Stated Clearly: The DNA evidence for Common Descent in ERVs

Here is a new video we have been working on for months that explains ERVs.

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This was very well done, although the link following the YouTube one is broken (it looks like part of the address was deleted somehow).

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Fixed the link. Thank you.

Wow. This is an amazing video. I learned a few things, and, in my expert capacity as a layman, I’m pleased to say it was very easy to follow. Well done!

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Hi Colt
What is the strongest creation counter argument?
Best
Bill

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That’s easy.

The best response is that ERVs do suggest CD, but there are separate creation models that can mimic this feature of the data (e.g. creation by modification of existing genomes).

Omphalos, in other words. I do wonder if Bill thinks omphalos arguments are worthwhile.

That isn’t omphalos :roll_eyes:

This response sure seems like special pleading on the part of creationists. In other words, there’s no particular reason to think a designer would plant inoperable genes in the genomes of various mammals in a way that is best represented mathematically as a nested hierarchy. Both parts of that observation (broken genes and nested hierarchy) are parsimoniously predicted by common descent, but they are not predicted by any parsimonious design hypothesis I have read, and I’ve read a lot of those. What am I missing here?

In my reading, the more common, special creation critique of the ERV argument is that they (supposedly) have real biological function in most every case. Aside from the exceedingly poor evidence for this creationist contention, it does not even attempt to address the nested hierarchy observation.

Best,
Chris

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I think you are missing the basic features of this proposal.

The idea is that ERVs enter our genomes in the same way that they do by common descent, by infections of individuals in the distant past. Just now, God is periodically creating new species from existing species, without cleaning up the ERVs as He does so (why should he?). Contingent on some details, there is reason to believe some version of this is consistent with the evidence.

That is neither a special pleading nor does it imply a deceptive God. However, it does seem difficult to motivate. I see it, at best, as a technical possibility for which I have no reason to adopt.

Hi Chris
This papers pretty short. Thoughts?

Great video.

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Of course it is. False evidence of ancient events in a non-existent human/chimp lineage that provided an appearance of age for that fictional lineage. What could be more omphalosy?

Depending on how that creation is done, it may not count as creation. It sounds more like common descent. Now if you’re going to claim that common descent is a form of creation, you’re abusing the language and sowing confusion.

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What do you think it means? Is it a challenge of some sort to evolution? If so, you will have to explain what the challenge is.

It seems more likely that the Designer designed some brains to not understand the nested and mathematical aspects of nested hierarchies. :wink:

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Excellent video! I would simply add that before DNA sequences were available, protein sequences could be used to draw the same conclusions. Of course protein sequences reflect the underlying DNA sequences. I do think that one thing missing, which maybe needs another video to explore, is that humans are not only have a common ancestor with the two species of chimp, but are more closely related to them than either is to gorilla. The evolutionary trees (phylogenies) made from different sorts of data match. You can make trees from different families of ERVs and they are very similar. Just saying we “have a common ancestor with” chimps is not quite good enough, because we also do, after all, have one with the oyster as well. And with yeast. And with the axolotl. And of course it was this consiliency of trees that underlay the evidence anatomists saw back in the 1700s, although they thought of it as consiliency of classifications.

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First of all, really impressive graphics. Secondly, great job showing thumbnails of all the scientific papers. Making those easy to identify strengthens the scientific case.

When it got to the beneficial, functional ERV part and I heard: “We can no longer produce without it…we are part virus” my reaction was something like chuckling and incredulousness. If the video was meant to convince creationists, then telling them - “btw this random evolutionary process is why we’re here today but also God did it with a virus,” made the idea seem silly to me.

I thought toward the end it got to be “preachy,” and instead of just presenting the evidence was intended to embarrass or ridicule anyone who thought differently into changing their mind - quotes like “Reluctant, yet rational person”… “More than Enough”…“beyond all reasonable doubt.” “We. Are. Family.” (As if it wasn’t obvious enough the point was that humans and chimps had a common ancestor, each word had to be punctuated.) And then Collins quote at the end.

