# News this Week

Science  05 Jun 2009:
Vol. 324, Issue 5932, pp. 1246
1. Particle Physics

# Chinese Scientists Hope to Make Deepest, Darkest Dreams Come True

1. Dennis Normile

Particle physicist Yue Qian had his eureka moment in front of the TV set. For over a decade, Chinese scientists have longed for an underground laboratory that would enable them to join efforts across the globe to detect dark matter, observe neutrinos, and watch for exotic particle physics phenomena. Searches for suitable sites repeatedly came up empty-handed. But last August, after Yue caught a news report on the completion of two tunnels piercing Jinping Mountain in Sichuan Province, he felt that the long quest for such a lab might finally be over.

After months of negotiations, on 8 May Tsinghua University in Beijing, where Yue is an associate professor, signed an agreement with the tunnels' owner, Ertan Hydropower Development Co., to hollow out an experimental chamber. The Jinping lab would be the deepest underground science facility in the world, edging out—by 100 meters or so—the Deep Underground Science and Engineering Laboratory that the U.S. National Science Foundation may build in an abandoned mine in Lead, South Dakota. By placing sensors deep in the earth, physicists hope to reduce spurious signals from cosmic rays. China's subterranean aspirations have been circulating in Asia for months; the international community will get its first glimpse of the project at a dark-matter workshop in Shanghai on 15 June and at an astroparticle and underground physics conference in Rome next month.

An underground lab has been a dream for several generations of Chinese scientists, says Wang Yifang, a particle physicist at the Institute of High Energy Physics of the Chinese Academy of Sciences in Beijing. Past candidate sites, including an underground aviation museum near Beijing and coal and gold mines around the country, all were judged too shallow or impractical.

Jinping, on the other hand, “looks ideal,” Wang says. The lab would have approximately 2500 meters of marble and sandstone above it: more shielding than any similar site in the world. Researchers will be able to make a 1-hour drive from a regional airport to the lab's front door. And the tunnels are sized for construction equipment, promising smooth delivery of instruments and supplies.

Wang cautions that the lab is not a done deal. “It's really at a very early stage,” he says. To start with, Yue's group must verify that the rock overburden really does screen out unwanted cosmic rays and that there is no unexpected radiation emanating from nearby rock or groundwater. To provide space for instruments, by the end of the year the team plans to have hollowed out a 5-meter-high, 5-meter-wide, 30-meter-long chamber. They will then measure cosmic ray flux and background radiation for about 6 months. And they will begin at least one experiment. Yue is forming a collaboration to install a germanium detector to search for a postulated component of dark matter known as WIMPs, or weakly interacting massive particles. Chinese physicists are also talking about observations of atmospheric and solar neutrinos as well as experiments to watch for neutrinoless double-beta decay, an extremely rare phenomenon that might help refine estimates of neutrino mass.

Yue doesn't yet know what the first phase will cost, as design efforts are just starting. “But [Tsinghua] university has promised strong support,” he says, and they are seeking funds from the science ministry. If the project develops as hoped, says Yue, “we would want to get more universities and institutions from China and around the world to join us and push this project ahead.”

The good fortune befell physicists thanks to a mammoth hydroelectric project about 350 kilometers southwest of Chengdu, the capital of Sichuan Province, where the Yalong River makes a 150-kilometer-long U-turn around Jinping Mountain. Ertan Hydropower is building two dams: Jinping 1 at the start of the U-turn and Jinping 2 at the end. To move workers and materials between the construction sites, Ertan blasted a pair of 17-kilometer-long access tunnels through the mountain. One will host the lab.

The hydropower project is controversial because some geologists think the weight of the impounded water could destabilize faults in the earthquake-prone region (Science, 8 May, p. 714). The prospect of an underground lab, though, is warmly welcomed by physicists throughout Asia. “It certainly is good news,” says Henry Wong, a physicist at Academia Sinica in Taiwan, who will collaborate with Yue on the dark-matter experiment. Wong says he expects the lab to strengthen scientific ties between Taiwan and mainland China. Kim Sun Kee, a particle physicist at Seoul National University, is also enthusiastic. “Compared to other regions, in Asia, we don't have many underground labs,” he says. Kim spearheads a collaboration hunting for dark matter in a lab in South Korea's Jeombong Mountain (Science, 6 July 2007, p. 32). But the Korean lab is only 700 meters beneath the surface, and more sensitive detectors now being contemplated by the community would need better shielding. Jinping, says Kim, “will be a great place for next-generation experiments.”

2. Research Facilities

# European Neutron Source Finally Finds a Home

1. Daniel Clery

After a frustrating decade watching their preeminence in neutron-beam science ebb away to newer facilities in the United States and Japan, European researchers got some good news last week: Their €1.4 billion dream machine, the European Spallation Source (ESS), which has been on the drawing board for more than 15 years, overcame a major hurdle when the countries interested in funding the project picked a site on which to build it in Lund, Sweden. “This is the real thing, something we can focus on and move forward,” says Robert Cywinski of the University of Huddersfield in the United Kingdom, spokesperson for the ESS preparatory phase project.

Government ministers are not getting out their checkbooks yet, as there is still much to sort out, including a final site-specific design and an environmental impact assessment, as well as obtaining planning permission and figuring out exactly which countries want to join. But as with other major European research facilities, choosing a site—Lund won out over rivals Debrecen in Hungary and Bilbao in Spain—is always a tense and deeply political part of the process. ESS will be “the first European experimental facility in Sweden and the first outside the big five E.U. nations.” says Colin Carlile of Lund University, who headed the effort to bring ESS there.

ESS will surpass current U.S. and Japanese neutron sources in power, unless they upgrade in the meantime. Neutron beams are used by a wide variety of researchers to probe how atoms are arranged within materials and how they interact. Beams of the particles can be produced using a nuclear reactor or by smashing a proton beam into a metallic target, a process known as spallation.

In the 1990s, Europe had the top two neutron sources: a reactor in France and a spallation source in the United Kingdom. U.S. researchers at the time were facing a neutron drought after a planned reactor was canceled in 1995. But the Spallation Neutron Source in Oak Ridge, Tennessee, got the green light in 1998 and opened for business in 2007 with a 1.5-megawatt beam. J-PARC, a multi-accelerator facility in Tokai-mura, Japan, is in the process of commissioning its 1-MW neutron beamline.

Although Europe drew up plans for a 10-MW spallation source in 1995, no European government seemed to want to pick up the ball and run with it. By 2003, ESS seemed all but dead, despite a cost reduction by downgrading to 5 MW. Cywinski blames this impasse on the fact that Europe “doesn't have one doorstep on which to put a proposal.” Instead, researchers have to find a government to champion their idea and build a group of collaborators, a process known in E.U. circles as “variable geometry.” Says Cywinski: “Variable geometry doesn't work, or we would have had ESS years ago.”

ESS finally got a shot in the arm from the European Strategy Forum on Research Infrastructures, an E.U. body that in 2006 drew up a list of facilities that would benefit European research, describing ESS as a mature project. That stamp of approval led to E.U. money for preparatory work and several countries stepping up to offer possible sites. The Swedish government, for example, offered to pay 50% of ESS's construction cost and 20% of operating expenses. The site at Lund will also be home to a new Swedish-built synchrotron, an intense source of x-rays for research, and ESS will aim to be carbon-neutral through a joint project with a wind-energy company.

Sweden worked hard to get neighboring countries in Scandinavia and the Baltic on board before the vote.The final decision was made on 28 May after a group of research ministers from 12 countries interested in participating met to discuss the bids and then the non-bidding countries voted. Seven declared they would join the Lund effort—Germany, France, Poland, Denmark, Norway, Estonia, and Latvia—and two others, Italy and Switzerland, backed the Lund site. Portugal voted for Bilbao.

Sweden must cement the collaboration over the next few months with a memorandum of understanding signed by the partners and attempt to bring Italy and Switzerland as well as defeated rivals Spain and Hungary into the collaboration. Construction is penciled in to start in 2012.

3. Geoscience

# The Quaternary Period Wins Out in the End

1. Richard A. Kerr

Geoscientists have cut the Gordian knot of geologic timekeeping. Ever since 19th century geologists divided the history of Earth into four periods—the Primary, Secondary, Tertiary, and Quaternary, oldest to most recent—their intellectual descendants have been dismantling that time scale. But the geologists, anthropologists, glaciologists, and paleoecologists studying the last couple of million years became quite attached to the Quaternary. They gave its name to their journals and even themselves—to the disgruntlement of strict constructionists, who have been insisting for decades that the modern rules for dividing up geologic time permitted neither the Quaternary nor quaternarists (Science, 25 January 2008, p. 402).

On 21 May, the final committee vote on the question was announced: The quaternarists will endure. Pending an almost certain ratification by the ultimate authority—the International Commission on Stratigraphy (ICS)—the Quaternary will officially take over the past 2.6 million years of the geologic time scale, when humans took up tools and the world began slipping in and out of the ice ages.

“The Quaternary Commission is greatly relieved and pleased,” says Philip Gibbard of the University of Cambridge in the United Kingdom, who is president of the commission, a subgroup of ICS. Nomenclature “is not set in stone, even in geology,” says Gibbard. “It's just a question of changing the label.”

