A press release turned up in the comments for a couple of my posts. While that's not as bad as Viagra-ad spam, it's not in the spirit of blogosphere. If you post a press release, it will be deleted. Post a comment in your own words, and it will stay.
One of the most exciting lines of research in evolution today is how parasites have become so good at making us sick. A case in point appears in the latest issue of Genome Biology (full text of paper here). It appears that parasites have stolen one of our best lines of defense and now use it against us.
When bacteria or other pathogens try to invade our bodies, we marshall an awesome system of biochemistry to ward them off. Recently, a group of French and German molecular biologists took a look at a key piece of that system, a molecule studding the surface of our cells called alpha-2-macroglobulin. Parasites penetrate a host cell by releasing enzymes that can punch a hole through the cell wall. But alpha-2-macroglobulin can snag these enzymes before they do damage, tucking them away in a cage where they can be destroyed.
You can find the gene for alpha-2-macroglobulin not only in humans but in other animals. The French and German researchers have identified a number of other versions of the gene in invertebrates by trawling through genome databases, looking for sequences that are similar to the alpha-2-macroglobulin gene. In some cases, other animals have evolved much more sophisticated variations on this particular defense than we have. Mosquitoes, for example, use 15 different versions of the gene. When you suck blood for a living, there’s a high premium on eradicating the parasites you slurp up as well.
It is now clear that the common ancestor of all animals on Earth evolved an ancestral version of alpha-2-macroglobulin, which was then passed down and gradually altered over a billion years of animal evolution. But the European researchers found some surprises as they hauled up their genomic nets. They found many versions of the alpha-2-macroglobulin gene in bacteria as well. Not in all bacteria, mind you, but in a wide range of species, most of which live inside animals. When the researchers looked at a family tree of bacteria, the ones carrying versions of alpha-2-macroglobulin were scattered across its branches. In many cases, their closest relatives lacked the gene.
Here’s the hypothesis that the researchers came up with to explain this weird pattern. An early animal equipped with alpha-2-macroglobulin was infected with a bacterium. The microbe accidentally acquired the animal gene and wove it into its own genome. (This has been documented happening many times among bacteria. They can scoop up genes from dead microbes, and viruses hopping between bacteria can deliver genes as well. But the exchange from animals to microbes hasn’t been studied very well till now.)
The stolen alpha-2-macroglobulin gene turned out to give the pathogen an advantage over others that lacked the gene. Specifically, it was able to use this host-defense molecule to defend itself from the host. It just so happens that animals also use enzymes to punch holes in the cell walls of their enemies. But while bacteria punch holes to invade a cell, animals do so in order to rip open pathogens and kill them. After one species of bacteria stole the alpha-2-macroglobulin gene from animals, it began to use the gene to trap their host’s hole-punchers. Later, it handed off the gene to other species of bacteria also living in animal cells. They also used it to defend themselves against their hosts.
The scientists point out that they still have to rule out the possibility (unlikely as they consider it) that the transfer went the other way: that animals acquired their alpha-2-macroglobulin defense from bacteria. But there’s a straightforward way to do that. They need to make a large-scale comparison of the version of the gene in bacteria, as well as in animals. If they’re right, then the tree will show that all of the bacterial versions descend from animal versions of the gene. If they’re wrong, the opposite pattern will emerge.
Either result would, however, point to one important conclusion: gene-swapping has been a big deal in the history of life. Scientists have known for a long time that it’s important for the rise of antibiotic resistance in bacteria. They’ve also known that the energy-generating mitochondria of our cells are actually captured degenerate bacteria. But it was hard to know how important gene-swapping was beyond these examples until entire genomes became available for study. When scientists first began to analyze genomes for evidence of gene-swapping, they sometimes claimed evidence for it that disappeared when more data came in. The most glaring example came in 2001, with the publication of the rough draft of the human genome. The authors of the draft claimed that a few percent of the human genome consisted of genes imported from bacteria. A comparison with more genomes later showed that this was not true.
