- INTERNATIONAL EXCHANGES
Secret Pyongyang Meeting Builds Science Ties Between Two Koreas
- Richard Stone*
SEOUL—In secret, some 200 researchers from South and North Korea met in the North Korean capital of Pyongyang last week to discuss ways to jumpstart scientific cooperation across the divided peninsula. The unprecedented gathering was “historic” in its scale and ambition, says attendee You-Hyun Moon, secretary general of the Korean Federation of Science and Technology Societies (KOFST) in Seoul.
Officials from the South Korean organizations that sponsored the event say they expect to catalyze joint projects in nanotechnology, information technology, environmental sciences, and biotechnology. Researchers in the south, aided by South Korea's $600,000 budget for inter-Korean science projects, must now raise money for specific goals. The long-term objective is to narrow the technological gap between North and South to make it easier to reunify Korea, says conference organizer Chan-Mo Park, president of Pohang University of Science and Technology.
The meeting has deep symbolic value, observers say. With six-party talks over North Korea's nuclear program stalled, “the South Korean government seems interested in expanding inter-Korean civic activities to break the current deadlock,” says Jekuk Chang, director of international cooperation at Dongseo University, who has worked with North Korea on sustainable development along the Tumen River. An expansion of scientific ties, adds Donald Gregg, president of the Korea Society in New York, “is a manifestation of the growing belief in South Korea that North Korea wants to become a more normal country and needs to be supported.”
The Korean Conference on Science and Technology, from 3 to 8 April, came close to being called off. Scheduled for March, it was postponed after North Korea protested joint South Korea-U.S. military exercises last month. And North officials told their South counterparts that the meeting would be scuttled if word leaked to the press beforehand. (Science agreed to an embargo in December.) In the hours before the event, Japan, citing a recent chill in relations with North Korea, barred 10 Korean-Japanese scientists from attending, says Park. “I could not sleep, worrying that it could be canceled at the last minute,” he says.
But everything went according to plan. Approximately 25 scientists from the South and an equal number of Korean scientists from China and the United States met with some 150 North Korean colleagues. After early awkwardness over language, “the ice melted once they began to talk about science,” says Park. “Participants spoke freely and with an open mind,” adds Moon.
Researchers zeroed in on a series of joint projects. One on software development aims to bridge the information technology gap between the two sides, says Park. North Korean scientists expressed a strong interest in alternative energy, breeding crops better suited to conditions in the North, and observing and mitigating the effects of dust storms from China. Plans are afoot to sample the flora of North Korea's uplands. In addition, South Korean scientists have proposed an ecological survey of the demilitarized zone between the nations, subject to approval by military officials from both sides.
The North Koreans emphasized that the projects must proceed on the initiative of individual scientists or nongovernmental organizations such as KOFST. Moon and others believe that ample money should be available from the South but that it will be more difficult to win approval for each project from the North Korean government. Last week's meeting included officials from a new North Korean agency, the People's Science and Technology Association, that is expected to be a major player in any North-South collaboration.
Past experience suggests that many challenges lay ahead. From 1999 to 2005, South Korea's science ministry spent $4.4 million on inter-Korean science projects, with little to show for the investment. Some projects have been delayed by export controls that limit high-tech transfers to the North. Others have languished for lack of communication. Several researchers have pointed to a common disappointment: After a connection is established, North Korean middlemen often have demanded cash up front before discussing substance. But the situation may be changing. Park says there was “hardly any money talk” in planning the meeting with his North Korean counterparts.
The most successful project by far focused on improving corn hybrids. Observers say the key to its success was the leadership of Soon-Kwon Kim of Kyungbuk University in Daegu, who has visited North Korea 27 times since 1998. “Science may be the best option to open North Korea, change North Korea, and help North Korea,” says Kim.
The conference is “a meaningful starting point,” says Moon, who notes that both sides will have to labor hard to get projects off the ground. A working-group meeting is planned for June in Shenyang, China, and if all goes well, a follow-up conference—“hopefully bigger than the one in Pyongyang,” Park says—will be held in in 2007. The South Korean government also intends to hold bilateral talks with the North in late 2006, with the aim of launching an “Inter-Korean Science Center” in Pyongyang.
- CLINICAL MEDICINE
Accident Prompts a Closer Look at Antibody Trials
- Eliot Marshall
CAMBRIDGE, U.K.—After investigating a clinical trial in London that sent six healthy volunteers into critical care last month, a U.K. agency has found no simple explanation for the accident. As a precaution, the Medicines and Healthcare Products Regulatory Agency (MHRA) announced that it will not approve any more “first-in-human” tests of antibodies like the one in this trial without first consulting “additional expert opinion.”
In an interim report on 5 April, MHRA said that it could find “no deficiency” in the manufacture of the test drug, TGN1412, a proposed therapy for autoimmune diseases. Nor did it find a flaw in the way the drug was administered. The inflammation that threatened volunteers' lives, MHRA concluded, was “most likely” caused by “an unpredicted biological action,” as many others had concluded (Science, 24 March, p. 1688).
The companies were relieved. Trial manager Parexel of Boston took comfort in the fact that the MHRA findings “support our internal review that best practices and policies and procedures were correctly followed.” TeGenero, a firm in Würzburg, Germany, that developed TGN1412 and paid for the trial, felt vindicated. “We observed the highest standards in developing this drug, and … these symptoms were both unexpected and unforeseeable,” the company said in a statement.
Details of the patients' symptoms have not been released, however. MHRA and the companies have declined to give out clinical data—to protect privacy, they say. (They also refused to release the consent form.) In its report, MHRA noted that Parexel described the patients' condition as “cytokine release syndrome,” which occurs when activated T cells produce a systemic inflammatory response. TGN1412 was designed to activate T cells, including a subset called regulatory T cells that help keep inflammation in check.
MHRA has asked Gordon Duff, a professor of molecular biology at Sheffield University, to head a committee that will report back in 3 months on what could be done to prevent another such accident.
Iraq Antiquities Find Sparks Controversy
- Susan Biggin,
- Andrew Lawler
TRIESTE, ITALY—Italian researchers in Iraq claim to have stumbled on an important cache of ancient clay tablets in one of the world's oldest cities. But others dispute the claim, and Iraqi authorities say the scientists have been acting illegally.
No archaeologist has been given permission to excavate since the U.S. invasion in March 2003 toppled Saddam Hussein. But last month, Italy's National Research Council announced that it had discovered some 500 rare tablets on the surface at Eridu, a desert site in southern Iraq. The team was reconnoitering artifacts and architecture for an online virtual museum project.
According to team member Giovanni Pettinato, an Assyriologist at the University of Rome “La Sapienza,” the tablets date from 2600 to 2100 B.C.E. and hold inscriptions featuring an unusually wide variety of literary, lexical, and historical content. He thinks they may have been part of a library.
But the find, which was widely publicized in recent weeks, has puzzled and outraged archaeologists in Iraq and abroad. Eridu was largely abandoned during the period in question, and Elizabeth Stone, an anthropologist at Stony Brook University in New York, says most real libraries were created much later than the dates the Italian team suggests. Stone, who was part of a U.S. team that inspected the site a month after the war began, says they did spot ancient bricks stamped with kings'names, but that such bricks are common and offer little historical information.
Donny George, chair of Iraq's State Board of Antiquities and Heritage, sent an irate e-mail to the Pettinato team on 6 April in search of an explanation. An Iraqi group sent recently to Eridu to investigate found no evidence of tablets, he wrote: “Why all this media propaganda … for something that is not real?” George also scolded the Italians for unauthorized work at nearby Ur, another ancient Sumerian city, where he says they have dug out “foundation stones and door sockets” and taken them to a nearby museum. As at Eridu, he wrote, they only had permission to take photos, so their actions are “a clear violation of the Iraqi antiquities law. … This means that you may be taken to an Iraqi court.”
In a statement to Science on 10 April, Pettinato confirmed that an inscribed foundation stone was taken to Nassiriya's museum following a judge's authorization. As for the Eridu find, he said the bricks and tablets have not been removed by the researchers.
Catalyst Combo Offers New Route for Turning Waste Products Into Fuel
- Robert F. Service
With oil prices approaching $70 a barrel and long-term oil supplies in doubt, researchers are scrambling to come up with fresh sources of transportation fuel. Now, chemists report a reaction that could squeeze fuel out of the waste from oil refineries.
When energy companies refine oil into gasoline, they break down or “crack” long-chain hydrocarbons in oil into medium-sized ones that make up an easily flowing liquid. But the process also generates many short and relatively inert hydrocarbons called alkanes that are far less useful. On page 257, researchers led by Alan Goldman, a chemist at Rutgers University in Piscataway, New Jersey, and Maurice Brookhart of the University of North Carolina (UNC), Chapel Hill, unveil a combination of two catalysts that can stitch together some of those short alkanes to make an ideal transportation fuel. Down the road, the catalysts could work the same magic on hydrocarbons from sources as diverse as renewable biomass, coal, and tar sands.
“It's a very clever idea,” says Robert Bergman, a chemist at the University of California, Berkeley. Bergman notes that researchers have been developing both types of catalysts independently in recent years. But this is the first time they've been paired. The new catalysts still work too slowly for large-scale use, Bergman says, but they probably can be improved: “I don't think this will be an industrial process tomorrow. But conceptually, it is important.”
