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  • richardmitnick 10:45 am on April 20, 2017 Permalink | Reply
    Tags: , , NYT   

    From NYT: “Is It O.K. to Tinker With the Environment to Fight Climate Change?” 

    New York Times

    The New York Times

    APRIL 18, 2017
    JON GERTNER

    Scientists are investigating whether releasing tons of particulates into the atmosphere might be good for the planet. Not everyone thinks this is a good idea.

    1

    For the past few years, the Harvard professor David Keith has been sketching this vision: Ten Gulfstream jets, outfitted with special engines that allow them to fly safely around the stratosphere at an altitude of 70,000 feet, take off from a runway near the Equator. Their cargo includes thousands of pounds of a chemical compound — liquid sulfur, let’s suppose — that can be sprayed as a gas from the aircraft. It is not a one-time event; the flights take place throughout the year, dispersing a load that amounts to 25,000 tons. If things go right, the gas converts to an aerosol of particles that remain aloft and scatter sunlight for two years. The payoff? A slowing of the earth’s warming — for as long as the Gulfstream flights continue.

    Keith argues that such a project, usually known as solar geoengineering, is technologically feasible and — with a back-of-the-envelope cost of under $1 billion annually — ought to be fairly cheap from a cost-benefit perspective, considering the economic damages potentially forestalled: It might do good for a world unable to cut carbon-dioxide emissions enough to prevent further temperature increases later this century.

    What surprised me, then, as Keith paced around his Harvard office one morning in early March, was his listing all the reasons humans might not want to hack the environment. “Actually, I’m writing a paper on this right now,” he said. Most of his thoughts were related to the possible dangers of trying to engineer our way out of a climate problem of nearly unimaginable scientific, political and moral complexity. Solar geoengineering might lead to what some economists call “lock-in,” referring to the momentum that a new technology, even one with serious flaws, can assume after it gains a foothold in the market. The qwerty keyboard is one commonly cited example; the internal combustion engine is another. Once we start putting sulfate particles in the atmosphere, he mused, would we really be able to stop?

    Another concern, he said, is “just the ethics about messing with nature.” Tall, wiry and kinetic, with thinning hair and a thick beard that gives him the look of the backcountry skier he is, Keith proudly showed me the framed badge that his father, a biologist, wore when he attended the landmark United Nations Conference on the Human Environment in Stockholm in 1972. Now 53, Keith has taken more wilderness trips — hiking, rock climbing, canoeing — than he can properly recall, and for their recent honeymoon, he and his wife were dropped off by helicopter 60 miles from the nearest road in northern British Columbia. “It was quite rainy,” he told me, “and that ended up making it even better.” So the prospect of intentionally changing the climate, he confessed, is not just unpleasant — “it initially struck me as nuts.”

    It still strikes him as a moral hazard, to use a term he borrows from economics. A planet cooled by an umbrella of aerosol particles — an umbrella that works by reflecting back into space, say, 1 percent of the sun’s incoming energy — might give societies less incentive to adopt greener technologies and radically cut carbon emissions. That would be disastrous, Keith said. The whole point of geoengineering is not to give us license to forget about the buildup of CO₂. It’s to lessen the ill effects of the buildup and give us time to transition to cleaner energy.

    Beyond these conceivable dangers, though, a more fundamental problem lurks: Solar geoengineering simply might not work. It has been a subject of intense debate among climate scientists for roughly a decade. But most of what we know about its potential effects derives from either computer simulations or studies on volcanic eruptions like that of Mount Pinatubo in 1991, which generated millions of tons of sunlight-scattering particulates and might have cooled the planet by as much as 0.5 degrees Celsius, or nearly 1 degree Fahrenheit. The lack of support for solar geoengineering’s efficacy informs Keith’s thinking about what we should do next. Actively tinkering with our environment — fueling up the Gulfstream jets and trying to cool things down — is not something he intends to try anytime soon, if ever. But conducting research is another matter.

    A decade ago, when Keith was among the few American scientists to advocate starting a geoengineering research program, he was often treated at science conferences as an outlier. “People would sort of inch away or, really, tell me I shouldn’t be doing this,” he said. Geoengineering was seen as a scientific taboo and Keith its dark visionary. “The preconception was that I was some kind of Dr. Strangelove figure,” he told me — “which I didn’t like.”

    Attitudes appear to have changed over the past few years, at least in part because of the continuing academic debates and computer-modeling studies. The National Academy of Sciences endorsed the pursuit of solar geoengineering research in 2015, a stance also taken in a later report by the Obama administration. A few influential environmental groups, like the Natural Resources Defense Council and the Environmental Defense Fund, now favor research.

