Complex Genetic Evolution of Self-Replicating Loops
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Transcript of Complex Genetic Evolution of Self-Replicating Loops
Complex Genetic Complex Genetic Evolution of Self-Evolution of Self-Replicating LoopsReplicating Loops
Chris SalzbergChris Salzberg1,21,2 Antony Antony Antony Antony33 Hiroki Sayama Hiroki Sayama11
1 1 University of Electro-Communications, JapanUniversity of Electro-Communications, Japan2 2 University of Tokyo, JapanUniversity of Tokyo, Japan
3 3 University of Amsterdam, the NetherlandsUniversity of Amsterdam, the [email protected]@cx.hc.uec.ac.jp
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SummarySummary We re-examined the evolutionary We re-examined the evolutionary
dynamics of self-replicating loops on dynamics of self-replicating loops on CA, by using new tools for complete CA, by using new tools for complete genetic identification and genealogy genetic identification and genealogy tracingtracing
We found in the loop populations:We found in the loop populations:1.1. Diversities in macro-scale morphologies Diversities in macro-scale morphologies
and mutational biasesand mutational biases
2.2. Genetic adaptationGenetic adaptation
3.3. Genetic diversification and continuing Genetic diversification and continuing explorationexploration
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Background: CA-based AlifeBackground: CA-based Alife
Universal constructor (Von Neumann Universal constructor (Von Neumann 1966; Codd 1968; Takahashi et al. 1990; 1966; Codd 1968; Takahashi et al. 1990; Pesavento 1995)Pesavento 1995)
Self-replicating loops (Langton 1984; Byl Self-replicating loops (Langton 1984; Byl 1989; Reggia et al. 1993)1989; Reggia et al. 1993)
Self-inspecting loops/worms (Ibanez et Self-inspecting loops/worms (Ibanez et al. 1995; Morita et al. 1995, 1996)al. 1995; Morita et al. 1995, 1996)
Self-replicating loops with additional Self-replicating loops with additional capabilities of construction/computation capabilities of construction/computation (Tempesti 1995; Perrier et al. 1996; (Tempesti 1995; Perrier et al. 1996; Chou et al. 1998)Chou et al. 1998)
Spontaneous emergence and evolution Spontaneous emergence and evolution of self-replicators (Lohn et al. 1995; of self-replicators (Lohn et al. 1995; Chou et al. 1997; Sayama 1998, 2000, Chou et al. 1997; Sayama 1998, 2000, 2003; Salzberg et al. 2003, 2004; Suzuki 2003; Salzberg et al. 2003, 2004; Suzuki et al. 2003, 2004)et al. 2003, 2004)
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Supposedly Limited Supposedly Limited Evolutionary Dynamics in Evolutionary Dynamics in
CACA McMullin (2000):McMullin (2000):
““[SR loop] does not embody anything like a [SR loop] does not embody anything like a general constructive automaton and general constructive automaton and therefore therefore has little or no evolutionary has little or no evolutionary potentialpotential.”.”
Suzuki et al. (2003):Suzuki et al. (2003):““Though there are many other variations of Though there are many other variations of
CA models for self-replication, CA models for self-replication, their their evolvability does not differ very muchevolvability does not differ very much.”.”
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QuestionQuestion
Did we truly understand what was Did we truly understand what was going on in this seemingly simple going on in this seemingly simple dynamics of our CA-based evolutionary dynamics of our CA-based evolutionary systems?systems?
We didn’t know we didn’t, until we We didn’t know we didn’t, until we have developed the formal framework have developed the formal framework and the sophisticated tools for detailed and the sophisticated tools for detailed analysis and visualization for those analysis and visualization for those systems.systems.
