Meyer-Ortmanns / Thurner Principles of Evolution

From the Planck Epoch to Complex Multicellular Life
1. Auflage 2011
ISBN: 978-3-642-18137-5
Verlag: Springer
Format: PDF
Kopierschutz: 1 - PDF Watermark

E-Book, Englisch, 388 Seiten

Reihe: The Frontiers Collection

With contributions from a team of leading experts, this volume provides a comprehensive survey of recent achievements in our scientific understanding of evolution. The questions it asks concern the beginnings of the universe, the origin of life and the chances of its arising at all, the role of contingency, and the search for universal features in the plethora of evolutionary phenomena. Rather than oversimplified or premature answers, the chapters provide a clear picture of how these essential problems are being tackled, enabling the reader to understand current thinking and open questions. The tools employed stem from a range of disciplines including mathematics, physics, biochemistry and cell biology. Self-organization as an overarching concept is demonstrated in the most diverse areas: from galaxy formation in the universe to spindle and aster formation in the cell. Chemical master equations, population dynamics, and evolutionary game theory are presented as suitable frameworks for understanding the universal mechanisms and organizational principles observed in a wide range of living units, ranging from cells to societies. This book will provide engaging reading and food for thought for all those seeking a deeper understanding of the science of evolution.

Hildegard Meyer-Ortmanns is full professor and head of the statistical physics group at Jacobs University in Bremen, Germany. Her area of expertise ranges from general relativity and theoretical particle physics to  statistical physics and its applications to complex systems. Stefan Thurner is Professor of Science of Complex Systems at the Medical  University of Vienna and external professor at the Santa Fe institute.  His area of interest extends from theoretical physics and applied  mathematics to complex systems theory and its applications in  life science and economics.

Autoren/Hrsg.

