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  • richardmitnick 3:48 pm on October 30, 2014 Permalink | Reply
    Tags: , , New York Times, Paleobiology,   

    From NYT: “From Ancient DNA, a Clearer Picture of Europeans Today” 

    New York Times

    The New York Times

    OCT. 30, 2014
    Carl Zimmer

    About 50,000 years ago, humans from Africa first set foot in Europe. They hunted woolly mammoths and other big game — sometimes to extinction. Eventually, they began grazing livestock and raising crops.

    They chopped down forests and drained swamps, turning villages into towns, then cities and capitals of empires. But even as they altered the Continent, Europeans changed, too.

    Their skin and hair grew lighter. They gained genetic traits particular to the regions in which they lived: Northern Europeans, for example, grew taller than Southern Europeans.

    Up till now, scientists have learned about evolution on the Continent mostly by looking at living Europeans. But advances in biotechnology have made it possible to begin extracting entire DNA from the bones of ancestors who lived thousands of years ago. Their genomes are like time machines, allowing scientists to see bits of European history playing out over thousands of years.

    Recently David Reich, a geneticist at Harvard Medical School, and his colleagues analyzed the genomes of nine ancient Europeans. Eight belonged to hunter-gatherers who lived about 8,000 years ago, seven in what is now Sweden and one in Luxembourg. The ninth came from a farmer who lived 7,000 years ago in present-day Germany.

    The scientists compared these genomes with those of living Europeans. As they reported last month in Nature, the study revealed something scientists never knew: Europeans today have genes from three very different populations.

    The oldest of these populations were the first Europeans, who appear to have lived as hunter-gatherers. The second were farmers who expanded into Europe about 8,500 years ago from the Near East.

    But most living Europeans also carry genes from a third population, which appears to have arrived more recently. Dr. Reich and his colleagues found the closest match in DNA taken from a 24,000-year-old individual in Siberia, suggesting that the third wave of immigrants hailed from north Eurasia. The ancient Europeans that the scientists studied did not share this North Eurasian DNA. They concluded that this third wave must have moved into Europe after 7,000 years ago.

    Last week, another team of scientists based at University College Dublin reported data from an even bigger haul of ancient European genomes — 13, all told. While Dr. Reich and his colleagues studied ancient Europeans separated by hundreds of miles, the Dublin team focused on just one region in Central Europe called the Great Hungarian Plain.

    The people whose genomes the scientists retrieved lived on the plain at various times between 7,700 years ago and 2,800 years ago.

    “What’s really exciting here is to have a transect through time,” said Johannes Krause, a co-director of the Max Planck Institute for History and the Sciences in Jena, Germany, who was not involved in the study. “It’s the first time that’s been done.”

    Archaeological digs have revealed evidence of farming on the plain as long as 8,000 years ago. People there raised crops like barley, and raised cattle and other livestock. Shards of pottery show that they consumed milk.

    The oldest genomes retrieved from human remains in the area — one from a man and one from a woman — date back to the dawn of agriculture on the plain. The woman’s DNA showed that she belonged to the ancient farming population documented by Dr. Reich and his colleagues.

    The man, however, did not have the genes of a farmer. He belonged to the oldest population of hunter-gatherers.

    “The archaeological information isn’t enough to say whether he was married to a local farmer,” said Ron Pinhasi, an archaeologist at University College Dublin and a co-author of the new study. It may even be that the man’s skull was a trophy of some sort, Dr. Pinhasi added.

    Archaeologists have found that early farming culture didn’t change drastically for the next 3,700 years. But about 4,000 years ago, the Bronze Age arrived. People started using bronze tools, trading over longer networks and moving into fortified towns.

    Dr. Pinhasi and his colleagues found that the era also brought a sudden shift in human DNA. A new population arrived on the Great Hungarian Plain, and Dr. Reich believes he knows who they were: the northern Eurasians.

    “It’s very exciting,” he said. “It documents that by this time in Central Europe, this Eastern influence had already arrived.”

    At the start of the Bronze Age, life settled down on the plain for a thousand years. But then came the Iron Age, bringing another shift in culture — and genes.

    People began traveling across the plain by horse-drawn chariots and wagons, and the genomes from 2,800 years ago show that the people of the Bronze Age had begun to be supplanted by a new Iron Age population. These are the people most closely related to living Hungarians.

    In the new study, Dr. Pinhasi and his colleagues also surveyed individual genes known to have changed over the course of European history.

    Today, for example, people in Hungary tend to have light skin and light brown hair, and half of them carry a mutation that lets them digest milk as adults. It took thousands of years for the genes for these traits to appear on the Great Hungarian Plain, the scientists found.

    The hunter-gatherer that lived 7,700 years ago, for example, probably had black hair and dark skin, along with blue eyes. His genes suggest that he also probably couldn’t digest milk — not surprising, since he came from a population that didn’t raise livestock.

    The ancient farmer woman, on the other hand, probably had dark brown hair and brown eyes. But like the hunter-gatherers, she lacked the genetic mutation for digesting milk.

    woman
    A 7,700-year-old skeleton of a woman found in Hungary has yielded DNA. Scientists have found that she belonged to a wave of early farmers who moved into Europe from the Near East. Credit Ron Pinhasi

    It is not until 6,400 years ago that the scientists find the first genetic evidence on the Great Hungarian Plain for light brown hair. And the milk mutation appeared even later, just 3,100 years ago.

    It is possible that these new genes and others were brought to the plain by successive waves of immigrants. But natural selection probably played a role in making these genes pervasive.

    Genetic mutations that enable people to drink milk as adults, for example, could have helped them survive famines. In cow-herding cultures, scientists have found, the milk-drinking mutation led to a 10 percent increase in the number of children.

    If that’s true, then for 4,600 years people on the Great Hungarian Plain were milking cows but lacked the ability to digest milk. Dr. Pinhasi suggested that they only used milk at first to make cheese and yogurt, which would have been easier to digest.

