This book examines life not from the reductionist point of view, but rather asks the questions: what are the universal properties of living systems, and how can one construct from there a phenomenological theory of life that leads naturally to complex processes such as reproductive cellular systems, evolution and differentiation? The presentation is relatively non-technical to appeal to a broad spectrum of students and researchers.
1 Introduction -- Problems in Molecular Biology 1.1 What is Life 1.2 A Half Century of Molecular Biology 1.3 Problems of Diversity 1.4 Context Dependent Behavior 1.5 Importance of Interaction 1.6 Is a life process a computer? 1.7 Problems of Stability 1.8 System that Works under Large Fluctuations 1.9 Universal features that are not reduced to Molecules 1.10 Necessity of New Framework 2 Constructive Biology 2.1 Understanding by Construction 2.2 Examples of Constructive Approaches to Biology 2.3 How can Biological Processes be Understood? 3 Basic Concepts in Dynamical Systems and Statistical Physics for Biology 3.1 Basic Concepts in Dynamical Systems 3.2 The Role of Fluctuations 3.3 Biological Plasticity 3.4 Representation of Biological ``Softness' 3.5 Coupled dynamical systems for biology 3.6 Itinerant Dynamics 4 The Origin of Hededity and Bioinformation 4.1 The Question to be Addressed: What is the Origin of Bioinformation 4.2 A Summary of the Theory: Minority Control 4.3 Model 4.4 A Summary of the Reslts: Origin of Bioinformation as Minority Control 4.5 Experiment: In Vitro Self-Replication of Chemical Networks, 4.6 Relevance to Biology 5 Origin of a Cell with Recursive Production and Evolvability 5.1 The Question to be Addressed: Origin of Recursiveness and Evolbabiliy 5.2 Logic; amplification and suppression of fluctuations 5.3 Models 5.4 Result; recursive growth and evolution of a cell 5.5 Experiment: towards Synthesis of Self-replicating Cells 5.6 Relevance to Biology 6 Universal Statistical Properties of a Cell with Recursive Production 6.1 The Question to be Addressed: universal property of a cell with recursiveness production 6.2 Logic; cascade catalytic process 6.3 Model 6.4 Universal Properties of Reaction Network 6.5 Experiment: Zipf's law and log-normal distribution 6.6 Relevance to Biology 7 Cell Differentiation and Development I 7.1 The Question to be Addressed: What Underlies the Stability of Development 7.2 A Summary of the Theory: Spontaneous Differentiation by Unstable Dynamics and Interaction 7.3 Constructive Computer Models 7.4 A Summary of the Results: Robustness of the Developmental Process 7.5 In Vitro Experiments: Differentiation of E. Coli 7.6 Relevance to Biology 8 Cell Differentiation and Development II: Stem Cells 8.1 The Question to be Addressed: What Regulates the Differentiation of Stem Cells 8.2 A Summary of the Theory: Regulation by Chaotic Dynamics and Stabilization of Plastic Dynamcis 8.3 Constructive Computer Models 8.4 Results from the Model 8.5 Stability and Irreversibility in the Development of a Cell Society 8.6 In Vitro Experiments: Construction of a System with Differenitaion by Synthetic Network in E. Coli 8.7 Relevance to Biology 9 Pattern Formation and the Origin of Positional Information 9.1 The Question to be Addressed: What is the Origin of Positional Information 9.2 A Summary of the Theory: Self-consistent Formation of Positional Information by Dynamic Differentiation 9.3 Constructive Computer Models 9.4 A Summary of the Results; Generation of Positional Information 9.5 In Vitro Experiments: Activin-controlled Tissue Generation 9.6 Relevance to Biology 10 The Evolution of Diversity 10.1 The Question to be Addressed: How does Interaction affect Sympatric Speciation 10.2 Summary of the Theory: Genetic Fixation of Interaction-induced Phenotypic Plasticity 10.3 Constructive Computer Models 10.4 A Summary of the Results: Robust S