Endogenous Retroviruses - Frequently Asked Questions

[Barry Desborough]

This thread lists and answers frequently asked questions (FAQs) from creationists about the case for common descent from endogenous retroviruses (ERVs).

retrovirus.jpg

Each question will be answered in a subsequent comment.

0. This looks hard. Do you have a simple introduction to the subject?


1. What is the "case for common descent" from ERVs?


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


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


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


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


6. ERVs do stuff. Doesn't that prove that they didn't originate from retroviruses, but were designed?


7. ERVs promote the transcription of host DNA. Doesn't this prove they are designed?


8. ERVs are essential in reproduction (syncytin and the formation of the placenta). How can this be?


9. Aren't the same ERV genetics in the same places in different species because they have to do the same job?


10. But how can you rule out design as an explanation?


11. How could a species survive a massive invasion of retroviruses into it's genome?


12. How could ERVs survive programmed cell death (apoptosis)?


13. The same retrovirus or ERV has been found in two species that evolutionists say are very distantly related. How is this possible?


14. What if we find an ERV in a common location in chimpanzees and gorillas, but not in humans?


15. David DeWitt at AiG says ERVs do not line up with the expected evolutionary progression. What gives?


16. What's all this about the Phoenix Virus? Sounds like a Michael Crichton science fiction story!


17. Hasn't the evolutionist's story about ERVs been debunked by scientists such as Dr. Yingguang Liu and Dr. Georgia Purdom?


18. Aren't you just a plagiarist? Why don't you attribute your sources? And who are you anyway?


19. Other articles on ERVs.

[shunyadragon]

Interesting!!!

Looking forward to more!

Unfortunately it will above the bar for most here on tweb, but interesting nonetheless.

[Barry Desborough]

0. This looks hard. Do you have a simple introduction to the subject?

Of Eloi and Morlocks

Time Machine.jpg

From The Time Machine 1960, directed by George Pal, based on the 1895 novel by H.G. Wells.

Adapted from Wikipedia: "By the year AD 802,701, humanity has evolved into two separate species: the Eloi and the Morlocks. The Eloi live a life of ease on the surface, while the Morlocks live underground, tending machinery and providing for the Eloi. Having nothing they need to do, the Eloi have slowly become like cattle, smaller than modern humans with sub-human intelligence. All they do is feed, play, and mate. When one of them, Weena, falls into a river, none of the other Eloi help her. She is rescued instead by the Time Traveler. Every so often the Morlocks capture individual Eloi for food, and because this typically happens on moonless nights, the Eloi are terrified of darkness."

How would we prove that the Eloi and the Morlocks had indeed both descended from modern humans? Well, we have signatures in our DNA that were written by retroviruses.

viruses-02-01110-ag (3).jpg

They put their DNA into the DNA of our cells to "fool" them into making new retroviruses.


Sometimes, a retrovirus puts its DNA into the DNA of an egg or sperm cell. When this happens, it becomes heritable - you can inherit it from your parents and pass it down to your offspring. These heritable bits of viral DNA are called ERVs - Endogenous RetroViruses. Fortunately, they no longer fully perform their original functions, otherwise humans would be extinct.


The signature of any endogenous retrovirus is that it can be found in exactly the same place in the DNA of every single one of your nuclear cells (every cell with a nucleus - which is most of them). The viral DNA ends up in the same place because it, along with all the rest of your DNA, is copied from the DNA of the original single cell you started out as. In contrast, the viral DNA that you have acquired from viruses in the environment is not present in all of your nuclear cells, and in those where it is present, the viral DNA ends up in different points in your DNA, comparing one infected cell with another.


To recap:


Viral DNA in the same place in the DNA of every cell means that it is inherited.
Viral DNA in different places in only some of your cells means that you have caught a virus from the environment.


Now if we find that all the Eloi have the same viral DNA as us, in every cell, in exactly the same places as us, we know that they must have inherited it from us, and therefore we are their ancestors.


The same goes for the Morlocks. The same viral DNA in the same places in every cell means that the Morlocks also descend from us.


Note that we do not even need to look at our own DNA! If we find the same viral DNA in the same places in every cell of every Eloi and Morlock, they have to have had common ancestors from which they inherited it.


Bear this in mind when the ERV FAQ mentions, not Eloi and Morlocks, but humans and chimpanzees!

