I’ve got a story on the cover of the latest issue of Time. It’s about the evolutionary origins of friendship. For a number of scientists, friendship–in a deep sense of the word–is not limited to our own species. The fact that friendship may be a widespread biological phenomenon could help us better understand why it has such a positive effect on our own health.

If you’re interested in the scientific literature, the best way in–and the way I first started to get familiar with it–is this review in the latest issue of Annual Review of Psychology by Dorothy Cheney and Robert Seyfarth, two of the world’s leading primatologists.

One thing that I delve into in the story is the question of just how widespread animal friendship really is. We don’t know, in large part because scientists haven’t done that many long-term field studies on wild animals. When scientists do watch dolphins or baboons for decades, they can see some bonds between unrelated individuals that last for long stretches. (Yet another value that comes from slow-cooked science.) On the other hand, what may look like friendship may just be anthropomorphic projection. In the article, I explain that a lot of cross-species “friendships” may be nothing like the kind seen in, say, chimpanzees. (As for the adorable dogs are on this week’s cover of Time, I note that the evidence about man’s best “friend” is quite thin.)

My story is behind a paywall, so you’ll need to subscribe or pick up a copy at a news stand. For a sense of the piece, here are the first few paragraphs–

Since 1995, John Mitani, a primatologist at the University of Michigan, has been going to Uganda to study 160 chimpanzees that live in the forests of Kibale National Park. Seventeen years is a long time to spend watching wild animals, and after a while it’s rare to see truly new behavior. That’s why Mitani loves to tell the tale of a pair of older males in the Kibale group that the researchers named Hare and Ellington.

Hare and Ellington weren’t related, yet when they went on hunting trips with other males, they’d share prey with each other rather than compete for it. If Ellington reached out a hand, Hare would give him a piece of meat. If one of them got into a fight, the other would back him up. Hare and Ellington would spend entire days traveling through the forest together. Sometimes they’d be side by side. Other times, they’d be 100 yards apart, staying in touch through the foliage with loud, hooting calls. “They’d always be yakking at each other,” says Mitani.

Their friendship—for that’s what Mitani calls it—lasted until Ellington’s death in 2002. What happened next was striking and sad. For all the years that Mitani had followed him, Hare had been a sociable, high-ranking ape. But when Ellington died, Hare went through a sudden change. “He dropped out,” says Mitani. “He just didn’t want to be with anybody for several weeks. He seemed to go into mourning.”

For anyone in the US who likes to know what it’s like inside a giraffe (hands up, people), it was frustrating to discover the show Inside Nature’s Giants airing on British TV. The best we could manage were snippets on YouTube. Now the show is here in the States. The other day I spent some time with one of the main scientists of the show, Joy Reidenberg, an anatomist at Mount Sinai School of  Medicine. I’ve written a profile of her, both as a researcher who’s discovering fascinating new things about whales, and as that most improbable thing: a celebrity anatomist. Check it out.

Be sure to take a look at the extras on the page, such as the podcast, video, and graphic instructions for how to dissect a 50-ton whale.

[Photo courtesy of Joy Reidenberg]

Michael Osterholm, his face a pink-cheeked scowl, looked out across the table, beyond the packed room at the New York Academy of Sciences, and out through the windows. The New York Academy of Sciences is housed on the fortieth floor of 7 World Trade Center, and their endless bank of windows affords a staggering view of Manhattan, Brooklyn, and New Jersey. One reason that its view is so magnificent is that there’s a huge gap in the skyline–and a huge gouge in the ground–where the Twin Towers once stood.

Osterholm had come here from Minnesota, where he runs a research center for infections diseases and terrorism, to talk Thursday night about the threat of a new kind of flu sitting in labs in the Netherlands and Wisconsin. In nature, it’s a flu that spreads easily between birds but doesn’t travel well from human to human. The Dutch and Wisconsin scientists had found ways to get this bird flu, known as H5N1, to move between ferrets. For Osterholm, ferrets were uncomfortably close to humans on the evolutionary tree. And so he, along with other members of an advisory board, issued a recommendation in December that key information in the papers about the research should be left out.

Osterholm looked out at the empty space beyond the windows. “Who would have imagined that you could use box cutters to take down the World Trade Center?” Osterholm asked. The risk from the new bird flu might seem equally unlikely, he warned, but it could end up being far more devastating. “We can’t afford to be wrong.”

The bird flu controversy first started to bubble up in September, when Ron Fouchier of the Erasmus Medical Center in Rotterdam described some of his unpublished results at a scientific meeting in Malta. It kicked into high gear when the National Science Advisory Board on Biosecurity issued their ruling, which Fouchier and Yoshihiro Kawaoka have agreed to. In January, the researchers agreed to stop doing any H5N1 research for two months, during which time the scientific community would try to come up with a plan about how to deal with such controversial research.

