News this Week

Science  03 Feb 2012:
Vol. 335, Issue 6068, pp. 508

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  1. Around the World

    1 - L'Aquila, Italy
    Italian Official Another Defendant in Earthquake Trial
    2 - Tokyo
    Japanese Experts Question Safety of—and Need for—Nuclear Power
    3 - Iquitos, Peru
    Andes Biodiversity Threatened
    4 - Lead, South Dakota
    Nobelists Lobby for Gigantic Neutrino Experiment

    L'Aquila, Italy

    Italian Official Another Defendant in Earthquake Trial


    Former Italian Premier Silvio Berlusconi (left) and Guido Bertolaso survey earthquake damage near L'Aquila.


    The former head of Italy's civil protection department, Guido Bertolaso, will be investigated for manslaughter alongside seven scientists and technicians who are currently on trial for allegedly having carried out a superficial seismic risk analysis and giving a false sense of security to people in the central Italian town of L'Aquila only days before the deadly earthquake of 6 April 2009 struck, killing 308 people.

    Bertolaso was implicated by a recording of a 30 March 2009 phone conversation between himself and regional civil protection officer Daniela Stati, a day before the seven experts met to discuss a seismic “swarm” in the region that had lasted several months. In the conversation, Bertolaso told Stati that the experts, members of a government advisory body known as the National Commission for the Forecast and Prevention of Major Risks, were to meet up “not because we are frightened and worried” by the tremors but because “we want to reassure the public.”

    The trial started last September, but with nearly 300 witnesses scheduled to testify, it is likely to last until at least the autumn.


    Japanese Experts Question Safety of—and Need for—Nuclear Power

    Japan is preparing for the possibility of a summer without nuclear power as utilities and safety experts squabble over the safety of the country's remaining reactors. Of Japan's 54 nuclear reactors, only three are currently operating, and they must shut down for periodic inspection by the end of April.

    In the wake of the Fukushima disaster, last summer the governing Democratic Party of Japan required “stress tests,” analyses of a facility's ability to withstand natural disasters, to be part of periodic inspections. Based on that analysis, Japan's Nuclear and Industrial Safety Agency (NISA) has concluded that two reactors at a plant in Ohi on the Japanese sea coast have passed. Operator Kansai Electric Power is seeking approval to restart the two reactors.

    But on 27 January, two members of a NISA advisory committee called the stress tests flawed, noting that the criteria for the tests should reflect new lessons from Fukushima, but that studies of the sequence of events that led to the disaster are still ongoing.

    A new national energy policy is due by the end of the summer, and observers expect it could call for a phase-out of nuclear power. A sudden and permanent shut down of all reactors, however, would be a huge surprise.

    Iquitos, Peru

    Andes Biodiversity Threatened

    At risk?

    The Cloud-forest Screech-owl (top) and the Black-faced Brush-finch are endemic to the Andes.


    A survey of herbarium and museum records dating back a century, combined with remote sensing data about vegetation and climate, has shown that despite large national nature reserves in Peru and Bolivia, a surprising number of endemic species are still unprotected there. Duke University's Jennifer Swenson and her colleagues compiled location and habitat information from 7000 specimens representing about 700 endemic plants, amphibians, birds, and mammals living in 1.25 million square kilometers of the eastern slope of the Andes. They predicted the current ranges of these species using satellite information to identify similar habitats where the species might also live. Birds and mammals were most diverse at about 2700 meters, with amphibians thriving at approximately 1200 meters, the researchers reported last week in BMC Ecology. The report noted that about 80% of the areas most in need of preservation are vulnerable. “The current protected areas aren't doing the best job” of saving biodiversity, comments Toby Pennington, a botanist at the Royal Botanic Garden Edinburgh in Scotland.

    Lead, South Dakota

    Nobelists Lobby for Gigantic Neutrino Experiment

    Forty-two theoretical physicists, including three Nobel laureates, sent a letter 19 January to the U.S. Department of Energy (DOE), urging it to build an enormous particle detector that they say is key to the United States' future in particle physics. The Long Baseline Neutrino Experiment would lurk in the abandoned Homestake gold mine in Lead, South Dakota, and snare particles called neutrinos fired 1300 kilometers through Earth from Fermi National Accelerator Laboratory (Fermilab) in Batavia, Illinois. If built deep enough, so that background radiation levels are very low, the detector could search for very weak signals, such as signs that protons decay, and detect neutrinos from supernovae. “This project is absolutely crucial to having a world-leading program in the United States,” says Jogesh Pati, of SLAC National Accelerator Laboratory in Menlo Park, California.

    The letter doesn't guarantee that DOE will build the $1.5 billion detector. In July 2010, 38 theorists, including the same three Nobelists, wrote to Secretary of Energy Steven Chu urging DOE to run Fermilab's atom smasher, the Tevatron, through 2014. But with Europe's higher-energy Large Hadron Collider up and running, DOE decided to shutter Tevatron last September as scheduled.

  2. Random Samples


    Light bulb moment: Thomas Edison is still number one when it comes to invention. The 2012 Lemelson-MIT Invention Index surveyed Americans aged 16 to 25 for their perceptions on invention. Asked to name who they thought was the greatest innovator of all time, 54% of the 1000 respondents named the inventor and holder of more than 1000 U.S. patents—taking a bite out of second-place holder and Apple Inc. co-founder Steve Jobs, who weighed in at 24%.

