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For Trees Under Threat, Flight May Be Best Response
New York Times, September 18, 2014

The whitebark pine grows in the high, cold reaches of the Rocky and Sierra Mountains, and some individuals, wind-bent and tenacious, manage to thrive for more than a thousand years.

Despite its hardiness, the species may not survive much longer.

A lethal fungus is decimating the pines, as are voracious mountain pine beetles. Making matters worse, forest managers have suppressed the fires that are required to stimulate whitebark pine seedlings.

Half of all whitebark pines are now dead or dying. In 2012, Canada declared the tree an endangered species, and in the United States it is currently a candidate for listing under the Endangered Species Act.

Now the tree faces a new threat: a swiftly changing climate. Temperatures are rising, and Forest Service researchers estimate that 97 percent of the whitebark pine’s natural range will disappear from the United States by 2100.

Mining for Antibiotics, Right Under Our Noses
New York Times, September 11, 2014

“Microorganisms are the best chemists on the planet,” declared Michael A. Fischbach, a chemist himself at the University of California, San Francisco.

For evidence, Dr. Fischbach points to the many lifesaving drugs that microorganisms produce. In 1928, for example, Alexander Fleming discovered that mold wafting into his lab produced a bacteria-killing chemical that he dubbed penicillin.

Later generations of scientists found drugmaking microorganisms in more exotic locales. In 1951, a missionary in Borneo named William Bouw shipped a box of jungle dirt to Edmund C. Kornfield, a chemist at Eli Lilly. In that soil, Dr. Kornfield discovered a species of bacteria that made a potent antibiotic, later named vancomycin.

Scientists today are still searching jungles, oceans and other corners of the world for microorganisms that make medicines. But in a new study published Thursday in the journal Cell, Dr. Fischbach and his colleagues suggest that we should also be looking inward.

How Caffeine Evolved to Help Plants Survive and Help People Wake Up
New York Times, September 4, 2014

Every second, people around the world drink more than 26,000 cups of coffee. And while some of them may care only about the taste, most use it as a way to deliver caffeine into their bloodstream. Caffeine is the most widely consumed psychoactive substance in the world.

Many of us get our caffeine fix in tea, and still others drink mate, brewed from the South American yerba mate plant. Cacao plants produce caffeine, too, meaning that you can get a mild dose from eating chocolate.

Caffeine may be a drug, but it’s not the product of some underworld chemistry lab; rather, it’s the result of millions of years of plant evolution. Despite our huge appetite for caffeine, however, scientists know little about how and why plants make it.

A new study is helping to change that. An international team of scientists has sequenced the genome of Coffea canephora, one of the main sources of coffee beans. By analyzing its genes, the scientists were able to reconstructhow coffee gained the biochemical equipment necessary to make caffeine.

The new study, published Thursday in the journal Science, sheds light on how plants evolved to make caffeine as a way to control the behavior of animals—and, indirectly, us.

Tiny, Vast Windows Into Human DNA
New York Times, September 1, 2014

In the history of biology, two little animals loom large.

In the early 1900s, scientists began studying Drosophila melanogaster, the common fruit fly. Research on these fast-breeding insects revealed that genes lie on chromosomes, which turned out to be true for other animals, including us. For more than a century, scientists have continued to glean clues from the lowly fly to other mysteries of biology, like why we sleep and how heart disease develops.

In the 1960s, another unassuming animal joined biology’s pantheon: a tiny worm called Caenorhabditis elegans. The biologist Sydney Brenner realized that its body, made up of just a couple of thousand cells, offered an singular opportunity to learn how a single egg gives rise to a complete animal. Today, many scientists are studying the worm for clues to how our own brains are wired and why we age.

Now the two species are providing even deeper insights in biology. A team of hundreds of scientists has exhaustively recorded the choreography of their genes as the animals develop from eggs to adults.

“It’s not just this gene or that gene,” said Robert H. Waterston, a geneticist at the University of Washington who is among the scientists working on the project, called modENCODE. “We can get a picture of the whole.”

Century After Extinction, Passenger Pigeons Remain Iconic—And Scientists Hope to Bring Them Back
National Geographic, August 31, 2014

People coming to the zoo to see the last passenger pigeon were disappointed by the bird, which barely budged off its perch. As Joel Greenberg writes in his recent book A Feathered River Across the Sky, some threw sand into its cage to try to force it to walk around. But on that first day of September a century ago, Martha no longer had to put up with such humiliations.

It was a quiet end to a noisy species. As recently as the mid-1800s, deafening flocks of billions of passenger pigeons swarmed across the eastern half of the United States. But they proved no match for humans, whose rapidly advancing technology drove the birds to extinction in a matter of decades.

Other species were also spiraling toward extinction in the late 1800s, but the destruction of the passenger pigeon happened on full public display. "It became the icon of extinction," says Mark Barrow, a historian at Virginia Tech and the author of Nature's Ghosts.

A hundred years later, the passenger pigeon remains iconic and is inspiring extravagant new technological feats. One team of scientists is even trying to bring the species back from extinction, using genetic engineering and cloning. Others are analyzing bits of passenger pigeon DNA to reconstruct its lost ways of life.

Parasites Practicing Mind Control
New York Times, August 28, 2014

An unassuming single-celled organism called Toxoplasma gondii is one of the most successful parasites on Earth, infecting an estimated 11 percent of Americans and perhaps half of all people worldwide. It’s just as prevalent in many other species of mammals and birds. In a recent study in Ohio, scientists found the parasite in three-quarters of the white-tailed deer they studied.

One reason for Toxoplasma’s success is its ability to manipulate its hosts. The parasite can influence their behavior, so much so that hosts can put themselves at risk of death. Scientists first discovered this strange mind control in the 1990s, but it’s been hard to figure out how they manage it. Now a new study suggests that Toxoplasma can turn its host’s genes on and off — and it’s possible other parasites use this strategy, too.

