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December 2004


December 31, 2004

The Whale and the AntibodyEmail This EntryPrint This Article

Ambulocetus.jpgEvolutionary biologists face a challenge that's a lot like a challenge of studying ancient human history: to retrieve vanished connections. The people who live in remote Polynesia presumably didn't sprout from the island soil like trees--they must have come from somewhere. Tracing their connection to ancestors elsewhere hasn't been easy, in part because the islands are surrounded by hundreds of miles of open ocean. It hasn't been impossible though: studies on their culture, language, and DNA all suggest that the Polynesians originally embarked from southeast Asia. We may never be able to retrieve the full flow of history that carried people thousands of miles to the middle of the Pacific, but we can know some things about it, and we can rest assured that some things are definitely not true (such as the sprouting-from-the-ground theory).

Whales are a lot like Polynesians. All living species of whales look a lot like each other, and not very much like any other animals. They all have horizontal tail flukes, blowholes, and smooth skin free of scales or fur. Darwin argued that whales were not simply created in the oceans in their current form, but instead descended from land mammals which had adapted to life in the ocean. He pointed out that whales share a number of traits with land mammals, such as milk and a placenta. Their blowhole connects to a set of lungs very much like those of land mammals and nothing like the gills of fish.

protolymph.gifDarwin wigged out more than a few people with this argument. Whales just seemed too different, too distinct to have evolved by small steps from a four-legged ancestor. And creationists loved to point out how unlikely this transition seemed--on par with turning a cow into a shark. They also liked to point out that no intermediate fossils had ever been found. But as I wrote in my book At the Water's Edge, paleontologists began to find those fossils in the 1980s. Today, the transition whales made from land to sea is wonderfully well documented. Paleontologists have found complete skeletons of creatures such as the 45 million year old Ambulocetus (reconstructed here by the gifted artist Carl Buell). The transformation was not some sudden macromutation, but a gradual series of changes over millions of years, featuring shrinking legs, lengthening tails, loosening hips, and migrating noses.

In the coming century, I suspect fossils will help scientists reconstruct other major transitions. But they'll also start reconstructing others that have left no record in rocks A fascinating case in point has been published on line at the Proceedings of the National Academy of Sciences. Jan Klein and Nikolas Nikolaidis of Penn State have drawn a rough map that charts the evolution of the immune system.

Our immune system is as awesome as a whale's body--in terms of the complexity of its parts and the way those parts work together so well. It keeps viruses, bacteria, tapeworms, and even cancer cells at bay, while generally sparing our own tissues from its withering attack. All animals share a rudimentary immune system, but Klein and Nikolaidis focused on a second system that is found only in vertebrates. Only we vertebrates have immune systems that can learn.

This learning system is a network of cells, signals, and poisons. Among its most important cells are T cells and B cells. They originate in the bone marrow, although the T cells have to finish their development in the thymus, an organ near the heart. These cells are unusual in many ways, most important of which are some of the receptors they make on their surface. The cells have a special set of tools that cut up the receptor genes and paste them into new arrangements, so that the genes produce receptors with new shapes. Depending on its shape, a receptor can grab onto certain molecules. Those molecules may come from a bacteria toxin, or they coat nerves or muscle cells. Our bodies can usually eliminate the immune cells that have an affinity for our own tissue. If they don't, we end up with autoimmune diseases such as muscular dystrophy.

The surviving B cells and T cells are introduced to molecules from invading pathogens (antigens) by other immune cells called macrophages. The macrophages devour bacteria or virus-infected cells and then put some of the molecules of their victims on their surface. They travel to the lymph nodes to show off their conquests. If T cells or B cells bump into one of these macrophages, their receptor may fit reasonably well onto an antigen. That fit sends a signal to their DNA, triggering them to multiply. Some of the cells they produce receptors cut and pasted into newer shapes, some of which do an even better job of fitting on the antigen. These winners get to reproduce more. In other words, our immune systems use a version of natural selection to fine tune their recognition of pathogens.

