Blogs / The Loom

Harper has put up a new page on Amazon for the reissued paperback of Evolution: The Triumph of an Idea. It will include an introduction I’ve written that surveys some of the important developments in both the science and politics of evolution in the five years since the book was published. The Amazon page doesn’t show the cover yet, but it’s in the fall catalog–a subset of these lovely eyes. The publication date is scheduled for November (cough…Christmas gifts…cough).

Last October, a lawsuit was leveled against an evolution web site at UC Berkeley, based on the claim that government funds had been used to promote religious belief. I contributed the section on the history of biological thought. Judy Scotchmoor, the project’s coordinator, just dropped me an email letting me know that the judge has dismissed the case. One less frivolous lawsuit clogging the courts. I’ve got to run, but if I get more information later, I’ll update this post.

Update: Berkeley press release here.

Natural selection can favor genes that allow children to grow up healthy. But in order to grow up healthy, they need nurturing from their mothers, both before and after birth. If a baby’s development puts a strain on a mother, she may end up having fewer children. That means she may spread fewer copies of her genes to later generations . That creates conditions in which natural selection may also genes that allow mothers to restrain their children. Our particular way of having kids puts genes in conflict.

I have an article in tomorrow’s New York Times on these conflicting genes, focusing on the visionary work of David Haig of Harvard University. As I explain in the article, Haig first wrote about his theory in the early 1990s. He made a number of predictions about pregnancy and fetal growth, many of which have only been tested in recent years. Many of them bolster his argument.

In articles such as this one, I usually have to struggle over which examples to include and which to leave out. Sometimes extemely cool ones demand a lot of explanation which would swamp the whole piece. In this case, I had to leave out a couple striking examples of how genes in conflict may create some of the most mysterious birth disorders around.

As I explain in the article, sometimes a mother’s or father’s copy of a gene is silenced. (This is sometimes called gene imprinting.) Haig argues that gene imprinting evolves to undercut the effect of genes from the other parent. A gene that stimulates growth in fetuses puts a strain on the mother. So the mother’s copy of the gene in the fetus is silenced, reducing the growth of the fetus. Imprinted genes are often linked to diseases, because only a single gene has to do a particular job, without backup from the other parent’s gene. And the effects of these disorders can reveal the evolutionary forces that drive the evolution of gene imprinting.

An estimated one in 25,000 babies is born with Prader-Willi syndrome, which causes them to show almost no interest in feeding. Prader-Willi syndrome has been linked to a set of imprinted genes. The syndrome may be triggered if a mutation deletes the father’s copies of these genes. So it may be that these are genes that drive the growth of babies by causing them to nurse more. Mothers hold the children back by silencing their copies of the genes.

By age three, children with Prader-Willi syndrome undergo a baffling change. They develop an insatiable appetite and an obsession with finding food. Prader-Willi can lead to severe obesity. Haig argues that this shift is also the result of genetic conflict. One clue is that it occurs right around the time when children are weaned. Weaning marks a major potential conflict for children and their parent. If a child can nurse longer, it may be more likley to thrive. But if a mother can wean her child, she doesn’t have to sacrifice more energy to make breast milk. Nursing also acts as a contraceptive, so putting a child onto solid food can make it possible for a mother to get pregnant again. The effects of Prader-Willi suggest that paternal genes are driving children to resist weaning. Mothers silence those genes to counteract that resistance.

Another enigmatic disorder is known as Angelman syndrome. Children with Angelman syndrome suffer from a number of symptoms, including retardation. But they’re most distinctive for abundant laughter and endless happiness. Angelman syndrome is caused by the disruption of imprinted genes. It’s the mother’s genes that are disrupted in Angelman syndrome, as opposed to the father’s in Prader-Willi.

What does it mean if disabling maternal genes causes children to laugh and be happy? In a paper in press, Lawrence Wilkinson and his colleagues at Cambridge University argue that babies use these sort of signals to get more attention from their mothers. So the genes that normally prevent Angelman syndrome may normally act as a brake on those signals.

These are speculations, but fascinating ones, and ones that line up with more thoroughly studied examples of genes in conflict. Fortunately, what can’t fit in the paper can always fit in the blog.

