Farming Human Pathogens: Ecological Resilience and Evolutionary Process / Edition 1

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Farming Human Pathogens: Ecological Resilience and Evolutionary Process introduces a cutting-edge mathematical formalism based on the asymptotic limit theorems of information theory to describe how punctuated shifts in mesoscale ecosystems can entrain patterns of gene expression and organismal evolution. The authors apply the new formalism toward characterizing a number of infectious diseases that have evolved in response to the world as humans have made it. Many of the human pathogens that are emerging out from underneath epidemiological control are 'farmed' in the metaphorical sense, as the evolution of drug-resistant HIV makes clear, but also quite literally, as demonstrated by avian influenza's emergence from poultry farms in southern China. The most successful pathogens appear able to integrate selection pressures humans have imposed upon them from a variety of socioecological scales. The book also presents a related treatment of Eigen's Paradox and the RNA 'error catastrophe' that bedevils models of the origins of viruses and of biological life itself.

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Product Details

  • ISBN-13: 9781441928269
  • Publisher: Springer New York
  • Publication date: 10/29/2010
  • Edition description: Softcover reprint of hardcover 1st ed. 2009
  • Edition number: 1
  • Pages: 216
  • Product dimensions: 6.14 (w) x 9.21 (h) x 0.48 (d)

Table of Contents

1 Introduction 1

1.1 Ecosystems as information sources 3

1.1.1 Coarse-graining a simple model 3

1.1.2 Ecosystems and information 5

1.2 Cognition as an information source 8

1.2.1 Immune cognition 12

1.2.2 Tumor control 14

1.2.3 A cognitive paradigm for gene expression 14

1.3 Darwinian genetic inheritance as an information source 18

2 Formal theory I 21

2.1 The cognitive modular network symmetry groupoid 21

2.2 Global and local symmetry groupoids 23

2.3 Internal forces breaking the symmetry groupoid 25

2.4 External forces breaking the symmetry groupoid 27

2.5 Emergence in information systems as a phase transition 28

2.6 Multiple workspaces: topological tuning 29

2.7 Phenomenological Landau theory 32

2.8 The dynamical groupoid: Phenomenological Onsager theory 34

2.9 Tuning the network of dynamic manifolds 41

2.10 The rate distortion manifold 41

2.11 No free lunch 48

2.12 Mesoscale resonance: Many Baldwin effects 50

2.13 Directed homotopy 51

2.14 Pathologies of gene expression 54

2.15 Traveling waves on cognitive modular networks 57

3 Formal theory II 63

3.1 The mean field model 63

3.2 Biological renormalization 66

3.3 Universality class distribution 71

3.4 Punctuated universality class tuning 72

3.5 Another network of dynamic manifolds and its tuning 75

3.6 Evolutionary implications of multiple models 75

4 Coevolution 77

4.1 The basic idea 77

4.2 Fragmentation and coalescence 77

4.3 Recursive interaction 83

4.4 Extending the model 86

4.5 The large deviations formalism 89

4.6 Farming a coevolutionary system 94

5 Eigen's paradox 97

5.1 Introduction 97

5.2 Reconsidering the Eigen model 99

5.3Capacity of a parallel channel 102

5.4 Rate distortion dynamics 102

5.5 Rate distortion coevolution 105

6 Farming human pathogens 109

6.1 Culture and the infection phenotype: a modeling exercise 109

6.1.1 Introduction 110

6.1.2 Universality class tuning 112

6.1.3 The adaptive mutator 114

6.1.4 Population stress and pathogen response 115

6.1.5 The phenotype coevolution ratchet 117

6.1.6 Implications of the model 118

6.2 Culture and the infection phenotype: case histories 121

6.2.1 Introduction 121

6.2.2 Genes, cognition, and culture 122

6.2.3 Immune cognition and culture 123

6.2.4 Malaria and the Fulani 124

6.2.5 'Heterosexual AIDS' in Northern New Jersey 127

6.2.6 Conclusions and speculations 129

6.3 Multiple Drug Resistant HIV in New York 131

6.3.1 Introduction 131

6.3.2 Evolutionary biology of HIV 135

6.3.3 Hierarchical diffusion 137

6.4 Avian influenza 141

6.4.1 Panic in the city 141

6.4.2 Farming deadly influenza 143

6.4.3 The political virology of offshore farming 145

6.4.4 Why Guangdong? Why 1997? 149

6.4.5 700 million chickens 151

6.4.6 Asian financial flu 155

6.4.7 Layers of complication 157

6.4.8 The political will for an epidemiological way? 159

7 Final Remarks 163

8 Mathematical Appendix I 169

8.1 The Shannon-McMillan Theorem 169

8.2 The Rate Distortion Theorem 171

8.3 Morse Theory 174

8.4 Geodesic flows 176

9 Mathematical Appendix II 181

9.1 Martingales 181

9.2 Nested Martingales 183

9.3 The Martingale Transform 184

9.4 Stochastic Differential Equations 185

10 References 191

Index 215

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