In the new issue of Smithsonian, I've got an article about life on Mars. I'm not writing about anything NASA has actually found, but instead about the difficulty of just recognizing life, even if the evidence is in your hand (or in your rover's spectrometer). While the chances of life existing today on the surface of Mars aren't fantastic, a lot of researchers are pretty optimistic that there are fossils to be found. But it turns out that fossils of microbes are even more difficult to identify. You just need to consider some of the fierce debates over some of the oldest fossils on Earth--a topic I've written about before on the Loom here.

Some magazines will only let you see their articles on-line if you subscribe. Sometimes you can read the text for free. Smithsonian, incredibly enough, puts pdf's of their articles online for a month. So if you want the full magazine experience coming out of your own printer, here's your chance. (Just be sure to scroll down to the bottom of the page.)

Update 10 AM: Drat. For some reason the pdf file is not linked. I will see if they plan on making it available and post another update when they do.

Update 10:30 AM: Now the link works, but the pdf is just text. Probably a copyright issue. Oh well. Perhaps my prose will be enough...

If anyone else is interested in sponsorship, and thereby reaching an incredibly desirable demographic (my dear readers), let me or the good people at corante.com know.

In tomorrow's issue of the New York Times, I have an essay that grew out of a meeting I went to earlier this month on natural history illustrations through the ages. The essay is accompanied by some of the cooler images I saw there, some of which are also included in the web version. Here's one that wasn't--one of the first illustrations of the legendary Victoria Regia water lily, so big that a single leaf could support a grown man. I explain in the essay why this picture was the 1854 equivalent of a high-resolution digital scan.

It's obvious from yesterday's vote that embryonic stem cells will continue to split the country (California versus Washington DC, for one thing). But in an ironic bit of timing researchers at the Reproductive Genetics Institute have just published some results at Reproductive BioMedicine Online that could--possibly--short-circuit some of the arguments against using embryonic stem cells.

The RGI researchers have figured out how to derive stem cells from a four-day old embryo--a stage known as a morula. Until now, scientists have been using older blastocysts, and have been destroying them in the process. But when the RGI team took a single cell from a morula, it still had the capacity to develop into a normal embryo. That means that parents who are doing IVF could conceivably agree to have a cell removed from their morula, which could then give rise to a line of stem cells, while the morula developed into an embryo ready for implanting. The stem cell line could be banked for therapy, or used for research.

I first read about this in an article published yesterday on News@Nature.com (unfortunately the article requires a subscription). Neither the article nor the abstract I linked to makes it clear whether this could be a viable source of stem cells for the large-scale research that scientists really want to do. But the results are enough to inspire a thought experiment.

Let's say you object to stem cell research because each blastocyst is a unique human being with a unique genome and the capacity for life. Destroying one is therefore murder. Would this "morula method" be acceptable to you? It seems like it has the benefits of adult stem cell research (no controversry over destroying embryos) and the benefits of embryonic stem cell research (the possibility of discovering therapies that can't be derived from adult stem cells). Or does any tinkering with embryos set off alarms? Perhaps we'll find out in a Senate hearing.

I've written a piece for Newsweek about how to program a cell. (The Newsweek International edition comes out this week; the US edition comes out next week.) I find the ongoing research exciting, but sometimes I wonder how much of its promise will become real. Programmable cells, for example, are an illustration of the exciting frontiers that can be explored with stem cells. It may be possible to wire the genetic circuits of a stem cell to make it grow into a particular sort of organ, produce a certain sort of hormone, etc. But it's hard to see how any of that will come to pass if stem cell research withers on the vine. And when I look elsewhere in this week's issue of Newsweek and see how we can't even handle flu vaccines, my hope for medical progress in general starts to dim.

Hope springs eternal, though.

See you September 13.

