Life: An Introduction to Complex Systems Biology

ISBN-13: 9783540326663 / Angielski / Twarda / 2006 / 374 str.

Kunihiko Kaneko

Opis

What is life? What type of system is life? How can we understand life? Or what does "understanding life" really mean? Sixty years since the publication of What Is Life? by Schrodinger ] and after the rise and success of molecular biology, have we reached the answer to these questions? In the recent years, I have often been asked by young researchers and students in biology: "I am afraid that such basic questions on a life system itself are not answered by the main-stream approach of c- rent biology that elucidates molecules and genes. We need some alternative approach. WhatamItodo?"Theyaresatis?edneitherwiththecurrenttrend in bioinformatics nor with the detailed computer models, and are striving for a framework complementary to molecular biology, a one that does not rely on enumerative approach. Responding to these voices, I have explained approaches my colleagues and I have been taking both theoretically and experimentally, in lectures and seminars. Although they show much interest, introduction of these rather interdisciplinary style of research is not easy, let alone discussing how we can understand life. Of course they ask for some books that describe a theoretical basis of our approach and the summaries of the recent studies. My desire to answer these requests from the students and researchers was the main force that had driven me to write the present book. On the other hand, those working in nonlinear dynamics and theoretical physicshavestrivedtosetupanoveltheoreticalframeworkthatiscompatible with biological systems.

Spis treści

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

Blurb

What is life? Has molecular biology given us a satisfactory answer to this question? And if not, why, and how to carry on from there?  This book examines life not from the reductionist point of view, but rather asks the question: 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 has been deliberately kept fairly non-technical so as to address a broad spectrum of students and researchers from the natural sciences and informatics.