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How a Weed, Once a Prehistoric Cavity Fighter
By RANJODH SINGH, The New York Times, August 18, 2014

Cyperus rotundus, commonly known as purple nutsedge or nutgrass, is considered one of the world’s worst invasive weeds. But new research suggests that prehistoric humans in what is now central Sudan may have gotten an unusual benefit from it.

Stephen Buckley, an archaeological chemist from the University of York in England, analyzed dental calculus — a form of hardened plaque — in fossilized teeth from people who lived thousands of years ago, in the pre-Mesolithic, Neolithic, and Meroitic periods.

In a paper published in the journal PLOS One, Dr. Buckley and his colleagues report that the teeth had remarkably few cavities and high levels of the chemical compounds found in purple nutsedge, suggesting that the plant may have protected against tooth decay.

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Tuberculosis Is Newer Than Thought, Study Says
By CARL ZIMMER, The New York Times, August 20, 2014

New research indicates that some seal species carried tuberculosis across the Atlantic Ocean.

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.”

But Helen Donoghue, an expert on ancient DNA at the University College London, rejected the idea that tuberculosis could have emerged so recently. “It just cannot be right,” she said, citing earlier fossil evidence of the disease.

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Neanderthals in Europe Died Out Thousands of Years Sooner Than Some Thought, Study Says
By KENNETH CHANG, The New York Times, August 20, 2014

Neanderthals, our heavy-browed relatives, spread out across Europe and Asia about 200,000 years ago. But when did they die out, giving way to modern humans?

A new analysis of Neanderthal sites from Spain to Russia provides the most definitive answer yet: about 40,000 years ago, at least in Europe. That is thousands of years earlier than some scientists have suggested, and it narrows the period that Neanderthals and modern humans overlapped in Europe.

“After that, we don’t think there are any Neanderthals on the continent anymore,” said Thomas Higham, the deputy director of the radiocarbon accelerator unit at the University of Oxford in England.

On the other hand, the dating also argues against the view that modern humans overwhelmed the Neanderthals as soon they arrived in Europe. While modern humans and Neanderthals do not appear to have intermingled in the same locales, the findings suggest they co-existed in neighboring regions for up to several thousand years.

The findings, reported Wednesday in the journal Nature, run counter to claims that pockets of Neanderthals persisted in Portugal, Spain and Gibraltar until just 30,000 years ago, even as modern humans spread outward.

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An artist's impression of Kulindadromeus zabaikalicus, a newly discovered dinosaur from the Jurassic Period that had feathers. Credit

New Find Hints at More Feathered Dinosaurs
By SINDYA N. BHANOO, The New York Times, JULY 25, 2014

A new dinosaur species, one with feathers, has been discovered in Russia.
The finding could mean that feathers were more widespread among
dinosaurs than previously thought, the researchers say.

The dinosaur, described in the journal Science, was about five feet
long and belonged to a group of herbivorous, beaked dinosaurs known as
ornithischia.

The first feathered dinosaur was discovered in China in 1996. A
number of others have been found since then, but those specimens were all
theropods, the suborder that includes Tyrannosaurus rex.

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When the Caregivers Need Healing
By CATHERINE SAINT LOUIS, The New York Times, JULY 28, 2014

“This has happened before,” she tells herself. “It’s nowhere near as bad as
before, and it will pass.”

Robbie Pinter’s 21-year-old son, Nicholas, is upset again. He yells. He
obsesses about something that can’t be changed. Even good news may
throw him off.

So Dr. Pinter breathes deeply, as she was taught, focusing on each
intake and release. She talks herself through the crisis, reminding herself
that this is how Nicholas copes with his autism and bipolar disorder.

With these simple techniques, Dr. Pinter, who teaches English at
Belmont University in Nashville, blunts the stress of parenting a child with
severe developmental disabilities. Dr. Pinter, who said she descends from
“a long line of the most nervous women,” credits her mindfulness practice
with giving her the tools to cope with whatever might come her way. “It is
very powerful,” she said.

All parents endure stress, but studies show that parents of children
with developmental disabilities, like autism, experience depression and
anxiety far more often. Struggling to obtain crucial support services, the
financial strain of paying for various therapies, the relentless worry over
everything from wandering to the future — all of it can be overwhelming.

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The Great Giant Flea Hunt
by: Carol Kaesuk Yoon, The New York Times, July 28, 2014

GIG HARBOR, Wash. — In the Pacific Northwest, we live among behemoths — snowcapped volcanoes, towering trees, great splashing salmon and lattes as big as a child’s head. Yet one of the region’s undeniably superlative titans has slipped beneath everyone’s radar.

The land of Bigfoot and Starbucks is also home to the world’s largest flea. The flea, Hystrichopsylla schefferi, is an awe-inspiring colossus that can reach nearly half an inch, its head alone the size of a cat or dog flea. Until last month, however, there existed not a single confirmed photograph of a live member of the species.

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A Sunken Kingdom Re-emerges
By Katrin Bennhold, The New York Times, June 23, 2014

BORTH, WALES — There is a poem children in Wales learn about the sunken kingdom of Cantre’r Gwaelod, swallowed by the sea and drowned forever after. On a quiet night, legend has it, one can hear the kingdom’s church bells ringing.

When the sea swallowed part of Britain’s western coastline this year and then spat it out again, leaving homes and livelihoods destroyed but also a dense forest of prehistoric tree stumps more exposed than ever, it was as if one had caught a faint glimpse of that Welsh Atlantis.

The submerged forest of Borth is not new. First flooded some 5,000 years ago by rising sea levels after the last ice age, it has been there as long as locals remember, coming and going with the tides and occasionally disappearing under the sand for years on end. But the floods and storms that battered Britain earlier this year radically changed the way archaeologists interpret the landscape: A quarter-mile-long saltwater channel cutting through the trees, revealed by erosion for the first time, provided a trove of clues to where human life may have been concentrated and where its traces may yet be found.


Ancient animal footprints on a beach near Borth, Wales. Archaeologists have had to race against time to study and preserve such remains before the sea further eroded them.

“We used to think of this as just as an impenetrable forest — actually this was a complex human environment,” said Martin Bates, a geoarchaeologist at the University of Wales Trinity St. David, who oversees the excavation work in Borth on a beach he played on as a toddler. “The floods have opened our eyes as to what’s really out there.”

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Searching for Answers in Very Old DNA
By Caludia Dreifus, The New York Times, June 23, 2014

As he puts it in the subtitle of his memoir, “Neanderthal Man,” Svante Paabo goes in search of lost genomes. Dr. Paabo, a 59-year-old Swede who leads his own laboratory at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, was the first to extract and sequence the genomes of the ancient humans called Neanderthals and Denisovans, and to compare them with those of modern humans. Genes, and the stories they tell, are texts he reads.

We recently spoke for three hours in Washington, and later on the telephone. Here is an edited and condensed version of our conversation.

Q. DID YOU ALWAYS WANT TO BE A GENETICIST?

A. I wouldn’t say so. When I was 13, my mother took me to Egypt. That made a big impression; afterward I thought I might become an Egyptian archaeologist. I had a very romantic idea what that would be
like: discovering mummies and pyramids and things like that. I even started studying Egyptology at the university. But there, my romantic ideas caught up with reality. In the 1970s, Swedish Egyptology was very linguistically oriented. It was about ancient word forms and translating hieroglyphics. I couldn’t imagine spending my life with it.

Q. HOW DID YOU COME TO INVENT AN ENTIRELY NEW RESEARCH AREA, THE GENETICS OF ANCIENT HUMANS?

A. In the late 1970s, while I was doing my medical studies [at Uppsala University in Sweden], these new techniques for studying DNA wereintroduced — cloning, sequencing. I was amazed by them and learned how to do them.
And that brought me to thinking again about Egyptian antiquities. I knew that there are hundreds of mummies stored in museums across Europe. Mummies, after all, are the dried-out bodies of dead people or animals. I wondered if in some, their DNA might still be preserved. If it was present, we could study it just as we study the DNA of people alive today.
My thought was, “If we could do this, we can answer many questions in history that we cannot otherwise answer.”

Q. SUCH AS?
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One day after the magnitude 9.2 earthquake on March 27, 1964, a section of an Anchorage street was several feet higher than another section. It is still the most powerful earthquake ever in North America.


A '64 Quake Still Reverberates
By Henry Fountain, The New York Times, April 7, 2014

When a strong earthquake rocked northern Chile on April 1, scientists were quick with an explanation: It had occurred along a fault where stresses had been building as one of the earth’s crustal plates slowly dipped beneath another. A classic low-angle megathrust event, they called it.

