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  • richardmitnick 6:10 am on February 24, 2015 Permalink | Reply
    Tags: Applied Research & Technology, English, Linguistics,   

    From NYT: “The Tangled Roots of English” 

    New York Times

    The New York Times

    FEB. 23, 2015

    The peoples of India, Iran and Europe speak a Babel of tongues, but most — English included — are descended from an ancient language known as proto-Indo-European. Scholars have argued for two centuries about the identity and homeland of those who spoke this parent language, but a surprisingly sudden resolution of this longstanding issue may be at hand.

    Many origins have been proposed for the birthplace of the Indo-European languages, but only two serious candidates are now under discussion, one of which assumes they were spread by the sword, the other by the plow.

    Historical linguists can reconstruct many words of proto-Indo-European from their descendants. For example, there was probably a word “kwekwlos,” meaning wheel, which is the ancestor of “kuklos” in classical Greek, of “kakra” in Old Indic and – because K shifts to H in Germanic languages – of “hweohl” in Old English, itself the ancestor of wheel in modern English.

    From the reconstructed vocabulary, the speakers of proto-Indo-European seem to have been pastoralists, familiar with sheep and wheeled vehicles. Archaeologists find that wheeled vehicles emerged around 4000 B.C., suggesting the proto-Indo-European speakers began to flourish some 6,500 years ago on the steppe grasslands above the Black and Caspian Seas. This steppe theory, favored by many linguists, holds that the proto-Indo-European speakers then spread their language to Europe, India and western China, whether by conquest or the appeal of their pastoral economy.

    This theory was challenged by Colin Renfrew, a Cambridge archaeologist who proposed in 1987 that the languages had been spread by the Neolithic farmers who brought agriculture to Europe. Under this scenario, the homeland of proto-Indo-European was in Anatolia, now Turkey, and its speakers started migrating some 8,000 to 9,500 years ago.

    Dr. Renfrew’s proposal carried weight because the expansion of farming peoples is an accepted mechanism of language spread, and the migration of Neolithic farmers into Europe is well documented archaeologically. Linguists objected that proto-Indo-European could not have fragmented so early because the wheel wasn’t invented 8,000 years ago, yet many Indo-European languages have related words for wheel that must be derived from a common parent. But Dr. Renfrew argued that, long after their dispersal, these languages could all have borrowed the word for wheel along with the invention itself.

    Source http://norse-mythology.org/indo-europeans-matter/ [Not from the article.]

    The standoff between the steppe and Anatolian theories of Indo-European origin persisted until 2003. Two New Zealand biologists, Russell Gray and Quentin Atkinson of the University of Auckland, entered the fray with an impressive method of constructing datable trees of language descent. Historical linguists had drawn up trees of how proto-Indo-European had split into its daughter languages, based on sets of related words known as cognates. The word for water is “wasser” in German, “vatten” in Swedish and “nero” in modern Greek. The similar English, German and Swedish words are said to be cognates, derived from an inferred proto-Indo-European word “wodr,” but the “nero” of modern Greek is not.

    Linguists had hoped that by comparing languages in terms of how many cognates they shared, the Indo-European tree could be dated. But after discovering that the rates of language change varied widely from one branch to another, they largely gave up.

    Dr. Gray and Dr. Atkinson realized that statistical methods developed by biologists for tracking the evolution of genes and proteins addressed many of the problems that exist in reconstructing trees of language descent. They represented each Indo-European language as a string of 1s and 0s, depending on whether it shared cognates for a list of words known to resist change. They then computed the likeliest of the many possible trees that would give rise to the observed data.

    Their preferred tree of Indo-European languages had the same shape as that constructed by historical linguists. But its lower branches could be dated from historical events like the split between Latin and Rumanian when Roman troops withdrew south of the Danube in A.D. 270. And with the lower branches anchored in time, they could date the root. Proto-Indo-European, they calculated, was spoken 7,800 to 9,800 years ago.

    That conclusion provided striking support for the Anatolian theory. Dr. Gray and Dr. Atkinson, with Remco Bouckaert and colleagues, dropped a second shoe in 2012 when they applied to the dispersal of proto-Indo-European a statistical model developed to track the geographical spread of viruses. It showed “decisive support for an Anatolian origin over a steppe origin,” the authors concluded in an article in Science.

    It seemed that with the biologists’ help, the archaeologists’ Anatolian theory had triumphed over the linguists’ steppe hypothesis. But two findings reported this month have abruptly tilted the weight of evidence toward the steppes.

    Though some linguists had dismissed the Gray and Atkinson result, others realized their computational approach had much to offer. Andrew Garrett, a linguist at the University of California, Berkeley, has teamed up with Will Chang, a linguist trained in computational techniques. They and colleagues noticed that in the 2012 article by Dr. Bouckaert and others, in eight cases where an ancient language is the widely assumed ancestor of a modern one, the modern language is shown as being descended from a hypothetical cousin of the ancient language.

    For example, the Romance languages are assigned to a hypothetical cousin of Latin, not Latin itself, and English to an inferred cousin of Old English.

    Dr. Garrett and Mr. Chang thought it would be more realistic for the tree to adopt generally accepted language ancestries, even though this required overruling its probability calculations.

    Origins of an Ancient Language
    Researchers place the homeland of the proto-Indo-European language, the ancestor of many modern languages spoken across Europe and Asia, in either the steppes north of the Black Sea or in Anatolia, modern Turkey.

    Sources: Wolfgang Haak et al., bioRchiv; “The Horse, the Wheel and Language” by David W. Anthony By The New York Times

    When the Bouckaert tree was forced to adopt the eight accepted language ancestries, Dr. Garrett and Mr. Chang and colleagues report in the journal Language, the whole tree shrank in age and its root stepped down to 6,500 years old, in agreement with the steppe hypothesis of Indo-European origins.

