Blogs / The Loom

The Tangled Bank is now officially out; I’m getting word back from readers that it’s actually showing up from Amazon. If you’re curious about it, here are a couple ways to find out more.

1. I’ve set up pages on my web site where you can download the introduction, look at some of Carl Buell’s artwork for the book, read reviews, and get contact information if you’re a teacher interested in a desk copy.

2. The New York Academy of Sciences has published an excerpt in the new issue of their magazine. It’s about the evolution of the eye, and you can read it online here.

3. Discover has another excerpt, about coevolution, in their November issue. The print issue is out now, and it should be posted online some time soon.

NOVA isn’t just a great television series; it’s also a formidable web site. (And, as with so many things media these days, it’s hard to draw the line between the two.)

They’ve just launched an evolution-rich site, with information on their evolution-related shows and lots of other goodies. (As you can see, it’s still beta.)

As part of the unveiling, NOVA asked me if I’d pick ten of the most important developments in evolutionary biology over the past decade. I came up with a far-from-exhaustive list. Check it out.

After weeks of manically scrubbing my hands with soap, Purel, and eye of newt, I ended up getting swine flu anyway. It’s not terribly surprising, since my entire town seems to have become a Petri dish for the viruses this week. I find a stunning clarity to the flu–you don’t feel a little sleep-deprived, or a little raspy. You are just a slave, heeding your body’s call to go to bed. I’m grateful that I am now on the mend, but I’m worried that with so many of us conking out, even a small percentage of serious cases will wreak havoc on hospitals. Someone please remind me why we still make our flu vaccines in chicken eggs?

It just so happens that swine flu was going to be one of the things I plan to talk about over the next few weeks as I head out for a series of talks to celebrate the 150th anniversary of the Origin of Species. I’d rather have to speak about the evolution of swine flu second-hand, but I guess I’ll talk as a former host.

Here are my movements…hope to meet some Loom readers along the way (but only if you’re healthy!)

Sunday November 1. Pasadena, CA: Caltech.

Thursday November 12. New Haven, CT: Yale Peabody Museum of Natural History

Saturday November 14. Ithaca, NY: Cornell University [details to come]

Thursday November 19. Vancouver, British Columbia: Beaty Biodiversity Museum

Thursday, December 3. Denver: Denver Museum of Nature and Science

Friday, December 11. Amherst: University of Massachusetts [details to come]

Saturday, January 16. Research Triangle Park, NC: Science Online 2010. (This is the only talk that’s not a public lecture. I’ll be on a panel discussing science journalism online. You have to register for the entire workshop. But this is definitely one workshop I’d recommend you sign up for.)

Meet Ardipithecus.

This introduction has been a long time coming. Some 4.4 million years ago, a hominid now known as Ardipithecus ramidus lived in what were then forests in Ethiopia. Fifteen years ago, Tim White of Berkeley and a team of Ethiopian and American scientists published the first account of Ardipithecus, which they had just discovered. But it was just a preliminary report, and White promised more details later, once he and his colleagues had carefully prepared and analyzed all the fossils they had unearthed. “Later,” it turned out, meant 15 years.

I’ve mentioned before how unfashionable this slow-cooked style of science can be. But sometimes, it’s the only way to do things right. Getting clues about HIV by observing sick chimpanzees in the wild takes years.  And so does reconstructing a fossil–particularly one as delicate as Ardipithecus happened to be. Today, the journal Science has handed many of its pages over to White and his colleagues, who have filled them with lots of details about Ardipithecus, plus a couple excellent articles by writer Ann Gibbons. Ardipithecus has gone from being an enigmatic collection of bones to a new touchstone for our early hominid ancestors.

To appreciate the importance of this new look of Ardipithecus, you have to step back into the history of hunting for hominid fossils. In the early 1970s, Tim White was part of a research team that found what was, at the time, the oldest hominid known: a 3.2 million year old fossil of Australopithecus afarensis. What made their discovery particularly spectacular was that they found a fair amount of a single A. afarensis individual, whom they named Lucy.

Combined with other A. afarensis fossils, paleonthropologists got a pretty decent picture of what hominids looked like. Lucy was a chimpanzee-sized ape with a brain that was only a little bigger than a chimp’s. She still had long arms and curving hands and other traits hinting that she could still climb in trees. But she also had feet with stiff, forward-facing toes, an adaptation for walking on the ground.