Such an explanation may seem straightforward now, but until well into the 20th century, scientists knew relatively little about the mechanism behind these large seismic events. But that all changed when a devastating quake struck south-central Alaska on March 27, 1964, nearly 50 years to the day before the Chilean quake.

Studies of the great Alaskan quake — undertaken largely by a geologist who, when he began, knew little about seismology — revealed the mechanism by linking the observed changes in the landscape to what was then a novel theory, plate tectonics.

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Fearing Punishment for Bad Genes
By KIRA PEIKOFF, The New York Times, APRIL 7, 2014

About 700,000 Americans have had their DNA sequenced, in full or in part, and the number is rising rapidly as costs plummet — to $1,000 or less for a full genome, down from more than $1 million less than a decade ago.

But many people are avoiding the tests because of a major omission in the 2008 federal law that bars employers and health insurers from seeking the results of genetic testing.

The Genetic Information Nondiscrimination Act, known as GINA, does not apply to three types of insurance — life, disability and long-term care — that are especially important to people who may have serious inherited diseases. Sponsors of the act say that they were well aware of the omission, but that after a 14-year effort to write and pass the law, they had to settle for what they could get.

That leaves many patients who may be at risk for inherited diseases fearful that a positive result could be used against them.

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Enceladus as viewed from NASA’s Cassini spacecraft. Gravity measurements taken by the craft align with the presence of a sea 20 to 25 miles below the moon’s surface, scientists say.

Under Icy Surface of a Saturn Moon Lies a Sea of Water, Scientists Say
By KENNETH CHANG, The New York Times, APRIL 3, 2014

Inside a moon of Saturn, beneath its icy veneer and above its rocky core, is a sea of water the size of Lake Superior, scientists announced on Thursday.

The findings, published in the journal Science, confirm what planetary scientists have suspected about the moon, Enceladus, ever since they were astonished in 2005 by photographs showing geysers of ice crystals shooting out of its south pole.

“What we’ve done is put forth a strong case for an ocean,” said David J. Stevenson, a professor of planetary science at the California Institute of Technology and an author of the Science paper.

For many researchers, this tiny, shiny cue ball of a moon, just over 300 miles wide, is now the most promising place to look for life elsewhere in the solar system, even more than Mars.

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When Trilobites Ruled the World
By Natalie Angier, March 3, 2014, The New York Times

WASHINGTON — Trilobites may be the archetypal fossils, symbols of an archaic world long swept beneath the ruthless road grader of time. But we should all look so jaunty after half a billion years.

At the Smithsonian’s National Museum of Natural History, Brian T. Huber, chairman of paleobiology, points to a flawless specimen of Walliserops, a five-inch trilobite that swam the Devonian seas around what is now Morocco some 150 million years before the first dinosaurs hatched. With its elongated, triple-tined head horn and a bristle brush of spines encircling its lower body, the trilobite could be a kitchen utensil for Salvador Dalí. Nearby is the even older Boedaspis ensifer, its festive nimbus of spiny streamers pointing every which way like the ribbons of a Chinese dancer.

In a back room of the museum, Dr. Huber opens a drawer to reveal a dark, mouse-size and meticulously armored trilobite that has yet to be identified and that strains up from its sedimentary bed as though determined to break free.

“A lot of people, when they see these fossils, don’t believe they’re real,” said Dr. Huber, who is 54, fit from years of fieldwork, and proud that the state fossil of his native Ohio is a trilobite. “They think they must be artists’ models.”

The fossils are real, and so, too, is scientists’ unshakable passion for trilobites (TRY-luh-bites), a diverse and illuminating group of marine animals, distantly related to the horseshoe crab, that once dominated their environment as much as dinosaurs and humans would later dominate theirs — and that still have a few surprises up their jointed sleeves.

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The Mammoth Cometh
By Nathaniel Rich, February 27, 2014, The New York Times

The first time Ben Novak saw a passenger pigeon, he fell to his knees and remained in that position, speechless, for 20 minutes. He was 16. At 13, Novak vowed to devote his life to resurrecting extinct animals. At 14, he saw a photograph of a passenger pigeon in an Audubon Society book and “fell in love.” But he didn’t know that the Science Museum of Minnesota, which he was then visiting with a summer program for North Dakotan high-school students, had them in their collection, so he was shocked when he came across a cabinet containing two stuffed pigeons, a male and a female, mounted in lifelike poses. He was overcome by awe, sadness and the birds’ physical beauty: their bright auburn breasts, slate-gray backs and the dusting of iridescence around their napes that, depending on the light and angle, appeared purple, fuchsia or green. Before his chaperones dragged him out of the room, Novak snapped a photograph with his disposable camera. The flash was too strong, however, and when the film was processed several weeks later, he was haunted to discover that the photograph hadn’t developed. It was blank, just a flash of white light.

In the decade since, Novak has visited 339 passenger pigeons — at the Burke Museum in Seattle, the Carnegie Museum of Natural History in Pittsburgh, the American Museum of Natural History in New York and Harvard’s Ornithology Department, which has 145 specimens, including eight pigeon corpses preserved in jars of ethanol, 31 eggs and a partly albino pigeon. There are 1,532 passenger-pigeon specimens left on Earth. On Sept. 1, 1914, Martha, the last captive passenger pigeon, died at the Cincinnati Zoo. She outlasted George, the penultimate survivor of her species and her only companion, by four years. As news spread of her species’ imminent extinction, Martha became a minor tourist attraction. In her final years, whether depressed or just old, she barely moved. Underwhelmed zoo visitors threw fistfuls of sand at her to elicit a reaction. When she finally died, her body was taken to the Cincinnati Ice Company, frozen in a 300-pound ice cube and shipped by train to the Smithsonian Institution, where she was stuffed and mounted and visited, 99 years later, by Ben Novak.

The fact that we can pinpoint the death of the last known passenger pigeon is one of many peculiarities that distinguish the species. Many thousands of species go extinct every year, but we tend to be unaware of their passing, because we’re unaware of the existence of most species.Read more... )





Out of Siberian Ice, A Virus Revived
By Carl Zimmer, March 3, 2014, The New York Times

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.

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Is Breast-Feeding Really Better?
By Nicholas Bakalar, March 4, 2014, The New York Times

Many women who are unable to breast-feed feel guilty about it and worry they may be depriving their children of a range of benefits. Groups like the American Academy of Pediatrics and the World Health Organization recommend six months of exclusive breast-feeding for all infants, citing studies that show breast milk is easily digestible and has nutrients that are superior to or absent from infant formulas, including immunological substances that reduce rates of infection and fatty acids important in brain development.

But now a new study suggests that many of the long-term benefits attributed to breast-feeding may be an effect not of breast-feeding or breast milk itself but of the general good health and prosperity of women who choose to breast-feed.

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Tracing Germs Through the Aisles
By SABRINA TAVERNISE, The New York Times, July 29, 2013

Twice a month for a year, Lance Price, a microbiologist at George Washington University, sent his researchers out to buy every brand of chicken, turkey and pork on sale in each of the major grocery stores in Flagstaff, Ariz. As scientists pushed carts heaped with meat through the aisles, curious shoppers sometimes asked if they were on the Atkins diet.

In fact, Professor Price and his team are trying to answer worrisome questions about the spread of antibiotic-resistant germs to people from animals raised on industrial farms. Specifically, they are trying to figure out how many people in one American city are getting urinary infections from meat from the grocery store.

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Hurricane Tips From Cuba
By JEAN FRIEDMAN-RUDOVSKY, The New York Times, July 29, 2013

HAVANA — Old computer processors whirred and paint crumbled from the walls in the National Prognostic Center of Cuba’s Meteorological Institute, set on a rise above Havana’s old city. Half a dozen meteorologists shifted their gaze between satellite images on large video screens and a giant overhead map of the United States.

They monitor the region’s weather every day, but their gaze grows especially intense in hurricane season. As the center’s director, José Rubiera, explained, almost every hurricane that strikes the Southern United States passes through Cuba first. “A hurricane that hits Cuba doesn’t ask for a visa before entering the United States,” he said.

This shared destiny has led to a rare truce between the two nations, which have had no bilateral relations for more than 50 years. Their meteorological agencies exchange satellite data, jointly analyze radar and collaborate on storm forecasting.

When a storm is approaching, “we call the National Prognostic Center or they call us, whoever gets to the phone first,” said Lixion Avila, a senior specialist at the United States government’s National Hurricane Center.

Dr. Avila called Cuba one of the United States’ most valuable meteorological partners. “Cuba has a long history of excellent forecasting with a tremendous record of data,” he said.