Stitching short alkanes together is usually an arduous task, in part because both their carbon-atom “backbones” and the hydrogen atoms sprouting from them are attached by strong single bonds. So the Goldman and Brookhart groups began by looking for a way to convert alkanes into more-reactive compounds. The Rutgers and UNC labs had developed a class of compounds called dehydrogenation catalysts that can do that. But the compounds produced, called olefins, slow down the catalysts. The researchers hoped to solve that problem by adding a second set of catalysts that would take olefins out of the system.
The team turned to compounds that promote a reaction known as olefin metathesis. Last fall, three researchers in the United States and France won the Nobel Prize in chemistry for developing these catalysts, which are now widely used to link olefins together to make everything from plastics to pharmaceuticals. The catalysts grab on to two olefin molecules at a time and rearrange the number of carbon atoms in them. Starting with hexane, a six-carbon chain, the researchers found that they could generate a wide range of compounds, including hydrocarbons up to 18 carbons long. One catalyst combo yielded primarily 10-carbon chains, an ideal component of ultraclean diesel.
The new catalytic duo is still much too slow to compete with commercial petrochemical catalysts. Goldman suspects that par t of the problem is that the olefin metathesis catalysts can break down under the 125° to 175°C temperatures in their reactor. The team is working to make them more stable at high temperatures.
Another “especially interesting” path forward could be to use the new catalysts to convert agricultural waste into liquid fuels, says James Dumesic, a chemist at the University of Wisconsin, Madison. Two years ago, Dumesic's group came up with a catalytic duo that can transform a derivative of glucose—a chief component of plant matter—into hexane. The new work shows that it's possible to convert hexane into the hydrocarbons in gasoline and diesel. If the two processes can be put together and made commercially viable, the combination could offer energy companies a way to produce gasoline from plant wastes. That could transform gasoline into a form of renewable energy and dramatically change the world's long-term energy outlook.
- NUCLEAR POWER
DOE Asked to Fill in the Blanks on Fuel Recycling Research Plan
- Eli Kintisch
The Bush Administration's plans for a grand research program aimed at eventually recycling nuclear waste aren't ready for prime time, legislators said at a pair of hearings last week. But they seem willing to support at least most of the $250 million price tag for next year.
Dubbed the Global Nuclear Energy Partnership (GNEP), the program was launched in February as a high-tech effort to expand nuclear power globally. At its technical core is a move to reprocess nuclear waste to extract fuel to be burned in so-called fast reactors. But although scientists are hashing out the particulars—researchers from nine Department of Energy (DOE) national laboratories met last week in Salt Lake City, Utah, to put together a research plan—the lack of detail is frustrating lawmakers.
“Why doesn't Congress know more about [GNEP]?” asked Michael Simpson (R-ID) at a 5 April meeting of the House Appropriations Energy and Water subcommittee, which funds DOE's civilian research programs. (The next day, a panel of the House Science Committee held another hearing on the project.) Simpson supports GNEP, but he's unhappy that DOE Assistant Secretary for Nuclear Energy Dennis Spurgeon couldn't provide a road map for the project that includes estimates of foreign contributions and full costs. Outside scientists are as flummoxed as policymakers. “I'm not sure anybody really knows what GNEP is,” says nuclear engineer and longtime DOE grantee Denis Beller of the University of Nevada, Las Vegas.
Part of the rationale for GNEP is to reduce the volume of waste that will require long-term storage. The government is responsible for disposal of some 55,000 metric tons of spent fuel rods at U.S. sites, but its designated repository—at Yucca Mountain in Nevada—isn't expected to open before 2020 and is expected to reach its legal capacity by then.
Subcommittee Chair David Hobson (R-OH) added nonbinding language to a spending bill last year instructing DOE to develop chemical reprocessing facilities that would extract fuel to be used in current U.S. reactors—a move DOE says would reduce the volume of wastes destined for Yucca by an estimated 10%. Now Hobson wants any reprocessing facilities DOE builds to offer storage for spent fuel rods. But DOE says it cannot legally hold the waste in such facilities. And DOE officials argue that burning recycled fuel in fast reactors would increase Yucca's capacity by at least sixfold.
GNEP's opponents, such as Tom Cochran of the Natural Resources Defense Council in Washington, D.C., say the dismal record of fast reactors abroad—the Monju reactor in Japan has yet to restart after a 1995 sodium fire—should be a lesson for DOE. And IBM physicist Richard Garwin, who supports an expansion of nuclear energy, told Science Committee Energy Subcommittee Chair Judy Biggert (R-IL) that DOE's plan to do detailed systems and cost analysis in parallel with GNEP was akin to “driving without a map.” Garwin also critiqued DOE's initial focus on the reprocessing of waste; he says showing that a fast reactor can be economical and safe is more important.
GNEP technical manager David Hill says an outline of the research plan hashed out at the Salt Lake City meeting should be available soon. And DOE manager Shane Johnson says the department would consider Garwin's advice to save money by scaling back recycling performance goals “if upon further investigation, that was [found to be] the correct form of action.” Such flexibility is exactly what Congress hopes to see as it mulls DOE's latest project.
- PEER REVIEW
Australia's Proposed U.K.-Style Merit Ranking Stirs Debate
- Elizabeth Finkel*
MELBOURNE—Australia is considering a radical overhaul of the way it allocates funds to universities and research institutions. But some academics worry that the changes, proposed in March by an expert panel, could be costly without significantly improving basic research.
The so-called Research Quality Framework (RQF) would rate all publicly funded research institutions and award block grants based on a new formula. Critics note that the United Kingdom, which pioneered a similar system, is now debating whether to scrap it because it is seen as unduly complex (Science, 31 March, p. 1848). The new Australian system could go into effect as early as 2008.
There's no doubt that RQF would have “dramatic effects” on universities, says Bradley Smith, a spokesperson for the Federation of Australian Scientific and Technological Societies (FASTS), which supports the concept of the framework but worries that its methods may be flawed. “It will drive the stronger groups and destroy the weak ones,” says Smith. Adds Judith Whitworth, director of the John Curtin School of Medical Research in Canberra: “We all agree that scarce resources need to be focused and that quality needs to be measured,” but “the devil lies in the detail.”
Some $614 million of the Australian government's current $4.4 billion investment on research comes in the form of block grants to 38 universities and research institutes. In 2004, then-Education Minister Brendan Nelson said it was time to develop a better rationale for allocating the money, which critics say is spread too thin. Physicist Gareth Roberts, president of Wolfson College at the University of Oxford and architect of the U.K.'s Research Assessment Exercise, led an advisory group that produced the RQF.
Government block grants are now awarded based on measures of productivity such as the number of publications and Ph.D. students completing degrees at an institution. The proposed RQF would use a system of peer review to assess research quality and add another parameter: “impact,” which would take account of social, environmental, and economic dividends. But some scientists worry that too much emphasis on impact could favor applied research at the expense of academic research.
There is also concern that the framework plan will impose a corporate, target-oriented culture onto the academic research sector. “We cannot set targets. We cannot say that next year we are going to produce 10 papers, and we are going to get x amount of funding from the outside,” says Patricia Vickers-Rich of Monash University's School of Geosciences. Virginia Walsh, executive director of the Group of Eight Universities (Australia's major universities), says, “There's no way we'd do justice to all the disciplines” if the government were to adopt the panel's proposal to have a dozen peer-review committees when the U.K. system used 67.
An advisory group headed by Australia's chief scientist Jim Peacock is expected to report by June on the weighting factors and other issues.
- U.S. IMMIGRATION
Congress Weighs Steps to Retain Foreign Talent
- Yudhijit Bhattacharjee
Fu Chiu spent months looking for a job as a technology transfer specialist with a U.S. biotech company after he received his Ph.D. in molecular biology from the University of Illinois, Urbana-Champaign. But the native of China couldn't hang around the United States indefinitely, because his student visa expired 1 year after his 2003 graduation. So Chiu crossed the Atlantic to work for a U.K. government-funded organization, then headed home to China to join a biotech firm in Shenzhen that specializes in gene therapy.
U.S. academic and business leaders have lobbied hard to include reforms in several pending bills that would make it easier for highly skilled foreigners like Chiu to stay. Such reforms are needed, they argue, if the country is to compete effectively in today's global economy. Last week, they lost their best chance to date to see them enacted, however, when a bipartisan immigration reform bill stalled in the U.S. Senate. But supporters haven't abandoned hope: They expect the issue to be back on the table when Congress returns later this month.
One key provision in the failed immigration bill would have granted automatic permanent residency, or “green cards,” to foreign students like Chiu who find a job in their field. Other measures include increasing the cap on H-1B visas—temporary visas for skilled workers—from the existing 65,000 to 115,000 annually, with a built-in provision to add 20% if the quota was filled in the preceding year, exempting spouses and minor children of foreign workers from this cap, and increasing the annual employment-based green card cap from 140,000 to 290,000 (see table). (Under current rules, foreign workers need their employers to sponsor them for a green card. The entire process can take several years.)
“There's a growing realization that this issue is not about immigration but about competitiveness,” says Bill Bates, vice president for government affairs at the Washington, D.C.-based Council on Competitiveness. “The prospects for some of these measures going through are definitely bright.” A cluster of bills introduced in January by senators Lamar Alexander (R-TN) and Jeff Bingaman (D-NM) (Science, 3 February, p. 594), and an upcoming measure sponsored by Senator John Cornyn (R-TX), may provide a home for such measures.
