Artificial Life Models in Software

446 Pages·2009·14.37 MB·English

by  Charles Ofria

Artificial Life Models in Software
Second Edition
Maciej Komosinski • Andrew Adamatzky
Editors
Artificial Life Models
in Software
Second Edition
123
Editors
Maciej Komosinski Andrew Adamatzky
Poznan University of Technology University of the West of England
Poznan Bristol
Poland UK
ISBN 978 -1-84882- 284-9 e-ISBN 978-1-84882-285-6
DOI 10.1007/978-1-84882-285-6
Springer Dordrecht Heidelberg London New York

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Preface
Artificial Life is an interdisciplinary field of science comprised of experts
fromcomputerscience,biology,physics,chemistry,andmathematics,aswell
as philosophers and artists. Artificial Life focuses on studying the phenom-
ena of life at all levels of complexity and organization – molecular, cellular,
organismic,andpopulation.Thesestudiesnotonlyemployconventionalcom-
puters (using both software and hardware) but also take place in wetware,
using techniques from the biochemical laboratory. Artificial Life research is
notlimitedtolife-formsthatcurrentlyexistontheEarth.Rather,itattempts
tostudythe generalprinciplesoflifethatarecommontoallinstancesoflife,
those both already recognized and yet unknown.
Contemporarymodelsoflifethatareimplementedinthehardwaremedium
are covered in the sister book Artificial Life Models in Hardware, which is
also published by Springer and edited by Andrew Adamatzky and Maciej
Komosinski. The book you are reading now is dedicated to software, the
most popular and widely employed medium in the artificial life research.
Software environments offer nearly unlimited opportunities for experiments
that are relatively inexpensive, and easily arranged and modified. Such ex-
periments can be performed with very precise descriptions of experimental
conditions and a high degree of reproducibility. Advances in computational
performance and efficiency allow for the collection of large amounts of data
at a density and resolution that are unavailable in the wetware biological
research environment.
This monograph1 provides an introduction and guide to modern software
toolsformodelingandsimulatinglife-likephenomena.Researchers,academi-
cians,andstudentsusethissoftwaretoverifymodelsandconceptsrelatedto
evolutionarydynamics, self-organization,the origins oflife, the development
ofmulticellularorganisms,naturalandartificialmorphogenesis,autonomous
1 Thepresentbookisanadvancement ofearlierpublications:
A.AdamatzkyandM.Komosinski,editors.ArtificialLifeModelsinSoftware,firstedition.
Springer,2005.
A.Adamatzky, editor.Kybernetes,32(1/2,specialissueonartificiallifesoftware),2003.
v
vi Preface
andevolutionaryrobotics,evolvablehardware,emergentcollectivebehaviors,
swarmintelligence, the evolution of communication, and the evolution of so-
cialbehaviors.Theartificiallifesoftwarepackagesdescribedhereareessential
componentsinundergraduateandpostgraduatecoursesinartificiallife,com-
plex adaptive systems, multi-agent systems, evolutionary biology, collective
robotics, and nature-inspired computing.
Software systems covered in this book are actively developed and sup-
ported by world experts in artificial life and software design. In most cases,
theseprogramsarecreatedwithbothprofessionalandamateurusersinmind,
andthesimulatorsareemployedinpublishedresearch.Eachchapterdescribes
a single, usually free-to-use software platform, but references to other simi-
lar software packages and related scientific works are included as well. The
origins of software packages, milestones in their development, and the most
important or interesting experiments are also reported.
Every chapter is self-contained and can be read independently. While the
compendiumofchaptersisdividedintofoursections,thepropertiesofthein-
dividualsoftwaremodelsoverlapsotherearenodistinctboundariesbetween
partsofthebook.Furthermore,whileeachpackagehasitsownspecificprop-
erties, the models presented in each chapter are quite general and can be
extended relatively easily to develop and utilize additional features depend-
ing upon their desired use.
The first part of the book – Virtual Environments – presents originalset-
tingsforagent-basedsimulation.ThechaptersintroduceAvida:adigitallab-
oratory for studying populations of evolving programs;Repast: an advanced
agent-basedsimulation toolkitfor studying developmentof naturaland arti-
ficialsocialstructures;Sodarace: anonline-basedinterface,learningsupport,
and environment for construction and competition between two-dimensional
mobilestructures;breve:apackagethatfacilitatesbuildingthree-dimensional
simulations of multi-agentsystems; and Framsticks: a platform for modeling
3D creatures that allows for simulation, evolution, and advanced analysis of
artificial life-forms and prototypes of bio-inspired robots.