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Subject: EvoloopSubject: Evoloop An evolvable SR An evolvable SR
loop by Sayama loop by Sayama (1999) constructed (1999) constructed on on nine-state five-nine-state five-neighbor fully neighbor fully deterministic CAdeterministic CA
Robust state-Robust state-transition rules transition rules give rise to give rise to evolutionary evolutionary behaviorbehavior
Mutation/selection Mutation/selection mechanisms are mechanisms are totally totally emergentemergent
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New Tools for Detailed New Tools for Detailed AnalysisAnalysis
At every birth, the newborn loop’s At every birth, the newborn loop’s genotype & genotype & phenotypephenotype and its and its genealogical informationgenealogical information is is detected and recorded in an event-driven fashiondetected and recorded in an event-driven fashion
Each genotype-phenotype pair is indexed in the Each genotype-phenotype pair is indexed in the Species DatabaseSpecies Database
genotypegenotype
G G G G C G C G T T G CC CC G
phenotypephenotype88
88
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Observation (1):Observation (1):Diversities in Macro-Scale Diversities in Macro-Scale
Morphologies and Morphologies and Mutational BiasesMutational Biases
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Huge Genetic State-Huge Genetic State-SpaceSpace
Permutation of genes (Permutation of genes (GG, , TT) and core ) and core states (states (CC) under constraints ) under constraints estimates estimates the number of viable the number of viable genotypesgenotypes to be to be
Size Size nn
# of species# of species Size Size nn
# of species# of species Size Size nn
# of species# of species
44 1515 99 11,44011,440 1414 9,657,7009,657,700
55 5656 1010 43,75843,758 1515 37,442,16037,442,160
66 210210 1111 167,960167,960 1616 145,422,675145,422,675
77 792792 1212 646,646646,646 1717 565,722,720565,722,720
88 3,0033,003 1313 2,496,1442,496,144 1818 2,203,961,42,203,961,43030
22nn-2-2nn-2-2
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Diversity in Growth Patterns Diversity in Growth Patterns (size-4)(size-4)
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Diversity in Growth Patterns Diversity in Growth Patterns (size-6)(size-6)
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Diversity in Mutational Biases Diversity in Mutational Biases (size-6)(size-6)
(new result not included in paper)
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Observation (2):Observation (2):Genetic AdaptationGenetic Adaptation
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Two Measures of (Possible) Two Measures of (Possible) FitnessFitness
Survival rate Survival rate (sustainability in (sustainability in competition):competition):— Characterized by an average of relative Characterized by an average of relative
population ratios of a species after a given population ratios of a species after a given period of time in competition with another period of time in competition with another speciesspecies
Colony density index Colony density index (growth speed):(growth speed):— Characterized by a quadratic coefficient of Characterized by a quadratic coefficient of
a parabola fitted to the population growth a parabola fitted to the population growth curve of each species in an infinite domaincurve of each species in an infinite domain
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Variety and Correlation Variety and Correlation (size-4)(size-4)
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Evolution Evolution in vivoin vivo(starting from size-8)(starting from size-8)
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Evolution Optimizes Evolution Optimizes “Fitness”“Fitness”
Evolutionary transitionactually observed inthe previous slide
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Observation (3):Observation (3):Genetic Diversification and Genetic Diversification and
Continuing ExplorationContinuing Exploration
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Non-Mutable SubsequencesNon-Mutable Subsequences
Certain subsequences are found Certain subsequences are found non-mutablenon-mutable::G{G{C*C*}}TT{{C*C*}}TTGG
A long non-mutable sub-sequence injected to A long non-mutable sub-sequence injected to ancestor causes a ancestor causes a relatively largerelatively large lower lower bound of viable sizesbound of viable sizes upon its descendants, a upon its descendants, a reduced size-based selection pressurereduced size-based selection pressure, and a , and a highly biased highly biased mutational tendency to larger mutational tendency to larger speciesspecies
Such “GMO” loops show long-lasting Such “GMO” loops show long-lasting evolutionary exploration processesevolutionary exploration processes
GGGGGGGGCCGGC C GGCCCCTTCCCCTTG GG G
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control
with long non-mutable subsequences
with subsequences + hostile environment
(new result not included in paper)
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ConclusionsConclusions
Huge diversityHuge diversity, , non-trivial genetic non-trivial genetic adaptationadaptation and and diversificationdiversification unveiled unveiled in the evoloop systemin the evoloop system
Hierarchical emergence Hierarchical emergence demonstrated, where demonstrated, where macro-scale macro-scale evolutionary changes of populations evolutionary changes of populations arises from micro-scale interactions arises from micro-scale interactions between elements much smaller than between elements much smaller than individual replicatorsindividual replicators, traversing , traversing multiple scalesmultiple scales
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References & AcksReferences & Acks Salzberg, C. (2003) Salzberg, C. (2003) Emergent Evolutionary Dynamics of Emergent Evolutionary Dynamics of
Self-Reproducing Cellular AutomataSelf-Reproducing Cellular Automata. M.Sc. Thesis. . M.Sc. Thesis. Universiteit van Amsterdam, the Netherlands.Universiteit van Amsterdam, the Netherlands.
Salzberg, C., Antony, A. & Sayama, H. Visualizing Salzberg, C., Antony, A. & Sayama, H. Visualizing evolutionary dynamics of self-replicators: A graph-based evolutionary dynamics of self-replicators: A graph-based approach. approach. Artificial LifeArtificial Life, in press., in press.
Sayama, H. Sayama, H. The SDSR loop / Evoloop Homepage.The SDSR loop / Evoloop Homepage. http://complex.hc.uec.ac.jp/sayama/sdsr/http://complex.hc.uec.ac.jp/sayama/sdsr/
Antony, A. & Salzberg, C. Antony, A. & Salzberg, C. The Artis Project Homepage.The Artis Project Homepage. http://artis.phenome.org/http://artis.phenome.org/
This work is supported in part by the Hayao Nakayama Foundation for Science, This work is supported in part by the Hayao Nakayama Foundation for Science, Technology & Culture, and the International Information Science Foundation, Technology & Culture, and the International Information Science Foundation, Japan.Japan.