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2016

How the Brown Rat Conquered New York City (and Every Other One, Too)
New York Times, October 27, 2016
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Millions of them live in New York, and billions more in cities and on farms across the globe. And wherever they scurry, they wreak havoc.

They devour food supplies and contaminate what they don’t eat with feces and urine. They spread a range of harmful viruses and bacteria. In delicate ecosystems around the world, they threaten other species with extinction.

“They’ll gnaw through walls. They’ll gnaw through wires. They’ll destroy cars,” said Jason Munshi-South, a biologist at Fordham University. “They’ve managed to spread wherever there are humans.”

Despite their ubiquity, Rattus norvegicus, otherwise known as the brown rat, remains surprisingly mysterious. Scientists have only a hazy idea of how it went from wild rodent to unwanted human companion.

Scientists think the common cold may at last be beatable
STAT, October 20, 2016
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Time and again, Martin Moore’s children get sick with a cold. He hauls them to their doctor, who then informs him that there’s nothing to be done aside from taking them home and waiting it out.

The experience is maddening for Moore — especially because he’s a virologist. For everything that virologists have learned about rhinoviruses — the cause of the majority of colds — they have not invented a vaccine for them.

In 2013, Moore wondered if he could make one. He consulted a rhinovirus expert for some advice. Instead, the expert told him, “Oh, there will never be a vaccine for rhinovirus — it’s just not possible.”

“I thought, ‘Well, let’s look into that,’” recalled Moore, an associate professor at Emory University and a research scholar at Children’s Healthcare of Atlanta.

How the First Farmers Changed History
New York Times, October 17, 2016
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Beneath a rocky slope in central Jordan lie the remains of a 10,000-year-old village called Ain Ghazal, whose inhabitants lived in stone houses with timber roof beams, the walls and floors gleaming with white plaster.

Hundreds of people living there worshiped in circular shrines and made haunting, wide-eyed sculptures that stood three feet high. They buried their cherished dead under the floors of their houses, decapitating the bodies in order to decorate the skulls.

But as fascinating as this culture was, something else about Ain Ghazal intrigues archaeologists more: It was one of the first farming villages to have emerged after the dawn of agriculture.

Around the settlement, Ain Ghazal farmers raised barley, wheat, chickpeas and lentils. Other villagers would leave for months at a time to herd sheep and goats in the surrounding hills.

As DNA reveals its secrets, scientists are assembling a new picture of humanity
STAT, October 7, 2016
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When Benedict Paten stares at his computer monitor, he sometimes gazes at what looks like a map of the worst subway system in the world. The screen is sprinkled with little circles that look like stations. Some are joined by straight lines — sometimes a single path from one circle to the next, sometimes a burst of spokes radiating out in many directions. And sometimes the lines bend into sweeping curves that soar off on express routes to distant stations.

A rainbow palette of colors makes it a little easier to digest the complexity. But if you stare a little too long, vertigo sets in.

This map is not a guide to any city on Earth. It is a sketch of the human gene pool.

What’s the Longest Humans Can Live? 115 Years, New Study Says
New York Times, October 5, 2016
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On Aug. 4, 1997, Jeanne Calment passed away in a nursing home in France. The Reaper comes for us all, of course, but he was in no hurry for Mrs. Calment. She died at age 122, setting a record for human longevity.

Jan Vijg doubts we will see the likes of her again. True, people have been living to greater ages over the past few decades. But now, he says, we have reached the upper limit of human longevity.

“It seems highly likely we have reached our ceiling,” said Dr. Vijg, an expert on aging at the Albert Einstein College of Medicine. “From now on, this is it. Humans will never get older than 115.”

A Single Migration From Africa Populated the World, Studies Find
New York Times, September 21, 2016
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Modern humans evolved in Africa roughly 200,000 years ago. But how did our species go on to populate the rest of the globe?

The question, one of the biggest in studies of human evolution, has intrigued scientists for decades. In a series of extraordinary genetic analyses published on Wednesday, researchers believe they have found an answer.

In the journal Nature, three separate teams of geneticists survey DNA collected from cultures around the globe, many for the first time, and conclude that all non-Africans today trace their ancestry to a single population emerging from Africa between 50,000 and 80,000 years ago.

“I think all three studies are basically saying the same thing,” said Joshua M. Akey of the University of Washington, who wrote a commentary accompanying the new work. “We know there were multiple dispersals out of Africa, but we can trace our ancestry back to a single one.”