Two-andthree-dimensionalgridmodelsaredealtwithinthesecondpart–
LatticeWorlds.Thefollowingsoftwareplatformsarediscussedinthissection
– StarLogo: an educational programming language for simulation of life-like
phenomena,frompopulationdynamicstoemergentbehaviorofcomplexsys-
tems;NetLogo:ageneralpurposeagent-basedenvironmentformodelingcom-
plex systems, describedhere from a specific biomedicalperspective; Discrete
Dynamics Lab: an interactive tool for designing and investigating dynam-
ics ofdiscrete dynamicalnetworks,including simulationof cellularautomata
anddecisionnetworks,generatingattractionbasins,andautomaticdiscovery
of mobile patterns; and EINSTein: a multi-agent simulator of land combat,
modeling individual traits of combatants.
The third part, Artificial Chemistries, comprises models capable of repre-
senting diverse systems of interacting and reacting molecules while abstract-
ingnaturalmolecularprocesses.Thispowerfulapproachisusedtostudyphe-
Preface vii
nomena in a variety of fields, including social and ecological modeling, and
evolutionary and chemical computing. Two chapters on artificial chemistries
discuss modeling of complex molecules in a mixed reactor and the behavior
ofsimple molecules inspatially extendednon-stirredreactors.Bothchapters
provide a review of available software tools.
The fourth and concluding section – Artificial Life Arts – includes three
chaptersfocusingonaesthetic issuesofartificiallife.The firstchapterinthis
section shows how to breed images and sounds using SBEAT (for graphics)
and SBART (for music) software packages; the computer programs allow
the selectionandbreeding ofgenotypesthatrepresentgraphicalandmusical
pieces. The next chapter brings out Eden: an interactive artwork including
hardwareimplementationofcellularautomataandagents,allowingobservers
tointeractwiththeinstallationandtoinfluencethedevelopmentoftheartifi-
cialecosystem.The lastchapterofthe book searchesfora phenomenological
understanding of what makes artificial life appealing to scientists, artists,
and laymen and presents an explanation of why people become attracted to
certain forms of creative computer art.
The Appendix contains a table that summarizes software packages de-
scribed in this book. For each environment, the table includes a short de-
scription, information about availability on various platforms and operating
systems, software requirements, license type, and the Internet web site ad-
dress.
The book covers hot topics related to computer science, evolutionary and
computational biology, simulation, robotics, cognitive science, cybernetics,
artificialintelligence,optimization,multi-agentsocieties,virtualworlds,com-
putergraphicsandanimation,neuroscience,andphilosophy.Webelieve that
academics, researchers, graduate students, and amateurs interested in these
fieldswillfindthismonographavaluableguidetoArtificialLifeandexcellent
supplementary reading.
Maciej Komosinski
May 2009 Andrew Adamatzky
Contents
Part I Virtual Environments
1 Avida: A Software Platform for Research in
Computational Evolutionary Biology ..................... 3
Charles Ofria, David M. Bryson and Claus O. Wilke
1.1 Introduction to Avida.................................. 3
1.1.1 History of Digital Life .......................... 4
1.2 The Scientific Motivation for Avida...................... 7
1.3 The Avida Software ................................... 8
1.3.1 Avida Organisms .............................. 8
1.3.2 The Avida World .............................. 17
1.3.3 Test Environments ............................. 22
1.3.4 Performing Avida Experiments .................. 23
1.3.5 Analyze Mode ................................. 24
1.4 A Summary of Avida Research.......................... 27
1.4.1 The Evolution of Complex Features .............. 27
1.4.2 Survival of the Flattest ......................... 28
1.4.3 Evolution of Digital Ecosystems ................. 30
1.5 Outlook.............................................. 31
References ................................................. 32
2 Foundations of and Recent Advances in Artificial Life
Modeling with Repast 3 and Repast Simphony ........... 37
Michael J. North and Charles M. Macal
2.1 Introduction.......................................... 37
2.1.1 Artificial Life.................................. 37
2.1.2 Agent-Based Modeling for Artificial Life .......... 38
2.1.3 Chapter Organization .......................... 40
2.2 REPAST............................................. 40
2.2.1 Repast 3...................................... 41
2.2.2 Repast Simphony .............................. 50
ix
x Contents
2.2.3 Using Repast 3 and Repast Simphony ............ 52
2.3 Repast Artificial Life Models ........................... 53
2.4 Conclusions .......................................... 57
References ................................................. 58