    Spider Can Inseminate Female From Afar


    The orb-web spider Nephilengys malabarensis is into rough sex—so rough that the male will often voluntarily break off his whole sex organ, or palp, while it's still lodged in the female's abdomen, rather than risk being eaten alive by her. Now a group of researchers think they know why evolution has allowed this dead-end dad to survive. They collected 25 pairs of spiders and introduced them to one another. After each pair had mated and the male's palp was left in the female, the researchers dissected the female and counted the sperm in her abdomen and the amount remaining in the embedded palp. That organ, they reported online 31 January in Biology Letters, continues to transfer sperm into the female long after the male has fled or been consumed. The longer it's embedded, the more sperm it transfers, and it's even more efficient when the male breaks it off himself to run away, rather than letting the female do it while eating him.

    They Said It

    “I think that there are ways … to recognize the sanctity of life, but nonetheless to look at fertility clinics where there are cells that are sitting there that are not going to be used to create life. … I hope the president will find a way to agree that there ought to be federally funded research.”

    —Newt Gingrich on 19 July 2001 discussing embryonic stem (ES) cell research

    “[Stem cell research] was the use of science to desensitize society over the killing of babies.”

    —Newt Gingrich 28 January. The next day, he vowed to ban ES research should he be elected president.

    Making Choices


    Women biochemists of all ages consider family-related factors to be as important as their professional surroundings in making career decisions, while their male counterparts place much more weight on working conditions. Some 1780 members of the American Society for Biochemistry and Molecular Biology answered a survey last year on the roles of gender and family in academic biochemistry. The survey, a first for the society, also found that the number of women in the academic workplace matches the number of men through the post-doctoral level but that men hold the lion's share of tenure-track and tenured positions.

    By the Numbers

    $5.7 billion The amount the Swiss drug company Roche Holding AG has offered in a hostile takeover bid for the San Diego–based DNA sequencing company Illumina.

    2% Percentage of plant collectors who have found more than 50% of the world's known species, according to a study in the Proceedings of the Royal Society B.

    Rock-a-Day Calendar


    A British seismologist has a geologic twist on the classic nightstand “word-a-day” calendar: the daily rock. In 2010, scientist-turned-shutterbug Ian G. Stimpson of Keele University in the United Kingdom set out to photograph a different rock for each day of the year, a project he dubbed Rock 365. And, as of 2012, he's back at it, posting new daily rock photos to Flickr and to his blog, Hypocentre. “How do you get better than Rock 365?” he asks. “You leave it to the leap year and do Rock 366.”



    For inspiration, Stimpson has turned to his university's large rock collection, which includes sheared limestones, trilobite fossils, and garnet-bearing schists (pictured) gathered from around the world. Digging through the collection was a learning experience, even for the veteran rock buff. He stumbled across rocks he wasn't familiar with—sometimes to his detriment. He handled a sample of orpiment, for example, before learning that it was an arsenic sulfide mineral.

    Toxins aside, Stimpson says his blogging marathon can be exhausting—not to mention inconvenient. At one point, he says, he found himself facing his own deadline while stranded in the airport at Casablanca, Morocco, without a geologic feature in sight. But when in doubt, look down: He turned his camera to the airport's granite floor. And this year, Stimpson plans to set sail on a cruise to the Baltic Sea for his 50th birthday. His solution for the days away from terra firma: A set of rocks, packed in his suitcase.

  3. Newsmakers

    Leukemia Drug and Magnet Material Net Japan Prizes

    A trio of American researchers will share one of this year's Japan Prizes for bringing their work on a leukemia drug from a basic discovery to a clinical success, while a Japanese materials scientist is taking the other prize for a breakthrough with permanent magnets.

    Clockwise from top left: Druker, Rowley, Sagawa, and Lydon.


    Janet Rowley of the University of Chicago, Brian Druker of the Oregon Health & Science University in Portland, and Nicholas Lydon of Blueprint Medicines in Cambridge, Massachusetts, jointly won the Healthcare and Medical Technology prize for developing a leukemia drug called imatinib, better known as Gleevec in the United States and Glivec elsewhere. Now used as a once-a-day pill, the drug has made chronic myelogenous leukemia (CML), once fatal within 3 to 5 years, “a manageable disease,” Druker said at the prize announcement press conference 25 January.

    Masato Sagawa, of Kyoto-based Intermetallics Co., won the prize in the field of Environment, Energy, and Infrastructure for work on the neodymium-iron-boron alloy which constitutes the high-performance permanent magnets at the heart of energy-efficient motors used in everything from hard disk drives to construction equipment.

    The three healthcare laureates will equally share one $650,000 award; Sagawa alone gets an equal sum. All four will receive their awards at an April ceremony in Tokyo.

    White House Gives Up on NOAA Science Chief Nomination

    The White House formally withdrew its nomination of geochemist Scott Doney, a senior scientist at the Woods Hole Oceanographic Institution in Massachusetts, to be chief scientist of the National Oceanic and Atmospheric Administration (NOAA) on 24 January. A U.S. Senate vote on Doney's nomination had been blocked for more than a year by Senator David Vitter (R–LA), who was unhappy with the Obama Administration's decision to impose a moratorium on offshore drilling in the wake of the April 2010 explosion of the Deepwater Horizon drilling rig in the Gulf of Mexico.

    Under U.S. Senate rules, a single lawmaker can place a “hold” on a nomination, effectively preventing a vote. Doney's nomination had been approved by a Senate committee, but never got a vote in the full Senate after Vitter announced a hold in December 2010.

    The withdrawal marks another setback for NOAA chief Jane Lubchenco. House Republicans have blocked her efforts to establish a new Climate Service within NOAA, and Doney's nomination marked an effort to raise the profile of the chief scientist's position. In October 2009, she announced a NOAA reorganization that included “reinstituting and elevating the role” to a presidential appointment.