    A second boost for the steppe theory has emerged from the largest study of ancient DNA in Europe, based on analysis of 69 people who lived 3,000 to 8,000 years ago. Patterns in the DNA bear evidence of a migration into Germany some 4,500 years ago of people from the Yamnaya culture of the steppes, the first to develop a pastoral economy based on wagons, sheep and horses. So extensive was this migration that three-quarters of the ancient people sampled in Germany bear Yamnaya-type DNA, says a team led by Wolfgang Haak of the University of Adelaide, Australia, and David Reich of Harvard Medical School. Their report was posted this month on bioRxiv.

    If so much of the population was replaced, the newcomers’ language probably prevailed, and the migration plausibly represents an expansion of Indo-European speakers from the steppes. “These results provide support for the theory of a steppe origin of at least some of the Indo-European languages of Europe,” the authors say.

    The three oldest branchings of the Indo-European tree, according to Don Ringe, a historical linguist at the University of Pennsylvania, are first, languages such as Hittite once spoken in Anatolia; second, Tocharian, a language group of western China; and third, the Italic and Celtic language groups of Europe. Archaeological evidence attests migrations out of the steppe in these directions in the right order, say Dr. Ringe and David Anthony, an archaeologist at Hartwick College, writing in the Annual Review of Linguistics.

    They also note that proto-Indo-European has borrowed words from proto-Uralic, the inferred ancestor of languages such as Hungarian, Finnish and Estonian, and from languages of the Caucasus. A location in the steppes, but not in Anatolia, would make such borrowings geographically plausible. The evidence for a steppe origin of the Indo-European languages “is so strong that arguments in support of other hypotheses should be re-examined,” Drs. Ringe and Anthony say.

    But the case is not yet closed. The two new pieces of evidence, Dr. Garrett’s correction of the Bouckaert tree and the ancient DNA data, may not be as conclusive as they seem.

    Dr. Renfrew, the author of the Anatolian hypothesis, considers it a “strong possibility” that the migration from the steppes to Europe recorded in ancient DNA may be a secondary phenomenon. In other words, Indo-European could have spread first from Anatolia to the steppes and from there to Europe.

    And the biologists who draw up statistically probable language trees do not believe the Garrett team is justified in making the trees conform to ancestry constraints. “The Garrett and Chang model is overzealous in forcing ancient languages to be directly ancestral – the data don’t support this,” said Dr. Atkinson, referring to new tests he has done.

    One reason is that written languages tend to be fossilized, said Paul Heggarty, a linguist at the Max Planck Institute for Evolutionary Biology: Living languages are likely to be descended from a spoken language that diverged from the written version.

    “The seemingly innocent assumptions which Garrett introduces,” Dr. Renfrew said, “turn out not to be so uncomplicated.”

    See the full article here.

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  • richardmitnick 5:34 am on February 24, 2015 Permalink | Reply
    Tags: Applied Research & Technology, , ,   

    From NYT: “I’ve Just Seen a (DNA-Generated) Face” 

    New York Times

    The New York Times

    Predictions of what people look like using a DNA analysis tool compared with photos of the actual people. Credit The New York Times; Images and renderings by Mark D. Shriver/Penn State University

    The faces here, which look a bit like video game avatars, are actually portraits drawn from DNA.

    Each rendering was created by plugging an individual genetic profile into a predictive tool created by Mark D. Shriver, a professor of anthropology and genetics at Penn State University. Dr. Shriver and his colleagues have studied the ways that genes influence facial development.

    Their software yields an image in a matter of minutes, rapidly drawing connections beween genetic markers and points on the face. In less time than it takes to make a cup of coffee, a sketch emerges inferred solely from DNA.

    How accurate or useful are these predictions? That is something that Dr. Shriver is still researching – and that experts are still debating. Andrew Pollack writes about the issues in an article on genetic sleuthing in Science Times.

    On The New York Times’s science desk, we wondered whether it would be possible to identify our colleagues based on the formula that Dr. Shriver has developed. So we tried a somewhat unscientific experiment.

    We asked New York Times employees if they could identify their colleagues based on these DNA renderings, explaining that these were not adjusted for age. Credit Mark D. Shriver/Penn State University

    John Markoff, a reporter, and Catherine Spangler, a video journalist, each volunteered to share their genetic profile, downloaded from 23andMe, a consumer DNA-testing company. The files we sent to Dr. Shriver did not include their names or any information about their height, weight or age.

    Dr. Shriver processed the genotype data and sent us renderings of the donors’ faces.

    We distributed the images to colleagues via email and a private Facebook group, and asked them if they could identify these individuals. We told them that because age and weight could not be determined from DNA, the person might be older or younger, heavier or lighter than the image suggested. At least a dozen people immediately responded that they could not guess because the images felt too generic. Among the 50 or so people who did venture guesses, none identified the man as Mr. Markoff, who is 65.

    The man who received the most votes was Andrew Ross Sorkin, a business columnist and editor of Dealbook. A number of other possibilities were suggested, too — mostly white men who work on the science desk.

    The correct answer — that no one guessed — was John Markoff. New York Times employees were shown the face, top right. Dr. Shriver’s team later adjusted for age and height and the bottom right image emerged.

    When it came to the computer’s DNA portrait of Ms. Spangler, 31, staffers had more luck. About 10 people correctly identified her.

    Although there was no close second, participants put forth the names of nearly 10 other women. About half of them were of European ancestry, half of Asian ancestry.

    To build his model, Dr. Shriver measured 7,000 three-dimensional coordinates on the face and analyzed their links to thousands of genetic variants. Though sex and ancestral mix are not the only predictor of face shape in this model, they are the primary influencers — something that has raised concerns about the potential for racial profiling.

    About ten employees correctly guessed Catherine Spangler. Employees were shown the top right image. The face, bottom right, was adjusted for age, weight and height

    Ms. Spangler’s ancestry is half Korean and half northern European. Mr. Markoff’s is almost entirely Ashkenazi Jewish, with a tenth of a percent Asian, according to his 23andMe analysis.

