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Junk DNA: Less junk than ever, it seems

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According to a recent paper:

Viruses and immunity are hot topics these days, and a new article in the Journal of Virology, “Switching Sides: How Endogenous Retroviruses Protect Us from Viral Infections,” has the potential to be a paradigm-shifter on the standard view that endogenous retroviruses (ERVs) are junk DNA. Consider this first line from the abstract. Though the authors are certainly not supportive of intelligent design, (ID), it’s another example of a line from a paper that sounds like it could have been written by a proponent of ID:

“Long disregarded as junk DNA or genomic dark matter, endogenous retroviruses (ERVs) have turned out to represent important components of the antiviral immune response. – Smitha Srinivasachar Badarinarayan and Daniel Sauter, “Switching Sides: How Endogenous Retroviruses Protect Us from Viral Infections,” Journal of Virology, 95(12): E02299-20 (June, 2021)

ERVs have long been a go-to argument against ID from those who believe that our genomes are full of undesigned junk. An outgrowth of this view is that ERVs have no functional importance, and that shared similar ERV sequences in similar genomic locations across different species (e.g., humans and apes) indicate their common ancestry. After, goes this way of thinking, ERVs were clearly not put there for any purpose.

If this paper is correct, however, then ERVs frequently have important immune functions and they should not be presumed to be “junk DNA.” This defeats both the “junk ERV” argument against the design of the genome (human and otherwise). It also challenges those who want to use the supposed junk-status of ERVs as an argument for common ancestry. After all, if ERVs have functions, then shared ERV sequences in similar locations across genomes of different species may reflect functional requirements rather than mere common ancestry.

Casey Luskin, “ Junk No Longer: ERVs Are “Integral” and “Important Components” of Immune Responses” at Evolution News and Science Today

The paper is open access.

Memories, memories: Wasn’t there a Darwinian blogger whose handle, sort of, was ERV? Wonder where she is now …

