I learned that Google has retooled its invitation system for Google+. Instead of manually adding names into a message field, I can just drop a link into this post and offer 150 invitations. So if you want to dabble in this new experiment in social media and enforced non-pseudonymity, please click here.

Last month I contemplated the staggering diversity of microbes in my bellybutton–an experience made possible by my participation in a survey of microbiome diversity carried out by scientists at North Carolina State University. At the time, I thought I was quite the host. I was informed there were 53 species living in my navel, some of which had never been seen on skin before and some of which were altogether new to science. I was even informed that I was a “wonderland.”

Well, the project is moving forward at quite a clip, and the scientists are starting to push more of their data online. Here you can see the species from the first 60 volunteers they’ve studied. The lists are coded by number–I’m B944. I appear to have lost a species so I’m down to 52. And 52 is, I’m seeing, nothing to blog home about. So far, the diversity champion is the anonymous owner of bellybutton B1288. 107 species! Now that’s a wonderland….

Lucas Brouwers, one of the new bloggers at Scientific American’s snazzy new blog network, takes a look at an intriguing paper (free pdf). The authors of the paper in examined many different strains of E. coli and come to a remarkable conclusion: they’ve been splitting apart so far that they may soon no longer be a single species. Check it out. (And, if you have a lot of time to spare, check out the rest of Scientific American’s fine line-up of bloggers.)

[Note: Some folks don't like the phrase "chlorine-based life." I welcome suggestions in the comments for a better shorthand descriptor]

Last year, a team of NASA-funded scientists claimed to have found bacteria that could use arsenic to build their DNA, making them unlike any form of life known on Earth. That didn’t go over so well. (See my two pieces for Slate for a quick recap: #1, #2.)  One unfortunate side-effect of the hullabaloo over arsenic life was that people were distracted from all the other research that’s going on these days into weird biochemistry. Derek Lowe, a pharmaceutical chemist who writes the excellent blog In the Pipeline, draws our attention today to one such experiment, in which E. coli is evolving into a chlorine-based form of life.

As I wrote in Microcosm, scientists have been contorting E. coli in all sorts of ways for years now to figure out what the limits of life are. Some researchers have rewritten its genetic code, for example, so that its DNA can encode proteins that include amino acids that are not used by any known organism.

Others have been tinkering with the DNA itself. In all living things, DNA is naturally composed of four compounds, adenine, cytosine, guanine, and thymine. Thymine, shown in the upper left panel here, is a ring of carbon and nitrogen atoms, with oxygen and hydrogens atoms dangling off the sides. Since the 1970s, some scientists have tried to swap thymine for other molecules, such as the one show to the lower left here. This compound is called 5-chlorouracil, the “chloro-” referring to the chlorine marked here in red. No natural DNA contains chlorine.

A team of German scientists recently published the details of an experiment that has taken them a long way towards E. coli that live only on chlorouracil. They didn’t simply sit down and type out a new sequence for E. coli’s genome–we just aren’t smart enough to make such predictions. Instead, they harnessed evolution. The scientists fed a population of E. coli chlorouracil, supplementing their dieet with a little thymine to keep them from starving to death. Bacteria that picked up mutations that allowed them to use some chlorouracil instead of thymine were favored by natural selection. They lowered the thymine levels to increase the pressure on the bacteria to evolve more.

After five months of this evolution, the E. coli underwent a noticeable change. For one thing, they changed shape. They started out in the normal capsule shapes in the top photo, turned into the worm-like shapes below, and then later became capsule-shaped again. The scientists also found that the bacteria were slurping up chlorouracil. Ninety percent of the thymine in their DNA was replaced by chlorouracil. As Lowe writes, the scientists found that the bacteria were still incorporating some thymine into their DNA through a pathway no one had discovered before (which just shows how marvelously mysterious E. coli remains after a century of intensive study). The scientists shut down this new pathway, and found that the bacteria still grew happily. But now they only had 1.5% thymine in their DNA.

This E. coli is different from ordinary E. coli, with over a thousand mutations that enable it to take up chlorouracil. But it is not quite yet off the grid. If it is fed thymine and no chlorouracil, it can switch back to a conventional way of life. So now we’ll see if scientists can further evolve the bacteria so that they can only live on chlorouracil, and starve on thymine.

I checked in with Steven Benner, a chemist who has raised a lot of concerns about the arsenic-life research last year. What did he think of the new research?

“It looks true,” he said.

Benner also pointed out that using chlorine in DNA is a pretty modest changed compared to what would have been required to substitute arsenic for phosphorus in the backbone of DNA. Swapping in chlorine doesn’t change how the compound reacts with other compounds, doesn’t change its size much, doesn’t change its stability much, and so on.