[Update 3/14: a little tinkering to clear up the beginning, per a commenter's request]

How do we know that we are kin to chimpanzees and howler monkeys and the other primates? For one thing, it’s by far the best explanation for the fossil record. For another, our DNA shows signs of kinship to other primates, much like the genetic markers that are shared by people from a particular ethnic group. There’s a third line of evidence that I find particularly fascinating: the viruses carried by humans and other apes.

Every day, viruses traffic in and out of human bodies. They invade people’s cells, make new copies of themselves, and then, if they’re lucky, infect a new host. Some viruses do this by stapling themselves into our DNA, so that their own genes are read by our cells much as they read their own genes. In many cases, infected cells die as they manufacture hundreds of new viruses that burst out of them. But in some cases the viruses get stuck. They sit in the cell’s genome, and the cell goes on living. When the cell duplicates, it duplicates the virus DNA as well. Just because the virus spares the cell is not necessarily a good thing. The virus may still be able to pop out of dormancy and wreak havoc. It may also trigger its host cell to duplicate like mad–giving rise to cancer. One in five cancers is associated with these viruses.

Now imagine what might happen if one of these viruses happened to infect an egg. The egg might well die. Or not. And if it started to divide (as a fertilized embryo), the virus would be passed down to all the daughter cells. In other words, a baby would be born with the virus throughout its body.

Too freaky, I know. Put it in a sci-fi script, and a movie producer will say, “Forget it kid. That’s as crazy as the zombie cockroach story some lunatic came in here with this morning.” But it has happened, and many times over. Scientists can identify viruses lurking in our genome (known as endogenous retroviruses) by their distinctive DNA. A fully-functioning retrovirus sequence contains three genes–one for copying DNA, one for a shell, and one for escaping and invading cells. These genes are flanked by a series of repeating DNA, which allow viruses to be inserted or snipped out of their host’s genome. The human genome carries full-fledged retroviruses, as well as viruses in various state of decay. Scientists have identified 98,000 of these viruses, along with about 150,000 fragments of defunct viruses. All told, they make up 8 percent of the human genome. In many cases, the virus genes have disappeared altogether, leaving behind flanking repeats, which have been duplicated to millions of copies that take up about 40 percent of the genome. As a point of comparison, our “own” genes–in other words, those that encode proteins that make up our bodies and allow our bodies live–make up only about one percent of the genome.

Some of these endogenous retroviruses are only found in some people and not others. They must have invaded someone’s genome and then spread to his or her descendants, but have not yet spread throug our entire species. Others appear to be ubiquitous–meaning that they are ancient passengers that had already spread throughout an ancestral population.

Other vertebrates carry their own collections of endogenous retroviruses. Mice have a particularly lively collection that continues to spread through their genome with each generation. And you can trace their history through evolutionary time. Domesticated cats, for example, share many endogenous retroviruses with their wild cousins. But they also carry other endogenous retroviruses of their own. The same goes for pigs, and their wild boar cousins. As pigs and boars stopped interbreeding, they could no longer spread newly acquired retroviruses to future generations.

Now, if you really don’t enjoy reading about evidence that you are related to a chimpanzee, now’s the time to close your browser window. Because now I must write about the endogenous retroviruses in chimpanzees, macaques, and other primates. It turns out that most of the viruses we carry can also be found in these other species. Our retroviruses can be grouped into families. They carry the same families. Our retroviruses usually appear in the same position in the genome, no matter whose genome you look at. Many of theirs are in the same place. These are all the sorts of evidence you’d expect if retroviruses had been carried down from distant primate ancestors. A particular retrovirus is not identical from one host primate to the next, but you wouldn’t expect that. Once each host lineage branched off, the viruses could acquire mutations. But the different versions of these retroviruses are still similar enough that scientists can reconstruct the DNA of original virus that infected some long-gone primate.

Retroviruses appear to have invaded the primate genome in a series of waves, starting over 55 million years ago and continuing until just a couple million years ago. As a result, some of the retroviruses in our genome are found only in some primates and not others. It’s not completely random as to which primates share these retroviruses. In general, they are the same species that other studies have shown to be our closest relatives.

