author : Mark A. Bedau

The papers are gathered under the following headings: • Origin of Life, Self-Organization, and Self-Replication • Development and Differentiation • Evolutionary and Adaptive Dynamics • Robots and Autonomous Agents • Communication, Cooperation, and Collective Behavior • Methodological and Technological Applications • The Broader Context

Contents

• Hector Fabio Restrepo, Daniel Mange, Moshe Sipper. A Self-Replicating Universal Turing Machine: From von Neumann's Dream to New Embryonic Circuits. 2000

• Alan Dorin. Creating a Physically-based, Virtual-Metabolism with Solid Cellular Automata. 2000

• Hiroki Sayama. Self-Replicating Worms That Increase Structural Complexity through Gene Transmission. 2000

• Uwe Tangen. Self-Organisation in Micro-Configurable Hardware. 2000

• Hugues Bersini. Reaction Mechanisms in the OO Chemistry. 2000

• Pietro Speroni di Fenizio. A Less Abstract Artificial Chemistry. 2000

• Yasuhiro Suzuki, Hiroshi Tanaka. Chemical Evolution among Artificial Proto-cells. 2000

• Harald Huning. A Search for Multiple Autocatalytic Sets in Artificial Chemistries based on Boolean Networks. 2000

• Ezequiel A. Di Paolo. Searching for Rhythms in Asynchronous Random Boolean Networks. 2000

• S. Kazadi, D. Lee, R. Modi, J. Sy, W. Lue. Levels of Compartmentalization in Alife. 2000

• Keith Downing. Exploring Gaia Theory: Artificial Life on a Planetary Scale. 2000

• Chikara Furusawa, Kunihiko Kaneko. Complex Organization in Multicellularity as a Necessity in Evolution. 2000

• Kunihiko Kaneko, Tetsuya Yomo. Sympatric Speciation from Interaction-induced Phenotype Differentiation. 2000

• Hiroaki Takagi, Kunihiko Kaneko. Evolution of Genetic Code through Isologous Diversification of Cellular States. 2000

• Thomas S. Ray, Joseph F. Hart. Evolution of Differentiation in Multithreaded Digital Organisms. 2000

• Cefn Hoile, Richard Tateson. Design by Morphogenesis. 2000

• Alistair G. Rust, Rod Adams, Hamid Bolouri. Evolutionary Neural Topiary: Growing and Sculpting Artificial Neurons to Order. 2000

• David G. Green, David Newth, Michael G. Kirley. Connectivity and Catastrophe---Towards a General Theory of Evolution. 2000

• Rob Shipman, Mark Shackleton, Marc Ebner, Richard A. Watson. Neutral Search Spaces for Artificial Evolution: A Lesson from Life. 2000

• Richard A. Watson, Torsten Reil, Jordan B. Pollack. Mutualism, Parasitism, and Evolutionary Adaptation. 2000

• Michael L. Best. Coevolving Mutualists Guide Simulated Evolution. 2000

• Eizo Akiyama, Kunihiko Kaneko. Evolution of Cooperation in Social Dilemma---Dynamical Systems Game Approach. 2000

• Takaya Arita, Reiji Suzuki. Interactions between Learning and Evolution: The Outstanding Strategy Generated by the Baldwin Effect. 2000

• Hideaki Suzuki. Evolvability Analysis: Distribution of Hyperblobs in a Variable-Length Protein Genotype Space. 2000

• Daniel Wagenaar, Christoph Adami. Influence of Chance, History and Adaptation on Evolution in Digitalia. 2000

• Stevan Jay Anastasoff. Ecology and Extinction---Macroevolutionary Extinction Dynamics in a Simulated Ecosystem. 2000

• Shinichiro Yoshii, Eiichi Miyamoto, Yukinori Kakazu. Quantification of Microscopic Events in the Process of Long-Term Evolutionary Dynamics. 2000

• Russell K. Standish. An Ecolab Perspective on the Bedau Evolutionary Statistics. 2000

