This is a doofy story running on MSNBC without an author byline: "Shrinking of Scottish sheep tied to warming". Why do I say "doofy"? Take a look at the way it describes natural selection:

The study upends the belief that natural selection is a dominant feature of evolution, noting that climate can trump that card.

"According to classic evolutionary theory," [study author Tim] Coulson added, the sheep "should have been getting bigger, because larger sheep tend to be more likely to survive and reproduce than smaller ones, and offspring tend to resemble their parents."

Yes, and classic evolutionary theory also says that if you stop killing the small ones, the population average is going to get smaller. Duh. A reduction will happen in a single generation as small individuals remain to become adults who would otherwise have been removed. The reduction may continue for a few generations, either by chance, or by changing the environmental component of variance in size. It can go on for many generations if there is a heritable component to size that confers a disadvantage on the largest individuals. Plausibly, larger individuals take longer to develop, there may be advantages to smaller size in females that are no longer opposed as strongly by antagonistic selection for larger size in males, or any number of other possibilities.

Has climate "trumped natural selection"? No. Cold and consequent food scarcity in this case is one cause of selection (killing small lambs). Possibly, one or more causes of stabilizing selection remain in force (maybe longer development time, but there are other possibilities). Or maybe not. Climate change has caused a change in the pattern of selection, by relaxing selection against small individuals who would otherwise have died from food scarcity.

The way the article describes selection is an old-time fallacy -- "survival of the fittest" is recast as "survival of the strongest", where strongest means "biggest". If the small are somehow fail to be eliminated, then natural selection is failing at its work. It's the eugenic fallacy, brought to 21st century climate change. It makes an eye-catching headline -- "Climate Change Overpowers Natural Selection". But it's false.

A more accurate headline would be "Wee Lambs, Once Doomed to Starve, Saved by Climate Change"

I happen to have been reading some of the earlier research on these sheep, so I know that the work is interesting because researchers actually know about the fitness outcomes for individuals across their study duration. The observed fitness outcomes indicate that larger individuals have more offspring within each generation, but the population nevertheless became smaller over time. That comes down to viability of small young individuals and the non-heritable (environmental) component of variance in size, in a fairly complicated way. I'll revisit the paper later to describe the study more fully. I just wanted to point out that this news story gets it totally wrong. Climate change is one of the big causes of the pattern of natural selection, it doesn't magically repeal it.

The NY Times profiles Southwest archaeologist Steve Lekson, "Scientist Tries to Connect Migration Dots of Ancient Southwest":

“Steve is possibly the best writer in Southwest archaeology,” said David Phillips, curator of archaeology at the Maxwell Museum of Anthropology at the University of New Mexico. “Our academic writing has this inherent gift of taking something interesting and making it dull and boring. And Steve doesn’t have that problem. He thinks outside the box, and the rest of us comb through his ideas.”

“Having said all that,” Dr. Phillips added, “I personally think that the Chaco meridian is a crock.”

Lekson has a new book coming out, History of the Ancient Southwest, which updates his "Chaco meridian" idea along with many other elements of Southwest archaeology. It seems to me that this is an interesting case study in the power of archaeology to test ideological versus ecological hypotheses -- that in a complex society with long-term occupations and stylistic elements for comparison.

But whenever you're talking about a hypothesis involving ideological causation, there's a tremendous potential for confirmation bias:

“Anyone can take any position and find evidence,” Dr. Phillips said. “Done properly, science means that you stop yourself and figure out what the opposite is — the null hypothesis — and you prove the null hypothesis couldn’t possibly be true. By process of elimination, your desired outcome becomes more plausible. This gets back to Karl Popper. You can only falsify.”

But Dr. Lekson insists that archaeology can advance only by pushing beyond the Popperian ideal, trying to make sense of all the data with plausible accounts of what was happening historically in the ancient Southwest.

“We were trained to treat ancient Pueblo societies like cultures in laboratory petri dishes,” he recently wrote. “Sprinkle the right amount of rainfall on the proper soil and up popped pueblos.” What has been neglected, he says, is an appreciation for the unquantifiable.

What they're talking about is different prior assumptions. How close to a meridian do sites have to be to confirm or reject the hypothesis that they're plotted on the meridian? How much can they overlap before they reject the hypothesis of mass relocation? It depends how committed you are to the idea to begin with -- and that depends on your prior expectations about the role of ideological and ecological forces on complex societies.

As for myself, I'm never surprised when a complicated scenario falls close to the mark. It's the simple ones that get my attention.

From The Guardian, via a reader:

God or Darwin? The world in evolution beliefs

Find out where on earth only 8% of people believe in evolution

The listing includes 10 countries, polled by The British Council, who have released the study to publicize a website called "Darwin Now". I suppose the title of "evolution leader" depends on how you interpret the poll. China has the greatest percentage who "agree that the scientific evidence for evolution exists," at 55 percent. But they also have a surprising number (19 percent) who think that "evolution should NOT be taught, only other theories."

