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]

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]

Steve Mirsky, host of the excellent Science Talk, a podcast at Scientific American, talked to me the other day about all sorts of things. Part one of our talk is now online. We talk about my recent story about evolution in New York City. (Scientific American has a special issue dedicated to cities this month.) Listen to the podcast here.

Steve will be posting the second part of the talk soon.

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 the wake of last year’s earthquake in Haiti, cholera arrived on the island for the first time in 60 years. According to the World Health Organization, 419, 511 Haitians got sick with cholera as of July 31, of which 5,968 died. The infection rate is dropping right now, but the arrival of Hurricane Irene could change that.

As I wrote in December, scientists applied evolutionary biology to find clues to how cholera–or, more precisely, the bacteria Vibrio cholerae– came to Haiti. They compared the DNA in the strain in Haiti to ones that have been found in other parts of the world. From this analysis, they drew a tree, which I’ve reprinted below.

The bacteria in Haiti was more closely related to strains in South Asia than ones from South America. So it was unlikely that cholera came to Haiti floating by water from a nearby country. The evolutionary tree led credence to idea that U.N. peacekeeping troops, some of whom came from Nepal, brought it with them by plane. An outbreak of cholera hit Nepal in September 2010, shortly before a battalion of Nepalese peacekeepers left for Haiti.

This analysis was a bit like a picture taken from 10,000 feet in the air. The bacteria that the scientists analyzed were just a small selection of the many strains that have made people sick over the past few decades. Notably missing from the tree were any bacteria from Nepal. That’s because those strains had not made their way into bacteria collections.

To get a picture up close–and to test the idea that U.N. peacekeepers brought cholera to Haiti–a team of Nepali, American, and Danish researchers collected 24 samples in Nepal at the end of last year. They sequenced the entire genomes of bacteria and compared them to the genomes of Haitian cholera. They reported their results today in the journal mBio.

And here’s their close-up tree. It clearly shows that the Haitian cholera strain evolved from one of four related lineages of V. cholerae circulating today in Nepal. It differs from the Nepalese strain by a single mutation.

It’s amazing that genome-sequencing methods have gotten so powerful that scientists can now use entire genomes to reconstruct an intercontinental outbreak. Yet ten months passed from the outbreak to the publication of this paper. In a blog at the mBio site, co-author Paul Keim explains why: politics. Governments can be reluctant to give up samples that might make them look bad. Building an evolutionary tree of a deadly outbreak takes more than data: it can take a lot of diplomacy, too.

Update: Martin Enserink, writing in Science, raises the question of whether the United Nations should compensate Haiti for the outbreak that this study now clearly lays at their doorstep. Hoo boy!

The biggest animals on Earth–the biggest animals to have ever lived, in fact–are baleen whales. They can grow to over 100 feet long thanks in part to their ability to snarf colossal amounts of food. To do so, they swing open their toothless lower jaws, which inflate like a parachute with water. Then they haul their lower jaw shut again and then use a titanic tongue to push out a school bus worth of water through a filter. The filter is baleen: a set of fronds that hangs from their upper jaws. They trap shrimp and other tiny creatures in the baleen, which the whales then swallow before preparing for the next gulp. Each one of these operations can snag a blue whale up to half a million calories.

The baleen whale is a mammal. It rears its young in the womb, complete with a placenta. It makes milk to feed its newborn calves. Yet the baleen whale is obviously a far cry from any mammal on land. This 30-million-year transformation is pretty irresistible, because it’s so radical and because it comes into sharper focus as the years go by. In my book At the Water’s Edge, I wrote about the first stage of this transition–the evolution of hoofed mammals into amphibious creatures about 50 million years ago, and then, by 40 million years ago, into legless, full-time residents of the sea.

But the first full-blown whales were still a long way from a blue whale or any other baleen whale. Rather than filtering their food, the early whales hunted for it. When they reached their prey, they bit down hard, using their powerful, sturdy jaws lined with massive teeth.

