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  Topic: Evolutionary Computation, Stuff that drives AEs nuts< Next Oldest | Next Newest >  

Posts: 2723
Joined: Sep. 2006

(Permalink) Posted: June 11 2009,14:12   

Quote (AnsgarSeraph @ June 11 2009,11:41)
Quote (Wesley R. Elsberry @ June 11 2009,11:29)
So, how much "evolution sucks" verbiage was generated by the people running the pre-1.4.1 versions? Was there any notice that people should re-run their experiments due to a pretty drastic change in program behavior?

To be fair (to a shoddy program? How odd), v. 1.4.1 still "demonstrates" all the genetic entropy problems that Sanford makes noise about. Whatever they fixed in terms of beneficial mutations, our runs at TWeb using 1.4.1 indicate that it's nowhere near enough; a 90% beneficial mutation rate with default "maximal benefit effect" still reduces fitness in a linear manner.


I think a key to understanding Mendel's Accountant is the so-called "Maximal beneficial mutation effects". It defaults to an extremely low number.

Mendel's Accountant User Manual: Maximal beneficial mutation effects – A realistic upper limit must be placed upon beneficial mutations. This is because a single nucleotide change can expand total biological functionality of an organism only to a limited degree. The larger the genome and the greater the total genomic information, the less a single nucleotide is likely to increase the total. Researchers must make a judgment for themselves of what is a reasonable maximal value for a single base change. The MENDEL default value for this limit is 0.001. This limit implies that a single point mutation can increase total biological functionality by as much as 0.1%. In a genome such as man’s, assuming only 10% of the genome is functional, such a maximal impact point mutation might be viewed as equivalent to adding 300,000 new information-bearing base pairs each of which had the genome-wide average fitness contribution. Researchers need to honestly define the upper limit they feel is realistic for their species. However it should be obvious that, in all cases, the upper limit for beneficial mutation effects ought to correspond to a very small fraction of the total genomic information (i.e. a small number relative to one).

There is something wrong with the analysis. They're comparing the selective value of a change to adding thousands of new bases to the genome. But adding 10% to a genome doesn't necessarily make an organism 10% fitter. On the other hand, a small change can often have a very high selective value. Consider a mutation making someone resistant to plague. Maybe he just tastes bad to fleas.

Also, I'm not sure what the number is supposed to represent. Does a value of 1 mean a change in fitness of 1? Shouldn't this scale with absolute fitness? Or is it a fractional? So does 1 represent 100% or a doubling of fitness? PS. I'm guessing the former, but my Accounting time has been somewhat limited.


You never step on the same tard twice—for it's not the same tard and you're not the same person.

  419 replies since Mar. 17 2009,11:00 < Next Oldest | Next Newest >  

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