    Daniel G. Bradley, a geneticist at University College Dublin and co-author of the new study, predicted more unexpected results would emerge as scientists gather more ancient DNA in Europe.

    “The past is going to be a different country,” he said, “and it’s going to surprise us.”

    See the full article here.

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  • richardmitnick 6:49 pm on October 20, 2014 Permalink | Reply
    Tags: , , New York Times   

    From NYT: “25 Years Ago, NASA Envisioned Its Own ‘Orient Express’” 

    New York Times

    The New York Times

    OCT. 20, 2014
    KENNETH CHANG

    The National Aero-Space Plane was to be a revolutionary advance beyond the space shuttle.

    plane

    In his 1986 State of the Union address, President Ronald Reagan promised “a new Orient Express that could, by the end of the next decade, take off from Dulles Airport and accelerate up to 25 times the speed of sound, attaining low-earth orbit or flying to Tokyo within two hours.”

    On Oct. 3, 1989, an article in Science Times, Designing a Plane for the Leap of Space (and Back), reported frenetic activity at NASA and the Defense Department.

    “Scientists and engineers are making rapid progress in developing technologies needed to build a 17,000-mile-an-hour ‘space plane’ that could escape earth’s gravity and circle the globe in 90 minutes,” the article began.

    “Their goal,” it continued, “is a space plane that could take off and land from virtually any airport in the world, carry satellites and other space cargo into orbit cheaply, shuttle between the earth and an orbiting space station, or carry a load of bombs deep into enemy territory as fast as an intercontinental missile.”

    Proponents contended the space plane would be far cheaper to operate than the shuttle.

    Others were dubious. The Air Force, which was providing most of the financing, had already tried to back out, but the National Space Council, headed by Vice President Dan Quayle, recommended continuing work at a slower pace.

    The target for the first flight of the first experimental version, known as the X-30, was originally 1993 but was pushed back to 1997.

    25 YEARS LATER The space plane, able to fly by itself to orbit, never took off. The X-30 died in 1994. Smaller-scale hypersonic programs came and went.

    Was the X-30 technologically feasible?

    “No, and it’s still not,” said Jess Sponable, a program manager in the tactical technology office at Darpa, the Defense Advanced Research Projects Agency. For X-30 to succeed, infant ideas would have had to have been developed into robust, reliable technologies — materials that could survive intense temperatures, air-breathing engines that could fly faster and higher.

    Nonetheless, “absolutely, it was worthwhile,” Mr. Sponable said, although he added perhaps not worth the more than $1.6 billion spent. “We learned a lot.”

    The pendulum for spacecraft design has since swung away from the cutting edge to the tried and true. The Orion craft, which NASA is building for deep-space missions, is a capsule, just like the one used for the Apollo moon missions but bigger. The two private company designs that NASA chose to take future astronauts to the space station are also capsules. (The loser in that competition was a mini-shuttle offering.)

    NASA Orion Spacecraft
    NASA/Orion

    But the dream of hypersonic space planes continues.

    At Darpa, Mr. Sponable heads the XS-1 space plane project. It is not a do-it-all-at-once effort like the 1980s space plane but a much simpler, unmanned vehicle that would serve as a reusable first stage.

    Mr. Sponable is eager to figure out how to send it up many times, quickly and cheaply; the goal is 10 flights in 10 days.

    “We want operability No. 1,” he said. With the quick launches, the issue of cost “just disappears, because we can’t spend a lot of money from Day 1 to Day 2 to Day 3.”

    Darpa has awarded contracts to three industry teams to develop preliminary designs. Mr. Sponable said the decision of a next step would come next spring.

    The space plane episode illustrates the recurring money woes that have bedeviled NASA for decades: A grandiose plan is announced with fanfare and a burst of financing that fades as delays and cost overruns undercut the optimistic plans. Then a new president or a new NASA administrator changes course.

    Most recently, the Obama administration canceled plans started under President George W. Bush to send astronauts back to the moon and told NASA to consider an asteroid instead.

    If the pattern continues, NASA priorities could zig again after the next president moves into the White House in 2017.

    See the full article here.

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  • richardmitnick 5:10 pm on October 8, 2014 Permalink | Reply
    Tags: , , , , , New York Times   

    From Dennis Overbye at the New York Times: “How to Make a Black Hole” 

    New York Times

    The New York Times

    On July 2, 1967, a network of satellites designed to detect tests of nuclear weapons recorded a flash of gamma rays coming from the wrong direction — outer space.

    And so it was that human astronomers were tipped to the existence of one of the most violent phenomena of nature. Today, they know that about once a day somewhere in the observable universe, an explosion called a gamma-ray burst occurs, releasing more energy in a few seconds than our galaxy does in a year.

    These magnificent cosmic conflagrations are as far away as they are rare, which is just as well. If one happened nearby, in our own galaxy, we could be swathed with radiation. The closest gamma-ray burst whose distance has been measured happened some 119 million light-years from us, far outside the so-called Local Group, which contains our own Milky Way galaxy. The farthest so far recorded is now 31 billion light-years away, as calculated by the mathematics of the expanding universe; it happened when the universe was only 500 million years old.

    local group
    Local Group

    Gamma-ray bursts are thought to be the final step in the series of transformations by which stars shrink and slump from blazing glory to oblivion, winding up as bottomless deadly dimples in the fabric of space-time — that is to say, as black holes.

    The hierarchy of dead stars goes like this: Stars like the sun, when they run out of thermonuclear fuel, shrink to cinders known as white dwarfs, the size of Earth. Stars more massive than the sun might collapse more drastically and undergo a supernova explosion, blasting newly formed heavy elements into space to enrich future stars, planets and perhaps life, and leaving behind crushed cores known as neutron stars. These weigh slightly more than the sun but are only 12 miles or so in diameter — so dense that a teaspoonful on Earth would weigh as much as Mount Everest.