Marfin @21 - Yes, exactly. And this sort of thing happens over and over. PaV @22, - Very nicely articulated in your previous post. Dead ends are necessary and helpful, but only if one is willing to acknowledge them as dead ends and then move on. Darwinism has been stuck in the 19th century and, unlike the other sciences, hasn't moved beyond or only reluctantly in a few cases. This, I believe the sad state of this area of science is due to a combination of ideological poisoning and social/peer pressure. But there's also a third factor. Academic pedantry/dogmatism. The way science is usually taught is that of a collection of immutable "facts," terminology, names, and dates. Works out nicely with multiple choice tests, but does nothing to promote inquisitiveness and understanding the scientific method. The well-researched, but tentative conclusions of scientific papers are routinely promoted as TRUTH in the classroom. Students are discouraged from scientific inquiry when they led to believe that everything has already been discovered by science and nothing can be challenged. This is nowhere near the truth. Sadly, I think Bob O'H has fled the thread. -Q Querius
Here's what I wrote about ERVs five years ago: PaV June 6, 2016 at 11:41 am I’ve read about half of Barbara McClintock’s seminal paper on transposons. And she makes clear that the occurence of the movement and placement of transposons is non-random. I personally believe that the organism/cell uses transposons to turn on, and to turn off, certain coding regions of the genome, and that it does so in accordance with its needs. How this happens, exactly, I don’t suppose to know; but, of course, this is worthy of examination, and, I suppose, is happening as we speak. My view is, naturally, in accordance with a theory of intelligent design. I say “theory” here because should enough information about transposons be obtained that indicates intelligent action on the part of organisms, then ID would be more than a hypothesis. Unless there is a reason for me to change my thinking about transposons, and their presumed mode of action, this, IMO, severely undermines the entire neo-Darwinian structure. Your thoughts. Isn't it interesting that the ID perspective leads you right where you need to go? And Darwinism? Where does it lead you? Isn't it to 'dead ends'? PaV
Bob o H - Bob simple question which side in the debate did the term "Junk DNA" come from in the first place hmm let me think. Marfin
Zweston, Yes, exactly. Before something became scientific dogma, it first survived being ignored, then ridiculed, then persecuted, and finally then being accepted as obvious. -Q Querius
Q @ 18... This is the way of the skeptic....keep really quiet about the problems until you can come up with some sort of solution, no matter how unscientific and ad hoc..... don't let the faithful know the boat is sinking! zweston
Martin_r @ 9, Yes, as Zweston said, great clip! It makes it obvious that Dawkins simply "evolves" his stories about how wonderful Darwinism is and how it predicted the new discovery all along. Completely bogus! I'm sorry that Bob O'H seems to do the same "we've known this for decades" BS. The same thing happened with 100+ "vestigial" organs that were used in the Scopes trial to "prove" evolution. How many "vestigial" organs are left from that list? Once again, the presumption of evolutionary junk rather than Intelligent Design is shown with boring regularity to be false. I predict that some time in the future when a new hypothesis for materialist change emerges, Darwin's racist theory will immediately be thrown under the bus and people like Dawkins and his dupes will boldly say something like,
"Oh, we knew ALL ALONG that Darwin's theory was a load of BS, but NOW . . . Now, we (meaning the person and their tapeworm) KNOW how everything emerged from molecules/quantum effects/a parallel universe/space aliens."
Sigh. -Q Querius
No no Sandy they lie it developed over millions of and gave them a survival advantage It’s humanists aka I’m moral without god that claim that They are a slightly different atheists that’s more intelligent then us roobs They read scripture according to Q And play call of Cthulhu They do so to protect themselves from the coming religious apocalypse that will befall them or that’s what they say on their website It’s really a group of Atheists nerds That play call of Cthulhu and sit around trying to find reasons to hate religion AaronS1978
Bob O'H Now? We’ve been saying this for decades.
Oh no, I thought that atheists never lie because they know will be held accountable by...The Son of king Clown from Mars middle Moon. We shouldn't believe the atheists even when they tell the truth. :))) Sandy
@14 Correct point in case they posted on papineau vs Egnor round 1 and NEVER again when papineau started to sound like joe biden in a debate Papineau “Hey man I don’t believe in the mind stuff because huh you know, I mean, you know the thing about stuff, I wrote a book man” AaronS1978
I notice Seversky and the like are very specific on which titles they respond to. And they are oft silent on posts with implications of disaster for their theory. Martin @ 9....really enjoyed that video clip... Just so and the "stuff happens theory" strikes again! Great stuff zweston
Darwinism is literally the god of gaps for this era There’s nothing it can’t explain which makes it every bit as guilty Of the same fallacy the original god of gaps was guilty of The only difference is that science is ever-changing and ever fluid so if it makes a mistake and was wrong about something it can’t be held guilty AaronS1978
BOB OH really man!? https://en.m.wikipedia.org/wiki/Non-coding_DNA They have not been saying this for years and saying don’t let reality get in the way of a good story is bull crap that’s the problem Darwinian theory is as soon as something comes up that doesn’t jive with the current thought you immediately retract and say oh we’ve been saying this sort of thing for years or this is what you would expect And what’s your definition of years four years two years or 30 years Again the appendix is a wonderful example of Darwinian evolution being bull crap The appendix has no function it’s just evolutionarily Sprandel 2007 rolls around I will look it looks like the appendix might have a function why would evolution Evo God extreme evolve it so many times 2014 rolls around oops looks like it has functionality and an important one don’t remove it unless you have too But for years it was just evolutionarily sprandle And I’m pretty sure Jerry Coyne one of your high priest still believes in junk DNA https://evolutionnews.org/2021/07/darwins-genie-misapplied-natural-selection-continues/ I hate quoting evolution news here because they are pretty much one and the same But this little article breaks down my issues pretty well which directly pertains to the ability for Darwinian evolution to be right even when it’s wrong There’s nothing that can disapprove Darwinian evolution, let me correct myself Darwinian philosophy There’s literally nothing that can, because everything is what you would expect and we’ve been saying that for years, which you have it And here’s the Darwinian algorithm Everything evolves to survive It’s survived therefore evolved Whatever treats it has gave it a survival advantage because it survived AaronS1978