After a couple months of merciless story deadlines, hard disk crashes, and strange viruses that you only find out about once you have kids, the Loom is creaking back to life. Expect several postings this week. For now, let me direct you to a review I wrote a couple weeks ago for The New York Times Book Review about Devil in the Mountain, a book about the Andes. The author, an Oxford geologist, dissects these mountains like a surgeon cutting open a living person. It reminded me of the times I've driven around with geologists; all of the landscape that blurs past most of us is a vast palimpsest to them, and waving their hand out the window, they tell you about hundreds of millions of years of mountain building and destruction. Short of grabbing a geologist for a ride, I'd suggest getting the book.

Chris Mooney has just blogged on a depressing new report that came out today that documents how the Bush administration puts politics before science.

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.

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.

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.

I'm in Cambridge at the MIT/Harvard Brain Boot Camp this week, so blogging will be light for a few days.

The Austin Chronicle has an interesting piece today on blogs, which marks the first time anyone's ever interviewed me about the Loom. Conclusion: no money, uncertain future, but much fun.

Check out Chris Mooney's post on the latest move in Washington to gut government science, which cloaks itself in bogus terms like "sound science." This dreadful campaign probably won't get much attention in the national media, but its effects--on conservation, climate change policy, and so on--could be profoundly bad.

Based on some feedback from subscribers and my own nosing around, I've decided to switch the subscription system to Bloglet. While this requires you to create a user name over at bloglet.com, the result of this minor chore seems better to me. The main attraction is that links and such don't turn into ugly, unreadable HTML. I will continue to send out the pre-bloglet notifications to those who have it, but you may want to switch over to the new system. Please drop me a note to let me know if you want to be taken off the old notification list.

Any further comments you may have will be most welcome.

We now return to our regularly scheduled blogging.

It's been a month since I've joined Corante, and my deep thanks go out to the many new readers who have visited the Loom. Daily visits reached a new high this Friday, January 9, with 900 pairs of eyeballs pointed this way. Please be sure to enter your email address in the subscription box in the lefthand column so that I can notify you of new posts.

I'm en route to Washington DC to talk tonight about Soul Made Flesh. If you're in the District, please come to Reiter's Bookstore at 2021 K Street NW at 6:30. On my web site I'm posting all my talks and radio interviews as they get confirmed.

In lieu of a blog of my own, let me point to a couple interesting items.

--At Quark Soup, David Appell gets righteously indignant about a new paper that predicts a major wave of extinction due to global warming. Actually, the paper could turn out to be a conservative underestimate (not to be confused with certain politically conservative underestimates of these sorts of things). Habitat loss, biological invasions, nitrogen pollution, increases in diseases, overfishing, and other impacts on endangered species may well work together synergistically, so that the whole of their damage is more than the sum of their parts.

--At the Intersection, Chris Mooney muses on genetically engineering mosquitoes to fight malaria. He's right to ask whether malaria-proof mosquitoes can compete in the evolutionary arena with wild mosquitoes. In fact, I just know I read some research published recently that indicated the bugs probably get knocked out. Evolution often works as a tradeoff between fighting off parasites and using that energy for other things, like moving or eating. Unfortunately, I don't have the time in transit to find it. In any case, all grand dreams of genetic modification need to take natural selection into account

Today's issue of Newsday has my review of Sea of Glory, Nathaniel Philbrick's history of the first great scientific U.S. expedition. The review gets pretty harsh towards the end, despite the fact that the book is an exquisitely researched narrative of a fascinating subject. (What makes it particularly fascinating is that the expedition's leader, Charles Wilkes, was practically insane.) It's this very potential that got me so frustrated. Here's a grand story about a journey to the ends of the Earth, about megalomaniacs, about the dawn of a great nation, about the birth of modern science, about the tragic dimension of empire, and yet Philbrick writes about all this in a style that's maddeningly pedestrian and dutiful. At one point he tries to offer some penetrating psychological insight into Wilkes's psyche by quoting from the pop-psychology book Emotional Intelligence. It was one of those moments when you have to tell yourself not to throw the book against the wall.

