News this Week

Science  01 Sep 2006:
Vol. 313, Issue 5791, pp. 1214
  1. PLUTO

    Underworld Character Kicked Out of Planetary Family

    1. Govert Schilling1
    1. 1Govert Schilling is an astronomy writer in Amersfoort, the Netherlands. With additional reporting by John Bohannon and Robert Coontz.

    PRAGUE, CZECH REPUBLIC—The debate wasn't even supposed to be about Pluto. Last week's vote by the International Astronomical Union (IAU) to define the term “planet” was intended to set rules for the classification of new discoveries in the outer solar system. Instead—in a pair of votes that made headlines around the world—IAU not only dropped the small, distant ice ball from the roster of planets but also all but guaranteed that no more planets would be discovered in the solar system in the future.


    Under new rules adopted by the International Astronomical Union, Pluto becomes one of three “dwarf planets” as well as the innermost member of a still-unnamed class of Kuiper belt objects.


    The decision, made here at the closing session of the IAU's triennial meeting,* reclassifies Pluto as a “dwarf planet”—but not a planet. That is “patently incorrect,” says astronomer and Pluto buff Alan Stern of the Southwest Research Institute in Boulder, Colorado, who heads the New Horizons mission that set off last January to explore the tiny ex-planet in 2015. “If the IAU wants to proclaim that the sky is green, that doesn't make it so.” But other astronomers and planetary scientists—including some who supported Pluto's planetary status—say it's time to move on.

    Pluto has always been an oddball. Smaller than Earth's moon, it follows a skewed, elongated orbit into a region known as the Kuiper belt, home to a population of countless “ice dwarfs”: rubble left over from the baby days of the solar system. After Pluto was discovered in 1930, IAU declared it a planet by fiat but never clearly defined what a planet is.

    The question became impossible to ignore in the summer of 2005, when Michael Brown, a planetary scientist at the California Institute of Technology in Pasadena, announced the discovery of 2003 UB313 (nicknamed “Xena”), an icy world farther from the sun than Pluto and some 10% larger. Had Brown discovered the 10th planet? Without a formal definition, there was no way to tell. So earlier this year, the IAU Executive Committee asked seven people (including award-winning science writer Dava Sobel) to write one.

    Chaired by Owen Gingerich, a professor of astronomical history at the Harvard-Smithsonian Center for Astrophysics in Cambridge, Massachusetts, the committee met in Paris on 30 June and 1 July and unanimously agreed that planet club membership would be open to any sun-circling body big and massive enough to become spherical under its own self-gravity. That would include not only Pluto and “Xena” but also Ceres, the largest member of the rocky asteroid belt between the orbits of Mars and Jupiter. The definition also opened the door for scores of yet-to-be-discovered Kuiper belt planets. In addition, the committee proposed that Pluto's large moon Charon should be considered a planet in its own right and that Pluto-like objects in the Kuiper belt should be called “plutons.”

    IAU presented the resolution to its General Assembly on 16 August, giving the roughly 2500 attendees more than a week to discuss it. But the committee expected clear sailing. “We felt we had a resolution that anybody could love,” Sobel says.

    Instead, the “12-planet proposal” went down in flames. Critics objected that planets should also be defined by their orbital dynamics, not just their size and shape. All eight “major” planets, they pointed out, were massive enough to sweep up, fling away, or gravitationally control all the debris in their parts of the early solar system, but Ceres and Pluto—and a host of other candidate “planets”—were not.

    Many astronomers lambasted the resolution during a tumultuous lunchtime meeting on 22 August. To Gingerich's argument that the proposal rested on physical criteria, asteroid researcher Andrea Milani of the University of Pisa in Italy, literally screamed, “Dynamics is not physics?” Other astronomers protested the committee's neglect of extrasolar planets, only to be angrily silenced by outgoing IAU President Ronald D. Ekers, who declared such issues to be “out of order!” Some in the audience expressed chagrin. “It should never have become this emotional,” says astronomer George Miley of Leiden University in the Netherlands.

    On the morning of 24 August—the day of the vote—IAU issued a revised resolution (5A) adding gravitational dominance to the requirements for planethood and omitting any reference to Charon or “plutons.” Ceres, Pluto, “Xena,” and other spherical sun-circling bodies were labeled “dwarf planets.” But to the surprise of many, IAU added an optional amendment (resolution 5B) that would have changed the term “planet” in resolution 5A into “classical planet.” By restricting the new definition to the eight existing “classical planets,” the second resolution implied that dwarf planets were a subcategory of planets, too. To “Pluto-bashing” planetary scientists, it looked as if the committee had made a final attempt to keep the small balls in the planet league.

    As it turned out, resolution 5A (including the dynamical criterion) passed by a margin so wide that no formal count was deemed necessary, and its sibling 5B was soundly defeated. At 3:32 p.m. European time, Pluto ceased to be a planet.

    The Plutonic wars aren't over yet. “This is a sloppy, bad example of how science should be done,” says Stern, who was not at the meeting. In protest, he and others have already withdrawn articles from an upcoming edition of a professional solar system encyclopedia after the editor requested them to change Pluto's status in the articles. A petition against the accepted planet definition is already circulating among planetary scientists.

    But 2003 UB313's discoverer Michael Brown (who is not an IAU member and thus had no say in the matter) urges peace. “It was the right scientific choice. As scientists, we should say, ‘It's fine. Let's let it go and get on with the business.'”

    The business includes coining a word for dwarf planets beyond Neptune, of which Pluto has been designated as the prototype, and setting an official name for dwarf planet 2003 UB313. Planetary scientists must also decide whether dwarf planets belong in their large and steadily growing list of minor planets or in a new catalog.

    And of course, schoolbooks have to be rewritten. Despite the flood of news stories speculating about the effect of the IAU vote on students' fragile psyches, Brown predicts that children will adapt easily to the revised solar system. “People are not as upset about schoolkids as they think they are,” he asserts. “They're actually upset about their memories of themselves as schoolkids. The kids will be fine.”

    • *26th General Assembly, International Astronomical Union, 14–25 August, Prague.


    Particle Physicists Want to Expand Open Access

    1. Jocelyn Kaiser

    Particle physicists have come up with a novel way to promote free, immediate access to journal articles. Led by CERN, the giant lab near Geneva, Switzerland, they want to raise at least $6 million a year to begin buying open access to all published papers in their field.

    The proposal adds fuel to the ongoing debate about public access to research results. Some private biomedical funding groups, such as the U.K.'s Wellcome Trust, now pay the author fees required for their grantees to publish in open-access journals. CERN's announcement goes further, say observers. “Across a discipline is new,” says Peter Suber, a philosophy professor at Earlham College in Richmond, Indiana, who closely follows open-access developments for the Scholarly Publishing and Academic Resources Coalition.

    CERN organizers cite next year's start-up of the Large Hadron Collider (LHC), the most powerful accelerator ever, as the proposal's motivation. That will be “a unique opportunity to reform the publishing paradigm of the particle physics community to ensure the widest, most efficient dissemination of results from this unique facility,” a task force of CERN, other particle physics funders, and scientific publishers concluded in a report issued in June.*

    To accomplish this goal, the task force proposed that a consortium of labs and funding agencies pay publication costs for particle physics papers. It would cost $6 million or more a year to include all the journals willing to offer an open-access option, the group estimated. That would cover up to half of the 6000 or so original theory and experimental papers published each year.

    Knowledge glut.

    The 5-year totals for 17,995 theoretical (top) and 2618 experimental (above) papers in open-access-ready journals.


    The task force hopes to start with $3 million to implement the policy at a few major journals. The practice would begin with the first LHC technical papers next year, says CERN's Rüdiger Voss.

