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  • richardmitnick 1:13 pm on April 16, 2017 Permalink | Reply
    Tags: , , , , NATURE, ,   

    From Nature: “Muons’ big moment could fuel new physics” 

    Nature Mag
    Nature

    11 April 2017
    Elizabeth Gibney

    1
    The Muon g-2 experiment will look for deviations from the standard model by measuring how muons wobble in a magnetic field. Credit: FNAL

    In the search for new physics, experiments based on high-energy collisions inside massive atom smashers are coming up empty-handed. So physicists are putting their faith in more-precise methods: less crash-and-grab and more watching-ways-of-wobbling. Next month, researchers in the United States will turn on one such experiment. It will make a super-accurate measurement of the way that muons, heavy cousins of electrons, behave in a magnetic field. And it could provide evidence of the existence of entirely new particles.

    The particles hunted by the new experiment, at the Fermi National Laboratory in Batavia, Illinois, comprise part of the virtual soup that surrounds and interacts with all forms of matter. Quantum theory says that short-lived virtual particles constantly ‘blip’ in and out of existence. Physicists already account for the effects of known virtual particles, such as photons and quarks. But the virtual soup might have mysterious, and as yet unidentified, ingredients. And muons could be particularly sensitive to them.

    The new Muon g−2 experiment will measure this sensitivity with unparalleled precision. And in doing so, it will reanalyse a muon anomaly that has puzzled physicists for more than a decade. If the experiment confirms that the anomaly is real, then the most likely explanation is that it is caused by virtual particles that do not appear in the existing physics playbook — the standard model.

    The Standard Model of elementary particles (more schematic depiction), with the three generations of matter, gauge bosons in the fourth column, and the Higgs boson in the fifth.

    2
    Adapted from go.nature.com/2naoxaw

    “It would be the first direct evidence of not only physics beyond the standard model, but of entirely new particles,” says Dominik Stöckinger, a theorist at the Technical University of Dresden, Germany, and a member of the Muon g−2 collaboration.

    Physicists are crying out for a successor to the standard model — a theory that has been fantastically successful yet is known to be incomplete because it fails to account for many phenomena, such as the existence of dark matter. Experiments at the Large Hadron Collider (LHC) at CERN, Europe’s particle-physics lab near Geneva, Switzerland, have not revealed a specific chink, despite performing above expectation and carrying out hundreds of searches for physics beyond the standard model. The muon anomaly is one of only a handful of leads that physicists have.

    Measurements of the muon’s magnetic moment — a fundamental property that relates to the particle’s inherent magnetism — could hold the key, because it is tweaked by interactions with virtual particles. When last measured 15 years ago at the Brookhaven National Laboratory in New York, the muon’s magnetic moment was larger than theory predicts.

    BNL RHIC Campus

    BNL/RHIC

    FNAL G-2 magnet from Brookhaven Lab finds a new home in the FNAL Muon G-2 experiment

    Physicists think that interaction with unknown particles, perhaps those envisaged by a theory called supersymmetry, might have caused this anomaly.

    Other possible explanations are a statistical fluke, or a flaw in the theorists᾽ standard-model calculation, which combines the complex effects of known particles. But that is becoming less likely, says Stöckinger, who says that new calculation methods and experimental cross-checks make the theoretical side much more robust than it was 15 years ago.

    “With this tantalizing result from Brookhaven, you really have to do a better experiment,” says Lee Roberts, a physicist at Boston University in Massachusetts, who is joint leader of the Muon g−2 experiment. The Fermilab set-up will use 20 times the number of muons used in the Brookhaven experiment to shrink uncertainty by a factor of 4. “If we agree, but with much smaller error, that will show definitively that there’s some particle that hasn’t been observed anywhere else,” he says.

    To probe the muons, Fermilab physicists will inject the particles into a magnetic field contained in a ring some 14 metres across. Each particle has a magnetic property called spin, which is analogous to Earth spinning on its axis. As the muons travel around the ring at close to the speed of light, their axes of rotation wobble in the field, like off-kilter spinning tops. Combining this precession rate with a measurement of the magnetic field gives the particles’ magnetic moment.

    Since the Brookhaven result, some popular explanations for the anomaly — including effects of hypothetical dark photons — seem to have been ruled out by other experiments, says Stöckinger. “But if you look at the whole range of scenarios for physics beyond the standard model, there are many possibilities.”

    3
    Fermilab is the home of the Muon g−2 experiment.

    Although a positive result would give little indication of exactly what the new particles are, it would provide clues to how other experiments might pin them down. If the relatively large Brookhaven discrepancy is maintained, it can only come from relatively light particles, which should be within reach of the LHC, says Stöckinger, even if they interact so rarely that it takes years for them to emerge.

    Indeed, the desire to build on previous findings is so strong that to avoid possible bias, Fermilab experimenters will process their incoming results ‘blind’ and apply a different offset to each of two measurements that combine to give the magnetic moment. Only once the offsets are revealed will anyone know whether they have proof of new particles hiding in the quantum soup. “Until then nobody knows what the answer is,” says Roberts. “It will be an exciting moment.”

    See the full article here .

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    Nature is a weekly international journal publishing the finest peer-reviewed research in all fields of science and technology on the basis of its originality, importance, interdisciplinary interest, timeliness, accessibility, elegance and surprising conclusions. Nature also provides rapid, authoritative, insightful and arresting news and interpretation of topical and coming trends affecting science, scientists and the wider public.

     
  • richardmitnick 8:14 am on March 10, 2017 Permalink | Reply
    Tags: , NATURE, Time Crystals, Time crystals' latest quantum weirdness   

    From COSMOS: “‘Time crystals’ latest quantum weirdness” 

    Cosmos Magazine bloc

    COSMOS

    10 March 2017
    Richard A Lovett

    1
    From this article
    Pixabay

    [Other depictions:

    2
    Scientists have confirmed a brand new phase of matter: time crystals – ScienceAlert

    3
    Popular Mechanics

    4
    Berkeley scientists unveil new form of matter known as time crystals

    Enough of that.]