So things stood for about 20 years. But then, with the discovery of Ardipithecus and a few other hominid fossils, the record of our ancestry got pushed back millions of years. The oldest fossil that’s been identified as a hominid, Sahelanthropus tschadensis, dates back between 6 and 7 million years old. But scientists have only found pieces of the Sahelanthropus skull. Another species, Orrorin tugenensis, is 6 million years old; it’s represented by little more than a leg bone.

Scientists have learned a lot from these pre-Lucy hominid fossils, but before now they weren’t able to make very detailed reconstructions of these creatures. Only about halfway along the journey from the first hominids to us did hominids come into full-bodied focus.

At first, Ardipithecus ramidus was yet another scrappy pre-Lucy fossil. The first report offered details about part of a 4.4 million-year-old jaw bone–a remarkable jaw bone, but just a jaw bone nonetheless. Soon after, White’s team found more fossil bones, from the hominid’s hand, skull, pelvis, feet, and on and on–110 pieces all told. But finding these pieces was just the start of the team’s labors. They picked away at the bits of rocks surrounding the fragile bits of fossils. They used a computer to manipulate CT-scans of the fossils to figure out how crushed fragments had originally fit together as a skull or a pelvis.

All this happened in strict secrecy. Some of us science writers knew a little about what the scientists were up to, but we could only guess when they’d finally finish working on the fossil. Sometimes when I’d speak to White, I’d inquire, and he’d politely say he wasn’t done yet.

Looking at the papers out today in Science, you can see that they’ve been very busy. I won’t even try to offer an all-encompassing account of their new results. In many cases, it wouldn’t actually be worth the effort, because these papers are just the first salvo in what will be a fascinating debate about how our ancestors evolved. I was speaking to University of Wisconsin paleoanthropologist John Hawks yesterday on another subject, and he was giddy about the papers’ imminent publication. “Tomorrow’s Christmas!” he said. (His young son overheard him on the phone and got very excited and confused. I had to give Hawks a few minutes  to explain the nature of metaphor. Not sure how well that went over.)

For now, I’ll point out a few of the results on Ardipithecus that are particularly intriguing.

Nice Guys With Little Teeth

Those of you reading this post that have a Y chromosome have canine teeth that are about the same size as those of my XX readers. The same rule applies to the teeth of some other primate species. But in still other species, the males have much bigger canines than the females. The difference corresponds fairly well to the kind of social lives these primates have. Big canines are a sign of intense competition between males. Canine teeth in some primate species get honed into sharp daggers that males can use as weapons in battles for territory and for the opportunity to mate with females.

Men have stubby canines, which many scientists take as a sign that the competition between males became less intense in our hominid lineage. That was likely due to a shift in family life. Male chimpanzees compete with each other to mate with females, but they don’t help with the kids when they’re born. Humans form long-term bonds, with fathers helping mothers by, for example, getting more food for the kids to eat. There’s still male-male competition in our lineage, but it’s a lot less intense than in other species.

White and his colleagues  found so many teeth of different Ardipithecus individuals that they could compare male and female canines with some confidence. The male teeth turn out to be surprisingly blunted. This result suggests that hominids shifted away from a typical ape social structure early in our ancestry. If this was a result of males forming long-term bonds with females and helping raise young, this shift was able to occur while hominids were still living a very ape-like life. Ardipithecus existed about 2 million years before the oldest evidence of stone tools, suggesting that technology was not the trigger for the evolution of nice hominid guys.

Walking, Of A Sort; And Climbing, Of A Sort

C. Owen Lovejoy of Kent State University spearheaded the studies on how Ardipithecus moved. He and his colleagues argue that its pelvis could support its upper body during bipedal walking. It wasn’t a fabulous walker, and was probably a terrible runner. Nevertheless, it had some of the same anchors for muscles that we have on our pelvis, and which chimpanzees and other apes lack. Its pelvis was, in other words, a mosaic. Lucy, we now can see, represents a later step in the journey towards out own walking-adapted anatomy.

Ardipithecus’s feet were mosaics too. The four little toes were adapted for walking on the ground. Yet the big toe was still opposable, much like our thumbs. This sort of big toe helped Ardipithecus move through the trees much more adeptly than Lucy.

