Don't retroviruses target particular locations in the DNA? Doesn't this explain corresponding ERVs?

https://barryhisblog.blogspot.com/p/relationship-between-integration-sites.html

No. If that was the case, then, creationists would be shouting it from the rooftops. From the spires and the minarets and the synagogues and from all street corners.

1. It would be great if we could use retroviral-like vehicles to precisely target positions in DNA. Think of the possibilities that would open up. It would be a wonderful tool for gene therapy, including cancer treatment, treatment for genetically inherited diseases, anti-viral therapy, genetic engineering, and pure research. That is why retroviral integration has been studied so carefully. Unfortunately, integrase, the enzyme that actually does the integration of a new DNA sequence into the DNA of the host organism, does not target specific loci. Update: Since the writing of the preceding, CRISPR interference has begun to become a powerful "gene editing" tool which has enormous possibilities because it can manipulate DNA in a very precise manner. Of course, CRISPR gene editing does not use retroviral-native integrases.
2. Actual studies of integration sites include HIV integration site selection: Analysis by massively parallel pyrosequencing reveals association with epigenetic modifications and Retroviral DNA Integration: ASLV, HIV, and MLV Show Distinct Target Site Preferences and many others. While the title of the second paper sounds interesting from the creationist point of view, it doesn't help. What these sorts of studies do is to survey real retroviral integration sites, using the same types of cell from the same individuals (identical DNA) in order to find any statistical 'preference' for certain types of area (in an existing gene, not in a gene, near a promoter etc.) Typically, they find some overall patterns, but no repetition of integration sites within 500 samples of the same cell type with the same retrovirus. This is not the locus specificity required to account for 200,000 integrations in precisely corresponding loci. Only common inheritance can account for them.

Yes, we know that ERVs can integrate in certain areas with a statistical preference. But this is not the base-level resolution targeting which would be required to question the endogenization hypothesis. I liken the issue to road traffic accident reports. Yes, certain stretches are road are more prone to accident to others, but it is extremely rare for a road traffic accident to involve a collision in exactly the same spot, and even more rare for them to involve exactly the same vehicles and the same occupants. It's far more likely that you are looking at duplicates of reports of the same accident.You could decide that these accidents were intelligently designed by some malicious supernatural force, or you could decide that the accident statistics are due to the particular road layouts, traffic patterns etc.

Update. Some creationists are putting the crotch area of their trousers under significant strain over their discovery of the discovery (by "evolutionist" scientists, note), of the highly site-specific integration of ZAM, a retroelement found integrated with the genome of Drosophila melanogaster (fruit flies), which is very similar in structure and replication cycle to mammalian retroviruses and is highly site-specific. However, as this paper, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2527525/ says, "Although different retroviruses have been shown to target distinctive chromosomal regions, few of them display a site-specific integration." The integrase involved is different than that found in retroviruses that have invaded mammalian genomes. Yes, It' is quite an exciting discovery for its potential for genetic research, gene therapy and genetic engineering, but sorry creationist guys, still your throbbing bits. It cannot account for site specificity in us mammals. Only common ancestry can do that.

How many ERVs are shared, in common locations, in the genomes of humans and chimps?

(Return to the ERV FAQ)

From table 11 of Initial sequencing and analysis of the human genome, ERVs found in humans (HERVs) include
112,000 ERV-class Is + 8,000 ERV(K)-class IIs + 83,000 ERV(L)-class IIIs = 203,000 ERVs.

From table 2 of Initial sequence of the chimpanzee genome and comparison with the human genome,
279 of the 203,000 ERVs are specific to chimps, and 82 are specific to humans.

The vast majority of the 203,000 ERVs are common to chimps and humans, and appear in corresponding locations in our genomes. See https://web.archive.org/web/20230531193743/http://www.evolutionarymodel.com/ervs.htm#Amount_of_Shared_ERVs






(Return to the ERV FAQ)

Isn't this just circular reasoning, assuming evolution to 'prove' evolution?

No. No assumption of evolution is made when concluding that commonly located ERVs are due to common ancestry.

A conclusion drawn from evidence and reasoning is not an assumption or a presupposition.

The conclusion is drawn from the following items of evidence -

1. ERVs have the same detailed structure as retroviral proviruses. This fact does not require us to assume evolution.
2. Retroviral integration does not target specific loci in DNA. This fact does not require us to assume evolution.
3. Inheritance places the same genetic material in the same locations in DNA. This fact does not require us to assume evolution.

But it does seem to me that evolution-deniers assume evolution is false when trying to prove it is false...

The accusation of "assumption" is especially risible coming from fundamentalists who adopt "presuppositions" based on thin air - nothing but the desire for something to be true. This is manifest in the "statements of faith" that are required by contributors to professional for-profit creationist blogs. 

What are Long Terminal Repeats (LTRs)?

