News this Week

Science  07 Jan 2011:
Vol. 331, Issue 6013, pp. 14
  1. U.S. Science Policy

    The Battle Over the 2011 Budget: What's at Stake for Research

    1. Jeffrey Mervis

    The 112th Congress convened this week amid cries from fiscal conservatives to shrink the federal budget and reduce the deficit. With revenues unlikely to grow much now that the outgoing Congress has extended Bush-era income tax cuts for the next 2 years, the immediate task of deficit hawks will be to convince their colleagues that individual agencies should receive less in 2011. But that begs an important question: Less than what?

    As federal officials ring in the new year, they are essentially marking time, fiscally speaking. Late last month, Congress agreed to extend 2010 spending levels until 4 March, a date nearly halfway through the 2011 fiscal year, while prohibiting agencies from starting anything new or canceling anything now under way. That means the new Congress—with Republicans controlling the House and Democrats holding a slim margin in the Senate—will decide what agencies can spend for the remainder of the fiscal year ending on 30 September. In the same week, the 111th Congress passed legislation giving some research agencies very specific orders about what to do—or not do—with any money they might receive.

    Aversive stimulus.

    Tea Party activists want the new Congress to roll back initiatives such as the massive 2009 spending package, which included billions for research.

    PHOTO CREDIT: BOB WEEKS

    How will Congress play the 2011 budget card? The answer could shape U.S. science for years to come.

    The new House speaker, Representative John Boehner (R–OH), says he wants to cut $100 billion from the current $1.1 trillion discretionary budget on the way toward reducing spending to 2008 levels. President Barack Obama has already embraced a 3-year freeze on nonsecurity discretionary spending. But that doesn't necessarily mean a flat science budget, he insists. “If we want to keep our competitive edge, we've got to invest in basic research—the same basic research that resulted in the Internet … [and] in GPS. All those things originated in research funded by the government,” Obama explained in a 22 December press conference.

    Budget breakdown

    It's not that the previous Congress ignored the budget process. Take the National Science Foundation (NSF). In 2010, legislators debated half a dozen bills with proposed 2011 funding levels for NSF that ranged from no increase to a 7.2% boost in its current $6.9 billion allocation.

    One of the bills, the America COMPETES Act of 2010, was actually passed by the lame-duck Congress on 21 December, 1 day before it adjourned. Among other things, it endorses annual increases for NSF of 7.2%, 5.1%, and 6.4% in 2011, 2012, and 2013, respectively. The first number matches what President Obama requested for NSF in his 2011 budget submission to Congress last February. A version of COMPETES passed in May by the House of Representatives would have been even more generous to NSF, with annual increases of 8%, 8.6%, and 7.8%.

    But as Winnie the Pooh might say, COMPETES is the wrong sort of budget bill. It's an authorization, meaning it sets guidelines but doesn't provide money to expand existing activities or implement any new policies and programs. The same thing happened to NASA in September, when Obama signed legislation that spells out a new policy for space exploration that would rely more heavily on commercial vehicles but doesn't appropriate the money to achieve that goal.

    Unfinished Business

    The 2011 budget is still a work in progress.

    Key: green -- appropriations bill; blue -- authorization bill; red -- continuing resolution.

    2010

    1 February:
    President Obama submits 2011 request to Congress.

    28 May:
    House passes COMPETES reauthorization.

    15 July:
    Senate spending panel approves agriculture and homeland security bills.

    22 July:
    Senate spending panel approves science (NSF, NASA, and Commerce Dept.) and energy bills.

    29 July:
    Senate spending panel approves NIH bill.

    16 September:
    Senate spending panel approves defense bill.

    30 September:
    CR extended to 3 December.

    11 October:
    President signs NASA reauthorization bill.

    3 December:
    CR extended to 17 December.

    9 December:
    House passes yearlong CR.

    16 December:
    Omnibus bill pulled from Senate floor.

    17 December:
    CR extended to 21 December.
    Senate passes COMPETES reauthorization bill.

    21 December:
    House passes Senate version of COMPETES Act, which goes to president.
    CR extended to 4 March.

    2011

    14 February:
    Obama submits 2012 request to Congress.

    4 March:
    CR expires.

    What's going on? The answer is that a federal budget process that has always been hideously complex has become even more fragmented. Congress is supposed to pass 12 separate appropriations bills to fund all branches of government by the start of the fiscal year on 1 October. That has happened less and less often in recent years, however. Instead, procrastinating legislators have adopted one or more short-term continuing resolutions (CRs), holding spending to current levels, before eventually wrapping several individual spending bills into something called an omnibus bill.

    This year, even that hope-and-a-prayer approach couldn't get the job done. Fresh from what Obama called an electoral “shellacking” by voters, the lame-duck Democratic majority in the House of Representatives passed in early December a modified CR for the rest of the year that would have exempted a few federal agencies and programs from being held to 2010 spending levels. None of the major funders of basic science—NSF, the National Institutes of Health (NIH), and the Department of Energy's Office of Science—was mentioned, meaning that their budgets would have remained flat.

    Senate Democrats, who lost six seats in the midterm elections but retain a three-seat majority, took a different approach. Senator Daniel Inouye (D–HI), chair of the appropriations committee, cobbled together an omnibus spending bill that provided detailed guidance and specific funding levels for every agency, including a 6% increase for NSF and a 2.5% increase for NIH. But that bill also contained $8 billion in so-called earmarks, spending that individual legislators have sought to benefit their constituents that was not requested by the agency whose budget would pay for these projects. On 16 December, Inouye withdrew his omnibus bill in the face of a threatened filibuster from Republicans, who have designated earmarks as Public Spending Enemy #1. The next week, both the House and the Senate approved the current CR, which maintains the status quo until 4 March.

    COMPETing for clout

    In parallel with appropriations bills, Congress also periodically reauthorizes programs at various federal agencies. These bills, both sweeping and detailed, can require or encourage agencies to move in new directions and can block or discourage activities deemed undesirable.

    Authorization bills sometimes carry great weight. The annual authorization bill for the Department of Defense, for example, typically lays down guidance for the year's spending bill that, as one congressional staffer notes, “appropriators ignore at their peril.”

    Historically, authorization bills for science agencies have had much less impact on spending panels. But the first COMPETES Act, in 2007, was an exception to that rule. Based on a 2005 National Academies report that Congress requested, it gained political strength from the endorsements of both President George W. Bush and Democratic congressional leaders. And Congress used the massive 2009 stimulus package to supplement funding for many of its provisions. In contrast, the 2010 COMPETES reauthorization quickly became partisan, with Democrats calling it the best way to ensure long-term economic prosperity and Republicans complaining that its cost would stifle job creation rather than encourage it.

    Even so, the 2010 law retains many of the features in the original authorization. It backs a 10-year doubling of the budgets of NSF, the Department of Energy's Office of Science, and the National Institute of Standards and Technology, as well as demanding better coordination across the federal government of science and math education and training programs. It also directs NSF to do things that don't require more money. For example, it nixes a proposed merging of programs to help minority undergraduates, orders NSF to shift some of the cost of its Graduate Research Fellowships from the education to the six research directorates, and tells the National Science Board, NSF's oversight body, to focus on NSF in its recommendations to Congress and the White House rather than cast its net across the entire government.

    NSF officials are prepared to implement those mandates, even if they may not like all of them. But congressional action on the 2011 and subsequent budgets could alter them. In particular, a future CR or appropriations bill could override some of those nonmonetary provisions, either through a blanket prohibition on “new starts” or by specifying what is kosher under a budget freeze.