    Last week, the American Physical Society announced that a $975 to $1300 payment to its two main journals would make an article available to all readers (Science, 25 August, p. 1031). Elsevier, the other major particle physics publisher, recently announced an open-access option for $3000, an amount not included in the task force's cost estimate. CERN's plan to sponsor journals would not be permanent: “We see it primarily as a transition scenario,” Voss says, after which funders would pay author fees for individual grantees.

    Nearly all particle physicists already share preprints of their articles on free servers such as at Cornell University Library. Voss, however, argues that the final, vetted article is still what academia values most and that physicists are losing access as budget-strapped libraries cut back on journal subscriptions. Paul Ginsparg, who runs, adds that journals serve as stable, long-term archives and offer extras such as searching for related papers in other journals.


    Genomes Highlight Plant Pathogens' Powerful Arsenal

    1. Erik Stokstad

    For farmers and botanists, Phytophthora unfortunately lives up to its name, which is Greek for “plant destroyer.” The 70-odd species of this eukaryotic genus include the pathogens behind root rot in soybeans, sudden oak death, and potato blight, which still causes upward of $5 billion of damage across the world. Just about all broadleaf plants suffer to some extent from Phytophthora, a distant relative of kelp and diatoms. “They've been terrifically successful as plant pathogens,” says Brett Tyler of Virginia Polytechnic Institute and State University in Blacksburg.

    On page 1261, a large team led by Tyler and Jeffrey Boore of the Joint Genome Institute in Walnut Creek, California, describes the first two genomes of this genus. The sequences reveal that P. sojae and P. ramorum, which cause soybean root rot and sudden oak death respectively, have a diverse array of proteins with which to attack their hosts. Plant pathologists are eager to learn more about such attacks and how to prevent the damage they cause. The sequences “open so many doors that we can now investigate; I'm very excited,” says William Fry of Cornell University.


    Zoospores of Phytophthora ramorum (inset) infected this coast live oak, Quercus agrifolia.


    Tyler and Boore's team began sequencing the two genomes in 2002. The team has so far identified 19,027 likely genes in P. sojae and 15,743 in P. ramorum. Fungal pathogens, in comparison, typically have 10,000 to 12,000 genes.

    One reason for the surfeit is that the two species have diversified their genetic repertoire for making substances that attack plants, such as toxins and enzymes to break down cell walls. In particular, the secretome—those genes that make proteins to be secreted—is evolving much more rapidly in each species than are the overall collection of protein-encoding genes. In P. sojae, for example, 17% of the 1464 genes for secreted proteins are at least 30% distinct from their peers; overall, it's just 9%. “It tells us that secreted proteins are diverging more rapidly,” Tyler says.

    Both species have about 350 genes that resemble so-called avirulence genes seen in bacterial plant pathogens. But such bacteria typically have only 20 to 30 of these genes. Avirulence proteins are highly targeted to particular hosts, and bacterial pathogens inject them into plant cells, lowering the plant's defenses or exploiting other weaknesses. “They're going after the generals inside the fortifications,” says genomicist Ralph Dean of North Carolina State University in Raleigh. “It's going to be absolutely amazing to figure out what these do” in Phytophthora.

    The hope is that researchers will eventually be able to slow the assault of Phytophthora pathogens, either by designing better chemical treatments or engineering stronger resistance into plants. Neither prospect is imminent. The genomes appear to contain complex arrays of genes with overlapping or redundant functions, making it difficult to find a single approach that will deliver a knockout blow. Nonetheless, the genome sequences are already proving their worth. In May, two team members used gene markers from the sequences to show that diversity of P. ramorum is much higher in nurseries than in forests, which further demonstrated the role of plant nurseries in the spread of the pathogen.

    Other findings reported in the Science paper include hundreds of Phytophthora genes apparently derived from red algae or cyanobacteria, bolstering a hypothesis that several kingdoms evolved from a photosynthetic ancestor. Meanwhile, researchers at the Broad Institute in Cambridge, Massachusetts, released a preliminary assembly in July of half of the much larger genome of P. infestans, the cause of potato blight.


    During a Hot Summer, Bluetongue Virus Invades Northern Europe

    1. Martin Enserink

    In a striking example of pathogens hopscotching the globe, a livestock virus originating in Africa appears to have hit three countries in northern Europe since 14 August. More than 70 farms in the Netherlands, Germany, and Belgium have been affected by bluetongue disease, an insect-borne infection of ruminants such as cows, sheep, goats, and deer. Scientists are trying to discover how the virus traveled and how far it might spread, while the European Union (E.U.) has implemented control measures, including some exports.

    The bluetongue virus, carried by tiny insects called Culicoides, or biting midges, is harmless to humans but causes a severe and sometimes fatal disease—symptoms include a blue tongue, a result of bleeding—in sheep and goats. Cows are reservoirs but usually don't get sick. The virus, for which 24 serotypes are known, occurs in many parts of the world, but until recently it was almost never seen in Europe. Since 1998, however, some serotypes have made dramatic incursions into Greece, Italy, Spain, Portugal, and the Balkan countries, a trend some scientists blame on climate change.


    Tiny Culicoides midges can carry a virus harmful to sheep and other ruminants.


    When the virus first turned up in the Netherlands on 14 August—much farther north than it had ever been seen—researchers assumed one of the southern European strains had taken another major leap, which in itself would have been “very surprising” given Culicoides's limited flying abilities, says bluetongue epidemiologist Bethan Purse of the University of Oxford. But a genetic analysis completed last weekend at the Institute for Animal Health (IAH) in Pirbright, U.K., revealed the virus to be of serotype 8, previously known to occur sporadically in sub-Saharan Africa, South America, and the Indian subcontinent. Its genetic fingerprint is closest to that of a Nigerian strain, which strongly suggests an African source, says IAH virologist Peter Mertens.

    It's a mystery how this strain reached northern Europe, because there is very little traffic of ruminants between Africa and Europe, says epidemiologist Aline de Koeijer of the Central Institute for Animal Disease Control (CIDC) in Lelystad, the Netherlands. Perhaps an imported zoo animal was infected, she suggests, or an infected midge may have hitched a ride on an airplane. The current outbreak is unusual in that some cows have gotten sick, but it's unclear whether this is typical of the little-studied serotype 8, says CIDC virologist Eugène van Rooij.

    In southern Europe, bluetongue's main vector is a species called C. imicola, which doesn't occur in the newly affected countries. Around stricken farms, a team led by medical and veterinary entomologist Willem Takken of Wageningen University in the Netherlands has found predominantly C. obsoletus—which lab studies have shown to be a potential vector for bluetongue—as well as eight other Culicoides species, Takken says. All will be tested for the presence of the virus.

    Once introduced, the virus may have benefited from the warm weather, which speeds up its life cycle; July was the hottest month on record in the Netherlands. Scientists are hoping that the northern European winter will kill off all infected midges and prevent a 2007 sequel.


    DOE Tightens Monitoring of Lab Collaborators

    1. Yudhijit Bhattacharjee

    In an effort to safeguard sensitive and classified information, the U.S. Department of Energy has decided that anyone who wants to access the agency's computers must first give DOE written permission to do some electronic snooping. Managers at DOE national labs say that the new rule could hinder collaborations between lab scientists and academic researchers and, at a minimum, be an administrative nightmare. But agency officials say researchers shouldn't worry because the rule won't be implemented as written.

    The rule, which builds on the National Defense Authorization Act of 2000, was published in the Federal Register on 19 July and went into effect 18 August. It mandates that anybody accessing information on computers owned by DOE and its contractors first provide the agency with “written consent” for investigators to check any DOE computer accessed by the individual for up to 3 years in the future. Currently, a warning banner appears whenever somebody logs on to a DOE computer—be it an employee at a national lab or an academic researcher logging on remotely from a university campus—asserting DOE's right to monitor the user's computer habits.

