My editor at the New York Times called me a few weeks ago and said, “Slime molds! Can you write something about them?” Moments like that fill me with gratitude.

Here’s my story, on the cover of tomorrow’s Science Times. I look at how they solve the evolutionary puzzles of altruism, build highway systems, and turn out to be some of the oldest life forms on land.

(And for more on the ever-expanding worldwide diversity of slime mold, check out the Eumycetezoan Project.]

[Image: myriorama/Flickr via Creative Commons]

The folks at Wired recently asked me to put together a guide to the human ecosystem. You can get it in the October issue as a centerfold–the kind of centerfold that shows someone who took off the clothes, and then took off the skin. Bugs in your eyes, in your ears, in your gut, influencing your mind and health–they’re all there. Check it out.

I’m thrilled to have a piece of mine in this year’s edition of Best of American Science Writing. The book, edited by Rebecca Skloot and her father Floyd, is officially published on Tuesday, 9/27, but you can order it now on Amazon. My semi-skeptical take on the Singularity is in there, as is lots of excellent stuff–including fellow Discover blogger Ed Yong’s tale of sushi genes in Japanese gut bugs. If I’m not mistaken, that’s the first time a blog post has made it into this series. So congratulations to Ed Yong for giving the old blogs-versus-journalism critics another reason to pull their hair out.

I’ve devoted a few posts (here and here and here) to the saga of a disputed link between chronic fatigue syndrome and a virus called XMRV. This week marks the next chapter in the story, with more evidence that the original results were at least partly due to contamination and a partial retraction of the original paper. Two great writers at Science, Martin Enserink and Jon Cohen, have put together an epic telling of this affair, from the first reports two years ago to the latest developments. The magazine has wisely put the piece out in front of their paywall. Do read it.

As Enserink and Cohen note, this is not the final word. That will probably come early next year, when a larger study led by Ian Lipkin of Columbia. We’ll see then if the link is buried at last, or lives to see another day.

Metaphors are essential to writing about science. Even scientists themselves use metaphors all the time, drawing from their familiar experiences to describe the unfamiliar. Building proteins is known as translation, for example, because the sequences of DNA and proteins are akin to words written in different languages. The cell has to translate one language into another using–another metaphor–the genetic code.

Metaphors can be powerful, but they can also trip us up if we mistake them for an equivalence. DNA isn’t really a human language, for example. In my latest column for Discover, I take a look at another tricky metaphor: the eye as camera. Some scientists are actually making that metaphor real, by building video cameras that can let blind people see. As I point out, however, eyes are not cameras, and the differences are fascinating. They’re also crucial to the future success in treating blindness with technology. Check it out. 

In tomorrow’s New York Times, I have a profile of Arthur Horwich, a medical geneticist who has spent a quarter century trying to figure out the workings of this beautiful molecular box. Today he won the Lasker Award, a prize for medicine that has often gone to scientists who later won the Nobel. Why all accolades for a little box? Because without it, you’d be dead. And as Horwich and others have discovered what goes on inside, they’ve helped change the way we understand the biology of the cell. Check it out.

[Image of GroEL from Molecular Chaperone Group, Birkbeck College]

Last year, while I was working on a profile for the New York Times of a virus hunter named Ian Lipkin, he told me he was consulting on a Hollywood movie about the outbreak of a new pathogen. Kate Winslet would be an epidemiologist. Lawrence Fishburne would work at the Centers for Disease Control. He was hanging out with Gwyneth Paltrow. The director was Steven Soderbergh.

I had a hard time picturing all this.

In fact, he was not blowing a single puff of smoke my way. It was all true. A couple weeks ago, I got a chance to see the movie–called Contagion–which will be released tomorrow. I liked it very much, but, of course, I have a thing for viruses (and for scary movies). So be sure to delicately place a grain of salt on top of my upturned thumb. I’ve embedded the trailer below.

On the occasion of the release, Slate asked me to join in a written dialogue with Arthur Allen, the author of the book Vaccine and frequent contributor to Slate. We’ve each contributed a piece today, and tomorrow we’ll each contribute another. Allen opens, I return…and we continue tomorrow to talk about the issues that the movie raises, such as how much we should worry about (and direct resources towards) the next big virus.

WARNING: While the trailer below gives away little, in my Slate pieces I give away all!

If you were this man, you’d be smiling too.