Only 9 percent of American respondents thought that evolution should not be taught, but only 33 percent agreed that evidence for evolution exists. That puts us behind Mexico and India, but way ahead of South Africa and Egypt -- those places on Earth where only 8 percent agree that evidence for evolution exists.

Michael Nielsen writes that the scientific publishing industry is set for a "disruption". It's an interesting read, and in a sample, he strikes on the same analogy that I used earlier in the week for grant agencies: the rugged fitness landscape:

The problem is that your newspaper has an organizational architecture which is, to use the physicists’ phrase, a local optimum. Relatively small changes to that architecture - like firing your photographers - don’t make your situation better, they make it worse. So you’re stuck gazing over at TechCrunch, who is at an even better local optimum, a local optimum that could not have existed twenty years ago:

Unfortunately for you, there’s no way you can get to that new optimum without attempting passage through a deep and unfriendly valley. The incremental actions needed to get there would be hell on the newspaper. There’s a good chance they’d lead the Board to fire you.

The essay is full of good one-liners ("The blogosophere has at least four Fields medallists (the Nobel of math), three Nobelists, and many more luminaries. The New York Times can keep its Pulitzer Prizes."). But is Nielsen right? Is a revolution is scientific publishing coming?

I think this insight has the most potential:

Scientific publishers should be terrified that some of the world’s best scientists, people at or near their research peak, people whose time is at a premium, are spending hundreds of hours each year creating original research content for their blogs, content that in many cases would be difficult or impossible to publish in a conventional journal. What we’re seeing here is a spectacular expansion in the range of the blog medium. By comparison, the journals are standing still.

The "world's best scientists" aren't worried about how to parcel their work into publishable units to impress review committees. The average scientist, on the other hand, has her hands full applying for grants.

So let's consider two big opportunities for a science publishing startup: (1) Make it easy to advance a body of work from informal to formal. (2) Find a way to bring grant descriptions and bibliographies into the system. Integrate grant applications with the results that follow, possibly years later. In some cases, grant agencies could require open access applications, reviewed on a rolling basis.

I also want to comment on one of Nielsen's final points: Start-ups have an opportunity to vastly improve online storage of original scientific data.

Developing high-quality web services requires deep knowledge and drive. The people who succeed at doing it are usually brilliant and deeply technically knowledgeable. Yet it’s surprisingly common to find projects being led by senior scientists or senior editors whose main claim to “expertise” is that they wrote a few programs while a grad student or postdoc, and who now think they can get a high-quality result with minimal extra technical knowledge. That’s not what it means to be technology-driven.

I've seen enough attempts to make databases in anthropology to see this weakness manifested repeatedly, in different ways. Lots of money and effort goes into database creation, only to build a result that requires potential users to develop specialized technical skills of their own. Many sets of data really need expert annotations about which observations are more or less reliable; ideally with photographic or other documentary evidence. The end result is that a bunch of people learn the database because it houses their data, but the collection is not generally useful. Students don't learn the database, and it falls into disuse. It's a bad enough problem in genetics, where some databases are highly trafficked, standardized and useful for building third-party applications. Anthro-related databases have a small set of potential users, fewer with the time and technical skill to make things work, and minimal resources for curation of the datasets.

So I agree there's an opportunity there, but it will be difficult to make work for small scientific communities. Something like Chemspider serves a vast community, with a rich dataset whose elements can be standardized in ways that may be difficult for many anthropological datasets.

No.

For a Sunday morning read, there's Gina Kolata's article in the NY Times: "Grant System Leads Cancer Researchers to Play It Safe":

Yet the fight against cancer is going slower than most had hoped, with only small changes in the death rate in the almost 40 years since it began.

One major impediment, scientists agree, is the grant system itself. It has become a sort of jobs program, a way to keep research laboratories going year after year with the understanding that the focus will be on small projects unlikely to take significant steps toward curing cancer.

“These grants are not silly, but they are only likely to produce incremental progress,” said Dr. Robert C. Young, chancellor at Fox Chase Cancer Center in Philadelphia and chairman of the Board of Scientific Advisors, an independent group that makes recommendations to the cancer institute.

The institute’s reviewers choose such projects because, with too little money to finance most proposals, they are timid about taking chances on ones that might not succeed.

The story goes through many of the problems with the current system of peer review, and profiles a few researchers whose "transformative" grants haven't been funded. This kind of story runs a risk: if you applied for grants and didn't get them, are you just whining? I mean, ninety percent of grant applications are not funded, so if you're even average good, you've got to submit 10 before you have any expectation of return.

The other risk of the story is that readers will draw that conclusion that there are so many deserving grants that go unfunded, all we need to do is raise the funding level. This overlooks the very high costs of the current review system -- flying all those people around for panels, handling the paperwork, paying the grant agencies' bureaucracies, plus the support staff at universities and other institutions to collect the grant money -- "indirect" costs of grants that cover administration now amount to nearly half of federal grant budgets. There's no question that this money could be better allocated.

The question raised by Kolata's article: Measured by progress in treatments, the money spent by NIH looks like a poor investment. Is there some way that we could invest the money in grants to yield faster progress? Many researchers (some disappointed in their pursuit of promising ideas) think that more money should be given to projects with higher risks of failure.