Not quite. “It makes no sense, it creates havoc, we're going to ignore it pretty much,” says marine geologist Marie-Pierre Aubry of Rutgers University in Piscataway, New Jersey, who with others vociferously opposed the change. The ICS committee's 16-to-2 vote, she notes, not only usurps the last 2.6 million years of the Neogene period for the Quaternary but also extends the subsidiary Pleistocene epoch from 1.8 million years ago to 2.6 million years at the expense of its predecessor, the Pliocene epoch. Everyone had agreed on how to identify the original time boundaries according to consistent rules, she says; the vote throws those rules out the window. “You have to respect scientific principles,” Aubry says. “If you don't, things don't make sense any more.”

“Technically, [Aubry] is absolutely right, but I don't think it's going to make a great deal of difference in our community,” says paleoceanographer Lloyd Keigwin of Woods Hole Oceanographic Institution in Massachusetts, who was not involved in the debate. Researchers analyzing the marine record are usually concerned with changes through time, he says, not so much where an event stands in relation to broadly spaced time markers. “From a practical standpoint, we may have to move on,” he concludes.

4. ScienceNOW.org

# From Science's Online Daily News Site

Preventing a Plant Apocalypse. Sometime between 100 million and 1 billion years from now, Earth will have lost so much carbon dioxide from its atmosphere that plants and trees will literally begin suffocating, eventually taking all life with them. In a new study, researchers propose one way to delay this Armageddon: reduce the pressure of the atmosphere, effectively creating conditions where we all feel like we're living at high altitudes. http://tinyurl.com/kqj3sc

A Billion-Year Hard Drive. That embarrassing home movie of you naked in the tub could still be around millions of years from now, along with your less-than-eloquent posts on Facebook and Twitter. Researchers have developed a new technology based on carbon nanotubes that promises to permanently preserve individual bits of data, such as those found on computer hard drives and DVDs. If so, the technology could lead to data archives holding the entirety of human thought and communications potentially forever. http://tinyurl.com/lxrffu

iPS Cells to the Rescue. Two papers published this week appear to bring the day closer when embryonic-like stem cells can be used to treat human diseases. One study describes what scientists say is the safest method yet to produce these cells. The other reports success in using the cells to begin correcting a rare genetic disorder known as Fanconi anemia. http://tinyurl.com/mogfdz

Quantum Widget. The strange rules of quantum mechanics govern the behavior of tiny objects and explain the structure of atoms, the subtleties of chemical bonding, and the inner working of electronic microchips. Ironically, although the theory is called quantum mechanics, physicists have never produced a machine whose motion demonstrates quantum weirdness. Now a team from the National Institute of Standards and Technology in Boulder, Colorado, has taken a step in that direction by forging a bizarre quantum connection called entanglement between two mechanical widgets. The devices don't look much like typical machines, however: Their moving parts are ions oscillating in electric fields.

So Long Aspirin, Hello Silver. Millions of people around the world are prone to dangerous blood clots. Now researchers have had early success with a new way to prevent them—and the strokes, heart attacks, and pulmonary embolisms they cause. Nano-sized particles of silver can stop sticky blood cells called platelets from clinging together in laboratory strains of mice, the team reports. http://tinyurl.com/lcof8s

5. U.S. Higher Education

# Report Finds No Gender Bias in Faculty Hiring, Resources

1. Jeffrey Mervis

A new report by the U.S. National Academies says that women are getting a fair shake from major research universities in being hired, promoted, and given access to resources—once they can grab onto the academic ladder and start climbing the rungs.

That conclusion may surprise those familiar with a stream of recent reports on the topic, including a 2006 academies' study that demanded an end to what it called the “bias and outmoded practices” hindering the progress of women in academic science. The good news, says the report, is that “men and women faculty … have enjoyed comparable opportunities, and gender does not appear to have been a factor in a number of important career transitions and outcomes.” The bad news, however, is that too many scientifically trained women are rejecting academia in favor of other career paths.

“I'd hate for anybody to read this report and think that we can be complacent,” says physicist Claude Canizares, vice president for research at the Massachusetts Institute of Technology in Cambridge and co-chair of the new report, Gender Differences at Critical Transitions in the Careers of Science, Engineering, and Mathematics Faculty. “While women can take some encouragement from the fact that there is no evidence of large-scale bias at these key transition points, the reasons for their continued underrepresentation need to be examined more closely.”