Toxoplasma manipulates its hosts to complete its life cycle. Although it can infect any mammal or bird, it can reproduce only inside of a cat. The parasites produce cysts that get passed out of the cat with its feces; once in the soil, the cysts infect new hosts.

Toxoplasma returns to cats via their prey. But a host like a rat has evolved to avoid cats as much as possible, taking evasive action from the very moment it smells feline odor.

Tuberculosis Is Newer Than What Was Thought, Study Says
New York Times, August 20, 2014

After a remarkable analysis of bacterial DNA from 1,000-year-old mummies, scientists have proposed a new hypothesis for how tuberculosis arose and spread around the world.

The disease originated less than 6,000 years ago in Africa, they say, and took a surprising route to reach the New World: it was carried across the Atlantic by seals.

The new study, published Wednesday in the journal Nature, has already provoked strong reactions from other scientists.

“This is a landmark paper that challenges our previous ideas about the origins of tuberculosis,” said Terry Brown, a professor of biomolecular archaeology at the University of Manchester. “At the moment, I’m still in the astonished stage over this.”

Our Microbiome May Be Looking Out for Itself
New York Times, August 14, 2014

Your body is home to about 100 trillion bacteria and other microbes, collectively known as your microbiome. Naturalists first became aware of our invisible lodgers in the 1600s, but it wasn’t until the past few years that we’ve become really familiar with them.

This recent research has given the microbiome a cuddly kind of fame. We’ve come to appreciate how beneficial our microbes are — breaking down our food, fighting off infections and nurturing our immune system. It’s a lovely, invisible garden we should be tending for our own well-being.

But in the journal Bioessays, a team of scientists has raised a creepier possibility. Perhaps our menagerie of germs is also influencing our behavior in order to advance its own evolutionary success — giving us cravings for certain foods, for example.

Maybe the microbiome is our puppet master.

Cyanobacteria Are Far From Just Toledo’s Problem
New York Times, August 7, 2014

Over the weekend, an entire city was brought to its knees by pond scum.

Toledo, Ohio, gets its drinking water from the western end of Lake Erie. A bloom of bacteria formed there last week, producing a dangerous toxin called microcystin. City officials warned half a million residents against drinking municipal water. At high doses, the toxin can cause liver failure.

The microbes that terrorized Toledo, known as cyanobacteria, are actually a worldwide menace.

Fertilizers and other pollutants, the consequences of modern agriculture and fossil fuel production, are flowing into rivers and lakes, promoting the growth of these waterborne bacteria. The result is a worldwide rise in cyanobacterial blooms.

Having More Than One Set of DNA Carries Legacy of Risk
New York Times, July 31, 2014

The family seemed to defy the rules of genetics.

When Meriel M. McEntagart, a geneticist at St. George’s University of London, met the family in May 2012, she suspected that three of the children had a rare genetic disorder called Smith-Magenis syndrome. They had many of the symptoms of the disease, such as trouble sleeping through the night. Dr. McEntagart confirmed that diagnosis with a genetic test. The children were all missing an identical chunk of a gene known as RAI1.

One of the children had a different father from the other two, and so the mother could be the only source of their altered gene. But when Dr. McEntagart ran a standard blood test on the mother, the results were not nearly so straightforward: The woman had a normal version of RAI1.

Dr. McEntagart and her colleagues suspected that the answer to this puzzle was that the mother was a genetic mosaic.

Study Gives Hope of Adaptation to Climate Change
New York Times, July 24, 2014

As we pour heat-trapping gases into the air, we’re running an experiment. We’re going to see what a rapidly changing climate does to the world’s biodiversity — how many species shift to new ranges, how many adapt to their new environment and how many become extinct.

We don’t have a very good idea of how the experiment will turn out. Scientists are coming to appreciate that there’s a lot about how climate affects life that they still don’t understand. That’s true, it turns out, even for species that scientists have been studying carefully for years.

In the early 2000s, Ary A. Hoffmann, a biologist then at La Trobe University in Melbourne, Australia, wondered how the many species in tropical rain forests would cope when their humid environment dried out.

It was conceivable that some species might adapt. Over the generations, natural selection ought to favor the individuals that could survive longer in dry air. Over time, the whole population should become more resistant.

Spark for a Stagnant Search
Co-authored with Benedict Carey
New York Times, July 21, 2014

One day in 1988, a college dropout named Jonathan Stanley was visiting New York City when he became convinced that government agents were closing in on him.

He bolted, and for three days and nights raced through the city streets and subway tunnels. His flight ended in a deli, where he climbed a plastic crate and stripped off his clothes. The police took him to a hospital, and he finally received effective treatment two years after getting a diagnosis of bipolar disorder.

“My son’s life was saved,” his father, Ted Stanley, said recently. When he himself was in college, he added, “those drugs didn’t exist; I would have had a nonfunctioning brain all the rest of my life.”

The older Mr. Stanley, 84, who earned a fortune selling collectibles, created a foundation to support psychiatric research. “I would like to purchase that happy ending for other people,” he said.

A Call to Fight Malaria One Mosquito at a Time by Altering DNA
New York Times, July 17, 2014

Every year, malaria-carrying mosquitoes kill more than 600,000 people, most of them children. Over the centuries, people have battled those mosquitoes in numerous ways, like draining swamps, spraying insecticides and distributing millions of bed nets. And yet malaria remains a menace across much of the world.

In papers published Thursday in the journals Science and eLife, scientists and policy experts propose fighting malaria in a new way: by genetically engineering the mosquitoes themselves.

A new technology for editing DNA may allow scientists to render the insects resistant to the malaria parasite, the authors contend. Or it might be possible to engineer infertility into mosquito DNA, driving their populations into oblivion.

