On an "Evolution" (fake) "News" article from Casey Luskin

On an "Evolution" (fake) "News" article from Casey Luskin - Junk No Longer: ERVs Are “Integral” and “Important Components” of Immune Responses

Here's Casey Luskin of the anti-science propaganda blog "EvolutionNews" (I call it "EvolutionFakeNews" exploiting the careless and thoughtless wording of a scientific article about the useful functions of some genetic components derived from endogenous retroviruses (ERVs). They should have known better than to encourage the fruitcakes. To learn more about ERVs, click on "ERV FAQ" at the top of the page.

As usual, my comments are in red. Luskin's comments are in black, and his extracts from the original article are in grey.

Casey Luskin

July 9, 2021, 6:02 AM

Image credit: lisichik, via Pixabay.

Luskin: 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,” (by Smitha Srinivasachar Badarinarayan and Daniel Sauter) 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. It’s another example of a paper that sounds like it could have been written by a proponent of intelligent design:

From Badainaarayan & Sauter: Long disregarded as junk DNA or genomic dark matter, endogenous retroviruses (ERVs) have turned out to represent important components of the antiviral immune response.

Nothing like an attention grabber to - grab attention! It has long been known that some ERV components (never an entire ERV) have useful, and even vital functions for the organisms that carry them. The authors should have known better than to encourage the cdesign proponetsists only fig-leaf defence against the slam-dunk evidence they provide for common ancestry.

So Luskin keeps repeating the same old cdesign proponentsist lie that "evolutionists" consider retroviral genetics to be "junk" and this "fact" is an important part of the "erroneous proof" of evolution from orthologous ERVs in different species. I deal with this utterly dishonest claim here. The "Not Junk" Anti-ERV Defence

Of course, as usual for cdesign proponentsist "literature", the evidence for ERVs being of retroviral origin is scrupulously ignored, because they have no answers to it.  

Luskin: 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. 

No. Sorry. The locus of a genetic complex is not critical to its function. See Aren't the same ERV genetics in the same places in different species because they have to do the same job? And they are not in "similar locations". They are in precisely corresponding locations, down to single base-pair resolution, in different species or "kinds". The only explanation for this is common inheritance. Common ancestry. 

And it has been long known by real scientists that retroviruses can confer protection from novel retroviral invasion. This is not "EvolutionFakeNews". It is real scientists, not cargo-cult fake "scientists" who have discovered this, and have published their findings in respectable scientific journals. So much for the conspiracy theory of a multi-generational multi-national "evolutionist" plot to try and fool us into accepting fake science. Luskin's piece, attempting to insinuate that this is new, and could be a "paradigm-shifter" is a lie, and he certainly knows it.

The scientific paper includes an extensive reference section of papers on this very same phenomenon, of function scavenged from ERV components, some of which go back at least a decade. True to form for bloggers for the cdesign proponentsist cult, he has probably not even read past the abstract of the paper. And why on earth does he think it is a surprise that viruses provoke an immune response? Was he a closet anti-vaxxer? Try to keep up, Casey.

Here is a summary of ERVs in relation to disease.

See also,

Human Endogenous Retroviruses Are Ancient Acquired Elements Still Shaping Innate Immune Responses

Studies of endogenous retroviruses reveal a continuing evolutionary saga

Virus hiding in our genome protects early human embryos

And so on.

Luskin: More Narrative Gloss

The irony is strong with this one.

Luskin: To be sure, the authors of the paper don’t see their results as defeating any evolutionary arguments. The subsequent sentences of the abstract immediately put a spin on ERVs — what we’ve in the past called a “narrative gloss” — to interpret them in an evolutionary context: 

Contentless gaffleblab.

From Badainaarayan & Sauter: These remnants of once-infectious retroviruses not only regulate cellular immune activation, but may even directly target invading viral pathogens. In this Gem, we summarize mechanisms by which retroviral fossils protect us from viral infections. One focus will be on recent advances in the role of ERVs as regulators of antiviral gene expression.

