News this Week

Science  14 Jan 2011:
Vol. 331, Issue 6014, pp. 130
  1. Genetic Testing

    New High-Tech Screen Takes Carrier Testing to the Next Level

    1. Jennifer Couzin-Frankel

    In the fall of 2008, Stephen Kingsmore, a longtime gene hunter, was approached by two biotech entrepreneurs. One of them, Craig Benson, had just learned that his 5-year-old daughter had juvenile Batten disease, a rare, fatal, inherited, neurological disorder. The pair had a question for Kingsmore: Could he develop a cheap, reliable genetic test for Batten and other equally horrible diseases, available to all parents to prevent the conception or birth of affected children? Their goal was simple: Do everything possible to eradicate these diseases, because, knowing now which genes cause them, we can.

    At the time this kind of screening, called carrier testing, was relatively uncommon. Both parents need to carry the same mutated gene for their child to develop a disease like Batten, and many of these recessive diseases are vanishingly rare. The number of affected children born each year can be in the single digits. Given that, it hasn't made fiscal sense to offer tests for dozens of diseases to everyone when so few couples will be carriers of any given one. In communities in which certain mutated genes pop up more often, such as Ashkenazi Jews, carrier testing has been common for years and has drastically reduced the number of babies born with diseases like Tay-Sachs.

    Missing DNA.

    A new genetic test identifies a four-base deletion that can cause Lesch-Nyhan syndrome, a rare childhood disease, when both parents carry the mutated gene. Here, “next generation sequencing” ran through one person's DNA many times for accuracy. The bottom line is from someone who doesn't carry the mutation.

    CREDIT: C. J. BELL ET AL., SCIENCE TRANSLATIONAL MEDICINE 3, 65 (12 JANUARY 2011)

    But DNA sequencing technology was moving fast and costs were dropping. What the two men proposed might now be doable, Kingsmore thought. He took on the project.

    Two years later, Kingsmore, bioinformaticist Callum Bell, and their colleagues describe in a paper published online this week by Science Translational Medicine (http://stm.sciencemag.org/content/3/65/65ra4.full) what appears to be the broadest application of “next-generation sequencing” to a medical problem. They used technology that, in Kingsmore's words, “sprays the genome with sequences” to look for mutations in the genes behind 448 childhood recessive diseases. The experience has been career-changing for Kingsmore: This week, he moves from the National Center for Genome Resources in Santa Fe, which conducts basic genetics research, to Children's Mercy Hospital in Kansas City, Missouri. There, with support from the hospital and the Beyond Batten Disease Foundation formed by Benson and his wife, Charlotte, he will work to make the test clinically available, he hopes for $500, before the end of the year. The test will be sold by the foundation, which will use some of the proceeds for research into Batten disease and support for families living with it.

    This carrier test is different from others now offered, including one for more than 100 diseases sold through physicians around the United States by the California company Counsyl. Those tests all hunt for previously identified genetic mutations for various diseases, working from a list that cobbles together what's been described in the scientific literature. This captures many carriers, but not all of them. “For some diseases, the mutations on these panels may only account for 20% of mutations” that can cause disease, says Wendy Chung, who directs the clinical genetics program at Columbia University. This means that someone could be told they're not a carrier when in fact they are.

    Next-generation sequencing changes that. Instead of starting with the mutations we know about, it sequences the same DNA again and again to reduce the likelihood of error, and then researchers look for any mutation in a gene involved in one of these rare diseases. The technology is being applied, still experimentally, across medicine, for instance, to diagnose uncommon diseases and to better understand cancer. But the first broad, real-world application will likely be carrier testing of prospective parents, because the medical challenge is straightforward and the technology is nearly ready.

    There are still kinks. Among the trickiest is determining whether gene variants that no one has seen before could, when paired with a mutation on the same gene from the other parent, cause disease. We all harbor gene variants that are harmless. Distinguishing those from the pathological is “going to be quite difficult,” says Lawrence Brody, chief of the genome technology branch at the National Human Genome Research Institute in Bethesda, Maryland.

    Brody should know: For the past 14 years, he's run a database of mutations in BRCA1 and BRCA2, genes involved in breast and ovarian cancer. About 10% of people tested for BRCA genes have a variant of uncertain significance. Brody and many others have been trying to determine which of these actually raise cancer risks.

    When it comes to Kingsmore's test, “how many people are going to be confident enough in discovering a new mutation that they'd be willing to terminate a pregnancy?” asks Stephen Quake, who studies biophysics and genomics at Stanford University in Palo Alto, California. Although one goal in all carrier screening is to encourage couples to screen prior to conception, that's currently rare.

    In their test, Kingsmore and colleagues screened 104 unrelated individuals; on average people carried mutations for about three of the 448 diseases. The group built computer software to analyze the DNA sequences and, among other things, determine whether they matched mutations already published. They've since expanded the test to cover 570 diseases and are testing it on hundreds more people.

    Kingsmore admits to a catch-22 when it comes to assessing whether a new variant is a problem: The best shot at doing so comes from carrier sequencing of many, many people, just as Brody is doing with BRCA1 and -2. But this means that “initially this test will not have perfect knowledge of all diseases.” He predicts it will be about a decade before that changes, and he isn't sure what, if anything, physicians and prospective parents should be told about variants of uncertain significance before then.

    One benefit of next-generation sequencing is that it's far more accurate than what came before it. When double-checking the mutations that showed up in Kingsmore's small sample against published work, about a fifth of those were wrong. For example, he cites a paper published about 20 years ago on a mutation in a very rare disease, Lesch-Nyhan syndrome, which reported a massive DNA deletion. In fact, the deletion Kingsmore's team found in one person (which was predicted, based on bioinformatics analysis, to have the biological effect described in that older paper) was just four DNA bases long. “They never intended that initial paper to be the definitive paper 20 years ago,” says Kingsmore. But as with work in so many rare diseases, studies are sparse and data often hard to come by. He and others hope that sequencing on a much bigger scale will change that, with time.

  2. High-Energy Physics

    Fermilab to End Its Quest for Higgs Particle This Year

    1. Adrian Cho

    U.S. researchers will soon abandon their search for the most coveted particle in high-energy physics because of a lack of funding.

    Researchers working at Fermi National Accelerator Laboratory (Fermilab) in Batavia, Illinois, had wanted to run their 25-year-old atom smasher, the Tevatron, through 2014 in hopes of spotting the so-called Higgs boson before their European counterparts could discover it with their newer, more powerful atom smasher. But officials at the U.S. Department of Energy (DOE), which funds Fermilab, informed lab officials this week that DOE cannot come up with the extra $35 million per year to keep the Tevatron going beyond September.

    “Unfortunately, the current budgetary climate is very challenging and additional funding has not been identified. Therefore, … operation of the Tevatron will end in [fiscal year 2011], as originally scheduled,” wrote William Brinkman, head of DOE's Office of Science, in a letter to Melvyn Shochet, chair of DOE's High Energy Physics Advisory Panel (HEPAP) and a physicist at the University of Chicago in Illinois. Pier Oddone, director of Fermilab, had stressed that the lab could not forsake future experiments to keep the Tevatron going. “Given the absence of additional funding, it's the right decision,” Oddone says.

    Brinkman's letter is the final chapter in a long, tense tale for scientists at Fermilab. Last February, officials at the European particle physics lab, CERN, near Geneva, Switzerland, announced that their Large Hadron Collider (LHC) would turn off for all of 2012 for repairs. That opened a window for physicists at Fermilab to spot the Higgs first—although CERN officials are now considering delaying repairs until 2013.

    “[T]he current budgetary climate is very challenging and additional funding has not been identified.”

    —WILLIAM BRINKMAN, U.S. DEPARTMENT OF ENERGY

    CREDIT: DOE

    In August, Fermilab's scientific advisory panel recommended that lab officials keep running the Tevatron through 2014 even if they didn't get another dime to do so. That advice didn't sit so well with Oddone, who announced a month later that he could squeeze $15 million from the lab's $410 million annual budget but needed DOE to provide $35 million more. In October, a HEPAP subpanel approved Oddone's plan but said the Tevatron should be shuttered if DOE came up empty-handed.