Viruses very often spark controversies, but often the controversy is between the scientists who study them and groups of people beyond the academy. Think of HIV denialism, of the non-existent link between vaccines and autism, of the purported connection between the XMRV virus and chronic fatigue syndrome. The new bird flu controversy is different. It’s split the scientific community wide open. I’ve written about this controversy in recent weeks over at Slate, as well as here at the Loom. Like most reporters covering the story, I’ve sampled the sharply opposing viewpoints of scientists over the phone or via emails. But on Thursday night, we got to see this debate in person. The New York Academy of Sciences brought together a group of experts to talk about new virus, and whether self-censorship is a prudent protection or a dangerous precedent. I wasn’t sure what to expect; I was a bit worried it might have turned out to be a fairly dry discussion of how to inspect the hood equipment in virus labs. Instead, we witnessed explosive confrontation between scientists who think we may be facing a world-destroying catastrophe, and others who think our fear of non-existent threats is going to destroy science’s power to help us out of clear and present dangers.

The panel included two members of the National Science Advisory Board on Biosecurity: Michael Osterholm and Arturo Casadevall of Albert Einstein College of Medicine. They both made it clear that they were speaking at the meeting as individuals, rather than as official spokesmen for the board. But they presented a fairly united front. The board has been around for eight years, and it has only considered issuing a recommendation twice. The first time was in 2005, when scientists unearthed the bodies of victims of the 1918 flu epidemic, which killed an estimated 50 million people. The researchers isolated the 1918 virus and sequenced its genes. The board decided they had no objections about publishing the research. But six years later, they decided that, as bad as the 1918 flu might have been, the risk of an H5N1 outbreak was worse.

One big factor in their recent decision was the mortality rate when H5N1 gets into people. The World Health Organization’s official estimate is 60%. The 1918 flu, by contrast, had a death rate of about two percent. If H5N1 could gain the ability to spread among humans–either naturally, or through a lab experiment–it could bring that fearsome death rate to the entire world. “It’s the lion king of infectious diseases,” Osterholm said, no doubt dismaying Disney lawyers across the country.

Sitting a few seats down the panel from Osterholm was Peter Palese, one of the world’s leading experts on flu, who works at Mount Sinai Medical School. Palese disputed Osterholm’s apocalyptic warnings. Where Osterholm burned hot, Palese kept cool, but he did not hide his utter rejection of the board’s decision. Just because a flu virus can be transmitted by another mammal species, he argued, doesn’t automatically mean it can spread among humans. In fact, ferrets are rather delicate in the face of a flu infections, easily suffering from brain damage. Our closer relatives among the primates, by contrast, don’t get sick from flu at all. (Jon Cohen explores the ferret question in depth in a news article for Science.)

Palese also questioned whether H5N1 is all that dangerous. He argued that the World Health Organization based its mortality rate only on the people who came into hospitals and tested positive for H5N1. But this particular strain of bird flu mostly strikes people in poor countries, especially in southeast Asia, where medical services are scarce. The people who make it to a hospital could well be a small fraction of all the people who come down with H5N1.

“The asymptomatic people are not being counted,” Palese said. If those extra people only got sick for a few days and then got on with their lives, the true mortality rate might be far less than 60% “It’s really much lower,” he said, pointing to surveys in Thailand and other countries that revealed evidence that a fair number of people had been exposed to H5N1 at some point in the past. (Palese recently published this same argument in the Proceedings of the National Academy of Sciences.)

This argument positively enraged Osterholm. He had clearly read Palese’s recent PNAS commentary and had prepared a rebuttal. “What you’re saying is just propaganda,” he told Palese. The trouble with Palese’s numbers were that they came from lousy studies, Osterholm argued. There are many ways to overestimate how many people have been exposed to a particular virus. A common test involves fishing for antibodies in blood samples. If your test isn’t precise enough, you may end up dredging up antibodies to other viruses. Osterholm had gone through surveys of H5N1 exposure, setting aside the lousy studies and tallying up the results from the best of the bunch. He came up with an estimate of .6% or less. If very few people have been exposed, the recorded deaths from H5N1 represent a frighteningly high rate.

Casadevall granted that perhaps H5N1 wasn’t 60% fatal. But it could be half that and still be a planetary nightmare. Even if it was ten times lower, it would still be far worse than the 1918 flu. “The numbers of unbelievable, any way you look at it,” he said.