The study, requested by Congress in 2002 and supported by a $1.3 million grant from the National Science Foundation, focuses on three important transitions: getting a tenure-track position, winning tenure, and being promoted to full professor. It's based on surveys of 500 departments at 89 institutions and of 1800 faculty members in those departments. Although legislators had initially wanted a sweeping review of “gender differences” among all faculty members at all institutions, the academy panel decided to save time and money by concentrating on full-time faculty members from six disciplines—biology, chemistry, civil and electrical engineering, mathematics, and physics—who work at the top tier of research universities. Within that population, the panel found that women are actually more likely than men to be interviewed for and offered tenure-track jobs (see graphic, p. 1251) and just as likely to be successful when they come up for tenure. But taking the first step is where the problems seem to lie. According to the report, many fewer women bid for tenure-track positions than would be expected based on their proportion of the Ph.D. pool. Although university outreach efforts had no apparent effect on attracting more women applicants, one factor did make a difference: Women are more likely to apply if a woman is chairing the selection committee or serving on it. Once women take the job, they also often face a tougher climb up the ladder than their male colleagues. The survey found that faculty women “were less likely to engage in conversation with their colleagues on a wide range of professional topics,” including research, salary, and benefits. The panel also found that women remain assistant professors significantly longer and that the attrition rate is higher before coming up for tenure. Donna Nelson, a chemistry professor at the University of Oklahoma who has done pioneering work on the status of women in academic science, says that the panel's findings match what she hears on campuses. “Women tell me all the time that they feel isolated. It's harder to feel good about your work, and be productive, if you're not being included in conversations and collaborations.” Nelson also emphasized the need for more women applicants to entry-level, tenure-track positions. “If universities narrow the pool at the onset,” she notes, “then women will have a harder time even getting on the radar screen.” Canizares said that the panel took the unusual step of conducting its own research because “there were no data to answer the questions we were interested in addressing.” He hopes that federal agencies and universities will recognize the need to gather longitudinal data on the career paths of women. “And I'd suggest that we start with our own graduate students.” 6. Newsmaker Interview # Eugenie Scott Toils in Defense of Evolution 1. Yudhijit Bhattacharjee As executive director of the California-based National Center for Science Education, anthropologist Eugenie Scott has spent the past 2 decades on the frontlines of the contentious battle over teaching evolution in U.S. public schools. She doesn't confine herself to the classroom and courthouse: Every year, she and geologist Alan Gishlick lead a rafting trip through the Grand Canyon, teaching a general audience about the science and natural history of the canyon and comparing the evidence with the creationist explanation of its origins. Last week, Scott won the inaugural Stephen Jay Gould Prize from the Society for the Study of Evolution, only weeks after Scientific American ranked her among the country's top 10 science and technology leaders for her self-described role as “Darwin's golden retriever.” Scott spoke to Science last week about where things now stand. Q:How has this battle changed in the past 20 years? E.S.:The enemy has become more diverse. When I started, it was just creation science. Now we have creation science, intelligent design [ID], and straight-up antievolution in the form of “evidence against evolution.” It used to solely be a K–12 issue. Now we are seeing that it crops up frequently in community colleges and even 4-year colleges. Q:What's the current situation in the various states? E.S.:Besides periodic assaults on science standards as we recently saw in Texas, we are concerned about antievolution legislation in different states under the guise of academic freedom bills. Just in the last few weeks, antievolution bills awaiting decisions in a number of states—Oklahoma, South Carolina, Alabama—died in committee. Louisiana passed antievolution legislation last year; we're now waiting to see how it plays out. We are also seeing closet creationism being introduced through wording not obvious to those unfamiliar with the history of the controversy. Q:Why has the ID movement survived the 2005 Dover trial? E.S.:ID proponents have repackaged ID and are promoting it as “evidence against evolution.” The Discovery Institute, an ID think tank, has published Explore Evolution that quotes a “number of problems” with evolution that they would like taught in biology class. Of course, these are standard creationist arguments. Q:Why hasn't the general public rejected ID? E.S.:Only 40% of adult Americans understand the nature of a scientific experiment. Remember that ID is primarily a marketing strategy to the general public, and unless that is directly opposed, people are going to be miseducated about science. We don't have to worry about medical schools teaching that AIDS is a curse from God, but we have to worry about teachers teaching well. Q:Why is it important to teach evolution? Can't doctors and most life scientists do their jobs without accepting evolution? E.S.:You can be a mechanic without understanding the niceties of the internal combustion engine. [But] wouldn't you rather go to a mechanic who has the big picture? Q:What should scientists do to help the cause? E.S.:Universities need to do a better job of teaching evolution because that's where high school teachers get their training. Evolution needs to be brought into every course of biology instead of getting tacked on as a unit to the intro class. What university scientists should not do is to force students to choose between religion and science. If a professor were to say that evolution proves there is no God, that's not just bad philosophy of science, it ensures that a significant number of students will stick their fingers in their ears. When explaining biological questions, such as the evolution of the eye, there is no need to say that God had nothing to do with it. It's an irrelevant comment. I don't think a classroom is an appropriate place to try to create more atheists any more than it is an appropriate place to create more fundamentalist Christians. 7. ScienceInsider # From the Science Policy Blog A call to include damage to oceans in climate policy, a trio of new government ministers in India, and a contrarian analysis of swine flu data were among the stories covered by ScienceInsider in the past week. Scientific academies have joined forces to warn world leaders about the dangers of ocean acidification. The InterAcademy Panel on International Issues, with members representing 69 countries, issued a statement this week recommending that the United Nations Framework Convention on Climate Change take up the issue before the U.N. Climate Change Conference in Copenhagen in December. The oceans are absorbing a quarter of industrial emissions of carbon dioxide, increasing their acidity and harming marine life. India's prime minister, Manmohan Singh, has named leaders with deep technical expertise to his cabinet. The new science minister is Prithviraj Chavan, a politician from western India who was educated as a mechanical engineer at the University of California, Berkeley. Singh appointed Kapil Sibal, a lawyer and respected former science minister, as minister of human resources development, which includes the education portfolio. Mechanical engineer Jairam Ramesh becomes minister of environment and forests. ScienceInsider's ongoing coverage of the swine flu outbreak includes an analysis that contradicts the view of the U.S. Centers for Disease Control and Prevention that cases in the country might have crested. Donald Olson, a New York City–based epidemiologist who runs the influenza monitoring project at the International Society for Disease Surveillance, says his data show “massive increases” in Boston and New York City, which look “mild” in the CDC regional data. Olson says New York City's drop and then rise in cases may soon be repeated around the country. Stay on top of the latest science policy news at blogs.sciencemag.org/scienceinsider. 8. The Biology of Genomes, 5–9 May 2009, Cold Spring Harbor, New York # Water Flea Boasts Whopper Gene Count Packed into a body no bigger than the letters on this page is a whale of a genome. The body belongs to Daphnia pulex, a crustacean common in lakes and ponds around the world. Since 2004, the Department of Energy Joint Genome Institute in Walnut Creek, California, and a consortium that now numbers 350 investigators from 17 countries have been sequencing and analyzing the 200-million-base genome from a Daphnia that lived in a pond along the Pacific coast of Oregon. It is one of just two noninsect arthropods to be deciphered to date. At first glance, the genome seemed to have about 25,000 genes—a lot, but no record-breaker. Eventually, however, gene-finding programs found 31,000, John Colbourne of Indiana University, Bloomington, reported at the meeting. And a variety of experiments have revealed as many as 8000 more genes that gene-finding annotation programs missed, he said.That tops the gene count of the newly sequenced genome of another tiny creature: the pea aphid, which sports 34,600 genes (see p. 1253). “It's a big surprise that critters that you think wouldn't have a high gene count do,” says Eric Green of the National Human Genome Research Institute in Bethesda, Maryland. These findings are further evidence that biological complexity does not directly correlate with gene number. But we are also “probably naïve in defining what is biological complexity,” Green adds. Part of the appeal for sequencing the genome of Daphnia is its ability to adapt—it usually clones itself but reproduces sexually under certain conditions. Eggs can hatch right away or lay dormant for more than a century. Daphnia thrive on algae and in turn are fodder for many fish and other predators, making them a key link in aquatic food webs. But, depending on the predator, they can sprout helmets, tail spines, or ridges called neck teeth. The genome is already helping researchers get to the genetic basis of this plasticity. Colbourne and his colleagues first made a microarray of all the organism's genome sequence rather than just pieces of the genes themselves. “The array is blind relative to the annotation,” Colbourne explains, and thus can pick up expressed DNA that gene-finding programs might miss. They have started using the array to study how gene expression changes under different conditions. In experiments that looked at Daphnia exposed to different predators, for example, they found “a set of genes that were hidden,” Colbourne reported. “And we expect there are still more” to be unearthed as they evaluate different environmental conditions. The new genes they're finding seem to code for proteins but not for any that look familiar. Colbourne wonders whether this gene-packed genome arose in part because of the complexity of the aquatic environment—this species can live where it's salty, acidic, hot, and so shallow that exposure to the sun is hazardous. “It's almost as if they have more than one genome” to be able to cope with this diversity,hesaid.Another reason for the high gene count could be a consequence of having both sexual and asexual reproduction. Whatever the cause, the high gene count comes from having many duplicated genes. This stands in contrast to the human genome, which generates a variety of different proteins by splicing genes into different configurations. Why the Daphnia genome evolved this way is a mystery, says John Werren of the University of Rochester, New York. “Some feature of the genome of Daphnia has pushed it to make more copies as opposed to [evolving] splicing.” 