Paleontologists are also documenting the second half of this metamorphosis, thanks to the discovery of some exceptional fossils. One of the best of these fossils is the 25-million-year-old Janjucetus, illustrated above by Carl Buell. Erich Fitzgerald, a paleontologist at Museum Victoria in Melbourne, has been studying this ten-foot whale for a number of years now. (I blogged about some of his earlier work here.) He has identified a number of traits that Janjucetus shares with baleen whales today, but not with any other whales. His analysis showed that it belongs to the oldest lineage of baleen whales, having branched off before the origin of many of the traits that baleen whales have today–most obviously, baleen.

Janjucetus makes it possible for us to understand how something as bizarre and complex as a mouth full of baleen evolved. The most important lesson–hammered home by study after study of evolutionary transitions–is that these sorts of things don’t evolve overnight. They evolve in a series of steps. Pieces of the system emerge and begin to work together, other pieces become incorporated along the way, and all the pieces take on new jobs. And at each step in the process, the transitional animals have fully working systems of bones and muscles they can use to stay alive.

In a new paper in Biology Letters, Fitzgerald takes a close look at the jaws of Janjucetus. In living baleen whales, the upper and lower jaws are shaped for maximum gulpiness. The upper jaws curve upwards and out to the sides. The lower jaws don’t connect at the front; instead, they’re joined by stretchy fibers. When a baleen whale opens its mouth, its lower jaws pull apart to increase the volume of water they can engulf. Janjucetus only had half of this anatomy, Fitzgerald has found. Its upper jaw was wider than in earlier whales. But its lower jaw was still fused together in front.

What could a whale have done with such a hybrid anatomy? Fitzgerald points to some living whales, like the pilot whale, for an answer. These whales have teeth, which they use to bite down on individual fish. But before they bite, they suck. By rapidly opening their jaws, they create negative pressure that pulls in a hapless fish. Their wide, blunt heads increase their pull. Fitzgerald argues that the upper jaw of Janjucetus evolved as a suction-boosting adpation as well. Only later, in more recent baleen whales, did the lower jaws separate, the teeth disappear, and baleen emerge. Only later, in other words, could they start the shift from chasing individual fish to dining on clouds of prey.

The skull of the dolphin-sized Janjucetus served it well. But in later whales, it became a machine for feeding a Leviathan.

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]

To understand how we evolved, we have to understand where we evolved. Natural selection exists because the environment is kinder to some individuals than others. Depending on the species, that environment may be a lake miles underneath Antarctic ice, an alpine meadow near the top of a mountain, or an oxygen-free swamp in the sweltering tropics. Each habitat creates its own set of conditions in which individuals thrive or die. We humans are no different. We are the product of where we have lived.

A century ago, paleontologists thought humans evolved in Central Asia. At the time the only known fossils of an ancient human relative (what we now call a hominin) came from Indonesia. The idea of humans evolving in dank rain forests did not appeal to Western scientists who lived in temperate climes. They looked to Central Asia’s windswept plains. In 1926, the American paleontologist Henry Fairfield Osborn laid out this line of thinking in an essay called “Why Central Asia?”

“In that environment, the struggle for existence was severe and evoked all the inventive and resourceful faculties of man,” he wrote. “While the anthropoid apes were luxuriating in the forested lowlands of Asia and Europe, the Dawn Men were evolving in the invigorating atmosphere of the relatively dry uplands.”

It’s hard to imagine worse timing for such a declaration. In 1925, the year before, Raymond Dart discovered the skull of a another hominin in South Africa. It was much older than the one in Indonesia, and it was a lot more ape-like. And since then, paleoanthropologists have found many more fossils of very old hominins in Africa, from South Africa to Kenya and up to Ethiopia and Chad. Hominins first split off from the ancestors of chimpanzees and bonobos (both found only in Africa) about seven million years ago. The oldest hominin fossils date back to about that age, and from seven million to 1.8 million years ago, the fossil record was exclusively African. Only then did hominins start popping up in places like Indonesia and the Caucasus Mountains. Hominins also continued to inhabit Africa, and evolve into new species. The first fossils of Homo sapiens, dating back about 200,000 years ago, are from Ethiopia.