    In the meantime, Keith’s own work at Harvard has progressed. This month, he is helping to start Harvard’s Solar Geoengineering Research Program, a broad endeavor that begins with $7 million in funding and intends to reach $20 million over seven years. One backer is the Hewlett Foundation; another is Bill Gates, whom Keith regularly advises on climate change. Keith is planning to conduct a field experiment early next year by putting particles into the stratosphere over Tucson.

    The new Harvard program is not merely intent on getting its concepts out of the lab and into the field, though; a large share of its money will also be directed to physical and social scientists at the university, who will evaluate solar geoengineering’s environmental dangers — and be willing to challenge its ethics and practicality. Keith told me, “It’s really important that we have a big chunk of the research go to groups whose job will be to find all the ways that it won’t work.” In other words, the technology that Keith has long believed could help us ease our predicament — “the nuclear option” for climate, as one opponent described it to me, to be considered only when all else has failed — will finally be investigated to see whether it is a reasonable idea. At the same time, it will be examined under the premise that it may in fact be a very, very bad one.

    Climate change already presents a demoralizing array of challenges — melting ice sheets and species extinctions — but the ultimate severity of its impacts depends greatly on how drastically technology and societies can change over the next few decades. The growth of solar and wind power in recent years, along with an apparent decrease in coal use, suggest that the global community will succeed in curtailing CO₂ emissions. Still, that may not happen nearly fast enough to avert some dangerous consequences. As Keith likes to point out, simply reducing emissions doesn’t reverse global warming. In fact, even if annual global CO₂ emissions decrease somewhat, the total atmospheric CO₂ may continue to increase, because the gas is so slow to dissipate. We may still be living with damaging amounts of atmospheric carbon dioxide a half-century from now, with calamitous repercussions. The last time atmospheric CO₂ levels were as elevated as they are today, three million years ago, sea levels were most likely 45 feet higher, and giant camels roamed above the Arctic Circle.

    Recently, I met with Daniel Schrag, who is the head of the Harvard University Center for the Environment, an interdisciplinary teaching and research department. Schrag, who helped recruit Keith to Harvard, painted a bleak picture of our odds of keeping global temperatures from rising beyond levels considered safe by many climate scientists. When you evaluate the time scales involved in actually switching our energy systems to cleaner fuels, Schrag told me, “the really depressing thing is you start to understand why any of these kinds of projections — for 2030 or 2050 — are absurd.” He went on: “Are they impossible? No. I want to give people hope, too. I’d love to make this happen. And we have made a lot of progress on some things, on solar, on wind. But the reality is we haven’t even started doing the hard stuff.”

    Schrag described any kind of geoengineering as “at best an imperfect solution that is operationally extremely challenging.” Yet to Schrag and Keith, the political and technical difficulties associated with a rapid transition to a zero-carbon-emissions world make it sensible to look into geoengineering research. There happens to be a number of different plans for how to actually do it, however — including the fantastical (pumping seawater onto Antarctica to combat sea-level rise) and the impractical (fertilizing oceans with iron to foster the growth of algae, which would absorb more CO₂). Some proposals involve taking carbon out of the air, using either immense plant farms or absorption machines. (Keith is involved with such sequestration technology, which faces significant hurdles in terms of cost and feasibility.) Another possible approach would inject salt crystals into clouds over the ocean to brighten them and cool targeted areas, like the dying Great Barrier Reef. Still, the feeling among Keith and his colleagues is that aerosols sprayed into the atmosphere might be the most economically and technologically viable approach of all — and might yield the most powerful global effect.

    It is not a new idea. In 2000, Keith published a long academic paper on the history of weather and climate modification, noting that an Institute of Rainmaking was established in Leningrad in 1932 and that American engineers began a cloud-seeding campaign in Vietnam a few decades later. A report issued in 1965 by President Lyndon B. Johnson’s administration called attention to the dangers of increasing concentrations of CO₂ and, anticipating Keith’s research, speculated that a logical response might be to change the albedo, or reflectivity, of the earth. To Keith’s knowledge, though, there have been only two actual field experiments so far. One, by a Russian scientist in 2009, released aerosols into the lower atmosphere via helicopter and appears to have generated no useful data. “It was a stunt,” Keith says. Another was a modest attempt at cloud brightening a few years ago by a team at the Scripps Institution of Oceanography at the University of California, San Diego.