    A Colorful Addition to a Berlin Museum

    With his signature mustache and a tendency toward floral ties, Johannes Vogel will be hard to miss in the halls of Berlin's Natural History Museum. Vogel, an expert on fern genetics, took over as director of the museum on 1 February. He had been Keeper of Botany at London's Natural History Museum since 2004. Vogel says his top priority for the new job will be shaping the Berlin museum as a bridge between science and the public, in part by increasing the visibility of the behind-the-scenes research. “I want people to see the live part, the part that is yet to be discovered,” he says. He'd also like to make the museum's 30-million zoological and geological samples more publicly accessible. “Amateur naturalists know more about some groups [of samples] than experts in the museum,” says Vogel, whose job comes with the honorary title professor of biodiversity at nearby Humboldt University. Ideally, he says, the museum would set up a glass-walled “biodiversity discovery factory” in which automated scanners could process samples, categorizing known species and flagging new ones, in full view of visitors.



    Vogel is mildly famous for his family connections as well. His wife, botanist Sarah Darwin, is the great-great-granddaughter of naturalist Charles.

    Wolf Prize Winners Announced

    Two U.S. nanoscientists are among this year's Wolf Prize winners, which recognize researchers at the top of their fields in chemistry, physics, mathematics, medicine, agriculture, and the arts.

    Like the other four scientists revealed on 19 January by Israel's Wolf Foundation, the chemistry duo honored—Paul Alivisatos of the Lawrence Berkeley National Laboratory in California and Charles Lieber of Harvard University—will take home a not-so small prize: $100,000. Alivisatos was recognized for his exploration of nanocrystal structure and design, while Lieber was noted for his work in building nanowires.

    The other awardees include physicist Jacob Bekenstein of the Hebrew University of Jerusalem, a prominent black hole researcher. Ronald Evans, a hormone guru at the Salk Institute in San Diego, California, will receive the Wolf Prize in medicine. Mathematicians Michael Aschbacher of the California Institute of Technology in Pasadena and Luis Caffarelli of the University of Texas, Austin, will each also walk away with a prize. Perhaps the biggest name in the awards this year, however, isn't a scientist: Famous tenor Placido Domingo has also won in recognition of his long tenure in music.

  4. Genomics

    China's Sequencing Powerhouse Comes of Age

    1. Dennis Normile

    With new sequencing centers in Europe and the United States, BGI hopes its growing clout will help deliver the benefits promised by genomics—and revenue to pay off a mounting debt.

    Heavy artillery.

    BGI claims it has more sequencing capacity than the entire United States.


    SHENZHEN, CHINA—On the sidelines of a genomics conference here last November, immunologist Lennart Hammarström sat down for a preliminary discussion with officials of the genome sequencing powerhouse BGI-Shenzhen. Hammarström, of the Karolinska Institute in Stockholm, had concluded that the best way to identify genetic mutations behind primary immunodeficiency disorders would be to sequence patient genomes. He hoped to gauge BGI's interest in cooperating—and got more than he expected. After 2 hours they had agreed on a vision and decided, “Let's do it,” he says. At the end of his presentation 2 days later, Hammarström donned a BGI T-shirt and with BGI Director Wang Jian signed an agreement under which the Shenzhen institute will sequence thousands of patient samples, the two sides will exchange graduate students, and Hammarström will head a new department of immunogenetics at BGI. Hammarström was awed by how quickly it all came together. “It's BGI speed, the speed of light,” he says.

    Such dealmaking is a central element of BGI's improbable emergence as a genomics superpower. Unlike other major sequencing centers that are attached to institutes with inhouse biology expertise and long-standing scientific programs, BGI, since its inception in 1999, has focused on developing its sequencing and bioinformatics capabilities while turning to outside teams in crop science, human disease, and microbiology to help define its research objectives.

    As a result, BGI has become the go-to organization for groups in need of sequencing. At the meeting, BGI inked deals with Johns Hopkins University in Baltimore, Maryland, to work on synthetic yeast and with the International Rice Research Institute (IRRI) in Los Baños, Philippines, to study genomic diversity of 3000 rice strains. Earlier last year, BGI agreed to collaborate to sequence 5000 cassava varieties and 10,000 autism patients and family members, and do heaps of sequencing for the international Human Variome Project (Science, 16 December 2011, p. 1487). And it's looking for partners on its own audacious goal to sequence a million human genomes, a million plant and animal genomes, and a million microbial genomes. To foster closer collaboration, BGI is establishing two sequencing centers in the United States and one in Europe, with more in the offing. The growing web of partnerships is turning BGI into the only genomics enterprise with a global footprint.

    In building its empire, BGI has made a huge gamble. To fuel its growth, BGI has borrowed heavily from a $1.5 billion line of credit from a government-owned bank—debt it must start to pay back in 10 years. Elsewhere, governments have invested in genomics and sequencing centers with the expectation of future payoffs in medicine and other areas. But none has taken as entrepreneurial an approach as China has in counting on a single institute to recoup its investment.

    BGI's triumvirate.

    From left: Chair Yang Huanming, Director Wang Jian, and Executive Director Wang Jun.


    Competitors are puzzled by the BGI phenomenon. “I don't think their model is very different in terms of interactions [with researchers],” says Richard Gibbs, director of the Human Genome Sequencing Center at Baylor College of Medicine in Houston, Texas, one of the big three sequencing centers funded by the U.S. National Human Genome Research Institute (NHGRI). Applying genomics to biomedicine is “pretty straightforward” in matching sequencing technology and expertise with funding and science, he says. Others worry that BGI's sheer size and mounting debt could skew priorities across the field if sequencing projects are determined by the likelihood of a payoff. Jack Gilbert, an environmental microbiologist at the University of Chicago and Argonne National Laboratory in Illinois, collaborates with and admires BGI. Nonetheless, he worries, “If one organization dominates the market and has an agenda, this could be bad for innovation in science.”