The surprising history of the war on superbugs — and what it means for the world today
STAT, September 12, 2016
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We may come to the end of antibiotics. We may run clean out of effective ammunition, and then how the bacteria and moulds will lord it.”

If you had to guess where those words came from, you might well say a recent news segment on TV, or perhaps an op-ed published by a frantic doctor. After all, these days there’s a lot of talk about our antibiotic resistance crisis. Bacteria that have evolved to withstand antibiotics kill 700,000 people each year, and ever more powerful strains are spreading around the world. Researchers are worried that we will enter a post-antibiotic age, in which we are infected by bacteria that can defeat every drug medicine has to offer. Next week, the United Nations will convene a high-level meeting to coordinate the global fight against these invisible enemies.

But perhaps you noticed something odd about those words above. They have a strangely old-fashioned sound. In fact, they were uttered back in 1954, by a British physician named Lindsey W. Batten.

Although mostly forgotten today, Batten and other like-minded scientists were warning of a coming antibiotic crisis over 60 years ago. They were right, but they were ignored. Their failure offers some important lessons for today’s new crusaders.

A 3.2-Million-Year-Old Mystery: Did Lucy Fall From a Tree?
New York Times, August 29, 2016
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In 1974, the paleoanthropologist Donald C. Johanson led an expedition to Ethiopia to look for fossils of ancient human relatives.

In an expanse of arid badlands, he spotted an arm bone. Then, in the area surrounding it, Dr. Johanson and his colleagues found hundreds of other skeletal fragments.

The fossils turned out to have come from a single three-foot-tall female who lived 3.2 million years ago. The scientists named her species Australopithecus afarensis, and the skeleton was dubbed Lucy.

Four decades later, Lucy remains one of the most famous discoveries in paleontology. Finding a single bone of that age would have been reason to celebrate; finding so much from a skeleton revealed a tremendous amount about Lucy — and about human evolution in general.

We’re all different in our DNA. We’re finally starting to understand when those differences matter
STAT, August 17, 2016
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I know it sounds strange, but I feel very grateful to a database. It saved me from a lifelong fear of dropping dead because my heart will give out.

The database is known as ExAC, and I had my first experience with it after I got my genome sequenced. For a few weeks, I brought it from one lab to another to ask scientists to help me make sense of it.

Their analysis brought up a doozy of a finding. I have a variant in a gene for heart muscles, called DSG2. Some studies have indicated that having a variant in just one of your two copies of DSG2 can cause a rare condition called arrhythmogenic right ventricular cardiomyopathy. Out of the blue, it can cause lethally irregular heartbeat rhythms. There is no cure.

From Fins Into Hands: Scientists Discover a Deep Evolutionary Link
New York Times, August 17, 2016
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To help his readers fathom evolution, Charles Darwin asked them to consider their own hands.

“What can be more curious,” he asked, “than that the hand of a man, formed for grasping, that of a mole for digging, the leg of the horse, the paddle of the porpoise, and the wing of the bat, should all be constructed on the same pattern, and should include similar bones, in the same relative positions?”

Darwin had a straightforward explanation: People, moles, horses, porpoises and bats all shared a common ancestor that grew limbs with digits. Its descendants evolved different kinds of limbs adapted for different tasks. But they never lost the anatomical similarities that revealed their kinship.

As a Victorian naturalist, Darwin was limited in the similarities he could find. The most sophisticated equipment he could use for the task was a crude microscope. Today, scientists are carrying on his work with new biological tools. They are uncovering deep similarities that have been overlooked until now.

Scientists Ponder an Evolutionary Mystery: The Female Orgasm
New York Times, August 1, 2016
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An eye is for seeing, a nose is for smelling. Many aspects of the human body have obvious purposes.

But some defy easy explanation. For biologists, few phenomena are as mysterious as the female orgasm.

While orgasms have an important role in a woman’s intimate relationships, the evolutionary roots of the experience — a combination of muscle contractions, hormone release, and intense pleasure — have been difficult to uncover.

For decades, researchers have put forward theories, but none are widely accepted. Now two evolutionary biologists have joined the fray, offering a new way of thinking about the female orgasm based on a reconstruction of its ancient history.

Memory researchers were rebuffed by science, and came roaring back
STAT, July 28, 2016
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Psychiatrists have been using hypnosis on patients for decades — to help them reduce their pain or kick a smoking habit, among other reasons.

But what, exactly, is happening to the patients’ brains when they are in a hypnotic state?