Palese was unmoved. The new H5N1 viruses might pose a risk–a small one, in Palese’s mind–but scientists could handle it. All the research that had triggered the controversy wasn’t conducted in someone’s backyard. It was carried out in well-protected labs. Palese noted that the board doesn’t seem to have any objections to the work that’s done these days on smallpox, a virus that killed millions of people every year until it was eradicated in the 1970s. If scientists can in fact safely experiment with dangerous viruses, there is no need to paralyze the scientific community over bird flu. “You can always assume the worst,” Palese said. “But where do we stop being afraid?”

Osterholm glowered at Palese. “You do not represent the mainstream of influenzologists when it comes to this issue on influenza,” he said. I glanced at some of the other journalist in the audience, wondering if Osterholm could see us scribbling notes.

Osterholm stressed that he was not against research on bird flu in general. He just wanted the scientific community to balance the potential costs and benefits. He didn’t see very much significance in the new bird flu work. It wouldn’t help public health workers monitoring H5N1 viruses for lineages that might be evolving into a human pathogen. Nor did he see any benefit for developing vaccines or antivirals. On the other hand, he saw a risk–a small one, possibly–of tremendous devastation.

But when it comes to viruses can we really calculate such ratios of costs to benefits? Vincent Racaniello, a Columbia University virologist who was also on the panel, doesn’t think so. We’re bad at estimating risks. In 1981, for example, Racaniello and his colleagues pioneered a method for making polio viruses: they stuck the virus’s genes on a ring of DNA called a plasmid, which they then inserted into E. coli bacteria. The engineered E. coli spewed out polio genes, which Racaniello could insert into human culture cells, which then made full-blown polio viruses. People worried that Racaniello’s bacteria would get into people’s guts and start a polio epidemic. (It didn’t.)

We’re also bad at determining the benefits of research. Racaniello recalled how microbiologists in the 1950s discovered that E. coli defend themselves against invading viruses by chopping up their genes. Nobody thought much of that discovery for over a decade. But then in the late 1960s, a few researchers realized that they could use E. coli’s enzymes to cut up DNA and then paste them into new combinations. The entire biotechnology industry was born from that late eureka.

“You could have never predicted that,” said Racaniello. “You never know who will do the right experiment. So that’s why you need to give the information to everyone.”

The way things stand right now, everyone will not be getting that information. I tried to follow the reasoning for holding back key parts of the studies, but, honestly, I can’t recount it in a way that makes sense. As far as I could tell, the thinking was somebody just fooling around out of curiosity would be able to use the full information to create a deadly flu. But the fact is that the scientists who produced the new bird flu used standard methods that have been published many times over. I was also confused by how Nature and Science, the two journals where the redacted papers are to be published, will handle distributing the information to those who need to know about it. An editor from Nature talked about how hard it would be to set up a system. I had been expecting them to have a system to unveil for us.

“None of us ever wants to see a redaction again,” said Casadevall. The most sensible way to avoid that would be to figure out a way to make decisions about risks and benefits much earlier in the life cycle of an experiment. If the mission of an experiment is to create a deadly virus, just to see if it can be done, the panelists agreed that that is probably not a study to run. But what kind of system can stop not just these experiments, but other experiments that might present unexpected dangers? Casadevall worries that every graduate student may have to fill out 100-page forms for even the most harmless of experiments. “You’ll kill science,” he said.

Casadevall was expressing a concern that all the scientists on the panel shared: they worry that this affair will keep them from doing research. For now, they’re trying to work out a fairly self-regulating system to handle this sort of controversial research, perhaps in the hopes that the government won’t come sweeping in. But there was one non-scientist on the panel who did her best to make the scientists aware of the world outside their community.

Laurie Garrett, an award-winning health reporter who now works at the Council on Foreign Relations, pointed out that the flu is not just something that American scientists study in their labs. It’s a global problem. There’s a huge amount of resentment in poor countries where bird flu is the biggest threat, not just to humans, but to the poultry industry. “Poor people are killing their chickens for you,” Garrett said. “They’re going bankrupt.”

Making matters worse, as Garrett has recently written, is the distrust that has developed in the developing world towards Western medical research and the pharmaceutical industry. Indonesia, where many of the H5N1 deaths have occurred, has been reluctant to share bird flu samples with Western scientists, for fear that they would make huge profits from vaccines developed from them. The World Health Organization has set up an international agreement for the exchange of wild bird flu strains between different countries, but it’s in fragile shape.

So for all the sparks that flew in New York Thursday night, the real fireworks over the flu are yet to come.

[Update 2/3 9 am: Corrected description of Racaniello's experiment. Thanks to Matt Frieman. 2:50 pm Fixed Fouchier's institution name and month of his talk. Thanks to Jon Cohen. 8 pm: Expanded Osterholm's "mainstream of influenzologists" quote after seeing his objection to a similarly truncated version in Christine Gorman's story for Scientific American and reviewing my own recording. It's a valid clarification .]