But Ardipithecus could not climb through trees as well as, say, chimpanzees. Chimpanzees have lots of adaptations in their arms and shoulders to let them hang from branches and climb vertically up trees with incredible speed. Ardipithecus had hands were not stiffened enough to let them move like chimpanzees. Ardipithecus probably moved carefully through the trees, using its hands and feet all at once to grip branches.

Just a Reminder: We Didn’t Evolve From Chimpanzees

Chimpanzees may be our closest living relatives, but that doesn’t mean that our common ancestor with them looked precisely like a chimp. In fact, a lot of what makes a chimpanzee a chimpanzee evolved after our two lineages split roughly 7 million years ago. Ardipithecus offers strong evidence for the newness of chimps.

Only after our ancestors branched off from chimpanzees, Lovejoy and his colleagues argue, did chimpanzee arms evolve the right shape for swinging through trees. Chimpanzee arms are also adapted for knuckle-walking, while Ardipithecus didn’t have the right anatomy to lean comfortably on their hands. Chimpanzees also have peculiar adaptations in their feet that make them particularly adept in trees. For example, they’re missing a bone found in monkeys and humans, which helps to stiffen our feet. The lack of this bone makes chimpanzee feet even more flexible in trees, but it also makes them worse at walking on the ground. Ardipithecus had that same foot bone we have. This pattern suggests that chimpanzees lost the bone after their split with our ancestors, becoming even better at tree-climbing.

Chimpanzees do still tell us certain things about our ancestry. Our ancestors had chimp-sized brains. They were hairy like chimps and other apes. And like chimps, they didn’t wear jewelry or play the trumpet.

But then again, humans turn out to be a good stand-in for the ancestors of chimpanzees in some ways–now that Ardipithecus has clambered finally into view.

[Reconstructions: Copyright 2009, J.H. Matternes. Cover: Copyright 2008 T.H. White]

I had a sudden drop in blood pressure when I checked out the new issue of Nature today. Evolutionary biologist Laurence Hurst wrote a two-book review: Richard Dawkins’s The Greatest Show on Earth, and my own The Tangled Bank. I revived when I saw that my book held up under Hurst’s comparison: “The book is billed as the first textbook on evolution for the general reader, and in that framework, it excels.”

Hurst used his review to pose an interesting question. He contrasts my style, which he describes as “authoritative and easy to read” with that of Dawkins, who “emerges like a prize-fighter, knocking out of the ring all objections.” Hurst then asks, “So which is the better strategy for explaining the difference between fact and fantasy, that of the quiet American or that of the British Rottweiler?”

Here’s my answer: this is a false choice. Dawkins and I did not write the same kind of book. Mine is a textbook, and Dawkins’s is not. Reading Hurst trying to equate the two gave me a vision of a college class on evolution. Spotlights swirl around the lecture hall. The professor jogs in. He’s wearing gold trunks and boxing gloves. As he pumps his arms over his head, Gary Glitter blares from the loudspeakers.

“Who here doesn’t think there are any transitional forms in the fossil record?” he roars.

One student meekly raises his hand, and immediately receive a devastating left hook. As he fades out of consciousness, he hears the professor bellowing his trademark battle-cry, “Ambulocetus!”

I can’t speak about Dawkins’s latest book, not having read it yet. But I can speak to my own thinking as I wrote The Tangled Bank. I envisioned my potential readers as curious people who didn’t know much about evolution–what the idea actually is and how scientists study it. I envisioned people who might be interested in learning the nuts and bolts of processes like selection and drift, and who might be intrigued by sexually deceptive wasps, whales with legs, the viruses that dominate our genome, and other features of life that evolution allows us to understand. My readers may not hear Gary Glitter in their mental loudspeakers as they work their way through my book. But, if I succeed, the music should still be sweet.

If you don’t already subscribe to Science and the City, a podcast from the New York Academy of Science, do so. They pick a great mix of intriguing topics, from the origin of the solar system to the physics of kite-flying. I was delighted that they gave me a call for their latest podcast to talk about The Tangled Bank. Our conversation ranged from the evolution of eyes to the power of good science illustrations. Listen here.

