Mom Genes

My Investigation into the Possibility of Adam & Eve—the First Human Pair

I have come to a conclusion. Perhaps if I had thought about it more carefully I would not be surprised. But it has only recently occurred to me that a great deal of the disturbance about evolution—yes, no, theistic, atheistic, guided, unguided, young earth, old earth, Darwinist, near-neutralist, whatever—is about human origins. Where did we come from? Are we descended from primates or not? And what did God have to do with it?

Nobody except specialist scientists would care whether the little tree frog turned out to be descended from a lobe-finned fish or, instead, was specially created with its special poison glands—unless it also had implications with regard to our origin. Not many people besides evolutionary biologists and entomologists would care one way or the other about the claim that butterflies were descended from a hybridization between onychophorans and insects (an idea that has been refuted, by the way¹). Most people wouldn't even know what that meant. They don't think about where butterflies came from at all.

However, people really do care about our origin, and specifically, about whether or not we share common ancestry with apes. They may not put it in so many words, but that's what their concern with evolution amounts to. People care about their own identity and origin, and many harbor a deep aversion to the idea of monkeys as their ancestors.

In 2011, when I first got involved in this question, I didn't quite see this. For me, the prior question was whether or not neo-Darwinism was true, whether it could explain the development and diversity of living things.

I had no fixed opinion about human origins. All I knew was that Darwinian evolution was insufficient to explain life, but I was hazy on the details of what that meant. I believed that God must have guided evolution, if evolution was the explanation for the grand diversity of life. I knew there were arguments for common descent based on DNA similarity between groups. Not that I had ever looked at any sequences, mind you. Or at arguments against.

I had never considered the question of whether we came from two first parents or from thousands of ape-like primates, because it was not an issue for me. I accepted the old age of the earth (I still do) and was prepared to accept that we came from a population of hominins that somehow became human. I had never thought deeply about it at all. And I can say with reasonable confidence that the statements in this paragraph would be true for the majority of scientists. But they are no longer true for me.

What follows is a description of how my mind has been changed since then. It began by doubting that Darwinian evolution was a sufficient explanation for life. What followed was a surprising journey prompted by a seemingly simple question—a journey that led me to think that an original first human pair, AKA Adam and Eve, might be possible.

A Simple Question

An email hit my inbox: "A philosopher I know is looking for a geneticist who can tell him how strong the evidence against Adam and Eve is. Contact him at. . . ."

So I wrote back, saying I didn't really know, but if I had to speculate . . . I would go look.

The philosopher's response to me was ecstatic beyond all proportion. He said he had been looking for years for a geneticist who would answer his question. "My word!" I thought. "What have I gotten involved in now?"

I emailed my friend Jay Richards and asked for his advice. "Sounds like destiny," was his laconic and slightly unnerving response.

So look I did. The first paper I found seemed to me to present a strong challenge. It was based on the observation that there is a great deal of diversity in some genes, too much diversity to have started from just two people and then increased to its current level in the time available. I found this paper first because of its title: The Myth of Eve: Molecular Biology and Human Origins.² Now that was a direct statement of intent, like the slap of a dueler's glove across the face.

The author, Francisco Ayala, was a former priest and an eminent evolutionary biologist. He claimed that population genetics analysis of an immune system gene called HLA-DRB1 indicated that we came from a starting population of at least 100,000 individuals, who between them carried 32 different versions of HLA-DRB1 at the time of our supposed split from chimps. According to his calculations, the effective population could never have been smaller than 4,000.

If Ayala was correct, that would be the end of Adam and Eve. Thirty-two copies of any gene are too many for just two people to have generated or carried. Each person has only one or two copies of every gene, so the maximum number of copies a couple like Adam and Eve could have had is four.

But then I discovered that the way Ayala did his calculations depended on the DNA he worked with having a background level of mutation, a background level of recombination, and a background level of selection. Otherwise, his estimates for the amount of evolutionary time passed would be off. Unfortunately, the small part of the gene he chose to study violated all of those requirements. This inflated his estimate for the number of variants, as was pointed out by Tomas Bergström and his colleagues a few years after Ayala's work was published.³ Their own study, using a nearby part of the gene not subject to the same flaws, dropped the estimate of the number of HLA-DRB1 variants at the beginning of humanity down to seven. Just seven. But still too many.

This story, plus Douglas Axe's and my protein studies and Casey Luskin's work on fossils and chromosome fusion, became the book Science and Human Origins, published in 2012.⁴

A Collaboration Begins

That same year, I began a collaboration with a Swedish population geneticist named Ola Hössjer that was aimed at making a population genetics model for testing the possibility of a first-couple origin. Ola and I met one December evening in the lobby of a Copenhagen hotel, he with his notepad and pencil and I with a head full of half-formed ideas. I described what I wanted: a mathematical model that could be used to generate and track genetic diversity over time in a population of humans, starting from two. We needed to be able to look for the effects on population statistics of various kinds of things, like the number of children born per women, mortality at various ages, migration, tribes, and so forth. I thought I was throwing an enormous, impossible pile on this gentle Swede.

