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  • richardmitnick 6:27 am on November 2, 2017 Permalink | Reply
    Tags: , , , , , , Earth-sized alien worlds are out there. Now astronomers are figuring out how to detect life on them, Exobiology, , JWST-James Webb Space Telescope, NASA Deep Space Climate Observatory, NASA HabEx, , NASA/WFIRST, Science,   

    From Science: “Earth-sized alien worlds are out there. Now, astronomers are figuring out how to detect life on them” 

    ScienceMag
    Science Magazine

    Nov. 1, 2017
    Daniel Clery

    Stephen Kane spends a lot of time staring at bad pictures of a planet. The images are just a few pixels across and nearly featureless. Yet Kane, an astronomer at the University of California, Riverside, has tracked subtle changes in the pixels over time. They are enough for him and his colleagues to conclude that the planet has oceans, continents, and clouds. That it has seasons. And that it rotates once every 24 hours.

    He knows his findings are correct because the planet in question is Earth.

    1
    An image from the Deep Space Climate Observatory satellite (left), degraded to a handful of pixels (right), is a stand-in for how an Earth-like planet around another star might look through a future space telescope.
    (LEFT TO RIGHT) NASA EPIC TEAM; STEPHEN KANE

    Kane took images from the Deep Space Climate Observatory satellite, which has a camera pointing constantly at Earth from a vantage partway to the sun, and intentionally degraded them from 4 million pixels to just a handful.

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    NASA Deep Space Climate Observatory

    The images are a glimpse into a future when telescopes will be able to just make out rocky, Earth-sized planets around other stars. Kane says he and his colleagues are trying to figure out “what we can expect to see when we can finally directly image an exoplanet.” Their exercise shows that even a precious few pixels can help scientists make the ultimate diagnosis: Does a planet harbor life?

    Finding conclusive evidence of life, or biosignatures, on a planet light-years away might seem impossible, given that space agencies have spent billions of dollars sending robot probes to much closer bodies that might be habitable, such as Mars and the moons of Saturn, without detecting even a whiff of life. But astronomers hope that a true Earth twin, bursting with flora and fauna, would reveal its secrets to even a distant observer.

    Detecting them won’t be easy, considering the meager harvest of photons astronomers are likely to get from such a tiny, distant world, its signal almost swamped by its much brighter nearby star. The new generation of space telescopes heading toward the launch pad, including NASA’s mammoth James Webb Space Telescope (JWST), have only an outside chance of probing an Earth twin in sufficient detail.

    NASA/ESA/CSA Webb Telescope annotated

    But they will be able to sample light from a range of other planets, and astronomers are already dreaming of a space telescope that might produce an image of an Earth-like planet as good as Kane’s pixelated views of Earth. To prepare for the coming flood of exoplanet data, and help telescope designers know what to look for, researchers are now compiling lists of possible biosignatures, from spectral hints of gases that might emanate from living things to pigments that could reside in alien plants or microbes.

    There is unlikely to be a single smoking gun. Instead, context and multiple lines of evidence will be key to a detection of alien life. Finding a specific gas—oxygen, say—in an alien atmosphere isn’t enough without figuring out how the gas could have gotten there. Knowing that the planet’s average temperature supports liquid water is a start, but the length of the planet’s day and seasons and its temperature extremes count, too. Even an understanding of the planet’s star is imperative, to know whether it provides steady, nourishing light or unpredictable blasts of harmful radiation.

    “Each [observation] will provide crucial evidence to piece together to say if there is life,” says Mary Voytek, head of NASA’s astrobiology program in Washington, D.C.

    In the heady early days following the discovery of the first exoplanet around a normal star in 1995, space agencies drew up plans for extremely ambitious—and expensive—missions to study Earth twins that could harbor life. Some concepts for NASA’s Terrestrial Planet Finder and the European Space Agency’s Darwin mission envisaged multiple giant telescopes flying in precise formation and combining their light to increase resolution. But neither mission got off the drawing board. “It was too soon,” Voytek says. “We didn’t have the data to plan it or build it.”

    Instead, efforts focused on exploring the diversity of exoplanets, using both ground-based telescopes and missions such as NASA’s Kepler spacecraft.

    NASA/Kepler Telescope

    Altogether they have identified more than 3500 confirmed exoplanets, including about 30 roughly Earth-sized worlds capable of retaining liquid water. But such surveys give researchers only the most basic physical information about the planets: their orbits, size, and mass. In order to find out what the planets are like, researchers need spectra: light that has passed through the planet’s atmosphere or been reflected from its surface, broken into its component wavelengths.

    Most telescopes don’t have the resolution to separate a tiny, dim planet from its star, which is at least a billion times brighter. But even if astronomers can’t see a planet directly, they can still get a spectrum if the planet transits, or passes in front of the star, in the course of its orbit. As the planet transits, starlight shines through its atmosphere; gases there absorb particular wavelengths and leave characteristic dips in the star’s spectrum.

    Astronomers can also study a transiting planet by observing the star’s light as the planet’s orbit carries it behind the star.

    Planet transit. NASA/Ames

    Before the planet is eclipsed, the spectrum will include both starlight and light reflected from the planet; afterward, the planet’s contribution will disappear. Subtracting the two spectra should reveal traces of the planet.

    Teasing a recognizable signal from the data is far from easy. Because only a tiny fraction of the star’s light probes the atmosphere, the spectral signal is minuscule, and hard to distinguish from irregularities in the starlight itself and from absorption by Earth’s own atmosphere. Most scientists would be “surprised at how horrible the data is,” says exoplanet researcher Sara Seager of the Massachusetts Institute of Technology in Cambridge.

    In spite of those hurdles, the Hubble and Spitzer space telescopes, plus a few others, have used these methods to detect atmospheric gases, including sodium, water, carbon monoxide and dioxide, and methane, from a handful of the easiest targets.

    NASA/ESA Hubble Telescope

    NASA/Spitzer Infrared Telescope

    Most are “hot Jupiters”—big planets in close-in orbits, their atmospheres puffed up by the heat of their star.