• Patricio Lerena. Mate Choice: Simple or Complex?. 2000

• Paul Domjan. A Discussion of the Use of Artificial Life Models to Evaluate Gould's Hypothesis about Progress in Evolution. 2000

• Tatsuo Unemi. Should Seeds Fly or Not?. 2000

• Bernard D. Reger, Karen M. Fleming, Vittorio Sanguineti, Simon Alford, Ferdinando A. Mussa-Ivaldi. Connecting Brains to Robots: The Development of a Hybrid System for the Study of Learning in Neural Tissues. 2000

• Stevan Jay Anastasoff. A ' Fitness Landscaping' Comparison of Evolved Robot Control Systems. 2000

• Hod Lipson, Jordan B. Pollack. Evolving Physical Creatures. 2000

• Edgar E. Vallejo, Ferdando Ramos. Evolving Insect Locomotion Using Non-uniform Cellular Automata. 2000

• Maciej Komosinski, Adam Rotaru-Varga. From Directed to Open-Ended Evolution in a Complex Simulation Model. 2000

• Masayasu Atsumi. Artificial Neural Development for Pulsed Neural Network Design---Generating Place Recognition Circuits of Animats. 2000

• Yuichi Sato, Takashi Nagai, Hiroshi Yokoi, Takafumi Mizuno, Yukinori Kakazu. Emergent SMA-Net Robot Control by Coupled Oscillator System. 2000

• Norman L. Johnson. Developmental Insights into Evolving Systems: Roles of Diversity, Non-Selection, Self-Organization, Symbiosis. 2000

• Josh C. Bongard. Reducing Collective Behavioural Complexity through Heterogeneity. 2000

• Shin I. Nishimura. Studying Attention Dynamics of a Predator in a Prey-Predator System. 2000

• Felix Flentge, Daniel Polani, Thomas Uthmann. On the Emergence of Possession Norms in Agent Societies. 2000

• James A. R. Marshall, Jonathan E. Rowe. Investigating the Mechanisms Underlying Cooperation in Viscous Population Multi-Agent Systems. 2000

• Lars Kroll Kristensen. Aintz: A Study of Emergent Properties in a Model of Ant Foraging. 2000

• Yoshiki Yamaguchi, Tsutomu Maruyama, Tsutomu Hoshino. A Co-evolution Model of Scores and Strategies in IPD Games: Toward the Understanding of the Emergence of the Social Morals. 2000

• Norberto Eiji Nawa, Katsunori Shimohara, Osamu Katai. On the Effect of "Stock Alerts" in an Agent-Based Model of a Financial Market. 2000

• Frederic Kaplan. Semiotic Schemata: Selection Units for Linguistic Cultural Evolution. 2000

• Luc Steels, Pierre-Yves Oudeyer. The Cultural Evolution of Syntactic Constraints in Phonology. 2000

• Carlo C. Maley, Stephanie Forrest. Modeling the Role of Neutral and Selective Mutations in Cancer. 2000

• Anthony Liekens. From Individuals to Populations, Approaches to the Study of Biological Emergent Phenomena. 2000

• Janos Albert. Towards a Comprehensive Alife-model of the Evolution of the Nervous System and Adaptive Behavior. 2000

• M. A. Gibney, N. R. Jennings, N. J. Vriend. Market-Based Call Routing in Telecommunications Networks Using Adaptive Pricing and Real Bidding. 2000

• Gina M. B. Oliveira, Pedro P. B. de Oliveira, Nizam Omar. Evolving Solutions of the Density Classification Task in 1D Cellular Automata, Guided by Parameters That Estimate Their Dynamic Behaviour. 2000

• V. J. Blue, J. L. Adler. Cellular Automata Model of Emergent Collective Bi-Directional Pedestrian Dynamics. 2000

• James Macgill. Using Flocks to Drive a Geographical Analysis Engine. 2000

• Una-May O'Reilly, Ian Ross, Peter Testa. Emergent Design: Artificial Life for Architecture Design. 2000

• Barry McMullin. John von Neumann and the Evolutionary Growth of Complexity: Looking Backwards, Looking Forwards. 2000