Charles Darwin was interested not just in how new things evolve, but also in how old things disappear. Often, they don’t disappear completely without a trace. We don’t have a visible tail like our primate ancestors did, but we still have a series of little bones tucked away at the bottom of the spine. While it may not function like a full-blown tail, it still anchors muscles around the pelvis. Blind cavefish may not have eyes of the sort found on their cousins in the outside world, but they still start to develop eyes as larva, before the cells start to die away.

Sometimes, though, the only place to look for vestiges of a lost trait is in a genome.

In the journal PLOS Genetics, Mark Springer of the University of California and his colleagues have published an intriguing study of how teeth–and the genes for teeth–have faded away over the past 50 million years. In particular, they looked at enamel, the tough covering that caps the teeth of humans and other vertebrates.

Enamel has three advantages for this kind of study: one is that it fossilizes well. For a lot of species, enamel is often the only thing left behind. Another advantage of enamel is that scientists also have a good understanding of the genes that build it–genes that are similar across a wide range of species. And the third advantage of enamel is that certain lineages of mammals have lost it. Baleen whales, anteaters, and pangolins have all lost their teeth entirely. (Baleen whales grow tooth buds, like cave fish grow eyes, but the buds die back without ever forming enamel.) Sloths, armadillos, pygmy sperm whales, and aardvarks still have teeth, but have no enamel left. This pattern suggests that enamel has been lost independently in several lineages of mammals.

In each lineage, these mammals have lost enamel as they’ve shifted away from depending on hard teeth. As I wrote about here, baleen whales descend from ancestors with formidable teeth for catching prey. But then their ancestors evolved a new way to eat, growing baleen–frond-like sheets of tissue that can filter out krill and other small animals from sea water. As anteaters came to only eat insects, the teeth of their ancestors became not just pointless but a hindrance. Their mouth became finely adapted for shooting a long tongue forward into ant nests. Big teeth would just get in the way.

So where did the enamel go? The scientists decided to test the possibility that the genes for enamel were still in the genomes of toothless mammals, but they had been shut down. In each species’s genome, scientists find a number of so-called pseudogenes, which can no longer encode a protein because of a crippling mutation. A mutation may, for example, insert a “stop” command, so that cells can no longer read the full sequence of a gene and make a full protein. Other mutations can shift a big chunk of DNA over a couple positions, garbling the code. Imagine shifting all the spaces in a sentence to the left. Y ouwou ldg etsomethi ngli kethis.

Despite these devastating mutations, pseudogenes often manage to retain a strong resemblance to their working counterparts. We, for example, have hundreds of pseudogenes that show a striking resemblance to hundreds of other genes that encode a variety of receptors in our noses. So Springer and his colleagues sequenced an enamel-building gene called ENAM in 49 mammal species, including toothless or enamel-less ones to see what happened to the gene along the way.

Their results were pretty much what they expected, but they’re still pretty amazing. There were no frameshift mutations in ENAM among the mammals with teeth. But 17 out of 20 species without teeth or enamel had at least one. In all 20 enamel-free species, a stop command (known as a stop codon) was present. These genes are shot.

The scientists then probed the evolution of the ENAM genes by taking advantage of the fact that only some letters in a gene encode a protein and others are ignored. Mutations that change the structure of a protein may have serious effects on an animal. They may be good effects or really bad ones–in either case, they may change the overall reproductive success of individuals who carry the mutation. On the other hand, silent mutations may have no effect (or at least just a small one).

It turns out that in mammals with teeth, the ENAM gene has experienced something call purifying selection. In other words, very few protein-changing mutations have endured for millions of years because tinkering with the recipe for enamel is a really bad thing to do if you need hard teeth to survive. In mammals without enamel, on the other hand, the ENAM gene evolved in a different way. It experienced what’s known as neutral evolution: the silent mutations and the protein-changing ones have occurred at about the same rate. It just doesn’t matter to the mammals anymore, because the genes are, as I mentioned before, shot.