    3
    In an artist’s concept, a petaled starshade flying at a distance of tens of thousands of kilometers from a space telescope blocks a star’s light, opening a clear view of its planets. NASA/JPL.

    The approach will pay much greater dividends after the launch of the JWST in 2019. Its 6.5-meter mirror will collect far more light from candidate stars than existing telescopes can, allowing it to tease out fainter exoplanet signatures, and its spectrographs will produce much better data.

    4
    https://jwst.nasa.gov/mirrors.html

    And it will be sensitive to the infrared wavelengths where the absorption lines of molecules such as water, methane, and carbon monoxide and dioxide are most prominent.

    Once astronomers have such spectra, one of the main gases that they hope to find is oxygen. Not only does it have strong and distinctive absorption lines, but many believe its presence is the strongest sign that life exists on a planet.

    Oxygen-producing photosynthesis made Earth what it is today. First cyanobacteria in the oceans and then other microbes and plants have pumped out oxygen for billions of years, so that it now makes up 21% of the atmosphere—an abundance that would be easily detectable from afar. Photosynthesis is evolution’s “killer app,” says Victoria Meadows, head of the NASA-sponsored Virtual Planet Laboratory (VPL) at the University of Washington in Seattle. It uses a prolific source of energy, sunlight, to transform two molecules thought to be common on most terrestrial planets—water and carbon dioxide—into sugary fuel for multicellular life. Meadows reckons it is a safe bet that something similar has evolved elsewhere. “Oxygen is still the first thing to go after,” she says.

    Fifteen years ago, when exoplanets were new and researchers started thinking about how to scan them for life, “Champagne would have flowed” if oxygen had been detected, Meadows recalls. But since then, researchers have realized that things are not that simple: Lifeless planets can have atmospheres full of oxygen, and life can proliferate without ever producing the gas. That was the case on Earth, where, for 2 billion years, microbes practiced a form of photosynthesis that did not produce oxygen or many other gases. “We’ve had to make ourselves more aware of how we could be fooled,” Meadows says.

    To learn what a genuine biosignature might look like, and what might be a false alarm, Meadows and her colleagues at the VPL explore computer models of exoplanet atmospheres, based on data from exoplanets as well as observations of more familiar planets, including Earth. They also do physical experiments in vacuum chambers. They recreate the gaseous cocktails that may surround exoplanets, illuminate them with simulated starlight of various kinds, and see what can be measured.

    Over the past few years, VPL researchers have used such models to identify nonbiological processes that could make oxygen and produce a “false positive” signal. For example, a planet with abundant surface water might form around a star that, in its early years, surges in brightness, perhaps heating the young planet enough to boil off its oceans. Intense ultraviolet light from the star would bombard the resulting water vapor, perhaps splitting it into hydrogen and oxygen. The lighter hydrogen could escape into space, leaving an atmosphere rich in oxygen around a planet devoid of life. “Know thy star, know thy planet,” recites Siddharth Hegde of Cornell University’s Carl Sagan Institute.

    Discovering methane in the same place as oxygen, however, would strengthen the case for life. Although geological processes can produce methane, without any need for life, most methane on Earth comes from microbes that live in landfill sites and in the guts of ruminants. Methane and oxygen together make a redox pair: two molecules that will readily react by exchanging electrons. If they both existed in the same atmosphere, they would quickly combine to produce carbon dioxide and water. But if they persist at levels high enough to be detectable, something must be replenishing them. “It’s largely accepted that if you have redox molecules in large abundance they must be produced by life,” Hegde says.

    Some argue that by focusing on oxygen and methane—typical of life on Earth—researchers are ignoring other possibilities. If there is one thing astronomers have learned about exoplanets so far, it is that familiar planets are a poor guide to exoplanets’ huge diversity of size and nature. And studies of extremophiles, microbes that thrive in inhospitable environments on Earth, suggest life can spring up in unlikely places. Exobiology may be entirely unlike its counterpart on Earth, and so its gaseous byproducts might be radically different, too.

    But what gases to look for? Seager and her colleagues compiled a list of 14,000 compounds that might exist as a gas at “habitable” temperatures, between the freezing and boiling points of water; to keep the list manageable they restricted it to small molecules, with no more than six nonhydrogen atoms. About 2500 are made of the biogenic atoms carbon, nitrogen, oxygen, phosphorus, sulfur, and hydrogen, and about 600 are actually produced by life on Earth. Detecting high levels of any of these gases, if they can’t be explained by nonbiological processes, could be a sign of alien biology, Seager and her colleagues argue.


    A. CUADRA/SCIENCE

    Light shining through the atmospheres of transiting exoplanets is likely to be the mainstay of biosignature searches for years to come. But the technique tends to sample the thin upper reaches of a planet’s atmosphere; far less starlight may penetrate the thick gases that hug the surface, where most biological activity is likely to occur. The transit technique also works best for hot Jupiters, which by nature are less likely to host life than small rocky planets with thinner atmospheres. The JWST may be able to tease out atmospheric spectra from small planets if they orbit small, dim stars like red dwarfs, which won’t swamp the planet’s spectrum. But these red dwarfs have a habit of spewing out flares that would make it hard for life to establish itself on a nearby planet.

    To look for signs of life on a terrestrial planet around a sunlike star, astronomers will probably have to capture its light directly, to form a spectrum or even an actual image. That requires blocking the overwhelming glare of the star. Ground-based telescopes equipped with “coronagraphs,” which precisely mask a star so nearby objects can be seen, can now capture only the biggest exoplanets in the widest orbits. To see terrestrial planets will require a similarly equipped telescope in space, above the distorting effect of the atmosphere. NASA’s Wide Field Infrared Survey Telescope (WFIRST), expected to launch in the mid-2020s, is meant to fill that need.

    NASA/WFIRST

    Even better, WFIRST could be used in concert with a “starshade”—a separate spacecraft stationed 50,000 kilometers from the telescope that unfurls a circular mask tens of meters across to block out starlight. A starshade is more effective than a coronagraph at limiting the amount of light going into the telescope. It not only blocks the star directly, but also suppresses diffraction with an elaborate petaled edge. That reduces the stray scattered light that can make it hard to spot faint planets. A starshade is a much more expensive prospect than a coronagraph, however, and aligning telescope and starshade over huge distances will be a challenge.

