From Jonathan McLatchie, "The Search for Adam and Eve"

Facebook readers, Facebook is lamentably primitive when it comes to formatting text. That is why I write blog pages. If you are seeing this on Facebook, go to the link, where the different sources are colour coded and indicated by indentation. It will be easier to read. I make no financial gain from clicks.

https://barryhisblog.blogspot.com/p/from-jonathan-mclatchie-search-for-adam.html

Jonathan McLatchie is Assistant Professor Of Biology at Sattler College, a Christian college. He has written about ERVs (endogenous retroviruses) before, in the mendaciously named "Evolution News" blog. I deal with that article here, @ "Do Shared ERVs Support Common Ancestry?" (https://barryhisblog.blogspot.com/p/do-shared-ervs-support-common-ancestry.html)

This present article, at his own blog, "The Search for Adam and Eve" (https://jonathanmclatchie.com/the-search-for-adam-and-eve-human-origins-according-to-scripture-and-science/) has a section on ERVs also. The article has rather heavy theological content, which is strange for someone who writes for intelligent design propaganda organs, and he is familiar with creationist attempts to defend their fantasies from the ERV evidence. As we shall see, he is now less than impressed by them, and has gone back on the ideas he expressed in the previous article.

As usual, original text in black and my comments in red.

"Primates are thought to have been on the scene for 50-55 million years. During that history, they have undergone many infections by retroviruses (RNA viruses that can reverse transcribe their RNA into DNA and integrate themselves into the genome of their host). Sometimes, those retroviruses infect the germ cells (those cells that are passed on to an organism’s progeny). When this happens, the retroviruses can be vertically inherited from one generation to the next, becoming permanent relics of past viral infections. These relics are referred to in the technical lingo as endogenous retroviruses (ERVs). There are literally hundreds of thousands of those endogenous retroviruses in the human genome. What evolutionary biologists have noticed is that the distribution of those retroviral sequences across the genomes of different primates forms a nested hierarchy, resembling a family tree — exactly what you would expect to observe on the hypothesis of common descent."

It is refreshing to read of an evolution-denier acknowledging the origin of ERVs in retroviruses. Some stick their fingers in their ears and deny that ERVs, and even retroviruses, exist at all!

"Furthermore, in addition to the placement of ERV sequences in orthologous loci (and its pertinent nested hierarchical pattern), we must also take into consideration the shared mutations among orthologous ERVs which also fall into very similar nested hierarchies."

McLatchie does not appear to understand what his own words are saying here. 

From Springer Link, (https://link.springer.com/referenceworkentry/10.1007%2F978-3-642-27833-4_1731-3) on orthology.

"Orthologous genes (or orthologs) are a particular class of homologous genes. They are found in different species and have diverged following the speciation of the species hosting them. Therefore, orthologous genes in different species derive from a common ancestral gene found in the ancestor of those species."

To continue with McLatchie, 

"Since mutation and ERV placement are independent factors, this is again best explained by the hypothesis of descent. Moreover, the comparative degrees of divergence between the long terminal repeat sequences on both termini of the retroviral sequence (which serve as retroviral promoters) among orthologous ERVs are also implicative of the common descent model. The long-terminal-repeat (LTR) sequences, on either end of the retroviral sequence, must be identical upon insertion. Since LTRs are identical upon reverse transcription and integration, greater mutational divergence (assuming common ancestry to be true) ought to correlate with an older insertion. This is precisely what we observe. Thus, this three-tiered evidence is quite surprising on the hypothesis of separate creation but not surprising at all given the truth of the scenario of common descent."

"Creationists have tended to respond to this evidence in one of two ways. The first is to point to functions that have been identified for these retroviral-like sequences in the context of the human genome, which many creationists take to suggest that these sequences are not of retroviral origin at all, but rather are endemic to the human genome. For example, the LTR sequences of ERVs in the human genome “have been shown to contribute promoter sequences that can initiate transcription of adjacent human genes.” Another example is the fusogenic syncytin proteins that fuse placental cells together to form the syncytiotrophoblast and which are known to be essential for placental formation. These proteins are coded for by the envelope (env) gene of an endogenous retroviral insert. However, these functions appear to have been acquired post-integration, since the evidence indicates quite strongly that these are indeed genuine inserts into the genome. The evidence for this has to do with the integrase enzyme which is responsible for integrating the viral DNA (after it has been reverse transcribed from RNA) into the host chromosome. Integrase breaks two phosphodiester bonds, one on each strand of the host DNA. Integrase does not simply break the bonds between two base pairs. Rather, it separates the breaks by several base pairs, resulting in a jagged cut. When nucleotides are added to fill in the gaps that have been created by integrase, the result is a target site duplication, which is the hallmarks of insertion by integrase. Thus, while there are plenty of examples of functions that may be identified for ERV sequences in the context of the human genome, this is of little value in responding to this argument for common descent, since those functions appear to have been acquired after integration of these retroviral-like sequences into the human genome."