Or as Michael T. Clegg, foreign secretary of the National Academy of Sciences, put it, “It seems that the substantial threat to the human population” posed by storms “is taken seriously enough to make cooperation more desirable.”

And some experts on both sides wish that cooperation would extend to the nonmeteorological aspects of storms. The countries’ disaster management agencies have no direct communication.

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Despite Two New Studies on Motives for Monogamy, the Debate Continues
By CARL ZIMMER, The New York Times, July 29, 2013

The golden lion tamarin, a one-pound primate that lives in Brazil, is a stunningly monogamous creature. A male will typically pair with a female and they will stay close for the rest of their lives, mating only with each other and then working together to care for their young.

To biologists, this deeply monogamous way of life — found in 9 percent of mammal species — is puzzling. A seemingly better evolutionary strategy for male mammals would be to spend their time looking for other females with which to mate.

“Monogamy is a problem,” said Dieter Lukas of the University of Cambridge in a telephone news conference on Monday. “Why should the male keep to one female?”

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D.N.A. Backs Lore on Pre-Columbian Dogs
By JACK HITT, The New York Times, July 15, 2013

BISHOPVILLE, S.C. — Inside a fenced acre on the swampy Lynches River flood plain in central South Carolina, seven of Don Anderson’s primitive dogs spring into high alert at approaching strangers. Medium-sized, they fan out amid his junkyard of improvised habitat: a few large barrels to dig under, an abandoned camper shell from a pickup, segments of black plastic water pipe and backhoed dirt mounds overgrown with waist-high ragweed.

These are Carolina dogs, and though they are friendly, one can instantly sense they are different from other dogs. Several rush to the gate, their whole bodies wagging eagerly. Others sprint off and take position — their jackal ears fully erect, their fishhook tails twitching like flags in a stiff wind. A black pup scrabbles away in crablike submission that eventually takes her into an underground den, dug deep enough that she is not seen again.

Walking into the pen is dangerous for only one reason: one of the dogs’ defining habits is digging snout pits, or gallon-size holes in the ground, perhaps to root for grubs or munch the soil for nutrients.

“It’s like a lunar landscape,” Mr. Anderson warns as we tread carefully into the underbrush.

Some Carolina dogs still live in the wild, and local people have long thought they were one of the few breeds that predated the European arrival in the Americas: “Our native dog,” as Michael Ruano, another enthusiast who often works with Mr. Anderson, put it. “America’s natural dog.”

Now, a new study of canine DNA backs up the folklore. A team led by Peter Savolainen at the Royal Institute of Technology in Sweden has reported that several dog breeds in the Americas — among them the Peruvian hairless, the Chihuahua and the Carolina dog — are without some genetic markers indicative of European origin, suggesting they arrived in an earlier migration from Asia.

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A Village Invents a Language All Its Own
By NICHOLAS BAKALAR, The New York Times, July 14, 2013

There are many dying languages in the world. But at least one has recently been born, created by children living in a remote village in northern Australia.

Carmel O’Shannessy, a linguist at the University of Michigan, has been studying the young people’s speech for more than a decade and has concluded that they speak neither a dialect nor the mixture of languages called a creole, but a new language with unique grammatical rules.

The language, called Warlpiri rampaku, or Light Warlpiri, is spoken only by people under 35 in Lajamanu, an isolated village of about 700 people in Australia’s Northern Territory. In all, about 350 people speak the language as their native tongue. Dr. O’Shannessy has published several studies of Light Warlpiri, the most recent in the June issue of Language.

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Hobbits’ Size Not Likely Linked to Growth Disorders
By JOHN NOBLE WILFORD, The New York Times, July 15, 2013

So much about the extinct little people nicknamed hobbits remains roundly contentious 10 years after their fossils were discovered on the Indonesian island of Flores. But a new study has weighed in with strong support for the original hypothesis about them: that they were remnants of a previously unknown distinct species of the genus Homo that lived as recently as 17,000 years ago.

Detailed comparisons show that the single skull among the skeletal remains is “clearly distinct” from skulls of healthy modern humans, the study said. Thus the fossil specimen may well deserve its designation as a representative of an extinct species, which scientists have called Homo floresiensis.

Much of the debate has centered on arguments by skeptics that these small-bodied, small-brained hominins were nothing more than modern Homo sapiens who had one of a number of growth disorders, possibly microcephaly, Laron syndrome or endemic hypothyroidism, known as cretinism.

In a paper in the journal PLoS One, the researchers said their findings “counter the hypotheses of pathological conditions.”

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The bended femurs of a 2-year-old member of the wealthy Medici family, indicating that the child may have had rickets.


Rickets Plagued Children of the Medicis
By DOUGLAS QUENQUA, The New York Times, June 17, 2013

The rich are different from you and me, F. Scott Fitzgerald once wrote. But according to a new study in The International Journal of Osteoarchaeology, children of the Medicis, one of history’s wealthiest families, may have had rickets, a disease typically associated with the inferior diet and cramped living conditions of the poor. What’s more, the family’s wealth may have been to blame.

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Saying Less and Doing More
By CORNELIA DEAN, The New York Times, June 17, 2013

When I received a diagnosis of breast cancer in 2009, my friend Caitlin was one of the first people I called. And when she came to see me, she said the perfect thing: nothing. Instead, she burst into tears, gave me a hug — and then took me shopping for wigs.

Caitlin has a genius for friendship. And because she had received her own diagnosis a year before, as a guide through breast cancer she was unparalleled.

She arranged for me to have eyebrows tattooed, so I would not look faceless when all my hair fell out under chemo. After my first treatment, she shaved my head in my kitchen sink. And after my mastectomy surgery, she presented me with a material assertion that there would be a life after reconstruction — a lacy bra.

Unfortunately, most people — even the most warmhearted — lack Caitlin’s intelligence and good sense. Letty Cottin Pogrebin’s new book is for us.

Ms. Pogrebin, a writer who, among other things, contributed to the founding of Ms., the feminist magazine, has produced a guide for people who have friends facing a wide range of troubles, including their own illness (or imminent death), the loss of a loved one, or the mental illness or drug addiction of a child.

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Poking Holes in Genetic Privacy
By GINA KOLATA, The New York Times, June 16, 2013

Not so long ago, people who provided DNA in the course of research studies were told that their privacy was assured. Their DNA sequences were on publicly available Web sites, yes, but they did not include names or other obvious identifiers. These were research databases, scientists said, not like the forensic DNA banks being gathered by the F.B.I. and police departments.

But geneticists nationwide have gotten a few rude awakenings, hints that research subjects in fact could sometimes be identified by their DNA alone, or even by the way their cells were using their DNA. The latest shock came in January, when a researcher at the Whitehead Institute, which is affiliated with the Massachusetts Institute of Technology, managed to track down five people selected at random from a database using only their DNA, ages and the states in which they lived. And he did it in just hours. He also found relatives — a total of close to 50 people.

This month an international group of nearly 80 researchers, patient advocates, universities and organizations like the National Institutes of Health announced that it wants to consolidate the world’s databases of DNA and other genetic information, making data easier for researchers to retrieve and share. But the security and privacy of the study subjects are paramount concerns, said Dr. David Altshuler of the Broad Institute of Harvard and M.I.T., a leader of the group.

“The problems are not yet solved in any general way,” Dr. Altshuler said. “We want to work to solve them.”

For years now, a steady stream of research has eroded scientists’ faith that DNA can be held anonymously.

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For Its Latest Beer, a Craft Brewer Chooses an Unlikely Pairing: Archaeology
By STEVEN YACCINO, The New York Times, June 17, 2013

CLEVELAND — The beer was full of bacteria, warm and slightly sour.

By contemporary standards, it would have been a spoiled batch here at Great Lakes Brewing Company, a craft beer maker based in Ohio, where machinery churns out bottle after bottle of dark porters and pale ales.

But lately, Great Lakes has been trying to imitate a bygone era. Enlisting the help of archaeologists at the University of Chicago, the company has been trying for more than year to replicate a 5,000-year-old Sumerian beer using only clay vessels and a wooden spoon.

“How can you be in this business and not want to know from where your forefathers came with their formulas and their technology?” said Pat Conway, a co-owner of the company.

As interest in artisan beer has expanded across the country, so have collaborations between scholars of ancient drink and independent brewers willing to help them resurrect lost recipes for some of the oldest ales ever made.

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4 Germs Cause Most of Infants’ Severe Diarrhea
By DONALD G. McNEIL Jr., The New York Times, May 20, 2013

Just four germs are responsible for most of the severe and fatal diarrhea among the world’s infants, according to a large new study.

