ERV FAQ: David DeWitt at AiG says ERVs do not line up with the expected evolutionary progression. What gives?

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Here's what DeWitt says.

• The ERVs are not always consistent with evolutionary expectations. For example, scientists analyzed the complement component C4 genes (an aspect of the immune system) in a variety of primates. Both chimpanzees and gorillas had short C4 genes. The human gene was long because of an ERV. Interestingly, orangutans and green monkeys had the same ERV inserted at exactly the same point. This is especially significant because humans are supposed to have a more recent common ancestor with both chimpanzees and gorillas and only more distantly with orangutans. Yet the same ERV in exactly the same position would imply that humans and orangutans had the more recent common ancestor. Here is a good case where ERVs do not line up with the expected evolutionary progression. Nonetheless, they are still held up as evidence for common ancestry.

He references this paper, Complement component C4 gene intron 9 as a phylogenetic marker for primates: long terminal repeats of the endogenous retrovirus ERV-K(C4) are a molecular clock of evolution.

Here is the abstract of the paper. It's a little heavy going, but you only need to read the first sentence, and you can skip to my observations that follow.

• The complement component C4 genes of Old World primates exhibit a long/short dichotomous size variation, except that chimpanzee and gorilla only contain short C4 genes. In human it has been shown that the long C4 gene is attributed to the integration of an endogenous retrovirus, HERV-K(C4), into intron 9. This 6.36 kilobase retroviral element is absent in short C4 genes. Here it is shown that the homologous endogenous retrovirus, ERV-K(C4), is present precisely at the same position in the long C4 gene of orangutan and African green monkey. Determination of the short C4 gene intron 9 sequences from human, three apes, two Old World monkeys, and a New World monkey allowed the establishment of consistent phylogenetic trees for primates, which favors a chimpanzee-gorilla clade. The 5' long terminal repeats (LTR) and 3' LTR of ERV-K(C4) in long C4 genes of human, orangutan, and African green monkey have similar sequence divergence values of 9.1%-10.5%. These values are more than five-fold higher than the sequence divergence of the homologous intron 9 sequences between the long and short C4 genes in higher primates. The latter is probably a result of homogenization or concerted evolution. We suggest that the 5' LTR and 3' LTR of an endogenous retrovirus can serve as a reliable reference point or a molecular clock for studies of gene duplication and gene evolution. This is because the 5'/3' LTR sequences were identical at the time of retroviral integration and evolved independently of each other afterwards. Our data provides strong evidence for the short C4 gene being the ancestral form in primates, trans-species evolution, and the "slow-down" phenomenon of the sequence divergence in great apes.

"The complement component C4 genes of Old World primates exhibit a long/short dichotomous size variation, except that chimpanzee and gorilla only contain short C4 genes." What does this mean? "Dichotomous" is just a fancy-ass way of saying, "distinctly different". The word is redundant in the sentence, as "size variation" is sufficient to convey the meaning. [Dismounts from hobby horse about unnecessarily high-falutin' language in scientific papers.]

This is what DeWitt does not make clear, and this is how he pulls the wool over the eyes of his unjustifiably trusting readers: In all Old World primates, except chimpanzees and gorillas, there are two forms of this "C4" gene. A short one without an ERV inserted in it, and a long one with an ERV inserted in it. How come chimps and gorillas only have the short gene?

When an ERV enters the germ-line, it starts with just one individual. It may immediately die out if that individual fails to pass it on to any progeny. It may get passed on, and an increasing number of descendants might inherit it, but then again, it might wane once more and disappear from the population. On the other hand, it might eventually become "fixed" in the population - everyone has it, therefore it is impossible not to inherit it. On the third hand, it may continue to fluctuate. Some will have the ERV, and some will not. This is the case with the long C4 gene in all Old World primates, including us, except for chimps and gorillas. "Genetic drift" is a term for how gene variants can wax and wane in frequency even when there is no selection pressure to either remove them, or replicate them. ERVs, as failed retroviral integrations, are a prime example of genetic material that is typically invisible to selection. It is pure chance whether they disappear, become fixed, or linger in a subset of the members of a species

Now what could have happened in the case of chimps and gorillas? If we can't come up with a plausible scenario, the case for common descent from shared ERVs is in trouble. But we can. The common ancestors of humans, chimps and gorillas could have had "dichotomous size variation", just like the species that have it today. Then, just by chance, or genetic drift, the long C4 variant disappeared in chimps and gorillas. It did not in us.

This is sleazy deception from DeWitt, when he says,

• the same ERV in exactly the same position would imply that humans and orangutans had the more recent common ancestor

No, it would not. More ERVs shared between humans and orangutans than those shared between humans and chimpanzees would imply it. But there are not. A credentialed scientist should know this. He would know about genetic drift and incomplete lineage sorting. In fact I'm sure he does. It is pretty basic evolutionary and genetic science. A respectable scientist would never try to deceive by omission and insinuation in this way. Respectable scientists are dedicated to the truth, as opposed to the Answers in Genesis Statement of Faith.

• By definition, no apparent, perceived or claimed evidence in any field, including history and chronology, can be valid if it contradicts the scriptural record. Of primary importance is the fact that evidence is always subject to interpretation by fallible people who do not possess all information.

Whoever wrote that has no right to try to use evidence to advance their case. They have already decided that evidence, whatever it is, is of no significance. And whoever they are, what sort of ego does it take to assume for themselves god-like powers of infallibility and total knowledge?

As always, do not take anything that appears in Answers in Genesis on trust. Do a bit of basic fact checking. You will soon see what a bunch of sleazy snake-oil salesmen they really are.

As Sir Winston Churchill said, "A lie gets half-way round the world before the truth gets a chance to put its trousers on."

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