Here are parts 1, 2, 3,a prelude to 4, and 4.
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Although it concludes the book, Ann Gauger's "The Science of Adam and Eve" in Science and Human Origins was the first chapter I'd seen. Excerpts had been posted suggesting the book made an argument for a population bottleneck that would allow for a real-world, literal, Adam and Eve. The idea intrigued me for a couple reasons -- how could intelligent design remain secular when its leading institution is publishing about a literal Adam and Eve? Will common descent be acceptable and the argument be instead that we were imbued with humanness at this bottleneck? How will the evidence of our long-term effective population size be treated?This was the genesis for the multi-part review that concludes here.
Although the rest of the book could be justified as building up to this point, Chapter 5 contains the presentation of the only original material in the book (as far as I know Gauger hasn't written about this before). The four chapters leading to this point have repeated old arguments, with minimal engagement with contemporary literature. If I have been scathing when reviewing these chapters, it is because I was expecting the Science from the book's title to have been taken more seriously. Yet not only have I found little concordance between any of the main claims made and the literature, I have found little evidence of engagement with the literature. But the final chapter has the promise of a little more. So get ready for it... everything has been building up to this.
To convince us of the possiblity of a literal Adam and Eve, Ann Gauger presents to us doubt over whether a single published paper from the 1990s truly supports a large human population since speciation. In this paper, Francisco Ayala had used the ancient polymorphisms in a 270 base-pair sequence of immune system DNA (exon 2 of HLA-DRB1) to suggest we must have had population far greater than two for the whole time since our lineage and the chimpanzee lineage separated. Because he found more than four alleles (versions of exon 2) that predated the splitting of the human and chimpanzee lineages, there could not have been a human population bottleneck of two people. In fact, Ayala's calculation supported a human population size of 100,000.
However, there is incongruence between the phylogenetic trees built from exon 2 and that built from its surrounding introns. Because recombination appears to be limited in the genomic region where HLA-DRB1 is found, Gauger argues that factors other than ancestral polymorphism might account for the exon 2 diversity. This limited recombination means that there are recognisable, major haplotypes of HLA-DR, and Gauger argues we should base our estimates of the number of ancient polymorphisms on these. Because these haplotypes contrain long introns, molecular dating for them is also more reliable than dating is on exon 2.
What Gauger then argues is that there are five major haplotypes but only three of the haplotypes are "ancient". Because up to four haplotypes could be inherited from two people, the existence of only three leaves the door open for an Adam-and-Eve bottleneck. Unfortunately for Gauger, even if we accept all parts of her argument up to here, we are forced to conclude that this final step is wrong if the book is to be internally consistent.
The other two major haplotypes might not "ancient", but they are still 4 to 6 million years old (Gauger agrees with this). While this does mean they originated in the hominoids, Gauger takes this as evidence they could have come from Adam and Eve. Why is this wrong? Well, if we recall Luskin's chapter, he argued that Homo habilis was seriously non-human. No self-contemplation for the habilines. Yet, H. habilis originated about 2.3 million years ago, and H. erectus did not arrive until about 1.8 million years ago, marking what Luskin accepts to be the start of humanness. Back at 4 million years ago when the last of the HLA-DR haplotypes originated, our closest relatives were Australopithecus. Anatomically modern humans were a long way away. So we can be sure that the five major haplotypes of HLA-DR all pre-date the genus Homo, and contradict the claim made by Gauger that:
The argument from population genetics has been that there is too much genetic diversity to pass through a bottleneck of two individuals, as would be the case for Adam and Eve. But that turns out not to be true.Instead, the argument from population genetics still definitively rules out the possibility of Adam and Eve, if Adam and Eve were human.
So far, I have only mentioned the one line of evidence around ancestral human population sizes as discussed in Gauger's chapter. But there are many more reasons to argue against a human two-person bottleneck. Unfortunately, Gauger does not engage with any of the modern literature that provides evidence of reasonably large human populations over our evolutionary history, instead only taking on Ayala's single-locus argument from the 1990s. I will discuss just one -- a compelling, modern examination of our ancestral population size.
When I first heard about this book, my immediate thought was, "What about Li and Durban (2011)?". Readers of Gauger's chapter might not know this paper, because she certainly doesn't discuss it. Li and Durban, however, trace effective population sizes (evolutionarily relevant estimates of the adult breeding population size) over our evolutionary history as a species, using comparisons of entire genomes from across a range of ethnic groups. At no point is there anything approaching an Adam and Eve population bottleneck at any point that correlates to the genus Homo. Again, when an earlier chapter has drawn the human/non-human distinction between Homo habilis and Homo erectus (i.e. approximately 2 million years ago) we can be quite well assured that a literal Adam and Eve are unsupported by population genetics.The figure below, from Li and Durban, suggests an effective population size of about 15,000 at the origin of Homo erectus.
In a section called "Take home message", the second-last of the book Gauger shifts to suggest that perhaps "we began from two intelligently designed first parents" and that if this were the case "all this analysis of how many ancient haplotypes we share with chimps doesn’t really matter".