    Many physicists believe that the hunt for the Higgs, the theoretical key to explaining how all particles obtain mass, is the most important challenge in the field. They argue that the Tevatron's lower-energy and cleaner collisions could help Fermilab beat CERN in the race to uncover the Higgs if its mass falls in the range indicated indirectly by measurements on other particles—between 121 and 144 times the mass of a proton. Because the Tevatron collides protons into antiprotons, it could also probe how a new particle interacts with, or “couples” to, certain other particles in order to prove whether it's really the Higgs. The LHC cannot probe those connections as easily because it collides protons with protons.

    “I think we presented a very good science case for continuing to run, but the fiscal realities just don't allow us to go forward,” says Rob Roser, a physicist at Fermilab and co-spokesperson for the 600 researchers working with the CDF particle detector, one of two fed by the Tevatron. But DOE gave scientists a fair hearing, he adds: “They have to make very difficult decisions based on the realities. I can't fault them for that.”

  3. Avian Influenza

    Transgenic Chickens Could Thwart Bird Flu, Curb Pandemic Risk

    1. Martin Enserink

    The chicken soup of the future might just be made from transgenic birds that can't get bird flu—if regulators decide they're safe and consumers don't object. U.K. scientists have created transgenic chickens that can't pass on avian influenza, a disease that decimates poultry flocks and that flu scientists fear could spawn an influenza pandemic among humans.

    The study, published in this week's issue of Science (p. 223), “is extremely interesting as a proof of principle,” says Timm Harder, a bird flu researcher at the Friedrich Loeffler Institute in Greifswald, Germany. But whether the chickens and their eggs are safe to eat—and whether the public will buy them—is an open question, Harder notes.

    Avian influenza, which comes in many different subtypes, is primarily a disease of wild birds, but it occasionally ends up infecting poultry flocks, in which so-called highly pathogenic strains can spread like wildfire. For the virus, infected poultry flocks are a potential bridge to the human population, and the worry is that avian viruses could trigger a pandemic if they adapt to humans, says Laurence Tiley, a molecular biologist at the University of Cambridge in the United Kingdom and the last author of the new paper. The team also included scientists from the Roslin Institute and the Royal (Dick) School of Veterinary Medicine, both part of the University of Edinburgh, and the Veterinary Laboratories Agency in Weybridge.

    Tiley and his colleagues equipped chickens with a so-called RNA-expression cassette, a piece of DNA that makes the birds produce a small, hairpin-shaped piece of RNA that acts as a decoy to polymerase, a key viral enzyme. Instead of binding to the virus's genome, which it helps replicate, polymerase now attaches itself to the hairpin RNA, rendering the enzyme useless. When transgenic chickens were exposed to the deadly H5N1 flu virus, they still succumbed to it. But they didn't pass the virus on to healthy cagemates—neither regular nor transgenic.

    That means that only one or a few chickens would become infected if H5N1 entered a flock—in itself a big improvement, says Tiley. But the ultimate goal is to make the chickens completely impervious to the disease by adding several more gene constructs, as well as to introduce resistance against Newcastle disease and Marek's disease, two other viral threats.

    Tiley and his colleagues chose their decoy carefully: It matches a short sequence on each of the eight genetic elements of the viral genome to which polymerase binds. To overcome resistance, the virus would have to change not only its polymerase enzyme but also the binding sequence in all eight gene segments, which Tiley says is extremely unlikely. It's “a smart strategy,” says Carlos Lois of the University of Massachusetts Medical School in Worcester, but perhaps not foolproof, given that flu is a “master of mutability.”

    Flu fighters.

    These transgenic chickens still die from bird flu; the ultimate goal is full resistance.

    CREDITS: THE ROSLIN INSTITUTE/UNIVERSITY OF EDINBURGH, PHOTOS BY NORRIE RUSSELL

    Flu-resistant chickens would have several advantages, says Harder. Bird flu vaccines work against only one subtype, they need to be updated frequently as the virus evolves, and they don't fully protect against infection, giving the virus a chance to spread silently. Flocks with built-in resistance would put an end to all that.

    Transgenic chickens could theoretically replace nontransgenic breeds worldwide in a few years, says Michael Greger, director of Public Health and Animal Agriculture at the Humane Society of the United States located in Washington, D.C. That's because the trade in both broiler and egg-laying chickens has become consolidated in a handful of companies, which essentially determine what stocks are used by chicken farmers worldwide.

    But Harder points out that these companies don't sell to the vast number of people in the developing world who have a small flock in their backyard or on their rooftop—and that's where avian influenza has been the most difficult to control. The strategy for reaching these small holders, says Tiley, would not be to make them buy their stock from big breeders; instead, he says, it should be possible to provide them with flu-free chickens that they can breed themselves.

  4. Research Funding

    Japan Boosts Competitive Grants at Expense of Big Science

    1. Dennis Normile

    TOKYO—Under what Prime Minister Naoto Kan calls “a budget for the reinvigoration of Japan,” the country's main research grants program is slated for a whopping 32% increase to $3.2 billion in the coming year. Rank-and-file researchers are sure to be pleased with the better odds of winning support under the fiercely competitive program, says Kazuaki Kawabata, the education ministry's director of research and development policy.

    For rent.

    A tight budget means the scientific drilling vessel Chikyu will spend half the year leased out for oil exploration.

    CREDIT: JAMSTEC/IODP

    With an emphasis on social welfare spending and “innovative research” to stimulate the economy, the record-breaking $1.1 trillion budget for the fiscal year starting in April is the first drawn up from scratch by Kan's Democratic Party of Japan, which captured the legislature in August 2009. Government-wide science spending has yet to be compiled. But the education ministry, which oversees most research, will see its S&T budget rise 3.3% to $20.2 billion. “Given the nation's fiscal circumstances, I think we have to be very grateful,” says Kawabata.

    The biggest percentage increase is going to Grants-in-Aid, the main source of support for individuals and small groups. In recent years only 20% of grant applications were successful, leaving a lot of deserving research unfunded, says Kawabata. In addition to giving the program its biggest single-year boost since its establishment in 1965, the administration is planning to relax rules requiring grants to be spent in the year they are awarded. Researchers have long wanted more flexibility in managing money.

    In response to other re quests from the scientific community, the new budget will expand existing programs and add new ones to foster the career development of younger researchers and ease the return of women to the research workforce after maternity leave, with support growing 5.4% to $414 million.

    The Democratic Party's strategy to lean on research to spur economic growth is evident in its support for “innovative” research in life sciences and green technologies, which is rising 9% to $932 million. The portfolio includes stem cells and other aspects of regenerative medicine, next-generation cancer treatments and neuroscience, and creation of a new program under the Japan Science and Technology Agency that will look for “game changing” research in areas such as cost-efficient solar panels, says agency president Koichi Kitazawa.

    For big science, however, the budget offers a mixed bag. Soon after coming to power, the Democratic Party staged a series of hearings that questioned spending on space, earth science, and a next-generation supercomputer (Science, 20 November 2009, p. 1046). The new budget, plus money from a supplementary budget adopted last November, provides funding to keep the supercomputer, planned to be the world's fastest, on track for completion in 2012. The space budget will rise a slim 0.8% to $2.2 billion, including $36 million to begin development of a second asteroid-return mission to succeed the Hayabusa sample-return project. Previous administrations had rejected a follow-up to Hayabusa, which was once thought lost in space. But popular interest after the craft returned to Earth this year with asteroid dust apparently warmed political hearts.

    Winners and losers.

    The education ministry's science budget will rise 3.3% to $20.2 billion in 2011, with small grants winning the lion's share of the increase.

    CREDIT: (SOURCE) MINISTRY OF EDUCATION

    Other big science efforts are in for a rough ride. Spending on atomic energy research will drop 3.7% to $2.5 billion. And polar, oceanographic, and earthquake research is being squeezed 2.4%, to $631 million, including a roughly 4% cut for the Japan Agency for Marine-Earth Science and Technology (JAMSTEC), to $433 million. It will be the second annual budget cut in a row for JAMSTEC, which operates the deep-ocean drill ship Chikyu. Asahiko Taira, a JAMSTEC executive director, says each of the agency's divisions will have to tighten its belt. And they plan to lease Chikyu for commercial oil drilling for half of the year.

