Geneticist Richard Buggs, Reader in Evolutionary Genomics at Queen Mary University of London, has just written an intriguing article in Nature: Ecology and Evolution (28 October 2017), titled, Adam and Eve: a tested hypothesis? Comments on a recent book chapter. It appears that Buggs is unpersuaded that science has ruled out Adam and Eve. He thinks it’s still theoretically possible that the human race once passed through a short, sharp population bottleneck of just two individuals, followed by exponential population growth. Buggs disagrees with the assessment of Christian biologist Dennis Venema, professor of biology at Trinity Western University in Langley, British Columbia, who forthrightly declared in chapter 3 of his 2017 book Adam and the Genome that it is scientifically impossible that the human lineage ever passed through a bottleneck of two, and we can be as certain about this fact as we are about the truth of heliocentrism.
Here’s Buggs’ take-down of the three methods employed by Venema to discredit the possibility of a single primal couple. As a layperson, I have to say it looks as if Buggs has done his homework:
Linkage disequilibrium within populations
…The methods assume that the populations at any given time point are at equilibrium and not expanding exponentially (the authors deliberately exclude the last 10,000 years from this analysis as they know that exponential population growth has occurred in this timeframe). It is hard to see how they could pick up on a short, sharp bottleneck even if one had happened. It would be nice to see this modelled, just to check.
PSMC method
…More recently, some simulations by a graduate student have shown that the PSMC method does not detect short, sharp bottlenecks, such as those caused by a pandemic or natural disaster. Thus I cannot see that PSMC analyses (many more of which have been done on human genomes since the original paper by Li and Durbin) can be cited as rigorously disproving a short, sharp bottleneck.
Incomplete lineage sorting
Venema makes an argument based on incomplete lineage sorting among humans, apes and gorillas, which gives a large estimated effective population size. This argument is not relevant if we are only interested in the human lineage (the occurrence of ILS does not require maintenance of large populations sizes in every lineage after speciation and so does not exclude a bottleneck in the exclusively human lineage).
Buggs adds:
We need to bear in mind that explosive population growth in humans has allowed many new mutations to rapidly accumulate in human populations (A. Keinan and A. G. Clark (2012) Science 336: 740-743). Hyper-variable loci like MHC genes or microsatellites have so many alleles that they seem to defy the idea of a single couple bottleneck until we consider that they have very rapid rates of evolution, and could have evolved very many alleles since a bottleneck.
In his conclusion, Buggs modestly refrains from claiming to have rebutted Venema’s arguments:
The question asked by my religious friends is different to the questions being asked in the studies discussed above. My religions (sic) 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…
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.
I would be interested to know what biologists think of Richard Buggs’ article. Is he right? Does science still leave open the possibility of Adam and Eve? Over to you.
vjtorley,
Using the argument on preservation of historic variation through the bottleneck, one is trying to ‘load the decks’ by making A & E more distantly related than two randomly selected members of an ancestral population. It’s actually more likely that they were more closely related than two ‘random’ members. Population genetic simplifications generally give populations a vigorous shake; in reality, matings tend to be much more local.
So God – for the usual peculiar and ad hoc reasons – has picked very distantly related individuals to survive a bottleneck, because He can’t generate variation any other way?
Spot on. Why can God conjure two working specimens of Homo sapiens out of thin air, but is then suddenly limited by the genetic variation contained in them? If we are to throw biological plausibility out of the window anyway, let us at least be consistent about it.
ETA: just realised that A&E were supposed to be founders from a previous population in this particular version. But I guess that since God is omnipotent He still should not be limited in this respect.
Also, can somebody explain to me why every possible aspect of the tale is sacrificed in order to salvage that humanity descended from a single pair?
Is that because of the theological implications of the fall, as keiths suggests?
Yes, Vincent mentioned this as well. It is probably a play on words that derives from the Sumerian (not Hebrew) language. Pretty neat.
Allan,
It’s not that he can’t generate variation any other way, but that he wants to lighten up on the miracles. It’s the Principle of Miracle Minimization, or PMM. By limiting the number of miracles, God makes the story slightly less ridiculous and enables later believers to accept it with less cognitive dissonance.
Unfortunately, the story is still ridiculous, and a much more sensible one — that Adam and Eve never existed — is available.
It is unfathomably unlikely that there was a Rumraket.
Hi Corneel and keiths,
I should point out that Dr. Steve Schaffner is a computational biologist in the Program in Medical and Population Genetics at the Broad Institute. We need to keep in mind what Dr. Schaffner wrote in his comment above:
So concerns about heterozygosity are misplaced. Here’s where the real problem lies:
The conclusion I draw is that an ancient Adam and Eve scenario is still biologically credible, provided that Adam and Eve were members of a large original population of hominins. In other words, the biological plausibility of Adam and Eve depends on the assumption of human evolution.
Corneel asks:
The Fall is a central doctrine in Christian teaching. No Fall, no Redemption. It’s difficult to explain how Adam’s Fall could affect the entire human race if he were not the ancestor of the entire human race. Other aspects of the Adam and Eve account are of secondary importance.
vjtorley,
I see. Thank you for explaining.