Luskin: The article continues with the narrative gloss, saying that 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.” So despite evidence for function of ERVs, we still see language suggesting that the only way to view them is that they were placed where they are by unguided mechanisms of viral insertion (e.g., “remnants of once-infectious retroviruses” or “retroviral fossils”). That’s one interpretation — and perhaps in some cases it is true. But the raw data — what we can directly observe and which is the focus of this paper — shows “important” immune functions for ERVs as regulators of gene expression and immune system activation. The article explains:"

The smear of "narrative gloss" is particularly ironic, in that narrative gloss is all Luskin has himself. It is is not gloss, but a solid fact, that at least 8% of the human genome is clearly of retroviral origin, for the reasons given in my link above.

Badainaarayan & Sauter: [M]any ERVs are not detrimental and have … important physiological functions in the host. Besides well-known examples, such as syncytins that regulate placental development, ERVs have become integral parts of immune defense mechanisms and help to fight off invading viral pathogens

Luskin then goes on to lifting from the paper, the details that the authors have identified. Note that none of this has been discovered by any "Discovery Institute" or any other cargo-cult outfit. Yes. We know components of some ERVs are useful. Some have even become essential. You can stop harping on about it now. It does not disprove common ancestry.

Badainaarayan & Sauter: This cooption of regulatory elements is not a rare phenomenon, and it has been estimated that about 20% of all transcription factor binding sites in humans are found in HERVs and other transposable elements. In line with this, a meta-analysis of chromatin immunoprecipitation sequencing (ChIP-Seq) data sets identified about 800,000 transcription factor binding sites within HERVs. 

Intriguingly, almost 90% of all HERVs represent so-called solo LTRs [long terminal repeats, which can serve as binding sites to regulate gene expression]. These HERVs lost the prototypical retroviral genes gag, pol, and env due to homologous recombination of their flanking LTR sequences, leaving single LTR promoters in the genome. Due to their activation upon immune stimulation, ERV LTRs have already been termed “landing strips for inflammatory transcription factors” (90), and evidence for their role in regulating cellular immune responses is growing.

Luskin: If you read that carefully, these ERV sequences don’t even resemble full “endogenous retroviruses” because they lack standard ERV genes (i.e., gag, pol, env) and simply represent long terminal repeats which can serve as binding sites for initiating or enhancing gene expression. This strongly suggests that not only can “ERVs” have function, but that some 90 percent of ERVs don’t even resemble actual “endogenous retroviruses” and may not deserve to be called “ERVs.” They are simply functional stretches of DNA in our genome used to regulate gene expression. 

Um - Casey, we know that the vast majority of ERVs are partial. Incomplete. Mutated. Epigenetically neutralised. We would be extinct if they were not. But some 200,000 ERVs and ERV fragments have been identified in your genome, and in the genome of your cousin, Charlie the chimp. 10% of ERVs are NOT solo-LTRs. That's 20,000 ERV remains! What is your explanation for them?

And BTW, LTRs only make sense in the context of the retroviral replication cycle. See "Long terminal Repeats and How They Confirm Common Ancestry".

Luskin: The article finally discusses an area for future research — ERVs may help fight cancer:

Finally, cancer research has already demonstrated that artificial induction of ERV expression can boost antitumor immune responses, and it will be important to investigate whether similar beneficial effects can be achieved for the therapy of viral diseases.

ERVs are implicated in a large range of late-onset diseases, notably cancers.

If any entity designed them, it was a malicious one. See "The Koala's Tale", and read Graeme Finlay's work, "Human Evolution: Genes, Genealogies and Phylogenies". Finlay is an expert in the role of retroviruses and ERVs in cancers, and BTW, he is a Christian, and a lay preacher to boot! 

Luskin: “ERVs” as Designed DNA Rather than Retroviral Insertions

From the evidence reviewed above, what we see is that not only are ERVs “important” and “integral” functional parts of our immune system for fighting off viral infections, but up to 90 percent of “ERVs” don’t even resemble true “endogenous retrovirus” sequences. They may show some similarities to true “endogenous retrovirus” DNA — but these similarities might be related to their function of fighting off viruses, and are not necessarily due to some ancient viral insertion. 