    Within the confines of that debate, the idea of doubling the budget of any federal agency is unlikely to get much traction. “There's going to be downward pressure on budgets, and the House will drive that process,” predicts one Senate aide. Joel Widder, a science lobbyist for the Washington, D.C., firm of Oldaker, Belair & Wittie, says he's “always hated” the concept of a freeze because of its imprecision—“When does it start and how long does it take?”—but that it's especially inappropriate in the current political climate. “Whether they get to 2008 levels or not, doubling doesn't seem to be on the minds of the new House leadership,” he notes.

    Although congressional Republicans have yet to describe the role of basic research in their overall philosophy of reducing the size and scope of government, Obama says his Administration is ready to rumble on the subject. “I expect we'll have a robust debate about this when we return from the holidays,” Obama said at his recent press conference. “[That] debate will have to answer an increasingly urgent question: ‘How do we cut spending that we don't need while making investments that we do need—investments in education, research and development, innovation, and the things that are essential to grow our economy in the long run, create jobs, and compete with every other nation in the world.’”

  2. Europe

    ESF Moves Toward Rebirth, But Change Worries Some

    1. Daniel Clery
    Home front?

    ESF chief Marja Makarow says no decision has been made on the future of the agency's HQ in Strasbourg, France.

    CREDITS: (PHOTOS) EUROPEAN SCIENCE FOUNDATION; EUROHORCS

    2011 will likely see the end of the European Science Foundation (ESF), at least in its current form. After 37 years of funding researchers, organizing collaborations, and convening meetings across the continent, ESF is expected to transform into a lobbying and strategy organization. But even as the details continue to be worked out, some observers are lamenting the change, particularly as certain science academies may be excluded from the resulting body. “The new organization will lose diversity, and … networking [among scientists] will be much weaker than promoted by the present ESF,” says Jüri Engelbrecht, president of ALLEA (All European Academies).

    The planned overhaul of ESF into a still-unnamed body, revealed by Science last year (Science, 11 June 2010, p. 1340), aims to produce a unified voice for the national research agencies that provide the vast majority of Europe's roughly €29 billion annual science spending. Those agencies finance 85% of Europe's science, while the European Union's (E.U.'s) research programs account for only about 5%. Yet E.U. research commissioners are arguably calling the shots on supranational science policy, with initiatives such as the European Research Area and the Innovation Union. The national agencies, which act collectively through an informal grouping called EUROHORCs, felt they should have more influence on regional science strategy.

    Those same agencies also form the majority of ESF members. (Other members currently include academies of science and learned societies.) Last year, the agencies decided to transform ESF from a funding body—with an annual budget of about €50 million—into an organization that will focus on research strategy and lobbying on behalf of EUROHORCs members. Because ESF is a formal body bound by statutes, the proposed transformation has had to be studied in detail, and decisions will be made at a special general assembly of ESF members in May. Yet signs of change are already apparent. ESF has canceled calls for proposals for two of its funding programs, which involve setting up cross-border collaborations and networks of researchers. Marja Makarow, chief executive of ESF, emphasizes that most existing projects will be honored.

    ESF's EUROCORES program supports large and complex cross-border collaborations between labs, but Makarow says non-ESF programs do a similar job. The European Union, for example, already funds the long-standing Cooperation in Science and Technology program and is also starting an initiative known as Joint Programming that identifies “grand challenges” such as neurodegenerative disease and then coordinates national agencies to collaborate on them rather than duplicating efforts. And then there are smaller groups of countries working together, such as the Scandinavian nations and the German-speaking grouping of Germany, Austria, and Switzerland. “If EUROCORES vanishes, it doesn't leave a void,” Makarow says.

    Engelbrecht and others remain to be convinced, however. Geophysicist Enric Banda, a former ESF chief who is now president of Euro science, an association of researchers, also regrets the loss of the current ESF, which he says was “a very good instrument” that didn't have the confidence of its member organizations. “It never really flew,” Banda says. Efforts such as Joint Programming are simply too bureaucratic, he adds. “It doesn't make sense that after 60 years of European union, [collaboration] is still done through formal intergovernmental agreements. We're not very European yet.” Banda thinks that what Europe really needs is “a reinforced ESF, concentrating on collaboration, with real money.”

    EUROHORCs wants to limit membership of the new body to organizations that fund research or carry out research, and that means excluding those national academies that operate principally as learned societies, such as the Royal Swedish Academy of Sciences. Engelbrecht says it would be a blow to the science community to exclude those academies because ESF, with its mix of members, was greater than the sum of its parts. Makarow says the new body will strive to maintain its relationship with the learned societies, possibly through an annual conference bringing together the new ESF-EUROHORCs organization, ALLEA, the European Union, universities, and the big European labs.

    So, without the funding and networking activities of ESF, what will the new body do? That's under discussion by a working group that is drawing up the body's mission statement. The EUROHORCs agencies, Makarow says, “are very powerful organizations, but they've been fragmented in the past. Now it is time to gather their strengths and direct science policy in Europe—align national policies and supranational policy.” Makarow says the new body will use scientific expertise to predict trends for policymakers; promote cross-border cooperation between member agencies; and, most urgently, help the European Union plan its next 7-year research program, which begins in 2014. Banda, for one, is surprised that the new body will focus so much on E.U. funding. “Why worry so much about this 5% of the cake and not the other 95%?” he says. Europe's science voice, it seems, still has some way to go before being unified.

  3. Chronic Fatigue Syndrome

    Studies Point to Possible Contamination in XMRV Findings

    1. Jocelyn Kaiser*

    The stormy debate over a potential cause of chronic fatigue syndrome (CFS) is nearing hurricane force. Last month, it prompted headlines suggesting that researchers have reached a dead end, scores of blog posts from disappointed patients, and accusations that scientists had gone beyond their data. The 14-month-old row intensified when four papers appeared in Retrovirology suggesting that reports linking the virus XMRV to CFS were based on false positives.

    The debate began in 2009 with a report in Science that XMRV, a retrovirus recently reported to have been found in prostate tumors, had been detected in 67% of a set of CFS patients but in only 4% of controls (Science, 9 October 2009, p. 215). Since then, one other group has found XMRV-like viruses in CFS patients' blood. But several teams have failed to detect the virus in CFS or cancer patients or in healthy people. Researchers have struggled to explain the discrepancies (Science, 17 September 2010, p. 1454).

    The potential link to CFS has had important consequences: Some CFS patients have begun taking antiviral drugs, which can have side effects. Last month, after being briefed on the original XMRV studies, advisers to the U.S. Food and Drug Administration recommended that CFS patients be barred from donating blood.

    The Retrovirology papers point to contamination as a possible source of positive results in previous studies. The polymerase chain reaction (PCR) test used to detect XMRV (a mouse retrovirus adapted to infect humans) could actually be picking up minute amounts of mouse DNA or similar mouse viruses.

    Two of the four studies in Retrovirology used highly sensitive assays for mouse DNA and found that samples positive for XMRV-like viruses also tested positive for mouse DNA. Another study found mouse viral RNA in a commercial PCR kit. And the fourth study argues that XMRV sequences previously reported in patient samples don't show the diversity expected if the virus were spreading through the human population. Instead, these authors report, the sequences are similar to those found in a popular prostate cancer cell line, 22Rv1. This cell line, used in lab experiments, was already known to contain an XMRV-like sequence.

    Greg Towers of University College London (UCL), who led the study of XMRV diversity, says the evidence linking this virus and human disease “is really looking pretty shaky now.” The Wellcome Trust, which cosponsored the research, and UCL issued a press release last week declaring flatly that the Towers study showed that “chronic fatigue syndrome is not caused by XMRV,” a message some newspapers repeated. Towers says he was “comfortable” with the release. But John Coffin of the U.S. National Cancer Institute (NCI) and Tufts University Sackler School of Graduate Biomedical Sciences in Boston, who co-authored two of the contamination papers, is wary. He says these studies “just point out how careful one must be.”

    Elusive.

    Scientists are still debating whether the XMRV virus has any connection to human disease.