Meyer-Ortmanns, Hildegard

Thurner, Stefan

Inhaltsverzeichnis

1;Preface;7
2;Contents;8
3;Contributors;10
4;1 Introduction;12
4.1;Hildegard Meyer-Ortmanns;12
4.1.1;1.1 A Short Chronology of Evolution;13
4.1.2;1.2 Scientific Reductionism;16
4.1.3;1.3 Universal Features, Universal Processes, and Striving for Universal Laws;19
4.1.4;1.4 The Concept of Self-Organization;22
4.1.5;1.5 Chicken-and-Egg Problems in Many Facets;24
4.1.6;1.6 A Quick Look into the Nanoworld;26
4.1.7;1.7 Playing the Tape Again;26
4.1.8;1.8 There is More than Intuition;28
4.1.9;1.9 Reduction of Complexity;29
4.1.10;1.10 How This Book Is Organized;30
4.1.10.1;1.10.1 Background;30
4.1.10.2;1.10.2 Rationale;30
4.1.10.3;1.10.3 About the Articles;32
4.1.11;References;51
5;Part I Principles of Evolution;53
5.1;2 Physical Principles of Evolution;54
5.1.1;Peter Schuster;54
5.1.1.1;2.1 Mathematics and Biology;55
5.1.1.2;2.2 Darwin's Theory in Mathematical Language;58
5.1.1.3;2.3 Evolution in Genotype Space;62
5.1.1.4;2.4 Modeling Genotype--Phenotype Mappings;65
5.1.1.5;2.5 Chemical Kinetics of Evolution;71
5.1.1.6;2.6 Evolution as a Stochastic Process;78
5.1.1.7;2.7 Concluding Remarks;85
5.1.1.8;References;86
5.2;3 The Interplay of Replication, Variation and Selection in the Dynamics of Evolving Populations;89
5.2.1;Richard A. Blythe;89
5.2.1.1;3.1 Hull's General Analysis of Selection;91
5.2.1.1.1;3.1.1 Instances of Hull's General Analysis of Selection;92
5.2.1.2;3.2 A Mathematical Analysis of Selection: The Price Equation;94
5.2.1.2.1;3.2.1 Derivation of the Price Equation;95
5.2.1.2.2;3.2.2 Applications of the Price Equation;96
5.2.1.3;3.3 Neutral Demographic Fluctuations: Genetic Drift;99
5.2.1.3.1;3.3.1 Models of Purely Neutral Evolution;100
5.2.1.3.2;3.3.2 Fixation Probability;101
5.2.1.3.3;3.3.3 Mean Fixation Time;102
5.2.1.3.4;3.3.4 Experimental Observation of Genetic Drift: Effective Population Size;103
5.2.1.4;3.4 Immigration and Mutation in Neutral Models;104
5.2.1.4.1;3.4.1 Recurrent Immigration;105
5.2.1.4.2;3.4.2 Nonrecurrent Immigration;108
5.2.1.4.3;3.4.3 Applications in Ecology and Cultural Evolution;116
5.2.1.5;3.5 Population Subdivision;117
5.2.1.5.1;3.5.1 Voter-Type Models on Heterogeneous Networks;120
5.2.1.5.2;3.5.2 Application to Theories for Language Change;123
5.2.1.6;3.6 Summary and Outlook;124
5.2.1.7;References;125
5.3;4 A Simple General Model of Evolutionary Dynamics;127
5.3.1;Stefan Thurner;127
5.3.1.1;4.1 Introduction;128
5.3.1.2;4.2 A General Model for Evolution Dynamics;131
5.3.1.2.1;4.2.1 A Notion for Species, Goods, Things, or Elements;132
5.3.1.2.2;4.2.2 Recombination and Production of New Elements;132
5.3.1.2.3;4.2.3 Selection, Competition, Destruction;133
5.3.1.2.4;4.2.4 The Active Production or Recombination Network;135
5.3.1.2.5;4.2.5 Spontaneous Creations, Innovations, Ideas, and Disasters;136
5.3.1.2.6;4.2.6 Formal Summary of the Model;136
5.3.1.2.7;4.2.7 An Evolutionary Algorithm;137
5.3.1.2.8;4.2.8 Random Interactions;137
5.3.1.3;4.3 Predictions of the Model;138
5.3.1.4;4.4 Model Variants;140
5.3.1.5;4.5 Understanding Evolutionary Dynamics;141
5.3.1.5.1;4.5.1 Evolutionary Dynamics as a Self-Organized Critical System;141