There is sharp disagreement on what those measures would do to high-tech employment, however. Ira Mehlman of the Federation for American Immigration Reform (FAIR) in Washington, D.C., which opposes the measures, says increasing high-tech immigration would dampen interest by native-born Americans in science and engineering by increasing the competition. That, in turn, depresses wages, he believes.
But Ralph Wyndrum Jr., president of the Institute of Electronic and Electrical Engineers-USA, thinks permanent residency will free well-trained foreign students from the limitations imposed by an H-1B visa and bolster salaries. “These people will be able to go around shopping for the best jobs,” Wyndrum says. “The free market shall prevail.”
Two Unexpected Players Add Twists to Liver's Comeback Story
- Gretchen Vogel
If only other organs had the regenerative power of the liver. Surgeons can remove more than two-thirds of the organ, and within weeks, it will regrow to its previous size. Scientists so far have found at least a dozen signals that seem to play a role in such regeneration, and now two groups have identified two new and unexpected players.
On page 233, scientists reveal that the concentrations of bile acids in the liver help control both the start and end of liver regeneration. And last week, a different research team published evidence that the neurotransmitter serotonin also governs the liver's regrowth (Science, 7 April, p. 104).
Serotonin is best known for its role in the brain; the family of antidepressants that includes Prozac works in part by influencing the brain's serotonin levels. But serotonin can also prompt cell division. Pierre-Alain Clavien of the University Hospital of Zurich, Switzerland, and his colleagues showed that knockout mice lacking the chemical had drastically reduced ability to regenerate their livers in response to partial surgical removal. That capacity was restored when the scientists gave the animals a serotonin precursor. A compound that triggers the serotonin receptor likewise resurrected the animals' regenerative powers. Clavien and his colleagues suggest that such molecules might speed regeneration in liver transplant patients.
The unexpected discovery that bile acids influence liver regeneration may provide as much insight into how the process ends as how it starts. These acids seem to tell the body when the organ is big enough to do its job. A healthy liver removes bile acids from the blood. The acids help digest fats, but they are toxic outside the digestive system. David Moore of Baylor College of Medicine in Houston, Texas, and his colleagues found that when mice ate diets rich in the bile acid cholic acid, their livers regenerated faster than did those of control mice following surgical removal of most of the organ. Mice fed a diet that lowers bile acid levels did not regenerate their livers as quickly as controls did.
The effect seems to involve the bile acid receptor called FXR; mice lacking FXR took much longer to begin regenerating their livers. Moore and his colleagues propose that FXR keeps tabs on the level of bile acids passing through the liver. If the liver isn't keeping up, the molecular sensor triggers the proliferation of new hepatocytes until the organ can handle the bile acid load, he says.
Both finds highlight that the liver has overlapping systems that can trigger regeneration in response to a variety of problems, says George Michalopolous of the University of Pittsburgh Medical Center in Pennsylvania. “There's a tremendous amount of redudancy,” he says. Liver regeneration is “like a car with 20 cylinders. You crank up the engine, all 20 cylinders fire. These are cylinders 21 and 22.”
Fossils Clinch Identity of Lucy's Ancestor
- Ann Gibbons
The meter-tall australopithecine named Lucy has reigned for 30 years as the world's most famous human ancestor. But who were Lucy's ancestors? A series of fossils from a stack of sediments more than a kilometer high in northeastern Ethiopia now helps prove what many researchers had suspected: that Lucy's species, Australopithecus afarensis, evolved from a 4-million-year-old upright hominid called Australopithecus anamensis.
The discoverers of the new fossils, who present their finds in this week's issue of Nature, also propose that an even older hominid called Ardipithecus, whose bones were found closer to the base of the rock layers, was the most likely ancestor of A. anamensis and all later australopithecines. Thus, they claim a three-part evolutionary series of human ancestors in a single river valley.
Many researchers are now convinced that A. anamensis was the long-sought ancestor of A. afarensis, which ranged across east Africa from 3 million to 3.6 million years ago. “It's clear you can see the trend over time from A. anamensis to A. afarensis,” says paleontologist Alan Walker of Pennsylvania State University in State College. But he and others aren't sure about Ardipithecus as direct ancestor of australopithecines. “It has been postulated but not demonstrated,” says paleoanthropologist William Kimbel of Arizona State University in Tempe.
Researchers from the international Middle Awash research project, co-led by Tim White of the University of California, Berkeley, found fossils of the three species in the Middle Awash valley over the past 12 years. In one area, they found the newly described A. anamensis fossils, including jaws, teeth, a finger, a toe, and a thighbone, directly below a younger rock layer containing A. afarensis fossils. The fossils confirm that A. anamensis's teeth and jaws were more primitive than those of A. afarensis, but the thighbone, the first from this species, was more like Lucy's species, suggesting upright walking, says White.
That fits with Kimbel's independent analysis of fossils from Kenya and Tanzania, to be published this spring in the Journal of Human Evolution. His team found that key skull and teeth traits support A. anamensis as A. afarensis's ancestor.
At another site, the Middle Awash team found a jawbone of A. anamensis just 80 meters above a 4.4-million-year-old layer with fossils of Ardipithecus ramidus. Changes in the teeth and skull, such as canines that get smaller, suggest that the two may have been members of a single lineage that evolved between 4.4 million and 4.2 million years ago, rather than separate lineages. However, “testing these hypotheses will require additional fossils from other sites,” admits White.
Others agree. “I don't think that the published evidence shows [the link between A. ramidus and A. anamensis] very convincingly,” says zoologist Meave Leakey of the National Museums of Kenya. Stay tuned: The discovery last year of another 4-million-year-old skeleton and more fossils of Ardipithecus under study could provide the missing data.
- ASTROBIOLOGY SCIENCE CONFERENCE 2006
Life Slow Enough to Live on Radioactivity
- Richard A. Kerr
ASTROBIOLOGY SCIENCE CONFERENCE 2006, 26–30 MARCH, WASHINGTON, D.C.
Life is slow at Earth's extremes—buried for millions of years beneath kilometers of cold ocean mud, say, or sweating out the heat in ancient rock 3 kilometers down in South Africa. Really, really slow. So slow, a new measurement suggests, that a substantial number of subsurface microbes might be surviving solely by consuming a product of feeble radioactive decay lingering from before Earth's formation. Even life on Mars, if any exists, could be hanging on beneath the martian surface living off such radiolysis.
At the meeting, geochemists Arthur Spivack, Guizhi Wang, and Steven D'Hondt of the University of Rhode Island (URI), Narragansett, explained how they used variations in the chemistry of 400 meters of cored sediment to gauge the pace of life beneath the sea floor of the eastern equatorial Pacific. Microbes there make a living by oxidizing organic matter—which was buried up to 12 million years ago—while chemically reducing sulfate, iron, and manganese. By tracking the changing concentrations of the carbon dioxide produced and the sulfate, iron, and manganese consumed with increasing depth beneath the sea floor, the URI group could calculate the rate of those reactions and thus the rate at which microbes could extract energy from them. Dividing by the number of cells seen in the sediment yields the rate at which a cell uses energy.
In the old and cold muds of the eastern equatorial Pacific, microbes “are utilizing very, very low levels of maintenance energy,” said Spivack. The rate comes to 2.8 × 10−16 kilojoules per cell per year, or 10,000 times lower than energy consumption in a slow-living bacterial culture in the laboratory. At that rate, sediment microbes are certainly not “thriving,” as the headlines often have it. They may not be doing any more than repairing the inevitable molecular decay due to radiation damage and the passage of time.
Such slow-mo microbes may point the way to creatures that live entirely “off the grid,” independent of the energy the sun supplies by means of photosynthesis. One way to live sun-free would be to consume the hydrogen gas generated when rock's natural store of radioactive uranium, thorium, and potassium decays and splits water molecules (Science, 28 February 2003, p. 1307). The URI group calculates that marine sediment in another core has enough natural radioactivity to “feed” 10% of the microbes there. In midocean sediments, which have much less organic matter, radiolysis may be the dominant energy source, they say. And a Mars soil, they calculate, could support a respectable 10,000 cells per cubic centimeter on radiolysis alone.
To astrobiologist Tori Hoehler of NASA's Ames Research Center in Mountain View, California, the vanishingly slow pace of life in deep-sea sediments is a vivid reminder that “there are energetic boundary conditions to the survival of life.” It's all well and good to find signs of past water on Mars, he says, as at the Opportunity rover landing site, but NASA needs to “follow the energy” as well. As the new sediment work shows, that could be a far greater challenge.
- ASTROBIOLOGY SCIENCE CONFERENCE 2006
Diversity Before Life
- Richard A. Kerr
ASTROBIOLOGY SCIENCE CONFERENCE 2006, 26–30 MARCH, WASHINGTON, D.C.
In the beginning, Darwin posited a “warm little pond” where life's chemical starting materials and then life itself first appeared. But lately, prebiotic chemists have favored sea-floor hot springs as the site where simple carbon compounds merged into the complex ones needed to begin life. At the meeting, prebiotic chemist George Cody warned that deep-sea hot springs couldn't have produced all of the necessary components. Instead, the final assembly of molecules leading to life must have happened somewhere between deep-sea vents, warm little ponds, and any number of other chemical stew pots.
Cody, who works at the Carnegie Institution of Washington's Geophysical Laboratory in Washington, D.C., has been a central player in the search for high-temperature and high-pressure reactions that produce the basic biochemistry of life. He's had some success producing carboxylic acids, key intermediates in sequences of biochemical reactions that extract energy from sugars. Metal sulfides commonly found in hot spring rocks make particularly good catalysts for such reactions, he found. And in other hydrothermal reactions, adding ammonia to the mix results in a variety of amino acids. But it takes unfamiliar starting components to get the metabolic intermediates, and the amino acids produced are not usually the ones life prefers. Worst of all, important sugars and nucleobases fall apart under hydrothermal conditions.