    Using DNA portraiture, would every male or female with these genetic percentages wind up looking exactly the same? Dr. Shriver says no.

    “People with same ancestry levels can come out looking different,” he said. But just how different — and how much like the actual flesh-and blood-person — is something he and his team are still testing.

    See the full article here.

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  • richardmitnick 5:11 am on February 24, 2015 Permalink | Reply
    Tags: Applied Research & Technology, , Siberian Times   

    From The Siberian Times: “Is this 415 million-year-old fish our earliest known human ancestor?” 

    Siberian Times

    The Siberian Times

    18 February 2015
    Derek Lambie

    Tests on tiny scull found in Siberia give breakthrough on evolution and could hint at the ‘missing link’ to mankind’s origins.

    ‘It’s a very interesting fossil, and it’s very small. It’s surprising that something so tiny could have so much information in it.’ Picture: Samantha Giles

    A tiny 415 million-year-old fish skull found in Siberia could provide the so-called ‘missing link’ to the origins of human kind, scientists have claimed. With many common characteristics to animals that live in the sea, many palaeontologists believe we began life in the water and evolved from fish. Now the miniscule remains, just two centimetres in width and still embedded in rock, have added weight to that theory and could give clues about what our earliest ancestor looked like. Originally uncovered in the 1970s on Putorana Plateau, the fossil was recently re-examined in the United Kingdom using state-of-the-art 3D scanning equipment. There are two main types of living jawed vertebrates: those made of bone and those made of cartilage. But what scientists found was that the ancient fish’s brain case had the characteristics of both modern-day bony fish, such as salmon and trout, and fish made of cartilage, including sharks and manta rays. It means the fossil is likely to be one of the common ancestors of the two groups, which split apart 420 million years ago, and could offer hints about the origins of all jawed vertebrates, including reptiles and humans. The findings, published in the international scientific journal Nature, have been heralded by some palaeontologists as being ‘truly remarkable’.

    Janusiscus schultzei is likely to be one of the common ancestors of the two groups, which split apart 420 million years ago, and could offer hints about the origins of all jawed vertebrates, including reptiles and humans. Picture: Samantha Giles

    Samantha Giles, the lead researcher and a paleobiology doctoral candidate at Oxford University, said: ‘It’s a very interesting fossil, and it’s very small. It’s surprising that something so tiny could have so much information in it. ‘There are over 60,000 species of living jawed vertebrates, and they encompass pretty much everything you can think of [with a backbone] that lives on land or in the sea. But we don’t really know what they looked like when they split.’ When the small fossil was first discovered, scientists classified the specimen as a bony fish and no further examination of it was done until recently. Ms Giles and her research team used a CT scanner to look at the skull and create a three-dimensional model by taking hundreds of images from different angles. The detailed scans showed that the fish had sensory line canals on its skull, like those used by bony fish on the outside of their bodies to sense changes in the pressure around them and avoid predators. But, crucially, it also shared characteristics with cartilaginous fish, with blood vessels inside the skull, above and between the jaws, to supply oxygen to its brain. The fossil was named Janusiscus schultzei in honour Janus the Roman god of transitions who is often shown with two faces, and Hans-Peter Schultze, from the University of Kansas and who first described it in 1977.

    Putorana Plateau, where the fossil was found in 1972. Picture: Cont

    Many believe humans evolved from some form of fish life, with a number of our current anatomical characteristics — including the way embryos are formed, the existence of the philtrum groove below our noses and the way in which people hiccup – thought to stem from our time in the water. John Long, a professor of palaeontology at Flinders University in Adelaide, described the findings at Oxford as ‘truly remarkable’. He told the Live Science website: ‘I think it is a highly significant discovery, as the origin and diversification of modern bony-jawed fishes is still shrouded in mystery. But Janusiscus takes us a big step closer to really understanding this major evolutionary transition, from primitive jawed fishes to the beginning of the modern jawed fish fauna.’ Sadly scientists were unable to find out more about the jawed fish because its jaw was actually missing from the fossil. Ms Giles said: ‘Presumably, the jaw is in a middle of the river somewhere in Siberia.’

    See the full article here.

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  • richardmitnick 4:36 am on February 24, 2015 Permalink | Reply
    Tags: Applied Research & Technology, , Giant Siberian Craters,   

    From Siberian Times: “How global warming could turn Siberia into a giant crater ‘time bomb’” 

    Siberian Times

    The Siberian Times

    25 December 2014
    Anna Liesowska & Derek Lambie

    Scientists say there is growing evidence that rising temperatures were catalyst for massive unexplained holes in ground.

    Scientists studying one of the massive holes on the Yamal Peninsula say there is growing evidence that rising temperatures is the main catalyst. Picture: Vladimir Pushkarev/Russian Centre of Arctic Exploration

    Global warming could leave parts of Siberia exposed to a wave of underground explosions like those behind the recent unexplained giant craters phenomenon. Scientists studying one of the massive holes on the Yamal Peninsula say there is growing evidence that rising temperatures is the main catalyst triggering the blasts. They believe warming air is melting the thick permafrost, leading to the accumulation and release of volatile ‘fire ice’ gases which then explodes to create the giant funnels. Overall temperatures in Yamal, in northwest Siberia, in the past 14 years alone have risen by at least two degrees Celsius. Any continued increase – as is predicted by meteorologists – could create the ideal conditions for more craters to be formed across the icy region, and other parts of Siberia.