Once viruses get established in a genome, they can take any of a number of evolutionary paths. They may still be able to break out of their resident genome, become full-blown viruses, and invade another cell in the body. If they’ve lost the ability to become true viruses, their DNA can still get accidentally copied and inserted back into the genome. These copies may accidentally get swapped, producing drastic changes in their host’s genome. And most remarkble, sometimes genes from viruses become useful to their hosts. It appears that virus genes have become vital for the development of primate placentas, and to carry out other essential tasks. While these genes retain distinctive sequences seen only in retroviruses, they show signs of having been preserved by natural selection, even as the viral genes that surround them have mutated into uselessness.

There’s one more use these viruses have to offer: they have preserved a precious record of our evolutionary history.

(For more information, see talk.origins for a discussion of retroviruses and primate evolution from a few years ago.)

In trying to navigate the new ethical territory of blogging, I’ve decided to delete part of one of my posts. The full explanation is below.

(more…)

Enceladus, a tiny moon of Saturn, suddenly gets interesting. It may be spewing liquid water. And since the only life we know of needs liquid water–and since Enceladus may now be the second place we know of in the solar system with liquid water–I want to buy a ticket there. Details and pictures here.

I’ve revisited the wrist walker story after a scientist involved accused me of spreading “empty gossip.” I don’t agree with that charge, but I do think I should retract some of what I wrote. But I’ve still got some nagging questions about the whole affair. Check it out.

I’ve been in low-blogging mode for a few days as I try to fire off a few dead-tree articles. But I wanted to write up a quick post to draw your attention to threetwo very interesting pieces of human evolution in the news.

1. Modern evolution. A new paper presents the results of a systematic scan for human genes that have experienced natural selection in the past few thousand years. An impressive 700 regions turned up. The fact that humans have been evolving during recorded history is not new. The ability to digest lactose in milk as an adult, resistance to malaria, and other traits have long been recognized as having experienced strong natural selection after the dawn of agriculture. But this new study certainly sets the standard for all future work in this area, because it is so thorough. (Gene Expression takes you through the steps. The original paper is here.) The next logical step would be to add new populations to the database. The new study compares only three populations–Yorubans from Nigeria, Chinese and Japanese, and people of European descent in Utah. I wonder how different the evolutionary pressures are in other groups. Inuits get no benefit from malaria resistance, for example. Lactase digestion turns up in people descended from cattle herders. Are there adaptations for eating rice, cassava, or blubber?

Adaptations for drinking milk are not the stuff of racial controversy, but brain genes certainly are. Last year there was quite a hullabaloo over findings that a couple brain genes were also evolving quickly over the past few thousand years. The fact that natural selection appeared to be occurring in those genes in Europeans and Asians generated a fair amount of commentary that at least had a whiff of racism to it. Those particular findings seem to dissipate in the new study, perhaps because it looks at a bigger sample of people. On the other hand, there are other brain genes that the new study identifies as evolving. Some are found only in one or two samples, and one is in all three. These results show no simple pattern that can be exploited for blithe generalizations. So I expect silence from pundits.

2. The Evolutionary Volume Knob. While working on my Smithsonian Intimate Guide to Human Origins, I was particularly struck by a visionary paper published in 1975. Mary King and Alan Wilson argued that the evolution of humans might have been dominated not by the emergence of new genes, but by new uses for old genes. At the time, scientists knew precious little about human DNA. They had yet to sequence a single human gene.

In Nature today, scientists published a study that investigates their proposal with all the tools biotechnology has to offer today. The scientists set up devices known as microarrays that can measure the activity of genes in cells. They measured the activity of over 1,000 genes in liver cells from four species of primates–humans, chimpanzees, orangutans, and rhesus monkeys. About sixty percent of the genes show the same levels of expression in all four species, suggesting that they have changed little since the common ancestor of monkeys and apes. But they found 14 genes in humans that buck that conservative trend, showing significantly higher or lower activity than in other primates. Interestingly, five of these genes encode proteins that turn on and off other genes (transcription factors). The authors note that in studies on closely related fruit flies, transcription factors don’t seem to have evolved very quickly. So it’s possible that the patterns found in the new study offer some clues as to why we humans are so different from chimpanzees compared to fruit flies separated by the same amount of evolutionary history.