Diarrhea is a major killer of children, with an estimated 800,000 deaths each year; it has many causes, and doctors want to focus on the most common ones to bring death rates down.

The study, financed by the Bill and Melinda Gates Foundation and published by The Lancet, found that the most common causes were rotavirus; a protozoan called Cryptosporidium; and two bacteria, Shigella and a toxin-producing strain of E. coli. In some areas, other pathogens, including the bacteria that causes cholera, were also important.

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From Neanderthal Molar, Scientists Infer Early Weaning
By JOHN NOBLE WILFORD, The New York Times, May 22, 2013

Modern mothers love to debate how long to breast-feed, a topic that stirs both guilt and pride. Now — in a very preliminary finding — the Neanderthals are weighing in.

By looking at barium levels in the fossilized molar of a Neanderthal child, researchers concluded that the child had been breast-fed exclusively for the first seven months, followed by seven months of mother’s milk supplemented by other food. Then the barium pattern in the tooth enamel “returned to baseline prenatal levels, indicating an abrupt cessation of breast-feeding at 1.2 years of age,” the scientists reported on Wednesday in the journal Nature.

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No Easy Choices on Breast Reconstruction
By RONI CARYN RABIN, The New York Times, MAY 20, 2013

By almost any measure, Roseann Valletti’s reconstructive breast surgery was a success. Although it was a protracted process, involving some pain and a nightmarish nipple replacement, she is pleased with how she looks.

But she is uncomfortable. All the time. “It feels like I’m wrapped up in duct tape,” said Mrs. Valletti, 54, of the persistent tightness in her chest that many women describe after breast reconstruction.

“They look terrific, to the eye,” added Mrs. Valletti, a teacher who lives Valley Stream, N.Y., and who learned she had early-stage cancer in both breasts five years ago. “But it’s never going to feel like it’s not pulling or it’s not tight. It took me a while to accept that. This is the new normal.”

Last week the actress Angelina Jolie announced in The New York Times that she had had a double mastectomy in February after testing positive for a genetic mutation that put her at high risk for breast and ovarian cancer. She also had reconstructive surgery.

Her disclosure was lauded by some advocates as a bold move that will inspire women to be proactive, learn about their family histories and risks, and consider genetic testing.

At the same time, some breast surgeons are discomfited that some might infer from the article that reconstructive surgery is a quick and easy procedure, and worry that Ms. Jolie inadvertently may have understated the risks and potential complications.

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New Research Tools Kick Up Dust in Archives
By JOHN MARKOFF, The New York Times, May 20, 2013

Seated recently in the special collections room at the Massachusetts Institute of Technology library, Anders Fernstedt raced through an imposing set of yellowing articles and correspondence.

Several years ago Mr. Fernstedt, an independent Swedish scholar who is studying the work of the 20th-century philosopher Karl Popper and several of his colleagues, would have scratched out notes and set aside documents for photocopying.

Now, however, his tool of choice is the high-resolution camera on his iPhone. When he found a document of interest, he quickly snapped a photo and instantly shared his discovery with a colleague working hundreds of miles away. Indeed, Mr. Fernstedt, who conducts his research on several continents, now packs his own substantial digital Popper library on the disk of his MacBook Air laptop computer — more than 50,000 PDF files that he can browse through in a flash.

In just a few years, advances in technology have transformed the methods of historians and other archival researchers. Productivity has improved dramatically, costs have dropped and a world distinguished by solo practitioners has become collaborative. In response, developers are producing an array of computerized methods of analysis, creating a new quantitative science.

However, the transformation has also disrupted many of the world’s historical archives, long known as sleepy places distinguished by vast and often musty collections of documents that only rarely saw the light of day. It has also created new challenges for protecting intellectual property and threatened revenue streams from document copying, creating financial challenges for some institutions.

“It gives me a bit of a chill,” said Henry Lowood, curator for History of Science and Technology Collections and Film and Media Collections in the Stanford University Libraries. “It’s not so much that we try to control things, it’s that we have agreements with people who give us their papers, and in order for us to monitor those agreements we need to monitor things at some level.”

The shift in archival research was documented in a report in December, “Supporting the Changing Research Practices of Historians,” financed by the National Endowment for the Humanities.

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In Pursuit of an Underwater Menagerie (and related slide show)
By C. DREW HARVELL, The New York Times, May 6, 2013

MAUNA LANI REEF, Hawaii — After a long, cold swim in the dark, we spotted it on the night reef with our dive lights: Octopus ornatus, the ornate octopus, a foot-long creature in an amber shade of orange with bright white spots and dashes along all its arms.

It sat stolidly in the light of the camera, 30 feet below the surface, unfazed by the attention. I reached out a finger and it touched me with its suctioned tentacles. When it scuttled in the other direction, I herded it between my cupped hands as it watched me attentively with searching golden eyes.

As if levitating, it smoothly lifted off and tried to jet over my head, but slowly enough that I could catch it gently in midair — like handling a large bird, albeit one with eight sticky tentacles. Holding it at eye level, I looked into its eyes. I felt connected, sort of an octopus whisperer.

Then a tentacle slapped the front of my mask. The octopus crawled up my arm and vanished into the night.

I’ve been a marine biologist my entire professional life, spending more than 25 years researching the health of corals and sustainability of reefs. I’m captivated by the magic of sessile invertebrates like corals, sponges and sea squirts — creatures vital to the ecosystem yet too often overlooked in favor of more visible animals like sharks and whales.

The filmmaker David O. Brown and I want to change that. To make a documentary, “Fragile Legacy,” we are on a quest to lure these elusive and delicate invertebrates in front of the camera lens.

Our inspiration springs from an unlikely source: a collection of 570 superbly wrought, anatomically perfect glass sculptures of marine creatures from the 19th century.

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Psychiatry’s Guide Is Out of Touch With Science, Experts Say
By PAM BELLUCK and BENEDICT CAREY, The New York Times, May 6, 2013

Just weeks before the long-awaited publication of a new edition of the so-called bible of mental disorders, the federal government’s most prominent psychiatric expert has said the book suffers from a scientific “lack of validity.”

The expert, Dr. Thomas R. Insel, director of the National Institute of Mental Health, said in an interview Monday that his goal was to reshape the direction of psychiatric research to focus on biology, genetics and neuroscience so that scientists can define disorders by their causes, rather than their symptoms.

While the Diagnostic and Statistical Manual of Mental Disorders, or D.S.M., is the best tool now available for clinicians treating patients and should not be tossed out, he said, it does not reflect the complexity of many disorders, and its way of categorizing mental illnesses should not guide research.

“As long as the research community takes the D.S.M. to be a bible, we’ll never make progress,” Dr. Insel said, adding, “People think that everything has to match D.S.M. criteria, but you know what? Biology never read that book.”

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Jeryl Lynn Hilleman with her sister, Kirsten, in 1966 as a doctor gave her the mumps vaccine developed by their father.



A Forgotten Pioneer of Vaccines
By RICHARD CONNIFF, The New York Times, May 6, 2013

We live in an epidemiological bubble and are for the most part blissfully unaware of it. Diseases that were routine hazards of childhood for many Americans living today now seem like ancient history. And while every mother could once identify measles in a heartbeat, now even the best hospitals have to call in their eldest staff members to ask: “Is this what we think it is?”

To a remarkable extent, we owe our well-being, and in many cases our lives, to the work of one man and to events that happened 50 years ago this spring.

At 1 a.m. on March 21, 1963, an intense, irascible but modest Merck scientist named Maurice R. Hilleman was asleep at his home in the Philadelphia suburb of Lafayette Hill when his 5-year-old daughter, Jeryl Lynn, woke him with a sore throat. Dr. Hilleman felt the side of her face and then the telltale swelling beneath the jaw indicating mumps. He tucked her back into bed, about the only treatment anyone could offer at the time.

For most children, mumps was a nuisance disease, nothing worse than a painful swelling of the salivary glands. But Dr. Hilleman knew that it could sometimes leave a child deaf or otherwise permanently impaired.

He quickly dressed and drove 20 minutes to pick up proper sampling equipment from his laboratory. Returning home, he woke Jeryl Lynn long enough to swab the back of her throat and immerse the specimen in a nutrient broth. Then he drove back to store it in the laboratory freezer.

The name Maurice Hilleman may not ring a bell. But today 95 percent of American children receive the M.M.R. — the vaccine for measles, mumps and rubella that Dr. Hilleman invented, starting with the mumps strain he collected that night from his daughter.

