Eckard Wimmer makes viruses from scratch. When he first made a polio virus out of raw ingredients in 2002, some congressmen drafted a resolution to condemn him. Today, he’s making viruses that act like vaccines.

Wimmer was one of several virologists I called over the past couple days to talk about the controversy swirling around altered bird flu viruses that have the scientific community deeply worried. Their reactions are all over the board, from those who think the research shouldn’t have even been done in the first place to others who want the research published in full and replicated many times over. My report is over at Slate. It’s a debate that gets to the heart of the scientific process in the twenty-first century. Check it out.

I’ve written a few times here about the battle over a virus called XMRV, and its supposed link to chronic fatigue system. I just wanted to point this morning to a few articles by some fine writers about the latest twist: the paper that first claimed a link has been completely retracted.

Ivan Oransky in Reuters

Jon Cohen in Science

Ewen Callaway in Nature

[Image: Wikipedia]

In this week’s issue of Nature, I write about the revolution that technology is bringing to the world of books. It’s a subject that’s been on my mind a lot recently. I’ve been experimenting with e-books myself, and I’ve been giving some talks about them (I’ll be helping to lead a discussion at Science Online 2012 in January).

My essay is accompanied by this funny picture. The guy looks a lot like me, but, strictly speaking, it should be my wife sitting atop the pile of books, with seagulls for company:

In the summer of 2010, on a tiny island off the coast of Maine, I saw the future of books. I had been invited to teach a writing course at Shoals Marine Laboratory on Appledore Island, a beautiful bulge of rock covered in scrub and herring-gull nests. During a break at the beach with my family, my wife finished reading her book with typical supersonic speed. She craved another, so decided to experiment with her new iPhone.

She tapped the screen. In seconds, an e-book had streamed invisibly through the air into her hand. Swiping her thumb like a windshield wiper, she soon finished it. She tapped the screen for another. Out of the ether, another e-book appeared.

Now I see, I thought. Everything was in place for a revolution in how we read and write. And the pace of that revolution has surpassed my expectations. Since Apple launched its iBooks application in April 2010, some 180 million books have been downloaded. Analysts estimate that Amazon will have sold 314 million e-books for the Kindle in 2011 alone. The radical change extends far beyond sales volume: the e-book ecosystem allows writers to reach readers in ways that did not exist before.

You can read the rest here. (Sub. required.)

Eric Michael Johnson, an historian of science, is also the writer behind an excellent blog, “The Primate Diaries.” The other day he gave me a call to talk about science writing. He put together a two-part Q&A that he published today (part one and part two) that ranges from the science writing in Moby Dick to the microscopic virtues of Twitter. I was particularly flattered to get a portrait done by Nathaniel Gold. Check it out!

Recently I blogged about a new strain of potentially dangerous flu that evolved during experiments in the Netherlands and Wisconsin. There I tried to counter the misconception that scientists had intentionally concocted this particular strain. Because these new flus actually evolved pretty quickly in laboratories, we now know we should take seriously the possibility that this transformation may happen in the outside world someday.

But there’s a second issue at play with this new virus: should the world get to see its genome?

As Martin Enserink reported last month, both teams of scientists have submitted their papers for publication. Normally, such a paper might include the entire genome of the new viruses. This was a touchy subject, so the papers went under review by the U.S. National Science Advisory Board for Biosecurity (NSABB).

Today, the editors at Science passed on the NSABB’s reccommendations. I’ll quote them here in full:

The National Science Advisory Board for Biosecurity (NSABB) made the following
recommendations regarding the publication of two manuscripts on highly pathogenic avian
influenza A/H5N1:

1. Neither manuscript should be published with complete data and experimental details.

2. Conclusions of the manuscripts be published but without experimental details and
mutation data that would enable replication of the experiments.

a) Text should be added describing: 1) the goals of the research, 2) the potential
benefits to public health (including informing surveillance efforts, pandemic
preparedness activities, and countermeasure development and stockpiling efforts), 3)
the risk assessments performed prior to research initiation, 4) the ongoing biosafety
oversight, containment, and occupational health measures, 5) biosecurity practices
and adherence to select agent regulation, and 6) that addressing biosafety, biosecurity,
and occupational health is part of the responsible conduct of all life sciences research.

b) The NSABB should develop a statement that explains their review process and
rationale for the recommendations. This statement will be provided to the journals to
consider for publication.

c) The USG should encourage the authors to submit a special
communication/commentary letter to the journals regarding the dual use research
issue.

