academy of Sciences, a former president of the American Association for the Advancement of Science and a winner of the National Medal of Science -- Dr. Ayala "has a bully pulpit," said Eugenie Scott, who heads the National Center for Science Education, a group that advocates for the teaching of evolution and against creationism in public schools. "When Francisco speaks, people listen."

Ayala is a fascinating person to talk to, and his vines make some of the best wine I've ever had. The article is a nice portrait of his current work.

...please reconsider, because it is an absolute waste of your time. Spend the time watching Nova's Judgment Day" documentary instead, which actually conveys both evolution and Intelligent Design creationism in a more intelligible way.

But if you absolutely, absolutely cannot ignore it -- for example, because you have students asking you what you think about it -- then you could do worse than Arthur Caplan's review of the movie. Caplan takes the focus off the distraction of the movie's premise, and back on to the movie's shortfalls in accurately describing Intelligent Design creationism, the historical context of the Holocaust, and the role of evolutionary theory in explaining life's diversification as opposed to its origin:

What is it that devotees of intelligent design believe that gets their colleagues in such a rage? Do they just want to invoke god as the starting point of the universe? Do they see god's hand in the design of every creature? Are they asking us to see the gods of every faith and tradition -- those posited in Catholicism, Hinduism, Mormonism, Islam, Buddhism, Sikhism, Rastafarianism, etc. -- in our DNA? Do they believe that competitive accounts of creation based on the Bible need to be in every American classroom? Do they see empirical proof of god in every molecule, plant, animal, rock, vegetable and fungus? "Expelled" never really tells us.

One suspects that sympathy for those portrayed in the movie as hapless pariahs might be reduced if the movie spent more time describing what it is this tiny handful of Ben Stein-proclaimed martyrs actually believe.

This paragraph seems to have the filmmaking style down to a T:

The movie's faux tale of an evolutionist led Inquisition is followed by Stein interviewing a short parade of self-avowed atheists who also are fervent Darwinians as they mock intelligent design in particular and religion in general. They also look frumpy. As an antidote we get deep, sincere ruminations mainly from some monumentally pompous thinker no one has ever heard of who is nevertheless stylishly attired and living in a gorgeous apartment in Paris. He assures what is hopefully an increasingly irritated audience that god and science can live together in peace. They can but for no reasons ever articulated by this fellow or in this film.

Maybe they're just saving the real explanations for "Expelled 2! The Wrath of Dawkins" or something?

Spring has finally come to us here in the North, and it's time to start thinking about planting. So, when I went to a seminar yesterday by John Willis, it was with dual motives.

Naturally, I was interested in hearing about his work relating the evolutionary ecology of Mimulus species to their genomics. As Willis and his many former and current lab members made clear in a recent review article in Heredity, monkeyflowers have become a really interesting model system for studying the dynamics of natural selection on genomes -- particularly, with relation to local ecological adaptation, and also with relation to speciation.

But I was also thinking about whether I could find a nice flower variety for my garden. I'm not particularly excited about peas, and I tolerate Arabidopsis when it comes up, but let's face it, it's not exactly a show flower. I'd love to get one of the prettier hawkweeds going (these have eponymical appeal as well as botanical interest) but the common ones are pretty boring.

Well, Willis's lab has been a center of development for Mimulus genetics. They have developed a store of SNPs and other markers (available at the Mimulus evolution website) for QTL mapping, and are using them to find genes responsible for ecological adaptations in different wild Mimulus populations. In the talk, Willis featured some of his collaborators' work finding genes involved in wet versus dry habitat adaptations and in early versus late flowering. These traits are connected to each other, as well as to other life history, plant size and flower size.

