Adam and Eve: Some of those just-a-myth citations turned out to be fig leaves

_{Denyse O'Leary

February 11, 2018

Genetics, Genomics, Human evolution, Intelligent Design, Religion, theistic evolution}

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They withered under study.

Fig Leaves 1 There’s been a lively discussion between geneticists Dennis Venema and Richard Buggs and about whether the human race must have had more than one pair of ancestors (Venema yes, Buggs no).

From Evolution News and Science Today:

Earlier, we saw that evolutionary genomicist Richard Buggs has been engaged in a dialogue with Venema about the latter’s arguments against a short bottleneck of two individuals in human history. Buggs is skeptical that methods of measuring human genetic diversity cited by Venema can adequately test such an “Adam and Eve” hypothesis. Buggs’s initial email to Venema thus concluded, “I would encourage you to step back a bit from the strong claims you are making that a two person bottleneck is disproven.”

Buggs agreed with Venema that one particular metric — human allelic diversity — might be capable of testing the issue. But he wanted to know more details about the population genetics models that Venema was relying on. In reply to Venema’s response to his initial email, Buggs asked Venema to provide a citation. He requested some backup for the repeated claims that human allelic diversity indicates we evolved from an ancestral population of about 10,000 individuals.

Ultimately Dr. Venema was unable to provide a scientific citation to substantiate his claim. To be fair to Venema, he says he believes that he has provided an adequate citation. And no doubt he sincerely does believe it. There is no accusation of bad faith here. But Buggs has clearly shown that Venema did not provide adequate backup. This means that Venema’s claims against Adam and Eve are scientifically suspect and intellectually unpersuasive. In fact, Buggs has shown that some of Venema’s citations don’t even address the question of the ancestral population size of humans. This gives the appearance of “citation bluffing,” however unwitting. More.

See also: Are Adam and Eve genetically possible? The latest: Richard Buggs (yes) replies to Dennis Venema (no)