3. [Update 3.11.06: I've decided to delete this last entry. I've explained why here]

Scientists are probably centuries away from drawing the full tree of life. For one thing, they have only discovered a small fraction of the species on Earth–perhaps only ten percent. They are also grappling with the relationships between the species they have discovered. Systematists (scientists who study the tree of life) rely mainly on DNA these days to figure out how species are related to one another. They compare the similarities and differences in a given gene in several different species to figure out which ones share the closest kinship. But they have actually sequenced DNA from relatively few species. And in many cases, that DNA may come from a single gene.

Systematists have made good use of this scanty data. They’ve been able to sort out relationships of many big groups of species, from mammals to plants–groups that sparked debate among systematists for decades. But these are just small tufts on the complete tree of life. The big picture has proven harder to pull into sharp focus.

When systematists try to make sense of billions of years of evolution, they must struggle with many foes. The DNA they study, for example, may send them a misleading signal. Some of the most common mutations are known as point mutations, because they change DNA at one point–changing a single base of DNA to another. Since there are are only four letters in the alphabet of DNA, it’s not surprising that over billions of years two lineages may acquire the same letter at the same position in the same gene. These two independent mutations may well give the illusion that two lineages share a close common ancestry.

Genes create another challenge when they jump from one species to another. For decades scientists have known that microbes can swap genes, primarily with the help of viruses that sometimes move between species, carrying some host DNA with their own. At first this hopping seemed like rare flukes. Then some systematists argued that gene swapping was so common that life’s history might be better represented by a web than a tree. Most experts disagree: they argue that this gene-swapping does not destroy the quest for the tree of life. It creates vines draped between the branches of the tree of life, but the branches of the tree are still visible.

It’s been hard to resolve this debate because until now most scientists have analyzed the tree of life by looking at just one gene in a number of species, or, in rare cases, a few genes. Fortunately, scientists now have entire genomes of a couple hundred species to analyze. In the new issue of Science, biologists at the European Molecular Biology Laboratory published the latest, most thorough glimpse at the tree of life.

It’s quite something to behold. I’ve posted a reduced version of the tree on this page, and you can get a closer look here, at a site dedicated to the project. To orient yourself, our species is at about two o’clock, next to the chimp, rat, and mouse.

The scientists took advantage of the fact that so many genomes have been sequenced over the past decade, and that it’s now possible to compare the DNA in different genomes relatively quickly (if you have a supercomputer, of course). Their strategy was to search for all the genes that could offer the clearest clues to the tree of life–genes that had not been swapped too much between species, for example. They searched the genomes of 191 species of animals, plants, fungi, protozoans, bacteria, and archaea (microbes that look superficially a lot like bacteria). They selected 36 universal genes, but then tossed out five of them because they appear to have been swapped.

This tree emerged from their analysis of the remaining 31 genes. The scientists kicked the tires, as it were, by running the tree through a series of statistical tests. Did the same pattern of branches emerge if they left out some species? What happened if they left out one gene or another from the analysis? Two-thirds of the branches turn out to have 100% support from these tests, and many of the others, while not so perfect, are still statistically robust. So this study suggests that gene-swapping does not end the quest for the true tree of life. (Other scientists came to a similar conclusion last year, which I wrote about here.)

Here’s a quick tour of the tree. Start at middle of the circle. The central point represents the last common ancestor of all living things on Earth. The tree sprouts three deep branches, which between them contain all the species the scientists studied. These deep branches first came to light in the 1970s, and are known as domains. We belong to the red domain of Eukaryota, along with plants, fungi, and protozoans. Bacteria (blue) and Archaea (green) make up the other two domains.

These lineages probably split very early in the history of life. Fossils of bacteria that look much like living bacteria turn up at least 3.4 billion years ago. Just a few lineages became multicellular much later, with some algae getting macroscopic about two billion years ago.

The length of the branches on this tree represent so-called genetic distance. The longer the branch, the more substitutions have accumulated in its genes. Since these genomes all come from living species, the branches all span the same period of time. The fact that some branches are long and some are short means that some lineages have evolved more than others. Many forces can stretch out genetic distance. A species may reproduce fast, or it may have a life that makes it prone to acquiring more mutations. The slash in the Bacteria branch represents a segment that the scientists left out to make the full tree easier to see.