The Genome Biology paper is an example of today's more thorough tests for gene-swapping. (In this case, they studied 32 species of bacteria, not to mention a wide range of animals.) It’s also an example of why this sort of research matters. Bacterial versions of alpha-2-macroglobulin could become excellent targets for drugs that would prevent the microbes from defending themselves against our hole-punching.
I always like book reviews that combine books that might not at first seem to have that much in common. In the new issue of Natural History, the neuroscientist Williams Calvin reviews Soul Made Flesh along with The Birth of the Mind, a fascinating book by Gary Marcus of NYU. If you haven't heard of Marcus's new book--which explores how genes produce minds--definitely check it out.
Do you know who George Williams is? If you don't, let me introduce you to one of the most influential evolutionary biologists ever to ponder natural selection. If you do know who he is, you may still be interested in my article in this week's Science about a symposium that was recently held in Williams's honor. Scientists studying everything from pregnancy to economic decision making explained how Williams's remarkably clear thinking about the nature of adaptation helped them in their research.
A pdf of the article is also available.
It's strange enough hearing yourself talking on the radio. It's stranger still to see a transcript someone makes of you talking on the radio. Recently I was interviewed about Soul Made Flesh on Australian Broadcasting Corporation's show "All in the Mind." Instead of an audio archive, ABC has posted a transcript of the show. While I can't claim I spoke in perfect paragraphs, we had an interesting talk about how the brain became the center of our existence.
I was asked a couple weeks ago to contribute a piece to a special series of articles in Newsweek about the future of Wi-Fi. I must admit that a fair amount of the stuff that's on the Wi-Fi horizon seems a little banal to me. It's nice to know that I will be able to swallow a camera-pill that will wirelessly send pictures of my bowels to my doctor, but it hardly cries out paradigm shift. On the other hand, I've been deeply intrigued and a little disturbed by the possibility that the next digital device to go Wi-Fi is the human brain. Here's my short essay on the subject.
Please accept my apologies for the vile spam comments that keep showing up here. I hope that the folks at Corante and I can find a way to permanently shut down the flow of craven obscenity.
I've been traveling again, and now I'm racing against a slew of deadlines, which leaves precious little time to blog. I hope to get back in the swing next week. More blogging, less spam is my goal for the Loom.
Jack Szostak, a scientist at Harvard Medical School, is trying to build a new kind of life. It will contain no DNA or proteins. Instead, it will based on RNA, a surprisingly mysterious molecule essential to our own cells. Szostak may reach his goal in a few years. But his creatures wouldn't be entirely new. It's likely that RNA-based life was the first life to exist on Earth, some 4 billion years ago, eventually giving rise to the DNA-based life we know. It just took a clever species like our own to recreate it.
My cover story in the June issue of Discover has all the details.
On the east coast, we're bracing for the howling emergence of a massive brood of 17-year cicadas in a couple weeks. Here's a nice piece in the Washington Post about the evolution of this strange life history.
There are only a few places on the surface of Earth where you can find really old rocks--and by old, I mean 3.5 billion years old or older. The rest have gotten sucked down into the planet's interior, cooked, scrambled with other rocks, and pushed back up to the growing margins of continental plates. The few formations that have survived are mere fragments, some the size of a football field, some a house. And generally they're are mess, shot through with confusion such as intrusions of lava from more recent volcanoes. Paleontologists are drawn and repulsed by these rocks, because they may hold the oldest clues about life on Earth, or lifeless mirages that only look like clues.
In the past couple years, scientists have been putting the oldest evidence of life on Earth under tough scrutiny. The oldest fossils, 3.45 billion year old bacteria from Western Australia, have been attacked as mere crud. Life not only leaves fossils behind but also can create peculiar ratios of isotopes in rocks. The oldest isotopic evidence for life came from 3.8 billion year old rocks in Greenland. But that also came under attack by critics who questioned whether the rocks were actually sedimentary (and thus might contain biological material) or belched up from a very nonbiological volcano.