    BGI officials say they are not bent on world domination. “I don't think this is the only [sequencing] model that fit s the entire field and should not be the only model,” says BGI Executive Director Wang Jun. But he adds that their approach to genomics “is probably a model no one else could easily follow.”

    As a research institute sponsored by the Shenzhen municipal government, BGI has set up private nonprofit institutes in Hong Kong, Europe, and the United States to manage its sequencing centers. It owns private companies that offer sequencing and clinical services. BGI also has a college in Shenzhen it hopes to turn into a university and an annual genomics conference, and it is launching a journal, GigaScience. Wang says they are simply trying to attract sufficient resources “to prove that the genome matters.”

    Seizing the day

    According to BGI brass, the center's rise was happenstance. “We went one step by one step,” says Yang Huanming, BGI's charismatic chair. “I don't think BGI had a long-term strategy, but it did have long-term dreams and it has been opportunistic,” adds Gane Ka-Shu Wong, a biosystems informaticist at the University of Alberta in Edmonton, Canada, who has been a BGI associate director from the start.


    Yang, Wang Jian, and a handful of colleagues formed Beijing Genomics Institute in 1999 to give their homeland a foothold in sequencing. That year, backed by seed funding from the Chinese Academy of Sciences (CAS) and promises of further government support, Yang persuaded the in ternational Human Genome Organisation to allow China to sequence 1% of the human genome. It was the only developing country in the landmark project, a fact that dominated news coverage in China when sequencing was completed in 2001.

    As work on the human genome wound down, BGI faced a problem: It had 150 people, sequencing machines, and supercomputers but no continuing funding. To win grants, “we had to do something else,” Yang says. They took aim at the rice genome, a project BGI initiated with Chinese partners. By the time they reported the draft sequence in Science in 2002, BGI's payroll had swelled to 300, and it was even hungrier for grants. “We decided we would take on any problem related to genomics,” Yang says.

    BGI joined with domestic partners and won grants for other sequencing projects deemed important for China's economy or prestige, including the chicken, silkworm, and panda genomes. And it expanded its overseas ties. BGI participated in the International HapMap Project, among others. In the process, it developed a recipe for success in its collaborations. For example, to tackle the pig genome, BGI took charge of sequencing and bioinformatics while Danish partners handled functional analysis. Every step of the way, Yang says, they sought to drive down costs, increase speed, and cover expenses.

    Room to grow.

    BGI is looking to agriculture and other fields to boost its revenues.


    In late 2003, riding political support for having quickly sequenced several strains of the SARS virus, BGI became a CAS institute. But it was a poor match. “There was serious conflict between CAS and BGI,” Yang says. CAS institutes have an academic structure, with senior scientists often heading small teams. BGI was building a large-scale sequencing operation staffed with an army of programmers and bioinformaticists. More important, Yang says there was little recognition of the importance of sequencing. There was “almost nothing” in funding for sequencing in China's 5-year plan that ended last year, he says.

    Shenzhen's government came to the rescue. In 2007, the prosperous special economic zone, eager to expand its economic base beyond manufacturing, offered 20 million yuan ($3.2 million) per year for 4 years and found BGI a home in a former shoe factory. Conflicting visions split BGI's scientists. Some chose to remain under CAS as the Beijing Institute of Genomics while Yang and his supporters decamped to Shenzhen.

    In early 2010, BGI hit the jackpot when the China Development Bank extended a 10 billion yuan ($1.58 billion) line of credit. The bank finances projects in line with central government policy, which includes support for biotech, Wang Jun says.

    BGI immediately bought 128 Illumina HiSeq 2000 sequencers, e ach capable of sequencing a human genome in a week. In one stroke, BGI acquired more sequencing power than any other center in the world. Winning an arms race was not the objective, Wang Jun says. “We just did a rough calculation: If we sequence the major farm animals and sequence the major medical genomes, how many instruments do we need?” They also predicted that the Illumina machines would not be trumped by a new generation of sequencers for at least 3 years.

    BGI Projects


    View a map of major genomics projects BGI is undertaking with international partners.


    Massive sequencing capacity is one prong of BGI's strategy. It has also strived to blaze a trail in bioinformatics by developing free software for the community. “They've been astonishingly open in the whole [bioinformatics] effort,” says Mark Edwards, a plant geneticist at Southern Cross University in Lismore, Australia.

    Bioinformatics has become increasingly important as sequencing volume has grown. For example, a BGI-Danish project called LuCamp sequenced all exomes, the genome's coding regions, of 1000 patients with metabolic disorders and 1000 controls. The project “was the first of its kind,” says team member Rasmus Nielsen, a computational biologist at the University of California, Berkeley. Earlier disease-related genomics efforts involved more limited sequencing and produced less data. Before starting, “you need to know how many samples and to what depth you have to sequence to maximize the statistical power to identify a particular gene or loci that is associated with a disease,” says Li Yingrui, who headed BGI's bioinformatics for LuCamp. The project required simulations and new statistical models on scales not previously attempted. Sequencing was completed in 2010; the first report from the ongoing functional analysis appeared in Nature Genetics in October 2010.

    Li's role in LuCamp highlights another facet of how BGI does things differently. When the project started in 2008, he was 21 years old and cutting master's degree courses, preferring to work on a real-world problem. “The textbooks are all behind the cutting edge,” Li says.

    When BGI put a student in charge of bioinformatics and staffed LuCamp with 20-somethings, its partners were understandably anxious. “We worried about whether they could deliver, given that most of the people working on the project were not trained scientists,” Nielsen says. But the team delivered the goods.

    Li eventually dropped out of grad school—“it was kind of a waste of time,” he says—and now heads a 400-strong group at BGI exploring future technologies.