Overall, the video will probably be very convincing to many people with seeming simplicity of the argument, and I would say that this is one of the tougher ones for creationists to wrestle with. But those few points I mentioned may be a turnoff to some creationists especially.

As for being told I’m not rational, well, probably not the first time. :slightly_smiling_face:

I would say, as far as I can tell, function is a YEC explanation.

This seems to only make sense in a progressive creation or some kind of similar idea, since YEC wouldn’t agree with infections before humanity fell into sin.

I was skimming through a creationist websites to see if there was a paper with a thorough YEC explanation. This one seems to be the most thorough I found in a quick search it if anyone is interested.

I thought I have learned a lot in 6-9 months, but wow, there are a lot of terms here. I mostly skimmed for now, as I need to read more material to understand it better. But honestly, if I was 20 years younger and wanted to go into biology, I would want to study this. As I mentioned in the other thread Colt started, ERVs fascinate me for some reason, and I’m not finding the evidence as intimidating as rh video wished to make it for me. Something or many unexpected things are going on. I think it may be the coolest, most fascinating part of the genome God created, we just have to learn more. (I already explained I’m not rational so give me a break on my excited comments). :relaxed::sweat_smile:

Abstract: Scattered in human and animal genomes are a class of repetitious genetic elements called endogenous retroviruses (ERVs), which bear sequence homology to retroviral genomes. They constitute about 8% of the human genome. Evolutionists assume that all endogenous retroviruses are remnants of germ line infection by exogenous retroviruses. However, the essential beneficial function of some ERVs and complex interaction between ERVs and other host DNA sequences suggest that some retroviruses were created in the cell as part of the host genome. The original ERV elements were endowed with the ability to package themselves in proteins and lipids and leave the host cell as infectious particles. Thus we speculate exogenous retroviruses were derived from endogenous retroviruses (exogenization, as opposed to endogenization). The ability of retroviruses to transpose within the host cell or to infect another host may have been designed for protein-coding, for gene regulation, and for DNA repair by homologous and non-homologous recombination. After the Fall, retroviral elements have been degraded by mutations. Retroviral insertion into the host genome also became deregulated, causing insertional mutagenesis. Deregulation of exogenous retroviruses resulted in pathogenesis.

Conclusion: ERVs were created to encode co-regulated proteins and to regulate dispersed host genes. Retrotransposition adds to the flexibility of the cellular genome, while intercellular transmission enables ERVs in horizontal gene transfer and homologous repair. Common design and controlled activities may explain the similarities between human and primate ERVs, while deregulation in viral replication and integration is responsible for the pathogenesis of modern retroviruses. Re-endogenization of degenerated exogenous retroviruses is mostly detrimental.

Predictions and Expectations

(1) Despite massive degeneration since the Fall, creationists expect to find more examples of complex, interdependent functions between ERVs and the host genome, which challenges the conception that ERVs are add-ins to pre-existing genomes.

(2) Discoveries are expected concerning the details of the interaction between ERVs and host cell DNA repair and maintenance, which would not be anticipated if ERVs were originally “selfish” exogenous entities.

(3) We expect more examples of degenerate and impaired functions, which may be repaired or restored by relatively small modifications (as with HERV-KCON (Lee and Bieniasz 2007).

(4) In line with their original design, creationists anticipate more examples of functional gene transfer by retroviruses between cells of the same host, between members of the same species, and possibly even between different species.

But why?

The video isn’t saying “but also God did it with a virus”. But what is silly about some ERVs some times evolving to be useful for the host?

No they argue this on the basis of evidence. It’s not an assumption. The video explains in part how that inference is made.

I invite you to consider in what way the functions of some tiny fraction of ERVs suggests this? To use that word “suggests” is to say that the functionality of ERVs is evidence for ERVs having been “created in the cell as part of the host genome”, but that just doesn’t follow from anything stated there. So how does it suggest this?

