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PROMISE AND CHALLENGES
N SYSTEMS MICROBIOLOGY
WORKSHOP SUMMARY
Patricia McAJams
Evonne Tang
Board on Life Sciences
Division on Earth and Life Studies
NATIONAL RESEARCH COUNCIL
OF THE NATIONAL ACADEMIES
THE NATIONAL ACADEMIES PRESS
Washington, D.C.
www.nap.eciu
OCR for page R2
THE NATIONAL ACADEMIES PRESS · 500 Fifth Street, N.W. · Washington, DC 20001
NOTICE: The project that is the subject of this summary 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 group responsible for the planning of the workshop were
chosen for their special competences and with regard for appropriate balance.
This material is based on work supported by the United States Department of Energy under
Grant DE-FG-02-OOER62941. Any opinions, findings, conclusions, or recommendations
expressed in this publication are those of the authors and do not necessarily reflect the views of
the Department of Energy.
International Standard Book Number 0-309-09167-5 (Book)
International Standard Book Number 0-309-53077-6 (PDF)
Additional copies of this summary are available from the National Academies Press, 500 Fifth
Street, NW, Lockbox 285, Washington, DC 20055; (800) 624-6242 or (202) 334-3313 (in the
Washington metropolitan area); Internet, http://www.nap.edu.
Copyright 2004 by the National Academy of Sciences. All rights reserved.
Printed in the United States of America.
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THE NATIONAL ACADEMIES
Advisers to the Nation on Stienre, Engineering, and Medicine
The National Academy of Sciences is a private, nonprofit, self-perpetuating society of distin-
guished scholars engaged in scientific and engineering research, dedicated to the furtherance of
science and technology and to their use for the general welfare. Upon the authority of the
charter granted to it by the Congress in 1863, the Academy has a mandate that requires it to
advise the federal government on scientific and technical matters. Dr. Bruce M. Alberts is
president of the National Academy of Sciences.
The National Academy of Engineering was established in 1964, under the charter of the
National Academy of Sciences, as a parallel organization of outstanding engineers. It is
autonomous in its administration and in the selection of its members, sharing with the National
Academy of Sciences the responsibility for advising the federal government. The National
Academy of Engineering also sponsors engineering programs aimed at meeting national needs,
encourages education and research, and recognizes the superior achievements of engineers.
Dr. Wm. A. Wulf is president of the National Academy of Engineering.
The Institute of Medicine was established in 1970 by the National Academy of Sciences to
secure the services of eminent members of appropriate professions in the examination of policy
matters pertaining to the health of the public. The Institute acts under the responsibility given
to the National Academy of Sciences by its congressional charter to be an adviser to the federal
government and, upon its own initiative, to identify issues of medical care, research, and
education. Dr. Harvey V. Fineberg is president of the Institute of Medicine.
The National Research Council was organized by the National Academy of Sciences in 1916
to associate the broad community of science and technology with the Academy's purposes of
furthering knowledge and advising the federal government. Functioning in accordance with
general policies determined by the Academy, the Council has become the principal operating
agency of both the National Academy of Sciences and the National Academy of Engineering in
providing services to the government, the public, and the scientific and engineering commu-
nities. The Council is administered jointly by both Academies and the Institute of Medicine.
Dr. Bruce M. Alberts and Dr. Wm. A. Wulf are chair and vice chair, respectively, of the
National Research Council.
