nothing in biology makes sense except in the light of evolution

I've been reading Mike Yarus's book: Life from an RNA world (Amazon). It's a very readable account of evolution from the perspective of sequences and the RNA world. Mike's a highly intelligent guy, and that and his wit inform every page. In one chapter, he gets Rob Knight and Steve Freeland to do an evolution simulation.

we let a computer write out a random string, mutate 1 in 100 characters in each generation, and select changes only if they match Dobzhansky

In my version:

in each generation we pick one position

if it already matches Dobzhansky, continue to the next generation

mutate to a random choice from the set of symbols

This isn't a very good model of evolution. It was just fun to spend a few minutes coding it.

Here is the beginning, middle and end of one run:

> python evolve.py 0 LVSTUknwIfGIRHFgHESZ M zthWtNQTk qgtoeMvjeJAzOidKWEZO ZwNjDyCvq 100 LVSTUknwIfGIRHFgHESZ M zthetNQTk qgtoeMvjeJAzOidKWEZO ZwNjDyCvq 200 LVSTUknwIfGIRHFgHESZ M zthetNQTk qgtoeMvjeJAzOidhWEZO ZwNjDyCvq 300 LVSTiknwIfGIRHFgHESZ M zthetNQ k qgtoeMvjeJAzOidhWEZO ZwNjuyivq 6100 notTing if biHlogy makes sense except iv the Oight of Zvolution 6200 notTing if biHlogy makes sense except iv the Oight of Zvolution 6300 nothing if biHlogy makes sense except iv the Oight of Zvolution 6400 nothing if biHlogy makes sense except iv the Oight of Zvolution 13800 nothing in biHlogy makes sense except in the light of evolution 13900 nothing in biHlogy makes sense except in the light of evolution 14000 nothing in biHlogy makes sense except in the light of evolution 14100 nothing in biHlogy makes sense except in the light of evolution 14167 nothing in biology makes sense except in the light of evolution 14167 nothing in biology makes sense except in the light of evolution

import random s = 'nothing in biology makes sense' s += ' except in the light of evolution' N = len(s) symbols = 'abcdefghijklmnopqrstuvwxyz ' symbols += symbols.upper() L = [random.choice(symbols) for i in range(N)] print ' 0 ' + ''.join(L) i = 0 while L != list(s): i += 1 v = i and not i % 100 if v: print str(i).rjust(5), j = random.choice(range(N)) if L[j] == s[j]: if v: print ''.join(L) continue c = random.choice(symbols) if c == s[j]: L[j] = c if v: print ''.join(L) print print str(i).rjust(5), s print str(i).rjust(5), ''.join(L)