    Direct imaging will provide much better spectra than transit observations because light will pass through the full depth of the planet’s atmosphere twice, rather than skimming through its outer edges. But it also opens up the possibility of detecting life directly, instead of through its waste gases in the atmosphere. If organisms, whether they are plants, algae, or other microbes, cover a large proportion of a planet’s surface, their pigments may leave a spectral imprint in the reflected light. Earthlight contains an obvious imprint of this sort. Known as the “red edge,” it is the dramatic change in the reflectance of green plants at a wavelength of about 720 nanometers. Below that wavelength, plants absorb as much light as possible for photosynthesis, reflecting only a few percent. At longer wavelengths, the reflectance jumps to almost 50%, and the brightness of the spectrum rises abruptly, like a cliff. “An alien observer could easily tell if there is life on Earth,” Hegde says.

    There’s no reason to assume that alien life will take the form of green plants. So Hegde and his colleagues are compiling a database of reflectance spectra for different types of microbes. Among the hundreds the team has logged are many extremophiles, which fill marginal niches on Earth but may be a dominant life form on an exoplanet. Many of the microbes on the list have not had their reflectance spectra measured, so the Cornell team is filling in those gaps. Detecting pigments on an exoplanet surface would be extremely challenging. But a tell-tale color in the faint light of a distant world could join other clues—spectral absorption lines from atmospheric gases, for example—to form “a jigsaw puzzle which overall gives us a picture of the planet,” Hegde says.

    None of the telescopes available now or in the next decade is designed specifically to directly image exoplanets, so biosignature searches must compete with other branches of astronomy for scarce observing time. What researchers really hanker after is a large space telescope purpose-built to image Earth-like alien worlds—a new incarnation of the idea behind NASA’s ill-fated Terrestrial Planet Finder.

    The Habitable Exoplanet Imaging Mission, or HabEx, a mission concept now being studied by NASA, could be the answer. Its telescope would have a mirror up to 6.5 meters across—as big as the JWST’s—but would be armed with instruments sensitive to a broader wavelength range, from the ultraviolet to the near-infrared, to capture the widest range of spectral biosignatures. The telescope would be designed to reduce scattered light and have a coronagraph and starshade to allow direct imaging of Earth-sized exoplanets.

    Such a mission would reveal Earth-like planets at a level of detail researchers can now only dream about—probing atmospheres, revealing any surface pigments, and even delivering the sort of blocky surface images that Kane has been simulating. But will that be enough to conclude we are not alone in the universe? “There’s a lot of uncertainty about what would be required to put the last nail in the coffin,” Kane says. “But if HabEx is built according to its current design, it should provide a pretty convincing case.”

    4
    NASA HabEx: The Planet Hunter

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  • richardmitnick 8:20 am on October 2, 2017 Permalink | Reply
    Tags: , , , , , , Kyoto University, Science, , University of Tübingen, University of Texas at Austin, University of Tokyo   

    From Science: “Sloshing, supersonic gas may have built the baby universe’s biggest black holes” 

    AAAS
    Science

    Sep. 28, 2017
    Joshua Sokol

    1
    Supermassive black holes a billion times heavier than the sun are too big to have formed conventionally. NASA Goddard Space Flight Center

    A central mystery surrounds the supermassive black holes that haunt the cores of galaxies: How did they get so big so fast? Now, a new, computer simulation–based study suggests that these giants were formed and fed by massive clouds of gas sloshing around in the aftermath of the big bang.

    “This really is a new pathway,” says Volker Bromm, an astrophysicist at the University of Texas in Austin who was not part of the research team. “But it’s not … the one and only pathway.”

    Astronomers know that, when the universe was just a billion years old, some supermassive black holes were already a billion times heavier than the sun. That’s much too big for them to have been built up through the slow mergers of small black holes formed in the conventional way, from collapsed stars a few dozen times the mass of the sun. Instead, the prevailing idea is that these behemoths had a head start. They could have condensed directly out of seed clouds of hydrogen gas weighing tens of thousands of solar masses, and grown from there by gravitationally swallowing up more gas. But the list of plausible ways for these “direct-collapse” scenarios to happen is short, and each option requires a perfect storm of circumstances.

    For theorists tinkering with computer models, the trouble lies in getting a massive amount of gas to pile up long enough to collapse all at once, into a vortex that feeds a nascent black hole like water down a sink drain. If any parts of the gas cloud cool down or clump up early, they will fragment and coalesce into stars instead. Once formed, radiation from the stars would blow away the rest of the gas cloud.

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    Computer models show how supersonic streams of gas coalesce around nuggets of dark matter—forming the seed of a supermassive black hole. Shingo Hirano

    One option, pioneered by Bromm and others, is to bathe a gas cloud in ultraviolet light, perhaps from stars in a next-door galaxy, and keep it warm enough to resist clumping. But having a galaxy close enough to provide that service would be quite the coincidence.

    The new study proposes a different origin. Both the early universe and the current one are composed of familiar matter like hydrogen, plus unseen clumps of dark matter.

    Dark Matter Research

    Universe map Sloan Digital Sky Survey (SDSS) 2dF Galaxy Redshift Survey

    Scientists studying the cosmic microwave background hope to learn about more than just how the universe grew—it could also offer insight into dark matter, dark energy and the mass of the neutrino.

    Dark matter cosmic web and the large-scale structure it forms The Millenium Simulation, V. Springel et al

    Dark Matter Particle Explorer China

    DEAP Dark Matter detector, The DEAP-3600, suspended in the SNOLAB deep in Sudbury’s Creighton Mine

    LUX Dark matter Experiment at SURF, Lead, SD, USA

    ADMX Axion Dark Matter Experiment, U Uashington

    Today, these two components move in sync. But very early on, normal matter may have sloshed back and forth at supersonic speeds across a skeleton provided by colder, more sluggish dark matter. In the study, published today in Science, simulations show that where these surges were strong, and crossed the path of heavy clumps of dark matter, the gas resisted premature collapse into stars and instead flowed into the seed of a supermassive black hole. These scenarios would be rare, but would still roughly match the number of supermassive black holes seen today, says Shingo Hirano, an astrophysicist at the University of Texas and lead author of the study.

