The Loom

The Loom Ends. The Loom Lives!

Tue, 01 Jul 2008 09:00:00 -0500

Okay--after some technical difficulties I won't bore you by recounting, I have an announcement. For the third time in this blog's life, I'm packing it up and moving it to a new home.

I would like offer my deepest thanks to Scienceblogs for hosting the Loom for two years. I got to know a great community of bloggers whom I will continue to follow closely as they flood my RSS stream. Virginia Hughes, Katherine Sharpe, Tim Murtaugh, and the rest of the folks behind the scenes at Scienceblogs have been wonderful to work with, always ready to get me out of whatever programming mess I fall into while never trying to control the content of the blog.

I'm moving the Loom because I'm starting a new incarnation as a columnist for Discover. Each month I'll be writing a column about the science at the intersection of brain and mind. Along with my column, I'll be joining some other excellent bloggers on Discover's web site, including Phil Plait at Bad Astronomy.

The new incarnation of the Loom will still contain its four-year archive of everything you've read before. And I will continue to blog the same disheveled mix of natural history, parasitic lore, evolutionary biology, and whatever else I find intriguing at the moment.

So goodbye, and hello.

The News Can Wait

Mon, 30 Jun 2008 23:22:46 -0500

Really, it's not like I've discovered a new element or anything. See you tomorrow.

Almost Ready...

Mon, 30 Jun 2008 17:06:07 -0500

...to spill beans. Any minute now, honest.

Some News...

Mon, 30 Jun 2008 01:12:49 -0500

...at 5 today. [That's 5 pm EST--sorry for the confusion.]

[Hint...I've turned off the comments till then.]

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A Tapeworm Mystery: Which Way Is Up?

Sat, 28 Jun 2008 23:36:53 -0500

I'm sure you'd like to pretend that you have nothing in common with a tapeworm.

A tapeworm starts off as an egg which then develops into a cyst. Inside the cyst is a ball-shaped creature with hooks that it can use to crawl around its host before growing into an adult. Many species are made up of dozens or hundreds of segments called proglottids. Each proglottid may be equipped with both eggs and sperm-making organs. As an adult, a tapeworm also grows a head-like end often equipped with suckers or hooks of its own. This strange organ is called the scolex. (The shark tapeworm in this photo is displaying its fearsome scolex.) While the tapeworm lives in the gut of its host, it uses its scolex to clamp down in place, although it may swim around to find an ideal spot from time to time.

And from time to time, a proglottid breaks off from the body of the tapeworm and ends up leaving the body. Actually, it can leave under its own steam. Proglottids have muscles and nerves that they can use to crawl out the back end and along the ground.

Tapeworms evolved from free-living flatworms, but they have undergone some radical changes. Along with the evolution of their proglottids, they also abandoned their digestive tract, opting instead to slurp up their food directly through their skin. They're so weird now that scientists haven't even been sure which end is which. Some people have suggested the scolex is the head of the tapeworm. But others have pointed out that while the tapeworm is still in its cyst, the hooks actually form on the other end of its body. What's more, in related flatworms with recognizable heads and tails, the sperm-organs are closer to the head than the ovaries. In tapeworms, the ovaries are closer to the scolex.

This morning at the second day of the American Society of Parasitologists, Peter Olson from the Natural History Museum in London, offered a potential solution to the puzzle. All animals--including us--use a set of master genes to determine the head-to-tail anatomy of developing embryos. The precise DNA sequence of these genes is different from species to species, but they show clear evidence of having evolved from a set of genes in a distant ancestor. Scientists have carried out most of their research on these genes in well-studied species like fruit flies and mice. Only recently have scientists started to look at how these so-called Hox genes work in other animals. Olson is studying the genes in tapeworms that live in mice, called Hymenolepis.

One key gene Olson described is called Post-2. It corresponds to genes that defines the tail end of insects and mammals. When tapeworms develop into little balls with hooks, Olson has discovered, Post-2 becomes active on the end of the ball with the hooks. That suggests that the hooks are growing at the tail-end of the animal, before it has yet grown a tail.

Later, when the tapeworm develops into an adult with proglottids, Post-2 becomes active at one end of each segment. It becomes active at the end furthest from the scolex. So the tail end of the animal appears to be pointing away from the scolex--in other words, the scolex really is the head after all. It may not be a head you're familiar with--sans teeth, sans eyes, sans taste, although not quite sans everything. But when the tapeworm grew its head, it knew where it was the same way you knew when you grew yours.

[Edited a bit to address questions from commenters.]

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Microcosm in tomorrow's New York Times Book Review

Sat, 28 Jun 2008 13:22:45 -0500

Science writer Peter Dizikes reviews my book Microcosm for the New York Times. It's great to see that he gets it--i.e., he understands what I'm trying to do with E. coli in the book. I actually appreciate that more than a positive review. Fortunately, he liked the book, too, calling it engrossing, vivid, and adroit. Check it out.

