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Adam and the Genome and “Predetermined Conclusions”

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Adam and the Genome

In two previous posts (here and here), we saw that evolutionary genomicist Richard Buggs and biologist Dennis Venema have been debating online about Venema’s argument in Adam and the Genome that human genetic diversity refutes a traditional view of Adam and Eve. (Find the rest of our series of posts on the book here.) Buggs explained that Venema’s allusion to human leukocyte antigen (HLA) genes (also called major histocompatibility complex, or MHC, genes) do not refute an original human couple. In his Nature Ecology & Evolution blog post, Buggs writes, “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.” Buggs also explained in a comment at The Skeptical Zone that the ability of MHC genes to evolve rapidly isn’t a good argument for a large ancestral population size:

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, 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.

Buggs isn’t the only qualified biologist who has looked at arguments from MHC genes against Adam and Eve and found them lacking. In the book Science and Human Origins, Ann Gauger considered the evidence, and found it compatible with an initial couple. She recounts her investigation of this topic:

When I began this study, I was prepared to accept that there was too much genetic diversity among these genes to have passed through just two first parents. To my surprise, I found that even this most polymorphic (most varied) region of our genome does not rule out the possibility of a first couple.

(Science and Human Origins, p. 106)

As Gauger points out, the evolutionary biologist Francisco Ayala had calculated that there were 32 different HLA alleles in existence when the human lineage diverged from chimps, requiring “that the minimum size of the ancestral population was no fewer than 4,000, with a long-term average effective population size of 100,000.” She explains why this supposedly refuted Adam and Eve:

Because of this minimal estimate of 4,000, Ayala claimed that at no time was it possible for the human population to have passed through a bottleneck of two. In his view, there is just too much ancestral diversity in HLA-DRB1.

(Science and Human Origins, p. 111)

After reviewing Ayala’s arguments, however, she found that his model had both explicit and implicit assumptions that were dubious:

These explicit assumptions include a constant background mutation rate over time, lack of selection for genetic change on the DNA sequences being studied, random breeding among individuals, no migrations in or out of the breeding population, and a constant population size. If any of these assumptions turn out to be unrealistic, the results of a model may be seriously flawed.

There are also hidden assumptions buried in population genetics models, assumptions that rely upon the very thing they are meant to demonstrate. For example, tree-drawing algorithms assume that a tree of common descent exists. The population genetics equations also assume that random processes are the only causes of genetic change over time, an assumption drawn from naturalism. What if non-natural causes, or even unknown natural causes that do not act randomly, have intervened to produce genetic change?

(Science and Human Origins, p. 112)

Gauger realized that in this case, Ayala had wrongly assumed a lack of selection on these genes, and wrongly assumed a constant background mutation rate. Another study that corrected for these problems found that only seven copies of HLA need have existed, which Gauger calls a “dramatically lower estimate for the number of HLA-DRB1 alleles in the ancestral population than the number Ayala found in his study (i.e. seven alleles versus thirty-two).” (p. 113) A later paper reported that HLA-DRB1 alleles numbered only four or five at the time of our supposed split from chimps. This number is low enough to have passed through a single couple.

Now of course Venema cites papers that looked at many other genes and their various alleles in the human genome. So there’s a lot more data that remains to be evaluated. But note why Gauger chose to study HLA genes:

I chose to look at the HLA-DRB1 story because it seemed to provide the strongest case from population genetics against two first parents. If it were true that we share thirty-two separate lineages of HLA-DRB1 with chimps, it would indeed cause difficulties for an original couple. But as we have seen, the data indicate that it is possible for us to have come from just two first parents.

(Science and Human Origins, p. 120)

For a short online summary of Gauger’s argument, see here.

A Prescient Warning

If perhaps the strongest argument against Adam and Eve — from population genetics — has fallen apart, what will happen when other genes are similarly scrutinized? Of course we should wait and see what the evidence says, but Gauger’s warning is prescient:

[O]ne thing is clear right now: Adam and Eve have not been disproven by science, and those who claim otherwise are misrepresenting the scientific evidence.