Constructing primate phylogenies from ancient retrovirus sequences
https://www.pnas.org/content/96/18/10254.full


https://barryhisblog.blogspot.com/p/long-terminal-repeats-ltrs.html

A quick overview follows in the next paragraph. More can be found out if you click on 'ERV FAQ' at the top of this page. 

Retroviruses replicate by converting their RNA genomes into DNA by reverse transcription and by inserting or 'integrating' the DNA version (the provirus) with the nuclear DNA of host cells. The host cells then dutifully produce more copies of the retrovirus by transcribing the proviral DNA back into RNA using RNA polymerase II under the influence of proviral promoter sequences. The promoters are necessary to promote transcription.

But RNA polymerase II does not normally transcribe promoters. Retroviruses have to make it do so, otherwise the newly replicated viruses would not be able to continue the replication cycle.

Retroviruses overcome this problem by polymerising copies of their promoters during reverse transcription, forming what are called long terminal repeats (LTRs) which can be transcribed back into RNA. LTRs appear at either end of the provirus and are always identical to one another when they are formed.

Upon examining LTRs from endogenous retroviruses, however, we find that many pairs of LTRs from ERVs have diverged. We call these divergences discontinuities. Discontinuities can be explained by mutation. The longer an ERV has been part of the species' genomes, the larger the discontinuity is likely to be. 

When discontinuities are inherited by cousin species from common ancestors, this data, together with the degree of discontinuity should reflect already established taxonomy and phylogeny. 

It does. 

This is a prediction from evolutionary science, borne out by direct observation, that neither "intelligent design" spotters nor creation "scienticians" can account for.

A2AIG

 

The Facebook group, "Answers to Answers in Genesis" https://www.facebook.com/groups/answers2aig+ has an admin who kept whining that I was "name calling", but repeatedly failed to say what the offending remarks were supposed to have been. I find it deeply infuriating, saddening and disappointing that I have been ejected from the group, without any adequate attempts at an explanation, especially in view of the fact that I am on a ban list from every single lying, conning, for-profit fanatical anti-science creationist group, not for bring aggressive or offensive, but merely because I know my stuff. I expect it from them, but not from those who are supposedly trying to defend knowledge and reason.

Disgusted is hardly adequate to express how I feel. /rant

Why do virologists and geneticists conclude that ERVs come from retroviruses? Isn't that just supposition on their part?

https://barryhisblog.blogspot.com/p/why-do-virologists-and-geneticists.html

Update: Here is Jon Perry of "Stated Clearly" and "Stated Casually" of YouTube renown explaining what all creationists avoid like the plague, evidence that ERVs are of retroviral origin. 

Much material in this page has been lifted from Stacey Smith.Hope you don't mind, Stacey, :D

Every detail of every full ERV is replete with complex and subtle details attesting to its origin in retroviruses. ERVs have the same structure as retroviral integrations. This is some -10 kilobases of genes specific to the retroviral replication cycle. All retroviruses and complete ERVs include genes we call gag, pol and env. The function of these genes will be gone into in detail in the following notes. In addition, several other features common to retroviral integrations and ERVs only make sense in terms of the requirements of the retroviral replication cycle.

"The gag gene encodes for ‘Gag’ the giant protein, which gets chopped into several smaller proteins, Matrix, Capsid, and Nucleocapsid (and sometimes a few more tiny ones, depending on the retrovirus)."

"Matrix is the structural protein just inside the envelope (the membrane the virus stole from its host cell). It has ‘outside’ functions (targeting the virus assembly to the right kind of cell membrane, keeping the outside protein env, in order) and ‘inside’ functions (targeting the reverse transcribed DNA to the new host cell nucleus). Jack of all trades protein, like lots of retroviral proteins. They run a tight ship."

"Capsid forms the viral ‘core’. Normally when you think of a ‘virus’, you think of this shape, an icosahedron. Retroviral ‘cores’ really look more like a cylinder-cone-thingie, like the bottom pic here. That particular pic is also worth a second look– More protein cuts to Capsid need to take place after a baby virus buds off from its host cell to make an immature virus mature. Blocking this maturation step is what the next family of anti-HIV-1 retrovirals do. *thumbs up*"

"Nucleocapsid is a structural protein that wraps up the retroviral genome to make sure its packaged properly into the Capsid."

Pol codes for all the enzymes a retrovirus needs:"

"Protease– Chomps big proteins into all the little functional proteins, like we saw with Gag getting chomped into Matrix/Capsid/Nucleocapsid. The name ‘protease’ can be a little confusing because all organisms have ‘proteases‘, but only the protease that the retrovirus carries with it is the ‘right‘ protease to cleave in all the ‘right’ spots to get all the ‘right’ proteins in the end. Instead of giving retroviral proteases a special name, they just named it ‘Protease’. heh. Protease inhibitors are a great target for anti-retrovirals."

