Farming Human Pathogens (eBook)

Preface 5
Contents 7
1 Introduction 10
1.1 Ecosystems as information sources 12
1.2 Cognition as an information source 17
1.3 Darwinian genetic inheritance as an information source 27
2 Formal theory I 29
2.1 The cognitive modular network symmetry groupoid 29
2.2 Global and local symmetry groupoids 31
2.3 Internal forces breaking the symmetry groupoid 33
2.4 External forces breaking the symmetry groupoid 35
2.5 Emergence in information systems as a phase transition 36
2.6 Multiple workspaces: topological tuning 37
2.7 Phenomenological Landau theory 40
2.8 The dynamical groupoid: Phenomenological Onsager theory 42
2.9 Tuning the network of dynamic manifolds 49
2.10 The rate distortion manifold 49
2.11 No free lunch 56
2.12 Mesoscale resonance: Many Baldwin effects 58
2.13 Directed homotopy 59
2.14 Pathologies of gene expression 62
2.15 Traveling waves on cognitive modular networks 65
3 Formal theory I I 71
3.1 The mean field model 71
3.2 Biological renormalization 74
3.3 Universality class distribution 79
3.4 Punctuated universality class tuning 80
3.5 Another network of dynamic manifolds and its tuning 83
3.6 Evolutionary implications of multiple models 83
4 Coevolution 85
4.1 The basic idea 85
4.2 Fragmentation and coalescence 85
4.3 Recursive interaction 91
4.4 Extending the model 94
4.5 The large deviations formalism 97
4.6 Farming a coevolutionary system 102
5 Eigen's paradox 105
5.1 Introduction 105
5.2 Reconsidering the Eigen model 107
5.3 Capacity of a parallel channel 110
5.4 Rate distortion dynamics 110
5.5 Rate distortion coevolution 113
6 Farming human pathogens 116
6.1 Culture and the infection phenotype: a modeling exercise 116
6.2 Culture and the infection phenotype: case histories 128
6.3 Multiple Drug Resistant HIV in New York 138
6.4 Avian influenza 148
7 Final Remarks 170
8 Mathematical Appendix I 175
8.1 The Shannon-McMillan Theorem 175
8.2 The Rate Distortion Theorem 177
8.3 Morse Theory 180
8.4 Geodesic flows 182
9 Mathematical Appendix II 187
9.1 Martingales 187
9.2 Nested Martingales 189
9.3 The Martingale Transform 190
9.4 Stochastic Differential Equations 191
10 References 196
Index 219