The Origins of Order: Self-organization and Selection in EvolutionStuart 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. |
Contents
Conceptual Outline of Current Evolutionary Theory | 3 |
ENLARGING THE FRAMEWORK | 16 |
SUMMARY | 25 |
Adaptation to the Edge of Chaos | 27 |
The Structure of Rugged Fitness Landscapes | 33 |
SelfOrganization and Selection | 34 |
FITNESS LANDSCAPES IN SEQUENCE SPACE | 36 |
THE NK MODEL OF RUGGED FITNESS LANDSCAPES | 40 |
BEDIANS PARADIGM FOR THE ONSET OF CODING | 364 |
SUMMARY | 366 |
Random Grammars Models of Functional Integration and Transformation | 369 |
TOWARD A NEW STRING THEORY | 372 |
APPROACHES TO STUDYING FAMILIES OF MAPPINGS OF STRINGS INTO STRINGS | 377 |
APPLICATIONS TO BIOLOGICAL NEURAL AND ECONOMIC SYSTEMS | 387 |
SUMMARY | 402 |
Order and Ontogeny | 405 |
SUMMARY | 66 |
Biological Implications of Rugged Fitness Landscapes | 69 |
PHYLOGENETIC IMPLICATIONS OF RUGGED LANDSCAPES | 70 |
ON RUGGED FITNESS LANDSCAPES | 95 |
SUMMARY | 117 |
The Structure of Adaptive Landscapes Underlying Protein Evolution | 121 |
ADAPTIVE MATURATION OF THE IMMUNE RESPONSE | 122 |
EVOLUTION OF NOVEL CATALYTIC FUNCTIONS | 142 |
DIRECT EXPLORATION OF DNA RNA AND PROTEIN SEQUENCE SPACES | 156 |
SUMMARY | 171 |
SelfOrganization and Adaptation in Complex Systems | 173 |
DYNAMICAL SYSTEMS AND THEIR ATTRACTORS | 175 |
SPONTANEOUS ORDER AND CHAOS IN COMPLEX DYNAMICAL SYSTEMS | 181 |
ADAPTATION IN DYNAMICAL SYSTEMS | 209 |
SUMMARY | 234 |
The Dynamics of Coevolving Systems | 237 |
COEVOLUTION IN ECOSYSTEMS | 242 |
COEVOLUTION TO THE EDGE OF CHAOS | 255 |
COEVOLUTIONARY CONCLUSIONS | 278 |
SUMMARY | 279 |
The Crystallization of Life | 283 |
The Origins of Life A New View | 287 |
BACKGROUND OF THE ORIGIN OF LIFE PROBLEM | 288 |
AUTOCATALYTIC SETS OF CATALYTIC POLYMERS | 298 |
GROWTH ON THE INFINITE GRAPH OF POLYMERS AND THERMODYNAMIC BEHAVIOR | 312 |
EXPERIMENTAL CONSEQUENCES | 337 |
SUMMARY | 340 |
The Origin of a Connected Metabolism | 343 |
CRYSTALLIZATION OF A CONNECTED METABOLISM AS A PERCOLATION PROBLEM | 346 |
NEW EXPERIMENTS | 354 |
SUMMARY | 355 |
Hypercycles and Coding | 357 |
The Architecture of Genetic Regulatory Circuits and Its Evolution | 411 |
INDEPENDENCE OF THE MOLECULAR EVOLUTIONARY CLOCK AND MORPHOLOGICAL EVOLUTION | 412 |
AN ENSEMBLE THEORY BASED ON RANDOM DIRECTED GRAPHS | 419 |
SUMMARY | 439 |
Differentiation The Dynamical Behaviors of Genetic Regulatory Networks | 441 |
AND THE BOOLEAN IDEALIZATION | 444 |
LARGESCALE FEATURES OF CELL DIFFERENTIATION | 454 |
CELL DIFFERENTIATION IN BOOLEAN NETWORKS | 462 |
GENERIC PROPERTIES | 470 |
IMPLICATIONS FOR ONTOGENY | 481 |
CELL TYPES AS A COMBINATORIAL EPIGENETIC CODE | 507 |
SUMMARY | 520 |
Selection for Cell Types | 523 |
THE FRAMEWORK | 524 |
GENOMIC NETWORK SPACE | 525 |
EXPERIMENTAL AVENUES | 533 |
SUMMARY | 534 |
Morphology Maps and the Spatial Ordering of Integrated Tissues | 537 |
INDUCTION AS A BASIC INTERCELLULAR CONVERSATION | 540 |
DUPLICATION REGENERATION AND POSITIONAL CONTINUITY | 549 |
TURING MODELS | 566 |
COMPARTMENTAL AND SEGMENTAL PATTERNS IN DROSOPHILA MELANOGASTER | 577 |
PATTERN FORMATION IN THE EARLY DROSOPHILA EMBRYO | 594 |
LONGITUDINAL DELETIONS AND MIRRORSYMMETRIC DUPLICATIONS | 601 |
A BIFURCATION SEQUENCE OF HIGHER HARMONICS ON THE EGG | 605 |
THE FOUR COLOR WHEELS MODEL OF POSITIONAL SPECIFICATION | 614 |
TURING AND BEYOND | 630 |
SUMMARY | 641 |
Epilogue | 643 |
Bibliography | 647 |
| 695 | |
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The Origins of Order: Self-Organization and Selection in Evolution Stuart A. Kauffman Limited preview - 1993 |
Common terms and phrases
activity adaptive walks alleles alter amino acids antibody antigen attractors autocatalytic sets basins of attraction behavior binding Boolean functions Boolean networks cell types changes chaotic Chapter coevolving combinatorial complex connected coupled cycle deletion developmental differentiation distribution Drosophila dynamical systems ecosystem edge of chaos eigen elements embryo ensemble enzyme epistatic evolution evolutionary evolve Figure fitness landscapes frozen component genetic genomic regulatory systems genomic systems genotype graph Hamming distance hence increases initial inputs interactions Kauffman large number length local optima loop metabolism molecular mutation rate Nash equilibria NK model number of cell occur one-mutant neighbors ontogeny optima optimum ordered regime organic molecules pairs parameters patterns of gene peaks peptides perturbations polymers population possible properties protein random reactions recombination region ribozyme RNA sequences rugged landscapes selection self-organization single spatial species strings substrates supracritical taxa theory tion tissue total number transformations transition typically values variables
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