    Two American teams of scientists have independently created the world’s first “time crystals”, but don’t order up a trip on the TARDIS anytime soon, because the crystals in question have nothing to do with time travel.

    Both sets of research have been published in Nature.

    The quest to crystallize time

    [Only one article is popping up. Totally unacceptable from Nature.]

    Here is one in Physical Review Letters.

    “I’m not responsible for its name,” laughs Mikhail Lukin, a physicist at Harvard University, Cambridge, Massachusetts, lead author on one of the papers.

    Chetan Nayak, principal researcher at Microsoft’s Station Q and a professor of physics at the University of California, Santa Barbara, puts it more simply. “What they observed is a new state of matter,” he says.

    Nayak is responsible for a third paper in the journal, explaining the significance of the discovery.

    What’s unique about the crystals, Lukin says, is that they have properties that repeat over time in a manner analogous to the way the atoms in crystal lattices repeat over space.

    Repeating phenomena, of course, aren’t a big deal. “Every year we have spring, summer, and fall,” Lukin notes.

    But most repeating phenomena are easily altered. An AC electrical current, for example, can be changed by altering the spin rate of the dynamo that produces it. The length of the Earth’s seasons would change if, heaven forbid, a giant asteroid hit us, altering our orbit.

    To understand time crystals, we need to start by considering liquids and gases. In these, Lukin says, molecules are uniformly distributed in a way that makes one point in the liquid or gas basically the same as all other points.

    But in crystals, atoms are arranged in repeating patterns that mean that once you know the position of one atom, you can pinpoint the locations of all the others. Furthermore, crystals are rigid. If you bash on one, you aren’t going to see one atom move one way, while another moves a different way, as would happen if you sloshed a tub of water or let the air out of a balloon.

    Crystals are common to our normal understanding of nature. Time crystals aren’t. In fact, it was only recently that anyone even hypothesized they might exist.

    Their atoms operate in a sort of time-array, as opposed to a physical array. The time crystal created by Lukin’s team was a synthetic black diamond, meaning that it was a diamond with a million or so “nitrogen vacancy” impurities — so many they made it appear black.

    The electrons in these impurities have spins: they can react to electromagnetic pulses by flipping 180 degrees, analogous to what happens to nuclei in the human body during magnetic resonance imaging.

    Normally, you would expect the spins to flip back and forth in synchronisation with the pulse. But that is not what happened. Instead, when Lukin’s team tried it with their black diamond, the spins flipped only once for every two or three pulses.

    Shivaji Sondhi, a theoretical physicist at Princeton University in New Jersey, who was part of the team that in 2015 first theorised that such crystals might be possible, compares the effect to repeatedly squeezing on a sponge.

    “When you release the sponge, you expect it to resume its shape,” he says. “Imagine that it only resumes its shape every second squeeze, even though you are applying the same force each time.”

    In the second study, a team lead by the Christopher Monroe, physicist at the University of Maryland, used a chain of 14 charged ytterbium ions, but got essentially the same result.

    Furthermore, the scientists found, varying the incoming electromagnetic pulse didn’t particularly alter the response. In other words, the time crystal’s response was stable, not strongly affected by variances that would normally scramble it and rapidly lead to disorder.

    Applications are up in the air. “It’s very early days,” says Nayak. “I think applications will become more clear as we expand the contexts in which we can create time crystals.”

    One possibility is that this might be used in futuristic quantum computers. “What a time crystal is doing is manipulating quantum information in a period manner,” says Nayak. “That’s potentially useful for quantum information processing.”

    Lukin says that another potential application is in developing sensing instruments capable of working on very small scales. These instruments could be designed with numerous tiny time crystals, tightly packed.

    The crystals would react to electrical or magnetic impulses in their local environment, but would not be easily perturbed by whatever is going on nearby. “We believe these will enable new approaches for [what are] basically quantum sensors,” Lukin says.

    See the full article here .

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  • richardmitnick 6:32 pm on March 7, 2017 Permalink | Reply
    Tags: , , NATURE, Science journalism can be evidence-based compelling — and wrong   

    From Nature: “Science journalism can be evidence-based, compelling — and wrong” 

    Nature Mag
    Nature

    07 March 2017

    1
    Many science journalists rely on peer review to check their stories are true.

    There has been much gnashing of teeth in the science-journalism community this week, with the release of an infographic that claims to rate the best and worst sites for scientific news. According to the American Council on Science and Health, which helped to prepare the ranking, the field is in a shoddy state. “If journalism as a whole is bad (and it is),” says the council, “science journalism is even worse. Not only is it susceptible to the same sorts of biases that afflict regular journalism, but it is uniquely vulnerable to outrageous sensationalism”.

    News aggregator RealClearScience, which also worked on the analysis, goes further: “Much of science reporting is a morass of ideologically driven junk science, hyped research, or thick, technical jargon that almost no one can understand”.

    How — without bias or outrageous sensationalism, of course — do they judge the newspapers and magazines that emerge from this sludge? Simple: they rank each by how evidence-based and compelling they subjectively judge its content to be. Modesty (almost) prevents us from naming the publication graded highest on both (okay, it’s Nature), but some names are lower than they would like. Big hitters including The New York Times, The Washington Post and The Guardian score relatively poorly.

    It’s a curious exercise, and one that fails to satisfy on any level. It is, of course, flattering to be judged as producing compelling content. But one audience’s compelling is another’s snoozefest, so it seems strikingly unfair to directly compare publications that serve readers with such different interests as, say, The Economist and Chemistry World. It is equally unfair to damn all who work on a publication because of some stories that do not meet the grade. (This is especially pertinent now that online offerings spread the brand and the content so much thinner.)

    The judges’ criterion of evidence-based news is arguably problematic, as well. Many journalists could reasonably point to the reproducibility crisis in some scientific fields and ask — as funders and critics are increasingly asking — just how reliable some of that evidence truly is. Mainstream science reporters have typically taken peer review as an official stamp of approval from the research community that a published finding is sufficiently robust to share with their readers. Yet this kind of evidence-based reporting is only as reliable as the evidence it reports on. And many scientists would complain (even if only among themselves) that some published studies, especially those that draw press attention, are themselves vulnerable to bias and sensationalism.

