I went recently to San Francisco to give a talk to a conference of scientists. The scientists were experts in gathering together mountains of biological data—genome sequences, results of experiments and clinical trials—and figuring out how to make them useful: turning them into new diagnostic tests, for example, or a drug for cancer. The invitation was an honor, but a nerve-wracking one. As a journalist, I had no genome scan to offer the audience.

We science writers do have one ace in the hole, though. Instead of being lashed to a lab bench for years, carrying out experiments to illuminate one particular fold in one particular protein, we get to play the field. We travel between different departments, different universities, different countries, and—most important of all—different disciplines. And sometimes we see links between different kinds of science that scientists themselves have missed. Which is why, when I arrived in San Francisco, walked up to the podium, and switched on my computer, I presented my audience with this photograph of a lake.

For the next hour, I tried to convince them that their bodies are a lot like that lake, and that appreciating this fact could help them find new ways to treat diseases ranging from obesity to heart disease to infections of antibiotic-resistant bacteria.

The lake, called Linsley Pond, is located in southern Connecticut, a short drive east of New Haven. It’s about a half a mile wide. It supports a typical assortment of species, including algae and bacteria, water fleas, lily pads and other aquatic plants, birds, turtles, and fishes. It looks utterly ordinary. But in the history of ecology, it’s one of the most significant places on Earth.

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Today I’ve got a story about some new research into evolvability–the potential to reach new adaptations. Scientists have explored the possibility of evolvability for some time now, but mostly through analyzing mathematical equations. Now a new study offers a fine-grained picture of evolvability in action.  Richard Lenski of Michigan State and his colleagues have watch evolvability help one line of bacteria beat out another one. It’s a Darwinian story of the tortoise and the hare. Check it out.

(For more on evolvability, check out this review by Massimo Pigliucci [pdf])

[Image: Wikipedia]

Earlier this month I was invited to deliver a keynote address at the Joint Summit on Translational Science in San Francisco. The meeting brings together scientists who seek to master the rising tide of biological data, in order to find new medical treatments. I urged them to think like ecologists, and treat the human body like an ecosystem of thousands of species.

I recorded my talk on my trusty iPhone, and I’ve posted the audio below. (You can download it.) It’s also here.

Carl Zimmer Keynote Lecture on the Human Microbiome by Carl Zimmer

And below are the lecture slides (also on Slideshare). (Thanks to everyone who responded to my query about the best way to present my talks. I hope later this week to turn the talk into a written post.) [UPDATE: Here's my essay, "The Human Lake."]

Why is ScienceOnline a meeting like no other? Because it’s the sort of meeting where a biologist named Rob Dunn can set up shop in the lobby to ask for samples of bellybutton shmutz that he can analyze for biological diversity. Not only is it a place where such a person will not be hustled out by security, but it’s a place where a whole bunch of people respond by grabbing Q-tips to do their part for science. And you can bet every last bit of your bellybutton lint that I was right up near the front of the line.

Ten days later, my sample is now thriving nicely on a Petri dish, awaiting a more detailed analysis of its DNA. And here are the rest of the samples from the meeting.

All I can say is, #974, what is going on in there?

I don’t usually make pleas on the Loom. It doesn’t suit my journalistic nature, and if I make a plug for one cause, it may seem like I am cruelly indifferent to all the other good causes out there. In this case, I’ll just fall back on self-interest! A few weeks back two young film-makers, Sam Gaty and George Costakis, stopped by my house to interview me about synthetic biology for a documentary they’re making on the subject. They’ve been filming across the country for the movie, but it won’t finished in time for next year’s Sundance unless they can raise a little scratch to get them through the summer. Over at the fund-raising site Kickstarter, Gaty makes the case–and offers a clip about goats making spider silk. If this movie doesn’t get made, I end up on the cutting room floor. Oh, the humanity! (Actually, I think the film would be pretty cool without me–but judge for yourself.)

