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  • richardmitnick 11:17 am on February 14, 2017 Permalink | Reply
    Tags: A Race to Document Rare Plants Before These Cliffs Are Ground to Dust, , , KAMPONG TRACH MOUNTAIN in Cambodia, Karsts, NYT   

    From NYT: “A Race to Document Rare Plants Before These Cliffs Are Ground to Dust” 

    New York Times

    The New York Times

    FEB. 13, 2017

    The chief of the Forestry Association of Kampong Trach, Ken Sam An, left, Neang Thy, a herpetologist at the Cambodian Ministry of Environment and Lorn Sokchan, a Cambodian entomology researcher, exploring the interior of a cave known as the “Bat Cave.” Credit Omar Havana for The New York Times

    KAMPONG TRACH MOUNTAIN, Cambodia — Millions of years ago, a cluster of coral reefs stood firm here as the water receded, leaving them surrounded by the marshy, mangrove-studded Mekong Delta.

    Today, these reefs have been carved by the wind and rain into spiky limestone cliffs known as karsts that stand stark against the Cambodian landscape, even as the lowland rain forest around them has been denuded by centuries of intensive rice cultivation and logging.

    The karsts are full of nooks and crannies that have nurtured highly specialized plants and animals found nowhere else. They are also important to humans, studded with small altars and temples that are thought to be homes to neak ta, landscape spirits in the local animist pantheon.

    Soon, they will be gone.

    A small group of scientists are now racing to document rare plant life in these limestone karsts before local companies quarry them to dust and grind them up for production of the cement that is fueling this country’s building boom.

    Most of the wood in mainland Southeast Asia has already been logged to support the region’s rapid economic growth and its relentless appetite for luxury hardwood. (Nearly all the forest cover in neighboring Thailand is gone and Cambodia is now experiencing the fastest acceleration of forest loss in the world, despite a putative ban on logging.) Cement and concrete are also in high demand, so the karsts are next in line.

    “They are the last refuges of what made it to the Mekong Delta, natural harbors for a specialized kind of vegetation that has very little timber value, sanctuaries of rare species,” said J. Andrew McDonald, a botany professor at the University of Texas Rio Grande Valley, who is spearheading the plant collection project with support from the International Union for Conservation of Nature.

    The limestone habitats can act as “arks” of biodiversity that replenish surrounding areas after ecological damage. But they are so complex that, once destroyed, they can never themselves be recreated.

    They have scant access to water for six months of the year, creating a harsh, alkaline environment that has led to the evolution of desertlike flora in the middle of a hot, wet country. Dr. McDonald calls them “Dr. Seuss-type plants,” ones that look and behave like cactuses and succulent desert flora, but are related to the local tropical foliage.

    There are fat, succulent grapevines, fig trees with thick, waxy leaves, and false cactuses — as spiky and segmented as those that grow in the American desert, but actually members of the poinsettia family that evolved independently. Perhaps most unusual are the large, phallic flowers known as Amorphophallus, which look like a cross between an orchid and a Muppet’s nose.

    The toughest and most determined plants nestle themselves into the fissures and cracks atop the karsts, or cling to the razor-sharp outcroppings exposed to the wind and sun. More delicate tropical flowers — feathery orchids and little white touch-me-nots — make homes in the grottoes within, sucking up the water that drips through the limestone. At the bottom, the karsts are like Swiss cheese, full of water-carved pockets that open up into large underground lakes where rare bats feed and mushrooms grow.

    Over four days in January, armed with rice sacks and pruning shears, Dr. McDonald and several colleagues and students pored over two linked karsts, Phnom Kampong Trach and Phnom Domrei, climbing atop their jagged surfaces and passing all the way through them in a network of caves.

    Dr. McDonald, 62, is a plain-spoken Texan with a mystical streak who spends his spare time working on a 1,000-page manuscript on the religious iconography of the lotus. He can clamber up and down the slippery, precipitous karsts like one of the mountain goats that live here (another anomaly in flat Cambodia).

    “Fruits! Flowers! Fruits! Flowers! Eyes on the prize!” he chanted, trying to urge the group to collect specimens. Among the group was a pair of technophilic Vietnamese botanists lugging huge cameras who kept falling behind to take close-up shots of the foliage.

    At first glance, Dr. McDonald was excited by a novel-looking parasitic Balanaflora with droopy, bulbous male flowers (“they latch onto this tree and have sex there”) and a huge, feathery white blossom at the edge of a grotto. It was an unusual variant of dogbane, a nocturnal plant with a dangling structure that dusts the underside of a visiting moth or bat with pollen. “I’ve never seen an Apocynaceae with an irregular flower like that!” he exclaimed, before gingerly tossing the specimens, one by one, across a huge fissure to the safe hands of a waiting colleague.

    Ultimately, over the course of two botanical excursions, the group found more than 130 species of vascular plants native to this patch of limestone, a comparatively rich assortment, including some thought to be new to science: an Amorphophallus and another related flower, a new type of jasmine, and a member of the coffee family.

    Kampot Cement (SCG) Quarry in Cambodia Video by Tony Whitten

    Along with discovering these rare species, the scientists wanted to document the karsts’s biodiversity and the ways in which different parts of the habitat work together before it is gone. Ultimately, they hope to persuade the government to make these two karsts a protected area and declare them off-limits to future cement quarrying.

    The team was accompanied by a representative of the Ministry of Environment who was to report back to his superiors on the merits of the protection proposal. The ministry is bereft of plant experts, so they sent Neang Thy, the country’s leading herpetologist, instead.

    “The vegetation you see here, you may not see anywhere else,” he said. “If it is destroyed, that is a problem.”

    Andrew McDonald, a researcher at the University of Texas Rio Grande Valley, holding an unknown flower specimen that he found on the Kampot Karst. Credit Omar Havana for The New York Times

    He said he hoped future trips would allow for a survey of animal life in the karsts. Similar limestone formations in Vietnam and Thailand are home to novel species of fish, lizards, crabs and insects that adapt to life inside caves by becoming pale, blind and wingless, often looking very different from their aboveground brethren.

    There are highly biodiverse karsts scattered across Southeast Asia, from Vietnam to Borneo, like desert islands surrounded by oceans of tropical rain forest. The destruction of karsts at the hands of cement companies, developers and tourists is a problem throughout the region.

    But it is particularly acute here, where government regulation is lax and the state of local scientific knowledge fledgling.

    “They are threatened, as they are elsewhere, but the difference is that there is almost nothing known about the biodiversity of the hills” in Cambodia, said Tony Whitten, the international regional director for Fauna and Flora International’s Asia-Pacific division, who coedited a book on the subject — “Biodiversity and Cultural Property in the Management of Limestone Resources: Lessons from East Asia.”

    Cambodia has almost no botanists and the study of plants in the country came to a standstill from 1970 to 1992 during an extended period of war and unrest punctuated by the trauma of the Khmer Rouge takeover from 1975 to 1979.

    The country’s main herbarium is a single room at the Royal University of Phnom Penh. It houses about 12,000 specimens, many of which have not been inventoried and are simply piling up on shelves. They are meant to be kept cool and dry by two air-conditioners, but one air-conditioner is broken and there is no money to fix it.

    “You talk about a herbarium in another country and it should be very big, but this is just one room,” said Ith Saveng, who runs the university’s Center for Biodiversity Conservation. “We hope to expand to another room within the next two years.”

    Rare plants found in karsts have to be shipped to Vietnam so better-trained scientists can do the precise work of matching species to species.

    In Kampot, the scientists were led through some of the more treacherous cave networks by Ken Sam An, a 61-year-old native of a village just below the Phnom Kampong Trach karst. He knows more about these caves than just about anyone else. As a teenager, he watched as the Viet Cong hid in the caves, resulting in retaliatory bombing campaigns by the United States that drove the population to flee. Soon, ultra-Communist rebels swept into the area and he was conscripted into a Khmer Rouge youth unit.