    The budget will go before the legislature for approval this month.

  5. ScienceInsider

    From the Science Policy Blog

    The British Medical Journal has accused gastroenterologist Andrew Wakefield of committing scientific fraud in the publication of a 1998 paper in The Lancet linking vaccines to autism. The paper had previously been retracted after a government investigation.

    Despite a grim employment picture for would-be academic researchers, an outside panel says that the U.S. National Institutes of Health (NIH) should maintain or even increase the number of graduate students and postdocs it supports. It's part of the latest review by the National Research Council of NIH's main training program, the National Research Service Award.

    A new study by the U.K. Academy of Medical Sciences finds that British biomedical researchers are drowning in paperwork. The study suggests a new independent agency to coordinate and streamline the system.

    New White House Chief of Staff William Daley believes that optimizing the federal innovation enterprise might require “reorganization” of agencies. “You can't understand how screwed up it is,” he said last month. Daley also defended a private-public joint research program from opponents on Capitol Hill during a stint as commerce secretary in the late 1990s.

    The America COMPETES Act, which President Barack Obama signed last week, seeks to strengthen education programs at NSF with changes to graduate training programs, more support for undergraduate research, and a new program to train prospective science teachers. Meanwhile, Energy Department officials were glad that the final version of the act, though stripped down, authorizes small but steady increases for the Office of Science through 2013.

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

  6. Paleontology

    Pint-Sized Predator Rattles The Dinosaur Family Tree

    1. Michael Balter

    The demise of Tyrannosaurus rex and most other dinosaurs some 65 million years ago may grab all the headlines. But paleontologists are equally concerned with puzzling out how these mighty beasts got their start. Who were their ancestors? Did they burst onto the scene, sweeping their older reptilian rivals before them, or take a quieter, more gradual route to world domination?

    On page 206, a team working in Argentina reports the discovery of a very early dinosaur—possibly a distant ancestor of T. rex—that lived about 230 million years ago, during what paleontologists call the dawn of the dinosaurs. The researchers say the new finds—two specimens that together make up a nearly complete skeleton of a diminutive, 1-meter-long dinosaur—and neighboring fossils show that dinosaurs didn't outcompete other reptiles, but rather gradually replaced them as their predecessors died out for other reasons. More controversially, the team says the fossils show that one of the most well-known early dinosaurs, Eoraptor, long considered an ancestor of meat eaters like T. rex, was actually an ancestor of gigantic plant-eating dinosaurs like Apatosaurus.

    “The new specimens are remarkable,” says Sterling Nesbitt, a paleontologist at the University of Washington, Seattle. Michael Benton, a paleobiologist at the University of Bristol in the United Kingdom, adds that the fossils—which the discovery team has assigned to a new species called Eodromaeus murphi—are “complete enough to add substantially to our knowledge” of early dinosaur evolution.

    Tracing the origins of the earliest dinosaurs has been a major challenge for paleontologists because there are no uncontested fossils from their earliest days on Earth. By the time Eoraptor and other undisputed early dinosaurs came on the scene about 230 million years ago, most researchers have concluded, dinosaurs had already evolved into three major lineages: ornithischians, which later gave rise to armored beasts like Stegosaurus and Ankylosaurus; sauropodomorphs, the lineage that led to giant plant eaters like Apatosaurus and Brachiosaurus; and the meat-eating theropods, such as T. rex and Allosaurus.

    The team that found Eodromaeus was led by the same two paleontologists who discovered and described Eoraptor in the early 1990s: Paul Sereno of the University of Chicago in Illinois, and Ricardo Martinez of the National University of San Juan in Argentina. In 1996, a volunteer from Japan working with Martinez in the Ischigualasto Valley of northwestern Argentina, also known as the Valley of the Moon, unearthed a small vertebra on the side of a hill. When Sereno arrived a couple of months later to help excavate the fossils, he and Martinez at first identified them as Eoraptor.

    Small daddy?

    Meter-long Eodromaeus, found in northwestern Argentina (top), sported serrated teeth and other similarities to later theropods (bottom).

    CREDITS (TOP TO BOTTOM): ILLUSTRATION BY TODD MARSHALL; PHOTO BY RICARDO MARTINEZ; PHOTO BY MIKE HETTWER

    Frustratingly, many of the fossils were embedded in a huge block of rock. “It was an extraordinarily difficult specimen to clean” and prepare for analysis, Sereno says. But once enough of the bones were visible, it became clear “that this was no Eoraptor.”

    Instead, the team concluded, the find was a new species of early theropod. Evidence included its very long, serrated teeth; long finger bones that aided in grasping prey; and pockets in its neck vertebrae for air sacs, which some researchers think helped drive air into the lungs as in today's birds, the descendents of theropod dinosaurs. “I have no doubt that this is a new taxon, a very important one from a critical time … near the beginning of the age of dinosaurs,” says Mark Norell, a paleontologist at the American Museum of Natural History in New York City. And Nesbitt says “the authors make a pretty good case that Eodromaeus is a theropod.”

    Sereno and Martinez themselves previously identified Eoraptor as the earliest known theropod. But after studying their original specimens more closely and comparing them with Eodromaeus and other dinosaurs, they now argue that Eoraptor was in fact an early plant-eating sauropodomorph. “No one, even ourselves, predicted this repositioning,” Sereno says.

    Other researchers are cautious. “Only further research by independent teams can evaluate” this radical shakeup of the early dinosaur tree, says Max Langer, a paleontologist at the University of São Paulo in Brazil. And Langer adds that the uncertainty about where to place Eoraptor “emphasizes how similar [early] theropods and sauropodomorphs” were to each other, which, he says, “is expected anyway in the early radiation” of an animal group.

    Dinosaur experts are happier with a broader conclusion in the Science paper. By 230 million years ago, the authors write, all three dinosaur lineages—ornithischians, theropods, and sauropodomorphs—had already evolved their characteristic dietary behaviors (meat eating versus plant eating) and modes of locomotion (bipedal theropods, four-footed sauropodomorphs). Yet they still made up only about 11% of all vertebrate species at Ischigualasto. Another 30 million years would pass before they became dominant—evidence, the team argues, that dinosaurs did not drive other species to extinction but rather filled ecological niches that other reptiles left empty.

    “Dinosaurs had all of their most noted advances prior to their takeover,” says Sereno. Benton, who has independently concluded that dinosaurs did not outcompete their rivals, says the new work confirms his own “opportunistic replacement” model for dinosaur ascendancy. “What is new is the greater precision they can bring to bear on its timing,” Benton adds.

  7. Digital Data

    Google Books, Wikipedia, and the Future of Culturomics

    1. John Bohannon

    BOSTON—Humanities scholars gathered for an unusual talk here on 8 May at the annual meeting of the American Historical Association. Jean-Baptiste Michel and Erez Lieberman Aiden, mathematicians at nearby Harvard University, focused on issues that are standard material for historians. They discussed, for example, the period of intense censorship in Nazi Germany that began with festive book burnings in 1933 and ended with the Nazi's surrender in 1945. Some of those books were written by Jewish intellectuals, others just contained ideas that were considered “un-German.” Some scholars and artists who were highly influential virtually disappeared from public discourse when the Nazi Party came to power, while those favored by Nazi propaganda vaulted to prominence.

    Working relationship.

    Improvements in Wikipedia will be needed for many research projects using Google's digitized books database.

    CREDITS (LEFT TO RIGHT): WIKIPEDIA; (SEDIMENT) MATEJ KRÉN, (PHOTO) GABRIEL URBÁNEK

    What was unusual was the method that Michel and Lieberman Aiden used to study censorship during that period. By tracking the rise and fall of people's names in millions of German and English books, the researchers identified not only people known to have been censored but also many whose suppression was not recorded. The mathematicians did not read those millions of books, of course. Instead, they performed a quantitative analysis of data they obtained from Google Books. “This is fantastic,” says Anthony Grafton, a historian from Princeton University who was sitting in the audience. Grafton stresses that the technique is “a new starting point” for historical analysis rather than a replacement. “But it is amazing that you get a coherent picture of censorship in the public sphere.”

