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2009

Scientists Start a Genomic Catalog of Earth's Abundant Microbes
The New York Times, December 29, 2009
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If you want to appreciate the diversity of life on earth, you will need a microscope.

There are about 5,400 species of mammals on the planet, but just a spoonful of soil may contain twice as many species of microbes. They can dwell in habitats where so-called higher life forms like us would quickly die, including acid-drenched mines and Antarctic deserts. By one rough estimate, there may be, all told, 150 million species of microbes.

''Microbes represent the vast majority of organisms on earth,'' said Hans-Peter Klenk, a microbiologist for the German Collection of Micro-organisms and Cell Cultures, a government microbiology research center.

What Is The Speed of Thought?
Discover, December 2009
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When Samuel Morse established the first commercial telegraph, in 1844, he dramatically changed our expectations about the pace of life. One of the first telegraph messages came from that year’s Democratic National Convention in Baltimore, where the delegates had picked Senator Silas Wright as their vice presidential nominee. The president of the convention telegraphed Wright in Washington, D.C., to see if he would accept. Wright immediately wired back: No. Incredulous that a message could fly almost instantly down a wire, the delegates adjourned and sent a flesh-and-blood committee by train to confirm Wright’s response--which was, of course, the same. From such beginnings came today’s high-speed, networked society.

Less famously but no less significantly, the telegraph also transformed the way we think about the pace of our inner life. Morse’s invention debuted just as researchers were starting to make sense of the nervous system, and telegraph wires were an inspiring model of how nerves might work. After all, nerves and telegraph wires were both long strands, and they both used electricity to transmit signals. Scientists knew that telegraph signals did not travel instantaneously; in one experiment, it took a set of dots and dashes a quarter of a second to travel 900 miles down a telegraph wire. Perhaps, the early brain investigators considered, it took time for nerves to send signals too. And perhaps we could even quantify that time.

Humanity’s Other Basic Instinct: Math
Discover, November 2009
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Numbers make modern life possible. “In a world without numbers,” University of Rochester neuroscientist Jessica Cantlon and her colleagues recently observed in the journal Trends in Cognitive Sciences, “we would be unable to build a skyscraper, hold a national election, plan a wedding, or pay for a chicken at the market.”

The central role of numbers in our world testifies to the brain’s uncanny ability to recognize and understand them -- and Cantlon is among the researchers trying to find out exactly how that skill works. Traditionally, scientists have thought that we learn to use numbers the same way we learn how to drive a car or to text with two thumbs. In this view, numbers are a kind of technology, a man-made invention to which our all-purpose brains can adapt. History provides some support. The oldest evidence of people using numbers dates back about 30,000 years: bones and antlers scored with notches that are considered by archaeologists to be tallying marks. More sophisticated uses of numbers arose only much later, coincident with the rise of other simple technologies. The Mesopotamians developed basic arithmetic about 5,000 years ago. Zero made its debut in A.D. 876. Arab scholars laid the foundations of algebra in the ninth century; calculus did not emerge in full flower until the late 1600s.

On The Origin of Tomorrow
Science, December 3, 2009
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In the final words of the final sentence of On the Origin of Species, Charles Darwin gave a nod to the future. "There is grandeur in this view of life, with its several powers, having been originally breathed into a few forms or into one; and that, whilst this planet has gone cycling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved."

Self-Destructive Behavior in Cells May Hold Key to a Longer Life
New York Times, October 6, 2009
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Deep down, we are all cannibals. Our cells are perpetually devouring themselves, shredding their own complex molecules to pieces and recycling them for new parts. Many of the details of our endless self-destruction have come to light only in the past few years. And to the surprise of many scientists, links are now emerging between this inner cannibalism and diseases like Alzheimer’s disease and cancer.

“There’s been an explosion,” said Daniel Klionsky of the University of Michigan. “All of a sudden, researchers in different fields are seeing a connection.”

In fact, as Dr. Klionsky wrote in a paper published online in Trends in Cell Biology, this cannibalism may extend our lifespan. Increasing our body’s ability to self-destruct may, paradoxically, let us live longer.