    This is one reason why the rise of the scientist (and non-scientist) as blogger, along with other forms of post-publication review, has been so valuable. Many scientists know about the problems with some fields of research. Many journalists do, too — articles on questionable practices from statistical fishing to under-powered studies are an increasing presence in most of the publications in the infographic. The relationship between science and media reporting is far from simple, and both sides should remember this.

    2
    An attempt to rank science news sites has caused controversy. American Council on Science and Health/RealClear Media Group

    See the full article here .

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    Nature is a weekly international journal publishing the finest peer-reviewed research in all fields of science and technology on the basis of its originality, importance, interdisciplinary interest, timeliness, accessibility, elegance and surprising conclusions. Nature also provides rapid, authoritative, insightful and arresting news and interpretation of topical and coming trends affecting science, scientists and the wider public.

     
  • richardmitnick 1:55 pm on February 5, 2017 Permalink | Reply
    Tags: “We outsource the choice to the Universe itself”, Cosmic test backs 'quantum spookiness', , Iconic experiment to confirm quantum theory, NATURE, , The Big Bell Test   

    From Nature: “Cosmic test backs ‘quantum spookiness'” 

    Nature Mag
    Nature

    02 February 2017
    Elizabeth Gibney

    1
    The light from distant stars is used to fix settings in a new version of the iconic Bell test. Dr Fred Espenak/Science Photo Library.

    A version of an iconic experiment to confirm quantum theory has for the first time used the light of distant stars to bolster the case for a phenomenon that Albert Einstein referred to as “spooky action at a distance”.

    Einstein disliked the notion that objects can share a mysterious connection across any distance of space, and scientists have spent the past 50 years trying to make sure that their results showing this quantum effect could not have been caused by more intuitive explanations.

    Quantum physics suggests that two so-called entangled particles can maintain a special connection — even at a large distance — such that if one is measured, that instantly tells an experimenter what measuring the other particle will show. This happens despite the fact neither particle has definite properties until it is measured. That unsettled some physicists, including Einstein, who favoured an alternative explanation: that quantum theory is incomplete, and that the outcomes instead depend on some predetermined, but hidden, variables.

    The latest effort to explore the phenomenon, to be published in Physical Review Letters on 7 February, uses light emitted by stars around 600 years ago to select which measurements to make in a quantum experiment known as a Bell test. In doing so, they narrow down the point in history when, if they exist, hidden variables could have influenced the experiment.

    “It’s a beautiful experiment,” says Krister Shalm, a quantum physicist at the US National Institute of Standards and Technology (NIST) in Gaithersburg, Maryland. Although few expected it to disprove quantum mechanics, such experiments “keep pushing alternative theories to be more and more contrived and ridiculous”, he says. Similar techniques could, in the future, help to protect against hackers who try to crack quantum-cryptography systems, he adds.

    Closing loopholes

    Physicists at the University of Vienna, along with colleagues in China, Germany and the United States, developed a new version of the Bell test — a protocol devised by the physicist John Bell in the 1960s to distinguish between two possible explanations for the seemingly strange behaviour of the quantum world.

    The test involves performing independent measurements on separated pairs of entangled quantum particles. Bell showed that, statistically, correlations between the results, once above a certain threshold limit, could not be explained by particles having hidden properties. Instead the coordinated outcomes seem to be the result of measurements on one particle mysteriously fixing the properties of the other.

    Although Bell tests have supported quantum theory many times, they include assumptions that leave wiggle room for non-quantum explanations, and physicists have been trying to close these ‘loopholes’ ever since.

    In 2015, they sealed a major victory when three separate teams, including Shalm’s, succeeded in simultaneously closing two major possible loopholes, by showing that entanglement could not be an illusion created by any speed-of-light communication between particles, or an artefact of only detecting certain photons.

    See the following:
    http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.115.250402
    http://www.nature.com/nature/journal/v526/n7575/abs/nature15759.html
    http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.115.250401

    Freedom of choice

    But they left open another loophole — one that is more subtle, and impossible to fully close, says Andrew Friedman, an astronomer at the Massachusetts Institute of Technology in Cambridge, and a co-author on the latest paper. Bell tests also assume that experimenters have free choice over which measurements they perform on each of the pair of photons. But some unknown effect could be influencing both the particles and what tests are performed (either by affecting choice of measurement directly, or more plausibly, by restricting the options that are available), to produce correlations that give the illusion of entanglement.

    To narrow this freedom-of-choice loophole, researchers have previously put 144 kilometres between the source of entangled particles and the random-number generator that they use to pick experimental settings.

    See
    http://www.pnas.org/content/107/46/19708

    The distance between them means that if any unknown process influenced both set-ups, it would have to have done so at a point in time before the experiment. But this only rules out any influences in the microseconds before: the latest paper sought to push this time back dramatically, by using light from two distant stars to determine the experimental settings for each photon. “We outsource the choice to the Universe itself,” says Friedman.

    The team, led by physicist Anton Zeilinger at the University of Vienna, picked which properties of the entangled photons to observe depending on whether its two telescopes detected incoming light as blue or red. The colour is decided when the light is emitted, and does not change during travel. This means that if some unknown effect, rather than quantum entanglement, explains the correlation, it would have to have been set in motion at least around 600 years ago, because the closest star is 575 light-years (176 parsecs) away, says Friedman, who hopes to eventually push back this limit to billions of years ago by doing the experiment with light from more distant quasars. Their results found a level of correlation that supports ‘action at a distance’.

    Protection against hackers

    Technically, the experiment is impressive, say Ronald Hanson, a quantum physicist at the Delft University of Technology in the Netherlands. But, unlike the loopholes closed in 2015, this one can never be fully closed; confining it to further in the past is only possible by making new assumptions — in this case, for example, by assuming that no one messed with the photons immediately before they hit the telescopes, he says.

    Others argue that although, fundamentally, the loophole is never closable, such experiments are valuable because new theories necessarily become more improbable and contrived, or eventually, end up assuming that everything in the Universe was determined at the time of the Big Bang — a philosophical view that most physicists reject. Reworking experiments to reduce and make better assumptions is therefore worthwhile, says Shalm.