9. The Biology of Genomes, 5–9 May 2009, Cold Spring Harbor, New York # Some RNA May Play Key Role in Repressing Genes, Slowing Cancer 1. Elizabeth Pennisi Protein-coding genes have long been the stars of the Human Genome Project, but now RNA is moving into the limelight. Over the past 3 years, researchers have come to realize that protein-coding genes account for barely a quarter of the DNA that gets transcribed. The rest leads to RNA strands of various lengths—but toward what end has been a mystery, because that RNA doesn't seem to lead to any proteins. Some experts have even argued that this RNA is little more than “transcriptional noise.” Yet, just as junk DNA proved to be more than junk, at least some of this “noise” translates into meaningful molecules that may play key roles in turning genes on and off. “For the past 5 to 10 years, researchers have been cataloging the presence of the noncoding RNAs,” says Thomas Gingeras, a molecular biologist at Cold Spring Harbor Laboratory in New York. “Now people want to understand what they do.” Chris Ponting of the University of Oxford in the United Kingdom and his colleagues took some of the first steps in that direction in 2007 by showing that 3000 long noncoding RNAs were conserved in evolution, with sequences that were quite similar among mice, rats, and humans—an indication that they serve some vital function. At the meeting, another team described progress in quantifying and assessing the function of a particular group of long RNA molecules. John Rinn of Harvard Medical School in Boston and his colleagues presented further evidence that at least some of these molecules seem to be important to a cell's survival, and they reported that by studying the molecules these RNAs associate with, they are beginning to glean how some of them may actually work. One, for example, seems critical to helping the tumor suppressor gene p53 keep cancer in check. “There are a lot more of these [RNAs], and they are probably more important than we thought,” says Richard Myers of the Hudson-Alpha Institute for Biotechnology in Huntsville, Alabama. Rinn and his colleagues study what he calls “large intervening noncoding RNAs” (lincRNAs), 2300 to 17,200 bases long, that are coded for in DNA between genes. Until recently, researchers knew of only about a dozen lincRNAs, notably XIST, an RNA that turns off the extra X chromosome in females, and HOTAIR, an RNA that directs the specialization of skin cells. Rinn's team has searched systematically for lincRNAs by looking outside gene boundaries for chemical signatures that they know mark the coding regions of active genes. They initially looked in four types of mouse cells, assuming that such marks signaled additional transcription. The survey initially turned up about 1500 candidates, Rinn graduate student Mitchell Guttman and colleagues reported online 1 February in Nature. At the meeting, Guttman reported that the team has expanded the search to 10 human tissues and has come up with 4000 definite lincRNAs. He estimates there are about 1000 more. Not everyone agrees that lincRNAs represent a true subclass of noncoding RNAs, as they worry that some of the DNA sequence encoding long noncoding RNAs may extend into genes, blurring the definition of “intervening.” “Making a new class may be premature,” Gingeras says. Guttman, Rinn, and their colleagues have also looked for patterns of coexpression between protein-coding genes and lincRNAs in 21 tissues. They found quite a few genelincRNA overlaps, from which they concluded that, broadly speaking, lincRNAs are involved in the regulation of the cell cycle, immunity, and stem cell differentiation, Guttman reported. For example, 39 associated with the tumor suppressor gene p53. One “is directly regulated by p53,” Rinn reported at the meeting. He thinks that particular lincRNA acts as a global repressor of the p53 pathway, because 1000 genes increased their expression when he disabled either p53 or that particular lincRNA. The story sounded vaguely familiar, for that is how HOTAIR and XIST seem to work. So Rinn and Guttman did an experiment to assess how many lincRNAs bind to polycomb protein complexes. These complexes remodel chromatin, reconfiguring this DNA-protein matrix to shut out transcription factors and silence certain genes. They found that almost 25% of the lincRNAs latch onto these complexes in one cell type or another. Furthermore, the RNAs were required for gene silencing. In total, 38% of the lincRNAs are tied in with one of four chromatin-remodeling complexes, Rinn reported. “We think RNA is a scaffold to [help] bring in the right proteins,” says Rinn. “Those results are very exciting,” says David Haussler, a bioinformaticist at the University of California, Santa Cruz. “This is far from being a mature scientific story, but there are tantalizing hints [of a repressive function].” Adds cancer geneticist Victor Velculescu of Johns Hopkins Kimmel Cancer Center in Baltimore, Maryland: “It reinforces the fact that these lincRNAs are likely to be important physiologically.” 10. The Biology of Genomes, 5–9 May 2009, cold Spring Harbor, New York # The Bug and the Bacterium: Interdependent Genomes 1. Elizabeth Pennisi Any successful relationship demands sacrifices. The partnership between the pea aphid and a tiny bacterium called Buchnera aphidicola is no exception. The newly sequenced DNA of this tiny insect, a common pest of legume crops, reflects a long history of give-and-take between the genomes of the bug and the bacterium. “The bargaining chips are genes, and the inventory reflects concessions during the course of negotiations,” says John Colbourne, an evolutionary biologist at Indiana University, Bloomington. Like other aphids, Acyrthosiphon pisum live off plant sap, a sugary mix low in protein. To make up for this nutritional shortfall, the insects depend on their microbial guests to supply essential amino acids. In return, the pea aphid has given up some of the genes that normally help fend off infections by Gram-negative bacteria such as Buchnera, Stephen Richards of Baylor College of Medicine in Houston, Texas, reported at the meeting. This loss “might account for the evolutionary success of aphids to obtain beneficial symbionts,” reported aphid consortium collaborator Shuji Shigenobu of Princeton University. Buchnera bacteria have tiny genomes, and genes number about 640. But they include key ones for providing the aphid with about nine amino acids that are missing from the sap that aphids feed on. A big surprise however, was that making almost every essential amino acid was a joint venture, with some steps occurring in each species. For example, Buchnera lacks the enzyme needed for the last step in making leucine, but it's in the aphid genome, so the finishing touches take place in the aphid. This division of responsibilities “dramatically underscores the dependent nature of symbiont-host relationships at the molecular level,” says Colbourne. The consortium had expected that some bacterial genes—such as ones missing in amino-acid-synthesis pathways—might have worked their way into the aphid genome. But relatively few have, Richards reported. The consortium found about 11. At least two are important to Buchnera for making the microbe's cell wall, and these are active in the nuclei of aphid cells specialized to house the microbes. Surprisingly, those genes didn't come from Buchnera, Richards reported: They appear to have come from a different type of microbe altogether, an alpha protobacteria. The aphid was rife with duplicated genes, with an estimated 34,604 protein-coding genes in all, double the number in Drosophila. It also has several new genes, not known in other species, that code for saliva proteins that likely help keep plant juices flowing once the aphid has broken into the plant. “If you ask how we are going to control aphids on plants, this is the interaction that you have to stop,” Richards says. “And now you have a molecular entry into that.” 11. Origins # On the Origin of Sexual Reproduction 1. Carl Zimmer* Why sex? In the sixth essay in Science's series in honor of the Year of Darwin, Carl Zimmer explores why so many species take such a labyrinthine path to reproduction, when straightforward routes are available. For Darwin, sex was a big question mark. “We do not even in the least know the final cause of sexuality; why new beings should be produced by the union of the two sexual elements,” he wrote in 1862. “The whole subject is as yet hidden in darkness.” Today, biologists understand the molecular nuts and bolts of sex fairly well. Each new human being (or bird or bee) needs a set of chromosomes from each parent. But that's the how. The why of sex is still fairly mysterious. Bacteria don't have to search for a mate; they just grow and divide in two. An aspen tree can simply send out shoots that grow into new trees. No muss, no fuss with finding a partner, fertilizing an egg, and joining two genomes. Why should so many species take such a labyrinthine path to reproduction, when straightforward routes are available? Biologists first began to give the question “Why sex?” serious attention about 40 years ago, and today they're using genomics and other 21st century tools to search for the answer. They are finding hidden signs of sex in the DNA of supposedly asexual organisms and are tracking the evolutionary impact of sex among living populations of animals and plants. Some use sophisticated mathematical models to assess the conditions under which sex can arise. These efforts are providing new hints about how sex first emerged some 2 billion years ago and about the forces that have made it so widespread. The studies bolster a handful of hypotheses: Sex may speed up evolution, for example, or it may provide a better defense against parasites. In the past, scientists have focused on just one of these hypotheses at a time, but today many argue that several forces may be at work at once. ## Mating of molecules Sex gives nature much of its spice. Fireflies flash through the night to find a mate; a flower's perfume lures insects to carry pollen to distant partners; male bullfrogs croak to impress females. But despite this dizzying diversity, all sexually reproducing organisms take the same key steps to make new offspring: They shuffle their own DNA and then combine some of it with the DNA of another member of their species to produce a new genome. The key to this novelty is a process called meiosis. As with those of other vertebrates, almost all human cells are diploid: Each one contains two copies of very similar, or homologous, chromosomes. As precursor sex cells divide, they give rise to haploid sex cells of sperm and eggs, each with only one chromosome from each pair. Only when one sex cell fuses with another does it become part of a new diploid genome. Meiosis creates new variations in two ways. There's a 50-50 chance that a parent will pass down either chromosome of a given pair to his or her offspring. And during the development of sex cells, homologous chromosomes undergo recombination: They line up with each other and swap segments of their DNA. So even if two siblings get the same chromosome from their mother, their chromosomes aren't identical. In 1971, the late British evolutionary biologist John Maynard Smith helped kick off the modern study of the evolution of sex by pointing out how costly sons are to a mother. An asexual female lizard, for example, produces just daughters, all of whom can reproduce. A sexually reproducing female lizard, on the other hand, produces, on average, a son for every daughter, half the reproductive potential. Yet despite this “twofold cost of sex,” as Maynard Smith called it, he observed that sex is widespread, as most animals and plants produce males and females. And he didn't even realize how widespread sex is. It's starting to seem as if just about all eukaryotes—the lineage that includes animals, plants, fungi, and protozoans—have some sort of sex. (Fungi and protozoans don't have males and females like we do; instead, they produce two or more “mating types.”) In April, for example, signs of sexual recombination were discovered in the seemingly asexual Leishmania, a protozoan that causes the tropical disease leishmaniasis (Science, 10 April, pp. 187, 265). Other asexual eukaryotes show signs of having evolved from sexual ancestors. Trichomonas vaginalis, a protozoan that causes vaginal infections, doesn't appear to reproduce sexually, for example. But in 2007, John Logsdon of the University of Iowa in Iowa City and his colleagues discovered that its genome contains almost all the genes necessary for meiosis, suggesting that it was once a sexual creature. Given how widespread sex and sex-related genes are, Logsdon says, “it's hard to escape the conclusion” that sex first evolved in the common ancestor of all eukaryotes some 2 billion years ago. ## The road to sex In trying to understand how this transition occurred, most scientists thought that meiosis and sex evolved together, as a package. But Adam Wilkins of the University of Cambridge in the United Kingdom and Robin Holliday of the Australian Academy of Sciences have recently argued that some key steps in meiosis—namely, the reduction of diploid cells into haploids—took place long before fullblown sex existed. “It turns the conventional thinking on its head,” says Wilkins. Wilkins and Holliday's scenario starts with the ballooning of the genomes of the early, asexual eukaryotes. Although the most ancient single-celled, amoebalike creatures were probably haploid, like modern bacteria, today the eukaryote genome can be thousands of times the size of a bacterial one, and many studies suggest that it was inflated billions of years ago by invading viruslike segments of DNA called mobile elements. At first, these early eukaryotes reproduced simply by duplicating their giant haploid genomes and dividing. But at some point, Wilkins and Holliday propose, diploid cells arose. Two haploid cells might have fused, for example, or a cell may have failed to divide after duplicating its DNA. Today, some fungi pass through these kinds of diploid stages. The combination of a big genome and a new diploid stage raised the risk that eukaryotes would make fatal mistakes while copying their DNA. A chromosome can potentially join any other chromosome wherever they share similar sequences. It's safe for this to happen between homologous chromosomes, because they will swap versions of the same genes during recombination. But when one chromosome recombines with a nonhomologous chromosome, “that leads to terrible problems,” says Wilkins. Each chromosome donates some of its genes but doesn't get the same genes back. A cell that inherits one of these deficient chromosomes may die. Wilkins and Holliday argue that this risk drove the evolution of a new defense. In one or more lineages of early eukaryotes, homologous chromosomes began to line up tightly with one another before cells divided. Now recombination could take place safely. If a chromosome swapped some of its genes with another chromosome, it would get versions of the same genes back. Meiosis thus evolved as a way to reduce the damage from mismatched recombinations. It would take millions of years more before eukaryotes shifted from a mostly haploid existence to spending most of their life cycle as diploids (as we do) and only sometimes producing the haploid cells necessary today for sexual reproduction. That shift to a sexual life cycle, however, still had to overcome the twofold cost of sex. Lilach Hadany of Tel Aviv University in Israel and Sarah Otto of the University of British Columbia, Vancouver, in Canada, have been building mathematical models to explore the evolutionary pressures that might have allowed a population of asexual eukaryotes to become sexual. They find that sex can come to predominate if it's only optional. Hadany