A Discrete Artificial Regulatory Network for Simulating the Evolution of Computation W. Garrett Mitchener College of Charleston Mathematics Department July, 22 http://mitchenerg.people.cofc.edu mitchenerg@cofc.edu W. Garrett Mitchener (C of C) Discrete ARN July, 22 / 37
Prelude Artificial life is hard W. Garrett Mitchener (C of C) Discrete ARN July, 22 2 / 37
Prelude Artificial life is hard W. Garrett Mitchener (C of C) Discrete ARN July, 22 2 / 37
Prelude So I made a toy W. Garrett Mitchener (C of C) Discrete ARN July, 22 3 / 37
Prelude So I made a toy http://legomyphoto.wordpress.com/2/6/23/day-327-2/ W. Garrett Mitchener (C of C) Discrete ARN July, 22 3 / 37
Prelude Prelude Learn how computation evolves Biochemical reaction networks Gene regulatory networks Neural networks W. Garrett Mitchener (C of C) Discrete ARN July, 22 4 / 37
Prelude Prelude Learn how computation evolves Biochemical reaction networks Gene regulatory networks Neural networks Combine Molecular genetics Population genetics W. Garrett Mitchener (C of C) Discrete ARN July, 22 4 / 37
Prelude Prelude Learn how computation evolves Biochemical reaction networks Gene regulatory networks Neural networks Combine Molecular genetics Population genetics Requirements Selection-mutation process Execution model W. Garrett Mitchener (C of C) Discrete ARN July, 22 4 / 37
Utrecht Machine Rationale: Operons Natural operon: space promoter polymerase binding site operator repressor binding site peptide code peptide code space W. Garrett Mitchener (C of C) Discrete ARN July, 22 5 / 37
Utrecht Machine Rationale: Operons Natural operon: space promoter polymerase binding site operator repressor binding site peptide code peptide code space Abstract instruction: j: switch pattern θ: threshold p: pattern q: pattern W. Garrett Mitchener (C of C) Discrete ARN July, 22 5 / 37
Utrecht Machine The Utrecht Machine (UM) State p A p 3 2 3 4 2 5 6 3...... Instructions ) + 6 2) 2 + 6 3) 4 + 6 4) 5 + 6 where n) j θ + p q means If A j θ then add to A p and subtract from A q W. Garrett Mitchener (C of C) Discrete ARN July, 22 6 / 37
Utrecht Machine UM as regulatory network Input NAND 5 Instruction 5 + - 6 4 Output If input is set, add to pattern 4 2 6 3 Instruction 2 + 6 - If activity of 6 is 3 or more, set output ) + 6 2) 2 + 6 3) 4 + 6 4) 5 + 6 W. Garrett Mitchener (C of C) Discrete ARN July, 22 7 / 37
Utrecht Machine Rationale: Complex mutations substitutions W. Garrett Mitchener (C of C) Discrete ARN July, 22 8 / 37
Utrecht Machine Rationale: Complex mutations substitutions deletions W. Garrett Mitchener (C of C) Discrete ARN July, 22 8 / 37
Utrecht Machine Rationale: Complex mutations substitutions deletions duplications W. Garrett Mitchener (C of C) Discrete ARN July, 22 8 / 37
Utrecht Machine Rationale: Recombination W. Garrett Mitchener (C of C) Discrete ARN July, 22 / 37
Utrecht Machine Analysis Detailed case study How are innovations discovered? Important molecular details? Aggregate analysis Appropriate bulk properties? Impact of parameters? W. Garrett Mitchener (C of C) Discrete ARN July, 22 / 37
Case Study Copy(2, ) problem Input Sender Receiver Output 3 3 4 8 2 2 W. Garrett Mitchener (C of C) Discrete ARN July, 22 / 37
Case Study Max score trajectory Max score trajectory 8 6 8 32 4 6 32 8 6 2 6 2k W. Garrett Mitchener (C of C) Discrete ARN July, 22 2 / 37