This does not mean that the fossil record has collapsed down to yesterday’s road kill. In other parts of Greenland, scientists have found slightly younger rocks (if you can call 3.7 billion year old rocks young) that are almost certainly sedimentary. And they contain a clear isotopic signature of life. The Danish geologist Minik Rosing, who has studied the rocks, argues that this particular fingerprint is so detailed he can tell what kind of life produced it: photosynthesizers. That's tantalizing for several reasons. One is that photosynthesizers give off oxygen, and yet there’s no record of any signifciant levels of oxygen in the atmosphere for well over a billion years after Rosing’s rocks formed. Another is that the early Earth may not have been a very friendly place for photosynthesizers—the oceans were hot and loaded with nasty metals.
The controversy over ancient fossils has forced some paleontologists to look for new kinds of evidence of life. For example, some bacteria can eat through glass, leaving behind microscopic pits. Volcanoes form glassy rocks such as obsidian, and in recently formed volcanic rocks sicentists have found tunnels that seem to have been created by hungry microbes. (They're even slathered with DNA and other biological material.). Today in Science, researchers reported that 3.5 billion year old rocks from Zimbabwe bear the same sorts of tunnels. They're also slathered in organic carbon with an isotopic fingerprint that looks like life. The evidence has impressed some researchers, but others are still skeptical. The possibility that these formations are formed without the help of microbes hasn't been eliminated yet.
I find all this work fascinating, but in one fundatmental way it's a bit pedestrian. These scientists are looking for the earliest signs of organisms that resemble organisms alive today, looking for the traits that are common to both. But a photosynthetic or glass-chewing bacterium is already pretty nicely evolved. Someday, a clever paleontologist is going to figure out how to identify something that no longer exists on Earth, such as an RNA-based organism. That discovery will push the fossil record back to a different chapter altogether in the book of life.
My book Soul Made Flesh looks at the roots of neuroscience in the 1600s. The first neurologists saw their work as a religious mission; they recognized that it was with the brain that we made moral judgments. In order to finish the book, I looked for living neuroscientists who carry on those early traditions today. I was soon fascinated by the work of Joshua Greene, a philosopher turned neuroscientist at Princeton. Greene is dissecting the ways in which people decide what is right and wrong. To do so, he poses moral dilemmas to them while he scans their brains. I mentioned Greene briefly in Soul Made Flesh and then went into more detail in a profile I wrote recently. Greene and I will join forces tomorrow on the show “New York and Company” on WNYC tomorrow around 12:30 pm. You can listen to us on the radio or on the web.
John Maynard Smith has died.
While many people know who Stephen Jay Gould was or Richard Dawkins is, I’d bet few would be able to identify Maynard Smith. That’s a shame, because he played a key role in building the foundations of modern evolutionary biology. (Underlining this point, I only learned about his death from Science's online new service. As far as I can tell, no one else has run an obituary.)
Maynard Smith came to evolution from a previous career as an engineer. In World War II he measured the stress on airplane wings. When he moved to evolution, he brought with him a gift to see the mathematical underpinnings of things, whether they are bridges or botflies. (An awful lot of creationists are engineers, for some reason; they would do well to consider Maynard Smith’s example.)
Maynard Smith saw evolution as a very complex mathematical equation that played out over time. Genes spread or faded depending on their fitness, which depended in turn on changes in the environment. Maynard Smith came up with brilliant new formulas to describe that change, in some cases borrowing methods from other disciplines. For example, economists have delved deep into game theory over the years, working out the ways in which players with different strategies can wind up winning or losing. Maynard Smith had the brilliant idea of apply game theory to evolution. The players in his game might be a population of elephant seals, each with its own genetically determined strategies for finding a mate. Different strategies would have different levels of success. One strategy might be to confront the biggest male on the beach, drive him away, and take his harem. That might work if a male was also big, but if he was small it was a strategy doomed to failure. So perhaps instead he might skulk at the edges of the colony and mate secretly with females from time to time, trying to avoid getting killed by the harem leader. It’s not a solution guaranteed to produce a lot of kids. But Maynard Smith showed that it’s also not necessarily a one-way ticket to extinction. Instead, it’s possible that the two strategies, one dominant and one minor, can come to a stable coexistence.