In essence: “Delete the recipe and the mutations.”

The editors at Science released a statement of their own, which I’ll quote in part:

The resulting virus is sensitive to antivirals and to certain vaccine candidates and knowledge about it could well be essential for speeding the development of new treatments to combat this lethal form of influenza. The NSABB has emphasized the need to prevent the details of the research from falling into the wrong hands. We strongly support the work of the NSABB and the importance of its mission for advancing science to serve society. At the same time, however, Science has concerns about withholding potentially important public‐health information from responsible influenza researchers. Many scientists within the influenza community have a bona fide need to know the details of this research in order to protect the public, especially if they currently are working with related strains of the virus.

Science editors will be evaluating how best to proceed. Our response will be heavily dependent upon the further steps taken by the U.S. government to set forth a written, transparent plan to ensure that any information that is omitted from the publication will be provided to all those responsible scientists who request it, as part of their legitimate efforts to improve public health and safety.

Science supports the 2003 joint Statement on Scientific Publication and Security, published in Science, Nature and PNAS. The statement notes that “open publication brings benefits not only to public health but also to efforts to combat terrorism.” It further emphasizes the need to publish “manuscripts of high quality, in sufficient detail to permit reproducibility,” and it recognizes that there may be occasions when a paper “should be modified, or not be published.”

In essence, “We haven’t decided yet. It would be nice if you let us know how responsible scientists could get hold of the data.”

Vincent Racaniello, a virologist at Columbia University, thinks taking this path is a bad idea. Here’s how he put it to me when I sent him the statements:

It doesn’t make any sense to publish Fouchier’s paper without complete data and experimental details. The point of a science paper is to enable others to duplicate the findings. Are we going to set a new precedent, where security matters override the reason for publication? This is setting a very dangerous precedent for virology and biological sciences in general.

I disagree with the NSABB recommendations, because they have no scientific basis…one cannot conclude that the mutations selected by Fouchier [the head of the Dutch research team] will have effects on transmission of the virus among humans. I understand that if you publish the plans for a nuclear weapon, that may enable a terrorist to make one, but the Foucher finding doesn’t enable anything except more experiments. And that is why the paper should be published – to allow virologists to extend his findings and determine what controls transmission of H5N1 viruses. Often the best experiments are done by scientific unknowns who take an interest in a problem and apply a fresh view. If you restrict dissemination of this information, you are limiting our eventual understanding of the problem.

Update: Looks like Racaniello’s concerns have fallen upon deaf ears. Martin Enserink reports that the virus researchers have decided to redact the contested parts of the papers, which are being considered by Science and Nature.

In 1494, King Charles VIII of France invaded Italy. Within months, his army collapsed and fled. It was routed not by the Italian army but by a microbe. A mysterious new disease spread through sex killed many of Charles’s soldiers and left survivors weak and disfigured. French soldiers spread the disease across much of Europe, and then it moved into Africa and Asia. Many called it the French disease. The French called it the Italian disease. Arabs called it the Christian disease. Today, it is called syphilis.

I’ve been intrigued by the murky history of syphilis for a few years now. The text above is from the start of an article I wrote for Science in 2008. At the time, scientists were split between two explanations for sudden appearance of syphilis at the end of the fifteenth century. According to one, it was caused by bacteria that had evolved in the New World and were brought back to Europe by Columbus’s crew. But other researchers found many skeletons with signs of syphilis in Europe, Africa, and Asia that appeared to have been from long before Columbus’s voyage. They argued that it must have started in the Old World, perhaps before people even left for the New World some 15,000 years ago.

As I explained in the article, one way to test these hypotheses is to survey the evolution of the bacteria. A group of researchers based at Emory University came across bacteria infecting Indians in Guyana that was genetically close, but not identical, to syphilis. They suggested syphilis had evolved in the New World from a common ancestor of both pathogens. Columbus’s crew may have picked it up when they visited the New World and then brought it home to Europe. Unfortunately, by the time doctors had gotten the bacteria from the jungles of Guyana to a laboratory where it could be analyzed, the DNA was in bad shape, so they couldn’t come to a firm conclusion.

