ScienceInsider

Breaking news and analysis from the world of science policy

  • Plant scientists plan massive effort to sequence 10,000 genomes

    An image of a freshwater alga in the genus Zygnema. It looks like a chain of oblong cells.

    Freshwater alga in the genus Zygnema would be one target of sequencing project.

    Norbert Hülsmann/Flickr (CC BY-NC-SA 2.0)

    SHENZEN, CHINA—Hopes of sequencing the DNA of every living thing on Earth are taking a step forward with the announcement of plans to sequence at least 10,000 genomes representing every major clade of plants and eukaryotic microbes. Chinese sequencing giant BGI and the China National GeneBank (CNGB) held a workshop yesterday on the sidelines of the International Botanical Congress, being held this week in BGI's hometown of Shenzhen, to discuss what they are calling the 10KP plan. About 250 plant scientists participated in the discussions and "are raring to go," says Gane Ka-Shu Wong, a genomicist and bioinformaticist at University of Alberta in Edmonton, Canada.

    The 10KP plan will be a key part of the Earth BioGenome Project (EBP), an ambitious and still evolving scheme to get at least rough sequence data on the 1.5 million eukaryotic species, starting with detailed sequences of one member of each of the 9000 eukaryotic families. The effort to sequence plants is moving ahead a bit faster than other aspects of EBP "because plant scientists are more collaborative," Wong says jokingly.

    The 10KP plan is also building on a previous 1000 plant (1KP) transcriptome project. That effort, launched in 2012 and now nearing completion, was also led by BGI, where Wong is an associate director. 

  • Sci-Hub’s cache of pirated papers is so big, subscription journals are doomed, data analyst suggests

    Sci Hub Map

    Sci-Hub activity on 5 February 2016.

    CREDITS: (DATA) SCI-HUB; (IMAGE/AUTOPLAY VIDEO) ADAPTED BY J. YOU/SCIENCE

    There is no doubt that Sci-Hub, the infamous—and, according to a U.S. court, illegal—online repository of pirated research papers, is enormously popular. (See Science’s investigation last year of who is downloading papers from Sci-Hub.) But just how enormous is its repository? That is the question biodata scientist Daniel Himmelstein at the University of Pennsylvania and colleagues recently set out to answer, after an assist from Sci-Hub.

    Their findings, published in a preprint on the PeerJ journal site on 20 July, indicate that Sci-Hub can instantly provide access to more than two-thirds of all scholarly articles, an amount that Himmelstein says is “even higher” than he anticipated. For research papers protected by a paywall, the study found Sci-Hub’s reach is greater still, with instant access to 85% of all papers published in subscription journals. For some major publishers, such as Elsevier, more than 97% of their catalog of journal articles is being stored on Sci-Hub’s servers—meaning they can be accessed there for free.

    Given that Sci-Hub has access to almost every paper a scientist would ever want to read, and can quickly obtain requested papers it doesn’t have, could the website truly topple traditional publishing? In a chat with ScienceInsider, Himmelstein concludes that the results of his study could mark “the beginning of the end” for paywalled research. This interview has been edited for clarity and brevity. 

  • Ding, ding, ding! CRISPR patent fight enters next round

    An artist's conception of the DNA cutting enzyme Cas9.

    An artist’s conception of the DNA-cutting enzyme Cas9.

    NIH 3D Print Exchange/Flickr (CC BY 2.0)

    The University of California (UC) has fired another legal salvo in the prolonged patent battle over CRISPR, the revolutionary gene-editing technology that has spawned a billion-dollar industry.

    UC leads a group of litigants who contend that the U.S. Patent Trial and Appeal Board (PTAB) wrongly sided with the Broad Institute in Cambridge, Massachusetts, and two partners—Harvard University and the Massachusetts Institute of Technology in Cambridge—in February when it ruled that the Broad group invented the use of CRISPR in eukaryotic cells. After that ruling, UC moved the battleground to the U.S. Court of Appeals for the Federal Circuit. In a 25 July brief to the Federal Circuit, the UC group contends that PTAB “ignored key evidence” and “made multiple errors.”

  • What can science learn from a child who has controlled HIV without drugs for more than 8 years?

    HIV

    Treating people soon after they become infected might reduce the size of the initial HIV reservoir in their bodies. 