The novelist Jonathan Franzen delivered quite a rant about e-books the other day. He’s deeply wrong, as I explain at the Crux by going shopping for a copy of The Great Gatsby. Check it out.

Charles Darwin recognized that natural selection can make eyes sharper, muscles stronger, and fur thicker. But evolution does more than just improve what’s already there. It also gives rise to entirely new things—like eyes and muscles and fur. To study how new things evolve, biologists usually have to rely on ancient clues left behind for hundreds of millions of years. But in a study published today, scientists at Michigan State University show that it’s possible to watch something new evolve in front of their eyes, in just a couple weeks.

The scientists were studying a virus, which evolved a new way of invading cells. As a result, their research not only sheds light on a fundamental question about evolution. It also suggests that it may worryingly easy for viruses such as influenza to turn into new epidemics. Check it out.

[Image of lambda virus: AJC1 on Flickr via Creative Commons]

In yesterday’s New York Times, I wrote about a new paper in which scientists report the evolution of single-celled yeast into multicellular snowflake-like “bodies.” Most (but not all) of the experts I contacted for the story had high praise for the study. (It also won an award when it was presented as a talk over the summer at the Society for the Study of Evolution.) Once the story appeared, however, some scientists took to Twitter to express their skepticism. As much as I like Twitter, this is one of the situations where it fails. You can’t have a conversation about genetics, lab strains versus wild types, etc., in 140 character chunks. At least not very satisfying ones.

So here’s what I decided to do last night. I used Storify to collect the comments of Leonid Kruglyak of Princeton and Michael Eisen of Berkeley, and then passed them on to Will Ratcliff, the lead author of the new study. He then responded. Below you’ll find the Storify tweets, and then Ratcliff’s response. Please continue the conversation in the comment thread. (And be sure to download the paper–it’s open access.)

Will Ratcliff responds:

Well, I don’t buy it that yeast are multicellular in nature. Certainly some yeast in nature form small clusters (like strain RM11), but as far as I know, these are the exception to the rule. Most strains isolated in nature are unicellular, or at most, flocculating (which I still count as unicellular but social). [CZ: "Flocculating" refers to the clumps that unrelated yeast cells form when they starve.]

Our yeast are not utilizing ‘latent’ multicellular genes and reverting back to their wild state. The initial evolution of snowflake yeast is the result of mutations that break the normal mitotic reproductive process, preventing daughter cells from being released as they normally would when division is complete. Again, we know from knockout libraries that this phenotype can be a consequence of many different mutations. This is a loss of function, not a gain of function. You could probably evolve a similar phenotype in nearly any microbe (other than bacteria, binary fission is a fundamentally different process). We find that it is actually much harder to go back to unicellularity once snowflake yeast have evolved, because there are many more ways to break something via mutation than fix it. The amazing thing we see is that we rapidly see adaptations to this adaptation. If we select for more rapid settling, snowflake yeast evolve to delay reproduction until the parent is larger, allowing it settle more quickly. We see the evolution of higher rates of apoptosis as a way to regulate the size and number of propagules produced. We show that the transition to multicellularity in yeast is surprisingly easy, and have no reason to suspect it would be any harder in other microbes with a reproductive process similar to yeast.

In the history of life, single-celled microbes have evolved into multicellular bodies at least 25 times. In our own lineage, our ancestors crossed over some 700 million years ago. In tomorrow’s New York Times, I write about a new study in which single-celled yeast evolved into multicellular forms–completely with juvenile and adult forms, different cell types, and the ability to split off propagules like plant cuttings. All this in a matter of weeks. Check it out.

(The paper is not yet online yet, but here’s the reference: “Experimental evolution of multicellularity,” William C. Ratcliff, R. Ford Denison, Mark Borrello, and Michael Travisano. Proceedings of the National Academy of Sciences. http://www.pnas.org/cgi/doi/10.1073/pnas.1115323109 )

Update: Here’s a Twitter-Storify-blog follow up on some reactions to the study.

Each year, literary agent and science salonista John Brockman poses a question about science and gets a slew of answers from scientists, writers, and other folks. This year’s question is

WHAT IS YOUR FAVORITE DEEP, ELEGANT, OR BEAUTIFUL EXPLANATION?

Brockman got 187 responses, totaling some 126,700 words. A book, you say! Well, if this year is like previous ones, this year’s answers will indeed become a book. But in the meantime, you can browse the answers for yourself, perhaps plucking out those of your favorite people. (Fellow Discover blogger cosmologist Sean Carroll chooses Einstein’s explanation of gravity, for example.)