These B cells and T cells can then fight off a disease. The T cells may destroy cells infected with the pathogen, because most cells in the human body have receptors they can use to display antigens. In other cases, they can whip up macrophages into a furious frenzy of killing. Or they may spur B cells to produce antibodies. The B cells spray out the antibodies into our bodies, and when they come into contact with their particular pathogen, they may drill into it, stop it from invading cells, or tag the pathogen to make it an easier target for macrophage attack. Some B cells and T cells that can recognize a pathogen sit out the battle. If we should be exposed to the same disease years later, these memory cells can leap into action so quickly that the new infection may not even make us sick.

You can find this same remarkable system in humans, albatrosses, rattlesnakes, bullfrogs, and all other land vertebrates. You can also find it in most fish, from salmon to hammerhead sharks to sea horses. There are some variations from species to species, but they've all got B cells, T cells, antibodies, thymuses, and the other essential components. But you won't find it in beetles, earthworms, dragonflies, or any other invertebrate on land. Nor will you find it in starfish, squid, lobsters, or lampreys in the water. All these other animals rely instead on rudimentary immune systems that cannot learn.

For those who reject evolution, this sort of pattern tells them nothing. Like everything else in nature, they can only wave their hands and declare it the inscrutable work of a designer (lower case d or upper case D as they are so inclined on a given day). But immunologists and other scientists who actually want to learn something about the immune system find this view useless. Instead, they look at how animals with an antibody-based immune system are related to one another. And what they find is both straightforward and astonishing. All of the living animals with an antibody-based immune system descend from a common ancestor, and none of the descendants of that common ancestor lack it. That means that the antibody-based immune system evolved once, about 470 million years ago.

I need to back up in the history of life a few hundred million years to explain how scientists know this. Studies on fossils and genes agree that everything we call an animal (including sponges and jellyfish) shares a common ancestor not shared by plants, fungi, or other major groups of organisms. Exactly when that ancestor lived is a subject of fierce debate, but one of the latest estimates puts the date at about 650 million years ago. This ancestor probably had a simple immune system, because all animals, from sponges on, have at least some sort of defense against pathogens. Over the next 100 million years or so, the major groups of animals branched off from one another, and while some branches evolved some new defenses of their own, the antibody-based immune system only appears in our own branch, the vertebrates.

Animals with some--but not all--of the key traits of vertebrates, such as heads and brains, lived at least 530 million years ago. The only living relics of these early branches are hagfish. Later, our ancestors also evolved a vertebral column, becoming true vertebrates. Lampreys represent the deepest branch of vertebrate evolution, splitting off perhaps 500 million years ago from their common ancestor with us. They lack many traits that other vertebrates have--most obviously a jaw. A number of other weird jawless vertebrates filled the oceans between about 500 and 360 million years ago, but except for lampreys, they're all long gone. One of these branches gave rise over 470 million years ago to fish with jaws--known as gnathostomes. Gnathostomes later gave rise to sharks and other "cartilaginous" fishes, as well as ray-finned fishes, and land vertebrates.

You may have already guessed the kicker of all this history. Lampreys and invertebrates don't have an antibody-based immune system. Sharks, ray-finned fish, and land vertebrates do. Sharks, ray-finned fishes, and land vertebrates all share a common ancestor that is not shared by lampreys or other invertebrates. The simplest way to explain this coincidence is to conclude that the antibody-based immune system evolved after lampreys branched off from our own lineage, but before sharks and other living gnathostomes began to branch apart. We can't dig up fossil antibodies, but we can know when they evolved.