Submarine hot springs no doubt could have played a role in brewing the primordial soup that gave rise to life, Cody said, but other environments must have contributed too. “If I said it all happened in hydrothermal vents, that won't move this field ahead,” he says. “Thinking more globally could open up something.” Perhaps the real action came along continental margins, he said. There, prebiotic compounds from deep-sea vents rose to meet drainage from the land's warm little ponds and fallout from atmospheric reactions triggered by lightning and sunlight. “This is a very good approach, quite novel,” says organic chemist Vera Kolb of the University of Wisconsin, Parkside. “People get bogged down with the particular conditions they're studying, but he wasn't pushing his own work.”
Such a “global origin” scenario, however, would make it less likely that life arose elsewhere in the solar system, Cody says. The subsurface oceans on the icy moons Europa and Enceladus might not have offered the required diversity of environments. And Mars may not have had even a short-lived ocean.
- NUCLEAR RADIATION
Return to the Inferno: Chornobyl After 20 Years
As health experts track the diseases caused by the world's worst nuclear accident, engineers prepare to slide a monumental tomb over the burnt-out reactor
HOMYEL, BELARUS, AND CHORNOBYL, UKRAINE—In a cavernous marketplace, radiologist Alla Oplachikova strides past stalls with slabs of beef and pork dangling from hooks, past canvas sacks brimming with grains and dried fruits, and makes a beeline for the produce section of the Central Bazaar in Homyel.* She stops at one vendor, flashes her badge, and picks a handful of mushrooms. “For analysis,” she tells the seller, then whisks the samples to a room at the back of the hall.
Every morning, Oplachikova's dawn patrol swings into action. As trucks roll into the bazaar, her team scans goods with a Geiger counter. “We measure every shipment,” she says. For good reason: 20 years ago this month, the Homyel region was drenched with radioactivity from an explosion at the nearby Chornobyl nuclear power plant. The aftereffects of the infamous disaster are still being felt here in southern Belarus, where levels of two radionuclides—cesium-137 and strontium-90—will remain high, in patches, for decades.
The threat of contamination keeps the Homyel rad-rangers on their toes. Oplachikova puts some mushrooms in a gray, lead-lined brick box wired to a radiometer and eyes the needle. A feeble tremor indicates that it's safe to eat. A few years earlier, she says, a fillet of wild boar drove the needle off the scale. “It's dangerous to handle that kind of sample,” Oplachikova says. “But we get paid extra.” Impounded food is buried, and tainted milk is diluted to acceptable levels of radioactivity and sold to consumers, she says. In recent months, her team has flagged only a few risky shipments. “The trend is getting better,” she says.
As the years have passed since the world's worst nuclear accident spewed fallout across Europe, the hardest-hit regions in Belarus, Russia, and Ukraine are slowly healing. In Belarus, fields are fertilized and limed to expel or bind radionuclides before sowing crops. Elderly evacuees have reclaimed their homes. And later this year, work will begin on a massive structure to isolate Chornobyl's destroyed reactor from the environment, permitting safe dismantlement and disposal of its toxic innards.
But scars run deep among the survivors. For some, Chornobyl was a death sentence: According to a U.N. report issued last September, an estimated 4000 people are expected to succumb to fallout-induced cancers, in line with predictions from studies of the survivors of the atomic bombs dropped on Hiroshima and Nagasaki (Science, 9 September 2005, p. 1663). Some experts have challenged that figure, contending that the cancer toll could climb into the tens of thousands. “There are many uncertainties. Nobody can say the exact number,” says Shunichi Yamashita, a radiation expert at the World Health Organization (WHO) who has studied Chornobyl victims for 15 years and affirms that the effects of low-dose radiation are diabolically hard to pin down. However, Yamashita believes the ultimate figure will be closer to the U.N. figure.
For many victims, life goes on—but with complications. Studies point to an elevated incidence of cataracts; anxiety and depression, linked to brooding over an invisible threat, are rampant. Some scientists in Belarus claim to have detected a rise in birth defects since the accident, although the general consensus is that this is an artifact of better reporting. Still, many agree that the story of Chornobyl-inflicted diseases is still unfolding. Says oncologist Alexey Okeanov of the International Sakharov Environmental University in Minsk, “Belarus is one big laboratory.”
In a grassy field, row upon ragged row of derelict vehicles used in the emergency are decaying in the Exclusion Zone, a Luxembourg-sized area around Chornobyl that's deemed uninhabitable for people of reproductive age or younger. The scene attests to the scale of the unparalleled operation 2 decades ago to stifle the burning nuclear reactor. From a 3-meter-tall viewing platform, you can see the motley assemblage of 2000 trucks, fire engines, armored bulldozers, and hulking gray military helicopters parked in front of a pine forest that's too dangerous to enter without protective gear.
The fatal events are now part of nuclear lore. In the early morning of 26 April 1986, Chornobyl's number four reactor exploded after a botched safety test, killing two technicians and exposing 28 other workers and firemen who raced to the scene that night to a lethal blast of radiation. The reactor burned for 10 days, disgorging 400 times the radioactivity released by the Hiroshima bomb.
In a secret operation, the Soviet military dispatched hundreds of thousands of “liquidators”—mainly soldiers, scientists, and engineers—to smother the fire in the reactor core, consolidate radioactive waste in several hundred dumps in the Exclusion Zone, and build a concrete-and-steel sarcophagus, now known as “the shelter,” over the destroyed reactor building. Each morning, as liquidators boarded buses from camps on territory deemed clean, they received a calming (and as many Soviet scientists believed, protective) glass of red wine, says Galina Lyatusova, a physician who headed a first aid station for liquidators in 1986 and now monitors the health of plant workers and scientists in Chornobyl village.
Of the 600,000 registered liquidators, about a third were deployed in the first months after the accident, the high-risk period. “We could see the influence of radiation on their blood,” Lyatusova recalls. “Their white blood cells were dropping. If the counts got too low, we wouldn't let them go to work the next day. The sickest people tried to go home. I don't know if they made it.” Only in the spring of 1988 did the Soviet government declassify information on Chornobyl research and cleanup operations.
To find out precisely how much radiation the liquidators absorbed, Vadim Chumak of the Scientific Center of Radiation Medicine in Kyiv and his colleagues in the mid-1990s began exploiting a reliable chronicle of dose: teeth. Their technique measures the warping of tooth enamel inflicted by radiation, detected in electron paramagnetic resonance. “Instead of throwing the teeth in the wastebasket, the dentists send them to us,” Chumak says; 6000 have been collected in Ukraine so far. After accounting for background radiation, including dental x-rays, they've concluded that liquidators generally received smaller doses than Chornobyl records indicate.
Chumak and his colleagues on the Ukrainian-U.S. team have found that cataracts, a hallmark affliction of Japanese atomic bomb survivors, are more prevalent among liquidators who received higher doses. And he says they have “some indication” of a small number of cases of radiation-induced leukemia among liquidators, although the analysis is not yet complete. An earlier study in Russia, however, failed to detect a heightened leukemia risk, although it did report high rates of stroke, high blood pressure, and digestive disorders. Okeanov, meanwhile, asserts that liquidators are far more likely to contract lung cancer. It may take years to sort through the conflicting claims, says Yamashita: “This high-risk group needs to be closely monitored.”
Discerning health effects among the general population is even trickier. The radiation “signal” is weak, easily swamped by other factors that degrade health, such as smoking, alcoholism, and poor nutrition. “There remains a lack of evidence of any measurable effect of Chernobyl radiation exposures on solid cancers in the general population except for childhood thyroid cancer,” notes the September 2005 report from the U.N.'s Chernobyl Forum.
Children were hardest hit. The presence of radioactive iodine-131 in fallout led to an epidemic of thyroid cancer in children: some 4000 cases to date, including nine deaths (Science, 20 April 2001, p. 420). Belarus was totally unprepared. “We didn't get any notice about the Chornobyl accident,” says Jacov Kenigsberg, chair of the National Commission of Radiation Protection in Minsk. Kept in the dark in the crucial first days after the accident, Belarusian officials did not begin to distribute iodine pills to children and evacuate hard-hit villages until a week after the accident—“too late,” Kenigsberg says. The developing thyroid gland absorbs iodine like a sponge; taking stable iodine as a pill blocks the uptake of the hazardous radioisotope, which has a half-life of 8 days. Children exposed to the highest levels of iodine-131, mainly through milk, suffered irreparable harm to their thyroids.
Despite the fallout cloud's huge footprint, studies have not established a link between Chornobyl and noncancer illnesses. But anecdotal data abound. Throughout the 1990s, doctors in Homyel and other contaminated regions registered increases “in all kinds of diseases,” from heart disease to endocrine and nervous system disorders—many lacking a plausible mechanistic link to radiation, says Valery Gurachevsky, a physicist who chairs Belarus's Committee for the Consequences of the Chernobyl Catastrophe. “This is a big riddle.” The likeliest explanation, he argues, is that a grab bag of woes—from pollution to lingering stress—has eroded public health. “So far, almost no serious research has been done on noncancer health effects,” says Okeanov. “Medical science says the danger is not that high, the situation is under control. But we need thorough studies.”