The long length of the Bacteria branch underscores one of the big messages of this tree: the diversity we can see with the naked eye reflect a pretty paltry snippet of life’s genetic diversity. Humans and mushrooms are tucked into a small part of the tree. Meanwhile, bacteria such as ones that cause strep throat (Streptococcous) and the ones that cause food poisoning (Salmonella) are divided by vast evolutionary gulfs. The diversity of microbes did not stop evolving billions of years ago. Escherichia coli, for example, emerged relatively recently, specializing on the warm guts of mammals and birds.

As the scientists point out, this tree challenges the traditional way that biologists classify living things into species, genus, family, class, phylum, and kingdom. Scientists named many of these groups in the eighteenth and nineteenth centuries, when they could only sort species by what they could see with the naked eye or a crude microscope. But there’s a vast amount of hidden biochemical diversity in living things, and that diversity is reflected in this new tree. The scientists compared the genetic distance among different groups. Animals in different phyla are separated by much less genetic distance than bacteria that are in the same phylum. If scientists were classifying life from scratch today based on genetic distance, they’d probably downgrade animal phyla to classes.

This discovery does not sit well with claims from creationists that evolution cannot account for the emergence of animal phyla. It is certainly true that the earliest fossils of several animal phyla emerge over a span of perhaps thirty million years around the beginning of the Cambrian period, 540 million years ago. But animal phyla are, in a sense, overrated. This new tree of life supports a growing consensus that relatively small genetic changes in animal evolution led to big changes in their bodies. (If you want to read a whole book on this, check out Endless Forms Most Beautiful.)

This tree supports some findings from other recent studies. Mushrooms are more closely related to us than they are to plants, for example. But it will also make some scientists unhappy in other ways. There’s a big debate going on these days about the animal kingdom. Some researhcers think that arthropods and nematodes belong to a “moulting” group. But this tree suggests that arthropods are more closely related to us vertebrates. The authors of the new study acknowledge that their tree may be unreliable in this respect. That’s because the animal genomes that have been sequenced may not belong to the best species to include in this sort of study. The fruit fly Drosophilia melanogaster or the mouse Mus musculus did not get their genomes sequenced so they could be put in the tree of life. They were chosen because scientists had studied their genes and physiology for decades. They would be able to make good use of the genomes of these animals for their research. It would help enormously if scientists could get the genomes of other animals that belong to different branches of the animal kingdom, such as ragworms and other obscure critters.

Fortunately, scientiss should be able to add these species to this tree very quickly. In the past, scientists have had to do a lot of their tree-building by hand, lining up genes, idenfitying cases of gene-swapping, and so on. But as the European scientists built this new tree, they were able to set up an automated pipeline. As new genomes are published, it will be possible to let a computer automatically compare them to older sequences and generate a new tree that does a better job of explaining all the evidence. None of us may live to see the full tree of life emerge, but at least we may be able to savor a better sneak preview.

Update, 3/5 9:45 am: Rhasgobel has put together a useful list of translations of the Latin names on the tree.

This image came out a couple months ago in Nature, but I just came across it today. I quite like the way it sums up the history of life–something that’s maddening hard to do, since the time scales are so vast. It shows how life’s diversity has been accumulating for billions of years. This chart shows the timing of the earliest paeolontological evidence for different kinds of life, ranging from fossils to chemical markers. A few definitions may help. Phototrophic bacteria can harness sunlight to grow. Cyanobacteria are also known as blue-green algae (aka pond scum). Eukaryotes are species such as amoebae, plants, fungi, and animals. Algal kindoms include red algae and green algae (closely related to land plants). Some of these bars may need to be pushed back in time when earlier evidence is discovered. Some studies on DNA suggests that a number of such “ghost lineages” remain to be discovered.

Go back far enough in our history–maybe about 650 million years–and you come to a time when our ancestors were still invertebrates. That is, they had no skulls, teeth, or other bones. They didn’t even have a brain.

