Table of Contents
Preface xii
Self-Organization
1 The Chemoton: A Model for the Formation of Long RNA Templates
Chrisantha Fernando and Ezequiel A. Di Paolo 1
2 Connecting Transistors and Proteins
Claudio Mattiussi and Dario Floreano 9
3 Designed and Evolved Blueprints for Physical Self-Replicating Machines
Efstathios Mytilinaios, Mark Desnoyer, David Marcus and Hod Lipson 15
4 Emergent Robustness and Self-Repair through Developmental Cellular Systems
Can Oztürkeri and Mathieu S. Capcarrère 21
5 On Self-referential Shape Replication in Robust Aerospace Vehicles
Mikhail Prokopenko and Peter Wang 27
6 An Evolving and Developing Cellular Electronic Circuit
Daniel Roggen, Yann Thoma and Eduardo Sanchez 33
7 An Environment for Simulating Kinematic Self-Replicating Machines
William M. Stevens 39
8 Towards an evolutionary-developmental approach for real-world substrates
Shivakumar Viswanathan and Jordan Pollack 45
9 Stepwise evolution of molecular biological coding
Peter R. Wills 51
Robotic Studies
10 Once More Unto the Breach: Co-evolving a robot and its simulator
Josh C. Bongard and Hod Lipson 57
11 Closing the loop: Evolving a model-free visually guided robot arm
Thomas Buehrmann and Ezequiel A. Di Paolo 63
12 Performance Evaluation of Neural Architectures for Sequential Tasks
Genci Capi and Kenji Doya 69
13 EvolGL: Life in a Pond
Santi Garcia Carbajal, Martin Bosque Moran and Fermin Gonzalez Martinez 75
14 Evolving Plastic Neural Controllers stabilized by Homeostatic Mechanisms for Adaptation to a Perturbation
Thierry Hoinville and Patrick Hénaff 81
15 A Stigmergic Cooperative Multi-Robot Control Architecture
Thomas G. Howsman, Daniel O'Neil and Michael A. Craft 88
16 Crawling Out of the Simulation: Evolving Real Robot Morphologies Using Cheap, Reusable Modules
Ian Macinnes and Ezequiel A. Di Paolo 94
17 Functional Freeform Fabrication for Physical Artificial Life
Evan Malone and Hod Lipson 100
18 Quadrupedal Locomotion: GasNets, CTRNNs and Hybrid CTRNN/PNNs Compared
Gary McHale and Phil Husbands 106
19 Evolving Simulated Mutually Perceptive Creatures for Combat
Michael J. T. O'Kelly and Kaijen Hsiao 113
20 Information Trade-Offs and the Evolution of Sensory Layouts
Lars Olsson, Chrystopher L. Nehaniv and Daniel Polani 119
21 Evolving Flying Creatures with Path Following Behaviors
Yoon Sik Shim, Sun Jeong Kim and Chang Hun Kim 125
22 Behavioural Categorisation: Behaviour makes up for bad vision
Emmet Spier 133
23 The Evolution of Control and Adaptation in a 3D Powered Passive Dynamic Walker
Eric D. Vaughan, Ezequiel A. Di Paolo and Inman Harvey 139
Language, Brain, Culture
24 Evolving Imitating Agents and the Emergence of a Neural Mirror System
Elhanan Borenstein and Eytan Ruppin 146
25 A Comparison of Population Learning and Cultural Learning in Artificial Life Societies
Dara Curran and Colm O'Riordan 152
26 A Computation Framework to Simulate the Coevolution of Language and Social Structure
Tao Gong, Jinyun Ke, James W. Minett and William S-Y Wang 158
27 Boom and Bust: Environmental Variability Favors the Emergence of Communication
Patrick Grim and Trina Kokalis 164
28 Expressing and Understanding Desires in Language Games
Michael Klein, Hans Kamp, Guenther Palm and Kenji Doya 170
29 The Evolution of Affect-Related Displays, Recognition and Related Strategies
Robert Lowe, Lola Cañamero, Chrystopher L. Nehaniv and Daniel Polani 176
30 Language, Altruism, and Docility: How Cultural Learning Can Favour Language Evolution
Marco Mirolli and Domenico Parisi 182
31 Evolution of Plastic Sensory-motor Coupling and Dynamical Categorization