5.3.1.5.2;4.5.2 Eigenvalues and Keystone Productions;141
5.3.1.6;4.6 Toward a Unified Mathematical Framework;144
5.3.1.6.1;4.6.1 Variational Principle for Deterministic Diversity Dynamics;144
5.3.1.6.2;4.6.2 Mean-Field Approximation;145
5.3.1.7;4.7 Applicability to Specific Evolutionary Systems;147
5.3.1.7.1;4.7.1 Macroeconomic Instruments;148
5.3.1.7.2;4.7.2 Chemical Reaction Networks;148
5.3.1.7.3;4.7.3 Lifetime Distributions of Species;148
5.3.1.8;4.8 Conclusions;150
5.3.1.9;References;151
5.4;5 Can We Recognize an Innovation? Perspective from an Evolving Network Model;153
5.4.1;Sanjay Jain and Sandeep Krishna;153
5.4.1.1;5.1 Introduction;153
5.4.1.2;5.2 A Framework for Modeling Innovation: Graph Theoryand Dynamical Systems;154
5.4.1.3;5.3 Definition of the Model System;156
5.4.1.4;5.4 Time Evolution of the System;157
5.4.1.5;5.5 Innovation;163
5.4.1.6;5.6 Six Categories of Innovation;164
5.4.1.6.1;5.6.1 A Short-Lived Innovation: Uncaring and Unviable Winners;164
5.4.1.6.2;5.6.2 Birth of an Organization: Cooperation Begets Stability;165
5.4.1.6.3;5.6.3 Expansion of the Organization at Its Periphery: Incremental Innovations;166
5.4.1.6.4;5.6.4 Growth of the Core of the Organization: Parasites Become Symbionts;167
5.4.1.6.5;5.6.5 Core-Shift 1: Takeover by a New Competitor;168
5.4.1.6.6;5.6.6 Core-Shift 2: Takeover by a Dormant Innovation;169
5.4.1.7;5.7 Recognizing Innovations: A Structural Classification;170
5.4.1.8;5.8 Some Possible General Lessons;172
5.4.1.9;5.9 Discussion;173
5.4.1.10;References;179
6;Part II From Random to Complex Structures:The Concept of Self-Organization for Galaxies,Asters, and Spindles;181
6.1;6 How Stochastic Dynamics Far from Equilibrium Can Create Nonrandom Patterns ;182
6.1.1;Gunter M. Schütz;182
6.1.1.1;6.1 Some Very Small Numbers;182
6.1.1.2;6.2 Some Models for Nonequilibrium Dynamics;186
6.1.1.2.1;6.2.1 Model 1: The Totally Asymmetric Simple Exclusion Process;186
6.1.1.2.2;6.2.2 Model 2: The TASEP with Random Sequential Update;188
6.1.1.2.3;6.2.3 Model 3: TASEP with Sublattice Parallel Update;189
6.1.1.2.4;6.2.4 Model 4: TASEP with Next-Nearest-Neighbor Interaction;189
6.1.1.2.5;6.2.5 Emergence of Order and Relaxation to Disorder;190
6.1.1.3;6.3 Some Conclusions;192
6.1.1.4;References;194
6.2;7 Structure Formation in the Universe;195
6.2.1;Matthias Bartelmann;195
6.2.1.1;7.1 The Framework;195
6.2.1.1.1;7.1.1 Concepts;195
6.2.1.1.2;7.1.2 Isotropy on Average;196
6.2.1.1.3;7.1.3 The Cosmic Expansion;197
6.2.1.1.4;7.1.4 Origin of the Light Elements and the CosmicMicrowave Background;198
6.2.1.1.5;7.1.5 Structures in the Cosmic Microwave Background;199
6.2.1.1.6;7.1.6 Cosmic Consistency;202
6.2.1.2;7.2 Structure Formation in the Universe;203
6.2.1.2.1;7.2.1 Concepts and Assumptions;203
6.2.1.2.2;7.2.2 Linear Structure Growth;204
6.2.1.2.3;7.2.3 Cold Dark Matter;205
6.2.1.2.4;7.2.4 Nonlinear Structure Growth;208
6.2.1.2.5;7.2.5 The Origin of Structures;209
6.2.1.3;References;209
6.3;8 The Need for Quantum Cosmology;211
6.3.1;Claus Kiefer;211
6.3.1.1;8.1 Introduction;211
6.3.1.2;8.2 Quantum Gravity;212
6.3.1.3;8.3 Quantum Cosmology;215