I may have such a strong reaction because I've read so many disappointing books on science. There are plenty of cases in which a solid, straight-ahead journalistic style is the right form for a science book to take. But there are also many opportunities in science to creat literary jewels, and generally those opportunities are squandered. For some reason this is considered a normal state of affairs. Critics rarely hold science writing to the same standards as, say, literary fiction. If a novel was riddled with the flat-footed cliches that plague so many science books, the critics would skewer it. On this score, it seems, most of the reviews of Sea of Glory give it a pass.

Craig Venter has followed up on his announcement that he and his coworkers have assembled a virus from its genome sequence. Now there's a paper available at the Proceeding of the National Academy of Science web site. A bleary-eyed late-night inspection suggests that this is not a flawless Xerox machine for viruses; the researchers had to cast away lots of misassembled versions. (Still, they were able to isolate a perfect sequence in just two weeks.) More interestingly, the authors talk a bit about how they can use this same method to cobble together chunks of much bigger genomes to make synthetic microbes. That's when things will get really interesting.

The paper ends on a grand note that takes a squirrely turn at the last moment:

"Synthetic genomics will become commonplace and will provide the potential for a vast array of new and complex chemistries altering our approaches to production of energy, pharmaceuticals, and textiles."

Textiles? Come on, folks. You may be on the verge of creating new life. Is this really the time to be talking about a new line of socks?

In February I wrote an article in Science about what Craig Venter's up to these days. In the late 1990s Venter made his mark by challenging the government human genome project to a race, promising to beat them to the full sequence for a fraction of their budget. Ultimately the race was a tie, and before too long Venter had been shown the door from his company. (I highly recommend James Shreeve's upcoming The Genome War for all the grisly details.) But he had also been working with the genomes of other organisms--particularly microbes--for years, and he went back to his first love. Not surprisingly, he was soon making headlines again, by setting out to build a microbial genome from scratch. His goal is to be able to tailor-make microbes for various applications, like providing clean energy or consuming carbon dioxide or other unwanted substances.

There was a lot of talk about playing God when Venter made his announcement, but when I spoke to other experts in the field, the general opinion was, "We'll believe it when we see it." Not that Venter wasn't a brilliant scientist who knew how to organize large-scale research with creativity and flair. In fact, many microbiologists were looking forward to seeing if he could just assemble a "minimal genome"--in other words, the lowest number of genes necessary to keep a microbe alive. But most believed that getting to his ultimate goal--designer microbes--was a lot harder than Venter was letting on. For one thing, when hundreds of genes start working together, the complexity gets pretty hairy. For another, microbes already do the sorts of things Venter's interested in--absorbing carbon dioxide, for example, or producing hydrogen. And it could well be that they've already evolved to their optimum. Engineering them drastically beyond what they do now might be like putting the muscles of an elephant in the body of a mouse.

This afternoon, Venter and the Department of Energy announced the first step on his long road ahead. They set out not to build a microbe, but a virus. This experiment is reminiscent of Venter's human genome work in many ways. Other scientists had built a virus from scratch before, but--like the government human genome project--they had done it very slowly. Venter's team found a faster way to build up accurate fragments of the genome and then to weld those fragments together in the right order to create a fully functioning virus. The virus in question infects bacteria, and Venter's reconstructed viruses did just as well as the originals. And instead of taking years, Venter needed two weeks. Faster, Venter, synthesize, synthesize!

Now that their test drive has turned out so well (the details are in press at The Proceedings of the National Academy of Sciences), it's on to microbes. Still, the same skeptical arguments about making designer bugs stand--although perhaps in a few years Venter will be knocking them down.

I'm writing this a few hours after the press conference, and I haven't seen too much comment on this announcement yet on the web. Presumably more will flood in tomorrow morning. But I'm struck by two things in the AP report on the press conference.

