If you could travel back to Spain about ten million years ago, you'd have no end of animals to watch, from apes to bear-dogs to saber-tooth tigers. With so many creatures jockeying for your attention (and perhaps chasing you down for lunch), you might well miss the creature shown here. Simocyon batalleri was roughly the size and shape of a puma, although its face looked more like a raccoon's. If anything were to draw your attention to Simocyon, it would probably be the animal's gift for climbing trees. Most big carnivorous mammals of the time were restricted to the ground; some may have been able to climb up tree trunks and onto bigger boughs. But judging from its fossils, Simocyon could have climbed trees out to their slender branches. It could do so because, unlike other carnivores, it had thumbs that it could use to grasp branches much like a monkey would. Those thumbs turn out to have a fascinating story to tell about the tinkering habits of evolution.

This story is a sequel of sorts. Part One was an essay that Stephen Jay Gould published in Natural History in 1978 called "The Panda's Peculiar Thumb." It's a classic example of Gould's skill at making a provocative argument about evolution with a flair so elegant that it could draw in the least scientific reader. (If you haven't read it, you really should check it out, either in Gould's collection of essays, The Panda's Thumb, or here. And also be sure to read the blog of the same name!)

In the essay, Gould complained that textbooks liked to illustrate evolution with examples of optimal design, such as insects that exquisitely mimicked a dead leaf. "Odd arrangements and funny solutions are the proof of evolution," he argued. Darwin himself spent a lot of effort uncovering the strange contortions by which organs changes shape and took on new functions. And to Gould, the thumb of the giant panda was the epitome of a funny solution.

Before a giant panda eats a piece of bamboo—its favorite meal—it grabs the shoot between its flexible thumb and finger and strips off the leaves. But this useful thumb is not really a thumb at all, at least in our sense of the word. Pandas descend from carnivorous mammal ancestors, as reflected in the many traits they share with bears, dogs, and other relatives. For one thing, its true thumb is lined up with its other fingers. What looks like its "thumb" is actually a wrist bone (the sesamoid) that evolved until it was so big that it stuck out to one side of its forepaw. The muscles that control the bone have become rearranged so that now it can move much like our own opposable thumb. Gould pointed out that the corresponding bone in the panda ankle is somewhat oversized, which he suggested was the result of genes that controlled the growth of the sesamoid in all its limbs. The large size of its ankle bones serve no function. Instead they're merely the byproduct of natural selection acting on other parts of the panda body.

I find Gould's essay a little peculiar to reread today. It's as if someone had drawn a picture of the head of a dime, and Gould said, "Outrageous—it's the tail that makes the dime!" Scientists who study the evolution of optimal design don't deny that evolution may be optimizing things with weird origins and which may have once had other uses. The wings of different species of bats are exquisitely well adapted to different ecological niches—open spaces, dense forests, and so on. But the biologists who study those wings would not deny that they originated from the forelegs of mammals, or that an entirely different sort of wing might actually do a better job. But my opinion may be colored by the fact that I'm reading the essay in 2005. Perhaps what seem like straw men today were genuine points of view in the 1970s. Of course, it's largely thanks to Gould that such overly adaptationist points of view are not so common today.

There's an interesting omission to "The Panda's Peculiar Thumb": the red panda. This bushy-tailed creature is the size of a small dog and climbs in trees. Found in East Asia, it eats bamboo, along with lichen, acorns, and even bird eggs. It earned its name from the similarities it bore to giant pandas. Those similarities include a false thumb that is actually an exaggerated sesamoid bone in the wrist.

More detailed studies raised doubts about whether the two pandas were closely related. But for a long time scientists had a difficult time determining their kinship. The picture has cleared up dramatically in the past few years thanks to large-scale studies of mammal DNA. These studies (such as this one and this one) indicate that giant pandas and red pandas are only distantly related. Their common ancestor lived 40 million years ago. One lineage gave rise to bears, including giant pandas. Another lineage gave rise to red pandas as well as skunks, raccoons, and weasels.

This research casts the panda's thumb in an interesting new light. It apparently evolved independently in two different lineages of carnivorous mammals. This is fascinating for a couple reasons. Two independently evolved sesamoid thumbs hint that carnivores are so constrained by their anatomy that they have only one pathway by which they can evolve something that will work like an opposable thumb. It's also intriguing that these two thumbed creatures also share a taste for bamboo. That coincidence may suggest that the same ecological shift from meat-eater to bamboo-eater drove the evolution of a bamboo-processing thumb. It's the sort of hypothesis that evolutionary biologists can test. They test it by digging up fossil relatives of living red pandas or giant pandas.

