The "Not Junk" Anti-ERV Defence (Fig Leaves)

https://barryhisblog.blogspot.com/p/the-not-junk-efence.html

If you don't know about Endogenous RetroViruses (ERVs) and how they prove common ancestry between different kinds of creatures, go to https://barryhisblog.blogspot.com/p/endogenous-retroviruses-frequently.html

Cdesign proponentsists often claim that the proof* of common descent from ERVs is falsified by the fact that elements of ERVs have been found to perform functions - sometimes vital functions, in the organisms in which they are found! It is true that they do, but this is a mere fig leaf to defend their antiscience creationism. It's all they have to try to cover up their nakedness when presented with the evidence from ERVs.

https://ncse.ngo/cdesign-proponentsists
https://barryhisblog.blogspot.com/p/what-is-case-for-common-descent-from.html

The fact that some elements of ERVs perform functions does not come as a surprise to virologists and geneticists. It is they, and not the creationist/ID "scientists", who found this out and published their findings in the first place (incidentally giving the lie to the theory that scientists are engaged in a multinational, multi-generational conspiracy to fool us about evolution).

I put scare-quotes ("") around creationist/intelligent designer spotter "scientists", because they have turned their backs on science. See https://barryhisblog.blogspot.com/p/aig-statement-of-faith.html

What is also a lie, and a big one, often repeated, is that this proof of common descent is dependent on all ERV genetics being useless "junk". It appears to be the only 'argument' deniers have in their creation bag** to try and hide the dreadfully unavoidable conclusion of common descent.

(The issue of whether "junk" DNA exists is a separate, different issue, but if you are interested in the topic, see "https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1004351" and "https://stonesnbones.blogspot.com/2012/12/junk-dna-and-junk-creationism.htm".)

No. The proof of common descent is based, not on any claim that ERV genetics are "junk", but on the fact that ERV genetics are derived from viruses. Typically, deniers fail to mention any of this evidence in their articles. A summary of this evidence may be found at, "https://barryhisblog.blogspot.com/p/why-do-virologists-and-geneticists.html"

But how can it be that ERVs derive from retroviruses? There are so many of them, in the DNA of every cell of our bodies. How is it that they do not kill us, or even worse, not allow us to develop at all?

The truth is that reverse transcription, the process by which retroviruses get their genomes copied from RNA to DNA prior to integrating it with our existing DNA, is very error prone. This results in many broken retroviruses that cannot get replicated. (We say that they are not "replication competent".)

So it is no surprise that ERVs are not replication competent. Any individual that got a fully functional retrovirus in a germ cell would not be able to produce viable offspring from it.

But retroviral genomes consist of many elements (see the link just above). The fact that an ERV is not replication competent does not mean that all its elements are broken.

It is well known, and published in the scientific literature, that certain elements of ERVs do perform functions. Most of these elements are promoters. You see, when a retrovirus integrates its genome into a host cell, it would not be able to induce the host's RNA polymerase to transcribe its genes back to RNA again unless the genome of the retrovirus already included transcription promoters. Now if you drop a promoter more-or-less at random into an existing genome, it is quite likely to promote the transcription of something or other downstream of it. This is true whether the downstream genetic material originated from the host or from the virus itself.

https://www.nature.com/scitable/topicpage/dna-transcription-426/

So a replication incompetent ERV cannot force the cell it is in to generate new viruses. How does it persist in our genomes? By good ole' natural selection! Any ERV component that assists its owner in getting all its owner's DNA replicated, including itself, via normal reproduction, will be likely to be found in more and more individuals as the generations pass.

It is the same with more complex ERV elements, the retroviral genes themselves. A striking example of this the case of the envelope (env) genes. These are the genes that allow a retrovirus to fuse with a host cell in the first place. They can also (HIV is an example), 'collect' more host cells and incorporate them into one large cell with then has multiple cell nuclei. This trick allows the HIV to counter T-cells more efficiently. The multi-nucleated cell is called a syncytium. Our bodies contain syncytia. Examples are muscles, and placentae. The genes that enable the production of syncytial placentae are very similar to ERV env genes and exist in ERV structures in the same relative position as retroviral env genes. What a coincidence!   

The other thing about syncytins that are involved in the development of placentae is that they are different in different lineages. They appear in different ERVs in different chromosomes and depend on whether you are  a rodent, a carnivore or an elephant etc. Same design - same designer? Not here! The phylogeny of syncytins is yet more evidence for evolution! (But the denialists will never tell you that.)

But how could placental mammals have survived and reproduced before placentae? The same way non-placental mammals survive and reproduce today. Now, of course, if you removed syncytins from all placental mammals by magic, they would all instantly become extinct. They have become dependent on this evolutionary innovation. This is a good example of "interlocking complexity", a prediction of evolutionary science established many decades before the cdesign proponentsists attempted to steal and pervert it under the banner of "irreducible complexity". See "The Mullerian Two-Step: or why Behe's "Irreducible Complexity" is silly". http://www.talkorigins.org/faqs/comdesc/ICsilly.html

I critique a number of denialist articles on ERVs here.
"Hasn't the evolutionist's story about ERVs been debunked?" https://barryhisblog.blogspot.com/p/hasnt-evolutionists-story-about-ervs.html

Another denialist wheeze is the "VIGE" idea. (Variation-Inducing Genetic Elements). I dismiss the question,"Could you have this backwards? Maybe retroviruses come from VIGEs?" See https://barryhisblog.blogspot.com/p/could-you-have-this-backwards.html

See also, But how can you rule out design as an explanation? https://barryhisblog.blogspot.com/p/in-science-we-apply-principle-of.html

And also,
https://barryhisblog.blogspot.com/p/ok-ill-admit-it-ervs-are-junk-dna-well.html
https://barryhisblog.blogspot.com/p/ervs-do-stuff-doesnt-that-prove-that.html
https://barryhisblog.blogspot.com/p/superinfection-exclusion.html
https://barryhisblog.blogspot.com/p/ervs-are-essential-in-reproduction.html

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*Some may object to my use of the word "proof", saying that it belongs exclusively to axiomatics such as mathematics and the measurement of the strength of alcoholic beverages, but the sense in which I am using the word is a respectable usage, found in law, viz. "proof beyond reasonable doubt". There are people who doubt the ERV evidence, but none of their doubts are reasonable.

**And now for a little light relief, a joke: When God finishes creating everything, he finds that he has two items left over in his creation goodie bag.

He asks Adam and Eve if they want them.

"What have you got?" asks Adam. 

"The ability to pee standing up", says God. 

"Gimme, gimme, gimme!" cries Adam. 

"OK", says God. 

"What have you got left?" asks Eve. 

"Multiple orgasms".