I left having my prior belief abundantly confirmed: botany is awesome. I mean, think about it. You can go outside, in your own neighborhood, and study biology. You can uproot your subjects and transplant them somewhere else, to watch how well they do. If they die, well, that's a data point, not an ethical emergency! Worried about gene-environment interactions? No problem, just put samples of all your subjects in the same greenhouse and wait. Need to isolate a QTL against a uniform genetic background? Cool, just repeatedly backcross it into an inbred line for a few generations, selecting for the trait each time. Want to study genetic correlations? Well, you can breed a thousand plants and select for any trait you want!

Oh, and if you want to, you can clone them.

Let's look at an example, from the Heredity review:

Recent work on floral evolution demonstrates that fundamental evolutionary questions can be addressed in Mimulus through the combination of field experiments and modern genomic approaches. Bradshaw et al. (1995, 1998) pioneered the application of genome mapping to study of ecologically important traits in Mimulus using RAPD and allozyme markers to map floral QTLs underlying the divergence between red-flowered, hummingbird-pollinated M. cardinalis and pink-flowered, bee-pollinated M. lewisii. The initial mapping experiments, with hybrid phenotypes measured in controlled greenhouse environments, revealed QTLs with major effects on virtually every floral character studied, from coloration and morphology to nectar production. To determine the effect of these QTLs on pollinator visitation and discrimination, Schemske and Bradshaw (1999) moved the genotyped hybrids to a field site near one of the few regions where the species coexist, and observed bee and hummingbird visitation behavior. Amazingly, the M. cardinalis allele at a single QTL, YELLOW UPPER (YUP), was responsible for an 80% loss of visitation by bee pollinators, and the M. cardinalis allele at a QTL responsible for variation in nectar production doubled hummingbird visitation (Schemske and Bradshaw, 1999). Bradshaw and Schemske (2003) subsequently created near-isogenic lines (NILs), where heterospecific alleles at YUP were reciprocally introgressed into the parental genetic backgrounds, and evaluated the response of pollinators to the NILs in the field. They observed an even clearer pattern of pollinator discrimination due to this locus, with a 74-fold increase in bee visitation in M. cardinalis NILs that carried the M. lewisii YUP allele, and a 68-fold increase in hummingbird visitation in M. lewisii NILs with the M. cardinalis YUP allele. Although the ecological context, in this case the community of potential pollinators, is certainly important to the evolution of new pollinator associations, these results also demonstrate that single genomic regions can have a large effect on major evolutionary transitions (Wu et al. 2008: 224-225).

The talk was mostly focused on the Mimulus guttatus complex, where some of the most pressing issues are life history, drought tolerance, and tolerance of high mineral concentrations, such as salt or copper. They were able to trace many QTL's of small effect with relation to the major differences in life history and moisture requirements in ecogeographic races of M. guttatus, to show that the within-population variation for these traits is caused by high-frequency (likely balanced) alleles rather than mutation-selection balance or rare alleles, and to find the correlated responses to selection of different plant traits based on different QTL's.

With respect to the genetics of speciation and ecogeographic race formation, they are helped by a long history of research on Mimulus. For example:

Macnair and Christie (1983) performed the first direct genetic analysis of hybrid incompatibilities in Mimulus. While studying the genetic basis of copper tolerance in California populations of M. guttatus, they noticed that some crosses between plants from the copper mines and certain other populations resulted in F1s that died as young seedlings. Further crossing studies revealed that the F1 lethality was caused by a deleterious epistatic interaction between the copper tolerance allele from the mine populations (or a gene tightly linked to it) and alleles at an unknown number of different loci from the other populations. Such deleterious interlocus interactions, usually referred to as Dobzhansky–Muller (D-M) incompatibilities, are thought to be the major cause of low hybrid fitness in plants and animals (reviewed in Coyne and Orr, 2004). Remarkably, it appeared that natural selection for copper tolerance had indirectly resulted in the evolutionary origin of the hybrid incompatibility (Wu et al. 2008:226).

So yes, say what you want, botany is awesome. Plus, there's one more thing: I sat through an entire lecture about natural selection and ecological differentiation of species and races, and never once heard the word, "bottleneck." It was like traveling to some kind of bizarro world where biologists still read Darwin!