    July 2014, the first scientific expedition has just returned from the site with first probes. Pictures: Marya Zulinova, Yamal regional government’s press service

    There is already speculation that Lake Baikal, the largest and oldest freshwater lake in the world, could also be sitting on a ‘time bomb’ ready to explode. The scenic stretch of water, which snakes for 400 miles through south-east Siberia, has massive reserves of the volatile ‘fire ice’ buried under ground. A number of craters have appeared across Siberia over the past few years, with the first spotted in 2013 by helicopter pilots 20 miles from a gas extraction plant at Bovanenkov. The second was in the same permafrost region of northern Russia, and the third on the Taymyr Peninsula, to the east, in the Krasnoyarsk region. Their emergence has baffled scientists, who have carried out extensive tests including taking ice probes, sampling gas levels and examining the crater walls. A number of expeditions have taken place to the Yamal hole, the latest of which was at the beginning of November. Since then several conferences, seminars and meetings have been held by scientists and other experts to share their opinions about what caused it.

    This new crater near the village of Nosok on Taimyr and in the Taz district, near the village of Antipayuta. Pictures: Local residents, Yamal regional government’s press service

    The latest data suggests the crater was formed at some point between October 9 and November 1, 2013. A consensus is beginning to grow that elevated levels of the crystallised ‘fire ice’ gas is causing the explosions in the same way as eruptions below the Atlantic may be behind the Bermuda Triangle phenomenon. It is thought permafrost at the sites could have one million times more methane hydrates locked inside than ordinary gas. But what is causing this gas to erupt has caused great divide, although many scientists now believe there is a link to the rising temperatures in the region. One of the first to view the site was Marina Leibman, a senior researcher at the Institute of the Earth’s Cryosphere, of the Siberian Branch of the Russian Academy of Sciences. She is convinced global warming is to blame, and told this to delegates at the recent Scientific Conference on Arctic Exploration. Dr Leibman told the Siberian Times: ‘We have agreed that in the area of Bovanenkovo there was an emission of gas and gas hydrates caused by the heating of the earth’s surface and geological features of the site. These phenomena caused the formation of crater. ‘In the last 14 years, the overall temperature in the depths of the Yamal has increased by at least two degrees Celsius. ‘In some areas of the region seasonal thawing of permafrost may affect the upper layers of ice and, under certain circumstances, cause thawing and dissociation of gas hydrates.’ She added: ‘I would argue this is a new process, which was not observed previously. It can be seen as a reaction to changes in the temperature, which releases gas, possibly hidden in the form of relic hydrate, from the upper layers of permafrost.’

    Marina Leibman and Andrey Plekhanov making measurments at the site. Pictures: Marya Zulinova, Yamal regional government’s press service

    One expert said more eruptions could prove deadly, with estimates that the total explosive power of the craters has been the equivalent of about 11 tonnes of TNT. Larissa Kozhina, the head of the laboratory centre of hydrocarbon resources and reserves at energy firm Gazprom, said: ‘The crater at Bovanenkovo is above the gas trap, where prospective reserves are estimated at 17 billion cubic meters. What does this mean? All fields, all pipelines and railway tracks could be affected by such dangerous objects behind them and should be monitored.’ Formed in a near-perfect cylinder, the Yamal crater is slightly wider at the surface and has smooth walls, with a frozen lake at the bottom. During recent examinations of the site, thawed out permafrost was found 200metres from the top of the crater. About a third of the crater is filled with water because of its melting walls and rain, and it is thought that within three years it will be almost full. Initially it was thought that by 2024 it will be difficult to see the 40 metres wide and 50 metres deep crater at all as it will be completely submerged by a lake. But Dr Leibman told the Siberian Times that the crater may already be under water from the melting ice by next year. She said: ‘Judging by the pace, by the end of next summer it may turn into a lake. ‘I once heard a theory that deep Yamal lakes were mostly the result of emissions of gas. Then I just laughed at it. Now I take back my laughter: I think that a lot of deep lakes on Yamal were formed in this way.’

    Scientists from ‘Gazprom VNIIGAZ’ and the Trofimuk Petroleum-Gas Geology and Geophysics Institute study the crater in September. Pictures: Gazprom

    Other scientists disagree with that theory, however, and say that the permafrost is being melted by underground heat from tectonic plates. ‘The Yamal crater is located at the intersection of tectonic faults,’ said Vladimir Olenchenko, a senior researcher in the Laboratory of Geo-electrics at the Institute of Petroleum Geology and Geophysics in Novosibirsk. ‘Despite the fact the region itself is seismically quiet area, there is an active tectonic life. Of course, it says the following: there was a slightly higher temperature, simply because heat rises from the centre of our planet via these cracks in the earth’s crust. It warmed the permafrost. ‘Or the warm stream could come from the oil and gas deposits lying under the funnel.’ There are two tectonic fault lines across the Yamal Peninsula, with one possibility being that the blow-out was caused by a deadly combination of heat leaving these rifts, a higher than normal air temperature, and the ‘fire ice’ melting. In November the Siberian Times told how scientists have been carrying out tests in the funnel to see if it could harness a new, highly efficient, gas energy source of the future. Japan, Canada and the United States have all ploughed millions of dollars into research projects to uncover and utilise global reserves of methane hydrate, as oil and coal dwindle. But now the discovery of the compound within the Siberian craters could give Russia the lead in the race to dominate the market over the next century.

    The latest expedition to Yamal crater was initiated by the Russian Centre of Arctic Exploration in early November 2014. Pictures: Vladimir Pushkarev/Russian Centre of Arctic Exploration

    When the Yamal hole first appeared, many odd theories were put forward to explain the phenomenon, including that it was a stray missile, a meteorite or even the work of aliens. A research team from the Trofimuk Petroleum-Gas Geology and Geophysics Institute said there is evidence all the craters could be linked to the Bermuda Triangle. Explosions under the Atlantic Ocean caused by high gas hydrate emissions are thought to explain part of the mystery of ships and aircraft disappearing. Ironically the name Yamal means ‘the end of the world’, the same description applied to the Bermuda Triangle, off the Florida coastline. Further tests at the site will take place in April, if there is sufficient funding in place. Dr Leibman said: ‘To understand and describe this phenomena fully, we need to do it seriously and not in a hurry. ‘I hope that we will have opportunity to go to the funnel next year. Now we have more information and we know better about which measurements we need and which equipment we need to take.’