    Such experiments also have practical value, argues Friedman, because if quantum mechanics turns out to be explained by a different underlying theory, that discovery could impact the security of technologies that rely on quantum theory, such as quantum encryption. And trying to close such loopholes is useful because minimizing the assumptions in an experiment serves to also beef up protection against hackers who might otherwise exploit them, says Shalm, whose team at the NIST is exploring whether Bell tests could be used in quantum cryptography.

    Harnessing cosmic phenomena is not the only way physicists are ensuring the independence of their measurement settings. In November, teams from around the world took part in the Big Bell Test, which tapped 100,000 game-playing volunteers worldwide to create random sequences of 0s and 1s, which physicists used to fix their measurement settings.

    Preliminary analysis indicates that in this case, most — and possibly even all — of the experiments yet again supported quantum mechanics, says Morgan Mitchell at the Institute of Photonic Sciences (ICFO) in Barcelona, Spain, which coordinated the event. “Sorry, Einstein,” he says.

    See the full article here .

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    Nature is a weekly international journal publishing the finest peer-reviewed research in all fields of science and technology on the basis of its originality, importance, interdisciplinary interest, timeliness, accessibility, elegance and surprising conclusions. Nature also provides rapid, authoritative, insightful and arresting news and interpretation of topical and coming trends affecting science, scientists and the wider public.

     
  • richardmitnick 4:55 pm on January 22, 2017 Permalink | Reply
    Tags: , , How Trump Could Unravel Obama’s Science Legacy, NATURE,   

    From SA: “How Trump Could Unravel Obama’s Science Legacy” 

    Scientific American

    Scientific American

    January 20, 2017
    Lauren Morello

    1
    Land in the Bears Ears region of Utah is among that designated a national monument by Barack Obama. Credit: Bureau of Land Management Flickr (CC BY 2.0).

    Barack Obama used his presidential powers to make changes that affect science. Once Donald Trump is inaugurated as president on 20 January, he will be able to do the same. These charts illustrate the government that Trump inherits as it relates to science and research, and explore how the new president might seek to take things in a different direction.

    Appointing leaders and freezing new hires

    As does every new president, Trump gets to fill out the ranks of federal science agencies with political appointees, from the agency chiefs who require Senate confirmation to lower-level bureaucrats. These jobs range from two spots at the US Geological Survey—the director and an assistant—to 358 positions at the Department of Energy. Trump has already nominated a handful of people to fill these slots, including former Governor of Texas Rick Perry, who has questioned the science underlying climate change, as energy secretary.

    2
    Credit: Nature, January 19, 2017, doi:10.1038/nature.2017.21327

    The much-larger ranks of non-political ‘career’ employees, meanwhile, could shrink under Trump, who has pledged to freeze federal hiring within his first 100 days in office. Staffing levels at science agencies—which stayed relatively flat under Obama, despite his enthusiasm for research— could eventually dwindle by attrition.

    Balancing basic and applied science

    Funding science involves a delicate balance. Science in the Obama years tilted the needle towards applied research—from the launch of the ambitious Precision Medicine Initiative to sequence the genomes of one million people, to the creation of a string of institutes to foster robotics and other innovative manufacturing technologies in partnership with private industry.

    3
    Credit: Nature, January 19, 2017, doi:10.1038/nature.2017.21327

    It is not clear which flavour of research Trump will favour, in part because he has said little publicly about science before or after the election. In September, Trump wrote that “scientific advances do require long term investment”, in response to questions from the advocacy group ScienceDebate.org. But the president-elect’s pick to lead the White House Office of Management and Budget, Representative Mick Mulvaney (Republican, South Carolina), has pushed for sharp cuts in government spending in recent years.

    Undoing Obama’s conservation triumphs

    More than any other president, Obama has used the Antiquities Act—a law that dates back to 1906—to protect public lands from development. He has declared 29 new national monuments, such as the Bears Ears buttes in Utah, and enlarged 5 others, preserving a total of around 553 million acres of land and water.

    4
    Credit: Nature, January 19, 2017, doi:10.1038/nature.2017.21327

    Some Republican politicians have suggested that Trump should remove protections from some or all of these areas, but most legal scholars say that only an act of Congress can reverse a monument designation. That might not stop the Trump administration from trying. The president-elect’s nominee to lead the Interior Department, Representative Ryan Zinke (Republican, Montana), told a Senate committee on 17 January that Trump could “amend”, if not fully rescind, the monuments that Obama created.

    Reversing stem cell and climate change policies?

    Faced with an often-hostile Congress, Obama enacted many of his signature policies by executive order—from reversing restrictions on research with human embryonic stem cells to helping communities prepare for climate change. That strategy now seems poised to backfire: Trump has vowed to reverse “every unconstitutional executive action, memorandum and order issued by President Obama” beginning on his first day in office, January 20.

    5
    Credit: Nature, January 19, 2017, doi:10.1038/nature.2017.21327

    See the full article here .

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    Scientific American, the oldest continuously published magazine in the U.S., has been bringing its readers unique insights about developments in science and technology for more than 160 years.

     
  • richardmitnick 11:15 am on January 22, 2017 Permalink | Reply
    Tags: Infection signals, NATURE, Phages caught sending chemical messages, phi3T   

    From Nature: “Do you speak virus? Phages caught sending chemical messages” 

    Nature Mag
    Nature

    18 January 2017
    Ewen Callaway

    1
    Viruses called phages hijack bacteria and use them to produce more copies of themselves. Now researchers have found they can also communicate. Animated Healthcare Ltd./SPL.

    Viruses sense chemical signals left behind by their forebears so they can decide whether to kill or just to infect their hosts.

    The discovery — in viruses that attack Bacillus bacteria — marks the first time that any type of viral communication system has ever been found. But researchers say that many other viruses could communicate with each other through their own molecular languages — perhaps even viruses that are responsible for human diseases. If that is the case, scientists might have found a new way to disrupt viral attacks.

    The secret viral code was spotted by a team led by Rotem Sorek, a microbial geneticist at the Weizmann Institute of Science in Rehovot, Israel. Their findings are published in Nature on 18 January [1].

