On August 21, 2008, Casey Luskin wrote Large Scale Function for Endogenous Retroviruses: Intelligent Design Prediction Fulfilled While Another Darwinist Argument Bites the Dust. In this post, Luskin uses a recent article in Bioinformatics by Conley et al. to attack a piece of evidence brought up by Douglas Theobald in his 29+ Evidences for Macroevolution. This article can be found at TalkOrigins, and is a must read for anyone who is interested in the evolution debate.
Luskin is not really addressing the evidence provided by Theobald. Luskin says that new evidence shows that endogenous retroviruses have function. Theobald never addressed this issue. Therefore, Luskin’s point is moot and should be disregarded as such.
The piece of evidence in question here concerns the presence of endogenous retroviruses (ERVs) found throughout genomes. When a retrovirus (such as HIV or HPV) infects a person, the virus gets incorporated into the person’s DNA. If a germ cell gets infected by one of these viruses, then it will become part of the offspring’s genome. Once it has become part of the genome, it is endogenous and will be passed down to successive generations.
Because these ERVs are passed down to offspring, one should be able to trace the introduction of different ERVs through evolutionary history by examining phylogenetic trees. As pointed out by Theobald, this is in fact what we see when we look at the ape family or the felines. We never see an ERV in the same position in two different distantly related apes without seeing it in the intervening species. So this provides strong support to evolutionary theory. An excellent overview of this can be found in episode 113 of the Evolution 101 podcast.
So how does Luskin try to disprove this evidence? He discusses the Bioinformatics article that points to ERVs affecting transcription of genes. Luskin states:
Douglas Theobald claims that “Endogenous retroviruses provide yet another example of molecular sequence evidence for universal common descent.” The presumption behind his argument is that endogenous retroviruses (ERVs) are functionless stretches of “junk” DNA that persist because they are “selfish”-but they have no function for the organism… The force of Theobald’s argument thus depends upon the premise that ERVs are selfish genetic “junk” that do not necessarily perform any useful function for their host.
However, this is not at all the point of Theobald’s argument. He says nothing about whether the ERVs are able to affect the function of genes. This is clearly a strawman that Luskin created for his uninformed readers.
The focus here is not if the ERVs have a function, it is do their positions in the genome match what a phylogenetic tree would predict. The fact that ERVs affect gene expression is not unknown or unexpected. For one thing, retroviruses utilize their host cell’s machinery to express their own genes. So if the retrovirus gets put into the genome near another gene, why wouldn’t it affect the gene?
The real thing to ask yourself, or someone from the Discovery Institute, is why a Designer would need to put the skeletons of retroviruses by genes to effect its expression? Other genes do not have these remnants of retroviruses and seem to function just fine. This should really be the focus of someone interested in reality, but we know proponents of intelligent design are not interested in what is going on.