While Osborn was wrong about the place where humans evolved, his vision of the invigorating atmosphere of dry uplands survived. Dart himself wrote in Nature that South Africa offered the same challenging grasslands as Central Asia.

“We must therefore conclude that it was only the enhanced cerebral powers possessed by this group [us] which made their existence possible in this untoward environment,” Dart concluded. For humans to split off from apes, he wrote, they required “a more open veldt country where competition was keener between swiftness and stealth, and where adroitness of thinking and movement played a preponderating role in the preservation of the species.”

Dart offered an early version of what came to be known as the “savanna hypothesis”–that moving from the forests to open grasslands drove the evolution of the hominin lineage, including the evolution of walking upright, a big brain, and even the loss of body hair.

In the decades that followed, scientists tried to reconstruct the ecosystems in which hominins lived. Plant fossils were scarce, but in many cases–particularly in the Rift Valley of East Africa–these studies pointed to open, savanna-like environments.

By the 1990s, however, things started to get confusing. James Shreeve, writing in this 1996 Discover article , explained how paleoanthropologists were finding evidence that the early hominins might actually have lived in more closed woodlands. The debate rolled on, fueled in part by the scarce information scientists had to rely on.

Eighty-six years after Dart first presented the savanna hypothesis in Nature, the journal has now published a spectacular chronicle of the environment in which our ancestors evolved. Thure Cerling of the University of Utah and his colleagues found a way to overcome the scarcity of plant fossils. Plants absorb carbon from the atmosphere to build their wood, stems, and leaves. Carbon in the atmosphere may have different numbers of neutrons–it may be isotopically “heavy” or “light.” Different kinds of plants will end up with a different balance of light and heavy carbon in their tissues. When the plants die, they add their carbon isotopes to the soil. And the soil itself can sometimes turn to rock–a substance known as a paleosol.

Cerling and his colleagues went to African forests and grasslands and measured the carbon isotopes in the soils. They found they could accurately predict the percentage of woody plant cover from the isotopes alone. With this method in hand, they then analyzed 1300 samples of paleosols that formed over the past seven million years from two sites that have yielded some of the richest troves of hominins: the Awash Valley in Ethiopia, and the Omo-Turkana Basin in Kenya. The result is a “tour de force,” according to Harvard paleoanthropologist Daniel Lieberman (who was not involved in the study).

Here is a massive graph summarizing their findings, which will become the benchmark against which future studies of hominin evolution will be measured.

The further to the left the curves are, the more wooded the habitats. The further to the right, the more open they were. In between are bars showing the age of different hominin fossils. The further to the right the bars are, the more small-brained and big toothed they are. The more to the left, the more like us they are. (You can see a bigger version of the graph here.)

Once you’ve grokked this image, join me at the bottom for an explanation of what it all may mean.

Cerling and his colleagues have found that seven million years ago, grasslands with sparse trees existed at these sites. The woody cover increased over the next few million years, reaching its greatest extent about 3.6 million years ago, when the sites were 40-60% woody cover. Then the woods began to retreat. By 1.9 million years ago, there was no place left with more than half woody cover. The environments continued to open up, the trend continuing till today.

I asked Lieberman, who studies the evolution of human anatomy, how he thinks hominin evolution played out against this ecological backdrop.

“Chances are we split from other apes in the forest,” Lieberman told me. He notes that chimpanzees, bonobos, and gorillas all live in the forest today. The fact that we don’t find early forest hominins is probably due to the fact that closed forests are lousy places for fossils to form. It’s probably no coincidence that scientists have found practically hardly any fossils of chimps or gorillas. They’ve lived in the wrong place.

Another crucial fact to consider is that the earliest known hominins have a number of features that hint that they were no longer knuckle walkers. A number of researchers argue that while they couldn’t walk as fast as we can and probably couldn’t run at all, they were already bipedal. So even though the earliest hominin fossils come from lightly wooded East African grasslands, Lieberman suspects that the origin of bipedalism took place earlier, and it took place in forests elsewhere on the continent. (Another paleoanthropologist, John Fleagle, expressed a similar sentiment to me.)