I view this as a basic reality of science: If you want to discover something new, you have to falsify some existing ideas. So if we want to make scientific progress, we have to invest money to disprove things that many people already believe to be true. It is a scientific mistake to allocate money to projects that do not challenge existing ideas.

As a practical matter, how much money should we invest in risk versus small incremental, low-risk projects? After all, there are ideas, and then there are ideas -- well-entrenched, hidebound, review panels goosestepping together ideas. I think a little R. A. Fisher is in order. Think of cancer research as a search space, where research advances are moving toward some (perhaps several) peaks. Now, the question is what kind of change will bring you closer to a peak?

Well, it depends how close to the peak you already are. If you're already close to a peak, a very large change can do nothing but take you further from it. An incremental change will be roughly halfway likely to take you up a small amount; halfway likely to take you down. So if you think you're already very close to an acceptable cure rate for cancer, you should focus on the very small incremental improvements.

On the other hand, if you're far from a peak, a large change is not unlikely to take you closer to the top, and it will certainly get you there a lot faster.

But worse, what if you're climbing some low peak, where the outcome -- even if you do everything entirely right -- is poor? A small incremental change will never do any better than the short peak you're on. But a large change has some chance of finding some other peak -- a radical shift in treatment that would bring much better outcomes. The likelihood of that for any particular change may be very low. But your coverage of the search space would be vastly larger -- making progress much faster.

That is, assuming you think that the present state of cancer science is far from the best possible treatment plan.

It seems to me that anytime there is a lot of government money involved in research, it's because the political process has come to some consensus that major, transformative changes are necessary. If you're not funding large, transformative research, you're wasting the people's money.

I'm remembering a story from earlier this year, that concluded that humanities grant panels rank "what is fascinating" over what is likely to be true. I wonder if NIH might do better to import some of those humanities panels to review their grants?

UPDATE (2009-06-28): Yes, I realize I suddenly switched from Fisher's mutation analogy to Wright's rugged landscape metaphor.

That image conjured by John Noble Wilford just had me tickled:

It so happens, as Dr. Conard and his co-authors, Susanne C. Münzel of Tubingen and Maria Malina of the Heidelberg Academy of Sciences, noted, the Hohle Fels flute was uncovered in sediments a few feet away from the carved figurine of a busty, nude woman, also around 35,000 years old. The discovery was announced in May by Dr. Conard.

Was this evidence of happy hours after the hunt? Fertility rites or social bonding? The German archaeologists suggested that music in the Stone Age “could have contributed to the maintenance of larger social networks, and thereby perhaps have helped facilitate the demographic and territorial expansion of modern humans.”

The description of the flutes is available in advance copy from Nature. This is one of my pet peeves -- papers in advance of print -- because I can't just enter them into my bibliographic database; there are no volume or page numbers. What a pain.

Mammoth ivory flutes were really hard to make.

The characteristics of these three fragments of ivory are known only from the ivory flute from the upper Aurignacian deposits of Geienklösterle archaeological horizon II (ref. 15). The technology for making an ivory flute is much more complicated than that for making a flute from a bird bone. It requires forming the rough shape along the long axis of a naturally curved piece of mammoth ivory, splitting it open at the interface of the cementum and dentine or along one of the other bedding plains in the ivory, carefully hollowing out the halves, carving the holes and then rejoining the halves of the flute with air-tight seals along the seams that connected the halves of the flute. The ivory flute from Geienklösterle preserves dozens of finely carved notches along the edges of the two halves to facilitate binding and sealing the flute (15). Although thousands of pieces of ivory-working debris and hundreds of ivory artefacts have been recovered from the Aurignacian deposits of Hohle Fels, Vogelherd and Geienklösterle, only the flute fragments have the form described above and preserve a hollowed-out convex morphology, finger holes and series of notches along the edge of the long axis. Thus, we can be confident that these finds represent fragments of ivory flutes similar to the one recovered from Geienklösterle. We recovered the ivory flute from Geienklösterle in 31 small fragments. Given the tendency of delicate ivory artefacts to break into many pieces, it is not unusual to find such pieces in isolation.

The tiny (~1 cm) fragments don't look like much by themselves. Several of them were found only by water screening of sediments. Much more than the "origin of music" angle, I think the attention of Conard's team is the real story here. They had an inkling what to look for, and they started finding the pieces. I wonder how many others may be floating around unrecognized within Upper Paleolithic collections. The thing working against a lot of unrecognized tiny flute fragments is that the Swabian sites seem to have involved dedicated ivory working on a scale that doesn't appear elsewhere.

The flutes made of bird bone are much simpler to manufacture and interpret.

The maker of the flute carved the instrument from the radius of a griffon vulture (Gyps fulvus). This species has a wing span of between 230 and 265 cm and provides bones ideal for large flutes. Griffon vultures and other vultures are documented in the Upper Palaeolithic sediments of the Swabian caves with several examples identified from Gravettian and Aurignacian deposits at Geissenklösterle.