    See the full article here.

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  • richardmitnick 4:04 am on February 24, 2015 Permalink | Reply
    Tags: Applied Research & Technology, , ,   

    From Huff Post: “Here’s What Will Happen To New York City If The World’s Ice Sheets Melt” 

    Huffington Post
    The Huffington Post

    Christopher Mathias


    A disconcerting report released last week revealed that New York City could see a 6-foot rise in sea levels by the end of this century. It would make nearly half a million New Yorkers vulnerable to flooding, and waterfront properties would be virtually uninhabitable.

    But what if climate change continues unabated for even longer? What will New York City look like if, say, both the Antarctic and Greenland ice sheets melt completely, raising sea levels an estimated 260 feet?

    Urban planner and cartographer Jeffrey Linn used computerized mapping to make a GIF demonstrating just that. Watch the city’s five boroughs disappear, with only the lofty heights of New Jersey’s Pallisades left as an island:


    Linn, who posted the GIF on his blog Spatialities, told The Huffington Post he wanted to show people what the city would look like after “the terminal point for ice caps melting,” which some scientists estimate could happen in 1,000 to 10,000 years.

    “What would the world around me look like, where I live, if in thousands of years, this is supposed to happen?” Linn said he wondered.

    Linn also made this mesmerizing map of New York City after only 100 feet of sea level rise. The city’s neighborhoods and parks are cleverly rechristened with more nautical nomenclatures: Central Park is Central Shark, Bushwick is Flushwick, the West Village is Wet Village, and so on:


    He’s made similarly alarming maps for his hometown of Seattle, as well as London and Montreal, among other cities.

    The polar ice caps are melting at an alarming rate, as manmade greenhouse gas emissions continue to trap the sun’s heat. Here, for example, is a 2012 video showing a lower Manhattan-sized piece of ice breaking off from the Greenland ice sheet:

    See the full article here.

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  • richardmitnick 3:52 am on February 24, 2015 Permalink | Reply
    Tags: Applied Research & Technology, , Great Dying   

    From CSIRO: “Understanding the Great Dying: does the secret to a past mass extinction lie in volcanic bubbles?” 

    CSIRO bloc

    Commonwealth Scientific and Industrial Research Organisation

    February 24, 2015
    Keirissa Lawson

    Trilobites graced the Earth for 270 million years until they were wiped out in the ‘Great Dying’. Image Credit: http://news.bbc.co.uk/2/hi/in_pictures/8398477.stm

    Around 250 million years ago, an extinction event took place that was unprecedented in its size and scale. Known colloquially as the ‘Great Dying’, the Permian Triassic extinction event wiped 90 percent of species (both marine and terrestrial) forever from the map. It is the largest recorded mass extinction event in Earth’s history, and was estimated to have set biological evolution back by tens of millions of years.

    There are many theories as to the cause of this Great Dying, ranging from giant meteor impacts to massive volcanic eruptions. In a paper published today in Nature Geoscience, a team of our researchers have supported the case for a much tinier – yet no less fascinating – contributor to the kill: methane-producing bacteria, fed from the bowels of the earth.

    Silent but deadly

    During this ancient era, massive methane-producing bacterial blooms, nourished by volcanic atmospheric nickel, are thought to have disrupted the carbon cycle and released toxic levels of methane and carbon dioxide – resulting in a runaway greenhouse effect on the Earth’s atmosphere.

    But how did these levels of nickel come to be released into the atmosphere? Rock records have revealed massive volcanic eruptions occurred during this period, yet the notion that nickel would be released into the atmosphere during eruptions was not widely believed by scientists who study magmas and volcanoes.

    Our research team, led by Dr Stephen Barnes in collaboration with Prof. James Mungall from the University of Toronto, are proposing that metals like nickel, which are normally concentrated at the bottom of magma chambers, hitched a ride to the atmosphere on the back of vapour bubbles, also forming rich ore deposits simultaneously with the ancient bacterial blooms.

    Raised on heavy metal

    A solidified sulphide liquid droplet (orange in diagram) with a silicate “cap” now recognised to be an infilled gas bubble (blue in diagram) from the Kharaelakh nickel deposit, Siberia, which was active during the Great Dying.

    Magma deep within the Earth’s crust commonly carry droplets of sulphur-rich melts that contain metals. But these sulphide melts are dense and would be expected to sink to the bottom of the magma reservoir.

    But the ‘vapour transport mechanism’ proposed by our researchers can explain how these dense metal sulphide melts are able to be found at shallower depths than expected.

    ‘In the lab we found that small droplets of the sulphide melt can attach to the vapour bubbles and use the buoyancy of the bubbles to float upwards,’ Steve said.

    ‘Even more interesting for us was the discovery that this transport mechanism provides a theoretical link between our understandings of how the magmatic and hydrothermal processes of metal ore formation from magma overlap .’

    The paper, Transport of metals and sulphur in magmas by flotation of sulphide melt on vapour bubbles, is available online from Nature Geoscience.

    For media enquiries, please contact Keirissa Lawson | Keirissa.Lawson@csiro.au | M: 0418 282 055

    See the full article here.

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    CSIRO campus

    CSIRO, the Commonwealth Scientific and Industrial Research Organisation, is Australia’s national science agency and one of the largest and most diverse research agencies in the world.

  • richardmitnick 5:40 pm on February 23, 2015 Permalink | Reply
    Tags: Applied Research & Technology, ,   

    From Rice: “Simulating superconducting materials with ultracold atoms” 

    Rice U bloc

    Rice University

    February 23, 2015
    Jade Boyd

    Using ultracold atoms as a stand-in for electrons, a Rice University-based team of physicists has simulated superconducting materials and made headway on a problem that’s vexed physicists for nearly three decades.