Scientists have sometimes treated the transition from rudimentary immune system to antibody-based immune system as a great leap. Lampreys don't have antibodies, B cells, T cells, thymuses, or the rest, and all gnathostomes do. Some creationists have even tried to turn this into an argument against evolution, claiming that something as complex as the adaptive immune system could not have emerged gradually. But it's important to bear in mind that tens of millions of years of evolution separate our common ancestor with lampreys and the earliest gnathostomes. And in their new paper, Klein and Nikolaidis argue that the evolution of the antibody-based immune system was a lot like the evolution of whales: a gradual, step-wise process.

Most of the components of the antibody-based immune system were actually already in place long before gnathostomes evolved. Lampreys, for example, don't have a thymus, but they do have the structures and cell types that form the thymus. In gnathostomes, the thymus develops as cells switch on special genes in a particular order. Lampreys have these genes, as so many other animals. Instead of building thymuses, they build other structures, such as eyes and gill arches. It would have only required altering the switches that determine when and where these genes become active to produce a new organ.

B cells and T cells are known as lymphocytes. Lampreys don't have lymphocytes, but Klein and Nikolaidis point out that they do have "lymphocyte-like cells." (The picture above shows what these cells look like.) Lymphocyte-like cells develop like lymphocytes, under the control of many of the same genes that control the development of lymphocytes. Once they are mature, these cells have almost the same structure and chemistry as lymphocytes--but they don't produce the antibodies and receptors of B cells and T cells. Exactly what they do in lampreys isn't clear.

What about those receptors and antibodies? Klein and Nikolaidis point out that they aren't quite as novel as they may look at first. They are made up of building-blocks of simple proteins arranged in different ways. And guess what--many of these simpler proteins are found in lampreys and invertebrates, where they serve other functions. The same goes for many of the proteins that B cells and T cells use to communicate with one another. Other proteins are made by genes that are unique to gnathostomes, but show a kinship to entire families of genes found in other animals. The most likely explanation is that an ancestral gene duplicated by accident, and later one of the copies was recruited to the evolving immune system.

Klein and Nikolaidis point out that some truly new things appeared as the antibody-based immune system emerged. But just because something is new doesn't mean that it couldn't have evolved. The best-understood example of a new feature is the cut-and-paste machinery that allows B cells and T cells to mix up their receptors into new shapes. Scientists have been working out its evolution for years now, but just last week some scientists from Johns Hopkins published a paper in Naturethat brought the picture into remarkable focus. Our genomes are rife with virus-like sequences known as transposable elements that produce enzymes whose sole function is to make copies of the transposable DNA and insert those copies somewhere else in our genomes. In a few cases, these transposable elements have evolved from pests to helpers, carrying out important functions in our cells. The genes that are responsible for cutting and pasting immune cell receptors bear a clear resemblance to transposable elements in other animals. So the evolution of a new cut-and-paste mechanism was actually just the domestication of an in-house virus.

I suppose that creationists might claim that these components could not possibly have come together into an antibody-based immune system. But there's no proof behind this sort of categorical dismissal, just a personal feeling of disbelief. These folks would still be left with the fact that the evolutionary tree of life and the biochemistry of vertebrates and other animals are all consistent with a gradual evolution of this system. It would all have to be a spectacular coincidence, or perhaps an intentional deception on the part of the designer. Who knows. Who cares, really? (Aside from certain Pennsylvania senators.) What's exciting here is the future research that could shed more light on this transition. Klein and Nikolaidis propose introducing lamprey genes into vertebrates and vice versa to see just how close the ancestors of lampreys had gotten to an antibody-based immune system before they branched off on their own. Obviously, some half a billion years of independent evolution will muddy up the results, but it should be possible to see whether gnathostome immune genes can organize the lamprey immune system to act more like our own. What I'd be even more excited by would be a deep-sea discovery of a living fossil--a jawless fish that is more closely related to us than lampreys. They filled the seas 400 million years ago, and perhaps a few are lurking in some deep sea trench. Such a fish might have a crude antibody-based immune system, with only a few genes recruited and others yet to be pulled in. Perhaps it could do a mediocre job of learning to recognize diseases--but a mediocre job is better than no job at all.