On my new podcast, I talk to Martin Blaser of New York University about Helicobacter pylori, best known as the microbe that causes ulcers. It’s also an ancient passenger in our stomachs, and has evolved a delicate balance with its human hosts. In fact, Blaser is worried by the disappearance of H. pylori from the modern world, thanks to antibiotics and hygiene. We may have to pay a price for its extinction, in the form of higher rates of asthma, esophageal cancer, and perhaps even obsesity. Check it out.

With this episode, the American Society for Microbiology is bringing the Meet the Scientist podcast series to a close. In the coming year, they’re going to be focusing their online efforts on some new projects you can look forward to on the Microbe World web site. (And they’ll be keeping all the episodes of Meet the Scientist on the site.) I’ve had a wonderful time over the past year hosting the podcast, and I’d like to thank all the scientists who shared their work with me and all the people at ASM who made this experience possible.

A lot of people are interested in my Slate story yesterday on the arsenic aliens. It’s still the most-read story of the site at the moment, Slashdot and others have linked to it, and I’m doing some more radio and maybe other media (details to come).

I think that what has gotten so much attention to the story is just how many scientists had such critical things to say. The verdict was not unanimous, but the majority was large. I was only able to quote a tiny bit from just a few of the scientists I communicated with, so I thought, for those who’d like to delve more deeply into this, that I’d post a list of everyone I spoke to, and, when possible, post their reactions. A lot of scientists replied to me by email or even attached word files where they went on at length. I put together a similar dossier for another biological controversy–the search for soft tissue in dinosaur fossils–and I think (or at least hope) that this sort of exercise can help further discussion.

Of course, as I and others have reported, the authors of the new paper claim that all this is entirely inappropriate. They say this conversation should all be limited to peer-reviewed journals. I don’t agree. These were all on-the-record comments from experts who read the paper, which I solicited for a news article. So they’re legit in every sense of the word. Who knows–they might even help inform peer-reviewed science that comes out later on.

I’m going to post everything under the fold here, but it will take a little while. I’ll just re-save the post every time I add a new one, and I should be done before too long. So keep refreshing, or just drop by again later…

PS–Science has made the paper at the center of this controversy free. Get it here.

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Rumors have been swirling this week about a press conference NASA is starting right now. Some people have speculated that they’re going to announce evidence for life on another planet.

Well, not quite. Scientists have found a form of life that they claim bends the rules for life as we know it. But they didn’t need to go to another planet to find it. They just had to go to California.

The search for alien life has long been plagued by a philosophical question: what is life? Why is this so vexing? Well, let’s say that you’re hunting for change under your couch so that your four-year-old son can buy an ice cream cone from a truck that’s pulled up outside your house. Your son offers to help.

“What is change?” he asks.

“It’s…” You trail off, realizing that you’re about to get into a full-blown discussion of economics with a sugar-crazed four-year-old. So, instead, you open up your hand and show him a penny, a nickel, a dime. “It’s things like this.”

“Oh–okay!” your son says. He digs away happily. The two of you find lots of interesting things–paper clips, doll shoes, some sort of cracker–which you set aside in a little pile. But you’ve only found seventeen cents in change when the ice cream truck pulls away. Tears ensue.

As you’re tossing the pile of debris into the trash, you notice that there’s a dollar bill in the mix.

“Did you find this?” you ask.

“Yes,” your son sobs.

“Well, why didn’t you tell me?”

“It’s not change. Change is metal. That’s paper.”

Scientists have proposed hundreds of definitions for life, none of which has emerged as the winner. (For more on this quest, see “The Meaning of Life,” a cover story I wrote for SEED.) NASA, which would like to find life elsewhere in the universe, has taken a very practical approach to the question, simply asking what sort of definition of life should would be the best guide for their search. Traditionally, they’ve put a priority on life as we know it. All life on Earth uses DNA or RNA to encode genes; all life on Earth uses the same basic genetic code to translate genes into proteins; all life uses water as a solvent. One reason that NASA has put so much emphasis on looking for life on Mars is that it’s plausible that life as we know it might have existed on Mars back when the planet was warm and watery. And besides, how are we supposed to look for a form of life we’ve never seen before?

