Re: Any real evidence for evolution, point on point.
Now do you see that mutation rate (u) and autosomal divergence (k) both have the same units and they include (indels). At least where they were counted (the paper I cited).
So you can not only use indels in the divergence calculation, you must use indels when you use the empirical value for mutation rate in humans, that of (1.1 x 10^-8 mutations per base pair per generation).
Remember the ratio of k/u must yield units of generation.
If I apply both the autosomal divergence percentage of (5%) and observed mutation rate (70 new mutations per generation) the time of human chimp common ancestor is beyond 40 million years...
Here is the simple version of divergence time used in calculating difference between species Without Ne. A simple approximation. I like simple.
d = 2*r*t or t = .5(d/r) where d = DNA differences between two individuals r = the measured mutation rate in the species or lineage t = time of origin derived from each origins model (in generations)
You are welcome to have the last substantive post on the topic. Is that a problem for you?
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Re: Any real evidence for evolution, point on point.
If I apply both the autosomal divergence percentage of (5%) and observed mutation rate (70 new mutations per generation) the time of human chimp common ancestor is beyond 40 million years...
This is halfwitted nonsense, for reasons that have been explained to you and explained to you and explained to you and explained to you and explained to you and explained to you and explained to you and explained to you and explained to you and explained to you and explained to you and explained to you and explained to you and explained to you and explained to you and explained to you and explained to you and explained to you and explained to you and explained to you and explained to you and explained to you and explained to you and explained to you and explained to you and explained to you and explained to you and explained to you and explained to you and explained to you and explained to you and explained to you and explained to you and explained to you and explained to you and explained to you and explained to you and explained to you and explained to you and explained to you and explained to you and explained to you and explained to you and explained to you and explained to you and 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Please find an argument that is not halfwitted nonsense.
quote:
Here is the simple version of divergence time used in calculating difference between species Without Ne. A simple approximation. I like simple. d = 2*r*t or t = .5(d/r) where d = DNA differences between two individuals r = the measured mutation rate in the species or lineage t = time of origin derived from each origins model (in generations)
Simple is good. Let's use a cartoon organism. It has a mutation rate of 1x10^-9/bp/gen and a genome of 1 billion base pairs, so on average there is 1 mutation per generation. Half of its mutations are single-base substitutions, and half are large indels. Let's look at a copy of the genome from each branch just one generation after they split. In that 1 generation, one copy acquired one single-base substitution. The other copy acquired an insertion of 10 million base pairs. As a result, the genomes now differ by 10,000,001 base pairs, or just over 1%.
Using your formula, t = 0.5*(.01/1e-9) = 5,000,000 generations. That's wrong by a factor of 5 million. What do you think might be wrong with your formula?
Zaius asked why it was dumb to just add up the unique sequence from each species to get the total divergence. Here's why. Consider two sequences, each 20 bp long:
The dashes are sequence that doesn't exist in that copy. 10 out of the 20 bp in each sequence are identical and ten are different. 50% of the sequence in each is unique to that copy (e.g. represents an insertion in its lineage). If we add up the fraction of unique sequence in both, we conclude that they have 0% of their bases in common, even though they are 50% identical.
quote:Simple is good. Let's use a cartoon organism. It has a mutation rate of 1x10^-9/bp/gen and a genome of 1 billion base pairs, so on average there is 1 mutation per generation. Half of its mutations are single-base substitutions, and half are large indels. Let's look at a copy of the genome from each branch just one generation after they split. In that 1 generation, one copy acquired one single-base substitution. The other copy acquired an insertion of 10 million base pairs. As a result, the genomes now differ by 10,000,001 base pairs, or just over 1%.
Do you read any of my citations? Think average...
This would be a problem if mutation rates were as simple as you think they are. From my citation:
Mutation Rate = # of mutations observed [30] (# of experimental lines [198]) x (average # of generations [339]) x (average # of base pairs sequenced [~21,000])
The citation I showed you directly counted base pairs in the indel over an average of measurements. Mutation rates are considered in the citation as averages. One case won’t cut it.
Examining the DNA sequences from their experimental animals (a total of over 4 million base pairs!), and comparing them with the controls, turned up a total of 30 mutations. 17 of these were insertions or deletions ("indels') ◦ 7 in exons all but 2 of which produced frameshifts and a premature STOP codon. ◦ 10 in introns or between genes 13 of these were single base substitutions ("point" mutations) ◦ 3 in exons : one "silent" producing a synonymous codon; two that changed the encoded amino acid. ◦ 10 in introns or between genes
I hope most who read this got over the indel being counted as one mutation a few posts back
Calculating Mutation Rate From these results I have pooled their data to calculate an approximate rate at which spontaneous mutations occur throughout the genome. Mutation Rate = # of mutations observed [30] (# of experimental lines [198]) x (average # of generations [339]) x (average # of base pairs sequenced [~21,000]) yielding a rate of 2.1 x 10-8 mutations per base pair per generation. The total C. elegans genome contains some 108 base pairs so this tells us that two new germline mutations occur somewhere in each of C. elegans's two haploid genomes in each generation.
quote:Zaius asked why it was dumb to just add up the unique sequence from each species to get the total divergence. Here's why. Consider two sequences, each 20 bp long:
Ask the authors of the papers claiming that you can add indels to divergence. That is not going on anyway read the paper.
Zaius asked why it was dumb to just add up the unique sequence from each species to get the total divergence. Here's why. Consider two sequences, each 20 bp long:
The dashes are sequence that doesn't exist in that copy. 10 out of the 20 bp in each sequence are identical and ten are different. 50% of the sequence in each is unique to that copy (e.g. represents an insertion in its lineage). If we add up the fraction of unique sequence in both, we conclude that they have 0% of their bases in common, even though they are 50% identical.
It looks to me as if you are comparing 30 bp with 2 indels. Your comparison is biased because you compare 20 bp on one side then 20 bp on the other. I would think that the comparison here would be 30 bp. The two outside indels are not in the same frame of your comparison.
Re: Any real evidence for evolution, point on point.
I hope no one is missing what's most amazing, because it isn't the rapidity of the touches. It's that the chimp looks at the numbers for only a second before hitting the circle that replaces them with white boxes. The chimp not only knows the ordering of the digits 1-9, he can remember them positionally after just a glance.
People are occasionally born with amazing talents, and since we're just animals it shouldn't be surprising that the same is true of animals. This chimp's talents seem similar in nature to a human savant's.
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