The New Science of Evolutionary Forecasting
Quanta Magazine, July 17, 2014

Michael Lässig can be certain that if he steps out of his home in Cologne, Germany, on the night of Jan. 19, 2030 — assuming he’s still alive and the sky is clear — he will see a full moon.

Lässig’s confidence doesn’t come from psychic messages he’s receiving from the future. He knows the moon will be full because physics tells him so. “The whole of physics is about prediction, and we’ve gotten quite good at it,” said Lässig, a physicist at the University of Cologne. “When we know where the moon is today, we can tell where the moon is tomorrow. We can even tell where it will be in a thousand years.”

Early in his career, Lässig made predictions about quantum particles, but in the 1990s, he turned to biology, exploring how genes evolved. In his research, Lässig was looking back in time, reconstructing evolutionary history. Looking ahead to evolution’s future was not something that biologists bothered doing. It might be possible to predict the motion of the moon, but biology was so complex that trying to predict its evolution seemed a fool’s errand.

Why do we have blood types?
Mosaic, July 15, 2014

When my parents informed me that my blood type was A+, I felt a strange sense of pride. If A+ was the top grade in school, then surely A+ was also the most excellent of blood types – a biological mark of distinction.

It didn’t take long for me to recognise just how silly that feeling was and tamp it down. But I didn’t learn much more about what it really meant to have type A+ blood. By the time I was an adult, all I really knew was that if I should end up in a hospital in need of blood, the doctors there would need to make sure they transfused me with a suitable type.

And yet there remained some nagging questions. Why do 40 per cent of Caucasians have type A blood, while only 27 per cent of Asians do? Where do different blood types come from, and what do they do? To get some answers, I went to the experts – to haematologists, geneticists, evolutionary biologists, virologists and nutrition scientists.

Hope for Frogs in Face of a Deadly Fungus
New York Times, July 14, 2014

In the 1990s, a disturbing silence began to settle across the world. From mountain lakes to tropical streams, the music of singing frogs began to disappear.

It took a few years for scientists to figure out what was happening. A species of fungus — Batrachochytrium dendrobatidis, or Bd for short — was infecting and killing amphibians.

Two decades later, Bd has proved itself an exceptional biological catastrophe. It afflicts amphibians on every continent, and scientists suspect it has driven hundreds of species to extinction since its discovery.

“Even Ebola doesn’t cause extinctions,” said Jason R. Rohr, an expert on the fungus at the University of South Florida. “This makes it arguably the second most deadly organism on the planet, behind humans.”

This Is Your Brain on Writing
New York Times, June 20, 2014

A novelist scrawling away in a notebook in seclusion may not seem to have much in common with an NBA player doing a reverse layup on a basketball court before a screaming crowd. But if you could peer inside their heads, you might see some striking similarities in how their brains were churning.

That’s one of the implications of new research on the neuroscience of creative writing. For the first time, neuroscientists have used fMRI scanners to track the brain activity of both experienced and novice writers as they sat down — or, in this case, lay down — to turn out a piece of fiction.

The researchers, led by Martin Lotze of the University of Greifswald in Germany, observed a broad network of regions in the brain working together as people produced their stories. But there were notable differences between the two groups of subjects. The inner workings of the professionally trained writers in the bunch, the scientists argue, showed some similarities to people who are skilled at other complex actions, like music or sports.

The research is drawing strong reactions. Some experts praise it as an important advance in understanding writing and creativity, while others criticize the research as too crude to reveal anything meaningful about the mysteries of literature or inspiration.

A Long-Ago Ancestor: A Little Fish, With Jaws to Come
New York Times, June 11, 2014

Half a billion years ago, a new study suggests, your ancestors may have looked like this:

This two-inch, 505-million-year-old creature belonged to the lineage that would later produce sharks, eels and other fish — along with birds, reptiles and mammals like us. This early vertebrate, known as Metaspriggina, was something of a mystery for years, known only from a pair of ambiguous fossils. But recently, scientists unearthed a trove of much more complete Metaspriggina fossils.

Putting a Price Tag on Nature’s Defenses
New York Times, June 5, 2014

After Hurricane Katrina devastated New Orleans, the United States Army Corps of Engineers got to work on a massive network of levees and flood walls to protect against future catastrophes. Finally completed in 2012, the project ended up costing $14.5 billion — and that figure didn’t include the upkeep these defenses will require in years to come, not to mention the cost of someday replacing them altogether.

But levees aren’t the only things that protect coasts from storm damage. Nature offers protection, too. Coastal marshes absorb the wind energy and waves of storms, weakening their impact farther inland. And while it’s expensive to maintain man-made defenses, wetlands rebuild themselves.

Protection from storms is just one of many services that ecosystems provide us — services that we’d otherwise have to pay for. In 1997, a team of scientists decided to estimate how much they are actually worth. Worldwide, they concluded, the price tag was $33 trillion — equivalent to $48.7 trillion in today’s dollars. Put another way, the services ecosystems provide us — whether shielding us from storms, preventing soil erosion or soaking up the greenhouse gases that lead to global warming — were twice as valuable as the gross national product of every country on Earth in 1997.

“We basically said, ‘It’s an imprecise estimate, but it’s almost definitely a pretty big number, and we’ve got to start paying attention,'” said Robert Costanza, a professor at Australian National University who led the study.

In a First, Test of DNA Finds Root of Illness
New York Times, June 4, 2014

Joshua Osborn, 14, lay in a coma at American Family Children’s Hospital in Madison, Wis. For weeks his brain had been swelling with fluid, and a battery of tests had failed to reveal the cause.

The doctors told his parents, Clark and Julie, that they wanted to run one more test with an experimental new technology. Scientists would search Joshua’s cerebrospinal fluid for pieces of DNA. Some of them might belong to the pathogen causing his encephalitis.