    Priya Natarajan, an astrophysicist at Yale University, says the new simulation represents important computational progress. But because it would have taken place at a very distant, early moment in the history of the universe, it will be difficult to verify. “I think the mechanism itself in detail is not going to be testable,” she says. “We will never see the gas actually sloshing and falling in.”

    But Bromm is more optimistic, especially if such direct-collapse black hole seeds also formed slightly later in the history of the universe. He, Natarajan, and other astronomers have been looking for these kinds baby black holes, hoping to confirm that they do, indeed, exist and then trying to work out their origins from the downstream consequences.

    In 2016, they found several candidates, which seem to have formed through direct collapse and are now accreting matter from clouds of gas. And earlier this year, astronomers showed that the early, distant universe is missing the glow of x-ray light that would be expected from a multitude of small black holes—another sign favoring the sudden birth of big seeds that go on to be supermassive black holes. Bromm is hopeful that upcoming observations will provide more definite evidence, along with opportunities to evaluate the different origin theories. “We have these predictions, we have the signatures, and then we see what we find,” he says. “So the game is on.”

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  • richardmitnick 7:09 am on September 27, 2017 Permalink | Reply
    Tags: After lengthy campaign, , , , Australia gets its own space agency, , , Science   

    From Science: “After lengthy campaign, Australia gets its own space agency” 

    AAAS
    Science

    Sep. 25, 2017
    Leigh Dayton

    1
    Australia will establish a space agency to pursue commercial and research activities. inefekt69

    Australia was the third nation after the United States and the USSR to build and launch a satellite from its own rocket range. But after the Weapons Research Establishment Satellite (WRESAT) took to the skies on 29 November 1967, the country’s space efforts dwindled. Australia’s last microsatellite—launched from a Japanese facility—died in 2007. Along with Iceland, Australia was one of only two Organisation for Economic Co-operation and Development nations without a space agency.

    But that’s about to change. The government announced today at the 68th International Astronautical Congress in Adelaide, Australia, that it will establish a national space agency.

    The decision caps a yearlong campaign to boost Australia’s space efforts, led by groups from universities, industry, and government bodies. “The creation of an Australian space agency is very exciting news,” says Michael Brown, a Melbourne, Australia–based Monash University astronomer.

    “The establishment of an Australian Space Agency is a strong nod of support for the current space sector in Australia,” says astronomer and astrophysicist Lee Spitler of Macquarie University here. He adds that what is left of the country’s space industry operates as a “grassroots movement across a small number of companies, university groups, and the defense sector.”

    Australia depends heavily foreign-built or operated satellites for communications, remote sensing, and astronomical research. Its share of the $330 billion global space economy is only 0.8%.

    Despite persistent calls for a national space agency, the current government took no steps until last July, when Arthur Sinodinos, the federal minister for industry, innovation and science, set up an expert review group to study the country’s space industry capabilities. To date, the group has received nearly 200 written submissions and held meetings across the country.

    Facing calls for action last week from the participants at the Adelaide meeting, Acting Industry Minister Michaelia Cash announced that the working group will develop a charter for the space agency that will be included in a wider space industry strategy.

    It is about time, says astronomer Alan Duffy at Swinburne University of Technology in Melbourne: “These announcements come at a special anniversary. It’s 50 years since the launch of WRESAT.”

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  • richardmitnick 11:07 am on September 25, 2017 Permalink | Reply
    Tags: , , Double-blind peer review, Nature Publishing Group (NPG) in London, Science   

    From Science: “Few authors choose anonymous peer review, massive study of Nature journals shows 

    AAAS
    Science

    Sep. 22, 2017
    Martin Enserink

    1
    Scientists from India and China far more often ask Nature’s journals for double-blind peer review than those from Western countries. Emily Petersen

    Once you’ve submitted your paper to a journal, how important is it that the reviewers know who wrote it?

    Surveys have suggested that many researchers would prefer anonymity because they think it would result in a more impartial assessment of their manuscript. But a new study by the Nature Publishing Group (NPG) in London shows that only one in eight authors actually chose to have their reviewers blinded when given the option. The study, presented here at the Eighth International Congress on Peer Review, also found that papers submitted for double-blind review are far less likely to be accepted.

    Most papers are reviewed in single-blind fashion—that is, the reviewers know who the authors are, but not vice versa. In theory, that knowledge allows them to exercise a conscious or unconscious bias against researchers from certain countries, ethnic minorities, or women, and be kinder to people who are already well-known in their field. Double-blind reviews, the argument goes, would remove those prejudices. A 2007 study of Behavioral Ecology found that the journal published more articles by female authors when using double-blind reviews—although that conclusion was challenged by other researchers a year later. In a survey of more than 4000 researchers published in 2013, three-quarters said they thought double-blind review is “the most effective method.”

    But that approach also has drawbacks. Journals have checklists for authors on how to make a manuscript anonymous by avoiding phrases like “we previously showed” and by removing certain types of meta-information from computer files—but some researchers say they find it almost impossible to ensure complete anonymity.

    “If I am going to remove every trace that could identify myself and my coauthors there wouldn’t be much left of the paper,” music researcher Alexander Jensenius from the University of Oslo wrote on his blog. Indeed, experience shows that reviewers can sometimes tell who wrote a paper, based on previous work or other information. At Conservation Biology, which switched to double-blind reviews in 2014, reviewers who make a guess get it right about half of the time, says the journal’s editor, Mark Burgman of Imperial College London. “But that’s not the end of the world,” he says. Double-blind review, he says, “sends a message that you’re determined to try and circumvent any unconscious bias in the review process.”

    In 2013 NPG began offering its authors anonymous peer review as an option for two journals, Nature Geoscience and Nature Climate Change. Only one in five authors requested it, Nature reported 2 years later—far less than editors had expected. But the authors’ reactions were so positive that NPG decided to expand the option to all of its journals.

