Why is evolution so controversial?

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The human and chimpanzee genomes differ in single-base substitutions at a rate of 1.23%. The single-base mutation rate is currently estimated to be roughly 1.1 x 10^-8/bp/gen. Using your other values, that gives t = 7.2 million years.

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As I understand the paper at Estimate of the Mutation Rate per Nucleotide in Humans | Genetics | Oxford Academic, (k) is estimate under a neutral model for total divergence between chimps and humans (their number 1.33%). Mutation rate by empirical measurement was found to be ~70 new mutations per generation (that is a mutation rate of 1.1 x 10^-8 mutations in the diploid genome per generation) that would be (u).The calculation they preformed estimating mutation rate was based on effective ancestral population (Ne), specie divergence and time of divergence being 5.6 million years. This produced a calculated mutation rate of ~175 mutations per generation (u) or(2.5 x 10^-8) to time of divergence. This is about twice the measured mutation rate in humans.You claim mutation rate of indels to be 1/7 that of substitutions, that would be ~ 10 per generation.This would give a new mutation rate of (1.3 x 10^-8) per generation. This has nothing to do with the (k).

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If you want to include indels, you have to increase the divergence by one-seventh. Unfortunately, we don't have a good independent estimate of the indel mutation rate, but a rate 1/7th that of substitutions is completely plausible.

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That is fine, I accept 1/7 that of the empirical value for substitutions.The actual value calculated for the generations from divergence did not change that much. Sorry.Edited by zaius137, : No reason given.Edited by zaius137, : correction...

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Just to select one: Are you even aware of what the so-called mitochondrial Eve really represents?

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Perfect time to present your understanding. I am familiar with the evo perspective but my personal view differs somewhat.

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If you use different numbers, you'll get a different result.

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You have pointed out an inconsistency in the way I was using the Nachman and Crowell paper. You are correct about mutation rates and Percent divergence.As you have suggested mutation rate of indels is less than that for substitutions. you say about 1/7 (u).Also I have been using the wrong (k). It must only consider indels.Following is my corrections:(u) for substations is ~70 per generation. 1/7 (u) makes (u’) = 10 mutation per generation in humans for indels only. (u’) is calculated by (10/6.4x10^9 ~ 2x 10^-9). (u’) for indels is ~ 2x10^-9A new number for (k) must be arrived at from the following:

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The major part of the genomic divergence could be attributed to indels (5.07%), while the nucleotide divergence was estimated as 1.52%. Thus the total divergence was estimated as 6.58%. When excluding repeats and low-complexity DNA the total divergence decreased to 2.37%. The chromosomal distribution of nucleotide substitutions and indel events was significantly correlated. Comparative Genomic Analysis of Human and Chimpanzee Indicates a Key Role for Indels in Primate Evolution | SpringerLink

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With repeats and low complexity DNA is excluded2.37% -1.52% Gives ~.8% for human and chimp divergence concerning indels this seems low but it must be true.Subbing in for indels gives:t= number of generations since divergence (Generation =20 years)
k= percentage of sequence divergence Estimated at .8% (for indels)
Ne= effective size of population ~10^5
(u')=mutation rate 2 x 10^-9 (for indels)t= .5(k/u-4Ne) from Estimate of the Mutation Rate per Nucleotide in Humans | Genetics | Oxford Academict = 1.8 million generations or 36 million years since divergence considering indels.So the HCLCA was about 36 million years ago.Edited by zaius137, : No reason given.

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That doesn't make any sense. Mitochondrial Eve is only a meaningful concept under the evolutionary perspective. The very calculations are, like everything else in biology, saturated in evolutionary theory.

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Yes I can accept the consensus on this:Using this much faster mutation rate from the two studies as a basis for a new mitochondrial clock speed, Eve can be calculated to have lived a mere 6500 or 6000 years ago, rather than 200,000 years ago.http://www.mhrc.net/mitochondrial.htm

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And the personal views you have been sharing with us, as pointed out by several posters, are contradicted by the evidence.

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Your presented evidence so far = 0

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That number is the number of bases that differ between. That is not the iindel count. A single indel can cause two genomes to vary by more than 1 base. That is what you keep getting wrong. Here is yet another example using two random sequences.

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Not knowing anything about the location or nature of the indel, you can not come to that conclusion.

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As sfs states, the good estimate for the indel rate is 1/7th of the substitution rate. Therefore, the number of mutations is (1.23)+(1.23/7)=1.4%. Not 5%.

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sfs has confused the (k) with the (u), sfs can correct me if I am wrong.

