Saturday, June 18, 2011

Did Adam and Eve Exist? (Part III)

[Note: This is the fourth post in a multipart series. The Introduction is at this link, Part I is at this link, and Part II is at this link.]

Having surveyed the science relating to the creation story of Genesis from a general point of view, we will now go into the latest findings from the science of genetics, including the subfield of population genetics. On the basis of the recent mapping of the human genome, by which the entire DNA sequence of the current human species was finally spelled out from start to finish, and on the basis of similar mappings of the gorilla and chimpanzee genomes, it has become possible to compare their relative similarities and differences with each other in mathematical detail. The results help to specify the likelihood that any two or more separate species shared a common ancestor, i.e., evolved from that ancestor, but along the way, through mutations, natural selection, genetic drift and geological or geographical factors contributing to speciation, separated from that common genome and developed in time as a species apart from other contemporary offshoots of that same ancestor.

Relationships determined by the mathematical analysis of genome maps can be compared in at least three ways, as described in more detail in this article. The three ways are based on what geneticists call homology, synteny, and the comparison of pseudogenes.

Two genes are said to be homologous when they have substantially the same DNA sequence. The article by Prof. Dennis Venema just linked describes the degree to which the human and chimpanzee genomes may be said to be homologous, depending on the criteria chosen (footnotes are omitted):
. . . The human genome has approximately 3.0 x 109 nucleotides [the basic building blocks of DNA]; of this number, 2.7 x 109 nucleotides match the chimpanzee genome with only a 1.23% difference between the species.

In short, the vast majority of the human genome matches the chimpanzee genome with only rare differences. The inclusion of sequence alignment gaps between the two genomes that are thought to have arisen through either insertions or deletions (so-called “indel” mutations) drives the identity of the two genomes down to about 95%. Restricting the comparison to the sequences responsible for coding for proteins raises the value to 99.4%. By any measure, humans and chimpanzees have genomes that are highly homologous and readily interpreted as modified copies of an original ancestral genome.
The article contains a detailed comparison chart (Figure 1) illustrating the variations in the DNA for insulin among humans, chimpanzees, gorillas, orangutans, horseshoe bats, and mice, and then shows another chart comparing insulin amino acid sequences for the same six species. This data, of course, focuses on a very tiny piece of the respective genomes, but illustrates the general aspects of homology discussed in the article.

Synteny is the word used by geneticists to describe the presence of two different genes on the same chromosome. By comparing the spatial arrangement of individual genes on chromosomes, the similarities or differences between two species may be seen gene-by-gene, instead of nucleotide by nucleotide. And under this yardstick, there are again a large number of synteny groups observed in comparing the human and chimpanzee genomes, which point to their having shared a common ancestor in the past. (References to the individual studies are footnoted in the Venema article.)

Pseudogenes (literally: "false genes") are sequences of DNA which are no longer thought functional, due to past mutations. (Recently, more detailed analysis is uncovering additional uses for, and functions of, many pseudogenes and similar "junk DNA".) They still have, however, a discernible sequential connection with other functioning genes in the genome (which points up the specific locations where mutations in the pseudogene occurred). If two different genomes share a lot of pseudogene sequences in common, that fact is evidence of their sharing a common ancestor in the past, due to having similar mutations at similar places in their DNA sequences. Such sequences are simply passed down through the generations with little further alteration, and preserve another record of a linked past.

The Venema article details the evidence about one pseudogene stemming from a very ancient ancestor (footnotes again omitted):
One protein used as a yolk component in egg-laying vertebrates is the product of the vitellogenin gene. Since placental mammals are proposed to be descended from egg-laying ancestors, researchers recently investigated whether humans retained the remnants of the vitellogenin gene sequence in pseudogene form. To assist in their search, this group determined the location of the functional vitellogenin gene in the chicken genome, noted the identity of the genes flanking the vitellogenin sequence, and located these genes in the human genome. They found that these genes were present side-by-side and functional in the human genome; then they performed an examination of human sequence between them. As expected, the heavily mutated, pseudogenized sequence of the vitellogenin gene was present in the human genome at this precise location. The human genome thus contains the mutated remains of a gene devoted to egg yolk formation in egg-laying vertebrates at the precise location predicted by shared synteny derived from common ancestry.
On the basis of multiple lines of evidence such as these, geneticists conclude that the human species "evolved" from primitive ancestors in the ancient tree of life. However, as we have seen in the earlier posts in this series, such a theory of evolution does not tell the whole story, if the basic precepts of Christianity are to be taken into account. In particular, straight evolution from ancient ancestors does not account for the appearance of, let alone the origins of and reasons for, "original sin" as taught in Christian theology.