It may sound like a crazy dream, but then again, so did walking whales.

Update 1/2/05: Panda's Thumb has more on the evolution of the immune system.
December 29, 2004

Ms. Schlafly, You Receive an FEmail This EntryPrint This Article

Phyllis Schlafly has suddenly become interested in evolution! She has written the most staggering display of buffoonery on the subject that I've read in a long time. She can't even tell the difference between Darwin and Lamarck--seriously. At least Steve Reuland at Panda's Thumb can dismantle this ignorant nonsense while retaining his sense of humor.
December 27, 2004

All the News That's Too Big To PrintEmail This EntryPrint This Article

Size matters. At least that's the result of some recent research on long-term evolutionary trends that I'll be reporting in tomorrow's New York Times. Here are the first few paragraphs...

Bigger is better, the saying goes, and in the case of evolution, the saying is apparently right.

The notion that natural selection can create long-term trends toward large size first emerged about a century ago, but it fell out of favor in recent decades. Now researchers have taken a fresh look at the question with new methods, and some argue that these trends are real.

Biologists have recently found that in a vast majority of animals and plants, bigger individuals are more successful at reproducing than smaller ones, whether they are finches, damselflies or jimsonweed.

Nor is this edge a fleeting one. Natural selection can steadily drive lineages to bigger sizes for vast stretches of time. The giant dinosaurs that made the earth tremble, for example, were the product of the long-running advantage of being big over tens of millions of years.

"I think it holds up very well, and a lot better than a lot of people have said over the years," said David Hone, a paleontologist at the University of Bristol. Mr. Hone and others argue the push toward bigger size is so strong and persistent that there must be significant forces pushing the other way. Otherwise, we would be living on a planet of giants.

You can read the rest of the article here.

As is so often the case, I wish the article could have ended with a big fat asterisk, along with a footnote reading, "There's more to the story, but you'll have to visit The Loom for it."

This notion about size increase, known as Cope's Rule, has a long, checkered history, and this history say a lot about how the entire science of evolutionary biology has changed over the years. Cope's Rule is named after the American paleontologist Edward Drinker Cope, who made a careful study of the fossils of North America in the late 1800s. Cope belonged to the first generation of scientists who grappled with Darwin's Origin of Species, published in 1859. Its reception was decidedly mixed. On the one hand, Darwin was hugely successful in persuading scientists that life had evolved over a long period of time, thanks to the huge amount of evidence he marshalled fossils, embryos, and the distribution of living species. But Darwin didn't fare so well in his argument about what drove the evolution of life. He was trying to quash the popular ideas of Lamarck, who had offered two mechanisms for evolution. First, traits acquired over an individual's lifetime are passed on to its descendants. Second, life contains a mysterious force that continually drives it from lowly primordial slime towards higher levels. Darwin rejected both of these mechanisms almost completely, replacing them with natural selection.

This second argument did not fare as well in the late 1800s as the first. Many biologists came to see life as the product of evolution, but they saw evolution as the product of various Lamarckian, long-term forces. Cope was one of these scientists. He looked at the early mammals of North America--tiny creatures, for the most part--and saw that later they were replaced by much larger species. Here, he decided, was evidence of an evolutionary force that could operate over millions of years, a force, moreover that was separate from natural selection. Others found similar patterns in other groups, such as corals and foraminfera.

In the mid-twentieth century, evolutionary biology went through a revolution known as the Modern Synthesis. Scientists came to understand how genes mutate, and how mutations helped make natural selection possible. Leftover Lamarckism found no vindication of its own, and faded away. Biologists still accepted Cope's Rule as a genuine pattern in the fossil record, but they offered a different mechanism than Cope originally had. Instead of some mysterious long-term trend, good old natural selection was at work. Bigger individuals were favored in populations, and over millions of years, this edge produced bigger and bigger species.