"Reverse Transcriptase– Another target for anti-retrovirals. Though the process of reverse transcription can be found in you and I (coooool), retroviruses need to carry an enzyme with them to convert viral RNA into DNA on demand. This process not only requires converting an RNA genome into a DNA genome, but also:"

"RNase H– The RT enzyme has (at least) two active sites. One performs the process of reverse transcription. Another active site has RNase activity (chops up RNA, specifically, RNA Hybridized with DNA haha!). RNase H chews up the old RNA template after a single strand of DNA has been made, so the single strand of DNA can be made into double stranded DNA, and subsequently inserted into the host cells genome. This might make more sense if you see this animation. *might* The process of reverse transcription is rather absurd."

"Integrase– Host cells don't come packed with the necessary biochemical machinery to move DNA out of the cytoplasm into the nucleus, to be inserted into the host DNA. So once again, retroviruses need to bring an enzyme capable of performing those activities. Integrase should be a perfect target for antiretrovirals… But we havent figured any out yet…"

Env. See http://scienceblogs.com/erv/2008/07/17/intro-to-ervs-envy-my-env/

LTRs. See this page. RNA polymerase's normal function is to convert nuclear DNA into messenger RNA that makes for proteins. It does not normally make RNA that 'codes" for promoters. Our bodies have no need for them. But retroviruses need their promoters to be converted back to RNA for when the replication cycle begins again. Long terminal repeats (LTRs) cause the RNA polymerase to produce them by a complicated "hack". The point is, that LTRs basic and original function is a part of the replication process of retroviruses. They cannot be part of any supposed original "design" of our genomes. That would not make any sense.

See http://barryhisblog.blogspot.fr/p/ervs-promote-transcription-of-host-dna.html and http://scienceblogs.com/erv/2009/07/16/intro-to-ervs-ltr-gator

Retroviruses exhibit the distinctive viral codon bias.

The Phoenix virus was resurrected from the multiple instances of an ERV which is to be found in each human cell. Each instance is a 'failed' retrovirus, but when a 'majority vote' for each base was taken, the resulting DNA produced, "viral particles that disclose all of the structural and functional properties of a bona-fide retrovirus, can infect mammalian, including human, cells, and integrate with the exact signature of the presently found endogenous HERV-K progeny." See also The "Phoenix Virus": an explanation of an experiment.

A retrovirus has been caught in the act of becoming endogenized: See The koala retrovirus KoRV and The Koala's Tale.

Retroviruses leave a telltale trace of integration in the form of a repeated host sequence either side of the integrated provirus. This is also evident in ERVs. From Virology Blog: Retroviral Integration and the XMRV Provirus, "The image below shows some of the characteristic features of retroviral integration. A the top is the unintegrated linear DNA of avian sarcoma/leukosis virus produced by reverse transcription. Upon completion of integration, two base pairs (AA•TT) are lost from both termini, and a 6-bp target site in host DNA (pink) is duplicated on either side of the proviral DNA. This target site varies in length from 4 to 6 bp among different retroviruses. The proviral DNA (middle) ends with the conserved 5′-T G…C A-3′ sequence. The provirus serves as a template for the production of the viral RNA genome (bottom)."

Answers in Science

https://barryhisblog.blogspot.com/p/answers-in-science.html

Emailed to science-editor@answersinscience.org @ https://answersinscience.org/index.html

Hello,

I'm a long-time campaigner for science and reason on the internet, particularly in my blog  @ https://barryhisblog.blogspot.com/2025/01/barryhisblog.html, which I am currently getting reorganised, and on multiple Facebook groups that discuss evolution and creationism. I have made a special study of endogenous retroviruses. See https://barryhisblog.blogspot.com/2025/01/the-erv-faq-endogenous-retroviruses.html

It occurred to me that there should be an internet site called "Answers in Science" which would counter Ken Ham's creationist site, Answers in Genesis (AiG) and other creationist and intelligent design sites. Lo and behold, Google came up with your site.

Your site is comprehensive, and looks to be a valuable resource for all of us who undertake to counter the anti-science sites like AiG, and I am recommending it to all like-minded people.

I have a number of suggestions and ideas for you, and I hope that you will consider them.

1) Sites like AiG have a very slick presentation, produced, by the looks of it, by professional-level web designers, be they volunteers or paid workers. I would like to see a site of that quality of presentation and 'feel', on the side of science and on the side of counter-creationism.

2) I would like to see the site open to ideas and contributions for content from people outside of the Tufts science departments, their contributions being subject to review and and necessary correction by an editorial body.

3) I would like to see appeals for donations from the public, to cover the cost of web site maintenance, design and promotion.

4) I would like to see a section designed for children like AiG's, to appeal to young people. Creating engaging content for young people is a specialist skill.

In order to 'nab' the name, I have created a Facebook page, "Answers in Science" @ https://www.facebook.com/groups/985398433559591 through which I intend to publicise your site and on which, people can comment and proffer material for inclusion in the site, be it original content or links to existing useful material.

I shall not be accepting requests to join, nor will I be inviting people, until I hear back from your good selves on my suggestions.

Yours faithfully,

Barry Desborough 15th Jan 2025