The final bit of evidence detailed in the Venema article has to do with the highly abstruse and technical subject of population genetics. Briefly speaking, geneticists can use their comparative data of the various genomes to calculate, retrospectively, the approximate size of an ancestor population for its descendants to have today the observed number and variety of genes in their gene pool. Venema provides this example of such a calculation (footnotes again omitted):
For example, a small, but significant, fraction of the human genome is more similar to the modern gorilla genome than to the chimpanzee genome. For this subset of sequences, our species tree does not match the gene tree (figure 2). This discordance is expected for closely related species that have diverged from each other in a short amount of time. Put another way, the reason our genome is overwhelmingly more similar to the chimpanzee genome is that we most recently shared a common ancestor with chimpanzees. Yet, in spite of this, we retain some regions of our genome that are more closely related to gorillas. This situation arises because the population that gave rise to the human-chimpanzee common ancestor was large enough, and genetically diverse enough, to transmit this variation to us without passing it on to chimpanzees. Chimpanzees and humans are thus separate genomic samplings of a diverse ancestral population. Had this pool been small, the human-chimpanzee gene trees would match the species tree in almost every case. The proportion of gene trees that do not match the species tree can therefore be used to estimate the population size of the ancestral population.
Prof. Venema explains that this method, in the latest large-scale studies which he references, returns a value of between eight to ten thousand individuals in the population at the time that human ancestors and gorilla ancestors began to speciate. Any larger, and the closeness of parts of the human-gorilla genomes would not be observed to the same degree; any smaller, and the population would most likely not have been able to keep the gorilla subcomponent separate, and preserve it distinct from the chimpanzee part until today. (See the species- and gene-tree diagrams in the article [Figure 2].)

Another method of population genetics, based this time on synteny data, provides confirmation of the results derived from the homologous data. The details are in the Venema article, but here is the bottom line (I have again omitted the footnote references, and have added the bold emphasis for reasons that will appear in my next post):
Studies based on SNP/LD [synteny] approaches have now estimated ancestral population dynamics for various human groups over time in more detail than is possible with mutation-based estimates. African groups have a higher effective population size (~7,000) than do non-African groups (~3,000) over the last 200,000 years. This approach, though based on methods and assumptions independent of previous work, nonetheless continues to support the conclusion that humans, as a species, are descended from an ancestral population of at least several thousand individuals. More importantly, the scalability of this approach reveals that there was no significant change in human population size at the time modern humans appeared in the fossil record (~200,000 years ago), or at the time of significant cultural and religious development at ~50,000 years ago.
The techniques of population genetics, as they become more and more refined, are like a microscope that uses ever and ever higher power to achieve ever greater resolution. In the short space of ten to fifteen years, we have gone from the data supporting an ancestral population of about ten thousand individuals into one that breaks into two groups: a larger, African group base of about 7,000; and a smaller, non-African base of about 3,000 individuals.

In the next post of this series I will put forth a tentative hypothesis that could, if it can withstand wider scrutiny, provide a bridge between the seemingly disparate genetic evidence sketched above and the ancient biblical literary evidence discussed earlier.


  1. Leaving aside the disputes over Darwinian theory -- the problems with it are serious, but we actually don't need to deal with them here -- you have a problem with the Christian view that man has dual natures, a spiritual and a physical. This is an early lesson in the RC catechism, but C.S.Lewis talks about it in a number of places, so it's also perfectly good Anglican doctrine.

    While the Roman Catholic Church has no position on evolution, it does have a position on Adam and the Fall, and that's related to the spiritual nature of humans. Humans, according to Christian doctrine, have a soul. Where did the soul come from? Did it "evolve"? Can you find the soul in DNA?