    With the new regulation in place, thousands of university researchers around the world—in addition to DOE and national lab employees—would need to agree in advance to those conditions in writing rather than electronically. The regulation “is not well suited to the collaborations we do at our lab,” says Dwayne Ramsey, computer protection program manager at Lawrence Berkeley National Lab in California. He adds that complying with the rule will be nearly impossible for grid computing projects, which often involve a fluid cast of users and computing resources. “Large international scientific collaborations increasingly depend on the trust of domains, not just people,” he says.

    Physicist James Shank of Boston University, who heads the U.S. grid computing effort for Atlas—an international particle physics experiment at CERN partly underwritten by DOE—says complying with the rule will also pose an unnecessary financial burden. “We will likely have to redirect somebody from the project or hire somebody to take care of the paperwork,” says Shank, who along with hundreds of academic colleagues routinely logs on to computers at DOE's Brookhaven National Laboratory in Upton, New York, in order to work on Atlas.

    A DOE spokesperson told Science that the agency plans to implement the rule in a way that will address these concerns. One possibility is for DOE to interpret “written consent” broadly so as to accept electronic signatures, which would enable users to click “I agree” on a consent form on the Web. One lab official calls that “a graceful way not to admit that the regulation is flawed.”


    USC Hires Prepackaged Team

    1. Yudhijit Bhattacharjee

    Academic departments typically grow in the way that crystals do, by adding faculty to their existing lattices one member at a time. But in a bold experiment that begins this fall, the University of Southern California (USC) in Los Angeles has hired seven scientists who pitched themselves to the institution as a package.

    The appointments by the Wrigley Institute for Environmental Studies (WIES) are part of the university's push to add 100 faculty members to its College of Letters, Arts, and Sciences. Three of the seven WIES hires are genomics experts; the rest specialize in marine biogeochemistry. Together, the septet plans to use gene sequencing as a tool to explore the dynamic relationship between microbial colonies and the ocean's chemical environment. The 11-year-old institute has some 30 faculty members and includes a marine biology station on Catalina Island.

    “By hiring researchers who are already organized into a team, we're starting out with a very strong basis for interdisciplinary scholarship,” says institute director Anthony Michaels, who sold the idea to the university. Michael Quick, dean of the college, says administrators felt that the concept fit USC's strategy of creating “niches within fields in which we can be leaders.”

    All for one.

    USC's Anthony Michaels sees faculty strength in numbers.


    The process began last year with ads for “an integrated group, a mix of Full, Associate, and Assistant Professors, who are innovative, entrepreneurial, interdisciplinary leaders.” Michaels says he wanted to invite big, novel ideas “to break the limits of our own imagination.” Another goal, he says, was “to achieve economies of scale. We thought that members of a group applying together would be much more willing to share resources than individuals hired separately.”

    Of the 100 applications, the search committee ended up liking three groups, all of whom shared an interest in applying genomic analysis to understanding marine geochemistry. At the committee's prodding, the three clusters merged and presented their work last fall at a seminar. “We knew they were going to get along,” says Michaels.

    “Working within such a group will allow us to focus on a range of big questions,” says John Heidelberg, who comes to the cluster from The Institute for Genomic Research in Rockville, Maryland. Another genomics expert in the cluster is his wife Karla, formerly at the neighboring J. Craig Venter Institute. Three members come from the Woods Hole Oceanographic Institution in Massachusetts: geobiologist Katrina Edwards; her husband Eric Webb, who specializes in cyanobacterial physiology and genomics; and James Moffett, an expert in trace metal ocean biochemistry. The team also includes oceanographer David Hutchins of the University of Delaware, Lewes, and trace metal biochemist Sergio Sañudo-Wilhelmy of Stony Brook University in New York.


    A Hurricane's Punch Still Knocks Out Forecasters

    1. Eli Kintisch

    A day and a half before Hurricane Charley hit Florida on 13 August 2004, the National Oceanic and Atmospheric Administration (NOAA) predicted it would probably be a Category 2 storm, “just shy of major hurricane status” and with maximum winds of 177 kilometers per hour. But the storm made landfall as a Category 4—with 241-km/h winds that killed 10 people and left billions of dollars of damage.

    Blown away.

    Hurricane Charley in 2004 turned out to be much more powerful than forecasters predicted 18 hours before Florida landfall.


    Decades of federally funded research have led to impressive gains in predicting where a hurricane will strike. But although forecasting a storm's track is largely influenced by nearby weather, sea, or land features, scientists say that knowing a storm's intensity also depends on the internal dynamics of a chaotic system. That's a much harder challenge and one that NOAA scientists admit they haven't solved. “We don't even know why [Charley] intensified,” confesses meteorologist Morris Bender of NOAA's Geophysical Fluid Dynamics Laboratory (GFDL) in Princeton, New Jersey. Nor, for that matter, do scientists know why Katrina dipped in intensity before it pounded the Louisiana coast 1 year ago this week.

    As the 2006 hurricane season unfolds, the best way to improve NOAA's ability to forecast storm strength is a pressing—and controversial—question. Agency officials say that a current $4 million project to create a new computational model is sufficient. But a recent report by a NOAA advisory panel disagrees and calls for massive new investment, research initiatives, and sharing arrangements. “NOAA's current program is moving in the right direction,” says meteorologist John Snow of the University of Oklahoma, Norman, who chaired the panel. “We think they can move much more aggressively.”

    NOAA's best current prediction tool is a statistical model that uses data from previous hurricanes to give a probable outcome of a storm given its initial conditions. But the agency would prefer to develop a computational model that dynamically approximates the behavior of local weather and sea conditions, as a particular storm may not match a historical situation. Last year, its current computational model, named for the New Jersey lab, only just matched the mediocre performance of its statistical competitor—a result GFDL developer Robert Tuleya, now a NOAA contractor, called “quite frankly … embarrassing.” After all, a computational model, if it accurately mimics a real system, should beat what amounts to a statistical guess. (The model gets good marks for predicting a hurricane's track.) Along with the new model, which will be made more realistic by including aspects of ocean behavior and cloud ice, the agency plans by 2009 to outfit hurricane-hunter planes with a $13 million storm-imaging radar system to supplement satellite data.

    But Snow and others question whether those efforts will be enough to solve the intensity riddle. NOAA's new modeling effort will image features on a 9-kilometer-square grid. But that's much too crude to detect clues about a key phenomenon called a “replacement cycle”—in which outer rainbands can dissipate or later strengthen the storm's most intense inner winds. Those events occur on scales as small as 1 kilometer, Snow says, adding that NOAA will be “consistently underestimating storms” unless it can image such features.

    Some scientists also feel that nascent efforts by NOAA to link ocean conditions and hurricane intensity are going too slowly. The modeling community and NOAA have available only a half-dozen data sets that relate ocean currents to hurricane strength, a situation physical oceanographer Lynn Shay of the University of Miami in Florida calls “pathetic.” The same shortcoming exists for ocean waves, says Shay, adding that “you can't do coupled models without having ocean and atmospheric data.”

    Shay would like NOAA to ask academic scientists to help it design buoys or probes to generate more data. Snow's group also proposed a new advisory board on hurricane modeling, drawn from the wider academic community, as well as a new, bolstered hurricane center that would include NOAA's applied research.

    NOAA, which received $3 million of supplemental funding this year to speed modeling efforts, defends its current intensity approach. The agency already spends $26 million a year for computing needs in weather, climate, and ocean prediction, and Louis Uccellini, head of NOAA's prediction operations in Camp Springs, Maryland, fears that focusing efforts on resolution alone would overshadow efforts to integrate data, study storm dynamics, or link atmospheric effects with the ocean. “There are no silver bullets,” he says. A model with finer resolution could also eat up the limited computing time the agency has to model a storm as it approaches. In fact, some scientists say it's impossible to know whether a 1-km-resolution model would actually lead to better intensity forecasting because the eye-replacement cycle is only one of a number of factors that might lead to better forecasts.