    Such an explosion, bright enough to be seen in daylight, happened in 1054, Earth time, as told by Chinese astronomers and the ancient inhabitants of Chaco Canyon in what is now New Mexico. That supernova left behind the Crab nebula, a tangle of glowing shreds of gas and a pulsar — a magnetized neutron star spinning 30 times a second, whipping the gas with magnetic fields that make it glow.

    Crab
    Crab Nebula

    Neutron stars, theorists say, are the densest stable form of matter, but they are not the end of the story. According to theory, too much mass accumulating on a neutron star can cause its collapse into a black hole, an abyss from which not even light can escape. The signature of such a cataclysm would be a gamma-ray burst, astronomers say.

    col
    Colliding neutron stars

    Supercomputer simulations by astronomers led by Luciano Rezzolla of the Institute of Theoretical Physics in Frankfurt have recently showed this would work.

    The simulation, as it unwound over six weeks of supercomputer time at the Max Planck Institute for Gravitational Physics, started with two neutron stars orbiting each other at a distance of 11 miles. That would not be unusual in the universe; most stars are in fact part of double-star systems and several pairs of pulsars orbiting each other are already known. They will eventually collide because such dense, heavy objects lose energy rapidly and spiral together.

    In the case of Dr. Rezzolla’s computation, it took seven milliseconds for tidal forces from the larger star’s gravity to rip apart the smaller star and unwind it into a spiral resembling flaming toothpaste writhing with magnetic fields and begin munching up the gas.

    The excess plasma forms a fat disk around the new black hole, and its magnetic fields, a billion times stronger than those in the sun, align to channel beams of radiation and particles out at the speed of light. The result is a gamma-ray burst visible across the universe, carrying the news of doom — the last astronomers will ever hear of these stars.

    For those two stars, the last bang was the best. Oblivion can be such a lovely sight.

    See the full article here.

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  • richardmitnick 8:36 pm on September 28, 2014 Permalink | Reply
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    From NYT: “Building an Ark for the Anthropocene” 

    New York Times

    The New York Times

    SEPT. 27, 2014
    JIM ROBBINS

    WE are barreling into the Anthropocene, the sixth mass extinction in the history of the planet. A recent study published in the journal Science concluded that the world’s species are disappearing as much as 1,000 times faster than the rate at which species naturally go extinct. It’s a one-two punch — on top of the ecosystems we’ve broken, extreme weather from a changing climate causes even more damage. By 2100, researchers say, one-third to one-half of all Earth’s species could be wiped out.

    ark

    As a result, efforts to protect species are ramping up as governments, scientists and nonprofit organizations try to build a modern version of Noah’s Ark. The new ark certainly won’t come in the form of a large boat, or even always a place set aside. Instead it is a patchwork quilt of approaches, including assisted migration, seed banks and new preserves and travel corridors based on where species are likely to migrate as seas rise or food sources die out.

    The questions are complex. What species do you save? The ones most at risk? Charismatic animals, such as lions or bears or elephants? The ones most likely to survive? The species that hold the most value for us?

    One initiative, the Intergovernmental Platform on Biodiversity and Ecosystem Services formed in 2012 by the governments of 121 countries, aims to protect and restore species in wild areas and to protect species like bees that carry out valuable ecosystem service functions in the places people live. Some three-quarters of the world’s food production depends primarily on bees.

    “We still know very little about what could or should be included in the ark and where,” said Walter Jetz, an ecologist at Yale involved with the project. Species are being wiped out even before we know what they are.

    Another project, the EDGE of Existence, run by the Zoological Society of London, seeks to protect the most unusual wildlife at highest risk. These are species that evolved on their own for so long that they are very different from other species. Among the species the project has helped to preserve are the tiny bumblebee bat and the golden-rumped elephant shrew.

    While the traditional approach to protecting species is to buy land, preservation of the right habitat can be a moving target, since it’s not known how species will respond to a changing climate.

    To complete the maps of where life lives, scientists have enlisted the crowd. A crowdsourcing effort called the Global Biodiversity Information Facility identifies and curates biodiversity data — such as photos of species taken with a smartphone — to show their distribution and then makes the information available online. That is especially helpful to researchers in developing countries with limited budgets. Another project, Lifemapper, at the University of Kansas Biodiversity Institute,

    “We know that species don’t persist long in fragmented areas and so we try and reconnect those fragments,” said Stuart L. Pimm, a professor of conservation at Duke University, and head of a nonprofit organization called SavingSpecies. One of his group’s projects in the Colombian Andes identified a forest that contains a carnivorous mammal that some have described as a cross between a house cat and a teddy bear, called an olinguito, new to science. Using crowd-sourced data, “we worked with local conservation groups and helped them buy land, reforest the land and reconnect pieces,” Dr. Pimm says.

    Coastal areas, especially, are getting scrutiny. Biologists in Florida, which faces a daunting sea level rise, are working on a plan to set aside land farther inland as a reserve for everything from the MacGillivray’s seaside sparrow to the tiny Key deer.

    To thwart something called “coastal squeeze,” a network of “migratory greenways” is envisioned so that species can move on their own away from rising seas to new habitat. “But some are basically trapped,” said Reed F. Noss, a professor of conservation biology at the University of Central Florida who is involved in the effort, and they will most likely need to be picked up and moved. The program has languished, but Amendment 1, on the ballot this November, would provide funding.

    One species at risk is the Florida panther. Once highly endangered, with just 20 individuals left, this charismatic animal has come back — some. But a quarter or more of its habitat is predicted to be under some three feet of water by 2100. Males will move on their own, but females will need help because they won’t cross the Caloosahatchee River. Experts hope to create reserves north of the river, and think at some point they will have to move females to new quarters.

    Protecting land between reserves is vital. The Yellowstone to Yukon Conservation Initiative, known as Y2Y, would protect corridors between wild landscapes in the Rockies from Yellowstone National Park to northern Canada, which would allow species to migrate.

    RESEARCHERS have also focused on “refugia,” regions around the world that have remained stable during previous swings of the Earth’s climate — and that might be the best bet for the survival of life this time around.

