Artificial Life X: Proceedings of the Tenth International Conference on the Simulation and Synthesis of Living Systems (Paperback)

Description

Artificial Life is an interdisciplinary effort to investigate the fundamental properties of living systems through the simulation and synthesis of life-like processes in artificial media. The field brings a powerful set of tools to the study of how high-level behavior can arise in systems governed by simple rules of interaction.

This tenth volume marks two decades of research in this interdisciplinary scientific community, a period marked by vast advances in the life sciences. The field has contributed fundamentally to our understanding of life itself through computer models, and has led to novel solutions to complex real-world problems--from disease prevention to stock market prediction--across high technology and human society. The proceedings of the biennial A-life conference--which has grown over the years from a small workshop in Santa Fe to a major international meeting--reflect the increasing importance of the work to all areas of contemporary science.

Luis M. Rocha is Associate Professor of Informatics, Computer Science, and Cognitive Science at Indiana University and Director of the Computational Biology Collaboratorium at the Gulbenkian Institute in Portugal.

Larry S. Yaeger is Professor in the School of Informatics at Indiana University.

Mark A. Bedau is Professor of Philosophy and Humanities at Reed College and Adjunct Professor of Systems Science at Portland State University.

Dario Floreano is Professor and Director of the Laboratory of Intelligent Systems and Institute for Systems Engineering at École Polytechnic Fédérale de Lausanne.

Robert L. Goldstone is Professor in the Department of Psychology at Indiana University.

Alessandro Vespignani is Professor of Informatics and Cognitive Science at Indiana University.

 

Table of Contents

Preface xi
 
 Bio-networks 
 
1. Dynamics of Scale-Free Semi-Synchronous Boolean Networks
M. Giacobini, Marco Tomassini, P. De Los Rios and E. Pestelacci 1
 
2. How Scale-free Type-based Networks Emerge from Instance-based Dynamics
Tom Lenaerts, Hugues Bersini and Francisco Santos 8
 
3. Evolving Biological Clocks using Genetic Regulatory Networks
Johannes F. Knabe, Chrystopher L. Nehaniv, Maria J. Schilstra and Tom Quick 15
 
4. Evolution of Repressilators Using a Biologically-motivated Model of Gene Expression
Barry Drennan and Randall D. Beer 22
 
5. A Nonlinear Continuous Stochastic Model for Genetic Regulatory Networks: Caveats for Microrray Data Analysis
Simon Rosenfeld 28
 
6. The Role of Redundancy in the Robustness of Random Boolean Networks
Carlos Gershenson, Stuart A. Kauffman and Ilya Shmuelevich 35
 
 Development 
 
7. An Endosymbiotic Model for Modular Acquisition in Stochastic Developmental Systems
John Rieffel and Jordan Pollack 42
 
8. Modeling of Pattern Formation in Cell Cultures
Scott Christley, Stuart A. Newman and Mark S. Alber 49
 
9. Investigating Ontogenetic Space with Developmental Cell Lineages
Nicholas Geard and Janet Wiles 56
 
10. Heterochrony and Evolvability in Neural Network Development
Artur Matos, Reiji Suzuki and Takaya Arita 63
 
11. Towards Shape and Structure Optimization with Evolutionary Development
Till Steiner, Markus Olhofer and Bernhard Sendhoff 70
 
12. Wriggraph: A Kinetic Graph Model That Uniformly Describes Ontogeny and Motility of Artificial Creatures
Koji Sano and Hiroki Sayama 77
 
13. A Morphogenesis Model for Multiagent Embryogeny
Gregory Beurier, Fabien Michel and Jacques Ferber 84
 
 Evolution 
 
14. Connecting Genotype with Phenotype using the Genome Template Model: Pleiotropy, Polygenic Traits, and Life-History Strategies
R. E. DeSimone, A. Boondirek and T. J. Newman 91
 