    The research was carried out by an international team of experimental and theoretical physicists and appears online this week in the journal Nature. Team leader Randy Hulet, an experimental physicist at Rice, said the work could open up a new realm of unexplored science.

    Randy Hulet

    Nearly 30 years have passed since physicists discovered that electrons can flow freely through certain materials — superconductors — at relatively elevated temperatures. The reasons for this high-temperature, or “unconventional” superconductivity are still largely unknown. One of the most promising theories to explain unconventional superconductivity — called the Hubbard model — is simple to express mathematically but is impossible to solve with digital computers.

    “The Hubbard model is a set of mathematical equations that could hold the key to explaining high-temperature superconductivity, but they are too complex to solve — even with the fastest supercomputer,” said Hulet, Rice’s Fayez Sarofim Professor of Physics and Astronomy. “That’s where we come in.”

    Hulet’s lab specializes in cooling atoms to such low temperatures that their behavior is dictated by the rules of quantum mechanics — the same rules that electrons follow when they flow through superconductors.

    “Using our cold atoms as stand-ins for electrons and beams of laser light to mimic the crystal lattice in a real material, we were able to simulate the Hubbard model,” Hulet said. “When we did that, we were able to produce antiferromagnetism in exactly the way the Hubbard model predicts. That’s exciting because it’s the first ultracold atomic system that’s able to probe the Hubbard model in this way, and also because antiferromagnetism is known to exist in nearly all of the parent compounds of unconventional superconductors.”

    Hulet’s team is one of many that are racing to use ultracold atomic systems to simulate the physics of high-temperature superconductors.

    “Despite 30 years of effort, people have yet to develop a complete theory for high-temperature superconductivity,” Hulet said. “Real electronic materials are extraordinarily complex, with impurities and lattice defects that are difficult to fully control. In fact, it has been so difficult to study the phenomenon in these materials that physicists still don’t know the essential ingredients that are required to make an unconventional superconductor or how to make a material that superconducts at even greater temperature.”

    Hulet’s system mimics the actual electronic material, but with no lattice defects or disorder.

    Rice University physicists trapped ultracold atomic gas in grids of intersecting laser beams to mimic the antiferromagnetic order observed in the parent compounds of nearly all high-temperature superconductors. Credit: P. Duarte/Rice University

    “We believe that magnetism plays a role in this process, and we know that each electron in these materials correlates with every other, in a highly complex way,” he said. “With our latest findings, we’ve confirmed that we can cool our system to the point where we can simulate short-range magnetic correlations between electrons just as they begin to develop.

    “That’s significant because our theoretical colleagues — there were five on this paper — were able to use a mathematical technique known as the Quantum Monte Carlo method to verify that our results match the Hubbard model,” Hulet said. “It was a heroic effort, and they pushed their computer simulations as far as they could go. From here on out, as we get colder still, we’ll be extending the boundaries of known physics.”

    Nandini Trivedi, professor of physics at Ohio State University, explained that she and her colleagues at the University of California-Davis, who formed the theoretical side of the effort, had the task of identifying just how cold the atoms had to be in the experiment.

    “Some of the big questions we ask are related to the new kinds of ways in which atoms get organized at low temperatures,” she said. “Because going to such low temperatures is a challenge, theory helped determine the highest temperature at which we might expect the atoms to order themselves like those of an antiferromagnet.”

    After high-temperature superconductivity was discovered in the 1980s, some theoretical physicists proposed that the underlying physics could be explained with the Hubbard model, a set of equations invented in the early 1960s by physicist John Hubbard to describe the magnetic and conduction properties of electrons in transition metals and transition metal oxides.

    Every electron has a “spin” that behaves as a tiny magnet. Scientists in the 1950s and 1960s noticed that the spins of electrons in transition metals and transition metal oxides could become aligned in ordered patterns. In creating his model, Hubbard sought to create the simplest possible system for explaining how the electrons in these materials responded to one another.

    The Hubbard model features electrons that can hop between sites in an ordered grid, or lattice. Each site in the lattice represents an ion in the crystal lattice of a material, and the electrons’ behavior is dictated by just a handful of variables. First, electrons are disallowed from sharing an energy level, due to a rule known as the Pauli Exclusion Principle. Second, electrons repel one another and must pay an energy penalty when they occupy the same site.

    “The Hubbard model is remarkably simple to express mathematically,” Hulet said. “But because of the complexity of the solutions, we cannot calculate its properties for anything but a very small number of electrons on the lattice. There is simply too much quantum entanglement among the system’s degrees of freedom.”

    Correlated electron behaviors — like antiferromagnetism and superconductivity — result from feedback, as the action of every electron causes a cascade that affects all of its neighbors. Running the calculations becomes exponentially more time-consuming as the number of sites increases. To date, the best efforts to produce computer simulations of two- and three-dimensional Hubbard models involve systems with no more than a few hundred sites.

    Because of these computational difficulties, it has been impossible for physicists to determine whether the Hubbard model contains the essence of unconventional superconductivity. Studies have confirmed that the model’s solutions show antiferromagnetism, but it is unknown whether they also exhibit superconductivity.

    Researchers used the optical technique called Bragg scattering to observe the symmetry planes that are characteristic of anti-ferromagnetic order. Credit: P. Duarte/Rice University

    In the new study, Hulet and colleagues, including postdoctoral researcher Russell Hart and graduate student Pedro Duarte, created a new experimental technique to cool the atoms in their lab to sufficiently low temperatures to begin to observe antiferromagnetic order in an optical lattice with approximately 100,000 sites. This new technique results in temperatures on the lattice that are about half of that obtained in previous experiments.

    “The standard technique is to create the cold atomic gas, load it into the lattice and take measurements,” Hart said. “We developed the first method for evaporative cooling of atoms that had already been loaded in a lattice. That technique, which uses what we call a ‘compensated optical lattice,’ also helped control the density of the sample, which becomes critical for forming antiferromagnetic order.”

