Evidence for God from Science

Does anybody have any information on endogenous retroviruses?
I can't seem to find any information against it.

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Jbuza wrote:Endogenous retroviruses are DNA sequences that get activated in the prescense of a virus. It is a communication tool that lets the body know the nature of the virus that has made it past the outer defenses.

It is commonly believed to be left over DNA from a hidden process that never happened. I am quite intrigued by IRs and think little has been done with it because it has been explained by the popularly accepted theory within biology.

Are you sure?

Title: The evolutionary dynamics of endogenous retroviruses
Author(s): Katzourakis A, Rambaut A, Pybus OG
Source: TRENDS IN MICROBIOLOGY 13 (10): 463-468 OCT 2005
Document Type: Editorial Material
Language: English
Cited References: 50 Times Cited: 0 Information
Abstract: Endogenous retroviruses (ERVs) are vertically transmitted intragenomic elements derived from integrated retroviruses. ERVs can proliferate within the genome of their host until they either acquire inactivating mutations or are lost by recombinational deletion. We present a model that unifies current knowledge of ERV biology into a single evolutionary framework. The model predicts the possible long-term outcomes of retroviral germline infection and can account for the variable patterns of observed ERV genetic diversity. We hope the model will provide a useful framework for understanding ERV evolution, enabling the testing of evolutionary hypotheses and the estimation of parameters governing ERV proliferation.
KeyWords Plus: MURINE LEUKEMIA-VIRUS; LONG TERMINAL REPEATS; HUMAN GENOME; INSERTIONAL POLYMORPHISMS; RESTRICTION GENE; MASTER GENES; TRIM5-ALPHA; FAMILY; REF1; MICE
Addresses: Pybus OG (reprint author), Univ Oxford, Dept Zool, S Parks Rd, Oxford, OX1 3PS England
Univ Oxford, Dept Zool, Oxford, OX1 3PS England

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I believe this was discussed on the old boards. Some interesting graphics to help explain the concept are posted there as well. Good stuff.

Jbuza wrote: No, but it seems reasonable, and their is some evidence to suggest that it might be so. IT is clear that HERVs have some role, but it is not clear what that role is.

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To understand the role endogenous retroviruses have in autoimmune disease, Dr. Adelman is studying the tissue and blood of patients with systemic lupus erythematosus to investigate how retroviruses mimic proteins that trigger the immune system.

The "role" being discussed here is how an endogeneour retrovirus plays a part in autoimmune disease. Are you saying that the purpose for their existance is to make us sick? I thought it was a communication of defence mechanism. Are you sure?

Jbuza wrote:The purpose of Dr. Adelman's study is to investigate the role of autoantibodies and antigenic or molecular mimicry by HERVs in autoimmune diseases. The premise of molecular mimicry is that a protein encoded by a HERV that is very similar to a self-protein (autoantigen) results in the production of autoantibodies that are cross-reactive between the two proteins.

Pathology arises when the autoantibodies form immune-complexes with autoantigens that subsequently are deposited in tissues, particularly the basement membranes of the kidneys.

Translation
Sickness happens when the immune system recognizes proteins made in the body as enemies. When these proteins embed in the cell wall of these cells the body attacks itself!

Jbuza wrote:Due to the widespread distribution of autoantigens, large numbers of immune-complexes are continuously produced and deposited, which result in the activation of complement and recruitment of inflammatory cells. Study results will have important implications for the development of treatments that block the causes of autoimmune diseases.

There is no protection going on here, some HERV's cause autoimmune diseases.
http://www.google.com/search?hl=en&lr=& ... ne+disease

Jbuza wrote: Our immune B cells of our immune system that can be shuffled around in near-limitless combinations. This means that with a relatively small set of "base" genes, our B cells can produce antibodies on demand against whatever infection we might be facing, without needing one gene for every possible antibody. However, this requires proteins that can "cut-and-paste" DNA to create these new combinations. We've seen this phrase before already … this is how DNA transposons move around!

This article isn't even related! What are you trying to do here!
I hope your not intentionally trying to be dishonest.

Jbuza wrote: HERV-K gag proteins are found in the cytoplasm of primary tumor cells of patients with seminoma. We identified HERV-K-specific T cells in patients with a past history of seminoma using the interferon-gamma ELISPOT assay and an MHC-HERV-K peptide-specific tetramer. A minority of apparently healthy subjects without evident germ cell tumors also made HERV-Kspecific T cell responses. In summary, we detected T cell reactivity to HERV-K peptides in both past seminoma patients and a minority of apparently healthy controls.

You left out the part where they stated 90% of endogeneous retroviruses do not encode for protein.