Okay, why? Doesn’t this conflict with the apparent reluctance you have to accept that an ERV insertion can evolve to become functional? Yet here AIG is suggesting that’s how ERVs were created, with the ability to move between hosts and infect their cells and result in useful functions. Presumably dependent on where and when they insert, right? So is it silly or not?

This is gibberish. The explanation they give for this in the paper appears to be a failure to apprehend how ERVs work. They reference a paper(this one:https://academic.oup.com/genetics/article/158/4/1665/6049491) that show ERVs(and many other random DNA fragments that happen to exist in the nucleus at any given time) are some times inserted at sites of double strand breaks when repaird. Yeah no wonder, that’s where retroviruses insert themselves. They don’t repair the DNA, they exploit the fact that it has become damaged to more easily insert themselves. This is facepalm inducing, and really shows how the authors of that “paper” aren’t really thinking about how biology works, but just making stuff up to sound technical and superficially convincing to ignorant laypeople, throwing anything and everything at the wall in hope something sticks.

Wait a minute. They’re pulling a fast one here. So how do they tell the difference between an endo-to-exo derived, and exo-to-endo derived retrovirus again? Have they tested how many of these supposedly originally created ERVs are detrimental when reactivated?

Most of these are actually rationalizations, or attempts to argue why ERVs aren’t evidence for evolution, they’re not really predictions from special creation.

Ahh, the “more examples” prediction. Shouldn’t they all be discovered to have been functionally important at one point? Now again we get this stuff that the discovery of a functional ERV “challenges” the idea that ERVs are derived from ancient retroviral infections. But why does it challenge this?

Really? What discoveries? How many? Which ones in particular? And what is it about them having once been bona fide retroviruses that makes it “not be anticipated” that an ERV here or there can have evolved to be functional?

But then the expectation has to be that ALL shared degraded ERV insertions must have once been functional, right? And that it should be possible to restore them all back to function beneficial ERVs to see how they work? Who is going to be doing this work?

This one is hilarious because it appears to have been invented as a “prediction” to try to stave off an argument that ERVs can evolve to become functional for the host organism by showing examples of where this has happened. The creationist can now account for all imaginable data. We are told up above that:

Re-endogenization of degenerated exogenous retroviruses is mostly detrimental.

That the discovery of a functional ERV:

…challenges the conception that ERVs are add-ins to pre-existing genomes.

In the “paper” they say:

If as claimed, these sequences were exploited de novo after endogenization of an ERV (exaptation), a burden of proof lies on evolutionists to demonstrate such vital functions could ever arise without catastrophe to the host.

@Thoughtful says:

So the AIG propaganda appears to have worked, and created this view that the “chance” evolution of a useful function from an ERV insertion is ridiculous (presumably because it must be miraculuously rare?).

But that last “prediction” (4) is now saying creationists expect to find that “in line with their original design” there are functionally beneficial genuine retroviruses that are supposed to be able to cross between cells, between individual hosts, and even between species.

So if we find nonfunctional or deleterious ERV insertions, this is evidence against evolution(see, these are detrimental/nonfunctional, so how could there ever evolve a functional/beneficial one? It must be miraculously rare!).
And if we find that some times some actual retroviruses are capable of moving between cells, hosts, and even species, and result in useful functions, well then this is evidence for creationism?

Perfect. With that set of “predictions” it’s become logically impossible to show evidence for the evolution of a functional ERV from a retroviral insertion, because the creationist will now just rationalize that it was created to be a functional one from the beginning.

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Dr. Swamidass explained it good. Unfortunately there are a lot of differing creationist views on this topic. The same as there there are many different beliefs of creationists in the area of science as well as theology.

Here is an article from Dr. Jonathan McLatchie that explains his view.

Colt

When making this video we discussed many ways that we could present this information and thought that limiting the “common ancestor” between Chimps and Humans was the most straightforward approach. Of course, we could present Gorillas, Gibbons and many others and show how the ERV evidence also shows common descent with these animals but we had to bound the video to a reasonable timeframe.