    Members of the team led by Dr. McDonald, center, prepare newspapers to dry the species collected during their expedition at the Kampot Karst, while Luu Hong Truong of the Vietnam Academy of Science and Technology takes a photograph of a specimen. Credit Omar Havana for The New York Times

    Whatever scientific research apparatus still existed was totally dismantled by the victorious Khmer Rouge government, which declared higher education anathema and sent city dwellers back to the land to work as rice farmers and dam builders. Although Mr. Ken Sam An possesses vast botanical knowledge, he has not attended school since the sixth grade.

    After the fall of the Khmer Rouge in 1979, Mr. Ken Sam An spent years working for a limestone quarrying company, but now he serves on a local committee that tries to preserve the karsts, urging local residents to stop stripping them and chopping off rocks to sell.

    “I tell them, ‘If you break the mountain, it’s not good for the environment, and if you work in tourism you can come and sell things to the tourists instead of breaking rocks.’”

    A far bigger risk is large-scale limestone quarrying by companies producing cement. Kampot (K) Cement, a joint venture between the well-connected local company Khaou Chuly Group and the Thai cement manufacturer Siam Cement, has claim to large karsts in the area. The site is churning out a million tons of cement a year.

    Another local company, Chip Mong, formed a partnership with a different Thai firm and started building a $262 million factory in the area last year, with the goal of producing 1.5 million tons a year. This is still not enough to slake Cambodia’s growing thirst for cement, expected to reach five million tons this year.

    Bags from the Kampot Cement company outside a hut in Chrokchey Village. The company is quarrying a limestone hill in the background. Credit Omar Havana for The New York Times

    The cement firms have also spawned a mini-land boom in Kampot, where prices have risen thirtyfold in the last decade, according to locals. In interviews, the inhabitants complained that rocks being blasted off the mountains were falling on their homes and angering the local neak ta, who had to be propitiated with offerings of roast pigs.

    Dr. Whitten said he had tried for years, fruitlessly, to determine whether environmental impact assessments had been carried out before cement companies were given permission to dynamite the karsts. The Ministry of Mines and Energy, which is responsible for granting and regulating concessions for limestone quarrying, declined to comment.

    Even when environmental assessments are conducted, they often focus on large mammals, overlooking plants and small species that are highly endemic to certain caves. The slimy, squishy invertebrates and strange plants that live in karsts can be a hard sell to donors, who prefer what are known as “charismatic megafauna”— cute, easy-to-anthropomorphize animals like elephants, tigers and dolphins that appeal to the public.

    “It takes a botanist to appreciate the charisma of a plant,” Dr. McDonald said.

    The karsts his group wants to protect have the advantage of already being a minor tourist attraction, with a Buddhist pagoda sprawling out at their feet, small shrines nestled into the caves and a set of stone steps leading down to an underground pond where monks bathe.

    “They are linked together — people come to pray at the pagoda and then they always go to the cave,” Mr. Ken Sam An said. It is also common for him and his neighbors to make offerings to the spirits believed to inhabit the karsts, going to different caves on different holy days. Each one is believed to be the domain of a different neak ta.

    Mr. Thy climbing at Kampot Karst. “The vegetation you see here, you may not see anywhere else,” he said. “If it is destroyed, that is a problem.” Credit Omar Havana for The New York Times

    Mr. Ken Sam An can rattle off their names as if they are members of his extended family: “There’s the Red Neck spirit, the Eight Heads spirit, the spirit of the 100 Rice Fields, the spirit of the Monk Who Lives in the Jungle, the White Elephant spirit, the Dragon’s Mouth spirit, the Magic Boy spirit, the Reincarnated Grandmother spirit and the Magic Mushroom spirit.”

    Altogether, the caves are thought by locals to be chambers in the stomach of a dragon that beached here when an ancient sea receded thousands of years ago — a tale not entirely different from the stories told by geologists and botanists.

    “This is what we lose when they take out a mountain,” Dr. McDonald said.

    See the full article here .

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  • richardmitnick 8:24 am on February 7, 2017 Permalink | Reply
    Tags: , Cholera, International Center for Diarrheal Disease Research known as the ICDDRB in Dhaka, , NYT, Vibrio cholerae   

    From NYT: “Turning the Tide Against Cholera” 

    New York Times

    The New York Times

    FEB. 6, 2017

    Two hundred years ago, the first cholera pandemic emerged from these tiger-infested mangrove swamps.


    It began in 1817, after the British East India Company sent thousands of workers deep into the remote Sundarbans, part of the Ganges River Delta, to log the jungles and plant rice. These brackish waters are the cradle of Vibrio cholerae, a bacterium that clings to human intestines and emits a toxin so virulent that the body will pour all of its fluids into the gut to flush it out.

    Water loss turns victims ashen; their eyes sink into their sockets, and their blood turns black and congeals in their capillaries. Robbed of electrolytes, their hearts lose their beat. Victims die of shock and organ failure, sometimes in as little as six hours after the first abdominal rumblings.

    Cholera probably had festered here for eons. Since that first escape, it has circled the world in seven pandemic cycles that have killed tens of millions.

    A fisherman in August in the Sundarbans, where cholera first emerged.

    Artists of the 19th century often depicted it as a skeleton with a scythe and victims heaped at its feet. It stalked revelers at a masked ball in Heinrich Heine’s “Cholera in Paris” and kills the protagonist in Thomas Mann’s “Death in Venice.” Outbreaks forced London, New York and other cities to create vast public water systems, transforming civic life.

    Today cholera garners panicky headlines when it strikes unexpectedly in places like Ethiopia or Haiti. But it is a continuing threat in nearly 70 countries, where more than one billion people are at risk.

    Now, thanks largely to efforts that began in cholera’s birthplace, a way to finally conquer the long-dreaded plague is in sight.

    A treatment protocol so effective that it saves 99.9 percent of all victims was pioneered here. The World Health Organization estimates that it has saved about 50 million lives in the past four decades.

    A child was treated at the International Center for Diarrheal Disease Research in Dhaka, Bangladesh, in August. It is the world’s largest diarrhea hospital.

    Just as important, after 35 years of work, researchers in Bangladesh and elsewhere have developed an effective cholera vaccine. It has been accepted by the W.H.O. and stockpiled for epidemics like the one that struck Haiti in 2010. Soon, there may be enough to begin routine vaccination in countries where the disease has a permanent foothold.

    Merely creating that stockpile — even of a few million doses — profoundly improved the way the world fought cholera, Dr. Margaret Chan, secretary general of the W.H.O., said last year. Ready access to the vaccine has made countries less tempted to cover up outbreaks to protect tourism, she said.

    That has sped up emergency responses and attracted more vaccine makers, lowering costs. “More cholera vaccines have been deployed over the last two years than in the previous 15 years combined,” Dr. Chan said.

    A Revolution in Recovery

    The treatment advances relied heavily on research and testing done at the International Center for Diarrheal Disease Research, known as the ICDDR,B, in Dhaka.

    A mother enters ICDDR,B with her child. The facility treats 220,000 patients a year.

    Although Dhaka may not be the first place one might look to find a public health revolution, the center is famous among experts in gut diseases.

    While its upper levels are quiet and scholarly, the center’s ground floor is the world’s largest diarrhea hospital. Its vast wards treat 220,000 patients a year, almost all of whom recover within 36 hours. Doctors there save hundreds of lives a day.

    The ICDDR,B was originally the Cholera Research Laboratory, founded in 1960 by the United States as part of that era’s “soft diplomacy.” Research hospitals were built in friendly countries both to save lives locally and to act as sentinels for diseases that might threaten America.

    The wards, which in the rainy season extend into circus-size tents in the parking lot, contain long rows of “cholera cots.” On each iron or wood frame is a plastic sheet with a hole in the middle. A bucket beneath the hole catches diarrhea, while another beside the cot fills with vomit. An IV pole completes the setup.

    The ICDDR,B wards contain long rows of “cholera cots.” Each has a plastic sheet with a hole in the middle. A bucket beneath the hole catches diarrhea and another is placed next to the cot for vomit. An IV pole completes the setup. Usually, the only patients who stay long in the hospital are malnourished infants.