• Seth Bullock. What Can We Learn from the First Evolutionary Simulation Model?. 2000

• David H. Ackley. Real Artificial Life: Where We May Be. 2000

• Ezequiel A. Di Paolo, Jason Noble, Seth Bullock. Simulation Models as Opaque Thought Experiments. 2000

• Alvaro Moreno. Artificial Life as a Bridge between Science and Philosophy. 2000

• J. McKenzie Alexander. Artificial Justice. 2000

• Edmund M. A. Ronald, Moshe Sipper. Engineering, Emergent Engineering, and Artificial Life: Unsurprise, Unsurprising Surprise, and Surprising Surprise. 2000

• Gary R. Greenfield. Art and Artificial Life---A Coevolutionary Approach. 2000

• Eleonora Bilotta, Pietro Pantano, Valerio Talarico. Synthetic Harmonies: An Approach to Musical Semiosis by Means of Cellular Automata. 2000

• Christa Sommerer, Laurent Mignonneau. Modeling Emergence of Complexity: The Application of Complex System and Origin of Life Theory to Interactive Art on the Internet. 2000

• Arantza Etxeberria. Artificial Evolution: Creativity and the Possible. 2000

Contents

• Carlos Gershenson. Classification of Random Boolean Networks. 2003

• Jean-Claude Heudin. Complexity Classes in Three-dimensional Gravitational Agents. 2003

• Tatsuya Nomura. Formal Description of Autopoiesis for Analytic Models of Life and Social Systems. 2003

• Kazumasa Oida. The Birth and Death Process of Hypercycle Spirals. 2003

• David Cornforth, David G. Green, David Newth, Michael G. Kirley. Do Artificial Ants March in Step? Ordered Asynchronous Processes and Modularity in Biological Systems. 2003

• Satoshi Kurihara, Kensuke Fukuda, Toshio Hirotsu, Osamu Akashi, Shinya Sato, Toshiharu Sugawara. Importance of Evolved Structure for Emerging Self-organization in a Complex Competitive Situation. 2003

• Eleonora Bilotta, Antonio Lafusa, Pietro Pantano. Is Self-replication an Embedded Characteristic of Artificial/Living Matter?. 2003

• Hiroki Sayama. Von Neumann's Machine in the Shell: Enhancing the Robustness of Self-Replication Processes. 2003

• Andre Stauffer, Moshe Sipper. Interactive Self-Replicating, Self-Incrementing and Self-Decrementing Loops. 2003

• Naoaki Ono, Takashi Ikegami. Selection of Catalysts through Cellular Reproduction. 2003

• Chrystopher L. Nehaniv. Evolution in Asynchronous Cellular Automata. 2003

• Thomas E. Portegys. An Abstraction of Intercellular Communication. 2003

• Hiroaki Takagi, Kunihiko Kaneko. Dynamic Relationship between Diversity and Plasticity of Cell types in Multi-cellular State. 2003

• Dennis L. Chao, Stephanie Forrest. Generating Biomorphs with an Aesthetic Immune System. 2003

• Takamasa Sawada, Atsuko Mutoh, Shohei Kato, Hidenori Itoh. A Model of Biological Differentiation in Adaptiogenesis to the Environment. 2003

• Jaime Lagunez-Otero, Pedro Pablo Gonzalez Perez, Maura Cardenas-Garcia, Octavio Rosa, Armando Franyuti. Cellulat. 2003

• Lucian Prodan, Gianluca Tempesti, Daniel Mange, Andre Stauffer. Embryonics: Electronic Stem Cells. 2003

• D. A. Mac Donaill. Tautomerism as a Constraint on the Composition of Alternative Nucleotide Alphabets. 2003

• Gianluca Tempesti, Daniel Roggen, Eduardo Sanchez, Yann Thoma, Richard O. Canham, Andy M. Tyrrell, Juan-Manuel Moreno. A POEtic Architecture for Bio-Inspired Hardware. 2003

• Wei-Min Shen, Cheng-Ming Chuong, Peter Will. Digital Hormone Models for Self-Organization. 2003