    “This is going to be one of those transformative papers,” says microbiologist Martha Clokie, who studies viruses that infect bacteria (known as bacteriophages, or phages) at the University of Leicester, UK.

    Infection signals

    Sorek’s team was looking for evidence that a bacterium called Bacillus subtilis might alert other bacteria to phages. The researchers knew that bacteria speak to their brethren through secreting and sensing an array of chemicals. This phenomenon, called quorum sensing, allows the bacteria to adjust behaviours according to the numbers of other bacteria around. For instance, bacteria use quorum sensing to decide whether to divide or when to launch an infection.

    Instead, the team found, to its surprise, that a viral invader of Bacillus bacteria — a phage called phi3T — makes a chemical that influences the behaviour of other viruses.

    Some phages can infect cells in two different ways. Usually, they hijack host cells and multiply until the hosts burst and die. Sometimes, however, phages insert their own genetic material into a host’s genome, then lie dormant until a trigger causes them to reawaken and multiply later.

    The newly discovered viral communication system alters the way phi3T infects.

    The team first injected phi3T into a flask of Bacillus subtilis bacteria, and found that the virus tended to kill the bacteria. Then they filtered the contents of this flask to remove bacteria and viruses — but keeping small proteins — and fed this ‘conditioned medium’ to a fresh culture of bacteria and phages. That changed what the phage did: it was now more likely to slip its genome into the bacteria, rather than kill it. The team named the mysterious molecule that they suspected was involved ‘arbitrium’ (after the Latin word for decision) and set out to identify it.

    ‘Annoyingly good’

    After a two-and-a-half year search, Sorek and graduate student Zohar Erez discovered that arbitrium was a short viral protein that seeps out of infected bacteria after death. When levels of arbitrium build up — after a large number of cells have died — phages stop killing off the remaining bacteria and retreat to lie dormant in bacterial genomes instead. Sorek, Erez and their colleagues identified two further phi3T proteins that measure levels of arbitrium and then influence the nature of subsequent infections.

    “It does make a lot of sense,” says Peter Fineran, a microbial geneticist at the University of Otago in Dunedin, New Zealand. “If the phage is running out of hosts, it would try and limit its destruction, and sit quiet and wait for the host to re-establish growth.”

    The new work is “annoyingly good”, says Clokie. “I’ve thought about doing those experiments to see if there’s something in the media.” She also expects other phage biologists will discover other communication systems. Sorek’s team found more than 100 different arbitrium-like systems, most of them in the genomes of other Bacillus viruses. “Phages broadcast in different frequencies. They speak in different languages and they can hear only the language that they speak,” he adds.

    He even wonders whether viruses that infect more complex organisms, such as people, could talk to one another. HIV and herpes viruses can cause both active and latent infections, he notes. “If you had a molecule that could drive viruses into complete latency, it would be a good drug.”

    See the full article here .

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    Nature is a weekly international journal publishing the finest peer-reviewed research in all fields of science and technology on the basis of its originality, importance, interdisciplinary interest, timeliness, accessibility, elegance and surprising conclusions. Nature also provides rapid, authoritative, insightful and arresting news and interpretation of topical and coming trends affecting science, scientists and the wider public.

     
  • richardmitnick 10:58 am on January 22, 2017 Permalink | Reply
    Tags: An open-science effort to replicate dozens of cancer-biology studies is off to a confusing start., , Cancer reproducibility project releases first results, , Muddy waters, NATURE   

    From Nature: “Cancer reproducibility project releases first results” 

    Nature Mag
    Nature

    18 January 2017

    Monya Baker
    Elie Dolgin

    An open-science effort to replicate dozens of cancer-biology studies is off to a confusing start.

    1
    Dozens of papers reporting efforts to attack cancer cells are being checked in an open-source project. Stanley Flegler/Visuals Unlimited, Inc./Science Photo Library

    Erkki Ruoslahti was on track to launch a drug trial in people with cancer this year, but his plan may now be in ­jeopardy. A high-profile project designed to gauge the reproducibility of findings from dozens of influential papers on cancer biology publishes results for its first five papers this week, including one by Ruoslahti. And scientists who tried to replicate his findings say that they can’t get his drug to work. For the other four papers, the replication results are less clear.

    Ruoslahti, a cancer biologist at the Sanford Burnham Prebys Medical Discovery Institute in La Jolla, California, disputes the verdict on his research. After all, at least ten laboratories in the United States, Europe, China, South Korea and Japan have validated the 2010 paper [1] in which he first reported the value of the drug, a peptide designed to penetrate tumours and enhance the cancer-killing power of other chemotherapy agents. “Have three generations of postdocs in my lab fooled themselves, and all these other people done the same? I have a hard time believing that,” he says.

    A single failure to replicate results does not prove that initial findings were wrong — and shouldn’t put a stain on individual papers, says Tim Errington, the manager of the reproducibility project, who works at the Center for Open Science in Charlottesville, Virginia. Investigators should take results as information, not condemnation, says Errington. “If we just see someone else’s evidence as ­making it hard for the person who did the original research, there is something wrong with our culture.”

    But Ruoslahti worries that the failure to reproduce his results will weaken his ability to raise money for DrugCendR, a company in La Jolla that he founded to develop his therapy. “I’m sure it will,” he says. “I just don’t know how badly.”

    Repeated attempts

    The Reproducibility Project: Cancer Biology launched in 2013 as an ambitious effort to scrutinize key findings in 50 cancer papers published in Nature, Science, Cell and other high-impact journals. It aims to determine what fraction of influential cancer biology studies are probably sound — a pressing question for the field. In 2012, researchers at the biotechnology firm Amgen in Thousand Oaks, California, announced that they had failed to replicate 47 of 53 landmark cancer papers [2]. That was widely reported, but Amgen has not identified the studies involved.

    The reproducibility project, by contrast, makes all its findings open — hence Ruoslahti’s discomfort. Two years in, the project downsized to 29 papers, citing budget constraints among other factors: the Laura and John Arnold Foundation in Houston, Texas, which funds the ­project, has committed close to US$2 million for it. Full results should appear by the end of the year. But seven of the replication studies are now complete, and eLife is publishing five fully analysed efforts on 19 January.

