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