    Officials say recent practice runs using a GFDL model souped up with code for cloud physics and other phenomena were on average 20% more accurate in predicting the intensity of major storms in the past 3 years. And the developers of the next-generation model should reap the benefits, says Bender: “We're making great strides.”


    Truth and Consequences

    1. Jennifer Couzin

    After making the difficult decision to turn in their adviser for scientific misconduct, a group of graduate students is trying to recover from the resulting damage to their careers

    Career conundrum.

    Chantal Ly, in her adviser's now-vacant lab, faced wrenching choices after she and fellow graduate students began questioning the contents of their boss's grant application.


    MADISON, WISCONSIN—In those first disorienting months, as fall last year turned to winter and the sailboats were hauled out of nearby lakes, the graduate students sometimes gathered at the Union Terrace, a popular student hangout. There, they clumped together at one of the brightly colored tables that look north over Lake Mendota, drinking beer and circling endlessly around one agonizing question: What do you do when your professor apparently fakes data, and you are the only ones who know?

    Chantal Ly, 32, had already waded through 7 years of a Ph.D. program at the University of Wisconsin (UW), Madison. Turning in her mentor, Ly was certain, meant that “something bad was going to happen to the lab.” Another of the six students felt that their adviser, geneticist Elizabeth Goodwin, deserved a second chance and wasn't certain the university would provide it. A third was unable for weeks to believe Goodwin had done anything wrong and was so distressed by the possibility that she refused to examine available evidence.

    Two days before winter break, as the moral compass of all six swung in the same direction, they shared their concerns with a university administrator. In late May, a UW investigation reported data falsification in Goodwin's past grant applications and raised questions about some of her papers. The case has since been referred to the federal Office of Research Integrity (ORI) in Washington, D.C. Goodwin, maintaining her innocence, resigned from the university at the end of February. (Through her attorney, Goodwin declined to comment for this story.)

    Although the university handled the case by the book, the graduate students caught in the middle have found that for all the talk about honesty's place in science, little good has come to them. Three of the students, who had invested a combined 16 years in obtaining their Ph.D.s, have quit school. Two others are starting over, one moving to a lab at the University of Colorado, extending the amount of time it will take them to get their doctorates by years. The five graduate students who spoke with Science also described discouraging encounters with other faculty members, whom they say sided with Goodwin before all the facts became available.

    Fraud investigators acknowledge that outcomes like these are typical. “My feeling is it's never a good career move to become a whistleblower,” says Kay Fields, a scientific investigator for ORI, who depends on precisely this occurrence for misconduct cases to come to light. ORI officials estimate that between a third and half of nonclinical misconduct cases—those involving basic scientific research—are brought by postdoctoral fellows or graduate students like those in Goodwin's lab. And the ones who come forward, admits ORI's John Dahlberg, often suffer a “loss of time, loss of prestige, [and a] loss of credibility of your publications.”

    Indeed, Goodwin's graduate students spent long hours debating how a decision to alert administrators might unravel. Sarah LaMartina, 29, who gravitated to biology after its appeal outshone her childhood plan to become a veterinarian, had already spent 6 years in graduate school and worried whether all that time and effort would go to waste. “We kept thinking, ‘Are we just stupid [to turn Goodwin in]?'” says LaMartina, whose midwestern accent reflects her Wisconsin roots. “Sure, it's the right thing to do, but right for who? … Who is going to benefit from this? Nobody.”

    Shock waves

    Goodwin, in her late 40s, had come to the University of Wisconsin in 2000 from Northwestern University in Chicago, Illinois, and was awarded tenure by UW soon after. Landing in Wisconsin was something of a homecoming for her; she had done a postdoc under Judith Kimble, a prominent developmental geneticist in the same department. Goodwin studied sex determination in worms during their early development and has published more than 20 papers on that and other subjects in various prominent journals (including, in 2003, Science). Goodwin was also the oldest of a crop of female faculty members hired in recent years by genetics department chair Michael Culbertson. “She was the role model,” he says.

    In the beginning, the Goodwin lab had a spark. Students recall being swept up in its leader's enthusiasm when, seeking a lab in which to settle, they rotated through for a month during their first year of graduate school. Goodwin pushed her students to believe that compelling scientific results were always possible, boosting their spirits during the low points that invariably strike Ph.D. hopefuls. She held annual Christmas parties at her home west of Madison. Once, she took the entire lab on a horseback-riding trip.

    Then, last October, everything changed. One afternoon, in the conference room down the hall from the lab, Ly told Goodwin she was concerned about her progress: The project she'd been working on, Ly felt, wasn't yielding usable results. Despite months of effort, Ly was unable to replicate earlier observations from the lab.

    “At that time, she gave me three pages of a grant [application],” Ly recalled recently. The proposal, which was under review at the National Institutes of Health (NIH), sought to broaden a worm genetics project that another student, third-year Garett Padilla, had begun. Goodwin, Ly says, told her that the project, on a new, developmentally important worm gene, was “really promising, but there's so many aspects of it there's no way he can work on everything.” Goodwin urged Ly to peruse the pages and see whether the gene might interest her as a new project.

    Reading the grant application set off alarm bells for Ly. One figure, she quickly noticed, was represented as unpublished data even though it had appeared in a 2004 paper published by Goodwin's lab.

    Ly and Padilla sat back to back at desks in the corridor outside the lab. When she showed him the pages from the grant application, he too was shaken. “There was one experiment that I had just not done,” as well as several published and unpublished figures that seemed to have been manipulated, he says. Two images apparently identical to those already published were presented as unpublished and as representing proteins different from the published versions. “I remember being overwhelmed and not being able to deal with it at that moment,” says Padilla.

    A bearish 25-year-old with a closely cropped beard and wire-rimmed glasses, Padilla speaks softly, with deliberation. Bored by bench work, he was considering leaving biology research for law school and had discussed the possibility with Goodwin. She had urged him to “stick it out,” he says. “Everybody goes through a phase where they don't want to be here,” he recalls Goodwin telling him.

    Happier times.

    The lab poses for a group shot, including (front row) Professor Elizabeth Goodwin in blue, Sarah LaMartina in white, Chantal Ly in gray, (back row) Garett Padilla in red, postdoc Scott Kuersten in black, and Mary Allen in green.


    At a loss after seeing the grant application, Padilla consulted two scientists for advice: his fiancée's adviser, a physiology professor at the university, and Scott Kuersten, a former postdoc in Goodwin's lab who had been dating LaMartina for several years and who happened to be in town. Kuersten and Padilla talked for about an hour and together examined the papers cited in the proposal. Kuersten, now at Ambion, a biotechnology company in Austin, Texas, advised Padilla to ask Goodwin for an explanation, as did the physiologist.

    Padilla steeled himself for a confrontation. On Halloween day, he paced nervously outside Goodwin's office, summoning the courage to knock. The conversation did not go well, says Padilla.

    In a computer log of events he had begun to keep at Kuersten's urging, which he shared with Science, Padilla wrote that Goodwin denied lifting a Western blot image from a published paper and presenting it as unpublished work, although, he added in the log, “She became extremely nervous and repeatedly said, ‘I fucked up.'” Padilla also noted: “I left feeling that no issues were resolved.” His confusion deepened when Goodwin later that day blamed the problem on a computer file mix-up.

    Meanwhile, word was leaking out to others in the lab that something was terribly wrong. Two days later, Padilla called a meeting of all current lab members: six graduate students and the lab technician. To ensure privacy, the group, minus Ly, who had recently had a baby girl, convened in the nearby engineering library. Padilla laid out the grant papers for all to see.

    In that meeting, ensconced in the library, the grad students hesitated at the thought of speaking with the administration. “We had no idea what would happen to us, we had no idea what would happen to Betsy, we had no idea how the university would react,” says LaMartina, who admits to some distrust of authority and also a belief that people who err deserve a second chance.