6.3.1.4;8.4 Boundary Conditions;216
6.3.1.4.1;8.4.1 No-Boundary Proposal;216
6.3.1.4.2;8.4.2 Tunneling Proposal;218
6.3.1.5;8.5 Inclusion of Inhomogeneities and the Semiclassical Picture;218
6.3.1.6;8.6 Arrow of Time and Structure Formation;220
6.3.1.7;References;223
6.4;9 Self-Organization in Cells;224
6.4.1;Leif Dehmelt and Philippe Bastiaens;224
6.4.1.1;9.1 The Origin of Cellular Organization;224
6.4.1.2;9.2 Self-Organization and Other Organizational Principlesin Cells;225
6.4.1.3;9.3 Emergence of Spatio-Temporal Gradients via Dynamic Feedback Systems;229
6.4.1.4;9.4 Stigmergy and Feedback Regulation in Directional Morphogenetic Growth or Transport Processes;232
6.4.1.5;9.5 Emergence of Complex Structures via Self-Organizationof Microtubules and Associated Motors;235
6.4.1.6;9.6 Emergence of Dynamic Structures in Actin Filament Treadmill Systems;238
6.4.1.7;9.7 Limits of Self-Organization in Cells;240
6.4.1.8;References;242
7;Part III Protocells In Silico and In Vitro;244
7.1;10 Approach of Complex-Systems Biology to Reproduction and Evolution;245
7.1.1;Kunihiko Kaneko;245
7.1.1.1;10.1 A Bridge Between Catalytic Reaction Networks and Reproducing Cells;246
7.1.1.1.1;10.1.1 Catalytic Reaction Network for a Protocell ;246
7.1.1.1.2;10.1.2 Long-Term Sustainment of Nonequilibrium State;247
7.1.1.1.3;10.1.3 Consistency Between Cell Reproduction and Molecule Replication;249
7.1.1.1.4;10.1.4 Minority Control: Origin of Genetic Information;251
7.1.1.2;10.2 Evolution;254
7.1.1.2.1;10.2.1 Fluctuations and Robustness;254
7.1.1.2.2;10.2.2 Evolutionary Fluctuation--Response Relationship;255
7.1.1.2.3;10.2.3 Relationship Between Fluctuations by Noise and by Mutation;256
7.1.1.2.4;10.2.4 Phenomenological Distribution Theory;259
7.1.1.2.5;10.2.5 Discussion;261
7.1.1.3;References;262
7.2;11 Wet Artificial Life: The Construction of Artificial Living Systems;264
7.2.1;Harold Fellermann;264
7.2.1.1;11.1 Introduction;264
7.2.1.2;11.2 Bits and Pieces;266
7.2.1.2.1;11.2.1 Chemical Information;266
7.2.1.2.2;11.2.2 Protocell Containers;268
7.2.1.2.3;11.2.3 Protocell Metabolisms;270
7.2.1.3;11.3 Bottom-Up Approaches to Artificial Cells;271
7.2.1.4;11.4 The Minimal Protocell;274
7.2.1.4.1;11.4.1 Design Principles;274
7.2.1.4.2;11.4.2 Building Blocks;275
7.2.1.4.3;11.4.3 Life Cycle of the Protocell;275
7.2.1.4.4;11.4.4 The Metabolism of the Protocell;277
7.2.1.4.5;11.4.5 Toward Inheritable Information and Darwinian Evolution;279
7.2.1.5;11.5 The Evolutionary Potential of Protocells;280
7.2.1.6;References;281
7.3;12 Towards a Minimal System for Cell Division;284
7.3.1;Petra Schwille;284
7.3.1.1;12.1 Two Concepts of Synthetic Biology;285
7.3.1.2;12.2 The Concept of a Minimal Cell;286
7.3.1.3;12.3 Minimal Systems for Cell Division: An Attempt;287
7.3.1.3.1;12.3.1 Step One: Modeling Membrane Morphogenesis -- Nature`s Solution to Compartmentation ;288
7.3.1.3.2;12.3.2 Step Two: Adding Mechanical Stability -- Creation of an Artificial Cortex/Cytoskeleton;291
7.3.1.3.3;12.3.3 Step Three: How Should the Division Site Be Defined? Pattern Formation and Self-Organization in Minimal Systems;293
7.3.1.4;12.4 Outlook;295
