I don't know if you have a point there or not. My point is that if it's nucleotide by nucleotide and gaps (indel) it's 96%. If it's gene comparisons and I do mean the actually number of genes in common, it's 96%. When you look at 3 billion base pairs and 4% of the divergence has to have happened since the split I don't see this happening by random mutations, genetic drift or any of the other normative evolutionary pathways.
I haven't done this in a while but lets try this one more time. Let's say we have 5 million years since the split. That means there has to be 35 million base pairs (bp) changed on a single substitution basis for 5 million years (that's a mean average of course). So you are looking at 7 per year or 140 per generation for 5 million years. Add to that another 3% of indels (insertions and deletions) which comes to 45 million in the respective genomes. Since those 45 million base pairs in the human lineage actually comes to 5 million indels we are talking 1 indel 9 base pairs long or 1 indel 180 base pairs per generation for 5 million years. That does not take into consideration 9 major chromosomal rearrangements, gene loss and gain and those ERV invasions that African Apes were besieged with and we were almost immune to.
Then you have to take into account that 2 million years ago the lineage leading up to humans has to have a genetic basis for a threefold expansion. This is perhaps the most conserved of the human organs with no known effects from genetic changes except disease and disorder. This would include on HAR1f regulatory gene that has not been substantially altered since the Cambrian allowing on two substitutions since the split between primate ancestors and chicken ancestors.
Pardon my incredulity but I can't even get a straight answer what the mutation rate would be. Maybe you would like to try:
In a word, it would have had to be mutations, primarily indels (aka length mutations). It is well known that length mutations have the lowest mutation rate at 2.3 x 10^-9. They are 10 times less common then single substitutions and yet they account for almost three times more divergence. This is the table based on 1.33% divergence:
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Table 3. Estimates of mutation rate assuming different divergence times and different ancestral population sizes
4.5 mya, pop.= 10,000 mutation rate is 2.7 x 10^-8
4.5 mya, pop.= 100,000 mutation rate is 1.6 x 10^-8
5.0 mya, pop.= 10,000 mutation rate is 2.5 x 10^-8
5.0 mya, pop.= 10,0000 mutation rate is 1.5 x 10^-8
5.5 mya, pop.= 10,000 mutation rate is 2.3 x 10^-8
5.5 mya, pop.= 10,000 mutation rate is 1.4 x 10^-8
6.0 mya, pop.= 10,000 mutation rate is 2.1 x 10^-8
6.0 mya, pop.= 100,000 mutation rate is 1.3 x 10^-8
Table 4. Estimates of mutation rate for different sites and different classes of mutation
Transition at CpG mutation rate 1.6 x 10^-7
Transversion at CpG mutation rate 4.4 x 10^-8
Transition at non-CpG mutation rate 4.4 x 10^-8
Transversion at non-CpG mutation rate 5.5 x 10^-9
All nucleotide subs mutation rate 2.3 x 10^-8
Length mutations mutation rate 2.3 x 10^-9
All mutations mutation rate 2.5 x 10^-8
Rates calculated on the basis of a divergence time of 5 mya, ancestral population size of 10,000, generation length of 20 yr, and rates of molecular evolution given in Table 1.
Calculations are based on a generation length of 20 years and average autosomal sequence divergence of 1.33%
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Estimate of the Mutation Rate per Nucleotide in Humans (Michael W. Nachmana and Susan L. Crowella
Genetics, 297-304, September 2000)
If you actually gave me a straight answer you would be the first. One person, actually a biologist, actually gave me the formula and later deleted it from the post. Everyone else just burys it under rationalizations and talk circles around it.
Care to give it a try?
My try is to wonder why you have that post archived and keep trotting it out every now and then as if it has never
been explained to you before.
Which of your labels works for that antic? Error of repetition while ignoring explanations?
Since you think copy and pasting posts you've made before is fine, I will c&p responses I've seen to this same claim of yours:
Let's look at the information
YOU keep presenting:
All nucleotide substitutions 2.3 x 10^-8
Length mutations 2.3 x 10^-9
All well and good, but look how you DISTORT this:
With 35 million base substitutions and 90 million indels you have a level of divergence that poses a mutation rate that no living system could sustain. In 5 million years to accumulate 125 million nucleotides worth of divergence it would require 7 single base substitutions and 1 indel, on average, 14 nucleotides long per year for five million years.
But we DON'T have 90 million indels! We have ~5 million!
And you keep forgetting that those numbers represent the total BETWEEN humans and chimps, which means we only have ~ HALF of those numbers! Why can you not grasp this? From the paper you cited:
On the basis of this analysis, we estimate that the human and chimpanzee genomes each contain 4045Mb of species-specific euchromatic sequence, and the indel differences between the genomes thus total ~90Mb. This difference corresponds to ~3% of both genomes and dwarfs the 1.23% difference resulting from nucleotide substitutions; this confirms and extends several recent studies. Of course, the number of indel events is far fewer than the number of substitution events (~5 million compared with ~35 million, respectively).