To tackle that question, David Spiegel, a psychiatrist at Stanford University School of Medicine, and his colleagues recently decided to scan patients’ brains and see if hypnosis left a mark. It did.

In a new study, published Thursday in the journal Cerebral Cortex, Spiegel and his colleagues report that they’ve found a distinctive signature in the brain when a patient has undergone hypnosis. What’s more, the changes in brain activity give scientists hints about what happens to the mind of hypnotized subjects. The discovery may ultimately lead to new insights about how to make hypnosis more effective.

DNA Study Reveals the One and Only Wolf Species in North America
New York Times, July 27, 2016
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The first large study of North American wolf genomes has found that there is only one species on the continent: the gray wolf. Two other purported species, the Eastern wolf and the red wolf, are mixes of gray wolf and coyote DNA, the scientists behind the study concluded.

The finding, announced Wednesday, highlights the shortcomings of laws intended to protect endangered species, as such laws lag far behind scientific research into the evolution of species.

The gray wolf and red wolf were listed as endangered in the lower 48 states under the Endangered Species Act in the 1970s and remain protected today, to the periodic consternation of ranchers and agricultural interests.

In 2013, the United States Fish and Wildlife Service recognized the Eastern wolf as a separate species, which led officials to recommend delisting the gray wolf. Conservationists won a lawsuit that forced the agency to abandon the plan.

Updated Brain Map Identifies Nearly 100 New Regions
New York Times, July 20, 2016
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The brain looks like a featureless expanse of folds and bulges, but it’s actually carved up into invisible territories. Each is specialized: Some groups of neurons become active when we recognize faces, others when we read, others when we raise our hands.

On Wednesday, in what many experts are calling a milestone in neuroscience, researchers published a spectacular new map of the brain, detailing nearly 100 previously unknown regions — an unprecedented glimpse into the machinery of the human mind.

Scientists will rely on this guide as they attempt to understand virtually every aspect of the brain, from how it develops in children and ages over decades, to how it can be corrupted by diseases like Alzheimer’s and schizophrenia.

Fecal Transplants Can Be Life-Saving, but How?
New York Times, July 15, 2016
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A fecal transplant is exactly what it sounds like: To treat certain gut disorders, doctors transfer stool from a healthy donor to a sick patient.

Just a few years ago, only a few doctors turned to fecal transplants, typically as a last resort. But in randomized trials, the procedure has proved remarkably effective against potentially fatal infections of bacteria known as Clostridium difficile.

The evidence has overwhelmed any squeamishness that physicians might have felt. “We’re doing this treatment almost weekly,” said Dr. Harry Sokol, a gastroenterologist at Saint-Antoine Hospital AP-HP in Paris.

Game of Genomes
STAT, July 11, 2016

In this three-part feature, I wrote about having my genome sequenced and getting scientists to help me understand it.
Links:
Part One | Part Two | Part Three

A scientist recently pointed me out to his colleagues. “That is not Carl Zimmer,” he declared.

The scientist was Mark Gerstein. He was sitting at a table in his office at Yale University, flanked by two members of his lab. “Really,” Gerstein said, pointing to a slim hard drive on the table, “this is Carl Zimmer.”

By “this,” he meant the sequence of my genome, which was being transferred from the drive onto a MacBook.

“I’m quite serious,” Gerstein said. “In about five minutes, he will be in this computer.”

Growing Pains for Field of Epigenetics as Some Call for Overhaul
New York Times, July 1, 2016
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Our genes are not just naked stretches of DNA.

They’re coiled into intricate three-dimensional tangles, their lengths decorated with tiny molecular “caps.” These so-called epigenetic marks are crucial to the workings of the genome: They can silence some genes and activate others.

Epigenetic marks are crucial for our development. Among other functions, they direct a single egg to produce the many cell types, including blood and brain cells, in our bodies. But some high-profile studies have recently suggested something more: that the environment can change your epigenetic marks later in life, and that those changes can have long-lasting effects on health.

Memory researchers were rebuffed by science, and came roaring back
STAT, June 23, 2016
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NEW YORK — Andre Fenton got to design his lab when he joined the Center for Neural Science at New York University a few years ago, and he made sure that he had a lot of closet space. But his closets do not contain brooms or shoes.

Each one is lined with black curtains and has wires and cameras hanging from the ceiling. In the middle of each closet is a disk where Fenton places mice or rats. As the rodents explore the arena, they soon discover that one section delivers a shock. It’s a lesson they don’t soon forget.