    Downstairs from Keith’s Harvard office, there is a lab cluttered with students fiddling with pipettes and arcane scientific instruments. When I visited in early March, Zhen Dai, a graduate student who works with Keith, was engaged with a tabletop apparatus, a maze of tubes and pumps and sensors, meant to study how chemical compounds interact with the stratosphere. For the moment, Keith’s group is leaning toward beginning its field experiments with ice crystals and calcium carbonate — limestone — that has been milled to particles a half-micron in diameter, or less than 1/100th the width of a human hair. They may eventually try a sulfur compound too. The experiment is called Scopex, which stands for Stratospheric Controlled Perturbation Experiment. An instrument that can disperse an aerosol of particles — say, several ounces of limestone dust — will be housed in a gondola that hangs beneath a balloon that ascends to 70,000 feet. The whole custom-built contraption, whose two small propellers will be steered from the ground, will also include a variety of sensors to collect data on any aerosol plume. Keith’s group will measure the sunlight-scattering properties of the plume and evaluate how its particles interact with atmospheric gases, especially ozone. The resulting data will be used by computer models to try to predict larger-scale effects.

    But whether a scientist should be deliberately putting foreign substances into the atmosphere, even for a small experiment like this, is a delicate question. There is also the difficulty of deciding on how big the atmospheric plumes should get. When does an experiment become an actual trial run? Ultimately, how will the scientists know if geoengineering really works without scaling it up all the way?

    Keith cites precedents for his thinking: a company that scatters cremation ashes from a high-altitude balloon, and jet engines, whose exhaust contains sulfates. But the crux of the problem that Harvard’s Solar Geoengineering Research Program wrestles with is intentionality. Frank Keutsch, a professor of atmospheric sciences at Harvard who is designing and running the Scopex experiments with Keith, told me: “This effort with David is very different from all my other work, because for those other field experiments, we’ve tried to measure the atmosphere and look at processes that are already there. You’re not actually changing nature.” But in this case, Keutsch agrees, they will be.

    During one of our conversations, Keith suggested that I try to flip my thinking for a moment. “What if humanity had never gotten into fossil fuels,” he posed, “and the world had gone directly to generating energy from solar or wind power?” But then, he added, what if in this imaginary cleaner world there was a big natural seep of a heat-trapping gas from within the earth? Such events have happened before. “It would have all the same consequences that we’re worried about now, except that it’s not us doing the CO₂ emissions,” Keith said. In that case, the reaction to using geoengineering to cool the planet might be one of relief and enthusiasm.

    In other words, decoupling mankind’s actions — the “sin,” as Keith put it, of burning fossil fuels — from our present dilemma can demonstrate the value of climate intervention. “No matter what, if we emit CO₂, we are hurting future generations,” Keith said. “And it may or may not be true that doing some solar geo would over all be a wise thing to do, but we don’t know yet. That’s the reason to do research.”

    There are risks, undeniably — some small, others potentially large and terrifying. David Santillo, a senior scientist at Greenpeace, told me that some modeling studies suggest that putting aerosols in the atmosphere, which might alter local climates and rain patterns and would certainly affect the amount of sunlight hitting the earth, could have a significant impact on biodiversity. “There’s a lot more we can do in theoretical terms and in modeling terms,” Santillo said of the Harvard experiments, “before anyone should go out and do this kind of proof-of-concept work.” Alan Robock, a professor of atmospheric sciences at Rutgers, has compiled an exhaustive list of possible dangers. He thinks that small-scale projects like the Scopex experiment could be useful, but that we don’t know the impacts of large-scale geoengineering on agriculture or whether it might deplete the ozone layer (as volcanic eruptions do). Robock’s list goes on from there: Solar geoengineering would probably reduce solar-electricity generation. It would do nothing to reduce the increasing acidification of the oceans, caused by seawater absorbing carbon dioxide. A real prospect exists, too, that if solar geoengineering efforts were to stop abruptly for any reason, the world could face a rapid warming even more dangerous than what’s happening now — perhaps too fast for any ecological adaptation.

    Keith is well aware of Robock’s concerns. He also makes the distinction that advocating research is not the same as advocating geoengineering. But the line can blur. Keith struck me as having a fair measure of optimism that his research can yield insights into materials and processes that can reduce the impacts of global warming while averting huge risks. For instance, he is already encouraged by computer models that suggest the Arctic ice cap, which has shrunk this year to the smallest size observed during the satellite era, could regrow under cooler conditions brought on by light-scattering aerosols. He also believes that the most common accusation directed against geoengineering — that it might disrupt precipitation patterns and lead to widespread droughts — will prove largely unfounded.

    But Keith is not trained as an atmospheric scientist; he’s a hands-on physicist-engineer who likes to take machinery apart. There are deep unknowns here. Keutsch, for one, seems uncertain about what he will discover when the group actually tries spraying particulates high above the earth. The reduction of sunlight could adversely affect the earth’s water cycle, for example. “It really is unclear to me if this approach is feasible,” he says, “and at this point we know far too little about the risks. But if we want to know whether it works, we have to find out.”