Lieberman suggests that the earliest hominins adapted to the margins of those early forests, where they had to travel further from tree to tree to find fruit. He and his colleagues have found that it’s four times more efficient for a human to walk a given distance than it is for an ape to knucklewalk. Saving energy on these trips could have translated into more babies.

By about seven million years ago, studies like Cerling’s now suggests, hominins were already moving around on two legs through open woodlands. Hominins evolved to be more efficient walkers. They also acquired big teeth and jaws. Lieberman argues that hominins need this new mouth equipment so that they didn’t have to rely on fruit alone. They could also chew on harder, tougher plants like tubers, which served as fall-back foods in the open woodlands.

Although tree cover increased for a couple million years, forests never came to dominate the East African landscape in the past seven million years. And when open grasslands returned with a vengeance, hominins underwent a dramatic change. They got tall and acquired traits that Lieberman argues were adaptations for running. Their teeth and jaws got small; their snouts disappeared.

Lieberman argues that this change marks a new way in which hominins coped with the increasing grasslands: they became hunter-gatherers, traveling long distances to stalk game. And once they began to enjoy this high-protein diet, one more change occurred: the energy-hungry hominin brain was able to expand towards its current size.

But he is quick to point out that there are some important facts about hominin evolution that don’t fit neatly into the scenario he sketched out for me, and a lot of other crucial facts thtat remain to be discovered. “Anybody who isn’t confused doesn’t know what’s going on,” he said. At least scientists now have a better backdrop for finding out exactly what did happen on the way to Homo sapiens.

[Image: Samburu National Reserve in Kenya, Thure Cerling, University of Utah]

Our cells are packed with various protein-stuffed sacs, each dedicated to carrying out essential tasks. One kind of organelle is peculiar, though. Mitochondria are jellybean-shaped structures whose jobs include making the fuel that our cells use to power everything they do. What makes mitochondria strange is that they carry their own DNA. It’s not a lot of DNA–just 37 genes–but mitochondria can make extra copies of it as they grow and divide. In other words, they act an awful lot like bacteria.

About a century ago, Russian biologists proposed that mitochondria actually started out as bacteria, which set up house in our single-celled ancestors. In the 1960s, University of Massachusetts biologist Lynn Margulis resurrected the idea, pointing to certain features in mitochondria, like their double membrane, found in bacteria but not in other organelles. In the 1970s, biologists began to invent the tools that allowed them to look at the DNA in mitochondria. As predicted, that DNA matched DNA from bacteria, not from animals.

Acquiring mitochondria over 2 billion years ago was a pivotal moment in our evolution. We are eukaryotes, as are trees, mushrooms, and amoebae. We all carry mitochondria (or organelles that started out as mitochondria). Once our eukaryotes acquired mitochondria, they could produce so much fuel that they could get very big. Eukaryote cells are much bigger than bacteria, and eukaryote cells have, on several occasions, stuck together to form multicellular bodies. You can thank your mitochondria for being more than a germ.

But what kind of bacteria did mitochondria come from? This is a lot harder to answer, because we know so little about the diversity of bacteria in the world. When scientists trace the origins of an organism, they compare it to other living things. In the case of birds, for example, scientists have compared them to other land vertebrates. In the big scheme of things, land vertebrates have never been particularly diverse. Scientists have a pretty good grasp of every group of land vertebrates that ever lived, and so they’ve been able to carefully compare birds to all of them. Birds did not evolve from frogs. They did not evolve from skunks. They evolved from feathered dinosaurs. There’s still plenty to learn about exactly which fossil dinosaur was the closest relative to the first birds. But in general terms, the origin of birds is pretty much settled.

When it comes time to compare mitochondria to bacteria, however, scientists face a much tougher challenge. Consider this: there are 5,000 species of mammals alive today. It’s big news when a mammalogist stumbles across a single new species of mammal. If you dig up a spoonful of dirt from your front yard, there may be 10,000 species of bacteria in it–many of which are new to science. If you’re anything like me, even your bellybutton is rife with exotic, undescribed bacteria.