On the other hand, it appears to have the advantage of being real.

[Update: Rosie Redfield, an outspoken critic of the arsenic-life research, just got back to me with nice things to say as well:

"This looks quite solid to me (I read it quickly). The technology is nice, very appropriate for the project. No red flags at all."]

It’s been very gratifying to listen to the conversation that’s been triggered by my essay in this Sunday’s New York Times on scientific self-correction. Here, for example, is an essay on the nature of errors in science by physicist Marcelo Gleiser at National Public Radio. Cognitive scientist Jon Brock muses on how to get null results published.

I also got an email from Eliot Smith, the editor of the Journal of Personality and Social Psychology who accepted the controversial clairvoyance paper I described in my essay. I wrote that three teams of scientists failed to replicate the results and that all three studies were rejected by the journal because they don’t accept simple replication studies.

Mr. Zimmer

Your recent Times column stated the following:

Best regards,
Eliot Smith

I’ve passed on Smith’s message to my editor at the Times, and I’ll also take this opporunity here to apologize for the error.

I’m not sure how meaningful it is in the context of my essay, since my point was that policies against publishing replication studies get in the way of science’s self-correction. But a mistake is a mistake.

Some people get a thrill from getting their genome sequenced and poring through the details of their genes. I’m a bit off-kilter, I guess, because I’m more curious about the genomes of the things living in my belly button. And let me tell you: it’s a jungle in there.

I first became curious about my navel in January. I was in Durham, North Carolina, to attend a meeting, and as I walked out of a conference room I noticed a cluster of people in the lobby handing out swabs. They were asking volunteers to stick the swabs in their belly button for the sake of science. Our bodies are covered with microbes, and scientists are discovering weirdly complex patterns to their biodiversity. From fingers to elbows to chin to forehead, different regions of our skin are dominated by different combinations of species. But the bellybutton remained terra incognita.

I happily donated my microbiome to the study, which is being conducted by Jiri Hulcr and Andrea Lucky, two post-doctoral researchers in the laboratory of Rob Dunn at North Carolina State University. After a few weeks, Hulcr sent me a photo of a Petri dish in which some of the bacteria from my bellybutton were thriving. Then Hulcr and Lucky got down to the serious work of identifying the species in the navels of their volunteers (90 and counting).

Yesterday, Dunn sent me a spreadsheet detailing my own results. “You, my friend, are a wonderland,” he wrote.

To catalog the biodiversity of bellybuttons, Hulcr and Lucky are extracting the genetic material from their collection of swabs. They then compare these fragments of DNA to the millions of sequences that are stored in public databases. (They limited themselves to DNA from bacteria, so for now they’re not cataloging the fungi, viruses, and other creatures that may be lurking in our navels.)

Some fragments of navel DNA precisely match the DNA of a known species of bacteria. In other cases, they’re close enough to a species for Hulcr and Lucky to assign them to a genus, a family, a class, or  some higher unit of classification. In a few cases, the bacterial DNA is so exotic that all they can say for sure at this point is that it is bacteria.

Hulcr, Lucky, and Dunn had lots of questions about the things that dwell in the human omphalos. Are they different from the species that live in other parts of the skin? Do they differ from one person to the next? Is there a core set of species found in all navels? To address these kinds of questions, they tallied up the number of volunteers who carried each species, and investigated how each species makes a living.

All told, I now discover, my belly button harbors at least 53 species of bacteria. This, Dunn informs me, is a “whopping” number.

I’m not sure whether to feel good or bad about this revelation. On the good side, I know that diversity can make ecosystems work better. One of the most important services that our microbial ecosystem performs for us is protecting us from pathogens. They can outcompete invaders, kill them with poisons, and otherwise ward them off. Scientists have run experiments to test the effect of diversity on infections. They manipulated mice so that some had no resident bacteria, and others had low levels of diversity. The researchers found that pathogens did a better job of invading low-diversity mice than high-diversity ones.

So perhaps my belly button is especially well-defended. Still, I can’t help but wonder if I ought to scrub it with some steel wool. There are some very exotic things in there. Only a small fraction of my belly button bacteria were common among the other 89 volunteers. The microbes I share with most other volunteers tend to be ordinary skin dwellers that are typically harmless (although sometimes they can turn nasty and cause problems ranging from acne to staph infections).

But out of 53 species, 35 were present in only 10 or fewer other volunteers. And 17 species in my navel didn’t show up in anyone else. In the column for notes in Dunn’s spreadsheet, he’s annotated these species with scientific descriptions like “weird one” and “totally crazy.”

Several species I’ve got, such as Marimonas, have only been found in the ocean before. I am particular baffled that I carry a species called Georgenia. Before me, scientists had only found it living in the soil.