Also if he were.
Glen Davidson
Its irrelevant from the point of view of the genetic arguments whether A+E were the only 2 individuals or part of a larger population.
Its sounds like you agree with a particular theological view that A+E were 2 members of a population that somehow God singled out, but they weren’t the only ancestors of humanity because we’re descended from other members of the same population as well
Vincent:
Any cross-species polymorphisms in which there are more than 4 alleles render a bottleneck of 2 individuals impossible. If there are any Y-linked cross-species polymorphisms at all, that’s just as bad. Or X-linked with more than 3 alleles. I don’t know about the latter two possibilities, but the first definitely exists in at least one HLA locus.
vjtorley:
Glen:
Indeed. Vincent, do you really think original sin is encoded in our genes? If yes, how exactly did that happen? Why has it been evolutionarily conserved?
If no, then what law of metaphysics requires original sin to be inherited vertically? Or inherited at all? And how was the Virgin Mary protected from it, despite the fact that both of her parents were afflicted?
John, to Vincent:
Unless there has been sufficient time post-bottleneck to plausibly explain the origin of the additional alleles by mutation. Right?
Wrong. That’s what “cross-species” contributes. Any allele shared with chimps was inherited from the common ancestor. You could of course invoke miracles.
Well, it appears that the biologists disagree.
John Harshman:
Richard Buggs:
Curiously, Buggs says nothing about HLA.
Would anyone like to comment? Professor Felsenstein, perhaps?
RodW:
No. The scenario I was considering (because I think this is what Buggs may have had in mind) is one where the entire hominin population gets wiped out worldwide, due to some natural catastrophe, leaving only two individuals (who were perhaps hiding in a cave) to populate the planet.
keiths,
No. It’s purely a privation, in Catholic theology. It simply means that we’re not born children of God, that’s all.
Well i would insist its got nothing to do with sumerians. Thats just a guess from somewhere.
The genesis story is the real one. possibly these sumerians just have a corrupted memory of the true story.
John:
Ah. Now I see what you were getting at.
Vincent,
Then what is your response to the second part of my comment?
Vincent,
Keep in mind that John is talking about cross-species polymorphisms. (I overlooked that too.)
If the number of matching alleles is greater than four, then the excess matching alleles must have originated independently in the two lineages.
Cuz.Robert sez so.
I have been occasionally reading this thread, but whenever I was tempted to make a point, darn it, someone then made it before I could.
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. 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.
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. 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.
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.
Steve Schaffner:
Hence the second part of my comment:
Steve:
Right, or more precisely, it depends on how reachable they are. An allele might be complex, but if (for example) it’s just a single nucleotide different from a complex predecessor that was present in the common ancestor, then it’s plausible for it to have arisen independently in the two lineages.
Steve,
I recall that you’re a Christian, so I’d be curious to know whether you accept the doctrine of original sin, and if so, how you would answer the questions I posed to Vincent above about its hereditary transmission.
Yes. You have forgotten that I was talking specifically of cross-species polymorphisms, not just polymorphisms. Was that somehow unclear?
Also, HLA loci are MHC loci.
What I find interesting about this topic is that with this, IDers give up all pretense about not being religiously motivated.
Here is an esoteric topic within an esoteric field that I would have thought was completely uninteresting and irrelevant to ID. There is no legitimate reason to doubt it and yet IDers have continued to attack it ineffectually. Their only reason is that it conflicts with a particular theological interpretation of a religious myth. At least the claims of Meyer, Behe etc can be justified as based on the objective observations of the complexity of living things and are sometimes even compelling to uninformed atheists such as Flew.
vjtorley,
You are a one for credentials, Vincent!
What I would like to see is a computational analysis by someone who advocates the two-individual bottleneck to try and generate a realistic pattern of modern diversity from those two individuals, gaming their initial ‘diversity’, as represented by their autosomal alleles, however they like. They can play God here, and tune the parameters as they wish. I’m inclined to think it can’t be done – that you can’t get here from there.
And, I actually don’t think heterozygosity a red herring. You have 4 alleles max to play with in a 2-individual bottleneck. If you reduce a population to 2 and then keep it at 2, you will lose heterozygosity much more rapidly than if you reduce it to (say) 10,000 and keep it at 10,000. It is only if you reduce it to 2 for the briefest of times and then immediately go into an exponential phase that you can retain that diversity – but it has still been bottlenecked, by only having 4 options max per locus (frequently fewer).
What claims? That life has functional complexity? And that if you define design as functional complexity then life is defined as designed?
Yes, if you define life as designed, it’s designed. Then you can just ignore the facts of biology that run counter to observed design results.
Well, if it can fool enough people it can provide substantial returns to Stephen Meyer, at least.
Glen Davidson
The claims that don’t involve trying to reconcile reality with a particular passage in Genesis.
VJTorely,
FWIW, I heard Joshua Swamidass of Biologos may accept a literal Adam and Eve. He may be worth looking up. He has posted here at TSZ before. Don’t quote me on that though, but I would be interested to know if that is true and he may have some scientific reasons for believing this.