    On page 176 of this issue (and published online 16 December 2010), a team led by Michel and Lieberman Aiden introduce this and many other examples of this data-intensive approach to the humanities, which they call culturomics (Science, 17 December 2010, p. 1600). The entire data set that underlies their study—a mapping of the words from 4% of all books ever published—is now online for any researcher to explore. “But even with all those data,” cautions Michel, “you'll need to carefully interpret your results.” One of the big challenges, for example, is to correctly extract the names of individual people from those 500 billion words. A potentially valuable resource for this type of analysis is Wikipedia, the massive online encyclopedia, which contains entries for nearly 750,000 people born since 1800. But its shortcomings, from the reliability of its information to the organization of its content, become quickly apparent to those who use it. Several efforts are under way to improve Wikipedia as a teaching and research tool, including one by the Association for Psychological Science (APS).

    Adrian Veres, one of the co-authors of the Michel et al. paper, experienced these problems firsthand. Veres, a chemistry and physics undergraduate at Harvard University, has been using Wikipedia to analyze the fame of scientists whose names appear in books over the centuries. His first task was to identify who among the myriad of people mentioned in books are actually scientists. He started by creating computer algorithms that scour Wikipedia for telltale words such as biologist, chemist, and physicist, as well as keywords that identify people in subfields such as ecology, physiology, and genetics.

    Wikipedia's content is created through cooperative—and often combative—editing by millions of volunteers. But even if the information is correct, “not all of it is structured data” with clear labels, says Veres. It was a serious challenge for his algorithms to extract biographical information, such as years of birth and death, profession, and nationality, from entries that are a “bag of words.” An online community effort called DBpedia has been enforcing structure onto Wikipedia entries, encouraging editors to sort the information into standard fields and then collecting those data for researchers to use. But that effort is only starting.

    Veres whittled down about 7000 candidates to a list of 4209 physicists, chemists, biologists, and mathematicians who were alive between the years 1800 and 2000. He then ranked them by “fame”—as measured by the frequency with which those scientists' full names appear in books. He shared the early results of this analysis with Science. You may be surprised who tops the list. You can view the Science Hall of Fame online at http://www.sciencemag.org/content/331/6014/143.3.full.

    Even so, Veres had to exclude the social sciences from his analysis because the Wikipedia entries were so unreliable. In the field of psychology, for example, Linda Bartoshuk, a psychophysicist and former APS president, was not detected as a scientist because of the paucity of details in her Wikipedia entry. (Bartoshuk was profiled in Science on 18 June 2010.)

    Psychologists are aware of the problem. “Unfortunately, the quality of information about psychological science in Wikipedia is uneven,” says Mahzarin Banaji, current APS president and a psychologist at Harvard. She is calling on psychology researchers, teachers, and students to improve Wikipedia themselves. APS is building a Web portal that will channel the effort with help from Robert Kraut and Rosta Farzan, computer scientists at Carnegie Mellon University in Pittsburgh, Pennsylvania, who specialize in human-computer interaction. The goal is to create “a more complete and accurate representation of our science,” says Banaji. The Web portal is slated to debut 1 February at www.psychologicalscience.org.

    When they first heard about the “culturomics” approach to the humanities, many scholars reacted “as if this were the coming of the antichrist,” says Grafton. “But my reaction is, God look at this new tool!”

  8. Environmental Technology

    Greenhouse–Power Plant Hybrid Set To Make Jordan's Desert Bloom

    1. Daniel Clery

    A novel combination of technologies that has the potential to turn large areas of desert green, producing commercial quantities of food and energy crops, fresh water, and electricity, looks set to have its first large-scale demonstration in Jordan. This week the governments of Jordan and Norway signed an agreement to work with the Sahara Forest Project (SFP), an environmental technology group based in Norway, to build a 20-hectare demonstration center near Aqaba on the Red Sea, which would begin operation in 2015. “It's a holistic approach that could be of major interest to a large number of countries,” says Petter Ølberg, Norway's ambassador to Jordan.

    The key to SFP is bringing seawater to the desert and evaporating it. A key component is the seawater greenhouse, developed by British inventor Charlie Paton. In Paton's scheme, seawater piped to the greenhouse trickles down over a grid structure that covers the windward side of the greenhouse. As natural breezes blow into the greenhouse through the grid, it evaporates the water, making an interior that is cool and moist—ideal conditions for growing crops. At the other end of the greenhouse, another grid evaporator, fed by seawater heated in black pipes on the greenhouse roof, loads more moisture into the air as it leaves the growing area. Now hot and very humid, the air passes through a maze of vertical polyethylene pipes cooled by cold seawater passing through them. Fresh water condenses on the pipes and trickles down into collectors, to be used for irrigation or drinking.

    Just add water.

    SFP's combination of technologies coaxes crops, electricity, and fresh water from unproductive desert.

    CREDIT: SAHARA FOREST PROJECT FOUNDATION/SCREENERGY

    Since 1992, Paton's Seawater Greenhouse company has built pilot projects in Tenerife, Abu Dhabi, and Oman. Its first commercial contract, a 2000-square-meter greenhouse in Port Augusta, Australia, approved in 2009, harvested its first crop of tomatoes last month. To everyone's surprise, still-moist air blowing out of the pilot greenhouses turns the seemingly arid surrounding soil fertile: Weeds spring up unaided there, but they could just as easily be crops.

    Paton teamed up with other experts in engineering, architecture, and environmental technology to form SFP. This group realized that a concentrated solar power plant would make an ideal partner for a seawater greenhouse.

    Unlike photovoltaic systems, which convert sunlight directly into electricity, concentrated solar power uses mirrors to focus light onto a heat collector, which then produces steam to drive a turbine generator. Such solar plants work well in sunny desert areas, but they also need water both for cooling at the end of the power cycle and for cleaning the mirrors. A greenhouse could easily share seawater with a power plant; at the same time, the moist greenhouse and nearby vegetation would act as a natural air scrubber, filtering out much of the dust that would otherwise coat the plant's mirrors. In return, the solar plant would power the greenhouse.

    Apart from Paton's prototype greenhouses, all of SFP's efforts so far have been theoretical. But a feasibility study drew plaudits at the COP15 climate summit in Copenhagen in 2009. “The Sahara Forest Project appears to be a very interesting example of the more integrated and holistic kind of thinking that we will need a lot more of in the future,” said the European Union's energy commissioner at the time, Andris Piebalgs.

    In June 2010, the project was presented to King Abdullah II of Jordan while he was visiting Oslo. The king invited an SFP team to visit Jordan in October and meet with five Jordanian ministers. And that led directly to this week's agreement. “The Jordanian authorities were very supportive and open,” says Ølberg.

    The agreement does not cover the construction cost of the demonstration center. Jordan will provide the 20-hectare site and a corridor to pipe salt water from the Red Sea. Norway will provide $600,000 for three studies: one to survey Jordan's potential for SFP-style facilities; a second to assess the Aqaba site; and a third to probe the possibility of building SFP plants alongside Jordan's planned pipeline to carry water from the Red Sea to the Dead Sea. Construction of the demonstration center will require private money; SFP chief Joakim Hauge says SFP is in discussions with several companies that are keen to invest in it.

    The planned demonstration center devotes 4 hectares to greenhouses and 16 hectares to open-air crops, solar reflectors, and support buildings. The solar plant will use linear Fresnel reflectors, long, flat mirror strips that concentrate light onto a pipe carrying a heat-absorbing fluid. Hauge says the center will try out a variety of crops, including algae and halophytes, salt-tolerant plants that can be irrigated with seawater and used as biomass fuel. Salty waste water from an existing desalination plant will also be evaporated to provide more moisture for open-air crops. “The aim is to test as many technologies and combinations of technologies as possible,” says Hauge.

    SFP aims to start building in 2012 and to begin operations in 2015. If the project is successful, the Aqaba authorities will provide another 200 hectares for expansion.

  9. ScienceNOW.org

    From Science's Online Daily News Site

    CREDIT: NASA

    First Earth-Sized Exoplanet Discovered Astronomers operating the Kepler telescope orbiting the sun in Earth's wake have discovered an extrasolar planet not much larger than Earth—the smallest exoplanet yet found.