    Ly felt less charitable toward Goodwin but confesses that at first she considered only her own predicament. In many ways, just reaching graduate school was a triumph for Ly, and she badly wanted that doctorate. In 1981, when Ly was 8 years old, her family fled Cambodia for the Chicago suburbs. Around Ly's neck hangs a goldplated French coin, a 20-franc piece her curator father had collected before he was killed in his country's civil war.

    In Chicago, Ly's mother worked long hours and put her daughter through Wellesley College in Massachusetts. When Ly moved to Madison, so did her husband, now an anesthesia resident, and her mother, who speaks little English and cannot drive. “Here I am, I've invested so much time in grad school, and this happens. If we let someone know …” she says, her voice trailing off.

    The students decided that Padilla needed to speak with Goodwin a second time, in hope of extracting a clear account of what went wrong or even a retraction of the grant application. Four days after his first nerve-wracking encounter, Padilla was in Goodwin's office again. This time, the conversation put him at ease. Padilla says Goodwin asked for forgiveness and praised him for, as he wrote in the log, “pushing this issue.” She told him that the grant application was unlikely to be funded—an assertion that turned out to be untrue given that NIH approved it—but offered to e-mail her NIH contact citing some of the problems in the application. Goodwin subsequently sent that e-mail, on which Padilla was copied. He left the encounter relieved.

    “At that point, I was pretty content to leave it alone,” he says. “I felt like we had compromised on a resolution.”

    A wrenching choice

    Another student, however, was finding little peace. Mary Allen, 25 and in her fourth year of graduate school, couldn't shake a sense of torment about what her mentor might have done. A bookworm who squeezed 3 years of high school into one and entered college at age 15, Allen is guided by unambiguous morals and deep religious convictions, attending a local church regularly and leading a youth group there. She could not fathom that Goodwin had falsified data; at one point, Allen refused even to examine another suspect grant application. But, concerned because Goodwin seemed to have admitted to some wrongdoing, Allen felt she needed to switch labs.

    Allen alerted Goodwin that she would likely be moving on. Their mentor then began offering additional explanations for the grant application, say Allen and the others. Goodwin told them that she had mixed up some files and asserted that the files had come to her unlabeled. In a private conversation with Allen, she adamantly denied faking data.

    As November wore on, the lab's atmosphere grew ever more stressful and surreal. When Goodwin was present, she chatted with the students about their worm experiments and their families—the same conversations they'd always had.

    Yet the strain was taking its toll. LaMartina's appetite declined, and she began losing weight, shedding 15 pounds before the ordeal was over. Padilla called former postdoc Kuersten nearly weekly for advice, and the students talked obsessively with one another. Careful to maintain confidentiality, “the only people we could bounce ideas and solutions off of were each other,” says Padilla. The tension even penetrated Goodwin's annual Christmas party. For the first time, several lab members didn't show up.

    Gathering place.

    Most students in Madison hit the Union Terrace for fun and food, but the lab's graduate students had weightier issues on their minds.


    Deeply worried about how speaking with administrators might impact the more senior students, lab members chose not to alert the university unless the desire to do so was unanimous. Gradually all, including Ly and LaMartina, the most senior among them, agreed that their mentor's denials left them uncomfortable and concerned that she might falsify data in the future. “My biggest worry was what if we didn't turn her in …and different grad students got stuck in our position,” says Allen.

    Two days before exams ended, on 21 December, Ly and Padilla met together with Culbertson and showed him the suspect grant pages. Culbertson didn't know what to think at first, he says, but “when somebody comes to me with something like that, I have to investigate.”

    A surprise resignation

    Culbertson quickly referred the matter to two university deans, who launched an informal inquiry to determine whether a more formal investigation was warranted. As is customary, Goodwin remained on staff at the university during this time. She vigorously denied the charges against her, telling Culbertson and the students in a joint meeting that the figures in question were placeholders she had forgotten to swap out. According to Padilla's log of that meeting, Goodwin explained that she “was juggling too many commitments at once” when the proposal was submitted.

    Two biology professors ran the informal inquiry, conducting interviews with Goodwin and her students. One of the two, Irwin Goldman, was also a dean, and he became the students' unofficial therapist and news source. At their first meeting in January, Goldman reassured the six that their salaries would continue uninterrupted.

    The informal inquiry wrapped up a few weeks later, endorsing a more formal investigation. Three university deans, including Goldman, appointed three faculty scientists to the task.

    At about this time, says Goldman, the university grew uneasy about possible fraud not only in the first grant application that the students had seen but also in two others that had garnered funding, from NIH and the U.S. Department of Agriculture. The school canceled all three grants. After a panicky 2 weeks during which the lab went unfunded, Goldman drew on money from both the college of agricultural and life sciences and the medical school. (Goodwin had a joint appointment at the two.) The students peppered Goldman regularly with questions, seeking advice on whether to talk to a local reporter or how their funding might shake out.

    Still, because privacy rules prevented sharing the details, “we felt isolated up on our floor,” says Padilla. “There were faculty nearby, but they didn't really know what was going on.” Goodwin, meanwhile, all but disappeared from the lab, appearing only once or twice after the investigation began. The students tried to keep up with their projects as they'd always done. They held lab meetings alone before being invited to weekly gatherings with geneticist Philip Anderson's lab.

    Most faculty members were aware that an investigation had been launched, and some had heard that Goodwin's students were the informers. That led to disheartening exchanges. A faculty member, asked by one of the students whether they'd done the right thing, told her he didn't know. Rumors reached the students that Goodwin had had “to fake something because her students couldn't produce enough data,” says Ly.

    In late February, Goodwin resigned. The students say they learned of her departure from a biologist who worked in a neighboring lab.

    Three months later, the university released its investigation report, which described “evidence of deliberate falsification” in the three applications for the cancelled grants, totaling $1.8 million in federal funds. In the school's report, which university officials shared with Science, investigators also raised questions about three published papers, in Nature Structural and Molecular Biology, Developmental Biology, and Molecular Cell.

    None has been retracted or corrected so far. “We are considering the implications” of the university report, said Lynne Herndon, president and CEO of Cell Press, which publishes Molecular Cell, in a statement. The editor of Nature Structural and Molecular Biology said she was awaiting the results of the ORI investigation, and the other authors of the Developmental Biology paper are reviewing the relevant data, says the journal's editor in chief, Robb Krumlauf of the Stowers Institute for Medical Research in Kansas City, Missouri.


    A University of Wisconsin investigation raised concerns about these three papers.

    The university investigators also noted other problems in the Goodwin lab. “It appears from the testimony of her graduate students that Dr. Goodwin's mentoring of her graduate students included behaviors that could be considered scientific misconduct—namely, pressuring students to conceal research results that disagreed with desired outcomes and urging them to over-interpret data that the students themselves considered to be preliminary and weak,” they wrote in their report.

    Seeking a new start.

    The possibility that her mentor had faked data left grad student Mary Allen determined to switch labs.


    Goodwin's lawyer in Madison, Dean Strang, disputes the reliability of the school's report. The investigation was “designed under the applicable UW rules to be an informal screening proceeding,” and, because Goodwin resigned, “there was no adjudicative proceeding at the administrative level or elsewhere,” Strang wrote in an e-mail message. He added that “there are no problems with the three published papers cited in the report (or any others).” Strang declined to address whether Goodwin pressed students to overinterpret data. “Dr. Goodwin will not respond at all to assertions of students in this forum,” he wrote.

    Uncertain future

    Culbertson distributed the investigating committee's report to all department faculty members; it even appeared on Madison's evening news. Still, the rapprochement some of the students had hoped for never materialized. “No one ever came up and said, ‘I'm sorry,'” Padilla says.

    As the graduate students contemplated their futures this spring, they did have one point in their favor: Ironically enough, the sluggish pace of their projects meant that almost none had co-authored papers with Goodwin. But when several of them sat down with their thesis committees to assess their futures, the prognosis was grim. Only one student of the six, who did not reply to Science's request for an interview, was permitted to continue with her original project. She has moved to another Wisconsin lab and hopes to complete her Ph.D. within about a year, according to the others.