This diversity makes comparisons difficult. It’s as if alien scientists wanted to figure out where humans came from, but they could only compare us to tulips and E. coli. Our DNA shows we are closer to tulips than E. coli, and so the alien scientists might be tempted to declare that we started out as flowers. If the alien scientists could compare the millions of eukaryote species that human scientists know about, however, they could see that plants and animals became multicellular on their own. We have no petals in our past.

Over the past twenty years, scientists have been finding bacteria that are closer and closer to mitochondria, and, in the process, they’ve been zeroing in on what the ancestors of mitochondria might have been like. Recently, J. Cameron Thrash at Oregon State University and his colleagues published a big new study of mitochondria and their relatives that brings them into even sharper focus. The open-access paper appears in the new journal Scientific Reports.

Initially, scientists recognized that mitochondria belonged to a big group of species called alphaproteobacteria. Then researchers sequenced a genome of Rickettsia, a group of alphaproteobacteria that cause diseases like typhus. They found a striking match between Rickettsia and mitochondria. Particularly intriguing was the fact that Rickettsia can only replicate inside eukaryote cells. One could imagine mitochondria starting out the same way, infecting some amoeba-like ancestor. Yet some researchers disputed this conclusion, arguing that the data wasn’t strong enough.

Then scientists went trawling for new bacteria in the oceans and, as they always do, found some surprises. They found new kinds of Rickettsia bobbing in the sea. This lineage of Rickettsia, called SAR11, does not need to infect a host to survive. Instead, this tiny microbe breathes oxygen and slurps up dissolved carbon.  Scientists now recognize SAR11 as one of the most successful lineages in all life: they make up 25% of all the bacteria in the ocean.

Thrash and his colleague did a massive comparison of SAR11 and other  bacteria, analyzing over 60 entire genomes. They concluded that SAR11 are more closely related to mitochondria than other bacteria, including other Rickettsia.

It’s possible, they argue, that our mitochondria did not start out as typhus-like pathogens. Instead, we might look to SAR11 for some clues. SAR11 bacteria breathe oxygen–a capacity that mitochondria gave to our ancestors. SAR11 bacteria also have extremely small genomes–probably because the bacteria were living on a meager food supply and so natural selection favored individual microbes with few genes. It’s likely that once mitochondria became established in our cells they lost many genes that they no longer needed. But this new research hints that they were already tiny, lean bacteria when they took their first step inward.

I can remember first learning of the history of mitochondria, and marveling that we are the offspring of a collective, of a cell that became a home for bacteria, which gave it a new breath of life. Now I will marvel again when I look out at the ocean and realize how, until recently, we didn’t know that our bacterial residents are cousins to an inconceivable number of microbes in the sea.

[Image: Wellcome Images]

[Update--Changed Giardia to E. coli. Dang polytomies]

In tomorrow’s New York Times, I’ve got a story about evolutionary biologists who make New York their Galapagos Islands. Working on this story was great fun–I traipsed around Manhattan parks and medians, checking out mice and ants and salamanders. I spoke to other researchers who study plants, fish, and bacteria in and around the city. All of them observe evolution unfolding in what might seem like a very unnatural place. But after four billion years, nothing can stop evolution. Not even New York.

The Times has posted some of Damon Winter’s wonderful photographs for the story along with some audio from some of the scientists I describe. You can also listen to the new podcast, which features the story too (link to come).

[ Photo: Creative Commons: NatalieTracy on Flickr ]

In March I wrote about two studies that raised the tantalizing possibility that the tree of life, which till now has appeared to have three main branches, turns out to have a fourth.

Some of the evidence for the fourth branch (or “domain,” as taxonomists would call it) came from a newly discovered and very strange group of viruses. They’re known as giant viruses, because they’re about a hundred times bigger than typical viruses and can have over a thousand genes. If there was indeed a fourth domain , it meant that giant viruses were part of one of the oldest lineages on Earth. By studying them we might learn about the earliest stages in life’s evolution.

Since then, there have been a couple developments that merit a follow-up. In April, Didier Raoult of Mediterranean University in Marseille and his colleagues published a new study on another species of giant virus. Their previous studies on the fourth domain involved giant viruses that were first discovered in the water in air conditioners, infecting amoebae called Acanthamoeba. But now scientists are finding giant viruses all over the world, in lots of different single-celled hosts. One of the newest of these discoveries is a giant virus that infects an ocean-dwelling amoeba called Cafeteria roenbergensis. which lives inside amoebae in the ocean.

