Creationist ERV Misinformation

I went to the Reasons to Believe website and searched their articles with the keywords "endogenous retroviruses". From what I can see, they all discuss the same misinformation already covered earlier in this thread.You searched for endogenous retroviruses - Reasons to Believe1. Retroviral insertion is not random enough. That's false. Even in a best case scenario, insertional bias will only produce ~1% shared ERV's.2. ERV's have function. Only a tiny fraction can be shown to have function, and even if they all had function they would still be smoking gun evidence for common ancestry.3. PtERV1 is found in chimps and gorillas but not humans or orangutans. They forget to mention that they are not at orthologous positions in the chimp and gorilla genomes.4. Departures from the expected phylogeny. There are known mechanisms that create these departures, such as ILS. It is expected that we will see a noisy phylogenetic signal if species evolved from a common ancestor. It is the ratio of noise to signal that matters, and they are reticent to even acknowledge the massive and overwhelming phylogenetic signal that sits out way above the noise.5. Retroviruses can't produce ERVs in the first place. They acknowledge the case of ERVs being produced by an exogenous retrovirus in koalas, but they tell their audience to just ignore it for no apparent reason.Nothing really original here. Just a rehash of what other creationist authors have written.

I ran across an article at ICR that made a claim about ERV's that I had not come across before:

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First, genetic data indicate that these sequences are not millions of years old. Using the comparative tools of evolutionary genetics, secular scientists compared the gene sequences of viruses to their counterparts in animal genomes and found that, at most, the variation in these sequences indicates they can be no more than 50,000 years old.2 So, if these viral-like sequences are not millions of years old, then where did they come from?

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[off topic note: the use of "secular scientist" still makes me giggle. What's next? Secular baseball players? Secular dentists?]That's a bit convoluted, but their claim is pretty clear. They are claiming that ERVs are not older than 50,000 years. To support this claim, they cite: Molecular Clocks and the Puzzle of RNA Virus OriginsSo what does the paper actually say?

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Although the ultimate origins of RNA viruses are uncertain, it seems reasonable to assume that these infectious agents have a long evolutionary history, appearing with, or perhaps before, the first cellular life-forms (38). While the RNA viruses we see today may not date back quite this far, the evidence that some DNA viruses have evolved with their vertebrate hosts over many millions of years (24) makes an equally ancient history for RNA viruses a natural expectation. Yet a very different picture of RNA virus origins is painted if their gene sequences are compared; by using the best estimates for rates of evolutionary change (nucleotide substitution) and assuming an approximate molecular clock (21, 33), it can be inferred that the families of RNA viruses circulating today could only have appeared very recently, probably not more than about 50,000 years ago. Hence, if evolutionary rates are accurate and relatively constant, present-day RNA viruses may have originated more recently than our own species.

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Well, that's a very different picture than the one painted by ICR. The scientific paper is saying that currently circulating RNA viruses originated no more than 50,000 years ago. It says nothing about ERVs originating within the last 50,000 years. On top of that, the article clearly states that there are examples of DNA viruses that have evidence for host/virus co-evolution over the last several million years. Strange that they didn't mention that (sarcasm implied). The paper also goes on to explain why comparison of circulating RNA viruses leads to these conclusions.The rest of the ICR article hits the usual misinformation bullet points, such as some ERVs having function and no examples of extant exogenous retroviruses producing heritable endogenous retroviruses (see Koala Retrovirus [KoRV]).

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The first example comes from the Discovery Institute.
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Do Shared ERVs Support Common Descent?

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The Article is in 3 parts if anyone wants to see all of them for full context
Revisiting an Old Chestnut: Retroviruses and Common Descent (Updated)
Do Shared ERVs Support Common Ancestry?
More Points on ERVs

TAQ:

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This means that out of the 203,000 ERV's reported in the human genome only 82 are not shared with chimps at the same base. ​

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Are you sure this is a valid method of calculating Orthologous ERV's? I tried to find an independent source and the best I could find was Orthologous endogenous retroviruses exhibit directional selection since the chimp-human split which says "Overall, we identified 336 chimp-human pairs of sequence from a variety of genomic locations".

Yes. ERV's are either orthologous or lineage specific. If they aren't lineage specific then they are orthologous. If only 82 human ERV's are lineage specific then the rest must be orthologous. The 203,000 human ERV's counted by the Human Genome Consortium was done by top scientists, so I see no reason to doubt it. They used several filters to narrow the field down which means they excluded a lot of ERV's from the study. They were looking for more recent insertions that are full length, so right away they are excluding about 90% of ERV's that are solo LTR's. Of the candidates, they further excluded older full length ERV's because they were focused on more recent insertions, as stated in the results section:

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We wanted to see if recently integrated proviruses accumulated mutations more quickly than neighbouring DNA. Our approach was to examine substitutions into ERVs and their neighbouring genomic sequence that lead to differences between human and chimpanzee. To achieve this goal we identified ERVs and their flanking DNA from both species.
Orthologous endogenous retroviruses exhibit directional selection since the chimp-human split - PMC

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They were NOT trying to measure the total number of ERV's in the human or chimp genome.

Is there anything you would like to see addressed that hasn't been so far?

I think you already covered this in #15.

Do you know of any creationist sources whose articles on ERV's are honest and consistent with the scientific literature? I have yet to find one.

Do you have similar data on shared ERVs with other mammals or with reptiles or fish?

Over time ERV's will accumulate mutations to the point that they can no longer be compared to one another. This is true for the vast majority of sequence in vertebrate genomes. Over those evolutionary distances (humans to distantly related mammals, reptiles, fish) it is better to compare conserved sequences which tend to be functional sequences. Since the vast majority of ERV's are not functional and accumulate mutations at a rate consistent with neutral drift they fade into the background much faster than functional DNA. There is also the problem of recombination and indels which can make synteny and orthology hard to determine.

Alright, understood. Thanks!

Taq:

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In table 2 of the chimp genome paper they report 82 human specific ERV's and 279 chimp specific ERV's.

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I don't see these numbers 82 and 279 in table 2. Could you explain to me where or how you got these numbers?Thanks!

Hi sensei,By adding ERV Class 1 to ERV Class 2.Mutate and Survive

Ah yes, thank you!