(Science and Human Origins, p. 121)

Indeed, much data remains to be examined. And Gauger and some of her colleagues, such as Ola Hössjer, have been addressing that data. They have published two peer-reviewed papers that present models for potentially testing population genetics arguments against a first couple at our origin: 

Their papers evaluate the assumptions underlying the standard evolutionary model of human origins and find “it is full of gaps and weaknesses.” The authors maintain that “a unique origin model where humanity arose from one single couple with created diversity seems to explain data at least as well, if not better.”

Created Founder Diversity

After reviewing five main mechanisms invoked by standard evolutionary models of population genetics to explain human genetic diversity (mutation, genetic drift, natural selection, recombination, and colonization and migration), the first paper observes:

Neo-Darwinism accounts for the above-mentioned mechanisms I-V, and among them germline mutations are essentially the only way by which novel DNA can arise. The theory does not allow for large amounts of new and suddenly appearing diversity. The reason is that neo-Darwinism is framed within methodological naturalism. This prevailing approach to science only allows for natural hypotheses. But if an intelligent designer is invoked as a possible explanation, and if humanity originates from one single couple, it is possible that their chromosomes were created with considerable diversity from the beginning.

Thus, the authors propose a sixth mechanism of genetic change, called created founder diversity. Created founder diversity is biologically plausible for DNA of non-sex chromosomes, and would allow for initial genetic diversity among all four sets of autosomes in the first couple.

The authors note that the “main argument against a unique origin is that the nucleotide diversity of human DNA data seems too high in order make a single founding couple possible.” But they argue it is possible that humans are descended from an initial couple if “they were created with genetic diversity in their autosomal and X-chromosome DNA.” They conclude: “Any common descent model faces a challenge to explain the genetic differences rather than the similarities with other species, the consequences of inbreeding depression and increased genetic entropy, human DNA mixture with archaic populations, and that our DNA resembles a mosaic of about four founder genomes.” Thus, they find, “The provisional conclusion is that a unique origin model seems more plausible.”

 Their second paper presents mathematical algorithms “for testing different historical scenarios of the human population,” including common ancestry models, and models where humans “all descend from one single couple.” Their mathematical approach can simulate human history by varying different parameters, including population expansion, bottlenecks, colonization and migration patterns, mating and reproduction schemes, and various types of mutations in autosomal chromosomes, sex chromosomes, and mitochondrial DNA. Additionally, “An important parameter of the model is the created diversity of the founder generation, since it facilitates a higher degree of genetic diversity for a relatively young population within autosomal and X chromosomal regions, and possibly also for mitochondrial DNA.”

Their algorithms incorporate what they identify as the six major mechanisms of genetic change: (i) genetic drift, (ii) genetic recombination, (iii) colonization and migration, (iv) mutations, (v) natural selection, and (vi) initial created founder diversity. They note that “common descent models only include the first five mechanisms, but (vi) is important in order to generate enough diversity for a population with only one founding couple.” Indeed, they observe that a “particularly important parameter is the created diversity, which makes it possible to obtain a substantial amount of genetic diversity for nuclear autosomal and X-chromosome DNA, during a relatively short period of time.”

After going through a detailed mathematical analysis of the model, they conclude, “In subsequent papers, we plan to simulate human DNA data from our proposed model in order to assess how well it fits real data,” with the ultimate goal of finding “the best fitting population history within a unique origin framework, and then to compare it with a best fitting common ancestry model.”