    CREDIT: REPRINTED WITH PERMISSION, CLEVELAND CLINIC CENTER FOR MEDICAL ART & PHOTOGRAPHY © 2009

    Virologists who have found a virus-disease link disagree with coverage of the Towers paper. “The data shown … do not justify some of the sweeping statements made,” says Ila Singh of the University of Utah, Salt Lake City, who has reported XMRV in prostate cancer samples. Moreover, the lead author of the Science paper on CFS and XMRV, Judy Mikovits of the Whittemore Peterson Institute (WPI) in Reno, Nevada, points out that PCR wasn't the only test her studies used: For example, Mikovits's team also showed that XMRV-positive patients make antibodies to the virus and that XMRV isolated from their blood can infect cultured human cells. Mikovits said in a statement, “Nothing that has been published to date refutes our data.”

    One outspoken scientist wavered on the significance of the Retrovirology papers. Columbia University virologist Vincent Racaniello, who runs a popular virology blog and podcast, initially e-mailed a Chicago Tribune reporter to say that they were “probably the beginning of the end of XMRV and CFS.” But he retracted that statement (and a similar comment to Science) after reviewing the studies more closely. “It's pretty complicated,” Racaniello concludes.

    Some had hoped that a project in which several U.S. labs are testing for XMRV in the same samples would clear up the picture. But so far this effort has been inconclusive. Four CFS patients' blood initially tested positive for XMRV at WPI and the U.S. Centers for Disease Control and Prevention but not at an NCI lab. When all three labs tested new samples from the same patients, none found XMRV—for reasons that aren't yet clear, says Coffin. The group now plans to test blood from several dozen CFS patients and controls.

    A bigger study is now under way. Funded by the U.S. National Institute of Allergy and Infectious Diseases, virologist W. Ian Lipkin of Columbia University is leading a project that will collect blood from 150 CFS patients and 150 controls from six U.S. clinical sites. The samples will be tested blindly by several labs. Because all the clinicians have agreed on standard methods, the study should help resolve concerns that differences in how CFS patients are selected or how samples are handled could explain clashing conclusions, Lipkin says: “Results will be definitive.”

    As the new study gets started, some wonder whether it's worth the $1.3 million it will cost. Jonathan Stoye of the MRC National Institute for Medical Research in London concedes that the Towers study was “overhyped.” But he says “it's pointing people in a certain direction,” away from chasing an elusive link to XMRV. Still, he says, a larger study may be the only way to satisfy patients.

    • * With reporting by Martin Enserink.

  4. Ecology

    A Slimy Invader Blooms in the Rivers of Patagonia

    1. Patricio Segura*

    Biochemist William Horvath was the first to sound the alarm. A Patagonian guide to kayakers from all over the world, Horvath was taking U.S. clients on the pristine Futaleufú River in Chile last year when he saw something that stopped him cold. In the water there “appeared to be toilet paper,” he says. Afraid of hepatitis, the kayakers turned back. Horvath decided to investigate. After ruling out pollution from a local water-treatment plant, he sent samples to the U.S. Geological Survey (USGS) in Fort Collins, Colorado. USGS ecologist Sarah Spaulding determined that it was natural material: the mucilaginous stalks of the algae known as Didymosphenia geminata, or Didymo.

    Coming to Chile?

    The invasive alga Didymosphenia geminata recently swept through New Zealand's South Island.

    CREDIT: NEW ZEALAND FISH AND GAME

    The discovery caused a stir, as Didymo is unwelcome wherever it blooms. It forms large colonies of brownish slime that cling to vegetation and streambeds, extending leathery trailers into the current. Known to hikers as “rock snot,” it is established in several Northern Hemisphere locations—including in Canada and the eastern United States, Europe, and Asia. But it was not seen in the Southern Hemisphere until 2004. That's when Didymo appeared in New Zealand; it has now spread to more than 40 watersheds in the country's South Island. In 2010, to the dismay of naturalists and Chile's tourism industry, it gained a foothold in Patagonia.

    A single water drop is enough to carry the diatom into new territory. The nontoxic organism is the only large-scale invasive species known in oligotrophic freshwater environments—those poor in phosphates, nitrates, and organic matter. It is capable of completely covering riverbeds with up to 20 centimeters of gunk, sometimes blocking water intakes for hydro plants and degrading fish breeding habitats.

    After Didymo's presence was confirmed in the Futaleufú River, Brian Reid, a limnologist at Chile's Center for the Research of Patagonian Ecosystems (CIEP) based in Coyhaique, in the Aysén Region, organized a survey in June of other rivers whose habitat, configuration, and stability made them potential reservoirs. Massive blooms of Didymo were confirmed in two spots within the Chilean Patagonia watershed, the Espolón River (a tributary of the Futaleufú) and Cea Creek; a macroscopic amount was found in the Cochrane River, part of the Baker Basin. Researcher Viviana Sastre of the Universidad Nacional de la Patagonia in Argentina reported a limited Didymo bloom in the Grande-Futaleufú River, which flows through Argentina and Chile.

    In October, a joint report by CIEP, the National Fisheries Service, and the Bureau of Water Management (DGA) identified three common factors in blooms: They occur in stable rivers downstream from lakes, near a main road that offers recreational access, and downriver from sources of nutrients such as waste treatment plants and fish farming operations. The link to nutrient sources does not jibe with earlier analyses. Historically, before its expansion in the United States and New Zealand, it was found in clean waters and places that weren't significantly impacted by humans—mostly in high latitudes and high elevations. Spaulding, who went to Chile in July to study the blooms, says, “We still don't understand why it is spreading so rapidly.”

    The propagation of D. geminata may be unstoppable, although officials in Chile have launched a massive effort to halt it. Since June, a permanent committee of state offices, research centers, and tourism operators has been coordinating fieldwork and educating communities on how to limit its spread. In October, authorities declared the Espolón and Futaleufú rivers “plagued areas” and the Simpson River as threatened.

    Pallaoor V. Sundareshwar, an associate professor of atmospheric sciences at the South Dakota School of Mines and Technology in Rapid City, who inspected the blooms in Chile last summer with Spaulding, says researchers plan to determine through DNA analysis whether Didymo in Patagonia is the same type detected in New Zealand and North America. Next they want to compare the environmental aspects of water in the affected regions. And Sundareshwar hopes they will be able to “solve the mystery of how Didymosphenia came to Chile, what is it doing, and why is it blooming.” He adds: “Maybe if we are lucky we will be able to figure out how to control it.”

    Sample takers themselves can be a problem, says Jorge O'kuinghtons of DGA. They're being trained in procedures for disinfecting gear and instruments. Training tourists and fishers will be more difficult. The immediate objective is to hold the line and prevent Didymo's expansion to other rivers on Patagonia and to the north of the country. “We are facing a threat to the primary patrimony of regional tourism products,” says Fabien Bourlon, director of the Patagonian Center for Scientific Tourism.

    The campaign has focused on prevention for a simple reason: “There is no effective and proven method that allows the eradication of Didymo” but also leaves the ecosystem intact, explains Manuel Martínez, an aquaculture engineer who is coordinating regional efforts to intercept the algae. Biocides can kill many organisms and have been ruled out.

    Three years ago, Spaulding warned in a paper that “rivers in the southern hemisphere are particularly at risk” to invasion and degradation by new species. The 2007 analysis, co-authored with conservationist Leah Elwell, said that environmental protection agencies in Australia, Argentina, Chile, and Peru should be aware of the “urgency of implementing decontamination procedures” to keep travelers from bringing in invasive species like Didymo. Chile did not move rapidly. Regional authorities hope it's not too late to restore the reputation of Patagonia's rivers as the most pristine on Earth.

    • * Patricio Segura is a freelance journalist in Coyhaique, Chile.