What evidence does she provide for this possiblity? She argues:
There certainly are surprising patterns of genetic variation within HLA-DRB1 that suggest unknown processes may be operating. Let me propose that a process exists which generates specific hypervariability within exon 2 and suppresses recombination elsewhere. The process is targeted to generate diversity precisely in the peptide-binding domain. I suggest that intelligent design had to be involved at the beginning, in order to rapidly generate HLA diversity after the foundation of our new species (assuming we came from two first parents). Evidence supporting this idea comes from the fact that HLA-DRB1 diversity has in fact increased very rapidly by anyone’s count, going from a handful of variants to over six hundred alleles in six million years or less. Also, the HLADRB1 variable regions in exon 2 show a patchwork, cross-species relationship to their surrounding DNA sequences, making their origin hard to account for by common descent. Their repeated use of similar motifs from different species may instead indicate common design. I further suggest that this process may be human-specific, since other primates don’t show nearly the same degree of allelic diversity within lineages as humans do.That is, verbatim, the argument for intelligent design that the book has been building towards: the second exon in a gene in the major histocompatibility complex (MHC) is highly variable, and the diversity in humans is higher than other primates. Gauger does not consider overdominant selection for immune system diversity in the rapidly expanding human population, as it spread from Africa across the world, which would seem to account for differences between human and other primate diversity at this locus.
She concludes by telling us:"it seems not unreasonable to propose that HLA-DRB1 diversity is the result of a process that generates specific hypervariability and/or gene conversion within exon 2 in order to rapidly generate HLA diversity. The existence of such a process essentially demolishes any population genetics arguments about ancestral population sizes." While this may indeed challenge the population genetics inferences drawn from exon 2, it does not demolish the population genetics argument about ancestral haplotypes, nor those based on loci outside the MHC.
We may have much to learn about the evolution of MHC diversity, but to reject common descent and postulate an intelligent designer who specially created us from an ancestral couple because of this is ludicrously at odds with the balance of evidence.
Closing thoughts on Science and Human Origins
I feel like I have written enough about this book to get away with tacking on a little conclusion here rather than making another post to sum up. Indeed, the review has run to a third of the length of the book itself (not hard: the text of those five chapters, less the references/endnotes, runs shy of 25,000 words).
I have been left wondering why the Discovery Institute, or intelligent design advocates in general, or biblical literalists feel a need to try and accommodate science when they have a belief in a supernatural entity capable of breaking natural laws. In the case of this book, it has left them needing to make all kinds of awkward criticisms of fields in which the authors clearly lack expertise. A lawyer is not the right guy to challenge the world's palaeoanthropologists, nor the world's geneticists. Certainly, he shouldn't be trying to take them all on at once. It will end with him trying to smear the reputation of scientists rather than engaging with their ideas. Accusations that the entire field of palaeoanthropology is driven by personal disputes and that Francis Collins is a bad Christian are simply not compelling reading in a book that is putatively about scientific argument.
By the end of the book I was left with a massive, if fairly obvious, incongruence. The reality is that the overwhelming majority of scientists in each of the fields addressed in this book share a broad consensus that is at odds with what the authors claim. And, despite the breathless accusations of a Darwinian conspiracy, mainstream scientists are a diverse bunch. Like Francis Collins and Francisco Ayala, who are both singled out in this book, many are themselves Christian yet accept the balance of evidence for our evolutionary past. They accommodate their beliefs with an uncompromised view of the science. This is because they have engaged openly with the evidence of their discipline and concluded that evolutionary principles best explain human origins. There is no atheist conspiracy to force evolution on the public; instead, it is all of the diverse and beautiful evidence of the world around us that points to evolution having shaped us and earth's biota. There is no shame in this, and it hardly makes us less human to acknowledge it.
And, of course, there are entirely different world views, such as the one taken by certain other religious folk. They choose to place their faith paramount to scientific evidence. Although I don't agree myself -- I value the conclusions of science ahead of those of personal revelation -- it is still a stronger position than that of intelligent design.
ID tries to straddle some in-between place, where it claims to disprove scientific consensus in a number of different fields, and then attributes the lack of a shifting consensus towards ID to bias and brainwashing. But, as this book amply demonstrates, the real problem is that ID fails to engage with much of the modern literature in those fields.
This book also demonstrates ID's difficulty with separating itself from Christianity in practice. The introduction, and four of the five chapters are framed in a Christian context. Concern over how Christian beliefs have been impacted by science, and the role of Christians who accept mainstream science are at the fore. Even issues like stem-cell research appear, given no context. The thrust of the whole book is to claim human exceptionalism, disprove our common descent with apes, and search for a real-life Adam and Eve. None of this is part of a secular programme to genuinely investigate the world. This is particularly clear because the authors are happy to create doubt about what they call Darwinism, rather than create positive cases for an alternative to it. This is an obvious echo of the Wedge Strategy on which the Discovery Institute was founded.
Science and Human Origins has to be described first and foremost as being anti-evolution rather than pro-intelligent-design, or pro-science. If it offers solace to those seeking evidence against evolution for their faith, the solace should be as incomplete as the arguments made in the book.
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