
Viruses as Complex Adaptive Systems
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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.
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Content
- Cover
- Title
- Copyright
- CONTENTS
- Preface
- 1. The Virosphere
- 1.1 Deep Microspace Field
- 1.2 The Expanding Viral Universe
- 1.3 Structural and Genetic Diversity
- 1.4 Viral Planet
- 2. Alive or Dead?
- 2.1 Computation and Life
- 2.2 Viruses as Replicating Machines
- 2.3 Viruses as Phases of Matter
- 2.4 Evolving Genome Reduction
- 2.5 The Space of Replicators
- 2.6 Adaptation at High Mutation Rates
- 2.7 Viral Quasispecies
- 2.8 Critical Genome Size
- 3. Landscapes
- 3.1 Climbing High
- 3.2 Symmetric Competition
- 3.3 Epistasis in RNA Viruses
- 3.4 Experimental Virus Landscapes
- 3.5 The Survival of the Flattest Effect
- 3.6 Virus Robustness
- 3.6.1 Intrinsic Mechanisms of Mutational Robustness
- 3.6.2 Extrinsic Mechanisms of Mutational Robustness
- 3.7 Selection: Fitness versus Robustness
- 4. Virus Dynamics and Arms Races
- 4.1 Virus-Host Interactions
- 4.2 HIV Multiscale Dynamics
- 4.3 Population Dynamics of HIV Infection
- 4.4 Spatial Dynamics of HIV-1
- 4.5 Antigenic Diversity Thresholds and AIDS
- 4.6 Viral Symbiosis
- 5. Epidemics
- 5.1 Outbreak
- 5.2 SIS Model
- 5.3 SIS Model in Space and Graphs
- 5.4 AIDS: Modeling HIV-1 Transmission
- 5.5 Halting Viruses in Scale-Free Networks
- 6. Emergent Viruses
- 6.1 Ecological Disturbance: Hanta- and Arenaviruses as Case Studies
- 6.2 The Genetics of Adaptation to Novel Host
- 6.2.1 Becoming Specialists
- 6.2.2 Becoming Generalists
- 6.2.3 The Causes of Specialization
- 6.3 Epidemics of Emergence
- 7. Origins
- 7.1 Are Viruses Inevitable?
- 7.2 Evidence from Digital Evolution
- 7.3 Where Do Viruses Come From?
- 7.3.1 Regressive Hypothesis
- 7.3.2 Cellular Origin Hypothesis
- 7.3.3 Protobiont Hypothesis
- 7.4 Viruses and the Origin of Cells
- 7.5 Viruses as Sources of Evolutionary Novelties
- 7.6 But . . . What Is a Virus Then?
- 8. Computer Viruses and Beyond
- 8.1 Viruses as Programs
- 8.2 Emergence of Computer Viruses
- 8.3 Cancer, Languages, and Minds
- References
- Index
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