1. Energy Secretary Spencer Abraham was not reported to have said a peep about whether publishing a how-to guide for building a virus from scratch in two weeks is dangerous or not. Of course, Venter's speed was due in large part to the massive computers and army of robot DNA sequencers at his disposal. This is not something a terrorist could whip up in his basement. But that doesn't necessarily mean that something bad can't come of this work. That, in turn, doesn't mean this research should be banned or kept secret, but at the very least, safeguards need to be put in place.

2. Here's something odd that Abraham did say (I'm quoting from the AP story here):

Abraham called the accomplishment "an extraordinary and exciting development" that will speed up "our ability to develop biology-based solutions for some of our most pressing energy and environmental challenges." As a result of the scientists' progress, Abraham said it is now "easier to imagine in the not-too-distance [sic!] future a colony of specially designed microbes living within emission-control system of a coal-fired plant, consuming its pollution and its carbon dioxide, or employing microbes to radically reduce water pollution or to reduce the toxic effects of radioactive water."

This is something Venter's been saying for months now. But I find it interesting that a member of the Bush cabinet now considers carbon dioxide such a pressing environmental challenge that it requires this sort of remedy. Isn't this the Administration that has consistently downplayed the danger of global warming?

UPDATE: Friday, 11/14, 11:30 am. Here's the full text of Abraham's speech. Nary a word about risks in it. Is Homeland Security taking care of that?

A lot of work has gone into reconstructing an entire human being in a computer. Computer scientists put in the precise dimensions of a person's body, factor in biomechanics, mimic facial expressions and so on. This work gets huge amounts of hype in the press, but for all the effort and all the attention, the results so far have left me pretty unimpressed. Does watching Kevin Bacon running around without his skin in Hollow Man really make all that work worthwhile?

Frankly, I'm much more impressed with work going on in places such as the Genetic Circuits Research Group at the University of California at San Diego. Led by Bernhard Palsson , the group recreates life from the ground up--simulating the interactions of hundreds or thousands of genes in a computer. In today's issue of the Proceedings of the National Academy of Sciences, Palsson and his colleagues offered up the newest example of this approach. They reconstructed a humble fungus--brewer's yeast, or Saccharomyces cervisiae.

Palsson's work would have been impossible before our genomic age. But the yeast genome is not the final answer to how these organisms work. It doesn't tell you how they feed, how they survive hard times, or even how fast they grow. To get those answers, you have to travel up from the genome to the organism itself, which is what Palsson has been doing.

As the yeast genome has been sequenced, Palsson and his colleagues have examined each gene, to understand how it functions. We typically think of genes making proteins and leave it at that, but actually many of these proteins turn around and influence the production of other proteins. In some cases, genes can't make their proteins at all unless another protein switches them on. In other cases, proteins can shut down the pathway that allows a protein to be made. This allows organisms to be more than just biological factories, blindly cranking out proteins. Instead, they produce proteins only as needed, in response to changes in the environment for example, or in order to take the next step in their life cycle. Genes are a lot like electrical components this way, wired together into metabolic circuits.

Palsson's team gathered information on 708 genes in yeast (about 16% of all their genes), and worked out their role in the yeast's metabolism. Then they turned those roles into equations (along the lines of "as production of protein A goes up, production of protein B goes down.") They then ran these equations in a computer--simulating a significant part of the yeast's metabolism.

To see how good their reconstruction was, they grew some virtual yeast in their computer. The virtual yeast grew at the same rate as real yeast under similar conditions. The model could predict how much glucose yeast take up, how much carbon dioxide they spewed out, and how much of the energy-carrying molecule ATP they could create along the way.

The new PNAS paper is the latest stage in a project that's now 13 years old. Palsson and his colleagues have already simulated simpler organisms, such as the bacteria E. coli. The latest wrok represents a big step up from bacteria, however, because yeast--like us--are eukaryotes, which all have far more complicated metabolisms than bacteria. Not surprisingly, then, the virtual yeast don't behave exactly like real ones. Palsson's team is adding more genes to the circuits to get better performance.