But in 2007 a National Academies of Science panel urged that we take a broader view of life, so that we wouldn’t miss the dollar bill in the couch. Other kinds of life were at least imaginable–such as organisms that used different backbones for their genes, or perhaps might swim through liquid methane like fish swim in water. (Here’s my write-up in the Times.) Some of the panelists–most notably, Steven Benner of the Foundation for Appllied Molecular Evolution–even endorsed a more radical notion. As I described in this feature for Discover, Benner and others speculate that maybe alien life is here on Earth.

A lot of evidence, for example, suggests that the first forms of life used RNA as both genes and enzymes. Later, double-stranded DNA evolved and DNA-based life wiped out RNA life. But perhaps RNA life still clings to existence in places where DNA-based life can’t drive them extinct. Benner suggests tiny pores in rocks that would be too small for bacteria.

No one has found RNA life yet, nor have they found any all-natural alien on Earth. But as I point out in Microcosm, there are definitely aliens among us.

They’re called E. coli.

Or, rather, they are laboratory stocks of E. coli that scientists have transformed so that they use new genetic codes or even use new nucleotides, the “letters” of DNA. No life that we know of has ever lived this way.

NASA’s press conference concerns another nearly-alien kind of life on our own planet. NASA has sponsored many expeditions to the toughest places on Earth for life to survive, from glaciers to deserts to acid-drenched mines. One of these expeditions was to Mono Lake, a practically toxic body of water, an extreme environment. It’s very salty, very alkaline, and is steeped in arsenic. The “weird life” report singled out arsenic-based life as one topic worth investigating, so Felisa Wolfe-Simon of the NASA Astrobiology Institute and her colleagues isolated a strain of bacteria and brought it back to the lab to study its growth.

As I mentioned earlier, life as we know it uses DNA for its genes (except for some viruses that use RNA). DNA has a backbone made of two alternating units: sugar and phosphate. Phosphate is one phosphorus atom and four oxygen atoms. It just so happens that arsenic–despite being a poison–has a lot of chemical properties similar to phosophorus. In fact, one arsenic atom and four oxygen atoms combine to form a molecule called aresenate that behaves a lot like phosphate.

Wolfe-Simon and her colleagues reared the bacteria in their lab, initially feeding them a typical diet of essential nutrients, including phosphate. But then they gradually reduced the phosphate in their diet and replaced it with arsenate. Before long, as they report today in Science, the bacteria were growing nicely on an all-arsenate diet, without a speck of added phosphate. The scientists then probed the DNA of the bacteria and concluded that they were sticking the arsenate into the DNA in place of phosphate. Phosphate is also vital for other molecules, such as proteins, and the scientists found arsenate in them as well. In other words–arsenic-based life.

Or…maybe not. In Science, reporter Elizabeth Pennisi writes that some scientists are skeptical, seeing other explanations for the results. One possible alternative is that the bacteria are actually stuffing away the arsenic in shielded bubbles in huge amounts.

I got in touch with Benner, who also proved to be a skeptic. “I do not see any simple explanation for the reported results that is broadly consistent with other information well known to chemistry,” he says. He pointed out that phosphate compounds are incredibly durable in water, but arsenate compounds fall apart quickly. It was possible that arsenate was being stabilized by yet another molecule, but that was just speculation. Benner didn’t dismiss the experiment out of hand, though, saying that it would be straightforward to do more tests on the alleged arsenic-DNA molecules to see if that’s what they really are. “The result will have sweeping consequences,” he said.

If Wolfe-Simon can satisfy the critics, this will be research to watch. The Mono Lake bacteria probably don’t actually exist in an arsenic-based form in nature, since they grow much faster on phosophorus. They’re aliens, but aliens in the same way unnatural E. coli are, thanks to our intervention. But Wolfe-Simon’s results suggest that life based on arsenic is at least possible. It might even exist naturally in places on Earth where arsenic levels are very high and phosphorus is very scarce.

Such a discovery would indeed be huge news–although not as huge as a similar discovery on another planet. For now, we will have to content ourselves with arsenic-laced dreams.

(PS: You should be able to watch the press conference live starting at 2pm Thursday 12/2 here.)