    Defying expectations, the ward smells only of the antiseptic that the floors are constantly mopped with.

    Patients with severe watery diarrhea arrive around the clock, many of them carried in — limp, dehydrated and barely conscious — by friends or family. A nurse sees each one immediately, and those close to death get an IV line inserted within 30 seconds.

    It contains a blend of glucose, electrolytes and water. Cholera spurs the intestines to violently flush themselves, but it does not actually damage the gut cells. If the fluid is replaced and the bacteria flushed out or killed by antibiotics, the patient is usually fine.

    Within hours, patients start to revive. As soon as they can swallow, they get an antibiotic and start drinking a rehydration solution. Most walk out within a day. The techniques perfected here are so effective that the ICDDR,B has sent training teams to 17 cholera outbreaks in the past decade.

    Usually, the only patients who stay long in the hospital are infants so malnourished that another bout of diarrhea would kill them. They live for up to a month in a separate ward with their mothers, who are taught how to cook nutritious porridges from the cheapest lentils, squash, onions, greens and oil.

    Only about 20 percent of the patients at the center have cholera. The rest usually have rotavirus, salmonella or E. coli. The same therapy saves them all, but the cholera cases are more urgent because these patients plummet so precipitously toward death.

    “I thought I was dying,” Mohammed Mubarak, a gaunt 26-year-old printing press worker, said one afternoon from his cot. His roommates had carried him in at 7 that morning, unconscious and with no detectable pulse.

    Now, after six liters of intravenous solution, he was still weak but able to sit up and drink the rehydration solution and eat bits of bread and banana.

    “His stool is changing from rice-water to green, so he is recovering,” said Momtaz Begum, the ward nurse who monitors the buckets and makes sure patients take in as much liquid as they lose.

    Mr. Mubarak had first fallen ill at about 2 a.m., a few hours after he drank tap water with his dinner. “Usually I drink safe water, filtered water,” he explained. “But I drank the city water last night. I think that is what did this.”

    Cholera, born in the swamps, arrived long ago in Dhaka. The city is home to more that 15 million, and a third of the population lives in slums. In some places, water pipes made of rubbery plastic are pierced by illegal connections that suck in sewage from the gutters they traverse and carry pathogens down the line to new victims, like Mr. Mubarak.

    The Korail slum in Dhaka. In some slums, water pipes suck in sewage from gutters. Cholera is a constant threat to hundreds of millions of people lacking safe drinking water in China, India, Nigeria and many other countries.

    Vibrio cholerae travels from person to person via fecal matter. In 1854, the epidemiologist John Snow famously traced cases to a single well dug near a cesspit in which a mother had washed the diaper of a baby who died of cholera and nd convinced officials to remove the well’s pump handle.

    Because cholera is a constant threat to hundreds of millions of people lacking safe drinking water in China, India, Nigeria and many other countries, scientists have long sought a more powerful weapon: a cheap, effective vaccine.

    Now they have one.

    Preventing a Plague

    Injected cholera vaccines were first invented in the 1800s and were long required for entry into some countries. But many scientists suspected they did not work, and in the 1970s studies overseen by the ICDDR,B confirmed that.

    In the 1980s, a Swedish scientist, Dr. Jan Holmgren, invented an oral vaccine that worked an impressive 85 percent of the time. But it was expensive to make and had to be drunk with a large glass of buffer solution to protect it from stomach acid.

    Transporting tanks of buffer was impractical. Making matters worse, it was fizzy, and poor Bangladeshi children who had never tasted soft drinks would spit it out as soon as it tickled their noses.

    In 1986, a Vietnamese scientist, Dr. Dang Duc Trach, asked for the formula, believing he could make a bufferless version. Dr. Holmgren and Dr. John D. Clemens, an American vaccine expert who at the time was a research scientist for the ICDDR,B, obliged.

    Jan Holmgren, Dr. Dang Duc Trach (his friends called him Dr. Chuck) and Dr. Clemens in a photo taken while on a vacation in Switzerland.

    “This isn’t an elegant vaccine — it’s just a bunch of killed cells, technology that’s been around since Louis Pasteur,” said Dr. Clemens, who is now the ICDDR,B’s executive director.

    He and Dr. Holmgren lost touch with Dr. Dang, largely because of Vietnam’s isolation in those days. But seven years later, Dr. Dang notified them that he had made a new version of the vaccine. He had tested it on 70,000 residents of Hue, in central Vietnam, and had found it to be 60 percent effective.

    Although his was not as effective as Dr. Holmgren’s, it cost only 25 cents a dose. If enough people in an area can be made immune through vaccination, outbreaks often stop spontaneously.

    In 1997, Vietnam became the first — and thus far, only — country to provide cholera vaccine to its citizens routinely, not just in emergencies. Cases dropped sharply, according to a 2014 study, and in 2003 cholera vanished from Hue, where the campaign focused most heavily.

    But Dr. Dang had not conducted a classic clinical trial, and Vietnam’s vaccine factory did not meet W.H.O. standards, so no United Nations agency was allowed to buy his vaccine.

    “This isn’t an elegant vaccine — it’s just a bunch of killed cells, technology that’s been around since Louis Pasteur,” said Dr. Clemens, center.

    Because no pharmaceutical company had an incentive to pay for trials or factories, his invention languished in “the valley of death” — the expensive gap between a product that works in a lab and a factory-made version safe for millions.

    In 1999, Dr. Clemens approached what is now the Bill & Melinda Gates Foundation, which was just getting organized.

    “They were literally operating out of a basement then,” he said. “I got a letter from Bill Gates Sr. It was very relaxed, sort of, ‘Here’s $40 million. Would you mind sending me a report once in a while?’

    “But without that,” Dr. Clemens continued, “this wouldn’t have seen the light of day.”

    With that money, Dr. Clemens reformulated Dr. Dang’s vaccine, conducted a successful clinical trial in Calcutta and found an Indian company, Shantha Biotechnics, that could make it to W.H.O. standards.

    Rolled out in 2009 under the name Shanchol, it came in a vial about the size of a chess rook, needed no buffer and cost less than $2 a dose. Even so, there was little interest, even from the W.H.O.

    The vaccine lacked the publicity campaign that pharmaceutical companies throw behind commercial products, and “cholera ward care” was saving many lives — when it could be organized. The new vaccine was not used in a cholera outbreak in Zimbabwe in 2009, or initially in Haiti’s explosive outbreak in 2010.

    The “valley of death” lengthened: Without customers, Shantha could not afford to build a bigger factory. The impasse was broken only when Dr. Paul Farmer, a founder of Partners in Health, which has worked in central Haiti since 1987, began publicly berating the W.H.O. for not moving faster.

    The vaccine is now used in Haiti, and has been deployed in outbreaks in Iraq, South Sudan and elsewhere. A second version, Euvichol, from South Korea, was approved in 2015.

    And later this year, Bangladesh — where it all began — hopes to begin wiping out its persistent cholera. A local company has begun making a domestic version of the vaccine, called Vaxchol. Dr. Firdausi Qadri, a leading ICDDR,B researcher, estimated last year that success there would require almost 200 million doses.

    An infant cholera patient with his mother in the general hospital ward at the ICDDR,B.

    The world finally has a vaccine that, with routine administration, could end one of history’s great scourges. But what will happen is still hazy.

    With 1.4 billion people at risk, the potential cost of vaccination in cholera-endemic countries is enormous. And the disease tends to move, surging and vanishing among the many causes of diarrhea.

    Even Bill Gates, who paid for much of the research, has asked: “We actually have a cholera vaccine, but where should it be used?”

    Looking back on his long struggle to prove the vaccine’s value, and then to win acceptance, Dr. Clemens offered an explanation that blended wistfulness and cynicism. “We’re probably not bad scientists,” he said, “but we were lousy advocates.

    “If this disease had been in American kids, there would have been trials as fast as the Sabin polio vaccine.”