    A package deal

    The dramatic decline in sequencing costs, from $50,000 for a human genome 5 years ago to approaching $1000 today, was expected to spur a “democratization” of sequencing. Instead it is sparking more-ambitious sequencing plans with ever-more-complex logistics and bioinformatics. That plays to BGI's strength, which is “the integration of both the sequencing and the bioinformatics,” Nielsen says. And it explains BGI's attraction to its growing stable of partners. For the rice project, after BGI sequences thousands of rice strains, IRRI intends to link biological characteristics to sequence data—in other words, connect phenotype to genotype. It aims to identify genes for desirable traits such as drought tolerance, pest resistance, and grain quality to improve commercial varieties. “BGI is the only one with the muscle” to carry out such a massive effort—sequencing 3000 strains and possibly 7000 more later—in a reasonable amount of time, says IRRI plant geneticist Hei Leung.

    Early achiever.

    Li Yingrui, 25, leads a 400-strong team.


    Hammarström, meanwhile, hopes to unravel the genetics of immune disorders. He and others have hunted for disease-related genes by looking at single-nucleotide polymorphisms in the genomic region associated with the major histocompatibility complex (MHC), a cell surface molecule that is key to the immune response. That approach has come up empty-handed, Hammarström says. Unraveling the genetics is tricky because many conditions are rare and likely involve multiple genes, hence the need for a huge number of samples. BGI will sequence the MHCs or exomes of 100,000 patients and controls in 5 years. The plan is “ambitious, yes, but within reach,” Hammarström says.

    The Center for Applied Genomics of Children's Hospital of Philadelphia (CHOP) is also partnering with BGI. CHOP and BGI had originally hoped to get NHGRI funding to set up a new sequencing center. When it became clear they would not win support, the two institutes dipped into their own resources to establish BGI@CHOP. Pediatrician Hakon Hakonarson, the center's director, says CHOP is already basing clinical decisions on the likely efficacy and side effects of medications by comparing patients' genotypes with samples in the hospital's biobank—the largest of its kind, with samples from most pediatric diseases along with data on medication, response, and side effects. Through whole-genome sequencing of samples, they expect to make more comprehensive and precise clinical decisions. “This is the future of medicine,” Hakonarson says.

    To execute this plan, BGI will set up a sequencing center at CHOP. It will start with 10 sequencers and could later add up to 40 more. One big advantage of the U.S. operation, Hakonarson says, is that BGI will have a better shot at winning National Institutes of Health grants. He envisions half of the sequencing capacity set aside for studies using CHOP's biobank and half for BGI's non-CHOP projects.

    CHOP is one of three beachheads that BGI is establishing outside China. Over the past year, it has announced plans to also set up sequencing operations in Copenhagen and at the Sacramento campus of the University of California, Davis. Centers are being mulled for southern Europe, Japan, and Australia. Baylor's Gibbs welcomes BGI's American ventures. “We're thrilled that we've got more people in the mix,” he says. He believes the U.S. centers have an advantage over BGI in expertise integrating sequencing, bioinformatics, and biology.

    Day of reckoning

    BGI may not be able to sustain its breakneck pace forever. Yang says that although BGI can sequence more economically than anyone, “we do not make money on it.” Thanks in part to services such as prenatal screening and genetic typing for bone marrow or organ recipients, BGI had about 1 billion yuan ($158 million) in revenue in the year through March 2011—enough to break even, Wang Jian says. They pay interest on the debt but must start paying back principal in 10 years. To generate more income, BGI is expanding its applied research portfolio. It launched an agricultural department in 2009 to use genomic techniques to improve cultivars, particularly of overlooked crops such as foxtail millet. BGI is developing genetically modified minipigs as models for breast cancer and degenerative diseases such as Alzheimer's and atherosclerosis, and it has high hopes for payoffs from synthetic biology.

    With partners in diverse fields, BGI could be better positioned than its rivals to benefit if genomics begins to produce long-promised rewards. “They're being very intelligent about picking their collaborators,” says Richard Cotton, a geneticist at the University of Melbourne in Australia who works with BGI on the Human Variome Project. “In the next 10 years,” Wang Jun predicts, “we will be able to develop something useful for ordinary people.” That may allow BGI to begin paying down its massive loan.

    BGI's day of reckoning is at least a decade away. For now, its bold ambitions are carrying the day. “They make you realize the sky is the limit,” Hammarström says.

  5. Ecology

    Rebuilding Wetlands by Managing the Muddy Mississippi

    1. Carolyn Gramling

    When spillways were opened to divert the flooding Mississippi last spring, scientists studying the waters sought data that might help restore the river's eroding delta.

    Water unleashed.

    The Mississippi pours through the 10-ton floodgate of the Morganza spillway.


    The Mississippi delta is in trouble. The thick lobe of sediments at the river's mouth—called the Bird's Foot delta for the three tributaries radiating from the main river channel into the Gulf of Mexico like the flexing claws of a large bird—marks where the mighty river has poured into the Gulf of Mexico for the past 600 to 800 years. Seasonal flooding along the river once swept pulses of sand, silt, and clay to the coast, forming a foundation for the vast wetlands. But these days, a complex network of humanmade river channels, levees, and dams, intended to control the river and save coastal communities from flooding, has cut sediment supply to the delta in half. Rising sea levels due to climate change and lowering land surface from groundwater pumping and oil and gas extraction are also taking their toll.