    Hulet said a second innovation was the team’s use of the optical technique called Bragg scattering to observe the symmetry planes that are characteristic of antiferromagnetic order.

    He said the team will need to develop an entirely new technique to measure the electron pair correlations that cause superconductivity. And they’ll also need colder samples, about 10 times colder than those used in the current study.

    “We have some things in mind,” Hulet said. “I am confident we can achieve lower temperatures both by refining what we’ve already done and by developing new techniques. Our immediate goal is to get cold enough to get fully into the antiferromagnetic regime, and from there we’d hope to get into the d-wave pairing regime and confirm whether or not it exists in the Hubbard model.”

    Additional co-authors include Tsung-lin Yang and Xinxing Liu, all of Rice; Thereza Paiva of Universidade Federal do Rio de Janeiro; Ehsan Khatami of both the University of California-Davis (UC-Davis) and San Jose State University; Richard Scalettar of UC-Davis; and David Huse of Princeton University. The research at Rice was supported by the Defense Advanced Research Projects Agency, the National Science Foundation, the Robert Welch Foundation and the Office of Naval Research.

    See the full article here.

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    Rice U campus

    In his 1912 inaugural address, Rice University president Edgar Odell Lovett set forth an ambitious vision for a great research university in Houston, Texas; one dedicated to excellence across the range of human endeavor. With this bold beginning in mind, and with Rice’s centennial approaching, it is time to ask again what we aspire to in a dynamic and shrinking world in which education and the production of knowledge will play an even greater role. What shall our vision be for Rice as we prepare for its second century, and how ought we to advance over the next decade?

    This was the fundamental question posed in the Call to Conversation, a document released to the Rice community in summer 2005. The Call to Conversation asked us to reexamine many aspects of our enterprise, from our fundamental mission and aspirations to the manner in which we define and achieve excellence. It identified the pressures of a constantly changing and increasingly competitive landscape; it asked us to assess honestly Rice’s comparative strengths and weaknesses; and it called on us to define strategic priorities for the future, an effort that will be a focus of the next phase of this process.

  • richardmitnick 5:20 pm on February 23, 2015 Permalink | Reply
    Tags: Applied Research & Technology, ,   

    From DOE Pulse: “NETL invents improved oxygen carriers” 


    National Energy Technology Lab

    February 23, 2015
    Linda Morton, 304.285.4543,

    Oxygen carriers are similar in texture to
    sand. The oxygen carrier pictured here
    blends magnesium oxide and hematite.

    One of the keys to the successful deployment of chemical looping technologies is the development of affordable, high performance oxygen carriers. One potential solution is the naturally-occurring iron oxide, hematite. “Hematite is pretty cheap,” says Doug Straub, Technical Coordinator for the National Energy Technology Laboratory’s Chemical Looping Combustion (CLC) projects and the just-completed Industrial Carbon Management Initiative (ICMI). “You just dig it out of the ground and run it through a screen.” That affordability makes hematite attractive as an oxygen-carrier material, but high performance at the conditions imposed by the chemical looping process is also important. Researchers at the DOE lab are investigating how to enhance hematite-based oxygen carriers so they can stand up to high reactor temperatures. Oxygen carriers also need to be resilient in the face of frequent impacts with reactor walls, with each other, and (in coal-burning reactors) with coal particles. Researchers are also improving oxygen carriers so that they more completely combust the fuel.

    Their work has paid off. Dr. Ranjani Siriwardane (who leads the CLC oxygen carrier research) and Dr. Duane Miller (a chemical engineer at NETL) have invented an oxygen carrier that pairs magnesium oxide with hematite. During a pilot-scale run through NETL’s fluidized bed reactor last year, their carrier showed better performance than carriers that contained just natural hematite.

    What’s next? In the words of Dr. Siriwardane, “this is a big scale-up problem,” and that scale-up can be difficult. The quantities of carriers used at the laboratory scale are small, and techniques for preparing them are easier to control. But, as Dr. Siriwardane explains, “some of the techniques we use for lab-scale preparations are not practical for large-scale preparations, where different techniques and equipment are used. Finding the proper production techniques for our carriers that still deliver the required performance is a big challenge.” However NETL researchers are clearly up to the challenge: when Drs. Siriwardane and Miller applied for the patent for their magnesium-oxide-and-hematite carrier, they had about 100 grams of material, just enough for a lab-scale run. Since then, they have worked with NexTech Materials, a commercial materials vendor, to prepare a 400-pound batch of the carrier for the pilot-scale test.

    In addition to the hematite-based carrier, NETL is also exploring alternative carrier materials, with the goal of optimizing carrier performance and affordability for specific chemical looping applications. A second carrier developed by Drs. Siriwardane and Hanjing Tian (formerly of NETL but now a West Virginia University faculty member) relies on manmade materials instead of natural hematite. Made of copper oxide, iron oxide, and alumina, it too is ready for pilot-scale testing.

    The oxygen carriers that NETL invents to enable CLC could have applications beyond electricity generation. CLC is also useful in industrial steam production, says Dr. Miller, and can be used for the production of hydrogen or syngas from methane. NETL scientists continue research to discover and develop carriers for such real-world applications with the expectation that the energy technologies they enable will one day be very green and very, very affordable.

    See the full article here.

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    DOE Pulse highlights work being done at the Department of Energy’s national laboratories. DOE’s laboratories house world-class facilities where more than 30,000 scientists and engineers perform cutting-edge research spanning DOE’s science, energy, National security and environmental quality missions. DOE Pulse is distributed twice each month.

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  • richardmitnick 4:54 am on February 23, 2015 Permalink | Reply
    Tags: Applied Research & Technology, ,   

    From NOVA: “In Once-Mysterious Epigenome, Scientists Find What Turns Genes On” 



    19 Feb 2015
    R.A. Becker

    A handful of new studies provide epigenetic roadmaps to understanding the human genome in action.(No image credit)

    Over a decade ago, the Human Genome Project deciphered the “human instruction book” of our DNA, but how cells develop vastly different functions using the same genetic instructional text has remained largely a mystery.