    These five paint a muddy picture (see ‘Muddy waters). Although the attempt to replicate Ruoslahti’s results failed [3], two of the other attempts [4], [5] “substantially reproduced” research findings — although not all experiments met thresholds of statistical significance, says Sean Morrison, a senior editor at eLife. The remaining two [6], [7] yielded “uninterpretable results”, he says: because of problems with these efforts, no clear comparison can be made with the original work.

    Muddy waters

    http://dx.doi.org/10.1126/scitranslmed.3001318
    http://dx.doi.org/10.1126/science.1183057
    http://dx.doi.org/10.1073/pnas.1121623109
    http://dx.doi.org/10.1016/j.cell.2011.08.017
    http://dx.doi.org/10.1038/nature11071

    “For people keeping score at home, right now it’s kind of two out of three that appear to have been reproduced,” says Morrison, who studies cancer and stem cells at the University of Texas Southwestern Medical Center in Dallas.

    Nature spoke to corresponding authors for all of the original reports. Some praised the reproducibility project, but others worried that the project might unfairly discredit their work. “Careers are on the line here if this comes out the wrong way,” says Atul Butte, a computational biologist at the University of California, San Francisco, whose own paper was mostly substantiated by the replication team.

    1
    Erkki Ruoslahti says he’s worried that the reproducibility project’s inability to validate his findings will affect his ability to launch a cancer drug trial.

    The reason for the two “uninterpretable” results, Morrison says, is that things went wrong with tests to measure the growth of tumours in the replication attempts. When this happened, the replication researchers — who were either at contract research labs or at core facilities in academic institutions — were not allowed to deviate from the peer-reviewed protocols that they had agreed at the start of their experiments (in consultation with the original authors). So they simply reported the problem. Doing anything else — such as changing the experimental conditions or restarting the work — would have introduced bias, says Errington.

    Such conflicts mean that the replication efforts are not very informative, says Levi Garraway, a cancer biologist at the Dana-Farber Cancer Institute in Boston, Massachusetts. “You can’t distinguish between a trivial reason for a result versus a profound result,” he says. In his study, which identified mutations that accelerate cancer formation, cells that did not carry the mutations grew much faster in the replication effort7 — perhaps because of changes in cell culture. This meant that the replication couldn’t be compared to the original.

    Devil’s in the details

    Perhaps the clearest finding from the project is that many papers include too few details about their methods, says Errington. Replication teams spent many hours working with the original authors to chase down protocols and reagents, in many cases because they had been developed by students and postdocs who were no longer with the lab. Even so, the final reports include long lists of reasons why the replication studies might have turned out differently — from laboratory temperatures to tiny variations in how a drug was delivered. If the project helps to bring such confusing details to the surface, it will have performed a great service, Errington says.

    Others think that the main value of the project is to encourage scepticism. “Commonly, investigators take published results at face value and move on without reproducing the critical experiments themselves,” says Glenn Begley, an author of the 2012 Amgen report.

    That’s not the case for Albrecht Piiper, a liver-cancer researcher at the University Hospital Frankfurt in Germany. Piiper has replicated Ruoslahti’s work in his own lab [8]. Despite the latest result, he says, he has “no doubt” about the validity of Ruoslahti’s paper.

    eferences

    1. Sugahara, K. N. et al. Science 328, 1031–1035 (2010).
    ArticlePubMedChemPort
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    2. Begley, C. G. & Ellis, L. M. Nature 483, 531–533 (2012).
    ArticlePubMedChemPort
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    3. Mantis, C. et al. eLife 6, e17584 (2017).
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    4. Aird, F. et al. eLife 6, e21253 (2017).
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    5. Kandela, I. et al. eLife 6, e17044 (2017).
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    6. Horrigan, S. K. et al. eLife 6, e18173 (2017).
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    7. Horrigan, S. K. et al. eLife 6, e21634 (2017).
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    8. Schmithals, C. et al. Cancer Res. 75, 3147–3154 (2015).
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    See the full article here .

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  • richardmitnick 11:50 am on December 19, 2016 Permalink | Reply
    Tags: , , Ephemeral antimatter atoms pinned down in milestone laser test, NATURE   

    From Nature: “Ephemeral antimatter atoms pinned down in milestone laser test” 

    Nature Mag
    Nature

    19 December 2016
    Davide Castelvecchi

    CERN ALPHA New
    The ALPHA antimatter experiment at CERN has measured an energy transition in anti-hydrogen. CERN.

    In a technical tour-de-force, physicists have made of the first measurements of how antimatter atoms absorb light.

    Researchers at CERN, the European particle physics laboratory outside Geneva, trained an ultraviolet laser on antihydrogen, the antimatter counterpart of hydrogen. They measured the frequency of light needed to jolt a positron — an antielectron — from its lowest energy level to the next level up, and found no discrepancy with the corresponding energy transition in ordinary hydrogen.

    The null result is still a thrill for researchers who have been working for decades towards antimatter spectroscopy, the study of how light is absorbed and emitted by antimatter. The hope is that this field could provide a new test of a fundamental symmetry of the known laws of physics, called CPT (charge-parity-time) symmetry.

    CPT symmetry predicts that energy levels in antimatter and matter should be the same. Even the tiniest violation of this rule would require a serious rethink of the standard model of particle physics.

    Randolf Pohl, a spectroscopist at Johannes Gutenberg University in Mainz, Germany, could barely contain his excitement. “WOW,” he told Nature in an email. “After all these years, these guys have finally managed to do optical spectroscopy in antihydrogen. This is a milestone in the investigation of exotic atoms.”

    “It is amazing that one can control antimatter to an extent that this is possible,” says Michael Peskin, a theoretical physicist at the SLAC National Accelerator Laboratory in Menlo Park, California.

    Cold anti-hydrogen

    Studying antimatter is extremely difficult, because it annihilates whenever it comes into contact with ordinary matter. In 2010, CERN’s ALPHA collaboration demonstrated how to hold antihydrogen in a magnetic trap — and since then, have been working towards studying its interactions with light.