The Geissenklösterle flute has previously been modeled to evaluate its sound characteristics; this has not been done for the new flutes:

The smaller, three-holed bone flute, made from the radius of a swan, that was recovered from the Aurignacian deposits of archaeological horizon II at the nearby cave of Geienklösterle can be played by blowing obliquely into its proximal end to produce four basic notes (10, 11, 12, 13). Three additional overtones can be produced by blowing more sharply into the flute. Given that the three-holed flute from Geienklösterle produces a range of notes comparable to many modern kinds of flute, we expect flute 1 from Hohle Fels to provide a comparable, or perhaps greater, range of notes and musical possibilities (14).

I for one am tired of the boring New-Agey flute music that has been creeping into documentaries about ancient people. So I hope that somebody out there will think a little more broadly about the kind of musical environment these flutes were part of. There would have been a huge potential variety of percussion artifacts. Singing and clapping. Probably not strings, although as long as we're going to talk seriously about arrows in the Upper Paleolithic, a good bowstring has a nice pluck to it.

Now if you're a composer of documentary caveman music, you don't want to take this too far. And by "too far", I mean Ewok celebration from Return of the Jedi "too far." That would not be my idea of a "happy hour." Kapiche?

References:

Conard NJ, Malina M, Münzel SC. 2009. New flutes document the earliest musical tradition in southwestern Germany. Nature (advance online) doi:10.1038/nature08169

For some reason, it's "bash evolutionary psychology" week. First, Sharon Begley writes a 7-page essay in Newsweek, "Don't Blame the Caveman.", and now David Brooks gamely takes on the subject in the New York Times: "Human Nature Today".

Brooks' target is Geoffrey Miller's new book, Spent: Sex, Evolution, and Consumer Behavior. I haven't seen Miller's book yet, maybe they'll send me one. I have a feeling there's more to it than Brooks' two-paragraph synopsis.

We are all narcissists, Miller asserts. We spend much of our lives trying to broadcast our excellence in these traits in order to attract mates. Even if we’re not naturally smart or outgoing, we buy products and brands that give the impression we are.

It seems to me that an evolutionary analysis of consumer behavior is a tall order. You have to account for the fact that nature didn't set up the mall; a lot of clever advertising people did. Just as David Kessler pointed out for restaurants, stores are busy trying to exploit innate biases toward products and to manipulate learned responses to them. Some of it is a novel environment, other parts are fairly old applications of information foraging. The combinations of old and new, cultural variations, and varying levels of group participation may make cooking a better analogy than foraging.

Putting the intrinsic challenge aside, I think David Brooks shoots wide of the mark. He lists a catalog of alleged excesses in Miller's book, and tries to pivot into the point that evolutionary psychology in general is overreaching in its interpretations of human behavior. These "criticisms" of evolutionary psychology are hardly new. Some of them may have some force yet, but in Brooks' hands they hardly slap harder than Ann Landers' famous "wet noodle":

But individuals aren’t formed before they enter society. Individuals are created by social interaction. Our identities are formed by the particular rhythms of maternal attunement, by the shared webs of ideas, symbols and actions that vibrate through us second by second. Shopping isn’t merely a way to broadcast permanent, inborn traits. For some people, it’s also an activity of trying things on in the never-ending process of creating and discovering who they are.

So what? Many kinds of sexual and status displays in nature are highly learned -- bowerbirds construct displays from physical objects, many songbirds learn songs based on features of the songs they hear. They're all trying to create and discover (which is highfalutin' way to say, learn) what to do. That doesn't mean that the behaviors don't evolve under selection -- it just means that an evolutionary account of the behaviors must explain the learning mechanism.

In humans, there's no question that status displays are part of mating and social competition. The outcomes of mating and social competition influence fitness. What remains unknown is the extent to which learning may be influenced by innate biases. How do we choose who to copy? Why do we respond to some signals (nowadays, products) and not others? Is familiarity enough -- old-fashioned, blank-slate type learning? How much do developing minds depend on cues other than repetition?

Nobody really knows the answers to these questions, at least not well enough to persuasively test hypotheses about the evolution of human minds. But Brooks implies that such questions aren't worth asking. He thinks that it's enough to claim that humans aren't "hard-wired" -- as if that (false) dichotomy actually conveys any information. In doing so, Brooks confuses the currency of evolution (that would be, fitness) with the currency of individual fulfillment. They're not the same, and in many cases they work against each other.

In the current Nature, the special section on science journalism (due to the upcoming World Conference of Science Journalists) includes an essay history of science writing, by Boyce Rensberger.

He traces the origin of the profession to H. G. Wells, and in his description, science writers have certainly had their moments:

In 1904 Adolph Ochs, founder of the modern New York Times, hired the legendary Carr Van Anda as his managing editor. Van Anda may have been the most scientifically astute news executive of the twentieth century. He had studied astronomy and physics at university, wrote science stories and encouraged his reporters to cover science. He stressed the need for accuracy: in an often-quoted anecdote, Van Anda corrected a mathematical error in a lecture of Albert Einstein's that The New York Times was about to print — after, of course, checking with Einstein.

