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.
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.
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.
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.
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
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).
Today marks the one-year anniversary of the Arsenic Life Affair. On December 2, 2010, NASA-funded scientists announced that they had discovered a microbe in Mono Lake that broke the rules of biology. They claimed it could build DNA from arsenic rather than phosophorus. It was a sensational claim, and it was greeted by a spectacular backlash.
Alan Boyle takes a close look at arsenic life on its first birthday over at MSNBC. Other scientists have yet to report whether they can replicate the results or not (the bet of many experts is on not). Meanwhile, other researchers are studying its biology, sequencing its genome, and otherwise investigating it as they would any new microbe. It seems as if the arsenic life affair is morphing into regular science. Which may be about as good of an ending as one could hope.
The year has been an intriguing one for me as a journalist–I’ve found writing about arsenic life as both science and the sociology of science to be very satisfying. Here’s a round-up of my main pieces:
I could not delve into the full details of the objections in my Slate piece, but I wanted to make sure readers could see that the critics were not shooting from the hip. So I posted their complete responses on my blog.
Nearly six months after arsenic life was announced, Science finally published the paper, along with lengthy criticisms. It felt fairly anti-climatic to me; at Slate, I wrote about what I thought was the important outcome of the whole affair: an experiment in open science and post-publication peer review.
As the Arsenic Life Affair was unfolding, several other high-profile papers were also under siege. Together, they got me interested in how science progresses: how scientific ideas are tested, and how difficult it can be for the wrong ones to be “de-discovered.”
The first big feature on arsenic life appeared in Popular Science. I warned that a folk tale about everything being the fault of those pesky bloggers was taking root. (Soon after, the author, Tom Clynes, sent a long message to me, which I posted on the blog.)
Along with Boyle’s piece, you can also plunge into Bora Zivkovic’s epic link round-up for more reading.
The New York Times has launched a series called Profiles in Science. When I was invited to join the undertaking, I proposed writing about the Harvard psychologist Steven Pinker. I had run into Pinker at the World Science Festival in June, and he had told me about his next book, The Better Angels of Our Nature, which was due out in the fall. In the 800+ page tome, Pinker argues that rates of human violence have been crashing for millennia, and he offers psychological explanations for the fall.
I’ve followed Pinker’s work since I first came across his 1994 book, The Language Instinct. In the wake of the book’s success, he quickly became a leading exponent of evolutionary psychology, coming out swinging against its critics such as Stephen Jay Gould. When Pinker described his book to me, I was intrigued. I wondered how someone who argued that human nature was shaped long ago by natural selection would end up arguing that human nature–or at least human experience–is now changing rapidly for the better. But there were other things I was wondering–how, for example, does a writer of massive books about human nature live inside the same body as an expert on irregular verbs?
So I headed up to Cambridge to ask a bunch of questions, out of which a profile emerged. You can read it in tomorrow’s Times, or on their web site.
Our brains are protected by an invisible fortress wall, keeping it safe from many dangers. Unfortunately, it also keeps out a lot of the drugs that could help cure diseases of the brain. In this month’s column for Discover, I look at some of the newest strategies for scaling the wall. Check it out.
Earlier this year in National Geographic, I wrote about how feathers evolved long before flight. This timing naturally raises the question, how did feathered dinosaurs take to the air? My article was accompanied by a picture from the University of Montana lab of Ken Dial, who argues that before dinosaurs flew, they flapped their wings to help them travel up and down inclines. While not all experts accept Dial’s hypothesis, it has the undeniable strength that he can gather evidence for it in living birds, rather than just inferring behavior from fossils alone.
This video shows some of the astonishing climbs birds can make with the help of some wing flapping. It’s a mix of lab climbs and footage from the wild, with an evolutionary tree of birds.
This is a skill that takes time for birds to develop, as shown in this video below. Dinosaurs might have gradually acquired the skill as well, as their arms evolved into more bird-like wings.
Dial argues that this flapping would also help on the way down, too. Here’s a young bird leaping to the ground, and flapping its wings to control its fall.
By the time dinosaurs had evolved the ability to use feathers to assist in climbs, they would have already developed the wing stroke used by birds today for true flight, as this video shows.
Even without full flight, Dial argues, flapping feathered wings would have given little feathered dinosaurs the boost they needed to escape hungry predators. And this behavior could have served as an evolutionary bridge from the land to the air.
Ten years ago this month, a team of University of Oxford scientists published a description of a family who struggled with words. By comparing their DNA, the scientists zeroed in for the first time on a gene associated with language, dubbed FOXP2. In my newest column in Discover, I look back at what scientists have learned over the past decade about how FOXP2 works, and what it tells us–or leaves us wondering–about how language evolved. Check it out.
Carl Zimmer is the author of twelve books and counting.
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“Carl Zimmer takes us behind the scenes in our own heads. He has ferreted out all the most wondrous, bizarre stories and studies and served them up in this delicious, sizzling, easy-to-digest platter of neuro-goodness.” —Mary Roach, author of Packing for Mars and Stiff
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"...among the joyous, heartless, ever-juvenile eternities, Pip saw the multitudinous, God-omnipresent, coral insects, that out of the firmament of waters, heaved the colossal orbs. He saw God's foot upon the treadle of the loom, and spoke it; and therefore his shipmates called him mad." --Moby Dick
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.
The New York Times has launched a series called 
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