And now they've found one—Simocyon batalleri.

In a paper that will be posted on-line this week by the Proceedings of the National Academy of Sciences, a team of paleontologists describe Simocyon batalleri, which turns out to be an ancient relative of red pandas. And like living red pandas, it had a thumb made out of a sesamoid bone. But its jaws, teeth, and other traits were not the sort you find in plant-eating mammals. Instead, it hunted or scavenged prey.

In the red panda lineage, in other words, the panda's thumb evolved before red pandas began to use it to strip bamboo. The researchers suggest that the thumb may have originally evolved for a different function: grasping branches. Simocyon may have used this skill to escape from bigger, faster predators. It might have even stolen dead prey cached in trees by saber-toothed cats and retreated out of range. Only after the panda's thumb evolved in a tree-climbing predator did some descendants co-opt it forfeeding on bamboo. In this respect, red pandas appear to have taken a different evolutionary path than giant pandas. No fossil of panda-like bears has shown any trace of a panda's thumb. Unlike the case with red pandas, the evolution of thumbs in giant pandas may have been tied to a shift from meat to plants.

Unfortunately, Stephen Jay Gould is not around to take delight in this new discovery (he died in 2002). I'd wager that he would have been particularly tickled by the fact that red pandas now embody not one but two of the concepts Gould championed in his career. He argued that evolutionary biologists must always remember that a structure that has one function today may have actually evolved millions of years ago for a different function altogether. Feathers, for example, don't seem to have evolved initially for flight. Some scientists liked to call these structures preadaptations, but Gould thought that term smacked of some kind of foreknowledge, which evolution cannot have. He preferred the term exaptation. The red panda's thumb turns out to be a striking exaptation—a tool for grasping branches that was turned into a tool for eating plants. It's an exaptation we humans can certainly appreciate. After all, our primate ancestors used their opposable thumbs to clamber around branches, perhaps alongside some of the ancient relatives of red pandas. While red pandas used their opposable thumbs to eat plants, hominids used them to make stone tools. Civilization and all the rest followed suit.

In October I wrote about the latest ideas about the evolution of autumn colors. The paper is now out.

When Judge John E. Jones III issued his decision in the Dover creationism trial on Tuesday, I downloaded the document with a vague sense of dread. It wasn't just that the decision was 139 pages long. I knew that Judge Jones had ruled that teaching intelligent design was unconstitutional, but I was worried that he might have accepted that it was anything but a warmed-over form of creationism.

Months of media coverage of the trial had nurtured my dread. Again and again, reporters felt an obligation to give "equal time" to intelligent design advocates, without feeling an equal obligation to fact-check the claims that the advocates were throwing out. I assumed Judge Jones would follow suit.

Once I started reading the decision, I realized I couldn't have been more wrong.

Judge Jones did not take the claims of intelligent design advocates at face value. They declared that intelligent design was not creationism. But he followed the long paper trail that linked creation scientists to the emergence of intelligent design in the 1980s. The Dover school board had its students to read the book "Of Pandas and People" to learn about intelligent design. Judge Jones observed that in the original draft of the book, the authors had used "creationism" and similar terms 150 times. In the final version, they had turned into "intelligent design."

The intelligent design advocates claimed that it was a serious field of scientific inquiry. In fact, Judge Jones wrote, intelligent design "has not generated peer-reviewed publications, nor has it been the subject of testing and research." Intelligent design advocates have tried to bolster their case by trying to find weaknesses in evolutionary biology. Judge Jones found that scientists had solidly rebutted these attacks. What's more, he recognized that simply attacking someone else's theory as wrong does not make yours right.

Journalists would do well to print Judge Jones's decision out and read it carefully. It's not up to a journalist to decide which side is right in a genuine scientific controversy. But it's wrong to let people use an article as a soapbox where they can make grand pronouncements about science, without looking into whether the science actually backs them up. Judge Jones fact-checked intelligent design and found it wanting. He did not shy away from this realization with worries that he was somehow being one-sided. Justice holds a balance in her hand, but balance is not what she seeks. Instead, she weighs the evidence to see which way it tips.

For the information hounds out there, Alan Templeton's paper, "Haplotype Trees and Modern Human Origins," on which I based my previous post is now published.

Judge Rules Against 'Intelligent Design'

Initial reaction: what a relief. Once I have a chance to read the decision, I'll have something vaguely more insightful to say...

Update: Oy. The decision turns out to be 139 pages. PDF here.