Reference: Wolfe-Simon et al, “A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus” Science, 10.1126/science.1197258

[Image of Mono Lake by .Bala via Flickr, under Creative Commons License]

[Update: Fixed Wolfe-Simon's name. Now I am left with images of wolf salmon roaming in packs.]

[Update: Fellow Discover bloggers Ed Yong and Phil Plait are on the case, too.]

[Update: I've been adding in various corrections pointed out by astute readers. Importantly, the researchers raised the bacteria with no *added* phosphate. But the medium did have a little phosphate in it anyway. More about this on Monday!]

[Upate: Well, Monday became Tuesday, but better late than never: Here's my new article on the arsenic backlash at Slate.]

Every now and then I take a moment at the Loom to marvel anew at the sophistication of a certain microbe. Today, I direct your attention to a report in New Scientist on E. coli that has been engineered to solve Sudoku puzzles. Frank Swain, the author, makes a good point: if E. coli is allowed to spread out the task among millions of individual microbes, it can tackle bigger problems. Let’s just hope that all the E. coli in our guts don’t figure this out on their own…

I’ve been invited to give a few talks in the wake of my article in the New York Times on the microbiome, and so I’m prowling for beautiful images that drive home the fact that we are microbial rain forests, rather than sterile mammals. Below is my favorite image of the day.

It’s from a survey of microbes across people’s bodies, published last year in Science. The inner circle shows the major lineages of bacteria found in all the subjects in each part of the body, while the ring shows the ones found in some people but not others.

This picture was stuffed away in the supplementary materials for the paper, so I missed it the first time around. I’m glad I found it–it’s a new Vitruvian man for our microbiomic age.

I’ve contributed my first article to Technology Review–a short profile of Tim Lu of MIT, one of TR’s 35 innovators under 35. Lu is engineering viruses to attack biofilms–not just the ones that make us sick, but the ones that gum up factories and HVAC systems. Elegant and practical at the same time. Congratulations to all the winners!

While I was away last week on vacation, the New York Times published my feature on the hidden jungle that each of us carries, known as the microbiome. I was very happy to come home to a lot of kind notes, tweets, and various communications about it. Yet I would never claim that my article delivered the Big Scoop on the subject. After all, we’ve known about the microbiome ever since Antonie Philips van Leeuwenhoek scraped his teeth over 300 years ago and discovered wee animacules in the scum. And as I wrote in my book Microcosm, Theodor Escherich discovered his eponymous Escherichia coli over a century ago in a quest to catalog the good microbes in babies’s guts, hoping to thereby identify the ones that were killing the children in droves. Even in the age of molecular biology, the microbiome has been well-chronicled. Jessica Snyder Sachs wrote a book back in 2007 called Good Germs, Bad Germs: Health and Survival in a Bacterial World that I heartily endorsed (and still do).

So why write a story now? That’s a question that science writers have to ponder a lot. Much of the most interesting science does not explode with a single experiment or the unearthing of a single fossil. It’s a stately unfolding, a long-running collaboration/competition. For me, the time seemed ripe thanks to a couple recent papers that catalogued vast amounts of DNA in the collective genome of our microbial lodgers. Scientists have long known that the genes in the microbiome outnumber human genes by perhaps 10 or 100 to 1. But now we’re finally getting a database of that genomic richness.

And then, at a recent conference, I heard about a fecal transplant that saved a woman’s life. I knew I had my lede. But I called my editor to make sure that I could kick off the article that way, given that so many readers peruse the Times over breakfast. You never know. To anyone who experienced a fascinated nausea, my apologies.

In the days since my article came out, a series of new papers on the microbiome have been published. Today the Times published an editorial about one of them, a study of the incredible diversity of bacteria-infecting viruses we carry. Even identical twins harbor different sets of viruses. And yesterday, Caltech researchers described how multiple sclerosis may be the result of the way bacteria manage our immune systems.

Still, I’m glad I didn’t wait for all the good science to emerge. I would still be waiting 20 years from now.

PS–Here is a list of links for my Times article:

The fecal transplant paper

Genomes of the microbiomes

A catalog of 3.3 million genes

Bacteria teaching the immune system

The paper on how microbes infect us at birth

The microbes of the lungs

[Image: A beautiful bacterial colony]