That sounds like the kind of story they would tell on the first day of science writing class. For me, the most important connection in the article is that it connects the dots between the environmental movement and the rise of "investigative" science reporting:

The 1970s offered increasing evidence of technology's potentially adverse effects, in part owing to controversies and crises such as the reactor meltdown at the Three Mile Island nuclear power plant near Harrisburg, Pennsylvania. By this time there was no way science journalists could ignore the social and political implications of their topic. And so the next great age of science journalism began — the 'Watchdog Age' — as science reporters became much more like their colleagues in other parts of the newsroom.

The quantity of science journalism boomed too, starting with the birth of a science section in The New York Times in 1978. By the boom's peak in 1987, according to one count, some 147 newspapers had at least a weekly science page, and four new popular-science magazines had joined the venerable Scientific American and Science News. Sadly, this upturn was short-lived.

I doubt the value of a "Science Section" -- I think it ghettoizes the science, generally in an attempt to drive subscriptions and defend editorial turf.

It is easy to forget that before this "golden age" of science reporting, big science (namely, NASA launches and before them other exploration) was covered on television and radio by mainstream news anchors, and science stories frontpaged national news magazines. Nowadays, that still happens but in a trivial, notably non-exciting way -- particularly for the never-changing nuggets of "health reporting". How many times do we need Robert Bazell to tell aging people to watch their cholesterol? It's not exactly Walter Cronkite and the moon landing.

Christopher Bird and Nathan Emery (2009) performed a number of tool use experiments on rooks -- birds related to crows (corvids) that do not use tools in the wild. Some other corvids, in particular New Caledonian crows, are expert tool users. People who work with New Caledonian crows compare their tool prowess with the great apes -- they can manufacture novel implements, put together two items into a compound tool, and use tools to make other tools. Each of these is a test that psychologists devised to differentiate human tool manufacture from animals. In each case, apes passed, and then the New Caledonian crows passed.

In the current paper, Bird and Emery find that rooks also can do these things, despite never having been observed to do any of them in the wild. They conclude that the birds likely do not have specialized cognitive adaptations for tool manufacture, but instead that they are solving novel problems using cognitive skills that are also useful for many other kinds of problems -- in short, domain general cognition:

Our results contradict suggestions that tool use was the driving force behind the evolution of advanced physical intelligence (2). It appears more likely that corvid tool use is a useful by-product of a domain-general “cognitive tool-kit” (31) rather than a domain-specific ability that evolved to solve tool related problems. Whether or not each species taps into this capacity for tool use may depend on their ecology (22, 32).

In hominoids, a shared basic ability for tool manufacture goes back at least to the Middle Miocene, based on its phylogenetic distribution. It is an open question whether early apes also were tool users. Some monkeys make and use tools in the wild, and if their abilities are homologous with ours, that would put the cognitive capacity for tool manufacture back into the Oligocene. Bird and Emery go through a similar train of logic for the corvids:

Rooks are highly innovative, social foragers (39), using their cognitive abilities in a number of nontool related ways (40). Our findings provide further support for recent claims of convergent evolution in the cognitive abilities of corvids and apes (31). New Caledonian crows and now rooks have been shown to rival, and in some cases outperform, chimpanzees in physical tasks, leading us to question our understanding of the evolution of intelligence.

The claim is that the cognitive resources useful for tool manufacture are probably also useful for other things, and therefore conserved in many if not all corvids. If they're useful for other things, there's no necessary reason for them to have evolved as adaptations for tool use or manufacture (although tool use in ancestral corvids remains possible). The same may be true of primates. For example, gorillas process some kinds of plant foods in complicated ways, using series of steps comparable in complexity to chimpanzee tool manufacture. But gorillas use tools very sporadically in the wild. Arguably, general-purpose cognitive abilities underlie both kinds of activities -- and social learning would facilitate both kinds of skills.

References:

Bird CD, Emery NJ. 2009. Insightful problem solving and creative tool modification by captive nontool-using rooks. Proc Nat Acad Sci USA 106:10370-10375. doi:10.1073/pnas.0901008106

On the intersection of science and art, the NY Times profiles former astronaut Alan Bean, who for nearly thirty years has painted what he experienced in spaceflight:

Critical attention has eluded Mr. Bean, 77, though he has developed, largely through word of mouth, a following among private collectors who pay up to $175,000 for one of his works. In July, the Smithsonian Air and Space Museum in Washington will mount a show of 45 of his works and will release a book of reproductions of his paintings. He has high hopes that the 40th anniversary of the moon landing may lure critics to take a look at his work.

I'm used to drawing and painting an entirely different kind of lifeless body. But the Moon poses unique challenges:

“People talk about nature being beautiful, and it is, but it’s not harmonized like a painting,” he said. “If Monet painted what he saw, we wouldn’t celebrate him today. He painted a little of what he saw but then he painted mostly the way he felt about it.”

Yet Mr. Bean’s methods still reflect his scientific side. He builds a scale model of every scene he paints, and uses a klieg light to simulate the sun and to get the shadows right. He works out the angle of the light and the positions of the people with mathematical precision. He wants the details to be historically correct.