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Chagas Disease Costs U.S. More Than Better-Known Illnesses
By DONALD G. McNEIL Jr., The New York Times, February 11, 2013

Chagas disease may be obscure, but the economic burden it imposes on the world is greater than that of better-known diseases, like cervical cancer or cholera, according to a new study. Even in the United States, the authors said, the costs of Chagas are commensurate with those of more publicized diseases, like Lyme disease.

(In the same league, perhaps, but not quite equal. In their study, published in Lancet Infectious Diseases, the authors calculated that Chagas cost the American economy $900 million a year. A 1998 study estimated that Lyme disease cost $2.5 billion.)

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Mice Fall Short as Test Subjects for Humans’ Deadly Ills
By GINA KOLATA, The New York Times, February 11, 2013

For decades, mice have been the species of choice in the study of human diseases. But now, researchers report evidence that the mouse model has been totally misleading for at least three major killers — sepsis, burns and trauma. As a result, years and billions of dollars have been wasted following false leads, they say.

The study’s findings do not mean that mice are useless models for all human diseases. But, its authors said, they do raise troubling questions about diseases like the ones in the study that involve the immune system, including cancer and heart disease.

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An artist's rendering of a placental ancestor. Researchers say the small, insect-eating animal is the most likely common ancestor of the species on the most abundant and diverse branch of the mammalian family tree.


Rat-Size Ancestor Said to Link Man and Beast
By JOHN NOBLE WILFORD, The New York Times, February 7, 2013

Humankind’s common ancestor with other mammals may have been a roughly rat-size animal that weighed no more than a half a pound, had a long furry tail and lived on insects.

In a comprehensive six-year study of the mammalian family tree, scientists have identified and reconstructed what they say is the most likely common ancestor of the many species on the most abundant and diverse branch of that tree — the branch of creatures that nourish their young in utero through a placenta. The work appears to support the view that in the global extinctions some 66 million years ago, all non-avian dinosaurs had to die for mammals to flourish.

Scientists had been searching for just such a common genealogical link and have found it in a lowly occupant of the fossil record, Protungulatum donnae, that until now has been so obscure that it lacks a colloquial nickname. But as researchers reported Thursday in the journal Science, the animal had several anatomical characteristics for live births that anticipated all placental mammals and led to some 5,400 living species, from shrews to elephants, bats to whales, cats to dogs and, not least, humans.

A team of researchers described the discovery as an important insight into the pattern and timing of early mammal life and a demonstration of the capabilities of a new system for handling copious amounts of fossil and genetic data in the service of evolutionary biology. The formidable new technology is expected to be widely applied in years ahead to similar investigations of plants, insects, fish and fowl.

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Researchers have found that mutations in pigeon DNA can control a variety of traits, including the directions their feathers grow, like in this Jacobin pigeon. Charles Darwin raised pigeons and was interested in their breeding as an extreme example of domestic selection. More Photos Here

Pigeons Get a New Look
By CARL ZIMMER, The New York Times, February 4, 2013

In 1855, Charles Darwin took up a new hobby. He started raising pigeons.

In the garden of his country estate, Darwin built a dovecote. He filled it with birds he bought in London from pigeon breeders. He favored the fanciest breeds — pouters, carriers, barbs, fantails, short-faced tumblers and many more.

“The diversity of the breeds is something astonishing,” he wrote a few years later in “On the Origin of Species” — a work greatly informed by his experiments with the birds.

Pigeon breeding, Darwin argued, was an analogy for what happened in the wild. Nature played the part of the fancier, selecting which individuals would be able to reproduce. Natural selection might work more slowly than human breeders, but it had far more time to produce the diversity of life around us.

Yet to later generations of biologists, pigeons were of little more interest than they are to, say, New Yorkers. Attention shifted to other species, like fruit flies and E. coli.

Now Michael D. Shapiro, a biologist at the University of Utah, is returning pigeons to the spotlight.

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Study Flags Duplicate Financing
By DOUGLAS QUENQUA, The New York Times, February 4, 2013

The government may be wasting millions of dollars by paying for the same research projects twice, according to a new analysis of grant and contract records.

Researchers from Virginia Tech and Duke University compared more than 600,000 grant summaries issued to federal agencies since 1985. What they found was almost $70 million that might have been spent on projects that were already at least partly financed. The results were published in the journal Nature.

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Myths of Weight Loss Are Plentiful, Researcher Says
By GINA KOLATA, The New York Times, JANUARY 30, 2013

If schools reinstated physical education classes, a lot of fat children would lose weight. And they might never have gotten fat in the first place if their mothers had just breast fed them when they were babies. But be warned: obese people should definitely steer clear of crash diets. And they can lose more than 50 pounds in five years simply by walking a mile a day.

Those are among the myths and unproven assumptions about obesity and weight loss that have been repeated so often and with such conviction that even scientists like David B. Allison, who directs the Nutrition Obesity Research Center at the University of Alabama at Birmingham, have fallen for some of them.

Now, he is trying to set the record straight. In an article published online today in The New England Journal of Medicine, he and his colleagues lay out seven myths and six unsubstantiated presumptions about obesity. They also list nine facts that, unfortunately, promise little in the way of quick fixes for the weight-obsessed. Example: "Trying to go on a diet or recommending that someone go on a diet does not generally work well in the long term."

Obesity experts applauded this plain-spoken effort to dispel widespread confusion about obesity. The field, they say, has become something of a quagmire.

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Drug-Dose Gender Gap
RONI CARYN RABIN, JANUARY 28, 2013, The New York Times

Most sleeping pills are designed to knock you out for eight hours. When the Food and Drug Administration was evaluating a new short-acting pill for people to take when they wake up in the middle of the night, agency scientists wanted to know how much of the drug would still be in users' systems come morning.

Blood tests uncovered a gender gap: Men metabolized the drug, Intermezzo, faster than women. Ultimately the F.D.A. approved a 3.5 milligram pill for men, and a 1.75 milligram pill for women.

The active ingredient in Intermezzo, zolpidem, is used in many other sleeping aids, including Ambien. But it wasn't until earlier this month that the F.D.A. reduced doses of Ambien for women by half.

Sleeping pills are hardly the only medications that may have unexpected, even dangerous, effects in women. Studies have shown that women respond differently than men to many drugs, from aspirin to anesthesia. Researchers are only beginning to understand the scope of the issue, but many believe that as a result, women experience a disproportionate share of adverse, often more severe, side effects.

"This is not just about Ambien - that's just the tip of the iceberg," said Dr. Janine Clayton, director for the Office of Research on Women's Health at the National Institutes of Health. "There are a lot of sex differences for a lot of drugs, some of which are well known and some that are not well recognized."

Until 1993, women of childbearing age were routinely excluded from trials of new drugs. When the F.D.A. lifted the ban that year, agency researchers noted that because landmark studies on aspirin in heart disease and stroke had not included women, the scientific community was left "with doubts about whether aspirin was, in fact, effective in women for these indications."

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Link to African Ebola Found in Bats Suggests Virus Is More Widespread
By DONALD G. McNEIL Jr., January 28, 2013, The New York Times

For the first time, scientists have found evidence of the African Ebola virus in Asian fruit bats, suggesting that the virus is far more widespread around the world than had been previously known.

That does not mean that outbreaks of hemorrhagic fever are inevitable, said Kevin J. Olival, leader of the bat-hunting team at EcoHealth Alliance. But the possibility exists: bats are believed to drink out of jars attached to trees to collect tasty date palm sap, and fatal outbreaks in Bangladesh of Nipah virus, which is not related to Ebola, have been blamed on fresh sap contaminated with bat saliva, urine or feces.

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An Oil Boom Takes a Toll on Health Care
By JOHN ELIGON, January 27, 2013, The New York Times

WATFORD CITY, N.D. — The patients come with burns from hot water, with hands and fingers crushed by steel tongs, with injuries from chains that have whipsawed them off their feet. Ambulances carry mangled, bloodied bodies from accidents on roads packed with trucks and heavy-footed drivers.

The furious pace of oil exploration that has made North Dakota one of the healthiest economies in the country has had the opposite effect on the region’s health care providers. Swamped by uninsured laborers flocking to dangerous jobs, medical facilities in the area are sinking under skyrocketing debt, a flood of gruesome injuries and bloated business costs from the inflated economy.

The problems have been acute at McKenzie County Hospital here. Largely because of unpaid bills, the hospital’s debt has climbed more than 2,000 percent over the past four years to $1.2 million, according to Daniel Kelly, the hospital’s chief executive. Just three years ago, Mr. Kelly added, the hospital averaged 100 emergency room visits per month; last year, that average shot up to 400.

