ACloserLookattheEvolutionaryDynamicsofSelf仔細看看自己的進化動力學課件

CreditsThisprojectispartofthesisworkleadingtotheMasterofSciencedegreeinComputationalScience.ResearchissupervisedbyDr.HirokiSayamaUniversityofElectro-Communications,Tokyo,JapanProjecttobecompletedbytheendofthisyear.1/6/20231SectionComputationalScience,UniversiteitvanAmsterdamCreditsThisprojectispartofLecturePlanStatementofProblemFormerworksANewDynamicEnvironmentIdentificationandClassificationGenealogyLarge-scaleSimulationsConclusions1/6/20232SectionComputationalScience,UniversiteitvanAmsterdamLecturePlanStatementofProbl1.StatementofProblemGoal:Tostudytheemergenceofcomplexevolutionaryphenomenathroughasimple,abstractmodel.Method:“…abstractfromthenaturalself-reproductionproblemitslogicalform.”(Neumann)Synthesizeusingcellularautomata(CA).1/6/20233SectionComputationalScience,UniversiteitvanAmsterdam1.StatementofProblemGoal:1/2.FormerWorks1/6/20234SectionComputationalScience,UniversiteitvanAmsterdam2.FormerWorks1/6/20234SectioTimelinerelatingcurrentworkVonNeumann’sUniversalConstructor19531970GameofLife(Conway)1994Tierra(Ray)1984SRLoop(Langton)1998Evoloop(Sayama)1/6/20235SectionComputationalScience,UniversiteitvanAmsterdamTimelinerelatingcurrentworkTheSelf-ReproducingLoopSheath:Outershellhousinggenesequence.Genes:7s(straightgrowth)and4s(turning).Tube:2swithinsheath.Arm:Extensibleloopstructureforreplication.sheathgenestubearm1/6/20236SectionComputationalScience,UniversiteitvanAmsterdamTheSelf-ReproducingLoopSheatState-transitionRulesLTCBRIRulestaketheformCTRLB>I.Localanddeterministic.1/6/20237SectionComputationalScience,UniversiteitvanAmsterdamState-transitionRulesLTCBRIRuLangton’sSRLoop8states5-cellneighbourhoodProgramforself-replicationcontainedingenesequence(genotype)Deathoccursviafunctionalfailure(limitedinfinitespace)1/6/20238SectionComputationalScience,UniversiteitvanAmsterdamLangton’sSRLoop8states1/6/2TheEvoloop9states(SRruleset+dissolvingstate)5-cellneighbourhoodModificationstoSRrulesetintroduceadaptivityleadingtoevolution.Deathoccursviastructuraldissolution.1/6/20239SectionComputationalScience,UniversiteitvanAmsterdamTheEvoloop9states(SRrulesEvoloopCAStatesStateNameFunction0[Black]Background1[Blue]CoreFillstubeofloop2[Red]SheathExternalstructure3[Purple]Structureofarm4[Green]GeneInfoforturningarm5[LightBlue]Messenger6[Yellow]Messenger/Guide/Finisher7[White]GeneInfoforstraightgrowth8[Grey]DissolverDissolvesloopstructure1/6/202310SectionComputationalScience,UniversiteitvanAmsterdamEvoloopCAStatesStateNameFuncPropertiesoftheDissolvingStateAppearsfromundefinedconfigurations.Travelsalongtubetodissolveneighbouringstates.Anycontiguousstructureisextinguished,creatingfreespacefornewloops.1/6/202311SectionComputationalScience,UniversiteitvanAmsterdamPropertiesoftheDissolvingSQualitiesoftheEvoloopCASimpleandscalable:Smallruleset(95=59049rules)NocentraloperatingsystemPurelydeterministic(nostochasticoperationsinruleset).Adaptable.Realizesanemergentevolutionaryprocess.1/6/202312SectionComputationalScience,UniversiteitvanAmsterdamQualitiesoftheEvoloopCASimPredictabilityoftheEvoloopContinuousself-reproductionleadstohigh-densitylooppopulations(nofreespace).Interactionofphenotypesfavourssmall-sizedloops.Evolutionendswithahomogeneoussingle-speciespopulation.Nodiversity,nospeciation,noevolution.1/6/202313SectionComputationalScience,UniversiteitvanAmsterdamPredictabilityoftheEvoloopCConclusion:modifytheenvironment.EvolutioninaPeriodicDomain1/6/202314SectionComputationalScience,UniversiteitvanAmsterdamConclusion:modifytheenviron3.ANewDynamicEnvironment1/6/202315SectionComputationalScience,UniversiteitvanAmsterdam3.ANewDynamicEnvironment1/TenthstateaddedtoEvoloopCA.Rulesnearlyidenticaltodissolvingstate,butpersistsintimeforafiniteperiodN(persistenceorlifetime).Purelypartoftheenvironment:loopswillneverproduceitontheirown.ThePersistentDissolvingState1/6/202316SectionComputationalScience,UniversiteitvanAmsterdamTenthstateaddedtoEvoloopCTheMemoryLayerMemorylayeractsascounter,decrementinglifetimeeachiterationifdissolvercellisabove.Whenlifetimereacheszero,counterisresetanddissolvercellisremoved.Doesnotdirectlyinteractwithneighbouringlooplayerstates.CTBLRILoopLayerMNMemoryLayer1/6/202317SectionComputationalScience,UniversiteitvanAmsterdamTheMemoryLayerMemorylayeraPersistenceandScaleThechoiceofthepersistenceNimposesafixedscaleonthesystem.Asdomainisexpanded(gridsize),Ncanbeusedto“scale”thepopulationclustersize.1/6/202318SectionComputationalScience,UniversiteitvanAmsterdamPersistenceandScaleThechoicPersistenceandScaleSignsofcomplexevolutionaryphenomena.Speciationandlong-termdiversity(phenotype).Conclusion:tounderstandwhat’shappening,weneedbetteranalysis…1/6/202319SectionComputationalScience,UniversiteitvanAmsterdamPersistenceandScaleSignsof4.IdentificationandClassification17d55555/13x131/6/202320SectionComputationalScience,UniversiteitvanAmsterdam4.IdentificationandClassifiNewDefinitionsGenotype:sequenceofstates‘0’,‘1’,‘4’,and‘7’insidealoop’stubestructure.Phenotype:sizeofinnersheath.Birth:appearanceofstate‘6’(umbilicalcorddissolver).Death:dissolutionofanyinnersheathstate.1/6/202321SectionComputationalScience,UniversiteitvanAmsterdamNewDefinitionsGenotype:sequePropertiesofLoopSpecies“Stationary”(identification):GenotypePhenotype“Reproductive”(classification):Existenceandidentityoffirst-bornoffspringinfreespace.1/6/202322SectionComputationalScience,UniversiteitvanAmsterdamPropertiesofLoopSpecies“StaIdentificationofLoopSpecies17d5555513x13Identifier:17d55555/13x13LoopReplicationGenotypePhenotype1/6/202323SectionComputationalScience,UniversiteitvanAmsterdamIdentificationofLoopSpeciesGenotype-basedCharacteristics41f55/6x613e95/6x65f541/6x6Speciesofthesamephenotypebutdifferentgenotypeexhibitdistinctdynamics:1/6/202324SectionComputationalScience,UniversiteitvanAmsterdamGenotype-basedCharacteristicsClassificationofLoopSpeciesStable:First-bornchildinfreespaceisidenticaltoparent.Transitional:First-bornchildinfreespaceisdifferentfromparent.Terminal:Speciesdoesnotreproduce.1/6/202325SectionComputationalScience,UniversiteitvanAmsterdamClassificationofLoopSpecies5.Genealogy1/6/202326SectionComputationalScience,UniversiteitvanAmsterdam5.Genealogy1/6/202326SectionGenealogyasaTreeTotrackgenealogy,ancestralinformationrecordedinparent/childform.Onlargegrids,resultsinhugegenealogytrees.Informationmissing:multipleparents(ancestors)forasinglechild(descendant).Conclusion:genealogynottree-based?1/6/202327SectionComputationalScience,UniversiteitvanAmsterdamGenealogyasaTreeTotrackgeGenealogyasaGraphLoopspeciesrepresentedbygraphnodes(vertices).Links(edges)representancestralrelations.Linktraversalfrequenciesbothtimeandspace-dependent.Graph-spacesizeon3Kx3Krun:5Knodes10Klinks1/6/202328SectionComputationalScience,UniversiteitvanAmsterdamGenealogyasaGraphLoopspeciClassificationinGraph-spaceStable:nodewithfree-spaceself-link(“buckle”).Transitional:nodewithfree-spacetoanothernode.Terminal:nodewithnofree-spacelinks.Free-spacelink:graph-spacelinktraversedinfreespace.1/6/202329SectionComputationalScience,UniversiteitvanAmsterdamClassificationinGraph-spaceSExampleofGraph-basedGenealogyA:5f541/6x6B:47d51/6x6C:27d5/5x5D:87d5/5x5E:9f5/4x4F:41f55/6x61/6/202330SectionComputationalScience,UniversiteitvanAmsterdamExampleofGraph-basedGenealoStatisticsfromGraph-BasedGenealogyRankSpeciesInLinksFrequency141f55/6x66542151927d/4x4642174437d/3x3621482RankSpeciesOutLinksFrequency120fa55/7x7855807878241f55/6x68214449632317d55555/13x1335155423(3Kx3Krun-compiledafter940Kiterations)1/6/202331SectionComputationalScience,UniversiteitvanAmsterdamStatisticsfromGraph-BasedGe6.Large-scaleExperiments1/6/202332SectionComputationalScience,UniversiteitvanAmsterdam6.Large-scaleExperiments1/6/Method3000x3000gridPersistence(N)=20,000timesteps.Initiatedwiththreeloopsofspecies17d55555/13x13.Blockofdissolvercellsbegininupper-rightcorner.Runfor29daysonDASII.1/6/202333SectionComputationalScience,UniversiteitvanAmsterdamMethod3000x3000grid1/6/2023“Bottlenecked”LifeCyclePeriodicdomainisdynamicallypartitionedbydissolver.Onespecies(5f541/6x6)narrowlyescapesextinction.Thisspeciesistheexclusiveancestorforallfuturegenerations.Predictingthiseventnearlyimpossible.1/6/202334SectionComputationalScience,UniversiteitvanAmsterdam“Bottlenecked”LifeCyclePerio“Bottlenecked”LifeCycle1/6/202335SectionComputationalScience,UniversiteitvanAmsterdam“Bottlenecked”LifeCycle1/6/2EvolutionaryStasisBetween400Kand1Miterations,twospecies(41f55/6x6,20fa55/7x7)dominateexclusively.1/6/202336SectionComputationalScience,UniversiteitvanAmsterdamEvolutionaryStasisBetween400EvolutionaryCoupling?Cycleingraph-spaceconnectsdominantspecies(41f55/6x6,20fa55/7x7).Systemsettlesingraph-space“potentialminimum”.A:41f55/6x6B:20fa55/7x7C:107d255/8x81/6/202337SectionComputationalScience,UniversiteitvanAmsterdamEvolutionaryCoupling?CycleinReturnoftheGiantsStasisabruptlyendsat940Kiterations.Large-sizedloops(size9,10,11,12,13)makeabriefreturn.Highdiversityforveryshortperiod(roughly80K).Punctuatedequilibrium(Tierra)?1/6/202338SectionComputationalScience,UniversiteitvanAmsterdamReturnoftheGiantsStasisabrReturnoftheGiants1/6/202339SectionComputationalScience,UniversiteitvanAmsterdamReturnoftheGiants1/6/2023397.ConclusionsDiversitycanbesynthesizedinaCAspace.Genealogycanbeviewedasagraph.ComplexevolutionaryphenomenacanemergefromadeterministicCAmodel:Evolutionary“bottlenecking”PunctuatedEquilibriumDescribingthepastiseasierthanprescribingthefuture.1/6/202340SectionComputationalScience,UniversiteitvanAmsterdam7.ConclusionsDiversitycanbeReferencesHirokiSayama,Anewstructurallydissolvableself-reproducingloopevolvinginasimplecellularautomataspace,ArtificialLife,vol.5,no.4,pp.343-365,1999.HirokiSayama:ConstructingEvolutionarySystemsonaSimpleDeterministicCellularAutomataSpace,Ph.D.Dissertation,DepartmentofInformationScience,GraduateSchoolofScience,UniversityofTokyo,December1998.Langton,C.G.:Self-reproductionincellularautomata,PhysicaD,10pp.135-144,1984WolframS.:ANewkindofscience,WolframMedia,2002.VonNeumann,J.editedbyBurks:TheoryofSelf-ReproducingAutomata,1966.Workinprogress:.1/6/202341SectionComputationalScience,UniversiteitvanAmsterdamReferencesHirokiSayama,AnewThanks!J1/6/202342SectionComputationalScience,UniversiteitvanAmsterdamThanks!J1/6/202342SectionCompCreditsThisprojectispartofthesisworkleadingtotheMasterofSciencedegreeinComputationalScience.ResearchissupervisedbyDr.HirokiSayamaUniversityofElectro-Communications,Tokyo,JapanProjecttobecompletedbytheendofthisyear.1/6/202343SectionComputationalScience,UniversiteitvanAmsterdamCreditsThisprojectispartofLecturePlanStatementofProblemFormerworksANewDynamicEnvironmentIdentificationandClassificationGenealogyLarge-scaleSimulationsConclusions1/6/202344SectionComputationalScience,UniversiteitvanAmsterdamLecturePlanStatementofProbl1.StatementofProblemGoal:Tostudytheemergenceofcomplexevolutionaryphenomenathroughasimple,abstractmodel.Method:“…abstractfromthenaturalself-reproductionproblemitslogicalform.”(Neumann)Synthesizeusingcellularautomata(CA).1/6/202345SectionComputationalScience,UniversiteitvanAmsterdam1.StatementofProblemGoal:1/2.FormerWorks1/6/202346SectionComputationalScience,UniversiteitvanAmsterdam2.FormerWorks1/6/20234SectioTimelinerelatingcurrentworkVonNeumann’sUniversalConstructor19531970GameofLife(Conway)1994Tierra(Ray)1984SRLoop(Langton)1998Evoloop(Sayama)1/6/202347SectionComputationalScience,UniversiteitvanAmsterdamTimelinerelatingcurrentworkTheSelf-ReproducingLoopSheath:Outershellhousinggenesequence.Genes:7s(straightgrowth)and4s(turning).Tube:2swithinsheath.Arm:Extensibleloopstructureforreplication.sheathgenestubearm1/6/202348SectionComputationalScience,UniversiteitvanAmsterdamTheSelf-ReproducingLoopSheatState-transitionRulesLTCBRIRulestaketheformCTRLB>I.Localanddeterministic.1/6/202349SectionComputationalScience,UniversiteitvanAmsterdamState-transitionRulesLTCBRIRuLangton’sSRLoop8states5-cellneighbourhoodProgramforself-replicationcontainedingenesequence(genotype)Deathoccursviafunctionalfailure(limitedinfinitespace)1/6/202350SectionComputationalScience,UniversiteitvanAmsterdamLangton’sSRLoop8states1/6/2TheEvoloop9states(SRruleset+dissolvingstate)5-cellneighbourhoodModificationstoSRrulesetintroduceadaptivityleadingtoevolution.Deathoccursviastructuraldissolution.1/6/202351SectionComputationalScience,UniversiteitvanAmsterdamTheEvoloop9states(SRrulesEvoloopCAStatesStateNameFunction0[Black]Background1[Blue]CoreFillstubeofloop2[Red]SheathExternalstructure3[Purple]Structureofarm4[Green]GeneInfoforturningarm5[LightBlue]Messenger6[Yellow]Messenger/Guide/Finisher7[White]GeneInfoforstraightgrowth8[Grey]DissolverDissolvesloopstructure1/6/202352SectionComputationalScience,UniversiteitvanAmsterdamEvoloopCAStatesStateNameFuncPropertiesoftheDissolvingStateAppearsfromundefinedconfigurations.Travelsalongtubetodissolveneighbouringstates.Anycontiguousstructureisextinguished,creatingfreespacefornewloops.1/6/202353SectionComputationalScience,UniversiteitvanAmsterdamPropertiesoftheDissolvingSQualitiesoftheEvoloopCASimpleandscalable:Smallruleset(95=59049rules)NocentraloperatingsystemPurelydeterministic(nostochasticoperationsinruleset).Adaptable.Realizesanemergentevolutionaryprocess.1/6/202354SectionComputationalScience,UniversiteitvanAmsterdamQualitiesoftheEvoloopCASimPredictabilityoftheEvoloopContinuousself-reproductionleadstohigh-densitylooppopulations(nofreespace).Interactionofphenotypesfavourssmall-sizedloops.Evolutionendswithahomogeneoussingle-speciespopulation.Nodiversity,nospeciation,noevolution.1/6/202355SectionComputationalScience,UniversiteitvanAmsterdamPredictabilityoftheEvoloopCConclusion:modifytheenvironment.EvolutioninaPeriodicDomain1/6/202356SectionComputationalScience,UniversiteitvanAmsterdamConclusion:modifytheenviron3.ANewDynamicEnvironment1/6/202357SectionComputationalScience,UniversiteitvanAmsterdam3.ANewDynamicEnvironment1/TenthstateaddedtoEvoloopCA.Rulesnearlyidenticaltodissolvingstate,butpersistsintimeforafiniteperiodN(persistenceorlifetime).Purelypartoftheenvironment:loopswillneverproduceitontheirown.ThePersistentDissolvingState1/6/202358SectionComputationalScience,UniversiteitvanAmsterdamTenthstateaddedtoEvoloopCTheMemoryLayerMemorylayeractsascounter,decrementinglifetimeeachiterationifdissolvercellisabove.Whenlifetimereacheszero,counterisresetanddissolvercellisremoved.Doesnotdirectlyinteractwithneighbouringlooplayerstates.CTBLRILoopLayerMNMemoryLayer1/6/202359SectionComputationalScience,UniversiteitvanAmsterdamTheMemoryLayerMemorylayeraPersistenceandScaleThechoiceofthepersistenceNimposesafixedscaleonthesystem.Asdomainisexpanded(gridsize),Ncanbeusedto“scale”thepopulationclustersize.1/6/202360SectionComputationalScience,UniversiteitvanAmsterdamPersistenceandScaleThechoicPersistenceandScaleSignsofcomplexevolutionaryphenomena.Speciationandlong-termdiversity(phenotype).Conclusion:tounderstandwhat’shappening,weneedbetteranalysis…1/6/202361SectionComputationalScience,UniversiteitvanAmsterdamPersistenceandScaleSignsof4.IdentificationandClassification17d55555/13x131/6/202362SectionComputationalScience,UniversiteitvanAmsterdam4.IdentificationandClassifiNewDefinitionsGenotype:sequenceofstates‘0’,‘1’,‘4’,and‘7’insidealoop’stubestructure.Phenotype:sizeofinnersheath.Birth:appearanceofstate‘6’(umbilicalcorddissolver).Death:dissolutionofanyinnersheathstate.1/6/202363SectionComputationalScience,