Update, 11:30 am: Okay, I've had a chance to give it a quick read, and while I'm not a lawyer, it seems to me like a pretty overwhelming decision. It didn't just focus on the school board's activities but demolished the entire project of intelligent design. For a legal document, it had some quite stirring passages, which I've excerpted here:

p 24: we conclude that the religious nature of ID would be readily apparent to an objective observer, adult or child.

p29 ID aspires to change the ground rules of science to make room for religion, specifically, beliefs consonant with a particular version of Christianity.

p31 The evidence at trial demonstrates that ID is nothing less than the progeny of creationism.

p64 We find that ID fails on three different levels, any one of which is sufficient to preclude a determination that ID is science. They are: (1) ID violates the centuries-old ground rules of science by invoking and permitting supernatural causation; (2) the argument of irreducible complexity, central to ID, employs the same flawed and illogical contrived dualism that doomed creation science in the 1980's; and (3) ID’s negative attacks on evolution have been refuted by the scientific community.

p71 ID is at bottom premised upon a false dichotomy, namely, that to the extent evolutionary theory is discredited, ID is confirmed.

[Conclusion] p137 Both Defendants and many of the leading proponents of ID make a bedrock assumption which is utterly false. Their presupposition is that evolutionary theory is antithetical to a belief in the existence of a supreme being and to religion in general. Repeatedly in this trial, Plaintiffs’ scientific experts testified that the theory of evolution represents good science, is overwhelmingly accepted by the scientific community, and that it in no way conflicts with, nor does it deny, the existence of a divine creator.

To be sure, Darwin’s theory of evolution is imperfect. However, the fact that a scientific theory cannot yet render an explanation on every point should not be used as a pretext to thrust an untestable alternative hypothesis grounded in religion into the science classroom or to misrepresent well-established scientific propositions.

The citizens of the Dover area were poorly served by the members of the Board who voted for the ID Policy. It is ironic that several of these individuals, who so staunchly and proudly touted their religious convictions in public, would time and again lie to cover their tracks and disguise the real purpose behind the ID Policy.

With that said, we do not question that many of the leading advocates of ID have bona fide and deeply held beliefs which drive their scholarly endeavors. Nor do we controvert that ID should continue to be studied, debated, and discussed. As stated, our conclusion today is that it is unconstitutional to teach ID as an alternative to evolution in a public school science classroom.

Those who disagree with our holding will likely mark it as the product of an activist judge. If so, they will have erred as this is manifestly not an activist Court. Rather, this case came to us as the result of the activism of an ill-informed faction on a school board, aided by a national public interest law firm eager to find a constitutional test case on ID, who in combination drove the Board to adopt an imprudent and ultimately unconstitutional policy. The breathtaking inanity of the Board’s decision is evident when considered against the factual backdrop which has now been fully revealed through this trial. The students, parents, and teachers of the Dover Area School District deserved better than to be dragged into this legal maelstrom, with its resulting utter waste of monetary and personal resources.

UPDATE: WEDNESDAY 12/21 9:30 AM I've cobbled together a few slightly more coherent thoughts on the Dover decision.

Blunt talk from L. Lynn Hogue, conservative law professor from Georgia via law.com. Hogue has signed an amicus brief in the Georgia textbook sticker case supporting the removal of the anti-evolution disclaimers. "I'm not religiously sympathetic to anti-evolutionists, who I think are lunatics." Professor Hogue, please drop a line to the President.

There are few things as fascinating to me as the question of how our ancestors evolved from small-brained, tree-dwelling apes. But sometimes it all can feel a bit abstract. After all, we're talking about things that happened six million years ago. Recently, though, I had a weird experience that brought our evolutionary history smack into my face. Some Yale psychologists came to my daughter Charlotte's pre-school looking for volunteers for a study that would compare how children and young chimpanzees learn. It turns out that chimpanzees can be a lot more logical than children, Charlotte included. I've written an essay about the experience that appears in tomorrow's New York Times.

(For those interested in the scientific background to this experience, here's the paper that inspired the new study.)

Over the weekend I was part of a panel at the American Anthropology Association, the topic of which was "Updating Human Evolution." I got to listen to ten presentations by scientists, each offering a look at how our understanding of our ancestry is changing with new research. While they were all interesting, I was particularly eager to hear one: Alan Templeton of Washington University. Templeton. Having just finished a book about human evolution, I knew that Templeton has been doing some groundbreaking work to figure out what our DNA has to say about our evolutionary history. I was looking forward to hearing about Templeton's latest results, and I wasn't disappointed.