Where Does Sex Live in the Brain? From Top to Bottom.
Discover, October 2009
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On April 11, 1944, a doctor named T. C. Erickson addressed the Chicago Neurological Society about a patient he called Mrs. C. W. At age 43 she had started to wake up many nights feeling as if she were having sex - or as she put it to Erickson, feeling “hot all over.” As the years passed her hot spells struck more often, even in the daytime, and began to be followed by seizures that left her unable to speak. Erickson examined Mrs. C. W. when she was 54 and diagnosed her with nymphomania. He prescribed a treatment that was shockingly common at the time: He blasted her ovaries with X-rays.

Despite the X-rays, Mrs. C. W.’s seizures became worse, leaving her motionless and feeling as if an egg yolk were running down her throat. Erickson began to suspect that her sexual feelings were emanating not from her ovaries but from her head. Doctors opened up her skull and discovered a slow-growing tumor pressing against her brain. After the tumor was removed and Mrs. C. W. recovered, the seizures faded. “When asked if she still had any ‘passionate spells,’” Erickson recounted, “she said, ‘No, I haven’t had any; they were terrible things.’”

Can Evolution Run in Reverse? A Study Says It’s a One-Way Street
The New York Times, September 29, 2009
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Evolutionary biologists have long wondered if history can run backward. Is it possible for the proteins in our bodies to return to the old shapes and jobs they had millions of years ago?

Examining the evolution of one protein, a team of scientists declares the answer is no, saying new mutations make it practically impossible for evolution to reverse direction. “They burn the bridge that evolution just crossed,” said Joseph W. Thornton, a biology professor at the University of Oregon and co-author of a paper on the team’s findings in the current issue of Nature.

Provocative New Study Warns of Crossing Planetary Boundaries
Yale Environment 360, September 23, 2009
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Human civilization has had a stable childhood. Over the past 10,000 years, as our ancestors invented agriculture and built cities, the Earth remained relatively stable. The average global temperature fluttered slightly, never lurching towards a greenhouse climate or chilling enough to enter a new Ice Age. The pH of the oceans remained steady, providing the right chemical conditions for coral reefs to grow and invertebrates to build shells. Those species, in turn, helped support a stable food web that provided plenty of fish for us humans to catch. The overall stability of the past 10,000 years may have played a big part in humanity’s explosion.

Now, ironically, civilization has become so powerful that it can reshape the planet itself. “We have become a force to contend with at the global level,” as Johan Rockstrom of the Stockholm Resilience Center in Sweden, puts it. Humans have changed the chemistry of Earth’s oceans, lowering their pH and causing ocean acidification. We are shifting the composition of the atmosphere, raising levels of carbon dioxide higher than they’ve been in at least the past 800,000 years.

A number of scientists have warned in recent years that if we keep pushing the planet this way, we will cause sudden, irreversible damage to the systems that made human civilization possible in the first place. Typically, they’ve just focused on one of these tipping points at a time. But in today’s issue of the journal Nature, Rockstrom and 27 of his fellow environmental scientists argue that we have to conceive of many tipping points at once. They propose that humans must keep the planet in what they call a “safe operating space,” inside of which we can thrive. If we push past the boundaries of that space - by wiping out biodiversity, for example, or diverting too much of the world’s freshwater - we risk catastrophe.

The Secrets Inside Your Dog's Mind
Time, Monday, Sep. 21, 2009
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Brian Hare, assistant professor of evolutionary anthropology at Duke University, holds out a dog biscuit.

"Henry!" he says. Henry is a big black schnauzer-poodle mix--a schnoodle, in the words of his owner, Tracy Kivell, another Duke anthropologist. Kivell holds on to Henry's collar so that he can only gaze at the biscuit.

"You got it?" Hare asks Henry. Hare then steps back until he's standing between a pair of inverted plastic cups on the floor. He quickly puts the hand holding the biscuit under one cup, then the other, and holds up both empty hands. Hare could run a very profitable shell game. No one in the room--neither dog nor human--can tell which cup hides the biscuit.

