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Geneticists Debate a First Human Pair — Continued; Where Is Dennis Venema?

human pair

Genuine scientific debate on fundamental issues that real people care about is such a rarity that when it happens, you almost want to pinch yourself to make sure you’re not dreaming. A biologist and theistic evolutionist, Dennis Venema, wrote a book, Adam and the Genome, telling fellow Christians how, among other things, they must give up belief in an original human couple. This, we’re told, is due to the undeniable conclusions of population genetic studies.

But a distinguished geneticist, Richard Buggs of Queen Mary University in London, weighed in on the question in a blog post for Nature Ecology & Evolution, part of the group of journals that includes Nature. No venue could be more mainstream. The Oxford University-trained Buggs informed Dr. Venema of Trinity Western University (near Vancouver) that he had said more than the relevant science itself says.

Buggs had listened carefully to the concerns of some friends:

The question asked by my religious friends is different to the questions being asked in the studies discussed above. My religious friends are not asking me if it is probable that humans have ever passed through a bottleneck of two; they are asking me if it is possible. None of the studies above set out to explicitly test the hypothesis that humans could have passed through a single-couple bottleneck. This is what we need to nail this issue down.

Buggs then asked for responses from fellow scientists:

If I am missing something, then I would very much like to know. Whilst this issue may seem trivial to many readers, for large numbers of religious believers in the world, this is a critical issue. Do they really face a binary choice between accepting mainstream science and believing that humans have, at some point in their history, all descended from a single couple? I am open to the possibility that they do face this dilemma, but I need more evidence before I am persuaded.

And guess what, he got some substantive responses from substantive people, not mere hissing from the Darwinist peanut gallery. Buggs at his blog directed readers to a discussion at The Skeptical Zone, and we followed him where he lead. A writer there had acknowledged Buggs for doing his “homework” and asked biologists what they thought. I noted one response earlier today from University of Washington geneticist Joseph Felsenstein.

Now in the same space Buggs interacts with computational biologist Stephen Schaffner of the Broad Institute, plus Felsenstein and biologist John Harshman, the latter of whom, unlike Venema, he thinks makes the “strongest case against a bottleneck of two”:

Thank you all for interacting with my Nature Ecology and Evolution Community blog, and thanks to Vincent Torley for posting here. Vincent kindly sent me a personal email pointing out this thread to me and asking me to specifically interact with comments made by Steve Schaffner and Joe Felsenstein. I will also comment on John Harshman’s comments as he is making the strongest case against a bottleneck of two, which was not mentioned explicitly by Dennis Venema in his book chapter.

First, I note that both Schaffner and Felsenstein agree with my point that the bottleneck hypothesis has not been directly tested.

Schaffner: “Buggs is right that existing tests have not been tested rigorously against an ancient Adam and Eve scenario. On the other hand, no one has shown that such a scenario would be undetectable by those tests either; it’s just not a scenario most geneticists are interested in.”

Felsenstein: “Most of the effort in analyzing these data has been to infer the past history of population size, rather than to make statements about A&E [Adam & Eve].”

Felsenstein goes further than this and suggests that it could never be entirely disproven: “If one poses the problem as whether we can absolutely certainly rule out A&E, that is asking for more than science can deliver. But if we ask whether it is made very improbable, that is not as hard to establish.”

Second, I note that neither of them are defending the PSMC argument, and Felsenstein implies that it is not necessarily reliable and new methods need to be developed

Felsenstein: “There are coalescent methods that use more information than PSMC, which only uses 2 haploid genomes at a time. Those methods need more development, but when they get it there will be more focused analyses.”

Thirdly, I note that no one so far has challenged my statements about the Tenesa at al paper based on linkage disequilibrium (I would welcome more comments on this paper).

Fourth, I need to respond to Schaffner’s comment: “The argument about total heterozygosity is a red herring. A tight but short bottleneck has a relatively modest effect on heterozygosity, but a dramatic effect on the distribution of allele frequencies. A bottleneck of two individuals eliminates all frequencies at less than 25% frequency, which is where the great majority of variants are.”