And by watching them learn that lesson, Fenton can learn how memories are made.

Cancer Is Contagious Among Clams. What About Us?
New York Times, June 22, 2016
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The ocean contains a vast number of living things, including many, many pathogens — from bacteria that thrive on coral to fungi that infect lobsters. A drop of seawater may hold 10 million viruses.

Recently, a team of scientists revealed a frightening member of this menagerie: free-floating cancer cells that cause contagious tumors in shellfish. Last year, they found one such cancer in a species of clam. On Wednesday, they reported that three more species were plagued with contagious cancers.

The cancers are specific to shellfish and do not appear to pose a danger to humans who eat them. But until now, infectious cancer was considered something of a fluke in the natural world, initially observed only in dogs and Tasmanian devils.

Scientists Hope to Cultivate an Immune System for Crops
New York Times, June 16, 2016
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The world’s crops face a vast army of enemies, from fungi to bacteria to parasitic animals. Farmers have deployed pesticides to protect their plants, but diseases continue to ruin a sizable portion of our food supply.

Some scientists are now investigating another potential defense, one already lurking beneath our feet. The complex microbial world in the soil may protect plants much like our immune system protects our bodies.

Scientists have known about so-called “suppressive soils” for decades. In 1931, a Canadian scientist named A. W. Henry discovered the spores of the common root rot, a fungus that strikes wheat crops, in a range of soil samples. But try as he might, he could almost never get the spores to grow.

New Fossils Strengthen Case for ‘Hobbit’ Species
New York Times, June 8, 2016
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Scientists digging in the Liang Bua cave on the Indonesian island of Flores years ago found a tiny humanlike skull, then a pelvis, jaw and other bones, all between 60,000 and 100,000 years old.

The fossils, the scientists concluded, belonged to individuals who stood just three feet tall — an unknown species, related to modern humans, that they called Homo floresiensis or, more casually, the hobbits.

On Wednesday, researchers reported that they had discovered still older remains on the island, including teeth, a piece of a jaw and 149 stone tools dating back 700,000 years. The finding suggests that the ancestors of the hobbits arrived on Flores about a million years ago, the scientists said, and evolved into their own distinct branch of the hominin tree.

Scientists Find Form of Crispr Gene Editing With New Capabilities
New York Times, June 3, 2016
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Just a few years ago, Crispr was a cipher — something that sounded to most ears like a device for keeping lettuce fresh. Today, Crispr-Cas9 is widely known as a powerful way to edit genes. Scientists are deploying it in promising experiments, and a number of companies are already using it to develop drugs to treat conditions ranging from cancer to sickle-cell anemia.

Yet there is still a lot of misunderstanding around it. Crispr describes a series of DNA sequences discovered in microbes, part of a system to defend against attacking viruses. Microbes make thousands of forms of Crispr, most of which are just starting to be investigated by scientists. If they can be harnessed, some may bring changes to medicine that we can barely imagine.

On Thursday, in the journal Science, researchers demonstrated just how much is left to discover. They found that an ordinary mouth bacterium makes a form of Crispr that breaks apart not DNA, but RNA — the molecular messenger used by cells to turn genes into proteins.

If scientists can get this process to work in human cells, they may open up a new front in gene engineering, gaining the ability to precisely adjust the proteins in cells, for instance, or to target cancer cells.

Tales of African-American History Found in DNA
New York Times, May 27, 2016
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The history of African-Americans has been shaped in part by two great journeys.

The first brought hundreds of thousands of Africans to the southern United States as slaves. The second, the Great Migration, began around 1910 and sent six million African-Americans from the South to New York, Chicago and other cities across the country.

In a study published on Friday, a team of geneticists sought evidence for this history in the DNA of living African-Americans. The findings, published in PLOS Genetics, provide a map of African-American genetic diversity, shedding light on both their history and their health.

Buried in DNA, the researchers found the marks of slavery’s cruelties, including further evidence that white slave owners routinely fathered children with women held as slaves.

Eske Willerslev Is Rewriting History With DNA
New York Times, May 16, 2016
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COPENHAGEN — As a boy growing up in Denmark, Eske Willerslev could not wait to leave Gentofte, his suburban hometown. As soon as he was old enough, he would strike out for the Arctic wilderness.