Henry could find the biscuit by sniffing the cups or knocking them over. But Hare does not plan to let him have it so easy. Instead, he simply points at the cup on the right. Henry looks at Hare's hand and follows the pointed finger. Kivell then releases the leash, and Henry walks over to the cup that Hare is pointing to. Hare lifts it to reveal the biscuit reward.

Henry the schnoodle just did a remarkable thing. Understanding a pointed finger may seem easy, but consider this: while humans and canines can do it naturally, no other known species in the animal kingdom can. Consider too all the mental work that goes into figuring out what a pointed finger means: paying close attention to a person, recognizing that a gesture reflects a thought, that another animal can even have a thought. Henry, as Kivell affectionately admits, may not be "the sharpest knife in the drawer," but compared to other animals, he's a true scholar.

Where Did All the Flowers Come From?
The New York Times, September 8, 2009
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Throughout his life, Charles Darwin surrounded himself with flowers. When he was 10, he wrote down each time a peony bloomed in his father’s garden. When he bought a house to raise his own family, he turned the grounds into a botanical field station where he experimented on flowers until his death. But despite his intimate familiarity with flowers, Darwin once wrote that their evolution was “an abominable mystery.”

Darwin could see for himself how successful flowering plants had become. They make up the majority of living plant species, and they dominate many of the world’s ecosystems, from rain forests to grasslands. They also dominate our farms. Out of flowers come most of the calories humans consume, in the form of foods like corn, rice and wheat. Flowers are also impressive in their sheer diversity of forms and colors, from lush, full-bodied roses to spiderlike orchids to calla lilies shaped like urns.

The fossil record, however, offered Darwin little enlightenment about the early evolution of flowers. At the time, the oldest fossils of flowering plants came from rocks that had formed from 100 million to 66 million years ago during the Cretaceous period. Paleontologists found a diversity of forms, not a few primitive forerunners.

Long after Darwin’s death in 1882, the history of flowers continued to vex scientists. But talk to experts today, and there is a note of guarded optimism. “There’s an energy that I haven’t seen in my lifetime,” said William Friedman, an evolutionary biologist at the University of Colorado, Boulder.

The Dark Matter of the Human Brain
Discover, September 2009
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Some of the common words we use are frozen mistakes. The term influenza comes from the Italian word meaning “influence” - an allusion to the influence the stars were once believed to have on our health. European explorers searching for an alternate route to India ended up in the New World and uncomprehendingly dubbed its inhabitants indios, or Indians. Neuroscientists have a frozen mistake of their own, and it is a spectacular blunder. In the mid-1800s researchers discovered cells in the brain that are not like neurons (the presumed active players of the brain) and called them glia, the Greek word for “glue.” Even though the brain contains about a trillion glia - 10 times as many as there are neurons - the assumption was that those cells were nothing more than a passive support system. Today we know the name could not be more wrong.

Glia, in fact, are busy multitaskers, guiding the brain’s development and sustaining it throughout our lives. Glia also listen carefully to their neighbors, and they speak in a chemical language of their own. Scientists do not yet understand that language, but experiments suggest that it is part of the neurological conversation that takes place as we learn and form new memories.

First Trace of Color Found in Fossil Bird Feathers
The New York Times, September 1, 2009
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Birds, more than any other group of animals, are a celebration of color. They have evolved to every extreme of the spectrum, from the hot pink of flamingos to the shimmering blue of a peacock’s neck. Yet, for decades, paleontologists who study extinct birds have had to use their imaginations to see the colors in the fossils. Several feather fossils have been unearthed over the years, but they have always been assumed to be colorless vestiges.

Now a team of scientists has discovered color-producing molecules that have survived for 47 million years in the fossil of a feather. By analyzing those molecules, the researchers have shown that they would have given a bird the kind of dark, iridescent sheen found on starlings and other living birds.

This new method may allow scientists not only to reconstruct ancient birds more accurately. Birds evolved from ground-running feathered dinosaurs, and now it may be possible to determine some of the colors on them as well.

