[Kings of Hell MC 04] • Gray's Shadow

Stuart Kauffman here presents a brilliant new paradigm for evolutionary biology, one that extends the basic concepts of Darwinian evolution to accommodate recent findings and perspectives from the fields of biology, physics, chemistry and mathematics. The book drives to the heart of the exciting debate on the origins of life and maintenance of order in complex biological systems. It focuses on the concept of self-organization: the spontaneous emergence of order that is widely observed throughout nature Kauffman argues that self-organization plays an important role in the Darwinian process of natural selection. Yet until now no systematic effort has been made to incorporate the concept of self-organization into evolutionary theory. The construction requirements which permit complex systems to adapt are poorly understood, as is the extent to which selection itself can yield systems able to adapt more successfully. This book explores these themes. It shows how complex systems, contrary to expectations, can spontaneously exhibit stunning degrees of order, and how this order, in turn, is essential for understanding the emergence and development of life on Earth. Topics include the new biotechnology of applied molecular evolution, with its important implications for developing new drugs and vaccines; the balance between order and chaos observed in many naturally occurring systems; new insights concerning the predictive power of statistical mechanics in biology; and other major issues. Indeed, the approaches investigated here may prove to be the new center around which biological science itself will evolve. The work is written for all those interested in the cutting edge of research in the life sciences. Cover Title Copyright Dedication Preface Contents Themes The Origins of Order 1. Conceptual Outline of Current Evolutionary Theory The Emergence of the Neo-Darwinian Synthesis Enlarging the Framework Summary PART I - ADAPTATION TO THE EDGE OF CHAOS 2. The Structure of Rugged Fitness Landscapes Fitness Landscapes in Sequence Space The NK Model of Rugged Fitness Landscapes Summary 3. Biological Implications of Rugged Fitness Landscapes Phylogenetic Implications of Rugged Landscapes Population Flow on Rugged Fitness Landscapes Summary 4. The Structure of Adaptive Landscapes Underlying Protein Evolution Adaptive Maturation of the Immune Response Evolution of Novel Catalytic Functions Applied Molecular Evolution: Direct Exploration of DNA, RNA, and Protein Sequence Spaces Summary 5. Self-Organization and Adaptation in Complex Systems Dynamical Systems and Their Attractors Spontaneous Order and Chaos in Complex Dynamical Systems Adaptation in Dynamical Systems Summary 6. The Dynamics of Coevolving Systems Coevolution in Ecosystems Structured Ecosystems and Self-Organized Criticality: Coevolution to the Edge of Chaos Coevolutionary Conclusions. Summary PART II - THE CRYSTALLIZATION OF LIFE 7. The Origins of Life: A New View Background of the Origin of Life Problem Autocatalytic Sets of Catalytic Polymers Growth on the Infinite Graph of Polymers and Thermodynamic Behavior Evolutionary Capacities of Autocatalytic Sets Without a Genome Experimental Consequences Summary 8. The Origin of a Connected Metabolism { Crystalization of a Connected Metabolism as a Percolation Problem New Experiments Summary 9. Hypercycles and Coding The Logic of Hypercycles Bedian’s Paradigm for the Onset of Coding Summary 10. Random Grammars: Models of Functional Integration and Transformation Jets and Autocatalytic Sets: Toward a New String Theory Infinite Boolean Networks and Random Grammars: Approaches to Studying Families of Mappings of Strings into Strings Applications to Biological, Neural, and Economic Systems Summary PART III - ORDER AND ONTOGENY 11. The Architecture of Genetic Regulatory Circuits and Its Evolution Independence of the Molecular Evolutionary Clock and Morphological Evolution Components in the Genetic Regulatory Systems of Prokaryotes and Eukaryotes An Ensemble Theory Based on Random Directed Graphs Summary 