The genetic study of human evolution really got off the ground in the 1980s. Allan Wilson of Berkeley and his colleagues compared the sequence of a gene in a sample of people and used their results to draw a genealogical tree. The gene came from mitochondria, energy-generating structures in our cells that also carry their own DNA. Wilson and his colleagues knew that we probably get all our mitochondria from our mothers. (Sperm apparently don't deliver their mitochondria to eggs during fertilization—only 23 chromosomes that will end up in the nucleus of the fertilized egg.) If a woman's mitochondrial DNA undergoes a mutation, she will pass that mutation down to her children, and her daughters will pass it down to their children. So finding people who share distinctive mutations allows scientists to see how closely related they are to one another. And since there was reason to think that the mutations arose at a relatively steady rate, they could even act as a molecular clock. If people shared an ancient ancestor, their mitochondria would be more different than if they shared a recent one.

The results of Wilson's study were quite striking. The tree he and his colleagues drew showed that all of the genes on the deepest branches of the tree belonged to people of African descent. Genes from Asians and Europeans were all more closely related to each other than to those from Africans. The researchers argued this meant that all living humans got their mitochondrial genes from a woman who lived in Africa less than 200,000 years ago. At a later date, one group of Africans moved out of the continent and colonized the rest of the world.

Before these results emerged, many paleoanthropologists argued that our species had evolved gradually over the past million years from Homo erectus, an ancestral hominid that lived in Africa, Europe, and Asia. Different populations evolved different traits, but enough interbreeding took place that they never became genetically isolated from one another, thus becoming a separate species. Neanderthals were thus the ancestors of living Europeans, and East Asian Homo erectus was the ancestor of Chinese and other people from that part of the world.

Many scientists saw in Wilson's tree a different story: Homo sapiens evolved much more recently in Africa, and then spread out into the other continents. Neanderthals and East Asian Homo erectus were actually separate species, and they did not leave any descendants among today's humans. If they did, the mitochondrial tree would have converged on a much older common ancestor. How they became extinct was an open question—perhaps through direct conflict or simply through competition for the food and other resources hominids needed to stay alive.

Adding more samples of mitochondrial DNA supported the basic outlines of Wilson's initial work. So did later studies of the Y chromosome. The Y chromosome acts a lot like mitochondria. Only men carry it, and they pass it down unchanged (except for mutations) to their sons. So it also serves as a good marker for genealogy. It showed much the same pattern as the mitochondria—a recent African origin and a subsequent spread to the rest of the Old World.

There's just one tricky thing about these results. All living men can trace the ancestry of their Y chromosome back to a man who lived an estimated 59,000 years ago, perhaps 100,000 years or more after "mitochondrial Eve." At the anthropology meeting, Alan Templeton explained the fundamental problem with these studies: a tree based on a single gene only tells you about the evolutionary history of that one gene. Genes may spread quickly or slowly through our species, sometimes due to natural selection and other times due to a chance-like process called genetic drift. The tree of a single gene on its own does not automatically reveal the evolutionary history of the species that carries it. People carrying the African Eve mitochondria might simply have interbred with people outside of Africa and passed their mitochondria on to later generations.

Fortunately, scientists are not limited any longer to just looking at mitochondria or the Y chromosome. Templeton has come up with a way to statistically compare the different trees of these genes, and use the comparison to test hypotheses about how our species evolved. Templeton published the first results of this method in 2002 in Nature, and at the anthropology meeting he described his newest results, in which he pushed his data set from 10 genes to 25 (the results will be published in the next issue of the Yearbook of Physical Anthropology, which should be online soon).

Templeton has found that he can easily reject the idea that all our genes come from the same 200,000 year old population of African humans. Instead, he finds evidence of three separate expansions out of Africa. The first he estimates to have occurred 1.9 million years ago—which just so happens to coincide with the earliest fossils of Homo erectus outside of Africa. Then he finds another expansion he dates to 650,000 years ago—which just so happens to coincide with the emergence of hominids in Europe of hominids that are believed to give rise to Neanderthals. The last expansion can be traced back 130,000 years ago.

His statistical study shows that Africans and Eurasians interbred enough to let genes flow back and forth for at least 1.5 million years (with 95% confidence). In fact, the results from a hemoglobin gene and the Y chromosome suggest a major expansion from Asia back into Africa after the latest expansion from Africa.

What's fascinating about Templeton's work (and other studies like it) is that it doesn't just take us back to a 1970-vintage view of human evolution. Humans really did expand out of Africa, as Wilson had claimed. But their expansion didn't prevent some genes from the hominids that were already there from surviving until today. Templeton doesn't have much to say on what happened when Africans moved into Eurasia—was interbreeding rare, or did the populations of pioneers and natives fuse together? Whichever is the case, Templeton would like people to think about human evolution less as a tree and more as a trellis. To that end, I've reproduced a figure from his new paper. (The thin lines show the flow of genes between different regions of the world, and the black arrows show major expansions of human populations from one region to another.)