A monumental task
In a bunkerlike office deep inside the Chornobyl shelter, Pyotr Lyushnya, a plant engineer, points to a diagram on the wall, a blueprint of the several-story reactor complex marked with radioactivity levels. The hottest recorded spot could deliver a lethal dose in minutes. The shelter's high humidity, from leaks of rain and melting snow, rusts the debris core, a hardened mixture of building materials and melted nuclear fuel, including about 180 metric tons of uranium. Dust in the building is studded with hot particles—radioactive howitzers that can riddle internal organs with alpha or beta particles. Lyushnya admits that this preternatural environment can be nerve-wracking, especially when he's the only one working the night shift. “It's natural to feel creepy,” he says, “when you have to make trips by yourself into the destroyed rooms.”
All work in the shelter is now focused on one goal: keeping the frail structure intact until a massive enclosure can be slid over it. After 10 years of arduous negotiations, construction of the $800 million New Safe Confinement (NSC) is set to start later this year. Two international consortia with Ukrainian partners—one led by CH2M Hill, the other by Novarka—are bidding for the contract. A decision is imminent, officials say.
Billed as the world's largest movable structure, the NSC is conceived as a steel lid 150 meters long and 100 meters high—taller than the Statue of Liberty. Its construction presents unprecedented perils. “There are very many interesting engineering problems. Not everything has been solved yet,” says Nikolai Steinberg, an official with the Ministry of Fuel and Energy of Ukraine who helped design the original shelter. After the accident, fuel elements and waste were buried haphazardly and will pose a risk during excavations for the NSC's foundations, says Serge Gronier, an engineer with Electricité de France, part of the NSC design consortium with Battelle Memorial Institute in Richland, Washington, Bechtel International Systems in San Francisco, and the Chornobyl Nuclear Power Plant.
Originally, engineers proposed building the NSC upright several hundred meters from the shelter and sliding it into place, says Eric Schmieman, a Battelle environmental engineer who was involved in the NSC's conceptual design. Health physicists knew that workers at ground level would be exposed to radiation from buried materials and to radiation emanating from the shelter. They were also concerned about “sky shine”: radiation emanating from the roof that's reflected downward by atmospheric particles. “As you go up in elevation, sky shine becomes more of a problem,” says Schmieman. To reduce dose (and the mundane risk of falling), the NSC will be constructed in segments on the ground and then hoisted up.
After completion, forecast for 2010, the NSC will be slid on rails over the shelter. The unique hazards won't end there. It will be essential to prohibit condensation on the inside of the NSC to prevent corrosion of the steel frame, for example. And air movement must be minimized to avoid stirring up and resurrecting the bane of shelter workers, radioactive dust. Calculating the fluid dynamics of this unusual milieu is no mean feat. “The modeling effort challenged the limits of computational capacity available even at the U.S. national laboratories,” Schmieman says.
Perhaps the biggest challenge will be to pick apart and permanently entomb what remains within the rickety shelter. Engineers will use remotely operated cranes for the disassembly. But the fuel-containing masses will stay put for the time being. “The technology does not yet exist to safely remove it,” Gronier says. With the NSC designed to last at least a century, the hope is that the fuel can eventually be moved to a deep geological repository. That will be a problem for the next generation to solve, he says.
A generation hence, most people will only vaguely recall one of the most notorious accidents of the 20th century. Already, symbols of the nightmare are disappearing. Most contaminated settlements in the Exclusion Zone have been torn down; the timber and other building materials have been buried in the sandy soil to reduce the amount of radioactivity dispersed by wildfires. The only indications of those former villages today are grassy barrows topped with yellow, triangular radiation-hazard signs.
In two generations, most of the radioactive cesium and strontium will have decayed, and most of the liquidators who put their lives on the line will be gone. But the generation that experienced the disaster is still haunted by memories. “The true story of Chornobyl,” says Ronald Chaser, a radio ecologist at Texas Tech University in Lubbock who carries out studies in the Exclusion Zone, “is the human tragedy.”
Once a Terminal Case, the North Aral Sea Shows New Signs of Life
- Christopher Pala*
A dike supported by the World Bank and repairs along the banks of the Syr Darya River have increased the water level dramatically
ALMATY, KAZAKHSTAN—By the early 1990s, much of the area around the northern end of the Aral Sea had become a salt-encrusted wasteland, desiccated by decades of ill-conceived cotton irrigation. Some ecologists seemed ready to write it off, but the World Bank decided in 1999 to support a rescue mission. Among other measures, the project created a 13-kilometer dike designed to raise the sea's level and decrease its salinity.
Managers settled in for a long haul, assuming that it would take up to 10 years for the water to rise 3 meters and cover 800 square kilometers of dry seabed (Science, 18 February 2005, p. 1032). They were wrong. Just 7 months after the dike's completion, the Small Aral Sea has reached the target level, 42 meters above the level of the Baltic Sea. Spare water is already flowing through the spillway—evidence of what may become one of the biggest reversals of an environmental catastrophe in history.
“We are very pleased,” says Masood Ahmad, the World Bank project coordinator. Looking back, Ahmad points to several factors that may have sped the project to an early success. All relate to the health of the Syr Darya River in the north, one of Central Asia's two great givers that flow into the Aral Sea and sustain it.
The Syr Darya itself deteriorated in the years following the collapse of the Soviet Union, as barriers along its banks fell into disrepair, lowering the amount of water it could carry safely. Another key problem, according to Ahmad and other specialists, was that Kyrgyzstan took an increasing volume of water during winter to run power turbines. To avoid flooding the eroded infrastructure downstream, this water had to be shunted off into lakes along the river, where it served no useful purpose. During summer, when the water level was naturally low, more water was withdrawn for crop irrigation. The result: Little water reached the sea.
Now, after several years of rehabilitation work on dams, sluices, and barrages along the Syr Darya in Kazakhstan, the river's capacity has been safely doubled to 700 cubic meters per second, which allows nearly all of the water released by Kyrgyzstan to reach the Aral, according to Ahmad. The increased flow may eventually bring enough water to the southern sea to slow the decline there as well, Ahmad says.
Nikolai Aladin of the St. Petersburg Academy of Sciences, a Russian biologist who has been studying the sea for nearly 3 decades, calls it “a paradise in the desert.” Even though it's only 10,000 years old and has no endemic species, the sea is exceptionally rich in both biodiversity and biomass, he says. And the Syr Darya River is home to one of the world's rarest sturgeon species, a half-meter-long shovelnose. “The bigger water flow is going to considerably increase the chances for recovery of this evolutionary relic,” says sturgeon specialist Phaedra Doukakis of the Pew Institute for Ocean Science. “The way and the speed with which the marine flora and fauna will expand with the water will be very instructive for future rehabilitation projects,” says Aladin.
Residents of Aralsk, the Aral Sea's main northern port—built on the shore in the 19th century—also have more than passing interest in sea life. Aralsk once boasted one of the biggest canneries in the Soviet Union. Lenin famously asked Aralsk fishers to send 17 wagons of fish to the front during the Civil War in the 1920s, an event immortalized in a huge mosaic mural in Aralsk's train station.
But starting in the 1960s, the Soviet government promoted the diversion of water from the Syr Darya and the Amu Darya in the south for cotton irrigation, making a calculated bet that cotton was more valuable than fish. By the time the Soviet Union collapsed, the sea had lost 70% of its surface and retreated 80 kilometers from Aralsk, leaving hundreds of rusting ships stranded along the way amid grazing horses and camels. The city's population dropped from 80,000 to 30,000, its airport closed, and its cannery is now an enormous, spindly steel skeleton.
But today, after the sea crept back to within 15 kilometers from Aralsk, the markets are already selling fresh fish at a fraction of the old price, says Marat Turemuratov, a hospital physician. He hopes the change will reduce chronic malnutrition and help abate a tuberculosis epidemic in Aralsk's children.
Michael Glanz, an Aral Sea specialist with the U.S. National Center for Atmospheric Research in Boulder, Colorado, calls the North Aral Sea project “a bright spot in a dismal landscape.” To the south, however, the Amu Darya River continues to shrink. Civil strife once prevented Afghanistan from drawing water from this river. But now Afghans in the relatively peaceful north are starting to draw from the river for irrigation—and they're planning to draw much more, Glanz says: “Once the Afghans start withdrawing a lot of water, the delta is going to dry up, and people upstream are going to suffer.”
Meanwhile, Kazakhstan has become flush with cash from high oil and metals prices. President Nursultan Nazarbayev announced a popular decision to raise the northern sea's level another 4 to 6 meters, senior Kazakh officials say. This would cover another 925 km 2 of dry seabed and bring the northern sea to about two-thirds of its size before desiccation began in the 1960s. It would also bring water back to within a few kilometers of Aralsk. Just how that is going to be done—by digging upstream canals, raising the dike, or other means—is still being studied, but Kazakhstani officials say they are committed to the project.
Targeting the Tolls
- Ingrid Wickelgren
On the front lines of the body's defense against microbes, toll-like receptors are choice targets for drugs to combat infectious diseases and inflammation
Tens of thousands of horticultural enthusiasts who attended a 1999 flower show in Holland were potentially exposed to something far more insidious than the sight and fragrance of exotic blossoms. Legionella pneumophila, the bacterium that causes Legionnaire's disease, contaminated the water in a whirlpool spa on display and a sprinkler system that misted the flowers, which probably dispersed the bacterium widely. More than 100 people fell ill, and 18 died.