    The result of this perfect storm of problems is that the delta's coastal wetlands—one of the most storied ecosystems in the world—are now rapidly ebbing away. River-borne sediments took about 7000 years to build the roughly 21,000-square-kilometer Mississippi delta region, but the ocean has reclaimed much of it in only a century. “Land loss and gain is closely coupled to the course and management of the Mississippi River and its sediment load,” says Alex Kolker, a geologist at Louisiana Universities Marine Consortium in Chauvin. Since 1900, he notes, about 4900 square kilometers of land have been lost—an area roughly the size of Delaware.

    The shrinking delta is a critical problem, and not just for naturalists: Louisiana's coastal ecosystem is big business, home to commercial and recreational fishing industries worth $3.5 billion a year, and the wetlands harbor plant and animal species that attract more than $220 million in tourism each year. And as the deadly impact of 2005's hurricanes Katrina and Rita highlighted, robust wetlands and barrier islands could also act as a natural buffer for the coast against storm surges and waves.

    Coastal managers and scientists have struggled to find ways to restore water flow through the wetlands and bring back the sediment. Oddly, a recent natural disaster, the 2011 Mississippi River floods, suggests that answers to the sediment-resupply problem may lie in some of the very coastal-management structures erected to chain the river. “No one had any idea, when [these structures] were put in place in the past century, that they could be used for rebuilding or restoring wetlands,” says Jeffrey Nittrouer, a geologist at the University of Illinois, Urbana-Champaign.

    The April and May 2011 floods along the Mississippi River—the second largest on record in the region, after the floods of 1927—claimed several lives and cost as much as $4 billion in damage. The toll would have been still higher, but to divert floodwaters bearing down on Baton Rouge and New Orleans, the U.S. Army Corps of Engineers controversially, and for the first time since 1973, decided to open the Morganza spillway.

    The released water flooded some oyster farms and crops and threatened towns downstream. But to Kolker, Nittrouer, and others interested in preserving or rebuilding the Mississippi delta, opening that spillway did offer a rare opportunity to conduct a large-scale natural experiment in real time. Some coastal managers and researchers have suspected that properly managing the Mississippi's annual floodwaters might be the most effective way to bring the sediment back to the wetlands. The idea, Kolker says, would be to partially divert the Mississippi, timing those diversions “so that you open them widest during a large flood and then close them during low-flow periods.”

    But there's a lack of data concerning how diverting the river might affect the large loads of sediment the floodwaters carry. Or at least there was until researchers such as Kolker and Nittrouer, many aided by rapid-response grants from the U.S. National Science Foundation, scrambled last spring to document the impact of the spillway's flooding on the delta. “We knew this was going to be a large event,” Kolker says. “The nice thing about a river flood is you can see it coming.”

    The natural experiment, as several research teams reported at the American Geophysical Union (AGU) meeting in December, gave mixed results: The floodwaters did carry enough sediment to help rebuild the wetlands, but that material didn't always stay where it could do the most good. However, Nittrouer notes, researchers gained valuable insights from the 2011 diversions—including ideas about how spillway design can help produce more targeted sediment deposits, and what volume of flow through the spillways might be required for effective wetland rebuilding.

    Parting the waters

    Before last year, Nittrouer and other scientists couldn't answer basic questions about what happens to the Mississippi's sediment during a large, managed flood. “There are no real strong science publications on coastal management and diversions,” Nittrouer says. For example, it wasn't clear if the released sediment would reach the wetlands or stay there, or even whether managed floodwaters actually carry enough sediment to make a difference. Even with managed diversions, the land might submerge faster than it could rebuild.

    When the Army Corps flipped the switch on the Morganza spillway on 14 May 2011, some answers to those questions began to rush in. This spillway diverts waters from the main Mississippi channel into the broad, shallow Atchafalaya Basin, just to the west of the river, and daily satellite images soon revealed a huge plume of sediment making its way through the basin. Keeping an eye on those images, Nittrouer and his team set to work on the ground, mapping not only the plume's path but also the volume and distribution of the sediment at different depths within the water. They also assessed the distribution of sediment sizes in the water, from sand to silt to clay. Cores in existing wetlands, he says, reveal that sand is best for wetland- and delta-building, because the larger grains settle out of the water earlier, and sandy sediment is easier for plants to colonize.

    Muddy waters.

    A surge of sediment carried by the Mississippi and Atchafalaya rivers reached the gulf on 17 May 2011.


    Kolker, too, was tracking the progress of the floodwaters and the plume of sediment, using current meters, salinity, and temperature data. His team found that most of the sediments in the floodwaters diverted through the Atchafalaya Basin ultimately went out onto the shelf rather than remaining in the basin. It's a disappointing result, he says, although not really a surprise. But what was heartening, he adds, is the volume of sediment in the floodwaters: “What this means in terms of coastal restoration is that these floods bring in huge pulses of material—and we have to figure out ways to keep these materials in the nearshore zone.”

    Nittrouer says he was also encouraged by the volume of sediment his team found in the floodwaters. Another useful piece of information, he says, is the discovery that the design of the spillways themselves has a major bearing on the fate of the sediments. His team found that out by comparing the sediment plume that passed through the Morganza spillway with another plume: one that traveled through the Bonnet Carré spillway, 19 kilometers west of New Orleans, which the Army Corps also opened in May to divert floodwater into Lake Pontchartrain.

    Both spillways have a forebay, a large pool where the floodwaters collect before the spillway is opened. The Morganza's forebay is many kilometers across—and acts like a big sediment trap, it turns out. Much of the floodwaters' sediment settled out into the forebay and never even made it to the Atchafalaya Basin, Nittrouer's team reported at the AGU meeting. By contrast, the Bonnet Carré's forebay is only 300 meters wide; sediment was shunted directly through the forebay and across the spillway into the lake. That's a key piece of information for possible restoration and management plans using diversions, Nittrouer notes. “The Bonnet Carré would be a design structure more analogous to a diversion plan,” he says.