    A section of the Driftless Area encompassing northeastern Iowa and southern Minnesota, also known as Little Switzerland, has ice beneath some of its ridges. The underground refrigerator means the land never gets above 50 or so degrees and has kept the Pleistocene snail, long thought extinct, from disappearing there. Other species might find refuge there as things get hot.

    A roughly 250-acre refugia on the Little Cahaba River in Alabama has been called a botanical lost world, because of its wide range of unusual plants, including eight species found nowhere else. Dr. Noss said these kinds of places should be sought out and protected.

    Daniel Janzen, a conservation ecologist at the University of Pennsylvania who is working to protect large tracts in Costa Rica, said that to truly protect biodiversity, a place-based approach must be tailored to the country. A reserve needs to be large, to be resilient against a changing climate, and so needs the support of the people who live with the wild place and will want to protect it. “To survive climate change we need to minimize the other assaults, such as illegal logging and contaminating water,” he said. “Each time you add one of those you make it more sensitive to climate change.”

    The Svalbard Global Seed Vault, beneath the permafrost on an island in the Arctic Ocean north of mainland Norway, preserves seeds from food crops. Frozen zoos keep the genetic material from extinct and endangered animals. The Archangel Ancient Tree Archive in Michigan, meanwhile, founded by a family of shade tree growers, has made exact genetic duplicates of some of the largest trees on the planet and planted them in “living libraries” elsewhere — should something befall the original.

    In 2008, Connie Barlow, a biologist and conservationist, helped move an endangered conifer tree in Florida north by planting seedlings in cooler regions. Now she is working in the West. “I just assisted in the migration of the alligator juniper in New Mexico by planting seeds in Colorado,” she said. “We have to. Climate change is happening so fast and trees are the least capable of moving.”

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  • richardmitnick 4:44 am on September 13, 2014 Permalink | Reply
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    From The New York Times: “A Lost-and-Found Nomad Helps Solve the Mystery of a Swimming Dinosaur” 

    New York Times

    The New York Times

    SEPT. 11, 2014
    KENNETH CHANG

    The first bones came in a cardboard box. Nizar Ibrahim, a paleontologist, was in the Moroccan oasis town of Erfoud at the edge of the Sahara, returning from a dinosaur dig in the sands. Inside the box, brought to him by a nomad, were sediment-encrusted pieces more intriguing than anything he had found himself, including a blade-shaped bone with a reddish streak running through the cross section. He took the bones to a university in Casablanca.

    That was April 2008.

    The next year, he was in Italy visiting colleagues at the Milan Natural History Museum who showed him bones that seemed to be from Spinosaurus aegyptiacus, a strange-looking predatory dinosaur larger than Tyrannosaurus Rex that lived in northern Africa about 95 million years ago.

    He looked at the spines, part of a giant distinctive sail on the back of Spinosaurus. He saw a familiar red line — possibly a passageway for blood vessels long since decayed away — in the cross section of a bone. “My mind started racing,” he said.

    big
    An artist’s interpretation of how Spinosaurus aegyptiacus might have looked and how its size might have compared with that of a human. Credit Davide Bonadonna

    Amazingly, the pieces in Milan and those he had seen a year earlier and 1,200 miles away were from the same ancient skeleton.

    That was the start of an odyssey of diligence and serendipity that led to the unveiling on Thursday of a new skeleton of Spinosaurus. The largest known predatory dinosaur, growing to at least 50 feet in length, Spinosaurus is also the only dinosaur known to be a swimmer that spent a large fraction of its life in the water.

    “It’s probably the most bizarre dinosaur out there,” said Dr. Ibrahim, a graduate student when he saw the first bones, and now a postdoctoral researcher at the University of Chicago.

    Spinosaurus had been an intriguing mystery for decades. The original fossil of the dinosaur, discovered in Egypt a century ago and moved to a German museum, was destroyed during World War II, leaving paleontologists with little more than a few drawings to ponder.

    The new partial skeleton is of a Spinosaurus not fully grown, about 36 feet long. Its forelimbs were large and strong, with scythe-like claws; its hind legs were short, with paddle-shaped feet.

    In an article published online on Thursday by the journal Science, Dr. Ibrahim and an international team of colleagues describe the features that made the dinosaur well suited for swimming and feasting on giant fish that lived in the rivers there.

    Conical teeth in a crocodilian snout overlapped like a snare for trapping fish, and it had nostrils halfway up the skull so it could stick its snout into the water and still breathe.

    With its flat feet, Spinosaurus may have paddled like a duck. It had a long, flexible tail, which it may have used for propulsion. “It’s like a cross between an aquatic bird and a crocodile,” said Paul C. Sereno, a paleontologist at the University of Chicago who was part of the research team.

    On land, Spinosaurus was ungainly. The researchers calculated that its center of mass would have been too far forward for it to have stood easily on its hind legs, like other predator dinosaurs; instead, it ambled on all four legs.

    “It does add significantly to the strangeness,” said Matthew C. Lamanna, a paleontologist at the Carnegie Museum of Natural History in Pittsburgh, who was not involved with the research. He described the evidence for Spinosaurus’s semiaquatic existence as “quite convincing.”

    model
    A life-size model of Spinosaurus aegyptiacus made from polystyrene, resin and steel. The model was created from computer scans of fossils, images of lost bones and educated guesses using bones from related dinosaurs. Credit Mike Hettwer/National Geographic

    An exhibition on Spinosaurus opens Friday at the National Geographic Museum in Washington. The National Geographic Society provided financing for the research.

    The new findings may return prominence to Ernst Stromer, the German paleontologist who first described Spinosaurus aegyptiacus, meaning “Egyptian spine lizard.”

    Stromer’s fossil, mounted in the Bavarian State Collection of Paleontology in Munich, included the lower jaw and parts of the spine.

