Gene Expression and Its Discontents (eBook)

Contents 6
1 Introduction 9
1.1 T o w ard new to ols 9
1.2 Epigenetic epidemiology 10
1.3 Ecosystem resilience 14
1.4 A rst surv ey of the ob esit y pandemic in the US 23
2 Models of development 35
2.1 The spinglass model 35
2.2 Shifting perspective: cognition as an information source 38
3 Groupoid symmetries 44
3.1 The first level 45
3.2 The second level 45
3.3 Spontaneous symmetry breaking 47
3.4 A biological example 48
4 Epigenetic catalysis 51
4.1 The basic idea 51
4.2 Rate Distortion dynamics 53
4.3 More topology 56
4.4 Inherited epigenetic memory 57
4.5 Multiple processes 58
4.6 `Coevolutionary' developmen t 59
4.7 Multiple models 61
4.8 Epigenetic focus 62
5 Developmental disorders 64
5.1 Net work information theory 64
5.2 Em b edding ecosystems as information sources 65
5.3 Ecosystems farm organismal development 66
5.4 A simple probability argument 69
5.5 Developmental shadows 70
5.6 Epigenetic programming of artificial systems for b i o t e c h n o l o g y 71
6 An interim perspective 73
7 The obesity pandemic in the US 76
7.1 Introduction 76
7.2 Stress and the HPA axis 77
7.3 HPA axis cognition 78
7.4 Interacting information sources 78
7.5 The simplest HPA axis model 80
7.6 Obesity as a developmen al disorder 84
7.7 Recent trajectories of structured stress in the US 85
7.8 Confron ting the obesity epidemic 92
8 Coronary heart disease in the US 101
8.1 Introduction 101
8.2 Cognition, immune cognition, and culture 104
8.3 Punctuated in terp enetration: adapting to pathogenic h i e r a r c h y 107
8.4 Implications for intervention 109
9 Cancer: a developmental perspective 112
9.1 Introduction 112
9.2 Context 113
9.3 Mutator dynamics 116
9.4 Implications and speculations 118
10 Autoimmune disorders 121
10.1 Introduction 121
10.2 Nonorthogonal eigenmodes of immune cognition 124
10.3 Circadian and other cycles 127
10.4 The retina of the immune response 130
10.5 Circadian-hormonal cycle synergism. 132
10.6 The cognitiv e HP A axis 133
10.7 Phase transitions of in teracting information systems 135
10.8 Autoimm une disease 136
10.9 An application to asthma 138
10.10 Images of pathogenic social hierarchy 139
11 Demoralization and obesity in Upper Manhattan 143
11.1 Introduction 143
11.2 Methods 144
11.3 Data Analysis 147
11.4 Modeling demoralization and chronic stress 148
11.5 Results 149
11.6 Discussion 154
11.7 Conclusion 157
11.8 Chapter App endix 158
12 Death at an early age: AIDS and related mortality in N e w Y o r k C i t y 161
12.1 Introduction 161
12.2 Data and analysis 164
12.3 Results 165
12.4 Discussion 171
12.5 Acknowledgment 178
12.6 Chapter Appendix 178
13 Final thoughts 181
14 Mathematical appendix 183
14.1 The Shannon Co ding Theorem 183
14.2 The `tuning theorem' 185
14.3 The Shannon-McMillan Theorem 187
14.4 The Rate Distortion Theorem 190
14.5 Group oids 193
14.6 Morse Theory 196
14.7 Generalized Onsager Theory 198
15 References 201