Gentaro Morimoto and Takashi Ikegami 188
33 Analogies between Genome and Language Evolution
Luc Steels 200
34 The Effects of Learning on the Evolution of Saussurean Communication
Edgar E. Vallejo and Charles E. Taylor 208
35 Minimum cost and the emergence of the Zipf-Mandelbrot law
Paul Vogt 214
Formal Games and Automata
36 Modeling Multicellular and Tumorous Existence with Genetic Cellular Automata
Armand Bankhead III, Nancy Magnuson and Robert B. Heckendorn 220
37 Whatever Emerges should be Intrinsically Useful
Hugues Bersini 226
38 Shaping collective behavior: an exploratory design approach
Pablo Funes, Belinda Orme and Eric Bonabeau 232
39 Updating Schemes in Random Boolean Networks: Do They Really Matter?
Carlos Gershenson 238
40 Reducing Prejudice: A Spatialized Game-Theoretic Model for the Contact Hypothesis
Patrick Grim, Evan Selinger, William Braynen, Robert Rosenberger, Randy Au, Nancy Louie and John Connolly 244
41 Quasi-Stable States in the Iterated-Prisoner's Dilemma
Philip T. Mueller 250
42 Evolving Memory: Logical Tasks for Cellular Automata
Luis Mateus Rocha 256
43 Complex Genetic Evolution of Self-Replicating Loops
Chris Salzberg, Antony Antony and Hiroki Sayama 262
44 Redrawing the Boundary between Organism and Environment
Tim Taylor 268
45 Imitation and Inequity in Avoiding the Tragedy of the Commons
Terry Van Belle and David H. Ackley 274
46 The Quantum Coreworld: Competition and Cooperation in an Artificial Ecology
Alexander Wait 280
47 Self-reproduction by glider collisions: the beehive rule
Andrew Wuensche 286
Evolutionary and Adaptive Dynamics
48 The value of death in evolution: A lesson from Daisyworld
Matthew Bardeen 292
49 The Flexible Balance of Evolutionary Novelty and Memory in the Face of Environmental Catastrophes
Andrew J. Buchanan, Mark Triant and Mark A. Bedau 297
50 Kin-Selection: The Rise and Fall of Kin-Cheaters
Sherri Goings, Jeff Clune, Charles Ofria and Robert T. Pennock 303
51 Homeostasis and Rein Control: From Daisyworld to Active Perception
Inman Harvey 309
52 Measuring Biological Complexity in Digital Organisms
Wei Huang, Charles Ofria and Eric Torng 315
53 The Role of Nearly Neutral Mutations in the Evolution of Dynamical Neural Networks
Eduardo Izquierdo-Torres 322
54 Sustained Evolution from Changing Interaction
George Kampis and Laszlo Gulyas 328
55 See How She Runs: Towards Visualising Artificial Red Queen Evolution
James A. R. Marshall and Simon Tokumine 334
56 Sexual reproduction and Muller's ratchet in digital organisms
Dusan Misevic, Richard E. Lenski and Charles Ofria 340
57 Chaotic Population Dynamics and the Evolution of Aging
Joshua Mitteldorf 346
58 The Role of Non-Genetic Change in the Heritability, Variation and Response to Selection of Artificially Selected Ecosystems
Alexandra Penn and Inman Harvey 352
59 Ecolab, Webworld and self-organisation
Russell Standish 358
60 Tierra's missing neutrality: case solved
Russell Standish 364
61 Drastic Changes in Roles of Learning in the Course of Evolution
Reiji Suzuki and Takaya Arita 369
62 Niche Construction and the Evolution of Complexity
Tim Taylor 375
Cellular Development
63 A Model for Exploring Genetic Control of Artificial Amoebae
Barry Drennan and Randall D. Beer 381
64 Asymmetric cell division and its integration with other developmental processes for artificial evolutionary systems
Peter Eggenberger Hotz 387
65 A Functional Model of Cell Genome
Alessandro Fontana and Walter Steven Fraccaro 393
66 Asynchronous Dynamics of an Artificial Genetic Regulatory Network
Jennifer Hallinan and Janet Wiles 399
67 Small World and Scale-Free Network Topologies in an Artificial Regulatory Network Model