15. Modeling Recombination's Role in the Evolution of HIV Drug Resistance
Richard K. Belew and Max W. Chang 98
 
16. An Evolutionary Model of Genotype Editing
Luis Mateus Rocha, Ana Maguitman, Chien-feng Huang, Jasleen Kaur and Sheetal Narayanan 105
 
17. A Structure of the Foothills of the Fitness Landscape in Protein Sequence Space
Yuuki Hayashi, Takuya Aita, Hitoshi Toyota, Yuzuru Husimi, Itaru Urabe and Tetsuya Yomo 112
 
18. The Role of Space in the Success of Coevolutionary Learning
Melanie Mitchell, Michael D. Thomure and Nathan L. Williams 118
 
19. Phat Phenotypes for Agents in Niche Construction
George Kampis and Laszlo Gulyas 125
 
20. Three Characteristics of Developmental, Self-repairable Cellular Systems to Improve Their Evolvability
Mathieu S. Capcarrere and Can Oztürkeri 132
 
21. Experimental Studies on Interaction among Correlated Traits
Haitao Zhang and Michael Travisano 139
 
 Prebiotic Evolution and Artificial Chemistries 
 
22. Quasi-Species and Aggregate Dynamics
Anders Eriksson, Olof Görnerup, Martin N. Jacobi and Steen Rasmussen 145
 
23. Simulation Model of Prebiotic Evolution of Genetic Coding
Sidney Markowitz, Alexei Drummond, Kay Nieselt and Peter R. Wills 152
 
24. The Role of Programmed Death in the Persistence of Life
Gordon C. Osbourn, Christina E. Warrender and Ann M. Bouchard 158
 
25. Complexity Scaling of a Minimal Functional Chemistry
Chris Salzberg 165
 
26. An Approach to Constructing Qualitative Models in Computational Cell Biology Using an Artificial Chemistry Based on Pattern Matching and Recombination
Kazuto Tominaga, Keiji Kobayashi, Tooru Watanabe, Kazumasa Koizumi and Koji Kishi 172
 
 Embodiment and Behavior 
 
27. Self-Organization of Communication in Evolving Robots
Davide Marocco and Stefano Nolfi 178
 
28. Measuring Spatiotemporal Coordination in a Modular Robotic System
Mikhail Prokopenko, Vadim Gerasimov and Ivan Tanev 185
 
29. Let it Roll -- Emerging Sensorimotor Coordination in a Spherical Robot
Ralf Der, Georg Martius and Frank Hesse 192
 
30. Synchronization within Homogeneous Neural Modules Controlling a Simulated Hexapod Robot
Mariagiovanna Mazzapioda and Stefano Nolfi 199
 
31. Incorporating Energy Expenditure into Evolutionary Robotics Fitness Measure
Gary McHale and Phil Husbands 206
 
32. TOPOS: Generalized Braitenberg Vehicles that Recognize Complex Real Sounds as Landmarks
Pablo González-Nalda and Blanca Cases 213
 
33. Automated Synthesis of Body Schema using Multiple Sensor Modalities
Josh C. Bongard, Victor Zykov and Hod Lipson 220
 
34. Spontaneous Emergence of Self-Replicating Structures in Molecube Automata
Gregory Studer and Hod Lipson 227
 
35. Developing a Reaching Behaviour in a Simulated Anthropomorphic Robotic Arm Through an Evolutionary Technique
Gianluca Massera, Angelo Cangelosi and Stefano Nolfi 234
 
36. Towards Evolvable Hovering Flight on a Physical Ornithopter
Will Regan, Floris van Breugel and Hod Lipson 241
 
37. Evolving an Integrated Phototaxis and Hole-avoidance Behavior for a Swarm-bot
Anders Lyhne Christensen and Marco Dorigo 248
 
