Friday, March 18, 2011

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)
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