The story doesn't cover the artistic side of NASA, and thereby may leave the impression that Bean is more of an anomaly than he really is. An immense attention to scientific illustration accompanied the development of the space program, as photorealistic renderings of space (and very early on, animated computer graphics) were an important part of spreading the science to the public. Bean's approach is, of course, very different and helps to extend the tradition outside the technical aspects into the humanistic sphere.

Jenny Tung of Duke University and colleagues report in Nature (online early) that yellow baboons have evolved a Duffy antigen-related defense against a baboon relative of malaria.

Most Africans carry a null allele for the Duffy antigen, coded by the DARC gene, which functions to protect them from vivax malaria. It's not the worst kind of malaria (that would be falciparum), but it is a major cause of disease outside those regions where the Fy*O allele is near fixation.

The baboon version of DARC is not convergent with the human null allele; the paper reports that it actually increases the gene activity, whereas the baboon variant allele actually increases the activity.

Presumably, the different defense in baboons is because they're fighting a different parasite:

Baboons are not generally infected by Plasmodium in the wild, but are vulnerable to infection by several closely related haematoprotozoans (4, 5) including Hepatocystis kochi, a blood parasite nested within the paraphyletic Plasmodium genus (15). Hepatocystis parasites do not produce the cyclical fever spikes typical of malaria in humans, but do produce anaemia and visible merocyst formation, followed by scarring on the liver (4).

They were able to show that the infection rate with Hepatocystis is significantly lower in baboons that cary the protective allele.

Based on their comparisons, the locus looks like a case of balancing selection:

We detected an increased level of population differentiation among East African baboon populations around FY, by comparing a FY-linked microsatellite with 35 neutral microsatellites (F_st = 0.31, P < 0.029; range of F_st for the neutral markers was 0.008–0.346; F_st is a metric describing genetic divergence between populations based on allele frequency differences at variable sites; Supplementary Fig. 3). We also detected a higher value for the Tajima's D statistic (D = 1.26) in this region relative to nine of nine other resequenced putative cis-regulatory regions in the Amboseli population and 11 of 12 resequenced transcribed regions (range of D for all other loci was -1.60 to 2.12). The only locus with a higher value of D, a transcribed portion of the gene MSR1, exhibited an even more extreme value than that identified for the MHC DQA1 promoter in baboons (22), which is known to evolve under strong trans-specific balancing selection (20).

A balance really would be necessary for them to be likely to have any evidence of selection. There's no reason to think that baboons are in the kind of demographic and disease transient that humans are in, so if a protective allele were always beneficial, it would likely be fixed. Still, it's not obvious what the disadvantage of the protective allele would be, although in humans it has been suggested that altering Duffy expression may impair immune response by reducing white blood cell count (Reich et al. 2009). Considering the high stress and cortisol levels of wild baboons, it may be that changes in immune activity have even more disadvantages.

One important aspect of the study is that the allele affects the cis-regulatory region of the gene; that's the general research topic covered by Gregory Wray's research group. I think that it's important because it raises the prospect that targeted sequencing of cis-regulatory elements in primate genomes might lead to the discovery of more adaptive variations within primate species. In their concluding paragraph, the authors emphasize the strengths of a combined field and in vitro approach to characterizing functional variants:

In vivo gene expression measurements are complicated by variation in genetic background and in the environment, both of which can modify functional cis-regulatory effects (25, 26). Indeed, our results show that even baboons that are homozygotes at the C/T site sometimes exhibit allelic imbalance in FY expression, suggesting that other, unidentified functional cis-regulatory variants are also segregating in the population. In contrast, in the in vitro comparisons, only a single cis-regulatory site differed between the experimental constructs, thus controlling for both environment and genetic backgrounds. Using both approaches in tandem can be synergistic: while in vitro experiments can help pin down specific functional sites, in vivo results demonstrate that these effects are relevant to the biology of individuals in the wild.

When it comes to primate genetics, looking for defenses to infectious diseases should be low-hanging fruit. Just take human genes that have alleles that defend against diseases, and sequence them for variations. Hopefully we'll find many others -- and in a few cases, those variations may prove useful in human health contexts, as they may reveal new pathways to deter or defeat pathogen infections.

References:

Tung J, Primus A, Bouley AJ, Severson TF, Alberts SC, Wray GA. 2009. Evolution of a malaria resistance gene in wild primates. Nature (advance online publication) doi:10.1038/nature08149

Reich D, Nalls MA, Kao WHL, Akylbekova EL, Tandon A, et al. 2009. Reduced Neutrophil Count in People of African Descent Is Due To a Regulatory Variant in the Duffy Antigen Receptor for Chemokines Gene. PLoS Genet 5(1): e1000360. doi:10.1371/journal.pgen.1000360

The Fitzwilliam Museum, Cambridge UK, is putting on an exhibition titled, "Endless Forms: Darwin, Natural Science and the Visual Arts."