In Japan.

When I learned this, I emailed Dunn to let him know I’ve never been to Japan.

“It has apparently been to you,” he replied.

While I may be a bit of an outlier in the belly button department, I’m not a freak. Among all 90 belly buttons Dunn and his colleagues have studied so far, they have found 1400 species of bacteria, a number of which have never encountered on human bodies before. These species are probably not so out of place as they may seem, however. The diversity of the world’s microbes is vast–far bigger than the whole animal kingdom combined. For the most of the history of microbiology, scientists have focused most of their attention on bacteria that make humans sick–ignoring the huge number of species that don’t harm us, or that live elsewhere in the world. Many species are turning out to have a much wider range than scientists have previously appreciated. Bacteria have also evolved to leap from one niche to another to another. Take Pantoena–a lineage Hulcr and Lucky have only found in my belly button and that of one other subject. Most species of Pantoena infect plants. But a few lineages have shifted from plants to people. As scientists add more branches to the tree of life, they will probably find more such transitions.

In ancient Greek mythology, Zeus release a pair of eagles to find the center of the world–the “omphalos,” which means belly button in Greek. Several statues, like the one shown above, were built around the Mediterranean to mark the supposed place where the eagles landed. It’s wonderful to be part of an experiment that gives a new meaning to this ancient word. Each of us carries a biological omphalos: a small, lint-clogged center of the microbial world.

(For more information, check out Dunn’s new book, The Wildlife of Our Bodies, for which I happily provided a cover blurb.)

[Image: University of Kentucky]

During the World Science Festival, I met Baba Brinkman, who performs hip hop about, among other things, evolution. He let me know that his “Rap Guide to Evolution” will be opening this Friday at the SoHo Playhouse in New York. Here are details about the venue and getting tickets.

Here are a couple videos from Baba…

Here’s a one called, “Performance, Feedback, Revision”:

Here’s Baba at TEDxKids:

The folks at 3 Quarks Daily are winnowing down the entrants for the best science blog post of the year. They want you to help select the finalists by voting for your favorite post from the 87 nominees. (The Loom makes an appearance at #76 with “The Human Lake.”) You can vote till June 8, 11:59 PM EST.

The folks at CreatureCast have created a new animation about the weirder corners of zoology. Behold Symbion pandora, an animal that clings to the mouthparts of lobsters, where it engages in the weirdest sex life I’ve ever heard of.

Charles Darwin was the original crowd-sourced scientist. He may have a reputation as a recluse who hid away on his country estate, but he actually turned Down House into the headquarters for a massive letter-writing campaign that lasted for decades. In her magisterial biography of Darwin, Janet Browne observes that he sometimes wrote over 1500 letters in a single year. Darwin was gathering biological intelligence, amassing the data he would eventually marshall in his arguments for evolution. In the letters he wrote to naturalists around the world, Darwin asked for details about all manner of natural history, from the color of horses in Jamaica to the blush that shame brought to people’s cheeks.

Given the skill with which Darwin used the nineteenth-century postal system, I always wonder what he would have done with the Internet. A new paper offers a clue: he might have enlisted thousands of citizen scientists to observe evolutionary change happening across an entire continent.

Darwin used his Victorian crowd-sourcing to collect evidence that was consistent with his evolutionary theory; he didn’t expect that he could actually document evolutionary change happening in his own lifetime. Ironically, he probably could have. Gregor Mendel worked out the basic rules of genetics around the time Darwin published The Origin of Species. At the time, pollution from England’s coal was turning trees dark, giving an evolutionary edge to dark moths over light ones. A naturalist even wrote directly to Darwin in 1878 to raise the possibility that natural selection was driving the shift in moth color. But it wasn’t until 14 years after Darwin’s death that a naturalist explicity put this idea into print.

In the decades after Darwin’s death, biologists translated Darwin’s ideas into the language of statistics. They figured out how to make measurements on animals and plants in the wild, and how to discover in those measurements the traits that led to the most reproductive success. Evolutionary biologists have now made thousands of measurements of natural selection in the wild. But each of those measurements has been hard won. To see natural selection, researchers must study dozens or hundreds of individuals. To get a sense of how tough this work is, read The Beak of the Finch: A Story of Evolution in Our Time, in which Jonathan Weiner chronicles the adventures of Peter and Rosemary Grant, who have traveled to an isolated island in the Galapagos Archipelago each summer for forty years in order to measure natural selection on Darwin’s finches.

But Jonathan Silvertown of The Open University in England and his colleagues have found a way to spread this kind of work far and wide. They set up a web site where volunteers could sign up to become amateur evolutionary biologists. They ende up with over 6,000 volunteers, who sent them measurements from across Europe.