    At the peer review congress last week, NPG’s Elisa De Ranieri presented data on 106,373 submissions to the group’s 25 Nature-branded journals between March 2015 and February 2017. In only 12% of cases did the authors opt for double-blind review. They chose double-blind reviews most often for papers in the group’s most prestigious journal, Nature (14%), compared to 12% for Nature “sister journals” and 9% for the open-access journal Nature Communications.

    The data suggest that concerns about possible discrimination may have been a factor. Some 32% of Indian authors and 22% of Chinese authors opted for double-blind review, compared with only 8% of authors from France and 7% from the United States. The option was also more popular among researchers from less prestigious institutes, based on their 2016 Times Higher Education rankings. There was no difference in the choices of men and women, De Ranieri noted, a finding that she called surprising.

    Burgman suspects that the demand for double-blind review is suppressed by fears that it could backfire on the author. “There’s the idea that if you go double blind, you have something to hide,” he says. That may also explain why women were not more likely to demand double blind reviews than men, he says. Burgman says he thinks making double-blind reviews the standard, as Conservation Biology has done, is the best course. “It has not markedly changed the kind or numbers of submissions we receive,” he says. “But we do get informal feedback from a lot of people who say: ‘This is a great thing.’”

    Authors choosing double-blind review in hope of improving their chances of success will be disappointed by the Nature study. Only 8% of those papers were actually sent out for review after being submitted, compared to 23% of those opting for single-blind review. (Nature’s editors decide whether to send a paper for review or simply reject it, and the editors know the identity of the authors.) And only 25% of papers under double-blind review were eventually accepted, versus 44% for papers that went the single-blind route.

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  • richardmitnick 1:22 pm on June 30, 2017 Permalink | Reply
    Tags: , , , , Science   

    From Science: “Cancer studies pass reproducibility test” 

    AAAS
    Science Magazine

    Jun. 27, 2017
    Jocelyn Kaiser
    1
    Though researchers have had general success reproducing cancer results, studies involving mice have proven difficult to replicate.
    Adva/Flickr (CC BY-NC 2.0)

    A high-profile project aiming to test reproducibility in cancer biology has released a second batch of results, and this time the news is good: Most of the experiments from two key cancer papers could be repeated.

    The latest replication studies, which appear today in eLife, come on top of five published in January that delivered a mixed message about whether high-impact cancer research can be reproduced. Taken together, however, results from the completed studies are “encouraging,” says Sean Morrison of the University of Texas Southwestern Medical Center in Dallas, an eLife editor. Overall, he adds, independent labs have now “reproduced substantial aspects” of the original experiments in four of five replication efforts that have produced clear results.

    In the two new replication efforts, however, one key mouse experiment could not be repeated, suggesting ongoing problems with the reproducibility of animal studies, says one leader of the Reproducibility Project: Cancer Biology.

    The unusual initiative was inspired by reports from two drugs companies that up to 89% of preclinical biomedical studies didn’t hold up in their labs. The project is having contract labs repeat key experiments from about 30 high-impact cancer papers published between 2010 and 2012. Whereas some researchers laud the effort, others have worried that contract labs lack the expertise to perform certain experiments as well as cutting-edge academic research labs and that any failures will unfairly tarnish the field.

    In January, critics’ fears were realized when the first five replications came out. Only two studies could be reproduced; one result was negative, and two studies were ruled inconclusive because of problems with mouse tumor models. The findings have led some experts to conclude that biomedicine suffers from a replication crisis.

    Now, scientists’ track records seem to be improving. In one of the new studies [eLIFE], a contract lab confirmed a 2010 report in Cancer Cell that mutations in genes called IDH1 and IDH2, found in some leukemias and brain cancers, cause cells to produce a metabolite that spurs cancer growth. The replicators also verified that levels of the metabolite in leukemia cells indicate whether a cancer patient has the IDH mutations. (The original paper’s lead author, Craig Thompson of Memorial Sloan Kettering Cancer Center in New York City, who co-founded a company that is testing IDH drugs in clinical trials, was traveling and unable to comment.)

    The second replication study [eLIFE]looked at a 2011 Nature paper reporting that a compound called a BET inhibitor, which controls whether genes are activated—can stop a type of leukemia. As in the original study, the compound, I-BET151, killed human leukemia cells in a dish and reduced their numbers in mice that had been injected with the cells. However, unlike in the original paper, these mice did not survive any longer than untreated mice with leukemia.

    Several scientists say that result doesn’t invalidate the overall conclusions that I-BET151 works against leukemia. The replication team did the mouse experiment differently, using a lower dose of I-BET151, for example. Given such differences, “I think we should be careful not to make too much of the absence of statistically significant differences in survival as an endpoint,” says Harvard University molecular biologist Karen Adelman, an eLife editor who oversaw reviews of the replication paper.

    And cancer biologist Tony Kouzarides of the University of Cambridge in the United Kingdom, who led the original Nature study, says this one negative result “highlights the pitfalls of biological research, namely that different labs may vary conditions that affect the outcome of a given experiment.”

    But Tim Errington of the Center for Open Science in Charlottesville, Virginia, which is co-sponsoring the reproducibility project, counters that the fact that the mouse survival experiment worked only under certain conditions raises questions about whether the paper’s overall findings are “robust.” He adds, “You want this to be generalizable.”

    The cancer biology project hopes to finish experiments for another 22 replications by the end of this year, when the grant funding the effort runs out, Errington says.

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  • richardmitnick 8:22 am on June 29, 2017 Permalink | Reply
    Tags: , , , , Reproducibility Project: Cancer Biology, Science, Scientists’ track records seem to be improving   

    From Science: “Cancer studies pass reproducibility test” 

    AAAS
    Science

    Jun. 27, 2017
    Jocelyn Kaiser

    1
    Though researchers have had general success reproducing cancer results, studies involving mice have proven difficult to replicate.
    Adva/Flickr (CC BY-NC 2.0)

    A high-profile project aiming to test reproducibility in cancer biology has released a second batch of results, and this time the news is good: Most of the experiments from two key cancer papers could be repeated.

