Why is evolution so controversial?

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The units they are using do match since they are using number of mutations for both.

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So am I....

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If that were so, then there would be no creationists since creationism is based purely on faith.

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And your faith in evolution takes more imagination than I could ever muster.

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how do you know the average generation is 20 years? chimps live for 35 years in the wild and reproduce at 12 years. And we don't know what the life cycles of our extinct ancestors where.

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Because evolutionist do no other reason.

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Show your work: given a plausible demographic model of the Out of Africa migration, and estimates for the amount of Neandertal admixture, calculate the probability that Neandertal mtDNA would have survived.

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I can not because the out of Africa model is a fraud. Neanderthals were fully human and actively interbreeding with other humans.

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Go back and read the post immediately before yours. It gives the units, and also explains why Nachman and Crowell's equation is just fine for single-base substitutions. Think about it until you understand it.

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(indels) are also quantifiable under neutral model calculations. They are in essence a slower molecular clock. If this was not true your 1/7 (u) could not work because you would not have a linear relationship in mutation rates.The majority of all papers dealing with indel variation, directly or indirectly, note that indels must be included in percentage similarity. The paper in question, discounted indels because the paradigm had not changed at that time.Indels must be included in the divergence calculation or you must throw out the entire premise of that calculation.

I respect your opinion.

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If that is the case how come they are so morphologically distinct? And so genetically separated?

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How are pigmies so morphologically distinct?My opinion: There has been a very recent bottleneck to a few individuals in very recent human history. At that bottleneck a lot of human diversity was lost. The surviving Neanderthal alleles were pre incorporated in the remaining human genome.

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Of course they are. But since we don't have a good direct estimate of their mutation rate, you can't independently check to see whether human/chimpanzee divergence in indels fits with the mutation rate. There's nothing to compare it to.

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So I have to scratch your 1/7(u)? I was hoping that you would not be so willing as to throw your number under the bus.Move those goal posts a little to the left.

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The vast majority of papers dealing with indels having to do with similarity. Indeed, the overall percentage similarity is of very little scientific interest.

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A minor exception would be the human chimp divergence time.

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What paper discounted indels? And what paradigm changed?

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Nachman and Crowell’s paper, I don’t think you want to claim it did.As the paradigm goes... The paradigm that indels are of no consequence.Since you are retracting the estimate of 1/7(u) that leaves me with a reduced but relevant argument.One last quick question do you agree with a mutation rate of 1.1 x 10^-8 in humans? Or are you moving those goal posts again?

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Fine. To go along with that, we'll also need the mutation rate in base pairs per generation. Do you know what it is for indels? It's not the rate you've been quoting -- that's the rate of mutations per generation. If you don't know it, you can't do the calculation.

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Well you gave me 1/7(u) for indel mutation rate and the empirical measurement of mutations per generation is 70 new mutations per generation or 1.1x 10^-8.

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They don't adjust anything. Alignment tools align the parts that align and show gaps where they don’t.

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They adjust the chimp genome to the human scaffold.You say tomato, I say tamato.And total Bp is not counted just the location of the insertion or deletion and if it is a multiple of 3. If you counted total bp the human chimp genome similarity would be below 70%.

I will be honest, you make a good point.

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The formula, as I stated, is found in Kimura's 1983 monograph on neutral evolutionary theory. And in this formula, k represents the rate of substitution mutations (see Kimura, 1986). This symbol, k, will be familiar to most students of molecular phylogenetics. It comes in handy in a bunch of formulas. But it represents the rate of substitution mutations, not the gross percent dissimilarity of sequences. Substitution mutations are not indels. They are thoroughly different, and equating the two in this formula is biologically incorrect -- and that's exactly what you've been doing.

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OK, so my technical language is not up to par.You know I have misplaced my pocket verseion of kimura,1986 also the 1983 copy. My notes from that class of molecular phylogenetics was eaten by my dog.
I do know that kimura along with others developed the Neutral theory of evolution. The theory as I understand it involves random drift as a mechanism for mutation. Indels are also subject to random drift which places them in the realm of the neutral theory of evolution. A clock is a clock although this one runs slower.It seems that the abstract in the following paper does equate substitution mutations with indel mutations

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Divergence due to insertions and deletions (indels) along with substitutions was examined separately for different genomic features (coding, noncoding genic, and intergenic sequence). 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%.