I found this year’s question particularly thought-provoking. Why is it that we call an equation or a theory “beautiful”? They don’t have pretty hazel eyes. They aren’t desert landscapes. I’m not sure of the answer. Scientific explanations seem to be beautiful if they give sense to confusing complexity in a very short space. Or maybe we just like the feeling we get when we consider how our puny human brains can interpret the universe.

For a lot of physicists, the beauty of an equation seems to be a good hint that it’s probably true. But I’m always a bit suspicious of beauty as a guide to the natural world. A number of contributors selected Darwin’s theory of evolution as their favorite explanation, and there’s no doubt that’s both beautiful and true. But there have been some wonderfully beautiful accounts of the natural world that have proven awesomely wrong. I was reminded of this fact while working on a new version of my evolution textbook (this one’s for biology majors). I was re-researching how scientists first came to appreciate the vast age of our planet, and realized it was a bit more complicated than I had previously appreciated. So that’s what I chose as my answer, which I’m reprinting here in full:

A Hot Young Earth: Unquestionably Beautiful and Stunningly Wrong

Around 4.567 billion years ago, a giant cloud of dust collapsed in on itself. At the center of the cloud our Sun began to burn, while the outlying dust grains began to stick together as they orbited the new star. Within a million years, those clumps of dust had become protoplanets. Within about 50 million years, our own planet had already reached about half its current size. As more protoplanets crashed into Earth, it continued to grow. All told, it may have taken another fifty million years to reach its full size—a time during which a Mars-sized planet crashed into it, leaving behind a token of its visit: our Moon.

The formation of the Earth commands our greatest powers of imagination. It is primordially magnificent. But elegant is not the word I’d use to describe the explanation I just sketched out. Scientists did not derive it from first principles. There is no equivalent of E=mc2 that predicts how the complex violence of the early Solar System produced a watery planet that could support life.

In fact, the only reason that we now know so much about how the Earth formed is because geologists freed themselves from a seductively elegant explanation that was foisted on them 150 years ago. It was unquestionably beautiful, and stunningly wrong.

The explanation was the work of one of the greatest physicists of the nineteenth century, William Thompson (a k a Lord Kelvin). Kelvin’s accomplishments ranged from the concrete (figuring out how to lay a telegraph cable from Europe to America) to the abstract (the first and second laws of thermodynamics). Kelvin spent much of his career writing equations that could let him calculate how fast hot things got cold. Kelvin realized that he could use these equations to estimate how old the Earth is. “The mathematical theory on which these estimates are founded is very simple,” Kelvin declared when he unveiled it in 1862.

At the time, scientists generally agreed that the Earth had started out as a ball of molten rock and had been cooling ever since. Such a birth would explain why rocks are hot at the bottom of mine shafts: the surface of the Earth was the first part to cool, and ever since, the remaining heat inside the planet has been flowing out into space. Kelvin reasoned that over time, the planet should steadily grow cooler. He used his equations to calculate how long it should take for a molten sphere of rock to cool to Earth’s current temperature, with its observed rate of heat flow. His verdict was a brief 98 million years.

Geologists howled in protest. They didn’t know how old the Earth was, but they thought in billions of years, not millions. Charles Darwin—who was a geologist first and then a biologist later—estimated that it had taken 300 million years for a valley in England to erode into its current shape. The Earth itself, Darwin argued, was far older. And later, when Darwin published his theory of evolution, he took it for granted that the Earth was inconceivably old. That luxury of time provided room for evolution to work slowly and imperceptibly.

Kelvin didn’t care. His explanation was so elegant, so beautiful, so simple that it had to be right. It didn’t matter how much trouble it caused for other scientists who would ignore thermodynamics. In fact, Kelvin made even more trouble for geologists when he took another look at his equations. He decided his first estimate had been too generous. The Earth might be only 10 million years old.

It turned out that Kelvin was wrong, but not because his equations were ugly or inelegant. They were flawless. The problem lay in the model of the Earth to which Kelvins applied his equations.

The story of Kelvin’s refutation got a bit garbled in later years. Many people (myself included) have mistakenly claimed that his error stemmed from his ignorance of radioactivity. Radioactivity was only discovered in the early 1900s as physicists worked out quantum physics. The physicist Ernst Rutherford declared that the heat released as radioactive atom broke down inside the Earth kept it warmer than it would be otherwise. Thus a hot Earth did not have to be a young Earth.