In the 1970s, a group of young paleontologists challenged some aspects of the Modern Synthesis. They rejected the idea that every long-term pattern in the fossil record could be neatly explained by short-term natural selection. And Cope's Rule became one of their favorite targets. A trend towards bigger sizes could appear in the fossil record, they pointed out, even if natural selection didn't favor bigger individuals. Small species, for example, might be more likely to survive mass extinctions, and would thus have been more likely to found major new groups of species. Because they were small, their descendants couldn't get much smaller before they hit a minimum size limit. But they'd have plenty of room at the larger end of the spectrum. Even without an inherent advantage to being big, the lineage would gradually get larger.

Although a number of paleontologists were involved in this rebellion, Stephen Jay Gould was its most outspoken member. He made Cope's Rule a favorite object of his derision, a case study of how our subjective biases ("bigger is better") shape our interpretation of the natural world. And from the 1970s to the 1990s, he had pretty good reason to be scornful. The evidence for Cope's Rule turned out not to be all that strong. Or to put it more precisely, scientists who promoted Cope's Rule did not test it rigorously against other possible explanations.

My article looks at some recent research that gives it the careful look it demands. And, in something of a surprise, Cope's Rule is enjoying a renaissance. In most living populations of animals and plants studied so far, natural selection shows a strong preference for larger size. In rigorous studies of the fossil record, lineages of dinosaurs and mammals show signs of having evolved to bigger sizes over millions of years thanks to natural selection.

So was Gould wrong? Yes and no. Cope's Rule is not, as he claimed, a "psychological artefact." But there must be more to the story than natural selection favoring bigger indvidiuals. Otherwise, we'd live on a planet of giants. In my article, I mention a few possible forces that work against Cope's Rule. One that I didn't have space to mention is a force near and dear to Gould's heart: species selection. Just as individuals are favored or disfavored by natural selection, species may also undergo a selection of their own, with some species giving rise to more descendant species, while others go extinct. In the case of size, what's good for the individual may not be so good for the species.

Species selection has been kicked around for quite some time to explain why Cope's Rule hasn't made everything enormous. Recently, a nice study of fossils came out that supported the idea. Paleontologist Blaire Van Valkenburgh of UCLA and her colleauges have documented how big size may have doomed two groups of canids-the ancient relatives of today's dogs and wolves-in North America. In both cases, the canids evolved to larger sizes over millions of years, only to dwindle away to extinction.

As Van Valkenburgh and her colleagues pointed out in Science in October, small canids could have found enough energy in rabbit-sized prey and other foods such as fruits. But once the canids got above about forty pounds, they could no longer survive on this fare. They would spend more energy running after prey than they got eating them. As the canids got bigger, Van Valkenburgh argues, they shifted to hunting prey as big as themselves or bigger. Consistent with this hypothesis, Van Valkenburgh has found that as both groups of canids got large, their jaws and teeth also evolved. They lost molars, their front teeth got larger, and their jaws became stout and strong. This shift put these canids in an evolutionary trap. If their large prey became extinct, they risked starving to death. Nor could they re-evolve the versatile teeth and jaws that had allowed their ancestors to eat different sorts of food. They didn't go extinct because they were big; they went extinct because they were specialized.

Scientists I spoke to for this article were confident that Cope's Rule would figure in a lot of research in coming years. They've now got the tools they need to dissect long-term trends like never before--from databases of fossils to detailed evolutionary trees to sophisticated statistical methods. After more than a century, Cope's Rule still has plenty of life in it yet.

December 16, 2004

When It Pays To Be DumbEmail This EntryPrint This Article

Intelligence is no different than feathers or tentacles or petals. It's a biological trait with both costs and benefits. It costs energy (the calories we use to build and run our brains) which we could otherwise use to keep our bodies warm, to build extra muscle, to ward off diseases. It's also possible for the genes that enhance one trait, such as intelligence, to interfere with another one, or even cause diseases. Over the course of evolutionary time, a trait can vanish from a population if its cost is too high.

