Introduction to Artificial Life

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 Percolationand 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

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.