!## a: }il'I ^it S■ yjs < -rm. 'iK'■ n 7^' j<JiU38|ou sinpies iu }ojudjaxjiA ROBUSTNESS AND EVOLVABE.ITY IN LIVING SYSTEMS PRINCETON STUDIES IN COMPLEXITY EDITORS Simon A. Levin (Princeton University) Steven H. Strogatz (Cornell University) Titles in the Series Lars-Erik Cederman, Emergent Actors in World Politics; How States and Nations Develop and Dissolve Robert Axelrod, The Complexity of Cooperation: Agent-Based Models of Competition and Collaboration Peter S. Albin, Barriers and Bounds to Rationality: Essays on Economic Complexity and Dynamics in Interactive Systems. Edited and with an introduction by Duncan K. Foley Duncan J. Watts, Small Worlds: The Dynamics of Networks between Order and Randomness Scott Camazine, Jean-Louis Deneubourg, Nigel R. Franks, James Sneyd, Guy Theraulaz, Eric Bonabeau, Self-Organization in Biological Systems Peter Turchin, Historical Dynamics: Why States Rise and Fall Andreas Wagner, Robustness and Evolvahility in Living Systems Mark Newman, Albert-Laszlo Barabasi, and Duncan Watts, eds.. The Structure and Dynamics of Networks J. Stephen Lansing, Perfect Order: Recognizing Complexity in Bali Joshua M. Epstein, Generative Social Science: Studies in Agent-Based Computational Modeling John H. Miller and Scott E. Page, Complex Adaptive Systems: An Introduction to Computational Models of Social Life ROBUSTNESS AND EVOLVABILITY IN LIVING SYSTEMS Andreas Wagner PRINCETON UNIVERSITY PRESS PRINCETON AND OXFORD Copyright © 2005 by Princeton University Press Published by Princeton University Press, 41 William Street, Princeton, New Jersey 08540 In the United Kingdom: Princeton University Press, 3 Market Place, Woodstock, Oxfordshire 0X20 ISY All Rights Reserved Third printing, and first paperback printing, 2007 Paperback ISBN-13: 978-0-691-13404-8 The Library of Congress has cataloged the doth edition of this book as follows Wagner, Andreas, 1967- Robustness and evolvability in living systems/Andreas Wagner, p. cm. Includes bibliographical references (p. ). ISBN 0-691-12240-7 (cloth : alk. paper) 1. Molecular evolution. 2. Mutation (Biology) 3. Biological systems—Stability. 4. Robust control. I. Title. QH390.W356 2005 572.8'38—dc22 2004054936 British Library Cataloging-in-Publication Data is available This book has been composed in Sabon Printed on acid-free paper. == press.princeton.edu Printed in the United States of America 10 9 8 7 6 5 4 3 For Elisabeth and Lani Wagner Contents List of Figures IX Acknowledgments Xlll 1. Introduction 1 PART I: ROBUSTNESS BELOW THE GENE LEVEL 13 2. The Genetic Alphabet 15 3. The Genetic Code 25 4. RNA Structure 39 5. Proteins and Point Mutations 62 6. Proteins and Recombination 78 PART II: ROBUSTNESS ABOVE THE GENE LEVEL 91 7. Regulatory DNA Regions and Their Reorganization in Evolution 93 8. Metabolic Pathways 104 9. Metabolic Networks 120 10. Drosophila Segmentation and Other Gene Regulatory Networks 143 11. Phenotypic Traits, Cryptic Variation, and Human Diseases 161 12. The Many Ways of Building the Same Body 175 PART III: COMMON PRINCIPLES 193 13. Neutral Spaces 195 14. Evolvability and Neutral Mutations 217 15. Redundancy of Parts or Distributed Robustness? 228 16. Robustness as an Evolved Adaptation to Mutations 247 Vlll CONTENTS 17. Robustness as an Evolved Adaptation to Environmental Change and Noise 270 18. Robustness and Eragility; Advantages to Variation and Trade-offs 281 PART IV: ROBUSTNESS BEYOND THE ORGANISM 295 19. Robustness in Natural Systems and Self-Organization 297 20. Robustness in Man-made Systems 310 Epilogue: Seven Open Questions for Systems Biology 321 Bibliography 323 Index 359 Figures Figure 2.1 The chemical structure of a G-C base pair. 17 Figure 2.2 The chemical structure of two base pairs that are not found in nature. 18 Figure 2.3 The number of complementary hydrogen donor- acceptor groups for different combinations of chemically stable bases. 20 Figure 3.1 The “universal” genetic code. 26 Figure 3.2 Biosynthetic pathways and codon assignments in Escherichia coli. 28 Figure 3.3 Histogram for the mean-squared deviation in polar requirement of amino acids encoded by neighboring codons, as obtained from 1 million randomly generated variants of the universal genetic code. 34 Figure 4.1 Two equivalent representations of RNA secondary structure. 40 Figure 4.2 Schematic illustration of interdigitating neutral networks for four secondary structures. 47 Figure 4.3 Neutral network exploration. 51 Figure 4.4 Genetic diversity of RNA sequences during episodic evolution. 54 Figure 4.5 Neutral changes that make a difference. 57 Figure 4.6 An unlikely change in the secondary structure of an RNA molecule. 58 Figure 4.7 A series of neutral mutations connects a hybrid ribozyme with the two ribozymes it is derived from. 59 Figure 5.1 Two globin molecules with very similar structures but little amino acid sequence similarity. 65 Figure 5.2 Evolutionary relationships among globins from 6 plants, 26 invertebrates, and 5 vertebrates. 66 Figure 5.3 Ribbon diagram of the fibronectin type III domain. 67 Figure 5.4 Lattice proteins. 70 Figure 6.1 An experiment shuffling cephalosporinase genes from four microbial species and the amino acid sequence of the most active chimera obtained. 80