The Osborns agreed, although they were skeptical that the test would succeed where so many others had failed. But in the first procedure of its kind, researchers at the University of California, San Francisco, managed to pinpoint the cause of Joshua’s problem — within 48 hours. He had been infected with an obscure species of bacteria. Once identified, it was eradicated within days.

The case, reported on Wednesday in The New England Journal of Medicine, signals an important advance in the science of diagnosis. For years, scientists have been sequencing DNA to identify pathogens. But until now, the process has been too cumbersome to yield useful information about an individual patient in a life-threatening emergency.

Stronger Brains, Weaker Bodies
New York Times, May 27, 2014

All animals do the same thing to the food they eat — they break it down to extract fuel and building blocks for growing new tissue. But the metabolism of one species may be profoundly different from another’s. A sloth will generate just enough energy to hang from a tree, for example, while some birds can convert their food into a flight from Alaska to New Zealand.

For decades, scientists have wondered how our metabolism compares to that of other species. It’s been a hard question to tackle, because metabolism is complicated — something that anyone who’s stared at a textbook diagram knows all too well. As we break down our food, we produce thousands of small molecules, some of which we flush out of our bodies and some of which we depend on for our survival.

An international team of researchers has now carried out a detailed comparison of metabolism in humans and other mammals. As they report in the journal PLOS Biology, both our brains and our muscles turn out to be unusual, metabolically speaking. And it’s possible that their odd metabolism was part of what made us uniquely human.

When scientists first began to study metabolism, they could measure it only in simple ways. They might estimate how many calories an animal burned in a day, for example. If they were feeling particularly ambitious, they might try to estimate how many calories each organ in the animal’s body burned.

A Theory on How Flightless Birds Spread Across the World: They Flew There
New York Times, May 22, 2014

Just a few centuries ago, Madagascar was home to a monstrous creature called the elephant bird. It towered as high as nine feet. Weighing as much as 600 pounds, it was the heaviest bird known to science. You’d need 160 chicken eggs to equal the volume of a single elephant bird egg.

The only feature of the elephant bird that wasn’t gigantic was its wings, which were useless, shriveled arms. Instead of flying, the elephant bird kept its head down much of the time, grazing on plants.

Scientists aren’t precisely sure when this strange creature became extinct, but it probably endured well into our human-dominated age.

In the Middle Ages, Marco Polo heard tales of a huge bird that stalked Madagascar. A French colonial governor of Madagascar wrote in 1658 about a giant bird that lived in the remote parts of the island. Today, scientists are trying to determine when the elephant bird became extinct by estimating the age of its youngest remains. It’s possible the birds were still thundering across Madagascar in the 1800s.

Strange Findings on Comb Jellies Uproot Animal Family Tree
National Geographic, May 21, 2014

“It's a paradox,” said Leonid Moroz, a neurobiologist at the University of Florida in Gainesville and lead author of a paper in today's Nature about the biology of the comb jelly nervous system. “These are animals with a complex nervous system, but they basically use a completely different chemical language” from every other animal. “You have to explain it one way or another.”

The way Moroz explains it is with an evolutionary scenario—one that's at odds with traditional accounts of animal evolution.

Moroz and his colleagues have been studying comb jellies, whose scientific name is ctenophores (pronounced TEN-o-fors), for many years, beginning with the sequencing of the genome of one species, the Pacific sea gooseberry, in 2007. The sea gooseberry has 19,523 genes, about the same number as are found in the human genome.

The scientists enlarged their library to the genes of ten other species of comb jelly (out of the 150 or so species known to exist) and compared them to the analogous genes in other animals. And when they looked at the genes involved in the nervous system, they found that many considered essential for the development and function of neurons were simply missing in the comb jelly.

When Predators Vanish, So Does the Ecosystem
New York Times, May 15, 2014

Mark D. Bertness, an ecologist at Brown University, began studying the salt marshes of New England in 1981. Twenty-six years later, in 2007, he started to watch them die. In one marsh after another, lush stretches of cordgrass disappeared, replaced by bare ground. The die-offs were wiping out salt marshes in just a few years.

“It’s unbelievable how quickly it’s moved in,” Dr. Bertness said.

Scientists have been witnessing a similar transformation in a number of plant species along coastlines in the United States and in other countries. And in many cases, it’s been hard to pinpoint the cause of the die-off, with fungal outbreaks, pollution, choking sediments stirred up by boats, and rising sea levels proposed as killers.

There is much at stake in the hunt for the culprit, because salt marshes are hugely important. They shield coasts from flooding, pull pollutants from water and are nurseries for many fish species.

“Acre for acre, they’re among the most valuable ecosystems on the planet,” Dr. Bertness said.

In the journal Ecology Letters, Dr. Bertness and his colleagues have now published an experiment that may help solve the mystery. The evidence, they say, points to recreational fishing and crabbing. A fisherman idly dangling a line off a dock may not appear to be an agent of ecological collapse. But fishing removes the top predators from salt marshes, and the effects may be devastating.

Antibiotic-Resistant Germs, Lying in Wait Everywhere
New York Times, May 8, 2014

The Lechuguilla Cave in New Mexico is a network of chambers stretching 1,600 feet underground. The bacteria that grow on the walls of its most remote recesses have been living in complete isolation for more than four million years.

In 2010, Gerry Wright, a microbiologist at McMaster University in Ontario, ran an experiment on those long-lost bacteria. He and his colleagues doused them with antibiotics, the drugs that doctors have used for the past 70 years to wipe out bacterial infections.

But many of the Lechuguilla bacteria would not die.

“Most of them were resistant to something,” said Dr. Wright. Some strains, he and his colleagues found, could resist 14 commercially available antibiotics.

Dr. Wright’s discovery didn’t fit the conventional story of antibiotics. Antibiotics were introduced in the mid-1900s. Each time a new drug was introduced, it would take years before bacteria that could resist it became common.