  5. ScienceNOW.org

    From Science's Online Daily News Site

    CREDIT: EUNICE WONG AND HANNAH SHEPPARD-BRENNAND/UNIVERSITY OF SYDNEY

    Some Don't Like It Hot As oceans continue to warm and acidify, the survival of the tiny floating young of marine mollusks (Haliotis coccoradiata) and sea urchins (Heliocidaris erythrogramma) looks bleak, researchers report online in the Proceedings of Royal Society B. Maria Byrne of the University of Sydney in Australia and colleagues found that young mollusks maturing in slightly warmer and more acidic seawater couldn't calcify their shells and formed amorphous blobs (picture, top right). Most died after only a 2°C rise in temperature. Sea urchins fared better but formed far fewer spines if the water was 4°C warmer (bottom right).

    You Could Have Fooled Me The “placebo effect” may work even if patients know they are taking fake pills, a new clinical trial suggests. Ted Kaptchuk of Harvard Medical School in Boston and colleagues gave either a placebo or no pill to 80 people with irritable bowel syndrome (IBS). All subjects were told that placebos contain no active ingredient but can have a powerful effect because the body responds to them “like Pavlov's dogs” to a bell. Three weeks later, those on the pills reported significant improvement, comparable to that seen in trials of real IBS drugs, the team reports online in PLoS ONE.

    Doll face.

    Researchers used morphed faces to test how humans decide whether a face is alive.

    CREDIT: CHRISTINE E. LOOSER/DARTMOUTH COLLEGE

    The Eyes Have It How do we judge whether a face is that of a living person or an inanimate object? Christine Looser and Thalia Wheatley of Dartmouth College had student volunteers look at pictures of human and doll faces, blended together to various degrees using software, and decide which ones were alive. Nearly all participants looked at the eyes more than the mouth, nose, or skin, suggesting that we rely on the eyes to judge whether a face has a mind behind it, the pair reports online in Psychological Science.

    Finger Points to New Type of Human By sequencing DNA from an ancient finger bone, researchers have confirmed the discovery of a new type of human that lived in the Altai Mountains in southern Siberia more than 30,000 years ago. The Denisovans, named after the Denisova cave in which the bone was found, lived at roughly the same time modern humans and Neandertals roamed the region but were more closely related to Neandertals. Before going extinct, they bred with modern humans; people from New Guinea and nearby islands appear to have inherited between 4% and 6% of their DNA from the Denisovans, lead author Svante Pääbo and scientists at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, report online in Nature.

    Read the full postings, comments, and more at http://news.sciencemag.org/sciencenow.

  6. ScienceInsider

    From the Science Policy Blog

    Brazil will pay more than €250 million over a decade to join the European Southern Observatory (ESO), becoming the first member from outside Europe. The agreement boosts Brazil's effort to strengthen its domestic science programs by joining big international projects such as ESO's cluster of telescopes in Chile.

    White House science adviser John Holdren sat down recently with ScienceInsider to talk about the joys of working for a president who "gets it" on science and the frustrations of never having enough time to plan ahead despite working 16-hour days. “I still find it more exhilarating than exhausting,” he says.

    The French medical system is in turmoil over the failure of the government to restrict or ban a diabetes drug called benfluorex that was widely prescribed as a weight-loss drug. A top official acknowledged “serious failures” in France's drug licensing system. Parliament has launched its own investigation.

    A new world of U.S. Environmental Protection Agency regulations regarding greenhouse gas emissions opened on 2 January. ScienceInsider provided a primer, with one post explaining the basic structure of the rules and a second analyzing the legal challenges facing the agency.

    An attempt to spur U.S. innovation died on the last day of the lame-duck Congress, as the House of Representatives failed to take up a Senate-passed bill that would have enlarged and broadened two long-running federal research programs that help hightech start-ups. The SBIR and STTR programs are due to expire at the end of the month.

    Dozens of U.K. scientists have urged the government to maintain its commitment to forensic science despite its decision to close the Forensic Science Service.

    For more science policy news, visit http://news.sciencemag.org/scienceinsider.

  7. Was North Africa the Launch Pad for Modern Human Migrations?

    1. Michael Balter

    A growing number of researchers suspect that long-neglected North Africa was the original home of the modern humans who first trekked out of the continent.

    Digging for our roots.

    Modern humans occupied many North African sites, like this one at Contrebandiers, Morocco.

    CREDIT: HAROLD DIBBLE

    Last year, archaeologists excavating at the Grotte des Contrebandiers (Smuggler's Cave) on Morocco's Atlantic coast unearthed a rare prize: the skull and partial skeleton of a 7- or 8-year-old child. The fossils, dated to 108,000 years ago, appear to belong to an early member of our species, although study of them has just begun.

    But one feature stands out already: “It has huge teeth,” says Harold Dibble of the University of Pennsylvania, co-leader of the dig team. That's a feature the child shares not only with other hominin fossils found across North Africa but also with some of the first modern humans to leave Africa. And so the new fossil may contain clues to an enduring mystery in human origins research: Just where in Africa did the modern humans who first colonized the rest of the world come from? “It's a very exciting specimen,” says anthropologist Jean-Jacques Hublin of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany.

    For Hublin, who was born in Algeria, the Contrebandiers child adds to growing evidence that North Africa was likely a major source of the modern humans who first left humanity's homeland and spread into Europe and Asia as early as 130,000 years ago. “If you look at a map and think how modern humans would have moved out, you would logically look at North Africa,” he says.

    Old youngster.

    This fossil child had big teeth.

    CREDIT: HAROLD DIBBLE

    Nevertheless, until very recently, most researchers studying the origins of Homo sapiens looked elsewhere, focusing instead on the fossils of East Africa and the sophisticated tools and ornaments of famed South African sites such as Blombos Cave (Science, 16 April 2004, p. 369). Few scientists thought that much of evolutionary significance had gone on in North Africa, or that the region's big-toothed, somewhat archaic-looking hominins might be closely related to the ancestors of many living people. “We've left North Africa off the map for so long, and now it deserves to be there,” says paleoanthropologist Chris Stringer of the Natural History Museum in London.

    Indeed, a flurry of research has now put the region firmly on the map of human evolution. Thanks to new excavations and more accurate dating, North Africa now boasts unequivocal signs of modern human behavior as early as anywhere else in the world, including South Africa. Climate reconstructions and fossil studies now suggest that the region was more hospitable during key periods than once thought. The data suggest that the Sahara Desert was a land of lakes and rivers about 130,000 years ago, when moderns first left Africa for sites in what is today Israel. And new studies of hominin fossils suggest some strong resemblances—and possible evolutionary connections—between North African specimens and fossils representing migrations out of Africa between 130,000 and 40,000 years ago.

    This barrage of new evidence is reported in recent papers and in two new edited volumes (see Additional Reading below). Human evolution researchers working in other parts of Africa are taking notice. The new studies are “long overdue,” says anthropologist Stanley Ambrose of the University of Illinois, Urbana-Champaign, who works in East Africa. They “show that North Africans may be responsible” for both early and later H. sapiens migrations out of Africa. Adds archaeologist Curtis Marean of Arizona State University, Tempe, “If I were not working in South Africa, I would probably be in North Africa.”

    North African hominin sites

    But a key question, Marean and other researchers say, is whether modern humans in North Africa were foremost among the migrants that eventually left Africa, or whether those populations represented an evolutionary cul-de-sac that was left behind when humans from other parts of the continent began moving into Asia and Europe. The evidence that North Africa was a population pool for migrations to Eurasia is not yet conclusive, says anthropologist Gerhard Weber of the University of Vienna. Marean is also cautious for now but says the new work should provide “some good answers in the future.”

    Old tools, new dates

    Given what researchers already know about modern human evolution, the long neglect of North Africa might seem surprising. Most anthropologists think that our species, H. sapiens, first evolved in sub-Saharan Africa about 200,000 years ago and began migrating out of Africa between 70,000 and 50,000 years ago, eventually colonizing the globe. And although the expansion has often been considered a single migration, many researchers are beginning to suspect that moderns left Africa in two or more waves.

