Table Of ContentARTIFICIAL CHEMISTRIES
ARTIFICIAL CHEMISTRIES
WolfgangBanzhafandLidiaYamamoto
TheMITPress
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London,England
©2015MassachusettsInstituteofTechnology
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ThisbookwassetinNewTimesRomanusingtheLaTeX—Memoirclass. PrintedandboundintheUnitedStatesof
America.
LibraryofCongressCataloging-in-PublicationData
Banzhaf,Wolfgang,1955—
Artificialchemistries/WolfgangBanzhafandLidiaYamamoto.
Includesbibliographicalreferencesandindex.
ISBN978-0-262-02943-8(hardcover:alk. paper)1. Biochemistry. 2. Molecularevolution. 3. Chemistry,Physicaland
theoretical.4.Evolution(Biology)5.Life—Origin.I.Yamamoto,Lidia.II.Title.
QD415.B242015
572—dc23
2014046071
10 9 8 7 6 5 4 3 2 1
artificial,a.,contrivedbyartratherthannature:”artificialflowers”;
http://www.thefreedictionary.com/artificial,accessed2014
Madeorproducedbyhumanbeingsratherthanoccurringnaturally,typicallyasa
copyofsomethingnatural.
https://www.google.ca,accessed2014
chemistry,n.,abranchofphysicalsciencethatstudiesthecomposition,structure,
propertiesandchangeofmatter,[fromGreek:χημ(cid:4)ια],
http://en.wikipedia.org/wiki/Chemistry,accessed2014
Theinvestigationofsubstances,theirpropertiesandreactions,andtheuseofsuch
reactionstoformnewsubstances.
http://www.oxforddictionaries.com/definition/english/chemistry,accessed2014
CONTENTS
Preface xi
I Foundations 1
1 Introduction 3
2 BasicConceptsofArtificialChemistries 11
2.1 ModelingandSimulation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
2.2 ChemistryConcepts. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
2.3 GeneralStructureofanArtificialChemistry . . . . . . . . . . . . . . . . . . . . . 25
2.4 AFewImportantDistinctions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
2.5 TwoExamples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
2.6 FrequentlyUsedTechniquesinACs . . . . . . . . . . . . . . . . . . . . . . . . . 38
2.7 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
3 TheMatrixChemistryasanExample 45
3.1 TheBasicMatrixChemistry . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
3.2 TheSimplestSystem,N=4 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
3.3 TheSystemN=9 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
3.4 SystemswithLargerN . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59
3.5 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
4 ComputingChemicalReactions 63
4.1 FromMacroscopictoMicroscopicChemicalDynamics. . . . . . . . . . . . . . 63
4.2 StochasticReactionAlgorithms . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65
4.3 SpatialandMulticompartmentalAlgorithms . . . . . . . . . . . . . . . . . . . . 71
4.4 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73
II LifeandEvolution 75
5 TheChemistryofLife 77
5.1 WhatIsLife? . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79
5.2 TheBuildingBlocksofLife . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80
5.3 TheOrganizationofModernCells . . . . . . . . . . . . . . . . . . . . . . . . . . 93
5.4 MulticellularOrganisms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 100
5.5 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 109
viii CONTENTS
6 TheEssenceofLife 111
6.1 AMinimalCell . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 111
6.2 OriginofLife . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 119
6.3 ArtificialChemistryContributionstoOriginofLifeResearch. . . . . . . . . . . 130
6.4 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 136
7 Evolution 139
7.1 Evolution:TamingCombinatoricstoImproveLife . . . . . . . . . . . . . . . . . 140
7.2 EvolutionaryDynamicsfromanACPerspective . . . . . . . . . . . . . . . . . . 141
7.3 ArtificialChemistriesforEvolution . . . . . . . . . . . . . . . . . . . . . . . . . . 154
7.4 SummaryandOpenIssues . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 157
8 ComplexityandOpen-EndedEvolution 159
8.1 Evolution:SteeringSelf-OrganizationandPromotingInnovation . . . . . . . . 159
8.2 CoevolutionaryDynamicsinEcologies . . . . . . . . . . . . . . . . . . . . . . . 161
8.3 RobustnessandEvolvability . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 165
8.4 ComplexityGrowth . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 169
8.5 TowardOpen-EndedArtificialEvolution . . . . . . . . . . . . . . . . . . . . . . . 175
8.6 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 177
III ApproachestoArtificialChemistries 179
9 RewritingSystems 181
9.1 LambdaCalculus . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 182
9.2 Gamma . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 184
9.3 TheChemicalAbstractMachine . . . . . . . . . . . . . . . . . . . . . . . . . . . 186
9.4 ChemicalRewritingSystemonMultisets . . . . . . . . . . . . . . . . . . . . . . 187