On the other hand, intelligence may offer some evolutionary benefits, by allowing us to find food, withstand the elements, locate the car keys our children have put in their dollhouses, etc. But it is by no means a given that intelligence is always a net plus. It all depends on the conditions in which we--and other animals--find ourselves in.

Scientists have come to appreciate how optional intelligence is through several sorts of experiments. Last year French scientists reported an experiment in which they bred fruit flies for their ability to learn. They would give the flies oranges and pineapples on which to lay their eggs, but they would dab one kind of fruit with a nasty tasting chemical. Some of the flies learned quickly to avoid the bad-tasting fruits, avoiding them even when the researchers didn't put the chemicals on them. These smarter flies were allowed to reproduce, passing on their learning genes to the next generation. (The researchers switched the bad taste between the fruits in each generation to make sure that the flies weren't simply evolving a distaste for oranges or pineapples.) This line of flies became significantly better at learning than their unevolved cousins in a few dozen generations. And in a reverse experiment, they succeeded in breeding stupid flies who did worse at learning than normal flies.

If it was so easy for the scientists to produce better learning in flies, why hadn't the ancestors of these insects already evolved this sort of intelligence in the wild? The answer is that this intelligence comes at a cost. The researchers put the larvae of the smart flies alongside some normal fly larvae and let them compete for a supply of yeast. They then counted how many of the larvae survived to adulthood. Then they did the same experiment with the dumb flies. They found that the larvae of smart flies are more likely to die off than the dumb ones.

Now comes another experiment in intelligence, this one conducted mainly by nature rather than scientists. Many of the streams that feed the Panama canal are inhabited by the same species of guppy, Brachyraphis episcopi. And in many of these streams, the guppies live in two different habitats: above and below waterfalls. Below the waterfalls, they face a lot of competition from other fish that are trying to eat the fruit and other foods that fall from the trees overhead, and they also have to cope with several predatory fish. But above the waterfalls the guppies enjoy a predator free existence. Researchers at the University of Edinburgh realized that this arrangement created excellent conditions for the evolution of different kinds of behavior within a species. Upstream guppies would not face the same evolutionary pressures that the downstream fish were. And if the researchers were right, they should find the pattern repeated in stream after stream.

The researchers netted guppies from four different streams, both from upstream and downstream populations. They then shipped the fish back to their lab in Scotland and tested their ability to make their way through mazes to find food. As they report in a paper in press at Behavioral Ecology, the fish from the low-predator upstream sites consistently outperformed their downstream counterparts. They figured out the mazes twice as quickly.

The researchers argue that the upstream fish do so well because they have been able to evolve a sort of single-mindedness. In the wild, the guppies appear to size up their stream and figure out the best place to wait for food to drop to the water. They head for that patch quickly and defend it from other guppies. This sort of learning translates well into a laboratory maze. The downstream guppies, on the other hand, would risk becoming easy prey if all they did were to search for the best patch of stream. Instead, they also have to get a better sense of their overall habitat, spotting predators, finding refuges, and so on. In the laboratory, they tended to explore more of the passageways of the maze than the upstream guppies, perhaps due to their instinct to get a lay of the land (or perhaps the lay of the water).

These results raise a sticky point about ourselves. They suggest that different populations of the same species (such as humans) can evolve differences in cognition in response to different environments. I don't think these results can be used to boost any notion of race-based difference in IQ, though, because we're not fish or laboratory fruit flies. I don't think the conditions that people in different parts of the world face are as different as these flies and guppies have faced. The most important lesson from these results, I think, is make us tone down our self-love a bit. Being intelligent does not make us superior to other animals. It only makes us superior in one respect.