These genomic vestiges don’t just provide evidence of how teeth were lost. They also provide some clues to when they were lost. By comparing closely related species that don’t have enamel, the scientists could tally up the mutations that had arisen since their last common ancestor. And since neutral mutations tend to pile up at a fairly steady rate, the scientists were able to estimate how long ago the ENAM gene turned from an essential gene to a useless one. In some cases, the scientists predict, paleontologists will find toothless members of these lineages millions of years older than the oldest known fossils without teeth–such as with pangolins, as this figure illustrates.. It is a remarkable convergence, of traces of history recorded in molecules tucked away in anteater cells, and skulls that have managed to turn to stone. But from them, a single picture emerges.

The stork UPS man pitched a box through the front door this morning. Inside was an advance copy of my new book, The Tangled Bank: An Introduction to Evolution. The paternal photographer in me took over, and now I have to show off my snaps. Above is a picture that I like for two reasons. One is the way it shows off Carl Buell’s lovely (and crowd-critiqued) cover. The other is the way it illustrates the book’s far-less-than-a-doorstop mass, which is all too typical for textbooks these days. In fact, the book’s smaller than Tino, our far-less-than-a-doorstop cat.

I also took some pictures of the inside, because I’m always astonished by how different pictures and text look when they’re actually on a physical book page, rather than on a monitor or spat out from a printer. (Fortunately, in this case, they look better.)

Here’s a typical chapter opener–living microbes growing in mats (known as stromatolites) above 3.5 billion year old fossils of stromatolites (some of the oldest evidence of life on Earth). To the right is paleontologist Abigail Allwood, who studies these fossils.

Conveying the vast time scales of life’s history is a perennial challenge. We chose to run a timeline across the front and back endpapers (the back one, covering the last 600 million years is in this picture).

Another challenge in a book like this is to get readers to start thinking about evolution in trees, rather than as linear marches of progress. Kevin Padian, a UC Berkeley paleontologist (and Tangled Bank advisor), has called for new illustrations he calls “evograms.” These are pictures that combining the branches of the tree of life with details showing homologies and fossil evidence. (Here’s an open-access paper he wrote about evograms last year.) I have a number of evograms in my book, like this one for birds. I think The Tangled Bank is the first textbook to use evograms, and now that they’re in print, I am glad I followed Kevin’s advice.

Of course, while the tree of life is a powerful metaphor for evolution, it does not work in some cases. I particularly liked the way the biologists Ford Doolittle and Tal Dagan have visualized the complex, web-like patterns of evolution brought about by horizontal gene transfer. So I included them in the book, too.

And, of course, the book includes as many paintings as we could squeeze out of Carl Buell. Here’s one showing the convergent evolution of saber toothed marsupials and placentals.

The book’s not perfect, of course; I see things I should have done better, and even a couple errors to be fixed at the soonest opportunity. I’ll set up an errata page when the book comes out in October, and I’ll welcome notes from readers. But, for now, I’m just reveling in the real-ness.

(To see what E.O. Wilson and other biologists have to say about The Tangled Bank, check out this post.)

Chimpanzees get AIDS.

This is an important discovery, but what intrigues me most about it is how the discovery was made. It is a story of two kinds of science, both of which are essential to getting a deeper understanding of life, but which today are staggeringly out of balance.

In the 1960s, Jane Goodall carried out some of the first long-term studies on chimpanzees in the wild. Goodall made important observations, noting that chimpanzees can be surprisingly cooperative but also quite violent, with troops engaging in war-like conflicts.

Goodall’s research was part of a long tradition of going to where the animals are, and tracking them for years on end. Goodall didn’t take giant crates of lab equipment with her to Tanzania; instead, she brought patience and careful observation.

Of course, doing this sort of science poses some serious challenges. Field biologists often end up studying relatively few individual animals, because they’re so hard to find. Small sample sizes always make sweeping generalizations risky. Animals in the wild are also embedded in a marvelously complex environment. They are influenced by a vast number of variables–the weather, the food supply, the latest disease outbreak, the latest kerfuffle between the top male and his younger rivals. The state of an animal at any moment may be influenced by many of these variables, making it even harder to uncover important underlying rules of its natural history. And since this kind of science takes so long, it can seem meager if you only learn about it through the papers that the scientists publish.

