Review of the Department of Energy’s Genomics: GTL Program
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NOTICE: The project that is the subject of this report was approved by the Governing Board of the National Research Council, whose members are drawn from the councils of the National Academy of Sciences, the National Academy of Engineering, and the Institute of Medicine. The members of the committee responsible for the report were chosen for their special competences and with regard for appropriate balance.
This study was supported by Contract DE-AM01-04PI45013 between the National Academy of Sciences and the U.S. Department of Energy. The content of this publication does not necessarily reflect the views or policies of the U.S. Department of Energy, nor does mention of trade names, commercial products, or organizations imply endorsement by the U.S. Government.
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COVER: Geobacter, a microorganism that can be used for bioremediation of uranium-contaminated groundwater and shows substantial promise for harvesting electricity from otherwise low-value energy sources. Photo by Derek Lovley, University of Massachusetts, Amherst. Design by Michael Dudzik, the National Academies Press.
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COMMITTEE ON REVIEW OF THE DEPARTMENT OF ENERGY’S GENOMICS: GTL PROGRAM
JENNIE HUNTER-CEVERA (Chair),
University of Maryland Biotechnology Institute, Rockville
CHARLES R. CANTOR,
Sequenom, Inc., San Diego, California
WAH CHIU,
Baylor College of Medicine, Houston, Texas
DOUGLAS R. COOK,
University of California, Davis
ERIC W. KALER,
University of Delaware, Newark
THOMAS KALIL,
University of California, Berkeley
DAVID T. KINGSBURY,
Gordon and Betty Moore Foundation, San Francisco, California
CLAUDIA NEUHAUSER,
University of Minnesota, St. Paul
GREGORY A. PETSKO,
Brandeis University, Waltham, Massachusetts
MARIAM STICKLEN,
Michigan State University, East Lansing
LARRY P. WALKER,
Cornell University, Ithaca, New York
JANET WESTPHELING,
University of Georgia, Athens
Staff
EVONNE P. Y. TANG, Study Director
FRANCES E. SHARPLES, Director,
Board on Life Sciences
ANN H. REID, Program Officer
JOSEPH C. LARSEN, Postdoctoral Research Associate
SETH STRONGIN, Senior Program Assistant (through September 2005)
ANNE F. JURKOWSKI, Program Assistant (since September 2005)
NORMAN GROSSBLATT, Senior Editor
BOARD ON LIFE SCIENCES
COREY S. GOODMAN (Chair),
Renovis, Inc., South San Francisco, California
ANN M. ARVIN,
Stanford University School of Medicine, Stanford, California
JEFFREY L. BENNETZEN,
University of Georgia, Athens
RUTH BERKELMAN,
Emory University, Atlanta, Georgia
DEBORAH BLUM,
University of Wisconsin, Madison
R. ALTA CHARO,
University of Wisconsin, Madison
DENNIS CHOI,
Merck Research Laboratories, West Point, Pennsylvania
JEFFREY L. DANGL,
University of North Carolina, Chapel Hill
PAUL R. EHRLICH,
Stanford University, Stanford, California
JAMES M. GENTILE,
Research Corporation, Tucson, Arizona
JO HANDELSMAN,
University of Wisconsin, Madison
ED HARLOW,
Harvard Medical School, Boston, Massachusetts
DAVID HILLIS,
University of Texas, Austin, Texas
KENNETH H. KELLER,
University of Minnesota, Minneapolis
RANDALL MURCH,
Virginia Polytechnic Institute and State University, Alexandria
GREGORY A. PETSKO,
Brandeis University, Waltham, Massachusetts
STUART L. PIMM,
Duke University, Durham, North Carolina
JAMES TIEDJE,
Michigan State University, East Lansing
KEITH YAMAMOTO,
University of California, San Francisco
Staff
FRANCES E. SHARPLES, Director
KERRY A. BRENNER, Senior Program Officer
ADAM P. FAGEN, Program Officer
DENISE GROSSHANS, Financial Associate
TOVA JACOBOVITS, Program Assiant
ANNE F. JURKOWSKI, Program Assistant
ANN H. REID, Program Officer
MARILEE K. SHELTON-DAVENPORT, Senior Program Officer
EVONNE P. Y. TANG, Senior Program Officer
ROBERT T. YUAN, Senior Program Officer
Preface
The Department of Energy (DOE) is one of the most complex of the U.S. government science agencies. It has led the nation in advancing many fields of science from physics and biology to large-scale computation. It was DOE that started the Human Genome Project and the first subsurface microbiology program and provided unparalleled capacity to the scientific community to define macromolecular structures in its synchrotrons. DOE has other user facilities, such as the Joint Genome Institute, which enables many researchers to benefit from the data acquired through whole genome sequences of both macroorganisms and microorganisms. Today, DOE maintains 17 national laboratories across the United States equipped with the latest technologies and housing some of the brightest minds in the country.