The exhibition is accompanied by a well-produced webiste, which includes descriptions of the collection, some material for educators (including visit information for the UK), and a virtual exhibition. Some of the text may be stretching Darwin's direct influence on the arts -- a naturalistic eye goes back farther than Audubon, for example, but several sections are interesting. Here's an excerpt from "Darwin and the Impressionists":

Edgar Degas, too, is known to have engaged directly with Darwinian theory, especially through reading Expression of the Emotions in Man and Animals soon after it was published in French in 1874. His images of dancers, singers, and criminals in the decades that followed stressed a kinship with animals in their features and gestures, and hinted at the possibility of human degeneration to an animal condition.

I think it's an open question how much Darwinism really affected popular culture. Several of the artists represented (e.g., Robert Farren) were already representing ancient creatures well before the publication of the Origin. Artists seem to have reacted to a greater understanding of nature, and science drew on that art as well as upon itself.

(via Jeff Hayes)

UPDATE (2009/06/23): I should mention that the BBC has a slideshow based on the exhibition. It doesn't have as much material, but it does have nice big versions of some of the included artwork. Plus, kinda depressing classical music.

In last week's Nature, Russell Ciochon has a remarkable essay:

For many years, I used Longgupo to promote this pre-erectus origin for H. erectus finds in Asia. But now, in light of new evidence from across southeast Asia and after a decade of my own field research in Java, I have changed my mind. Not everyone may agree; such classifications are always open to interpretation. But I am now convinced that the Longgupo fossil and others like it do not represent a pre-erectus human, but rather one or more mystery apes indigenous to southeast Asia's Pleistocene primal forest. In contrast, H. erectus arrived in Asia about 1.6 million years ago, but steered clear of the forest in pursuit of grassland game. There was no pre-erectus species in southeast Asia after all.

I think it's interesting how much speculation Nature is willing to publish about hominid evolution in Asia. The 2005 review article by Robin Dennell and Wil Roebroeks, "An Asian perspective on early human dispersal from Africa," speculated that the origin and early evolution of Homo may have been in Asia, not Africa. And of course, several papers on the hobbits have included speculations about the pattern of early Homo in Asia, in pursuit of ways to derive Homo floresiensis from early hominids not yet found in Asia.

Ciochon's essay is part of this new tradition, but it bucks the trend. Instead of arguing that Asia was the home to an undiscovered diversity of hominids, he instead argues that the hominids have been overestimated (in part by himself) and that some fossils represent an undiscovered diversity of apes.

Ancient orangutans (Pongo) and Gigantopithecus are already known from China. Ciochon proposes a third lineage of great ape, one that would be similar to the earlier Lufengpithecus from China and Thailand:

Later, we had to field a serious proposal that Longgupo belonged to Lufengpithecus (4, 5). Although the age disparity remained troubling, the dental similarities could not be denied. I began to imagine a mystery ape as a possible solution to the problem.

The "age disparity" Ciochon refers to is that Lufengpithecus is known from the Late Miocene and very earliest Pliocene, but not the Late Pliocene. Still, if the teeth look like Lufengpithecus, it seems probable that the "mystery ape" actually is a late-surviving Lufengpithecus, or at least a close relative. Reference 5 is a paper by Dennis Etler, Tracy Crummett and Milford Wolpoff, which is available (PDF) from Etler's excellent website. Wolpoff refers to this in his 1999 book, Paleoanthropology:

The Longgupo mandible is actually a fossil ape that is related to Lufengpithecus, the missing P₃ was sectorial in shape.  However the prestigious British Journal Nature hastily published it as a hominid, with a picture of the specimen on its cover, and subsequently refused to accept papers establishing its identity.  The misidentifications actually started decades ago, when G.H.R. von Koenigswald identified an ancient australopithecine-like hominid from South China based on worn, isolated teeth, which he named “Hemianthropus.” These turned out to be worn postcanine teeth of a medium-sized Pongo species. The resemblances of the other materials to Australopithecus species were real enough, but they were not unique resemblances. A. Kramer and Zhang Yinyun have each shown there are no synapomorphies that support the hypothesis of Asian australopithecines.

So it's not a new idea that Longgupo represents an ape, or that the ape was different in size and morphology from Pongo or Gigantopithecus. It is probably natural that early paleontologists might associate these ape teeth with the hominids -- until 40 years ago, most paleontologists thought that hominids went back far into the Miocene. They were wrong, but a mistake like "Hemianthropus" was a natural one. The opposite mistake -- "Meganthropus" as an australopithecine-like hominid -- was also a natural consequence of the assumption that an unrecognized hominid diversity existed in Asia. That assumption has outlived Meganthropus, as we've seen.

Ciochon adds the idea that the ape may also be represented at other contemporary or later sites, and is apparently unwilling to attribute them to Lufengpithecus, at least not yet. He does not mention the isolated upper incisor from Longgupo, but he does appear to accept the claim that the two stone artifacts from the site are intrusive elements that are not contemporary with the jaw. The same is probably true of the incisor, which Etler and colleagues found morphologically most like living East Asians.