The man is Lee Berger, a paleoanthropologist at the University of Witwatersrand in South Africa. He’s holding the skull of Australopithecus sediba, a 1.98 million year old relative of humans, otherwise known as a hominin. In April 2010 Berger and his colleagues first unveiled the fossil in the journal Science. As I wrote in Slate, Berger argued that A. sediba was the closest known cousin to our genus Homo. Hominins branched off from other apes about 7 million years ago, but aside from becoming bipedal, they were remarkably like other apes for about five million years. Among other things, they were short, had long arms, and had small brains. Berger and his colleagues saw in A. sediba what biologists often find in transitional forms–a mix of ancestral and newer traits. It has Homo-like hands, a projecting nose, and relatively long legs. It was intermediate in heigh between earlier hominins and the tall Homo. And it still had a small brain and long arms. (In August, Josh Fishman wrote a feature for National Geographic on A. sediba, complete with excellent reconstructions.)

It wasn’t just finding such a potentially significant fossil that would make you smile if you were Lee Berger. It’s how much stuff he and his colleagues have found. The skull that Berger holds would be enough to keep several scientists busy for years. But Berger and his team have much more. In fact, A. sediba is, in some ways, now even better represented than far more recent hominin relatives.

Today, Science has turned over much of this week’s issue to follow-up papers from Berger’s team, in which they share some of the goodies. Here, for example, is A. sediba’s hand. Before this specimen came to light, paleoanthropologists had much less to look at to study the origin of the human hand. The best specimen came from a 1.75 million year old hominin called Homo habilis. It got the name Homo in part because the fossils were found along with stone tools, which were considered a sign of a very human-like creature. Researchers also found bones from its hand–but only 13 fragments. In this picture of A. sediba‘s hand, just about every bone is real. This is what paleoanthropologists dream about at night.

Tracy Kivel, a paleoanthropologist at the Max Planck Institute, led a team of researchers who compared A. sediba’s hand to the hands of humans, chimps, gorillas, and extinct hominins. They found even more mingling of old and new traits than before. The hand has ridges for powerful muscles that run up the length of the hand. Chimpanzees have muscles like these, which give them stronger grips as they climb around in trees. Earlier hominins have them too. We don’t. Instead, we have long thumbs and fleshy pads on our finger tips, which are great if you’ve come to depend on your skill to make and use tools. A. sediba has them too.

Scientists have found likely hominin stone tools dating back 2.6 million years ago; last year a team of researchers kicked up some controversy by claiming to have found signs of stone tools 3.4 million years ago. It’s clear that by the time A. sediba came on the scene, hominins had been using stone tools for hundreds of thousands of years. It’s too bad that Berger and his colleagues haven’t found any tools alongside A. sediba’s bones, to see what they could do with these transitional hands. Then again, why should he get all the fun?

Things got particularly intriguing when Kivel and company compared A. sediba‘s hand to Homo habilis’s. Remember, Homo habilis is about 250,000 years younger than A. sediba. Yet A. sediba‘s hand is actually more like our own than that of Homo habilis. It’s got some wrist bones that are shaped to handle strong forces transmitted from the thumb–the sort of forces you might expect from whacking stones together to make a cleaver, for example. Evidence such as this suggests that Homo habilis branched off first from the ancestors of A. sediba and later hominins like ourselves, and then later A. sediba branched off from our own lineage. Along the way, the hand gradually became less adapted for tree-climbing, and acquired more traits we use to handle tools.

In other papers, scientists take a look at A. sediba‘s brain and hips. The two are more intimately associated than you might think at first. We have huge brains even at birth, which make child-bearing a tricky proposition in our species, because they have to be able to pass through the birth canal. We humans have wide hips compared to other apes, and some researchers have argued that they evolved in tandom with our expanding brains. (See this column I wrote recently for more compensations in our bodies for big brains.) But it turns out that A. sediba–which had a small brain–already had broader hips than earlier hominins. Whatever drove its hip expansion, a big head wasn’t it.

While the A. sediba brain was small, it demonstrates that in hominin brain evolution, size isn’t everything. The skull Berger holds here contains a beautifully preserved cavity inside. When he and his colleagues put the fossil in a scanner, they were able to reconstruct the shapes of a lot of the left hemisphere of the brain and the front chunk of its right. The shapes of some parts of the brain (in particular, a part of the brain called orbitofrontal cortex) are more like our own than like earlier hominins.

Reading this, I can’t help but dabble in a little paleo-phrenology. The orbitofrontal cortex is a crucial node in our emotional network, where neurons assign value to things and can tamp down or ramp up our automatic responses of fear and delight. Did a glimpse of human feelings mark this great transition, long before human-sized brains evolved?