Their measurements came from an animal that’s at once humble and iconic. The land snail Cepaea is common in gardens, ditches, forests, and meadows throughout Europe. The snails come in a beautiful variety of colors, as this photograph from Poland demonstrates. The patterns are encoded in genes, which the snails pass down to their offspring. In the early 1900s, many naturalists considered the patterns to be pretty but insignificant. They were just the result of random mutations that cropped up and then spread through the snail population thanks to chance.

Starting in the 1930s, a team of Oxford scientists took a close look at which snails lived and died. They could do so because the snails are a favorite meal for thrushes, which like to pick up their prey and carry the snails into the air, whereupon they drop the snails onto rocks below to crack the snails. The Oxford researchers were able to catalog these smashed shells, noting their colors and stripes.

The researchers found that some colors and stripes were more common among the shell debris than you’d expect from chance alone. It turns out that the birds are more likely to pick out the snails that stand out against the background. So snails that are better camouflaged are more likely to survive. Which pattern works best depends on where a snail lives; what hides a snail crawling over a dark forest floor doesn’t work so well in a field grazed short by cattle. The researchers found that the most common patterns were, indeed, well-matched to where the snails lived.

This research on Cepaea snails helped establish natural selection as a powerful force in evolution–although bird-driven natural selection turns out to be http://www.ncbi.nlm.nih.gov/pubmed/10983823“>not the sole force at work. Studies across Europe revealed, for example, that southern European snails are more likely to have yellow shells than their darker northern cousins. The difference is probably due to the climate: yellow shells bounce sunlight away and keep the southern snails cool.

A few years ago, Silvertown and his colleagues set out to gather a new batch of observations on Cepaea to compare with these historical records. They wondered, for example, if the warming that Europe has experienced might have made northern snails more yellow. Through the web site Evolution Megalab, they enlisted people from 15 different countries, who set out into their own neighborhoods to find the snails and note their colors. Combining the new observations with the old, the scientists ended up with half a million snails, organized in a geographical database along with information such as the habitat where the snails lived, as well as the temperature and rainfall at each location. Nothing quite like it has ever been achieved by evolutionary biologists–professional or otherwise.

The collection chronicles fifty years of snail evolution, over the course of about twenty generations. In that time, the researchers didn’t detect a continent-wide change in the frequency of yellow shells. Only in populations that lived on beach dunes did yellow shells become more common. Silvertown and his colleagues suspect that most snails have been coping with the warming temperatures in Europe by spending more time in the shade. On the treeless dunes, however, that’s not an option. As a result, natural selection has favored the yellow snails, which can stay cooler without the help of foliage.

But Silvertown and his colleagues did find other shifts that took place across all of Europe. Snails without a stripe on their shell declined by about 10%, while snails with a mid-line band increased by 5%. The scientists doubt that the rise of striped snails has anything to do with a shifting climate. Indeed, the striped snails have become more common in southern Europe than in northern Europe–the opposite of what you’d expect if stripes were a defense against heat.

The scientists don’t know for sure what’s behind this evolution, but they have an idea. The song thrushes that eat the snails have been declining in some places for the past thirty years. It’s possible that the change in the predatory pressure of birds is shifting the force of natural selection.

It’s the sort of idea you could imagine Darwin coming up with as he sat in his study, paging through letters from his farflung correspondents. But now Silvertown and his colleagues are going to test it, taking advantage of the original citizen scientists: birders. And if you’re reading this in Europe, you can be part of the investigation.

PS: In case you don’t know how to hunt for a snail, here is a charming video from the Megalab:

Via fellow Discover blogger Sean Carroll, I came across Jorge Cham’s podcast/comic/video about cosmology. I’m embedding it here, not just because it’s a very good summary of where we stand in understanding the stuff of the cosmos, but because Cham–he of PhD comics–has done something fascinating here. He has combined three different media into something new. I think, on the whole, it works very well. It moves a bit too fast for my eye sometimes, and can get a little herky jerky. But a living comic illustration of a scientist talking? Me likes.

Dark Matters from PHD Comics on Vimeo.

The Browser, one of my favorite sites for gathering interesting reads I can wield in my perpetual battle on behalf of procrastination, has a great feature called FiveBooks. From time to time, they ask a writer to select five of their favorite books on some particular topic, and then interview them about their choices. I was honored to be interviewed for today’s FiveBooks (just after Ian McEwan–yikes!). I chose the theme of “the strangeness of life” and then scanned my bookshelves for some favorite books that deal with it in one way or another. If you have any interest in good writing on natural history (including human natural history), I’ll wager you’ll like them all. Check it out.