    See the full article here .

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  • richardmitnick 9:07 am on January 24, 2017 Permalink | Reply
    Tags: Altered DNA, Ants, , , Hypersociality, NYT   

    From NYT: “Gene-Modified Ants Shed Light on How Societies Are Organized” 

    New York Times

    The New York Times

    JAN. 23, 2017

    Dr. Daniel Kronauer, shown in a double exposure, above, studies ants with altered DNA in order to understand complex biological systems. Credit Béatrice de Géa for The New York Times

    Whether personally or professionally, Daniel Kronauer of Rockefeller University is the sort of biologist who leaves no stone unturned. Passionate about ants and other insects since kindergarten, Dr. Kronauer says he still loves flipping over rocks “just to see what’s crawling around underneath.”

    In an amply windowed fourth-floor laboratory on the east side of Manhattan, he and his colleagues are assaying the biology, brain, genetics and behavior of a single species of ant in ambitious, uncompromising detail. The researchers have painstakingly hand-decorated thousands of clonal raider ants, Cerapachys biroi, with bright dots of pink, blue, red and lime-green paint, a color-coded system that allows computers to track the ants’ movements 24 hours a day — and makes them look like walking jelly beans.

    The scientists have manipulated the DNA of these ants, creating what Dr. Kronauer says are the world’s first transgenic ants. Among the surprising results is a line of Greta Garbo types that defy the standard ant preference for hypersociality and instead just want to be left alone.

    The researchers also have identified the molecular and neural cues that spur ants to act like nurses and feed the young, or to act like queens and breed more young, or to serve as brutal police officers, capturing upstart nestmates, spread-eagling them on the ground and reducing them to so many chitinous splinters.

    Dr. Kronauer, who was born and raised in Germany and just turned 40, is tall, sandy-haired, blue-eyed and married to a dentist. He is amiable and direct, and his lab’s ambitions are both lofty and pragmatic.

    “Our ultimate goal is to have a fundamental understanding of how a complex biological system works,” Dr. Kronauer said. “I use ants as a model to do this.” As he sees it, ants in a colony are like cells in a multicellular organism, or like neurons in the brain: their fates joined, their labor synchronized, the whole an emergent force to be reckoned with.

    “But you can manipulate an ant colony in ways you can’t easily do with a brain,” Dr. Kronauer said. “It’s very modular, and you can take it apart and put it back together again.”

    Dr. Kronauer and his co-authors describe their work in a series of recent reports that appear in Proceedings of the National Academy of Sciences, The Journal of Experimental Biology and elsewhere.

    See the full article here .

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  • richardmitnick 8:35 am on January 10, 2017 Permalink | Reply
    Tags: , , , , NYT, or TADs, , Syndactyly, topologically associating domains   

    From NYT: “A Family’s Shared Defect Sheds Light on the Human Genome” 

    New York Times

    The New York Times

    JAN. 9, 2017

    Headcase Design

    They said it was their family curse: a rare congenital deformity called syndactyly, in which the thumb and index finger are fused together on one or both hands. Ten members of the extended clan were affected, and with each new birth, they told Stefan Mundlos of the Max Planck Institute for Molecular Genetics, the first question was always: “How are the baby’s hands? Are they normal?”

    Afflicted relatives described feeling like outcasts in their village, convinced that their “strange fingers” repulsed everybody they knew — including their unaffected kin. “One woman told me that she never received a hug from her father,” Dr. Mundlos said. “He avoided her.”

    The family, under promise of anonymity, is taking part in a study by Dr. Mundlos and his colleagues of the origin and development of limb malformations. And while the researchers cannot yet offer a way to prevent syndactyly, or to entirely correct it through surgery, Dr. Mundlos has sought to replace the notion of a family curse with “a rational answer for their condition,” he said — and maybe a touch of pioneers’ pride.

    The scientists have traced the family’s limb anomaly to a novel class of genetic defects unlike any seen before, a finding with profound implications for understanding a raft of heretofore mysterious diseases.

    The mutations affect a newly discovered design feature of the DNA molecule called topologically associating domains, or TADs. It turns out that the vast informational expanse of the genome is divvied up into a series of manageable, parochial and law-abiding neighborhoods with strict nucleic partitions between them — each one a TAD.

    The hand of a woman with syndactyly, the congenital fusion of fingers. The deformity may range from a slight degree of webbing to almost complete fusion as shown here. Credit SPL/Science Source

    Breach a TAD barrier, and you end up with the molecular equivalent of that famous final scene in Mel Brooks’s comedy, “Blazing Saddles,” when the cowboy actors from one movie set burst through a wall and onto the rehearsal stage of a campy Fred Astaire-style musical. Soon fists, top hats and cream pies are flying.

    By studying TADs, researchers hope to better fathom the deep structure of the human genome, in real time and three dimensions, and to determine how a quivering, mucilaginous string of some three-billion chemical subunits that would measure more than six-feet long if stretched out nonetheless can be coiled and compressed down to four-10,000ths of an inch, the width of a cell nucleus — and still keep its operational wits about it.

    “DNA is a super-long molecule packed into a very small space, and it’s clear that it’s not packed randomly,” Dr. Mundlos said. “It follows a very intricate and controlled packing mechanism, and TADs are a major part of the folding protocol.”

    For much of the past 50 years, genetic research has focused on DNA as a kind of computer code, a sequence of genetic “letters” that inscribe instructions for piecing together amino acids into proteins, which in turn do the work of keeping us alive.

    Read Between the Folds

    Most of the genetic diseases deciphered to date have been linked to mishaps in one or another protein recipe. Scanning the DNA of patients with Duchenne muscular dystrophy, for example, scientists have identified telltale glitches in the gene that encodes dystrophin, a protein critical to muscle stability.

    At the root of Huntington’s disease, which killed the folk singer Woody Guthrie, are short, repeated bits of nucleic nonsense sullying the code for huntingtin, an important brain protein. The mutant product that results soon shatters into neurotoxic shards.

    Yet researchers soon realized there was much more to the genome than the protein codes it enfolded. “We were caught up in the idea of genetic information being linear and one-dimensional,” said Job Dekker, a biologist at the University of Massachusetts Medical School.

    For one thing, as the sequencing of the complete human genome revealed, the portions devoted to specifying the components of hemoglobin, collagen, pepsin and other proteins account for just a tiny fraction of the whole, maybe 3 percent of human DNA’s three billion chemical bases.

    And there was the restless physicality of the genome, the way it arranged itself during cell division into 23 spindly pairs of chromosomes that could be stained and studied under a microscope, and then somehow, when cell replication was through, merged back together into a baffling, ever-wriggling ball of chromatin — DNA wrapped in a protective packaging of histone proteins.

    Stefan Mundlos of the Max Planck Institute for Molecular Genetics in Germany studies the origin and development of limb malformations, some of which are caused by a novel class of genetic defects. Credit Norbert Michalke/Max Planck Institute for Molecular Genetics, Berlin

    What was the link, scientists wondered, between the shape and animation of the DNA molecule at any given moment, in any given cell — and every cell has its own copy of the genome — and the relative mouthiness or muteness of the genetic information the DNA holds?

    “We realized that in order to understand how genetic information is controlled, we had to figure out how DNA was folded in space,” said Bing Ren of the University of California, San Diego.

    Using a breakthrough technology developed by Dr. Dekker and his colleagues called chromosome conformation capture, researchers lately have made progress in tracking the deep structure of DNA. In this approach, chromatin is chemically “frozen” in place, enzymatically chopped up and labeled, and then allowed to reassemble.

    The pieces that find each other again, scientists have determined, are those that were physically contiguous in the first place — only now all their positions and relationships are clearly marked.

    Through chromosome conformation studies and related research, scientists have discovered the genome is organized into about 2,000 jurisdictions, and they are beginning to understand how these TADs operate.