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DISABLED Almost all the other skeletons at the Man Bac site, south of Hanoi, are straight. But the man now called Burial 9 was laid to rest curled in a fetal position that suggests lifelong paralysis.



Ancient Bones That Tell a Story of Compassion
By JAMES GORMAN, The New York Times, December 17, 2012

While it is a painful truism that brutality and violence are at least as old as humanity, so, it seems, is caring for the sick and disabled.

And some archaeologists are suggesting a closer, more systematic look at how prehistoric people — who may have left only their bones — treated illness, injury and incapacitation. Call it the archaeology of health care.

The case that led Lorna Tilley and Marc Oxenham of Australian National University in Canberra to this idea is that of a profoundly ill young man who lived 4,000 years ago in what is now northern Vietnam and was buried, as were others in his culture, at a site known as Man Bac.

Almost all the other skeletons at the site, south of Hanoi and about 15 miles from the coast, lie straight. Burial 9, as both the remains and the once living person are known, was laid to rest curled in the fetal position. When Ms. Tilley, a graduate student in archaeology, and Dr. Oxenham, a professor, excavated and examined the skeleton in 2007 it became clear why. His fused vertebrae, weak bones and other evidence suggested that he lies in death as he did in life, bent and crippled by disease.

They gathered that he became paralyzed from the waist down before adolescence, the result of a congenital disease known as Klippel-Feil syndrome. He had little, if any, use of his arms and could not have fed himself or kept himself clean. But he lived another 10 years or so.

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In Gun Debate, a Misguided Focus on Mental Illness
By RICHARD A. FRIEDMAN, M.D., The New York Times, December 17, 2012

In the wake of the terrible shooting at an elementary school in Newtown, Conn., national attention has turned again to the complex links between violence, mental illness and gun control.

The gunman, Adam Lanza, 20, has been described as a loner who was intelligent and socially awkward. And while no official diagnosis has been made public, armchair diagnosticians have been quick to assert that keeping guns from getting into the hands of people with mental illness would help solve the problem of gun homicides.

Arguing against stricter gun-control measures, Representative Mike Rogers, Republican of Michigan and a former F.B.I. agent, said, “What the more realistic discussion is, ‘How do we target people with mental illness who use firearms?’ ”

Robert A. Levy, chairman of the Cato Institute, told The New York Times: “To reduce the risk of multivictim violence, we would be better advised to focus on early detection and treatment of mental illness.”

But there is overwhelming epidemiological evidence that the vast majority of people with psychiatric disorders do not commit violent acts. Only about 4 percent of violence in the United States can be attributed to people with mental illness.

This does not mean that mental illness is not a risk factor for violence. It is, but the risk is actually small. Only certain serious psychiatric illnesses are linked to an increased risk of violence.

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Journal Offers Dose of Fun for Holiday
By LAWRENCE K. ALTMAN, M.D., The New York Times, December 17, 2012

LONDON — Dutch and Norwegian scientists say they have solved a glowing mystery: why Rudolph the reindeer’s nose is red.

By traveling to the Arctic and using video-microscope and thermal imaging technology, the scientists showed that the glow is from tiny blood vessels that are more abundant in the noses of reindeer than in humans’. Yes, seriously. The findings are being reported next week in BMJ, formerly known as The British Medical Journal, a publication with a quirky holiday tradition.

For the past 30 years, BMJ has devoted its Christmas-week issue to a lighter and sometimes brighter side of medicine, publishing unusual articles that vary from simply amusing to bizarre to creative or potentially important. All are based on methodologically sound science.

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A view of Pauline avibella, a shrmplike marine creature, from a computer-generated model.

Fossils of New Species Discovered in England
By SINDYA N. BHANOO, The New York Times, December 17, 2012

A tiny, fossilized crustacean that lived 425 million years ago has been discovered, remarkably intact, in a rock formation in Herefordshire, England. Paleontologists say it represents a new genus and species, belonging to a class of shrimplike marine creatures called ostracods.

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The crustacean is named Pauline avibella, after Dr. Siveter’s deceased wife, Pauline.
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Genomic Study Traces Roma to Northern India
By SINDYA N. BHANOO, The New York Times, December 10, 2012

The Roma people of Europe, often called Gypsies, are long thought to have originated in India because of similarities between Roma and Indian languages. But historical records are scanty.

Now a wide-ranging genomic study appears to confirm that the Roma came from a single group that left northwestern India about 1,500 years ago.

“Some genetic studies have also pointed to India before, but it was not clear what part of India,” said an author of the study, David Comas, an evolutionary biologist at Pompeu Fabra University in Barcelona.

Dr. Comas led the study with Manfred Kayser from Erasmus University Rotterdam in the Netherlands. They and other colleagues report their findings in a recent issue of Current Biology.

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How to Control an Army of Zombies
By CARL ZIMMER, The New York Times, December 5, 2012

In the rain forests of Costa Rica lives Anelosimus octavius, a species of spider that sometimes displays a strange and ghoulish habit.

From time to time these spiders abandon their own webs and build radically different ones, a home not for the spider but for a parasitic wasp that has been living inside it. Then the spider dies — a zombie architect, its brain hijacked by its parasitic invader — and out of its body crawls the wasp’s larva, which has been growing inside it all this time.

The current issue of the prestigious Journal of Experimental Biology is entirely dedicated to such examples of zombies in nature. They are far from rare. Viruses, fungi, protozoans, wasps, tapeworms and a vast number of other parasites can control the brains of their hosts and get them to do their bidding. But only recently have scientists started to work out the sophisticated biochemistry that the parasites use.

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Divining the Weather, With Methods Old and New
By DAN BARRY, The New York Times, December 9, 2012

In these times of upset and uncertainty, comfort comes in knowing that dental floss can cut a dense cheesecake more cleanly than any knife. That cloves of garlic will send ants scurrying. That a cow requires at least 15 pounds of hay per day. That the state bird of South Dakota is the ring-necked pheasant.

For the 217th consecutive year, useful facts and tips like these have been assembled in J. Gruber’s Hagerstown Town and Country Almanack, a deceptively slim volume that is available to farmers, merchants and all good citizens — especially those residing in the Middle Atlantic States — at the nominal cost of $4.99.

Contained within its 82 pages is the accumulated wisdom of many generations of farmers who lived and worked according to the arc of the sun and the pull of the moon. This means that in addition to reporting that our nation’s fifth vice president was Elbridge Gerry and that the gift of a daffodil represents unrequited love, Gruber’s Almanack also provides “conjecture of the weather and other astronomical information.”

For example, if you want to know what weather to expect in New England next Thanksgiving Day, the almanac offers an answer with a better-than-even shot at accuracy: “Snow, heavy south.”

This is the educated guess of Bill O’Toole, 70, a retired college math professor who, for more than four decades, has served as the almanac’s seventh prognosticator — or conjecturer, or calculator — a line of work that began in 1797 with a star-savvy blacksmith. Mr. O’Toole is tall and bearded, with large eyes that convey wonder in all things, and a business card that declares in black and white his gray-area profession.

Working from desk space carved out of the book clutter of a brick row house here in Emmitsburg, about a mile south of the Pennsylvania line, Mr. O’Toole endeavors to divine the weather as much as 18 months in advance. He does so with a conjurer’s brew of age-old wisdom and 21st-century technology that includes a range of tools, from a software program of astronomical data produced by the United States Naval Observatory to the meticulous tracking — through some 30 computer programs he has written — of all things lunar.

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Bid to Preserve Manhattan Project Sites in a Park Stirs Debate
By WILLIAM J. BROAD, The New York Times, December 3, 2012

A plan now before Congress would create a national park spread over three states to protect the aging remnants of the atomic bomb project from World War II, including an isolated cabin where grim findings threw the secretive effort into a panic.

Scientists used the remote cabin in the seclusion of Los Alamos, N.M., as the administrative base for a critical experiment to see if plutonium could be used to fuel the bomb. Early in 1944, sensitive measurements unexpectedly showed that the silvery metal underwent a high rate of spontaneous fission — a natural process of atoms splitting in two.

That meant the project’s design for a plutonium bomb would fail. J. Robert Oppenheimer, the project’s scientific head, was so dismayed that he considered resigning.

But he and his colleagues pressed ahead with a new design. On July 16, 1945, the world’s first atom bomb — a lump of plutonium at its core — illuminated the darkness of the central New Mexican desert with a flash of light brighter than the sun.

The plan for a Manhattan Project National Historical Park would preserve that log cabin and hundreds of other buildings and artifacts scattered across New Mexico, Washington and Tennessee — among them the rustic Los Alamos home of Dr. Oppenheimer and his wife, Kitty, and a large Quonset hut, also in New Mexico, where scientists assembled components for the plutonium bomb dropped on Japan.