Ciochon suggests that some of the Hemianthropus collection may be his mystery ape:

Von Koenigswald viewed Hemanthropus as a distant relative of African Australopithecus. Later research revealed that these were worn or atypical orangutan teeth and Hemanthropus was quickly abandoned. But, had von Koenigswald actually discovered evidence of the mystery ape? In October 2005, I examined the original Hemanthropus collection. Among the many worn orangutan teeth I found several small ape teeth that very closely resembled the mystery ape teeth from Mohui. Perhaps von Koenigswald was the first to lay hands on the mystery ape.

It's not an easy task to sort through large samples of teeth trying to sort them into sets. Particularly not with these teeth -- sure, Gigantopithecus falls right out, but worn orangutan teeth aren't very easy to tell from hominids, much less "mystery apes." Ciochon ends his essay with a plan to revisit the existing samples of teeth, trying to document the variation in the mystery lineage. Sounds like a good topic for a TV show. There's a historical angle, lots of museums, a personal hook, reversal of fortune, the whole "mystery ape" thing....

Meanwhile, the introductory paragraph at the top of the post raised two issues, not one. The first is the focus of the rest of the essay: Longgupo represents a third ape in Pleistocene China; smaller than both Gigantopithecus and Pongo. The second idea is covered briefly near the end of the essay, but I think it deserves more consideration. Is it true that humans reached China 1.6 million years ago, and then "steered clear of the forest"?

Here's what Ciochon writes:

Homo erectus, it seems from this perspective, hunted grazing mammals on open grasslands, and did not or could not penetrate the dense subtropical forest. In fact, there is no record of early hominins living in tropical or subtropical forested environments in Africa or Asia.

In resolving the mystery, two other Asian sites come to mind: Jianshi (Hubei province, China) and Tham Khuyen (Lang Son province, Vietnam). At both sites, teeth labelled variously as Australopithecus, H. erectus and Meganthropus are most likely to be the mystery ape instead. Others have come to similar conclusions; a 2009 paper identifies a tooth from Sanhe Cave (Chongzuo, Guangxi province, China) as belonging to an unidentified ape.

The map accompanying the article is mysteriously depauperate of actual early hominid sites in China. Considering their locations relative to the proposed distribution of subtropical forest in Pleistocene China, I don't see an immediate objection to the hypothesis. The earliest Chinese archaeological sites, from the Nihewan basin near Beijing (Majuangou and Xiaochangliang) and also from around the Yellow River (Gongwangling and Xihoudu), are north of the Stegodon--Ailuropoda fauna. Yuanmou may have been forested at this time, but the hominid teeth there appear to be later (Hyodo et al. 2002), when the Ciochon's forest-plains biogeographic proposal may no longer hold. Josette Sarel and colleagues (2009) report on stone tools from Baerya Cave, which does preserve the Stegodon--Ailuropoda fauna, but these are so far undated and the stratigraphy has not been worked out. For all we know, the association is no clearer than at Longgupo, but that may change.

The other early Chinese sites with hominid teeth, Ciochon suggests are not hominids -- Mohui and Sanhe. Since he has examined the Mohui teeth (Wang et al. 2007), this isn't an idle speculation, and it would be odd for humans to drop their teeth around these sites without dropping a single stone tool. If he's right, that would make the earliest clear evidence of human occupation of South China into the Middle Pleistocene in age.

So, it's an interesting generalization. It remains to be seen how true it may be -- was early Homo really limited to a biogeographic strip of plains and savanna as it left Africa, or were the early humans more broadly adapted -- or adaptable?

References:

Ciochon RL. 2009. The mystery ape of Pleistocene Asia. Nature 459:910:911. doi:10.1038/459910a

Ciochon R, Long VT, Larick R, González L, Grün R, de Vos J, Yonge C, Taylor L, Yoshida H, Reagan M. 1996. Dated co-occurrence of Homo erectus and Gigantopithecus from Tham Khuyen Cave, Vietnam. Proc Nat Acad Sci 93:3016-3020.

Etler DA, Crummett TL, Wolpoff MH. 2001. Longgupo: Early Homo colonizer or Late Pliocene Lufengpithecus survivor in South China? Hum Evol 16:1-12.

Hyodo M, Nakaya H, Urabe A, Sagua H, Xue S, Yin J, Ji X. 2002. Paleomagnetic dates of hominid remains from Yuanmou, China, and other Asian sites. J Hum Evol 43:27-41. doi:10.1006/jhev.2002.0555

Sarel J, Zhang P, Weng Z. 2009. Recent discoveries in Baerya Cave (Bijie District, Northern Province of Guizhou, China). Antiquity 83 (online).

Wang W, Potts R, Yuan B, Huang W, Cheng H, Edwards RL, Ditchfield P. 2007. Sequence of mammalian fossils, including hominoid teeth, from the Bubing Basin caves, South China. J Hum Evol 52: 370-379. doi:10.1016/j.jhevol.2006.10.003

Zhu RX, Potts R, Xie F, Hoffman KA, Deng CL, Shi CD, Pan YX, Wang HQ, Shi RP, Wang YC, Shi GH, Wu NQ. (2004). New evidence of the earliest human presence at high northern latitudes in Northeast Asia. Nature 431:559-562.