December 13, 2004

Taking Crichton Down a PegEmail This EntryPrint This Article

The folks at Real Climate have hit the ground running. They carefully demonstrate how misleading Michael Crichton's new book State of Fear is on global warming. Let's hope they can keep this quality up.
December 10, 2004

Climate: A Promising BlogEmail This EntryPrint This Article

I just heard about Real Climate, a blog authored by some of the best climatologists in the business. The blogosphere has been flooded by awful gibberish about climate change that tries to make the most out of flimsy bits of research while making the least of the overwhelming scientific consensus. So I'll definitely be putting this one on my daily reading list.

Idealogy Versus IsotopesEmail This EntryPrint This Article

Imagine you're a columnist. You decide to write something about how the National Park Service is allowing a creationist book to be sold in their Grand Canyon stores, over the protests of its own geologists, who point out that NPS has a mandate to promote sound science. Hawking a book that claims that the Grand Canyon was carved by Noah's Flood a few thousand years ago is the polar opposite of this mandate. So what do you write? Well, if you're Republican consultant Jay Bryant, and you're writing for the conservative web site Town Hall, you declare that this as a clear-cut case of Darwinist atheists censoring freedom of speech in a desperate attempt to squelch Intelligent Design.

I don't blog much about science and politics, because I don't have the time and because others do it better than I could (see Chris Mooney and Prometheus for starters). But there's something so simple and basic about the Grand Canyon affair--with plain scientific fact on one side and eye-popping rhetorical nonsense on the other--that I can't help but register disbelief at it from time to time.

Hominid SculptureEmail This EntryPrint This Article

floresiensis.gifThe Australian media are doing a fantastic job of keeping up with the developments with Homo floresiensis. Here's the first three-dimensional reconstruction I've seen of the little hominid, made by an Australian archaeologist. It's published on the Australian Broadcasting Corporation's web site. I'm sure that as more bones emerge, the image will improve, but this is still a wonderful first look.

December 09, 2004

Bones on the LooseEmail This EntryPrint This Article

Homo floresiensis update: The Economist weighs in on the "borrowing" of the fossils. They mention that when the bones were removed, they were simply stuffed in a leather bag. This is not exactly the sort of procedure you see in protocols for avoiding contamination of ancient DNA. In the Australian, the discoverers of "Florence" vow to return to the fossil site, and this time they'll put their discoveries in a really good safe. Wise move.

December 06, 2004

Resurrecting GenomesEmail This EntryPrint This Article

mammaltree.gifIn tomorrow's New York Times, I have an article about how to reconstruct a genome that's been gone for 80 million years. The genome in question belongs to the common ancestor of humans and many other mammals (fancy name: Boreoeutheria). In a paper in this month's Genome Research, scientists compared the same chunk of DNA in 19 species of mammals. (The chunk is 1.1 million base pairs long and includes ten genes and a lot of junk.) The researchers could work their way backwards to the ancestral genetic chunk, and then showed they could be 98.5% certain of the accuracy of the reconstruction.

There are some pretty astonishing implications of this work. For one thing, it should be possible to synthesize this chunk of DNA and put it in a lab animal to see how it worked in our ancestor. For another, the scientists are now confident that they will be able to use the same technique to reconstruct the entire genome in the next few years, if the sequencing of mammal genomes continues apace. Could scientists some day clone a primordial Boreoeutherian? It's not impossible.

On the down side, this method will not work for just any group of animals you want to pick. Mammal evolution was rather peculiar 80 million years ago: a lot of branches sprouted off in different directions in a geologically short period of time. That makes the 19 species the scientists studied like 19 different fuzzy images of the same picture. Other groups of species had a very different evolutionary history, and one that may make genome reconstruction impossible. If you yearn for the day when Jurassic Park becomes real, you will have to conect yourself with a swarm of shrew-like critters. If they did somehow manage to break out of a lab, I suspect they would get eaten by the first cat to cross their path.

December 03, 2004

Hobbit UpdateEmail This EntryPrint This Article

The tension continues to mount over the locking-up of the Homo floresiensis fossils, according to this new article in the Australian. (via Gene Expression)