and Otto created a mathematical model of eukaryotes in which most of the organisms were asexual, but some carried genes that let them reproduce sexually when under stress. This reflects real life: Today, yeast and many species of plants reproduce sexually only during times of stress and reproduce asexually the rest of the time. The researchers found that over the generations, from one crisis to the next, the sex genes spread. By triggering organisms to reproduce sexually, these genes could become combined with new sets of genes that were better able to withstand the crisis, leading to the greater proliferation of the “sexual” individuals. Once the crisis was over, the sex genes turned off, allowing the advantageous combinations of genes to remain intact. However, this strategy “doesn't happen because sex is good for the population,” Hadany points out. Instead, the model suggests that genes for sex spread thanks to their own self ish drive to generate ever more copies of themselves. If sex started out as an optional way to reproduce, then a new question emerges: How did sex later become mandatory in many species, including our own? Hadany suspects that the answer has to do with sexiness—that is, with the preference sexually reproducing organisms often have to mate with some individuals over others. Female guppies, for example, like to mate with male guppies with bright spots; in some frog species, the females choose to mate with the males that croak loudest. Hadany and Tuvik Beker, then at Hebrew University of Jerusalem, built a mathematical model in which the frequency of sex as well as the mating preferences could evolve. Under these conditions, they found, the population evolved to reproduce sexually more and more often until asexual reproduction ceased all together. The sexy individuals were driving this evolution. Because they could attract so many more mates from the opposite sex, they could have more offspring through sexual reproduction than by just cloning themselves. (The female's advantage comes in part from sexy sons that achieve reproductive success through mate preference.) As a result, mutations that increased the amount of sex increased these organisms' success. These genes passed down to more offspring and eventually spread through the entire population. ## Here to stay Although sexiness may help explain how sexual reproduction took over, it can't fully explain why sex has managed to reign for billions of years. Because they don't have to pay the twofold cost of sex, under the right conditions, any new cloners ought to spread rapidly in a population, challenging sexual reproduction. However, given the rarity of asexuals, something must be getting in the way. Over the years, scientists have proposed about 20 different hypotheses to explain the failure of asexuality to regain much of a foothold. Logsdon calls the three with the most support from both experiments and mathematical analysis “the good, the bad, and the ugly.” The “good” refers to the ability sexual species have to adapt faster than asexual ones. If an asexual organism picks up a beneficial mutation, it can only pass the mutation down to its direct offspring. If another organism picks up a different beneficial mutation in a different gene, then there's no way for it to be combined into the same genome as the first mutation to make a more optimal genome. Sexual reproduction, on the other hand, splits up genes and recombines them into new arrangements, joining beneficial mutations. In this way, sexual reproduction may improve the fitness of a population faster than asexual reproduction. In 2005, Matthew Goddard and colleagues at the University of Auckland in New Zealand genetically engineered some yeast that could only reproduce sexually and others that could only reproduce asexually. (Typically, yeast can do both.) When Goddard raised both mutants on a near-starvation diet, the sexual yeast were able to adapt faster. As they evolved, their growth rate increased 94%, while the asexual strain increased only 80%. The difference in growth would allow the sexual yeasts to rapidly take over a population. The “bad” refers to slightly harmful mutations and what sex does to purge them. Over time, a population of asexual organisms may pick up mutations that slow their growth rate. Each mutation may be only slightly deleterious, and so natural selection fails to eliminate it from the population. As generations pass, more and more harmful mutations accumulate, dragging down the expansion of the population. Eventually, these slightly deleterious variants may replace all the undamaged versions of these genes in a population, permanently compromising fitness. Sexual organisms, on the other hand, can trade in a defective version of a gene for a working one through recombination, keeping healthy genomes intact. Real examples that celibacy can be bad for the genome exist. In 2006, for example, Susanne Paland and Michael Lynch of Indiana University, Bloomington, looked at mutations in Daphnia pulex, a species of water flea. Populations of asexual water fleas carried more harmful mutations than sexual ones. Along with the “good” and the “bad,” there is the “ugly”: namely, parasites, against which sex may be a powerful defense. In the 1970s, several researchers built mathematical models of how parasites influenced the evolution of their hosts and vice versa. Their research suggested that both partners go through cycles of boom and bust. Natural selection favors parasites that can infect the most common strain of host. But as they kill off those hosts, another host strain rises to dominate the population. Then a new parasite strain better adapted to the new host strain begins to thrive, leaving the old parasite strain in the dust. This model of host-parasite coevolution came to be known as the Red Queen hypothesis, after the Red Queen in Lewis Carroll's book Through the Looking Glass, who takes Alice on a run that never seems to go anywhere. “Now here, you see, it takes all the running you can do to keep in the same place,” the Red Queen explains. The Red Queen conundrum, some researchers have argued, may give an evolutionary edge to sex. Asexual strains can never beat out sexual strains, because whenever they get too successful, parasites build up and devastate the strain. Sexual organisms, meanwhile, can avoid these dramatic booms and busts because they can shuffle their genes into new combinations that are harder for parasites to adapt to. Red Queen models for sexual reproduction are very elegant and compelling. But testing them in nature is fiendishly hard, because biologists need asexual and sexual organisms that share the same environment and parasites. One of the few test cases scientists have found is Potamopyrgus antipodarum, a snail that lives in New Zealand lakes. Some snails have to mate to reproduce; others don't. Curt Lively of Indiana University, Bloomington, and his colleagues have spent nearly 30 years painstakingly studying the snails and one of their parasites, a fluke that can sterilize them. In a paper in press at The American Naturalist, Lively and collaborators Jukka Jokela of the Swiss Federal Institute of Aquatic Science and Technology and Mark Dybdahl of Washington State University, Pullman, present some of the most compelling evidence gathered so far for the Red Queen at work. Over the course of the past 15 years, Lively and his colleagues have documented a parasite-driven boom-and-bust cycle in asexual snails, a cycle just as the Red Queen would predict. In a New Zealand lake in 1994, the most common strains of asexual snails were initially resistant to the most common flukes. Over time, the snails became more and more vulnerable, as a well-adapted fluke strain infected them. By 2004, the snails had all but disappeared. Meanwhile, a rare strain of asexual snails in 1994 became the most common, apparently because it was resistant to the fluke strain sickening the previous dominant strain of snails. “We didn't expect to see such a dramatic shift in our lifetimes,” says Lively. As the flukes drove the asexual snails through boom and bust, the population of sexual snails has remained relatively steady, Lively says. That stability is consistent with the idea that the Red Queen effect can give sexual organisms an edge. Yet Lively doesn't think that the Red Queen on its own can fully account for the staying power of sex. Once an asexual strain of hosts becomes rare, its parasites become rare, too. So the Red Queen can't wipe out asexual reproduction altogether. It's possible that the Red Queen may be able to work more effectively to promote sex by cooperating with another force. For example, the Red Queen may drive asexual populations down to small numbers, which may make it easier for harmful mutations—the “bad”—to build up. “There are a lot of people who don't like this fusing of hypotheses,” admits Lively. “It gets messy, and it gets hard to test.” Yet Lively and some other researchers think that messiness is no reason to reject the possibility that sex has many masters. It won't be surprising if a mystery so hidden in darkness turns out to have more than one answer. ## References N. Akopyants et al., "Demonstration of Genetic Exchange During Cyclical Development of Leishmania in the Sand Fly Vector." Science 324, 265 (2009). L. Hadany and J. M. Comeron, "Why Are Sex and Recombination So Common?" Annals of the New York Academy of Sciences 1133, 26 (2008). J. Jokela et al., "The Maintenance of Sex, Clonal Dynamics, and Host-Parasite Coevolution in a Mixed Population of Sexual and Asexual Snails." The American Naturalist 174, July Supplement (2009). S.-B. Malik et al., "An Expanded Inventory of Conserved Meiotic Genes Provides Evidence for Sex in Trichomonas vaginalis." PLoS ONE 3(8): e2879 (2008). M. A. Miles et al., "Leishmania Exploit Sex." Science 324, 187 (2009). A. M. Schurko et al., "Signs of sex: what we know and how we know it." Trends in Ecology & Evolution 24, 208 (2009). J. A. G. M. de Visser and S. F. Elena, "The evolution of sex: empirical insights into the roles of epistasis and drift." Nature Reviews Genetics 8, 139 (2007). A. Wilkins and R. Holliday, "The Evolution of Meiosis From Mitosis." Genetics 181, 3 (2009). • * Carl Zimmer's latest book is Microcosm: E. coli and the New Science of Life. 12. Transportation Research # Hydrogen Cars: Fad or the Future? 1. Robert F. Service The Obama Administration wants to end the hydrogen fuel cell vehicles program, which proponents see as the ultimate clean-car technology. In May 2007, engineers from General Motors pumped 8 kilograms of compressed hydrogen gas into each of two GM Sequels, among the company's most advanced hydrogen fuel cell cars. The fuel, produced by splitting water into hydrogen and oxygen, was generated using renewable electricity from nearby Niagara Falls, on the U.S.-Canadian border. The two cars were driven 482 km, from Rochester to Tarrytown, New York. Instead of emitting roughly 90 kilograms of carbon dioxide (CO2) during the journey, their tailpipes puffed only water vapor. “It was the world's first 300-mile drive that was petroleum-free and emissions-free on a single tank of fuel,” explained GM's R&D chief, Larry Burns, at an alternative fuel vehicles meeting in March 2008. The drive may have been historic, but it didn't impress the Obama Administration. Last month, Energy Secretary Steven Chu announced that the Department of Energy (DOE) was putting the brakes on research into automotive hydrogen fuel cells. Chu cites the cost and durability of vehicle fuel cells, the inability to store large volumes of hydrogen fuel, the absence of a carbon-free way of generating the hydrogen, and the need to build a nationwide refueling infrastructure. The issue came down to a simple question, says Chu: “Is it likely in the next 10 or 15 or even 20 years that we will convert to a hydrogen-car economy? The answer, we felt, was no.” But many scientists and energy experts believe Chu asked the wrong question and, therefore, made the wrong call. No alternative-vehicle technology will make a major impact on carbon emissions, petroleum use, or anything else within the next 20 years, they say, because it takes longer than that for a new technology to displace what is already on the road. In the long run, they say only two technologies—hydrogen fuel cells and electric vehicles—are capable of getting the job done. And only one variation, plug-in hybrids, will be on the market anytime soon. “There are uncertainties with both these technologies,” says Joan Ogden, who heads the sustainable transportation energy program at the University of California, Davis. “So the idea of taking one off the table seems shortsighted.” Some influential politicians are also unhappy with Chu's proposed policy shift and have vowed to block the cuts. “I, for one, am not interested in shutting down these research projects,” says Senator Byron Dorgan (D–ND), who chairs the spending panel that will act on the president's 2010 budget request, which saves$100 million by eliminating the vehicle portions of the program while maintaining $68 million for stationary fuel-cell power plants viewed as closer to the market. Speaking at a hearing last month during which Chu laid out the Administration's plans, Dorgan declared, “We are going to do everything we can to continue the [vehicle program].” ## Making the case Invented in 1839, fuel cells use catalysts to combine hydrogen and oxygen to produce water and electricity. Their ability to generate electricity without CO2—at least within the fuel cell itself—has spawned recurring visions of a carbon-free hydrogen economy. The Bush Administration embraced the idea in 2003 when it rolled out what became a$1.5 billion research program to make hydrogen fuel cell vehicles practical and affordable. Since then, car companies have spent billions of dollars of their own money and produced two generations of cars, 318 of which remain on the road. Toyota, GM, and Honda have said that they will continue to invest in the technology regardless of what DOE decides to do.