    Some of these early migrants may have gone east, across the Red Sea and along the southern coast of Arabia. But the earliest known modern human fossils outside Africa suggest a northern route, perhaps through the Nile Valley: Modern human skulls and other bones discovered in the early 20th century in the Skhul and Qafzeh caves in Israel are now dated to between 100,000 and 130,000 years ago, although researchers debate whether these early colonizers traveled any farther at that early date (Science, 9 October 2009, p. 224).

    O pioneers.

    Early modern humans like this one from Dar es-Soltan (computer reconstruction, right) may have spread across North Africa and into Eurasia.

    CREDIT: RECONSTRUCTION BY HUBLIN AND NEUBAUER

    Despite this early connection to the Middle East, not so long ago most experts thought that modern humans occupied North Africa itself relatively late. The earliest known modern human fossils were from East Africa: Skulls and bones found near Kenya's Omo River by Richard Leakey and others are now dated to 195,000 years ago, and skulls found at Herto in Ethiopia clock in at about 160,000 years old. Then, in recent years, Hublin, Stringer, and others convinced most anthropologists that a 160,000-year-old skull from Jebel Irhoud in Morocco was that of an archaic modern human and not a Neandertal, as previously thought. But that skull was considered an anomaly, perhaps representing a population that got trapped north of the Sahara and then died out.

    This picture of North African hominins as Johnny-come-latelies was reinforced by assumptions about the dates of characteristic stone tools in the region. Called Aterian after their discovery in 1917 at the site of Bir el Ater in eastern Algeria, the tools include triangular objects that some suggested were used as arrowheads or spear points (see photo, p. 23). At least 100 Aterian sites have now been uncovered across North Africa, including in what is now the Sahara Desert. But when archaeologists radiocarbon-dated these sites, they tended to throw out any results older than 40,000 years, says archaeologist Elena Garcea of the University of Cassino in Italy, because such dates were at the limit of the radiocarbon technique and considered unreliable (Science, 15 September 2006, p. 1560). “In the past, the Aterian was thought to be relatively late and not terribly exciting, … a sideline or a dead end,” says archaeologist Nick Barton of the University of Oxford in the United Kingdom.

    By 1998, however, it began to look like archaeologists might be throwing away the wrong dates. That year, researchers used the new techniques of optically stimulated luminescence (OSL) and thermoluminescence (TL) to date Aterian sites in Libya back to 70,000 years, and soon afterward similar dates using these and other methods were found at other Aterian sites in the region.

    European connection?

    Some features, such as the molars, of these 40,000-year-old specimens from Romania resemble those of earlier North African hominins.

    CREDIT: H. ROUGIER ET AL., PNAS 104 (23 JANUARY 2007) © 2007 NATIONAL ACADEMY OF SCIENCES, U.S.A.; E. TRINKAUS ET AL., PNAS 100 (30 SEPTEMBER 2003) © 2003 NATIONAL ACADEMY OF SCIENCES, U.S.A.

    During the past 2 years, the dates have gotten even older. In 2009, Barton and Abdeljalil Bouzouggar of the National Institute of Archaeological and Heritage Sciences in Rabat reported OSL dates of at least 110,000 years from the Aterian site of Dar es-Soltan in Morocco; and in a new volume edited by Garcea, the team reports similarly old dates from three other Moroccan caves. Then in September, TL dates of about 145,000 years were reported for Ifri n'Ammar in Morocco. “The Aterian goes back at least 145,000 years,” Stringer says. “That's an incredible length of time.”

    Those early dates are coupled with a growing realization that the Aterians were just as behaviorally sophisticated as modern humans in other parts of Africa. In addition to their skillfully made tools, they made personal ornaments—a key sign of modern, symbolic behavior—from shell beads 82,000 years ago at Morocco's Grotte des Pigeons (Pigeon Cave). That's somewhat earlier than when the same genus of shells, Nassarius, was used to make beads at Blombos Cave thousands of kilometers away in South Africa 75,000 years ago. Nassarius beads show up at Qafzeh in Israel even earlier, at least 100,000 years ago (Science, 23 June 2006, p. 1785). Researchers are now studying 108,000-year-old perforated Nassarius shells from Contrebandiers to determine whether they, too, were used as personal ornaments.

    All this implies that the Aterian was not a sideshow but a “[cultural] package that may be linked with the emergence of modern human behavior,” says Barton. That's not direct evidence that the Aterians were the source of out-of-Africa migrations, but it suggests that they met an important prerequisite: Rather than being a small, isolated population unlikely to go on the move, they apparently were part of extensive social networks that used ornaments to signal the identities of different groups that were in contact with one another, perhaps across long distances (Science, 9 April, p. 164).

    Facing the past.

    The Max Planck's Jean-Jacques Hublin sees similarities between the Aterians and the first modern humans to leave Africa.

    CREDIT: PETER ENDIG

    This is in contrast to recent genetic research, which has suggested that the humans who dispersed to Europe, Asia, and Australia by 50,000 years ago originated in sub-Saharan Africa (Science, 1 May 2009, p. 575). But Hublin argues that such studies, which are based on the genetic diversity of humans today, might not capture past patterns. For example, some of the Aterians in the Sahara area—along with their genes—may have moved east or south when the Sahara became hotter and drier after 60,000 years ago.

    Leading geneticists support the idea that some of the populations that live south of the Sahara today may have Aterian roots. “This is entirely plausible,” says Sarah Tishkoff of the University of Pennsylvania. “We can only study populations present today, and their present-day distribution probably doesn't reflect where they originated from tens of thousands of years ago.”

    Rain over the Sahara

    Today, no sensible hominin would think of trying to cross the Sahara Desert. This vast landscape of sand dunes, rocky plains, and plateaus covers 5 million square kilometers from the Atlantic Ocean in the west to the Red Sea in the east. The Sahara overall receives less than 8 centimeters of rain each year, and the driest parts might not see rain for years on end. But during key periods in human prehistory, new data from multiple sources suggest, at least parts of the Sahara featured lakes, rivers, and trees.

    Scientists are now working to correlate the cyclical greening of the Sahara with archaeological signs of human occupations. For example, satellite radar imaging has revealed a system of more than 800 kilometers of channels, some more than 5 kilometers wide, buried under the eastern Sahara sands. A 2008 study of 120,000-year-old snail shells suggests that these are river corridors, which could have supported human migrations (http://scim.ag/wetsahara). And trees increased markedly 120,000 and 50,000 years ago, according to work published last year on isotopes from plant leaves in a marine core off the coast of northwest Africa.

    Other recent work suggests that Libya, Chad, Tunisia, and Egypt were dotted with huge “megalakes” about 120,000 years ago; about 10% of Libya might have been underwater around that time, concludes geographer Nick Drake of King's College London. These wet phases lasted for thousands of years.

    “One of the wettest times was around 120,000 to 130,000 years ago,” says geologist Jennifer Smith of Washington University in St. Louis (WUSTL). That's about when modern humans first left Africa and are found in the Israeli caves of Skhul and Qafzeh.

    A wet Sahara between 100,000 and 130,000 years ago may also help explain how shell bead ornaments ended up in both North and South Africa some tens of thousands of years later, says Hublin, if farflung populations were in touch across the continent. “If you look before 100,000 years ago, North Africa was very much connected to the rest of Africa,” he says, adding that fossils of sub-Saharan animals such as rhinos, giraffes, and hippos have been found at North African sites. “We had a network of early modern populations all over Africa, sometimes connected and sometimes separated.”

