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I am confused by Mark's latest post. Most of it shows clear evidence of a common ancestor for humans and chimps. I thought he was arguing against this.
Understanding Mark's posts helps if you understand that Mark doesn't really understand what he is posting about. Mark has the habit if confusing numbers and terms with each other, which leads him to confuse the issues and others to have a hard time understanding what he is saying in the first place.
Best to look at his post as a puzzle, where you have to find out which numbers he actually used and what they actually refer to.
As an aside, I went to a conference recently and saw the authors of the "human accelerated regions" present their work. All of it shows 100% support for evolution in general and the common descent of humans/chimps in particular.
__________________
Tom
'What luck for rulers, that men do not think.'
-Ascribed to Adolf Hitler-
`Contrariwise,' continued Tweedledee, `if it was so, it might be; and if it were so, it would be; but as it isn't, it ain't. That's logic.'
-Through the Looking Glas by Lewis Caroll-
Statistics are like a bikini. What they reveal is suggestive, but what they conceal is vital.
Best to look at his post as a puzzle, where you have to find out which numbers he actually used and what they actually refer to.
Here's a puzzle for you Tom, what is the rate when the divergence is calculated at 5% instead of 1.33%?
The average mutation rate was estimated to be 2.5 x 10-8 mutations per nucleotide site or 175 mutations per diploid genome per generation...Using conservative calculations of the proportion of the genome subject to purifying selection, we estimate that the genomic deleterious mutation rate (U) is at least 3. This high rate is difficult to reconcile with multiplicative fitness effects of individual mutations and suggests that synergistic epistasis among harmful mutations may be common.
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%
“Gärtner, by the results of these transformation experiments, was led to oppose the opinion of those naturalists who dispute the stability of plant species and believe in a continuous evolution of vegetation. He perceives in the complete transformation of one species into another an indubitable proof that species are fixed with limits beyond which they cannot change.” (G. Mendel)
You need to edit this because you've seen quite a few honest answers. You've also been told why comparing apples and oranges isn't correct. The sentence should read something like "I would like to see an answer where people agree with me."
__________________ (The Library of Alexandria) questioned the permanence of the stars, but did not question the justice of slavery - Carl Sagan in Cosmos
Here's a puzzle for you Tom, what is the rate when the divergence is calculated at 5% instead of 1.33%?
That would depend on the number of indels, which would give an estimate of the mutation rate. It would not depend on the length of these indels.
The average mutation rate was estimated to be 2.5 x 10-8 mutations per nucleotide site or 175 mutations per diploid genome per generation...Using conservative calculations of the proportion of the genome subject to purifying selection, we estimate that the genomic deleterious mutation rate (U) is at least 3. This high rate is difficult to reconcile with multiplicative fitness effects of individual mutations and suggests that synergistic epistasis among harmful mutations may be common.
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%
For nucleotide substitution only (which would cause the 1.33% divergence) according to this article it would be 2.3X10-8.
For length mutations (ie, the remaining 3.7%) about 2.3X10-9, if I read the article correctly.
Averaged over number of mutations per nucleotide this would mean an average of 2.5X10-8. My opinion is that one can question how useful this number is, because of divergence within sites.
For substitution mutations, the mutation rate calculated would (according to the article) mean that every generation would have around 175 new mutations. This correlates very well with other estimates I have seen on substitutions.
Given that the mutation rate for length mutations is around 10 times lower than for base subsitutions, one would expect around 17 to 18 new indels per generation. That means individual mutation events, not number of base pairs. The number of base pairs may be much higher, since indels can insert large stretches of bases. I haven't seen estimates on these rates arrived at in a different way, although I have searched for them in the past. They do not seem to high to me, but I really cannot tell whether this conforms with other estimates.
Does that answer your question (again).
Just once I would like to see an honest answer.
I and others have given you plenty of honest answers. The problem is that even though the differences between the numbers you bandy about and what they signify keep being misunderstood by you and you show no active interest in getting an accurate understanding of them.
__________________
Tom
'What luck for rulers, that men do not think.'