In the decades since, this trend has turned into a crisis. Last week, the World Health Organization reported that antibiotic resistance is now a major threat to public health across the entire planet. “We will soon hit the wall,” warned Joseph Nesme, a microbiologist at the University of Lyon in France.

Laser Cowboys and the Fossils of the Future
Popular Mechanics, May 2, 2014

One morning in November 2011, trucks were roaring down the Pan-American Highway, carrying loads of ore from mines in the Atacama Desert to the port town of Caldera, Chile. The trucks screamed past a young goateed American paleontologist named Nicholas Pyenson, who was standing at the side of the road, gazing at a 250-meter-long strip of sandstone that construction workers had cleared in preparation for building new lanes.

Pyenson, the curator of fossil marine mammals at the Smithsonian Institution, spends much of his time searching for fossils of whales. For over a year his Chilean colleague Mario Suárez had been nagging him to come to see whale fossils that had been exposed as construction workers widened the highway. Pyenson envisioned a few skull fragments wedged in a road cut—a very low priority. After completing his work at another fossil site in Chile, Pyenson finally agreed to go see the remains. And standing by the highway, he realized why Suárez had been so insistent. The road crew had uncovered not just a few whale bones but an entire whale graveyard. At least 40 prehistoric whales, some 30 feet long, were spread out before him. It would turn out to be the densest collection of fossil whales discovered anywhere in the world.

Whales may be some of the most remarkable animals in the history of life—they evolved, after all, from deerlike mammals on land and became top predators of the sea. But their fossils can be a nightmare for paleontologists. "I wouldn't wish a whale fossil on anyone," Pyenson says. "Especially not 40."

Young Blood May Hold Key to Reversing Aging
New York Times, May 4, 2014

Two teams of scientists published studies on Sunday showing that blood from young mice reverses aging in old mice, rejuvenating their muscles and brains. As ghoulish as the research may sound, experts said that it could lead to treatments for disorders like Alzheimer’s disease and heart disease.

“I am extremely excited,” said Rudolph Tanzi, a professor of neurology at Harvard Medical School, who was not involved in the research. “These findings could be a game changer.”

The research builds on centuries of speculation that the blood of young people contains substances that might rejuvenate older adults.

In the 1950s, Clive M. McCay of Cornell University and his colleagues tested the notion by delivering the blood of young rats into old ones. To do so, they joined rats in pairs by stitching together the skin on their flanks. After this procedure, called parabiosis, blood vessels grew and joined the rats’ circulatory systems. The blood from the young rat flowed into the old one, and vice versa.

Later, Dr. McCay and his colleagues performed necropsies and found that the cartilage of the old rats looked more youthful than it would have otherwise. But the scientists could not say how the transformations happened. There was not enough known at the time about how the body rejuvenates itself.

In 1918 Flu Pandemic, Timing Was a Killer
New York Times, April 30, 2014

Sometimes a virus can cause more devastation than all the world’s armies. In 1918, at the end of World War I, influenza spread around the planet, reaching even Pacific islands and Arctic villages. The virus infected a third of all people on earth, and caused an estimated 50 million deaths — more than three times the number of people killed in World War I.

Since 1918, four new global flu pandemics have struck. None have come anywhere close to 1918’s toll, leaving scientists to puzzle about why 1918 was so deadly.

Adding to the mystery was that people in their late 20s were at greatest risk of dying in 1918. Typically, children and old people are more likely to die in flu outbreaks.

In a provocative new study published recently in The Proceedings of the National Academy of Sciences, a team of scientists argues that there wasn’t anything particularly sinister about the 1918 virus. The pandemic was the result of some disastrously bad luck.

The Continuing Evolution of Genes
New York Times, April 28, 2014

Each of us carries just over 20,000 genes that encode everything from the keratin in our hair down to the muscle fibers in our toes. It’s no great mystery where our own genes came from: our parents bequeathed them to us. And our parents, in turn, got their genes from their parents.

But where along that genealogical line did each of those 20,000 protein-coding genes get its start?

That question has hung over the science of genetics ever since its dawn a century ago. “It’s a basic question of life: how evolution generates novelty,” said Diethard Tautz of the Max Planck Institute for Evolutionary Biology in Plön, Germany.

New studies are now bringing the answer into focus. Some of our genes are immensely old, perhaps dating all the way back to the earliest chapters of life on earth.

But a surprising number of genes emerged more recently — many in just the past few million years. The youngest evolved after our own species broke off from our cousins, the apes.

Springing Forward, and Its Consequences
New York Times, April 23, 2014

This is a busy time of year for Richard B. Primack, a biologist at Boston University. He and his colleagues survey the plants growing around Concord, Mass., recording the first day they send up flowers and leaves.

Compared to the last five springs, things are pretty slow right now around Concord, in large part because of the relatively cold winter and chilly March.

But Dr. Primack wouldn’t call this a late spring. “It’s just much later compared to our recent memories of spring,” he said.

Dr. Primack knows this thanks to Henry David Thoreau. During the 1850s, Thoreau carefully recorded the arrival of spring at Walden Pond, one of Concord’s most famous sites. Dr. Primack has combined Thoreau’s data with his own and those of other naturalists to create a record of the seasons stretching across 160 years.

As Dr. Primack writes in his new book “Walden Warming,” spring has started earlier and earlier over the decades. It now arrives about three weeks sooner than in Thoreau’s time.

Plants That Practice Genetic Engineering
New York Times, April 17, 2014

In the debate over genetically modified crops, one oft-said word is “unnatural.” People typically use it when describing how scientists move genes from one species into another.

But nature turns out to be its own genetic engineer. Genes have moved from one species of plant to another for millions of years.

Scientists describe a spectacular case this week in The Proceedings of the National Academy of Sciences in which ferns acquired a gene for sensing light from a moss-like plant called hornwort. Gaining the gene appears to have enabled the ferns to thrive in shady forests.