    Thesis committees and faculty members told Ly, LaMartina, and fourth-year Jacque Baca, 27, that much of their work from Goodwin's lab was not usable and recommended that they start over with a new doctoral project. The reason wasn't necessarily data fraud, the students say, but rather Goodwin's relentless optimism that some now believe kept them clinging to questionable results. Allen, for example, says she sometimes argued but gave in to Goodwin's suggestions that she stick with molecular data Allen considered of dubious quality or steer clear of performing studies that might guard against bias. Ly, on her third, floundering project, says, “I thought I was doing something wrong experimentally that I couldn't repeat these things.”

    Despite her setback, Baca has chosen to stay at Wisconsin. “It's kind of hard to say” how much time she'll lose, says Baca, who notes that her thesis committee was supportive in helping her find a new lab.

    The other four—Ly, LaMartina, Padilla, and Allen—have scattered. Only Allen plans on finishing her Ph.D. Determined to leave Wisconsin behind, she relocated in late March to the University of Colorado, Boulder, where she hopes to start fresh. Members of her church, her husband, and her parents persuaded her to stay in science, which she adores, but she still wonders about the future. “We unintentionally suffer the consequences” of turning Goodwin in, Allen says, noting that it will now take her 8 or 9 years in all to finish graduate school. To her husband's disappointment, their plans for having children have been deferred, as Allen always wanted to wait until she had completed her degree.

    For Padilla, the experience cemented the pull of the law. In late July, a month after his wedding, he and his wife moved to Minneapolis-St. Paul, Minnesota, not far from where Padilla grew up, because his wife's adviser, the physiologist, had shifted his lab there. Padilla began law school in the city last week.

    LaMartina spent 2 months in a different Wisconsin genetics lab, laboring over a new worm project she'd recently started under Goodwin. That project, however, fell apart in June. She then spent 3 weeks in Seattle and Alaska with Kuersten. During the trip, LaMartina abandoned her Ph.D. plans, and in July, she left Wisconsin for Texas, joining Kuersten at Ambion as a lab technician.

    When Ly learned from her thesis committee that her years in the Goodwin lab had come to naught, she left the program and, as a stopgap, joined a cancer lab as a technician. “I decided that I had put my life on hold long enough,” Ly says. She intends to leave science altogether and is considering business school.

    For Goldman, the dean who supported the graduate students, the experience was bittersweet. Impressed by the students' professionalism and grace under trying circumstances, he came to believe strongly that science needs individuals like them. And although he admits that it's “horrible” that so many of the students were told to start over, “I don't see us changing our standards in terms of what a Ph.D. means,” he says.

    Still, Goldman does plan to craft formal policies for students who might encounter this situation in the future. The policies, he says, would guarantee that the university protects students from retribution and that their funding remains secure. He hopes that codifying such safeguards will offer potential whistleblowers peace of mind.

    In a building with a lobby graced by a fountain shaped like DNA, the Goodwin lab now sits deserted on the second floor. Incubators, pipettes, and empty plastic shoeboxes that once held worms litter its counters. Ly's original fear months before, that something bad would happen to the lab, had proved more prescient than she had imagined.


    From Making a Killing to Saving a Species

    1. Diane Garcia
    1. Erik Stokstad

    A retired financier turned philanthropist is making an unprecedented investment in conservation science to help save the big cats

    Thomas Kaplan was a long way from his usual Wall Street habitat. The wealthy financier spent 4 days last year tracking a 3-year-old leopard named Ngoye in the humid woodlands of northern KwaZulu-Natal Province in South Africa. Along with Luke Hunter, a wildlife biologist for the New York-based Wildlife Conservation Society (WCS), and Guy Balme, a graduate student at the University of KwaZulu-Natal, Durban, Kaplan was silently willing Ngoye to cross from private lands, which were off-limits to the trio, into the Phinda Game Reserve so they could replace her radio collar. Just as they were about to give up and head back to Cape Town, Ngoye finally entered the reserve. Balme quickly tranquilized her and replaced her collar.

    The trek turned out to be a pivotal experience—and not just for the 43-year-old Kaplan, who was fulfilling a lifelong dream to study big cats. After he learned that Balme was struggling to find the money to complete his master's degree, Kaplan wrote a $20,000 check to cover Balme's expenses for 2 years. That philanthropic act was just the start: Kaplan decided there and then to launch a grants program with WCS for graduate students working on cat conservation. So far, he has given $307,000 to 20 students at institutions all over the world, with a goal of spending $500,000 a year. Balme says he now plans to pursue a Ph.D. in zoology.

    On the move.

    Biologist Alan Rabinowitz searches for tigers in Laos.


    Graduate students aren't the only beneficiaries of Kaplan's largess. Since his trek, Kaplan has pledged $13 million over 10 years for a variety of cat-related conservation efforts, making him quite possibly the largest individual source of research support for such efforts around the world. Conservation scientists say that his long-term philanthropic commitment promises not only to give them more tools with which to save these magnificent beasts but also to nurture the next generation of conservationists. “I don't think anyone else is in this bracket,” says conservation biologist John Seidensticker of the Smithsonian Institution's National Zoo in Washington, D.C.

    Cat lover

    Kaplan, who grew up in New York City, says books such as Jim Corbett's The Man-Eating Leopard of Rudraprayag fueled his passion for big cats. By the age of 11, he had tracked bobcats in Florida, sighted a panther, and searched for jaguars in the Amazon. “Their gait is self-assured, their bearing confident, their coats are brilliant and practically glow with the richest hues,” he enthuses.

    Despite his interest in animals, Kaplan decided to make his mark in the financial world. After finishing a Ph.D. in history from Oxford University, Kaplan managed hedge funds before founding Apex Silver Mines in 1993. Helped by an investment from the Soros family, Apex became one of the world's largest silver-mining companies; Forbes magazine estimated that Kaplan's 20% stake in the company was worth $70 million in 2000. In late 2004, Kaplan retired from Apex; since then, he has founded an energy company and another firm that explores for precious metals around the world.

    However, those interests leave him plenty of time for philanthropy. He endowed The Lillian Jean Kaplan Renal Transplantation Center at the University of Miami, Florida, after his mother died of kidney disease in 2002 and helped set up a prize for research on the disease.

    Kaplan was introduced to modern conservation efforts through reading Jaguar, a book by WCS wildlife biologist Alan Rabinowitz about setting up the world's first jaguar preserve in Belize. “I felt an immediate, indeed, filial, affection for the man and a knowing connection to the depth of his passion,” Kaplan says. “I resolved one day to help him fulfill his biggest ambitions in the way that he had unknowingly lived all of mine.”

    After leaving Apex, Kaplan called Rabinowitz, who suggested that Kaplan familiarize himself with WCS by visiting Hunter's project in South Africa. “I've dealt with donors since 1978 … I could tell he was real,” Rabinowitz says. “It's very rare for someone to say big cats have been a lifelong passion.”

    Setting targets

    Experts warmly welcome Kaplan's decision to continue supporting the work of students he has funded. Explains Seidensticker: “The problem for many graduate students is that they get a degree, go back to their countries, and there are no support bases. They get drawn away from the field.” The 20 graduate students currently receiving funding are conducting research on wild cats in Africa, Asia, Central and South America, and elsewhere. Their projects include a conservation plan for the 15 remaining Armenian leopards and a study of how young cougars disperse through developed lands around Yellowstone National Park.

    Radio contact.

    Tom Kaplan (left) helps Guy Balme change Ngoye's radio collar after sedating the leopard inside the Phinda Game Reserve in South Africa.