P. Dwight Kuo and Wolfgang Banzhaf 404
68 Inertia of Chemotactic Motion as an Emergent Property in a Model of an Eukaryotic Cell
Shin I. Nishimura and Masaki Sasai 410
69 Phenotypic Variability in Canalized Developmental Systems
Sean Psujek and Randall D. Beer 415
70 Self-repairing and Mobility of a Simple Cell Model
Keisuke Suzuki and Takashi Ikegami 421
71 Evaluating an Evolutionary Approach for Reconstructing Gene Regulatory Networks
Dion J. Whitehead, Andre Skusa and Paul J. Kennedy 427
Artificial Chemistries
72 Bonding as an Emergent Phenomenon in an Abstract Artificial Chemistry
Dominique Chu and Rune Vabø 433
73 Evolution of Robust Developmental Neural Networks
Alan Hampton and Christoph Adami 438
74 A Functional Self-Reproducing Cell in a Two-Dimensional Artificial Chemistry
Tim J. Hutton 444
75 Metabolic Closure in (M,R) Systems
Juan-Carlos Letelier, Jorge Soto-Andrade, Flavio Guinez-Abarzua, Athel Cornish-Bowden and Maria-Luz Cardenas 450
76 Flows of information in spatially extended chemical dynamics
Kristian Lindgren, Anders Eriksson and Karl-Erik Eriksson 456
77 Cellular Dynamics in a 3D Molecular Dynamics System with Chemistry
Duraid Madina and Takashi Ikegami 461
78 Lipidia: An Artificial Chemistry of Self-Replicating Assemblies of Lipid-like Molecules
Barak Naveh, Moshe Sipper, Doron Lancet and Barak Shenhav 466
79 Towards the Simulation of Reaction Networks in Astrochemistry
Pierre Philippe, David Weiss Solis, Tom Lenaerts and Hugues Bersini 472
80 Homochirality as Fixed Point of Prebiotic Chemistry
Raphael Plasson, Hugues Bersini and Auguste Commeyras 478
81 An Evolvable Artificial Chemistry Featuring Continuous Physics and Discrete Reactions
Thomas E. Portegys 484
82 The Role of RNA Editing in Dynamic Environments
Luis Mateus Rocha and Chien-feng Huang 489
83 A Tangled Hierarchy of Graph-Constructing Graphs
Chris Salzberg, Hiroki Sayama and Takashi Ikegami 495
84 Graded Artificial Chemistry in Restricted Boundaries
Barak Shenhav, Ran Kafri and Doron Lancet 501
85 Spacial Representation for Artificial Chemistry Based on Small-World Networks
Hideaki Suzuki 507
Art and Philosophy
86 Behavioral Adaptive Autonomy. A milestone in the Alife route to AI?
Xabier Barandiaran 514
87 A Physiological Approach to the Generation of Artificial Life Forms
Marc Cavazza, Simon Hartley, Louis Bec, François Mourre, Gonzague Defos du Rau, Remy Lalanne, Mikael Le Bras and Jean-Luc Lugrin 522
88 Mechanistic and ecological explanations in agent-based models of cognition
Jason Noble and Manuel de Pinedo 528
89 Empiricism in Artificial Life
Eric Silverman and Seth Bullock 534
90 Using the Universal Similarity Metric to Model Artificial Creativity and Predict Human Listeners Response to Evolutionary Music
Nils Svangard, Jon Klein and Peter Nordin 540
91 Playing Music by Conducting BOID Agents
Tatsuo Unemi and Daniel Bisig 546
Agents Ants and Swarms
92 An Evolutionary Approach to Complex System Regulation Using Grammatical Evolution
Saoirse Amarteifio and Michael O'Neill 551
93 Analyzing Evolved Fault-Tolerant Neurocontrollers
Alon Keinan 557
94 Tracking Information Flow through the Environment: Simple Cases of Stigmergy
Alexander S. Klyubin, Daniel Polani and Chrystopher L. Nehaniv 563
95 Ant Foraging Revisited
Liviu A. Panait and Sean Luke 569
96 Learning Ant Foraging Behaviors
Liviu A. Panait and Sean Luke 575
97 Systems Biology Thought Experiments in Human Genetics Using Artificial Life and Grammatical Evolution
Bill C. White and Jason H. Moore 581
Author Index 587
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