    The latest replication studies, which appear today in eLife, come on top of five published in January that delivered a mixed message about whether high-impact cancer research can be reproduced. Taken together, however, results from the completed studies are “encouraging,” says Sean Morrison of the University of Texas Southwestern Medical Center in Dallas, an eLife editor. Overall, he adds, independent labs have now “reproduced substantial aspects” of the original experiments in four of five replication efforts that have produced clear results.

    In the two new replication efforts, however, one key mouse experiment could not be repeated, suggesting ongoing problems with the reproducibility of animal studies, says one leader of the Reproducibility Project: Cancer Biology.

    The unusual initiative was inspired by reports from two drugs companies that up to 89% of preclinical biomedical studies didn’t hold up in their labs. The project is having contract labs repeat key experiments from about 30 high-impact cancer papers published between 2010 and 2012. Whereas some researchers laud the effort, others have worried that contract labs lack the expertise to perform certain experiments as well as cutting-edge academic research labs and that any failures will unfairly tarnish the field.

    In January, critics’ fears were realized when the first five replications came out. Only two studies could be reproduced; one result was negative, and two studies were ruled inconclusive because of problems with mouse tumor models. The findings have led some experts to conclude that biomedicine suffers from a replication crisis.

    Now, scientists’ track records seem to be improving. In one of the new studies, a contract lab confirmed a 2010 report in Cancer Cell that mutations in genes called IDH1 and IDH2, found in some leukemias and brain cancers, cause cells to produce a metabolite that spurs cancer growth. The replicators also verified that levels of the metabolite in leukemia cells indicate whether a cancer patient has the IDH mutations. (The original paper’s lead author, Craig Thompson of Memorial Sloan Kettering Cancer Center in New York City, who co-founded a company that is testing IDH drugs in clinical trials, was traveling and unable to comment.)

    The second replication study looked at a 2011 Nature paper reporting that a compound called a BET inhibitor, which controls whether genes are activated—can stop a type of leukemia. As in the original study, the compound, I-BET151, killed human leukemia cells in a dish and reduced their numbers in mice that had been injected with the cells. However, unlike in the original paper, these mice did not survive any longer than untreated mice with leukemia.

    Several scientists say that result doesn’t invalidate the overall conclusions that I-BET151 works against leukemia. The replication team did the mouse experiment differently, using a lower dose of I-BET151, for example. Given such differences, “I think we should be careful not to make too much of the absence of statistically significant differences in survival as an endpoint,” says Harvard University molecular biologist Karen Adelman, an eLife editor who oversaw reviews of the replication paper.

    And cancer biologist Tony Kouzarides of the University of Cambridge in the United Kingdom, who led the original Nature study, says this one negative result “highlights the pitfalls of biological research, namely that different labs may vary conditions that affect the outcome of a given experiment.”

    But Tim Errington of the Center for Open Science in Charlottesville, Virginia, which is co-sponsoring the reproducibility project, counters that the fact that the mouse survival experiment worked only under certain conditions raises questions about whether the paper’s overall findings are “robust.” He adds, “You want this to be generalizable.”

    The cancer biology project hopes to finish experiments for another 22 replications by the end of this year, when the grant funding the effort runs out, Errington says.

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  • richardmitnick 2:07 pm on June 16, 2017 Permalink | Reply
    Tags: , , , Science,   

    From Science: “Designer protein halts flu” 

    AAAS
    Science Magazine

    June 12, 2017
    Robert Service

    1

    A designer protein (brown and orange) fits snugly on top of the influenza virus’s hemagglutinin protein (green), which helps the virus latch onto and infect cells.
    Eva-Maria Strauch

    There’s a new weapon taking shape in the war on flu, one of the globe’s most dangerous infectious diseases. Scientists have created a designer protein that stops the influenza virus from infecting cells in culture and protects mice from getting sick after being exposed to a heavy dose of the virus. It can also be used as a sensitive diagnostic. And although it isn’t ready as a treatment itself, the protein may point the way to future flu drugs, scientists say.

    “It’s impressive,” says James Crowe, an immunologist at Vanderbilt University in Nashville, who was not involved in the study. But because it hasn’t yet been tested in humans, “it [still] has a long way to go,” he says.

    Influenza severely sickens 3–5 million people each year, and it kills between 250,000 and 500,000, mostly the elderly and people with weakened immune systems. Every year, public health officials survey the three flu subtypes circulating in humans and design a vaccine for the next winter season that covers them all. But those vaccines are far from perfect: They don’t always exactly match the viruses actually going around, and in some people, the shots fail to trigger a vigorous immune response.

    Drugs are another line of defense. Most focus on the proteins on the virus’s outer coat, neuraminidase and hemagglutinin (HA). Some drugs that block neuraminidase, which helps the virus escape already infected cells, are starting to bump up against viral resistance. HA is scientists’ next target. The mushroom-shaped protein specializes in infecting cells, first by binding a trio of sites on its head to three separate sugar molecules on the surface of targeted cells. Once the virus latches on, parts of HA’s stem act as a grappling hook to pull the virus in close, allowing it to fuse with the cell membrane and release its contents inside.

    In 2011, researchers led by David Baker, a computational biologist at the University of Washington in Seattle, created a designer protein that binds HA’s stem, which prevented viral infection in cell cultures.

    Dr. David Baker, Baker Lab, U Washington

    But because the stem is often shrouded by additional protein, it can be hard for drugs to reach it.

    Now, Baker’s team has designed proteins to target HA’s more exposed head group. They started by analyzing x-ray crystal structures that show in atomic detail how flu-binding antibodies in people grab on to the three sugar-binding sites on HA’s head. They copied a small portion of the antibody that wedges itself into one of these binding sites. They then used protein design software called Rosetta to triple that head-binding section, creating a three-part, triangular protein, which the computer calculated would fit like a cap over the top of HA’s head group.

    Rosetta@home project, a project running on BOINC software from UC Berkeley

    My BOINC

    Next, they synthesized a gene for making the protein and inserted it into bacteria, which cranked out copies for them to test.

    In the test, Baker’s team immobilized copies of the protein on a paperlike material called nitrocellulose. They then exposed it to different strains of the virus, which it grabbed and held. “We call it flu glue, because it doesn’t let go,” Baker says. In other experiments, the protein blocked the virus from infecting cells in culture, and it even prevented mice from getting sick when administered either 1 day before or after viral exposure, they report today in Nature Biotechnology.