    Finally, what if something goes wrong either in research or in deployment? David Battisti, an atmospheric scientist at the University of Washington, told me, “It’s not obvious to me that we can reduce the uncertainty to anywhere near a tolerable level — that is, to the level that there won’t be unintended consequences that are really serious.” While Battisti thought Keith’s small Scopex experiment posed little danger — “The atmosphere will restore itself,” he said — he noted that the whole point of the Harvard researchers’ work is to determine whether solar geoengineering could be done “forever,” on a large-scale, round-the-clock basis. When I asked Battisti if he had issues with going deeper into geoengineering research, as opposed to geoengineering itself, he said: “Name a technology humans have developed that they haven’t used. I can’t think of any. So we can work on this for sure. But we are in this dilemma: Once we do develop this technology, it will be tempting to use it.”

    Suppose Keith’s research shows that solar geoengineering works. What then? The world would need to agree where to set the global thermostat. If there is no consensus, could developed nations impose a geoengineering regimen on poorer nations? On the second point, if this technology works, it would arguably be unethical not to use it, because the world’s poorest populations, facing drought and rising seas, may suffer the worst effects of a changing climate.

    In recent months, a group under the auspices of the Carnegie Council in New York, led by Janos Pasztor, a former United Nations climate official, has begun to work through the thorny international issues of governance and ethics. Pasztor told me that this effort will most likely take four years. And it is not lost on him — or anyone I spoke with in Keith’s Harvard group — that the idea of engineering our environment is taking hold as we are contemplating the engineering of ourselves through novel gene-editing technologies. “They both have an effect on shaping the pathway where human beings are now and where will they be,” says Sheila Jasanoff, a professor of science and technology studies at Harvard who sometimes collaborates with Keith. Jasanoff also points out that each technology potentially enables rogue agents to act without societal consent.

    This is a widespread concern. We might reach a point at which some countries pursue geoengineering, and nothing — neither costs nor treaties nor current technologies — can stop them. Pasztor sketched out another possibility to me: “You could even have a nightmare scenario, where a country decides to do geoengineering and another country decides to do counter-geoengineering.” Such a countermeasure could take the form of an intentional release of a heat-trapping gas far more potent than CO₂, like a hydrochlorofluorocarbon. One of Schrag’s main concerns, in fact, is that geoengineering a lower global temperature might preserve ecosystems and limit sea-level rise while producing irreconcilable geopolitical frictions. “One thing I can’t figure out,” he told me, “is how do you protect the Greenland ice sheet and still have Russia have access to its northern ports, which they really like?” Either Greenland and Siberia will melt, or perhaps both can stay frozen. You probably can’t split the difference.

    For the moment, and perhaps for 10 or 20 years more, these are mere hypotheticals. But the impacts of climate change were once hypotheticals, too. Now they’ve become possibilities and probabilities. And yet, as Tom Ackerman, an atmospheric scientist at the University of Washington, said at a recent discussion among policy makers that I attended in Washington: “We are doing an experiment now that we don’t understand.” He was not talking about geoengineering; he was observing that the uncertainty about the potential risks of geoengineering can obscure the fact that there is uncertainty, too, about the escalating disasters that may soon result from climate change.

    His comment reminded me of a claim made more than a half-century ago, long before the buildup of CO₂ in the atmosphere had become the central environmental and economic problem of our time. Two scientists, Roger Revelle and Hans Suess, wrote in a scientific paper, “Human beings are now carrying out a large-scale geophysical experiment of a kind that could not have happened in the past nor be reproduced in the future.”

    If anything could sway a fence-sitter to consider whether geoengineering research makes sense, perhaps it is this. The fact is, we are living through a test already.

    See the full article here .

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  • richardmitnick 8:24 am on April 19, 2017 Permalink | Reply
    Tags: , Climate Change Reroutes a Yukon River in a Geological Instant, , , , Kaskawulsh Glacier, NYT, Slims River Valley   

    From NYT: “Climate Change Reroutes a Yukon River in a Geological Instant” 

    New York Times

    The New York Times

    APRIL 17, 2017
    JOHN SCHWARTZ

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    An aerial view of the ice canyon that now carries meltwater from the Kaskawulsh Glacier, on the right, away from the Slims River. “River piracy” refers to one river capturing and diverting the flow of another. Credit Dan Shugar/University of Washington-Tacoma

    In the blink of a geological eye, climate change has helped reverse the flow of water melting from a glacier in Canada’s Yukon, a hijacking that scientists call “river piracy.”

    This engaging term refers to one river capturing and diverting the flow of another. It occurred last spring at the Kaskawulsh Glacier, one of Canada’s largest, with a suddenness that startled scientists.