I doubt scientists will ever answer that question, but not to worry: there are many more answers A. sediba will be able to provide.

[Images: Berger, courtesy of Lee Berger and University of Witwatersrand; hand and pelvis by Peter Schmid, courtesy of Lee Berger and University of Witwatersand; brain, photo by ESRF/KJ Carlson, courtesy of Lee Berger and the University of Witwatersrand]

I’m among the 800,000 people in Connecticut without power thanks to Irene, so I won’t be blogging much for the foreseeable future. But before I get to other matters like dragging branches around, let me point you to my latest piece for Yale Enivronment 360. I take a look at a new concept called the climate relict. Around the world, there are pockets of plants and animals living hundreds of miles away from their main species ranges. They were left behind in refuges at the end of the last Ice Age, as others moved towards the poles in response to the warming climate. As the climate now warms even more, climate relicts have a lot to teach us about how to manage biodiversity. Check it out.

[Update: bad link to Yale e360 fixed]

It’s been a while since we’ve treated to the spectacle of Ann Coulter lecturing about evolution, but she’s at it again. She’s just written an op-ed in the wake of Rick Perry’s recent statement that Texas teaches evolution and creationism [his word] because evolution is “just a theory out there.”

Coulter takes this opportunity to remind us that she dedicated a third of her 2006 book Godless to demolishing evolutionary biology. Apparently the scientists who have published over 59,000 papers on the topic of evolution since she published her book didn’t get the memo.

To rectify that situation, Coulter now informs us that “it is a mathematical impossibility, for example, that all 30 to 40 parts of the cell’s flagellum — forget the 200 parts of the cilium! — could all arise at once by random mutation.”

Of course, nobody is saying they evolved all at once by random mutation. Nobody except for Ann Coulter. To see what scientists are actually saying, you can start by reading this review that presents a detailed hypothesis about the incremental evolution of the flagellum and the cilium, based on actual experiments. In a case of wonderful timing, it came out just last month in the Journal of Cell Biology. I’m sure it’s right at the top of Coulter’s reading stack.

Reading Coulter’s new attack on evolution, I got a fond flash of nostalgia. You see, five years ago, I had the mixed pleasure of discovering that I was actually in Godless. Here’s the text of the post I wrote at the time:

I just want to make one thing clear. When Ann Coulter talks about her Giant Raccoon Flatulence Theory, she’s talking about me. Don’t let anyone else tell you that they are a giant flatulent raccoon. They’re all just a bunch of wannabes. For I am the One True Giant Flatulent Raccoon.

Allow me to explain…

Coulter dedicates the last four chapers of her new book Godless to evolution. She claims that it is nothing more than the religion of liberalism (as opposed to the foundation of modern biology, as 92 national scientific academies and dozens of scientific societies attest.)

When I first heard about this bizarre news, I didn’t pay much attention to it. I certainly didn’t sit down to read the book, since I had more pressing matters to attend to, such as reading papers written by actual scientists about actual science. And as early reports on the treatment of evolution in Godless began emerge–documenting copious errors, illogical arguments, and other sorts of intellectual dreadfulness (see, for example, talkreason, Panda’s Thumb, and Pharyngula)–I decided I had made the right choice.

But then a friend told me that I, or at least one of my articles, was in the book. Now the bizarre had become the personal. I had to investigate. And when I did, I discovered that I had inspired the Giant Flatulent Raccoon Theory.

You see, last July my appendix nearly burst. I got to the hospital in time to have it safely removed, and as I recuperated I wondered why I had an appendix in the first place. After all, it had nearly killed me and now I was perfectly healthy without it. When I mentioned this to my editor, she said, Cool–sounds like an essay. I agreed. I started to read scientific studies of the appendix, and I spoke to some scientists who had written about its evolutionary origins. The question remains open, I discovered, in large part because scientists have a lot of work left to do to trace its history in mammals and to understand its function in us and in other special.species.

The existence of unanswered questions in science sometimes come as a shock to non-scientists, but there are plenty. How does the brain develop in a baby, for example? Scientists have identified some important genes, but they only have the vaguest idea of how those genes work together to create the cerebellum, the cerebral cortex, and all the other parts of the brain. That doesn’t make their work inconsequential or wrong. It just means they’ll be busy for a few more centuries.

I eventually wrote an essay (which you can read here or here) in which I explained what is and is not known of the appendix. I included a speculation from one of the scientists, Rebecca Fisher of Midwestern University, about why the appendix is still with us. She suggested that the appendix provided a net evolutionary benefit. It killed some people with appendicitis, but it also protected them by boosting the immune function in children. Testing this hypothesis is possible, although it will demand an analysis of a lot of medical records. But it is certainly plausible, since biologists have documented similar trade-offs.