In 2013, I discovered that Bergström's lab had gone on to sequence a number of full-length variants of HLA-DRB1. His team reported a coalescence to four lineages, just four, though which lineages they meant was ambiguous.⁵ That number four caught my eye, though, because that is the number of lineages Adam and Eve could have carried if they were both heterozygous for the gene HLA-DRB1.

A Revealing Tree

Swedish biologist Jenny von Salomé and her colleagues produced a graph that I stared at for a long time. It showed the tree of relatedness for variants of the gene HLA-DRB1 in humans. I have drawn an exaggerated, cartoon version here.

When you look from left to right, you are looking from the deep past to the present. The data is on the right. The individual little lines like teeth in a comb represent individual gene variants here in the present. I have drawn 21. We know their DNA sequences, so we can compare them and figure out which are most like each other and which are most different—how they are related. We group them according to family, and then if necessary, group them again.

This is a vastly oversimplified gene tree, but it captures three things. The length of the branches corresponds to time or to genetic distance. What geneticists actually measure is how different DNA sequences are—the genetic distance between them—and then they convert that to evolutionary time by using a factor based on fossil evidence from elsewhere. So when you see really long branches like the ones in this tree, that means the DNA in each branch is distinctive, different from the others. The question is, Why?

Is it because they diverged over a long time period, or is it because they were made to be different—that there was primordial diversity from the beginning? This is the key question.

The other thing to notice is that all the diversity happened really recently. On the real graph, the average age is about 450,000 years. On a scale of 50 million years, that's lightning fast. A veritable DRB1 explosion. Note the age.

The last thing to notice is that there are four lineages, four long branches for a very long time (30 million years). Or one could say, four distinct genes with distinct sequences. Sound familiar?

When I saw these things, I knew I had something potentially very important. It might be a signal of our origin from the distant past—not from a population of thousands, as Ayala had proposed, but from a population of two, perhaps 500,000 years ago, the origin of two, followed by the steady increase and diversification going forward of their offspring.

I was excited!

Getting It Done

But still we needed a catalyst. And that catalyst came in the form a new book to be written that had to address "the Adam and Eve question." A loose coalition came together to brainstorm about the best way forward. We needed genetics, fossils, and an answer to the population genetics challenge. Ola's model rapidly came together (he's a wonder!). From that collaboration came two papers, published in 2016, that described Ola's magnificent model,⁶ and three chapters for a book.⁷ At that stage, the model had yet to be programmed.

The next phase required someone with programming expertise. In 2017 we found a programmer with considerable talent for population genetics. I watched things happen, with amazing speed, offering comments and suggestions as they occurred, but the work was in Ola’s supervisory hands now.

By the end of 2018 the job was done. All that was left was to see the paper published.

The Result?

It's very simple. The tree was right. We could have come from a first pair with primordial diversity 500,000 years ago. We can start from two individuals with initial diversity in their chromosomes, then let the population grow at a reasonable rate to a steady state of 16,000. Using standard mutation rates and so forth, and no special assumptions—in other words, a parsimonious model—we can duplicate current population statistics like allele frequency spectra (AFS) and linkage disequilibria (LD).

AFS has to do with how many rare and how many common variants there are in the population, and how they are distributed. In the graph, the rare ones are bunched up as a sharp peak to the left because, while each variant is rare, there are many rare variants. The LD graphs are more complex. They are measures of recombination—how DNA shuffles itself into new combinations in each generation. The graphs are a beautiful sight—the alignment between actual genomic data and the data Ola's program generates is amazing.

It started with a simple question. How strong is the evidence against Adam and Eve? Not as strong as they thought, it turns out. 

Postscript: The paper has now been published and can be viewed and downloaded at https://bio-complexity.org/ojs/index.php/main/article/view/BIO-C.2019.1/BIO-C.2019.1. A more reader-friendly description of the model is available at https://evolutionnews.org/2019/10/new-bio-complexity-paper-we-could-have-come-from-two. Are all questions answered? No. But it seems we could have come from two!

Notes
1. pnas.org/content/106/47/19906.
2. Francisco J. Ayala, "The Myth of Eve: Molecular Biology and Human Origins, Science 270 (1995): 1930–1936.
3. Tomas F. Bergström, et al., "Recent Origin of HLA-DRB1 Alleles and Implications for Human Evolution," Nature Genetics 18 (1998): 237–242.
4. Ann Gauger, Douglas Axe, and Casey Luskin, Science and Human Origins (Discovery Institute Press, 2012).
5. Jenny von Salomé et al., "Full-length sequence analysis of the HLA-DRB1 locus suggests a recent origin of alleles," Immunogenetics 59 (2007): 261–271.
6. Ola Hössjer, Ann Gauger, and Colin Reeves, "Genetic Modeling of Human History": "Part 1: Comparison of Common Descent and Unique Origin Approaches," BIO-Complexity 2016(3), 1–15: doi:10.5048/BIO-C.2016.3; "Part 2: A Unique Origin Algorithm," BIO-Complexity 2016(4), 1–36: doi:10.5048/BIO-C.2016.4.
7. J. P. Moreland, Stephen Meyer, Wayne Grudem, Christopher Shaw, and Ann Gauger, eds., Theistic Evolution: A Scientific, Philosophical and Theological Critique (Crossway Books, 2017).