• Marc Metivier, Claude Lattaud, Jean-Claude Heudin. A Stress-based Speciation Model in LifeDrop. 2003

• Gary R. Greenfield. On Attaining Maximal Fitness or How to Evolve Virtual Redwoods. 2003

• Russell K. Standish. Diversity Evolution. 2003

• Xin-She Yang. Characterization of Multispecies Living Ecosystems With Cellular Automata. 2003

• Lee Spector. Adaptive Populations of Endogenously Diversifying Pushpop Organisms are Reliably Diverse. 2003

• Joshua Mitteldorf, David H. Croll, S. Chandu Ravela. Multilevel Selection and the Evolution of Predatory Restraint. 2003

• James R. Watson, Nicholas Geard, Janet Wiles. Stability and Task Complexity: A Neural Network Model of Evolution and Learning. 2003

• Dale Thomas. Aesthetic Selection of Developmental Art Forms. 2003

• Hideaki Suzuki, Hidefumi Sawai. Chemical Genetic Algorithms -- Coevolution between Codes and Code Translation. 2003

• Alastair D. Channon. Improving and Still Passing the ALife Test: Component-Normalised Activity Statistics Classify Evolution in Geb as Unbounded. 2003

• Shengxiang Yang. Adaptive Crossover in Genetic Algorithms Using Statistics Mechanism. 2003

• Daniel W. Franks, Jason Noble. The Origins of Mimicry Rings. 2003

• Seth Bullock. Will Selection for Mutational Robustness Significantly Retard Evolutionary Innovation on Neutral Networks?. 2003

• Gina M. B. Oliveira, Jose C. Bortot, Pedro P. B. de Oliveira. Multiobjective Evolutionary Search for One-Dimensional Cellular Automata in the Density Classification Task. 2003

• Hiroshi Ito, Takashi Ikegami. Evolutionary Dynamics of a Food Web with Recursive Branching and Extinction. 2003

• Takashi Ikegami, Tomoharu Iwata, Koh Hashimoto. A Network of Dynamic Keystone Species. 2003

• Tom Lenaerts, Anne Defaweux, Piet van Remortel, Joke Reumers, Bernard Manderick. Multi-level Selection and Immune Networks: Preliminary Discussion of an Abstract Model. 2003

• Tim F. Cooper, Charles Ofria. Evolution of Stable Ecosystems in Populations of Digital Organisms. 2003

• Andre Skusa, Mark A. Bedau. Towards a Comparison of Evolutionary Creativity in Biological and Cultural Evolution. 2003

• Peter Eggenberger Hotz, Gabriel Gomez, Rolf Pfeifer. Evolving the Morphology of a Neural Network for Controlling a Foveating Retina -- and its Test on a Real Robot. 2003

• Janne Haverinen, Juha Roning. A Stochastic Evolutionary Neuron Migration Process with Emerged Hebbian Dynamics. 2003

• Amelie Schmolke, Hanspeter A. Mallot. Territory Formation in Mobile Robots. 2003

• Elaine Catterall, Kristof Van Laerhoven, Martin Strohbach. Self-Organization in Ad Hoc Sensor Networks: An Empirical Study. 2003

• Bertrand Mesot, Eduardo Sanchez, Carlos-Andres Pena, Andres Perez-Uribe. SOS++: Finding Smart Behaviors Using Learning and Evolution. 2003

• Tom Smith, Philip Husbands, Andy Philippides, Michael O'Shea. Temporally Adaptive Networks: Analysis of GasNet Robot Control Networks. 2003

• Matthias Scheutz, Paul Schermerhorn. Steps Towards a Systematic Investigation of Possible Evolutionary Trajectories from Reactive to Deliberative Control Systems. 2003

• Andy Philippides, Philip Husbands, Tom Smith, Michael O'Shea. Fast and Loose: Biologically Inspired Couplings. 2003

• Matt Quinn, Lincoln Smith, Giles Mayley, Philip Husbands. Evolving Teamwork and Role-Allocation with Real Robots. 2003