9.5 Psystems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 188
9.6 MGS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 191
9.7 OtherFormalCalculiInspiredbyaChemicalMetaphor . . . . . . . . . . . . . . 193
9.8 L-SystemsandOtherRewritingSystems . . . . . . . . . . . . . . . . . . . . . . . 193
9.9 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 194
10 AutomataandMachines 195
10.1 FiniteStateAutomata . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 196
10.2 TuringMachines . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 197
10.3 VonNeumannMachines . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 198
10.4 CellularAutomata . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 200
10.5 ExamplesofArtificialChemistriesBasedonTuringMachines . . . . . . . . . . 202
10.6 ArtificialChemistriesBasedonvonNeumannMachines . . . . . . . . . . . . . 207
10.7 ArtificialChemistriesBasedonCellularAutomata . . . . . . . . . . . . . . . . . 215
10.8 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 222
11 Bio-inspiredArtificialChemistries 225
11.1 String-BasedArtificialChemistries . . . . . . . . . . . . . . . . . . . . . . . . . . 225
11.2 Lock-and-KeyArtificialChemistries . . . . . . . . . . . . . . . . . . . . . . . . . 234
11.3 Networks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 240
11.4 SpatialStructuringandMovementinArtificialChemistries . . . . . . . . . . . 248
11.5 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 254
CONTENTS ix
IV OrderConstruction 255
12 TheStructureofOrganizations 257
12.1 BasicDefinitions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 259
12.2 Generators . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 262
12.3 BringingOrderintoOrganizations . . . . . . . . . . . . . . . . . . . . . . . . . . 263
12.4 NoveltyandInnovation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 265
12.5 ExamplesoftheStaticsofOrganizations . . . . . . . . . . . . . . . . . . . . . . . 266
12.6 HowtoCalculateClosedandSelf-MaintainingSets . . . . . . . . . . . . . . . . 270
12.7 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 273
13 TheDynamicsofOrganizations 275
13.1 Flows,StoichiometryandKineticConstants . . . . . . . . . . . . . . . . . . . . 275
13.2 ExamplesoftheDynamicsofOrganization . . . . . . . . . . . . . . . . . . . . . 277
13.3 ObservingOrganizations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 282
13.4 ProbabilisticNotionsofClosureandSelf-Maintenance . . . . . . . . . . . . . . 283
13.5 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 285
14 Self-OrganizationandEmergentPhenomena 287
14.1 ExamplesofSelf-OrganizingSystems. . . . . . . . . . . . . . . . . . . . . . . . . 288
14.2 ExplanatoryConceptsofSelf-Organization . . . . . . . . . . . . . . . . . . . . . 289
14.3 TheEmergenceofPhenomena . . . . . . . . . . . . . . . . . . . . . . . . . . . . 295
14.4 ExplanatoryConceptsofEmergence . . . . . . . . . . . . . . . . . . . . . . . . . 298
14.5 EmergenceandTop-DownCausation . . . . . . . . . . . . . . . . . . . . . . . . 304
14.6 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 306
15 ConstructiveDynamicalSystems 307
15.1 Novelty,Innovation,Emergence. . . . . . . . . . . . . . . . . . . . . . . . . . . . 307
15.2 BirthProcessesattheSameLevel . . . . . . . . . . . . . . . . . . . . . . . . . . . 309
15.3 TheEmergenceofEntitiesonaHigherLevel . . . . . . . . . . . . . . . . . . . . 317
15.4 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 319
V Applications 321
16 ApplicationsofArtificialChemistries 323
16.1 RobotsControlledbyArtificialChemistries . . . . . . . . . . . . . . . . . . . . . 324
16.2 ACsforNetworking . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 330
16.3 LanguageDynamicsandEvolution . . . . . . . . . . . . . . . . . . . . . . . . . . 334
16.4 MusicCompositionUsingAlgorithmicChemistries . . . . . . . . . . . . . . . . 338
16.5 ProofSystems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 339
16.6 ArtificialChemistryandGeneticProgramming . . . . . . . . . . . . . . . . . . . 340
16.7 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 344
17 ComputingwithArtificialChemistries 345
17.1 Principlesofimplementation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 346
17.2 SearchandOptimizationAlgorithmsInspiredbyChemistry . . . . . . . . . . . 355
17.3 DistributedAlgorithmsUsingChemicalComputing . . . . . . . . . . . . . . . . 358
17.4 InSilicoSimulationofWetChemicalComputing. . . . . . . . . . . . . . . . . . 366
17.5 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 372
Description:An introduction to the fundamental concepts of the emerging field of Artificial Chemistries, covering both theory and practical applications. The field of Artificial Life (ALife) is now firmly established in the scientific world, but it has yet to achieve one of its original goals: an understanding