Reconstructing life in a computer this way potentially has a lot more to offer than Hollow Man. It may become possible to engineer new yeasts or bacteria to make new compounds or absorb pollutants by running virtual versions of them on a computer. Eventually, it may be possible to reconstruct human cells in a computer as well. That could allow scientists to study how genetically engineered human cells would behave in the body. Ultimately, it might be possible to see how groups of cells function together--something like studying the way computers linked in a network behave. Reconstructing a whole person in a computer--trillions of cells, each with 30,000 or so genes--is insanely complex, but no one can say what the limits are to this sort of work.

Books have been bubbling up from the comments cauldron. Jim Harrison has asked what I think of Simon Conway Morris's Life's Solution. Web Webster says Cosmos was his first favorite science book and asks for suggestions. Humboldt and Feyerband make an appearance too. It's ironic that two forms of reading that are competing furiously these days for my free time--books and blogs--meet at this crossroads.

Let me just say that I have four books on my desk, that I am trying to dig into. They're either just out or about to come out. For the most part, I can't tell you that they're great or lousy, because I haven't really started them yet, but I am intensely curious about them. Take the following as partially-informed recommendations.

1. Life's Solution. This book is by Simon Conway Morris, a great paleontologist. Conway Morris thinks that Stephen Jay Gould's emphasis on contingency in evolution does an injustice to repeated trends in the history of life--towards certain ways of flying, for example. In a sense, then, we may be an inevitable product of evolution (i.e., intelligent, self-aware life). He also explores the potential religious implications of his scientific argument. Conway Morris has an incisive mind and has done spectacular work on the origin of complex animals (like the first vertebrates). On the other hand, what I've read and heard of his ideas about convergence in the past have left me a bit skeptical. Convergence is fascinating, but I don't know if you can hang the sort of significance Conway Morris wants to on it. Another downside is that his writing is not always crystal clear, shall we say. And being a great scientist may not necessarily make him a good philosopher (or theologian). But I am certainly curious.

2. Sea of Glory, by Nathaniel Philbrick. Philbrick wrote the NBA winning In the Heart of the Sea, about the voyage that Moby Dick was based on. Now he's writing about the first great scientific expedition in US history which stretched from 1838 to 1842. Six ships full of scientists wandered the Pacific for four years and did spectacular work. I anticipate a ripping maritime yarn that also delivers good information on early American science, a fascinating topic in my opinion.

3. The Genome War, by James Shreeve. Shreeve's a great science writer, and this is his first book since The Neanderthal Enigma. He tells the story of the Human Genome Project. "Again?" you yawn. Stay with me--I've started this one, and I can say that Shreeve has written the first book I know of that actually tells the story right--a story of big egos, big science, and big stakes. (Plus excellent descriptions of genetics.) Craig Venter, James Watson, and all the other players are coming alive on the page. I suspect this one will get finished first.

4. Radiant Cool, by Dan Lloyd. I first came across Lloyd's work in the Journal of Cognitive Neuroscience. He had written a paper on consciousness, and at first I too yawned, "Again?" But then I started reading it, and it was really fascinating. He was exploring a new way to use neuroimaging to find a signature of consciousness--not as a blob on a scan indicating some "consciousness organ" but a running comparison of activity all over the brain. It was sketchy but intriguing. Now he's written a book to explain his ideas on consciousness, in the form of a detective novel. That's a first.

I write about science, and in a recent overhaul of my web site, I decided it was a good time to add a blog. I'll be posting thoughts about new research in the fields that I can't get enough of--the brain and the body, how they evolved, and where they're going. I'm still getting the hang of iblog, and so the first few posts will probably be pretty clunky. And until I can figure out how to post comments, please feel free to email me. I will try to post some messages from time to time in my own posts.