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

CreditsThisprojectispartofthesisworkleadingtotheMasterofSciencedegreeinComputationalScience.ResearchissupervisedbyDr.HirokiSayamaUniversityofElectro-Communications,Tokyo,JapanProjecttobecompletedbytheendofthisyear.7/27/20231SectionComputationalScience,UniversiteitvanAmsterdamCreditsThisprojectispartofLecturePlanStatementofProblemFormerworksANewDynamicEnvironmentIdentificationandClassificationGenealogyLarge-scaleSimulationsConclusions7/27/20232SectionComputationalScience,UniversiteitvanAmsterdamLecturePlanStatementofProbl1.StatementofProblemGoal:Tostudytheemergenceofcomplexevolutionaryphenomenathroughasimple,abstractmodel.Method:“…abstractfromthenaturalself-reproductionproblemitslogicalform.”(Neumann)Synthesizeusingcellularautomata(CA).7/27/20233SectionComputationalScience,UniversiteitvanAmsterdam1.StatementofProblemGoal:7/2.FormerWorks7/27/20234SectionComputationalScience,UniversiteitvanAmsterdam2.FormerWorks7/27/20234SectiTimelinerelatingcurrentworkVonNeumann’sUniversalConstructor19531970GameofLife(Conway)1994Tierra(Ray)1984SRLoop(Langton)1998Evoloop(Sayama)7/27/20235SectionComputationalScience,UniversiteitvanAmsterdamTimelinerelatingcurrentworkTheSelf-ReproducingLoopSheath:Outershellhousinggenesequence.Genes:7s(straightgrowth)and4s(turning).Tube:2swithinsheath.Arm:Extensibleloopstructureforreplication.sheathgenestubearm7/27/20236SectionComputationalScience,UniversiteitvanAmsterdamTheSelf-ReproducingLoopSheatState-transitionRulesLTCBRIRulestaketheformCTRLB>I.Localanddeterministic.7/27/20237SectionComputationalScience,UniversiteitvanAmsterdamState-transitionRulesLTCBRIRuLangton’sSRLoop8states5-cellneighbourhoodProgramforself-replicationcontainedingenesequence(genotype)Deathoccursviafunctionalfailure(limitedinfinitespace)7/27/20238SectionComputationalScience,UniversiteitvanAmsterdamLangton’sSRLoop8states7/27/TheEvoloop9states(SRruleset+dissolvingstate)5-cellneighbourhoodModificationstoSRrulesetintroduceadaptivityleadingtoevolution.Deathoccursviastructuraldissolution.7/27/20239SectionComputationalScience,UniversiteitvanAmsterdamTheEvoloop9states(SRrulesEvoloopCAStatesStateNameFunction0[Black]Background1[Blue]CoreFillstubeofloop2[Red]SheathExternalstructure3[Purple]Structureofarm4[Green]GeneInfoforturningarm5[LightBlue]Messenger6[Yellow]Messenger/Guide/Finisher7[White]GeneInfoforstraightgrowth8[Grey]DissolverDissolvesloopstructure7/27/202310SectionComputationalScience,UniversiteitvanAmsterdamEvoloopCAStatesStateNameFuncPropertiesoftheDissolvingStateAppearsfromundefinedconfigurations.Travelsalongtubetodissolveneighbouringstates.Anycontiguousstructureisextinguished,creatingfreespacefornewloops.7/27/202311SectionComputationalScience,UniversiteitvanAmsterdamPropertiesoftheDissolvingSQualitiesoftheEvoloopCASimpleandscalable:Smallruleset(95=59049rules)NocentraloperatingsystemPurelydeterministic(nostochasticoperationsinruleset).Adaptable.Realizesanemergentevolutionaryprocess.7/27/202312SectionComputationalScience,UniversiteitvanAmsterdamQualitiesoftheEvoloopCASimPredictabilityoftheEvoloopContinuousself-reproductionleadstohigh-densitylooppopulations(nofreespace).Interactionofphenotypesfavourssmall-sizedloops.Evolutionendswithahomogeneoussingle-speciespopulation.Nodiversity,nospeciation,noevolution.7/27/202313SectionComputationalScience,UniversiteitvanAmsterdamPredictabilityoftheEvoloopCConclusion:modifytheenvironment.EvolutioninaPeriodicDomain7/27/202314SectionComputationalScience,UniversiteitvanAmsterdamConclusion:modifytheenviron3.ANewDynamicEnvironment7/27/202315SectionComputationalScience,UniversiteitvanAmsterdam3.ANewDynamicEnvironment7/TenthstateaddedtoEvoloopCA.Rulesnearlyidenticaltodissolvingstate,butpersistsintimeforafiniteperiodN(persistenceorlifetime).Purelypartoftheenvironment:loopswillneverproduceitontheirown.ThePersistentDissolvingState7/27/202316SectionComputationalScience,UniversiteitvanAmsterdamTenthstateaddedtoEvoloopCTheMemoryLayerMemorylayeractsascounter,decrementinglifetimeeachiterationifdissolvercellisabove.Whenlifetimereacheszero,counterisresetanddissolvercellisremoved.Doesnotdirectlyinteractwithneighbouringlooplayerstates.CTBLRILoopLayerMNMemoryLayer7/27/202317SectionComputationalScience,UniversiteitvanAmsterdamTheMemoryLayerMemorylayeraPersistenceandScaleThechoiceofthepersistenceNimposesafixedscaleonthesystem.Asdomainisexpanded(gridsize),Ncanbeusedto“scale”thepopulationclustersize.7/27/202318SectionComputationalScience,UniversiteitvanAmsterdamPersistenceandScaleThechoicPersistenceandScaleSignsofcomplexevolutionaryphenomena.Speciationandlong-termdiversity(phenotype).Conclusion:tounderstandwhat’shappening,weneedbetteranalysis…7/27/202319SectionComputationalScience,UniversiteitvanAmsterdamPersistenceandScaleSignsof4.IdentificationandClassification17d55555/13x137/27/202320SectionComputationalScience,UniversiteitvanAmsterdam4.IdentificationandClassifiNewDefinitionsGenotype:sequenceofstates‘0’,‘1’,‘4’,and‘7’insidealoop’stubestructure.Phenotype:sizeofinnersheath.Birth:appearanceofstate‘6’(umbilicalcorddissolver).Death:dissolutionofanyinnersheathstate.7/27/202321SectionComputationalScience,UniversiteitvanAmsterdamNewDefinitionsGenotype:sequePropertiesofLoopSpecies“Stationary”(identification):GenotypePhenotype“Reproductive”(classification):Existenceandidentityoffirst-bornoffspringinfreespace.7/27/202322SectionComputationalScience,UniversiteitvanAmsterdamPropertiesofLoopSpecies“StaIdentificationofLoopSpecies17d5555513x13Identifier:17d55555/13x13LoopReplicationGenotypePhenotype7/27/202323SectionComputationalScience,UniversiteitvanAmsterdamIdentificationofLoopSpeciesGenotype-basedCharacteristics41f55/6x613e95/6x65f541/6x6Speciesofthesamephenotypebutdifferentgenotypeexhibitdistinctdynamics:7/27/202324SectionComputationalScience,UniversiteitvanAmsterdamGenotype-basedCharacteristicsClassificationofLoopSpeciesStable:First-bornchildinfreespaceisidenticaltoparent.Transitional:First-bornchildinfreespaceisdifferentfromparent.Terminal:Speciesdoesnotreproduce.7/27/202325SectionComputationalScience,UniversiteitvanAmsterdamClassificationofLoopSpecies5.Genealogy7/27/202326SectionComputationalScience,UniversiteitvanAmsterdam5.Genealogy7/27/202326SectionGenealogyasaTreeTotrackgenealogy,ancestralinformationrecordedinparent/childform.Onlargegrids,resultsinhugegenealogytrees.Informationmissing:multipleparents(ancestors)forasinglechild(descendant).Conclusion:genealogynottree-based?7/27/202327SectionComputationalScience,UniversiteitvanAmsterdamGenealogyasaTreeTotrackgeGenealogyasaGraphLoopspeciesrepresentedbygraphnodes(vertices).Links(edges)representancestralrelations.Linktraversalfrequenciesbothtimeandspace-dependent.Graph-spacesizeon3Kx3Krun:5Knodes10Klinks7/27/202328SectionComputationalScience,UniversiteitvanAmsterdamGenealogyasaGraphLoopspeciClassificationinGraph-spaceStable:nodewithfree-spaceself-link(“buckle”).Transitional:nodewithfree-spacetoanothernode.Terminal:nodewithnofree-spacelinks.Free-spacelink:graph-spacelinktraversedinfreespace.7/27/202329SectionComputationalScience,UniversiteitvanAmsterdamClassificationinGraph-spaceSExampleofGraph-basedGenealogyA:5f541/6x6B:47d51/6x6C:27d5/5x5D:87d5/5x5E:9f5/4x4F:41f55/6x67/27/202330SectionComputationalScience,UniversiteitvanAmsterdamExampleofGraph-basedGenealoStatisticsfromGraph-BasedGenealogyRankSpeciesInLinksFrequency141f55/6x66542151927d/4x4642174437d/3x3621482RankSpeciesOutLinksFrequency120fa55/7x7855807878241f55/6x68214449632317d55555/13x1335155423(3Kx3Krun-compiledafter940Kiterations)7/27/202331SectionComputationalScience,UniversiteitvanAmsterdamStatisticsfromGraph-BasedGe6.Large-scaleExperiments7/27/202332SectionComputationalScience,UniversiteitvanAmsterdam6.Large-scaleExperiments7/27Method3000x3000gridPersistence(N)=20,000timesteps.Initiatedwiththreeloopsofspecies17d55555/13x13.Blockofdissolvercellsbegininupper-rightcorner.Runfor29daysonDASII.7/27/202333SectionComputationalScience,UniversiteitvanAmsterdamMethod3000x3000grid7/27/202“Bottlenecked”LifeCyclePeriodicdomainisdynamicallypartitionedbydissolver.Onespecies(5f541/6x6)narrowlyescapesextinction.Thisspeciesistheexclusiveancestorforallfuturegenerations.Predictingthiseventnearlyimpossible.7/27/202334SectionComputationalScience,UniversiteitvanAmsterdam“Bottlenecked”LifeCyclePerio“Bottlenecked”LifeCycle7/27/202335SectionComputationalScience,UniversiteitvanAmsterdam“Bottlenecked”LifeCycle7/27/EvolutionaryStasisBetween400Kand1Miterations,twospecies(41f55/6x6,20fa55/7x7)dominateexclusively.7/27/202336SectionComputationalScience,UniversiteitvanAmsterdamEvolutionaryStasisBetween400EvolutionaryCoupling?Cycleingraph-spaceconnectsdominantspecies(41f55/6x6,20fa55/7x7).Systemsettlesingraph-space“potentialminimum”.A:41f55/6x6B:20fa55/7x7C:107d255/8x87/27/202337SectionComputationalScience,UniversiteitvanAmsterdamEvolutionaryCoupling?CycleinReturnoftheGiantsStasisabruptlyendsat940Kiterations.Large-sizedloops(size9,10,11,12,13)makeabriefreturn.Highdiversityforveryshortperiod(roughly80K).Punctuatedequilibrium(Tierra)?7/27/202338SectionComputationalScience,UniversiteitvanAmsterdamReturnoftheGiantsStasisabrReturnoftheGiants7/27/202339SectionComputationalScience,UniversiteitvanAmsterdamReturnoftheGiants7/27/202337.ConclusionsDiversitycanbesynthesizedinaCA