“I really do think we are moving from dinosaurs in black and white to dinosaurs in Technicolor,” said Julia Clarke, a University of Texas paleontologist who was a co-author of the new paper, published in the journal Biology Letters.

On the Origin of Eukaryotes
Science, August 7, 2009
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You may not feel as though you have much in common with a toadstool, but its cells and ours are strikingly similar. Animals and fungi both keep their DNA coiled up in a nucleus. Their genes are interspersed with chunks of DNA that cells have to edit out to make proteins. Those proteins are shuttled through a maze of membranes before they can float out into the cell. A cell in a toadstool, like your own cells, manufactures fuel in compartments called mitochondria. Both species' cells contain the same molecular skeleton, which they can break down and reassemble in order to crawl.

This same kind of cell is found in plants and algae; single-celled protozoans have the same layout as well. Other microbes, such as the gut bacterium Escherichia coli, lack it. All species with our arrangement are known as eukaryotes. The word is Greek for "true kernel," referring to the nucleus. All other living things that lack a nucleus, mitochondria, and the eukaryote LEGO-like skeleton are known as prokaryotes. "It's the deepest divide in the living world," says William Martin of the University of Dusseldorf in Germany.

First Comes Global Warming, Then An Evolutionary Explosion
Yale Environment 360, August 3, 2009
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In 1997, Arthur Weis found himself with an extra bucket of seeds. Weis, who was teaching at the University of California at Irvine at the time, had dispatched a student, Sheina Sim, to gather some field mustard seeds for a study. When Sim was done with her research, Weis was left with a lot of leftover seeds. For no particular reason, he decided not to throw the bucket out. “We just tossed it in a cold, dry incubator,” said Weis.

Weis is glad they did. When a severe drought struck southern California, Weis realized that he could use the extra bucket of seeds for an experiment. In 2004 he and his colleagues collected more field mustard seeds from the same sites that Sim had visited seven years earlier. They thawed out some of the 1997 seeds and then reared both sets of plants under identical conditions. The newer plants grew to smaller sizes, produced fewer flowers, and, most dramatically, produced those flowers eight days earlier in the spring. The changing climate had, in other words, driven the field mustard plants to evolve over just a few years. “It was serendipity that we had the seeds lying around,” says Weis.

Weis is convinced that his experiment is just a harbinger of things to come. Global warming is projected to drastically raise the average global temperature, as well as producing many other changes to the world’s climate, such as more droughts in California. And in response, Weis and other researchers contend, life will undergo an evolutionary explosion.

Scientists Find a Microbe Haven at Ocean’s Surface
The New York Times, July 28, 2009
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The world’s oceans are like an alien world. The National Oceanic and Atmospheric Administration estimates that 95 percent of them remain unexplored. But the mysteries do not start a mile below the surface of the sea. They start with the surface itself.

Scientists are now discovering that the top hundredth-inch of the ocean is somewhat like a sheet of jelly. And this odd habitat, thinner than a human hair, is home to an unusual menagerie of microbes. “It’s really a distinct ecosystem of its own,” said Oliver Wurl, of Canada’s Institute of Ocean Sciences.

Stop Paying Attention: Zoning Out Is a Crucial Mental State
Discover, July/August 2009
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I am going to do my best to hold your attention until the very last word of this column. Actually, I know it’s futile. Along the way, your mind will wander off, then return, then drift away again. But I can console myself with some recent research on the subject of mind wandering. Mind wandering is not necessarily the sign of a boring column. It’s just one of the things that make us human.

Blink Twice if You Like Me
The New York Times, June 30, 2009
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LINCOLN, Mass. -- Sara Lewis is fluent in firefly. On this night she walks through a farm field in eastern Massachusetts, watching the first fireflies of the evening rise into the air and begin to blink on and off. Dr. Lewis, an evolutionary ecologist at Tufts University, points out six species in this meadow, each with its own pattern of flashes.

