Stated Clearly: The DNA evidence for Common Descent in ERVs

You’ve already said that you don’t understand nested hierarchies yet.

I think that to better promote understanding an explanation of nested hierarchy outside biology would be preferred:

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Nested Hierarchies from Berkeley.edu

Is this helpful?

@rumraket I just keep finding fun stuff. :slight_smile: The last article I quoted had a reference to Mer41, but didn’t really explain.

This one explains more: How Viruses Infiltrated Our DNA and Supercharged Our Immune System - The Atlantic

When we suffer from infections, two proteins called IRF and STAT coordinate our immune responses. They hover over our DNA, looking for particular sequences that they can stick to. When they find these docking sites, they land and activate nearby genes. And when Chuong looked at these docking sites, he found that many of them came from ERVs. By hopping around our genomes, these viruses created new ports for IRF and STAT, and changed the portfolio of immune genes that they turn on.

This pattern isn’t unique to humans. The team found that a different virus had littered the genome of mice with docking stations for STAT. And the MER41 viruses have independently invaded the genomes of many other mammals, including lemurs, bats, mice, cows, and dogs, perhaps affecting the activity of different immune genes in each family. Time and again, it seems that viruses have shaped the evolution of the mammalian immune system—and not just by giving it something to push against, but by giving it new ways of pushing.

It’s the scope of the discovery that’s impressive says Guillaume Bourque from McGill University. While other scientists have shown that ERVs can control the activity of specific genes in specific animals, Chuong has shown that many families of ERVs can influence an entire branch of the immune system in many species. “This really demonstrates that importance that [such sequences] have played, and probably continue to play, in the evolution of mammalian gene regulation.”

Sure, but that leaves one huge mystery: why exactly would a virus contain sequences that act as docking stations for human proteins like STAT, and that can activate nearby human genes.

They answer:

Many of these viruses, like HIV, infect immune cells. They could have evolved genetic tricks for manipulating their host’s immune system to boost their own reproduction. The hosts could then have co-opted those same tricks to re-wire their defenses against the viruses!

Maybe that’s not the irony - the irony could be the hosts already had the tricks.

But now, I’m kinda getting why the other article said infiltrations only happened 30-40 occasions.

Is that really robust enough to create a nested hierarchy that is reliable?

Anyway, excited to read that article that ERVs are as fascinating as I thought.

It has everything to do with nested hierarchies. Each retroviral insertion that’s present in humans and chimps but no other species implies a branch on a tree of life connecting humans and chimps exclusive of other species in that tree. Though the video doesn’t mention it, other retroviral insertions connect the human-chimp branch to gorillas, that branch to orangutans, etc. Groups within groups, that’s what a nested hierarchy is.

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Lmao…

Nested hierarchies and phylogenies are related concepts..

@Rumraket provided links to a couple of accessible YouTubes I found high yield for understanding how genetic phylogenies are constructed here.

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This is way too complicated!

The fossils in sedimentary rocks came from fossilization and ERVs came from viruses.

:slight_smile:

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Look at the abstract (especially the boldened parts):

The authors used the LTRs of six HERV loci (or positions) to reconstruct the phylogeny of primates. They used these LTRs for several reasons, one of which is their lack of function making them subject to neutral evolution. Neutrally evolving sequences accumulate mutations at a fairly constant rate and we can use that to figure out important information like the age of the ERVs.

The phylogeny derived from the analyses of those LTR sequences matched the standard phylogeny of primates, that is, chimps and bonobos were most closely related to humans, than gorillas etcetera. Biology is messy, so (unsurprisingly) there were deviations from the expected pattern, and the authors offered several explanations for them.

This nested hierarchy gleaned from the HERV LTRs and other parts of the genome across primates and other animals is extremely powerful evidence for common descent. @John_Harshman can explain this better than I.

There certainly is, but this is a good place to start, as the authors indicate in their abstract:

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https://en.wikipedia.org/wiki/Matryoshka_doll#/media/File:Russian-Matroshka.jpg

I know that the big one is the ancestral primate, and I’m the little one. But it looks like the big one is gorilla and the litttle one is a mouse lemur

Hi Joshua,

You misunderstood what I wrote. Here’s what I said:

they [“inoperable genes” and “nested hierarchy”] are not predicted by any parsimonious design hypothesis I have read. [emphasis added]

What I said, and what you said I said, are not the same thing.

Also, note that I included the word parsimonious. You evidently agree with me because you have said the model in question would be ad hoc. A model cannot be both parsimonious and ad hoc, would you not agree?

But let’s move on.