Sal
Hi Allan Miller,
I think that’s an excellent proposal, and I’d like to second it. I wonder if Dr. Ann Gauger would be interested in taking it up.
Hi Sal,
I’ve invited Dr. Swamidass to contribute to this discussion, so he may join us in the next day or so.
You might want to read his review of Scot McKnight and Dennis Venema’s book,
Adam and the Genome: http://peacefulscience.org/reviewing-adam-and-the-genome/
See also this more recent article of his, dated October 24, 2017:
http://peacefulscience.org/genealogical-rapprochement/
Dr. Swamidass acknowledges “the genetic evidence in which it appears (1) our ancestors arise as a population, not a single couple, and that (2) we share ancestry with the great apes.” But he also tentatively puts forward an additional hypothesis of a recent Adam and Eve, whose offspring interbred with biological humans who lacked any awareness of God:
Hi John Harshman,
No. What was unclear was how one can tell that a polymorphism is indeed a cross-species polymorphism, in the sense you intend: namely, one inherited from the common ancestor of humans and chimps. The fact that alleles are common to humans and chimps doesn’t necessarily mean they were inherited from the common ancestor of both.
And keiths writes, in a similar vein:
Once again, I’m not clear as to why the presence of “matching alleles” necessarily implies that all of these alleles were inherited from the common ancestor of humans and chimps.
“Impossible” is a strong word. I notice that Professor Felsenstein doesn’t seem to be using it. He seems to think a human bottleneck of two in the distant past is highly improbable, without putting a figure on it:
However, I’m not a scientist, so if someone would care to set the record straight, they are welcome to do so.
Hi keiths:
Original sin is not “inherited” in a genetic sense of the word. Rather, we should speak of a privilege forfeited by our first parents, to which their descendants can no longer lay claim. Of course, if God chooses to bestow that privilege on some individual at a subsequent stage in history, that is His choice.
There is no way to “set the record straight”. All you have done is abandon science, whose results are always provisional even if the alternative is vanishingly improbable. There is no proof in science, and what we mean by “impossible” is “a probability so small that we can afford to ignore it as an explanation”. Now, what you are apparently proposing is that the within-locus phylogeny of HLA is incorrect, and that the alleles we think are more closely related to homologs in chimps are in fact more closely related to other human alleles, and that the similarities are convergent across species. That is certainly possible, especially if you allow for miracles, but is it probable enough to consider seriously barring the miracles? I would say not, and I don’t think you can justify any contrary claim.
Then why doesn’t he bestow that privilege on everyone? Are we to be condemned on a whim because of something one of our many ancestors did and in which we had no part? How does that make even surface sense?
Are you citing a Catholic doctrine here? Can you point me to the source?
Something appears to be in the works:
http://bio-complexity.org/ojs/index.php/main/issue/view/30
Should we just ignore the evidence that men are in fact sinners?
Mung,
Speak for yourself. And, if you feel like getting all judge-y on my ass, I have a couple of Bible quotes primed and ready to go.
I presume here you’re talking about the particular set of alleles I inherited from my parents and the unique set of mutations that came along with the process. If so, the improbable nature of the kinds of genetic changes it would take to account for extant human genetic diversity to evolve from a single breeding pair, are very different from the rather mundane event it is that a new human is born with some set of “standard” mutations.
Each banana is unfathomably unlikely. And yet, bananas!
Joe Felsenstein,
What do you base your mutation rate on?
How do you know or calculate what the mutation rate was say… 5000 years ago?
Hi everyone,
Just a quick update: Dr. Buggs has informed me by email that he has tweeted a link to my blog post, and that when he next writes a blog on this topic, he intends to refer to the comments on this site. I would like to thank Dr. Buggs for his kind acknowledgement.
Hi John Harshman,
Now we come to the nub of the matter:
I wasn’t proposing any miracles. So your claim is that an independent origin for the alleles in question is vanishingly improbable. If that’s correct, then we can rule out Adam and Eve, for all practical purposes.
As many readers are doubtless aware, Dr. Ann Gauger has a different take on the matter:
However, I don’t know what Dr. Buggs thinks of her arguments, as he hasn’t mentioned her work.
Erik and John Harshman,
You asked me about the Catholic understanding of original sin. I’ll simply refer you to what the Catechism of the Catholic Church says on the subject:
It can be seen that original sin is a privation or deprivation. The Catechism speaks of it being “transmitted,” but it should be apparent that they’re not speaking of anything genetic, here.
vjtorley:
So the proper Catholic answer to my question…
…is “we have absolutely no idea, and it makes no sense. We just believe it in order to prop up Christian doctrine.”
The Catechism basically admits that here:
“A mystery” is Christian shorthand for something that is deeply irrational but part of the dogma, like the Trinity. The doctrine of original sin is nonsensical, and it makes a mockery of the notion of a just and loving God. But orthodox Christianity falls apart without it, and so Christians embrace the ridiculous.
Vincent,
Which puts you in a bind. If all of Creation was perfect, with no privations, then why did Adam and Eve rebel?
It’s clear that Creation was not perfect, and that God himself is ultimately responsible for the sin of Adam and Eve, and hence for the Fall.