Hydrogen proponents don't dispute that hydrogen fuel cell technology lags a few years behind plug-in hybrids. However, they argue that it's improving rapidly in virtually all areas. “We cannot abandon one of the most promising technologies around just because it is not ready for commercialization in the next 2 years,” says Ronald Grasman, an automotive engineer who manages fuel-cell market development for Daimler in Kirchheim, Germany.

Grasman and others point out that the ultimate goal is not how quickly alternative-fuel vehicles are adopted but how fast greenhouse gas emissions and the use of petroleum can be reduced. Even if plug-in hybrids hit the market first, their impact on carbon emissions will be modest initially because they rely on electricity generated primarily by burning fossil fuels. A recent analysis by C. E. “Sandy” Thomas, whose Virginia company H2Gen Innovations makes reformers that convert natural gas into hydrogen, found that hydrogen cars would actually reduce CO2 emissions more than plug-ins would by 2030, and the gap widens as the decades pass.

A big reason is their source of power. Most electricity in the United States is generated by burning coal, Thomas notes, and coal emits nearly twice as much carbon as does natural gas, the fuel most commonly used to generate hydrogen. In addition, fuel-cell electric engines are twice as efficient as the combustion engines that are still required in hybrids. A clean, carbon-free source of energy is needed for either fuel cell or electric vehicles to meet their potential, Thomas acknowledges.

The Obama Administration has already called for cutting U.S. carbon emissions 80% below 1990 levels by 2050. In the transportation sector, which accounts for more than one-quarter of all carbon emissions, “you can't accomplish that without hydrogen vehicles,” says Robert Shaw Jr., a venture capitalist and founder of Aretê Corp. in Center Harbor, New Hampshire. Shaw was vice chair of a National Research Council (NRC) panel that looked at the viability of hydrogen cars and their potential impact by 2050.

The NRC report, published last year, concluded that improvements in conventional vehicles, switching to gas-electric hybrids, and using biofuels would be the best first step in reducing CO2 emissions. But “hydrogen offers greater longer-term potential,” reads the report. “The greatest benefits will come from a portfolio of R&D technologies that would allow the United States to achieve deep reductions in oil use” by 2050. A follow-on NRC panel is now reviewing the role of plug-ins.

DOE officials, from Chu on down, would probably agree with that overall assessment of the promise of hydrogen vehicles. But that doesn't mean they think they're a safe bet. “There is really a lot of progress, but issues remain,” says Sunita Satyapal, who directs DOE's hydrogen program.

One major concern is price, in particular, the high cost of precious-metal catalysts. Today's fuel cell engines could be built for $73 a kilowatt if mass-produced, according to a recent DOE estimate, a 74% drop since 2002 but still more than twice the 2015 target price. The range of today's cars is also a problem. High-pressure tanks used by today's fuel cell cars hold enough fuel for the average fuel cell car to travel 320 km, according to the latest tally from researchers at the National Renewable Energy Laboratory in Golden, Colorado. By 2015, DOE hopes to achieve 480 km, a distance that would satisfy consumers. Durability is another issue. Some of the fuel cell cars have operated for 2000 hours without need of servicing, the equivalent of driving 96,000 km, and DOE would like to boost that number to 5000 hours. Finally, despite hydrogen's widespread use in industry, no infrastructure exists for producing vast amounts of hydrogen and delivering it to drivers when and where they need it. Given these hurdles, Chu and his DOE colleagues argue that it makes more sense to focus on areas with the potential to make the quickest impact, notwithstanding that the average car stays on the road for 15 years. “With plug-in vehicles, you can start that process now,” says Patrick Davis, who heads DOE's Vehicle Technologies Program in Washington, D.C. “With other technology, you have to start that clock later.” Mass-produced hydrogen cars may be 2 decades away. And if the onboard hydrogen-storage problem isn't solved, customers simply won't buy the cars. Fuel-cell cars aren't the only alternatives facing a rough road, however. Battery electric vehicles (BEVs) have cost and technology problems of their own. Mass-produced BEVs with a range of more than several dozen kilometers are years away. And better batteries will be expensive. A 2007 study by automotive engineers John Heywood and Matthew Kromer at the Massachusetts Institute of Technology in Cambridge projected the cost of various advanced technologies and found that all make a bigger dent in the wallet than advanced internal combustion engines. A plug-in hybrid with an all-electric range of only 16 km would cost an extra$3000, for example, whereas an electric vehicle with a range of 320 km would add $10,200 to the sticker price. The long-distance winner, a hydrogen car that could travel 400 km between fill-ups, would cost an extra$3600.

“None of these technologies are free,” Shaw says. Adds Heywood: “It's really battery cost versus fuel-cell cost. Cost reduction is a major challenge for both these paths.” Klaus Bonhoff, managing director for Germany's National Organization for Hydrogen and Fuel Cell Technology, agrees: “People are overselling battery technology today. They will not be able to do the [complete] job that people expect.”

Both technologies need to develop a better way to deliver energy to consumers. Hydrogen would appear to face the bigger challenge: Only 71 hydrogen refueling stations exist in the United States and Canada, and the distribution system is likewise scant. The NRC panel estimated that the U.S. federal government would need to spend about $10 billion between 2008 and 2023 to develop a self-sustaining hydrogen-fuel infrastructure and another$44 billion on tax credits and other subsidies, while industry invests $145 billion. In comparison, the nation already has an electric utility grid, and a 2006 study by researchers at the Pacific Northwest National Laboratory found that the existing grid could charge up to 70% of all cars and light trucks in the United States if they were plug-ins that were charged overnight when idle generation capacity is available. But battery-powered cars also need sockets into which to plug. A 2008 study by researchers at the Idaho National Laboratory estimated it would cost$878 to $2146 to add the home circuits needed to charge a plug-in. And recharging takes several hours, compared with just a few minutes for a hydrogen fill-up. Then there's fuel storage, which DOE's Satyapal says remains a “significant challenge” for hydrogen cars. In recent years, DOE has backed research on some 200 different storage materials, ranging from packing hydrogen into metal solids called metal hydrides to a slurry of alane powder in a light mineral oil. To date, none meets DOE's targets for storing and releasing enough hydrogen fuel on demand. But automotive engineers don't seem overly concerned. Daimler's new B-class fuel-cell engines have a range of 400 km using a tank that pressurizes hydrogen to 700 bar, and GM's Sequels have already gone farther than that. In addition, reducing the size and weight of the fuel cells and other electronic systems has left more room for larger storage tanks. “Storage technology is not the issue,” Daimler's Grasman concludes. The trends are similarly positive with respect to improving the durability of fuel-cell engines, lowering the cost of producing hydrogen, and finding a low-carbon means of doing so. Lab-based fuel cells have far surpassed DOE's 5000-hour benchmark, and natural gas can be turned into hydrogen for$3 per kilogram of hydrogen (the equivalent to how far a car will go on a gallon of gasoline). As renewable-energy technologies improve, they can be used to generate hydrogen as well as electricity.

Given this progress, many hydrogen experts were caught off-guard by Chu's announcement last month. “Everybody I know in the hydrogen field is just puzzled by this decision,” Shaw says. Philip Ross, a retired chemical engineer from Lawrence Berkeley National Laboratory and member of a DOE technical panel that is supposed to advise DOE's upper management on the hydrogen program, says Chu did not contact the committee before announcing his new direction.

Chu and his aides also did not reply to requests from Science for comment. However, when he announced DOE's fiscal year 2010 budget, Chu said the department is not giving up on fuel cells altogether. In addition to continuing to support stationary fuel cells, DOE will back basic research to improve the catalysts and other components of the systems.

Even if Congress restores the program's funding, some hydrogen backers worry that Chu's statements have already damaged the industry. “It has really hurt the public perception of this field,” Grasman adds. Such skepticism, when combined with the industry's overall financial woes, could undermine corporate support for the technology, Grasman contends.

That outcome would leave Chu in the position of supporting a policy that could significantly delay the potential climate and energy-security benefits he believes alternative vehicles can deliver. Says Shaw: “If you want to get to the volumes [of cars] necessary to make an impact, you have to begin immediately.”

13. Marine Biology

# Persevering Researchers Make a Splash With Farm-Bred Tuna

1. Dennis Normile

A 30-year effort has paid off in raising bluefin tuna in captivity, but the benefit for wild stocks of the embattled predator may be years more away.

OHSHIMA, JAPAN—With a snap of its jaws, a meter-long bluefin tuna grabs a fish tossed into its circular enclosure and darts away in murky Kushimoto Bay. “They're excellent swimmers,” says Yoshifumi Sawada, a fisheries biologist at Kinki University's Ohshima Experiment Station, as he shovels fish into the water. The note of pride in his voice is understandable: The bluefins in the pen are the product of a 30-year effort to rear second-generation captive tuna—something no other group in the world has accomplished. It's “a magnificent achievement,” says Daniel Pauly, a fisheries biologist at the University of British Columbia, Vancouver.

