Episomal latency.
I’ve asked you at least three times (now four) why hasn’t life on the planet died out from GE after 3.5 billion years?
The more you avoid the problem for GE the sillier you look defending it. 
Because he sincerely believes he is right.
Do you understand that in science the empirical evidence always tops sincere beliefs? The empirical evidence shows the GE idea is dead wrong, full stop. What Sanford sincerely believes matters not one iota.
Here is Sanford’s response to your objection , which I share for the most part:
My primary thesis is not that everything is going extinct (although I do hold that view), but is that many levels of evidence show that the neo-Darwinian theory is false. The mutation/selection process cannot create the genome, it cannot even stop the genome continuous degeneration. Given only mutation / selection (given only neo-Darwinian theory) - all species must go extinct. I realize that conceivably there may be a counter-force to Genetic Entropy other that natural selection. That counterforce might be God, or aliens, or some unknown natural force. But if we are given only strict neo-Darwinian theory - yes, all life forms are doomed to extinction. ( Genetic Entropy, p 229)
LOL! So your and Sanford’s answer is “I can’t explain the 3.5 BY fossil record so maybe God or Space Aliens are magically counteracting genetic entropy”.
Does that sound like a valid scientific explanation to you? 
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Recombination is random, right? If the insertion is flawed the virus does not activate. And if the insertion is in a “seed” tissue (ovaries or testies), the inactive genome is passed to the next generation.
If a deleterious mutation happens in one viral genome, how are the descendants of that virus able to outcompete the viruses without that mutation?
As far as I am aware, only DNA viruses are able to persist through this type of latency. Influenza A is an RNA virus.
Sanford hasn’t shown that there is continuous degeneration. That is the first problem. For all we know, slightly beneficial mutations are just as numerous as slightly deleterious mutations, not to mention the reversion of slightly deleterious mutations as they begin to saturate the genome. Sanford just assumes that most selectively neutral mutations are deleterious by some measure, but he never supports this assumption.
It was common knowledge among the working geneticists that I know.
Sure, it’s relevant, since you keep making claims like this (in the very next sentence):
I told you how I was defining ‘functional DNA’: sequence-specific DNA that affects the organism’s health or ability to reproduce or even just its phenotype. Under that definition, which is not peculiar at all among biologists, there’s no conflict at all where you think there is. The fact that you are making statement after statement about biology that are just plain wrong is what I’m discussing.
No, I think we can mutate 90% of the genome without changing anything else about our bodies. The bulk presence of DNA is a different question.
And there are multiple reasons that Graur’s number is an overestimate of the number of offspring actually needed. The biggest one is soft selection.
You’re off by about a factor of two, since the functional fraction of the genome is more like 10%. Beyond that, what’s your point? That people who don’t understand biology don’t understand biology?
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As others have pointed out, there’s a big difference between saying “this sequence has no sequence-specific function” and “this sequence can be deleted without any ill effects”. Even if we were to assume that the entire length of a TAD is essential for function (which is objectively not true, as lengths vary quite considerably in different species), the majority of sequence would only “function” as a spacer, meaning the sequence itself is unimportant, only that it approximately Xbp long. If the sequence itself can mutate freely without any ill effects on fitness, then it’s not relevant to any genetic entropy scenario.
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All reasonable discussion ended with the claim God or Space Aliens are supplying an undetectable counteracting force to make it look like GE isn’t happening.
Creation “science” never ceases to amuse.
What do you mean “essential for function” spare tires aren’t essential for most functioning of a car but they have function.
The sequences of DNA affect its structural properties! It can be compromised with slight changes.
Robust systems have DEEP redundancy. Are robustness and redundancy “essential function”? Even if they weren’t that doesn’t make them non functioning.
Do you mean one nucleotide in isolation or 90% simultaneously? There is a difference since aggregate changes do make a difference that can’t be detected individually.
Then how do you explain much higher sequence conservation in exons as compared to introns within the same genes?
The physical characteristics of polymers like DNA are affected by sequence. The characteristics affect folding, bending, and other conformations. It’s naive to think we can just freely mutate 90% of the DNA and in aggregate expect there is no compromise in the 4D nucleome.
But here is another perspective:
According to Phys.org, “Rattling DNA hustles transcribers to targets” –
New simulations of DNA as a transport conduit could shatter the way scientists have thought about how large molecules called transcription factors diffuse on their way to carry out genetic missions, according to a study by researchers at the Georgia Institute of Technology. The simulations add important brush strokes to our picture of elusive inner mechanics of cells.
The simulations strongly support the hypothesis that, in a live cell, DNA is in constant motion, making it the dominant mover of transcription factors, to their target sites on DNA. There, the factors regulate the transcription of genetic code into life-sustaining action.
How do you think such supposedly deeply redundant systems have persisted given that they’re evidently not conserved in terms of their sequence? I’ll repeat myself yet again, this type of “function” even granting that it exists, isn’t relevant to genetic entropy.
Over long distances? Not really. Once you get beyond a few thousand base pairs the bendiness of the polymer is no longer driven by sequence.
How so? Do you have any references whatsoever that backs up your claims? How is the bladderwort able to get away with a genome size of just 0.083 billion bases while the onion genome has a genome size of 16 billion bases, and humans with 3 billion bases.
But independent of the supposed number of kids, Dr. Felsenstein also believes there must be a limit to how many mutations can be tolerated in functional regions:
he mutational load calculation continues to be relevant to understanding whether
most eukaryotic DNA has any function that is visible to natural selection. Recent announcements (Encode Project Consortium, 2012) that 80% of human DNA is “functional”, based on finding some transcription or binding of transcription factors in it
are very misleading. Junk DNA is still junk DNA, however often its demise has been
announced. – page 121 Theoretical Evolutionary Genetics
So, if the genome is mostly functional, then evolution is wrong. Whether Graur says it or Dr. Felsenstein.