It’s true that radioactivity does give off heat, but there isn’t enough inside the planet is to account for the heat flowing out of it. Instead, Kelvin’s real mistake was assuming that the Earth was just a solid ball of rock. In reality, the rock flows like syrup, its heat lifting it up towards the crust, where it cools and then sinks back into the depths once more. This stirring of the Earth is what causes earthquakes, drives old crust down into the depths of the planet, and creates fresh crust at ocean ridges. It also drives heat up into the crust at a much greater rate than Kelvin envisioned.

That’s not to say that radioactivity didn’t have its own part to play in showing that Kelvin was wrong. Physicists realized that the tick-tock of radioactive decay created a clock that they could use to estimate the age of rocks with exquisite precision. Thus we can now say that the Earth is not just billions of years old, but 4.567 billion.

Elegance unquestionably plays a big part in the advancement of science. The mathematical simplicity of quantum physics is lovely to behold. But in the hands of geologists, quantum physics has brought to light the glorious, messy, and very inelegant history of our planet.

[Post-script: Thanks to responses from readers, I can see how this essay is confusing. I added some passages from the papers I cite below down in the comment thread, which I hope can clear things up a bit.]

[Update: For an up-to-date review of the age and formation of the Earth, see this paper [abstract, free pdf] For a great look at Kelvin’s work, see this piece in American Scientist or the more technical paper on which it was based (free pdf).]

[Image: Photo by Hawaiian Sea - http://flic.kr/p/8AyKnC via Creative Commons]

Over on Facebook, David Hillis, an evolutionary biologist at the University of Texas, took up my question as to whether anyone can define life in three words. His short answer was no, but his long answer, which I’ve stitched together here from a series of comments he wrote, was very interesting (links are mine):

Like all historical entities (including other biological taxa), it is only sensible to “define” Life ostensively (by pointing to it, noting when and where it began, and following its lineages from there) rather than intensionally (using a list of characteristics). This applies to the taxon we call Life (hence capitalized, as a formal name). You could define a class concept called life (not a formal taxon), but then that concept would clearly differ from person to person (whereas it is much less problematic to note examples of the taxon Life). So, I’d say that I can point to and circumscribe Life, and that it the appropriate way to “define” any biological taxon. A list of its unique characteristics is then a diagnosis, rather than a definition. So, I’d argue that any intensional definition of Life is illogical (does not recognize the nature of Life), no matter how many words are used.

Defining Life (the taxon) is like defining other particular historical entities. We don’t “define” Carl Zimmer or the United States of America by listing out their attributes. Instead, we point to their origin and history. The same should be true for Life. If we ever discover a Life2, we’ll have a new origin and history to point to.

The question people actually want to ask is “Are there entities in the universe that are similar to the Life we know about here on Earth?” The answer, of course, depends on what people mean by the arbitrary meaning of “similar”. One person might answer “I mean ‘self-replicating with variations’.” Then, the answer is yes: humans have created imperfectly self-replicating systems (“artificial life”) here on Earth. But then someone else says “But that is not what I meant by similar…I meant that they had to have metabolism and cellular structure and a nucelic-acid-based genetic system.” OK, then we have to keep looking to find something that similar. But then someone else says “But that’s pretty arbitrary…I’d still consider it alive if it didn’t have cellular structure.” Exactly…it is indeed arbitrary to argue over how similar something has to be to consider it “similar” to Life. So, in the end, we can ostensively define Life (by referencing its origin and history), and we can do the same for other historical entities that some people might also want to say are alive, but there can be no simple “right” answer that will satisfy everyone about which entities should be considered alive, because we all emphasize different characteristics in defining an arbitrary class concept of “life”.

We are all sure we know what life is, but if you try to actually define it, things get tricky fast. I wrote a feature about the scientific struggle to define life in 2007 for Seed, and I’ve been keeping tabs on the evolution of this metaphysical quandary ever since. I was particularly intrigued to discover recently that one scientist thinks he can define life–and do so in just three words. I’ve written an essay about his short and sweet definition for the web magazine Txchnologist. Check it out.

I’ve just written a profile of the astrophysicist Neil deGrasse Tyson, perhaps the best-known scientific figure in America. Here’s how it opens:

On a hay-mown crest, dozens of people are crouching in the dark. The Earth has turned away from the sun, and the sky has flowed down a color chart, from light gray to orange to bluish-black. A sliver of a waxing moon has appeared briefly and then slipped below the western horizon, leaving the sky to blinking airplanes rising from La Guardia fifty miles to the south, to satellites gliding in low orbit, to Jupiter and its herd of moons and to the great river of the Milky Way beyond.

The crowd that sits in this chilly field in North Salem, New York, is surrounded by a ring of telescopes. There’s a Dobsonian, a giant barrel-shaped contraption that’s so tall you have to climb a stepladder to look through its eyepiece. Small, squat Newtonian cylinders sit on tripods, rigged to computers that give off a weak lamp-glow from their monitors. A few older men are fussing over the telescopes, but everyone else is huddled on the grass.

