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Author | Topic: Why is evolution so controversial? | |||||||||||||||||||||||||||||||
zaius137 Member (Idle past 3439 days) Posts: 407 Joined: |
quote: So am I....
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zaius137 Member (Idle past 3439 days) Posts: 407 Joined: |
quote: And your faith in evolution takes more imagination than I could ever muster.
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zaius137 Member (Idle past 3439 days) Posts: 407 Joined: |
quote: Because evolutionist do no other reason.
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zaius137 Member (Idle past 3439 days) Posts: 407 Joined: |
quote: 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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zaius137 Member (Idle past 3439 days) Posts: 407 Joined: |
quote: (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.
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zaius137 Member (Idle past 3439 days) Posts: 407 Joined: |
I respect your opinion.
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zaius137 Member (Idle past 3439 days) Posts: 407 Joined: |
quote: 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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zaius137 Member (Idle past 3439 days) Posts: 407 Joined: |
quote: 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.
quote: A minor exception would be the human chimp divergence time.
quote: 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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zaius137 Member (Idle past 3439 days) Posts: 407 Joined: |
quote: 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.
quote: 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%.
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zaius137 Member (Idle past 3439 days) Posts: 407 Joined: |
I will be honest, you make a good point.
quote: 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
quote:Comparative Genomic Analysis of Human and Chimpanzee Indicates a Key Role for Indels in Primate Evolution | SpringerLink quote:Divergence between samples of chimpanzee and human DNA sequences is 5%, counting indels - PMC It 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.
quote: Well, I will just take that long needed vacation and spend it locked in a room with all the research I can dig up.
quote: 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.
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zaius137 Member (Idle past 3439 days) Posts: 407 Joined: |
I just realized something You posted the following:
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. 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
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zaius137 Member (Idle past 3439 days) Posts: 407 Joined: |
(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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zaius137 Member (Idle past 3439 days) Posts: 407 Joined: |
quote: 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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zaius137 Member (Idle past 3439 days) Posts: 407 Joined: |
quote: 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 | SpringerLink I 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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zaius137 Member (Idle past 3439 days) Posts: 407 Joined: |
quote: 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).
quote: I was meaning to address this point Since 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.
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