His twin brother, Rane, shared his obsession. On vacations, they retreated to the woods to teach themselves survival skills. Their first journey would be to Siberia, the Willerslev twins decided. They would make contact with a mysterious group of people called the Yukaghir, who supposedly lived on nothing but elk and moose.

When the Willerslev twins reached 18, they made good on their promise. They were soon paddling a canoe up remote Siberian rivers.

“Nobody knew what you would see on the other side of a mountain,” said Eske Willerslev, who is now 44. “There were villages on the maps, and you wouldn’t even see a trace of them.”

Climate Change and the Case of the Shrinking Red Knots
New York Times, May 12, 2016
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Animal migrations combine staggering endurance and exquisite timing.

Consider the odyssey of a bird known as the red knot. Each spring, flocks of the intrepid shorebirds fly up to 9,300 miles from the tropics to the Arctic. As the snow melts, they mate and produce a new generation of chicks. The chicks gorge themselves on insects, and then all the red knots head back south.

“They are there less than two months,” said Jan A. van Gils, an ecologist at the Royal Netherlands Institute for Sea Research. “It’s a very tight schedule.”

It is also a vulnerable one. The precipitous decline of the red knots that winter in West Africa may provide a small but telling parable of the perils of climate change.

Bacteria-Infected Mosquitoes Could Slow Spread of Zika Virus
New York Times, May 4, 2016
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If there is ever a contest for Least Appreciated Creature on Earth, first prize should go to a microbe called Wolbachia.

The bacterium infects millions of invertebrate species, including spiders, shrimps and parasitic worms, as well as 60 percent of all insect species. Once in residence, Wolbachia co-opts its hosts’ reproductive machinery and often greedily shields them from a variety of competing infections.

Ever since the Zika outbreak began in Brazil last year, scientists have suspected that Wolbachia might protect mosquitoes from the virus. Now, researchers have confirmed this hunch, providing the first solid evidence that releasing Wolbachia-infected mosquitoes into the wild could help quell the epidemic.

Foxes That Endure Despite a Lack of Genetic Diversity
New York Times, April 21, 2016
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The Channel Islands, off the coast of Southern California, are a natural laboratory for a particularly adorable experiment in evolution.

A unique species called the island fox has lived there for several thousand years, their bodies shrinking over the generations until now each is smaller than a house cat. Adult island foxes weigh as little as 2.35 pounds.

Now a team of scientists has discovered another way in which island foxes are extraordinary: Genetically, they are nearly identical to one another. In fact, a fox community on one island has set a record for the least genetic variation in a sexually reproducing species.

Oliver A. Ryder, the director of genetics at the San Diego Zoo Institute for Conservation Research, said the new research posed a biological puzzle.

Scientists Unveil New ‘Tree of Life’
New York Times, April 11, 2016
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A team of scientists unveiled a new tree of life on Monday, a diagram outlining the evolution of all living things. The researchers found that bacteria make up most of life’s branches. And they found that much of that diversity has been waiting in plain sight to be discovered, dwelling in river mud and meadow soils.

“It is a momentous discovery — an entire continent of life-forms,” said Eugene V. Koonin of the National Center for Biotechnology Information, who was not involved in the study.

The study was published in the journal Nature Microbiology.

In his 1859 book “On the Origin of Species,” Charles Darwin envisioned evolution like a branching tree. The “great Tree of Life,” he said, “fills with its dead and broken branches the crust of the earth, and covers the surface with its ever branching and beautiful ramifications.”

Fathered by the Mailman? It’s Mostly an Urban Legend
New York Times, April 8, 2016
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Five days a week, you can tune into “Paternity Court,” a television show featuring couples embroiled in disputes over fatherhood. It’s entertainment with a very old theme: Uncertainty over paternity goes back a long way in literature. Even Shakespeare and Chaucer cracked wise about cuckolds, who were often depicted wearing horns.

But in a number of recent studies, researchers have found that our obsession with cuckolded fathers is seriously overblown. A number of recent genetic studies challenge the notion that mistaken paternity is commonplace.

“It’s absolutely ridiculous,” said Maarten H.D. Larmuseau, a geneticist at the University of Leuven in Belgium who has led much of this new research.

The term cuckold traditionally refers to the husband of an adulteress, but Dr. Larmuseau and other researchers focus on those cases that produce a child, which scientists politely call “extra-pair paternity.”

Tapeworms and Other Parasites Can Make Good Guests
New York Times, March 31, 2016
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The kakapo, a large flightless parrot that can live 95 years and perhaps longer, is dangerously close to extinction. Once found throughout New Zealand, the population has dwindled to fewer than 150.