Raoult and his colleagues took a close look at the Cafeteria virus’s genes. A number of its genes don’t exist inside other known giant viruses. The ancestors of Cafeteria may have picked up them from hosts, or from unknown viruses. (This shuttling of genes from species to species is called horizontal gene transfer.)

But Raoult and his colleagues found some genes shared by the Cafeteria virus and by other giant viruses. They compared some of these shared genes to versions found in other forms of life, like bacteria and eukaryotes (we are eukaryotes, as are plants, fungi, and amoebae). Raoult and his colleagues found that the most compelling evolutionary tree joining these genes together had a four-branch structure. They concluded that the Cafeteria virus “unabiguously” points to the existence of a fourth domain.

But in June a new study came out that raises some serious doubts about the fourth domain.

The new study is the work of Tom Williams, Martin Embley, and Eva Heinz of the University of Newcastle. They felt that Raoult and his colleagues might have been tricked by the slippery nature of evolution. One of the big challenges in drawing evolutionary trees based on DNA is that similarities can be deceiving. Just because two species have stretches of DNA that look alike doesn’t necessarily mean that they inherited that DNA from a recent ancestor. The DNA may have independently evolved into a similar state in each lineage.

This is no big secret. Everybody in the business of reconstructing evolutionary history from DNA knows they have to contend with this kind of mirage, called homoplasy. Scientists can reduce homoplasy’s confusion by steering clear of genes that are prone to homoplasy. They can look at particular kinds of elements of DNA that are particularly unlikely to suffer from homoplasy. They can also take into account experiments on living organisms that show how likely different kinds of mutations are. Knowing those probabilities can help scientists figure out how likely an evolutionary tree is to be accurate.

Embley and his colleagues performed some new tests on the DNA that was used in the fourth-domain studies. They concluded that Raoult and his colleagues had used an evolutionary model that did a bad job of avoiding homoplasy. Embley and his colleagues then carried out an analysis of their own, using other models that took into account some details of biology that Raoult and his colleagues didn’t think were important. There are twenty amino acids that proteins can be built from, for example. But that doesn’t mean that during evolution a pariticular amino acid can switch to any of the other nineteen. Some switches are simply impossible. So Embley and his colleagues built these constraints into their model.

When Embley and his colleagues redrew the tree of life, the support for a fourth domain “effectively disappeared,” they write. They could not reject the possibility that the supposedly ancient genes in giant viruses are not ancient at all. Instead, the viruses picked the genes up more recently from their amoebae hosts. Once inside the viruses, these genes quickly evolved so that they ended up looking different from their original forms.

I got in touch with Jonathan Eisen of the University of California at Davis to get his comment on the new paper. Eisen, as I wrote in March, was an author on a study on microbial genes scooped up from the ocean; he and his co-authors suggested that the genes might be pointing to a fourth domain, although they were a lot more tentative in their conclusions than Raoult and his colleagues. Eisen thinks Embley’s probably right. “Paper looks pretty sound,” he wrote in an email to me.

For now, Eisen’s undecided on where giant viruses fit into the tree of life. They could have branched off early, he says, “but I think it is equally plausible that even the big viruses have stolen their cellular-organism-like genes from hosts of some kind.”

One way to cut down on the uncertainty would be to fill in more branches on the tree of life. It’s easy to forget that for all the millions of species scientists have discovered, there are millions–maybe tens of millions–more that are waiting to be found. Right now, scientists are forced reconstruct the tree of life by comparing species that are separated by hundreds of millions or billions of years of evolution. The more species scientists add to the tree of life, the closer those comparisons will become. And there’s no telling what sort of strange branches the tree will turn out to have.

“There very well may be some weird stuff out there,” Eisen said.

PS: I also contacted Raoult to comment on Embley’s paper and have yet to hear back. I’ll add his responses when I do.

[Update: revised post to clarify that the host is named Cafeteria. ]