The feat could hold vital significance for one of the ocean's keystone predators. In recent decades, the bluefin tuna's succulent belly meat has become the favorite of sushi and sashimi aficionados, driving the price sky high. Tunas auctioned at Tokyo's Tsukiji fish market routinely fetch tens of thousands of dollars; in 2001, a prize 202-kilogram specimen sold for an astounding ¥20.2 million, or roughly $1000 per kilogram. To satiate rising demand, dozens of tuna farms have sprung up off Japan's coasts. Each year, Japanese fishers capture 300,000 to 400,000 young bluefins from the open ocean and fatten them in pens before shipping them off to wholesalers. But removing juveniles from the wild has only increased pressure on the heavily fished species, leaving some populations on the brink of collapse (see sidebar). The bluefin's eccentricities have contributed to its downfall. “The bluefin tuna has habits that are completely wrong for species survival,” says Gary Sakagawa, a fisheries biologist at the U.S. National Oceanic and Atmospheric Administration's Southwest Fisheries Science Center in San Diego, California. For instance, young tuna congregate in coastal areas in spring and summer as they feed on schooling fish, making them easy prey for fishers, Sakagawa says. The researchers at Kindai, as the university is known locally, hope their breakthrough will give wild tuna a reprieve. “We want to supply all of the farmed bluefin tuna harvested in Japan,” says Sawada. They have a long way to go. This year, Sawada says they hope to sell up to 20,000 juveniles to fish farms, a small fraction of what's needed. “This technology will take a while to have a positive impact on the conservation of tuna,” says Pauly. Kindai's tuna program started in 1970, when “it seemed Japanese were eating up all the world's tuna,” says university trustee Hidemi Kumai, a fisheries biologist who led the Kindai research for years. Concerned that the country would be blamed for depleting wild tuna stocks, Japan's Fisheries Agency funded three groups, including one at Kindai, to try raising bluefin tuna from eggs. As a private university with campuses scattered across a rugged peninsula that juts into the Pacific Ocean southeast of Osaka, Kindai emphasizes “practical studies” attuned to the needs of local agricultural and fishing communities, Kumai says. Kindai had already succeeded in raising yellowtail, sea bream, sole, and other fish from eggs. The university sells fry to farmers and harvests mature fish for the market, then sinks the proceeds into research. The know-how gleaned from farming other fish, however, didn't readily transfer to bluefins. “Tuna have many unique characteristics that make culturing them difficult,” says Sawada. For starters, bluefin tuna, one of the larger oceanic predators, are simply much bigger than other farmed fish. A half-century ago, before overfishing started to take its toll, 4-meter-long tuna tipping the scales at half a ton were common. These days, mature bluefins can exceed 2 meters in length and weigh 250 kilograms. When it comes to captive breeding, more than size matters. Tuna, unlike most pelagic fish, are warm-blooded. And like some sharks, they must move continuously to force water over their gills; otherwise, they suffocate. “They swim all day, all through their lives,” Sawada says. Bluefins are built for both speed and endurance: They can accelerate as quickly as a sports car, and they crisscross the Atlantic several times a year. For these reasons, tunas require pens much bigger than those used for other captive fish. It took the Kindai group 4 years to learn how to keep penned tuna alive longer than a few months. Then it took another 5 years, until 1979, to get them to spawn. That was a world first, Kumai says, but his team couldn't keep the spawned fish alive. Then, for more than a decade, they couldn't get captive tuna to spawn at all. Facing similar difficulties, the two competing research groups gave up, and Kumai worried that Kindai's program would get the ax. At one point, he confessed to Kindai's president that his team had “no results despite spending a lot of money.” “The president said to me, ”You have to take the long view when considering living creatures,‘” Kumai recalls. With such encouragement, he says, the group resolved to “succeed in this project at any cost.” (The price of success is hard to quantify, he says, as the Fisheries Laboratory, with an annual budget of about$25 million, doesn't itemize expenses by project.) Finally, in 1994 their captive tunas spawned again.

Through sheer persistence, the team has gained a trove of information about tuna biology. Postmortems on dead juveniles revealed that many fish were snapping their necks by swimming into the walls of the square enclosures. Such injuries tapered off after fish passed their 80th day. In juvenile tuna, the tail f in, used for propulsion, develops more quickly than the pectoral and abdominal fins, which adults use to steer and brake, Kumai says. “The only thing [juvenile] tuna can do is dash straight ahead,” he says. To reduce the number of deadly collisions, the researchers switched to circular enclosures.

After numerous other tweaks to rearing techniques, the Kindai team eventually bred mature fish. Six fish spawned in 1995, and 16 from the class of 1996 survived to adulthood. Those fish spawned in 2002, and Kindai is now rearing the third generation. “We've completed the life cycle,” Kumai says. That, says Sakagawa, “gives us some idea what may be going on in nature.” The Kindai group has identified behavioral triggers for spawning and clarified that the time of first spawn is more closely related to size than age. The group acknowledges that they still have a lot to learn. Kumai figures they get mature fish from only about 1% of eggs, compared with 60% for sea bream.

The Kindai group now hopes to develop an attractive product. They are selectively breeding tuna for fast growth, disease resistance, and higher-quality meat, Sawada says. The group does not plan to genetically engineer tuna out of concerns about unforeseen consequences if fish were to escape into the wild. But they are introducing the use of molecular markers, small DNA fragments that identify desirable traits, says Yasuo Agawa, a molecular biologist who cut his teeth on Drosophila and recently joined the Kindai team. Pauly, however, worries that the feed requirements of scaled-up tuna farming could harm wild stocks of feed fish, many of which are a staple for people in developing countries.

That might be avoided if the Kindai group's most ambitious plan succeeds: to transform their captives into vegetarians. Sawada says they intend to gradually substitute plant protein for fish feed, in part to improve the program's sustainability. Pauly, for one, is skeptical. “This is where these plans veer off into science fiction,” he says. He notes that despite decades of trying, the Norwegian salmon industry has not weaned farmed salmon off a fish diet.

It is unclear what impact the landmark breeding success might have on wild tuna stocks. Sakagawa worries that replacing fish caught for farms with juveniles raised from eggs might simply expand the market, as happened when Australian fisheries started pen-rearing captured Southern Pacific bluefins. He says he appreciates Kindai's contributions to understanding tuna reproductive biology. However, Sakagawa says, “I don't think it's a solution for conservation of wild stocks.”

Toward that end, Japan's Fisheries Research Agency is working to raise tuna from eggs for release. To have an impact on natural populations, a restocking effort would have to be massive—and “many issues need to be solved before [we can] start to release tuna,” says agency official Kazumasa Ikuta. But as the Kindai team has demonstrated in their decades-long effort to breed tuna, patience is a virtue.

14. Marine Biology

# Scientists Get No Respect From Fishery Managers

1. Dennis Normile

A 2008 report on the health of the bluefin tuna stock in the East Atlantic and Mediterranean recommended setting a catch quota of 15,000 tons starting in 2009. Fishery managers responded by setting quotas of 22,000 tons in 2010, 19,950 tons in 2011, and 18,500 tons in 2012.

Last June, when a scientific panel met to review the health of the bluefin stock in the East Atlantic and Mediterranean, they were miffed to find they had so little to go on. Only three of 48 member countries and regions of the International Commission for the Conservation of Atlantic Tunas (ICCAT) had reported 2007 catch data. Despite that handicap, the ICCAT advisory panel gleaned that the situation was grave: The 2007 bluefin catch, they estimated, was roughly 61,000 tons—more than double ICCAT's limit.

In its report,* the Standing Committee on Research and Statistics warned that overfishing “will most probably lead to further reduction in spawning stock biomass with high risk of fisheries and stock collapse.” To forestall that disaster, the scientists recommended that ICCAT set a quota of 15,000 tons starting in 2009. ICCAT's response: quotas of 22,000 tons in 2010, 19,950 tons in 2011, and 18,500 tons in 2012. “Even in 3 years, the quotas will be higher than what scientists recommended the quotas be immediately,” fumes Rebecca Lent, an economist in charge of international affairs for the U.S. National Oceanic and Atmospheric Administration's National Marine Fisheries Service.

ICCAT's problems run deeper than quota setting. In a September 2008 report, an independent review panel chaired by Glenn Hurry, CEO of the Australian Fisheries Management Authority in Canberra, concluded that ICCAT's management of bluefin tuna fisheries for sustainable fishing “is widely regarded as an international disgrace.”

In response to an e-mail asking for comment on the catch quotas, ICCAT Assistant Executive Secretary Victor Restrepo wrote, “We abstain from interpreting how or why the Commission makes decisions.” He added that a meeting on ICCAT's future planned for next August will address questions raised by the review panel.

Stock mismanagement hasn't yet dealt a crippling blow to bluefin stocks in the Western Atlantic and the Pacific. Although stock assessments are clouded by gaps in the data, scientists recommended there be no increase in Pacific bluefin catches above the current 23,000 tons a year. This covers taking mature tuna but not capturing juveniles for pen-fattening.

15. Astronomy

# The Tales Told by Lonely Galaxies

To what extent is a galaxy shaped by its surroundings? To find out, astronomers are seeking the rare ones that appear to be isolated.

GRANADA, SPAIN—Laden with 400 billion stars, countless planets, and vast clouds of gas, our Milky Way galaxy pinwheels through the void. Its spiral arms stretch 50,000 light-years and revolve once every 220 million years, as we plunge at 400,000 kilometers per hour toward the neighboring Andromeda galaxy. That's well known, but it's less clear how the Milky Way—or any other galaxy—came to appear as it does.