“Just get snuggly. There’s nothing wrong with that. Get snuggly.”

The voice is deep and loud–not loud from shouting, but from some strange acoustic property that gives it a conversational boom. It comes from a man who looms in the dark at the edge of the crowd.

“We still have the remnants of what we typically call the Summer Triangle,” he says. “And the Summer Triangle is three stars that are about equally bright. So, one is here–”

“Oh my God,” the crowd murmurs.

The looming figure is Neil Tyson, the director of the Rose Center for Earth and Space at the American Museum of Natural History. He has just put the crowd into a swoon by switching on a laser and pointing it towards the zenith of the sky. The green beam seems to reach up from the field and touch the star.

“And one is here, and here,” he says, sweeping the laser across the sky to mark a stellar triangle. The squatters gasp, swear again, and laugh at themselves. Tyson’s laser is creating an optical illusion: he seems to pull the sky down into a dome that floats close overhead, like an astronomical Sistine Chapel.

“Here we have Deneb,” he says. “Everyone say Deneb!”

“Deneb!”

“Good. And down here we have Altair.”

“Altair!”

“And up here we have Vega.”

“Vega!”

“One of the telescopes is actually trained on a star that’s in the middle of this triangle,” Tyson says, moving his laser to a faint dot, called Albireo. “It’s right there. It doesn’t look very interesting at first, but when you whip out a telescope, what you’ll find is that this star is not alone, as a solo star. It has a companion star. Albireo is in fact my favorite star of the night sky. If you look closely, one star is this brilliant, beautiful blue color and the other is gold. And we know from astrophysics what must be true if an object is glowing at one or the other of those colors. Unlike what an artist will tell you, something glowing red-hot is the coolest among all the hots. You get way hotter than red-hot. If you crank the temperature, it becomes white hot. Crank it some more, it then begins to glow blue.”

Tyson moves the laser to other regions of the sky, to the feeble North Star, to Cassiopeia, to Sagittarius. As he talks, the people huddling on the ground blast questions at him. Where is Venus? Is that a satellite? Is that a satellite? Is the Chinese calendar based on the lunar cycle? Tyson stops to answer each question. He twirls his laser in a tight circle midway down the handle of the Big Dipper.

“If you look really carefully at it, you should be able to see two stars there,” he says. “How good is your vision?”

“Awesome!” a boy says.

“I can see it!” says another.

“Okay, who cannot see two stars inside my little circle here?” Tyson asks.

“Me,” says a third.

“Okay, therefore you cannot be drafted into the Roman army,” says Tyson. “That was their eye test. So this pair of stars is called Mizar and Alcor. Mizar is the brighter of the two. Alcor is the dimmer of the two. This is a very loosely bound double-star system. If you take out a telescope and point it on Mizar, that’s a double star. Then if you take the telescope and point it on the brighter of the two stars that is the bright of these two stars, that’s a double star. So what you have here,” Tyson says, “is a double-double-double star system. All in mutual, harmonious orbit around their common center of gravity. Such is the lay-out of this cosmic ballet that we call the universe.”

For most of the people huddling on the ground, tonight is the first time they’ve spent such an extended period looking up at the sky. For three hours, Tyson keeps his audience staring so hard at the heavens he cramps their necks. He speaks of galaxies and the delusions of astrology, how to calculate latitude, the fate of the universe. It is not a lecture. He delivers something more akin to a solo concert. Although he is a card-carrying astrophysicist with a long list of scientific papers in publications like Astrophysical Journal, Tyson has turned himself into a rock-star scientist. He plays to sold-out houses. He appears on the Daily Show with Jon Stewart, on the New York Times bestseller list, on Twitter (@neiltyson, with 242,400 followers as I write this). He is now shooting a remake of Carl Sagan’s classic Cosmos series, which will air on Fox in 2013.

Tyson spreads himself so wide for two reasons. One is that there’s so much in the sky to talk about. The other reason is down here on earth. For all the spectacular advances American science has made over the past century–not just in astrophysics but in biology, engineering, and other disciplines–the best days of American science may be behind us. And as American science declines, so does America. So here, in the dark, under the stars, Tyson is going to try to save the future, one neck cramp at a time.

The profile appears in the new issue of Playboy. It’s not online at their site, but I’ve posted the full story on carlzimmer.com. Check it out.

[Image: Photo by Greyhawk68, Flickr, via Creative Commons]

In 2011, the Loom reached its eighth birthday. Thanks to everyone who’s paid a visit or become a loyal reader in that time. With the year coming to a close, I spent a little time this week perusing the Loom’s archive, reflecting on the things that obsessed me during 2011.