    Donald Bliss and Sriram Subramaniam, NIH

    PARIS—An HIV-infected child in South Africa who is controlling the virus without antiretroviral (ARV) drugs has reinvigorated the push to find ways to allow people to control the virus for prolonged periods without treatment.

    The child, whose gender hasn't been revealed to help protect anonymity, was born to an HIV-infected mother and was given ARVs starting at 8 weeks old; the treatment was stopped at 40 weeks as part of a controlled clinical trial. Now, more than 8.5 years later, the virus hasn't rebounded and the child is doing fine, researchers reported here yesterday at an international AIDS conference. That doesn't mean the HIV infection has been cured, they stressed; the child still harbors low levels of the virus, invisible with standard tests but easily detected with ultrasensitive ones.

    But the case may offer fresh clues to what makes long-term remission possible. In most people living with HIV who stop taking drugs, the virus comes roaring back within weeks. If long drug holidays were possible, it could simplify people’s lives, slash the costs of treatment, and reduce long-term side effects. And the research into what some call "sustained viral remission" could help inform the search for a complete cure.

  • Senate spending panel would squeeze science agencies but exceed Trump request

    Dome of the U.S. Capitol, with an American flag in front of it.

    Shawn Clover/Flickr (CC BY-NC 2.0)

    A Senate spending panel voted today to reduce funding in 2018 below current levels for several science agencies under its jurisdiction.

    Even so, the move by the Senate Commerce, Justice, and Science appropriations subcommittee would erase most of the cuts that President Donald Trump requested next year for the National Science Foundation (NSF), the National Institute of Standards and Technology (NIST), and the National Oceanic and Atmospheric Administration (NOAA). The exception is NASA’s science program, which would get less under the Senate panel’s plan than the president has requested.

    Senator Richard Shelby (R–AL), chair of the panel, blamed the tight proposed spending levels on the panel’s overall allocation of $53.4 billion for agencies under its jurisdiction, some $3.2 billion below 2017 levels. He said it forced lawmakers into making “difficult but responsible decisions.”

  • Researchers think they’ve found a much better way to conduct the 2030 U.S. census

    a man hands another man a form

    Researchers are thinking about ways to reduce the number of face-to-face visits needed to conduct the census.

    U.S. Census Bureau

    The decennial census is supposed to be a tally of everybody living in the United States. But it actually starts out as a master list of addresses. That list, updated once a decade by the U.S. Census Bureau, is then used to send out an army of workers to collect basic demographic information from whoever answers the door at those addresses.

    The approach allows the agency to meet its constitutional requirement to provide Congress with the data needed to apportion seats in the U.S. House of Representatives. But the 2010 census also cost $12.3 billion, and future censuses that use that approach may be prohibitively expensive (see our story yesterday on issues facing the 2020 census). It also assumes that households, not people, should be the key unit of measurement.

  • It will be much harder to call new findings ‘significant’ if this team gets its way

    the number 5

    Joanna Poe/Flickr (CC BY-SA 2.0)

    A megateam of reproducibility-minded scientists is renewing a controversial proposal to raise the standard for statistical significance in research studies. They want researchers to dump the long-standing use of a probability value (p-value) of less than 0.05 as the gold standard for significant results, and replace it with the much stiffer p-value threshold of 0.005.

    Backers of the change, which has been floated before, say it could dramatically reduce the reporting of false-positive results—studies that claim to find an effect when there is none—and so make more studies reproducible. And they note that researchers in some fields, including genome analysis, have already made a similar switch with beneficial results.

    “If we’re going to be in a world where the research community expects some strict cutoff … it’s better that that threshold be .005 than .05. That’s an improvement over the status quo,” says behavioral economist Daniel Benjamin of the University of Southern California in Los Angeles, first author on the new paper, which was posted 22 July as a preprint article on PsyArXiv and is slated for an upcoming issue of Nature Human Behavior. “It seemed like this was something that was doable and easy, and had worked in other fields.”

  • Australian government to roll back marine protections

    Crayfishing camps, Houtman Abrolhos Islands, Australia

    Fishing camps in western Australia’s Houtman Abrolhos Islands. Controversial new marine reserve plan seeks to balance habitat protection with sustainable fishing. 