Here is a list of questions that the speculation that ERVs were designed raises. Nobody has ever been able to come up with coherent answers to these. 

a) What is reverse transcriptase designed to do? Why was it designed? To what purpose?
b) What is integrase designed to do? Why was it designed. To what purpose?
c) Why were ERVs designed with a viral codon bias?
d) What is the design purpose of re-transcribable promoters?
e) What were the HERVs that produced the consensus sequence that generated Phoenix designed for?
f) What is the design purpose of both exogenous and endogenous KoRV? 
g) If chimps and humans have commonly located ERVs, what is the design purpose of giving these common ERVs common disabling mutations?
h) What is the design purpose of giving some people certain HERVs and not others? 
i) What is the design purpose of creating different syncytins in different placental lineages?

See "But how can you rule out design as an explanation?"

Luskin: Perhaps some of these ERV-like sequences do reflect ancient ERV viral insertions, but it’s also possible that what evolutionary biologists call “endogenous retroviruses” frequently aren’t actually ancient viral “fossils.” Indeed, that very view of “ERVs” as ancient viral insertions may be what caused them to be “long disregarded as junk DNA,” as the paper puts it. 

Thus, perhaps DNA sequences that are often called “ERVs” often did not originate as viral insertions, but were intelligently designed as vital parts of our genome which play important immunoresponse roles to viral infections. Under this view, the reason these ERV-like sequences resemble (to one degree or another) viral DNA is because these similarities are required for their functional role to mimic or interact with real viral DNA during an immunoresponse. This is an intriguing new way to understand “ERVs” — not as viral fossils, but as vital components of our immune system.

Casey Luskin

EvolutionFakeNews:ASSOCIATE DIRECTOR, CENTER FOR SCIENCE AND CULTURE

Casey Luskin is a geologist and an attorney with graduate degrees in science and law, giving him expertise in both the scientific and legal dimensions of the debate over evolution. He earned his PhD in Geology from the University of Johannesburg, and BS and MS degrees in Earth Sciences from the University of California, San Diego, where he studied evolution extensively at both the graduate and undergraduate levels. His law degree is from the University of San Diego, where he focused his studies on First Amendment law, education law, and environmental law.

So. No virology. No genetics. Just a religiously derived presupposition that evolution is not correct, and a willingness to lie for Jesus. It shows.

And the "theological" aspects of this make no sense whatsoever. What would a disembodied unnatural intelligent designer be doing designing both viruses and defences against them? The "Fall"? What are the mechanics of such a fantasy idea? And what about the idea of intelligent design NOT being a theological concept in an attempt to circumvent the separation principle in 'murcan schools? ID is a discredited, intellectually bankrupt, meaningless, nonsense joke. 

Chris Dicus writes, 

"It’s hard to overstate just how ridiculous this article is. It’s just as bad as the YECster approach to “debunking” by citing active LTRs as evidence of genomic function. The unstated conclusion by creationists is ERVs are not the remnants of past retroviral infections, and that conclusion is absurd cannot be justified.

The evidence ERVs provide for common ancestry rests in shared distribution patterns. Creationists need to change the story to perceived function because they can’t answer the shared distribution patterns. Through the red herring of “function” creationists move through their unstated conclusion that can’t be justified and declare victory in the ultimate game of pigeon chess. And, as always, creationists confuse causal role with selected effect function, so they can’t even get that right.

In this article ERV deregulation has consequences, specifically on the interaction with the immune response and directly with viruses. So what? That’s going to happen when ERV fragments are transcribed, and it is only a tiny fraction of ERVs that do this.

Unmentioned in Luskin’s hatchet job are the large number of negative effects from ERV deregulation. Transcription of ERVs before they are epigenetically silenced during embryological development is thought to be a major driver of miscarriage. ERV deregulation is associated with MS. It is associated with psoriasis. It is associated with diabetes. ERV transcription is associated with many negative outcomes.

This article is just as bad as what I would expect from a young earth creationism propaganda mill."