“It’s a way to help educate the next generation,” said Cynthia C. Kelly, president of the Atomic Heritage Foundation, a private group in Washington that helped develop the preservation plan.

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‘Famous’ Wolf Is Killed Outside Yellowstone
By NATE SCHWEBER, The New York Times, December 8, 2012

Yellowstone National Park’s best-known wolf, beloved by many tourists and valued by scientists who tracked its movements, was shot and killed on Thursday outside the park’s boundaries, Wyoming wildlife officials reported.

The wolf, known as 832F to researchers, was the alpha female of the park’s highly visible Lamar Canyon pack and had become so well known that some wildlife watchers referred to her as a “rock star.” The animal had been a tourist favorite for most of the past six years.

The wolf was fitted with a $4,000 collar with GPS tracking technology, which is being returned, said Daniel Stahler, a project director for Yellowstone’s wolf program. Based on data from the wolf’s collar, researchers knew that her pack rarely ventured outside the park, and then only for brief periods, Dr. Stahler said.

This year’s hunting season in the northern Rockies has been especially controversial because of the high numbers of popular wolves and wolves fitted with research collars that have been killed just outside Yellowstone in Idaho, Montana and Wyoming.

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X-Ray Scans at Airports Leave Lingering Worries
By RONI CARYN RABIN, The New York Times, AUGUST 6, 2012

Even before she was pregnant, Yolanda Marin-Czachor tried to avoid the full-body X-ray scanners that security officers use to screen airport passengers. Now she's adamant about it: She'll take a radiation-free pat-down instead any day.

"I had two miscarriages before this pregnancy," Ms. Marin-Czachor, a 34-year-old mother and teacher from Green Bay, Wis., recalled, "and one of the first things my doctor said was: 'Do not go through one of those machines. There have not been any long-term studies. I would prefer you stay away from it.' "

There are 244 full-body "backscatter" X-ray scanners in use at 36 airports in the United States. They operate almost nonstop, according to the Transportation Security Administration. Other airports use millimeter wave scanners, which look like glass telephone booths and do not use radiation, or metal detectors.

Most experts agree that as long as the X-ray backscatter machines are functioning properly, they expose passengers to only extremely low doses of ionizing radiation.

But some experts are less sanguine, and questions persist about the safety of using X-ray machines on such a large scale. A recent study reported that radiation from the machines can reach organs through the skin. In another report, researchers estimated that one billion X-ray backscatter scans per year would lead to perhaps 100 radiation-induced cancers in the future. The European Union has banned body scanners that use radiation; it is against the law in several European countries to X-ray people without a medical reason.

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In Crises at Sea, Chivalry Dies First
By NICHOLAS BAKALAR, The New York Times, August 6, 2012

As the Titanic began to sink in the early hours of April 15, 1912, the captain ordered women and children first to the lifeboats. Ultimately, he went down with the ship.

The order has long been held up as an example of modern chivalry, an unwritten law of the sea. But a new review of historical records suggests that in maritime disasters, “every man for himself” is a rule more commonly applied, and that women and children die at significantly higher rates than male passengers and crew members.

Two researchers at Uppsala University in Sweden examined records of 18 ship accidents from 1852 until 2011, which involved more than 15,000 passengers and crew members. They selected accidents for which there is complete data on survivors and decedents by number and sex, and they limited their sample to wrecks involving 100 people or more in which at least 5 percent died or 5 percent lived.

Their findings suggest that the events on the Titanic, where 20 percent of men and 70 percent of women and children lived to tell the tale, were highly unusual, if not unique.

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Peru: Antibodies Seen in Amazon Dwellers Suggest That Rabies May Be Survivable
By DONALD G. McNEIL Jr., The New York Times, August 6, 2012

Defying conventional wisdom about rabies, a new study suggests that the disease may not be 100 percent fatal.

Scientists who took blood samples from 63 relatively healthy villagers in the Amazon jungle in Peru, where vampire bat bites are common, found seven people who had antibodies to rabies. Only one reported ever having had a rabies shot (which would also produce antibodies).

The study, led by scientists from the Centers for Disease Control and Protection and Peru’s Health Ministry, was published Aug. 1 in The American Journal of Tropical Medicine and Hygiene.

Rabies kills about 55,000 people a year, mostly in Africa and Asia; many are children bitten by dogs. But in Peru, 81 percent of known rabies deaths are from bats.

More than half the Amazon villagers interviewed said they had been bitten; vampire bats can drink without awakening their victims.

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Iron Age Creativity in a Turkish King’s Image
By SINDYA N. BHANOO, The New York Times, August 6, 2012

Archaeologists have discovered a giant statue of a Turkish king that dates back 3,000 years.

The partly broken sculpture of the king’s head and torso stands nearly five feet tall, and the full sculpture may have been more than 10 feet, said Timothy P. Harrison, an archaeologist from the University of Toronto who was part of the team that made the discovery.

The piece demonstrates that creativity and intellect flourished in the Iron Age, though cities and kingdoms were small and independent — unlike the centralized system of the earlier Bronze Age. “This counters our intuition that big empires are what produced creativity,” Dr. Harrison said.

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Another Tick-Borne Disease to Guard Against
By JANE E. BRODY, The New York Times, JULY 30, 2012

Despite its many delights, summer also brings its fair share of pestilence. One, called babesiosis, has only recently been widely recognized as a potentially serious outdoor hazard. According to a very detailed study conducted on Block Island, R.I., it could eventually rival Lyme disease as the most common tick-borne ailment in the United States.

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Disease Diagnosed in a 500-Year-Old Mummy
By SINDYA N. BHANOO, The New York Times, July 30, 2012

An Inca girl who lived 500 years ago suffered from a bacterial lung infection just before she died, report scientists who have examined her mummy.

The girl, thought to be 15, was sacrificed by the Andean Inca at the summit of Llullaillaco, a 22,000-foot volcano in the province of Salta, Argentina, said Angelique Corthals, a forensic anthropologist at the City University of New York. The girl had a large sore on one leg, leading Dr. Corthals to believe she may have been unwell when she was buried, alive but unconscious, on the mountain.

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Flu That Leapt From Birds to Seals Is Studied for Human Threat
By CARL ZIMMER, The New York Times, July 31, 2012

Four times in the past century, a new strain of flu has emerged that can spread quickly in humans. One of those strains, which emerged in 1918, killed an estimated 50 million people.

All human flu strains evolved from flu viruses that live in birds. To understand how these transitions happen, scientists have recently been tinkering with a strain of bird flu to see how many mutations it takes until its spreads from mammal to mammal.

When news of their efforts emerged last fall, a fierce debate broke out about the wisdom of publishing the experiments in full.

Eventually, the scientists got the go-ahead from a federal advisory board, and earlier this year they described how a few mutations of a strain called H5N1 enabled it to spread among ferrets. But the controversy still rages: Responding to worries about an accidental release of an engineered virus, leading flu scientists agreed in January to a moratorium on further research, and experts are debating when it should be lifted.

Scientists may respect moratoriums, but nature does not. Evolution recently carried out an influenza experiment of its own on the coast of New England. Last fall, 162 dead harbor seal pups washed up on the beaches of New Hampshire and Massachusetts.

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Artifacts Revive Debate on Transformation of Human Behavior
By JOHN NOBLE WILFORD, The New York Times, July 30, 2012

In the widening search for the origins of modern human evolution, genes and fossils converge on Africa about 200,000 years ago as the where and when of the first skulls and bones that are strikingly similar to ours. So this appears to be the beginning of anatomically modern Homo sapiens.

But evidence for the emergence of behaviorally modern humans is murkier — and controversial. Recent discoveries establish that the Homo sapiens groups who arrived in Europe some 45,000 years ago had already attained the self-awareness, creativity and technology of early modern people. Did this behavior come from Africa after gradual development, or was it an abrupt transition through some profound evolutionary transformation, perhaps caused by hard-to-prove changes in communication by language?

Now, the two schools of thought are clashing again, over new research showing that occupants of Border Cave in southern Africa, who were ancestors of the San Bushmen hunter-gatherers in the area today, were already engaged in relatively modern behavior at least 44,000 years ago, twice as long ago as previously thought. Two teams of scientists reported these findings Monday in the journal Proceedings of the National Academy of Sciences.

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Good News for Mental Illness in Health Law
By RICHARD A. FRIEDMAN, M.D., The New York Times, July 9, 2012

Americans with mental illness had good reason to celebrate when the Supreme Court upheld President Obama’s Affordable Care Act. The law promises to give them something they have never had before: near-universal health insurance, not just for their medical problems but for psychiatric disorders as well.