“Ad hoc” is a pretty good synonym for “is based on special pleading,” IMO.

IMO they are quite far apart.

A Christian who Accepts the Science of Evolution (CASE) would accept that speciation happens via mechanisms identified by biologists, such as fixation of different mutations in different populations, copy-and-modify mutations, constructive neutral evolution, horizontal gene transfer, natural selection, etc. Such a Christian would generally believe that God providentially and perhaps miraculously guides the whole process at every moment. (If it even makes sense to distinguish between providence and miracles, a discussion which is beyond my pay grade.)

The progressive creation adherent, on the other hand, tends to reject the mechanisms identified by biologists as an explanation for the diversity of life–at the level of class, phylum, and kingdom, at least.

Another reason the model you presented could be considered special pleading is that it would either: (1) be impossible to distinguish from standard evolution models, or (2) not be capable of yielding meaningful predictions. Here’s why: such a genomic copying model would necessarily involve one of two possibilities:

  1. A nucleotide-for-nucleotide copy of an existing genome, with the resulting new population being placed in a new environment for subsequent developments; OR
  2. A copy-with-modification in which the modifications set a new direction for the resulting new population.

The first alternative (nucleotide-for-nucleotide copy) would be indistinguishable from standard evolution models.

The second alternative (copy-with-modification) would make scientific predictions impossible because scientists would have no way to predict or even identify after the fact what modifications an infinitely wise and powerful Creator might have made.

So the 2 alternatives are copy-with-no-modifications or copy-with-modifications, and neither alternative yields a model which would be scientifically viable IMO.

Assuming this analysis is valid, I have nothing further to add. I’ve said quite a bit about why the model you have put forth in this thread leans heavily on special pleading and is not what a Christian who Accepts the Science of Evolution would favor. I leave the last word to you, should you care to say anything else.

Best,
Chris

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haha. I understand that. I just don’t “get” why nested hierarchies are such good evidence for evolution. Maybe it’s just me - maybe I’m terribly dense about it… It seems that when ever other arguments against evolution seem to have a lot of merit, and the argument for evolution over common design breaks down, the response is “but nested hierarchies!” It’s the trump card.

I was doing some searching; as far as I could tell this is the only paper everyone is citing. Interesting that everything that came up in google searches are forum posts and a few Evolution News blogs disputing this paper. Thanks for the explanation.

Because we know from the early history of studying them that retroviruses incorporate human genes. The first to be thoroughly studied were those that caused tumors in chickens and rodents because they carried activated versions of oncogenes found in the host genome: src, myc, ras, erbB.

There is no “huge mystery.”

Didn’t you recently write that you don’t understand nested hierarchies?

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limiting [it to] the “common ancestor” between Chimps and Humans was the most straightforward approach.
It is worth noting that for a creationist who is concerned to show that there is no common ancestor of chimps and humans, this is highly relevant. For an evolutionary biologist who starts with all life being genealogically related, it is boring and uncontroversial that humans and chimps have a common ancestor. After all, so do all pairs of species.
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Very simple, really. We naturally expect nested hierarchies to result from common descent with divergence. We have no other hypothesis that would naturally result in such a thing. Creation could do it, but we have no reason to suppose that it would unless there was an attempt to simulate common descent. And that involves a deceitful God.

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Actually, no. The big one is all primates. In a nested hierarchy, everything inside the big doll counts as part of the big doll. Matryoshka dolls are actually a poor example of nested hierarchy. There would have to be a big doll with lots of little dolls inside it, some of them inside different medium-sized dolls within the big doll.

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Ok, so it’s a requirement of evolution for evolution to make sense. But creationists can’t claim it would fit common design + evolution within kinds because it makes God deceptive. Therefore evolution is true, because a designer has to be good and any designer that makes something that men have decided is common descent isn’t good?

What about exceptions to nested hierarchy?

My strategy is to start with a nonthreatening case…

I’m afraid that it just muddies up the explanation for no gain.

Not at all. A designer doesn’t have to be good, but I doubt that you would accept a lying designer. Was I wrong about that? Evolution is true as far as we can tell, because it’s the only hypothesis that explains the data. A lying designer explains nothing, because that designer could have shown us anything he felt like, so his existence is compatible with any data at all. It’s a useless hypothesis.

What about them? We expect certain categories of exceptions due to simple homoplasy, lineage sorting, horizontal transfer, hybrid speciation, and, very occasionally, real convergence. That doesn’t change the general pattern, and common descent explains that pattern.

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I’m not the pro, but I think this is backwards. Nested hierarchy is observed. Common Descent is the hypothesis that makes sense of it.

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