-Ascribed to Adolf Hitler-
`Contrariwise,' continued Tweedledee, `if it was so, it might be; and if it were so, it would be; but as it isn't, it ain't. That's logic.'
-Through the Looking Glas by Lewis Caroll-
Statistics are like a bikini. What they reveal is suggestive, but what they conceal is vital.
That would depend on the number of indels, which would give an estimate of the mutation rate. It would not depend on the length of these indels.
You are looking at 5 million events in each species so figure 1 event per year or 20 per generation just to keep it simple and straightforward. You can plug in whatever population size you like but the per nucleotide mutation rate paper uses 10,000 and 100,000:
The analysis of modest-sized insertions reveals ~32 Mb of human-specific sequence and ~35 Mb of chimpanzee-specific sequence, contained in ~5 million events in each species
45% of events cover only 1 base pair (bp), 96% are <20 bp and 98.6% are <80 bp),
70,000 indels larger than 80 bp comprising 73% of the affected base pairs) (FIGURE 5).
Indels >80 bp fall into three categories:
(1) about one-quarter are newly inserted transposable elements;
(2) more than one-third are due to microsatellite and satellite sequences;
(3) and the remainder are assumed to be mostly deletions in the other genome.
[indent]
For nucleotide substitution only (which would cause the 1.33% divergence) according to this article it would be 2.3X10-8.
For length mutations (ie, the remaining 3.7%) about 2.3X10-9, if I read the article correctly.
Averaged over number of mutations per nucleotide this would mean an average of 2.5X10-8. My opinion is that one can question how useful this number is, because of divergence within sites.
For substitution mutations, the mutation rate calculated would (according to the article) mean that every generation would have around 175 new mutations. This correlates very well with other estimates I have seen on substitutions.
Given that the mutation rate for length mutations is around 10 times lower than for base subsitutions, one would expect around 17 to 18 new indels per generation. That means individual mutation events, not number of base pairs. The number of base pairs may be much higher, since indels can insert large stretches of bases. I haven't seen estimates on these rates arrived at in a different way, although I have searched for them in the past. They do not seem to high to me, but I really cannot tell whether this conforms with other estimates.
Does that answer your question (again).
Not really, the divergence changes from 1.33% to 5%. Length mutations are 2.3X10-9 with the actual indels broken down into nucleotides. The overall mutation rate is 2.5X10-8. Both of these are calculated using the formula given in the mutation rate per nucleotide paper. Just assume the rate is applied uniformly across the genomes.
I say again, does it change when the overall divergence changes from 1.33% to 5%?
I and others have given you plenty of honest answers. The problem is that even though the differences between the numbers you bandy about and what they signify keep being misunderstood by you and you show no active interest in getting an accurate understanding of them.
I understand it's a simple enough formula that the question can be understood well enough to plug in the overall divergence.
Just plug in 5% where 1.33% is and show me the mutation rate. Do that and I will shut up about it.
Have a nice day.
Mark
__________________
“Gärtner, by the results of these transformation experiments, was led to oppose the opinion of those naturalists who dispute the stability of plant species and believe in a continuous evolution of vegetation. He perceives in the complete transformation of one species into another an indubitable proof that species are fixed with limits beyond which they cannot change.” (G. Mendel)
You need to edit this because you've seen quite a few honest answers. You've also been told why comparing apples and oranges isn't correct. The sentence should read something like "I would like to see an answer where people agree with me."
What I would like is the formula used in the Mutation rate per nucleotide paper applied when the divergence goes from 1.33% to 5%. I don't care if you agree with me or not.
Have a nice day
Mark
__________________
“Gärtner, by the results of these transformation experiments, was led to oppose the opinion of those naturalists who dispute the stability of plant species and believe in a continuous evolution of vegetation. He perceives in the complete transformation of one species into another an indubitable proof that species are fixed with limits beyond which they cannot change.” (G. Mendel)
Here's a puzzle for you Tom, what is the rate when the divergence is calculated at 5% instead of 1.33%?
