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



Posts: 533
Joined: Sep. 2008

(Permalink) Posted: June 16 2009,14:42   

Quote (Zachriel @ June 15 2009,19:00)
         
Quote
John Sanford: That is easily re-set, but one has to consider if it is reasonable to realistically build up a genome by increments of 10% (I am speaking of internal complexity - not adaptation to an external environmental factor). I think that is like going up Mt. Improbable using a helicopter.

Which goes to show that he doesn't understand his own simulation. Mendel's Accounant doesn't model "internal complexity". It purports to abstract selective differences.

A specific limit to beneficial mutations may not make sense. Some mutations may sweep over a population rapidly. It is certainly conceivable that a seemingly minor mutation could dramatically increase reproductive success, perhaps many-fold, such as when there is only one male that reproduces.

I think it is even worse that that Zach, for three reasons:

Firstly, the parameter in question is the "maximal fitness effect of a beneficial mutation". This has nothing to do with the physical makeup of the genome, as Dr Sanford seems to imply.  It seems absurd to link this parameter to some implication of "affected base pairs", much less some inferred "infusion of information" into the genome, as the description of this parameter in the MA manual below seems to imply:
         
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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).


Call me cynical, but when this much handwaving is applied to a point,  I suspect it means that this is a crucial parameter when it comes to justifying the conclusion that "genetic entropy" leads inevitably to genetic meltdown.

Secondly, there seems to be no reason to limit the maximal fitness effect of a beneficial mutation to a very small number.  Clearly, as pointed out by Z and others, in a competitive environment, there seems to be no reason a single beneficial mutation cannot virtually guarantee reproductive success. In other words, why can't the maximal fitness benefit of a beneficial mutation be something close to unity?

Lastly, the parameter in question is implemented as a scale factor on the probability distribution of fitness effect, which, for no apparent reason, is hard coded to be identical to the shape of the PDF of fitness effects of deleterious mutations  (whose scale factor is hard coded to be -1, i.e. instant death).
 The effect of this fitness effect PDF scaling is even more significant when one considers that the PDF shape is already heavily skewed so that the vast majority of mutations fall "under the radar" of selection. So now, all beneficial mutations are 1000-fold (default value 0.001) less likely to become fixed in the population through selection, hard or soft.  That seems unrealistic to me, so say the least.

To mitigate the above bias against beneficials,  I recommend setting the maximal beneficial fitness parameter close to unity, which will symmetrize the fitness effect probability distribution, and then play with the parameter that determines the proportion of beneficial mutations ( i.e. set the ratio of beneficial to deleterious mutations to .001 or whatever).
 My guess is that this will "level the playing field" and have a significant effect on the overall fitness trend.

Maybe someone who has MA up and running (Zach, Sam?) could try this and report?

P.S. I occurs to me that the PDF shape symmetry might also help account for the effects of the mutational "flipping" of deleterious to beneficial and vice versa.

ETA clarification: "be fixed by selection" is now "become fixed in the population through selection"

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The majority of the stupid is invincible and guaranteed for all time. The terror of their tyranny is alleviated by their lack of consistency. -A. Einstein  (H/T, JAD)
If evolution is true, you could not know that it's true because your brain is nothing but chemicals. ?Think about that. -K. Hovind

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

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