Recently, I caught up with one of the scientists on the team, Kristin Harper, who is now at Columbia University. She didn’t have any new genetic results to talk about, unfortunately, although she may before long. In the meantime, she pointed me to a new review she has published in the Yearbook of Physical Anthropology. She and her colleagues took a look at the bones that scientists have pointed to as evidence for the antiquity of syphilis in both the New and Old World, and passed judgment about just how good the evidence was that they did, indeed, have syphilis, and not some other disease that can deform bone. The scientists also took a close look at the dating of the bones, since the timing of syphilis’s origin is so crucial to the entire debate.

The trouble with a lot of past research, Harper says, is that scientists have come up with new ways to diagnose syphilis in ancient bones without offering good evidence that their criteria are good. “Paleopathology is kind of the wild west of science, in that the ‘rules’ are still in their infancy,” Harper said. “We set ourselves the challenge of using only evidence-based diagnostic criteria in this paper and tried to be similarly stringent about dating.”

The scientists looked at 54 reports from both hemispheres. Most of the Old World bones failed to meet at least one of the standard requirements for a diagnosis of syphilis, such as distinctive pits on the skull or swelling in the long bones of the arms and legs. But when they looked at the Old World bones that had been dated to before 1492 that did make the grade, they ended up throwing all of those bones out, too. The evidence that these Old World bones were from before 1492 turned out to be weak. They tended to come from coastal regions, where people eat lots of fish. Fish are full of carbon from deep in the ocean, which has a different balance of isotopes than that found on the land. The ocean carbon gets into the bones of coastal people, where it can throw off estimates of their age by centuries. A close examination of these coastal Old World bones led the Emory scientists to conclude that they belonged to Europeans who died shortly after Columbus’s voyage.

“In contrast,” Harper told me, “we found definite cases of treponemal disease [syphilis] hailing from the New World that stretched back thousands and thousands of years.”

Harper and her colleagues conclude that there’s no good evidence for syphilis in the Old World, and plenty in the New World. They continue to argue that syphilis traveled east across the Atlantic.

It’s intriguing if Harper turns out to be right. Europeans brought smallpox and other pathogens to the New World which decimated its residents. Syphilis, it seems, is one pathogen that went the other way.

[Image of Columbus voyage: Wikipedia]

[Update, 12/19 7 pm: Some of the comments prompted me to edit this piece for clarity.]

We take in streams of information of radically different forms: photons through the eyes, textures through the skin, air vibrations through the ears, molecules through the nose. Marvelously, we manage to integrate all that information into a unified, coherent feel of the world. It turns out that as we draw in these different streams, we use information from one sense to shape what we take in from others. It’s an efficient way to make the most of our imperfect perceptions. But it also leaves us vulnerable to some remarkable illusions, like the one illustrated in this video.

In my latest column for Discover, I explore our powers of multi-sensory integration. Check it out.

Last year I decided to play in the ebook sandbox. I brought together some of my favorite pieces about the brain in an anthology I entitled Brain Cuttings: Fifteen Journeys Through the Mind. I teamed up with the publishers George Scott and Charles Nix, and we produced an ebook.

Along the way, we learned a lot. I recounted some of the lessons in this piece for the Atlantic, and others in this conversation with the writer Steve Silberman. Suffice to say, publishing ebooks is by no means a frictionless utopia for writers. Nevertheless it remains strangely addictive. Perhaps we writers get the same jolt of dopamine that readers get when they tap a glass screen and are rewarded with a new book.

It just so happens I now have some new material to keep fueling my addition. I’ve continued to write about the brain, and recently I selected another crop of favorites. This new ebook has made it down the digital assembly line, and is now available for $7.99: More Brain Cuttings: Further Exporations of the Mind (Amazon, Barnes & Noble).

You’ll find a range of subjects here. How a 100 billion cells use 100 trillion connections to create a working brain. How the ringing in our ears may tell us important things about the nature of consciousness. How dancing cockatoos may reveal how we’re pre-adapted to love music.

I hope you enjoy the book. The brain unfolds like a flower; the more I have explored neuroscience, the more it has rewarded me with new stories. I expect there will be many more to come.

Long before Darwin published The Origin of Species, there was talk of evolution. The more acquainted naturalists became with the major groups of animals, the gaps between them grew smaller. Once it seemed as if mammals were profoundly different than other vertebrates, for example. And then European explorers encountered the platypus, a mammal that laid eggs. Perhaps the major groups of animals had not been separately created, some naturalists suggested. Perhaps life had changed over time.