12. Differentiation: The Dynamical Behaviors of Genetic Regulatory Networks Simple Genetic Circuits and the Boolean Idealization Large-Scale Features of Cell Differentiation The Conceptual Framework: Cell Differentiation in Boolean Networks Ensembles of Genetic Regulatory Systems: Generic Properties Implications for Ontogeny Cell Types as a Combinatorial Epigenetic Code Summary 13. Selection for Cell Types The Framework Genomic Network Space Experimental Avenues Summary 14. Morphology, Maps, and the Spatial Ordering of Integrated Tissues Induction as a Basic Intercellular Conversation Evidence for Long-Range Order in Tissues: Duplication, Regeneration, and Positional Continuity The Spontaneous Generation of Spatial Patterns: Turing Models Compartmental and Segmental Patterns in Drosophila Melanogaster Pattern Formation in the Early Drosophila Embryo Spatial Harmonics Suggested by Mutants Affecting Segmentation: Longitudinal Deletions and Mirror-Symmetric Duplications Sinusoidal Transcription and Protein Patterns: A Bifurcation Sequence of Higher Harmonics on the Egg The Four Color Wheels Model of Positional Specification Turing and Beyond Summary Epilogue Bibliography Index Stuart Kauffman Here Presents A Brilliant New Paradigm For Evolutionary Biology, One That Extends The Basic Concepts Of Darwinian Evolution To Accommodate Recent Findings And Perspectives From The Fields Of Biology, Physics, Chemistry And Mathematics. The Book Drives To The Heart Of The Exciting Debate On The Origins Of Life And Maintenance Of Order In Complex Biological Systems. It Focuses On The Concept Of Self-organization: The Spontaneous Emergence Of Order Widely Observed Throughout Nature. Kauffman Here Argues That Self-organization Plays An Important Role In The Emergence Of Life Itself And May Play As Fundamental A Role In Shaping Life's Subsequent Evolution As Does The Darwinian Process Of Natural Selection. Yet Until Now No Systematic Effort Has Been Made To Incorporate The Concept Of Self-organization Into Evolutionary Theory. The Construction Requirements Which Permit Complex Systems To Adapt Remain Poorly Understood, As Is The Extent To Which Selection Itself Can Yield Systems Able To Adapt More Successfully. This Book Explores These Themes. It Shows How Complex Systems, Contrary To Expectations, Can Spontaneously Exhibit Stunning Degrees Of Order, And How This Order, In Turn, Is Essential For Understanding The Emergence And Development Of Life On Earth. Topics Include The New Biotechnology Of Applied Molecular Evolution, With Its Important Implications For Developing New Drugs And Vaccines; The Balance Between Order And Chaos Observed In Many Naturally Occurring Systems; New Insights Concerning The Predictive Power Of Statistical Mechanics In Biology; And Other Major Issues. Indeed, The Approaches Investigated Here May Prove To Be The New Center Around Which Biological Science Itself Will Evolve. The Work Is Written For All Those Interested In The Cutting Edge Of Research In The Life Sciences. Conceptual Outline Of Current Evolutionary Theory -- The Structure Of Rugged Fitness Landscapes -- Biological Implications Of Rugged Fitness Landscapes -- The Structure Of Adaptive Landscapes Underlying Protein Evolution -- Self-organization And Adaptation In Complex Systems -- The Dynamics Of Coevolving Systems -- The Origins Of Life : A New View -- The Origin Of A Connected Metabolism -- Hypercycles And Coding -- Random Grammars : Models Of Functional Integration And Transformation -- The Architecture Of Genetic Regulatory Circuits And Its Evolution -- Differentiation : The Dynamical Behaviors Of Genetic Regularity Networks -- Selection For Cell Types -- Morphology, Maps, And The Spatial Ordering Of Integrated Tissues. Stuart A. Kauffman. Includes Bibliographical References (p. 647-694) And Index. This monograph extends the basic concepts of Darwinian evolution to accommodate recent findings and perspectives from the fields of biology, physics, chemistry and mathematics. It explains how complex systems, contrary to expectations, can spontaneously exhibit degrees of order.