The new research builds on a 2004 study on ferns carried out by Kathleen M. Pryer of Duke University and her colleagues. They traced the evolutionary history of ferns by comparing samples of DNA from 45 fern species.

The scientists found that roughly 100 million years ago, ferns exploded into a number of new lineages. Eighty percent of today’s fern species can be traced to that evolutionary burst.

How Lives Become Long
An Introduction to The Oldest Things in the World, by Rachel Sussman (University of Chicago Press, April 2014)

It is easy to feel sorry for the gastrotrich. This invertebrate animal, the size of a poppy seed and the shape of a bowling pin, swarms by the millions in rivers and lakes. After it hatches, it takes only three days to develop a complicated body, complete with a mouth, a gut, sensory organs, and a brain. Having reached maturity in just seventy-two hours, the gastrotrich starts laying eggs. And after a few more days, it becomes enfeebled and dies of old age.

To squeeze a whole life into a week seems like one of nature’s more cruel tricks. But that’s only because we are accustomed to measure our lives in decades. If the ancient animals and plants featured in this book could look upon us, they might feel sorry for us as well. We humans marvel at the longest-living human on record, Jean Calment, who lived from 1875 to 1997. But for a 13,000-year-old Palmer’s oak tree, Calment’s 122 years rushed by as quickly as a summer vacation.

Watch Proteins Do the Jitterbug
New York Times, April 10, 2014

If you could shrink down to the size of a molecule and fly into a cell, what would you see?

In 2006, a team of scientists and illustrators offered a gorgeous answer in the form of a three-minute video called “The Inner Life of the Cell.” Nothing quite like it had ever been made before, and it proved to be a huge hit, broadcast by museums, universities and television programs around the world.

The video was a collaboration between BioVisions, a scientific visualization program at Harvard’s department of molecular and cellular biology, and Xvivo, a scientific animation company in Connecticut.

Delving into the scientific literature, the scientists and animators created a video about an immune cell. The cell rolls along the interior wall of a blood vessel until it detects signs of inflammation from a nearby infection.

Antibiotics Have Turned Our Bodies From Gardens Into Battlefields
Wired, March 2014

We’re in the midst of an extinction crisis, and it doesn’t involve Siberian tigers. Microbiologist Martin Blaser of New York University School of Medicine says that many species of germs are disappearing from our bodies—and that’s a problem.

In his new book, Missing Microbes: How the Overuse of Antibiotics Is Fueling Our Modern Plagues, Blaser argues that while antibiotics have saved countless lives, they’re an assault on our microbiome. His experiments have linked the resulting extinctions to disorders from asthma to obesity. WIRED spoke to Blaser about the need to look at our bodies less as battlefields to be conquered and more as gardens to be tended.

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Enlisting a Computer to Battle Cancers, One by One
New York Times, March 27, 2014

When Robert B. Darnell was a graduate student in the early 1980s, he spent a year sequencing a tiny fragment of DNA. Now Dr. Darnell is an oncologist and the president of the New York Genome Center, where the DNA-sequencing machines can decode his grad-school fragment in less than a ten-thousandth of a second.

As an oncologist, Dr. Darnell is firmly convinced that this technological advance will change how cancer is treated. “It’s inspiring for me, and it’s inspiring for lots of doctors,” he said in an interview.

The idea is simple. Oncologists will get a tumor biopsy and have its genome sequenced. They will identify the mutations in the cancer cells, and they will draw up a list of drugs to treat each patient’s particular mix of mutations.

This isn’t pure science fiction. Oncologists have already created such drug cocktails for a handful of cancer patients. But that doesn’t mean people with cancer should expect personalized treatments any time soon. Unfortunately, the path from a genome to a treatment is blocked by a colossal bottleneck.

“We know that the devil’s in the details, and a lot of the mystery is still there,” said Dr. Darnell.

A Growth Spurt at 1,500 Years Old
New York Times, March 17, 2014

Signy Island, which lies 375 miles off Antarctica, has too harsh an environment to support a single tree. Its mountains are girdled instead by banks of moss.

“It’s just like a big, green, spongy expanse,” said Peter Convey, an ecologist at the British Antarctic Survey who has worked on Signy Island for 25 years.

Only the top inch of the moss banks is growing. The lack of sunlight turns the older moss brown, and eventually it becomes permanently frozen. Blankets of permafrost have grown on the island for thousands of years, since the glaciers retreated at the end of the last ice age.

But when Dr. Convey and his colleagues have drilled to the gravel bed and examined the cores they drew up, they have seen something odd.

Take a Breath and Thank a Sponge
New York Times, March 13, 2014

If Tim Lenton is right, we all owe sponges a deep debt of gratitude. It may be hard to give much credit to these simple animals, which spend their uneventful lives on the sea floor trapping floating bits of food. But Dr. Lenton, an earth systems scientist at the University of Exeter, suspects that sponges played a crucial role in the rise of the animal kingdom.

Some 700 million years ago, he and his colleagues argue, sponges re-engineered the planet. The sponges unleashed a flood of oxygen into the ocean, which before then had scarcely any oxygen at all. Without that transformation, we might not be on earth today.

“This story is about the first animals bootstrapping the environment into one where more complex animals could evolve,” said Dr. Lenton. “This is essentially the birth of the modern world.”

The Oldest Rocks on Earth
Scientific American, March 2014

The Nuvvuagittuq greenstone belt doesn't look like a battlefield. It lies in peaceful, roadless isolation along the northeastern edge of Hudson Bay in Canada, more than 20 miles from Inukjuak, the nearest human settlement. From the shoreline, the open ground swells into low hills, some covered by lichens, some scraped bare by Ice Age glaciers. The exposed rocks are beautiful in their stretched and folded complexity. Some are gray and black, shot through with light veins. Others are pinkish, sprinkled with garnets. For most of the year the only visitors here are caribou and mosquitoes.