So we come down to the really difficult question: which variety am I going to plant? Mimulus glabratus is native here in Wisconsin, including Dane County, but it is not very showy, and prefers wet habitat. That makes it a poor fit for my native plant patch, which is dry/mesic, and which I never water unless the black-eyed Susans and bee balms start to wilt. Mimulus ringens is prettier, with bigger, lavender flowers, but also likes it wet.

I guess I'll have to keep looking. M. lewisii is a pretty variant, if I can find a good source for it, and I can keep it in one of the wetter corners of the yard. I would try for M. cardinalis, since we have hummingbirds sometimes, but I'd like to get Lobelia cardinalis going also, and it's a lot easier to find. Besides, it hardly looks like a monkey!

References:

Wu CA, Lowry DB, Cooley AM, Wright KM, Lee YW, Willis JH. 2008. Mimulus is an emerging model system for the integration of ecological and genomic studies. Heredity 100:220-230. doi:10.1038/sj.hdy.6801018

This Saturday (2/8/2008) is Darwin Day here at UW. My lab will be putting a display together at the Geology Museum in the afternoon -- you can find a full schedule and flyer at the UW Darwin Day website.

The real Darwin Day is February 12 (just like Lincoln!), and he was born in 1809 (just like Lincoln!). In honor of the occasion, Nature prints an essay by Kevin Padian reviewing Darwin's scientific legacy.

In the past century and a half, Darwin's ideas have inspired powerful images and insights in science, humanities and the arts. Meanwhile, countless commentators ignorant of his meaning have borrowed his eloquence to plump their own chickens -- from capitalism to 'evolutionary psychology'. Darwin has been invoked as the demon responsible for a variety of perceived heartless ills of society, including atheism, Nazism, communism, abortion, homosexuality, stem-cell research, same-sex marriage, and the abridgement of all our natural freedoms. One can scarcely imagine the horror that Darwin would feel at the misunderstanding, misappropriation and vilification of his ideas in the 125 years since his death.

The essay is a list of "big ideas" from Darwin, along with some of their later developments. Natural selection, monogenism, genealogical classification, the action of imperceptible forces over long periods of time ("deep time"), biogeography, sexual selection, coevolutionary relationships, gradualism, and natural economy all merit entries, along with a few others.

I particularly liked this passage describing Darwin's conception of coevolution:

One of Darwin's lesser-known books is On the Various Contrivances by which British and Foreign Orchids are Fertilised by Insects and on the Good Effects of Intercrossing (1862). It encapsulates the concept that species of very different origins have evolved mutual ecological relations through time that have come to affect critical aspects of their morphologies. An African orchid was discovered that had a corolla nearly a foot long. Darwin inferred that there must be a moth with a tongue long enough to extract its pollen. When the moth sub-species was eventually discovered, it was given the name praedicta. Today we can identify groups of plants and their insect predators, vertebrates and their parasites, lichens composed of an alga and a fungus, and many other associations that can only reasonably be explained by co-evolution through diversification over millions of years (Padian 2008:633).

Padian includes about the amount of unwarranted hagiography you might expect. Darwin's being "less emphatic than Wallace about the pre-eminence of natural selection among other mechanisms of evolutionary change" seems good, until you reflect on the "other mechanisms" in the running -- mainly Lamarckism. And maybe Darwin didn't share Malthus' "bleak view" of the poor, but he certainly displayed a bleak view of Australian and South American native peoples in Voyage of the Beagle. Darwin should be forgiven the prejudices of the age, but it ill serves us to whitewash them.

Darwin's Origin ends famously with a passage that evokes poetic interpretation. Padian ends his essay with a quote from Thomas Hardy, one of the literary figures he describes as a recipient of Darwin's influence:

As Hardy put it: "Let me enjoy the earth no less / Because the all-enacting Might / That fashioned forth its loveliness / Had other aims than my delight." This child of the Enlightenment was well aware of more ancient world views, and humbled by what the new investigations of the cosmos revealed. Humans are animals, one species of many on the planet, bound by common ancestry to all other species, part of an ages-old dance of reproduction, accommodation, survival and alteration.