It is a common defence in intelligent design/creationist articles to point out that components of ERVs have been found to have function. Here, McLatchie is agreeing that this is not evidence for design. He also agrees that ERV correspondence with the already established nested hierarchy and that the LTR discontinuities are what we expect from common ancestry, evidence rarely acknowledged in creationist/ID 'literature'. He does not offer any reason why the creator or intelligent designer should have been constrained to carefully mimic what we would expect from common ancestry.  

"The second creationist attempt to deal with this evidence is to point to target-site preferences. However, while statistical biases for integration do exist (for example regions of the chromosome that are rich in expressed genes, and near transcription start sites) these biases are not anywhere close to sufficiently locus-specific to make a significant statistical difference. In fact, these biases require thousands of trials just to detect. Integration of retroviruses into a host genome therefore seem to be rather random."

This is not what McLatchie was trying to insinuate in his previous piece. (See the first link I give.) He has come to acknowledge that a statistical tendency to integrate in certain general types of regions does not explain the precise, base-pair level resolution of common ERV DNA loci.

"To recap, we have seen that, while the evidence indicates that a transition from a chimp-like ancestor to humans is unlikely to have occurred by an unguided evolutionary process, there is nonetheless genomic evidence confirmatory of common descent of primates that cannot be ignored. I do not believe evolutionists have adequately responded to the former evidence, and I do not believe creationists have adequately responded to the latter evidence."

"How can one make sense of those apparently conflicting sets of evidence?"

What? No conflicting evidence has thus far been presented!

"The model I would propose is that God brought new forms of life into being by miraculous divine action, using the genome of a previously-existing species as a template. This suggestion would account for the presence of evolutionary relics in the human genome and yet would also account for the data that shows the strong implausibility of an evolutionary transition having occurred by unguided natural processes. A literal historical Adam and Eve is certainly compatible with the scenario I have proposed."

Some might worry that this solution is ad hoc. However, given the overwhelming scientific evidence that life is the result of design and that unguided processes are demonstrably inadequate to explain the complex features of biology, I think it is legitimate to explore alternative explanations for data that appears on first blush to point to common descent.

Hitchens' Razor is applicable here.

"If there is no natural way to account for the transition from A to B, then how can we be so confident that the transition from A to B in fact occurred at all? Moreover, I do not believe the fossil record at all supports a smooth and gradual transition from the australopithecines to our genus Homo. In fact, one paper put it, “We, like many others, interpret the anatomical evidence to show that early H. sapiens was significantly and dramatically different from…australopithecines in virtually every element of its skeleton and every remnant of its behavior.” The famed late evolutionary biologist Ernst Mayr likewise stated that “The earliest fossils of Homo, Homo rudolfensis and Homo erectus, are separated from Australopithecus by a large, unbridged gap. How can we explain this seeming saltation? Not having any fossils that can serve as missing links, we have to fall back on the time-honored method of historical science, the construction of a historical narrative.”"

This appears to be pure argument from personal incredulity, plus the determined ignoring of the evidence that McLatchie himself has just described! I am at an utter loss to understand why intelligent, informed scientists like Jonathan McLatchie, Todd Wood (http://toddcwood.blogspot.com/2009/10/microbes-continue-retroviruses.html) and Kurt Wise (https://barryhisblog.blogspot.com/p/sadly-honest-creationist-creation.html) can stare the evidence in the face, understand it and acknowledge it, and still refuse to accept what it is clearly telling them!

Update, 25 March 2021. I have contacted "Evolution News" with the following message.

Good day, ladies and gentlemen,

Please take note that Jonathan McLatchie, who wrote this piece for you ten yeas ago https://evolutionnews.org/2011/05/do_shared_ervs_support_common_/, has completely changed his mind on this issue, and has concluded that shared ERVs do indeed support common ancestry. I analysed a recent piece of his @ https://barryhisblog.blogspot.com/p/from-jonathan-mclatchie-search-for-adam.html Please read it and mine and Jonathan's comments.

I think, in all intellectual honesty, you should give people the news about it, or simply withdraw the old article.

Thank you for your attention,

Regards,

Barry Desborough


29 Aug 2021. Did they withdraw it? Did they hell!