The contrast between Goodall’s kind of science and, what goes on in, say, a virology lab is enormous. Instead of just watching viruses, scientists can run experiments to test hypotheses–experiments that are controlled with exquisite precision. Scientists can genetically alter viruses to discover how each bit of its genetic material helps (or doesn’t help) it infect its host. They can carefully select the hosts to infect, comparing two sets of hosts for instance that might differ only in one particular cell receptor. They can trace the virus’s journey through the cell and out again; they can sequence viral genes as easily as you might crack open a fortune cookie. And they can churn out many papers a year on what they discover.

The divide between these different kinds of biology has existed for decades, as I wrote in this essay for PLOS Computational Biology. That divide has led to some unfortunate biases. Natural history is sometimes treated like glorified butterfly-collecting. Meanwhile, lab-based molecular biology is sometimes seen as sterile and pointlessly reductionist. But it would be a mistake for one side to think it could live without the other. Understanding the origin of AIDS is a case in point.

In 2007, an estimated 33 million people worldwide had HIV infections, and an estimated 3.1 million people were dying of AIDS-related causes every year. Yet, as diseases go, HIV is a latecomer. Scientists only became aware of it in the early 1980s, when it was still relatively rare, after which it swiftly became a global epidemic. Scientists have tried to search through medical records and blood samples for earlier cases of HIV infection that might have been overlooked. The earliest sample of HIV comes from a blood sample taken from a patient in Kinshasa, the capital of the Democratic Republic of Congo, in 1959.

The mysterious appearance of HIV led to many speculations about where it came from–including accusations that vaccination campaigns introduced it into people with vaccines contaminated with a monkey virus. But when scientists reconstruct the evolutionary tree of the virus and its relatives, they can reject those claims.

As soon as scientists discovered HIV, it was clear that it belonged to a group known as the lentiviruses. Lentiviruses are small particles with spiky knobs on their surface, and they encode their genes in RNA. They infect mammals, such as cats, horses, and primates, typically invading certain types of white blood cells. Genetic studies revealed that HIV is most closely related to strains of lentivirus that infect monkeys and apes–known as simian immunodeficiency virus, or SIV for short. HIV is not actually a single lineage. It is several different strains with different origins.

There are two main forms of HIV, HIV-1 and HIV-2. HIV-2, which is relatively mild, evolved from SIV that live in a monkey called the sooty mangabey. The story of HIV-1, which  causes the vast majority of AIDS cases, is more complicated, as this diagram shows. (It comes from my upcoming book, The Tangled Bank: An Introduction to Evolution.) This tree reveals that it is actually several strains, all of which jumped from chimpanzees.

Scientists first discovered SIV in chimpanzees by looking at captive animals. But in order to get a sense of the true diversity of the virus, they had to leave the relative comforts of laboratories and head out to the places where chimpanzees live. Wild chimpanzees don’t take very well to a blood draw, so scientists developed methods for extracting virus DNA from the feces chimpanzees leave behind. But in order to find those chimp feces, you have to find the chimps (and the trees in which they spend the night).

These studies showed that two subspecies of chimpanzees carry SIV, but HIV-1 has only evolved from one, P. troglodytes trogloydytes, found in west Africa around Kinshasa (marked Ptt on this tree). Goodall’s central African chimpanzees, Pan troglodytes schweinfurthii, have SIV of their own (Pts).

These studies indicate that SIV evolved into HIV as hunters killed apes and monkeys to sell in a growing “bush-meat” industry. Viruses in the blood of the primates could have entered cuts in the skin of the hunters, where a few of them mutated and evolved adaptations to their new host.

Knowing the structure of the HIV tree allows scientists to pinpoint those adaptations. It turns out, for example, that as all three strains of HIV-1 evolved from chimp virus ancestors, they all acquired the same new amino acid in the same position in the same protein. No strain of SIV in chimpanzees produces that amino acid. This mutation altered a gene encoding the shell of the virus, and experiments suggest that it was crucial to the success of the new HIV strains in humans. It’s possible that the mutation allowed the virus to do a better job of manipulating its new hosts into building new copies of itself.

Of course, AIDS is more than just a virus. Once a person is infected with HIV, it may take years for the virus to wipe out his or her immune system, allowing a menagerie of parasites to move in. When scientists studied captive chimpanzees infected with SIV, they didn’t see anything that looked like AIDS. This was intriguing to say the least. Perhaps the chimpanzees and the viruses had coevolved to a peaceful coexistence. When HIV-1 jumped to humans, its evolution took a nasty turn.

