The PCs am familiar with are just fine with evolution, and do not try to get all sciency about God, ala Behe.
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Would you provide me a link that explains nested hierarchy of ERVs? Or maybe @Chris_Falter has one since heâs been mentioning it too.
You wrote a lot of words, and Iâd like to respond to more, but I donât understand this topic well enough to do any justice to a response right now. Your statement may be close to hitting the mark, except is there anything that mainstream scientists wonât rationalize to be evolved from the beginning? Sometimes I feel that way also 
I know itâs not saying that. But if youâre trying to convince someone who is not sure evolution is true, probably mostly because of their faith/interpretation of the Bible, theyâre going to think of Godâs plan to create humanity. The idea that God would decide that a random virus insertion would ensure the latter development of all mammals including humans doesnât make much sense. Instead it immediately gives the creationist the idea that the inference that this is an insertion should be questioned, or something smells rotten in the state of Denmark.
Perhaps finding special regulation around humans is a prediction of special creation. I was reading this yesterday, but finished the article this morning. The Viruses That Made Us Human | NOVA | PBS
The team identified genes derived from the human endogenous retrovirus HERV-K that were active around the time when the embryo was just eight cells. Of the many known edogenous retroviruses in humans, HERV-K is the newestâit inserted itself as recently as 200,000 years ago. Itâs so new that several of its copies in the human genome can still produce viral protein. To prevent this, adults keep a tight control on HERV-K by switching it off, though this isnât the case in very young embryos, Reijo Pera and Wysocka found. But far from being detrimental, HERV-K activates key genes that help transform a single cell into a fully-formed infant. These HERV-K viral particles and proteins also help protect the tiny ball of cells from being infected by other viruses, the researchers showed in a 2015 Nature paper .
A follow-up study in Nature Genetics , published in early 2016, found another, HERV-H, which produced RNA molecules that also switch other genes on and off. The 13 HERV-H switches identified by Reijo Pera and Wysockaâs team help keep the early embryonic cells pluripotent, ready for any job as an adult cell. When the researchers blocked the production of HERV-Hâs RNA molecules, they stopped embryo development in its tracks. Further experiments showed that HERVH-derived RNAs are also required to turn adult cells back into pluripotent stem cells.
âThis DNA, what we used to think of as junk DNA, is actually modulating our development,â Reijo Pera says.
This pair of studies followed on the heels of a 2015 paper in Cell Stem Cell that showed researchers could identify the specific stage of development of an embryonic cell based on which set of endogenous retroviruses were active. When the embryo had just one or two cells, it had the most endogenous retroviruses active, says Jonathan Göke, a computational biologist at the Genome Institute of Singapore and first author of the 2015 study. As the embryo got larger, viral activity dropped dramatically, though it still continued in specific groups of cells as the fetus developed.
âWe know that theyâre active. We know that theyâre important, but we still donât know exactly what they do,â he says.
The work is still preliminary, says virologist John Coffin at Tufts University, who has spent much of his long career studying retroviruses, including endogenous retroviruses. âYou can clearly see the pattern of expression of these genes, but their actual role still remains to be established,â he says.
Blurry Boundary
HERV-K may also have played an important role in separating some of the first humans from their primate ancestors by making small adjustments in when certain genes were switched on or off, according to Reijo Peraâs research. But with tens of thousands of viruses embedded in our genomes, scientists have only just begun to explore their potential effects. In a recent paper in Science , University of Utah geneticist Cedric Feschotte found that these viruses played a key role in the evolution of the mammalian immune system and, even now, continue to tell certain immune system genes when to turn on and off.
âThese viruses put us on the fast track to evolve all the bells and whistles needed to evade other viruses,â Feschotte says. âThese viruses are already equipped with all kind of weapons to evade our immune systems that now can be recycled.â
Although one of the viruses in question, Mer41, infiltrated the genome 45 to 60 million years ago, one of the proteins it controls is only found in humans.
All of this reading about embryonic development and viruses makes me wonder if ERVs have anything to do with morning sickness. 
I have no idea of that makes any biological sense, but just canât help the thought coming to mind since itâs been my life for the past 4 months.
The process requires an astonishingly rare set of circumstances be met, Katzourakis says. âAlthough endogenous retroviruses make up a pretty large proportion of our genome, in terms of the number of times theyâve infiltrated our genome over the past sixty or so million years, it only comes down to about 30 or 40 distinct occasions,â he says.