www. nationa l-academies.org
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PLANNING GROUP FOR THE WORKSHOP ON PROGRESS AND
PROMISE IN SYSTEMS MICROBIOLOGY
JOHN C. DOYLE (Cochair), California Institute of Technology, Pasadena
ABIGAIL SAYLERS (Cochair), University of Illinois, Urbana-Champaign
ALAN HASTINGS, University of California, Davis
DEREK R. LOVELY, University of Massachusetts, Amherst
MICHAEL SAVAGEAU, University of California, Davis
LYLE WHYTE. McGill University, Quebec, Canada
Staff
EVONNE TANG, Study Director
ROBIN SCHOEN, Senior Program Officer
FRANCES SHARPLES, Director, Board on Life Sciences
BRIDGET AVILA, Senior Project Assistant
DANIELLE GREENE, Research Intern
NORMAN GROSSBLATT, Senior Editor
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BOARD ON LIFE SCIENCES
COREY S. GOODMAN, (Chair) University of California, Berkeley
RUTH BERKELMAN, Emory University, Atlanta, Georgia
R. ALTA CHARD, University of Wisconsin, Madison
DENNIS CHOI, Merck Research Laboratories, West Point, Pennsylvania
JOANNE CHORY, The Salk Institute for Biological Studies, La Jolla,
California
JEFFREY L. DANGL, University of North Carolina, Chapel Hill
PAUL R. EHRLICH, Stanford University, Palo Alto, California
{AMES M. GENTILE, Hope College, Holland, Michigan
LINDA GREER, Natural Resources Defense Council, Washington,
District of Columbia
ED HARLOW, Harvard Medical School, Cambridge, Massachusetts
DAVID HILLIS, University of Texas, Austin
KENNETH F. KELLER, University of Minnesota, Minneapolis
RANDALL MURCH, Institute for Defense Analyses, Alexandria, Virginia
GREGORY A. PETSKO, Brandeis University, Waltham, Massachusetts
STUART L. PIMM, Columbia University, New York, New York
BARBARA A. SCHAAL, Washington University, St. Louis, Missouri
{AMES TIEDIE, Michigan State University, East Lansing
KEITH YAMAMOTO, University of California, San Francisco
Senior Staff
FRANCES SHARPLES
v'
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Preface
n 1993, the National Research Council's Board on Biology established a
series of workshops on biotechnology. The purpose of the discussions is
to foster open communication among scientists, administrators, policy-
makers, and others engaged in biotechnology research, development, and
commercialization. The neutral setting offered by the National Research
Council is intended to promote mutual understanding among government,
industry, and academe and to help develop imaginative approaches to prob-
lem solving. However, the objective is to illuminate issues, not to resolve
them. Unlike study committees of the National Research Council, work-
shops cannot provide advice or recommendations to any government agency
or other organization. Similarly, summaries of workshops do not reach
conclusions or present recommendations but instead reflect the variety of
opinions expressed by the participants. The comments in this report reflect
the views of the workshop participants as indicated in the text.
The first workshop, held in 1996, focused on intellectual property rights
issues related to plant biotechnology. Other workshops have focused on
broad issues related to developing an agricultural genome project, privacy
in biomedical and clinical research, and the field of bioinformatics.
On August 19, 2003, the Board on Life Sciences held the workshop on
"Progress and Promise in Systems Microbiology." The systems approach
attempts to use comparative, high-throughput assays and mathematical or
computational models to generate a picture of system-wide activity that can
yield insight into processes operating within the system. The workshop
brought together scientists in academe, government, and other institutions
. .
v''
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. . .
vail
PREFACE
with representatives of the US Department of Energy, the National Science
Foundation, and the National Academies. The focus of the workshop was
on communication among scientists in different disciplines pertinent to the
application of systems biology to microbial ecology, with a goal of facilitat-
ing transition among science and application and information dissemina-
tion. The training of next-generation scientists with an emphasis on the
interface of biology and computational biology was also stressed during the
workshop.
Several themes emerged during the discussions, which began with con-
crete case studies of particular microbial systems and proceeded to research
and educational needs to support further development of the field. Micro-
bial ecosystems offer unique opportunities for practical bioengineering
applications and attractive mode! systems for basic biological research. Sub-
stantial basic research is needed to develop the theory, software tools, and
experimental methods required to support systems microbiology, but the
case studies showed that progress has already been made by coupling math-
ematical modeling with experimentation. There was wide agreement that
tight interactions of too! development with practical applications is needed,
not only to keep too! development relevant and motivated but also because
the current challenges for microbiologists in dealing with the enormous
complexity of their systems and data can benefit from incremental progress
in modeling, simulation, and analysis tools.
John C. Doyle
Cochair, Workshop on Progress and
Promise in Systems Microbiology
Evonne Tang
Study Director
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Acknowledgments
his document presents the rapporteur's summary of the workshop
discussions and does not necessarily reflect the views of the round-
table members or other participants.
This summary has been reviewed in draft form by individuals chosen
for their diverse perspectives and technical expertise, in accordance with
procedures approved by the NRC's Report Review Committee. The pur-
pose of this independent review is to provide candid and critical comments
that will assist the institution in making its published summary as sound as
possible and to ensure that the summary meets institutional standards for
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 individuals for
their review of this summary:
Timothy Donohue, University of Wisconsin, Madison
Phil Harriman, EPSCoR Centers Development Initiative
Reinhard Laubenbacher, Virginia Polytechnic Institute and State University
Gary S. Sayler, University of Tennessee, Knoxville
The review of this summary was overseen by George Kenyon, University
of Michigan. Appointed by the National Research Council, he was respon-
sible 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 summary rests entirely with the institution.
Nix
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Contents
1 INTRODUCTION
2 WORKSHOP PROCEEDINGS
Microbial Systems: Case Studies, 3
Exploring Microbial Systems, 9
Modeling The Too! for Understanding Systems, 12
Tools for Systems-Microbiology Studies, 18
Looking Ahead Collaboration and Education, 23
Concluding Remarks, 26
3 SUMMARY OF KEY POINTS
APPENDIXES
A AGENDA
B PARTICIPANT BIOGRAPHIES
x'
1
3
27
29
31
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