    In April 1944, the British Royal Air Force dropped a bomb on the museum, and Spinosaurus — and every Egyptian dinosaur fossil known at the time — burned.

    After that, some isolated bones of Spinosaurus were found, but nothing as complete as Stromer’s specimen. Some evidence, like the conical teeth, suggested Spinosaurus ate fish, but perhaps it just waded into a river and caught them like a grizzly bear.

    One fossil, uncovered in Morocco around 1975, had been thought to be part of the lower jaw of a crocodile, but a decade ago, Cristiano Dal Sasso of the Milan museum realized that interpretation was upside down. “There were too many bones to be the lower jaw,” he said.

    It was actually from the top half of a snout of a huge adult Spinosaurus.

    In 2008, an Italian geologist showed the new Spinosaurus bones to Dr. Dal Sasso, who then showed them to Dr. Ibrahim.

    But the scientists were missing crucial geological information about where the bones had been excavated.

    Dr. Ibrahim needed to find the nomad, so last year, he returned to the Erfoud area.

    A researcher helping him, Samir Zouhri, of University Hassan II Casablanca, asked how they would locate the man, whether Dr. Ibrahim had a name or an address or a phone number.

    “I didn’t want to disappoint my Moroccan colleague,” Dr. Ibrahim said, “so I told him I distinctly remember that the man had a mustache.”

    Dr. Zouhri did not seem impressed. “He basically thought that was not an adequate starting point for our wild-goose chase,” Dr. Ibrahim said.

    The search indeed proved fruitless, and they were sitting in a cafe, about to give up, when a mustachioed man walked past.

    It was the nomad who had showed Dr. Ibrahim the Spinosaurus bones five years earlier.

    “I had to run, because he was walking fast,” Dr. Ibrahim said. “He recognized me, and I convinced him to take us to the site.”

    The nomad, who Dr. Ibrahim said did not want public attention, remains anonymous.

    A few months later, Dr. Ibrahim and other members of the research team returned, uncovering more bone fragments and confirming that the fossils Dr. Ibrahim had seen in 2008 and those in Milan were all from the same dinosaur.

    The partial skeleton — about a quarter to a third of the animal, Dr. Sereno estimated — did not tell the whole story. The researchers made a three-dimensional digital model of the bones and added pieces scanned from other fossils like the Milan snout and the Stromer drawings.

    The new fossil also served as a Rosetta stone. A second dinosaur fossil of Stromer’s turned out to be a Spinosaurus; some of its bones matched those from the Moroccan find.

    Putting all the pieces together and making educated guesses from close relatives of Spinosaurus, the researchers came up with a complete skeleton and produced a life-size model for the National Geographic exhibition.

    The dearth of swimming dinosaurs has been something of a mystery. Among other groups of animals, some species did move from land to water — for instance, the mammals that evolved into whales. Even among birds, the modern-day descendants of dinosaurs, some like penguins and ducks spend copious time in the water.

    “Dinosaurs were landlubbers,” Dr. Sereno said. “Until this one.”

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  • richardmitnick 12:46 pm on September 3, 2014 Permalink | Reply
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    From Dennis Overbye at The New York Times: “The V838 Monocerotis Star Still Has Astronomers’ Heads Exploding” 

    New York Times

    The New York Times

    SEPT. 3, 2014
    Dennis Overbye

    For astronomers and aficionados of cosmic violence, an obscure star known as V838 Monocerotis has turned out to be a gift that has kept on giving for a long, long time.

    http://upload.wikimedia.org/wikipedia/commons/thumb/d/d3/V838_Mon_HST.jpg/600px-V838_Mon_HST.jpg838
    In January 2002, a dull star in an obscure constellation suddenly became 600,000 times more luminous than our Sun, temporarily making it the brightest star in our Milky Way galaxy. The mysterious star, called V838 Monocerotis, has long since faded back to obscurity. But observations by NASA’s Hubble Space Telescope of a phenomenon called a “light echo” around the star have uncovered remarkable new features. These details promise to provide astronomers with a CAT-scan-like probe of the three-dimensional structure of shells of dust surrounding an aging star.

    NASA Hubble Telescope
    NASA/ESA Hubble

    The star forms part of the shoulder of an imagined unicorn in the constellation Monoceros, 20,000 light-years away, and in January 2002, astronomers saw it blow up. Over the next few months, it became a million times as luminous as the sun and swelled in diameter to a billion miles, comparable to the orbit of Jupiter. It was briefly one of the most luminous stars in the galaxy.

    Astronomers are still arguing and speculating about what happened. Measurements of the star’s light output showed that the explosion happened in three stages, flaring and then dimming three times from January to March 2002.

    Some scientists have suggested that V 838 swallowed planets in its orbit. Others have proposed that V 838 was actually two stars orbiting each other, and that the explosions were a result of their atmospheres merging into a common envelope of gas.

    The answer could be relevant to our plight. Someday, a few billion years from now, the sun will run out of fuel and become a red giant,swallowing Mercury and frying the Earth and Venus.

    Whatever it was that made V 838 erupt, astronomers are still watching it go.

    The star, it turns out, is embedded in a cloud of dust trillions of miles across. Most likely, astronomers say, these wreaths of dust gave rise to V 838 perhaps four million years ago. They would usually be invisible, but the pulses of light traveling outward from the explosion have illuminated shells of dust previously kicked off the star. The Hubble Space Telescope has recorded images of these so-called light echoes, and viewing them in succession calls to mind the explosion of Darth Vader’s Death Star — except that in this case, nothing is moving but the outward-rushing light wave; the dust is standing still.

    As a result, the death of V 838 Monocerotis is giving astronomers a rare look at the circumstances that gave it birth. Dust to dust and ashes to ashes. So it goes.

    Nothing lasts forever, but in the universe, nothing is ever really gone, either. As the Columbia University astrophysicist Caleb Scharf pointed out in an essay on his blog recently, long after you and I are dead, the light reflected off our faces today will still be traveling across space, ever fainter with distance, but always there. For somebody with a big enough telescope somewhere, we will be immortal.