    Despite these early successes, Baker and Crowe caution that the newly designed protein isn’t likely to become a medicine itself. For starters, Baker says, the protein doesn’t bind all flu strains that commonly infect humans. That means a future drug may require either a cocktail of HA head group binding proteins or work in combination with stem-binding versions. Second, the safety of designer proteins will have to be studied carefully, Crowe says, because they are markedly different than natural HA-binding antibodies. “The further you get away from a natural antibody, the less you can predict what will happen,” Crowe says.

    But down the road, Baker says, the new designer protein could serve as the basis for a cheap diagnostic—akin to a pregnancy test—for detecting flu and possibly even medicines able to knock it out.

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  • richardmitnick 3:23 pm on April 15, 2017 Permalink | Reply
    Tags: , , Science, Teleocrater   

    From Science: “Curious fossil could rewrite early days of the dinosaurs” 

    AAAS
    Science Magazine

    Apr. 12, 2017
    Carolyn Gramling

    1
    In this artist’s rendition of life in the middle Triassic, carnivorous Teleocrater rhadinus, newly identified as a very early ancestor of dinosaurs and pterosaurs, feasts on mammallike reptile Cynognathus. Natural History Museum, London, artwork by Mark Witton

    How did the dinosaur become the dinosaur? Somewhere along the line, the ancestor of dinosaurs diverged from the ancestor of crocodiles, a momentous split in the evolution of vertebrates that ultimately set the stage for the age of dinos. But the details of that split remain mysterious, thanks to a dearth of fossils of early dinosaur relatives. Enter the newly identified 247-million- to 242-million-year-old Teleocrater rhadinus, a close relative of dinosaurs that also happened to walk on all fours and share some key features with the ancestors of crocodiles. These shared features, the authors say, suggest that it’s time to rethink what we thought we knew about dinosaurs’ earliest ancestors.

    “We’ve been waiting a long time to find fossils like this that fit in this part of the family tree,” says Randall Irmis, a paleontologist at the Natural History Museum of Utah in Salt Lake City, who was not involved in the work. “This has pretty big implications for how we understand the early evolution of dinosaurs.”

    Some 251 million years ago, at the end of the Permian period, a mass extinction wiped out most of life on Earth. In its wake arose a group of egg-laying reptile precursors called archosaurs, the common ancestors of dinosaurs, flying reptiles known as pterosaurs, and crocodiles. At some point during the next period, the Triassic, pterosaurs and dinosaurs split off from the crocodile lineage.

    Those two different lineages, avian versus crocodilian, have long been identified by their types of ankle joints. Dinosaurs and pterosaurs all have a version of a hinged, birdlike ankle, rather than the crocodilelike ankle with ball-and-socket joint.

    But exactly what early dinosaurs and their closest relatives looked like has been something of a mystery, because few fossils exist from the dawn of the dinosaurs. And many of the fossils that do exist, collected perhaps decades to a century ago, languish unidentified in museum drawers.

    Indeed, Teleocrater isn’t a completely new discovery. A specimen was first unearthed in what is now Tanzania in the 1930s and sat in London’s Natural History Museum until 1956, when Ph.D. candidate Alan Charig (later a paleontologist at the museum) dubbed it T. rhadinus (referring to the shape of the animal’s hip and its slender body). Charig, who died in 1997 but is included as an author on the new paper, speculated that it was some sort of early dinosaur relative. But the fossil was in pieces, just bits of vertebrae and pelvis and limb, and difficult to place on the family tree.

    Then in 2015, Sterling Nesbitt, a paleontologist at Virginia Polytechnic Institute and State University in Blacksburg, and a team of researchers headed back to southern Tanzania to take another look at the middle Triassic rocks where Teleocrater was first discovered. This time, the rocks—estimated to be about 247 million to 242 million years old—yielded several individuals of the same species. With that new bounty, the researchers were able to catalog many more of the creature’s features—enough to place it on the vertebrate family tree.

    Teleocrater, Nesbitt and his co-authors report online today in Nature, belongs at the very base of the avian lineage that later gave rise to dinosaurs. It has a characteristic muscle scar on the upper leg bone that is found only in the avian lineage of birds and dinosaurs and is missing in crocodiles and their relatives. But Teleocrater also had a crocodilelike ankle, with a ball-and-socket joint. That suggests that the crocodile ankle came first, and the bird ankle evolved later.

    That’s key, because the ankle joint has been used for decades as an indicator of avian versus crocodilian lineage, so Teleocrater must be close to the split between them. And in several respects, Nesbitt says, “Teleocrater looks more like the relatives of the crocodiles than the relatives of dinosaurs.” The carnivorous animal, which was roughly the size of a small lion, walked on all fours, its forelimbs and hindlimbs are similar in proportion, and the limbs themselves are pretty short relative to the length of the body.

    Seemingly small details like these can produce ripples throughout paleontology collections, because they can help researchers properly classify fossils that had seemed to be walking contradictions. “These fossils exist in museums around the world, but until you find a keystone—something that helps you understand the full anatomy [of a species]—you won’t understand where these animals go on the tree of life,” Nesbitt says.

    After identifying Teleocrater as an ancestor along the avian lineage, the authors could group it with several other difficult-to-place animals, including Dongusuchus and Spondylosoma, naming a new group of long-necked, carnivorous quadrupeds dubbed Aphanosauria (hidden or obscure lizards, in Greek). Aphanosaurs, they suggest, are the earliest group in the avian stem lineage to diverge from the crocodile lineage. And that suggests that these bird and dinosaur ancestors were far more diverse and widely distributed across the globe during the middle Triassic than once thought.

    The find may also alter what paleontologists hunt for in the field, as well as how they understand existing collections, says Max Langer, a paleontologist at the University of São Paulo in Rio Claro, Brazil. “Now that we know the diagnostic features of this group of archosaurs, everybody working on middle Triassic rocks will be looking for something similar.”

