Understanding Complex Systems

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 process6.3 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 Speciation 10.5 In Vitro Experiments: Artificial Evolution of E Coli 10.6 Relevance to Biology 11 Remarks on Other Biological Problems from the Perspective of Complex Systems Biology 11.1 The Origin of Recursive Multicellular Organisms 11.2 Construction of Symbiosis 11.3 Dynamic Memory and Learning 11.4 Dynamic Proteins: Loose vs Tight Couplings 11.5 Signal Transduction and Dynamic Bottlenecks 12 Summary 12.1 Summary: Basic Concepts for a Biological System 12.2 Necessity of Constructive Biology 12.3 Phenomoenological Theory for Developmental Process 12.3 Fluctuation-Response Relationship: Relevance to Evolution 12.4 Law of Irreversible Loss of Plasticity 12.5 From Plastic Dynamics to Logical Processes