7.3.1.5;References;296
8;Part IV From Cells to Societies;297
8.1;13 Bacterial Games;298
8.1.1;Erwin Frey and Tobias Reichenbach;298
8.1.1.1;13.1 Introduction;299
8.1.1.2;13.2 The Language of Game Theory;300
8.1.1.2.1;13.2.1 Strategic Games and Social Dilemmas;300
8.1.1.2.2;13.2.2 Evolutionary Game Theory;302
8.1.1.2.3;13.2.3 Nonlinear Dynamics of Two-Player Games;305
8.1.1.3;13.3 Games in Microbial Metapopulations;307
8.1.1.3.1;13.3.1 Cooperation;307
8.1.1.3.2;13.3.2 Pattern Formation;309
8.1.1.3.3;13.3.3 The Escherichia coli Col E2 System ;309
8.1.1.4;13.4 Stochastic Dynamics in Well-Mixed Populations;311
8.1.1.4.1;13.4.1 Extinction Times and Classification of Coexistence Stability;311
8.1.1.4.2;13.4.2 Cyclic Three-Strategy Games;315
8.1.1.5;13.5 Spatial Games with Cyclic Dominance;316
8.1.1.5.1;13.5.1 The Role of Mobility in Ecosystems;316
8.1.1.5.2;13.5.2 Cyclic Dominance in Ecosystems;317
8.1.1.5.3;13.5.3 The May--Leonard Model;317
8.1.1.5.4;13.5.4 The Spatially Extended May--Leonard Model;319
8.1.1.5.5;13.5.5 Pattern Formation and Reaction--Diffusion Equations;321
8.1.1.6;13.6 Conclusions and Outlook;325
8.1.1.7;References;328
8.2;14 Darwin and the Evolution of Human Cooperation;331
8.2.1;Karl Sigmund and Christian Hilbe;331
8.2.1.1;14.1 Darwin on Complexity;331
8.2.1.2;14.2 The Riddle of Cooperation;332
8.2.1.3;14.3 Kin Selection;334
8.2.1.4;14.4 Relatedness and Assortment;335
8.2.1.5;14.5 Darwin on Kin Selection;336
8.2.1.6;14.6 Political Animals;337
8.2.1.7;14.7 Reciprocal Altruism;338
8.2.1.8;14.8 Indirect Reciprocity;341
8.2.1.9;14.9 Competition of Moral Systems;342
8.2.1.10;14.10 Exceptionalism;344
8.2.1.11;14.11 Team Efforts;345
8.2.1.12;14.12 Group Selection;346
8.2.1.13;References;347
8.3;15 Similarities Between Biological and Social Networks in Their Structural Organization;348
8.3.1;Byungnam Kahng, Deokjae Lee, and Pureun Kim;348
8.3.1.1;15.1 Introduction;348
8.3.1.2;15.2 Branching Tree and Fractal Structure ;349
8.3.1.2.1;15.2.1 Scale-Free and Critical Branching Structure;349
8.3.1.2.2;15.2.2 Fractality ;350
8.3.1.3;15.3 The Phylogenetic Tree ;352
8.3.1.3.1;15.3.1 Database;352
8.3.1.3.2;15.3.2 Structural Features;352
8.3.1.4;15.4 Evolution of Protein Interaction Networks ;353
8.3.1.4.1;15.4.1 The Solé Model;353
8.3.1.4.2;15.4.2 Numerical Results;354
8.3.1.5;15.5 Evolution of a Coauthorship Network;357
8.3.1.5.1;15.5.1 Data Collection;357
8.3.1.5.2;15.5.2 Evolution of a Large-Scale Structure;358
8.3.1.5.3;15.5.3 Fractal Structure and Critical Branching Tree;360
8.3.1.6;15.6 Conclusions;363
8.3.1.7;References;363
8.4;16 From Swarms to Societies: Origins of Social Organization;365
8.4.1;Alexander S. Mikhailov;365
8.4.1.1;16.1 What Is a Society?;365
8.4.1.2;16.2 Swarms and Active Fluids;366
8.4.1.3;16.3 Internal Dynamics and Communication;367
8.4.1.4;16.4 Synchronization;368
8.4.1.5;16.5 Clustering;368
8.4.1.6;16.6 Hierarchies;370
8.4.1.7;16.7 Networks;372
8.4.1.8;16.8 Coherent Patterns and Turbulence;373
8.4.1.9;16.9 Feedback and Control;374
8.4.1.10;16.10 Social Evolution;376
8.4.1.11;16.11 Open Questions and Perspectives;376
8.4.1.12;References;377
9;Index;379