    The telescope stared for months on end at the same 150,000 stars in the constellation Cygnus looking for the telltale dimming of a star as a planet passes in front of it. One star, 560 light-years away and designated Kepler-10, dimmed 0.015% every 0.84 days, indicating a planet, dubbed Kepler-10b, orbiting 20 times closer to its star than Mercury orbits the sun. The planet has a diameter 1.42 times Earth's and a density 8.8 times Earth's, and local temperatures are a blazing 1833 K, the team announced this week at the winter meeting of the American Astronomical Society in Seattle, Washington. It's improbable that such a planet could harbor life, but with this milestone behind them, the Kepler team could be announcing the discovery of an Earth-like, habitable exoplanet within a few years.

    Mental Retardation Drug Shows Promise A phase II clinical trial of a drug for treating Fragile X syndrome, the most common inherited form of mental retardation, has delivered encouraging results—but only for patients with a particular genetic mutation.

    Sébastien Jacquemont, a medical geneticist at Centre Hospitalier Universitaire Vaudois in Lausanne, Switzerland, and Baltazar Gomez-Mancilla, a neurologist at Novartis Institutes for Biomedical Research in Basel, Switzerland, studied the effects of a drug called AFQ056, developed by the pharmaceutical company Novartis, on 30 young men with Fragile X. They saw no improvement in patients' learning or memory. However, based on questionnaires filled out by the patients' caregivers, seven patients showed reduced repetitive behaviors, hyperactivity, inappropriate speech, and social withdrawal, the team reports online in Science Translational Medicine.

    These responsive patients all had something in common: an inactive version of FMR1, the gene that is mutated in Fragile X. This is a discouraging sign, perhaps, for those without that marker, but a potentially useful tool for identifying the patients most likely to respond to treatment. Next, a larger clinical trial involving 160 people with Fragile X will test the effects of AFQ056 when taken for 3 months.

    Lunar Core Finally 'Seen' Two groups analyzing decades-old data taken by seismometers left on the moon by Apollo astronauts say they have detected lunar seismologists' prime target: a core of iron that is still molten 4.5 billion years after the moon's formation.

    A team led by planetary scientist Renee Weber of NASA's Marshall Space Flight Center in Huntsville, Alabama, and a second group led by seismologist Raphaël Garcia of the University of Toulouse in France combed recordings made by the Apollo seismic experiment, which stopped transmitting data back to Earth in the mid-1970s, for signs of moonquake waves that may have reflected off the core. The groups took different approaches, but both came to the conclusion that the moon, like Earth, has a liquid core, they reported at last month's meeting of the American Geophysical Union. The core's radius is about 330 kilometers, Weber and her colleagues report online in Science. If the seismic results hold up, researchers say, they would be by far the strongest evidence yet for a liquid core.

    CREDIT: JOHANNA JAMES-HEINZ

    Bumblebees in a Slump Several species of bumblebees, which are important pollinators, have declined substantially over the past 2 to 3 decades in the United States, according to a new survey.

    A team led by entomologist Sydney Cameron of the University of Illinois, Urbana-Champaign, and colleagues used museum collection databases and field samples to assess historical and current populations of eight of the nearly 50 bumblebee species. Four species thought to be in decline had plummeted by as much as 96%, and their ranges had shrunk by between 23% and 87%, the researchers report online in the Proceedings of the National Academy of Sciences. In contrast, four species thought to be stable fluctuated but seemed healthy overall.

    The team also found that the rate of infection of Nosema bombi, a single-celled parasite that afflicts bees in Europe, was much higher in populations of dwindling species. Cameron and her colleagues are now investigating whether Nosema is to blame for the bumblebee decline. In the meantime, Cameron says, it's important to keep breeding facilities disease-free.

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

  10. Social Neuroscience

    Why Loneliness Is Hazardous to Your Health

    1. Greg Miller

    New research suggests that chronic loneliness can cause changes in the cardiovascular, immune, and nervous systems.

    CREDIT: EDWARD HOPPER/THE BRIDGEMAN ART LIBRARY

    Everyone knows what it's like to be lonely. It often happens during life's transitions: when a student leaves home for college, when an unmarried businessman takes a job in a new city, or when an elderly woman outlives her husband and friends. Bouts of loneliness are a melancholy fact of human existence.

    But when loneliness becomes a chronic condition, the impact can be far more serious, says John Cacioppo, a social psychologist at the University of Chicago in Illinois. Cacioppo studies the biological effects of loneliness, and in a steady stream of recent papers, he and collaborators have identified several potentially unhealthy changes in the cardiovascular, immune, and nervous systems of chronically lonely people. Their findings could help explain why epidemiological studies have often found that socially isolated people have shorter life spans and increased risk of a host of health problems, including infections, heart disease, and depression. Their work also adds a new wrinkle, suggesting that it's the subjective experience of loneliness that's harmful, not the actual number of social contacts a person has. “Loneliness isn't at all what people thought it was, and it's a lot more important than people thought it was,” Cacioppo says.

    Colleagues credit him with building an impressive network of collaborations with researchers in other disciplines to pioneer a new science of loneliness. “He's placed it on the scientific map,” says one collaborator, Dorret Boomsma, a behavioral geneticist at Vrije Universiteit Amsterdam in the Netherlands. “He's doing very creative work,” says Martha Farah, a cognitive neuroscientist at the University of Pennsylvania. “He's created a new way of thinking about the biology of interpersonal relationships.”

    A new beginning

    Cacioppo hasn't always studied loneliness. In the 1980s and '90s, he made a name for himself with meticulous laboratory studies on various aspects of emotion and cognition, and he's a founder of the field of social neuroscience, which seeks to understand the brain's role in social behavior. (Last month, colleagues elected him president of the newly formed Society for Social Neuroscience.)

    Cacioppo says a 1988 Science paper suggesting that social isolation increases mortality (29 July 1988, p. 540) prompted him to change the focus of his research. Since then, scores of studies have found that people who lack social support are more prone to a variety of ailments. An analysis of 148 of these studies, published in the July 2010 issue of PLoS Medicine, suggests that social isolation increases the risk of death about as much as smoking cigarettes and more than either physical inactivity or obesity.

    Compelling as these epidemiological studies are, Cacioppo says, they leave unanswered many questions about the mechanisms involved and about what aspects of social isolation are responsible. In the early 1990s, he set out to tackle these questions. He began by handing out questionnaires to thousands of students at Ohio State University in Columbus, where he was based at the time, and following up with physiological and psychological testing in the lab. For the past 10 years, he has been testing hundreds of Chicago-area residents, working closely with psychologist Louise Hawkley and other University of Chicago colleagues.

    This work has convinced Cacioppo that loneliness is a health risk on its own, apart from conditions such as depression or stress that are common fellow travelers. More specifically, it seems to be the subjective experience of loneliness that's important for people's well-being rather than any objective measure of social connectivity (the number of close contacts someone has, for example). It's an important distinction that most previous studies had ignored, says Daniel Russell, a psychologist at Iowa State University in Ames. “Some people are socially isolated and they're not lonely,” Russell says. “By contrast, some people are lonely even if they have a lot of social contacts.”

    As a graduate student in the 1970s at the University of California, Los Angeles (UCLA), Russell helped develop the scale Cacioppo now uses in most of his research. The UCLA Loneliness Scale is based on a questionnaire that tries to size up how people perceive their social situation, with questions about how often they feel a lack of companionship, feel they have no one to talk to, or feel out of tune with those around them.

    “Loneliness … [is] a lot more important than people thought it was.”

    —JOHN CACIOPPO, UNIVERSITY OF CHICAGO

    CREDIT: DAN DRY/COURTESY UNIVERSITY OF CHICAGO

    Sympathetic feelings

    When people score high on the UCLA Loneliness Scale, Cacioppo and colleagues have found, they also tend to exhibit several physiological changes that effectively put the body in a state of alert. In one early study, they found that lonely people exhibit higher vascular resistance, a tightening of the arteries that raises blood pressure. That forces the heart to work harder and can contribute to wear and tear on vessels.