    As with city neighborhoods, TADs come in a range of sizes, from tiny walkable zones a few dozen DNA subunits long to TADs that sprawl over tens of thousands of bases and you’re better off taking the subway. TAD borders serve as folding instructions for DNA. “They’re like the dotted lines on a paper model kit,” Dr. Dekker said.

    TAD boundaries also dictate the rules of genetic engagement.

    Scientists have long known that protein codes are controlled by an assortment of genetic switches and enhancers — noncoding sequences designed to flick protein production on, pump it into high gear and muzzle it back down again. The new research indicates that switches and enhancers act only on those genes, those protein codes, stationed within their own precincts.

    Because TADs can be quite large, the way the Upper West Side of Manhattan comprises an area of about 250 square blocks, a genetic enhancer located at the equivalent of, say, Lincoln Center on West 65th Street, can amplify the activity of a gene positioned at the Cathedral of St. John the Divine, 45 blocks north.

    But under normal circumstances, one thing an Upper West Side enhancer will not do is reach across town to twiddle genes residing on the Upper East Side.

    Scientists have learned that disruptions of the genome’s boundaries may cause syndactyly and other diseases, including some pediatric brain disorders that affect the brain’s white matter. Credit Living Art Enterprises, LLC/Science Source

    “Genes and regulatory elements are like people,” Dr. Dekker said. “They care about and communicate with those in their own domain, and they ignore everything else.”

    Breaking Boundaries

    What exactly do these boundaries consist of, that manage to both direct the proper folding of the DNA molecule and prevent cross talk between genes and gene switches in different domains? Scientists are not entirely sure, but preliminary results indicate that the boundaries are DNA sequences that attract the attention of sticky, roughly circular proteins called cohesin and CTCF, which adhere thickly to the boundary sequences like insulating tape.

    Between those boundary points, those clusters of insulating proteins, the chromatin strand can loop up and over like the ribbon in a birthday bow, allowing genetic elements distributed along the ribbon to touch and interact with one another. But the insulating proteins constrain the movement of each chromatin ribbon, said Richard A. Young of the Whitehead Institute for Biomedical Research, and keep it from getting entangled with neighboring loops — and the genes and regulatory elements located thereon.

    The best evidence for the importance of TADs is to see what happens when they break down. Researchers have lately linked a number of disorders to a loss of boundaries between genomic domains, including cancers of the colon, esophagus, brain and blood.

    In such cases, scientists have failed to find mutations in any of the protein-coding sequences commonly associated with the malignancies, but instead identified DNA damage that appeared to shuffle around or eliminate TAD boundaries. As a result, enhancers from neighboring estates suddenly had access to genes they were not meant to activate.

    Reporting in the journal Science, Dr. Young and his colleagues described a case of leukemia in which a binding site for insulator proteins had been altered not far from a gene called TAL1, which if improperly activated is known to cause leukemia. In this instance, disruption of the nearby binding site, Dr. Young said, “broke up the neighborhood and allowed an outside enhancer to push TAL1 to the point of tumorigenesis,” the production of tumors.

    Now that researchers know what to look for, he said, TAD disruptions may prove to be a common cause of cancer. The same may be true of developmental disorders — like syndactyly.

    In journals like Cell and Nature, Dr. Mundlos and his co-workers described their studies of congenital limb malformations in both humans and mice. The researchers have detected major TAD boundary disruptions that allowed the wrong control elements to stimulate muscle genes at the wrong time and in the wrong tissue.

    “If a muscle gene turns on in the cartilage of developing digits,” Dr. Mundlos said, “you get malformations.”

    Edith Heard, director of the genetics and developmental biology department at the Institut Curie in France, who with Dr. Dekker coined the term TAD, said that while researchers were just beginning to get a handle on the architecture of DNA, “suddenly a lot of things are falling into place. We’re coming into a renaissance time for understanding how the genome works.”

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  • richardmitnick 12:38 pm on January 3, 2017 Permalink | Reply
    Tags: Bogoslof Island, NYT,   

    From NYT: “An Alaskan Volcano Erupts, Largely Out of View” 

    New York Times

    The New York Times

    DEC. 30, 2016

    An image of an eruption plume from Bogoslof was captured on Dec. 20 from an airplane window. Credit Paul Tuvman/Alaska Volcano Observatory.

    For a mere flyspeck, Bogoslof Island has been causing quite a commotion recently.

    The island is the exposed summit of a volcano that sits in 6,000 feet of water in the Bering Sea about 40 miles west of the Alaskan island of Unalaska, which is part of the Aleutian chain. Bogoslof has had a series of eruptions over the last several weeks, spewing gases and ash into the skies and prompting aviation warnings.

    An eruption on Friday, which produced an ash cloud that was believed to rise to about 20,000 feet, was the sixth since Dec. 20. But Michelle Coombs, a geologist with the United States Geological Survey and scientist-in-charge of the Alaska Volcano Observatory, said that analysis of seismic data revealed several more eruptions earlier in the month.

    Alaska, where the Pacific Ocean plate is slowly sliding, or subducting, beneath the North American plate, is home to many volcanoes, 52 of which have been active in the last three centuries. But only about 30 of them have seismometers and other instruments to readily detect eruptions.

    Bogoslof, which last erupted in 1992, is remote and all of its exposed land — about a quarter of a square mile — is protected as part of the Alaska Maritime National Wildlife Refuge. As a result, there are no instruments there.

    Instead, the volcano observatory relies on equipment installed at other locations, as well as satellites, to determine if an eruption has occurred. “It’s a fun bit of detective work trying to put all the pieces together,” Dr. Coombs said.

    Among the information they use is data from the World Wide Lightning Location Network, which has sensors in 40 locations to detect and pinpoint lightning flashes. Dr. Coombs said ash clouds, like thunder clouds, produce lightning, and since thunderstorms are rare in that part of Alaska, “if we see lightning that is geographically near a volcano, the odds are pretty good that that could be from an eruption.”

    Satellite images show that the volcano is erupting from a vent that is just offshore, under the water, and as new material piles up it is changing the shape of the island. “You can see in these images that a new volcanic cone is being built,” Dr. Coombs said. “If it continues, it might build a cone that is above seawater.”

    There is some risk that a larger eruption could result in an ashfall on Unalaska and its port, Dutch Harbor, which has a total population of about 4,000. But the main concern about Bogoslof, Dr. Coombs said, is its potential to affect aviation in what is a busy corridor for flights to and from Asia.

    Flying through volcanic ash can damage or destroy a plane’s engines, so if the eruption is big enough and the ash cloud is high enough, air travel can be shut down, as it was in much of Europe in April 2010 because of the eruption of Eyjafjallajökull, a volcano in Iceland.

    The Bogoslof eruptions are much smaller, and although warnings have been issued and some flights rerouted, so far there has been no need to shut down airspace over the Aleutians.

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  • richardmitnick 3:51 pm on December 23, 2016 Permalink | Reply
    Tags: , , , New Ebola Vaccine Gives 100 Percent Protection, NYT   

    From NYT: “New Ebola Vaccine Gives 100 Percent Protection” 

    New York Times

    The New York Times

    DEC. 22, 2016

    Health workers in November 2015 with Mibemba Soumah, infected by Ebola, at a treatment center in Conakry, Guinea. Credit Samuel Aranda for The New York Times.

    In a scientific triumph that will change the way the world fights a terrifying killer, an experimental Ebola vaccine tested on humans in the waning days of the West African epidemic has been shown to provide 100 percent protection against the lethal disease.

    The vaccine has not yet been approved by any regulatory authority, but it is considered so effective that an emergency stockpile of 300,000 doses has already been created for use should an outbreak flare up again.

    Since Ebola was discovered in the former Zaire in 1976, there have been many efforts to create a vaccine. All began with a sense of urgency but then petered out for lack of money. Although only about 1,600 people died of Ebola over those years, the grotesque nature their deaths — copious hemorrhaging from every orifice — has lent the disease a frightening reputation.

    Ultimately, only the huge, explosive 2014 outbreak that took 11,000 lives in Africa and spread overseas, reaching a handful of people in Europe and the United States, provided the political and economic drive to make an effective vaccine.