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A Talk With Paul Ehrlich About The State of the World

Sat, 28 Jun 2008 09:00:41 -0500

I'm back on bloggingheads.tv, talking this week with Paul Ehrlich about everything from climate change to Polynesian canoe oars to the origins of human culture to why cars are best for teenagers to make out in. Check it out.

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Nice and Weird: Dispatches from The Depths of Parasitology

Fri, 27 Jun 2008 18:51:29 -0500

It feels like a homecoming: I'm among hundreds of people who live for parasites.

I arrived in Arlington Texas this afternoon to attend the annual meeting of the American Society of Parasitologists. I'm going to give a talk tomorrow about the public awareness of parasitology, talking about my long-term relationship with the beasties in books, articles, blogs, and beyond. But till then, I get to hang out with parasitologists. I've met a lot of the people here over the years, like the leech-master Mark Siddall, and I've read the work of a lot of people I'm just meeting (work on things like how lice jumped from gorillas to human ancestors).

And I'm also hearing new people talking about research I've never heard before--"nice and weird," as one parasitologist described the species she studies. I heard about a parasite in Nebraska, a flatworm called a trematode (Halipegus eccentricus), that scientists discovered living in the ears of bullfrogs. But the trematodes in their ears are all adults. Matt Bolek from the University of Nebraska described how he and his colleagues had figured out the rest of the parasite's life cycle. The parasites release their eggs from the frog ears, which then get scarfed up by snails, where they hatch and start to develop. Then they leave the snails and swim in search of little aquatic invertebrates called ostracods. The ostracods get eaten by the larvae of damselflies, which then mature and fly into the air, only to be devoured by frogs. The parasites escape the damselflies and move through the bodies of the frogs to their ears. One trematode, four hosts.

And you thought your commute was long.

Tomorrow I'll blog about more of these marvelous beasts.

[Image courtesy of Matthew Gilligan]

[Update: In answer to commenters--that's an invertebrate known as a isopod that's eaten the fish's tongue and is now sitting where the tongue used to be. Nice and weird, baby.]

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The Ten-Mile-Wide Bullet

Thu, 26 Jun 2008 12:38:22 -0500

In 1980, Walter Alvarez, a geologist at the University of California, Berkeley, and his colleagues proposed that the dinosaurs had been exterminated by an asteroid that smashed into the Earth. I was fourteen at the time, and that mix of dinosaurs, asteroids, and apocalyptic explosions was impossible to resist. I can still see the pictures that appeared in magazines and books--paintings of crooked rocks crashing into Earth, sometimes seen from the heavens, sometimes from the point of view of an about-to-become-extinct dinosaur. Suddenly the history of life was more cinematic than any science fiction movie.

By luck rather than foresight, I eventually became a science writer. I had the good fortune to start the job in the early 1990s, as the impact story was still unfolding. Until then, I knew Walter Alvarez only as a name on a page. Now I could call Alvarez and talk to him about new evidence other scientists were finding to support his impact hypothesis--evidence showing not only that the impact did come at the end of the Cretaceous period, but even revealing where it hit: a site called Chixculub, along the coast of the Yucatán Peninsula. "It ties everything together," Alvarez told me with delight in 1991. I had the wonderful privilege of watching the story continue to develop--as a bull's-eye ring a hundred miles across came to light under the Gulf of Mexico, as a piece of the asteroid itself was fished from the Pacific.

By 1997, the story had matured enough that Alvarez himself was ready to offer a firsthand account in T. rex and the Crater of Doom. It is an intimately readable look at how great science gets done. Scientists notice odd things that seem out of place, they contemplate ludicrous hypotheses, and then they doggedly test those hypotheses for years. T. rex and the Crater of Doom illustrates an important rule about science: some of the most revealing discoveries come not from deep within a single discipline, but at the borders between disciplines. The impact hypothesis would probably have come to nothing if not for the combined efforts of experts on everything from geochronology to pollen fossils to nuclear explosions.

That's the beginning of my foreword to Princeton University Library's new edition of Alvarez's book. I've posted the entire introduction here.

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Reminder: I'm talking tonight in Los Angeles

Wed, 25 Jun 2008 05:38:42 -0500

I'm bound for LA today to talk about Microcosm. My talk is part of the Zocalo lecture series. I'll be talking tonight at 7:30 pm at the Skirball Cultural Center. Here are the details.

Of Bacteria and Throw Pillows

Tue, 24 Jun 2008 21:05:04 -0500

The strange thing about E. coli, as I explain in my book Microcosm, is that it has played a central part not just in the modern science of life, but in the political conflicts over life. It may come as a surprise that a humble gut germ could get involved in culture wars. But you need only consider how much attention creationists have been lavishing on E. coli in recent years, hoping to use it as evidence that life did not evolve--that it was created or designed instead.