This caused Coulter a great snit, which appears on page 214 of Godless:

So there it is: the theory of evolution is proved again. When the appendix’s use was a mystery, it proved evolution. When the appendix was thought to help humans resist childhood diseases–well, that proved evolution, too! Throw in enough words like imagine, perhaps, and might have–and you’ve got yourself a scientific theory! How about this: Imagine a giant raccoon passed gas and perhaps the resulting gas might have created the vast variety of life we see on Earth. And if you don’t accept the giant raccoon flatulence theory for the origin of life, you must be a fundamentalist Christian nut who believes the Earth is flat. That’s basically how the argument for evolution goes.

For some people, this outburst has come to epitomize Coulter’s empty rhetoric. A pretty good analysis of her scientific errors published Friday on the web site Media Matters is entitled, “Ann Coulter’s ‘Flatulent Raccoon Theory.’” The report has triggered the spread of the flatulent raccoon meme around here at scienceblogs, and elsewhere. It has even earned its own Wikipedia entry (although its survival is still up for grabs). [Update: The deliberations at Wikipedia are over: the giant raccoon theory is now a subsection of the Ann Coulter entry.]

There are plenty of passages in Godless’s evolution chapters that are as wrong-headed as the Giant Flatulent Raccoon Theory. But having witnessed my own work go through Coulter’s mangling machine, I can’t help marvelling on just how wrong-headed it is. Coulter conveniently leaves out the fact that when I decribed Fisher’s trade-off hypothesis, I stated clearly that it was just that: a hypothesis. I even pointed out that it was one of several possible hypotheses that might be worth examining. (See, for example, this Scientific American article by George Williams and Randolph Nesse in which they propose that it can’t get any smaller without causing more infection). Again, that’s how science works: people come up with hypotheses that are consistent with the evidence, and then they think about ways to test those hypotheses with new evidence. Instead, Coulter portrays Fisher’s hypothesis as “the answer the Times gave” as to why the appendix has not disappeared–making it sound as if the Grey Lady was handing down absolute truth. She then goes one step further, and transforms a hypothesis-turned-answer into the indisputable proof of evolution. I wonder if Coulter actually read my essay–in which case she presumably knows she is misrepresenting it–or if someone just handed her a passage to quote and told her to make up a joke about farts. In any case, she manages to create a truly laughable straw man.

The theory of evolution is not a pile of imagines and might-haves. It has been tested by generations of scientists and found to be the best explanation science can provide for how the natural world has gotten to be the way it is. Naturally the theory has matured over the past 150 years, and naturally many aspects of it generate fierce debates. That is how science works. If Coulter can only wage her war against evolution by misrepresenting a speculative hypothesis in an essay by a science writer, she really ought to stop and think for a moment.

If she actually did, it might occur to her that she really doesn’t even understand what evolution is, or what evolutionary biologists are setting out to explain. I pointed out in my essay that the appendix does not seem to be intelligently designed. “If I understand the concept of the survival of the fittest,” she responds, “the appendix doesn’t do much for the theory of evolution either. How does a surival-of-the-fittest regime evolve an organ that kills the host organism? Why hasn’t evolution evolved the appendix away? (Another sign that your scientific theory is in trouble: When your argument against an opposing theory also disproves your own.)”

“If I understand…” If only. Here, as elsewhere, Coulter writes about natural selection as if it were a process that can do no wrong. So she thinks that if she just points out flaws in nature she has disproven evolution. Just before Coulter contemplates my appendix, she writes,

But, you say, there must be some characteristics that are inherently desirable without regard to whether or not the organism survived, such as intelligence, strength, or–to take something really obvious–a tendency to avoid eating poison. In one experiment attempting to prove evolution (and those are the only evolution experiments allowed by law), fruit flies were bred to avoid eating poison. One would think that if we could settle on one characteristic that is a priori “fit,” it would be: “Avoid eating posion.” (p.213)

Coulter is then shocked to discover that fruit flies bred to avoid eating poison are outcompeted by ordinary flies. “Yes, it’s been observed for centuries that it’s the truly stupid who are the most successful, live the longest, are the happiest, the wealthiest, the most desirable, and so on,” she scoffs.