    The test results of the trial in Guinea were released Thursday in The Lancet.

    The vaccine was not ready in time to stop the outbreak, which probably began in a hollow, bat-filled tree in Guinea and swept Liberia and Sierra Leone before being defeated. But the prospect of a vaccine stockpile now has brought optimism among public health experts.

    “While these compelling results come too late for those who lost their lives during West Africa’s Ebola epidemic, they show that when the next outbreak hits, we will not be defenseless,” said Marie-Paule Kieny, the World Health Organization’s assistant director-general for health systems and innovation and the study’s lead author. “The world can’t afford the confusion and human disaster that came with the last epidemic.”

    The vaccine opens up new, faster, more efficient ways to encircle and strangle the virus. The many small Ebola outbreaks that occurred between 1976 and 2014 were all stopped in remote villages by laborious methods: medical teams flew in, isolated the sick, and donned protective gear to treat them and bury the dead.

    A volunteer receiving the experimental Ebola vaccine at a clinic in Conakry, Guinea, in 2015. Credit Yann Libessart/Medicins Sans Frontieres, via European Pressphoto Agency

    But that tactic failed in 2014 when the virus reached crowded capital cities, where it spread like wildfire and dead bodies piled up in the streets.

    The new vaccine has some flaws, experts said. It appears to work only against one of the two most common strains of the Ebola virus, and it may not give long-lasting protection. Some of those who get it report side effects like joint pain and headaches.

    “It’s certainly good news with regard to any new outbreak — and one will occur somewhere,” said Dr. Anthony S. Fauci, director of the National Institute for Allergy and Infectious Diseases, which makes many vaccines and did some early testing on this one. “But we still need to continue working on Ebola vaccines.”

    The Lancet study was done in 11,841 residents of Guinea last year. Among the 5,837 people who got the vaccine, none came down with Ebola 10 or more days later. There were 23 Ebola cases among the thousands of others not immediately vaccinated.

    (The 10-day window was important because the trial used the “ring vaccination” technique developed during the drive to eliminate smallpox. Once a confirmed case was found, researchers contacted everyone in the circle of family, friends, neighbors and caregivers around the victim. About half the “circles” were offered vaccine. No one who fell ill within the first nine days after vaccination was counted, however, because it was assumed that they had already been infected before vaccination.)

    The Ebola trial was led by the World Health Organization, the Guinean Health Ministry, Norway’s Institute of Public Health and other institutions. The vaccine, known as rVSV-ZEBOV, was developed over a decade ago by the Public Health Agency of Canada and the United States Army and is now licensed to Merck.

    Its genetic “spine” is that of a vesicular stomatitis virus, which sickens cattle but usually does not infect humans. Spliced into the spine is the gene coding for an Ebola virus surface protein that prompts the immune system to make antibodies.

    Tests in monkeys showed that one shot protected all of them when it was given at least a week before they were given a high dose of Ebola. The shot even protected a few monkeys who received it a day after being infected with Ebola.

    The Ebola virus has five known subtypes, the most common of which are Ebola-Zaire, the one that caused the West African outbreak, and Ebola-Sudan. Ebola is also related to Marburg virus, which is similarly lethal.

    An ideal vaccine would protect against all Ebola strains and Marburg. However, Dr. Kieny said, it may not be possible to make a shot effective against several strains if it is t based on the VSV spine because VSV triggers a lot of side effects.

    Risks that are acceptable in the midst of a deadly epidemic are not acceptable in a preventive vaccine given to healthy children and adults, several experts noted.

    The new vaccine is “a step in the right direction but not the ultimate solution,” said Dr. Gary J. Nabel, chief scientific officer for global health research at the Sanofi pharmaceutical company, who designed a different Ebola vaccine in the 1990s when he worked at the National Institutes of Health.

    A randomized clinical trial involving tens of thousands of subjects is the preferred way to test any vaccine, he noted. But by the time testing could start in mid-2015 in West Africa, isolation and treatment of the sick in tent hospitals had made Ebola cases so rare that researchers had to switch to ring vaccination around the few they could find.

    A likely candidate for a routine Ebola vaccine is one now being developed by GSK, Dr. Nabel said. It uses two shots: the first has the Ebola surface protein attached to a chimpanzee adenovirus that can infect humans without harming them; the second uses a weakened pox virus similar to that used in smallpox vaccine.

    Dr. Seth F. Berkley, chief executive of Gavi, the Vaccine Alliance, said his organization’s board voted in late 2014 to spend up to $390 million for 12 million doses of an Ebola vaccine. At the time, several companies had candidates but none had been fully tested in humans. “That was at a time when the epidemic was raging and we did not know if it could be controlled without a vaccine,” he said.

    By early last year, when preliminary results suggested the Merck vaccine worked well, Gavi gave the company $5 million to make 300,000 doses as an emergency supply to be used if Ebola-Zaire exploded again.

    It is not yet clear how big a stockpile will eventually be created. Merck is now required to seek approval of its vaccine from the World Health Organization, which itself requires licensing by a major regulatory agency like the United States Food and Drug Administration or the European Medicines Agency.

    See the full article here .

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  • richardmitnick 9:21 pm on December 20, 2016 Permalink | Reply
    Tags: , , , , NYT   

    From NYT: “Cancer-Free: One Recovery Inspires Another — and Could Help Thousands” 

    New York Times

    The New York Times

    DEC. 19, 2016

    Melinda Bachini, left, whose cancer treatment inspired Celine Ryan, right, with her sons Liam and Decklan, to pursue the same. Credit Left: Lynn Donaldson for The New York Times Right: Laura McDermott for The New York Times

    In this story, the science reporter Denise Grady provides human backstory about her article about a woman who, remarkably, recovered from colon cancer after treatment with cells from her own immune system.

    I’ve been meeting more and more people with cancer lately who would be desperately ill — or worse — had they not taken matters into their own hands and found their way into clinical trials in which they received experimental treatments that put the disease in remission.

    There were no guarantees. New treatments don’t always work, and experiments have risks. [My own wife died after, first, immunotherapy that did not work and then clinical trial which at best did not work and at worst possibly killed her.] The patients I met are here to tell their stories because they’re among the lucky few, the successes. Still, the cancer landscape does seem to be brightening, if only just a bit, in large part thanks to immunotherapy, which includes various treatments that help the patient’s own immune system to fight cancer.

    The latest good news from the cancer front came last week, from Celine Ryan, a 51-year-old woman from Rochester Hills, Mich., a suburb of Detroit. She homeschools her five children, the youngest of whom is seven years old. Ms. Ryan has colon cancer, and two years ago, doctors found that despite surgery, radiation and chemotherapy, the cancer had spread and invaded her lungs, where scans detected 10 tumors.

    Ms. Ryan is an engineer and database programmer, and to her scientific mind, it seemed highly unlikely that more chemo would control the disease. Chemo made her sick the first time around, and she had every reason to belief it would do so again. She and her husband, who is also an engineer, agreed that she should forgo chemo and instead try to tap into a major research center for help.

    “I remembered that I had read about another cancer patient, Melinda Bachini. It stuck in my brain,” Ms. Ryan said. “I found out about this trial she did, and I said, ‘That’s what I want to do.’”

    A front-page article I wrote in May 2014 about Ms. Bachini, a paramedic in Billings, Mont., might have been the article that Ms. Ryan remembered. Ms. Bachini had a deadly cancer, cholangiocarcinoma, that had started in her bile duct; Ms. Bachini underwent surgery and several grueling rounds of chemo, but the cancer nontheless spread to her liver and lungs. In April 2012, her life expectancy was a matter of months. Ms. Bachini, 43 at the time, had six children and, like, Ms. Ryan, did not think further chemotherapy would help.

    Instead, she combed the internet looking for clinical trials and came upon one, run by Dr. Steven A. Rosenberg, at the National Cancer Institute, that made sense to her.