Some of the most pressing scientific and societal challenges that DOE has to deal with are finding alternative bioenergy sources, bioremediation of mixed wastes (radionuclide-contaminated organics), and enhancing carbon sequestration potentially to decrease the rate of global warming. All three of these fields of multidisciplinary research require understanding of complex biological systems starting at the organismal level and working down to the molecular level and vice versa. Recognizing that one cannot put the cart before the horse, especially if one is to design experiments at the bench to fit the reactor (applications in the field), DOE developed a forward-thinking program called Genomics: GTL (formerly Genomes to Life). The immediate goal of Genomics: GTL is to understand biological systems well enough to predict their behavior accurately with mechanistic computational models; the long-term goal of the program is to be able to develop microorganisms with capabilities for producing alternative energy sources, clean-
ing up the Cold War legacy of contaminated waste sites, and elucidating carbon cycling and sequestration.
The National Research Council (NRC) was asked to put together an ad hoc committee to review the design of the Genomics: GTL program and its infrastructure plan. We heard from various academic, industry, and national-laboratory scientists both funded and not funded by the program or involved with GTL, and we visited DOE headquarters in Germantown, Maryland, to meet and hear the perspective of the program’s managers. The committee met twice to discuss our findings and writing tasks and held numerous phone conferences over the 5-month period during which this report took shape.
Our task was not an easy one by any standard, given the complexity of the science being evaluated and the need to unravel the Genomics: GTL components in order to understand better the planned future user facilities. The work of the committee was in some ways analogous to the Genomics: GTL program itself—examining the inner workings of a complex system so as to be able to design its functions for optimal output.
I thank the committee members and the NRC staff for being so giving of their time and talent. It was an honor to serve as chair of such a distinguished group of scientists. We were on a very tight schedule to finish the report and had much to review and digest in a very short time. The committee’s discussions were stimulating and forward-thinking as to the role that DOE’s Genomics: GTL program could play in our country’s future in taking fundamental basic research all the way to translational research in the field, generating both important curiosity-driven discoveries and applied solutions for the most pressing challenges in bioremediation, bioenergy, and carbon sequestration.
We came from many different backgrounds with diverse perspectives based on personal experiences, and yet we came together as a team focused on one mission, that of making a difference and moving DOE’s Genomics: GTL program to new heights based on the strong foundation it has established to date. Although the Genomics: GTL program had a “roadmap,” the committee paved its own road, bumps included, to reach a final consensus that the Genomics: GTL program is critical to the success of DOE’s mission and future as a leader in systems biology. Starting from this premise, the committee came up with a set of recommendations aimed at ensuring that this program would establish DOE as a world leader in microbial systems biology. The opportunity that Genomics: GTL offers scientists to advance both fundamental and applied knowledge in not only the mission focus areas of DOE but many other scientific endeavors worldwide is tremendous.
Jennie Hunter-Cevera
Chair, Committee on Review of the Department of Energy’s Genomics: GTL Program
Acknowledgments
This report is a product of the cooperation and contributions of many people. The committee would like to thank all the speakers who attended the first meeting of the committee, on September 25-26, 2005, and others who provided information and input.
This report has been reviewed in draft form by persons chosen for their diverse perspectives and technical expertise in accordance with procedures approved by the National Research Council’s Report Review Committee. The purpose of this independent review is to provide candid and critical comments that will assist the institution in making its published report as sound as possible and to ensure that the report meets institutional standards of objectivity, evidence, and responsiveness to the study charge. The review comments and draft manuscript remain confidential to protect the integrity of the deliberative process. We wish to thank the following for their review of this report:
Nitin Baliga, Institute for Systems Biology, Seattle, Washington
Peter Bottomley, Oregon State University, Corvallis
Steven P. Briggs, University of California, San Diego
Jeffrey L. Dangl, University of North Carolina, Chapel Hill
Edward Dougherty, Texas A&M University, College Station
Jed Fuhrman, University of Southern California, Los Angeles
David Galas, Battelle, Columbus, Ohio
Robert Haselkorn, University of Chicago, Chicago, Illinois
Kenneth Keegstra, Michigan State University, East Lansing
Karl Sanford, Genencor International, Palo Alto, California
John Wooley, University of California, San Diego
Although the reviewers listed above have provided constructive comments and suggestions, they were not asked to endorse the conclusions or recommendations, nor did they see the final draft of the report before its release. The review of this report was overseen by Dr. Christopher R. Somerville. Appointed by the National Research Council, Dr. Somerville was responsible for making certain that an independent examination of this report was carried out in accordance with institutional procedures and that all review comments were carefully considered. Responsibility for the final content of this report rests entirely with the author committee and the institution.