    A process that would ordinarily take thousands of years — or more — happened in just a few months in 2016.

    Much of the meltwater from the glacier normally flows to the north into the Bering Sea via the Slims and Yukon Rivers. A rapidly retreating and thinning glacier — accelerated by global warming — caused the water to redirect to the south, and into the Pacific Ocean.

    Last year’s unusually warm spring produced melting waters that cut a canyon through the ice, diverting more water into the Alsek River, which flows to the south and on into Pacific, robbing the headwaters to the north.

    2
    Jim Best, a researcher, measuring water levels on the lower-flowing Slims River in early September. Credit Dan Shugar/University of Washington-Tacoma

    The scientists concluded that the river theft “is likely to be permanent.”

    Daniel Shugar, an assistant professor of geoscience at the University of Washington-Tacoma, and colleagues described the phenomenon in a paper published on Monday in the journal Nature Geoscience.

    River piracy has been identified since the 19th century by geologists, and has generally been associated with events such as tectonic shifts and erosion occurring thousands or even millions of years ago. Those earlier episodes of glacial retreat left evidence of numerous abandoned river valleys, identified through the geological record.

    In finding what appears to be the first example of river piracy observed in modern times, Professor Shugar and colleagues used more recent technology, including drones, to survey the landscape and monitor the changes in the water coursing away from the Kaskawulsh Glacier.

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    Kaskawulsh glacier junction from air
    29 August 2014
    Author Gstest

    The phenomenon is unlikely to occur so dramatically elsewhere, Professor Shugar said in a telephone interview, because the glacier itself was forming a high point in the landscape and serving as a drainage divide for water to flow one way or another. As climate change causes more glaciers to melt, however, he said “we may see differences in the river networks and where rivers decide to go.”

    Changes in the flow of rivers can have enormous consequences for the landscape and ecosystems of the affected areas, as well as water supplies. When the shift abruptly reduced water levels in Kluane Lake, the Canadian Broadcasting Corporation reported, it left docks for lakeside vacation cabins — which can be reached only by water — high and dry.

    The riverbed of the Slims River basin, now nearly dry, experienced frequent and extensive afternoon dust storms through the spring and summer of last year, the paper stated.

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    The ice-walled canyon at the terminus of the Kaskawulsh Glacier, with recently collapsed ice blocks. This canyon now carries almost all meltwater from the toe of the glacier down the Kaskawulsh Valley and toward the Gulf of Alaska. Credit Jim Best/University of Illinois

    The impacts of climate change, like sea level rise or the shrinkage of a major glacier, are generally measured over decades, not months as in this case. “It’s not something you could see if you were just standing on the beach for a couple of months,” Professor Shugar said.

    The researchers concluded that the rerouted flow from the glacier shows that “radical reorganizations of drainage can occur in a geologic instant, although they may also be driven by longer-term climate change.” Or, as a writer for the CBC put it in a story about the phenomenon last year, “It’s a reminder that glacier-caused change is not always glacial-paced.”

    4
    Looking up the Slims River Valley, from the south end of Kluane Lake. The river used to flow down the valley from the Kaskawulsh glacier. (Sue Thomas)

    The underlying message of the new research is clear, said Dr. Shugar in a telephone interview. “We may be surprised by what climate change has in store for us — and some of the effects might be much more rapid than we are expecting.”

    The Nature Geoscience paper is accompanied by an essay from Rachel M. Headley, an assistant professor of geoscience and glacier expert at the University of Wisconsin-Parkside.

    “That the authors were able to capture this type of event almost as it was happening is significant in and of itself,” she said in an interview via email. As for the deeper significance of the incident, she said, “While one remote glacial river changing its course in the Yukon might not seem like a particularly big deal, glacier melt is a source of water for many people, and the sediments and nutrients that glacier rivers carry can influence onshore and offshore ecological environments, as well as agriculture.”

    Her article in Nature Geoscience concludes that this “unique impact of climate change” could have broad consequences. “As the world warms and more glaciers melt, populations dependent upon glacial meltwater should pay special attention to these processes.”

    Another glacier expert not involved in the research, Brian Menounos of the University of Northern British Columbia, said that while glaciers have waxed and waned as a result of natural forces over the eons, the new paper and his own research underscore the fact that the recent large-scale retreat of glaciers shows humans and the greenhouse gases they produce are reshaping the planet. “Clearly, we’re implicated in many of those changes,” he said.

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  • richardmitnick 7:43 am on April 4, 2017 Permalink | Reply
    Tags: , , NYT, We Have Some God News on the California Drought. Take a Look   

    From NYT: “We Have Some God News on the California Drought. Take a Look.” 