Case Study Step : first bit Step : Transmission of one bit #2244: ; ; ; Input Sender Receiver Output 3 8 3 4 5 2 2 W. Garrett Mitchener (C of C) Discrete ARN July, 22 3 / 37
Case Study Step 2: partial second bit Step 2: Partial second bit #7245: ; ; ; Input Sender Receiver Output 8 3 4 7 7 3 2 2 4 42 5 W. Garrett Mitchener (C of C) Discrete ARN July, 22 4 / 37
Case Study Step 2: partial second bit Gene history 6563 7) 8 3 2 6658 7) 8 3 2 7576 7) 8 3 2 7) 8 3 2 7845 ) 8 5 3 28 666 ) 8 5 3 28 ) 8 5 3 2 686 6557 ) 8 3 6 ) 8 3 6 662 ) 8 3 6 6252 ) 8 3 6 7584 ) 8 3 6 ) 8 3 44 ) 8 6 3 ) 8 3 44 6) 8 3 5 67542 6) 8 3 5 67744 6) 8 3 5 665 6) 8 3 5 6) 8 3 5 6) 8 3 5 7) 3 5 7) 8 3 5 7) 3 5 7) 8 3 5 7) 8 3 5 W. Garrett Mitchener (C of C) Discrete ARN July, 22 5 / 37
Case Study Step 3: both bits Step 3: Second bit #2682 Receiver Output Input Sender 6 3 3 3 4 3 2 8 3 2 3 6 42 5 4 W. Garrett Mitchener (C of C) Discrete ARN July, 22 6 / 37
Case Study Step 4: both bits + timing Step 4: Also stop on time #225284 Input Sender 8 3 3 6 47 3 2 5 7 3 Receiver 4 7 22 3 4 3 42 5 4 47 2 4 Output 3 6 6 5 3 2 2 W. Garrett Mitchener (C of C) Discrete ARN July, 22 7 / 37
Case Study Step 4: both bits + timing Step 4: Also stop on time #225284 Input Late activation 8 3 3 Early activation 3 5 6 cruft 3 7 Sender 47 2 Receiver 4 7 22 3 4 3 42 5 4 Timing 47 2 4 Output 3 6 6 5 Pre-boost 3 2 2 W. Garrett Mitchener (C of C) Discrete ARN July, 22 7 / 37
Case Study Step 4: both bits + timing Step 4: Also stop on time #225284 5 5 2 W. Garrett Mitchener (C of C) Discrete ARN July, 22 7 / 37
Aggregate analysis Considerations Aggregate analysis & comparison Weak 2 new agents bred from top plus new from whole pop of 5 plus keep top 2 Strong 3 new agents bred from top plus keep top 2 Very strong 3 new agents bred from top plus keep top 2 W. Garrett Mitchener (C of C) Discrete ARN July, 22 8 / 37
Aggregate analysis Considerations Aggregate analysis & comparison Paying attention to: Search time? Genome length? W. Garrett Mitchener (C of C) Discrete ARN July, 22 / 37
Aggregate analysis Comparisons Length vs. Time 25 2 5 5 Weak W. Garrett Mitchener (C of C) Discrete ARN July, 22 2 / 37
Aggregate analysis Comparisons Length vs. Time 25 2 5 5 Strong W. Garrett Mitchener (C of C) Discrete ARN July, 22 2 / 37
Aggregate analysis Comparisons Length vs. Time 25 2 5 5 Very strong W. Garrett Mitchener (C of C) Discrete ARN July, 22 2 / 37
Aggregate analysis Comparisons Fraction of runs with major innovations from outliers..8.6.4.2 With Without W. Garrett Mitchener (C of C) Discrete ARN July, 22 2 / 37
Aggregate analysis Comparisons Weak selection densities Runs with/without outlier major innovations 2 2 5 5 5 5 5 without 5 with W. Garrett Mitchener (C of C) Discrete ARN July, 22 22 / 37
Aggregate analysis Comparisons Tunneling W. Garrett Mitchener (C of C) Discrete ARN July, 22 23 / 37
Aggregate analysis Comparisons Tunneling W. Garrett Mitchener (C of C) Discrete ARN July, 22 23 / 37
Conclusion Lessons Molecular details are important Complex mutations Recombination Network formation mechanisms Chicken-and-egg solutions W. Garrett Mitchener (C of C) Discrete ARN July, 22 24 / 37
Conclusion Lessons Molecular details are important Complex mutations Recombination Network formation mechanisms Chicken-and-egg solutions Weak selection Generally faster Generally shorter solutions Innovation from outliers W. Garrett Mitchener (C of C) Discrete ARN July, 22 24 / 37