The Best Treatment of This Issue

Probably the best treatment of this issue found anywhere is the chapter “An Alternative Population Genetics Model,” by Ann Gauger, Ola Hössjer, and Colin Reeves in the book Theistic Evolution: A Scientific, Philosophical, and Theological Critique. There, they find key human genomic diversity evidence is highly compatible with Adam and Eve:

Block Structure of DNA. A large part of our autosomal and X-chromosomes have apparently been recombined into blocks of varying length. Many of them are of the order 10,000 nucleotides long, but the variation in length is large. But even though the blocks are long, there is still very little variation within them. Each block comes in just a few variants, four for many parts of the genome. Our chromosomes are different mosaics of these block variants.

This DNA block structure is remarkably consistent with a unique origin hypothesis. If Adam and Eve were created with DNA diversity, there would have been four different copies of each autosomal chromosome — two in Adam and two in Eve. Their four chromosomes have since been scrambled by ancestral recombinations, and today each of us has one mosaic of the four founder chromosomes inherited from our father, and another one from our mother.

After reviewing various aspects of the genetic evidence, they conclude:

We have argued that a unique origin model (with a young or old age of humanity) with created diversity should have at least the same explanatory power for human genetic data as the most popular common descent scenario of today. Any model must be able to explain the big genetic differences between humans and other species, solve the problem of inbreeding depression, support the viability of human and archaic population admixtures, and give reasons why our DNA resembles a mosaic of about four founder genomes. The conclusion is that the unique origin model seems more plausible.

They end their chapter by discussing the models they are currently in the process of testing (the aforementioned technical papers).

We are currently working on implementing a model based on backward simulation. The intent is to validate it with real data. This is a long-term project, whose outcome we hope to publish elsewhere. Using this approach, it may be possible to demonstrate that a unique origin model is able to replicate current human diversity as well or better than the common descent model. That is the purpose of the model—to test this possibility. Therefore, if more than one plausible account of human origins can explain the data, the common descent model of our origin from ape-like ancestors can no longer be claimed as conclusive proof that there could not have been a single first pair. Thus, it would be premature to discard traditional interpretations of the reality and historicity of Adam and Eve. [Emphasis added.]

Obviously  more work remains to be done. But if Venema wants to maintain that Adam and Eve are truly refuted, he’s going to have to contend with this modelling research, which isn’t complete, but already points in a promising direction.

In fact, Venema did respond — though only very briefly, and very dismissively — to this work. As we explained here, on the BioLogos website Venema called the papers “a (poor) attempt to argue for a predetermined conclusion that humans were specially created as a pair in the Middle East. It does not offer a mechanism to deal with the obvious problems of such an approach other than an appeal to ‘created diversity.’” University of Stockholm mathematician Ola Hössjer, who co-authored the papers, responded:

Venema basically criticizes the Middle East version of the unique origin model, saying the African DNA looks older than non-European DNA, both from single locus allele frequency statistics and from two locus linkage disequilibrium patterns. But we also point out that this is a drawback of the Middle East unique origin model (on the other hand we argue that a ME origin has other advantages, for instance less inbreeding depression). We offer some tentative explanations (reference 50, for instance) of why African DNA could look older even if humanity originated in the Middle East. Venema rules out these explanations as inadequate. This may very well be true, but it remains to be seen when the model is implemented.

It’s worth stating that these papers offer a model that can be used to test many scenarios, not just that of a single couple at our origin. The model will allow the examination of the effects of mutation rate, selection, recombination, population structure, and population history on patterns of genetic variability, in order to determine which scenarios best reproduce modern genetic diversity. As for the hypothesis of a single pair with created diversity, which Venema labels a “predetermined conclusion,” it is simply one hypothesis to be tested among many.

Moreover, initial “created diversity” is a legitimate, testable mechanism. We know how genetics works and we can decide whether (within the bounds of genetics) initial high diversity could account for present-day observations.

Unfortunately, critics of this work seem to want to reject the proposed model before it’s even been fully implemented. Dr. Venema complains of “predetermined conclusions.” But the criticism could be turned right around and applied to him, instead.

Image: Adam and Eve, by Tintoretto [Public domain], via Wikimedia Commons.