Beneficial mutation rates not a problem

I originally posted this in a different thread, but since I continue to see claims that beneficial mutations are too rare to bother with, I thought I'd repost it here (with slight edits) so it would get more attention.

First of all, estimates on beneficial mutation rates are almost non-existent. Even estimates on mutation rates in general are sketchy, so I would caution against drawing any rigorous conclusions from this data. That said, based on the numbers I could dig up, mutations are not a problem for evolution.

The only hard numbers I could find on beneficial mutations were from the paper Fitness effects of advantageous mutations in evolving Escherichia coli populations. The authors estimate the number of beneficial mutations in an E.coli population to be 4x10^-9 per cell and generation. It should also be noted that the authors consider this to be a conservative estimate. So what does this mean? Well, I took an estimate of the number of total mutations in E.coli from the paper Rates of Spontaneous Mutation at 0.0025 per cell and generation. Based on these rates, 1 in every 625000 mutations is beneficial. This may sound like beneficial mutations are ridiculously rare, but keep in mind that E.coli populations are huge (supposedly an individual human poops out between 100 billion and 10 trillion E.coli every single day). Just like winning the lottery may be rare, if enough people play, someone will win.

But let's put this into another context: human evolution. From the same Rates of Spontaneous Mutation paper, the estimated mutation rate for humans is 1.6 mutations per effective genome per sexual generation. Note, I highlighted "effective genome". This is due to the fact that many more mutations occur in humans (typical estimates are over 100), but most are in non-protein coding DNA. But in the E.Coli genome, almost the entire genome is considered the "effective genome". Therefore, for the purposes of this comparison I'm going to compare rates in effective genome only. I should also point out that 1.6 mutations is one of the lower estimates I've seen (some estimates are over 4 per human per generation).

Assuming the same ratio of beneficial mutations to total mutations, this means the rate of beneficial mutations in humans is 2.56x10^-6. How does this affect human evolution? Consider the scenario of human versus chimp evolution. Humans and chimps are estimated to have diverged anywhere from 5 to 10 million years ago. I'm going to go with the lower end of 5 million. If I assume 5 million years of evolution, an average generation time of 20 years, and a stable population size of 100 000 individuals, this means that during that time 64000 beneficial mutations could occur in the human population.

So what does that mean? Well, the estimated difference between human and chimp genomes is typically less than 2% (though one study put the difference between critical genes at only 0.6%). I'll assume 2% in this scenario. Based on the estimated size of the protein-coding portion of the human genome (45 million base pairs; or 30 000 genes @ ~1500 base pairs per gene), we need a difference of 900 000 base pairs. But the chimp line is also evolving, so in the human population we only need to account for half of the difference or 450 000 base pairs.

I also calculated a rough estimate based on the paper DNA sequence and comparative analysis of chimpanzee chromosome 22 and arrived at a 168000 mutation difference in coding DNA between humans and chimps.

Could these mutations account for the difference? Sure, especially given that the 64000 mutations is only based on strictly beneficial mutations and lower end time frame of 5 million years. This doesn't take into account fixation of neutral or even possibly deleterious mutations which could account for many more differences between humans and chimps. Plus, the 64000 mutations is based on a relatively conservative estimate of both beneficial mutation rates and effective mutation rates in humans. Conceivably, there could numbers of beneficial mutations that are magnitudes higher.

So are mutations a problem for evolution? Based on limited and conservative data, the answer is no.

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Creationism has not made a single contribution to agriculture, medicine, conservation, forestry, pathology, or any other applied area of biology. Creationism has yielded no classifications, no biogeographies, no underlying mechanisms, no unifying concepts with which to study organisms or life. - Botanical Society of America's Statement on Evolution

I nominate this for the quiet thread.

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The high, the low, all of creation God gives to humankind to use. If this privilege is misused, God's Justice permits creation to punish humanity~~ Hildegard of Bingen cited in, Earth Prayers from around the World

great post! thanks. if you had rep turned on, you'd be getting some now.

indeed, i could even imagine that most of the changes would be of this type. especially since humans are much more similar to chimps in the protein coding part of DNA (98.5%) than if you consider non-coding portions as well (95%). also, if i remember correctly, there are several different codons that will code for the same amino acid, so you could mutate a base pair and still end up with the same protein. human and chimp proteins are 99% similar. so according to these numbers, beneficial mutations would only need to account for 1% of the difference between chimps and humans, while neutral mutations, which occur much more commonly, can account for the remaining 4% difference. also, keep in mind that this difference between chimps and humans occured partly in the chimp line, and partly in the human line, so there could be only half the genetic distance between humans or chimps and the human/chimp common ancestor, as compared to the genetic distance between humans and apes.

Thank you. But reps are the tool of the devil. You heard it here first.

Actually, I completely ignored non-coding regions of the genomes for the purposes of the comparison and subsequently based everything on mutation rates of coding DNA only. If I took into account all types of mutations based on rates for the entire genome, you'd wind up with literally trillions of possible mutations over the 5 million year period. So yeah, the difference in non-coding regions is a piece of cake.

And yes, I took into account that the lines evolved seperately and therefore one only needs to account for half the genetic distance within a single line.

__________________
Creationism has not made a single contribution to agriculture, medicine, conservation, forestry, pathology, or any other applied area of biology. Creationism has yielded no classifications, no biogeographies, no underlying mechanisms, no unifying concepts with which to study organisms or life. - Botanical Society of America's Statement on Evolution

So soon? Surely you're not expecting creationists to ignore this thread.

__________________
Creationism has not made a single contribution to agriculture, medicine, conservation, forestry, pathology, or any other applied area of biology. Creationism has yielded no classifications, no biogeographies, no underlying mechanisms, no unifying concepts with which to study organisms or life. - Botanical Society of America's Statement on Evolution

*bump*

__________________
Creationism has not made a single contribution to agriculture, medicine, conservation, forestry, pathology, or any other applied area of biology. Creationism has yielded no classifications, no biogeographies, no underlying mechanisms, no unifying concepts with which to study organisms or life. - Botanical Society of America's Statement on Evolution

Excellent thread.

Given all the insufficiency claims against 'naturalistic' means of evolution, it'd be fun to see an IDer or two address this.

Mark Kennedy, where are you?

Facts and figures are involved, so I wouldn't expect to see him any time soon.

Indeed, although one must avoid the common mistake of the opposition who declare victory in the absence of a response.

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"The true index of civilization is how we behave towards people to whom we owe nothing." - Hugo Gryn

*bumpity bump*

__________________
Creationism has not made a single contribution to agriculture, medicine, conservation, forestry, pathology, or any other applied area of biology. Creationism has yielded no classifications, no biogeographies, no underlying mechanisms, no unifying concepts with which to study organisms or life. - Botanical Society of America's Statement on Evolution