    Yet despite some evidence, for example from the tree study, that parts of the Sahara continued to experience wet periods as late as 50,000 years ago, the climate data suggest that the Sahara had greatly expanded by that time. Indeed, Garcea says, no Aterian sites are found in the Sahara after about 60,000 years ago, although the Aterian continues until about 40,000 years ago all along Africa's northern Mediterranean coast.

    Signs of sophistication.

    The Aterians made personal ornaments (above) and advanced stone tools (below).

    CREDITS (TOP TO BOTTOM): IAN R. CARTWRIGHT ©INSTITUTE OF ARCHAEOLOGY/UNIVERSITY OF OXFORD; ROBERTO CECCACCI

    Bones tell a new tale

    Did the Aterians themselves die out, or did they live on to join the exodus out of Africa? The bones they left behind offer some tantalizing clues. The Aterians were kind to human evolution researchers: They left not only ample artifacts but also one of Africa's best collections of modern human fossils. Now new analyses of Aterian faces and teeth suggest that at key times, populations across North Africa and the Middle East were “relatively closely related,” says paleoanthropologist Katerina Harvati of the University of Tübingen in Germany. For example, in a paper in an upcoming volume co-edited by Hublin, Harvati and Hublin compared an Aterian skull with those of other early hominins. They analyzed the facial features of a partial skull found at Dar es-Soltan—now dated to about 80,000 years ago—using the three-dimensional coordinates of 19 facial landmarks. The Dar es-Soltan skull most closely resembled two 100,000-year-old skulls from Qafzeh as well as the 160,000-year-old Jebel Irhoud skull; it showed much less affinity with Neandertal skulls or with younger modern humans from any continent.

    In a second paper, Hublin, along with dental experts Shara Bailey of New York University and Tanya Smith of Harvard University, compared the size and shape of more than 50 hominin teeth from Aterian sites with more than 200 teeth from Neandertals as well as modern humans from several continents. The Aterian teeth, which have very large molars and a distinctive pattern of cusps, clustered most closely with those from Qafzeh and Skhul. And they also strikingly resembled those of the earliest known modern humans in Europe: a cranium and mandible, dated to about 40,000 years ago, from the site of Peştera cu Oase in Romania.

    Earlier, other researchers had also found resemblances—such as the robust shape of the lower jaw and forward-facing cheekbones—between Oase and a 40,000-year-old skull from the site of Nazlet Khater in Egypt, providing another potential North African link to the earliest Europeans. “There are indeed some affinities between Oase and Nazlet Khater,” says anthropologist Hélène Rougier of California State University, Northridge, who worked on some of these studies, although she notes that the contemporaneous skulls differ in other traits.

    The big teeth “certainly potentially link the Aterians with Oase,” says the Natural History Museum's Stringer, making the Aterians candidates for the ancestors of later Europeans.

    But to nail down those evolutionary relationships, Stringer says, “we need good samples from northeast Africa,” because most Aterian fossils are from Morocco in northwest Africa. “The people in Morocco could have been marginal.” He adds that the early Oase skull from Romania might not have been closely related to the modern humans who later colonized the rest of western Europe and left the famed Aurignacian and Gravettian cultures; those cultures could represent a later wave of more gracile, smaller-toothed H. sapiens.

    Other researchers remain even more skeptical. Paleoanthropologist Erik Trinkaus of WUSTL, who has extensively studied the Oase fossils and thinks they represent admixture between Neandertals and moderns, rejects any close connection between them and the Aterians. He sees “some superficial resemblances in terms of large molars” between Oase and Aterian specimens but few other similarities. In fact, he thinks the Aterians weren't fully modern humans but “archaics” living in an isolated corner of Africa who were an evolutionary dead end. North Africa was “just another cul-de-sac,” he says.

    But that view of the Aterians is rejected by many other anthropologists. The emerging evidence, Hublin and others say, suggests that at the critical time, prehistoric North Africans enjoyed the right climate, engaged in the right symbolic behavior, and possessed the right anatomy to be leading candidates for the ancestors of at least some of the H. sapiens who left Africa. So for a growing number of researchers, North Africa is a very promising place to look. Says Dibble: “We have exactly the kind of thing everyone has been searching for, right here.”

    Additional Reading:

  8. Cell Biology

    The Power of One

    1. Mitch Leslie

    Rather than probe masses of cells all at once, scientists are now applying new research techniques to individual cells.

    Small sample size.

    Researchers are exploring new ways of investigating individual cells such as this human white blood cell.

    CREDIT: ANNE WESTON/CANCER RESEARCH UK/VISUALS UNLIMITED, INC.

    1) Measure out a heaping portion of cells.

    2) Grind until thoroughly mixed.

    3) Analyze.

    Cellular studies still pretty much stick to this traditional recipe, whether the goal is probing bacterial metabolism, following differentiation of stem cells, or tabulating gene activity in tumors. But mashing up a multitude of cells—one common method of studying gene expression typically requires more than 10,000—obliterates key differences between cells, researchers have come to realize. “If you take an average of a large number of cells, you get an average answer,” says analytical chemist Renato Zenobi of the Swiss Federal Institute of Technology in Zurich.

    That's why more and more scientists are opting for the alternative approach of taking the measure of individual cells. Although much of this work is in its early stages, “there is an increasingly diverse set of examples where single-cell studies have provided qualitative insights that couldn't be obtained from population-level studies,” says biophysicist Michael Elowitz of the California Institute of Technology in Pasadena.

    Scientists have already recorded the most accurate measurements of how much an individual cell weighs and gauged how much oxygen one requires. They've flagged specific cancer cells resistant to chemotherapy and developed ways to pinpoint rare, disease-causing bacteria among swarms of harmless microbes. Developmental biologists have tallied gene activity as a fertilized egg starts its course of division and specialization, work that might help clarify the factors that spur a cell in the embryo to become one tissue and its seemingly identical next-door neighbor to become something else. And Elowitz and other researchers have spelled out how individual cells not only cope with but actually benefit from “noise,” random fluctuations in their internal and external conditions.

    Of course, scientists have paid attention to single cells ever since the first microscopes were invented. What's changed is that researchers are now applying to individual cells the powerful techniques, including genome sequencing, mass spectrometry, and gene expression analysis, that formerly required batches of cells. “Real biological tissues are complex, and if you want to dissect that complexity and heterogeneity, you have to have tools to do it at the single-cell level,” says biophysicist Stephen Quake of Stanford University in Palo Alto, California.

    Good technique

    Single-cell research tools range from old standbys to cutting-edge inventions (see sidebar for a sample of methods). Many of them allow researchers to get into what Quake calls “production mode,” analyzing large numbers of individual cells in parallel or over a short period of time. The technology he calls “absolutely central” to the surge in single-cell research is microfluidics, which uses miniaturized networks of channels, valves, pumps, and chambers to control microscopic quantities of liquid. So-called lab-on-a-chip devices combine microfluidic circuits and can perform several analytical steps.

    An example of how microfluidics can elucidate single-cell behavior comes from Quake, his Stanford colleague Markus Covert, and their colleagues. Last July in Nature, the team reported using a microfluidic chip to dose individual cells with different concentrations of tumor necrosis factor α (TNF-α), a protein that can trigger inflammation and cell suicide. Previous work on cells en masse suggested that they respond to a range of TNF-α concentrations. But the researchers found that sensitivity to TNF-α varied from cell to cell—a result that might help clarify how the body fine-tunes TNF-α's effects.

    Single-cell techniques also allow researchers to ferret out rare troublemakers such as Escherichia coli bacteria of the O157:H7 strain. Just a handful of the malignant microbes in undercooked hamburger could be enough to cause fatal food poisoning, so detection methods need high sensitivity. Last year, biophysical chemist Richard Mathies of the University of California (UC), Berkeley, and colleagues revealed a strategy that can finger a single cell of the lethal strain from among as many as 100,000 normal E. coli. The key step in their method, which the researchers described in Analytical Chemistry, involves a microfluidic circuit that creates tiny, uniform oil droplets in which DNA sequences from normal and lethal bacteria are copied.