Extra stuff Extra stuff W. Garrett Mitchener (C of C) Discrete ARN July, 22 25 / 37
Extra stuff Interesting solutions Shortest genome Run 32 W. Garrett Mitchener (C of C) Discrete ARN July, 22 26 / 37
Extra stuff Interesting solutions Shortest genome Run 32 Input 8 6 Sender 3 4 34 32 3 Receiver 2 Output 2 2 3 4 35 W. Garrett Mitchener (C of C) Discrete ARN July, 22 26 / 37
Extra stuff Interesting solutions Shortest genome Run 32 5 W. Garrett Mitchener (C of C) Discrete ARN July, 22 26 / 37
Extra stuff Interesting solutions Longest genome Run 25 W. Garrett Mitchener (C of C) Discrete ARN July, 22 27 / 37
2 8 2 45 2 26 4 2 6 4 8 3 2 4 6 4 6 3 6 7 44 5 2 3 5 8 7 8 Input Extra stuff 3 6 2 2 38 6 4 3 5 7 3 8 32 2 22 4 7 4 3 Interesting solutions 35 7 26 8 4 2 5 25 8 8 6 4 4 5 7 7 2 52 3 6 2 3 37 44 7 7 Receiver 6 38 3 3 2 8 32 6 8 35 5 2 25 2 4 4 6 62 6 Output 4 6 3 8 Sender 28 Longest genome Run 25 8 4 7 52 3 5 3 3 W. Garrett Mitchener (C of C) Discrete ARN July, 22 27 / 37
Extra stuff Interesting solutions Longest genome Run 25 5 W. Garrett Mitchener (C of C) Discrete ARN July, 22 27 / 37
Extra stuff Synaptic codes Typical / Atypical Codes..8.6.4.2 Atypicalcode Typical code W. Garrett Mitchener (C of C) Discrete ARN July, 22 28 / 37
Extra stuff Timing & Genome length Time to first perfect solution V Str Str Wk 2 3 4 5 6 W. Garrett Mitchener (C of C) Discrete ARN July, 22 2 / 37
Extra stuff Timing & Genome length Genome lengths V Str Str Wk 5 5 2 W. Garrett Mitchener (C of C) Discrete ARN July, 22 3 / 37
Extra stuff Timing & Genome length Time to first perfect solution 6 6 5 6 4 6 3 6 2 6 6 T A T A T A * = all, T = typical codes, A = atypical codes W. Garrett Mitchener (C of C) Discrete ARN July, 22 3 / 37
Extra stuff Timing & Genome length Genome lengths 2 5 5 T A T A T A * = all, T = typical codes, A = atypical codes W. Garrett Mitchener (C of C) Discrete ARN July, 22 32 / 37
Extra stuff Timing & Genome length *Hic* Run 23 W. Garrett Mitchener (C of C) Discrete ARN July, 22 33 / 37
Extra stuff Timing & Genome length *Hic* Run 23 5 W. Garrett Mitchener (C of C) Discrete ARN July, 22 33 / 37
Extra stuff Timing & Genome length *Hic* Run 23 Input 3 8 2 5 7 6 Sender 3 Receiver Output 4 2 2 2 3 3 6 W. Garrett Mitchener (C of C) Discrete ARN July, 22 33 / 37
Extra stuff Timing & Genome length Bee Bop Run 2 W. Garrett Mitchener (C of C) Discrete ARN July, 22 34 / 37
Extra stuff Timing & Genome length Bee Bop Run 2 5 W. Garrett Mitchener (C of C) Discrete ARN July, 22 34 / 37
Extra stuff Timing & Genome length Bee Bop Run 2 Sender 6 2 2 5 5 3 Input 6 48 2 23 2 37 8 3 22 3 4 3 Receiver Output 5 4 2 2 48 2 6 2 5 3 2 W. Garrett Mitchener (C of C) Discrete ARN July, 22 34 / 37
Extra stuff Timing & Genome length Timing repairs 8 6 4 2 6 7 8 6 7 8 6 7 8 after figuring out nth bit W. Garrett Mitchener (C of C) Discrete ARN July, 22 35 / 37
Tools Prelude 2 Utrecht Machine 3 Case Study Max score trajectory Step : first bit Step 2: partial second bit Step 3: both bits Step 4: both bits + timing 4 Aggregate analysis Considerations Comparisons 5 Conclusion W. Garrett Mitchener (C of C) Discrete ARN July, 22 36 / 37
Tools 6 Extra stuff Interesting solutions Synaptic codes Timing & Genome length 7 Tools W. Garrett Mitchener (C of C) Discrete ARN July, 22 37 / 37