Scientists have found lots of these so-called evolutionarily stable stategies. Some male salmons who take the sneaky route actually commit their whole bodies to the strategy. Instead of bulking up their bodies and developing big sexual displays such as long jaws, they become small and invest their energies into growing massive testes that give them a large enough supply of sperm to make the most of their few tristes. Some evolutionarily stable stragies cycle from prominence to rareness and back over time, in a sort of rock-scissors-paper game. Bacteria may reach evolutionarily stable strategies that leave some of them killers and others harmless. Evolutionary stable strategies may have a lot to tell us about human behavior as well. Genes have a role in personality, intelligence, and behavior, and there’s obviously a lot of variation in all these factors. It’s possible that these genes have, over millions of years, reached an evolutionarily stable state with one another. And these games may also be a model for how something as peculiar as cooperation evolved in our own species. (You can read a good recent review of evolutionary games written by Martin Nowak here.)
Maynard Smith realized that some of the equations that he developed for these sorts of social interactions might also carry over to more fundamental questions about the evolution of life. When life was just getting started on Earth, for example, genes might have settled into certain strategies for getting replicated—arranged on chromosomes, for example--in the same way animals settle into strategies for surviving. Maynard Smith came to see the history of life as a series of transitions to new ways of processing information--from the origin of life to the first sexually reproducing cells to the appearance of multicellular life to the emergence of animal societies, and finally, human language and culture. Each new transition created a new playing field for a new set of games.
All this may sound a bit daunting, but Maynard Smith was gifted with a disarmingly simple way of explaining his ideas. Check out his final book, The Origins of Life, to see what I mean.
Update 4/22: The obits are emerging now.
Update 4/23: The definitive JMS site. Via Panda's Thumb.
No, I didn’t get hit by a car. Instead, I got hit by your typical crush of deadlines, traveling, and a bout of laryngitis. But tranquility is returning, and I’m firing up the blogotron again.
This week I am in England to give some talks about Soul Made Flesh, which has just been published here. In addition to talking on the BBC, I'll be talking at Blackwell's in Bristol on Tuesday, and at the Museum of the History of Science at Oxford University on Wednesday. I've posted details and links to even more details on the talks page of my web site.
It's a bit daunting coming here, the very place where much of my book is set. But the response has been kind so far. This morning the eminent historian Lisa Jardine wrote a generally good review in the Sunday Times. Meanwhile, stateside, another Brit (Adam Zeman) wrote a positive review in The New York Times Book Review.
While I'm here, I hope to have a little spare time to blog a bit on some interesting new research (and fisk the latest creationist shenanigans). If logistics get the better of me, I'll definitely get back on track next week when I get home.
I'm in Cambridge at the MIT/Harvard Brain Boot Camp this week, so blogging will be light for a few days.
Rowland Institute Library Blog: creating life with RNA molecules?
Les Jones Blog: John Maynard Smith RIP
Gene Expression: JM Smith dies
idiolect.org.uk: The Panda's Thumb
Muck and Mystery: Own Goals
The Panda's Thumb: A very groovy brain gene
Tom H. on Battle of the Hole Punchers
Paul Orwin on Battle of the Hole Punchers
Carl Zimmer on Mister Adaptation
Joe Dunckley on Mister Adaptation
Van Aurum (Aurangzeb) on Right and Wrong and Radio
the bunyip on Mister Adaptation