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  • richardmitnick 7:18 pm on February 24, 2017 Permalink | Reply
    Tags: , , Science   

    From Science: “Spinning black holes could fling off clouds of dark matter particles” 

    ScienceMag
    Science Magazine

    Feb. 22, 2017
    Adrian Cho

    1

    A spinning black hole (white) should produce huge clouds of particles called axions (blue), which would then produce detectable gravitational waves, a new calculation predicts. Masha Baryakhtar

    Few things are more mind bending than black holes, gravitational waves, and the nearly massless hypothetical particles called axions, which could be the mysterious dark matter whose gravity holds galaxies together. Now, a team of theoretical physicists has tied all three together in a surprising way. If the axion exists and has the right mass, they argue, then a spinning black hole should produce a vast cloud of the particles, which should, in turn, produce gravitational waves akin to those discovered a year ago by the Laser Interferometer Gravitational-Wave Observatory (LIGO). If the idea is correct, LIGO might be able to detect axions, albeit indirectly.

    “It’s an awesome idea,” says Tracy Slatyer, a particle astrophysicist at the Massachusetts Institute of Technology (MIT) in Cambridge, who was not involved in the work. “The [LIGO] data is going to be there, and it would be amazing if we saw something.” Benjamin Safdi, a theoretical particle physicist at MIT, is also enthusiastic. “This is really the best idea we have to look for particles in this mass range,” he says.

    A black hole is the intense gravitational field left behind when a massive star burns out and collapses to a point. Within a certain distance of that point—which defines the black hole’s “event horizon”—gravity grows so strong that not even light can escape. In September 2015, LIGO detected a burst of ripples in space called gravitational waves that emanated from the merging of two black holes.

    The axion—if it exists—is an uncharged particle perhaps a billionth as massive as the electron or lighter. Dreamed up in the 1970s, it helps explain a curious mathematical symmetry in the theory of particles called quarks and gluons that make up protons and neutrons. Axions floating around might also be the dark matter that’s thought to make up 85% of all matter in the universe. Particle physicists are searching for axions in experiments that try to convert them into photons using magnetic fields.

    But it may be possible to detect axions by studying black holes with LIGO and its twin detectors in Louisiana and Washington states, argue Asimina Arvanitaki and Masha Baryakhtar, theorists at the Perimeter Institute for Theoretical Physics in Waterloo, Canada, and their colleagues.

    If its mass is in the right range, then an axion stuck in orbit around a black hole should be subject to a process called superradiance that occurs in many situations and causes photons to multiply in a certain type of laser. If an axion strays near, but doesn’t cross, a black hole’s event horizon, then the black hole’s spin will give the axion a boost in energy. And because the axion is a quantum particle with some properties like those of the photon, that boost will create more axions, which will, in turn, interact with the black hole in the same way. The runaway process should thus generate vast numbers of the particles.

    But for this to take place, a key condition has to be met. A quantum particle like the axion can also act like a wave, with lighter particles having longer wavelengths. For superradiance to kick in, the axion’s wavelength must be as long as the black hole is wide. So the axion’s mass must be extremely light: between 1/10,000,000 and 1/10,000 the range probed in current laboratory experiments. The axions wouldn’t just emerge willy-nilly, either, but would crowd into huge quantum waves like the orbitals of the electrons in an atom. As fantastical as that sounds, the basic physics of superradiance is well established, Safdi says.

    The axion cloud might reveal itself in multiple ways, Baryakhtar says. Most promising, axions colliding in the cloud should annihilate one another to produce gravitons, the particles thought to make up gravitational waves just as photons make up light. Emerging from orderly quantum clouds, the gravitons would form continuous waves with a frequency set by the axion’s mass. LIGO would be able to spot thousands of such sources per year [Physical Review D], Baryakhtar and colleagues estimate in a paper published 8 February in Physical Review D—although tracking those continuous signals may be harder than detecting bursts from colliding black holes. Spotting multiple same-frequency sources would be a “smoking gun” for axions, Slatyer says.

    The axion clouds could produce indirect signals, too. In principle, a black hole can spin at near light speed. However, generating axions would sap a black hole’s angular momentum and slow it. As a result, LIGO should observe that the spins of colliding black holes never reach that ultimate speed, but top out well below it, Baryakhtar says. Detecting that limit on spin would be challenging, as LIGO can measure a colliding black hole’s spin with only 25% precision.

    Safdi cautions that the analysis assumes that LIGO will see lots of black-hole mergers and will perform as expected. And if LIGO doesn’t see the signals, it won’t rule out the axion, he says. Still, he says, “This is probably the most promising paper I’ve seen so far on the new physics we might probe with gravitational waves.”

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  • richardmitnick 11:29 am on January 22, 2017 Permalink | Reply
    Tags: , , How white blood cells rip holes in your blood vessels—and how your blood vessels recover, Science   

    From Science: “How white blood cells rip holes in your blood vessels—and how your blood vessels recover” 

    ScienceMag
    Science Magazine

    1
    A. Barzilai et. al. Cell Reports 18, 3 (17 January 2017) © 2017 Elsevier Inc.

    Jan. 17, 2017
    Emma Hiolski

    White blood cells are constantly tearing holes in your blood vessel walls. But these guardians of the immune system are doing it to protect you: Once they ride through the bloodstream to infected tissues—where they make antibodies and eat foreign invaders—they need a way to get inside. Now, scientists have discovered just how they do it without permanently damaging blood vessels, which they slip into and out of up to 10 times each day. First, researchers added fluorescent tags to their nuclei and to the structural fibers of blood vessel walls, which keep out foreign particles and seal in blood, plasma, and immune cells. The researchers then tracked the process with video-microscopy. They found that blood vessel cells were not the ones making the openings, as previously thought. Instead, immune cells make their own way across. By softening their bulky nuclei and pushing them to the front edge of their cells, white blood cells probe apart scaffolding in the blood vessel walls and squeeze through, researchers report online today in Cell Reports. This process (seen above) snaps smaller, threadlike fibers that form the flexible scaffolding of blood vessel walls; the cells easily repair that breakage later as part of routine cellular maintenance. The researchers hope to use their discovery to better understand how metastatic cancer cells migrate into the bloodstream and spread cancer throughout the body.

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