[Barry Desborough]

1. ERV FAQ: What is the "case for common descent" from ERVs?

Here is a brief overview. Much more detail can be found by googling, "Three Layers of Endogenous Retroviral Evidence for the Evolutionary Model".
Further posts will go into the following points in more depth.

viruses-02-01110-ag (3).jpg

1. Retroviruses replicate by invading the cells of host organisms, converting their RNA genomes into DNA, and inserting (integrating, in the jargon) the DNA into the DNA of the host cell. The integrated DNA is called a "provirus". The host cell then "reads" the provirus, converting it back into RNA, resulting in the production of more viruses.


2. Retroviruses tend to target certain types of cells. Their "environment" proteins tend to be specialized to attach to the surfaces of these cells.


3. The insertion is made by a retroviral enzyme called integrase. While certain retroviruses can show a general tendency to insert their DNA in certain types of regions in a host cell's DNA, they do not target specific points (loci). This means that in an infected individual, not all cells will be infected, and in those that are, the retroviral integration will be in a different place or places in the DNA of each cell.


4. We find, in the genomes of creatures such as ourselves and chimpanzees, inherited structures that appear to be broken retroviral insertions. Some are more complete than others, but many have the full set of genes that would be necessary for a complete retrovirus, were they not faulty. We call these structures endogenous retroviruses (ERVs). Unlike the case where each cell is individually infected, they appear in the exact same spots in the DNA of every single nuclear cell (cells with nuclei containing DNA).


5. Although certain components of some ERVs perform functions in the host, some even being essential in some species, no complete ERVs are functional. Design, as an explanation for ERVs, does not make any sense. A designer would have no need to include specifically retroviral genes in its designs, which now do nothing, or may even cause harm. There would also be no need to design in non-functional traces of the action of integrase, traces of which are present in ERVs.


6. The only explanation that makes any sense is that ERVs are the result of retroviral insertions into germ-line DNA - egg cells or sperm cells, followed by reproduction and consequent cell division. Cell division will duplicate the ERVs in the same positions in the DNA of every cell. Separate, parallel infection would not infect every cell, and the proviruses would end up in different locations, comparing one infected cell with another.


7. All human beings have some 200,000+ ERV and ERV fragments in the DNA of every one of their cells. Most of them are in identical DNA locations going from cell to cell, and person to person. This means that we all share common ancestors - the ancestors that first acquired each of the the germ-line retroviral infections.


8. All human beings and chimpanzees have some 200,000+ ERV and ERV fragments in the DNA of every one of their cells. Most of them are in precisely corresponding DNA locations going from cell to cell, and individual to individual. This means that we all share common ancestors - the ancestors that first acquired each of the the germ-line retroviral infections. See http://www.evolutionarymodel.com/erv...of_Shared_ERVs

[Barry Desborough]

Interesting!!!

Looking forward to more!

Unfortunately it will above the bar for most here on tweb, but interesting nonetheless.

Thankyou! I shall continue the answers as and when I can afford the time. ;)

[Tassman]

Thankyou! I shall continue the answers as and when I can afford the time. ;)

Yes, please do. And welcome to TWeb.

[Barry Desborough]

Yes, please do. And welcome to TWeb.

Thank you! :)

[rogue06]

Great to see you around again.

[Barry Desborough]

Great to see you around again.

Thanks! :)

[Barry Desborough]

2. ERV FAQ: Why do virologists and geneticists think that ERVs come from retroviruses? Isn't that just supposition on their part?

Provirus structure.jpg

Much material in this post has been lifted from Abbie Smith. Hope you don't mind Abbie, :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 haven't figured any out yet…"


Env. See http://scienceblogs.com/erv/2008/07/...s-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 Post #7 and http://scienceblogs.com/erv/2009/07/...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. At 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)."

[Lili]

Very interesting topic. ERVs are one of the best types of evidence for common descent and evolution. I'm familiar with Abbie's blog, too. Very informative.

[HMS_Beagle]

Very interesting topic. ERVs are one of the best types of evidence for common descent and evolution. I'm familiar with Abbie's blog, too. Very informative.

Looks like her blog ERV hasn't been updated in over a year. anyone know what she's up to these days? One of my all time great web memories is of her • Edited by a Moderator •of the mouthy and arrogant IDiot Casey Luskin.

Moderated By: Littlejoe

That's way too crude. Let's watch it please

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Contact the forum moderator or an administrator in Private Message or email instead. If you feel you must publicly complain or whine, please take it to the Padded Room unless told otherwise.

[Barry Desborough]

3. ERV FAQ: Isn't this just circular reasoning, assuming evolution to 'prove' evolution?

circular reasoning.jpeg
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 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.