evolution calculations

You gave your answer in your question: It give us the mutation rate as determined by comparing human and chimp DNA. It doesn't necessarily "promote" the TOE, it is based upon the TOE, since it assumes common ancestry for human and chimp. Importantly, nothing in the study falsifies the TOE.Most evolutionary genetics research does not "promote" the TOE in the sense that it states "our data alone shows the TOE to be correct". Generally such research is gathering and analyzing data, adding detail to an already enormous amount of data that collectively supports the TOE.

No. Hardy-Weinberg is a theoretical model (with lots of assumptions and limitations) that shows how alleles can become fixed in a population.OTOH, Orr's equations can show how cumulative mutations can result in hybrid incompatibilities leading to speciation that absolutely guarantees evolution happens. Since I have no clue how to post complex equations here, I can only reference the article where he puts forward his theoretical model:H. Allen Orr, 1995, "The Population Genetics of Speciation: The Evolution of Hybrid Incompatibilities", Genetics 139:1805-1813

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Speciation often results from the accumulation of complementary genes, ie., from genes that, while having no deleterious effect within species, cause inviability or sterility when brought together with genes from another species. Here I model speciation as the accumulation of genic incompatibilities between diverging populations. Several results are obtained. First, and most important, the number of genic incompatibilities between taxa increases much faster than linearly with time. In particular, the probability of speciation increases at least as fast as the square of the time since separation between two taxa. Second, as Muller realized, all hybrid incompatibilities must initially be asymmetric. Third, at loci that have diverged between taxa, evolutionarily derived alleles cause hybrid problems far more often than ancestral alleles. Last, it is easier to evolve complex hybrid incompatibilities requiring the simultaneous action of three or more loci than to evolve simple incompatibilities between pairs of genes. These results have several important implications for genetic analyses of speciation.

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IOW, speciation has to happen.

Hardy-Weinberg certainly models evolution, albeit in a simple way, in terms of changes in allele frequency. It doesn't suggest that any evolution other than allelic frequency changes should occur.TTFN,WK

I think the contrary. With genetic drift and constant mutations occuring I think there must be a selective pressure there to mantain and organisms form. The pressue is, however, to stay where it is. This would be true if it at an adaptive peak in a reasonably constant environment.

That's certainly what I thought it did, but what other evolution were you thinking of? Doesn't "allelic frequency changes" pretty much cover it?

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No. Hardy-Weinberg is a theoretical model (with lots of assumptions and limitations) that shows how alleles can become fixed in a population.

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No, Hardy-Weinberg says nothing about fixation of alleles. It just tells you (in a particular model), what the relationship is between allele frequencies and genotype frequencies (i.e. how many heterozygotes and homozygotes you'll find given an allele frequency). One of the assumptions of H-W is that of an infinite population size, so that genetic drift does not occur.

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IOW, speciation has to happen.

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In a particular model. Models are not reality, and are only valid to the extent to which they have been tested against reality.

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I think the contrary. With genetic drift and constant mutations occuring I think there must be a selective pressure there to mantain and organisms form. The pressue is, however, to stay where it is. This would be true if it at an adaptive peak in a reasonably constant environment.

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Right. Or you could specify a model in which any genetic change is fatal, in any environment. That leads either to stability or extinction (which is a sort of stability, I suppose), depending on whether the environment changes significantly.

"The conventional view of evolution is that, though the action of natural selection, organisms have come to exhibit those characteristics that best enable them to survive and reproduce in their environments. The fact that, in standard evolutionary theory, it is alwyas changes in organisms rather than changes in environments that are held responsible for generating teh organism-environment "mathching" relationship is made explict by the terms used to describe the process of evolutionary change itself, "adaptation." Organisms are assumed to adapt to their environments, but environments are not assumed to "adapt" to their organisms. The same term, however, is used to describe the every changing products of natural selection, the "adaptations' that organisms exhibit. This double usage of "adaptation" provided the clearest possible indication that the process of adaption, whereby organisms respond to their environments, is usually regarded as the only process thought to be capable of generating complementarity between organisms and environment in evolution.One consequence is that, hitherto, the most commone evolutionary approaches to the study of humans have been "adaptationist" in nature, in the sense that they have placed sole emphasis on the process of selectionand on purported adaptations that underlie human behavior (Laland and Brown 2002). Sociobiologists and evolutionary psychologists provide explanations for the characteristics of human behavior, human relationships, and human instiutions in terms of natural seleciton's furnishing our ancestors with functional solutions to problems posed by ancestral environments. Hence, any match that is observed between the characters or features that humans posses and the factors in the environments that thier ancestors experienced is assumed to ahve come about by either chance of exclusively through natural selection^1. Yet, in chpater 2, we saw that niche construction provides a second evolutionary route to the dyanmic match between organism and environment."in Niche Construction, The Neglected Process in Evolution byOdling-Smee,Laland and Feldman.