    New York Times

    The New York Times

    1

    MARCH 22, 2017
    MIKE McPHATE
    DEREK WATKINS
    JIM WILSON

    The majestic beauty of California’s Sierra Nevada never fails to impress. But the mountain range, which stretches hundreds of miles, is much more than a stunning vista. It’s a linchpin that helps make living in an arid state possible.

    That’s because one of California’s most important water supplies is melted snow. Each spring and summer, the Sierra sends runoff down its slopes that recharges rivers and reservoirs, allowing crops to be irrigated and drinking glasses to be filled.

    Knowing with precision how much snow has accumulated is crucial for farmers and water managers.

    That’s where a mapping project at NASA’s Jet Propulsion Laboratory known as the Airborne Snow Observatory comes in.

    2

    Using measurements gathered by specialized instruments on a plane, scientists have been able to gain an unprecedented understanding of the amount of water present in the Sierra’s snow.

    This year, after California’s very wet winter, the totals have been remarkably big.

    Using the NASA data, we compared this year’s snowpack with that of 2015, when the state was in the grip of drought (which, at least officially, is still ongoing). In the interactive maps below, the white areas had a meter, or 3.3 feet, or more of snow on the ground in March.

    High in the mountains, this year’s snow blankets the ground in layers tens of feet deep in many places.

    At the lower elevations around the Hetch Hetchy reservoir, which collects most of the melting snow runoff in this area and supplies water to millions, there was almost no snow to speak of in 2015. This year, the snowpack reached down to within a few hundred feet of the reservoir’s edge.

    These maps show parts of the Tuolumne Basin, which in late February was blanketed by 1.2 million acre-feet of snow-water equivalent, or the amount of water that would result if the snow were instantly melted.

    That’s about 10 times the amount as the same time in 2015, said Thomas Painter, a snow hydrologist at the NASA Jet Propulsion Laboratory/California Institute of Technology, who leads the NASA program.

    He added, “And it keeps on coming.”

    The pattern has held for the central Sierra region as a whole:

    3

    The airborne observatory has been detecting snow depths in the mountains ranging from a few feet at lower elevations to more than 70 feet in avalanche areas.

    “Some of the snowdrifts have faces of 25 to 40 feet,” said Jeffrey Payne, a water resources manager at the Friant Water Authority who has analyzed the NASA data. “So we’ve got some pretty serious snow.”

    4
    Strong winds created huge snowdrifts near the western cliffs of the Minarets in the central Sierra Nevada. Photo by Jim Wilson/The New York Times

    4
    Trees on a slope in the snow-covered eastern Sierra Nevada. Photo by Jim Wilson/The New York Times

    Ski resorts that typically close in the spring are so deeply blanketed that they have been making plans to extend their seasons.
    Officials at Squaw Valley, in the Lake Tahoe area, and Mammoth Mountain, below, in the eastern Sierra, said they anticipated staying open well into summer.

    6
    Skiers at Mammoth Mountain. Photo by Jim Wilson/The New York Times

    7
    A snow-covered ridge on the western slope of the central Sierras. Photo by Jim Wilson/The New York Times

    The snow observatory project, which began flights over the Sierra in 2013, is a groundbreaking initiative in California, where aging infrastructure, a warming climate and rapid population growth have made water management a high-stakes job.

    For decades, state officials have estimated snowpack levels by extrapolating from ground-based data gathered at points across the range.

    The margin of error, unsurprisingly, has been huge.

    “It’s like turning on your TV screen and four of the pixels turn on, and you can only use those four every single time you watch ‘Breaking Bad,’” Dr. Painter said.

    Every one to four weeks, the NASA crew circles above the Sierra Nevada in an airplane that fires laser pulses toward the ground. By measuring how fast the pulses bounce back, the scientists are able to create detailed topographical maps.

    Compare those with maps of the mountains when bare and factor in the snow’s density, and they can tell how much water is present.

    With the view from the sky, Dr. Painter said, “we turn on the whole screen, every pixel.”

    8
    Thomas Painter on the steps of the plane NASA uses to gauge snow depth. Photo by Jim Wilson/The New York Times

    9
    Dr. Painter with a device that uses laser beams to precisely measure topography.

    The observatory also measures the reflection of sunlight off the snow, which is critical to understanding how much energy the snow absorbs and how fast it could melt.

    Mr. Payne of the Friant Water Authority, which manages water for agricultural land in the San Joaquin Valley, said the new snow data was game-changing for farmers, who will be able to plan their crops with greater confidence.

    “We need to be smarter about how we approach water resource management,” Mr. Payne said. “And this new technology is sort of a beacon of hope.”