• Jason Teo, Hussein A. Abbass. Multi-Objectivity for Brain-Behavior Evolution of a Physically-Embodied Organism. 2003

• Hiroyuki Iizuka, Takashi Ikegami. Simulating Turn-Taking Behaviours with Coupled Dynamical Recognizers. 2003

• Jon Klein. breve: a 3D Environment for the Simulation of Decentralized Systems and Artificial Life. 2003

• Dario Floreano, Nicolas Schoeni, Gilles Caprari, Jesper Blynel. Evolutionary Bits'n'Spikes. 2003

• Chrystopher L. Nehaniv, Daniel Polani, Kerstin Dautenhahn, Rene te Boekhorst, Lola Canamero. Meaningful Information, Sensor Evolution, and the Temporal Horizon of Embodied Organisms. 2003

• Jin Akaishi, Takaya Arita. Misperception, Communication and Diversity. 2003

• Steven Mascaro, Kevin B. Korb, Ann E. Nicholson. ALife Investigation of Parental Investment in Reproductive Strategies. 2003

• O. Burchan Bayazit, Jyh-Ming Lien, Nancy M. Amato. Better Group Behaviors in Complex Environments using Global Roadmaps. 2003

• Zachary Mason. Programming with Stigmergy: Using Swarms for Construction. 2003

• Pedro Mariano, Luis Correia. The Effect of Agreements in a Game with Multiple Strategies for Cooperation. 2003

• Jason Noble, Daniel W. Franks. Social Learning Mechanisms Compared in a Simple Environment. 2003

• Tamon Oboshi, Shohei Kato, Atsuko Mutoh, Hidenori Itoh. Collective or Scattering: Evolving Schooling Behaviors to Escape from Predator. 2003

• Mark Dras, K. David Harrison. Emergent Behavior in Phonological Pattern Change. 2003

• Anders Eriksson, Kristian Lindgren. Cooperation in an Unpredictable Environment. 2003

• Dominique Gross, Barry McMullin. The Creation of Novelty in Artificial Chemistries. 2003

• Tatsuo Unemi. SBEAT3: A Tool for Multi-part Music Composition by Simulated Breeding. 2003

• Pavel O. Luksha. Formal Definition of Self-reproductive Systems. 2003

• Stephen Jones. Organizing Relations and Emergence. 2003

• Alan Dorin, Jon McCormack. Self-Assembling Dynamical Hierarchies. 2003

Contents

• James P. Crutchfield. Is anything ever new? Considering emergence. 1994

• James P. Crutchfield, J. Doyne Farmer, Norman H. Packard, Robert S. Shaw. Chaos. Sci. Am., 254(12), 46-58. 1986

• Philip W. Anderson. More is Different. Science, 177, 393-396. 1972

• Andrew M. Assad, Norman H. Packard. Emergent Colonization in an Artificial Ecology. 1992

• Stephen Wolfram. Undecidability and intractability in theoretical physics. Phys.Rev.Lett 54:735-738. 1985

• Daniel C. Dennett. Real patterns. The Journal of Philosophy 87. 1991

As Dennett says in the introduction, the ideas here are utterly central to his thinking. It covers the ontological status of abstract objects, including patterns, particularly those obscured by more or less noise. It moves on to patterns in the Game of Life, and a nice description of his three stances: physical (for describing the underlying cellular automaton with cells changing state), design (for describing gliders, glider guns, etc: moving patterns), and intentional (for describing what a GoL CA emulating a chess playing program is doing at the level of "wanting to play chess"). This leads to a discussion of the reality of the intentional patterns. Dennett's position is somewhere between the (implausible) extremes of Realism and Instrumentalism.