More than many years, this one reminded me just how huge science is. Even if you limited yourself to the most important stories of this past year, there was just too much to keep up with. (Here’s Discover’s top 100 picks.) As a science writer, my focus is biology, but that didn’t ease my year-long case of head-spinning. The anchors that kept me from spinning away completely were the very small and the very complicated.

At the small end of the spectrum were, among other things, the bacteria that call us home. Like every year, 2011 saw outbreaks, such as the E. coli that sickened thousands in Germany. But now that we can read the genomes of these killers,  as I noted in Newsweek, we can see how chillingly fast new pathogens can evolve.

But the good germs also gained more recognition in 2011. The science of the microbiome is blooming at an astonishing pace, as you can see in the map I created for the September issue of Wired. As I got more familiar with the microbiome, it became clear to me that scientists won’t be able to handle its complexity without thinking like ecologists. I made that point in a talk this spring called “The Human Lake,” which I turned into a blog post in April. (I was delighted when it was selected as one of the best pieces of 2011 by The Browser and Longreads, and was picked to be including in the 2012 edition of Open Lab.)

The microbiome, I predict, is going to become very intimate in years to come. It’s a strangely thrilling experience to discover 53 species of bacteria living in one’s belly button, as I found out this year. In the future, doctors may check our bug types just as they check our blood types today. But all this new knowledge about the microbiome will bring us unexpected  ethical quandaries, some of which I discussed in December in the New York Times.

Bacteria may be small, but they’re positively plus-sized compared to viruses, the subject of my book A Planet of Viruses, which came out in May. (You can read excerpts in Audubon and i09.) Working on the book opened my eyes to just how abundant, diverse, and powerful viruses are–a point I tried to get across in the talks I gave in the spring. The two that I was happiest with were an interview on Science Friday on NPR, and a talk I gave at the Long Now Foundation in San Francisco. As always happens when I write a book about a fast-moving field, the science of virology offered up lots of surprises after the book came out–such as the biggest virus ever, a possible ancestor of hepatitis C in dogs, and signs of a battle between viruses and bacteria in our mouths. When the movie Contagion came out in September, I took a look in Slate at how realistic its story of a new world-wide pandemic was. I found it real enough to be very scary. And in an eerie bit of timing, this fall scientists developed a strain of bird flu that some researchers worry could make the movie a reality.

At the other end of the spectrum from bacteria and viruses is the human brain, those 100 billion neurons that make the universe aware of itself. There seems to be no end of revelatory research coming out of neuroscience and psychology. At the World Science Festival, I talked with three scientists doing extraordinary work on the mystery of sleep (you can watch the video here). In my own stories, I explored genes for language, teen brains, music in the brain, the neuroscience of smiles, how our brains make us capable of both war and peace, and the minds of Neanderthals. A lot of the pieces I wrote first appeared in the New York Times or magazines, but some of them have gotten a new lease on life. I published a new ebook in December, More Brain Cuttings, and my feature on the possibility of uploading our brains to achieve immortality was selected for The Best of American Science Writing 2011.

In 2011, it wasn’t just new science that was in the news. The nature of science was, too. Over the course of 2011, some high-profile papers came under fierce criticism, including arsenic-based life and a link between viruses and chronic fatigue syndrome. These studies prompted a debate about how science gets done in the first place, and how some of it then gets “de-discovered.” I pondered the nature of de-discovery in the New York Times in July, and the emergence of a more transparent discussion of science in Slate.

A lot of that discussion happened on Twitter. Twitter was just one of many new media that became more widespread this year. And just as scientists were getting comfortable with these channels of communication, science writers were too. I spent a fair amount of time in 2011 experimenting with different formats. On Twitter, I went after some egregiously bad science with a hashtag: #Greenfieldism. When I wasn’t on Twitter, I was often on Facebook, Tumblr, and Google+. Each medium has different strengths, I’ve found, which only emerge after playing around with it for a while. Google+ has spurred some fascinating discussions; Twitter is a fast way to spread links. I spent some time working with the folks at Radiolab this year, including the newly minted Macarthur genius Jad Abumrad. It was fascinating to see them turn spoken words into symphonies, such as this episode entitled “Patient Zero.” Another form of storytelling can be found at Story Collider, where people tell tales live in front of an audience. An invitation to be a part of a Story Collider evening led me to talk about how a trip to a war zone made me realize just how deeply science speaks to me. And at the end of the year I published Science Ink, a book born out of a blog-based obsession with science tattoos.

It was a strange year indeed when a traditional book felt like a fresh new format. And it makes me eager for the surprises waiting for us in 2012.

[Image: Wikipedia]