Iâd love an explanation of how this scientists is saying infiltrations only happened 30-40 occasions if there are hundreds of ERVs in the genome. Iâm actually just curious about it. It was surprising to read that sentence.
Then what makes them PCs? Do you consider that just another name for god-guided evolution?
This is still special pleading.
Why would God choose to copy non-functional, âaccidentalâ sequences in a genome? There is no particular reason that proceeds by necessity from any model of Godâs work as revealed in Scripture.
Iâll give an example: I have occasionally copied software code from one project to another. When I have done so, I have always taken care to delete the parts of the copied code which are not relevant to the new project.
Why would God, who is infinitely wiser than I, not exercise similar care?
This is why, my friend Joshua, the OEC model you cite contains special pleading. The feature of not deleting anything (even the ugly, inessential stuff) when making a copy is a form of special pleading. Copy-without-taking-care is only in the model to align the model with the nested hierarchy that is so powerfully present in the genomic data. Thatâs what makes it a special pleading.
The GAE model also contains an instance of special pleading, but its special pleading has the theological advantage of relying on exactly one miracle, and of that miracle being explicitly mentioned (according to a certain, traditional interpretation) in the Holy Scriptures.
Copy-without-taking-care, conversely, appeals to thousands of miracles that are nowhere mentioned in the Bible. The special pleading in copy-without-taking-care has no more theological justification than YEC special pleadings such as:
- acceleration in radioactive decay rates to explain radiometric dating
- local super-inflation of space to explain why Noah, his family, and the entire planet did not instantly vaporize during that orders of magnitude acceleration in radioactive decay
- runaway subduction during a global flood
I do not have time to list all the special pleadings in YEC geology and physics, of course. I am not inclined to accept them, and I am not inclined to accept the special pleading in the OEC speciation-by-copy-with-ERVs-and-pseudogenes model that you have mentioned, Joshua.
Thanks for listening,
Chris
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No it is not. It is just a straight forward analysis of the model, an analysis you had incorrect when you claimed that it would not produce nested clades in mammals.
The model itself might be ad hoc or poorly motivated, but that isnât a special pleading. We canât know if it is ad hoc for sure without hearing from people who prefer it what precisely draws them to it.
It is notable that this particular model of creation is very close to theistic evolution in which God guides evolution at times, a model that you (@Chris_Falter ) have no problem with as I understand you. So the aversion to this PC model does not seem well motivated.
What model? âProgressive creationâ is at most a catchphrase, not a model.
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Did you even look at the video that started this thread?
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Here you go.
Yes, I watched it twice. What does that have to do with nested hierarchies?
Thank you, but it looks too technical for me. Is there something beyond primate phylogenies?
You left out one feature of the model: God places the new copies in the same places as the species they were copied from.
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Iâm still trying to figure this out: if Satan embedded billions of fossils in miles of sedimentary rocks to plant false evidence of evolution, was it Satanâs intent to make us follow evolution and weaken our YEC faith?
Or if God can plant thousands of ERVs in the genomes of thousands of species, again with every semblance of an evolutionary process, was His intent to make us accept evolution, again to undermine Genesis?
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I have a couple of questions. I had thought about starting a thread in order to ask questions like these, but they seems to fit inside of this discussion pretty well. Please feel free to break this out if it is too much off topic. Here are my questionsâŠ
If God created the heavens, land, sea and all life upon and within them, and chose to do so through the processes we observe in the natural world, why would he âneedâ to guide those processes? I understand that he might choose to guide them based on prerogative, but why does he need to guide them?
My follow up question is, why are some Christians compelled to show that God guides these processes? Is there a reason why Christians need to show that these processes are guided?
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Youâve already said that you donât 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. The last article I quoted had a reference to Mer41, but didnât 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 isnât 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 systemâand not just by giving it something to push against, but by giving it new ways of pushing.
Itâs the scope of the discovery thatâs 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. âThis really demonstrates that importance that [such sequences] have played, and probably continue to play, in the evolution of mammalian gene regulation.â
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 hostâs 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 thatâs not the irony - the irony could be the hosts already had the tricks.
But now, Iâm 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 thatâs 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 doesnât mention it, other retroviral insertions connect the human-chimp branch to gorillas, that branch to orangutans, etc. Groups within groups, thatâs what a nested hierarchy is.
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LmaoâŠ
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.
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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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