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.

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