Path: utzoo!attcan!uunet!husc6!ukma!uflorida!novavax!proxftl!tomh From: tomh@proxftl.UUCP (Tom Holroyd) Newsgroups: sci.bio Subject: Genetics Message-ID: <247@proxftl.UUCP> Date: 1 Jun 88 17:19:48 GMT Organization: Proximity Technology, Ft. Lauderdale Lines: 79 This is from sci.physics, where it grew from a discussion of molecular modeling.. In article <1617@vaxb.calgary.UUCP>, radford@calgary.UUCP (Radford Neal) writes: ]Well, I've just gone out and (to some extent) read Holland's book ]("Adaptation in Natural and Artifical Systems"). I'll summarize ]his main algorithm, since this will illuminate the roles of cross-over ]and mutation. ] ]You've got a bunch of potential structures (e.g. organisms), each of ]which has a "goodness" (e.g. fitness). You're trying to find the ]best structure. You maintain a "population" of structures, and apply ]the following algorithm: ] ] 1) Fill the population up with randomly-chosen structures. ] ] 2) Repeat: ] ] a) Randomly select two structures, X and Y, from the population, ] biasing your selection in favour of "better" structures. ] ] b) Compute a new structure, Z, from X and Y. ] ] c) Add Z to the population, deleting a randomly (uniformly) chosen ] structure to make room. ] ]Structures are represented by linearly-ordered attributes (e.g. alleles ]of genes). Step (b) is accomplished as follows: ] ] A) For each attribute of X, randomly change it with some (rather ] low) probability (Mutation). ] ] B) Sometimes do the following: Randomly select a segment of X and ] reverse the order of attributes within it (Inversion). ] ] C) Sometimes do the following: Randomly select a segment of X and ] replace its attributes with the analogous attributes of Y (Cross- ] over). ] ]The resulting modified X is what is called Z in step (b). ] ]Roughly, the roles of (A) to (C) are as follows: ] ] (A) Mutation: ensures that no attribute disappears entirely from the ] population, or constantly cycles in new attributes if the ] number of possibilities is greater than can be held at once ] in the population. ] ] (B) Inversion: Moves around attributes so that closely-related ones ] can form closely-linked groups. ] ] (C) Cross-over: Combines attributes from various successful structures ] in a fashion that is unlikely to break up closely-linked groups. ] ]It all sounds very plausible. I may try it out soon on my current ]intractible optimization problem. ] ] Radford Neal I have two questions for all you genetic engineers (I hope this is the right place to post this): 1. Is this model of genetic evolution in keeping with current biological thinking? (I know it's incomplete, I just want to know if it's crazy.) 2. It doesn't address the growth of chromosomes, or the creation of new ones. In fact, it doesn't talk about chromosomes at all. What can you say about a) where chromosomes "come from", and b) does their structure play a role in evolution (as the term 'crossover' seems to imply)? For b), it seems that keeping genes for different organs on distinct chromosomes would be an advantage, since you wouldn't be wasting time crossing eyeballs and fins. This is probably a simplistic view, but.. Tom Holroyd UUCP: {uunet,codas}!novavax!proxftl!tomh The white knight is talking backwards.