I don’t think it is a red herring, as (1) it is worth pointing out to the non-specialist that the results of a short bottleneck are far less devastating than a long one, where inbreeding would eventually eliminate all allelic variation; (2) during a bottleneck of two, most variability has to be carried by heterozygosity within the two individuals, so this is important; (3) because there are four DNA bases, two individuals can potentially carry all possible alleles at any given SNP locus. In response to his final sentence above, I note that it is the high frequency alleles in the human population that most require explanation in terms of ancestral variation, and those alleles at less than 25% frequency are also the ones most easily explained by recent mutation.

Fifth, I’m really glad to hear that Steve Schaffner has done some simulations. This is exactly what I think needs to be done to nail down this issue.

Schaffner: “I doubt anyone has ever made a formal test, but having played around with simulations I think an absolute minimum of several hundred thousand years would be required to generate something like the observed frequency spectrum for humans; half a million years is a more plausible lower bound… It’s not clear how many creationists are interested in a half million year old Adam anyway.”

I very much hope that Schaffner will write these up for publication. I agree with his final comment, but a creationist (in the conventional sense of the word) would not be concerned about this entire topic as it assumes common ancestry and creationism can have genetic diversity front-loaded into Eve’s ova anyway, thereby avoiding the whole issue of genetic diversity. I suspect many Christians, Jews and Muslims would be interested in the idea of a half million year old ancestral bottleneck of two.

Sixth, to come to John Harshman’s comments: John is making an argument from huge allelic diversity of HLA (human MHC) alleles and signatures of incomplete lineage sorting among these. This is the strongest argument being made in this thread against an ancestral bottleneck. Schaffner and Felsenstein have commented on this:

Schaffner (on HLA): Buggs is suggesting that some of the alleles shared between species could represent homoplasies, presumably as a result of similar selective pressures. How likely that is depends on how complex the alleles are.

Felsenstein: “Just saying that rates of mutation are high and so the pattern could occur is insufficient. One needs a more quantitative analysis with estimated mutation rates. HLA is a hard case for A&E — it would be even better to find more polymorphisms involving multiple haplotypes and put all that information together.”

I agree with both of these points. More work is needed to show in detail whether or not MHC diversity renders a bottleneck impossible. My major overarching point here would be that we need to look at genome-wide patterns of polymorphism to get a reliable picture of past effective population sizes. MHC loci are pretty exotic. Several studies show that they evolve fast and may be under sexual selection, pathogen-mediated selection, and frequency-dependent selection; they may also have heterozygote advantage (see e.g. [LINK]). The maintenance of MHC polymorphism is still “an evolutionary puzzle” ([LINK]). There is some evidence for convergent evolution of HLA genes ([LINK], [LINK], [LINK]). If the whole case for large human ancestral population sizes rests on MHC loci, I think this is inadequate to prove the point, given our current state of knowledge on MHC evolution. As Felsenstein says “— it would be even better to find more polymorphisms involving multiple haplotypes and put all that information together.”

These scientists can speak for themselves. But the conversation so far seems to provide evidence Venema was wrong about one thing: that religious believers currently face, as Buggs puts it, a “binary choice between accepting mainstream science and believing that humans have, at some point in their history, all descended from a single couple.” On the contrary, mainstream science on the subject speaks in multiple voices.

The question of a first pair has not been “nailed down,” and theistic evolutionists are mistaken to imply that it has been. What does Dennis Venema say to all this? Dr. Buggs calls him the “go to expert on this issue within the organisation BioLogos.” However, Dr. Venema’s BioLogos blog, mainly concerned with arguing against intelligent design, has not been updated since June 8. So I have no idea.

UPDATE: Venema has now replied to Buggs, after promising to do so in the same thread at The Skeptical Zone. A Part 1 is up. He originally received Buggs’s challenge in an email dated May 10, but explains, “I’m typically running behind on my email inbox at the best of times, and a reply to Dr. Buggs was clearly not going to be a note that I could dash off in a spare few minutes.” He maintains the comparison with geocentrism:

I agree with Buggs that science has not “disproven” that humans could have descended uniquely from just two people (and also I’m acutely aware that this last sentence is particularly ripe for selective quoting). In the same breath, I also don’t think that science has “disproven” geocentrism – the idea that the earth is the immobile center of the universe.

Oddly, the reply is dated November 10 and so doesn’t currently appear on the front page of his “Letters to the Duchess” blog. Must be a glitch.

Image credit: A human couple, by Hans, via Pixabay.