Life as a Complex System: An Introduction to Complex Systems Biology (eBook)

Preface 6
Contents 9
1 How Should Living Systems Be Studied? 15
1.1 What Is Life? 15
1.2 A Half Century of Molecular Biology 17
1.3 The Reemergence of Diversity and the Enumerative “-ome” Doctrine 21
1.4 Diversity and Dependence on Environmental Circumstances 24
1.5 Systems of Strongly Interacting Elements 27
1.6 Are Living Organisms "Computing Machines”? 29
1.7 Problems with the "Program” Point of View 32
1.8 The Problem of Stability 34
1.9 Systems Evolving Amongst Fluctuations 36
1.10 Spontaneity 38
1.11 How the Parts Composing the Whole Are Determined by the Whole 41
1.12 Universal Properties That Cannot Be Traced Back to Molecules 42
1.13 Transcending Enumeration 45
2 Constructive Biology 51
2.1 The Understanding Obtained Through Construction 51
2.2 The "Way” of Construction 53
2.3 Examples of Studies in Constructive Biology 54
2.4 On the Mode of Understanding 58
3 Basic Concepts in Dynamical Systems and Statistical Physics for Biological System 61
3.1 Basic Picture in Dynamical Systems 61
3.2 The Role of Fluctuations 71
3.3 Plasticity 77
3.4 Representation of "Softness” 80
3.5 Coupled Dynamical Systems for the Study of Cell System 85
3.6 Chaotic Itinerancy 88
4 Origin of Bioinformation 94
4.1 Question to Be Addressed 94
4.2 Logic: Minority Control Hypothesis 102
4.3 Toy Model 104
4.4 Result 107
4.5 Minority-Controlled State 110
4.6 Experiment 113
4.7 Relevance to Biology 118
5 Origin of a Cell with Recursive Growth 123
5.1 Question to Be Addressed 123
5.2 Logic 124
5.3 Model 126
5.4 Result 130
5.5 Experiment 139
5.6 Relevance to Biology 144
6 Universal Statistics of a Cell with Recursive Growth 146
6.1 Question to Be Addressed 146
6.2 Logic 148
6.3 Model 150
6.4 Result 151
6.5 Experiment 159
6.6 Relevance to Biology 163
7 Cell Differentiation and Development 169
7.1 Question to Be Addressed: Stability of Development 169
7.2 Logic: Isologous Diversiffcation 177
7.3 Model 180
7.4 Results 184
7.5 Further Results on Robustness and Dynamics of Differentiation 190
7.6 Experiment 194
7.7 Relevance to Biology 197
7.8 Appendix: An Example of Model Equation 200
8 Irreversible Differentiation from Stem Cell and Robust Development 203
8.1 Question to Be Addressed: Regulation for Differentiation of Stem Cell 203
8.2 Logic: Chaotic Stem Cell 208
8.3 Model 211
8.4 Results 212
8.5 Experiment 228
8.6 Relevance to Biology 232
9 Pattern Formation and Origin of Positional Information 236
9.1 Question to Be Addressed: Origin of Positional Information 236
9.2 Logic 241
9.3 Model 241
9.4 Results 242
9.5 Experiment 250
9.6 Relevance to Biology 252
9.7 Appendix: Model for Recursive Growth of Multicellular Organism 260
10 Genetic Evolution with Phenotypic Fluctuations 264
10.1 Question to Be Addressed 264
10.2 Logic 267
10.3 Model and Result of the Simulation 272
10.4 Experiment 275
10.5 Relevance to Biology 280
11 Speciation as a Fixation of Phenotypic Differentiation 289
11.1 Question to Be Addressed 289
11.2 Logic: Interaction-Based Speciation 294
11.3 Model 296
11.4 Result 298
11.5 Further Remarks on the Differentiation Scenario 302
11.6 Constructive Experiment 312
11.7 Relevance to Biology 316
12 Conclusion 323
12.1 Summary 323
12.2 Machine Versus Life Revisited 330
12.3 Fluctuations, Response, and Stability 332
12.4 The "Law” of Decreasing Plasticity in a Closed System 339
12.5 The Restoration of Plasticity in an "Open” System 340
12.6 A Theoretical Approach to Plasticity Dynamics 344
12.7 Developmental Phenomenology: Stability, Irreversibility, Operations, Equation of State 349
12.8 Toward an Understanding of the Dynamics of Cognition and Human Society 353
References 356
Index 372
More eBooks at www.ciando.com 0

Reading rehearsal currently not available.