    She was accepted into the study, and got very lucky. Dr. Rosenberg’s team found that she had a type of cancer-killing immune cell that could destroy her tumors without harming normal cells. The researchers multiplied those cells in the lab and dripped more than 100 billion of them back into her. Ms. Bachini’s tumors melted away.

    Inspired by Ms. Bachini’s story, Ms. Ryan called the cancer institute. She was deferred twice because her tumors were not big enough to yield enough immune cells. But she persisted, and even sent the researchers screen shots from her scans, with measurements of tumors that she and her husband thought met the trial criteria. Eventually, she was accepted into the study and, like Ms. Bachini, was one of the fortunate ones: Now, thanks to the cell treatment and surgery, she is cancer-free.

    Ms. Ryan’s case made medical history, because it was the first time researchers found cells that could attack a common cancer causing mutation — a finding that may help thousands of other patients with the same mutation.

    In November 2015, after the first scan showed that her tumors had shrunk markedly, Ms. Ryan tracked down Ms. Bachini and emailed her. “Call me!” Ms. Bachini replied. Ms. Bachini and Ms. Ryan have been friends ever since and stay in touch by phone and on Facebook.

    “When Celine and I connected, I was so unbelievably happy for her,” Ms. Bachini said.

    They hope to meet in person, maybe by coordinating their checkups at the cancer institute. Both try to help other patients who are looking for help and considering clinical trials.

    Ms. Bachini needed more treatment recently, because tumors in her lungs began to grow again. She had surgery and was given an immunotherapy drug, a type called a checkpoint inhibitor, which has begun shrinking the tumors.

    “I spend a lot of time talking to patients, doing cancer advocacy stuff,” Ms. Bachini said. “It’s how I can pay it forward.”

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  • richardmitnick 8:58 am on December 15, 2016 Permalink | Reply
    Tags: America’s First Offshore Wind Farm Spins to Life, , , NYT   

    From NYT: “America’s First Offshore Wind Farm Spins to Life” 

    New York Times

    The New York Times

    DEC. 14, 2016

    The Block Island Wind Farm’s turbines off the coast of Rhode Island in August. They began spinning on Monday and will deliver electricity to Block Island, a community nearby. Credit Kayana Szymczak for The New York Times

    Until this week, all of the wind power generated in the United States was landlocked.

    But in a first for America, the ocean breeze is now generating clean, renewable power offshore — electricity that will supply a small island community off the coast of Rhode Island. Renewable energy, including from offshore wind, is crucial to the effort to avoid some of the worst effects of climate change, according to environmentalists and some elected officials.

    On Monday, the country’s first offshore wind farm, developed by a company called Deepwater Wind and helped along by the state’s political leadership, started spinning its turbines to bring electricity to Block Island, a vacation destination with few year-round residents that had previously relied on diesel-fueled generators for power.

    “This is a historic milestone for reducing our nation’s dependence on fossil fuels, and I couldn’t be more thrilled that it’s happening here in the Ocean State,” Senator Sheldon Whitehouse, Democrat of Rhode Island and co-founder of the Senate Climate Action Task Force, said in a statement from Deepwater Wind.

    Though the Block Island Wind Farm is small — made up of five turbines, which were built by a division of General Electric, and capable of powering about 17,000 homes — it is the first successful offshore wind development in the United States, and it sets up the possibility for offshore wind projects elsewhere along the coast.

    According to a spokeswoman for Deepwater Wind, about 90 percent of the island’s needs will be met by the wind-generated power, and more will go back to the grid. Current estimates are that the wind farm will supply 1 percent of the state’s electricity, the spokeswoman said.

    Despite its modest size, the wind farm, which cost about $300 million to build, still represents a significant reduction in carbon dioxide emissions — about 40,000 tons per year.

    Deepwater Wind will receive a federal tax credit for the project, and first-year rates for Rhode Island customers of National Grid, the utility company laying one of the cables to the wind farm, may be higher than what customers currently pay.

    Environmentalists, members of the Obama administration and government officials in several states see significant potential for offshore wind energy, given that winds over the ocean usually blow stronger and more steadily than those on land.

    Earlier this year, the Obama administration announced a lease for a wind farm off the coast of Long Island, and the Department of Energy has said that if wind farms were built in all of the suitable areas, including in the Great Lakes, they could provide up to twice as much electricity as the country now uses.

    In the past, offshore wind farms have faced significant opposition in the United States for a few reasons: high costs, complicated rules about who gets to build on the seafloor and what they build, and complaints from people who do not want their ocean view obstructed.

    In Europe, however, thousands of wind turbines have sprouted up along the coast, and an additional 3,000 megawatts of wind power were added last year (about 100 times the amount of power provided by the Block Island Wind Farm).

    There has been some opposition to offshore wind projects in Europe, including from President-elect Donald J. Trump, who unsuccessfully fought to block construction of a wind farm off the coast of Scotland near one of his golf courses.

    Mr. Trump has expressed skepticism of wind power, saying in an interview with The New York Times that “the wind is a very deceiving thing.” And an email written by Thomas J. Pyle, who is running the Department of Energy transition for the president-elect, said that the Trump administration might be looking to get rid of all energy subsidies.

    Mr. Trump has also been accused of exaggerating the harmful effects of wind turbines on bird populations, which Mr. Pyle also addressed in the email, writing, “Unlike before, wind energy will rightfully face increasing scrutiny from the federal government.”

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  • richardmitnick 10:35 pm on December 12, 2016 Permalink | Reply
    Tags: , , , NYT, Where Will NASA Go in the Age of Trump?   

    From NYT: “Where Will NASA Go in the Age of Trump?’ 

    New York Times

    The New York Times

    DEC. 12, 2016
    Dennis Overbye

    Elwood Smith

    Two weeks after a presidential election that could have vaulted him to the head of NASA, John Grunsfeld reached across his peanut curry at a small restaurant on the Far West Side of Manhattan, grabbed my notebook and sketched out a plan for a trip to Mars.

    Dr. Grunsfeld, astronomer, astronaut, and former associate administrator of NASA, was in town to promote a National Geographic TV series about Martian exploration. On his shirt was a picture of a space shuttle and the Hubble Space Telescope.

    We’ve been having a kind of Mars moment lately. Audiences filled theaters last year to watch Matt Damon as The Martian. Personalities as diverse as President Obama and Elon Musk have declared the Red Planet the next great destination.

    In the days leading up the election, Dr. Grunsfeld said, NASA was thinking about a Mars mission to get ready for the transition. He himself was rumored to be on the short list to run the space agency should Hillary Clinton have won.

    “NASA has never had a scientist as administrator; you and I would have had fun,” he said.

    Now, nobody knows where NASA’s rockets are going on their biblical smoke pillars. Donald J. Trump’s one mention of the space program during his campaign was to tell a kid that potholes on Earth need fixing first.

    But he also campaigned on the promise to “make America great again,” and hardly anything in recent history says that more clearly than the Apollo moon landings. That has some space buffs hoping that a Trump administration will put its weight behind another grand adventure in space, most likely a return for good to the moon.

    At the same time, there is no evidence that Congress would give NASA any more money than it is already getting to carry out these adventures. Mr. Trump’s potholes, a military buildup and tax cuts beckon.

    Early in December, the first member of Mr. Trump’s transition “landing team,” Christopher Shank, policy director for the House Committee on Science, Space and Technology and a former member of NASA arrived at its headquarters to begin taking stock of the agency. He did not respond to an email request for an interview and none of the other members of the team, which now numbers seven, have commented publicly.

    Even NASA insiders are reduced to reading tea leaves and possible smoke signals, clues scattered by Mr. Trump and Republican space and science insiders during the last year. In a recent speech in Washington, Bob Walker, a former congressman who advised the Trump campaign on space, reiterated his desire for NASA to concentrate on basic science and exploration and farm out climate research, which he has referred to as “politicized science,” to other agencies like NOAA. That’s a notion that alarmed climate scientists regard as either naïve or cynical.

