bFast
Posts: 44
Joined: Mar. 2008
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The question that I present is, how easy is it for natural selection to favor an advantageous point mutation (signal) in light of the various destractions (noise)?
I see noise in four areas:
1 - Allele populations. Organisms, such as myself, consist of a mishmash of alleles that exist within the community of origin. As such, any one individual will not have an ideal mix of alleles. If an organism, such as myself, has the lucky slightly beneficial point mutation, will natural selection be able to favor it dispite all of the other alleles flying around in the population.
2 - New alleles. Each individual organism will be hit with zero to a few mutations within the active DNA. The fact that each organism is de-idealized by these mutations increases the noise, making it more difficult for natural selection to be able to favor a slightly beneficial point mutation.
3 - The fickleness of natural selection. In two given contexts natural selection will favor different alleles. For instance, I am more intelligent than most. As such, I have a good allele set wrt intelligence. I am decidedly less athletic than most. As such, I don't have a good allele set wrt athletics. If a given opportunity for selection involves me and a friend trying to outrun a hungry bear, in all likelihood my above average intelligence will do me no good, and I'll be lunch. To make matters worse, I think that natural selection is probably best at ignoring allele mixes altogether, and causing one to be removed from the pool for no reason other than being in the wrong place at the wrong time.
4 - Bulk-editing. Alleles come with an entire gene full of baggage. Our dear lucky mutation has to happen within an existing allele. This existing allele may not be a rising star. Now a new allele exists which may be marginally better than its falling star cousin, but may not be sufficiently advantageous to beat out other alleles floating around in the population. When organisms such as myself produce offspring, we generally exchange genetic data in bulk units called chromosomes. So even if a gene is a particularly good one, I think that the fact that it is packaged up in a chromosome presents a challenge.
Now, I have produced a simulation that selects out issue number 1. The question is, is noise source 1 in itself sufficient to disable natural selection for a slightly beneficial mutation?
My sim's algorithm is as follows:
Initialization accepts 3 parameters: gene count, population, mutant count.
- Per population, I create an organism
- Per organism, I create an array of 'gene count' elements.
- Each element is initialized with a random 0 or 1, representing allele #0 or allele #1 where we assume that the #1 allele is 'fitter' than #0.
- Each element is given a 'fitness' number -- the total of 1's in its genes.
- for 'mutant count', organisms are selected at random, and the first gene is boosted to allele #2. The 'fitness' number is adjusted.
Processing accepts 1 parameter: cycles and returns the total number of active mutants.
- Per cycle:
- two organisms are selected at random
- the less fit of the two is decomissioned, and replaced by:
- two organisms are selected at random
- through the genes of these organisms, either the first or 2nd organism's allele will be selected.
- the 'fitness' of the new organism is measured.
One "generation" is considered to be Population cycles (on average, the death/replacement of each individual.)
The general results of my sim are as follows (I haven't run lots of simulations yet, nor have I done careful logging yet.):
- when there are 200 alleles per organism, the mutant dies very about 9 times out of 10. If the mutant lives to get about 20 organisms to contain it, it rather quickly becomes fixed. Dying or fixing doesn't seem to have much to do with population.
- when there are 2000 alleles per organism, the mutant dies rather often, often enought that I have skipped past early processing and seeded the system with multiple mutants. If it has 50 mutants in a 1000 population, the mutant usually survives, and fixes rather quickly.
- when there are 20,000 alleles per organism, the population of the mutant seems to wander like it is influenced by the throwing of a dice -- genetic drift. I have been seeding with 100 in a population of 1000, and have yet to be able to get it to fix.
NOTE: As all allele 1s are motivated to increase in popularity, one may consider that a bunch of them have fixed within this process. As they fix, the amount of noise, the number of alleles in the population decreases. I have not yet measured the number of fixed alleles in the calculation, but I suspect that with the small counts, the reason NS grabs the beneficial mutation so solidly at some point is because the noise has significantly decreased.
Now, in real world organisms, there is (almost) always an abundance of available alleles. In fact, when there are not, it is conserning. This is caused, of course, by other organisms obtaining mutants that have infiltrated the population. Populations always have many alleles, so the mutant of interest fixing because all of the nearby alleles fixing is an artificial situation.
A major question that I have as I present this sim is, how many alleles are there in a population. I could envision that there are a whole lot. I know that I contain 2 sets of genes, each set has 25,000 coding genes. My wife also has 2 sets of genes. So between the two of us, let alone our neighbors, we have 100,000 coding genes. But, for how many of those genes is there only one allele within the population? For how many of those genes are there literlally hundreds of alleles? Bottom line, how many alleles are disguising my lucky beneficial mutation. My sim suggests that somewhere less than 20,000 is too many, that it produces too much noise for natural selection to filter out, when selecting a beneficial point mutation -- and that, dispite the other sources of noise as described above.
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