Conservation biologists are doing everything they can to keep the kakapo from vanishing. And so, when they discovered a few years ago that a pair of captive kakapos were infected with tapeworms, they did the obvious thing: They dewormed the birds.

Hamish G. Spencer, a geneticist at the University of Otago in New Zealand, thinks that was unwise. If endangered species are going to escape extinction, he argues, they may need parasites to survive.

“Some of these parasites may turn out to be quite good for their hosts,” Dr. Spencer said.

Researchers Find Fish That Walks the Way Land Vertebrates Do
New York Times, March 24, 2016
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It’s one of the most famous chapters in evolution, so familiar that it regularly inspires New Yorker cartoons: Some 375 million years ago, our ancestors emerged from the sea, evolving from swimming fish to vertebrates that walked on land.

Scientists still puzzle over exactly how the transition from sea to land took place. For the most part, they’ve had to rely on information gleaned from fossils of some of the intermediate species.

But now a team of researchers has found a remarkable parallel to one of evolution’s signature events. In a cave in Thailand, they’ve discovered that a blind fish walks the way land vertebrates do.

The waterfall-climbing cave fish, Cryptotora thamicola, has even evolved many of the skeletal features that our ancestors did for walking, including a full-blown pelvis.

Ancestors of Modern Humans Interbred With Extinct Hominins, Study Finds
New York Times, March 17, 2016
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The ancestors of modern humans interbred with Neanderthals and another extinct line of humans known as the Denisovans at least four times in the course of prehistory, according to an analysis of global genomes published Thursday in the journal Science.

The interbreeding may have given modern humans genes that bolstered immunity to pathogens, the authors concluded.

“This is yet another genetic nail in the coffin of our oversimplistic models of human evolution,” said Carles Lalueza-Fox, a research scientist at the Institute of Evolutionary Biology in Barcelona, Spain, who was not involved in the study.

Unappetizing Experiment Explores Tools’ Role in Humans’ Bigger Brains
New York Times, March 9, 2016
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Scientists recently turned Harvard’s Skeletal Biology Laboratory into a pop-up restaurant. It would have fared very badly on Yelp.

Katherine D. Zink, then a graduate student, acted as chef and waitress. First, she attached electrodes to the jaws of diners to record the activity in the muscles they use to chew food. Then she brought out the victuals.

Some volunteers received a three-course vegetarian meal of carrots, yams or beets. In one course, the vegetables were cooked; in the second, they were raw and sliced; in the last course, Dr. Zink simply served raw chunks of plant matter.

Study Finds Surprising Benefit of Viral DNA: Fighting Other Viruses
New York Times, March 3, 2016
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What could be more alien than a virus? It’s a nanobiological weapon — a microscopic protein shell holding a few genes that hijack a cell’s internal machinery, forcing it to make new viruses. The battles we fight with these alien enemies brings malaise, scars and even death.

Yet as foreign as viruses may seem, the boundary between us and them is turning out to be remarkably blurry. We use DNA from viruses to do things that are essential to our own survival, scientists are finding. Somehow, we have managed to domesticate some of these invaders.

A number of viruses replicate by inserting their DNA into our own genes. On rare occasions, their genes get passed down to future generations.

Inside the secret defense systems of giant viruses
STAT, February 29, 2016
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The strangest life forms on Earth just got a lot stranger.

In 2003, Didier Raoult of Aix-Marseille University in France and his colleagues discovered a new kind of virus lurking inside single-celled protozoans. Like other viruses, it couldn’t grow on its own, lacking the biochemical machinery to build proteins and genes. Instead, it had to infect host cells and use their material to produce new viruses.

But this new virus was enormous, measuring hundreds of times bigger than any previously known virus. What’s more, it was far more complex. Typical viruses may have just a few genes. The new virus had over 900 — more than many species of bacteria.

DNA Under the Scope, and a Forensic Tool Under a Cloud
New York Times, February 26, 2016
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Marina Stajic worked for nearly three decades as director of the forensic toxicology lab at the medical examiner’s office in New York City. Last week Dr.. Stajic, 66, filed a lawsuit against the city, claiming she had been forced into retirement last year in part because of a disagreement with her superiors over the accuracy of certain DNA tests.