The tragedy piqued the curiosity of infectious disease specialist Annelies Verbon of the Academic Hospital Maastricht in the Netherlands. Why did a handful of people get sick, whereas most came away unharmed? Verbon, along with a research team led by immunologist Alan Aderem of the Institute for Systems Biology in Seattle, Washington, and Thomas Hawn, an infectious disease specialist at the University of Washington Medical Center in Seattle, came up with an intriguing answer. When the researchers analyzed the DNA of groups of attendees, they discovered that a higher percentage of those who fell ill carried a single mutation in the gene for an immune cell surface protein called toll-like receptor (TLR) 5. The team found that the mutation cripples the receptor, apparently preventing immune cells from recognizing the whiplike tail of L. pneumophila and rendering those with the mutation more susceptible to severe Legionnaire's disease.
That finding, published in 2003, is part of an avalanche of research on TLRs. TLR5 is a member of a family of at least 10 human TLRs discovered within the past 7 years. Their discovery has “revolutionized immunology,” in the words of Luke O'Neill, an immunologist at Trinity College in Dublin, Ireland.
Scientists had long known that the immune system has an initial line of defense that triggers the inflammatory response and recruits B and T cells to mount an attack on invading microbes. But they didn't know how that initial alarm was sounded. TLRs have turned out to be the key. “These are the sensors of the microbial world that turn on the immune system,” says O'Neill. And more recent evidence suggests that they also play important roles in autoimmunity and inflammatory conditions such as heart disease.
All this has caught the collective fancies of immunologists and biomedical researchers around the globe. Some 3500 papers on these immune sentinels have appeared to date, and at least nine biotech companies have compounds that stimulate or inhibit TLRs in clinical and preclinical trials for illnesses as diverse as hepatitis, cancer, asthma, and allergies. In the past year, big pharma has moved in too, with companies such as GlaxoSmithKline and Novartis buying up or inking deals with smaller firms developing TLR-based drugs. Commercial interest in TLRs is “suddenly hot,” says O'Neill, who has himself founded a company, Opsona Therapeutics in Dublin, that is now collaborating with Wyeth Pharmaceuticals on TLR-targeting drugs for inflammatory diseases.
Many more experimental TLR-based drugs are in earlier stages of development, including ones designed to treat or prevent allergies, inflammatory bowel disease, and autoimmune afflictions. Basic researchers, meanwhile, are uncovering a slew of additional drug targets as they identify the cascade of enzymes and other molecules involved in transmitting the messages sent by TLRs to the interior of the cell. In the past 3 years, researchers have unveiled 15 previously unknown proteins activated by TLRs and have now cataloged about 30 of the estimated 40 to 50 components of TLR signaling pathways, says Bruce Beutler, an immunologist at the Scripps Research Institute in San Diego, California.
Of course, many hurdles remain before most of these compounds can be marketed. And some, such as pediatric immunologist Jean-Laurent Casanova of Necker Medical School in Paris, contend that more work must be done to prove the importance of TLRs in human immunity, as most studies on these receptors involve animal models of infection. “Enthusiasm for TLRs is deserved,” cautions Casanova, “but it should be tempered.”
The explosion of interest in human TLRs had humble beginnings: the 1988 discovery of a protein involved in fruit fly development. German researchers noted that flies lacking the protein looked toll, the German word for “weird” or “far out.” The insects' bodies were disordered, with bottom body parts mixed with parts that belonged on top, and vice versa. It wasn't until 1996 that scientists learned that the protein, Toll, had a second job, helping defend against fungi. Flies with mutated versions of the protein or its signaling partners more readily succumbed to fungal infections, according to work by Jules Hoffmann and colleagues at the National Center for Scientific Research in Strasbourg, France.
That curious finding led immunologists to wonder whether humans have a corresponding protein. Two years earlier, it turned out, Nobuo Nomura and his colleagues at the Kazusa DNA Research Institute in Chiba, Japan, had unveiled a human protein that bore strong resemblance to the fly Toll. It was later dubbed TLR1. In 1997, Yale University scientists unveiled the second human TLR (now called TLR4), and soon thereafter, researchers at DNAX in Palo Alto, California, identified five more TLR proteins in people.
A year later, Beutler and his colleagues provided the first evidence that a TLR plays a part in mammalian immunity: They found that mice with a defective version of TLR4 could survive injections of endotoxin, a cell-wall component of some bacteria that invariably kills normal mice and in humans can incite a deadly inflammatory disorder called sepsis. The work, Beutler says, “proved that TLR4 was the receptor for endotoxin.” The receptor suddenly became a hot drug target for sepsis, a killer of 750,000 Americans each year.
After that, discoveries came thick and fast. Immunologist Shizuo Akira of Osaka University in Japan and his colleagues systematically deleted the mouse genes for TLRs to reveal their specific functions. Several groups determined which compounds trigger individual receptors. Akira, in collaboration with Aderem and Hawn, for example, determined that flagellin, a protein in the flagella of bacteria, activates TLR5. Others traced out signaling pathways inside the cell that connect to the TLRs, discovering that triggering these receptors can prompt a range of immune responses. These include the release of cytokines such as interferon—a powerful antiviral agent—and other messenger molecules that stimulate the immune system's storm troopers, T cells and antibody-producing B cells.
The unveiling of TLRs and their specific activities (see chart) has given immunologists new respect for the body's frontline defenses, known as the innate immune system. Long considered an evolutionary holdover that provides broad protection before the more specific adaptive immune system of T cells and B cells kicks in, innate immunity is turning out to wield a rather precise set of counter-measures. It is the TLRs that direct the innate immune system's responses, and immunologists are realizing that those responses in turn guide the subsequent adaptive immune reaction that is even more targeted. “The two go hand in glove,” says O'Neill. “You wouldn't get any adaptive response without the innate.” Adds Kleanthis Xanthopoulos, who heads Anadys Pharmaceuticals, a San Diego firm developing antiviral drugs that target TLRs: “The innate immune system had always been viewed as the ‘low-tech immune system.’ Only now do we understand that innate immunity has significant molecular specificity.”
Revving up immune responses
The more scientists learn about TLRs, the more excited they—and drug company executives—get about the potential of stimulating the receptors to combat everything from infectious diseases to cancer. Among the early targets is the hepatitis C virus. Once the virus sets up a chronic infection, it can be very difficult to dislodge: The current treatment—nearly a year of interferon injections combined with an oral antiviral—clears only about half the infections with the most resistant strain, and its side effects can be debilitating. Anadys recently tested a compound that stimulates TLR7 on 32 patients chronically infected with hepatitis C. The injectable drug lowered blood levels of the virus by 82%—a response comparable to injected interferon—in eight of the 12 patients who received the highest dose daily for a week. Only a few patients had side effects, and those were mild to moderate, Anadys scientists reported in the September 2005 issue of Hepatology. The results were promising enough to inspire Novartis to collaborate with Anadys on a pill version of the drug.
Coley Pharmaceutical Group in Wellesley, Massachusetts, a company founded by University of Iowa immunologist Arthur Krieg, has also begun clinical tests of a TLR stimulator aimed at hepatitis C. In a trial with 60 patients, a drug called Actilon that stimulates TLR9 elicited a dose-dependent release of the body's own interferon-α without producing serious side effects, Coley scientists reported at the November 2005 meeting of the American Association for the Study of Liver Diseases. Among the 13 patients who received the highest dose levels of Actilon once or twice a week for 4 weeks, 11 achieved greater than 90% reduction in blood levels of viral RNA.View this table:
Krieg started working on TLR stimulators in the mid-1990s—but he wasn't aware of it at the time. He discovered that short sequences of nucleotides containing cytosine (C) followed by guanine (G), which are common in viruses and bacteria, could powerfully activate B cells in mice. At about the same time, immunologist Eyal Raz and cancer biologist Dennis Carson of the University of California, San Diego (UCSD), and their colleagues observed that T cells respond to loops of bacterial DNA called plasmids, which also contain these so-called CpG sequences. In 2000, Akira's group connected both sets of findings to the world of TLRs: The researchers reported that mice lacking TLR9 fail to generate the immune response typically produced by CpG DNA. Since then, several groups, including Krieg's, have used CpG sequences to construct TLR stimulators for a variety of applications, including cancer treatments.
At a cancer meeting last year, Coley scientists and their collaborators reported that one such compound—a 24-base DNA sequence with four CG pairs—plus chemotherapy shrank lung tumors in 37% of 75 patients with advanced forms of lung cancer, compared to just 19% of 37 patients who received chemotherapy alone. The data also show a positive trend toward increased survival after 1 year. The results are “preliminary—but potentially very exciting,” says Trinity's O'Neill. Pfizer, which pledged up to $515 million for the rights to develop the Coley drug last year, started large-scale trials in November.
Several companies are using TLR stimulants as adjuvants, boosting the immune system's response to vaccines to increase their efficacy. Coley has developed a CpG-based adjuvant called VaxImmune that seems to improve the human immune response to the anthrax vaccine. GlaxoSmithKline recently bought Corixa, a Seattle-based company devoted to TLR therapeutics, for $300 million and is sponsoring large-scale trials of Corixa's MPL, a derivative of bacterial endotoxin that stimulates TLR4, as an adjuvant in a vaccine against human papillomavirus, which causes cervical cancer. And scientists at Dynavax in Berkeley, California, are conducting large-scale human trials of a hepatitis B vaccine in which a CpG DNA sequence is linked to a surface protein from the virus. Early trials suggest that the adjuvant generates a more robust immune response in older adults—and a faster response in young adults—than does the current vaccine.
