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On Prejudiced Models and Human Origins

human origins

The question of human origins has been stirring the religious world for a number of years. Recently Dennis Venema joined with Scot McKnight to publish a book, Adam and the Genome, in which they claim that there never was an original pair of humans like Adam and Eve, and we can be as sure of that as that the earth goes round the sun:

As our methodology becomes more sophisticated and more data are examined, we will likely further refine our estimates in the future. That said, we can be confident that finding evidence…that we descend from only two people just isn’t going to happen. Some ideas in science are so well supported that it is highly unlikely new evidence will substantially modify them, and these are among them. The sun is at the center of our solar system, humans evolved, and we evolved as a population.

Put most simply, DNA evidence indicates that humans descend from a large population because we, as a species, are so genetically diverse in the present day that a large ancestral population is needed to transmit that diversity to us. [Emphasis added.]

However,  population geneticist Richard Buggs called Venema’s bluff and as the debate has raged over at BioLogos, it has attracted the attention of another population geneticist at the top of his field, Steve Schaffner (alias glipsnort).

As you likely know, Discovery Institute advocates for the theory of intelligent design, which is a scientific claim based on scientific evidence, not a theological claim, and likewise it does not take a position on Adam and Eve. However, when scientists such as Venema made claims about human origins, and Adam and Eve in particular, it opened up the question as to whether their science is correct. In addition, this debate about origins reveals the same dynamic as debates about intelligent design. This particular exchange has revealed that although most scientists, if asked, have strong opinions against the idea of a first couple, their opinion is not really based on science. They have not used the process of science to properly  address the question. We see the same thing all the time in critical responses to intelligent design.

Here is why the question of a first pair has not been properly addressed. Almost all scientific models make simplifying assumptions, which is perfectly sensible and reaonable, and population genetics is no different. However, this means the models are only valid if the assumptions are appropriate to the case you are studying.

The biggest and most obvious problem is that most mainstream models assume a large and/or constant population of humans (or hominins) all the way back in time, past the theorized common ancestors with apes. Clearly this is incompatible with there being a time when there were only two. But if you use a model that assumes Adam and Eve didn’t exist, then you can’t use that model to test whether they existed or not. That would be circular reasoning. And yet, that is kind of what Dennis Venema has been doing.

A second assumption is that if you want to date the age of a population you should date it back to a single ancestor. When it comes to genetic information, that means a single chromosome of each type, not a single human. But humans are diploid (two chromosomes of each type) and there are two people in the first pair, giving four chromosomes, and up to four original alleles at every locus.

This idea has prompted computational biologist Joshua Swamidass to explore how much of a difference that makes: instead of tracing ancestry back to the earliest one copy of an allele, he traces back to the earliest four copies. His work is quite impressive and the tool he used, ARGweaver , is pretty cool too. Swamidass stresses that he does not actually believe all humanity derived from a single couple but he has shown that it is possible, if the couple lived more than 300,000 years ago. To be more precise and extra specially careful: he shows that a particular study being waved about by Venema as evidence against a single couple origin is nothing of the sort. The core finding is that coalescence back to four alleles takes about one third of the time it takes to coalesce back to one, and so the minimum age since Adam and Eve could have existed falls by a factor of 3, down to about 340,000 years. Here is the post by Swamidass on the subject.

Notice that Swamidass is defending someone else’s position from an unfair or poorly reasoned or overly confident attack. Wouldn’t it be nice to see more of that in all these debates?

Having said that, I think Swamidass’s new work further illustrates the difficulty of answering far-out questions using mainstream methods. The tool used, ARGweaver, is fantastic in that it combines an enormous amount of real genetic information to model the past genetic history of humans. For this reason it gives the impression of being truly objective, and so when I first read it, I thought he had proved that there could be no bottleneck earlier than 300,000 years.

However, a little digging into how ARGweaver works reveals that it too assumes a constant population, and uses this assumption to assign probabilities to ancestry trees. Therefore, again, it is not clear if it is really appropriate for asking questions about Adam and Eve. The particular reason why it is a problem is a bit technical: coalescence (branching but backwards in time) happens much more slowly in a large population. In a large population, the last few coalescents could take thousands of generations. But what if you have a small number of generations, drawing to a smaller and smaller population and terminating in a single couple? All the lineages will coalesce (down to at most four as explained above) but at a faster rate.

How much faster? Well, say Adam and Eve had ten children. That’s a lot of children, but not unknown amongst modern humans. In that case you could easily see 16 coalescents happen in one generation! Meanwhile ARGweaver’s internal probability model is strongly biased to believe those 16 coalescents would take at least 10,000 generations (250,000 years)! ARGweaver adds a lot of real data as well, but will that do enough to outweigh an error of four orders of magnitude? I doubt it. But to be honest I don’t know, and when we don’t know, its best to say so, rather than, for example, insist we need to reinvent the theology of a thousands-years-old religion.

This is not the end of the question, of course, just a note that there is more work to do. Swamidass also points out there are  multiple scientific models that suggest any single-couple origin would have to be well beyond 100,000 years (such as “Y-chromosome Adam,” and “mitochondrial Eve”). And the one that everyone keeps coming back to is the MHC (major histocompatibility complex). I bet we haven’t heard the last about that.

Photo credit: Pixel2013, via Pixabay.