    Mr. Walker also said that Vice President-elect Mike Pence would be presiding over a reinstated National Space Council, last used during George W. Bush’s administration, to oversee and coordinate civilian and military space efforts. One of its jobs would be to decide how much NASA should depend on commercial space entrepreneurs like Mr. Musk and Jeff Bezos to shoulder the rocket load.

    Last summer many of these insiders, including Michael Griffin, a former NASA former administrator, gathered around a television at Mr. Shank’s house to cheer on Eileen Collins, the first woman to command a space shuttle mission, as she spoke at the Republican National Convention. Denouncing what she saw as a lack of American leadership, at least as far as human spaceflight was concerned, she noted that it had been five years since an American was launched into space from American soil.

    “We are a nation of explorers,” she declared. “Nations that lead on the frontier lead in the world.”

    Ever since John Glenn orbited Earth in 1962, the United States space program has limped through a series of auspicious starts and stops. Americans landed on the moon in 1969 and abandoned it in 1972. We built the space shuttle and then retired it; we embarked on the Constellation program to return to the moon, then canceled it in favor of eventually going to Mars. The International Space Station was supposed to get us ready for deep space travel, but we haven’t gone anywhere.

    Mr. Glenn died last week, at age 95. Reflecting on the long arc of his life and the space program, Dr. Grunsfeld asked, “What do we have to show for it?”

    Are we in for another outer space pivot back to the moon?

    Among the many Trump advisers is Newt Gingrich, who promised a lunar colony by 2020 when he was running for president four years ago, quipping that it could apply for statehood someday.

    At the time eyes rolled, but times have changed. Recently Jeb Bush declared it a “cool” idea. Europe, China and Russia are all reportedly eager to establish a base on the moon.

    Jim Bridenstine, an Oklahoma congressman rumored to be in the hunt for NASA administrator, said in a recent speech: “This is our Sputnik moment [Quoting former D.O.E. Secretary Stephen Chu]. America must forever be the pre-eminent spacefaring nation, and the moon is our path to being so.”

    Among the attractions of a lunar base, its adherents say, would be the ability to mine ice at the moon’s poles to produce rocket fuel. According to recent studies, refueling at the moon, or nearby, would be the cheapest way to go to Mars.

    It could be the mother of all infrastructure projects, perhaps a notion attractive to Mr. Trump’s developer instincts, in effect paving a highway to Mars and beyond.

    It would also take a lot of money, time and political capital.

    “The moon’s a nice place to visit, but you wouldn’t want to live there,” Dr. Grunsfeld said.

    But we can go to Mars without breaking NASA’s budget, Dr. Grunsfeld said, reaching for my notebook.

    First he drew a line of rockets.

    Forget the giant heavy-lift super booster rocket. Assemble a Mars spacecraft in orbit using the kinds of rockets like Atlas or Delta we already have.

    Suppose it takes 10 launches to get all the pieces up there, he said. At $350 million a launch, that adds up to $3.5 billion.

    Adding in another $500 million to launch the crew brings the total to $4 billion.

    If the spaceship segments themselves cost $1 billion apiece, the whole Mars ship is $14 billion.

    Make two, just to be on the safe side.

    “For $4 billion a year for seven years you get a Martian spaceship including a full spare,” he said.

    Where does the money come from?

    As it happens, this is the amount of money NASA now spends on the space station every year, money that will be available one day to go someplace.

    They could only go around Mars, without landing . But it would still be an epochal voyage, the interplanetary version of Apollo 8’s Christmas voyage around the moon in 1968, setting the stage for what is to come if people are ever going to live off-planet.

    Someone should do it. All that money would be spent here — on things we say we care about, like science, technological development and education, things that stimulate the economy and inspire generations.

    “Going to Mars would make NASA great again,” Dr. Grunsfeld said.

    I asked him how long it would all take. Seven to 10 years, he texted me later. “Whenever someone decides to start.”

    See the full article here .

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  • richardmitnick 11:07 am on December 11, 2016 Permalink | Reply
    Tags: Colombia Reports Major Rise in Birth Defect Amid Zika Crisis, NYT, ,   

    From NYT: “Colombia Reports Major Rise in Birth Defect Amid Zika Crisis” 

    New York Times

    The New York Times

    DEC. 10, 2016

    Colombia, which suffered a Zika epidemic that peaked in February, has reported four times as many cases of babies born with microcephaly this year as it did in 2015, providing more proof that the Zika virus causes brain damage in infants.

    Because births of microcephalic infants peaked five months after the epidemic did, at about nine times the numbers of the previous July, scientists feel sure that the greatest risk is to babies whose mothers were infected during their first trimesters or early in their second.

    The numbers were reported in a study released Friday by the Centers for Disease Control and Prevention and conducted jointly by scientists from the C.D.C. and Colombia’s national health institute.

    With 105,000 suspected Zika cases, Colombia has had the second-largest Zika epidemic after Brazil. Brazil has had proportionally many more cases of microcephaly, and the reason has remained a mystery, although its population is four times larger than Colombia’s and it experienced a much longer, more intense epidemic in 2014 and 2015, especially in the northeast.

    As of Thursday, Brazil had reported 2,211 cases of microcephaly in which Zika infection had been confirmed to the World Health Organization, while Colombia had reported only 60.

    W.H.O. reports of confirmed cases have sometimes lagged weeks behind local reports. The study released by the C.D.C. found 476 cases of microcephaly in Colombia between January and mid-November. Of those, only 147 — about 30 percent — had laboratory evidence of Zika virus infection. But many others were not tested, and the virus is not always detectable months after it damages a fetus, so the true numbers may be higher.

    About 4 percent of the fetuses tested had evidence of other infections that can cause microcephaly, such as toxoplasmosis, herpes, cytomegalovirus or syphilis. Many other fetuses were not tested or their microcephaly had no clear cause.

    Of the total, 432 of the microcephaly cases were in babies born alive, and 44 were in fetuses that were stillborn, miscarried or aborted. One theory — still unproven — is that Colombia had fewer microcephaly cases than expected because many fearful women aborted their pregnancies, legally or illegally. Abortion is much more restricted in Brazil than in Colombia.

    The number of confirmed cases of microcephaly is in line with predictions made by health officials after they declared an end to the Zika epidemic in Colombia in July. Early in the year, based on Brazil’s experience, Dr. Fernando Ruiz, the vice minister for public health, estimated that Colombia would have 700 cases of Zika-related microcephaly this year. In August, he changed that estimate to between 100 and 250.

    Although Colombia is widely believed to have a better disease-surveillance system than Brazil, it still relies on doctors to voluntarily report birth defects. They may have been underreported in 2015, before microcephaly was in the news.

    See the full article here .


    There is a new project at World Community Grid [WCG] called OpenZika.
    Zika depiction. Image copyright John Liebler, http://www.ArtoftheCell.com
    Rutgers Open Zika

    WCG runs on your home computer or tablet on software from Berkeley Open Infrastructure for Network Computing [BOINC]. Many other scientific projects run on BOINC software.Visit WCG or BOINC, download and install the software, then at WCG attach to the OpenZika project. You will be joining tens of thousands of other “crunchers” processing computational data and saving the scientists literally thousands of hours of work at no real cost to you.

    This project is directed by Dr. Alexander Perryman a senior researcher in the Freundlich lab, with extensive training in developing and applying computational methods in drug discovery and in the biochemical mechanisms of multi-drug-resistance in infectious diseases. He is a member of the Center for Emerging & Re-emerging Pathogens, in the Department of Pharmacology, Physiology, and Neuroscience, at the Rutgers University, New Jersey Medical School. Previously, he was a Research Associate in Prof. Arthur J. Olson’s lab at The Scripps Research Institute (TSRI), where he ran the day-to-day operations of the FightAIDS@Home project, the largest computational drug discovery project devoted to HIV/AIDS, which also runs on WCG. While in the Olson lab, he also designed, led, and ran the largest computational drug discovery project ever performed against malaria, the GO Fight Against Malaria project, also on WCG.

    Rutgers smaller


    Please help promote STEM in your local schools.

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