How invertebrates became vertebrates is a fascinating question, made all the more fascinating because the answer tells us something about how we got to be the way we are. In order to reconstruct what happened, scientists can study several different kinds of evidence. They can look at the bodies of invertebrates to find the ones that share traits with vertebrates not found in other invertebrates. Those common traits may be signs of common ancestry. Scientists can look for signs of this ancestry by studying the DNA of vertebrates and invertebrates. They can also examine the fossil record, to discover transitional forms that offer clues to the transitions that can’t be found in living species.

When scientists consider this evidence, the answers don’t come pouring into their lap like coins from a slot machine. They have to put together hypotheses that do the best job of explaining vertebrate origins.They can then test those hypotheses against new evidence. Sometimes the old hypotheses hold up. Sometimes it turns out they were based on a misreading of the evidence. New hypotheses emerge to take the place of old ones. But those new hypotheses have to be better than the old ones. Scientists do not just suddenly declare that any explanation will do.

This is how science works. It occurred to me that this fact bears repeating when I read a recent comment to this blog. The comment emerged in a discussion about some observations from Randy Olson, a movie director, on how to communicate effectively about evolution. Some people agreed with Olson’s ideas on livening things up, while others worried that he just wanted to dumb science down. The differences were real, but the discussion was productive–at least until a couple creationists chimed in.

These creationists claimed to offer some helpful advice, but it’s pretty clear from their comments (and their links to creationist web sites) that they really had nothing of the sort in mind. They don’t actually want to help people understand evolution; they’re just exploiting some common misunderstandings about evolution, and about science in general.

They do provide one service, by showing which misundertsandings they think they can exploit most effectively. “Anonymous” writes:

“But you need to be honest about the scientific accuracy. How often does a new discovery come out that requires a rewrite of the evolutionary timelines and trees. If memory serves, I’ve read at least 2 posts on this blog in the last year with statements to that effect. How can you say Evolution is Science and Science is Truth and then in the next statement that Evolutionary scenarios must be rewritten. The public hears this.”

If only I could put words in the mouths of people I write about–life would be so much easier. Anonymous might as well have written, “You say that your cat can speak Mandarin. The public hears this.” Not from me.

Scientists learn new things about the world. They revise their theories. They do not pull away a curtain, to reveal Truth with a capital T, and walk away. And just because they do not deal in Truth with a capital T does not mean that they deal in pure nonsense. Their knowledge improves, although it never reaches perfection.

The origin of vertebrates is a case in point. Among living invertebrates, scientists have identified certain groups as being closer to us than to other invertebrates. The biggest group are echinoderms, which include starfish. They may not have skulls or brains like ours, but they do share some peculiar traits. In other invertebrates, for example, a hole in the early embryo called the blastopore becomes the mouth. In echinoderms and vertebrates, it becomes the anus.

Along with echinoderms, a few less familiar species have also shown strong links to vertebrates. One group is called the tunicates. These include the sea squirt, a truly bizarre animal. It begins life as a tiny tadpole. It swims with a tail made of a stiff rod called a notochord, along which runs a hollow nerve cord. It also has slits in its throat for swallowing food. These traits are not found in echinoderms or other invertebrates, suggesting a close link to vertebrates. Remarkably, most of its vertebrate-like traits disappear when it gets to be an adult. It lands on the sea floor on its head, rotates its organs ninety degrees, and eats its own nervous system. It then sits on the sea floor, filtering food and making new tadpoles.

Then there are the lancelets. These creatures (such as the one in the picture here) look like sardines with their heads cut off. They have a similar life cycle to sea squirts, swimming as larvae and then settling to the sea floor. But they have more traits in common with vertebrates. The tip of their nerve cord, for example, shows many striking similarities to the overall organization of the verebrate brain, even down to the genes that build each. It also has muscles arranged into blocks along its length–the same sort of blocks that you can get your fork into when you have fish for dinner. They don’t degenerate into a sac as adults. They just dig into the sediment and stick their heads out, so they can filter food passing by.

Many scientists argued that the ancestors of echinoderms branched off from our ancestors first. Then, after our ancestors acquired throat slits and a notochord, the ancestors of sea squirts branched off. Then our ancestors acquired rudiments of a brain, blocks of muscles, and other traits, after which the lancelet lineage branched off. At this point, the vertebrate body plan was still only partially built. Evolution had not yet produced skulls, spinal columns, eyes, and other features found in all living vertebrates. All that came later.