    The scholarships are funded through Panthera, a foundation Kaplan created that is also contributing $10 million (half of it from Michael Cline, a venture capitalist in Greenwich, Connecticut) toward a conservation project in Asia called Tigers Forever. The project works with local governments and landowners to address conservation issues and is modeled after Rabinowitz's jaguar conservation program in Latin America. (In April, Rabinowitz helped persuade eight governments in the region to incorporate a jaguar corridor within the ongoing Mesoamerican Biological Corridor initiative, running from Mexico to Panama.)

    The novelty of Tigers Forever, Rabinowitz says, is the setting of specific recovery targets—an average 50% increase over 10 years across the nine sites at which WCS works. “It holds our feet to the fire and makes us more accountable than anything ever done in conservation before,” Rabinowitz says. “That's an extraordinary thing to do,” says Seidensticker.

    Two months ago, Kaplan finalized plans with WCS for Project Leonardo, which will evaluate the status of lions in Africa and plan for their conservation. Kaplan and WCS have each committed $750,000 over 3 years for the effort, named for Kaplan's 4-year-old son, and he anticipates extending his commitment if the project meets its goals.

    This fall, he plans to start an annual $50,000 lifetime achievement award for big cat conservation, joined next year by a $25,000 young scientist award in the field. With other projects in mind, Kaplan expects his commitment to top $20 million within 5 years. “I hope to collaborate with likeminded people who have passion for big cats,” he says. “I'm willing to put serious money to get this done.”


    Plant Wannabes

    1. Elizabeth Pennisi

    Sea slugs that take in chloroplasts or algae make the photosynthesizers feel right at home

    VIENNA, AUSTRIA—Some sea slugs have figured out how to act like plants or at least like coral. Several species of these shell-less mollusks carry algae or chloroplasts in cells of their digestive glands. The slugs acquire the algae or the organelles from their diet and harvest the carbohydrates or lipids the chloroplasts produce by photosynthesis.

    Researchers have known for decades about these partnerships, but only through histological studies. Now, they are watching them in action. In presentations here last month at the International Symbiosis Society Congress, two research teams described how they have brought sea slugs into the lab and begun to use the latest molecular techniques to reveal the secrets of the symbiotic relationships.

    They reported that algae and even naked chloroplasts can function for months inside a slug and that one sea slug species has acquired algal genes to help such a partnership thrive. The discoveries are “nice examples of coevolution,” says Jörg Ott, a marine biologist at the University of Vienna.

    Ingo Burghardt, a zoologist at Ruhr University in Bochum, Germany, has focused on Phyllodesmium, a sea slug genus with species that salvage algae from the soft corals they eat. Working with Heike Wägele of the University of Bonn, Burghardt has demonstrated that slugs hosting microscopic algae called zooanthellae can last without food for up to 260 days, thanks to contributions from the algae. The longevity of the zooanthellae—and the sea slug's ability to withstand starvation—seems tied in par t to the slug's evolution of a complex midgut that houses the algae, Burghardt reported.

    Dietary supplements.

    The flowing branches of this sea slug house photosynthesizing algae (brown) taken from the soft coral it eats.


    To understand how sea slug-zooanthellae partnerships arose, Burghardt has been working out the Phyllodesmium family tree by comparing each species' ribosomal DNA. At the same time, he has been examining the digestive systems of slugs within this group. He uses a fluorometer, which measures energy released in the form of fluorescence during photosynthetic reactions, to monitor the efficiency of photosynthetic activity when the slugs are given no access to food.

    So far, he's found that various sea slug species differ in the complexity of their digestive gland, the size of dorsal appendages that contain these branches, and their ability to keep zooanthellae. When such features are overlaid onto the slug family tree, “you can see that species that have similar digestive gland structures group together,” he said. Moreover, there is a correlation between a species' success at keeping zooanthellae—and itself—alive and the degree of branching in its digestive gland. “Species with highly branched glands hold on to their zooanthellae a longer time,” he reported.

    The algae turn Phyllodesmium slugs the same color as the soft corals they eat, and Burghardt suspects that this camouflaging originally prompted the evolution of a relationship between the two. Only later, he surmises, did the slugs evolve the ability to use the zooanthellae's photosynthesizing as a food source. And as it did, it made more room by adding on to its digestive glands. “What we see,” says Ott, “is an interplay between dependence on symbiosis and the development of special organs.”

    Mary Rumpho, a biochemist at the University of Maine, Orono, and her colleagues have been studying an even more intriguing relationship: the sea slug Elysia chlorotica's dependence on chloroplasts. They found that Elysia eggs hatch into free-floating larvae that harbor no chloroplasts, but when University of Maine colleague Mary Tyler filmed juvenile sea slugs munching on their favorite seaweed, Vaucheria litorea, “we could literally watch the sea slug suck the chloroplasts out of the alga,” says Rumpho. The ability to harness chloroplasts is critical: If the juveniles don't have access to this organelle, “they don't make it,” Rumpho reported. Moreover, despite being removed from its normal algal home, the chloroplasts can continue to photosynthesize within the sea slug for most of the animal's 10-month life. “That's pretty spectacular,” says Margaret McFall-Ngai of the University of Wisconsin, Madison.

    Leaves of the sea.

    This sea slug harvests chloroplasts from its seaweed meals and depends on them for some of its energy needs.


    It's perhaps not too surprising that sea slugs can house zooanthellae: These algae can survive on their own if they have to. But chloroplasts are dependent on proteins that are typically provided by the plant's nuclear genome. Elysia, it turns out, has what it takes to make the slug-chloroplast partnership work. At the meeting, Rumpho's graduate student Jared Worful described his discovery of large parts of two plant genes in the sea slug's DNA. “When [the sea slug] takes in the chloroplast, it has the machinery to keep the chloroplast active and happy,” says David Richardson, a lichenologist at Saint Mary's University in Halifax, Canada.

    Because these genes are not normally found in animals, Rumpho is convinced they originally came from ingested algae. “We're seeing the evolution of photosynthesis in an animal,” says Rumpho.


    Auxin Begins to Give Up Its Secrets

    1. Gretchen Vogel

    Auxin controls the growth of plants and their interactions with their environment, but only now are researchers understanding the basics of this hormone

    Sweet effects.

    Auxin helps prompt the growth and maturation of strawberries and other fruits.


    Next time you bite into a deliciously juicy strawberry or tomato, thank the seeds. As a fruit forms, its seeds produce a plant hormone called auxin, prompting the fruit to grow and ripen. Without seeds—and without auxin—fruit stays shrunken on the stem.

    The wonders auxin works on strawberries and tomatoes are just the start. The hormone controls almost every aspect of plant growth, from putting down roots to determining where to start a new stem or leaf. It allows plants to react to their environment, shaping the response to signals such as light, gravity, and even the presence of bacteria. Auxin is so fundamental that one leading researcher has called it the brains of the plant world. “I got in a fair amount of trouble for saying that” in a radio interview, Ottoline Leyser of the University of York in the United Kingdom ruefully admits, cautioning that the comparison can be taken too far. “But the useful analogy is that it's an information-processing system.”

    Auxin has fascinated and puzzled plant scientists for more than 100 years. In 1880, Charles Darwin and his son Francis wrote in The Power of Movement in Plants about a substance that seemed to be produced at the tip of growing plant shoots, prompting them to bend toward light. It was one of the first scientific descriptions of the action of auxin. (There are several closely related hormones known collectively as auxin.) But it wasn't until the 1930s that scientists identified the chemical structure of the most common plant auxin, indole-3-acetic acid (IAA). Since then, auxins and their synthetic cousins have been used to boost plant growth—and to kill weeds. Too much auxin is actually deadly to plants; the herbicide 2,4-D is a synthetic auxin, and Agent Orange contains a combination of synthetic auxins.

    Several recent advances have helped give scientists a better picture of this multitalented hormone. They have finally identified the receptor that senses auxin's presence, and the transport system that plants use to control levels of the hormone is becoming clearer. Researchers have also found clues to the fundamental mystery of how plants make auxin—still a surprisingly difficult question. They are even unearthing new roles for auxin in plants' defenses against pathogens. To tackle such complexities, several groups are developing computer models that can keep track of dozens of genes that control or respond to auxin in growing roots or new branches.