    “Those were landmark investigations” that got other researchers interested in potential biological effects of loneliness, says Chris Segrin, a behavioral scientist at the University of Arizona in Tucson.

    Lonely people also have elevated molecular markers of stress. Cacioppo's group has found that cortisol and epinephrine are elevated in saliva and urine, respectively. That might help explain why lonely people report feeling more stressed in situations most people experience as only moderately stressful, such as public speaking, Cacioppo says.

    Together, these findings point to activation of the sympathetic nervous system, which coordinates the body's fight-or-flight responses. It's as if loneliness prepares the body for some looming threat. Cacioppo thinks that makes evolutionary sense. He argues that being alone, for our distant ancestors, meant abandoning the protection of the group and jeopardizing one's genetic contribution to the next generation. He posits that the physiological changes and anxiety that accompany loneliness are a warning that an individual's social ties have gotten too weak: “It's an aversive signal that motivates us to change our behavior in a way that's good for our genetic survival.” In his view, loneliness is a double-edged sword—adaptive in the short term but dangerous when it becomes chronic.

    Clusters of loneliness.

    Loneliness tends to spread among people on the fringes of social networks, according to a 2009 study. Blue dots represent people who reported feeling lonely three or more days a week, green corresponds to two lonely days, and yellow corresponds to less than two lonely days.

    CREDIT: J. CACIOPPO ET AL., JOURNAL OF PERSONALITY AND SOCIAL PSYCHOLOGY, 97 (DECEMBER 2009) AMERICAN PSYCHOLOGICAL ASSOCIATION

    Cacioppo and colleagues have also found evidence that loneliness has a direct impact on the immune system. In a 2007 study in Genome Biology, Cacioppo teamed up with UCLA genomics researcher Steve Cole and other colleagues to investigate gene activity across the genome in the white blood cells of 14 participants in a longitudinal study of loneliness among Chicago-area residents. The volunteers selected scored in either the top or the bottom 15% of the study cohort on the UCLA Loneliness Scale.

    Two differences between the groups stood out: Lonely people exhibited increased activity for several genes encoding signaling molecules that promote inflammation and decreased activity for genes that normally put the brakes on inflammation. They also showed diminished activity in genes that help mount a defense against viral invaders.

    Cole says that jibes with epidemiologic findings that socially isolated people are more susceptible to viruses, from the common cold to HIV, and to cardiovascular disease, which has been linked to excess inflammation. Cole says the team will soon publish a replication of the findings in a group of about 120 participants in the Chicago study. He notes that just feeling a little left out isn't likely to throw the immune system out of whack. “It really takes a person who has taken and consolidated a lonely view of the world to show these changes in gene expression,” he says.

    Loneliness not only increases wear and tear by keeping the body in alert mode but also may prevent people from recharging their batteries with rest and relaxation. In the March 2010 issue of Health Psychology, Cacioppo and colleagues reported that although lonely people sleep a normal number of hours, they report more fatigue the next day, suggesting that their quality of sleep isn't as good. Segrin says his group has recently replicated this finding and extended it to show that lonely people derive less satisfaction from leisure activities. Their findings are in press at Health Communications.

    The lonely brain

    Studies by Cacioppo and others before him have found that lonely people tend to rate their own social interactions more negatively and form worse impressions of people they meet. Researchers are beginning to show how these biases may be encoded in the brain. In a 2008 study in the Journal of Cognitive Neuroscience, Cacioppo and colleagues used functional magnetic resonance imaging to measure metabolic activity in the brains of 23 undergraduate women at the University of Chicago. Those who were lonelier, as rated by the UCLA Loneliness Scale, exhibited less activation in the ventral striatum, a component of the brain's reward circuitry, when they viewed pictures of smiling faces.

    Unrewarding.

    Lonely people take less enjoyment from social interactions and exhibit less activity (blue) in the ventral striatum.

    CREDIT: J. CACIOPPO ET AL., JOURNAL OF COGNITIVE NEUROSCIENCE, 21 (JANUARY 2009)

    In another study, Cacioppo and colleagues asked lonely and nonlonely people to perform the Stroop test, a workhorse task in experimental psychology in which people see words presented in colored text one by one on a computer screen, then indicate what color it was. When lonely people saw words that evoked negative social interactions, such as “isolate” or “reject,” they took a split second longer to identify the color than they did for negative nonsocial words, such as “vomit.” Nonlonely people showed no such delay. To Cacioppo, the findings, as yet unpublished, suggest that lonely people pay extra attention to negative social cues. “It suggests the brain is on the alert for social threats,” he says.

    A recent study by researchers at Duke University in Durham, North Carolina, meshes with these findings. Neuroscientist Ahmad Hariri and colleagues set out to replicate previous reports that people with anxious tendencies (but not a clinical diagnosis) exhibit more activity in the amygdala, a brain region crucial for threat detection, when they see images of angry or fearful faces. But Hariri's group found that this was true only for the subset of the volunteers who also reported below-average levels of social support. (They did not measure loneliness per se.) To Hariri, the findings, published online 31 August in Neuropsychologia, suggest that people's perceptions of social support may calibrate how the amygdala assesses social threats, which in turn could influence their risk for anxiety disorders or other conditions.

    Loneliness may also affect the prefrontal cortex, a region important for what cognitive scientists call executive control. In daily life, that often translates to restraint—as in not eating cheeseburgers at every meal or putting the stopper back in the wine bottle after one or two glasses. Epidemiological studies have suggested that people with poor social networks are more likely to eat poorly, consume more alcohol, and exercise less. Several studies have found that lonely people perform poorly on lab tests that require executive control, and at least one study, published in the June 2006 issue of Social Neuroscience, found reduced prefrontal cortex activity in socially isolated people.

    Contagious … but curable

    Evidence that loneliness is partly heritable has emerged from a collaboration between Cacioppo and Boomsma, who oversees a database of Dutch twins and their family members. They've found that genetics accounts for up to half of the individual variation in loneliness. Their most recent study, published in the July 2010 issue of Behavioral Genetics, used an abbreviated version of the UCLA Loneliness Scale in a survey sent to 8683 twins and family members. In this group, genetics accounted for 37% of the variability in loneliness, somewhat lower than in some previous studies. Overall, the heritability of loneliness is comparable to that of depression, Boomsma says, but less than that of traits such as high blood pressure and cholesterol levels.

    In his 2008 book, Loneliness: Human Nature and the Need for Social Connection, Cacioppo hypothesizes that there is a “genetic thermostat” for loneliness that's set differently in different people. That setting determines the degree of distress triggered by social isolation. “You're not inheriting loneliness; you're inheriting how painful it feels to be alone,” Cacioppo says.

    But environment matters, too, as studies by Russell have shown. College freshmen rank among the loneliest populations he and his colleagues have studied, because they've left behind their family and high school friends and are trying to find their way in a new social ecosystem, Russell says.

    According to some measures, society is changing in ways that may make people even lonelier. The U.S. Census Bureau estimates that nearly 29 million people live alone in the United States, a 30% increase from 1980. A widely cited 2006 study in American Sociological Review asked a representative sample of the U.S. population how many people they would feel comfortable discussing an important personal issue with. Between 1985 and 2004, the average number dropped from three to two, and the percentage of people who reported having no such confidants rose from 10% to 25%.

    And like certain other health risks, loneliness may be contagious. Cacioppo recently teamed up with James Fowler of UC San Diego and Nicholas Christakis of Harvard University to investigate the spread of loneliness through social networks. Scrutinizing data on thousands of people participating in the Framingham Heart Study, Fowler and Christakis have reported that everything from smoking habits to happiness appears to spread from person to person within social networks (Science, 23 January 2009, p. 454). So, too, can loneliness, the trio reported in December 2009 in the Journal of Personality and Social Psychology.

    The news isn't all bad, however. Even for hard cases, Cacioppo believes loneliness can be overcome. He and colleagues recently conducted a meta-analysis of 20 studies on interventions for loneliness. Simply providing social support doesn't seem to work, especially if people know they're being looked after. “If you know people are stopping by to check on you, it makes you feel like more of a loser,” Cacioppo says. The most effective interventions were those that borrowed methods from cognitive behavioral therapy to shift people's attention and interpretation of social situations in a more positive direction, the team reported online 17 August 2010 in Personality and Social Psychology Review.

