My thoughts on an Evolution News post on ERVs

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That’s not an explanation for ERVs. As in, you are not explaining their locations, distribution, sequence properties, or anything. You’re just asserting they were made to have some function. That doesn’t explain any of their attributes. This is why creationism is not even a scientific hypothesis because it doesn’t actually explain, or even attempt to explain, any of the interesting attributes or patterns in the data.

Why should it be the case that a sequence that clearly contains GAG, POL, and ERV, is flanked by LTRs exactly as you would find in a genuine virus, in order to have this serve as nothing but binding spots for regulatory proteins, when any sequence could in principle serve the same role? Why stuff an entire virus genome into a multicellular animal if all you want is to express some surrounding genes?

But hey, creationists say it’s not actually a virus geneome. It just looks exactly like one by mere accident. Or deliberately was made to look like one to make us think that a virus infected some distant ancestor, just like viruses do today.

No explanation on creationism. It’s just whim. The designer just wanted to do it that way and nobody knows why.

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64

you are doing the same when you asserting that these are the result of viral insertions. you also believe that the host survived somehow without that ERVs. although you have no evidence for that claim.

actually some of these genes also have a function. so its not just the LTR sequence:

https://royalsocietypublishing.org/doi/full/10.1098/rstb.2012.0507

https://jvi.asm.org/content/89/8/4047

again this make sense if these ERVs are integral part of the genome.

incorrect. its possible that all these retroviruses evolved from ERVs and thus they are very similar.

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We can compare what?

Yeah, that isn’t an explanation. It doesn’t fit the evidence that ERVs appear in genomes with no precursor sequences, that they resemble retroviruses in sequence, that retroviruses actually do insert into genomes, and that most of them, the older ones, can no longer function as retroviruses or as anything else.

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66

How is it irrelevant? The entire line of evidence is based on the extremely low probability of a retrovirus inserting at the same base in two different insertions.

If DNA is transcribed into RNA it does not mean the DNA has to have function. Junk DNA can be transcribed into junk RNA. Viral promoters acting as viral promoters does not mean the RNA transcription they promote is functional.

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We can observe retroviruses producing new ERVs right in front of us. It isn’t an assertion.

There are species that don’t have these ERVs. How do they survive?

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lets see…

what is the problem? many creatures have unique genes. ERVs are not exceptional.

if retroviruses evolved from ERVs it make sense.

and the opposite is also possible.

since they got many mutations over time it make sense. like any other pseudogene.

its relevant because we do find such cases in nature. although according to the evolutionery calculations it should be very unlikely.

because they have other gene instead of that ERV. so you just moved the problem.

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We can observe retroviruses producing new ERVs right in front of us. That makes the most sense.

How often do two independent insertions occur at the same base (not within 100 kbp, but at the same base)?

That’s the solution. The ancestors had different genes which means they could survive without the ERV. If the ERV insertion became beneficial then it would have been selected for, and over time the descendants could have become dependent on it as other genes changed. It’s not that hard to figure out.

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Yes they are. Unique genes come from somewhere, either from previously existing non-coding sequences or from duplication of existing sequences. ERVs do come from somewhere, but it’s from retroviruses, not the organismal genome.

You are confusing the ancient origin of retroviruses with the origin of retroviral insertions. It’s the latter we’re talking about here.

Of course. In fact that’s why retroviruses insert. But that’s not where retroviral insertions come from.

So you agree that they’re non-functional, contra your earlier claims.

You are confusing “at the same base” with “within 100,000 bases”.

Exactly. A little thought should reveal how ancestral taxa could get along without the ERV.

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71

No, I am deriving that conclusion from the fact that it has all the components of virus genomes. Viruses which really do insert their genomes into hosts.

So no, I’m not doing the same. Our inferences are not equivalent at all. We have reason to believe that IF a virus were to insert it’s genome into the host, it would look like these retroviral insertions. But you don’t have a reason to believe that a transcriptional promoter for some host gene needs to look like a virus genome.

First of all I do have evidence for that, since this very data is what evidence for that would look like: Consilience of independent phylogenies, both of different ERV sequences, and other data sets.

Second is that hosts generally survive just fine without viral infections.

Yes, some ERVs have become functional. Still not evidence that any significant portion of ERVs are functional.

You keep just waving your hand towards a combination of a handful of isolated examples, and mere transcriptional activity.

That’s a suggestion of a remarkable evolutionary trajectory to hear coming from a creationist. It suggests numerous required gain of function mutations to turn an ERV, from merely serving as a collection of transcriptional promoters(or whatever other functions you might conjecture ERVs serve), into a functional retrovirus that can transmit between hosts. So basically the evolution of an irreducibly complex, replicating molecular machine, from a collection of genes with separate functions(or none at all).

But not only that, you’re literally saying that is how all retroviruses evolved from ERVs. So it must have happened many, many times. And within the last 6000 years, probably even less.

