The Role of Theory in Advancing 21st-Century Biology: Catalyzing Transformative Research (2008)

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THE ROLE OF THEORY IN ADVANCING 21ST-CENTURY BIOLOGY Catalyzing Transformative Research Report of the Committee on Defining and Advancing the Conceptual Basis of Biological Sciences in the 21st Century Board on Life Sciences Division on Earth and Life Studies 

THE NATIONAL ACADEMIES PRESS  500 Fifth Street, NW  Washington, DC 20001 NOTICE: The project that is the subject of this report was approved by the Govern- ing Board of the National Research Council, whose members are drawn from the councils of the National Academy of Sciences, the National Academy of Engineer- ing, and the Institute of Medicine. The members of the committee responsible for the report were chosen for their special competences and with regard for appropri- ate balance. This material is based on work supported by the National Science Foundation under Grant No. DBI–0633909. Any opinions, findings, and conclusions or rec- ommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation, nor does mention of trade names, commercial products, or organizations imply endorsement by the U.S. government. International Standard Book Number-13:  978-0-309-11249-9 (Book) International Standard Book Number-10:  0-309-11249-4 (Book) International Standard Book Number-13:  978-0-309-11250-5 (PDF) International Standard Book Number-10:  0-309-11250-8 (PDF) Library of Congress Control Number:­­  2007940783 Additional copies of this report 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. Cover:  Design by Francesca Moghari; artwork by Nicolle Rager Fuller (www.sayo-art.com). Copyright 2008 by the National Academy of Sciences. All rights reserved. Printed in the United States of America 

The National Academy of Sciences is a private, nonprofit, self-perpetuating society of distinguished 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 Acad- emy has a mandate that requires it to advise the federal government on scientific and technical matters. Dr. Ralph J. Cicerone 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 en- gineers. 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 engineer- ing programs aimed at meeting national needs, encourages education and research, and recognizes the superior achievements of engineers. Dr. Charles M. Vest is presi- dent 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 Insti- tute 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 Sci- ences 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 communities. The Coun- cil is administered jointly by both Academies and the Institute of Medicine. Dr. Ralph J. Cicerone and Dr. Charles M. Vest are chair and vice chair, respectively, of the National Research Council. www.national-academies.org 



COMMITTEE ON DEFINING AND ADVANCING THE CONCEPTUAL BASIS OF BIOLOGICAL SCIENCES IN THE 21ST CENTURY DAVID J. GALAS (Chair), Battelle Memorial Institute and Institute for Systems Biology, Seattle, Washington CARL T. BERGSTROM, University of Washington, Seattle, Washington VICKI L. CHANDLER, University of Arizona, Tucson, Arizona PAUL G. FALKOWSKI, Rutgers University, New Brunswick, New Jersey DOUGLAS J. FUTUYMA, Stony Brook University, Stony Brook, New York JAMES GRIESEMER, University of California, Davis, California LEROY E. HOOD, Institute for Systems Biology, Seattle, Washington DAVID JULIUS, University of California, San Francisco, California JUNHYONG KIM, University of Pennsylvania, Philadelphia, Pennsylvania KARLA A. KIRKEGAARD, Stanford University, Stanford, California JANE MAIENSCHEIN, Arizona State University, Tempe, Arizona EVE E. MARDER, Brandeis University, Waltham, Massachusetts CARLOS MARTÍNEZ DEL RIO, University of Wyoming, Laramie, Wyoming JOSEPH H. NADEAU, Case Western Reserve University, Cleveland, Ohio JOAN ROUGHGARDEN, Stanford University, Stanford, California JULIE A. THERIOT, Stanford University School of Medicine, Stanford, California GUNTER P. WAGNER, Yale University, New Haven, Connecticut Staff KERRY BRENNER, Study Director ANN H. REID, Senior Program Officer EVONNE P.Y. TANG, Senior Program Officer FRANCES E. SHARPLES, Director, Board on Life Sciences TOVA JACOBOVITS, Senior Program Assistant REBECCA WALTER, Program Assistant  