when you look at the original article, Darwinists will tell you the following story:
"... some 8 percent of the human genome “represent[s] remnants of once infectious exogenous retroviruses that became fixed in our DNA” and that “the host cell has coopted fossils of possibly once harmful retroviruses to limit the spread of current viral pathogens."
i like the word "coopted" ... "the host cell has coopted ...." I would like to add another example where ERVs were "coopted" for some function, and in this case, very very important KEY function, a function, that has to work at the first attempt, otherwise no evolution, because no reproduction .... look at this miracle (from a mainstream Darwinian paper):
Domestication of the syncytin genes represents a dramatic example of convergent (repeated) evolution via the cooption of a retroviral gene for a key biological function in reproductive biology. In fact, syncytin domestication from a retroviral envelope gene has been previously shown to have independently occurred at least seven times during mammalian evolution https://www.pnas.org/content/109/7/2184
A cooptionn then another cooption and then, somewhere else, another cooption, and elsewhere another cooption and another cooption and so on ... Seriously... who buys this stuff ? martin_r
Dawkins wrote in his fantasy books about junk DNA. Clueless people like Dawkins done a lot of harm to science and even worse to all humans that believed him . Many thought that his books is science when in fact were about made-up fairytales post hoc explanations :) Sandy
BobOH @5
"We’ve been saying this for decades.".
yeah, yeah... in this case, look at this... see/hear it on your own ... here is a very funny Dawkins video on this subject, it is only 2 minutes long (someone took the time to cut various Dawkins interviews .... very funny, you Darwinists are funny clowns...) "Dawkins contradictions on Junk DNA" https://www.youtube.com/watch?v=IH6CVwTHkXc martin_r
BobOH @5 reminds me on Richard Dawkins. Here is a 2012 interview with Dawkins (see on your own https://youtu.be/roFdPHdhgKQ)
Dawkins: "I have noticed that there are some creationists who are jumping on [the ENCODE results] because they think that’s awkward for Darwinism. Quite the contrary it’s exactly what a Darwinist would hope for, to find usefulness in the living world…." Whereas we thought that only a minority of the genome was doing something, namely that minority which actually codes for protein, and now we find that actually the majority of it is doing something. What it’s doing is calling into action the protein-coding genes. So you can think of the protein-coding genes as being sort of the toolbox of subroutines which is pretty much common to all mammals — mice and men have the same number, roughly speaking, of protein-coding genes and that’s always been a bit of a blow to self-esteem of humanity. But the point is that that was just the subroutines that are called into being; the program that’s calling them into action is the rest [of the genome] which had previously been written off as junk.
We can see another textbook example of Darwinian insanity... as we can see, both theories are OK. If the 'junk" DNA has no function, it is an evidence for evolution. If the 'junk' DNA has a function, it is also an evidence for evolution - like Dawkins said - "it’s exactly what a Darwinist would hope for, to find usefulness in the living world" it is like in some mental hospital.... martin_r
ID does not officially say anything about so called junk DNA. If it does, who determines what is official? Science has determined that some of what is/was called junk DNA has positive function. Not all. I doubt any ID proponent claims all will be shown to have function. That would actually be a big plus for Darwinism, which is just modern day genetics. jerry
Bob O'H:
We’ve been saying this for decades.
And yet Moran and Graur say the opposite. Many biologists and biochemists say the human genome is 90% junk. ET
And now “maintream” science finally acknowledges that the assumption of “junk” might have been a tad problematic.
Now? We've been saying this for decades. But don't let reality get in the way of a good story. Bob O'H
So at some point in the future, the biologists are going to "discover" that the DNA system processes information. Rational input, as well as rational output. They will discover that the DNA bases, which everyone already considers as being chosen from 4 possible bases, is chosen, in a reasoned and informed way. Then they will discover, that the brain also processes information, and is much of an extension of the DNA system as being an information processor. It seems all so totally obvious. mohammadnursyamsu
Even Darwinists should never have assumed that part of an organism is junk. The constant and speedy action of "smart mutations" automatically removes all ENERGY-WASTING portions of the organism, leaving only the efficient Green parts. Gaia must be satisfied at all times by evolution. polistra
and that shared similar ERV sequences in similar genomic locations across different species (e.g., humans and apes) indicate their common ancestry.
ID confirmed, common ancestry claim questionable ... PS: with every new discovery, Darwinian just-so-stories proven wrong over and over again ... martin_r
“Long disregarded as junk DNA or genomic dark matter, endogenous retroviruses (ERVs) have turned out to represent important components of the antiviral immune response. – Smitha Srinivasachar Badarinarayan and Daniel Sauter, “Switching Sides: How Endogenous Retroviruses Protect Us from Viral Infections,” Journal of Virology, 95(12): E02299-20 (June, 2021)
And now "maintream" science finally acknowledges that the assumption of "junk" might have been a tad problematic. Had scientists used the Intelligent Design paradigm--the assumption of designed purpose--then, scientific progress on non-coding DNA and endogenous retroviruses wouldn't have been unnecessarily delayed for decades by the now obsolete, racist, 19th century Darwinism. And yes, Susumu Ohno did suggest an evolutionary purpose for "junk" DNA in his 1972 paper. -Q Querius

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