    In one of the biggest surprises, Nittrouer says, measurements taken at the Bonnet Carré spillway revealed that even the uppermost 5 meters of water contained a significant amount of sediment, particularly sand. That's important, because the spillways decant only the top 10% to 20% of the floodwaters. Computer models of river diversions seriously underestimate that portion's sediment, Nittrouer says, because they average sediment concentrations across many tens of kilometers of river length instead of zooming in on how the twists and turns of the river affect sediment dynamics and sediment load. “What we found is that these local effects of sediment transport conditions … are extremely important for getting sediment out of these diversions,” concludes Nittrouer, who helped organize the AGU session.

    How to take such information and build it into models aiding coastal restoration management is now the challenge facing researchers. More data may be arriving soon: On 12 January, Louisiana's Coastal Protection and Restoration Authority (CPRA), created in 2006 to study how to combat the coastal erosion, released a draft of its 50-year plan to shore up Louisiana's coastline. A team of CPRA scientists, engineers, and administrators, with advice from an independent scientific board, spent 2 years analyzing nearly 400 proposed scientific projects, including restoration projects such as river diversions and marsh rebuilding, as well as risk-reduction projects, such as building new levees to protect against storm surge or floodproofing structures. The new draft selects 145 projects for funding, at a cost of $50 billion, divided equally between restoration and risk-reduction plans. Following a public-comment period that lasts through 25 February, the plan will move on to the Louisiana Legislature on 26 March.

    “This whole attempt to reconstruct the Louisiana coastline is truly novel because of the scope and scale,” says William Dennison, a marine scientist at the University of Maryland's Center for Environmental Science who chaired CPRA's independent science board. “The whole thing is a big experiment.”

    Nittrouer acknowledges that conclusions based on the data from the spillway openings are too preliminary to shape policy about diversions and coastal management. But it's a start. “Ultimately, if we're going to understand something about delivering water and sediment from the main channel to wetlands, it's important to get the timing and magnitude down,” he says.

    And the bottom line, he adds, is good news: Diverting enough sediment to kick-start wetland restoration won't necessarily require a flood on the scale of the 2011 disaster. Even with much smaller flows, the extensive network of flood-control devices along the Mississippi means that “you can efficiently and effectively route sediment outside of the main channel for the sake of constructing new coastal landscape. … It's something that you could reproduce in the future.”

  6. Oil Resources

    Technology Is Turning U.S. Oil Around But Not the World's

    1. Richard A. Kerr

    The high price of oil is driving technological innovation that has reversed the decline in U.S. oil production, but the world will increasingly depend on OPEC and “non-oil” oil.

    Saudi Arabia of the north.

    The new technologies of fracking and horizontal drilling are driving an oil boom in North Dakota.


    The 1 October 2011 Wall Street Journal headline was none too subtle: “How North Dakota Became Saudi Arabia.” Blatant boosterism, perhaps, but not complete fantasy. Hard against the Canadian border, North Dakota has a full-blown oil boom under way. The state's oil production recently quadrupled in 3 years, making it the fourth largest oil-producing state in the world's third largest oil-producing country. And that gusher has been instrumental in reversing the 2-decade-long decline in U.S. oil production.

    For technological optimists, North Dakota's oil boom demonstrates the future of oil outside of the Organization of Petroleum Exporting Countries (OPEC). Oil production “is a high-technology industry, [and] I don't think the innovation will come to an end,” says Daniel Yergin, chair of IHS Cambridge Energy Research Associates (CERA) in Massachusetts.

    Up, down, and up again.

    U.S. oil production peaked in 1970, declined through years of low prices, but lately rose again with high prices and new drilling technologies.


    New techniques such as the “fracking” that is now unlocking North Dakota's oil riches will frustrate the oil “peakists,” Yergin writes in his recent book, The Quest. For at least 20 years, peakists have been warning of an imminent maxing out of world oil production . Yergin thinks not.

    Instead, Yergin says, technological innovation driven by higher prices will make hard-to-extract North Dakota “tight oil,” Canadian oil sands, and far-offshore deposits accessible and profitable. That opening of new, abundant sources will help put off the much-feared peak until “perhaps sometime around mid-century,” Yergin writes.

    Less-optimistic analysts remain unconvinced. “Technology does make a difference,” says oil analyst Richard Nehring of Nehring Associates in Colorado Springs, Colorado. But “the question is how big that difference is going to be.” Many think it will barely offset the declining output of aging fields. “You can definitely keep squeezing more out of what you've found, but everything gets harder,” notes energy analyst David Greene of Oak Ridge National Laboratory in Tennessee. Because harder means slower, Yergin's mid-century timing of the peak remains dubious for many analysts. “We're getting pretty close to it right now,” Nehring says.

    The big squeeze

    For drillers outside of OPEC, cheap, easy oil is now a thing of the past. Fields that gushed oil on their discovery in the 1930s, '40s, and '50s are well on their way to a dribble. And discoveries of truly huge oil fields capable of easily delivering a half-billion barrels or more are now few and far between. That suggests to some that world production is about to peak.

    U.S. oil production, once the world's largest, peaked in 1970. It has since been in decline except when it temporarily plateaued in the early 1980s as Alaskan oil was tapped and high oil prices drove a frenzy of drilling. Although prices rose again through the 2000s, U.S. production continued to decline as oil production outside of OPEC plateaued for the past 8 years or so.

    For years, no one outside of OPEC seemed able to produce oil any faster, price incentives or not. But U.S. drillers have been getting serious. Some borrowed technology from the natural gas industry that frees up gas bound in nearly impermeable rock (Science, 25 June 2010, p. 1624). In such hydrofracturing or “fracking,” wells are drilled down into layers of gas-bearing shale and bored horizontally for great distances; then high-pressure water is pumped in, cracking the surrounding rock. By raising production in North Dakota and elsewhere in the west, fracking of “tight oil” has now boosted U.S. oil production by almost half a million barrels a day.

