Viruses as Complex Adaptive Systems

by Ricard Solé, Santiago F. Elena

Overview

How complex systems theory sheds new light on the adaptive dynamics of viral populations

Viruses are everywhere, infecting all sorts of living organisms, from the tiniest bacteria to the largest mammals. Many are harmful parasites, but viruses also play a major role as drivers of our evolution as a species and are essential regulators of the composition and complexity of ecosystems on a global scale. This concise book draws on complex systems theory to provide a fresh look at viral origins, populations, and evolution, and the coevolutionary dynamics of viruses and their hosts.

New viruses continue to emerge that threaten people, crops, and farm animals. Viruses constantly evade our immune systems, and antiviral therapies and vaccination campaigns can be powerless against them. These unique characteristics of virus biology are a consequence of their tremendous evolutionary potential, which enables viruses to quickly adapt to any environmental challenge. Ricard Solé and Santiago Elena present a unified framework for understanding viruses as complex adaptive systems. They show how the application of complex systems theory to viral dynamics has provided new insights into the development of AIDS in patients infected with HIV-1, the emergence of new antigenic variants of the influenza A virus, and other cutting-edge advances.

Essential reading for biologists, physicists, and mathematicians interested in complexity, Viruses as Complex Adaptive Systems also extends the analogy of viruses to the evolution of other replicators such as computer viruses, cancer, and languages.

Product Details

ISBN-13:	9780691158846
Publisher:	Princeton University Press
Publication date:	12/11/2018
Series:	Primers in Complex Systems , #6
Pages:	240
Product dimensions:	5.40(w) x 8.30(h) x 0.80(d)

About the Author

Ricard Solé is research professor and head of the Complex Systems Lab at Pompeu Fabra University in Barcelona. His books include Phase Transitions and Self-Organization in Complex Ecosystems (both Princeton). Santiago F. Elena is professor and head of the Evolutionary Systems Virology Lab at the Spanish National Research Council (CSIC) in Valencia.

Table of Contents

Preface ix

1 The Virosphere 1

1.1 Deep Microspace Field 1

1.2 The Expanding Viral Universe 7

1.3 Structural and Genetic Diversity 9

1.4 Viral Planet 15

2 Alive or Dead? 19

2.1 Computation and Life 19

2.2 Viruses as Replicating Machines 22

2.3 Viruses as Phases of Matter 25

2.4 Evolving Genome Reduction 33

2.5 The Space of Replicators 36

2.6 Adaptation at High Mutation Rates 43

2.7 Viral Quasispecies 45

2.8 Critical Genome Size 53

3 Landscapes 55

3.1 Climbing High 55

3.2 Symmetric Competition 62

3.3 Epistasis in RNA Viruses 68

3.4 Experimental Virus Landscapes 73

3.5 The Survival of the Flattest Effect 77

3.6 Virus Robustness 82

3.6.1 Intrinsic Mechanisms of Mutational Robustness 85

3.6.2 Extrinsic Mechanisms of Mutational Robustness 86

3.7 Selection: Fitness versus Robustness 87

4 Virus Dynamics and Arms Races 91

4.1 Virus-Host Interactions 91

4.2 HIV Multiscale Dynamics 95

4.3 Population Dynamics of HIV Infection 98

4.4 Spatial Dynamics of HIV-1 105

4.5 Antigenic Diversity Thresholds and AIDS 108

4.6 Viral Symbiosis 116

5 Epidemics 120

5.1 Outbreak 120

5.2 SIS Model 125

5.3 SIS Model in Space and Graphs 130

5.4 AIDS: Modeling HIV-1 Transmission 137

5.5 Halting Viruses in Scale-Free Networks 141

6 Emergent Viruses 149

6.1 Ecological Disturbance: Hanta- and Arenaviruses as Case Studies 152

6.2 The Genetics of Adaptation to Novel Host 154

6.2.1 Becoming Specialists 156

6.2.2 Becoming Generalists 158

6.2.3 The Causes of Specialization 161

6.3 Epidemics of Emergence 162

7 Origins 168

7.1 Are Viruses Inevitable? 168

7.2 Evidence from Digital Evolution 170

7.3 Where Do Viruses Come From? 176

7.3.1 Regressive Hypothesis 176

7.3.2 Cellular Origin Hypothesis 177

7.3.3 Protobiont Hypothesis 178

7.4 Viruses and the Origin of Cells 185

7.5 Viruses as Sources of Evolutionary Novelties 187

7.6 But… What Is a Virus Then? 188

8 Computer Viruses and Beyond 190

8.1 Viruses as Programs 190

8.2 Emergence of Computer Viruses 191

8.3 Cancer, Languages, and Minds 197

References 203

Index 219

What People are Saying About This

From the Publisher

“This book demonstrates how viruses, besides being fascinating organisms, can provide experimental tests and case studies for many of the evolutionary processes that are important to biologists.”—Lin Chao, University of California, San Diego

“This stimulating and timely book addresses questions central to virus population dynamics from the conceptual framework of complex systems theory. Clearly structured and easy to read, it fills a gap and will appeal to scientists in a diversity of fields, from virology to mathematical biology.”—Fernando García-Arenal, Universidad Politécnica de Madrid

“Viruses as Complex Adaptive Systems covers the evolution, diversity, and behavior of viruses from a mathematical perspective, providing a broad range of vignettes on the subject that are clear and engagingly written. The book also serves as a useful introduction to some aspects of theoretical biology.”—Oliver Pybus, University of Oxford

“Solé and Elena bring together in one place a variety of different concepts and approaches that are normally treated separately, offering detailed discussions of the rapid contemporary variation of some viruses along with the medium and long-term evolution of others. I know of no other book like this one.”—Colin R. Parrish, Cornell University

Editorial Reviews

This book demonstrates how viruses, besides being fascinating organisms, can provide experimental tests and case studies for many of the evolutionary processes that are important to biologists.”—Lin Chao, University of California, San Diego

From the Publisher