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Hardy-Weinberg certainly models evolution, albeit in a simple way, in terms of changes in allele frequency. It doesn't suggest that any evolution other than allelic frequency changes should occur.

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I don't think H-W models evolution at all. It just shows the relationship between alleles and genotypes in a population with random mating, large population size, no selection, etc. The genotypic frequencies may change, but not the allelic frequencies.Now, variations of H-W certaintly do show allelic frequency changes. These are the ones that include selection coefficients, genetic drift coefficients, mutation rates, etc. I'm not sure if these are considered H-W theorems, since I thought H-W specifically referred to H-W equilibrium.If you were referring to the latter, then this is just semantics since I can see how one could consider the equations which involve the different coefficients H-W theorems.

You're right, I misspoke. H-W deals with allele frequencies and how they change over time leading to specific ratios (equilibrium). It also shows that a variant can never be lost from a population once it's there. Among others like completely random mating, non-overlapping generations, no mutation, no immigration/emigration, and no natural selection (although you can add a selection coefficient to H-W and get a reasonable result that still fits with the original equations). Right. That's why I'm not a theoretician. I prefer to use models that at least attempt to reflect something like reality. H-W doesn't reflect reality, Orr comes a bit closer but he's dealing with something completely different than the basic pop-gen equations.

You are right of course, Ned, I was too casual in my formulation. There must be non-zero selective pressure. It's just that it weeds out changes in a constant environment, instead of weeding out maladaptation in a changing environment.Dawkins ("The Blind Watchmaker", chapter 9) has it thus:

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[...] if lineages go for many generations in the wild without changing, this is not because they resist change {something that was discussed earlier, P.} but because there is no natural selection pressure in favour of changing {emphasis mine, P}. They don't change because individuals that stay the same survive better than individuals that change.

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I guess I initially oversaw the phrase "in favour of changing".The late Mayr ("What Evolution Is", appendix B, item 12: "How can long-lasting stasis be explained?") had this to say on the subject:

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Stasis apparently indicates the possession of a genotype that is able to adjust to all changes in the environment without the need for changing its basic phenotype. To explain how this is done is the task of developmental genetics.

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We are all atheists about most of the gods that humanity has ever believed in. Some of us just go one god further. - Richard Dawkins

I think I see a way of getting some sort of equation for you. You said

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i saw that research which determined that the mutation rate in humans is 175 neutral mutations, 3 deleterious, and a few beneficial.

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This is for a diploid genome, so 175 mutations in 6 billion bases. The chimp genome is about the same size. I'm not sure what the chimp mutation rate is, but let's assume that it is about 175 mutations per generation per diploid genome. I'm sort of going out on a limb, but lets use 15 years as the chimp generation time and 30 years for humans. Let's also use the range of 5-7 million years since the chimp lineage and the human lineage separated. A lot of assumptions, I know, but I think they are all pretty reasonable.From this, we would expect that the difference between the chimp genome and the human genome would be within the range of the mutation rate, realizing of course that natural selection and genetic drift will eliminate some mutations.So, for humans we get:(low range)
5x10^6/30= 166,666 generations
166,666 x 175 mutations = about 29 million mutationsHigh range (skipping the write up) = about 41 million mutationsFor chimps (it would be double of the human range due to the generation time):low range = 58 million
high range = 82 millionSo combined (adding together the mutations in humans and the mutations in humans) we would expect between 87 million and 123 million bases to be different. Of course, not all mutations are point mutations, but for the moment let's pretend they are since these would make the smallest difference.What is the difference between the chimp and human genome? 1.3% different. For a diploid genome of 6 billion, a difference of 1.3% is 78 million mutations, well within the measured mutation rate even if detrimental mutations are subtracted out.Someone may nit-pick my assumptions (or math, might want to double-check it), but I think this is a reasonable assessment. The differences between man and chimp can be favorably compared with the measured muation rate. If nothing else, it is a fun little excersize.This message has been edited by Loudmouth, 02-08-2005 17:30 AM

There's a question I've been wanting to ask that goes to the issue of "Use of Language".One quote that's come up here is... With your background and grounding in math, can you tell me which is larger, 3 or a few?

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Aslan is not a Tame Lion

I think I have all of the pop genetics stuff I learned classified in my head under Hardy-Weinberg. You are right of course that there is not any change in allele frequency in fact the whole point of H-W equilibrium is that there is no significant change in allele frequency.My bad.TTFN,WK

That, and the fact that under any of the H-W equations + additional coefficients no allele is ever lost in a population. Ever.