But this tranquil site is indeed a battleground—a scientific one. For almost a decade rival teams of geologists have traveled to Inukjuak, where they have loaded canoes with camping gear and laboratory equipment and trekked along the coast of the bay to the belt itself. Their goal: to prove just how old the rocks are. One team, headed by University of Colorado geologist Ste- phen J. Mojzsis, is certain that the age is 3.8 billion years. That is pretty ancient, though not record setting.

Jonathan O’Neil, who leads the competing team at the University of Ottawa, argues that the Nuvvuagittuq rocks formed as long as 4.4 billion years ago. That would make them by far the oldest rocks ever found on Earth. And that is not the least of it. Rocks that old would tell us how the planet’s surface formed out of its violent infancy and just how soon after that life emerged—a pivotal chapter in Earth’s biography that has so far remained beyond reach.

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Out of Siberian Ice, a Virus Revived
New York Times, March 4, 2014

Siberia fills the heads of scientists with dreams of resurrection. For millions of years, its tundra has gradually turned to permafrost, entombing animals and other organisms in ice. Some of their remains are exquisitely well preserved — so well, in fact, that some scientists have nibbled on the meat of woolly mammoths.

Some researchers even hope to find viable mammoth cells that they can use to clone the animals back from extinction. And in 2012, Russian scientists reported coaxing a seed buried in the permafrost for 32,000 years to sprout into a flower.

Now a team of French and Russian researchers has performed a resurrection of a more sinister nature. From Siberian permafrost more than 30,000 years old, they have revived a virus that’s new to science.

“To pull out a virus that’s 30,000 years old and actually grow it, that’s pretty impressive,” said Scott O. Rogers of Bowling Green State University who was not involved in the research. “This goes well beyond what anyone else has done.”

Stupider With Monogamy
New York Times, February 27, 2014

Forcing male flies into monogamy has a startling effect: After a few dozen generations, the flies become worse at learning.

This discovery, published on Wednesday in the Proceedings of the Royal Society, isn’t a biological excuse for men who have strayed from their significant other. Instead, it’s a tantalizing clue about why intelligence evolved.

The new study was carried out by Brian Hollis and Tadeusz J. Kawecki, biologists at the University of Lausanne in Switzerland. They investigated a fly species called Drosophila melanogaster that normally has a very un-monogamous way of life.

Seeking a Break in a 252 Million-Year-Old Mass Killing
New York Times, February 20, 2014

Sam Bowring is officially a geologist at M.I.T. Unofficially, he’s a homicide detective trying to solve the ultimate cold case. Dr. Bowring wants to understand how an estimated 96 percent of all species on Earth became extinct at the end of the Permian Period 252 million years ago. It was the biggest of the five mass extinctions recorded in the fossil record. But because this killing happened so long ago, the culprit has evaded discovery for decades.

Dr. Bowring and his colleagues have now gotten an important break in the case. They’ve made the most precise measurement yet of how long it took for all those species to become extinct. Writing in the Proceedings of the National Academy of Sciences, they report that the extinction took less than about 60,000 years. That’s a geological blink of an eye — a fact that will help scientists evaluate different hypotheses for what triggered the mass extinction.

For now, however, the new result has Dr. Bowring puzzled. “I just think there’s probably something really fundamental that we don’t understand,” he said.

Scientists have long known that something big happened 252 million years ago, at the end of the Permian Period and the beginning of the Triassic. By the mid-1800s, they had collected enough fossils to notice that this boundary marked a dramatic change in the diversity of life on Earth. Before the Triassic, for example, horseshoe-crab-like creatures called trilobites left scads of fossils on the floors of the world’s oceans. Afterward, they left none.

Phantom Melodies Yield Real Clues to Brain’s Workings
New York Times, February 13, 2014

In 2011, a 66-year-old retired math teacher walked into a London neurological clinic hoping to get some answers. A few years earlier, she explained to the doctors, she had heard someone playing a piano outside her house. But then she realized there was no piano.

The phantom piano played longer and longer melodies, like passages from Rachmaninov’s Piano Concerto number 2 in C minor, her doctors recount in a recent study in the journal Cortex. By the time the woman — to whom the doctors refer only by her first name, Sylvia — came to the clinic, the music had become her nearly constant companion. Sylvia hoped the doctors could explain to her what was going on.

Sylvia was experiencing a mysterious condition known as musical hallucinations. These are not pop songs that get stuck in your head. A musical hallucination can convince people there is a marching band in the next room, or a full church choir. Nor are musical hallucinations the symptoms of psychosis. People with musical hallucinations usually are psychologically normal — except for the songs they are sure someone is playing.

The doctors invited Sylvia to volunteer for a study to better understand the condition. She agreed, and the research turned out to be an important step forward in understanding musical hallucinations. The scientists were able to compare her brain activity when she was experiencing hallucinations that were both quiet and loud — something that had never been done before. By comparing the two states, they found important clues to how the brain generates these illusions.

If a broader study supports the initial findings, it could do more than help scientists understand how the brain falls prey to these phantom tunes. It may also shed light on how our minds make sense of the world.

A Catalog of Cancer Genes That’s Done, or Just a Start
New York Times, February 6, 2014

Cancer is a disease of genes gone wrong. When certain genes mutate, they make cells behave in odd ways. The cells divide swiftly, they hide from the immune system that could kill them and they gain the nourishment they need to develop into tumors.

Scientists started identifying these cancer genes in the 1970s and their list slowly grew over the years. By studying them, scientists came to understand how different types of cancer develop and in some cases they were even able to develop gene-targeting drugs. Last May, for example, the Food and Drug Administration approved a drug known as Tarceva as a first-line treatment for lung cancer in which a gene called EGFR has mutated.