As I mentioned earlier, there are a couple ways to test this hypothesis. One is to look at the fossil record. Do the traits seen in echinoderms, sea squirts, lancelets, and vertebrates tend to turn up together in extinct animals, or do are they scattered all over the animal kingdom? Do paleontologists discover lobsters with skulls, earthworms with fish-like gills? No. They do find lancelet-like animals that have well-formed brains and even skulls–which is exactly what you’d expect as invertebrates evolved into vertebrates. They also find peculiar fossils that might be closely related to vertebrates or to the common ancestor of echinoderms and vertebrates. This sort of ambiguity is not surprising, because in the early days of these groups, you’d expect to find species that had not yet acquired the distinctive traits found in living groups. The same pattern turns up in the earliest hominids–they are so much like other apes that it can be hard to say whether they are ape-like hominids or hominid-like apes.

Another way to test an hypothesis about the origin of vertebrates is to look at DNA. In this week’s issue of Nature, a team of French scientists publish the results of just such a study–the biggest of its kind, both in terms of the range of animals studies and the mass of DNA analyzed in each one. They looked for the evolutionary tree that offered the best explanation for the differences and similarities in the DNA carried by each species. They put their results through a series of statistical tests to see if they were solid, or if they were just misleading illusions (removing one species from the study, for example, to see if a different tree emerged).

Their evolutionary tree has the overall shape of trees produced from other kinds of evidence. The French scientists find that humans and chickens are more closely related to each other than either is to frogs. Lampreys and hagfish are more distantly related to us, but closer than lancelets or echinoderms. Even among the invertebrates, patterns turn up that have been seen before. Insects are more closely related to us than jellyfish, for example, and jellyfish are more closely related to us than mushrooms.

The fact that studies based on anatomy, various genes, and fossils, all converge on these same patterns indicates that they’re onto something real. If someone shows you twwenty species and has you connect them with a family tree, there are over 200 billion billion different possible trees you could draw. But the trees that emerge from these studies only only minor variations on one another, not a random sample of all the possible trees. The odds of this happening by pure coincidence are incredibly tiny. But it’s exactly what you’d expect if they represented real evolutionary relationships.

The new tree does have a couple interesting surprises. One is that sea squirts–those weird nerve-eaters–are closer to us than lancelets. The other is that lancelets may actually be more closely related to echinoderms than to vertebrates and sea squirts.

If this conclusion is supported by more studies, lancelets may turn out to be a lot like the common ancestor we share with starfish. That lancelet-like ancestor then gave rise to some lineages in which some radical changes occurred. Once the echinoderm ancestors of starfish branched off, they must have lost some traits we still carry, such as a main nerve cord running along the back and throat slits. That conclusion would jive with some early fossils of echinoderms that appear to have slits.

The study suggests that sea squirts also changed a lot from a lancelet-like ancestor. They lost the muscle blocks of their ancestors and their nervous system must have become much simpler. Their odd sedentary filter-feeding evolved only after their ancestors branched off from our own. Rather than primitive, sea squirts may actually be highly specialized proto-vertebrates.

But as different as sea squirts may have become, scientists may still be able to learn a lot about our own origins by studying them. Much of what distinguishes us from invertebrates–eyes, teeth, and such–develops from a distinctive group of cells called neural crest cells. They first emerge along the back of the vertebrate embryos and then move through the body, giving rise to lots of different structures. Both lancelets and sea squirts have neural-crest-like cells. But only in sea squirts do they migrate as they do in our own bodies. By studying how these cells move, scientists may be able to understand a key step in vertebrate evolution.

There is one obvious way to test this scenario: sequence the genomes of other close vertebrate relatives. Previous studies have suggested that echinoderms share a close common ancestor with acorn worms, which have throat slits among other vaguely vertebrate-like traits. Including their DNA in a new study may support this current study, or pose a new challenge. That sort of result may disappoint those who would like science to deliver Truth in one perfect lump. But for scientists, it’s the sort of fresh challenge that gets them out of bed in the morning.

Update 2/23 8 am: Thanks to Dr. David Hone for giving me precise numbers for the possible trees.

This is why I was so lucky to get Carl Buell to illustrate my first book.