You should be able to show that on a phylogenetic analysis, then. Show which retroviruses derive from which ERVs in differen’t species’ genomes.

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This is another argument for the prevalence of junk DNA. If viruses were commonly inserted into functional DNA, the cell would likely die and the virus would not be able to do its stealth reproduction.

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you are begging the question. on the same base i can say that since all retroviruses have host components, this prove that they evolved from the host.

actually transposons and retrotransposons already doing something similar. so i see no problem with that. you just need to move existing parts of the genome to other places.

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again, we can see the opposite too (a part of a retrovirus that was created from host genes).

remember that its not just insertions since we also need to include natural selection, so its more problematic calculation than you think. but its irrelevant since the chance to get it within 100 kbp is very low, and yet we do find such cases.

its not. im talking about the same function (placenta formation) with different gene. on second thought im not sure if other creatures using a gene that isnt ERV for the placenta formation. but they do using different ERVs for the same function. so its basically the same problem: how the creature survived before it got this gene? i gave you a simple example from a cell-phone. a minimal cell-phone needs at least few parts to be functional. so you cant remove too much parts without making it non-functional.

not always. some groups of creatures have a bunch of genes that other groups dont. here are few examples:

“Our analysis identified 154 human genes that have orthologs in mouse, dog, and the elephant shark, but not in the teleost fish genomes”

or…

“Our analysis identified 107 teleost fish genes that have orthologs in the elephant shark assembly, but not in the human, mouse, and dog genomes” ( Survey Sequencing and Comparative Analysis of the Elephant Shark Genome).

no. if its possible once its possible many times.

im talking about the possibility that a retrovirus evolved from ERVs.

i never said otherwise. many of them are probably indeed non functional.

i dont confusing anything. see above.

you probably meant to “a little imagination”.

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No, we don’t. We don’t see supernatural deities creating genomes with fake retroviral insertions in them.

They are found at the same base, not within 100 kbp.

It is.

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What point are you trying to make here? This is more about gene loss than gene origin.

Then you’re not talking about anything. ERVs come from retroviral insertions. Some (though only quite recent) ERVs are transcribed to produce new retroviruses. But those ERVs came from retroviral insertions. That doesn’t support your original claim at all.

“Evolved” is the wrong word. You’re trying to make a claim that some retroviruses originated from ERVs that were not actually ERVs, i.e. not actual retroviral insertions. There is no evidence for any such thing. There is however plenty of evidence for insertions and transcriptions.

If you don’t confuse anything, you have misspoken frequently. And even the “within 100,000 bases” assumes a uniform distribution of insertion probabilities, which is not true.

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77

Do you have a reference?

Otherwise this is no more convincing than “we can created a nested hierarchy for vehicles”.

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I don’t offhand, but I understand it’s not uncommon for a transcribed retroviral genome to pick up a few adjacent bits of the host genome. Viruses are at least a frequently hypothesized vector for horizontal transfer.

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That makes sense, but scd seems to be implying that retroviruses arise from host DNA that isn’t retroviral in any way.

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Right. The problem isn’t with what he said but with what he meant.

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If you think that is possible, then you implicitly accept that evolution can and does evolve complex new function. At the very least you should be as skeptical of this as you are about anything else claimed to have evolved.

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82

No. Retroviruses really do insert their genomes into the host. Many ERVs really do contain a full retrovirus genome. GAG, POL, ERV, LTRs, the whole shebang. It simply wouldn’t make sense that retroviral genes should be flanked by LTRs if those LTRs did not once serve the function of LTRs in genuine retroviruses, since these sequences are critical to the viral replication and integration process.

Well you could say the words but you’d just be making a blind assertion. There’s just no reason to think that, and no known function of any piece of an ERV insertion in any host has been shown to need presence of GAG, POL, ERV, with flanking LTRs, much less why there would need to be many distinct such apparent ERV insertions scattered throughout the host genome. It simply doesn’t make sense.

You can make up scenarios and conjectures about what functions this could serve, but you have no evidence for them. You’d be making it up. But we do have direct evidence for retroviruses inserting themselves in the genome of the host, providing an immediate and experimentally confirmed explanation for their presence in our genomes. Our ancestors were infected by viruses. It’s so incredibly simple.

No they aren’t. Straightforwardly false. Neither transposons nor retrotransposons produce viral capsids, coats, or envelopes, in order to facilitate transmission between different host cells.

That’s not the only thing genuine retroviruses are doing. HIV, for example, can move from one host cell to another, and from one multicellular organism to another by constructing a complex genome-carrying vehicle, a rather large and complicated molecular machine, the virus particle made of proteins and lipids, that bind to antigens and other types of receptor molecules on the surfaces of other cells.

But you suddenly see no problem with that. Irreducible complexity evolving is just fine, simply because you feel the need to invoke such a hypothesis in order to avoid admitting that ERV insertions are evidence for common descent. I’ll have to remember this going forward.

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