Originally, creationists claimed that structures in E. coli showed clear evidence of being created--they were complex, made up of lots of parts, and seemed to work like manmade machines. The flagellum--the tail E. coli spins hundreds of times a second--was one of their favorite examples. It reminded them of car engines, of outboard motors. This sort of thinking reached its climax a couple years back in the Dover Trial, in which parents claimed their school board was introducing religion into school in the guise of "intelligent design." One lawyer joked that it should have been called the Flagellum Trial. In journalist Lauri Lebo's excellent new account of the trial, The Devil in Dover, she recounts how one of the plaintiff parents came dressed as a flagellum, with a little tail poking out of her pants.

The school board lost, and in the scientific arena--where scientists publish their experiments in peer-reviewed journals--so have the advocates of a designed flagellum. The evolutionary history of the flagellum is becoming increasingly clear as scientists discover related copies of flagellar genes in other structures. But there are still people ready to sell you an intelligently designed flagellum throw pillow (or beer stein or apron).

Now E. coli poses a new quandary for creationists. As I wrote earlier this month, scientists at Michigan State University have been tracking the evolution of E. coli in their lab for 20 years. They've been experiencing natural selection as they've adapted to this environment, and in one of the twelve lines of these microbes, the bacteria evolved the ability to digest citrate. The lack of citrate metabolism has been, till now, a hallmark of E. coli as a species. The scientists don't know precisely how the bacteria evolved this capacity, but it appears to have involved a series of mutations that happened over several thousand generations.

This new paper has apparently touched a creationist nerve. There have been two sorts of responses. One has been to downplay the finding. Unless E. coli actually evolves into a human being in front of someone's eyes, then its evolution is insignificant. "It's important for us all to remember that when we read science news that seems to 'confirm' evolution, it's never a true threat to the biblical worldview and the creation account because God's Word never changes but man's fallible ideas do," Answers in Genesis consoles us.

Some have responded by suggesting there must be some mistake in the experiment, perhaps even fraud. Perhaps there was some contaminating DNA that endowed the bacteria with the ability to feed on citrate, for example. Andrew Schlafly, who runs a site called Conservapedia that's supposed to be a conservative alternative to Wikipedia, wrote a letter to the senior author on the E. coli, Richard Lenski. He demanded that Lenski "post the data supporting your remarkable claims so that we can review it."

Lenski responded politely at first that as far as he could tell, the relevant data Schlafly wanted was in the paper, which Schlafly had not bothered to read closely. When Schlafly repeated his demands--and as the discussions on the Conservapedia site veered to accusations of Piltdown-Man-level fraud--Lenski wrote a barbed reply that's definitely worth reading in full. You can see the whole correspondence at Panda's Thumb or Bad Science.

It is surreal to watch people with Conservapedia claim to be champions of science. Conservapedia has a densely detailed entry for Young Earth creationism, and another for Flood Geology. But their entry for Big Bang Theory is tiny--and taken up in large part by the objections of creationists. The entry for parasites informs us of the young Earth view that parasites are the result of Adam's sin. What's not surreal is to see E. coli at the eye of the storm. It's business as usual for the little bug.

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On the Radio Today: Mass Extinctions, Past and Future

Tue, 24 Jun 2008 10:18:36 -0500

At noon EST, I'll be talking on "Word of Mouth," a radio show coming from New Hampshire Public Radio. The topic will be my recent article on global warming and mass extinctions in Yale Environment 360. You can listen live (look for the mp3 stream here, or look for a podcast on the show page.)

My Microbial Muse

Tue, 24 Jun 2008 09:09:42 -0500

The British edition of Microcosm is coming out on July 3 (Brits can pre-order here, and here's a link for Americans). In conjunction with its publication, the Telegraph asked me to explain why I love E. coli so. Here's why.

Microcosm Infects The Journal Science

Mon, 23 Jun 2008 12:02:53 -0500

It's nice to get book reviews in both the popular press and academic journals. I hope everyone will read my books, but I also hope that scientists will consider them good science. And, speaking of Science, the journal of said name just published a lovely review of Microcosm by the evolutionary biologist Daniel Rankin:

A popular science book on E. coli may not sound like the most interesting read. However, Microcosm is just that. The next time you hear of an outbreak of nasty E. coli on the news, spare a thought for this minute creature, which has arguably helped advance humanity far further than any other organism. Not only has it inhabited human guts for as long as we have existed, it has benefited almost all areas of the biosciences, from genetic engineering to evolutionary theory. To really understand life, it seems we must pay close attention to this bug's life.

Source: "Learning Much from a Bug's Life."

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The Octopus: Smart, Dumb, Other?

Sun, 22 Jun 2008 23:50:44 -0500

I've been pretty quiet on the blog while I've been off visiting grandparents in other states this past week. But in the meantime, Slate has published a piece I wrote for them on the beguiling mystery of octopus brains. I wonder if this guy would find it enlightening.

Update: A couple readers pointed out to me that I should have said octopuses jet water, not air. Sorry for the slip--it should be fixed shortly.

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