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All you have to do is go back a few generations in your own family. Your paternal grandfather's mother (your great grandmother) contributed just as much DNA to your autosomal genome as any other great grandparent (as averaged across all births), and yet she did not give you your mitochondrial DNA. Your mothers', mother's, mother did that. So you carry a lot of DNA from other women that were not your great-grandmother responsible for your mitochondrial DNA.

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I am confused, here is a question you can answer about mitochondrial Eve.If Neanderthals interbred with humans 40,000 to 60,000 years ago but diverged from humans 200,000 to 250,000 years ago.That means they lived before mitochondrial eve who was around ~100,000 years ago. Would there be a reintroduction of ancestral mitochondria at that interbreeding?There should not be a mitochondrial Eve, since the humans and Neanderthals remixed ancestral mitochondria around 40,000 years ago.How can that be?

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The mutation rate measures the number of mutations, while the divergence you're using measures the total number of bases changed.

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That is number of mutations per generation. not total. The (u).Divergence is the total percentage of number of bases changed. The (k).Maybe we are talking about the same thing and you are not labeling them.No I am not comparing apples against oranges. All my variables are in terms of indels. Which by current thinking must be accounted for under a neutral modeling.I know you would like to reject indels altogether, all evolutionists would.

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Quite. And what you're doing is counting the total number of mutations that have occurred (u x total number of generations since human/chimpanzee chromosomes diverged) and assuming it should give you k, the total number of bases different between the two chromosomes. That only works if each mutation changes one base; that's the assumption in the Nachman & Crowell paper. It's not true for indels. Your equation is wrong for indels.

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No, (u) and (k) are related by:u = k/(2t+4Ne)You measure the (k) and calculate a (u). if you have (k) and (u) you can back calculate (t).P.S. indels are quantifiable under a neutral mutation regiment. Otherwise there would not be a 1/7 (u) relationship. Get it?

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As you are using them, (u) and (k) do not have the same units. That's the problem. Number of mutations and number of bases changed are different units. You need to put them in the same units.

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Well I guess you better notify Michael W. Nachman, and Susan L. Crowell that the units do not match in the equation they used for this paper. By the way do you know the units of (k) and (u)?My guess is the following, might save you some embarrassment.k = is mutations (%)
u = is mutations per generation (rate)k/u = generationt = generationand 20 years per generationThe problem is where?(t) x 20 years = yearsEdited by zaius137, : No reason given.Edited by zaius137, : No reason given.

RAZD,I really like your posts, but this one is a bit far out.

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Although we have onlycranialmaterial fromSahelanthropus, studies so farshow thisspecies had a combination of ape-like and human-like features.

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Only cranial material? Keep in mind I am a narrow minded creationist who needs more proof than a speculation.I think I will use this one in future debates thanks.Edited by zaius137, : No reason given.

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Only if modern human men mated with neanderthal women. We would only see their mitochondrial DNA if there is an unbroken chain of women from present time back to that neanderthal mother. If there is a man in that chain, the the mitochondrial DNA chain is broken. However, the rest of the neanderthal genome passed down from that neanderthal mother can still be passed down.

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Are you claiming interbreeding populations (by the way the populations at this point were relatively large) did not have a female female linage? That is what would have to happen again and again.You accuse me of having improbable mechanisms? That is total nonsense.I think the average human would find the Neanderthal woman very attractive. You know the Elmer Fud types.

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Which is it? The number of mutations or the percentage difference?

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Units are mutations and represent variance is percentage. Any way the mutation units (what ever they may be) are canceled in the first division.k/u leaves generation. (t) is in units of generation.

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If you have two identical genomes, except that one of them has had an insertion mutation of 30 million base pairs, 1 out of 100 bases is different, but only 1 out of 3,000,000,000 sites has mutated. The mutation rate counts this as 1 event, while the percentage difference counts it as 30,000,000 differences.

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OK let us count every site difference between the two genomes and see what percentage of variance comes up. The number is bp adjusted via alignment tool.

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Counting the number of mutations is never going to get you to the percentage difference unless you know how big the mutations are.

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Again bp is not completely counted, it is defiantly the adjusted percentage difference between the human chimp genome. Look, if you did a bruit force comparison between base pairs, human against chimp, the similarity of base pairs would be in the 65% range. You do not want to go there. So saying that all base pairs are accounted for in variance is just not true.I used to write algorithms for variance (not for biology). The alignment tools used in these comparisons adjust for distances and gaps and bp, in the genomes.

You are a agenda driven evolutionist and I am a faith driven creationist.

It is great far better than my chicken scratch. How do you get to the generation units of (t)?Remember:t = .5(k/u - 4Ne).Units of (u) cancel all units of (k) except the generation unit. Does your point even matter?My point may not be as pretty, but it carries more weight.