But what about chimpanzees out in the real world? Do they get AIDS? That’s a very short question that has taken a very long time to answer. A team of scientists set up shop at Jane Goodall’s study site in Gombe National Park, and took advantage of her decades of field work to track 94 individual chimpanzees for nine years. They searched chimpanzee feces for SIV, and then kept track of the chimpanzees themselves, observing their health, their offspring, and their lifespan. When the chimpanzees died, the scientists autopsied them to see what effect, if any, SIV had on them.

The results, published today in Nature, are stark. Out of the 94 chimpanzees, 17 had SIV. The SIV-infected chimpanzees had a mortality rate 10 to 16 times higher than the uninfected chimpanzees. Fewer infected female chimpanzees gave birth than uninfected ones, and none of their babies survived to a year. Pathologists found that dead infected chimpanzees looked like they had AIDS, with a lower level of immune cells called CD4+ T cells and damaged lymph tissue.

This discovery raises all sorts of questions. The Gombe chimps get sick, but not as sick as humans do from HIV-1. Why? There’s no evidence that SIV jumped into humans from P. t. schweinfurthii. Instead, it jumped three or more times from P. t. troglodytes. As far as anyone knows, those chimpanzees don’t get AIDS. But, then again, nobody has yet published a study like the one that has just come out on the Gombe chimps. What will that study reveal, if anyone ever carries it out? Is P. t. trogolodytes the source of a recent infection of both humans and the Gombe chimps?

And what’s particularly interesting, to me at least, is the fact that scientists had not noticed chimp AIDS before. Robin Weiss, an HIV researcher at University College London, and Jonathan Heeney of the University of Cambridge, published a commentary in Nature in which they suggest that the artificial conditions in which captive chimpanzees live protect them from AIDS. Out in the real world, where chimpanzees face an onslaught of pathogens, infections may activate the immune system in a way that brings on the virus’s attack and, ultimately, AIDS.

In other words, only the slow-cooked science pioneered by Jane Goodall allowed scientists to discover one of the most fundamental facts about a virus that has become one of the most devastating scourges humanity has faced in modern history. Slow-cooked science may provide more clues in the future–but only if its value is recognized, and only if chimpanzees can survive SIV and all the other threats to their survival these days.

[Goodall image: Jane Goodall's Chimpanzees]

In response to my post on the endorsements for The Tangled Bank: An Introduction to Evolution, a lot of commenters had questions and reactions. I’ve responded in the comment thread here.

My publisher has been sending out copies of The Tangled Bank: An Introduction to Evolution to some leading biologists for possible endorsements when it comes out in October. Here’s what we’re hearing back so far…

“The Tangled Bank is the best written and best illustrated introduction to evolution of the Darwin centennial decade, and also the most conversant with ongoing research. It is excellent for students, the general public, and even other biologists.” –Edward O. Wilson, Harvard University, author of Consilience

“Carl Zimmer’s excursion through the evolutionary epic is without equal.  His gift for the scientific narrative is on full display through The Tangled Bank, and he leads his readers onward with an energy and delight that never disappoints. This marvelous text is an extraordinary introduction to the depth and richness of evolutionary science.” –Kenneth Miller, Brown University, author of Only a Theory: Evolution and the Battle for America’s Soul and co-author of Miller & Levine’s Biology

“Zimmer has produced a wonderfully thorough introduction to evolutionary biology. With his prose and color diagrams by leading artists produced specially for this volume, The Tangled Bank will be a powerful tool to introduce students to the explanatory power of evolution and the way that it integrates different fields of knowledge. I have no doubt that this important volume will find its way into diverse courses in the curriculum.” –Neil Shubin, University of Chicago, author of Your Inner Fish

“One rarely says of a textbook, ‘I couldn’t put it down,’ but that was how I felt reading Carl Zimmer’s Tangled Bank. Zimmer has applied his award-winning communication skills to producing a readable yet up-to-date and thorough treatment of evolutionary biology. Were I teaching evolution, this is the book I would use.” — Eugenie Scott, Executive Director of the National Center For Science Education and winner of the 2009 Stephen Jay Gould Prize