In addition to revving up immune defenses, researchers are also investigating ways of using TLRs to turn them down. One such strategy may provide faster and safer immunotherapy for allergic conditions.
Current allergy immunotherapy regimens are cumbersome, requiring weekly or monthly shots for 3 to 5 years. They can also be dangerous, causing symptoms from swelling to anaphylaxis in some patients. UCSD's Raz and Carson have discovered that bacterial CpG DNA may offer another solution. By stimulating TLR9, such DNA spurs macrophages and other innate immune cells to kill the so-called T helper 2 (TH2) cells whose overzealous activity characterizes allergy and asthma. Following up on the UCSD team's work, Dynavax is developing medication that may safely prevent allergies in just 6 weeks. The compound—a CpG molecule bound to DNA encoding the culprit allergen—elicits an anti-TH2 response in animals that is stronger than that from separately administered CpG DNA. The company has already sponsored some clinical tests of this strategy and at the March meeting of the American Association of Allergy, Asthma & Immunology reported promising results for ragweed-allergic adults.
A more obvious way of taming the immune system through TLRs is to block one or more of the receptors. This may be useful for inflammatory conditions such as the autoimmune disorder lupus and sepsis. Last year, for example, Seattle's Hawn and Aderem reported that the nonworking TLR5 variant they had implicated as a risk factor in Legionnaire's disease was about half as common in lupus patients as it was in their unaffected relatives, suggesting that inactivating TLR5 may protect people against the disorder. And researchers at Eisai Inc. in Teaneck, New Jersey, are already testing a TLR-blocking compound against sepsis. The compound, dubbed eritoran, is a molecular mimic of a portion of the endotoxin molecule; it binds with TLR4 but does not activate it. In a trial of nearly 300 hospital patients diagnosed with sepsis, a large dose of eritoran reduced the death rate by 12%, compared to a placebo, in the 80% of participants who fully complied with the regimen. In the patients at highest risk for death, a large eritoran dose reduced the death rate by 18%, Eisai announced in August. Beutler calls the results “encouraging,” given how hard it is to administer a drug soon enough to save sepsis patients. The work also shows that TLR blockers are possible. “It sets a precedent for making small molecule antagonists to other TLRs,” he says.
Hope for the heart
Drugs that hinder TLRs might one day treat heart disease as well. Accumulating evidence suggests that TLR activity contributes to atherosclerosis, perhaps by stimulating inflammation.
Hints of this role appeared in 2001 when Moshe Arditi, an infectious disease specialist at Cedars-Sinai Medical Center in Los Angeles, California, and his colleagues found that TLR4 was abundant in atherosclerotic plaques from the coronary arteries of five patients needing bypass surgery but scarce in four normal arteries. More recently, they have found that atherosclerosis-prone mice lacking the TLR4 gene developed arterial lesions that were about 25% smaller than those in the same mice with the TLR4 gene. And if such mice lacked the gene for MyD88, which is involved in the signaling of several TLRs, the atherosclerosis in their aortas dropped by nearly 60%, the researchers reported in 2004. The study “really shows that TLR4 and MyD88 play a role in the production of atherosclerosis,” says Arditi.
TLR1 and TLR2 are also implicated. These receptors have been found to be much more prevalent in plaque-pocked human arteries than in normal ones. And when immunologist Linda Curtiss and her colleagues at The Scripps Research Institute deleted the TLR2 gene in atherosclerosis-prone mice, the animals' arterial lesions shrank by almost 50% compared to similar mice that retained the TLR2 gene. What's more, injecting susceptible mice with a compound that activates TLR2 greatly worsened their lesions.
“It looks like the innate immune system is going to be very clearly involved in the pathogenesis of atherosclerosis,” says Arditi. If so, new treatments could include drugs that block TLR4, TLR2, and MyD88. Such drugs might cripple a person's infection-fighting ability if delivered systemically, but administering them locally to the arteries could reduce that risk, Arditi suggests.
Despite this flurry of activity, there is still uncertainty about the receptors' role in human immunity. There are rare cases in which people have a mutation in an enzyme in the signaling pathway shared by TLRs and the interleukin-1 (IL-1) receptor, making the receptors useless, and yet these people still seem to resist most types of viral, fungal, and parasitic infections, Necker Medical School's Casanova and his colleagues reported in Science in 2003 (28 March 2003, p. 2076). What immune impairment these people do experience could conceivably be caused by an IL-1 pathway defect, Casanova suggests. Because there is no human genetic defect that selectively impacts the TLRs, Casanova says, “there is so far no conclusive evidence that human TLRs are critical, nonredundant players in protective immunity in infection.”
Even if TLRs are vital and unique players in human immunity, as many researchers believe, almost all of the TLR-based experimental therapies must undergo further testing. It's also worth remembering that turning up or down the volume of the human immune system—by means of TLRs or any other method—is a risky proposition. Attempts to dampen dangerous inflammatory responses by means of TLRs could cripple the immune system and cause patients to succumb more easily to infectious diseases, for example. On the other hand, TLR-stimulating compounds could rev up the immune system too much or for too long, leading to sepsis or autoimmune diseases.
“These are huge challenges,” says Beutler. “But they could have rich payoffs.” A growing number of companies are betting on that.
- COMPUTER SCIENCE
Life in Silico: A Different Kind of Intelligent Design
- Kim Krieger*
Engineers and computer scientists are trying to establish a standard tool kit for an emerging field of biology
A biologist sits in front of her computer screen, staring at a model of a bacterium, pondering which metabolic pathway it would use if it were buried deep in the ice of Jupiter's moon Europa. She goes online and searches a database. Within seconds, she finds what she's looking for: Models of three metabolic pathways have been designed and archived by other biologists from past projects. She downloads them, plugs them into her bacterium, programs in the icy environmental conditions, and starts the model running to see which works best.
Futuristic? Yes. But a growing cadre of systems biologists and computer scientists believes it's possible. Just as engineers use the program AutoCad to create structures in virtual space, if an enterprising team of researchers has its way, biologists will have their own software to design and assemble models of organisms and their components. One group has already ventured into this exotic territory—a computer group at Harvard University led by mathematician Jeremy Gunawardena. They soon plan to unveil what they consider the first truly modular program for bio design, called “Little b.”
The name is a play on a powerful computer programming language called C. (Gunawardena's group had planned to call their software “B,” for biology, but realized the name was already taken by C's predecessor.) Gunawardena outlined the program and some of its uses in talks last October at the Council for the Advancement of Science Writing meeting. One of his goals is to bring more consistency to the young field of computer simulation of biological systems. Although biological modeling has shown early promise in pharmaceutical research and the study of complex diseases, he believes it is still a “cottage industry” in sore need of standardization. Existing model systems are “not proper scientific objects,” because they're not easy to reproduce or build upon.
Several other efforts to standardize biological models for easy sharing are under way. The European Bioinformatics Institute (EBI) in Hinxton, U.K., for example, has gathered more than 50 models in its online collection, called BioModels Database (www.ebi.ac.uk/biomodels). It makes them freely available for downloading. Models in this collection are validated for internal consistency and annotated for legibility. But Gunawardena and his collaborators have something more ambitious in mind: a future in which not just biological models but all the pieces of models should be sharable. In this utopia, models should be able to swap computer code for protein cascades as easily as Mr. Potato Head swaps noses.
In concept, Little b bears a resemblance to computer-aided design (CAD) software, which allows engineers to model a new machine in virtual space by combining different parts from a menu of possibilities. The engineer can take the best stock part and tweak it if necessary to make the best fit. Similarly, Little b would allow biologists to build a reaction chain, cell, or organism in silico, picking and choosing proteins and cell parts from a menu of modular parts. If a novel part is needed, the modeler could alter an existing module or write a new one. Once finished, the new module could just be plugged in.
Modularity is a fairly sophisticated software concept. The Little b group “is looking at this from the standpoint … of software engineering,” which is a good thing, says Michael Hucka, a computer scientist at the California Institute of Technology in Pasadena. “They're ahead of the curve.” Both Hucka and Herbert Sauro, a systems biologist and software engineer at the Keck Graduate Institute in Claremont, California, are principal engineers on another effort to standardize biological systems models called the SBML project, for Systems Biology Markup Language. In the past 5 years, SBML has become the standard—and pretty much the only—way for computational biologists to exchange models in a mutually readable format. SBML and Little b are entirely different beasts, however; Little b is a modeling language, whereas SBML is a file format. Like a Word document or pdf, it's simply a way of encoding a model so that it is readable by different machines.
SBML allows computational biologists to e-mail their models to other researchers, who can then run the models on the SBML-compatible software of their choice. The BioModels Database at EBI has collected and curated the best SBML-compatible models. Several journals, including Nature, now require all biological models described in their articles to be submitted to the BioModels Database as well. But neither the database nor SBML requires modularity, as Little b does.
This aspect of Little b promises a unique mix-and-match flexibility. Consider how the program deals with the cell lattice, a construct that describes how cells connect to one another in two or three dimensions. A conventional computer simulation that explores the effect of different cell lattices on embryo development, for example, treats the lattice structure as an integral part of the model. It would be difficult to change from a square to an irregular grid without altering the entire program. The connectivity in lattices can affect a number of conditions—the shape of the cell, which chemical signals it is exposed to, how much light it gets—altering development.
