Blogs / The Loom

Last month I wrote in the New York Times about Spore, a highly anticipated game that let you follow life from microbe to intergalactic civilization. I had a couple evolutionary biologists play around with it to get their reaction, and contact a couple others who had had a chance to play the game. They gave it positive–though decidely mixed–marks. In today’s issue of Science, John Bohanon describes the reactions of a number of other biologists, and they really don’t like it at all. Here’s what Ryan Gregory has to say:

“The problem is that the game features virtually none of the key ingredients of evolution as we understand it,” says Gregory. “There’s no shared common descent between species, since every single creature in Spore can trace its lineage back to a different single-celled organism that arrives from space.” Spore also lacks biological variation. “When you run into other members of your species, they are always identical clones of you.” Nor does it have natural selection. “There are no consequences for dying, since you just reappear at your nest.” Your organism does evolve, says Gregory, “in the sense that it changes over time, but it really has no bearing on how things evolve in the real world.”

I believe the article is behind a subscription wall, but you can check out a wiki Bohanan set up for an in-depth report card.

The Boston Globe has set up an insanely beautiful feature called “The Big Picture.” Each week, they pick out a dozen or more stunning pictures on some topic and display them at huge size. The latest theme is “Earth From Above,” and the pictures are all from photographer Yann Arthus-Bertrand. I don’t know why, but this picture really spoke to me (click through for the full size shot). It’s a fresh expanse of lava in Iceland that has cooled down enough for moss and other organisms to colonize it. Life always finds a way.

We’ve cast our votes…and here are the winners. As a judge, let me extend best wishes to the winners and all the entrants to the National Academies of Sciences Communication Award.

Have you ever seen a fungus firing its spores to the tune of the Anvil Chorus from Il Travatore?

I’ll take that as a no.

Nicholas Money, an expert on fungi at Miami University, has been playing around with very fast video. Ultra fast. As in 250,000 frames-a-second fast. He knew exactly what this kind of video was made for. To film fungi that live on dung as they discharge their spores. These tiny fungi can blast spores as far as six feet away, boosting the odds that they’ll land on a clean plant that a cow or other grazing animal may eat. The fungi develop inside the animal, get pooped out with its dung, and fire their spores once more.

Money’s results were not just significant, but beautiful. The fungi fire their spores up to 55 miles an hour–which translates to an acceleration of 180,000 g. Money calls it “the fastest flight in nature.”

Money has just published his results in the journal PLOS One, and his students, in a justified fit of ecstasy, have created the first fungus opera. Behold:

I just found that Carl Sagan’s Cosmos, the 1980 TV series on life and the universe, is now on Itunes. You can get it here, at $1.99 an episode.

I’ve downloaded the first two episodes, which I don’t think I’ve seen since they first aired 28 years ago. I remember watching every episode intently as a 14-year old at the end of the Carter administration. The passage of time has revealed some hokiness around the edges.  The music, much of it by Vangelis, sometimes makes me think I’ve walked into a crystal shop. Sagan is fitted in corduroy blazers and what seems to be the precursor of the Members Only jacket. Some of the images still look good–like Sagan’s calendar of the cosmos–but there are also painfully long pans across a cardboard diorama of ancient amphibians, reptiles, and mammals. We are so spoiled today by Jurassic Park.

For some reason, what struck me as hokiest about Cosmos was the spaceship Sagan uses to coast around space to show off galaxies and pulsars. It is meant as a deeply profound experience–a voyage of the imagination across billions of light years (say it slowly, in proper Sagan style). But Sagan sits in a plastic bucket chair that survives today only in aging bus stations and flea markets.

The picture of science Sagan presents is also a bit too simple for my taste now (at least in the first two episodes I’ve watched again). He offers a black-and-white picture of science versus the forces of superstition, war, and other bad things. Greeks love knowledge, Dark Ages fall, Kepler rises! Only science will save us from the evils of nuclear war! Of course, Kepler’s discoveries were motivated by his mystical reading of the Bible. And, of course, science and war (hot or cold) have been intimately intertwined for the past century. The people who sacked the library of Alexandria did not build the atomic bomb. The generation of physicists who taught Sagan did.

