Contents

• Contents
• List of Figures
• List of Tables
• Introduction
  • The Big Picture
  • Organisation of the Thesis
  • Major Contributions
  • Typographical Conventions
• Evolution and Life
  • Two Views of Life
    • The Evolutionary View
    • The Ecological View
    • Hybrid Definitions
  • The Origin of Life
  • The Pattern of Life
    • Evolutionary Progress
    • Different Types of Complexity
    • Driven and Passive Trends
    • Major Evolutionary Transitions
    • Contingency in Evolution
  • Playing the Game
  • Definition of Terms
  • Summary
• Artificial Life
  • What is Artificial Life?
    • Weak Artificial Life versus Strong Artificial Life
    • Is Artificial Life Possible?
    • Relation to Theoretical Biology
  • Previous Work
    • Self-Reproduction
    • Open-Ended Evolution
    • Self-Organisation and Origin of Life Models
  • Methodology and Design Issues for Artificial Life Platforms
    • Methodology
    • Self-Reproduction
    • Representation
• Design Details of the Cosmos Platform
  • Cosmos Design Philosophy
  • Preliminary Issues
    • Representation of Information
    • Spatial Structure
    • Time Slicing and the Top-Level Algorithm
    • Naming of Organisms
  • The Structure of an Individual Cell
    • Overview
    • The Genome
    • Regulators: Promoters and Repressors
    • The Translator
    • The Energy Token Store
    • Cell Division and Reproduction
    • Inter-Organism Communication Structures
    • Other Structures
    • Parallel Programs (Multicellular Organisms)
  • The Programming Language and Representation
  • The Environment
    • The Grid
    • Distribution of Energy Tokens
    • Collection of Energy Tokens
    • Moving around the Grid
    • Inter-Organism Communications
    • Environmental Information
    • Mutations and Flaws
  • Actions and Interactions
    • Implications of Intercellular and Inter-Organism Communications
  • The Top-Level Algorithm
  • Global Parameters
  • Input and Output Files
  • Major Differences between Cosmos and Tierra
  • Summary
• Cosmos Experiments 1:
  Detailed Analysis of a Standard Run
  • Analysis and Visualisation Techniques
    • Individual-based Measures
    • Visualisation of Spatial Distributions
    • Population-based Measures
    • A Neutral Shadow
  • Detailed Analysis of a Standard Run
    • Program Length
    • Replication Period
    • Age at Death
    • Population Size and Diversity
    • Flaw Period and Proportion of Unfaithful Replications
    • Activity Measures
    • Analysis of Significant Genotypes
    • Spatial Distribution
    • Summary of Results
• Cosmos Experiments 2: Exploring the Parameter Space
  • The Role of Chance^6.2
    • Method
    • Results
    • Activity Wave Diagrams
    • Discussion
  • Re-running the Standard Model
    • Results
  • Mutations and Flaws
    • High Mutation and Flaw Rates
    • Low Mutation and Flaw Rates
  • The CPU-time Distribution Scheme
    • Results
  • Energy
    • High Energy Levels
    • Private Energy Collection
    • Energy Gradient
    • Random Distribution
  • Reading Neighbouring Code
  • Inoculation with Sexual Ancestors
  • Summary and Discussion
• Reappraisal of the Approach
  • Problems with Tierra-like Models
    • Lack of an Explicit Theoretical Grounding
    • Predefined Organism Structure
    • Restricted Ecological Interactions
    • No Competition for Matter or Energy
    • Evolving a Self-Reproduction Algorithm
  • Self-Reproduction and Evolution Revisited
    • Some Definitions
    • General Issues of Reproduction
    • Self-Reproduction and Open-Ended Evolution
  • Improving the Approach
    • Beyond Digital Naturalism: The Need for Clear Goals^7.20
    • A Full Specification for Open-Ended Evolution
    • Evolution and Life Revisited
• Summary
• Cosmos System Details
  • Global Parameters
    • Inoculation
    • Start of Run
    • Termination
    • Environment
    • Organism
    • Cell
    • Mutations and Flaws
    • Input and Output
  • The REPLiCa Instruction Set
  • Predefined Ancestor Programs
    • Ancestor A1
    • Ancestor A2
  • Running Cosmos
  • Format of Input and Output Files
    • Input Files
    • Output Files
  • Implementation Details
• Details of the Reported Cosmos Runs
  • Default Values for Minor Parameters in Cosmos
  • The Standard Ancestor Program, 348AAAA
  • The Sexual Ancestor Program, 1314AAAA
  • Genetic Code
  • RNG Seeds for Runs in Chapter 6
    • The Role of Chance
    • Re-Running the Standard Model
    • Mutations and Flaws
    • The CPU-time Distribution Scheme
    • Energy
    • Reading Neighbouring Code
    • Inoculation with Sexual Ancestors
• Bibliography