    As for preventing loneliness, Cacioppo says it helps to know where your own thermostat is set and strive to stay in your comfort zone. In Loneliness, he writes: “The degree of social connection that can improve our health and our happiness … is both as simple and as difficult as being open and available to others.”

  11. Archaeology

    Did the First Cities Grow From Marshes?

    1. Andrew Lawler

    The world's earliest large settlements may owe their existence as much to the swamps of southern Iraq as to irrigation and agriculture.

    Swamp cities?

    The Iraq marsh may be a last remnant of wetlands that spurred urban evolution.

    CREDIT: CARRIE A. HRITZ/THE PENNSYLVANIA STATE UNIVERSITY

    In his dying moments, Goethe's Faust foresees a happy day when a nearby foul swamp is replaced by green and fertile fields “where men and herds may gain swift comfort from the new-made earth.” He might have had a more benign view of marshlands had he pored over the data gathered by a young archaeologist who recently led the first American archaeological research team to Iraq in a quarter-century. She suggests that cities and civilization didn't rise along riverbanks, as most archaeologists have supposed, but out of swamps, which provided rich animal and plant resources to complement irrigation agriculture and animal husbandry. “Almost everywhere we look,” says Jennifer Pournelle of the University of South Carolina, Columbia, “the biggest and earliest [human settlements] are in that marsh environment.”

    Pournelle is on a quest to understand the role of marshes in southern Iraq between 4000 B.C.E. and 3000 B.C.E., when humans first began to live in a network of cities. After a decade of work with satellite and aerial images, she and two colleagues finally got a chance to see the region up close last September, on an expedition with the University of Basra. She presented the team's findings at a meeting in November and hopes to return to Iraq this year.

    If she is right, says her former adviser, Guillermo Algaze of the University of California, San Diego, “we may have to rethink how Mesopotamian civilization began.” “It's very intriguing,” adds archaeologist Jason Ur of Harvard University. “She's proposing a radically different environmental context for the first cities.” But additional on-the-ground data will be crucial to convince interested but skeptical colleagues.

    Pournelle's view of the importance of marshes goes up against a half-century-old idea that early cities were born along the great rivers of the Near East from advances in farming and irrigation, which created food surpluses that could sustain large settled populations. Archaeologist Robert Adams of the University of Chicago in Illinois, who surveyed southern Iraq in the 1960s and 1970s, found evidence that early settlements were strung along ancient canals or rivers.

    As a graduate student with Adams a decade ago, Pournelle led a project to reconstruct the ancient Mesopotamian landscape by combining archaeological site maps with aerial and satellite imagery. During this initial work, Pournelle noticed that the early settlements—from modest villages to sizable cities—showed up on what appeared to be narrow boat paths through dense marsh. Since then, her colleagues have nearly doubled the number of known ancient sites, which have come into view as the modern marshes have been dried up by drought, Turkish dams, and the actions of Saddam Hussein. “The settlements are not pearls on a chain, or cities on rivers, but are located on delta marshlands,” concludes Pournelle, who became a remote-sensing expert in her previous career as a military analyst interpreting spy satellite data.

    Meanwhile, research on the ancient Persian Gulf environment shows a dramatic rise in sea levels. The waters reached a peak in 4000 B.C.E., flooding the lower reaches of today's southern Iraq and prompting the growth of marsh in the flat, low-lying plain—and coinciding with the growth of the first protocities. Pournelle's remote-sensing studies show that as the waters rose, people built permanent settlements on small ridges, called turtlebacks, that rise only a meter or so above the plain. She believes these ridges offered shelter during flood season and eventually a dry place for storehouses, temples, and administrative centers, some of which have been identified by previous research. These settlements were the core of what became early population centers, such as Eridu, in the 4th millennium B.C.E., and the marshes provided an array of foods and building materials.

    Rising tide.

    Waters flooded ancient Iraq.

    CREDIT: ADAPTED FROM JENNIFER R. POURNELLE/UNIVERSITY OF SOUTH CAROLINA

    By about 3500 B.C.E., other urban centers like Uruk—famed as the first true city and birthplace of writing—were developing on small deltas on the northern fringes of the marsh, formed when water coming from upstream broke into multiple channels. Such locations offered year-round water transportation and less flooding while still providing access to birds and fish.

    Pournelle argues that the role of irrigation in sustaining large populations has been overstated. “At the very least, marsh resources were an important part of a triad” that included agriculture and cattle grazing, she says. The rise of multiple cities around 3000 B.C.E., therefore, was due in part to their proximity to the rich marshes. She notes that delicate fish and bird bones at sites like Eridu and Uruk have been largely ignored by archaeologists, both because of the focus on sheep and goats and because such bones are not easily preserved. The same is true of reeds, which were important but overlooked materials for constructing houses and ziggurats, she says.

    It was the retreat of the Persian Gulf during the 3rd millennium B.C.E. that prompted the first extensive canal systems, Pournelle says. In her view, the canals were a response to this crisis rather than an attempt to expand food surpluses.

    Adams praises Pournelle's scientific work but warns that the distinction between marshes, fields, and grazing land may be more blurred than she contends. He and others say that further on-the-ground work is necessary, and Pournelle agrees. She hopes to return with her team in late spring to drill cores to find more clues to the ancient environment—and, perhaps, insight into how civilization was born of the swamps so despised by Faust.

  12. American Geophysical Union

    Tectonic Blow Ended Mountain Building, Fired Up Volcanoes

    1. Richard A. Kerr

    Fifty-five million years ago, Siletzia arrived on North American shores with nary a bump. But the 500-kilometer-wide chunk of drifting oceanic plate had far-reaching geologic effects across the continent's western third, according to a presentation at the meeting.

    Fifty-five million years ago, Siletzia arrived on North American shores with nary a bump. But the 500-kilometer-wide chunk of drifting oceanic plate had far-reaching geologic effects across the continent's western third, according to a presentation at the meeting. New seismic imaging shows Siletzia throwing a monkey wrench into the gears of the plate tectonics machine and thus reshaping western North America.

    Shutdown.

    The Farallon plate delivered Siletzia, stopping the sinking of the older plate (darker green).

    CREDIT: B. SCHMANDT AND E. HUMPHREYS, GEOLOGY (PRE-ISSUE PUBLICATION DATE, 5 JANUARY 2011) © GEOLOGICAL SOCIETY OF AMERICA

    Before Siletzia arrived, things tectonic were humming along nicely. The Farallon oceanic plate was creeping northeastward and diving into the mantle beneath North America. But unlike most subducting plates, the Farallon plate wasn't diving very deeply. Instead, it was leveling off and sliding hard against the underside of the North American plate. The drag of the Farallon plate tended to squeeze the overlying plate, crumpling its surface into mountains like a wrinkled rug. The mountain building extended as far as the Black Hills of South Dakota and included the Laramie Mountains of Wyoming. But starting about 50 million years ago, the Farallon plate began diving more steeply into the mantle, ending the era of so-called Laramide mountain building. Geologists wondered why.

    The reason subduction steepened, seismologist Eugene Humphreys of the University of Oregon (UO), Eugene, said at the meeting, was the arrival of a thicker patch of the plate called Siletzia. Humphreys and UO colleague Brandon Schmandt reached that conclusion by using seismic waves from earthquakes to image what remains of the Farallon plate in the mantle beneath North America. Using seismic waves the way radiologists use x-rays to form CT images, they drew on the newest records from a dense network of seismometers known as the USArray project (Science, 25 September 2009, p. 1620). “We now have a lot more data,” says Humphreys. “Now I believe the structures we see.”

    Still hangin'.

    Seismic imaging reveals a “curtain” of old ocean plate (blue, right) left dangling since Siletzia arrived 40 million years ago.

    CREDIT: B. SCHMANDT AND E. HUMPHREYS, GEOLOGY (PRE-ISSUE PUBLICATION DATE, 5 JANUARY 2011) © GEOLOGICAL SOCIETY OF AMERICA

    Most geologists think the thicker Siletzia section of the Farallon plate jammed at the edge of the continent and stopped subduction across the Pacific Northwest. In the OU scenario, however, the Farallon plate didn't just stop; it tore clean through beneath the southern edge of Siletzia. That left the remaining shallowly subducting plate to the south to peel off the base of North America and progressively fall away southward.