BOARD ON LIFE SCIENCES KEITH YAMAMOTO (Chair), University of California, San Francisco, California ANN M. ARVIN, Stanford University School of Medicine, Stanford, California RUTH BERKELMAN, Emory University, Atlanta, Georgia DEBORAH BLUM, University of Wisconsin, Madison, Wisconsin VICKI L. CHANDLER, University of Arizona, Tucson, Arizona JEFFREY L. DANGL, University of North Carolina, Chapel Hill, North Carolina PAUL R. EHRLICH, Stanford University, Stanford, California MARK D. FITZSIMMONS, John D. and Catherine T. MacArthur Foundation, Chicago, Illinois JO HANDELSMAN, University of Wisconsin, Madison, Wisconsin KENNETH H. KELLER, Johns Hopkins University School of Advanced International Studies, Bologna, Italy JONATHAN D. MORENO, University of Pennsylvania, Philadelphia, Pennsylvania RANDALL MURCH, Virginia Polytechnic Institute and State University, Alexandria, Virginia MURIEL E. POSTON, Skidmore College, Saratoga Springs, New York JAMES REICHMAN, University of California, Santa Barbara, California BRUCE W. STILLMAN, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York MARC T. TESSIER-LAVIGNE, Genentech, Inc., South San Francisco, California JAMES TIEDJE, Michigan State University, East Lansing, Michigan CYNTHIA WOLBERGER, Johns Hopkins University School of Medicine, Baltimore, Maryland TERRY L. YATES, University of New Mexico, Albuquerque, New Mexico Staff FRANCES E. SHARPLES, Director KERRY A. BRENNER, Senior Program Officer ADAM P. FAGEN, Program Officer ANNA FARRAR, Financial Associate MERC FOX, Program Assistant TOVA G. JACOBOVITS, Senior Program Assistant ANN H. REID, Senior Program Officer vi 

MARILEE K. SHELTON-DAVENPORT, Senior Program Officer EVONNE P.Y. TANG, Senior Program Officer REBECCA WALTER, Program Assistant ROBERT T. YUAN, Senior Program Officer vii 



Acknowledgments This report is a product of the cooperation and contributions of many people. The members of the committee thank all of the speakers who briefed the committee. (Appendix C presents a list of presentations to the committee.) 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 people for their review of this report: Douglas Cook, University of California, Davis Daniel Dennett, Tufts University, Medford, Massachusetts Robert Full, University of California, Berkeley Lou Gross, University of Tennessee, Knoxville Alan Hastings, University of California, Davis J. Woodland Hastings, Harvard University, Cambridge, Massachusetts Douglas Lauffenburger, Massachusetts Institute of Technology Simon Levin, Princeton University Kenneth Nealson, University of Southern California, Los Angeles ix 

 ACKNOWLEDGMENTS Jeffrey Platt, Mayo Clinic, Rochester, Minnesota Tom Pollard, Yale University, New Haven, Connecticut Rino Rappuoli, Chiron Corp, Siena, Italy Hudson Kern Reeve, Cornell University, Ithaca, New York Gene Robinson, University of Illinois, Urbana-Champaign Michael Ryan, University of Texas, Austin Kevin Strange, Vanderbilt University Keith Yamamoto, University of California, San Francisco Although the reviewers listed above provided constructive comments and suggestions, they were not asked to endorse the conclusions or recom- mendations, nor did they see the final draft of the report before its release. The review of this report was overseen by Dr. May Berenbaum, University of Illinois. Appointed by the National Research Council, Dr. Berenbaum 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. 

Contents SUMMARY 1   1 Introduction 13   2 The Integral Role of Theory in Biology 25   3 Are There Still New Life Forms to Be Discovered? The Diversity of Life—Why It Exists and Why It’s Important 38   4 What Role Does Life Play in the Metabolism of Planet Earth? 67   5 How Do Cells Really Work? 81   6 What Are the Engineering Principles of Life? 90   7 What Is the Information That Defines and Sustains Life? 110   8 What Determines How Organisms Behave in Their Worlds? 130   9 How Much Can We Tell About the Past—and Predict About the Future—by Studying Life on Earth Today? 145 10 Education: Learning to Think About the Elephant 157 11 Findings and Recommendations 162 xi 

xii CONTENTS REFERENCES 168 APPENDIXES A Statement of Task 187 B Biographical Sketches of Committee Members 188 C Workshop on Defining and Advancing the Conceptual Basis of Biological Sciences for the 21st Century 196