    Every 15 minutes or so, the ALPHA group can produce around 25,000 antihydrogen atoms. To make them, the physicists combine positrons, emitted by a radioactive substance, with antiprotons, produced by a particle accelerator and then slowed down and cooled.

    Most of these atoms are too ‘hot’ — moving too fast, and in too high an energy state — for spectroscopy studies. So the researchers must let them escape the magnetic trap, leaving just a handful of the slowest, lowest-energy antihydrogen atoms. Perfecting this technique took years, says ALPHA spokesperson Jeffrey Hangst. “Making antihydrogen is relatively easy; making cold antihydrogen is really difficult,” he says.

    Finally, the ALPHA team was able to see whether, when the researchers shone a laser at a particular frequency, the antihydrogen atoms would act like their hydrogen counterparts. The group says they do: the energy transition is consistent to a precision of 2 parts in 10 billion, they report on 19 December in Nature.

    “You put so much effort into something, and it finally succeeds. There are almost no words to describe it,” says Hangst.

    Next, the researchers hope to probe the antihydrogen with a large range of laser energies. That could provide a more stringent test of matter–antimatter equivalence and of CPT symmetry.

    Many theories — such as string theory — that venture beyond the standard model by combining gravity with the three other fundamental forces of subatomic physics, do involve some kind of CPT violation, says Peskin. “So it is not at all clear that CPT is a true symmetry of nature,” he says.

    Two other experiments at CERN — called ATRAP and ASACUSA — were competing with ALPHA to measure antimatter spectroscopy. Gerald Gabrielse, the leader of ATRAP and a physicist at Harvard University in Cambridge, Massachusetts, says he first proposed nearly 30 years ago measuring the particular energy transition in antihydrogen that the ALPHA team have reported. “We started ten years earlier and they got to this result first,” he says. ”Congratulations to ALPHA.”

    See the full article here .

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  • richardmitnick 6:14 am on December 16, 2016 Permalink | Reply
    Tags: , , NATURE, Waterworld   

    From Nature: “Solar System’s biggest asteroid is an ancient ocean world” 

    NASA JPL Banner

    JPL-Caltech

    From JPL-Caltech
    Where is the Ice on Ceres? New NASA Dawn Findings

    News Media Contact
    Elizabeth Landau
    Jet Propulsion Laboratory, Pasadena, Calif.
    818-354-6425
    elizabeth.landau@jpl.nasa.gov

    Nature Mag
    Nature

    15 December 2016
    Alexandra Witze

    1
    This graphic shows a theoretical path of a water molecule on Ceres. Some water molecules fall into cold, dark craters at high latitudes called “cold traps,” where very little of the ice turns into vapor, even over the course of a billion years. Other water molecules that do not land in cold traps are lost to space as they hop around the dwarf planet.

    The graphic features an enhanced color image from NASA’s Dawn spacecraft (see PIA20182).

    Asteroids might look dry and barren, but the Solar System’s biggest asteroid — Ceres — is chock full of water, NASA’s Dawn spacecraft has found.

    3
    This movie of images from NASA’s Dawn spacecraft shows a crater on Ceres that is partly in shadow all the time. Such craters are called “cold traps.” Dawn has shown that water ice could potentially be preserved in such place for very long amounts of time. Credit: NASA/JPL-Caltech/UCLA/MPS/DLR/IDA

    “It’s just oozing,” says Thomas Prettyman, a nuclear engineer at the Planetary Science Institute in Tucson, Arizona. He led the team that built the neutron-counting instrument aboard Dawn, which reported its findings on 15 December in Science.

    NASA Dawn Spacecraft
    NASA Dawn Spacecraft

    Today, the water is either frozen as ice, filling pore spaces deep inside Ceres, or locked inside hydrated minerals at the surface. But billions of years ago, early in Ceres’s history, heat left over from the Solar System’s formation probably kept the asteroid warm inside. This allowed the water to churn and flow, helping to separate Ceres into layers of rock and ice.

    “We know the water and the rock have separated and interacted over time,” said Carol Raymond, a planetary scientist at NASA’s Jet Propulsion Laboratory in Pasadena, California, at a meeting of the American Geophysical Union in San Francisco on 15 December.

    The discovery adds to a growing awareness of Ceres as an active, wet world that pushes the boundary of what it means to be a planet. Today it sports a 4-kilometre-high ice volcano and bright spots of salt mixed with ice and rock.

    At 940 kilometres across, Ceres is so big that it contains roughly one-third of all the mass in the asteroid belt — and it is technically both an asteroid and a dwarf planet. Researchers knew that Ceres was rich in water on the basis of its estimated density, by studying light reflecting off the hydrated minerals on its surface and because they spotted water apparently steaming from it. But they did not know exactly how much water was there until Dawn showed up in March 2015.

    Hydrogen highs and lows

    The spacecraft studies chemical elements by counting the gamma-rays and neutrons reflecting off Ceres as cosmic rays bombard it. Prettyman’s team generated a map of the asteroid’s hydrogen, which appears in water ice and hydrated minerals.

    Hydrogen levels were richest in the middle to high latitudes, with the greatest concentrations — up to 30% water — present at the north pole. Around the equator, frozen water has probably sublimated into space and dried out Ceres’s surface, Prettyman says. An astronaut there would have to dig down about 1 metre to find frozen water, whereas at the north pole, a visitor “would just swipe and find the ice table”, he says.

    Ceres’s dampness stands in stark contrast to Vesta, a much drier asteroid visited by Dawn in 2011–12. On average, Ceres is more than 100 times richer in hydrogen than Vesta, Prettyman says.

    A second paper, appearing on 15 December in Nature Astronomy, shows where other frozen water might lie. A team led by Thomas Platz of the Max Planck Institute for Solar System Research in Göttingen, Germany, studied 634 craters on Ceres that are always in the dark. Ten of those have bright areas on the crater floor, and spectral studies of one of them found that it consisted of water ice.

    Similarly to the Moon and Mercury, the airless Ceres apparently manages to trap frozen water in dark areas on its surface, the team says.