    As of yesterday, it became a bit less mysterious. A massive NIH consortium called the Roadmap Epigenomics Program published eight papers in the journal Nature which report on their efforts to map epigenetic modifications, or the changes to DNA that don’t alter its code. These subtle modifications make genes more or less likely to be expressed, and the collection of epigenetic modifications is called the epigenome.

    One of the eight studies mapped over 100 epigenomes characterizing every epigenetic modification occurring in human tissue cells. “These 111 reference epigenome maps are essentially a vocabulary book that helps us decipher each DNA segment in distinct cell and tissue types,” Roadmap researcher Bing Ren, a professor of cellular and molecular medicine at the University of California, San Diego, said in a news release. “These maps are like snapshots of the human genome in action.”

    This kind of mapping has challenged the field because of the huge amount of data needed to make sense of the chaotic arrangements of genes and their regulators. “The genome hasn’t nicely arranged the regulatory elements to be cheek by jowl with the elements they regulate,” Broad Institute director Eric Lander told Gina Kolata at The New York Times. “It can be very hard to figure out which regulator lines up with which genes.”

    Here’s how Lander described the detective process used to Kolata:

    If you knew when service on the Red Line was disrupted and when various employees were late for work, you might be able to infer which employees lived on the Red Line, he said. Likewise, when a genetic circuit was shut down, certain genes would be turned off. That would indicate that those genes were connected, like the employees who were late to work when the Red Line shut down.

    Diseases can be linked to epigenetic variations as well. For example, another of the eight papers published yesterday proposed that the roots of Alzheimer’s disease lie in immune cell genetic dysfunction and epigenetic alterations in brain cells.

    Creating an epigenetic road map is a huge step, but it’s just a first step. As Collins wrote in 2001 when the human genome had been mostly mapped, “This is not even the beginning of the end. But it may be the end of the beginning.”

    See the full article here.

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    NOVA is the highest rated science series on television and the most watched documentary series on public television. It is also one of television’s most acclaimed series, having won every major television award, most of them many times over.

  • richardmitnick 3:40 pm on February 20, 2015 Permalink | Reply
    Tags: , Applied Research & Technology, ,   

    From FightAIDS@Home at WCG: “The end of the beginning is near for FightAIDS@Home” 

    WCG new
    World Community Grid


    20 Feb 2015
    The FightAIDS@Home research team

    Thanks to the incredible generosity of World Community Grid volunteers, the FightAIDS@Home project team has finished with an important stage of their project. The research team has refocused on analyzing their existing results and preparing for the end of this historic grid computing stage.


    FightAIDS@Home has been running on World Community Grid in some form almost since the beginning of World Community Grid itself: our project launched in 2005. Thanks to the enormous and ongoing support of our worldwide community of volunteers, we have expanded the scope of our research and explored new targets and drug candidates that we simply could not imagine at the outset. It hardly seems sufficient to say thank you for donating over 330,000 years of processing time to support our research, but once again, from all of us to all of you: thank you. Clearly we could not do this research without you.

    With your help, we have reached a new milestone: no new AutoDock (AD) or AD Vina docking experiments are currently being generated. Put another way: we’re done creating new work tasks. The AutoDock queue is now empty, and the AD Vina queue has more than a year’s worth of jobs left. Most of our efforts have shifted towards analysis.

    The analysis of the FightAIDS@Home data has several levels of difficulty due to the sheer amounts of data, which are comprised of several structures of any drug target as well as millions of small molecules, resulting in hundreds of millions of data points. We are attempting to use a couple of approaches to mine this data, one of which includes examining amino-acids involved in top-ranked dockings. Another approach is to investigate the atomic coordinates of important interactions (pharmacophore) between the protein and the small molecule that was docked. Figures 1 and 2 (below) illustrate a simple example of inhibitor TL3 (Figure 1) and the predictions of 1 experiment (Figure 2, ~5.5 million dockings on 1 protein structure). Of course, these evaluations must be done with a large set of known inhibitors and across myriad protein structures. Once these methods pass a high level of confidence, molecules will be bought and sent to collaborators to be tested.

    Figure 1. Docked pose of known HIV-1 protease inhibitor TL3 in an HIV-1 protease structure (not shown). Spherical representations (accompanied with dots, orange for TL3, green for a water molecule) represent important locations for protein-ligand interactions that are used to evaluate if a molecule may be a good drug candidate. The green sphere represents the location of an important (“flap”) water molecule often observed in HIV-1 protease co-crystal structures. The 2 orange spheres directly below the green sphere represent two locations of an interaction with significant amino acids (Asp25) of HIV-1 protease.

    Figure 2. Same docked pose of TL3 in HIV-1 protease as Figure 1 with top percentage of interactions from 1 experiment (pink spheres) and several predictions (transparent surfaces) for important protein-ligand interactions. Note that the water molecule (green) and the 2 orange interactions below it are always predicted.

    See the full article here.

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    FightAIDS@Home is a project run by the Olson Laboratory that uses distributed computing to contribute your computer’s idle resources to accelerate research into new drug therapies for HIV, the virus that causes AIDS. FightAIDS@Home made history in September 2000 when it became the first biomedical Internet-based grid computing project. FightAIDS@Home was started with Scott Kurowski, founder of Entropia. People all around the World continue to donate their home computer’s idle cycles to running our AutoDock software on HIV-1 protease inhibitor docking problems. With the generous assistance of IBM, we joined World Community Grid in late 2005, and launched FightAIDS@Home on World Community Grid on 21 November, 2005.

    How do I join the FightAIDS@Home Project?

    All you need to do is download and install the free client software. Once you have done this, your computer is then automatically put to work and you can continue using your computer as usual.

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