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Comparative Genomic Analysis of Human and Chimpanzee Indicates a Key Role for Indels in Primate Evolution | SpringerLink

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The conclusion is the old saw that we share 98.5% of our DNA sequence with chimpanzee is probably in error. For this sample, a better estimate would be that 95% of the base pairs are exactly shared between chimpanzee and human DNA. In this sample of 779 kb, the divergence due to base substitution is 1.4%, and there is an additional 3.4% difference due to the presence of indels.

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Divergence between samples of chimpanzee and human DNA sequences is 5%, counting indels - PMCIt looks to me as if you can add divergence of indels directly to substitutions. If you want to maintain that indel mutation can not be added directly you must provide citations The ones you did just are not up to date, that doesn’t mean they are bad, just outdated.As I have stated before, new evidence includes indels as significant factors of evolution.

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You might want to read up on the statistical and bioinformatics literature when it comes to alignment methods.

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Well, I will just take that long needed vacation and spend it locked in a room with all the research I can dig up.

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Obviously. If there were no such adjustments, alignment methods would be neglecting a very important part of biological reality -- indels. So gaps are introduced to account for indels, and parsimony (and other methods) are used to determine the most optimal alignment.
At this point, the discussion is so convoluted and such a mlange of talking points that it can be hard to follow. But really, I suggest you actually make sound arguments and actually read the papers you cite.

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I always try and understand what I use in my citations. If you feel that I am in error, you too can cite away, but not from some dusty text book that is out of print since 1990.

I just realized something You posted the following: The k in the paper we are discussing is the autosomal sequence divergence not the rate of substitution mutations. (u) is the rate of substitution mutations.Thought I would clear that up Maybe my def. was better.Estimate of the Mutation Rate per Nucleotide in Humans | Genetics | Oxford Academic

(k) is autosomal sequence divergence (a percentage).(u) is the mutation per generation figure (rate of mutations).You don’t get it the (u) and (k) are reversed. Look at the paper

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It seems that the abstract in the following paper does equate substitution mutations with indel mutations

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No, it does not equate the two. It simply analyzes the two. But they aren't equated, because they're different -- especially when you're using them in mol clock equations.

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Could you add the percentage if they are different?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%.From that citation... Did they add the percentages or not?So I can add apples and oranges to figure out how much citrus in the fruit bowl?

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They describe total changes, not total number of bases changed. They have the accession numbers for the genes they compared, so I may try to do my own alignments at a later time to show that multiple base indels are counted as single changes.

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I assume the same holds true with how indels were counted alongside substation sequences, presented in the paper I cited.Comparative Genomic Analysis of Human and Chimpanzee Indicates a Key Role for Indels in Primate Evolution | SpringerLinkI think it might be a good intro to your endeavor. I am making that very argument They describe total changes, not total number of bases changed.Looking forward to your finding. Also I am curious how insertions in multiples of 3 are counted (those that change open reading frames).

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The problem is that you are not adding two percentages. You are adding the percentage of bases changed for substitutions to the number of indel events for your mutation rate. You need to convert the number of indel events to the number of bases changed if you want to add the two together for your mutation rate.

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I disagree with the premise that the percentage includes total base pair changed. When long segments are compared together between the species, alleles, are not always in one piece. The gap is probably a insertion (previously discarded). It depends if those bp’s are counted as a singular event, if so the percentages are addable. But if you start to count bp totals even in SNP divergence, all bets are off in the resulting divergence numbers. My guess is Nachman and Crowell’s paper did not include indels in the autosomal sequence divergence (there number is too low).

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I already did this math earlier. Indels are 1/7th the number of substitutions. If the number of substitutions is 70, then there are 10 indels. The average size of an indel is 20 bases. Therefore, the mutation rate in the units of bases changed is 70 bases from substitutions and 200 bases from indels for a total of 270.

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I was meaning to address this pointSince indel mutations are on a longer term than SNPs, they probably will not show up in the study that found 70 mutations per generation (unless they are included. As pointed out by sfs the mutation rate per generation is not nailed down in a study that produced 70 mutations per generation. It surprised me that sfs would present a number like 1/7(u). The implication is that there are 10 mutations, including the bp count, totaled in the number (u) of 70 new mutation per generation. That is a question for further investigation.The 270 new mutations per generation is not possible on a number of levels. One being the genome load for humans.