So, a rational, educated reading tells us:
~35 million point mutations
~5 million indels (involving 40-45 Mbs)
There are 7 times more point mutations than indels!
So, this claim of yours:
In 5 million years to accumulate 125 million nucleotides worth of divergence...
is patently false. It should read: In 5 million years to accumulate 80 million nucleotides worth of divergence spread across 35 million single nucleotide substitutions and 5 million indels...
The fact that despite your protestations, you still appear to think that the individual nucleotides in indels must be accounted for by a higher overall mutation rate even though you conflate indel numbers and indel amounts from 2 species.
Until you admit that you are confused, I will do what is necessary. What you think are points that you are making are actually elementary errors.
Oh, well, I guess I am all wrong. Let's see if those chaps - whose paper came out 5 years before the paper that actually directly compared the entire genomes - include indels in their analysis:
All nucleotide substitutions 2.3 x 10^-8
Length mutations 2.3 x 10^-9
and then what happens? Right:
All mutations 2.5 x 1-^-8
Hmmm... So what does this mean?
Why, it means that ALL mutations - including indels - occur at a rate of ~2.5 x 10^-8 in the human genome.
And what is that rate? It is per nucleotide site/year, producing about 175 MUTATIONS per diploid genome per generation. That does not mean 175 point mutations, it means 175 EVENTS, and according to their numbers anyway, very roughly 17 of them are INDEL events, the rest are point mutations.
Nowehere in the paper do they indicate that the 175 accommodates for within indel nucleotide numbers.
Gee, I guess nobody should try to find errors, and merely accept your statements at face value as absolutley correct.
Like when you say '90 million indels'. we should just sit back and say, 'Wow - 90 million indels - that is a lot!' and not even wonder if your numbers have merit...
Right - because 95% is totally different than 99% and has a substantially, dramatically different impact on the whole claim.
Yup, I am sure that is exactly what happened.
It is not an error to understand that the total nucleotide divergence is made up of point mutations as well as mutations of length, and that the length mutations are single mutational events that can add or remove up to 10s of 1000s of nucleotides at once, and that such events are rarer than point mutations and so should comprise their own rate of occurrance.
It IS an error to take the 10,000 nucleotides 'altered' in a single mutational event and dictate that all 10,000 must be accounted for individually.
I don't know how else to put it. It seems that many others have put it to you before and you just refuse to acknowledge your error. I suspect this invincible ignroance on your part is part of the reason why so many peopel simply blow you off, as they see that it is futile to try to correct your many error-riddled ideas and assertions.
I'll bet you don't know what you are talking about. Your Wiki expertise can only get you so far.
I cannot decipher that gibberish. You have certainly implied and inisted that the nucleotides must be accoutned for - why else would you cut-and-paste this claim of your's so often if you did not:
With 35 million base substitutions and 90 million indels you have a level of divergence that poses a mutation rate that no living system could sustain.
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Yeah, I guess it is me that thinks that despite the fact that a paper I frequently cut and paste from and cite clearly says that each species (each referring to human and chimp) possesses 40-45 Mb of nucleotide difference attributed to indels that I keep writing that we have to account for 90 million Mb (or 90 millionindels) of mutational change and this is too high a mutation rate. Yup - that's me!
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This is just incredible. First, you insist that you do not claim that the number of nucleotides in indels must each be accounted for, then you turn around a few paragraphs later and imply exactly that.
I suggest you actually read the Britten paper for once to try to understand what the 1-5% actually means, because you clearly dfon't get it. That or you do get it and are just being obstinate and obnoxious.
Here is a hint - the rates do not have to change because the 5% divergence merely 'counts' the number of nucleotides within indels instead of counting them as single events.
I know explaining that is lost on you, but I am hoping that some lurker will get the picture and understand how foolish of an argument you are making.
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Does it matter? NO. Did you actually read that paper to understand it ? NO. If you did, you would have seen that they count indels as occurrences, not by the number of nucleotides.
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Then why do you keep referring to it?
And the divergence has no impact on their estimate because they counted the indels the right way in terms of rate, but you don't understand that because you have no education or understanding of biology or genetics.
I won't bring what up?
1.23% divergence as the result of nucleotide substitutions (~35 million), ~3% as the result of indels (~5 million).
nuc. substitutions = 7/year (140/generation)
indels = 1/year (20/ generation)
What is the big deal? You seem to think this makes evolution impossible, but it is right in line with expectations. Viruses mutate about 10x that rate. You are just blowing smoke.
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Right. Whatever.