    For now, the observatory is taking measurements for most of the central Sierra Nevada. The hope is to get more buy-in from state officials and expand to the whole range, Dr. Painter said.

    It has been an increasingly easy sell.

    “It really has gotten to the point now where we don’t call on anyone,” Dr. Painter said. “We are simply responding to phone calls.”

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  • richardmitnick 7:19 am on March 28, 2017 Permalink | Reply
    Tags: , , , , NYT,   

    From NYT: “A Dream of Clean Energy at a Very High Price”, a Now Too Old Subject 

    New York Times

    The New York Times

    MARCH 27, 2017
    HENRY FOUNTAIN

    1
    Source: ITER Organization Mika Gröndahl/The New York Times

    SAINT-PAUL-LEZ-DURANCE, France — At a dusty construction site here amid the limestone ridges of Provence, workers scurry around immense slabs of concrete arranged in a ring like a modern-day Stonehenge.

    It looks like the beginnings of a large commercial power plant, but it is not. The project, called ITER, is an enormous, and enormously complex and costly, physics experiment. But if it succeeds, it could determine the power plants of the future and make an invaluable contribution to reducing planet-warming emissions.

    ITER, short for International Thermonuclear Experimental Reactor (and pronounced EAT-er), is being built to test a long-held dream: that nuclear fusion, the atomic reaction that takes place in the sun and in hydrogen bombs, can be controlled to generate power.

    First discussed in 1985 at a United States-Soviet Union summit, the multinational effort, in which the European Union has a 45 percent stake and the United States, Russia, China and three other partners 9 percent each, has long been cited as a crucial step toward a future of near-limitless electric power.

    ITER will produce heat, not electricity. But if it works — if it produces more energy than it consumes, which smaller fusion experiments so far have not been able to do — it could lead to plants that generate electricity without the climate-affecting carbon emissions of fossil-fuel plants or most of the hazards of existing nuclear reactors that split atoms rather than join them.

    Success, however, has always seemed just a few decades away for ITER. The project has progressed in fits and starts for years, plagued by design and management problems that have led to long delays and ballooning costs.

    ITER is moving ahead now, with a director-general, Bernard Bigot, who took over two years ago after an independent analysis that was highly critical of the project. Dr. Bigot, who previously ran France’s atomic energy agency, has earned high marks for resolving management problems and developing a realistic schedule based more on physics and engineering and less on politics.

    “I do believe we are moving at full speed and maybe accelerating,” Dr. Bigot said in an interview.

    The site here is now studded with tower cranes as crews work on the concrete structures that will support and surround the heart of the experiment, a doughnut-shaped chamber called a tokamak. This is where the fusion reactions will take place, within a plasma, a roiling cloud of ionized atoms so hot that it can be contained only by extremely strong magnetic fields.

    2
    By The New York Times

    Pieces of the tokamak and other components, including giant superconducting electromagnets and a structure that at approximately 100 feet in diameter and 100 feet tall will be the largest stainless-steel vacuum vessel ever made, are being fabricated in the participating countries. Assembly is set to begin next year in a giant hall erected next to the tokamak site.

    3
    At the ITER construction site, immense slabs of concrete lie in a ring like a modern-day Stonehenge. Credit ITER Organization

    There are major technical hurdles in a project where the manufacturing and construction are on the scale of shipbuilding but the parts need to fit with the precision of a fine watch.

    “It’s a challenge,” said Dr. Bigot, who devotes much of his time to issues related to integrating parts from various countries. “We need to be very sensitive about quality.”

    Even if the project proceeds smoothly, the goal of “first plasma,” using pure hydrogen that does not undergo fusion, would not be reached for another eight years. A so-called burning plasma, which contains a fraction of an ounce of fusible fuel in the form of two hydrogen isotopes, deuterium and tritium, and can be sustained for perhaps six or seven minutes and release large amounts of energy, would not be achieved until 2035 at the earliest.

    That is a half century after the subject of cooperating on a fusion project came up at a meeting in Geneva between President Ronald Reagan and the Soviet leader Mikhail S. Gorbachev. A functional commercial fusion power plant would be even further down the road.

    “Fusion is very hard,” said Riccardo Betti, a researcher at the University of Rochester who has followed the ITER project for years. “Plasma is not your friend. It tries to do everything it can to really displease you.”

    Fusion is also very expensive. ITER estimates the cost of design and construction at about 20 billion euros (currently about $22 billion). But the actual cost of components may be higher in some of the participating countries, like the United States, because of high labor costs. The eventual total United States contribution, which includes an enormous central electromagnet capable, it is said, of lifting an aircraft carrier, has been estimated at about $4 billion.