But as I was tallying up the shortcomings of the show, something funny happened. My daughters, 7 and 4, are pretty well-trained now to stay out of the office. But as I was watching Cosmos on my computer, they snuck in and ended up sitting on my lap, captivated by the stately unwinding of DNA and the majestic trip through the cell. I could see they were starting to understand things that I’ve been trying to explain without much luck. In an age of hyper-fast editing cuts and soundtracks always turned to eleven, Cosmos can still mesmerize a child and give her an introduction to the natural world. Sagan’s accounts are sometimes a bit dated now, but nobody has done a better job of conveying a sense of the scale of nature, from that calendar to that bus-station spaceship to the dive into the cell–and it’s thanks largely to Sagan’s exceptional ability to talk about science in clear, even poetic terms. It is, I’m realizing, a show that shaped the way I look at the world, even now that I’m getting close to Sagan’s age when he filmed it. And for that, I can forgive any fashion faux pas.

This morning: grey clouds and low tide on White Island, home to an empty lighthouse, thousands of terns, and thousands more mosquitoes. And red algae.

George Orwell is about to start a blog.

I’m heading off to Appledore Island for a few blog-free days of yapping sea gulls and dissected sharks. I’ll schedule a few science tattoo posts for while I’m gone, but I will be mum till my return.

Last week I wrote about a talk by genome pioneer Craig Venter on the future of biotech, biofuels, and bio-everything. Here’s the talk, posted on Fora.tv. (Note to friends and family: the question at about 48:30 is from me.)

I’ve got a pretty lax attitude towards comments. Creationists are free to add theirs. But there are limits.

In response to a post on evolution Friday, the first comment I got a very long announcement about “A PARAGON OF SCIENTIFIC ACHIEVEMENT!” [sic]–a book that proved evolution was wrong. It came from someone named C. David Parsons.

Others responded.

Jeered might be the right word.

One commenter, named Paul Burnett, called Parsons sad.

And then someone named Steve Larimore attacked Burnett. “I’ll bet he’s never read the book. If he had, he would crawl back into the hole from whence he wonders out at night to do his evil deeds.”

A quick check of IP addresses revealed Larimore and Burnett Parsons share the same computer. Probably the same brain, I’d wager. In any case, that’s a bannable offense around here.

[Update–Sorry, Paul, for the typo]

I’ve been offered a few islands to do my work.

Craig Venter said this in passing, almost under his breath, as he spoke Wednesday night about the future of biology at the Oxonian Society in New York. It was a perfect Venterism. Venter, of course, is the scientist who declared he would lead a project to sequence the human genome faster, better, and much cheaper than the official government effort. He’s the guy who then had the audacity last year to publish the most accurate genome sequence to date–his own. He’s the guy who sailed around the world and trawled six million new genes, which he hopes to use to engineer a microbe that will overthrow the petroleum industry and save us from what he considers the biggest threat to civilization: global warming. He’s the one trying to synthesize a genome from scratch–what some might called creating life. That guy.

These audacious projects create a lot of attention for Venter. In fairness, Venter does not use that attention to give a snake-oil spiel. His talk probably surprised a lot of people in the audience, who may have expected lots of simple-to-understand, over-the-top promises about genome sequencing. In fact, Venter had a habit of slipping into tech talk, waxing rhapsodic about the restriction endonucleases that microbes use to cut up the DNA of invading parasites. But every now and then Venter allowed himself a touch of outrageousness. One questioner asked what was being done to make sure that no one went off and used synthetic biology for evil purposes, and mentioned the sci-fi clunker The Island, in which cloned humans are raised for body parts. Venter mentioned–in passive voice, of course–the offer of islands where he could do his research unpestered. We were all left, of course, with an image of Venter mysteriously at work out in the Carribean–perhaps doing his best impression of Dr. Moreau?