Along one edge of the meadow are Photinus greeni, with double pulses separated by three seconds of darkness. Near a stream are Photinus ignitus, with a five-second delay between single pulses. And near a forest are Pyractomena angulata, which make Dr. Lewis’s favorite flash pattern. “It’s like a flickering orange rain,” she said.

The Gene Puzzle
Newsweek, June 27, 2009
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Ten years ago, the human genome was medicine's holy grail. Playing the part of King Arthur's knights were rival teams of biologists racing to sequence all the genetic instructions required to make a human being. And just as the actual Holy Grail was believed to have miraculous healing powers, some promised that the genome would change medicine forever. Biotech companies raced to cash in--Human Genome Sciences, for instance, filed patents on 100,000 genes and, in 1999, saw its stock quadruple. But genomic science didn't deliver fast breakthroughs. Today Human Genome's stock price is down below $3, and its vast patent portfolio looks like overkill, considering that a human has only about 20,000 genes altogether.

Scientists have made plenty of progress over the past decade in generating genomic data. The Human Genome Project, after employing hundreds of scientists for many years at a total cost of $3 billion, produced in 2000 an error-riddled collage of several people's DNA. Since then, scientists have published complete genomes of five people. And this summer, Complete Genomics, a biotech firm in Mountain View, California, plans to announce that it will sequence an individual genome for $5,000. Data, however, is not the same thing as insight. Rather than finding cures for cancer, diabetes, and other intractable diseases, scientists have mainly learned just how staggeringly complicated genomes are.

New Technologies Allow Scientists to Watch Cells in Motion
The New York Times, June 9, 2009
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It’s easy to imagine the cells in our bodies like bricks in a house, all cemented into place. But we are actually seething with cells that creep, crawl, and squirm. They start wandering soon after conception, and, throughout our lives, our bodies continue to hum with cellular traffic.

Some cells burrow into old bone so that new bone can be laid down in their wake. The tips of new blood vessels snake forward, dragging the cells behind along with them. White blood cells race along on flickering lobes to chase down bacteria before they can make us sick.

The fact that cells can move is old news. How they move is just now being understood. In the mid-1600s, Antonie van Leeuwenhoek built one of the first microscopes and observed single-cell organisms making what he called “pleasing and nimble” movements. But he had no idea what was going on inside those cells, and three centuries later, scientists were still baffled.

Thomas Pollard, a biochemist at Yale, started studying crawling cells in the 1960s, when, he said, “Exactly zero was known.” Today Dr. Pollard and his colleagues have identified many of the key proteins that work together to let cells navigate through our bodies. Scientists can even see some of these proteins at work in living cells and measure their forces.

“My dream was always to be a little gremlin, to get inside the cell and watch all this stuff,” Dr. Pollard said. “This is almost like being a little gremlin.

On the Origin of Sexual Reproduction
For Darwin, sex was a big question mark. "We do not even in the least know the final cause of sexuality; why new beings should be produced by the union of the two sexual elements," he wrote in 1862. "The whole subject is as yet hidden in darkness."

Today, biologists understand the molecular nuts and bolts of sex fairly well. Each new human being (or bird or bee) needs a set of chromosomes from each parent. But that's the how. The why of sex is still fairly mysterious. Bacteria don't have to search for a mate; they just grow and divide in two. An aspen tree can simply send out shoots that grow into new trees. No muss, no fuss with finding a partner, fertilizing an egg, and joining two genomes. Why should so many species take such a labyrinthine path to reproduction, when straightforward routes are available?

Can a Single Neuron Tell Halle Berry From Grandma Esther?
Discover, June 2009
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Four decades ago, an MIT neuroscientist named Jerry Lettvin had a sudden inspiration about how our brains make sense of the world. What if each of us had a special set of neurons in our head whose only job was to recognize a particular person, place, or thing? It was a strange idea, but given what Lettvin knew about the brain, it was plausible. To describe his idea to his students, he made up a story.

