Introduction to Artificial Life

ISBN-13: 9781461272311 / Angielski / Miękka / 2013 / 376 str.

Christoph Adami

Opis

This book and CD-ROM package has been developed in a lab-oriented course taught at Cal Tech in 1995 and 1996, and simultaneously augmented by artificial life research conducted there. These courses were attended by an interdisciplinary group of students from physics, computer science, and the computational neural sciences. The authors assume a pre-requisite understanding of statistical physics and thermodynamics, basic biology, as well as familiarity with computer architectures and scientific computing techniques. This project brings together the necessary theoretical groundwork for understanding the dynamics of systems of self-replicating information, as well as the results of initial experiments carried out with artificial living systems based on this paradigm.

Spis treści

1 Flavors of Artificial Life.- 1.1 Whither a Theory of the Living State?.- 1.2 Emulation and Simulation.- 1.3 Carbon-Based Artificial Life.- 1.4 Turing and von Neumann Automata.- 1.5 Cellular Automata.- 1.6 Overview.- 2 Artificial Chemistry and Self-Replicating Code.- 2.1 Virtual Machines and Self-Reproducing CA.- 2.2 Viruses and Core Worlds.- 2.3 The tierra System.- 2.4 avida, amoeba, and the Origin of Life.- 2.5 Overview.- 3 Introduction to Information Theory.- 3.1 Information Theory and Life.- 3.2 Channels and Coding.- 3.3 Uncertainty and Shannon Entropy.- 3.4 Joint and Conditional Uncertainty.- 3.5 Information.- 3.6 Noiseless Coding.- 3.7 Channel Capacity and Fundamental Theorem.- 3.8 Information Transmission Capacity for Genomes.- 3.9 Overview.- 4 Statistical Mechanics and Thermodynamics.- 4.1 Phase Space and Statistical Distribution Function.- 4.2 Averages, Ergodicity, and the Ergodic Theorem.- 4.3 Thermodynamical Equilibrium, Relaxation.- 4.4 Energy.- 4.5 Entropy.- 4.6 Second Law of Thermodynamics.- 4.7 Tèmperature.- 4.8 The Gibbs Distribution.- 4.9 Nonequilibrium Thermodynamics.- 4.10 First-Order Phase Transitions.- 4.11 Overview.- 5 Complexity of Simple Living Systems.- 5.1 Complexity and Information.- 5.2 The Maxwell Demon.- 5.3 Kolmogorov Complexity.- 5.4 Physical Complexity and the Natural Maxwell Demon.- 5.5 Complexity of tRNA.- 5.6 Complexity in Artificial Life.- 5.7 Overview.- 6 Self-Organization to Criticality.- 6.1 Self-Organization and Sandpiles.- 6.2 SOC in Forest Fires.- 6.3 SOC in the Living State.- 6.4 Theories of SOC.- 6.5 Overview.- 7 Percolation.- 7.1 Site Percolation.- 7.2 Cluster Size Distribution.- 7.3 Percolation in 1D.- 7.4 Higher-Dimensional Euclidean Lattices.- 7.5 Percolation on the Bethe Lattice.- 7.6 Scaling Theory.- 7.7 Percolation and Evolution.- 7.8 Overview.- 8 Fitness Landscapes.- 8.1 Theoretical Formulation.- 8.2 Example Landscapes.- 8.3 Fractal Landscapes.- 8.4 Diffusive and Nondiffusive Processes.- 8.5 RNA Landscapes.- 8.6 Fitness Landscape in avida.- 8.7 Overview.- 9 Experiments with avida.- 9.1 Choice of Chemistry.- 9.2 A Simple Experiment.- 9.3 Experiments in Adaptation.- 9.4 Experiments with Species and Genetic Distance.- 9.5 Overview.- 10 Propagation of Information.- 10.1 Information Transport and Equilibrium.- 10.2 The Artificial Life System sanda.- 10.3 Diffusion and Waves.- 10.4 Comparison: Theory and Experiment.- 10.5 Overview.- 11 Adaptive Learning at the Error Threshold.- 11.1 Information Processing at the Edge of Chaos.- 11.2 Adaptation to Computation in avida.- 11.3 Eigen’s Error Threshold.- 11.4 Molecular Evolution as an Ising Model.- 11.5 The Race to the Error Threshold.- 11.6 Approach to Error Threshold in avida.- 11.7 Overview.- A The avida User’s Manual.- A.1 Introduction.- A.2 A Beginner’s Guide to avida.- A.3 Time Slicing and the Fitness Landscape.- A.4 Reproduction.- A.5 The Virtual Computer.- A.6 Mutations.- A.7 Installing avida.- A.8 The Text Interface.- A.9 Configuring avida Runs.- A.10 Guide to Output Files.- A.11 Summary of Variables.- A.12 Glossary.- References.

O autorze

For students, researchers and professional scientist eager to gain insight into the emerging frontiers of Artifical Life, Chris Adami's work provides the basic underpinnings for properly understanding this interdisciplinary research area. The CD-ROM accompanying the book invites readers to actively experience artificial evolution in "real time" by using a proprietary simulation software program, AVIDA, which is contained on the CD.