News flash: natural selection does not produce traits that are “inherently desirable.” It favors mutations that increase reproductive fitness under a particular set of ecological conditions. And the relationship between mutations and fitness is made even more complicated by trade-offs. Coulter may want to mock the fly research (which for some reason she failed to mention was published in that pseudoscientific rag, the Proceedings of the Royal Society of London), but the fact remains that the scientists found that flies bred for better learning did pay a cost in terms of how well they competed. That may not square with Coulter’s experience with smart people, but it wasn’t people the scientists were studying. Evolution is influenced by all sorts of trade offs, and scientists have done enormous amounts of research on them, in everything from viruses to swans. For heaven’s sake, does Coulter even know about the classic trade-off, sickle cell anemia? What Coulter portrays as the death-blow to the idea that the appendix is the product of evolution is nothing of the sort.

As others have observed, it would take many more pages to explain everything that Ann Coulter got wrong about evolution in Godless than she wrote herself. I will content myself with two pages of a book that now sits atop the bestseller list. And I hereby declare this blog the Original Home of the Giant Flatulent Raccoon!

[Note: The raccoon picture comes from a wonderful new children's book from my old friend Ian Schoenherr, Little Raccoon's Big Question.]

Update 11:30 am: Comments about Coulter’s physical appearance (and other personal details) are irrelevant and, in my view, mean-spirited. They will not be accepted here.

In 1833, John Obadiah Westwood, a British entomologist, tried to guess how many species of insects there are on Earth. He extrapolated from England to Earth as a whole. “If we say 400,000, we shall, perhaps, not be very wide of the truth,” he wrote. Today, scientists have found over a million species of insects and keep finding more every year.

The question of how many species there are on Earth has been a tricky one ever since Westwood’s day. I’ve written a story for the New York Times about a new estimate that was published today: 8.7 million.

What makes the paper particularly interesting is that it introduces a new method for estimating biodiversity. The method is based on Linnean taxonomy. While we have lots of new species left to find, we may have found most of the classes, orders, and phyla. It turns out that for a number of groups–mammals, birds, and so on–the numbers of each of these rankings rise as you descend the hierarchy.

Here’s a diagram that summarizes this striking pattern (courtesy of the Census of Marine Life). I couldn’t fit it into the story, so I thought I’d show it here:

The scientists reasoned that we’re probably closer to having found most kingdoms, classes, and other high level groups. So they used this relationship to estimate how many species there are in well-studied groups like mammals and birds. They found this method got them a number close to the actual number of species. So they applied to other groups, such as plants and fungi.

As I write in the article, some experts love this method, and some don’t think much of it. I couldn’t get into deep details in a 1,000 word piece. Here’s part of a long email I got from Lucas Joppa, an ecologist at Microsoft Research in Cambridge, England. Joppa thinks the new method is important and intriguing. And he added some interesting thoughts about why knowing this number matters–aside from just being a very basic question that’s worth answering because we can–

I do think that it matters that we try to estimate this number, although given that we are talking about millions, I don’t really think it changes our daily perception of how many species there are (the human mind has problems with any number larger than a few hundred!). Moreover, I’m not quite so sure it matters if we are able to put an exact figure of how many species there really are, as when you look at the scope of the problem (2 million currently described, likely 7 million more!) it is unlikely that we will ever reach a full census of life on earth.

That said, the goal of coming up with a sensible estimate is not only noble, but worthy from a conservation perspective…the species currently unknown to science (at least in a terrestrial sense for well-known groups such as flowering plants) are likely to have ecological traits that are correlated with extinction risk (small ranges, rare within those ranges, etc.). Because of this, putting a number on the total number of species gives us insight into the number of missing species, and thus insight into the increase in the estimated numbers of species threatened with extinction around the world. In a recent paper in the Proceedings of the National Academy of Sciences, Stuart Pimm and I, along with collaborators, show that at least for one taxonomically important group (flowering plants), those species currently “missing” (ie, undiscovered) are most likely to be found in places that are already identified as global conservation priorities.

So, the good news is that even without having a full catalogue of life, the global conservation community is already actively engaged in protecting those places where species are most at risk (ie, Biodiversity Hotspots, locations with high number of species found nowhere else, but with extensive (>70%) of natural habitat loss). The bad news is that most new species will come from places around the world most at risk! As you can see from that direct example, while knowing every single species on earth is not a likely scenario, estimating information about those species, as Mora et al. do, can drastically change the way we view current estimates of species extinction risk around the world.

In tomorrow’s New York Times, I take a look at a new study on the generosity of chimpanzees. Check it out. (And also check out Ed Yong’s take at Not Exactly Rocket Science.)

[Image courtesy of Frans de Waal]