    U.S. drillers using other, incrementally improving technologies inched out into the once-inaccessible “ultradeep” waters of the Gulf of Mexico. Offshore oil production in shallow to deep waters had been declining since 2003. But with the newly developed ability to drill in waters deeper than 1500 meters, oil began to flow from these ultradeep waters in 2005. By 2009, ultradeep-water production had reversed the decline in Gulf of Mexico production and returned it to its peak of the early 2000s.

    New, high-tech ways for getting at hard-to-extract oil haven't been limited to the United States. Rather than drilling for oil, Canadians have been digging for it in the so-called oil sands of Alberta, where subsurface sands come coated with a tarry substance that is convertible to oil. With refined technology, Canadians have been digging or steam-extracting more oil of late, hitting 1.5 million barrels per day in 2010. Yergin projects that oil sands production could double by 2020.

    Unconventional sorts of oil such as tight oil and oil sands are “expanding the definition of oil,” Yergin writes. Going further, he and various authorities now consider natural gas liquids (NGLs)—the lightweight hydrocarbons that condense from gas once it has left the ground—as part of the “liquids” that will meet the world's growing demand for anything like crude oil. Organizations such as the U.S. Energy Information Agency (EIA) and oil giant BP now even include biofuels in the liquids category. “I can't tell what it is that's going into my car's tank,” says BP's senior U.S. economist, Mark Finley in Washington, D.C. “They all go into the mix.”

    Sufficiency or scarcity?

    With high prices driving so much innovation, Yergin is optimistic. The headline of his 17 September 2011 Wall Street Journal article says it all: “There Will Be Oil.” CERA has projected that the world's liquids production will grow from 93 million barrels per day (mb/d) in 2010 to about 110 mb/d in 2030, meeting expected demand. BP's Energy Outlook 2030, released last month, shows similar gains by 2030.


    Daniel Yergin sees rising oil production.


    According to BP's projections, non-OPEC liquid supply will grow. Growth in production of U.S. and Brazilian biofuels and of oil from Canadian oil sands, Brazilian deep water, and U.S. tight oil will offset continued declines in aging non-OPEC fields. “We don't perceive a world facing a global resource constraint,” says Finley. And tight oil and offshore oil will even hold off any further decline in U.S. crude oil production through at least 2035, according to an EIA report released late last month.

    Peakists—along with other analysts who would decline that label—are far less sanguine. For starters, they would leave biofuels out of the discussion. Biofuels aren't oil, they note, and their development is even more uncertain than oil production is. For that matter, natural gas liquids are not part of the resource that has been the subject of the decades-long peak oil debate.

    But beyond the creeping redefinition of oil, critics of projected production growth see an overabundance of optimism. True, there are trillions of barrels of oil left in the ground, they say, but how fast can it be produced? “It's about rates,” Greene says. Perhaps the most fundamental rate in the debate is the growth rate's opposite number, the decline rate: how fast production in existing fields is falling. That's how fast new production must be added just to keep overall production steady. In his book, Yergin cites a CERA study that came up with a decline rate of 3%. But other estimates are more like 5%, including a 2008 estimate by the International Energy Agency in Paris.

    OPEC ascendant.

    BP projects non-OPEC oil output (pink wedge and below) to plateau as OPEC's market share (dotted line) rises.

    CREDIT: © BP

    Whatever the decline rate, many projected rates of growth in oil supply are inflated by enthusiasm for new sources that have yet to prove themselves, says geologist Arthur Berman of Labyrinth Consulting Services in Sugar Land, Texas. Drillers, naturally enough, have been targeting the most promising tight-oil prospects first, he notes. But elsewhere, good productivity is likely to be frustratingly patchy. And production typically soars in the first year only to plummet in later years. Nehring has looked at prospective tight-oil fields around the United States and concluded that “many are called, but few are worth choosing.”

    Likewise, oil sands may have rocketed Canada to number two in proven oil reserves, right behind Saudi Arabia, but sands won't come close to compensating for the depletion of aging fields. Yergin writes that production could double there by 2020, to 3 mb/d; that would be only a few percent of world production. And there is nothing else in the world like Alberta's sands.

    There are “world-class” amounts of oil in the deep offshore, Nehring concedes. But deep-water projects take 10 to 20 years to develop, he notes, spreading the contributions from the deep offshore over many years. So he calls the deep water “a plateau-prolonging source of oil.”

    All in all, peakists and other pessimists see the non-OPEC oil plateau of the past 8 years continuing. BP more or less agrees. Excluding biofuels, non-OPEC oil production in the BP outlook rises only about 3% by 2015 to a plateau that continues through 2030.

    As in outlooks by other energy organizations, BP assumes that OPEC countries can and will increase production to meet any demand above what non-OPEC countries can cover. OPEC's production of natural gas liquids increases by more than 4 mb/d, or about 60% in the BP projection, but BP still sees a need for OPEC oil production to rise by almost 8 mb/d, or about 25%.

    Six million barrels per day of that OPEC oil increase is slated to be split between Saudi Arabia and Iraq. In the past, Saudi Arabia has always increased its production capacity ahead of demand. But Iraq and other OPEC countries such as Venezuela and Iran have been far less reliable. “The challenges the world faces are much more above ground than below it,” says Finley, referring to the political, social, and economic forces that already constrain production from abundant resources below ground. So that makes for three things to watch: the price of oil, the level of non-OPEC production, and the state of affairs in the OPEC countries.