[snipped]
All of this was in the paper
Calculations are based on a generation length of 20 years and average autosomal sequence divergence of 1.33%
This you made up. 1.33% is the result of the calculation, not an a priori assumption
As the paper says:
the amount of divergence, k, between sequences drawn from two species is given by
k=2µt + 4Neµ
where t is the time since the species have diverged measured in generations, µ is the mutation rate, and Ne is the ancestral effective population size
A less misleading question on your part would have been "what is the effect on the divergence if the mutation rate counted indels as a sequence of individual events"
The answer to this question is (assuming the peer review process failed utterly and such a silly un-evidenced hypothesis was considered valid) is that the divergence would be larger.
My response would be "so what?" 1.3%, 5%, 10%. None of it invalidates the model.
Mark, you behave like this "satan" character fundies drone on about, you take a whole bushel of truth and add a sprinkling of lies.
Last edited by Blayz; 20th August 2007 at 12:19 AM.
This you made up. 1.33% is the result of the calculation, not an a priori assumption
The 1.33% was from the mutation rate by nucleotide paper and the 5% was from the Chimpanzee genome paper. The a priori assumption is of a common ancestor.
As the paper says:
the amount of divergence, k, between sequences drawn from two species is given by
k=2µt + 4Neµ
where t is the time since the species have diverged measured in generations, µ is the mutation rate, and Ne is the ancestral effective population size
A less misleading question on your part would have been "what is the effect on the divergence if the mutation rate counted indels as a sequence of individual events"
The answer to this question is (assuming the peer review process failed utterly and such a silly un-evidenced hypothesis was considered valid) is that the divergence would be larger.
My response would be "so what?" 1.3%, 5%, 10%. None of it invalidates the model.
These calculations are based on divergence of 1.33%. The Chimpanzee Genome paper puts divergence at 5% so what would that make the mutation rates in Table 3?
Mark, you behave like this "satan" character fundies drone on about, you take a whole bushel of truth and add a sprinkling of lies.
Just once I would like to see an honest answer to this question. You have the formula, use it.
__________________
“Gärtner, by the results of these transformation experiments, was led to oppose the opinion of those naturalists who dispute the stability of plant species and believe in a continuous evolution of vegetation. He perceives in the complete transformation of one species into another an indubitable proof that species are fixed with limits beyond which they cannot change.” (G. Mendel)
Calculations from table 1 of the cited paper put
k =0.0133
t = 4.5 x 10^6 (years) / 20 (generation time) Ne = 10^4
Lets consider the first line of the table
0.0133 = 2 x µ x 4500000 / 20 + 40000µ
0.0133 = µ450000 + 40000µ
µ = 0.0133/490000
µ = 2.7 x 10^-8
Last line
t = 6 x 10^6
Ne = 10^5
0.0133 = 2 x µ x 6000000/20 + 400000µ
0.0133 = µ600000 + 400000µ
µ = 0.0133/10000000
µ = 1.3 x 10^-8
I can but hope you don't need me to do the other lines of the table
Anyway, you want me to plug in a divergence (not mutation rate) of 5%
first line
µ=0.05/490000=1.02 x 10^-7
last line
µ = 0.05/1000000 = 5 x 10^-8
Which is to say, all values go up by ~5x
__________________ I hear stories from the chamber / How Christ was born into a manger
And like some ragged stranger / Died upon the cross
And might I say it seems so fitting in its way
He was a carpenter by trade / Or at least that's what I'm told
--Mercy Seat, Nick Cave and the Bad Seeds
* For the lurkers, in Mark's scenario some thousands of species on the Ark hyper-evolved into the millions of species we see on Earth and in the fossil record in the 4,000 years since the Flood but somehow, to him, brain growth in Homo over about 5 million years is utterly impossible.
__________________ You will do me the justice to remember, that I have always strenuously supported the Right of every Man to his own opinion, however different that opinion might be to mine. He who denies to another this right, makes a slave of himself to his present opinion, because he precludes himself the right of changing it.
-- Thomas Paine
Last edited by RichardT; 23rd August 2007 at 12:59 PM.
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