Chemicals in Dragon’s Glands Stir Venom Debate
The New York Times, May 19, 2009
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The Komodo dragon is already a terrifying beast. Measuring up to 10 feet long, it is the world’s largest lizard. It delivers a devastating bite with its long, serrated teeth, attacking prey as big as water buffaloes.

But in a provocative paper to be published this week, an international team of scientists argues that the Komodo dragon is even more impressive. They claim that the lizards use a potent venom to bring down their victims.

10 Genes, Furiously Evolving
The New York Times, May 5, 2009
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Evolutionary biology may sometimes seem like an arcane academic pursuit, but just try telling that to Gavin Smith, a virologist at Hong Kong University. For the past week, Dr. Smith and six other experts on influenza in Hong Kong, Arizona, California and Britain have been furiously analyzing the new swine flu to figure out how and when it evolved.

The Big Similarities & Quirky Differences Between Our Left and Right Brains
Discover, May 2009
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There is nothing more humbling or more perception-changing than holding a human brain in your hands. I discovered this recently at a brain-cutting lesson given by Jean-Paul Vonsattel, a neuropathologist at Columbia University. These lessons take place every month in a cold, windowless room deep within the university’s College of Physicians and Surgeons. On the day I visited, there were half a dozen brains sitting on a table. Vonsattel began by passing them around so the medical students could take a closer look. When a brain came my way, I cradled it and found myself puzzling over its mirror symmetry. It was as if someone had glued two smaller brains together to make a bigger one.

As Climate Warms, Species May Need to Migrate or Perish
Yale Environment 360, April 20, 2009
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In the gentle hills outside York, England, a controversial experiment is quietly unfolding. It began in the summer of 2000 when Steven Willis, a biologist at the University of Durham, and his colleagues drove to a wildlife preserve called Wingate Quarry. In the back of their car was a cage full of butterflies called Marbled Whites. Willis and his colleagues removed the cage from the car, opened it, and let 500 butterflies flutter away across the scrubby meadows.

Marbled Whites are common in Europe and southern England, but in 2000 the northern edge of their range was 65 kilometers south of Wingate Quarry. Yet Willis and his colleagues suspected that they might do well there. Thanks to global warming, Wingate Quarry might now be mild enough for the butterflies to survive.

From Developing Limbs, Insights That May Explain Much Else
The New York Times, April 7, 2009
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For its first four weeks, a human embryo looks like a crumpled tube. But around its twenty-seventh day of development, four buds bulge from its sides. Over the next few days, the buds grow like tulips, stretching out into flattened stalks and blooming into crowns of fingers and toes. Inside these developing limbs, bones condense. Muscle cells, tendons, blood vessels and nerves all find their respective places. The embryo now has hands with thumbs to suck, legs ready to deliver a kick.

Could a Dose of Ether Contain the Secret to Consciousness?
Discover, April 2009
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I was looking forward to my first experience with anesthesia. I had been laid out on a stretcher, and nurses and doctors were prepping my midsection so they could slice it open and cut out my appendix. After a bout of appendicitis, a short vacation from consciousness seemed like a pleasant way to spend a few hours. I had no idea what anesthesia would actually feel like, though, and suddenly I was seized by skepticism. I tried to hoist myself up, already swabbed in iodine, as I suggested that I ought to pop into the men’s room before the scalpels came out. I wouldn’t want to interrupt the surgery with a bathroom break. “Don’t worry,” one of the nurses replied. “We’ll do that for you.”

I lay back down, puzzling over that. After a nurse put the IV into my hand, I had to interrupt again: The anesthesia flowing into my arm was not working. I just couldn’t believe that anything would keep me asleep while someone was knitting up my intestines. The nurses and doctors nodded in my direction as I tried to explain the problem to them, but I was sure they weren’t taking me seriously. I took a long, slow blink. And then there were no doctors and nurses around me. I was lying alone in a new room, recovering from my surgery.