The National Institutes of Health, hoping to speed up the identification of cancer genes, started an ambitious project in 2005 called the Cancer Genome Atlas. They analyzed 500 samples from each of over 20 types of cancer and found a wealth of new genes. The data have helped scientists discover more of the tricks cancer cells use to thrive at our expense.

“The Cancer Genome Atlas has been a spectacular success, there’s no doubt about that,” said Bruce Stillman, the president of Cold Spring Harbor Laboratory.

But now, as the Atlas project is coming to an end, researchers at the Broad Institute of M.I.T. and Harvard have published a study in the journal Nature that has scientists debating where cancer research should go next. They estimated that scientists would need to examine about 100,000 cancer samples —10 times as many as the $375 million Cancer Genome Atlas has gathered — to find most of the genes involved in 50 cancer types.

Secrets of the Brain
National Geographic, February 2014

Van Wedeen strokes his half-gray beard and leans toward his computer screen, scrolling through a cascade of files. We’re sitting in a windowless library, surrounded by speckled boxes of old letters, curling issues of scientific journals, and an old slide projector that no one has gotten around to throwing out.

“It’ll take me a moment to locate your brain,” he says.

On a hard drive Wedeen has stored hundreds of brains—exquisitely detailed 3-D images from monkeys, rats, and humans, including me. Wedeen has offered to take me on a journey through my own head.

“We’ll hit all the tourist spots,” he promises, smiling.

This is my second trip to the Martinos Center for Biomedical Imaging, located in a former ship-rope factory on Boston Harbor. The first time, a few weeks ago, I offered myself as a neuroscientific guinea pig to Wedeen and his colleagues. In a scanning room I lay down on a slab, the back of my head resting in an open plastic box. A radiologist lowered a white plastic helmet over my face. I looked up at him through two eyeholes as he screwed the helmet tight, so that the 96 miniature antennas it contained would be close enough to my brain to pick up the radio waves it was about to emit. As the slab glided into the cylindrical maw of the scanner, I thought of The Man in the Iron Mask.

Neanderthals Leave Their Mark on Us
New York Times, January 29, 2014

Ever since the discovery in 2010 that Neanderthals interbred with the ancestors of living humans, scientists have been trying to determine how their DNA affects people today. Now two new studies have traced the history of Neanderthal DNA, and have pinpointed a number of genes that may have medical importance today.

Among the findings, the studies have found clues to the evolution of skin and fertility, as well as susceptibility to diseases like diabetes. More broadly, they show how the legacy of Neanderthals has endured 30,000 years after their extinction.

“It’s something that everyone wanted to know,” said Laurent Excoffier, a geneticist at the University of Bern in Switzerland who was not involved in the research.

Neanderthals, who became extinct about 30,000 years ago, were among the closest relatives of modern humans. They shared a common ancestor with us that lived about 600,000 years ago.

Seeing X Chromosomes in a New Light
New York Times, January 20, 2014

The term “X chromosome” has an air of mystery to it, and rightly so. It got its name in 1891 from a baffled biologist named Hermann Henking. To investigate the nature of chromosomes, Henking examined cells under a simple microscope. All the chromosomes in the cells came in pairs.

All except one.

Henking labeled this outlier chromosome the “X element.” No one knows for sure what he meant by the letter. Maybe he saw it as an extra chromosome. Or perhaps he thought it was an ex-chromosome. Maybe he used X the way mathematicians do, to refer to something unknown.

Today, scientists know the X chromosome much better. It’s part of the system that determines whether we become male or female. If an egg inherits an X chromosome from both parents, it becomes female. If it gets an X from its mother and a Y from its father, it becomes male.

But the X chromosome remains mysterious. For one thing, females shut down an X chromosome in every cell, leaving only one active. That’s a drastic step to take, given that the X chromosome has more than 1,000 genes.

This Week’s Forecast: What Flu Season May Look Like
New York Times, January 16, 2014

Jeffrey Shaman, an environmental health scientist at Columbia University, hopes that he and his colleagues will someday change the nightly news. “The way you get pollution reports and pollen counts on the local weather report, you could also have a flu forecast on there,” said Dr. Shaman.

Each year, the flu season arrives like clockwork. But once it strikes, it can unfold in surprising ways. In 2012, for example, it arrived in November, four weeks ahead of the typical flu season. Some years it can be especially brutal, and in others, very mild. Infection rates may start climbing in some parts of the United States when they are already falling in others.

Scientists like Dr. Shaman are reducing this uncertainty with computer models that make predictions about flu seasons in the United States. Last year, Dr. Shaman and his colleagues carried out their first flu forecasts in real time. They are now making predictions about the current outbreak, and this week they set up a website where you can see their predictions for yourself.

Battle for Survival May Yield the Rain Forest’s Diversity
New York Times, January 2, 2014

The diversity of a tropical rain forest can be hard to fathom for people who have not seen one. Three acres of jungle may be home to more than 650 species of trees — more species than grow in the entire continental United States and Canada combined.

It’s tempting to look at all those species living so close together as a picture of peaceful coexistence. But Phyllis D. Coley and Thomas A. Kursar, a husband-and-wife team of ecologists at the University of Utah, see them as war zones. Hordes of insects threaten the survival of plants, which respond with chemical warfare. The result, they argue, is the remarkable biodiversity we see today.

“It’s not harmonious,” Dr. Coley said. “It’s a constant battle to stay alive, to stay in the game.” Dr. Coley and Dr. Kursar outline their hypothesis in this week’s issue of Science.

This hypothesis is a departure from the classical explanation for tropical diversity. Traditionally, ecologists argued that all the species in a tropical forest could coexist through specialization to their physical environment. Some species might be able to live in deep shade, for example, while others could gain minerals beyond the reach of other plants.

But this explanation has fallen out of favor in recent years. “There just aren’t enough different ways to take advantage of light or nutrients or water,” Dr. Coley said. “There must be something else going on.”

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