The first time, I read that last word as "alliteration." I guess it's my inner English major coming out...

References:

Padian K. 2008. Darwin's enduring legacy. Nature 451:632-634. doi:10.1038/451632a

A letter to the editors of Nature by Jasmina Muzinic notes the new translation of Darwin's works into Croatian:

Charles Darwin's On the Origin of Species and The Descent of Man have at last been translated into Croatian, thanks to the work of the renowned science and theology translator Josip Balabanic. Other European countries -- including Denmark, the Netherlands, France, Germany, Italy, Poland, Russia and Sweden -- had access to Darwin's works in their mother tongue during his lifetime. But it was not until this year that Croatian students of biology could read them in their own language.

Cool.

Stories about genetics, paleoanthropology, and other stuff have been falling this week faster than I can keep up, but happily I'm not alone. Here are some of the more interesting blog-takes on recent stuff:

Pigment use by Neandertals

Julien Riel-Salvatore writes about recent work by Maria Soressi and Francesco d'Errico establishing that Mousterian pigment nodules were used as crayons:

The reason why this ongoing study is so convincing is that the authors used replicative referents that objectively establish the microscopic and rugosimetric features of blocks of coloring materials worked in different manners and with different tools. This provides an objective baseline against which to compare the characteristics of objects found in assemblages attributed to Neanderthals and to determine whether they bear evidence of having been purposefully manufactured by human action.

I'll write more about this when I get a chance, but Julien's post is valuable and provides translated (from French) excerpts of the relevant papers.

Genetic diversity in African cattle

Razib writes about a New York Times Magazine article that details the cultural and economic pressures around cattle breeding in Uganda. People are bringing in Holsteins, because even though they are finicky in the African climate, they can give as much as 20 times the milk of the native Ankole cattle. The Ankole breed resembles those that American cattlemen would call "Watusi."

Here's a passage from the article:

Not everyone in Uganda, however, agrees that the foreign breeds are an upgrade. President Yoweri Museveni once imposed a ban on imported semen. Museveni belongs to the Bahima ethnic group. When he was a baby, in a sort of Bahima baptism ritual, his parents placed him on the back of an Ankole cow with a mock bow and arrow, as if to commit him symbolically to the defense of the family's herd. Museveni, now in his 60s, still owns the descendants of that very cow, and he retains a strong bond to the Ankole breed. Two years ago, I accompanied a group of Ugandan journalists on a daylong trip to one of the president's private ranches, where he proudly showed us his 4,000-strong herd of Ankole cattle. At one point, a reporter asked if the ranch had any Holsteins. "No, those are pollution," Museveni replied. "These," he said, referring to his Ankoles, "the genetic material is superior."

Razib's comment on another passage:

I guess it's nice that [the author] put quotes around [genetic] dilution, but the rest of the article suggests to me that the author hasn't internalized that genetics is discrete, and that information isn't destroyed through cross-breeding. Rather, it seems that a good program of cross-breeding could result in a superior breeds of Holstein optimally suited to the local climate. That's what happened with indigenous African lineages as they hybridized with introduced South Asian ones 2,000 years ago to produce the Ankole according to the article! This sort of piece in a widely circulated publication such as The New York Times Magazine could have been a serious examination of agricultural and quantitative genetics, and just how much we depend on these unsexy sciences to feed the world. As it is, there's a lot of hand-waving scare-mongering....

The usual argument in favor of preserving diversity of domesticated species is as a hedge against future uncertainties like climate change or novel diseases. Another reason is to preserve local flavor -- that's why people grow "heirloom" vegetables, for instance. But it is quite certain that the pasturage devoted to traditional breeds of cattle well decline if imported breeds provide a net economic advantage. In that case, the best way to preserve diversity is cross-breeding -- which also has the direct advantage of introducing locally adapted genes into the descendants of the foreign breed.