Ever since that experience, I’ve wondered what exactly happened in my head. It didn’t feel like sleep. It was not a blackout, either. It was as if the surgeons had simply cut a few hours out of my life and joined together the loose ends. So I decided to get more familiar with the science behind anesthesia. To my surprise, I discovered that anesthesiologists are a bit in the dark themselves. “How anesthesia works has been a mystery since the discovery of anesthesia itself,” writes Michael Alkire, an anesthesiologist at the University of California at Irvine School of Medicine, in the new Encyclopedia of Consciousness.

Is Patriotism a Subconscious Way for Humans to Avoid Disease?
Discover, March 2009
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The long battle between humans and infectious microbes has left its marks all over us.

It shows up most obviously in the way our bodies are constructed. The thousands of species of bacteria that swarm over us cannot penetrate our multilayered skin. Entry points, such as the eyes and nose, are bathed in moisture to help flush out pathogens. The lining of our lungs releases bacteria-killing compounds. Viruses that manage to infect cells are greeted by proteins that attempt to shred them into genetic confetti. Any pathogen that sneaks past all these defenses then faces an army of immune cells, which can devour and destroy the invaders. Immune cells can also manufacture antibodies, which allow them to launch swift attacks if they encounter the same infection elsewhere in the body.

This elaborate defense system dates back billions of years. Our single-celled ancestors were infected with viruses; when they got bigger they were infected with bacteria; and after they evolved guts, those guts were infected with worms. Any mutation that offered even a little protection against those pathogens had a chance to be favored by natural selection. Over thousands of generations, mutation upon mutation built up our diversity of immune cells, signals, and weapons. There was never a point at which our defenses stopped evolving, because the pathogens were evolving as well. New generations of invaders slipped past our lines of defense, spurring the evolution of immune upgrades.

But it is not just our bodies that have been shaped by this tug-of-war. A number of scientists now argue that the battle against disease has left an indelible imprint on our minds as well.

The Awe of Natural History Collections
Seed, February 12, 2009
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A natural history museum is really two museums, and when you’re in one of them, you can hardly imagine the other. I don’t know how many times I’ve wandered around the halls of the American Museum of Natural History, among the armored fish and the stegosaurs. But it wasn’t until I was a 26-year-old science writer that I had the chance to pass through to the other side. I wanted to learn about pterosaurs, those stork-faced, bat-bodied reptiles that soared for 150 million years. I found out about a Brazilian man named Alexander Kellner who was getting his Ph.D. at the museum, studying new fossils of pterosaurs from the Santana Formation. Kellner invited me to the museum, to take a look at the bones and talk about his ideas about what pterosaurs had actually been like in life.

I followed his directions and came to the Grand Gallery. I waited by the Great Canoe, and eventually a gangly paleontologist emerged from the acoustic fog of school groups on field trips. He led me through exhibit halls, and then, between two dioramas, he stopped. At first I thought he was lost in thought, and then maybe that he had forgotten something. There was no reason, after all, to stop by a dim wall between a pair of displays. But then I heard keys ringing in Kellner’s hand. He slipped one into an invisible lock, and the wall swung open. We slid through and Kellner locked the door behind us. I was in the other museum.

The Ever Evolving Theories of Darwin
Time, February 12, 2009
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What do Harry Potter, Sherlock Holmes, G.I. Joe and Charles Darwin have in common? They will all be coming to movie theaters this year. The only real person on that list will be played by Paul Bettany in the biopic Creation. And in true celebrity fashion, Darwin will be everywhere this year. In a convergence of anniversaries, Darwin would have turned 200 years old on Feb. 12, and his landmark book, On the Origin of Species, turns 150 on Nov. 24. There will be documentaries, lectures, conferences and museum exhibits. Darwin-themed blogs are being launched, and a cartload of Darwin-related books are being published. A replica of H.M.S. Beagle, the ship that carried Darwin around the world, will retrace his path. This January, Stanford University let a group of 90 people do likewise--albeit more comfortably, on a private Boeing 757.

It's only fitting to recognize the accomplishments of a great biologist. But there's a risk to all this Darwinmania: some people may come away with a fundamental misunderstanding about the science of evolution. Once Darwin mailed his manuscript of On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life to his publisher, the science of evolution did not grind to a halt. That would be a bit like saying medicine peaked when Louis Pasteur demonstrated that germs cause diseases.

