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

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Joined: Sep. 2006

(Permalink) Posted: June 17 2009,19:39   

Quote (sledgehammer @ June 17 2009,16:39)
Sanford: A setting of 1.0 means that a single mutation can double fitness - creating as much biological functionality as the entire rest of the genome.

I don't buy that argument either.
This is from:
J. Sanford, J. Baumgardner, W. Brewer, P. Gibson, and W. Remine. Mendel's Accountant: A biologically realistic forward-time population genetics program. SCPE. 8(2), July 2007, pp. 147-165.
3.2. Prescribing Fitness Effects of Mutations. ...These scale factors are meaningful relative to the initial fitness value assumed for the population before we introduce new mutations. In Mendel we assume this initial fitness value to be 1.0. For deleterious mutations, since lethal mutations exist, we choose dsf del = -1.
For favorable mutations, we allow the user to specify the (positive) scale factor dsf fav. Normally, this would be a small value (e.g., 0.01 to 0.1), since it is only in very special situations that a single beneficial mutation would
have a very large effect.

Seems to me that if the scale factor for deleterious mutations of -1 represents lethality, (i.e. no chance of reproduction), then it's inverse for beneficial mutations, +1, would represent guaranteed reproductive success, not "doubling of fitness".

Relative fitness compares different genotypes in a population, and is defined as the ratio of the average numbers contributed to the next generation with one genotype set arbitarily at 1. So if genotype-A contributes 300 and normal genotype-B contributes 200, then genotype-A has a relative fitness of 1.5 compared to genotype-B. Relative fitness can be most any non-negative number.

Absolute fitness is calculated for a single genotype as simply the ratio of the numbers in the new generation to the old after selection. So if the population of the genotype increases from 100 to 200, then it has an absolute fitness of 2. Again, absolute fitness can be most any non-negative number.

I've been trying to independently implement Mendel's Accountant, but keep running into such definitional problems. Heritability. Fitness. And how they're handling probability selection. I'm working with a simplified model, but Mendel's Accountant should be able to handle the simple cases with obvious results.

I'm assuming that if fitness increases by 1, then it goes from 1 to 2 (100% increase), or from 2 to 3 (50%) and so on. It shouldn't be additive, but multiplicative so it scales. Sanford's complaint is that if we use multiplicative, then it can never reach zero. So he is clearly assuming his conclusion.

It's not easy to resolve some of these problems. If we scale fecundity with fitness, then that solves the problem of very low fitness. But introduces a problem if the fitness levels climb so that we may be radically multiplying the reproductive rate.

Of course, "generation" is an abstraction, so it may represent an undefined breeding season. Frankly, the whole thing is an abstraction, so any strong claims about the specifics of biology are invalid anyway.


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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