[Update: Templeton's paper is now online.]

I've been asked to review a couple books about global warming. Climate change and evolution, which I mainly write about, are intimately related, since life is a potent source of greenhouse gases (methane from bacteria, etc.) and abrupt climate change has triggered profound changes in the biosphere. This assignment has me taking a particularly close look to all the new research and political news emerging these days.

And I'm getting a funny sense of deja vu.

Those who pay close attention to the work of creationists know that they have a penchant for quote mining--for snipping out a passage from a scientific paper that conveys a completely different message once it's taken out of context. Typically, this qutoe mining makes it sound as if a scientist is admitting the evolutin is one big hoax, but if you actually look at the full context, you see that it's part of a consideration about what sort of mechanism is more or less important in some particular aspect of evolution. You can see over 100 examples here.

So today I come across an article on Fox News in their "Junk Science" column, by Steve Milloy. He endorses the US's refusal to budge on carbon dioxide controls at a meeting in Montreal, casting worries about global warming as hysteria.

A more sober reality, though, is that whatever slight impact humans might have on the climate, it is too small to measure – a point made in a study just published by Swiss researchers in the journal Quaternary Science Reviews (November 2005).

The study reviewed prior efforts to reconstruct global temperatures of the last 1,000 years. It concluded that natural temperature variations over the last millenium may have been so significant that they would “result in a redistribution of weight towards the role of natural factors in [causing] temperature changes, thereby relatively devaluing the impact of [manmade] emissions and affecting future predicted [global climate] scenarios.”

“If that turns out to be the case,” the researchers stated, “agreements such as the Kyoto protocol that intend to reduce emissions of anthropogenic greenhouse gases, would be less effective than thought.”

So senior U.S. climate negotiator Harlan Watson was on very firm ground when he stated this week in Montreal that, “I reject the premise that the Kyoto-like agreement is necessary to address the issue."

It didn't seem to me that the quotation was fitting very tightly into Milloy's claims, so I wondered if I could get hold of the paper itself. In about five seconds I had it (pdf). It hardly makes Fox News's case. The quoted passage comes at the very end of this 3-page review. But Milloy drops the last sentence. Here's the full final paragraph, with bold face added:

So, what would it mean, if the reconstructions indicate a larger (Esper et al., 2002; Pollack and Smerdon, 2004; Moberg et al., 2005) or smaller (Jones et al., 1998; Mann et al., 1999) temperature amplitude? We suggest that the former situation, i.e. enhanced variability during pre-industrial times, would result in a redistribution of weight towards the role of natural factors in forcing temperature changes, thereby relatively devaluing the impact of anthropogenic emissions and affecting future predicted scenarios. If that turns out to be the case, agreements such as the Kyoto protocol that intend to reduce emissions of anthropogenic greenhouse gases, would be less effective than thought. This scenario, however, does not question the general mechanism established within the protocol, which we believe is a breakthrough.

Hm. Do you think he couldn't fit that last sentence in because he ran out of space?

Now I'm sure that global warming skeptics don't like to be put in the company of creationists. But if that notion really does bother them, they should not take a page out of the creationist handbook. And when it comes to creationism, there's one more interesting connection to make here. You can look through the Junk Science archive at Milloy's previous columns, which attack all sorts of things Milloy claims are nonsense. And yet, despite all the headlines about intelligent design in the news these days, nowhere in the archive can I find a single column attacking creationism. Deja vu all over again.

Update: To be fair and balanced, The Day After Tomorrow was nuts.

Light blogging this week is due to my frantic fragment of a week, returning from Thanksgiving and preparing to head down to DC to participate on a panel at the American Anthropological Association. The panel is called "Updating Human Evolution: Bringing Anthropological and Public Coneceptions into Contemporary Perspective," and will take place Saturday afternoon starting at 1:45 pm. Ten anthropologists are going to talk about new advances in our understanding of human evolution, from humans as prey to the evolution of the sexes. (You can find the full line up here. Search the pdf for the title of the panel.) The panel will also discuss how the public comes to learn about this sort of research. The discussion is where I come in, along with Ann Gibbons, a reporter for Science magazine and the author of the upcoming The First Human, a book about the oldest hominids which I suspect will be fantastic. I'm looking forward to the session for both parts of its goals, and I plan to blog about it afterwards.

Writing about paleontology without illustrations is like directing a movie without a camera. When I wrote my first book, At the Water's Edge, I had the good fortune to join forces with Carl Buell, who brought walking whales and fish with fingers to life. Now he has come to the other side, with a blog of his own, complete with pictures. Check it out.