“Carl Zimmer’s The Tangled Bank is a joy to read. He draws readers into the excitement of the rapidly expanding science of evolutionary biology, as he explains why life on earth is so diverse and how the web of life evolved to be so entangled.  He explains, through elegant prose and beautiful illustrations, the remarkable progress that has been made in recent years in understanding the evolutionary process.” –John Thompson, University of California, Santa Cruz, author of The Geographic Mosaic of Coevolution

“This engagingly written and well-organized book is a wonderful introduction to evolutionary biology.  It beautifully synthesizes the conceptual basis of evolutionary theory with the empirical evidence that evolution has occurred.  The book is remarkably up-to-date, seamlessly moving from discussion of fossils to genomes, and nicely illustrates that evolutionary biology is a vigorous field that increasingly takes an experimental approach.” — Jonathan Losos, Harvard University

[Update 7/6: Two new ones below]

“In clear, accessible prose, Carl Zimmer explains how 21st century science confirms the 19th century’s most radical idea. If you want to understand life’s remarkable past and uncertain future, read The Tangled Bank.” –Andrew Knoll, Harvard University, author of Life on a Young Planet: The First Three Billion Years of Evolution on Earth

“Zimmer weaves cutting-edge findings and essential concepts around the personalities and adventures of the biologists themselves. The result is superb: an up-to-date, articulate, and gorgeously illustrated introduction to modern evolutionary biology. We sorely needed a text aimed at the nonmajor undergraduate, and Zimmer was exactly the right person to write it.” –Douglas J. Emlen, Professor of Biology, University of Montana

To all of these biologists, many thanks from this old English major.

(And, by the way, that is the final cover. Thanks to the 1018 people who cast votes on their favorite mock-ups, as well as to the many who didn’t like any of them and asked, “Where’s the tangled bank?”  You spoke, I listened. In the end, I decided to go with Tiktaalik, but give it some extra company–both animal and vegetable–based on fossils that also date back to this sort of ecosystem 370 million years ago. Thanks to Carl Buell, as ever, for making that idea into a cover.)

Fireflies are the topic of my story on the cover of the New York Times science section tomorrow. It’s the result of a visit I paid last Friday evening to a meadow in Massachusetts, where I listened to Sara Lewis of Tufts University explain the sultry, complex tale of sex, deception, and death that was playing out in front of me.

I first got to know Lewis’s work last summer, when I decided I wanted to include fireflies in my next book, The Tangled Bank: An Introduction to Evolution. Lewis co-authored a fascinating review of firefly biology last year (free pdf from Lewis’s web site). I particularly liked this chart, which shows how different species have evolved different flash signals.

The male, flying around, releases a certain pattern of flashes–a single one second pulse followed by a five secondin the case of Photinus pyralis, for one example. And if a female P. pyralis, sitting on a blade of grass, likes what she sees, she responds three seconds later. Not one. Not six. Three. If she responds at the right interval, he knows he’s found a female of his own species and zeroes in, sending more flashes. She may also be signalling other males at the same time; which male she chooses may come down to subtle features of the flash pattern–for example, a rapid series of pulses as opposed to a slow one.

You can, as I discovered, speak their language with a penlight. You can even play the male or the female, depending on your mood.

There’s lots of strange business going on out among the fireflies. I didn’t have room in the article to describe some of Lewis’s new areas of research. Because female fireflies mate with several males, they can end up with sperm from several males inside them at once. Studies on other animals have suggested that females can choose which male’s sperm they’ll use to fertilize their eggs. Males can also inject chemicals with their sperm that increase their odds of fertilization. It’s clear that in many species, female preferences and male competition can continue after mating ends.

No one knows how this struggle plays out in fireflies. Adam South, one of Dr. Lewis’s graduate students, is investigating this side of the evolutionary equation. He is mating female fireflies with two males apiece and then collecting the eggs they lay. Using DNA tests, he’s determining the paternity of the eggs. Perhaps the males with more attractive flashes have more offspring.

What scientists like Lewis know about fireflies is remarkable, but it’s dwarfed by what they don’t know. Are fireflies on the decline, for example? Unfortunately, there’s no good long-term data. But that’s now an opportunity for some citizen-science you can get involved in. Lewis and some former students have helped organize Firefly Watch, based at the Boston Museum of Science. You can make your backyard part of biology’s new frontier.