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Author | Topic: Why is evolution so controversial? | |||||||||||||||||||||||||||||||
sfs Member (Idle past 2563 days) Posts: 464 From: Cambridge, MA USA Joined: |
quote:Or just take 1.1e-8 and divide by 7, giving 1.6e-9 mutations/bp/generation. quote:Sorry, but this is just wrong. As others have pointed out, you're comparing apples and oranges. The mutation rate measures the number of mutations, while the divergence you're using measures the total number of bases changed. Since indels frequently change more than 1 base, you cannot use the Nachman and Crowell formula to predict the divergence (or calculate the number of generations). Not unless you know the mean length of an indel. Note that the estimate I gave for the indel mutation rate comes from the chimpanzee genome paper, in which there are 1/7th as many indel events seen as single-base substitutions. Comparing human and chimpanzee divergence at indels will just give you that 1/7th rate back again, since the mutation rate and divergence are coming from the same data.
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sfs Member (Idle past 2563 days) Posts: 464 From: Cambridge, MA USA Joined: |
quote:Consider yourself corrected.
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zaius137 Member (Idle past 3439 days) Posts: 407 Joined: |
quote: I am confused, here is a question you can answer about mitochondrial Eve. If Neanderthals interbred with humans 40,000 to 60,000 years ago but diverged from humans 200,000 to 250,000 years ago. That means they lived before mitochondrial eve who was around ~100,000 years ago. Would there be a reintroduction of ancestral mitochondria at that interbreeding? There should not be a mitochondrial Eve, since the humans and Neanderthals remixed ancestral mitochondria around 40,000 years ago. How can that be?
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zaius137 Member (Idle past 3439 days) Posts: 407 Joined: |
quote: That is number of mutations per generation. not total. The (u). Divergence is the total percentage of number of bases changed. The (k). Maybe we are talking about the same thing and you are not labeling them. No I am not comparing apples against oranges. All my variables are in terms of indels. Which by current thinking must be accounted for under a neutral modeling. I know you would like to reject indels altogether, all evolutionists would.
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Taq Member Posts: 10085 Joined: Member Rating: 5.1 |
Not knowing anything about the location or nature of the indel, you can not come to that conclusion. We do know what the location and nature of the indels is. It is found in the chimp genome paper. There are 5 million indels combined between the human and chimp lineages, 1/7th the number of substitutions. "Through comparison with the human genome, we have generated a largely complete catalogue of the genetic differences that have accumulated since the human and chimpanzee species diverged from our common ancestor, constituting approximately thirty-five million single-nucleotide changes, five million insertion/deletion events, and various chromosomal rearrangements. . . On the basis of this analysis, we estimate that the human and chimpanzee genomes each contain 40—45 Mb of species-specific euchromatic sequence, and the indel differences between the genomes thus total ~90 Mb. This difference corresponds to ~3% of both genomes and dwarfs the 1.23% difference resulting from nucleotide substitutions; this confirms and extends several recent studies63, 64, 65, 66, 67. Of course, the number of indel events is far fewer than the number of substitution events (~5 million compared with ~35 million, respectively)." (Supplementary Information ‘Genome evolution’ and Supplementary Fig. S5)."Initial sequence of the chimpanzee genome and comparison with the human genome - PubMed So there are about 5 million indels with an average of ~20 bases per indel.
sfs has confused the (k) with the (u), sfs can correct me if I am wrong. If you change the divergence from 5% to 1.4%, this won't change anything in the calculations? Edited by Taq, : No reason given. Edited by Taq, : No reason given. Edited by Taq, : No reason given.
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Taq Member Posts: 10085 Joined: Member Rating: 5.1 |
That is number of mutations per generation. not total. The (u). Divergence is the total percentage of number of bases changed. The (k).
Already, you have a conflict. A single mutation can change 10 bases, or even 10,000 bases.
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Taq Member Posts: 10085 Joined: Member Rating: 5.1 |
If Neanderthals interbred with humans 40,000 to 60,000 years ago but diverged from humans 200,000 to 250,000 years ago. That means they lived before mitochondrial eve who was around ~100,000 years ago. Would there be a reintroduction of ancestral mitochondria at that interbreeding?
Only if modern human men mated with neanderthal women. We would only see their mitochondrial DNA if there is an unbroken chain of women from present time back to that neanderthal mother. If there is a man in that chain, the the mitochondrial DNA chain is broken. However, the rest of the neanderthal genome passed down from that neanderthal mother can still be passed down. I am sure you can find examples of how mitochondrial lineages go extinct in families that you know. All you need is a mother or grandmother who does not have any daughters or grandaughters. Over time, lineages die off which just leaves one dominant lineage. Added in edit: Always have a tough time finding this photo, but it has always been the best one for explaining the difference between mtDNA and the rest of your genome.