38. An Improved System for Artificial Creatures Evolution
Thomas Miconi and Alastair Channon 255
 
39. Evolution of Virtual Catapults
Nicolas Chaumont, Richard Egli and Christoph Adami 262
 
40. The Evolution of Structural Organization in Digital Organisms
Matthew Rupp, Eric Torng and Charles Ofrica 268
 
 Biologically-inspired Computing and Technology 
 
41. Role of Inhibitions in Neural Networks for the Orientation Behaviour of Sand Scorpions
DaeEun Kim 275
 
42. Passive Sensing and Active Sensing of a Biomimetic Whisker
DaeEun Kim and Ralf Möller 282
 
43. A Cytoskeletal-Based Robotic Controller
Jeffrey O. Pfaffmann, Monica Brockmeyer and Silvano Colombano 289
 
44. Alternate Recruitment Strategies for SDS
Darren R. Myatt, Mark Bishop and Slawomir J. Nasuto 296
 
45. DNA as a Medium for Storing Digital Signals
Sotirios A. Tsaftaris, Vassily Hatzimanikatis and Aggelos K. Katsaggelos 303
 
46. Noise-Mediated Intermittent Sychronization of Collective Behaviors in the Probabilistic Cellular Automata Model of Neural Populations 310
 
 Information and Complexity 
 
47. Measuring Informational Distances Between Sensors and Sensor Integration
Lars Olsson, Chrystopher L. Nehaniv and Daniel Polani 316
 
48. Evolving Coordinated Behavior by Maximizing Information Structure
Olaf Sporns and Max Lungarella 323
 
49. Evolution of Neural Structure and Complexity in a Computational Ecology
Larry S. Yaeger and Olaf Sporns 330
 
50. Relevant Information in Optimized Persistence vs. Progeny Strategies
Daniel Polani, Chrystopher L. Nehaniv, Thomas Martinetz and Jan T. Kim 337
 
51. A Simple Modularity Measure for Search Spaces Based on Information Theory
Peter Dauscher, Daniel Polani and Richard A. Watson 344
 
52. Sensorimotor Information Flow in Genetic Regulatory Network Driven Control Systems
Tom Quick, Chrystopher L. Nehaniv, Kerstin Dautenhahn and Graham Roberts 351
 
 Collective Behavior and Population Dynamics 
 
53. Influence of the Level of Polyandry and Genetic Architecture on Division of Labour
Danesh Tarapore, Dario Floreano and Laurent Keller 358
 
54. On Prey Grouping and Predator Confusion in Artificial Fish Schools
Hanspeter Kunz, Thomas Züblin and Charlotte K. Hemelrijk 365
 
55. Ideal Free Distribution in Agents with Evolved Neural Architectures
Virgil Griffith and Larry S. Yaeger 372
 
56. EPICURE: An Agent-Based Foraging Model
Michael E. Roberts and Robert L. Goldstone 379
 
57. A Particle Swarm Selects for Evolution of Gliders in Non-Uniform 2D Cellular Automata
J.J. Ventrella 386
 
58. On Self-Regulated Swarms, Societal Memory, Speed and Dynamics
Vitorino Ramos, Carlos Fernandes and Agostinho C. Rosa 393
 
59. Representing Classical Structures in Cellular Automata
Peter R. Wills 400
 
60. Asymmetry between Even and Odd Levels of Recursion in a Theory of Mind
Masanori Takano and Takaya Arita 405
 
61. SWAGES--An Extendable Distributed Experimentation System for Large-Scale Agent-Based Alife Simulations
M. Scheutz, P. Schermerhorn, R. Connaughton and A. Dingler 412
 
62. Real-time Evolving Swarms for Rapid Pattern Detection and Tracking
Christopher Middendorff and Matthias Scheutz 419
 
63. Pushing Up The Daisies
J. G. Dyke and I. R. Harvey 426
 
 Evolutionary and Collective Games 
 
64. Emergence of Cooperation in Heterogeneous Structured Populations
F. C. Santos, J. M. Pacheco and Tom Lenaerts 432
 
65. A Minimal Information Prisoner's Dilemma on Evolving Networks
L. Luthi, M. Giacobini and Marco Tomassini 438
 
66. Game-Theoretic Robustness in Cooperation and Prejudice Reduction: A Graphic Measure
Patrick Grim, Randy Au, Nancy Louie, Robert Rosenberger, William Braynen, Evan Selinger and Robb E. Eason 445
 