Until now, people with mental illness and substance disorders have faced stingy annual and lifetime caps on coverage, higher deductibles or simply no coverage at all.

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Study Says Meeting Contraception Needs Could Cut Maternal Deaths by a Third
By SABRINA TAVERNISE, The New York Times, July 9, 2012

A new study by researchers at Johns Hopkins University shows that fulfilling unmet contraception demand by women in developing countries could reduce global maternal mortality by nearly a third, a potentially great improvement for one of the world’s most vulnerable populations.

The study, published on Tuesday in The Lancet, a British science journal, comes ahead of a major family planning conference in London organized by the British government and the Bill and Melinda Gates Foundation that is an attempt to refocus attention on the issue. It has faded from the international agenda in recent years, overshadowed by efforts to combat AIDS and other infectious diseases, as well as by ideological battles.

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C.I.A. Vaccine Ruse May Have Harmed the War on Polio
By DONALD G. McNEIL Jr., The New York Times, July 9, 2012

Did the killing of Osama bin Laden have an unintended victim: the global drive to eradicate polio?

In Pakistan, where polio has never been eliminated, the C.I.A.’s decision to send a vaccination team into the Bin Laden compound to gather information and DNA samples clearly hurt the national polio drive. The question is: How badly?

After the ruse by Dr. Shakil Afridi was revealed by a British newspaper a year ago, angry villagers, especially in the lawless tribal areas on the Afghan border, chased off legitimate vaccinators, accusing them of being spies.

And then, late last month, Taliban commanders in two districts banned polio vaccination teams, saying they could not operate until the United States ended its drone strikes. One cited Dr. Afridi, who is serving a 33-year sentence imposed by a tribal court, as an example of how the C.I.A. could use the campaign to cover espionage.

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In Dieting, Magic Isn’t a Substitute for Science
By GINA KOLATA, The New York Times, July 9, 2012

Is a calorie really just a calorie? Do calories from a soda have the same effect on your waistline as an equivalent number from an apple or a piece of chicken?

For decades the question has percolated among researchers — not to mention dieters. It gained new momentum with a study published last month in The Journal of the American Medical Association suggesting that after losing weight, people on a high-fat, high-protein diet burned more calories than those eating more carbohydrates.

We asked Dr. Jules Hirsch, emeritus professor and emeritus physician in chief at Rockefeller University, who has been researching obesity for nearly 60 years, about the state of the research. Dr. Hirsch, who receives no money from pharmaceutical companies or the diet industry, wrote some of the classic papers describing why it is so hard to lose weight and why it usually comes back.

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FOR THE AGES Single-celled foraminifera helped to create the materials used in some of the world's great monuments, and are also very valuable in telling Earth's history because they produce shells that make good fossils.


‘Nature’s Masons’ Do Double Duty as Storytellers
By SEAN B. CARROLL, The New York Times, June 25, 2012

GUBBIO, Italy — North of Rome, in Umbria, a series of picturesque, ancient towns perch on the tops or sides of the foothills of the Apennine Mountains. Their placement here was a defensive imperative for successive Umbrian, Etruscan, Roman and Christian occupants over the millenniums. But these hillside locations were also of great advantage for constructing massive buildings, fortified walls and aqueducts, because of to unlimited local supplies of limestone.

Tourists flock to places like Gubbio, on the slope of Mount Ingino, to admire its impressive medieval churches and palazzos. But no one gives any thought to the tiny creatures that helped to create the materials necessary for making such spectacular, long-lived monuments.

Limestone is composed largely of crystallized calcium carbonate. Some of it comes from the skeletal remains of well-known creatures like corals, but much of the rest comes from less appreciated but truly remarkable organisms called foraminifera, or forams for short.

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Immigrants Are Crucial to Innovation, Study Says
By ANDREW MARTIN, The New York Times, June 25, 2012

Arguing against immigration policies that force foreign-born innovators to leave the United States, a new study to be released on Tuesday shows that immigrants played a role in more than three out of four patents at the nation’s top research universities.

Conducted by the Partnership for a New American Economy, a nonprofit group co-founded by Mayor Michael Bloomberg of New York, the study notes that nearly all the patents were in science, technology, engineering and math, the so-called STEM fields that are a crucial driver of job growth.

The report points out that while many of the world’s top foreign-born innovators are trained at United States universities, after graduation they face “daunting or insurmountable immigration hurdles that force them to leave and bring their talents elsewhere.”

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Really? Eating Soy Increases the Risk of Breast Cancer
By ANAHAD O'CONNOR, The New York Times, JUNE 25, 2012

THE FACTS

Soy milk, tofu and other soy products contain phytoestrogens, chemicals that can mimic the behavior of the hormone estrogen. Because estrogen fuels many breast cancers, soy has long been a source of concern: Can it heighten the risk of breast cancer or raise the odds of recurrence?

In the lab, phytoestrogens can stimulate the growth of breast cancer cells. But in human studies, scientists have not found that diets high in soy increase breast cancer risk. In fact, most have found the reverse.

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Fast Access to Records Helps Fight Epidemics
By MILT FREUDENHEIM, The New York Times, June 18, 2012

Public health departments around the country have long scrutinized data from local hospitals for indications that diseases like influenza, tuberculosis, AIDS, syphilis and asthma might be on the rise, and to monitor the health consequences of heat waves, frigid weather or other natural phenomena. In the years since 9/11, this scrutiny has come to include signs of possible bioterrorism.

When medical records were maintained mainly on paper, it could take weeks to find out that an infection was becoming more common or that tainted greens had appeared on grocery shelves. But the growing prevalence of electronic medical records has had an unexpected benefit: By combing through the data now received almost continuously from hospitals and other medical facilities, some health departments are spotting and combating outbreaks with unprecedented speed.

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ROUGH SEAS A 19th-century engraving depicts John Cabot on his second voyage, reaching what is now Newfoundland in 1497. His first voyage was aborted, and his third was a mystery, with Cabot thought to have perished at sea.


Discovery of a £16 Advance Sheds Light on John Cabot’s Adventures
By GUY GUGLIOTTA, The New York Times, June 18, 2012

In early 1496, a Venetian sea captain named Giovanni Caboto appeared in the southern English port city of Bristol. He had no money, but carried a warrant from King Henry VII to obtain a ship and sail on a voyage of trade and discovery.

England would call him John Cabot, and from 1496 to 1498 — less than a decade after Christopher Columbus — he set sail three times for the New World. The first voyage was aborted, but on the second he made landfall in what is now Newfoundland and claimed North America for England and the Roman Catholic Church.

That much is known. But of his third voyage there is nothing. He left Bristol and apparently vanished — slaughtered by enemies, taken by disease or swallowed by the sea.

And that is not the only enduring mystery about Cabot. Who helped him? Who bankrolled him? Did he really disappear?

But scholars first had to untangle another mystery: the authenticity of spectacular claims made by Alwyn Ruddock, a historian at the University of London who had researched Cabot for more than half her life.

Dr. Ruddock several times promised a book, but never wrote it. Instead, before she died in 2005 at 89, a childless widow, she ordered her executor to destroy her research. Seventy-eight bags of papers were shredded and incinerated, leaving scholars astounded.

Now an important piece of the Ruddock riddle has been solved. In 2010, an international team of scholars working together in what is called the Cabot Project came upon a set of 514-year-old Italian ledgers that Dr. Ruddock had found decades earlier but which had disappeared from view. They showed that in the spring of 1496, Cabot received seed money for his voyages from the London branch of a Florentine banking house called the Bardi.

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To Advance, Search for a Black Cat in a Dark Room
By SANDRA BLAKESLEE, The New York Times, June 18, 2012

Many people think of science as a deliberate process that is driven by the gradual accumulation of facts. Legions of smart scientists labor to piece together the evidence supporting their discoveries, hypotheses, inventions and progress itself.

But according to Stuart Firestein, a professor of neuroscience at Columbia University, this view is fallacious. Working scientists don’t get bogged down in factual swamps, he says, because they don’t care all that much for facts. Facts are not what science is all about. It’s only when the facts fail that scientists really put on their thinking caps.

Scientists, Dr. Firestein says, are driven by ignorance.

In this sense, ignorance is not stupidity. Rather, it is a particular condition of knowledge: the absence of fact, understanding, insight or clarity about something. It is a case where data don’t exist, or more commonly, where the existing data don’t make sense.

To show how scientists depend on ignorance, Dr. Firestein has written a short, highly entertaining book aimed at nonscientists and students who want to be scientists.

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