This is what African herders have been doing for thousands of years, as evidenced by the spread of zebu genes across the continent. These European imports are merely the newest version.

What are genetic tests good for?

Hsien-Hsien Lei has an invited post by Ann Turner, noted for her book, Trace Your Roots With DNA. Turner comments on the new genetic tests from deCODEme and 23andMe:

Since I'm interested in genetic genealogy, I am more attuned to the ancestry components of the deCODEme results. The admixture results are interesting to anyone who suspects they may have ancestors from different geographical areas. The detailed chromosome graphs also show the potential for tracing segments of DNA shared with even more distant relatives. For instace, it was recently found that a block carrying a colon cancer gene could be traced back to a couple who arrived in the US in the early 1600's. This sort of thing might very well show up in the "Compare Me" feature.

Evo-devo and its detractors

On the subject of guest posts, Carl Zimmer is running an essay from Jerry Coyne. The essay is a response to a blog post by Olivia Judson, in which she reviewed the ideas of Richard Goldschmidt and suggested that the macromutation theory may be primed for a comeback, using recent results from evolutionary developmental biology (evo-devo) as a jumping-off point. Coyne has been one of the foremost critics of the idea that evo-devo is somehow "changing" basic conceptions in evolutionary biology.

Unfortunately, her piece is inaccurate and irresponsible, especially for a journalist with a strong science background (Judson has a doctorate from Oxford). I've admired Judson's columns and her whimsical and informative book Dr. Tatiana's Sex Advice to All Creation. But this latest posting is simply silly. As an evolutionary biologist, I'm used to seeing our field twisted out of shape to satisfy the demands of journalists who love sensational new findings--especially if they go against long-held Darwinian beliefs like the primacy of gradual, stepwise evolution. But I'm not used to seeing one of my own colleagues whip up excitement about evolutionary biology by distorting its findings.

I have to say I find the entire concept of a "New York Times blog" to be interesting. They have quite a lot of them now, and they are not clearly demarcated from other editorial content at the Times website. That's not a criticism, but it does mean that readers tend to think they come with the full authority of the Times' editors. To me, they read just like any other blog post anywhere, but for a picture of how people perceive their importance, just look at their comment sections.

That was enough in this case to bring Jerry Coyne out of the woodwork. I think his slapdown is a little extreme (Remind me not to get on his bad side!). But Judson was clearly mistaken to equate today's evo-devo results with Goldschmidt's ideas -- a link that evolutionary developmental biologists themselves deny. At any rate, Coyne's forceful advocacy for his point of view makes for good reading, and I would recommend it to anybody interested in where evolutionary developmental biology is going and how it will influence our ideas about evolution over the next few years. Here at Wisconsin I am at one of evo-devo's epicenters, and I can see a number of ways that it may transform our ideas of human evolution. So in that sense, I am more sanguine than Coyne about the prospects for understanding morphological changes with developmental insights. At the same time, I agree substantially that the genetic questions must ultimately be answered in genetic terms.

The discussion in Zimmer's comments section digresses into what Stephen Jay Gould may or may not have thought about saltational changes in evolution. I think that is essentially unenlightening, in the sense that quote-pulling out of Gould can reinforce almost any point of view.

The Beagle Project Blog lists me as one of the top ten senders of traffic to their site, which reports on the efforts to replicate the original voyage:

We aim to celebrate Charles Darwin's 200th birthday by building a sailing replica of HMS Beagle and recreating the Voyage of the Beagle with an international crew of researchers, aspiring scientists and science communicators. The voyage will apply the techniques of 21st century science to Darwin's journey, inspiring a new generation of scientists and promoting the public understanding of evolution and wider science.

So, I thought I would post to send them a little more!