Edited by Taq, : No reason given. Edited by Taq, : No reason given. Edited by Taq, : No reason given. Edited by Taq, : No reason given.
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sfs Member (Idle past 2563 days) Posts: 464 From: Cambridge, MA USA Joined: |
quote:Quite. And what you're doing is counting the total number of mutations that have occurred (u x total number of generations since human/chimpanzee chromosomes diverged) and assuming it should give you k, the total number of bases different between the two chromosomes. That only works if each mutation changes one base; that's the assumption in the Nachman & Crowell paper. It's not true for indels. Your equation is wrong for indels. quote:Get stuffed. It's possible that you will someday post an accurate statement about genetics or evolution, but if you do, it will be by accident.
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zaius137 Member (Idle past 3439 days) Posts: 407 Joined: |
quote: No, (u) and (k) are related by: u = k/(2t+4Ne) You measure the (k) and calculate a (u). if you have (k) and (u) you can back calculate (t). P.S. indels are quantifiable under a neutral mutation regiment. Otherwise there would not be a 1/7 (u) relationship. Get it?
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Taq Member Posts: 10085 Joined: Member Rating: 5.1 |
No, (u) and (k) are related by: As you are using them, (u) and (k) do not have the same units. That's the problem. Number of mutations and number of bases changed are different units. You need to put them in the same units.
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RAZD Member (Idle past 1435 days) Posts: 20714 From: the other end of the sidewalk Joined: |
... I could reduce this to a simple logic point by saying that we are genetically closer to the HCLCA than to chimps. Seeing as both branches diverge from the Human-Chimp Last Common Ancestor it is logical that each is more closely related to the HCLCA than each other. This would be true for all species descendant from a common ancestor, so this should not be a problem.
Now does the HCLCA look more like a chimp or a human? Paleoanthropology would most defiantly say a chimp. ... Not really:
sfs Message 801: ... Using your (correct) formula from Nachman and Crowell, and the values you specified for ancestral population size, generation time and mutation rate, and using the best estimate for human/chimpanzee divergence, the estimated divergence time is 7.2 million years. ... Sahelanthropus tchadensis | The Smithsonian Institution's Human Origins Program
quote: Seeing as this is very close to the time of divergence we would expect this ape/hominid to be very very close to the last common ancestor with chimps, and it may even BE the last common ancestor species. Sahelanthropus - Wikipedia
quote: That is what I would expect the HCLCA skull to look like.
... But our genes would say that human genes have to be closer to the HCLCA than a chimp. Do you see a dichotomy here? Nope. Do you? Enjoy.by our ability to understand Rebel☮American☆Zen☯Deist ... to learn ... to think ... to live ... to laugh ... to share. Join the effort to solve medical problems, AIDS/HIV, Cancer and more with Team EvC! (click)
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sfs Member (Idle past 2563 days) Posts: 464 From: Cambridge, MA USA Joined: |
quote:Exactly. Multiply the mutation rate (= (number of mutations)/bp/generation) by the mean size of the mutation (= (number of bases changed)/mutation) and you'll get (number of bases changed)/bp/generation. Multiply that by the number of generations, and you've got k, the fraction of bases that differ (= (number of bases changed)/bp). For single-base substitutions, it doesn't matter, since it's 1 (base changed)/mutation.
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zaius137 Member (Idle past 3439 days) Posts: 407 Joined: |
quote: Well I guess you better notify Michael W. Nachman, and Susan L. Crowell that the units do not match in the equation they used for this paper. By the way do you know the units of (k) and (u)? My guess is the following, might save you some embarrassment. k = is mutations (%)u = is mutations per generation (rate) k/u = generation t = generation and 20 years per generation The problem is where? (t) x 20 years = years Edited by zaius137, : No reason given. Edited by zaius137, : No reason given.
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zaius137 Member (Idle past 3439 days) Posts: 407 Joined: |
RAZD,
I really like your posts, but this one is a bit far out.
quote: Only cranial material? Keep in mind I am a narrow minded creationist who needs more proof than a speculation. I think I will use this one in future debates thanks. Edited by zaius137, : No reason given.
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zaius137 Member (Idle past 3439 days) Posts: 407 Joined: |
quote: Are you claiming interbreeding populations (by the way the populations at this point were relatively large) did not have a female female linage? That is what would have to happen again and again. You accuse me of having improbable mechanisms? That is total nonsense. I think the average human would find the Neanderthal woman very attractive. You know the Elmer Fud types.
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