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  • richardmitnick 3:06 pm on August 28, 2014 Permalink | Reply
    Tags: , , New York Times,   

    From The New York Times: “Parasites Practicing Mind Control” 

    New York Times

    The New York Times

    AUG. 28, 2014
    Carl Zimmer

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

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

    image
    A microscopic cyst in the brain of a mouse containing thousands of Toxoplasma gondii parasites. New research has found that the parasite is able to exert a form of mind control by turning its host’s genes on and off. Credit Jitender P. Dubey/U.S.D.A.

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

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

    Experiments on rats and mice have shown that Toxoplasma alters their response to cat smells. Many infected rodents lose their natural fear of the scent. Some even seem to be attracted to it.

    Manipulating the behavior of a host is a fairly common strategy among parasites, but it’s hard to fathom how they manage it. A rat’s response to cat odor, for example, emerges from complex networks of neurons that detect an odor, figure out its source and decide on the right response in a given moment.

    Within each of the neurons in those networks, thousands of genes are producing proteins and other molecules essential for relaying all of the necessary information throughout the body. Simple Toxoplasma seems ill-equipped to take over such a complicated system.

    But a new study published in the journal Molecular Ecology hints that the parasite can do so by relying on an eerily elegant strategy. Think of the genes in a host as keys on a piano. Toxoplasma, it seems, simply plays some of the keys differently to produce a new melody.

    A rat is made up of lots of different kinds of cells, from the neurons in its brain to the bone-producing cells in its skeleton to the insulin-making cells in its pancreas. Yet all of them carry the same 20,000 genes. Depending on the function of a particular cell, some of its genes are switched on and others are shut down.

    Genes may be switched off, or silenced, by the attachment of molecular caps called methyl groups, a process called methylation. In order to switch a gene on again, the caps are removed.

    Methylation does more than just allow cells to develop into a variety of organs. It lets them change the way they work in response to signals from the outside. In the brain, for example, neurons rely on this process to lay down long-term memories and change how an animal responds to its environment.

    Ajai Vyas, a neurobiologist at Nanyang Technological University in Singapore, wondered if Toxoplasma might wreak changes on rats by changing methylation in the rat brain — an idea “just hiding in plain sight,” he said.

    In earlier research, Dr. Vyas and his colleagues had found that infected rats produced extra amounts of a neurotransmitter called arginine vasopressin. The neurotransmitter is manufactured by a small set of neurons buried in a structure of the brain called the medial amygdala.

    Perhaps, Dr. Vyas thought, the parasite switched on the gene for arginine vasopressin in those cells. To find out, he and his colleagues ran a series of tests.

    First they looked at the gene for arginine vasopressin in the medial amygdala of rats. In infected rats, they found, many of the molecular caps were missing, suggesting that Toxoplasma had “unsilenced” the gene in order to increase production of the neurotransmitter. The arginine vasopressin then might alter their response to cats.

    If that were true, Dr. Vyas reasoned, then counteracting the parasite’s strategy should change the rat’s behavior.

    He and his colleagues injected an extra supply of the molecular caps into infected rats. Some of the caps attached to the arginine vasopressin gene, and the rats became more fearful of the odor of cats.

    That experiment led Dr. Vyas to see if he could make the rats behave as if they were being controlled by parasites — but without the parasites.

    He and his colleagues removed molecular caps from the arginine vasopressin gene, mimicking what Toxoplasma might be doing to its hosts. The rats became reckless, feeling no fear at the whiff of cats.

    “The animals looked like they were infected, even though there was no parasite around,” said Dr. Vyas.

    “I think they could be on to something interesting,” said Michael Eisen, a biologist at the University of California, Berkeley, who has researched Toxoplasma in mice and was not involved in the new study. But he thought more experiments would have to be done to make a compelling case that the parasites really are using methylation to control their hosts.

    Kami Kim of Albert Einstein College of Medicine, who also was not involved in the study, was more enthusiastic about the research. She also suggested that the strategy may be not be uncommon. In a review published this spring in the American Journal of Pathology, Dr. Kim and her colleagues survey a number of species that may use methylation to turn host genes on and off.

    The bacteria that cause leprosy, for example, invade certain kinds of neurons and change some of their molecular caps. This methylation causes the neurons to change into stem cells much like those in an embryo. In this new state, the infected cells leave the nervous system and migrate through the body, spreading the bacteria with them.

    “It looks like it will be a general strategy used by pathogens,” said Dr. Kim.

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  • richardmitnick 2:42 pm on August 24, 2014 Permalink | Reply
    Tags: , , New York Times,   

    From The New York Times: “Methane Is Discovered Seeping From Seafloor Off East Coast, Scientists Say” 

    New York Times

    The New York Times

    AUG. 24, 2014
    HENRY FOUNTAIN

    Scientists have discovered methane gas bubbling from the seafloor in an unexpected place: off the East Coast of the United States where the continental shelf meets the deeper Atlantic Ocean.

    seeps
    Methane bubbles flow in small streams out of the sediment on an area of seafloor offshore Virginia north of Washington Canyon.

    The methane is emanating from at least 570 locations, called seeps, from near Cape Hatteras, N.C., to the Georges Bank southeast of Nantucket, Mass. While the seepage is widespread, the researchers estimated that the amount of gas was tiny compared with the amount released from all sources each year.

    In a paper published online Sunday in the journal Nature Geoscience, the scientists, including Adam Skarke of Mississippi State University and Carolyn Ruppel of the United States Geological Survey, reported evidence that the seepage had been going on for at least 1,000 years.

    They said the depths of the seeps suggested that in most cases the gas did not reach the atmosphere but rather dissolved in the ocean, where it could affect the acidity of the water, at least locally.

    But methane is a potent, if relatively short-lived, greenhouse gas, so the discovery should aid the study of an issue of concern to climate scientists: the potential for the release of huge stores of methane on land and under the seas as warming of the atmosphere and oceans continues.

