2. Genetic Programming and Biology 신수용

2.1 Minimal requirements for Evolution to Occur u Four essential preconditions for the occurrence of evolution by natural selection  Reproduction of individuals in the population  Variation that affects the likelihood of survival of individuals  Heredity in reproduction  Finite resources causing competition

2.2 Test Tube Evolution - A study in Minimalist Evolution u Evolution occurs even in simple non-living systems, such as in vitro(test tube) environments  enzyme Q  replicase and RNA [Orgel 1979] l The structure and function of the RNA in the test tubes evolves l The mix of RNA in the last test tube varies l Different initial conditions result in a final mix specifically adapted to those conditions l the RNA that evolves in these test tube experiments would have been extremely unlikely to evolve by random chance  demonstration of the poser of simple evolutionary search  SELEX by Teurk and Gold l diverse population l affinity column -> fitness function l iterative in vitro selection

2.2 (2) u Lessons for GP  A simple system may evolve as long as the elements of multiplication, variance, and heredity exist  Evolutionary learning may occur in the absence of life or of self-replicating entities  Evolutionary learning may be a very efficient way to explore learning landscapes  Evolution may stagnate unless the system retains the ability to evolve  The selection mechanism for evolutionary learning may be implicit in the experimental setup(Orgal) or may be explicitly defined by the experimenter(SELEX) u Evolution is not the complexity itself  Occam’s Evolutionary Razor

2.3 The Genetic Code - DNA as a Computer Program u DNA  the principal constituent of the genome, may be regarded as a complex set of instructions for creating an organism  3 DNA base pairs -> codon l codes for the production of an amino acid  sequences of codons code for the assembly of amino acid -> RNA, polypeptides(protein fragments), proteins, functional RNA  -> organisms

2.3.1 The DNA Alphabet u Four different bases appear in DNA  A(adenine), G(guanine), C(cytosine), T(thymine)  A = T, G  C

2.3.2 Codons and Amino Acid Synthesis u Codon  three consecutive RNA bases  template for the production of a particular amino acid or a sequence termination codon  ex) ATG -> methionine  ex) CAA, CAG -> glutamine  ex) TAA -> termination  4 3 = 64 different codons  but, only 20 amino acid l several different codons that produce the same amino acid l redundancy

2.3.2 (2) u Redundancy in DNA (in GP views)  The efficiency of different codons in producing the same amino acid can vary widely from codon to codon. l Random mutation ( 구성은 바뀌지만 단백질은 큰 변화 없음 )  neutral mutation l 동일한 단백질을 만드는 다른 핵산으로 변화 u DNA polarity  DNA not only has instructions with specific meanings, the instructions have an implicit order of execution also

2.3.3 Polypeptide, Protein, and RNA Synthesis u DNA transcribes RNA molecules

2.3.4 Genes and Alleles u Adjacent sequences of DNA do act together to affect specific traits, DNA at widely scattered places on the DNA molecule may affect the same trait u The portions of the DNA that engage in transcriptional activity are separated by long sequences of DNA(junk DNA) u The portions of DNA that engage in transcriptional activity are located in the regions between the long junk DNA sequences.  Exons : transcribe for proteins  Introns : junk DNA  recombination 시 정보를 보존하는 역할 u DNA’s functions are much more complex than the translation of polypeptides and proteins

2.3.5 DNA without Function - Junk DNA and Introns u GP 에서도 중요한 역할  Ch 7 참조

2.4 Genomes, Phenomes and Ontogeny u In 1909, Johannsen: phenotype and genotype u Genotype  the DNA of that organism  genetic changes: mutation, recombination u Phenotype  set of observable properties of an organism  natural selection u Ontogeny  the development of the organism from fertilization to maturity

2.4 (2) u In GP views  Evolution is possible even where there is no physical difference between the genotype and the phenotype  Evolution is possible with or without ontogeny

2.5 Stability and Variability of Genetic Transmission u Genetic transmission must be simultaneously stable and variable

2.5.1 Stability in the Transmission of Genetic Material u Principal mechanisms of stability  Redundancy  Repair  Homologous Sexual Recombination l recombination’s most vital function is probably the repair of damaged DNA

2.5.2 Genetic Variability u 3 principal forces  mutation l changes from one bp to another l additions or deletions of one or more bps l large DNA sequence rearrangements  Homologous and Non-Homologous Genetic Transfer in Bacteria l Hfr Conjugation l Transposons  Homologous Sexual Reproduction

2.5.3 Homologous Recombination u Mutation causes random changes in DNA u Homologous exchange encourages changes in DNA of a very narrow and specified type u Homologous exchange conditions  can only occur between two identical or almost identical DNA segments  can occur only if the two DNA segments to be exchanged can be matched up so that the swap point is at functionally identical points on each strand u non-homologous recombination is nothing more than a massive mutation u GP crossover is clearly NOT homologous

2.6 Species and Sex u In asexual populations, mutation is the primary driving force of evolution  most mutations are damaging to the organism  Muller’s rachet l mutation 이 진행됨에 따라 더욱 나빠짐 u Sexual recombination 장점  allows the species to combine numerous favorable mutations into one individual much more rapidly than asexual reproduction  probably ameliorates the effect of Muller’s rachet