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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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