Evolution as Computation: DIMACS Workshop, Princeton, January 1999Laura F. Landweber, Erik Winfree The study of the genetic basis for evolution has flourished in this century, as well as our understanding of the evolvability and programmability of biological systems. Genetic algorithms meanwhile grew out of the realization that a computer program could use the biologically-inspired processes of mutation, recombination, and selection to solve hard optimization problems. Genetic and evolutionary programming provide further approaches to a wide variety of computational problems. A synthesis of these experiences reveals fundamental insights into both the computational nature of biological evolution and processes of importance to computer science. Topics include biological models of nucleic acid information processing and genome evolution; molecules, cells, and metabolic circuits that compute logical relationships; the origin and evolution of the genetic code; and the interface with genetic algorithms and genetic and evolutionary programming. |
Contents
Genome System Architecture and Natural Genetic Engineering | 1 |
Evolutionary Computation as a Paradigm for DNABased Computing | 15 |
A Paradigm for the Maturation of the Humoral Immune Response | 41 |
The Evolutionary Unfolding of Complexity | 67 |
Biologically Inspired Computation That Creatively Solves Nontrivial Problems | 95 |
Is Ours the Best of All Possible Codes? | 125 |
The Impact of Message Mutation on the Fitness of a Genetic Code | 140 |
Genetic Code Evolution in the RNA World and Beyond | 160 |
The Example of Bacteriophage T7 | 201 |
Using Artificial Reagents to Dissect Cellular Genetic Networks | 210 |
Computational Aspects of Gene UnScrambling in Ciliates | 216 |
Universal Molecular Computation in Ciliates | 257 |
Toward in vivo Digital Circuits | 275 |
Evolution of Genetic Organization in Digital Organisms | 296 |
Toward Code Evolution By Artificial Economies | 314 |
Mechanism and Evolvability | 179 |
Other editions - View all
Evolution as Computation: DIMACS Workshop, Princeton, January 1999 Laura F. Landweber,Erik Winfree No preview available - 2012 |
Evolution as Computation: DIMACS Workshop, Princeton, January 1999 Laura F. Landweber,Erik Winfree No preview available - 2011 |
Common terms and phrases
activation affinity agents amino acids anticodons antigen aptamers arginine behavior binding Biol biological cells CH₂ ciliates circuit codon codon position coli complex components configuration constellation create crossover denoted distribution DNA computing dynamics encoding entropy Evol evolution strategies evolutionary algorithms Evolutionary Computation evolved example expression filter fitness functions frequency gene genetic algorithms genetic code genetic programming genome genotypes graph H₂N-C-H Hayek2 hi-excision/reinsertion hypermutation IESS individual inductors initial input instruction interactions inverted Koza lambda macroscopic maximum clique problem MDSS mechanism micronuclear molecular molecules multiple mutation Natl nodes nucleotide operator optimization organisms output pair pattern phage phenotype pointer population portal problem Proc promoter protein random recombination repressor RNA polymerase scrambled selection sequence signal simulation solution specific stack stereochemical strands string structure structure-preserving subbasin subtree synthesis telomere tion transcription translation unscrambling