In 1837, a profoundly paradoxical creature was shipped from West Africa to London, packed in clay. It was destined for Richard Owen, the greatest British anatomist of his age. He picked away the clay, to reveal a creature that looked like a fish. It has a knife-shaped body, gills, and fins. “If indeed the species had been known only by its skeleton,” Owen wrote, “no one could have hesitated in referring it to the class of Fishes.”

But inside its body, Owen found what he could only call lungs. Its whisker-like fins had a chains of bones that faintly resembled arms. Owen was a fierce opponent of all the transformationists of his day, and he was determined to find a way to push this creature–what Owen called Lepidosiren and what we today commonly call a lungfish–to one side of the divide or the other. He finally found an antidote to evolution in its nose.

Owen’s examination led him to conclude that the nostrils of the lungfish did not connect to its mouth. They seemed to end in a blind pouch. That was a hallmark of fish, and the trait banished lungfish from the tetrapods–the land vertebrates such as reptiles, birds, and mammals. “According to this test, Lepidosiren is a Fish…simply by its nose,” he wrote.

As I write in my book At the Water’s Edge, Owen turned out to be wrong. In 1860, a year after Darwin published his theory of evolution, an Irish anatomist named Robert M’Donnel discovered a passageway from the lungfish’s nose to its mouth. It was, he concluded, a transitional creatures, with some traits from our fishy past mixed with traits also found in tetrapods. “I know of no animal more calculated leading to the adoption of the theory of Darwin, than the Lepidosiren,” he wrote.

Since then, scientists have amassed an overwhelming amount of evidence that lungfish are close kin to tetrapods. Their kinship is inscribed in their DNA, for example: genetic tests consistently show that of the 30,000-odd species of fish, lungfish are the closest (or among the closest) relatives to tetrapods.

On the other hand, we shouldn’t rush to the conclusion that the lungfish is a living fossil, a snapshot of our own ancestry. Lungfish and tetrapods share a common ancestor that lived some 400 million years ago. Since then, the lungfish lineage has gone through drastic changes. Some 350 million years ago, rivers and coastal waters were loaded with a diversity of lungfishes, including massive predators the size of sailboats. Today, lungfish are a whisper of that former glory, a few species eking out an existence in Australia, Brazil, and Africa. The living lungfishes are different from each other in some important ways. The lungfish in Africa have wispy fins and dig into the mud to survive droughts. The lungfish of Australia have stout lobe-shaped fins and never escape droughts in the mud.

Once scientists can sort out what’s new about lungfishes, they can then take a look at what’s old. And therein lie some intriguing clues about our own origins. Today, scientists at the University of Chicago published a study of lungfish that sheds light on the origin of one of the most essential behaviors for a tetrapod: the ability to walk. In their own weird way, lungfish can walk, too.

Tetrapods walk in many different ways. Lions race, sloths lumber, salamanders squirm. But all tetrapod walks are built on the same foundation. A tetrapod typically alternates its forelegs and hind legs, pushing each limb against the ground to propel itself forward. Early tetrapods bent their trunks from side to side as they moved, and amphibians like salamanders still do today. Other tetrapods modified their walks; most mammals keep their trunk from bowing out to the sides, instead flexing it up and down.

That’s a far cry from the typical way fishes move. They propel themselves forward through the water with their tails, adjusting their fins to help them control their movements. They mainly flap their pectoral fins (which correspond to our arms). One glaring exception to this kind of locomotion is a deep-water fish known as the coelacanth. It swims by alternating its lobe-shaped fins. And it just so happens that the coelacanth is the only other aquatic animal that shares the same close kinship to tetrapods as lungfish.

Some researchers who have observed lungfishes in the wild have noticed that they also seem to move their fins in an alternating pattern. To see whether that was actually true, Heather King of the University of Chicago and her colleagues have been filming lungfish in lab tanks and then analyzing their movement on computers.

King found that the lungfishes regularly moved around their tank by pushing off the bottom with their pelvic fins (which correspond to hind legs). They alternated between the fins in a walk-like pattern, sometimes switching to a bounding, synchronous gait. With each step, the lungfishes lifted their bodies up and forward, much like tetrapods do while walking. (The movie below shows a few samples of her footage.)

It’s pretty remarkable that lungfish can come so close to walking. They have no pelvis to help them transmit the force they generate pushing off the bottom of the tank to the rest of their body. Their their fins contain thin chains of bones, with no foot or ankle. King’s research suggests that an animal doesn’t need all that much tetrapod anatomy to walk.