    I think you're allowing yourself to confuse the physical and the spiritual here, although this is a confusion that the "positivist" or not-fully-accurately-named "scientific" world view promotes. You seem to be using DNA to argue a spiritual issue, the existence of Adam and the implications of the apple, which is simply a non-sequitur.

    Let's acknowledge that only a few thousand humans existed at one time. But if you go to church, even a breakaway Anglican church, you are in some way also acknowledging a world-view that includes original sin and its promulgation at a very early stage among those few thousand humans.

    Where did they come from? This DNA-based version of the creation story is giving us no answer to that question. XX percent of the human genome matches chimpanzees, but almost as much matches pumpkins, and even the staunchest Darwinist doesn't argue that we actually evolved from chimps -- they simply claim that both evolved from something else, but they won't say what.

    At what point did these few thousand get souls, which you must acknowledge they had? I doubt that their souls just sorta-kinda improved via natural selection from australopithecenes, whose souls had greater ankle-flexibility than those of chimps! There must have been some sort of divine intervention to make that happen. (Otherwise, you're wasting your time Sunday mornings, after all.)

    Is it your intent to rewrite Genesis to make it more "scientific"? I chatted about this with my wife, a retired attorney, who remarked that it's not unusual for attorneys to decide they're experts in fields other than the law. I find your legal opinions worthwhile. However, in this area, I think the term "dilettante" may apply, for which I'm sorry.

  2. John, it appears I can do nothing with your preconceptions -- did you even read the full post? Did you see, in particular, this paragraph in the middle?

    "On the basis of multiple lines of evidence such as these, geneticists conclude that the human species 'evolved' from primitive ancestors in the ancient tree of life. However, as we have seen in the earlier posts in this series, such a theory of evolution does not tell the whole story, if the basic precepts of Christianity are to be taken into account. In particular, straight evolution from ancient ancestors does not account for the appearance of, let alone the origins of and reasons for, 'original sin' as taught in Christian theology."

    We are in much more agreement than you realize: the soul did not "evolve" in my scheme of things, either. But before I could take issue with the genetic science in my next post, I had to lay it out first. Sorry if it is all seeming dilettantish to you.

  3. The paragraph you cite says nothing that Bishop Spong would disagree with, either. I'm sure he, Bishop Bennison, Presiding Bishop Schori, and many others have vague words to say on all such subjects. But in the last sentence of your post, you call the Bible "literary", which I'm not completely sure that even Spong, Bennison, or Schori would agree with. The Bible is not literature. The Iliad and the Odyssey are literature; Genesis isn't.

    Your paragraph also doesn't answer the problem I raised in my comments on Post II: where did the X,000 early humans come from? It's worth repeating the Darwinian problem that we have no observed instance of one species "evolving" from another in real time, such that we can explain how a certain population of protospecies A breeds successfully to produce new species B. The DNA experts still can't identify which protospecies produced homo sapiens, for example. So you're simply accepting on faith some Canadian's assertion that X,000 humans just happened, as far as I can see.

    And you're saying that it's "preconceptions" that are getting in the way. But aren't juries supposed to bring "preconceptions" like common sense into their deliberations?

  4. As an anthropolgists, I'm always trying to push back to earlier antecedents. How are we to interpret the universal burial of rulers in red ochre, a symbol of blood?

    H.B.S. Cooke and his associates report the discovery of the oldest known human burial, between 46,000 and 80,000 years old in the the Lebombo Mountains in Swaziland. The grave held a small boy, buried with a seashell pendant and covered in red ochre. A man buried 45,000 years ago at La Chapelle-aux-Saints in southern France, was packed in red ochre. “The Red Lady of Paviland” in Wales was buried in red ochre about 20,000 years ago. Her skeletal remains and burial artifacts are encrusted with the red ore.

    P.L. Kirk reports that prehistoric Australian aboriginal burials reveal pink staining of the soil around the skeleton, indicating that red ochre had been sprinkled over the body. The remains of an adult male found at Lake Mungo in southeastern Australia were copiously sprinkled with red ochre.

    The ‘Fox Lady’ of Doini Vestonice, Czechoslovakia (near Russia) who was burial 23,000 years ago, was also covered in red ochre.