    As evidence for this scenario, the scientists point to a vertical “curtain” of colder rock they see stretching 600 kilometers down into the mantle beneath Idaho. The curtain, they say, is the dangling remnant of the subducted plate that tore away from the rest of the Farallon plate.

    All of this fits with what geologists have inferred happened at the surface, Humphreys said. The ocean crust melting on the hanging slab would have fueled the so-called Challis volcanism through Idaho and into Canada. The broad loss of shallowly subducting plate would have triggered the switch from North American compression and mountain building to the crustal stretching seen today. And the progressive falling away of Farallon plate would have allowed hot mantle rock to rise and drive the flare-up of volcanism seen to the south.

    The sharper view of the mantle “ties the tectonic history of the crust with what you can now see in the mantle,” says geologist Ray E. Wells of the U.S. Geological Survey in Menlo Park, California. It also helps tie the geology in the north with that in the south, he says: “Now that we can see things under there, they're starting to integrate processes across wide areas.”

  13. American Geophysical Union

    What Heated Up the Eocene?

    1. Richard A. Kerr

    Fifty-five million years ago, carbon dioxide gushed into the atmosphere over as little as a millennium, acidifying the ocean and scorching the world of the Eocene epoch with a 5˚C greenhouse warming. In one presentation, earth systems modelers suggested an ocean source for all that carbon dioxide.

    Talk about your global warming. Fifty-five million years ago, carbon dioxide gushed into the atmosphere over as little as a millennium, acidifying the ocean and scorching the world of the Eocene epoch with a 5°C greenhouse warming. At least two more progressively weaker “hyperthermals” would strike during the next few million years. So where did all that carbon dioxide come from?

    The possibilities are expanding, from the sea floor to an ice-free Antarctica. In one presentation, earth systems modeler Andrew Ridgwell of the University of Bristol in the United Kingdom and his colleagues suggested an ocean source. Earth is always wobbling on its axis like a spinning top, and its orbit about the sun is rhythmically stretching into an ellipse and relaxing to more of a circle. By changing how much sunlight falls at different latitudes in different seasons, these orbital variations can make for exceptionally warm summers with extra-cold winters, for example.

    Ridgwell and his colleagues included orbital variations in a computer model of early Eocene climate, when the world was slowly warming under a strengthening greenhouse. When the orbital variations in the model combined to make an extreme contrast between summer and winter temperatures, the model's ocean circulation would slow and stagnate. That allowed the deep ocean to warm, warming the sea floor. And that's where natural methane hydrates reside—the “ice that burns.” Warm them and they decompose into water and methane. That methane can escape the sea floor, oxidize to carbon dioxide, and warm the world.

    In the next talk, paleoceanographer Robert DeConto of the University of Massachusetts, Amherst, and his colleagues claimed that a larger source of carbon dioxide in Eocene times would have been the permanently frozen ground of polar regions. No ice sheets covered polar ground in Eocene times, and the land area of Antarctica was far larger than it is today, DeConto said. That would have made for widespread permafrost, storing organic matter that—if thawed and decomposed—would yield large amounts of carbon dioxide. In their model, extremes of orbital variations caused permafrost to melt in summer and release its carbon dioxide. Enough would have come out fast enough to drive the observed warming, DeConto said.

    “I think both Andy and Rob may be right,” says paleoceanographer James Zachos of the University of California, Santa Cruz. “I think you're getting contributions from both.” Bad news for future warming.

  14. American Geophysical Union

    Worry But Don't Panic Over Glacial Losses

    1. Richard A. Kerr

    Glaciers are suddenly galloping to the sea in Greenland and the "weak underbelly" of Antarctic ice is beginning to give way, but a couple of glaciologists at the meeting say that at least in the short term, the situation, while bad, is not always quite as bad as it looks.

    With glaciers suddenly galloping to the sea in Greenland and the “weak underbelly” of Antarctic ice beginning to give way, it's hard to keep a cool head, but a couple of glaciologists at the meeting gave it a try. At least in the short term, they said, the situation, while bad, is not always quite as bad as it looks.

    Glaciologist Ian Joughin of the University of Washington, Seattle, reported on his and his colleagues' study of the forces acting on the Jakobshavn Glacier of southern Greenland. Jakobshavn accelerated toward the sea early in the decade after warming ocean water destroyed part of its floating ice tongue that had been helping to restrain it.

    Jakobshavn is still accelerating and thus increasing the rate of sea level rise—plenty of cause for worry—but Joughin cautioned that Jakobshavn is not totally off its leash. Judging by the glacier's behavior from season to season, restraining forces such as friction with rock at the glacier's sides will likely keep it from accelerating by more than a factor of 3 in this century, not the factor of 10 sometimes bandied about. And even at the slower rate, by 2100 it will have retreated up onto dry land, where friction must slow it greatly.

    Faster.

    Jakobshavn Glacier's acceleration has its limits.

    CREDIT: AMAP/© KONRAD STEFFEN/CIRES/UNIVERSITY OF COLORADO

    Still, glaciologist Richard Alley of Pennsylvania State University, University Park, saw cause for some worry as well. Glaciers draining the West Antarctic Ice Sheet are also flowing faster these days. New ocean warmth has melted the floating tongues of some glaciers there, loosening their hold on bumps on the sea floor that had been restraining glacier flow and accelerating ice loss. Flow will slow only when the ice again becomes stuck on a sea-floor bump somewhere farther upstream. Such pulses of ice loss are inevitable and for many glaciers unpredictable, Alley warned, because no one is sure where the bumps are.

    If researchers are going to predict such glacial surges, “we'll need to understand what's under the ice,” notes glaciologist Robert Bindschadler of NASA's Goddard Space Flight Center in Greenbelt, Maryland. In the meantime, he advises not focusing on just a few glaciers like Jakobshavn. “If we do,” he says, “we're likely to get too excited when they accelerate and too relieved when they pause.” His advice: Keep your eye on measures of the overall losses from an ice sheet. Those will be steadier, and plenty worrisome.

  15. American Geophysical Union

    Snapshots From the Meeting

    1. Richard A. Kerr

    Snapshots from the meeting include new evidence showing that the Sierra Nevada mountains of east-central California are rising at the rate of about 1 millimeter per year and geophysical quirks that worsened the air-traffic disruption caused by the eruption of the Eyjafjallajökull volcano.

    Showstopper.

    Several characteristics of Eyjafjallajökull worsened air-traffic disruption.

    CREDIT: JOHANN HELGASON/ISTOCKPHOTO.COM

    Whoa there! Geodesists have found that the Sierra Nevada mountains of east-central California are rising so fast that they could have achieved their 3-kilometer height in just the past 3 million years, not the past 30 million years, as suggested by some geologists. William Hammond of the Nevada Bureau of Mines and Geology in Reno and his colleagues reported that GPS measurements combined with satellite radar observations of vertical ground motions show the central and southern Sierras are rising at about 1 millimeter per year. “If that number stands, it would be a rip-roaring uplift rate,” says geologist Craig Jones of the University of Colorado, Boulder.

    Hammond says the high rate across so much of the Sierras argues that they aren't bouncing upward after a heavy piece of the continental plate beneath them peeled off and fell into the mantle. Instead, some aspect of the West Coast's helter-skelter plate tectonics must be responsible.

    Blame all around. Remember those millions of airline passengers kept from the skies last spring by the ash of that unpronounceable Icelandic volcano? They can fault any number of geophysical quirks, according to volcanologists gathered at the meeting. There was the persistently ill-directed wind that blew over Eyjafjallajökull volcano toward Europe, of course. But other factors peculiar to Eyjafjallajökull combined to aggravate the problem. Magma melted glacial ice on the summit of the volcano and drove the water to steam that energized the early phase of the eruption, raising a high plume full of particularly fine, far-traveling ash. In addition, the magma carried an unusual amount water of its own. And it was a particularly thick, sticky magma for an Icelandic volcano, which made for an even more explosive eruption.

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