There is more at stake here than Dr. Stajic’s retirement. The cutting-edge technique at the center of this legal dispute, called low copy number DNA analysis, has transformed not just police work, but also a range of scientific fields including cancer biology, in vitro fertilization, archaeology and evolutionary biology. Yet some of the technique’s applications have triggered scientific controversy.

The medical examiner’s office has become a strong advocate for the technique. It is the only public lab in the United States that uses low copy number DNA to develop profiles for use in criminal cases. But experts have long warned that investigators must take particular care in interpreting these tests: analyzing so few DNA molecules can lead to errors.

In Neanderthals’ DNA, Ancient Humans May Have Left Genetic Mark
New York Times, February 17, 2016
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In 1997, scientists found the first scrap of Neanderthal DNA in a fossil. Since then, they have recovered genetic material, even entire genomes, from a number of Neanderthal bones, and their investigations have yielded a remarkable surprise: Today, 1 to 2 percent of the DNA in non-African people comes from Neanderthals.

That genetic legacy is the result of interbreeding roughly 50,000 years ago between Neanderthals and the common ancestors of Europeans and Asians. Recent studies suggest that Neanderthal genes even influence human health today, contributing to conditions from allergies to depression.

Now scientists have found that the genes flowed both ways. In a study published on Wednesday in Nature, a team of scientists reports that another instance of interbreeding left Neanderthals in Siberia with chunks of human DNA.

A Parasite, Leopards, and a Primate’s Fear and Survival
New York Times, February 11, 2016
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Many of our primate ancestors probably ended up in the bellies of big cats. How else to explain bite marks on the bones of ancient hominins, the apparent gnawing of leopards or other African felines?

Big cats still pose a threat to primates. In one study of chimpanzees in Ivory Coast, for example, scientists estimated that each chimp ran a 30 percent risk of being attacked by a leopard every year.

A new study suggests that the big cats may be getting some tiny help on the hunt. A parasite infecting the brains of some primates, including perhaps our forebears, may make them less wary.

Scientists Investigate How Viruses Like Zika Cause Birth Defects
New York Times, February 8, 2016
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The Zika virus has quickly gained Ebola-level notoriety as it has spread through the Western Hemisphere in recent months. Researchers in Brazil, where it was first detected in May, have linked infections in pregnant women to a condition known as microcephaly: infants born with undersize heads.

Where birth defects are concerned, however, the Zika virus is far from unique. A number of other viruses, such as rubella and cytomegalovirus, pose a serious risk during pregnancy. Researchers have uncovered some important clues about how those pathogens injure fetuses — findings that are now helping to guide research into the potential link between Zika and microcephaly.

“I think we’ll discover a lot of parallels,” said Dr. Mark R. Schleiss, the director of pediatric infectious diseases and immunology at the University of Minnesota Medical School.

DNA Study of First Ancient African Genome Flawed, Researchers Report
New York Times, February 4, 2016
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When scientists first started to figure out how to extract DNA from ancient skeletons, their success was met with astonishment. One minute, scientists were fishing Richard III’s genes from his royal bones, and the next they were showing off DNA retrieved from 5,00-year-old Incan mummies.

The idea that DNA could survive for thousands of years — let alone be reassembled into an entire genome — seemed little short of miraculous.

Despite the field’s rapid advances in recent years, though, ancient DNA is still hard to find and hard to make sense of. Potential errors lurk around every corner. Even little oversights can cause big headaches.

Tribes’ Win in Fight for La Jolla Bones Clouds Hopes for DNA Studies
New York Times, January 29, 2016
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The San Diego Archaeology Center holds a pair of extraordinary skeletons. Dating back about 9,500 years, they are among the oldest human remains ever found in the Americas.

A number of scientists would love to study the bones, using powerful new techniques to extract any surviving DNA.

“These skeletons of such antiquity are so important for helping us understand what happened in the past in North America,” said Brian Kemp, a molecular anthropologist at Washington State University.

Telling Jewels From Junk in DNA
New York Times, January 21, 2016
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When you learned about genes in high school, chances are it went something like this:

Our DNA holds about 20,000 protein-coding genes. To make a protein, a cell makes a copy of the corresponding gene, in the form of a single-stranded molecule called RNA. The cell uses the RNA molecule as a template to make the protein. And then the protein floats off to do its job.

That’s certainly true. But there’s more to the story.

Some of our genes don’t encode proteins; instead, they create long RNA molecules that don’t serve as protein templates. They have different jobs.