    Despite the recent progress there are still plenty of doubts about ITER, especially in the United States, which left the project for five years at the turn of the century and where funding through the Energy Department has long been a political football.

    The department confirmed its support for ITER in a report last year and Congress approved $115 million for it. It is unclear, though, how the project will fare in the Trump administration, which has proposed a cut of roughly 20 percent to the department’s Office of Science, which funds basic research including ITER. (The department also funds another long-troubled fusion project, which uses lasers, at Lawrence Livermore National Laboratory in California.)

    Dr. Bigot met with the new energy secretary, Rick Perry, last week in Washington, and said he found Mr. Perry “very open to listening” about ITER and its long-term goals. “But he has to make some short-term choices” with his budget, Dr. Bigot said.

    Energy Department press aides did not respond to requests for comment.

    Some in Congress, including Senator Lamar Alexander, Republican of Tennessee, while lauding Dr. Bigot’s efforts, argue that the project already consumes too much of the Energy Department’s basic research budget of about $5 billion.

    “I remain concerned that continuing to support the ITER project would come at the expense of other Office of Science priorities that the Department of Energy has said are more important — and that I consider more important,” Mr. Alexander said in a statement.

    While it is not clear what would happen to the project if the United States withdrew, Dr. Bigot argues that it is in every participating country’s interest to see it through. “You have a chance to know if fusion works or not,” he said. “If you miss this chance, maybe it will never come again.”

    But even scientists who support ITER are concerned about the impact it has on other research.

    “People around the country who work on projects that are the scientific basis for fusion are worried that they’re in a no-win situation,” said William Dorland, a physicist at the University of Maryland who is chairman of the plasma science committee of the National Academy of Sciences. “If ITER goes forward, it might eat up all the money. If it doesn’t expand and the U.S. pulls out, it may pull down a lot of good science in the downdraft.”

    In the ITER tokamak, deuterium and tritium nuclei will fuse to form helium, losing a small amount of mass that is converted into a huge amount of energy. Most of the energy will be carried away by neutrons, which will escape the plasma and strike the walls of the tokamak, producing heat.

    In a fusion power plant, that heat would be used to make steam to turn a turbine to generate electricity, much as existing power plants do using other sources of heat, like burning coal. ITER’s heat will be dissipated through cooling towers.

    There is no risk of a runaway reaction and meltdown as with nuclear fission and, while radioactive waste is produced, it is not nearly as long-lived as the spent fuel rods and irradiated components of a fission reactor.

    To fuse, atomic nuclei must move very fast — they must be extremely hot — to overcome natural repulsive forces and collide. In the sun, the extreme gravitational field does much of the work. Nuclei need to be at a temperature of about 15 million degrees Celsius.

    In a tokamak, without such a strong gravitational pull, the atoms need to be about 10 times hotter. So enormous amounts of energy are required to heat the plasma, using pulsating magnetic fields and other sources like microwaves. Just a few feet away, on the other hand, the windings of the superconducting electromagnets need to be cooled to a few degrees above absolute zero. Needless to say, the material and technical challenges are extreme.

    Although all fusion reactors to date have produced less energy than they use, physicists are expecting that ITER will benefit from its larger size, and will produce about 10 times more power than it consumes. But they will face many challenges, chief among them developing the ability to prevent instabilities in the edges of the plasma that can damage the experiment.

    Even in its early stages of construction, the project seems overwhelmingly complex. Embedded in the concrete surfaces are thousands of steel plates. They seem to be scattered at random throughout the structure, but actually are precisely located. ITER is being built to French nuclear plant standards, which prohibit drilling into concrete. So the plates — eventually about 80,000 of them — are where other components of the structure will be attached as construction progresses.

    A mistake or two now could wreak havoc a few years down the road, but Dr. Bigot said that in this and other work on ITER, the key to avoiding errors was taking time.

    “People consider that it’s long,” he said, referring to critics of the project timetable. “But if you want full control of quality, you need time.”

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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
    JULIA WALLACE

    1
    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.”

    3
    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.

    4
    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.

    5
    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.

    6
    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.

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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
    DONALD G. McNEIL Jr.
    Photographs by ISMAIL FERDOUS FOR THE NEW YORK TIMES

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

    1

    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.

    2
    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.

    3
    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.

    4
    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.

    5
    6
    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.

    7
    8
    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.

    9
    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.

    10
    “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.

    10
    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
    NATALIE ANGIER

    1
    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
    NATALIE ANGIER

    1
    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.

    2
    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.

    3
    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.

    4
    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.”

    See the full article here .

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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
    HENRY FOUNTAIN

    1
    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.

    See the full article here .

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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
    DONALD G. McNEIL Jr.

    1
    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.

    2
    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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