    A 20,000 year old burial site in Bavaria reveals a thirty-year-old man entirely surrounded by a pile of mammoth tusks and nearly submerged in a mass of red ochre. Native Americans used red ochre for ceremonies and also to bury their dead.

    From the earliest times humans (not chimps) have sought to overcome or defeat death through the blood. Where did they get this idea?

    They valued red ochre so much that they actually dug tunnel mines in the Lebombo Mountains. The mines were in operation between 80,000 to 100,000 years ago. We are not speaking here of small hallows in the earth, but of major mining operations.

    “One of the largest sites evidenced the removal of a million kilos of ore. At another site half a million stone-digging tools were found, all showing considerable wear. All of the sites in fact produced thousands of tools and involved the removal of large quantities of ore; and while some were open quarries, others had true mining tunnels.” (

    The Orthodox Church holds a somewhat different view of sin and the Fall. The Fall brought death into the world and sin and death are two sides of the same coin. This is probably what St. Paul means when he says that by Adam sin entered the world and with sin came death. The Western Church stresses the sin-death sequence but to Eastern Church stress the death-sin sequence.

    I'm enjoying this series and look forward to the next one.

    Typical lawyer! Lay out the facts in an orderly fashion. I love it.

  5. Except that the lawyer's opening argument doesn't say what he's going to prove, other than some vague thing that maybe there was an Adam, or maybe not, we've gotta wait to find out.

    When I do jury duty, the lawyers are pretty specific: the evidence will show my client was 500 miles away when the crime took place, for instance. Not here!

    Typical lawyer? Maybe in the courtroom.

  6. You'll have to stand the suspense a bit longer, John -- these posts, believe it or not, take time to research, check, and include all the relevant links I can find.

    And no, I have not promised to "prove" anything -- I do not have a client here who is on trial. When the fourth installment appears in a few days, you will see that it presents simply a rational scenario for the original pair.

  7. I'm still puzzled. The title of the series is "Did Adam and Eve Exist?", which makes me think that if you pose the question you have some sort of answer in mind -- and in fact, you've said we're closer than I think in our opinions, which makes me think you do have something you mean to argue.

    But now you're saying you've still got to get certain ducks in a row. Now, I was patient, I guess, for dorm room bull sessions 40-odd years ago, but I walked into this expecting to hear from an educated person skilled in exposition, and so far, I'm still disappointed.

    I think the term "desultory" may also apply here, to the other d-word I suggested earlier.

  8. Fascinating reading - albeit I skimmed more than I absorbed, and I'm not much of a scientist. So if this goes a bit off-topic, I apologize. According to Genesis, Adam clearly predates Eve (2:18-20, roughly stated, points out that Adam pretty much had to discount the existing choices - animals - as suitable partners before it became apparent that none of these were acceptable - thus Eve came to be). How outlandish would it be that the gene pool was already stirred up before Eve came to be Adam's partner?

    (I am not presenting this theory with much thought put into it; I am a novice when it comes to theology, the bible, and science)

    I'm not saying the NAB (the current translation I'm reading) or any other version implies Adam had intimacies with his pre-Eve choices - really it just says God brought them to Adam, who in turn gave them names. But what if he did?

    Subsequently, what if Eve was the evolutionary bottleneck?

    (Of course that would mean a new understanding of the biblical birth of Eve from Adam's rib).

    I hope I haven't offended anyone. Even if this is a gross misrepresentation or interpretation of science or Bible, I guess the point is, perhaps the picture is still much bigger than either side is able to (yet) comprehend.

    (By the way, I only found myself here after days of mapping out descendants of Noah and getting frustrated with the lack of knowledge on the origins of the Horites - talk about going down a rabbit hole!)

  9. (comment after previous post) Of course, I suppose Dennis R. Venema addresses this in some fashion in his article (linked on your intro). His data indicates my theory is flawed. LOL. I don't know enough to argue the point. Perhaps I'll modify my theory a bit. Either way, I still say the box is way to big for any of us to get out of at the moment.

  10. Huey, This should help you on that rabbit trail:

    The Horites were a caste, not an ethnicity. Ethnically, they were Kushites.

    Best wishes,