In the century since the first distant ones were recognized, astronomers have learned much about how galaxies form and evolve. But they still don't know to what extent a galaxy's properties are determined by its inner workings or through interactions with its surroundings—such as the Milky Way's potential collision with Andromeda in 3 billion years. In short, astronomers want to know how much of a galaxy's character is set by nature and how much by nurture.

To solve that puzzle, some astronomers are searching for rare galaxies well isolated from their neighbors. By comparing these loners to their more-gregarious brethren, researchers hope to tease apart the inherent inner workings of galaxies and the effects of interactions. Last month, 120 researchers gathered here to discuss such efforts.*

“If there really are significant numbers of isolated galaxies, and if we can collect large enough samples of them, then they're certain to provide some sort of fundamental insight into galaxy evolution,” says Jack Sulentic, an astronomer here at the Institute for Astrophysics of Andalusia (IAA). Astronomers have searched for isolated galaxies before, but recent massive galaxy surveys may unearth many more of the gems.

The notion of an isolated galaxy may be something of an oxymoron, however. Galaxies form through a “hierarchical process” in which smaller ones merge to make bigger ones, researchers think. So each galaxy is in fact the product of galaxy interactions. “I think there are no isolated galaxies,” says Bärbel Koribalski, an astronomer at the Australia Telescope National Facility in Epping. Still, the few galaxies that appear to be lingering alone are worth studying, says Christian Theis, a theoretical astrophysicist at the University of Vienna in Austria. “Even if they're not formed in isolation, they may have evolved in isolation for some time,” he says. “So they can give some insight into the inherent processes of evolution.”

## Gathering the outcasts

The first major catalog of isolated galaxies was created in 1973 by Valentina Karachentseva of Taras Shevchenko National University of Kyiv in Ukraine, working with her husband, Igor Karachentsev of the Special Astrophysical Observatory in Nizhnij Arkhyz, Russia. “We divided our work,” she says. “Igor worked with the pairs, and I work on the isolated galaxies.”

Karachentseva analyzed photos taken in the 1950s with a 1.2-meter telescope in the famed Palomar Observatory Sky Survey. She declared a galaxy isolated if no neighboring galaxy lay closer than 20 times the neighbor's radius or was more than four times as big in diameter as the galaxy in question. Those rules selected galaxies that had not suffered an interaction in roughly 3 billion years. The Karachentseva catalog of 1051 galaxies is “still the best game in town,” say Sulentic, who works on the Analysis of the Interstellar Medium of Isolated Galaxies (AMIGA) project at IAA.

Now, however, astronomers are trawling the enormous data sets produced in the past decade in ever-bigger sky surveys. In optical wavelengths, the Six-Degree Field Galaxy Redshift Survey has used a 1.2-meter telescope on Siding Spring Mountain, Australia, to pinpoint a total of 125,071 galaxies; the Two-Degree Field Galaxy Redshift Survey has used a neighboring 4-meter telescope to spot 221,414 more; and the Sloan Digital Sky Survey has used a 2.5-meter telescope on Apache Point, New Mexico, to bag 930,000 of them.

The new data allow astronomers to fix a galaxy's position in three-dimensional space, not just on the two-dimensional celestial sphere. As the universe expands, the galaxies speed apart. The more distant a galaxy, the faster it recedes. The motion stretches a galaxy's light to longer, redder wavelengths, so by measuring that “redshift,” astronomers can deduce the galaxy's speed and distance.

Using Sloan data, Hong Bae Ann of Pusan National University in South Korea has sifted through 100,000 galaxies lying between 275 million and 700 million lightyears away to find about 500 isolated ones. Meanwhile, Karachentsev has used data from all three big surveys to pick out 513 isolated galaxies lying within 135 million lightyears. Karachentseva has spied 3227 of them using data from the near-infrared Two Micron All-Sky Survey conducted with twin 1.3-meter telescopes on Mount Hopkins, Arizona, and Cerro Tololo, Chile.

But as catalogs proliferate, so do the criteria used to define isolation and the tensions between them. Ann focuses on the galaxies' masses and separations, and he can set his criteria so that his list recaptures 80% of the 1973 Karachentseva catalog. However, Ann seeks extremely isolated galaxies, and when he tightens his criteria the lists do not overlap at all, he says.

Whether a galaxy appears isolated may also depend on the method used to observe it, says Oded Spector of Tel Aviv University in Israel. He used the 1-meter telescope at the Wise Observatory near Mitzpe Ramon, Israel, to spot 27 extremely isolated galaxies. He then compared the optical data with data from ALFALFA, a radio survey using the 305-meter dish at the Arecibo Observatory in Puerto Rico that can detect hydrogen gas and reveal galaxies too faint to be seen with optical and infrared instruments. The ALFALFA data showed that nine of Spector's galaxies had companions after all. “One of these had seven neighbors,” he says.

## Compare and contrast

Still, the few isolated galaxies there are may shed light on galaxy content, behavior, and structure, researchers say. Theorists generally agree that the cosmos took shape after the big bang as dark matter—the mysterious stuff whose gravity binds the galaxies—coalesced into clumps. Smaller clumps merged to make bigger clumps and form a vast “cosmic web” of filaments and sheets separated by voids. Meanwhile, the dark matter clumps or “halos” drew in hydrogen gas from which stars and galaxies formed like raindrops condensing in clouds.

Researchers hope to fill in some of the details within this big picture. One question is whether star formation depends on a galaxy's environment. Galaxies in crowds are often “red and dead”: Their stars are reddish in color, and the galaxies have stopped making new ones. That could be a natural effect of aging, as the radiation from the galaxies themselves blows out the gas needed to make new stars. Or interactions with other galaxies may have stripped out the gas.

Striking a blow for interactions and nurture, Angela Iovino of the Astronomical Observatory of Brera in Milan, Italy, and colleagues tallied galaxies as far away as 11 billion light-years (a redshift of 100%) using the Very Large Telescope on Cerro Paranal, Chile. They find signs that isolated galaxies fade from blue to red more slowly than those in groups do. “Isolated galaxies stay younger longer,” Iovino says.

But Jeremy Tinker, a theorist at Lawrence Berkeley National Laboratory in California, argues for nature. Simulations of the large-scale structure of the cosmos reproduce the observed distribution of galaxy clusters and voids only if a galaxy's color and fertility depend on the mass of its dark matter halo alone, he says. “The probability of being red has to be independent of the environment,” he says.

Other studies are probing the tricks of a galaxy's heart. A galaxy can possess a radiation-spewing “active galactic nucleus” (AGN) that presumably arises when gas falls into the supermassive black hole in the galaxy's center and heats up to a temperature of millions of degrees. Researchers think that can happen when one galaxy jostles another. But can it happen in an isolated galaxy?

To find out, IAA's José Sabater looked for AGNs as part of the AMIGA project, which reanalyzes the galaxies in Karachentseva's 1973 catalog using new data. With data from the Sloan survey and elsewhere, he found that 21% of 353 isolated galaxies had AGNs. That's well below the 33% rate that M. Angeles Martinez of the University of Zaragoza in Spain found in her study of galaxies in groups. The results don't necessarily prove that a galaxy can toss gas on its own heart to make an AGN, Sabater says: An isolated galaxy with an AGN may have been perturbed while consuming a now-vanished companion.

Still, the results put a limit on what a galaxy can do alone. AGNs come in two types: those that emit radio waves and those that are “radio quiet.” Sabater finds only radio-quiet AGNs in isolated galaxies. “We can conclude that the environment is fundamental for triggering a radio AGN,” he says.

Astronomers would also like to know what sorts of structures a galaxy can generate by itself. Theorists generally agree that bloblike elliptical galaxies can form only through galaxy mergers, whereas a well-isolated galaxy has a strong tendency to form a spiral. Data seem to back that up: The various studies suggest that fewer than 20% of isolated galaxies are elliptical.

Isolated galaxies have already given theorists modeling structure something to puzzle over, however. AMIGA researchers find that at least two-thirds of the isolated spirals lack the prominent bulges often seen in spiral galaxies such as the Milky Way. “Bulgeless spirals are a challenge to the simulations, because they don't produce them in great numbers,” says Evangelia Athanassoula of the Astronomy Observatory of Marseilles Provence in France. So theorists may have to rethink certain details of galaxy structure formation.

## A loner and its companions

The question of what counts as isolation among galaxies can be subtle, as becomes clear when researchers turn to the Milky Way. The Milky Way has remained relatively unmolested for billions of years, and theorists need invoke no external influence to explain its properties, says François Hammer, an astronomer at the Observatory of Paris. By that measure, “I would say that the Milky Way is isolated,” Hammer says.

But the Milky Way is surrounded by tiny dwarf galaxies—“mosquitoes,” conference attendees call them—some of which it is shredding. “The companions of the Milky Way definitely feel its effect,” says Eric Wilcots of the University of Wisconsin, Madison. Given that it's ripping its neighbors apart, the Milky Way might also exemplify an interacting galaxy.

Such ambiguity aside, the search for isolated galaxies seems likely to continue as ever more data become available. The Sloan survey measured the positions of 930,000 galaxies; the proposed 8-meter Large Synoptic Survey Telescope would pinpoint billions. The data might reveal inherent and environmental effects too small to be seen now. “I think we have a good chance to solve this problem” of the relative importance of nature and nurture in galaxy evolution, Hammer says. However, the answer may depend on how precisely you define the question.

• * Galaxies in Isolation: Exploring Nature vs. Nurture, 12–15 May.