Comments

cornu: "haploid genome" instead of "haploid chromosome."PaV_{February 14, 2018
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Really not sure what youa are aiming at with this calculation. Why is the expected arrival time of a SNP dependant on the mutation rate per chromosome (or actually per genome if you're talking about human mutation rates)?cornu_{February 13, 2018
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Bob O'H: The size of the population becomes a factor when you compute the time for the fixation of a particular mutation; that is, a nucleotide change at a particular locus leading to an a.a. change. If evolution is to take place randomly, this is just a basic step. Here's my numbers, and assumptions Arrival Time= 3 x 3 x 10^9/2Nv ~ 10^10/200Nv=5 x 10^7/N Fixation Time=1/probability of fixation= 1/1/4N=4N(*) v=mutation rate= 100/haploid chromosome/generation (This is my best stab at a 'table') Pop Size: N=100 // N=10,000 // N=100,000 // N=1,000,000 Arrival Time: 500, 000 // 5,000 // 500 // 50 Fixation Time: 400 // 40,000 // 400,000 // 4,000,000 Total Time: 500,400 // 45,000 // 400,500 // 4,000,050 [*] 1/4Ne is Kimura's number for the 'average time for fixation of a mutation.' Very clearly, the optimal population size is around 10,000. When you're not concerned about a particular location, then all mutations are the same, and you get a generic mutation flow rate through a populations. When you ask about a particular location, then population size does come into play.PaV_{February 13, 2018
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I am not entirely sure about PaV's personal observation that if one wants to maximize the speed at which mutations arise and become fixed, then a population of 10,000 is around optimal. I say this on the basis of two things. First, was a paper looking at the spread of mutations over 300 years in Quebec that indicates this process happens faster in small populations at the frontier of the advancing wave front of civilization (Science 334, 1148 (2011); Claudia Moreau, et al.). Second, I am currently working on a program that simulates evolution, with several variables that can be played with. It seems to me, from preliminary runs, that if you want to maximize the speed at which mutations arise and become fixed, then you want a lot of small (100), independently evolving populations, similar to what we probably had as human settlement spread as small tribal groups out across Asia, Europe, Africa and, eventually, the Americas. Essentially, a lot of small, independently evolving populations can take off in all sorts of directions, unimpeded by a large population mass. Eventually, when they coalesce into one large population, you have enormous variation well established in the overall population. I have a lot more work, and a lot of runs to do, each requiring about 24 hours or more of run time for just one data point, so I can't show this yet in the form of graphs, but I plan to, and plan to publish the results. I'm just speaking from preliminary runs as I fine-tune the program to more closely to model reality. But I have run population sizes up to 100,000 and the larger the population and the fewer independently evolving populations, the slower the rate of accumulation of mutations if I use a reproduction rate of 10% (which can also be varied).KD_{February 13, 2018
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Bob O'H: I've just remembered how I did the calculations, and how I arrived at my conclusion. Details to follow when I have time.PaV_{February 13, 2018
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Bob O'H: I found the book. On my bookshelf. Was looking at it, but didn't see it. The calculation I'm referring to is on p.101-102. I no longer remember what I used for the probability of fixation, but I'm guessing is was likely 1/2Ns generations, which, as you indicate, should just cancel out in terms of 2Nmu mutations/generation. I just don't remember now where that trade-off came from at this point. I've done a google search looking for a post where I may have carried out a calculation, and I don't find any. I've looked at a number of my earlier posts--171 of them, and can't pinpoint one. I just can't waste more time looking around. But, I hope making all those calculations back then wasn't a big waste of time. I'm wondering if I left out the 2N factor when calculating the time needed for the mutation to occur. If that's so, then my 10,000 number is of no relevance. With that said, however, I have no idea, then, where this figure of 10,000 comes from that Venema insists upon. Where does it come from, exactly? BTW, I went back to a 2007 post, and there you were!!PaV_{February 12, 2018
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That's Kimura's argument for the neutral theory from genetic load. It can't be the basis for the claim you made in 8, as Kimura assumes many mutations are not neutral. As Bob says, undergrads learn that the fixation rate is independent of Ne for neutral variants. If you want to increase the rate of adaptive substitutions then larger populations are always better. (With very large populations you will run into 'soft sweeps' where alleles that are identical in terms of their genetic sequence actually arrive from independent mutations. You could argue these are not true substitutions since the alleles that fix are not identical by descent. But that would be some next-level quibbling and not really relevant to the biology).cornu_{February 12, 2018
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Bob O'H: I've misplaced my copy of Kimura's "Neutral Theory of Evolution." He made a calculation for a population of elephants using standard selection theory, I believe, and I simply followed his calculation. I don't have time now to scour my room; but, if I get my hands on the book, I can review it and respond. IIRC, population size did matter. It didn't just simply cancel out. So, once found, and assuming I remember things correctly, I'll have a 'citation.' But, not really, since I'm 'citing' my own experience. I haven't been a "scientist" since I left graduate school in 1973. I quickly became an engineer; and then even moved on from there. (It's hard to keep up with me. :) Posting at UD is simply an avocational interest, one that's waned substantially over the last five or six years. )PaV_{February 12, 2018
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PaV @ 8 -
The smaller the population, the fewer mutations arise; and, the larger the population, the longer it takes (4Ne replications) for a neutral mutation to become fixed. There’s a trade-off.
Yes, and the effect of population size on the probability of fixation cancels out: this is undergrad stuff.
And, if you crunch enough numbers enough times, you then zoom-in on the figure of around 10,000 as the ideal population size.
Can you show me an example of the figures being crunched?
Why would there be a citation?
Because if you have something more solid than "I say it is like this", it becomes much easier to accept your claims, and might also provide some more insight into what's going on.Bob O'H_{February 12, 2018
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Bob O'H: My claim should not be surprising. The smaller the population, the fewer mutations arise; and, the larger the population, the longer it takes (4Ne replications) for a neutral mutation to become fixed. There's a trade-off. And, if you crunch enough numbers enough times, you then zoom-in on the figure of around 10,000 as the ideal population size. Why would there be a citation? Why would evolutionists want it to come out that the numbers they throw around are just favorable estimates they like to use? And, if you "expect a scientist making that claim to have either a model or data to back it up," then why can't Venema, when telling Christians that science tells us that the minimum population size for the human lineage is 10,000, give us a citation? I think I've given the real reason why.PaV_{February 12, 2018
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PaV - the result you claim is surprising so I would expect that you have something more formal than a comment in a blog post. I would expect a scientist making that claim to have either a model or data to back it up, so they would be able to point to a paper or manuscript reporting it.Bob O'H_{February 12, 2018
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Bob O'H: You want a citation for something I've noticed on my own? Am I missing something? What are you looking for? I just reread my post. Are you being sly? Are you saying that I have no citation, just as Venema has no citation; ergo, a 'Mexican standoff'?PaV_{February 12, 2018
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Source for Venema?: Recent human effective population size estimated from linkage disequilibrium, Albert Tenesa, Pau Navarro, [...], and Peter M. Visscher "Overall, the estimates of Ne appear to be much lower than the usually quoted value of 10,000 (Takahata 1993). Earlier studies using mtDNA data suggested an Ne in the range of 1000–6000 (Rogers and Harpending 1992; Harpending et al. 1993; Sherry et al. 1994), for a population ?200,000 yr ago (?10,000 generations ago). Erlich et al. (1996) estimated a recent population size of ?10,000 from HLA polymorphisms. Sherry et al. (1997) estimated an ancestral population size of ?17,800 during the last one to two million yr from Alu repeats evolution." https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1832099/ Takahata N. Allelic genealogy and human evolution. Mol. Biol. Evol. 1993;10:2–22. [PubMed] Erlich H.A., Bergstrom T.F., Stoneking M., Gyllensten U., Bergstrom T.F., Stoneking M., Gyllensten U., Stoneking M., Gyllensten U., Gyllensten U. HLA sequence polymorphism and the origin of humans. Science. 1996;274:1552–1554. [PubMed]redwave_{February 12, 2018
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You cannot use standard evolutionary claims to test for Adam and Eve who would have been designed to evolve/ adapt.ET_{February 12, 2018
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Over the years I’ve noticed that if you want to maximize the speed with which mutations arise and become ‘fixed,’ the optimal population size for animal populations is right around 10,000.
Oh, that's interesting. Do you have a citation for it?Bob O'H_{February 12, 2018
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It seems like the reality is, rather than the data forcing anyone into the idea of a population of 10,000, the real fact is that 10,000 is the working model of a lot of individual biologists. That's a *huge* difference for someone trying to make the argument that the science dictates that there were more than two individuals. Saying "science dictates X" is drastically different than "scientists generally prefer X as a working hypothesis". I have not read the book, but, based on what I've heard about it, the idea that science dictates that there were more than two people is pretty much the foundational starting point that the rest of the book works from. And it turns out that the starting point may not even be controversial, just wrong.johnnyb_{February 11, 2018
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Over the years I've noticed that if you want to maximize the speed with which mutations arise and become 'fixed,' the optimal population size for animal populations is right around 10,000. I suspect that is the true origin of this number: that is, Venema won't find, and will be unable to give Buggs, any citation that documents this number. It's just a convenient number that, repeated enough times, becomes 'fact.' Oh, how wonderful the scientific methods in the hands of some!PaV_{February 11, 2018
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