    “It highlights a really key area where we can test some of the more radical hypotheses about climate change,” said John Kessler, a professor at the University of Rochester who was not involved in the research.

    Methane seeps occur in many places, but usually in areas that are tectonically active, like off the West Coast of the United States, or connect to deep petroleum basins, as in the Gulf of Mexico. The Atlantic margin, as the region where the shelf meets the deeper oceanic crust is known, is tectonically quiet, and most of the seeps are not thought to be linked to oil and gas deposits.

    “This is a large amount of methane seepage in an area we didn’t expect,” Dr. Skarke said. “That raises new questions for us.”

    Dr. Ruppel said that at about 40 of the seeps — those in water depths exceeding 3,300 feet — the methane may be migrating up through the sediments from deeper reservoirs of the gas. Further studies would be needed to confirm this, she said.

    If the gas is found to be originating from reservoirs, then oil companies could potentially be interested in determining whether the reservoirs can be tapped.

    But Dr. Ruppel said most of the seeps had been found in depths of about 800 to 2,000 feet, where the methane, which is produced by microbes, is most likely trapped in sediments near the seafloor , within cagelike molecules of ice called hydrates. Natural variability in water temperatures, caused by ocean circulation and other factors, may be warming these hydrates just enough to release the gas.

    Hydrates at such relatively shallow depths “are exquisitely sensitive to small changes in temperature,” she said. “You don’t have to change things very much to get the methane to come out.”

    Dr. Kessler, author of an article reviewing the findings in the same journal, said that because the Atlantic margin was unaffected by tectonic activity or other factors, it should prove to be a convenient location to conduct long-term studies of links between climate change and methane releases.

    “How will those release rates accelerate as bottom temperature warms, or how will they decelerate if there are some cooling events?” Dr. Kessler said. “We don’t really have all of the answers. But this is a great place to try to find them.”

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  • richardmitnick 2:57 pm on August 19, 2014 Permalink | Reply
    Tags: New York Times, ,   

    From The New York Times: “The Intelligent-Life Lottery” 

    New York Times

    The New York Times

    AUG. 18, 2014
    George Johnson

    Almost 20 years ago, in the pages of an obscure publication called Bioastronomy News, two giants in the world of science argued over whether SETI — the Search for Extraterrestrial Intelligence — had a chance of succeeding. Carl Sagan, as eloquent as ever, gave his standard answer. With billions of stars in our galaxy, there must be other civilizations capable of transmitting electromagnetic waves. By scouring the sky with radio telescopes, we just might intercept a signal.

    But Sagan’s opponent, the great evolutionary biologist Ernst Mayr, thought the chances were close to zero. Against Sagan’s stellar billions, he posed his own astronomical numbers: Of the billions of species that have lived and died since life began, only one — Homo sapiens — had developed a science, a technology, and the curiosity to explore the stars. And that took about 3.5 billion years of evolution. High intelligence, Mayr concluded, must be extremely rare, here or anywhere. Earth’s most abundant life form is unicellular slime.

    Since the debate with Sagan, more than 1,700 planets have been discovered beyond the solar system — 700 just this year. Astronomers recently estimated that one of every five sunlike stars in the Milky Way might be orbited by a world capable of supporting some kind of life.

    That is about 40 billion potential habitats. But Mayr, who died in 2005 at the age of 100, probably wouldn’t have been impressed. By his reckoning, the odds would still be very low for anything much beyond slime worlds. No evidence has yet emerged to prove him wrong.

    Maybe we’re just not looking hard enough. Since SETI began in the early 1960s, it has struggled for the money it takes to monitor even a fraction of the sky. In an online essay for The Conversation last week, Seth Shostak, the senior astronomer at the SETI Institute, lamented how little has been allocated for the quest — just a fraction of NASA’s budget.

    “If you don’t ante up,” he wrote, “you will never win the jackpot. And that is a question of will.”

    Three years ago, SETI’s Allen Telescope Array in Northern California ran out of money and was closed for a while. Earlier this month, it was threatened by wildfire — another reminder of the precariousness of the search.

    Allen Telescope Array
    Allen Telescope Array

    It has been more than 3.5 billion years since the first simple cells arose, and it took another billion years or so for some of them to evolve and join symbiotically into primitive multicellular organisms. These biochemical hives, through random mutations and the blind explorations of evolution, eventually led to creatures with the ability to remember, to anticipate and — at least in the case of humans — to wonder what it is all about.

    Every step was a matter of happenstance, like the arbitrary combination of numbers — 3, 12, 31, 34, 51 and 24 — that qualified a Powerball winner for a $90 million prize this month. Some unknowing soul happened to enter a convenience store in Rifle, Colo., and — maybe with change from buying gasoline or a microwaved burrito — purchase a ticket just as the machine was about to spit out those particular numbers.

    According to the Powerball website, the chance of winning the grand prize is about one in 175 million. The emergence of humanlike intelligence, as Mayr saw it, was about as likely as if a Powerball winner kept buying tickets and — round after round — hit a bigger jackpot each time. One unlikelihood is piled on another, yielding a vanishingly rare event.

    In one of my favorite books, “Wonderful Life,” Stephen Jay Gould celebrated what he saw as the unlikelihood of our existence. Going further than Mayr, he ventured that if a slithering creature called Pikaia gracilens had not survived the Cambrian extinction, about half a billion years ago, the entire phylum called Chordata, which includes us vertebrates, might never have existed.

    Gould took his title from the Frank Capra movie in which George Bailey gets to see what the world might have been like without him — idyllic Bedford Falls is replaced by a bleak, Dickensian Pottersville.

    For Gould, the fact that any of our ancestral species might easily have been nipped in the bud should fill us “with a new kind of amazement” and “a frisson for the improbability of the event” — a fellow agnostic’s version of an epiphany.