• Brian P. McLaughlin. The Rise and fall of British Emergentism. From Emergence or Reduction?. 1992

• Carl Hempel, Paul Oppenheim. On the idea of Emergence. From Aspects of Scientific Explanation. 1965

• John R. Searle. Reductionism and the Irreducibility of Consciousness. From The Rediscovery of the Mind. 1992

• Brian P. McLaughlin. Emergence and supervenience. Excerpt, Intellectica 25. 1997

• William C. Wimsatt. Aggregativity: reductive heuristics for finding emergence. Philosophy of Science 644. 1997

• Paul Humphreys. How properties emerge. Philosophy of Science 64. 1997

• Jaegwon Kim. Making sense of Emergence. Philosophical Studies 95. 1999

• Mark A. Bedau. Downward causation and autonomy in weak emergence. Principia Revista Internacional de Epistemologica 6. 2003

• Thomas C. Schelling. Micromotives and macrobehaviour. Excerpt. 1978

• Herbert A. Simon. Alternative views of complexity. From The Sciences of the Artificial. 1996

• Robert B. Laughlin, David Pines. The theory of everything. PNAS 97. 2000

• Edmund M. A. Ronald, Moshe Sipper, Mathieu S. Capcarrere. Design, Observation, Surprise! A test of emergence. Artificial Life 5. 1999

• Steen Rasmussen, Nils A. Baas, Bernd Mayer, Martin Nillson. Ansatz for dynamical hierarchies. Artificial Life 7. 2001

• Steven Weinberg. Newtonianism, Reductionism, and the art of Congressional testimony. Nature 330. 1987

• Ernest Nagel. Teleology revisited. Excerpt. 1982

• Jerry A. Fodor. Special sciences, or the disunity of science as a working hypothesis. Synthese 28. 1974

• David Chalmers. Supervenience. Excerpt from The Conscious Mind. 1996

• Jaegwon Kim. The nonreductivist's troubles with mental causation. From Mental Causation. 1993

Contents

• Aristotle. De Anima (selections). 2010

• René Descartes. Treatise on Man. 1985

• Immanuel Kant. Critique of the teleological power of judgment (selections). 2001

• Erwin Schrödinger. What is Life? (selections). 1967

• Alexander I. Oparin. The nature of life. 1964

• Ernst Mayr. What is the meaning of "life"?. 1997

• Tibor Gánti. The principles of life (selections). 2003

• Leslie E. Orgel. The origin of life: a review of facts and speculation. 1998

• Robert Shapiro. Small molecule interactions were central to the origin of life. 2007

• Iris Fry. Are the different hypotheses on the emergence of life as different as they seem?. 1995

• Norman R. Pace. The universal nature of biochemistry. 2001

• Steven A. Benner, Alonso Ricardo, Matthew A. Carrigan. Is there a common chemical model for life in the universe?. 2004

• Kenneth H. Nealson. Searching for life in the universe: lessons from Earth. 2001

• Carol E. Cleland, Shelley D. Copley. The possibility of alternative microbial life on Earth. 2005

• National Research Council of the National Academies. Introduction to the limits of organic life in planetary systems. 2007

• Elliott Sober. Learning from Functionalism--Prospects for Strong Artificial Life. 1992

• Marc Lange. Life, "artificial life," and scientific explanation. 1996

• Margaret A. Boden. Alien life: how would we know?. 2003

• Hod Lipson, Jordan B. Pollack. Automatic design and manufacture of robotic life forms. 2000

• David W. Deamer. A giant step towards artificial life?. 2005

• Pier Luigi Luisi, Francesca Ferri, Pasquale Stano. Approaches to semi-synthetic minimal cells: a review. 2006

• Evelyn Fox Keller. Creating "real life". 2002

• Carl Sagan. Definitions of life. 1970

• Daniel E. Koshland. The seven pillars of life. 2002

• Kepa Ruiz-Mirazo, Juli Peretó, Alvaro Moreno. A universal definition of life: autonomy and open-ended evolution. 2004

• Carol E. Cleland, Christopher Chyba. Does 'life' have a definition?. 2007

• Lynn Margulis, Dorion Sagan. Sentient symphony. 2000

• Kim Sterelny, Paul E. Griffiths. What is life?. 1999

• Richard Dawkins. Universal Darwinism. 1983

• Stuart A. Kauffman. What is Life?. 1997

• Mark A. Bedau. Four puzzles about life. 1998