    Bill Bachman/Alamy Stock Photo

    TOWNSVILLE, AUSTRALIA—Five years after the Australian government created one of the world’s largest networks of marine reserves, it has unveiled a heavily revised management blueprint that would curtail conservation. Some scientists are assailing the plan as deeply flawed. “I suppose you could say it’s an insult to the science community. It’s not evidence-based,” says David Booth, a marine ecologist at the University of Technology in Sydney, Australia.

    Australia is fringed by some of the richest marine ecosystems in the world. Recognizing the need to protect those resources, in 2012, after years of input from scientists and the public, the Australian government strung together a necklace of marine reserves encircling the continent. But following elections a few months later, the new conservative government commissioned an independent review to gather more public input. The draft plan, released on Friday, retains the 2012 plan’s boundaries but scales back protections in some areas to allow for more fishing.

    The proposal, which will undergo a 60-day public review period before heading to Parliament, which is expected to approve the plan, covers 44 marine reserves encompassing 36% of Australia’s exclusive economic zone—the wide ring of ocean from about 5 kilometers offshore to 370 kilometers out. In maps showing which activities will be allowed where in the reserves, large swaths of no-take “green” zones designated in 2012—areas in which no fishing or mining would be allowed—have been converted to “habitat protection zones,” where sea floor–ravaging activities such as trawling are barred but other types of fishing are permitted. Under the new plan, only 20% of the reserves would be green zones and more permissive “yellow” habitat protection zones would increase from 24% to 43%.

  • Rising costs hamper mega–neutron beam facility

    aerial of European Spallation Source construction site

    The European Spallation Source, under construction in Lund, Sweden, may not reach its design power of 5 megawatts.

    Perry Nordeng/ESS

    The world’s most powerful source of neutron beams will be less than half as powerful as planned when the facility begins scientific experiments in 2023. The European Spallation Source (ESS), under construction in Lund, Sweden, was designed to reach 5 megawatts (MW), but ballooning costs means that it will only achieve 2 MW in 6 years’ time—a reduced level that will likely limit the range of scientific studies it can carry out.

    Although the ESS council, the project’s main decision-making body, is considering plans that would boost power to 5 MW by 2025, some scientists fear that the facility will remain stuck at 2 MW for good. “There are some people with persuasive voices who say you don’t need 5 MW,” says Colin Carlile, a physicist at Uppsala University in Sweden and former ESS director. “But theirs are siren voices. It would be tragic if that happens.”

    Like x-rays, beams of neutrons are a way for scientists to explore the atomic structure of materials. But where x-rays scatter off the cloud of electrons surrounding an atom, neutrons scatter off atomic nuclei. That capability helps scientists, for example, to locate hydrogen, which, with only one electron, is a more elusive target for x-rays. Neutron beams can also differentiate between nuclei of different isotopes. And, because neutrons carry a spin, they can reveal the magnetic properties of the material in question. 

  • With unusual candor, Senate appropriators ‘reject’ cuts to energy research

    Senate wing of the United States Capitol building

    OGphoto/iStockphoto

    Many observers hoped Senate budgetmakers would oppose cuts to the Department of Energy's (DOE's) basic and applied research programs proposed by the White House in May. But they may not have expected them to be quite so blunt about it. The detailed report that accompanies the Senate version of the so-called energy and water bill, which funds DOE, contains several passages in which Senate appropriators express their objections to cuts in unusually frank language.

    For example, in its budget request for fiscal year 2018, which begins 1 October, the White House seeks to eliminate the Advanced Research Projects Agency-Energy (ARPA-E), the 8-year-old agency that aims to quickly transform the best ideas from basic research into budding energy technologies. House of Representatives appropriators have voted to go along with that elimination, but Senate appropriators are having none of it. "The Committee definitively rejects this short-sighted proposal," the report says. Instead, Senate appropriators would increase ARPA-E's budget by 8% to $330 million. Their report expressly forbids DOE from using money to shut down ARPA-E.

    Similarly, within DOE's Office of Science, the White House has called for cutting spending on biological and environmental research (BER) by 43% to $349 million. But the Senate appropriations committee "rejects the short-sighted reductions proposed in the budget request." Instead, Senate budgetmakers would boost BER research by 3% to $630 million. Senate appropriators also would give DOE's applied research in its Office of Energy Efficiency & Renewable Energy $1.937 billion, a 7% cut from last year, but far above the $636 million proposed by the White House.

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