Crunching the Data for the Tree of Life
The New York Times, February 10, 2009
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Michael Sanderson is worried. Dr. Sanderson, a biologist at the University of Arizona, is part of an effort to figure out how all the estimated 500,000 species of plants are related to one another. For years now the researchers have sequenced DNA from thousands of species from jungles, tundras and museum drawers. They have used supercomputers to crunch the genetic data and have gleaned clues to how today’s diversity of baobabs, dandelions, mosses and other plants evolved over the past 450 million years. The pace of their progress gives Dr. Sanderson hope that they will draw the entire evolutionary tree of plants within the next few years. “It’s within striking distance,” Dr. Sanderson said.

There’s just one problem. “We have no way to visualize such a tree at the moment,” he said. If they tried, they would end up with a blurry, inscrutable thicket. “It would be ironic,” Dr. Sanderson said. “We’d be saying, ‘We’ve built it, but we can’t show it to you.’ ”

How Google Is Making Us Smarter
Discover, February 2009
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Our minds are under attack. At least that’s what I keep hearing these days. Thumbing away at our text messages, we are becoming illiterate. (Or is that illiter8?) Blogs make us coarse, YouTube makes us shallow. Last summer the cover of The Atlantic posed a question: “Is Google Making Us Stoopid?” Inside the magazine, author Nicholas Carr argued that the Internet is damaging our brains, robbing us of our memories and deep thoughts. “As we come to rely on computers to mediate our understanding of the world,” he wrote, “it is our own intelligence that flattens into artificial intelligence.”

I have a hard time taking these Cassandras of the Computer Age seriously. For one thing, they are much more interested in our fears than in the facts. In his new book, Txtng: The Gr8 Db8, the English linguist David Crystal demonstrates that many of the dire warnings about texting are little more than urban legends. Texting doesn’t lead to bad spelling, he finds. In fact, Crystal writes, “texting actually improves your literacy, as it gives you more practice in reading and writing.”

More significantly, the ominous warnings feed on a popular misconception of how the mind works. We tend to think of the mind as separated from the world; we imagine information trickling into our senses and reaching our isolated minds, which then turn that information into a detailed picture of reality. The Internet and iPhones seem to be crashing the gate of the mind, taking over its natural work and leaving it to wither away to a mental stump. As plausible as this picture may seem, it does a bad job of explaining a lot of recent scientific research. In fact, the mind appears to be adapted for reaching out from our heads and making the world, including our machines, an extension of itself.

On the Origin of Life on Earth
Science, January 8, 2009
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An Amazon of words flowed from Charles Darwin's pen. His books covered the gamut from barnacles to orchids, from geology to domestication. At the same time, he filled notebooks with his ruminations and scribbled thousands of letters packed with observations and speculations on nature. Yet Darwin dedicated only a few words of his great verbal flood to one of the biggest questions in all of biology: how life began.

The High-Tech Search For A Cleaner Biofuel Alternative
Yale Environment 360, January 5, 2009
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Craig Venter is ready for his next incarnation.

In the 1990s, Venter became familiar to the world as a maverick who would sequence the human genome faster and cheaper than a huge team of government scientists. Six years ago he made headlines by announcing his plan to synthesize an entire genome from scratch, insert it into a cell, and manufacture a new species. In both cases, Venter has followed up his promises with some hard results. He published the first gold-standard sequence of an individual's complete genome (his own). And while he hasn't made an artificial life form yet, he and his colleagues at the J. Craig Venter Institute have achieved a series of landmarks, from synthesizing large chunks of DNA to performing the world's first "genome transplant"on a microbe.

Now Venter says he wants to help save the environment. For some time, he has speculated that genetically engineered microbes could help wean the world off oil and reduce greenhouse gases at the same time. In 2005 Venter set up a company, Synthetic Genomics, to pursue that goal. And now, according to Venter, the company is seeking the capital to move forward. "We're ready to build a pilot plant right now," he says.

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