    Dynamic fluids.

    With microfluidic chips like this one, researchers can sort single cells, copy their DNA, measure their gene activity, and perform other kinds of analysis.

    CREDITS: PAUL C. BLAINEY/STEPHEN R. QUAKE GROUP/STANFORD MICROFLUIDICS FOUNDRY

    Predicting which patients will benefit from cancer treatment could be another use of single-cell methods. Immunologist Garry Nolan of Stanford and colleagues have profiled individual cancer cells with phosphospecific flow cytometry, a technique for determining whether proteins have undergone certain chemical modifications that can change cell behavior. For cancers such as acute myeloid leukemia and lymphoma, Nolan and colleagues showed that some abnormal cells contain patterns of protein modifications indicating resistance to chemotherapy. Based on these patterns, “you could pick out patients who would respond to chemo and [those] who wouldn't,” he says.

    Gone genome fishing

    Microbial ecologists and microbiologists are looking to single-cell techniques for help with their culture problem. More than 99% of microbial species remain enigmatic because they refuse to grow under lab conditions and scientists can't obtain enough of the microbes' DNA to sequence their genomes. To fill in the gaps, researchers have turned to metagenomics (Science, 30 March 2007, p. 1781), trawling environments such as the open ocean and the human colon for any microbial DNA and then sequencing it to identify genes. Such an analysis can reveal the metabolic capabilities of an entire microbial community, and in a few cases researchers have been able to piece together an unculturable bacterium's genome from the jumble of DNA fragments. But it's usually impossible to pin down which genes belong to a specific microbe. That means researchers can't determine which species perform which ecological roles or reconstruct their evolution, notes microbial ecologist Ramunas Stepanauskas of the Bigelow Laboratory for Ocean Sciences in West Boothbay Harbor, Maine.

    In 2001, however, genome biologist Roger Lasken, now at the J. Craig Venter Institute in Rockville, Maryland, and colleagues unveiled a method called multiple displacement amplification (MDA) that can expand the minute amount of DNA in a single bacterial cell by a billion times, thus providing enough material for sequencing. “The great excitement is that we have access to this whole world of bacteria that's been hidden,” Lasken says.

    His group provided the first glimpse into this world in 2005, sequencing an uncultured microbe that they dug out of the soil. Genomes from previously furtive bacteria have been trickling in ever since.

    Microbial rainbow.

    Although these bacteria are genetically identical, random fluctuations in gene expression turn them different colors.

    CREDIT: M. B. ELOWITZ ET AL., SCIENCE 297 (16 AUGUST 2002)

    Four years ago, Quake and colleagues announced that they had used the technique on microbes from a dark and mysterious environment: the human mouth. The researchers scraped the teeming gunk from the gum line of a volunteer who hadn't brushed his teeth for 5 days. Then the scientists sequenced the genome of an unknown bacterium they sifted from the samples with a microfluidic chip. And in 2009, Stepanauskas and colleagues added genome sequences for two unidentified bacteria they'd fished from the Gulf of Maine. Stepanauskas says that thanks to MDA, he expects a flood of genomes for unculturable microbes in the next few years.

    MDA can't capture the entire genome; typically the coverage falls between 40% and 90%, says Lasken. But that's enough to furnish a wealth of information about an organism's way of life, says Stepanauskas: “Even if we only recover 50% of the genome of groups that are driving the biogeochemistry of the planet, that's great.”

    Going their own way

    Other researchers are using single-cell techniques to pinpoint molecular events in the embryo, probing the key time when cells begin to specialize and follow disparate developmental paths. “It's always been a goal for developmental biologists to understand, at the single-cell level, what decisions are being made” as this process unfolds, says molecular developmental biologist Paul Robson of the Genome Institute of Singapore. However, researchers didn't have the tools to detect changes in individual cells, he notes.

    Now they do. Robson and colleagues, for example, used a microfluidic chip to track the activity of 48 genes as a single-celled zygote morphed into a 64-cell blastocyst, which harbors three cell types. The study revealed surprising behavior by transcription factors, proteins that latch onto DNA to flip genes on or off. Researchers had assumed that differentiation would involve activation of previously silent transcription factors, which would then nudge the cell in a new direction. But as Robson and colleagues reported last year in Developmental Cell, mouse embryonic cells appear to differentiate at least partly by subtraction: Transcription factors expressed throughout the embryo switch off in a cell starting down a particular developmental path.

    Researchers can use such single-cell techniques to study other embryonic stages, Robson says: “We can capture cell fate decisions anywhere in development.” This work might provide insight into how birth defects originate. And by identifying factors that hasten or hinder cell differentiation, such studies might also improve researchers' ability to nurture embryonic stem cells and to guide their development into the desired tissues.

    Vive la différence

    Single-cell research has also prodded scientists to rethink their ideas of how cells control and coordinate actions. We tend to imagine cells as governed by clockwork circuits of genes and proteins, which keep neighboring cells performing in sync like musicians in an orchestra. But evidence that began to accumulate in the late 1950s has shown that cellular variables such as gene activity fluctuate randomly. The supposedly clockwork networks are riddled with what researchers call noise.

    When it's making a protein, for example, a cell typically doesn't pour out a steady stream of the molecule. Instead, it blurts out pulses of the protein at irregular intervals. Such molecular vagaries create differences between even genetically identical cells in a uniform tissue. The discovery of this variability “opens up the question, how do cells do anything, [if] it's so noisy?” says molecular biologist Jeff Hasty of UC San Diego.

    In many cases, recent studies suggest, cells capitalize on such noise to guide their development, coordinate gene activity, and perform other tasks. “Heterogeneity is useful, not just a nuisance,” says molecular cell biologist Michael White of the University of Liverpool in the United Kingdom.

    A study of single cells by White and colleagues, published in 2010 in the Proceedings of the National Academy of Sciences, provides an example. The researchers tracked how individual mouse or human cells manage NF-κB, which flits in and out of a cell's nucleus, turning on genes that spur inflammation when it's inside. Two closely related proteins shut down NF-κB, but cells stagger production of the two inhibitors. White's group tweaked the production delay in individual cells and found that the delay's natural length is fine-tuned to accentuate differences in NF-κB activity between cells, thus increasing the amount of noise. “I suggest that the system is optimized to make the cells as asynchronous as possible,” White says. By keeping neighboring cells out of step, the strategy might prevent release of a large, potentially harmful burst of inflammation-triggering molecules.

    Even development, which seems so orderly, might rely on noise. Elowitz and colleagues have probed that possibility by dissecting differentiation in the microbe Bacillus subtilis. Although the changes a single bacterium undergoes are a far cry from the development of a plant or an animal, the simplicity of bacteria can provide insights into the more complex cases, researchers say. When a bacterium such as B. subtilis is stressed out, for example, it can gain the ability to absorb DNA from its surroundings—an altered state called competence that might boost its genetic variation. In studies of individual B. subtilis cells over the past few years, Elowitz's group has concluded that random fluctuations within a two-gene network control whether one of the bacteria becomes competent. Similar noisy circuits, says Elowitz, “may apply to differentiation in more complex systems,” such as in biofilms that comprise multiple kinds of bacteria or in the development of multicellular animals.

    The spotlight on a cell's internal noise is a direct result of the ability to study one cell at a time rather than masses of them. And researchers predict that the best is yet to come for single-cell studies, as they hone an expanding repertoire of techniques and apply them to new questions. “I think this will be one of the great new areas where advancing bioanalytical technologies combine with cell biology,” Mathies says.

  9. Single-Cell Tech Primer

    1. Mitch Leslie

    Microfluidics, gene expression, flow cytometry, and mass spectrometry are enabling researchers to delve into individual cells.