Obama’s big bet on science
STAT, January 18, 2016
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To anyone who follows science, President Barack Obama’s announcement of a “moonshot” to cure cancer last week brought on a strong sense of déjà vu. It was, in fact, the third time in less than three years that he has launched a high-profile effort to solve a complex biomedical problem.

A year ago, in his 2015 State of the Union address, Obama announced the Precision Medicine Initiative, which is intended to usher in what he called “a new era of medicine — one that delivers the right treatment at the right time.”

And in an April 2013 speech at the White House, Obama unveiled the BRAIN Initiative, which he described as “the next great American project,” designed to help figure out how the brain works.

“Think about what we could do once we do crack this code,” Obama said. “Imagine if no family had to feel helpless watching a loved one disappear behind the mask of Parkinson’s or struggle in the grip of epilepsy. Imagine if we could reverse traumatic brain injury or PTSD for our veterans who are coming home.”

Searching for Cancer Maps in Free-Floating DNA
New York Times, January 14, 2016
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Loose pieces of DNA course through our veins. As cells in our body die, they cast off fragments of genes, some of which end up in the bloodstream, saliva and urine.

Cell-free DNA is like a message in a bottle, delivering secrets about what’s happening inside our bodies. Pregnant women, for example, carry cell-free DNA from their fetuses. A test that analyzes fetal DNA has proved to be more accurate in screening for Down syndrome than standard blood tests.

In 2012, Jay Shendure, a geneticist at the University of Washington, and his colleagues were able to reconstruct the entire genome of a fetus from cell-free DNA in a pregnant woman’s saliva. A team of Stanford University researchers collected DNA fragments from the blood of patients who had received heart transplants and managed to find DNA from their donated hearts. (Tellingly, levels were highest in patients who were rejecting their hearts.)

U.S. Restricts Movement of Salamanders, for Their Own Good
New York Times, January 12, 2016
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The Fish and Wildlife Service is barring the door against 201 species of salamanders, making it illegal to import them or move them across state lines, the agency announced on Tuesday. Scientists hope the ban will help prevent a devastating outbreak from driving native salamander species extinct.

In 2013, scientists in the Netherlands discovered a species of fungus infecting native fire salamanders. Later research revealed that the fungus, called Batrachochytrium salamandrivorans, or Bsal, was carried by Asian salamanders that were imported into Europe as pets. While the fungus was harmless to the Asian amphibians, it was lethal to the Dutch ones.

Although Bsal has continued to spread in Europe, there is no sign that it has taken hold in the United States. But if the vigorous pet trade goes unchecked, scientists fear that it is only a matter of time before Bsal threatens some of the 190 salamander species that live in the United States. The Fish and Wildlife Service estimated that from 2004 to 2014, nearly 2.5 million live salamanders, representing 59 species, were imported into the United States.

Genetic Flip Helped Organisms Go From One Cell to Many
New York Times, January 12, 2016
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Narwhals and newts, eagles and eagle rays — the diversity of animal forms never ceases to amaze. At the root of this spectacular diversity is the fact that all animals are made up of many cells — in our case, about 37 trillion of them. As an animal develops from a fertilized egg, its cells may diversify into a seemingly limitless range of types and tissues, from tusks to feathers to brains.

The transition from our single-celled ancestors to the first multicellular animals occurred about 800 million years ago, but scientists aren’t sure how it happened. In a study published in the journal eLife, a team of researchers tackles this mystery in a new way.

The researchers resurrected ancient molecules that once helped single-celled organisms thrive, then recreated the mutations that helped them build multicellular bodies.

Scientists unearth bacteria from stomach of 5,300-year-old iceman
STAT, January 7, 2016
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In 1991, a German couple hiking in the Alps came across the body of a middle-aged man lying face down in a snowfield. It took days for a recovery team to hack him out of the ice and haul him by helicopter and truck to a lab in Austria. There, scientists determined the man had died 5,300 years ago.

Ötzi, as the man was nicknamed (after the nearby Ötztal Valley), has kept scientists very busy for the past 24 years. They’ve even built an entire research center — the Institute for Mummies and the Iceman in Bolzano, Italy — to house Ötzi and study him. They’ve slowly extracted one clue after another about how Ötzi died and, more importantly, how he lived.

But Ötzi still has much left to tell us. On Thursday, researchers reported in the journal Science that they have reconstructed the entire genome of a species of bacteria that lived in his stomach. Now Ötzi may be able to tell us not just about ancient humans. He can tell us about ancient microbiomes, too.

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