    “We came this close (put your thumb about a millimeter away from your index finger), thousands and thousands of times, to erasure by the veering of history down another sensible channel,” he wrote. “Replay the tape a million times,” he proposed, “and I doubt that anything like Homo sapiens would ever evolve again. It is, indeed, a wonderful life.”

    Other biologists have disputed Gould’s conclusion. In the course of evolution, eyes and multicellularity arose independently a number of times. So why not vertebrae, spinal cords and brains? The more bags of tricks an organism has at its disposal, the greater its survival power may be. A biological arms race ensues, with complexity ratcheted ever higher.

    But those occasions are rare. Most organisms, as Daniel Dennett put it in “Darwin’s Dangerous Idea,” seem to have “hit upon a relatively simple solution to life’s problems at the outset and, having nailed it a billion years ago, have had nothing much to do in the way of design work ever since.” Our appreciation of complexity, he wrote, “may well be just an aesthetic preference.”

    In Five Billion Years of Solitude, by Lee Billings, published last year, the author visited Frank Drake, one of the SETI pioneers.

    “Right now, there could well be messages from the stars flying right through this room,” Dr. Drake told him. “Through you and me. And if we had the right receiver set up properly, we could detect them. I still get chills thinking about it.”

    He knew the odds of tuning in — at just the right frequency at the right place and time — were slim. But that just meant we needed to expand the search.

    “We’ve been playing the lottery only using a few tickets,” he said.

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  • richardmitnick 7:50 am on August 14, 2014 Permalink | Reply
    Tags: , , , , New York Times   

    From The New York Times: “Our Microbiome May Be Looking Out for Itself” 

    New York Times

    The New York Times

    AUG. 14, 2014
    Carl Zimmer

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

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

    microbe
    A highly magnified view of Enterococcus faecalis, a bacterium that lives in the human gut. Microbes may affect our cravings, new research suggests. Credit Centers for Disease Control and Prevention

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

    Maybe the microbiome is our puppet master.

    “One of the ways we started thinking about this was in a crime-novel perspective,” said Carlo C. Maley, an evolutionary biologist at the University of California, San Francisco, and a co-author of the new paper. What are the means, motives and opportunity for the microbes to manipulate us? They have all three.

    The idea that a simple organism could control a complex animal may sound like science fiction. In fact, there are many well-documented examples of parasites controlling their hosts.

    Some species of fungi, for example, infiltrate the brains of ants and coax them to climb plants and clamp onto the underside of leaves. The fungi then sprout out of the ants and send spores showering onto uninfected ants below.

    How parasites control their hosts remains mysterious. But it looks as if they release molecules that directly or indirectly can influence their brains.

    Our microbiome has the biochemical potential to do the same thing. In our guts, bacteria make some of the same chemicals that our neurons use to communicate with one another, such as dopamine and serotonin. And the microbes can deliver these neurological molecules to the dense web of nerve endings that line the gastrointestinal tract.

    A number of recent studies have shown that gut bacteria can use these signals to alter the biochemistry of the brain. Compared with ordinary mice, those raised free of germs behave differently in a number of ways. They are more anxious, for example, and have impaired memory.

    Adding certain species of bacteria to a normal mouse’s microbiome can reveal other ways in which they can influence behavior. Some bacteria lower stress levels in the mouse. When scientists sever the nerve relaying signals from the gut to the brain, this stress-reducing effect disappears.

    Some experiments suggest that bacteria also can influence the way their hosts eat. Germ-free mice develop more receptors for sweet flavors in their intestines, for example. They also prefer to drink sweeter drinks than normal mice do.

    Scientists have also found that bacteria can alter levels of hormones that govern appetite in mice.

    Dr. Maley and his colleagues argue that our eating habits create a strong motive for microbes to manipulate us. “From the microbe’s perspective, what we eat is a matter of life and death,” Dr. Maley said.

    Different species of microbes thrive on different kinds of food. If they can prompt us to eat more of the food they depend on, they can multiply.

    Microbial manipulations might fill in some of the puzzling holes in our understandings about food cravings, Dr. Maley said. Scientists have tried to explain food cravings as the body’s way to build up a supply of nutrients after deprivation, or as addictions, much like those for drugs like tobacco and cocaine.

    But both explanations fall short. Take chocolate: Many people crave it fiercely, but it isn’t an essential nutrient. And chocolate doesn’t drive people to increase their dose to get the same high. “You don’t need more chocolate at every sitting to enjoy it,” Dr. Maley said.

    Perhaps, he suggests, the certain kinds of bacteria that thrive on chocolate are coaxing us to feed them.

    John F. Cryan, a neuroscientist at University College Cork in Ireland who was not involved in the new study, suggested that microbes might also manipulate us in ways that benefited both them and us. “It’s probably not a simple parasitic scenario,” he said.

    Research by Dr. Cryan and others suggests that a healthy microbiome helps mammals develop socially. Germ-free mice, for example, tend to avoid contact with other mice.

    That social bonding is good for the mammals. But it may also be good for the bacteria.

    “When mammals are in social groups, they’re more likely to pass on microbes from one to the other,” Dr. Cryan said.

    “I think it’s a very interesting and compelling idea,” said Rob Knight, a microbiologist at the University of Colorado, who was also not involved in the new study.

    If microbes do in fact manipulate us, Dr. Knight said, we might be able to manipulate them for our own benefit — for example, by eating yogurt laced with bacteria that would make use crave healthy foods.

    “It would obviously be of tremendous practical importance,” Dr. Knight said. But he warned that research on the microbiome’s effects on behavior was “still in its early stages.”

    The most important thing to do now, Dr. Knight and other scientists said, was to run experiments to see if microbes really are manipulating us.

    Mark Lyte, a microbiologist at the Texas Tech University Health Sciences Center who pioneered this line of research in the 1990s, is now conducting some of those experiments. He’s investigating whether particular species of bacteria can change the preferences mice have for certain foods.

    “This is not a for-sure thing,” Dr. Lyte said. “It needs scientific, hard-core demonstration.”

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