67. How Spatial Locality Can Affect the Evolution of Niche Construction
Reiji Suzuki and Takaya Arita 452
 
68. Cross-level Interactions Between Conflict Resolution and Survival Games
Matthias Scheutz 459
 
 Language and Learning 
 
69. A Cross-situational Learning Algorithm for Damping Homonymy in the Guessing Game
Joachim De Beule, Bart De Vylder and Tony Belpaeme 466
 
70. Collectivism and the Emergence of Linguistic Universals
Georg Theiner 473
 
71. Strategies for Fast Convergence in Semiotic Dynamics
Andrea Baronchelli, Luca Dall'Asta, Alain Barrat and Vittorio Loreto 480
 
72. Generalization in Languages Evolved for Mobile Robots
Ruth Schulz, Paul Stockwell, Mark Wakabayashi and Janet Wiles 486
 
73. On Crossing Fitness Valleys with the Baldwin Effect
Robert Mills and Richard A. Watson 493
 
74. On the Influence of Lifetime Learning on Selection Pressure
Ingo Paenke, Tadeusz Kawecki and Bernhard Sendhoff 500
 
75. Learning on a Continuum in Evolved Dynamical Node Networks
Eduardo Izquierdo-Torres and Inman Harvey 507
 
 Philosophy and Formal Models 
 
76. ALife Models as Epistemic Artefacts
Xabier Barandiaran and Alvaro Moreno 513
 
77. Computational Modelling, Explicit Mathematical Treatments, and Scientific Explanation
John Bryden and Jason Noble 520
 
78. Representations: The Hard Problem for Artificial Life
Harry Halpin and Simon McGregor 527
 
79. Is Adaptiveness a Coherent Idea?
Simon McGregor 534
 
80. The Fallacy of General Purpose Bio-inspired Computing
Seth Bullock 540
 
81. Formalising Agency-Inducing Patterns in World Dynamics
Tibor Bosse and Jan Treur 546
 
82. Inductive Formalization of Self Reproduction in Dynamical Hierarchies
Janardan Mishra 553
 
 Author Index 559

描述

《人工生命》是一項跨學科的努力，通過在人工媒介中模擬和合成類似生命過程來研究生命系統的基本特性。該領域為研究高層行為如何在由簡單互動規則控制的系統中產生帶來了強大的工具。

這第十卷標誌著這個跨學科科學社區二十年的研究，這一時期在生命科學方面取得了巨大的進展。通過計算機模型，這個領域對我們對生命本身的理解做出了基本貢獻，並在高科技和人類社會的各個領域中提供了從疾病預防到股市預測的新解決方案。兩年一次的人工生命會議的論文集反映了這項工作對當代科學各個領域的日益重要性。

Luis M. Rocha是印第安納大學的信息學、計算機科學和認知科學副教授，也是葡萄牙古爾本基金會計算生物學合作實驗室的主任。

Larry S. Yaeger是印第安納大學信息學院的教授。

Mark A. Bedau是里德學院的哲學和人文學教授，也是波特蘭州立大學系統科學的兼職教授。

Dario Floreano是洛桑聯邦理工學院智能系統實驗室和系統工程研究所的教授和主任。

Robert L. Goldstone是印第安納大學心理學系的教授。

Alessandro Vespignani是印第安納大學的信息學和認知科學教授。

目錄

前言 xi
生物網絡
1. 無尺度半同步布爾網絡的動力學
M. Giacobini, Marco Tomassini, P. De Los Rios和E. Pestelacci 1
2. 如何從基於實例的動力學中產生無尺度類型的網絡
Tom Lenaerts, Hugues Bersini和Francisco Santos 8
3. 使用基因調控網絡進化生物鐘
Johannes F. Knabe, Chrystopher L. Nehaniv, Maria J. Schilstra和Tom Quick 15
4. 使用生物學模型的基因表達進化的抑制器
Barry Drennan和Randall D. Beer 22
5. 一個非線性連續隨機基因調控模型
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