    All of this is helping to explain how a relatively simple molecule such as auxin can perform such versatile tasks. “It's a very general signaling system,” says Leyser.

    Target found

    Last year, scientists solved one of the biggest outstanding questions in plant biology when two groups reported that they had finally identified the auxin receptor (Science, 27 May 2005, p. 1240). It turns out that the long-sought protein was hidden in plain sight.

    In papers published simultaneously in Nature, Leyser and her colleagues and Mark Estelle of Indiana University, Bloomington, and his research group showed that auxin binds directly to a protein called TIR1. Scientists already knew that the hormone's presence in plant cells triggers TIR1 to bind to a class of proteins called Aux/IAA, which repress genes known to be triggered by auxin. But most people assumed that auxin turned on such genes by setting off a long signaling cascade, involving numerous proteins and feedback loops.

    One way.

    Auxin transporters such as PIN2 (green) help determine which way the hormone flows in growing root tissues.


    In fact, the cascade is just a few steps: Auxin binds to TIR1, which is part of a molecular complex that attaches the cell's garbage tag, ubiquitin, to proteins destined to be recycled. Auxin, by glomming onto TIR1, helps the complex ubiquitinate Aux/IAA proteins. When the Aux/IAA proteins are broken down, the genes they had repressed turn on. The find “has really simplified things,” Estelle says. Adds Leyser: “I'm just massively relieved that we have a signal-transduction pathway that starts at auxin and ends at gene expression, and that all the parts are there.”

    The find also triggered interest beyond the auxin field. TIR1 is one of roughly 700 so-called F-box proteins already identified in plants and long suspected of playing a role in ubiquitination. The auxin connection suggests that similar small molecules in plants might join with these F-box proteins to direct the breakdown of proteins, Estelle says. Animals, too, have hundreds of F-box proteins.

    A deeper look at the auxin-TIR1 interaction has turned up a surprise. Estelle and structural biologist Ning Zheng of the University of Washington, Seattle, have teamed up to solve the crystal structure of TIR1—both with and without auxin. Small molecules that interact with proteins such as TIR1 often change the shape of the target protein. But, as Estelle and Zheng have described at meetings this summer, TIR1 keeps its shape when united with auxin. Auxin, Zheng says, appears to act as “a molecular glue,” helping TIR1 bind to the Aux/IAA proteins. Zheng, who works in a pharmacology department, says this discovery serves as a reminder for drug developers: Instead of just seeking molecules that disrupt binding, it might be useful to also search for those that encourage binding.

    Transport streams

    Before auxin can interact with TIR1 to unleash gene activity, it needs to get to the right place in the right amount. A picture is gradually emerging, says Leyser, of a system of checks and balances that provide stable yet flexible auxin signals for plant growth and development. A plant regulates auxin levels in its cells by manipulating auxin production, making use of specialized transporters that either allow auxin into a cell or pump it out, and adjusting how quickly cells break down the molecule.

    One key to this tight control of auxin is a family of proteins called PIN-FORMED or PINs, named for the pin-shaped, flowerless shoots grown by Arabidopsis mutants lacking the proteins. In May, Eva Zazimalova of the Institute of Experimental Botany in Prague, Czech Republic, and her colleagues confirmed suspicions that this growth defect was due to an auxin dysfunction. They showed that PIN proteins can transport the hormone between cells and that they are distinct from a second group of well-known auxin transport proteins, called the PGPs (Science, 12 May, p. 914). In the same issue of Science, Jiri Friml of the University of Tü;bingen, Germany, and his colleagues report that the specific type and combination of different members of the PIN family, which localize to different sides of a plant cell, determine which direction auxin flows.

    Other clues about auxin are coming from computer models that can begin to weave together the effects of dozens of genes. Several groups, including Elliot Meyerowitz of the California Institute of Technology in Pasadena and his colleagues, have developed transgenic Arabidopsis plants in which the PIN genes, among others, glow green during plant growth. The scientists film the plants' growth and use the digitized images to build models of the roles and reactions of key development genes in response to auxin. They can then use such a “virtual plant” to better understand how changing levels of the hormone affect different cells and tissues.

    Illustrating the complexity of the task, Gerd Jü;rgens and his colleagues at the University of Tü;bingen have shown in several recent papers that, among other factors, specific combinations of the 29 different Aux/IAA proteins and 22 so-called auxin response factors control a plant cell's response to the hormone.

    A strategic defense

    Growing evidence suggests that RNA strands also play an important role in the auxin story. In April, for example, Jonathan Jones of the John Innes Centre in Norwich, U.K., and his colleagues revealed that RNAs appear to dampen auxin signaling when a plant is infected with certain bacteria. Plants can sense the presence of bacterial flagella and turn various genes on and off in response. And Jones's team showed that when a plant senses the bacteria, it ramps up production of certain microRNAs (miRNAs), short stretches of RNA that can interfere with the manufacture of specific proteins. They also showed that the miRNAs thwart the production of TIR1 and several related proteins.

    Why would a plant interrupt its own auxin response? Perhaps to control plant-dwelling bacteria that also make auxin, says Estelle. Such bacteria, he speculates, use the hormone as part of their colonizing strategy. Extra auxin can trigger growth of new leaves, which might give the bacteria more living space. Indeed, says Estelle, there seems to be a sort of battle to control auxin between plant and pathogen. When the scientists disrupted the miRNA's ability to work, plants more easily succumbed to bacterial infection (Science, 21 April, p. 436).

    Misdirected development.

    Unlike a normal Arabidopsis (left), plants lacking several genes involved in auxin synthesis have flowers that fail to form properly (right).


    The microbe-induced response isn't the first to implicate RNA interference in auxin signaling. Bonnie Bartel of Rice University in Houston, Texas, and her colleagues have found that miRNAs interfere with the expression of several auxin-responsive genes. She predicts that such interactions may be a common way plants regulate auxin's powers. Plant miRNAs “seem to have an overabundance of auxin-implicated genes in their repertoire of clearer control,” says Bartel.

    Although the regulation and effects of auxin are coming into focus, plant biologists have a somewhat embarrassing problem: They still do not know exactly how plants make the hormone. Researchers have worked out how bacteria produce auxin, but the technique used by plants has remained a mystery because it's not just complex but also multiplex. The hormone is so crucial to plant development that a nearly fail-safe system of backup production has evolved. If scientists try to knock out a gene that plays a role in the hormone's synthesis, another is available to jump in and take its place, thus obscuring the initial gene's importance.

    A recent paper in Genes and Development, however, may have broken the impasse. Yunde Zhao and his colleagues at the University of California, San Diego, showed that a family of genes named after a growth-defective Arabidopsis mutant called yucca seems to play a key role in producing auxin during development. Although knocking out a single member of the gene family left the mustard plant's growth unperturbed, knocking out three or four at once generated severely misshapen leaves and flowers. Adding auxin back through the stem didn't rescue the plants, but by inserting a bacterial auxin-producing gene attached to a yucca promoter, the scientists produced nearly normal-looking plants.

    The paper “is a huge step forward” in understanding the specific genes involved in plant auxin production, Estelle says. But Jerry Cohen of the University of Minnesota, Twin Cities, cautions that the story is far from solved: “Nothing has gotten to the point that you can say, ‘This is how it's made.'”

    As scientists sort out the pieces of how auxin is produced, moved, and blocked and broken down, it becomes clearer, says Leyser, that all the processes “interact and intertwine and interreact in horribly complicated feedback mechanisms.” That makes any one part of the auxin system difficult to understand on its own. “It's necessary to think about it as an integrated system,” she says. “It's hard science. You have to be moderately obsessed to stick with it. But that's also why it's so exciting.”

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