Gunawardena's group has created a model of embryonic development but made the lattice a flexible module. In Little b, it can be altered or replaced without reprogramming any other part, allowing the same experiment to be run on a wide array of cell-lattice patterns.
Little b can also be used to model complete organisms. There's a Drosophila melanogaster living in silico on a laptop at Harvard Medical School, designed completely by Gunawardena's group in Little b. Many research groups are modeling entire organisms and might well make use of a modular approach.
Although it doesn't aim to model whole organisms, the integrative cancer biology program of the National Cancer Institute (NCI) in Bethesda, Maryland, is considering a modular approach to modeling. “It's the Holy Grail to take all these individual modeling components, plug them together, and get a comprehensive view of what's going on,” says Daniel Gallahan, the associate director of NCI's division of cancer biology.
Other researchers agree that modularity is necessary if computational biology is to advance. Sauro, for one, decries the “huge waste of grant money” in the “chronic reinvention” of computer tools that employ one-off models. The redundancy is amazing, he says. For example, the BioModels Database has tens of models just of the MAP kinase cascade, a signal pathway in mammalian cells. And no matter how many MAP kinase cascade models there are available, or how well curated they may be, without modularity they're next to useless to a researcher who wants one ready-made to integrate into a larger model. There's simply no way to plug it in.
Whether Little b succeeds will depend in part on how it evolves and how widely it is accepted. Not everyone is enchanted with it, because it's based on an abstract language called LISP originally devised for artificial intelligence applications. Sauro suggests that the best way to get biologists to adopt a modeling language like this would be to give it a friendly graphical interface. No one has started a project like that, to his knowledge. Several computational biologists also say Little b's developers have not shared much information about their efforts thus far. Without input from the biology community, they ask, how can it satisfy everyone's needs?
Gunawardena says his group plans to begin teaching Little b to students at Harvard soon; he's preparing a paper that he hopes to publish this year. Then the test of community acceptance will begin in earnest.
- NUCLEAR PHYSICS
Scheme for Boiling Nuclear Matter Gathers Steam at Accelerator Lab
- Adrian Cho
Physicists hope to glimpse that violent transformation by running a gargantuan particle collider in lowest gear
UPTON, NEW YORK—Coiling through the woods and buried beneath meters of sandy Long Island loam, a vast atom smasher here at Brookhaven National Laboratory (BNL) has transported physicists back to the big bang. Since 2000, researchers have used the 4-kilometer-long Relativistic Heavy Ion Collider (RHIC) to produce a superhot, ultrathin soup of fundamental particles called quarks and gluons (Science, 22 April 2005, p. 479). The observation of the quark-gluon plasma sheds light on the type of matter that filled the infant universe and has opened a new frontier in nuclear physics. To explore it, though, researchers need a landmark—and they hope to find it by boiling nuclei like water in a kettle.
Imagine a map of nuclear matter with temperature increasing to the north and density increasing to the east. Ordinary nuclei fill a spot on the chilly southern edge, and RHIC has explored the low-density, high-temperature western border (see diagram). Most theorists believe that somewhere to the north and east in the “phase diagram” lies a special point beyond which the transformation from ordinary nuclear matter to free-flying quarks and gluons becomes violent, like the boiling of water. RHIC might be able to reach that “critical point,” and in March, more than 50 physicists gathered here to consider whether to try.
The critical point is “the landmark on the phase diagram,” says Krishna Rajagopal, a theorist at the Massachusetts Institute of Technology in Cambridge and Lawrence Berkeley National Laboratory in California. “If it's not there, then we don't have even a qualitative understanding of the diagram,” which also predicts an exotic “color superconductor” state of nuclear matter in neutron stars. Others say the discovery of the critical point would merit a Nobel Prize.
Searching for the critical point may be tricky, however. Pressing eastward on the phase diagram means producing higher density nuclear matter. That requires ratcheting RHIC's energy down to as little as 1/40 of its normal level—a challenge akin to driving a Formula 1 race car at jogging pace without stalling. And nobody knows exactly where the critical point should be or how experimenters will recognize it.
Still, previous experiments may have spotted hints of it, and researchers here are eager for the search. “It's something that's definitely going to happen at some time,” says BNL's Timothy Hallman, spokesperson for STAR, one of three ongoing particle-detector experiments at RHIC (see photo). William Zajc, a physicist at Columbia University and spokesperson for a second experiment, called PHENIX, says the project would add a new dimension to research at RHIC. “By going down in energy, not only do you have the potential for discovery, you're going out in a whole new direction,” he says.
Glued together with gluons, quarks ordinarily bind so tightly that they're always found either in groups of three—as in the protons and neutrons in atomic nuclei—or in quark-antiquark pairs in fleeting particles called mesons. To liberate quarks, RHIC smashes gold nuclei with such energy that they rip through each other and leave behind a tiny volume of vacuum heated to a million billion degrees. From the void, unfettered gluons, quarks, and antiquarks emerge like violets blooming in spring. In an instant, the wispy plasma cools, and the quarks and antiquarks bind into the particles that spray into RHIC's particle-detector experiments.
As far as RHIC researchers can tell, however, the transition they've observed from ordinary particles to plasma and back is smooth. Conceptually, bound-up nuclear matter and quark-gluon plasma resemble water and steam. Squeeze water to 218 times atmospheric pressure, and the distinction between liquid and vapor blurs, so that it's possible to go smoothly from one state to the other by raising the temperature past 374°C. In the same way, at low densities, the transition from bound to unbound quarks is seamless.
But that transition should be more dramatic in higher-density plasmas, theorists predict, just as at lower pressures water boils violently to become steam and then condenses into distinct droplets to return to the liquid state. If researchers can increase the density of the plasma, then nuclear matter should essentially boil in the collisions and condense as the plasma cools—a process known as a “first-order phase transition.” The critical point is the density and temperature at which those effects kick in, Rajagopal says. “You want to go to the place where you start seeing the formation of droplets” in the cloud of plasma, he says.
To make a denser plasma, RHIC researchers must collide nuclei at energies much lower than normal. That would leave matter from the nuclei lingering in the hot vacuum, driving up the density. RHIC's two overlapping circular accelerators speed ions in opposite directions and crash them together inside the particle detectors spaced around the ring. The accelerators typically boost gold nuclei to energies of 100 billion electron volts (100 GeV) per nucleon—that is, 100 GeV for every proton and neutron in the nucleus. To reach the densities hoped for, RHIC would have to accelerate ions to just 2.5 GeV per nucleon.
Turning the energy that low may push the limits of the equipment, says BNL accelerator physicist Todd Satogata. “It's like doing the limbo,” he says. “How much do your knees hurt as you go lower and lower?” RHIC uses magnets to focus and guide the beams, and those magnets have never been tested at the low fields needed to control such low-energy beams, Satogata says.
Making the beams collide may also pose a problem, says BNL accelerator physicist Angelika Drees. Ordinarily, accelerator operators guide the beams into each other by sensing neutrons from the collisions. But low-energy neutrons won't trigger the neutron detectors, Drees says: “If we don't have a signal to steer with, you may not have collisions at all.”
Nevertheless, accelerator physicists see no insurmountable hurdles to running RHIC at very low energies. For example, Drees says, RHIC's particle detectors could be outfitted with new monitors for steering. And Satogata says accelerator physicists should be able to tell what they're up against after just a single day of test runs.
Even if RHIC can deliver the collisions, experimenters must be able to recognize the critical point when they reach it. The signs of the quark-gluon plasma itself are quite subtle. The minuscule puff of plasma blinks out of existence in less than a billionth of a billionth of a second, leaving visible only the thousands of ordinary particles gushing in all directions.
But in that torrent of particles, researchers have found evidence of the plasma of unbound quarks and gluons. For example, an elongated puff rebounds so that it quickly becomes shorter and fatter, like a squeezed water balloon returning to its round shape. Such “hydrodynamic flow” is a hallmark of the quark-gluon plasma. Researchers have also shown that the tiny cloud appears to drag on jets of highly energetic particles moving through it and snuff them out. That “jet quenching” is another sign of the plasma.
The signs of the critical point would be subtler still. For example, the flow should cease when the transition from bound quarks to free quarks becomes violent like boiling, says Horst Stoecker, a theorist at Johann Wolfgang Goethe University in Frankfurt am Main, Germany. More generally, near the critical point, conditions within the superhot cloud of nuclear matter should begin to fluctuate wildly, leading to event-to-event variations in the number of particles such as mesons, K mesons, and protons and in other variables.
In fact, researchers working on another experiment may have already glimpsed signs of the first-order transition. From 1996 to 2002, researchers at the European particle physics laboratory CERN near Geneva, Switzerland, slammed lead nuclei into a stationary lead target. At energies of about 7 GeV per nucleon, the ratio of K mesons to mesons peaked dramatically. That and other signs suggest that the collisions pushed around the east side of the critical point, says Marek Gazdzicki, an experimenter at the University of Frankfurt and the Swietokrzyska Academy in Kielce, Poland. He has proposed taking more data at CERN, although that won't happen for at least 3 years, he says. Meanwhile, researchers at Germany's GSI laboratory in Darmstadt are developing an accelerator that could also take up the search in 2012.
Still, Gazdzicki and others agree that with its wide energy range and two large particle detectors, RHIC is ideally suited to hunt for the critical point. The best opportunity should come after researchers upgrade the STAR detector in 2009. In the meantime, interest in the critical point is building like pressure in a boiling tea kettle.