    Dawn’s next steps

    Dawn began its extended mission phase in July, and is currently flying in an elliptical orbit more than 4,500 miles (7,200 kilometers) from Ceres. During the primary mission, Dawn orbited and accomplished all of its original objectives at Ceres and protoplanet Vesta, which the spacecraft visited from July 2011 to September 2012.

    Dawn’s mission is managed by JPL for NASA’s Science Mission Directorate in Washington. Dawn is a project of the directorate’s Discovery Program, managed by NASA’s Marshall Space Flight Center in Huntsville, Alabama. UCLA is responsible for overall Dawn mission science. Orbital ATK Inc., in Dulles, Virginia, designed and built the spacecraft. The German Aerospace Center, Max Planck Institute for Solar System Research, Italian Space Agency and Italian National Astrophysical Institute are international partners on the mission team. For a complete list of mission participants, visit:

    http://dawn.jpl.nasa.gov/mission

    More information about Dawn is available at the following sites:

    http://dawn.jpl.nasa.gov

    http://www.nasa.gov/dawn

    See the full Nature article here .
    See the JPL-Caltech article here .

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  • richardmitnick 6:21 am on November 26, 2016 Permalink | Reply
    Tags: , , NATURE, UK scientists excited by surprise £2-billion government windfall   

    From Nature: “UK scientists excited by surprise £2-billion government windfall” 

    Nature Mag
    Nature

    23 November 2016
    Elizabeth Gibney

    1
    UK Chancellor of the Exchequer Philip Hammond has announced a large boost in funding for research and development.

    British scientists are not used to hearing about large increases in national research spending. So when Prime Minister Theresa May promised on 21 November that her government would invest an extra £2 billion (US$2.5 billion) per year in research and development (R&D) by 2020, scientists gave the speech a cautious welcome.

    But the funding hike seems to be no financial sleight of hand, according to UK Treasury documents released on 23 November after Chancellor of the Exchequer Philip Hammond gave an address on the nation’s finances. The government is expecting to spend an extra £4.7 billion on R&D between now and 2020–21, it says, and the final year’s £2-billion boost will represent a rise of around 20% in total government R&D spending.

    “It seems that this is genuinely new money, which is fantastic news,” says James Wilsdon, who studies research policy at the University of Sheffield, UK.

    Still, it remains unclear how the cash will be allocated, and how much will make its way to funding basic, blue-skies research.

    “It is a real boost to see UK strength in science being championed by the prime minister and backed with what is the most significant investment in R&D I can remember,” says Sarah Main, director of the London-based Campaign for Science and Engineering.

    Industrial challenges

    Some of the money will go directly to applied R&D through a new Industrial Strategy Challenge Fund, modelled on the US Defense Advanced Research Projects Agency (DARPA), the Pentagon’s high-risk research arm. That fund will be aimed at supporting cross-disciplinary “collaborations between business and the UK’s science base”, according to Treasury documents, and will “set identifiable challenges for UK researchers to tackle”.

    It will be managed by Innovate UK, a government body that funds R&D primarily through businesses, and by the seven UK research councils, agencies that mainly fund university research. The money will be allocated according to an “evidence-based process”, the Treasury says.

    Other cash will go towards “innovation, applied science and research”. Although the Treasury was vague on what exactly this entailed, it said that the extra funding would be used “to increase research capacity and business innovation, to further support the UK’s world-leading research base and to unlock its full potential”.

    UK Research and Innovation (UKRI) — an agency that has not yet been created, but is expected to unite the research councils and Innovate UK — will award the funding on the basis of “national excellence”, with grant funding through Innovate UK getting a “substantial increase”, said the Treasury.

    The documents make no clear reference to spending any of the new cash on basic research, but Main says she would be surprised if it was excluded. “I think it will be really important that this funding goes to both blue-skies and challenge-driven research. It is clear from the document that there is money there just to increase the UK’s research capacity, and that this money is going to be channelled through UKRI. It will be important for UKRI to consider the balance of how that money is distributed,” she says.

    Funding will begin to ramp up next year, when the government plans to spend an extra £425 million compared with 2016–17, followed by an additional £820 million in 2018–19, £1.5 billion in 2019–20 and £2 billion in 2020–21. The government said that it also plans to review the nation’s R&D tax-credit system; a Treasury spokesperson confirmed that any changes, which could provide tax breaks for companies carrying out R&D, would not count towards the extra funding.

    Brexit ahead

    Scientists had been eagerly awaiting the speech, known as the Autumn Statement, hoping that it would signal the new government’s approach to science. The budget was dominated by forecasts of the country’s slowed economic growth as a result of Brexit, its forthcoming exit from the European Union. But research and innovation also took top billing, with Hammond beginning the announcement of a string of new investments by reiterating the £2-billion pledge.

    “We do not invest enough in research, development and innovation,” he said. “As the pace of technology advances and competition from the rest of the world increases, we must build on our strengths in science and tech innovation to ensure the next generation of discoveries is made, developed and produced in Britain.”

    Scientists were also pleased with an infrastructure announcement: a new direct rail link between Oxford and Cambridge, which researchers shuttling between universities in the two cities have been wanting for decades. Hammond called it a “transformational tech-corridor drawing on the world-class strengths of our two best-known universities”.

    But what was “sorely missing” from the statement was any reference to the impact on science from Brexit, says Stephen Curry, a structural biologist at Imperial College London and a member of the advisory board for the campaign group Science is Vital. “I’d like to know how the loss of EU funding will impact decisions on allocation of the new investments announced today.”

    Hammond’s opposition counterpart, Labour Party shadow chancellor John McDonnell, responded to his speech by saying that the rise in R&D funding was not enough: it would lift the proportion of UK gross domestic product spent on R&D from 1.7% to only 1.8%, whereas the Organisation for Economic Co-operation and Development recommends that developed countries should be spending 3%.

    See the full article here .

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    Nature is a weekly international journal publishing the finest peer-reviewed research in all fields of science and technology on the basis of its originality, importance, interdisciplinary interest, timeliness, accessibility, elegance and surprising conclusions. Nature also provides rapid, authoritative, insightful and arresting news and interpretation of topical and coming trends affecting science, scientists and the wider public.

     
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