This discovery offers a new way to interpret some enigmatic track marks dating back to the time when the first tetrapods evolved. These trackways seem to have been formed by a limbed animal with an alternating gait. But there are no toe marks preserved with them. It’s possible, King suggests, that early relatives of tetrapods made them, with limbs as simple as those of lungfishes.

It also underscores one of the most counterintuitive facts about how our ancestors evolved into land-walking vertebrates. Our limbs are so well-adapted for moving around on land that it’s tempting to think that they must have first evolved expressly for that purpose. Indeed, for much of the 1900s, many scientists believed tetrapods evolved when fish had to crawl from pond to pond to survive droughts. It’s clear, however, that many of the key elements of a walking body–such as limbs that an animal could move in an alternating gait to push itself forward–evolved long before our ancestors came on land. The lungfish, M’Donnel might say, is more calculated than ever to lead to the adoption of the theory of Darwin.

King et al, Behavioral evidence for the evolution of walking and bounding before terrestriality in sarcopterygian fishes. PNAS. http://www.pnas.org/cgi/doi/10.1073/pnas.1118669109

[Photo by Joel Abroad Flickr/Creative Commons]

I’ve been doing some research on the long cultural history of tattoos in preparation for my talk about Science Ink at Harvard on Tuesday. I’m a hard-core Moby Dick fan (this blog’s name comes from there), so it was a delight to stumble across a passage on tattoos, which I had forgotten.

Queequeg, readers may recall, was covered with tattoos. Here’s how Ishmael describes them:

This tattooing had been the work of a departed prophet and seer of his island, who, by those hieroglyphic marks, had written out on his body a complete theory of the heavens and the earth, and a mystical treatise on the art of attaining truth; so that Queequeg in his own proper person was a riddle to unfold; a wondrous work in one volume; but whose mysteries not even himself could read, though his own live heart beat against them; and these mysteries were therefore destined in the end to moulder away with the living parchment whereon they were inscribed, and so be unsolved to the last.

[Image: Rockwell Kent, Plattsburgh State Art Museum]

There are 100 trillion microbes that live in your body. Do you own them? Do they deserve the same protections as your own genes and cells? If someone genetically alters a microbe and claims that if you swallow it, it will let you lose weight, should that living germ be regulated as a drug?

These are a few of the questions I mull in a piece that appears in the Sunday Review section of today’s New York Times. I’ve been writing a lot about the microbial world for a few years now, but only recently did I encounter a group of bioethicists who are now pondering what sort of ground rules we should set up to govern science and medicine as we gain understanding and power over the microbiome. Check it out.

If you’re interested in reading more about all this, here are a few new papers (some free, some behind paywalls).

The Human Microbiome Project: lessons from human genomics: Trends in Microbiology (in press)

“Who owns your poop?”: insights regarding the intersection of human microbiome research and the ELSI aspects of biobanking and related studies, Kieran O’Doherty, BMC Medical Genomics 4 (1), (07 Oct 2011) info:doi/10.1186/1755-8794-4-72

Community Health Care: Therapeutic Opportunities in the Human Microbiome Justin Sonnenburg and Michael Fischbach, Science Translational Medicine 3 (78), April 13, 2011 info:doi/10.1126/scitranslmed.3001626

There will also be a book coming out next year edited by Rosamond Rhodes of Mount Sinai Medical School, but it’s not on the radar just yet. For now, here’s a powerpoint of a recent presentation from her research group (pdf)

[Image: Andrea Wan for the New York Times]

It’s been a busy week for Science Ink!

1. Science Ink was on TV. The Daily Planet, a Canadian science news show on the Discovery Channel, interviewed me about my favorite tattoos.

2.The Irish Times put Science Ink on top of its list of science books for holiday gifts. (As did MSNBC and io9.)

3. Der Spiegel takes a look.

4. The Toronto Star has a whole package on Science Ink in Saturday’s issue: A Q&A with yours truly, an article by Megan Ogilvie about Toronto-area scientists with tattoos, and a slide show of their tattoos. (I was amazed that there were lots of tattoos I had never seen before!)

5. Just a reminder to folks in Boston: I will be giving a lecture at the Harvard Museum of Natural History on Tuesday, 12/13 at 6 pm. The lecture is free and open to the public. (The parking is free too!) Details are here.

[This tattoo of cyanide is from David Lighthart.]