Actually, Venter doesn’t much like science fiction. When people asked about the ethics of cloning, he complained that people bring science fiction plots to the problem, imaginging things like armies of killer clones, destroying everything that came across their zombie-like march. He pointed out that the clones would be no more similar to one another than twins. In fact, he said, the problem isn’t that scientists are too wild in their ambitions. The problem is that they’re boring.

I assume he considers himself an exception. After all, during his talk, Venter sketched out a plan to copy genes from deep-sea microbes to produce organisms that could slurp up highly concentrated carbon dioxide and spew out hydrogen gas–killing two environmental birds with one stone by simultaneously providing clean energy and drawing down current levels of greenhouse gases in the atmosphere to more bearable levels. The first step towards this goal will be to compose a genome on a computer, synthesize it from scratch, and insert it into a microbe without killing it. I’ve been wondering when Venter will take that step (see my conversation with him last fall on Bloggingheads.tv). Back then, Venter said some time in 2008. During the Q&A after his talk, I asked how the experiment was going. He said he still hoped to finish it this year. I felt like such a nag.

The other audience members who asked questions, I noticed, were less interested in energy than in people. I guess we all want to understand ourselves, and think that a genome sequence will do the trick. For someone who has put so much effort into sequencing human DNA, Venter went to great lengths to downplay what genomes can tell us at this point. He considers gene therapy a bust at this point, based on a hopelessly simplistic notion of how the genome works. He doesn’t think a whole lot of personal genomes at this point, either. If you go to 23&me or some other personal genome sequencing company, they’ll look at 500,000 genetic markers in your DNA. That’s less than one-thousandth of your entire genome. What’s more, they’ll only zero in on a couple dozen genes in their report. It’s a good introduction to genomics, but not your inner book of life.

And when the subject of race came up, Venter went to great pains to explain why he was against race-based medicine. The color of a person’s skin is crude guide at best to the genome within. Last year, James Watson, the co-discoverer of the structure of DNA, said some outrageous things about race and intelligence. Venter came down hard against Watson (who later apologized). But apparently the two were still on speaking terms when Watson later discovered that his genes have some African ancestry. Venter described how he talked to Watson on the phone just after the story broke; Watson said he was looking at pictures of his grandparents and just couldn’t see it. Venter told him to get a paternity test.

Venter also had some news about Watson and himself. Watson, it just so happens, had his own genome sequence published last year by another group of scientists who work not far from me here on the Connecticut shoreline. At the talk, Venter described a paper coming out soon that details a comparison of the two men’s genomes. “My biggest fear was that we’d be too similar,” Venter joked.

But not to worry. Humans, Venter and other researchers are finding, are more genetically variable than the earlier estimates. Our DNA does not just vary letter by letter, but by entire genes–some of us are missing some genes entirely, and others have extra copies. Venter discovered that he has two copies of a gene variant that speeds up the metabolism of some toxins. Watson’s variants don’t. It turns out that Watson’s variants are very rare in people of European descent, but very common in China. He’s becoming a veritable melting pot.

[A producer from Fora TV told me they’ll be posting a video of the talk in a few days–I’ll embed it when it’s ready.]

Image PLOS Biology/Creative Commons License

Just a quick note: over to the right you’ll see a blog roll of some of my favorite blogs. I’m having a little trouble dumping all my favorite blogs at once into the right place on the back end, so I’ll just add them now and then. Today’s addition is a baby blog–The Rough Guide to Evolution. It’s by Mark Pallen, a British microbiologist and evolutionary biologist I’ve interviewed several times (see this National Geographic article for starters). You may also know Mark for his Origin of Species dub. Despite having his hands full (see image), Mark has just hammered out an eponymous book that will be published at the end of the year, and he promises to post on his blog every day till then…and beyond? Anyway–check it out.