3 Sodarace: Continuing Adventures in Artificial Life........ 61
Peter W. McOwan and Edward J. Burton
3.1 The Sodarace Project.................................. 61
3.2 Introduction.......................................... 62
3.2.1 Sodarace: The Story Begins ..................... 62
3.2.2 Previous Work................................. 63
3.3 Sodarace, the Scientific Background ..................... 64
3.3.1 Sodaconstructor:The Physics Engine of Sodarace .. 64
3.3.2 Sodarace: The Racing Environmental Variables .... 65
3.3.3 Taking Sodarace Out and About................. 66
3.4 Software for Artificial Life in Sodarace ................... 67
3.5 LessonsLearnedonApproachesfor Artificial Life in Sodarace 67
3.5.1 Easy-to-Use Point-and-Click Racing .............. 68
3.5.2 Amoebamatic: An Easy Start for the New Engineer 69
3.5.3 AI and the Travelling Kiosk Software............. 69
3.6 Interactions in Sodarace: The Evolution of the Forums ..... 71
3.6.1 Community Development of Peer-to-PeerLearning
Web Sites..................................... 72
3.6.2 The Pandora’s Box: An Example of the
Spontaneous Development of Scientific Method .... 72
3.6.3 Interdisciplinary Interaction: Art and Music Meet
Science and Engineering in Sodarace ............. 73
3.6.4 Sodarace in Schools ............................ 74
3.7 Experiments with Sodarace............................. 74
3.8 Summary: The Future of Sodarace ...................... 76
References ................................................. 77
4 3D Multi-Agent Simulations in the breve Simulation
Environment ............................................. 79
Jon Klein and Lee Spector
4.1 Overview............................................. 79
4.1.1 Agent-Based Modeling Paradigms................ 80
4.1.2 ComparisontoOtherAgent-BasedModelingSystems 82
4.2 Motivations .......................................... 84
4.2.1 A PersonalMotivation.......................... 84
4.2.2 Design Principles and Goals..................... 84
4.3 Writing Simulations in breve............................ 86
4.3.1 Object Orientation and the Built-in breve Classes.. 86
4.3.2 The Controller Object .......................... 86
4.3.3 The breve Simulation Loop...................... 87
4.3.4 Defining Callbacks and Agent Behaviors .......... 89
Contents xi
4.3.5 The steve Programming Language ............... 90
4.3.6 The Python Programming Language ............. 91
4.4 Breve Features and Technical Details .................... 91
4.4.1 3D Spatial Simulation .......................... 91
4.4.2 Physical Simulations ........................... 92
4.4.3 Visualization .................................. 93
4.4.4 The Push ProgrammingLanguage ............... 94
4.5 Development History and Future Development ............ 95
4.5.1 Transition to Open Source ...................... 95
4.5.2 Push3 ........................................ 95
4.5.3 Python Integration............................. 96
4.5.4 Future Development............................ 96
4.6 ALife/AI Research with breve .......................... 96
4.6.1 Evolving Swarms .............................. 97
4.6.2 Evolution of Cooperation ....................... 98
4.6.3 Division Blocks ................................ 98
4.6.4 Genetic Programming Research.................. 98
4.7 Educational Applications of breve ....................... 100
4.7.1 Artificial Life and Braitenberg Vehicles ........... 100
4.7.2 Reactive Bouncy Balls for Kids .................. 100
4.7.3 Biology and SuperDuperWalker.................. 101
4.7.4 Artificial Intelligence in 3D Virtual Worlds ........ 102
4.7.5 Algorithmic Art ............................... 103
4.8 Conclusion ........................................... 104
References ................................................. 104
5 Framsticks: Creating and Understanding Complexity of
Life....................................................... 107
Maciej Komosinski and Szymon Ulatowski
5.1 Available Software and Tools ........................... 108
5.2 Simulation ........................................... 111
5.2.1 Creature Model................................ 111
5.2.2 The Three Modes of Body Simulation ............ 111
5.2.3 Brain......................................... 114
5.2.4 Receptors and Effectors......................... 116
5.2.5 Communication................................ 116
5.2.6 Environment .................................. 119
5.3 Genetics and Evolution ................................ 120
5.4 Scripting ............................................. 123
5.4.1 Creating Custom Script-Based Neurons........... 124
5.4.2 Experiment Definitions ......................... 125
5.4.3 Illustrative Example (“Standard Experiment”
Definition) .................................... 126
5.4.4 Popular Experiment Definitions.................. 127
5.5 Advanced Features for Research and Education ........... 129