    Microfluidics is the hot technique in the single-cell field (see main text). However, it's just one of the methods that are enabling researchers to delve into individual cells.

    • Gene Expression

    Many modern gene-expression studies apply the mingled contents of thousands of cells to devices called microarrays that look like glass slides or microchips. But with microfluidic chips, researchers can make the same measurements on one cell. Take the gene-expression chips from California-based Fluidigm, a company co-founded by Stephen Quake of Stanford University in Palo Alto, California. The devices isolate samples from individual cells and mix them with the chemicals necessary for quantitative polymerase chain reaction, a technique that determines gene activity by measuring how much messenger RNA a gene makes. The company's most powerful version allows researchers to simultaneously gauge the activity of 96 genes in 96 individual cells, churning through a batch in about 4 hours.

    Another new technology, known as RNA-seq, provides an alternative to microfluidic chips for measuring gene activity in one cell. An offshoot of next-generation genome sequencing, the procedure involves converting a cell's mRNA molecules back into short strands of DNA, sequencing those DNA fragments, and then matching them up with the gene that originally spawned the mRNAs. Last May in Cell Stem Cell, molecular geneticist M. Azim Surani of the University of Cambridge in the United Kingdom and colleagues reported one of the first studies to apply the RNA-seq technique to single cells, revealing the expression of 385 genes in individual embryonic stem cells. Fans of RNA-seq emphasize that it can measure more genes at once than can microfluidic chips. Meanwhile, chip devotees tout their method's superior speed.

    • Flow Cytometry

    A classic technique, flow cytometry sifts and counts cells based on characteristics such as the presence of certain proteins on their surface. Researchers use it today for single-cell work because it can handle large numbers of cells quickly. Garry Nolan of Stanford and colleagues have turned to phosphospecific flow cytometry, a version that detects whether some of a cell's signaling proteins have been tagged with phosphate groups, which are chemical switches that can turn the proteins on or off. Measuring the phosphorylation status of the proteins in a circuit that controls a particular cellular function provides an indication of a cell's status: how other cells have influenced it and how it might respond in the future.

    Along with more accurate cancer prognoses, potential uses of phosphospecific flow cytometry include drug screening, Nolan says. The technique is even more powerful when combined with mass spectrometry, he notes. In phosphospecific flow cytometry, the small number of fluorescent tags limits researchers to measuring about 15 of a cell's phosphorylated proteins. But a new instrument developed by DVS Sciences in Canada uses different isotopes of elements such as lanthanum as labels and mass spectrometry to detect the tags, hiking the number of proteins researchers can monitor to approximately 100. “This is not your grandmother's flow cytometry,” Nolan says.

    • Mass Spectrometry

    Mass spectrometry alone might also provide insights into individual cells. Renato Zenobi's lab at the Swiss Federal Institute of Technology in Zurich, for example, is one of several taking advantage of the method to tally the products of biochemical reactions one cell at a time. The cellular concentrations of metabolic compounds such as ATP, the molecule cells use to store energy, are well within the sensitivity of mass spectrometry, he says. The trick now, adds Zenobi, is figuring out what questions biologists can answer by performing mass spectrometry on an individual cell. “We need to show a really hot application of the data, and that will convince” more researchers that adopting it is a good idea.

  10. National Science Foundation

    Meeting for Peer Review at a Resort That's Virtually Free

    1. John Bohannon

    More than 19,000 scientists travel to NSF headquarters each year to take part in grant evaluation panels. Could their avatars do the job as well?

    Face-to-face, almost.

    An alternative way to bring scientists together for confidential reviews.

    CREDITS: WILLIAM SIMS BAINBRIDGE/NSF

    The view from the terrace is stunning. Sunlight glimmers across a wind-riffled ocean right to the horizon. Over the past year, William Sims Bainbridge, a sociologist and program director at the U.S. National Science Foundation (NSF), has invited scientists here to take part in grant-review panels. “We usually work over there,” he says, walking to a ring of stools. “This is Vannevar Bush, our patron saint,” he says, admiring a framed portrait of the computer scientist who helped create NSF in 1950. Bainbridge rubs his hands together, and a floating cube the size of a refrigerator box grows out of thin air. It rotates, each face covered with scientific plots and data. “Let's teleport upstairs so I can show you around.” He vanishes.

    That was Bainbridge's avatar, of course, and the glimmering ocean nothing more than code in the online world of Second Life. Bainbridge helped build this virtual scientific resort for NSF as an experiment. Can the hard work of grant review be done without face-to-face meetings? With budgets tightening, scientific organizations like NSF are exploring ways to reduce the number of their physical meetings. Proponents see it as a win-win scenario, saving not only time and money but also carbon emissions. Whether the technology is up to the task is another matter.

    Over the past year, more than 19,000 scientists traveled to NSF headquarters in Arlington, Virginia, to take part in traditional review panels. Most of them worked for two solid days, huddled in groups of six to 10, carefully reading, discussing, and scoring dozens of research proposals competing for over $6 billion in grants. It's the scientific equivalent of jury duty. NSF covers expenses, but the small honorarium—typically $500—hardly covers a scientist's time, especially considering the days lost to travel. But how else can NSF evaluate the merits of all those proposals?

    The U.S. National Institutes of Health (NIH) has an equally heavy load. Over the past year, 17,000 reviewers evaluated 61,000 proposals competing for more than $15 billion in NIH grants. But nearly 20% of those scientists never met face to face, relying instead on combinations of phone and video conferencing, says Antonio Scarpa, director of the NIH Center for Scientific Review. Starting this year, NIH has been testing a technology called Cisco TelePresence, a videoconferencing system used by the military and large corporations. Strategically placed screens, speakers, and microphones make it seem as though remote participants are sitting around the same table. “It is so convincing that people reach for coffee cups that are not really there,” says Scarpa. Although the system is expensive—NIH declined to cite a number because they are currently negotiating the price—Scarpa predicts that it will eventually reduce the cost of face-to-face meetings “by one-third.”

    Although very few scientists currently have access to a Cisco TelePresence station, anyone can log in to Second Life with a laptop. Since March 2009, six grant-review panels have convened on NSF's island in Second Life, known as IISLand. “Realworld panelists are provided with some resources,” says Bainbridge. “So it was felt appropriate to provide them with the cost of a decent set of virtual clothes.” Once the scientists had created avatars, they each received 1000 Linden dollars—which cost NSF $4—to shop in Second Life's virtual stores. (They also received a $240 honorarium of real money per day.)

    Aside from those virtual quirks, the format of the meetings followed a traditional schedule, and all of the work was completed on time. Bainbridge estimates that switching to virtual review can save as much as $10,000 per panel. NSF pays $3600 in rent per year to Linden Labs, the company that operates Second Life, he says, so “just one normal-sized panel pays for the island more than twice over.”

    Not everyone liked it. “The work got done,” says a cognitive scientist who took part in a Second Life panel in April, “but as soon as the computer turns off, you're gone. I much prefer the pain of going somewhere, hanging out, and having meals together.” But virtual meetings are better than video-conferencing, he notes, because “at least you can sit around in your pajamas.”

    Other scientists say that the advantages of virtual and video meetings are too good to pass up. “Is what is missing about physical presence relevant at all to making scientific recommendations? In my experience, it is not,” says Douglas Fisher, a computer scientist at Vanderbilt University in Nashville, Tennessee, who has taken part in other virtual meetings. “The real impediment to change is discomfort” with the virtual environment. That may be less of an issue for a younger generation of scientists accustomed to avatars in online gaming worlds. Then again, says Bainbridge, “I just turned 70. So age is no barrier.”

    NSF is now evaluating the Second Life panels to decide whether to expand the program. Eventually, Bainbridge calls it “plausible” that as much as 50% of grant review could be done in virtual worlds.

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