UniversiteitvanAmsterdamNewDefinitionsGenotype:sequePropertiesofLoopSpecies“Stationary”(identification):GenotypePhenotype“Reproductive”(classification):Existenceandidentityoffirst-bornoffspringinfreespace.1/6/202364SectionComputationalScience,UniversiteitvanAmsterdamPropertiesofLoopSpecies“StaIdentificationofLoopSpecies17d5555513x13Identifier:17d55555/13x13LoopReplicationGenotypePhenotype1/6/202365SectionComputationalScience,UniversiteitvanAmsterdamIdentificationofLoopSpeciesGenotype-basedCharacteristics41f55/6x613e95/6x65f541/6x6Speciesofthesamephenotypebutdifferentgenotypeexhibitdistinctdynamics:1/6/202366SectionComputationalScience,UniversiteitvanAmsterdamGenotype-basedCharacteristicsClassificationofLoopSpeciesStable:First-bornchildinfreespaceisidenticaltoparent.Transitional:First-bornchildinfreespaceisdifferentfromparent.Terminal:Speciesdoesnotreproduce.1/6/202367SectionComputationalScience,UniversiteitvanAmsterdamClassificationofLoopSpecies5.Genealogy1/6/202368SectionComputationalScience,UniversiteitvanAmsterdam5.Genealogy1/6/202326SectionGenealogyasaTreeTotrackgenealogy,ancestralinformationrecordedinparent/childform.Onlargegrids,resultsinhugegenealogytrees.Informationmissing:multipleparents(ancestors)forasinglechild(descendant).Conclusion:genealogynottree-based?1/6/202369SectionComputationalScience,UniversiteitvanAmsterdamGenealogyasaTreeTotrackgeGenealogyasaGraphLoopspeciesrepresentedbygraphnodes(vertices).Links(edges)representancestralrelations.Linktraversalfrequenciesbothtimeandspace-dependent.Graph-spacesizeon3Kx3Krun:5Knodes10Klinks1/6/202370SectionComputationalScience,UniversiteitvanAmsterdamGenealogyasaGraphLoopspeciClassificationinGraph-spaceStable:nodewithfree-spaceself-link(“buckle”).Transitional:nodewithfree-spacetoanothernode.Terminal:nodewithnofree-spacelinks.Free-spacelink:graph-spacelinktraversedinfreespace.1/6/202371SectionComputationalScience,UniversiteitvanAmsterdamClassificationinGraph-spaceSExampleofGraph-basedGenealogyA:5f541/6x6B:47d51/6x6C:27d5/5x5D:87d5/5x5E:9f5/4x4F:41f55/6x61/6/202372SectionComputationalScience,UniversiteitvanAmsterdamExampleofGraph-basedGenealoStatisticsfromGraph-BasedGenealogyRankSpeciesInLinksFrequency141f55/6x66542151927d/4x4642174437d/3x3621482RankSpeciesOutLinksFrequency120fa55/7x7855807878241f55/6x68214449632317d55555/13x1335155423(3Kx3Krun-compiledafter940Kiterations)1/6/202373SectionComputationalScience,UniversiteitvanAmsterdamStatisticsfromGraph-BasedGe6.Large-scaleExperiments1/6/202374SectionComputationalScience,UniversiteitvanAmsterdam6.Large-scaleExperiments1/6/Method3000x3000gridPersistence(N)=20,000timesteps.Initiatedwiththreeloopsofspecies17d55555/13x13.Blockofdissolvercellsbegininupper-rightcorner.Runfor29daysonDASII.1/6/202375SectionComputationalScience,UniversiteitvanAmsterdamMethod3000x3000grid1/6/2023“Bottlenecked”LifeCyclePeriodicdomainisdynamicallypartitionedbydissolver.Onespecies(5f541/6x6)narrowlyescapesextinction.Thisspeciesistheexclusiveancestorforallfuturegenerations.Predictingthiseventnearlyimpossible.1/6/202376SectionComputationalS