Seminoma is a cancer of the germ cells(testicle). This is a study ofseminoma and it's relationship to HERV. Please don't confuse the issue.

Jbuza wrote: http://www.liebertonline.com/doi/abs/10 ... alCode=aid
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Retroviruses have been suggested as possible pathogenic factors in multiple sclerosis (MS), supported by the observation that endogenous retroviruses are activated in MS patients.
[can we say cause and effect?] The objective of the study was investigation of cell-mediated immune responses of MS patients to retrovirus
http://www.mult-sclerosis.org/news/May2 ... andMS.html
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This article is stating that there is a possible relationship between multiple sclerosis and retroviruses.

When a retrovirus enters a cell it inserts its code into the DNA of the host cell to produce proteins for the production of more viruses.
http://users.rcn.com/jkimball.ma.ultran ... ruses.html

So in short this is what we know about endogeneous retroviruses.

They appear to be snippets of code for retroviruses.
Most of them are deactivated due to mutations(changes in their sequence).
Some of them do encode for proteins which provoke an immune responce. Just as if the body were under attack from the real thing.

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Jbuza wrote:IT is a demonstration that the immune system and retroviruses are strongly linked. Simply because I posted the articles doesn't mean that I completley agree with their conclusions. Retroviruses can behave much the same as a flu shot does also.

Jbuza wrote:

Our immune B cells of our immune system that can be shuffled around in near-limitless combinations. This means that with a relatively small set of "base" genes, our B cells can produce antibodies on demand against whatever infection we might be facing, without needing one gene for every possible antibody. However, this requires proteins that can "cut-and-paste" DNA to create these new combinations. We've seen this phrase before already … this is how DNA transposons move around!

Bgood wrote

This article isn't even related! What are you trying to do here!
I hope your not intentionally trying to be dishonest.
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I disagree I think it is very much related.

"However, retroposons resembling retroviruses and transposons resembling DNA viruses have been found across all kingdoms."
http://en.wikipedia.org/wiki/Talk:Retrovirus

Completeley unrelated!
PLEASE try to understand the subject material before making any rash and uneducated links. They are in the same sentance not because they are the same but because of a similar trait, transposability!

We can discuss this in another thread if you wish but the supposed link you provided only understates your lack of knowledge on the subject!

Jbuza wrote:-----
Bgood Wrote
You left out the part where they stated 90% of endogeneous retroviruses do not encode for protein.

Yes if you go back and look you will find I left out numerous PAGES from the sources, in fact I left out numerous sources that I reviewed. In the future would you like me to post everything I read?

Yes but it's a major fact regarding this subject. You seem to be selectively choosing certain findings and deliberately leaving out other facts. Why?

Jbuza wrote: I belive that I have clearly demonstrated that there are retroviruses associated with numerous viral and cancerous diseases and that often they (the retrovirus or protein products ) illicit some type of immune response. Some are proposing an unproven causal link.

There is very little known and to simply say they are remnants of the past without any actual proof is couter productive. Simply because it has been decreed from the slanted instituation of science does not make it so.

???
Nothing is being decreed. We can bring up the actual data and go into how retroviruses work if you wish.

There is a reason we can identify ERV's and it is due to their similarity with exogenic retroviruses.

Once we work out how retroviruses may have originated, and that fact coupled with the fact that most ERV's are inactive, it leads to some interesting conclusions.

But we won't go there if you agree to just drop it. Don't pretend to be an expert, the above shows this is far from the case.

Or I'll drop it if people want to be misinformed, and they explicitly tell me so. Then I won't bother correcting misleading and incorrect statements.

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Jbuza wrote:Sure you run with that.

There are certian sequences within the DNA and RNA that have virus like traits, and those DNA and RNA sequences are inextricably lilnked to the immune system.

Not quite, there are sequences within the DNA which signial a start of a gene. If this is missing or there is a premature stop signal no proteins is formed.
http://users.rcn.com/jkimball.ma.ultran ... odons.html

Jbuza wrote:I guess my lack of understanding of exactley how virus like DNA and RNA sequences are involved with external virul sequences and how the interelate with immunology makes my like every other organism on this planet.

No, I am not saying that I know everything, but it is anoying when you it is clear to me you don;t know the subject and then begin misconstruing and misunderstanding ideas and using that as arguments. If you want to go into more detail on what exactly an endogenous retrovirus is we can do so.

Jbuza wrote:Perhaps I should attack you and call you ignorant as well. Would that help?

Please just admit that you do not fully understand the subject. It is painful to argue in this way, we can bring you up to speed if you want to take the time to study.

Jbuza wrote:If you fail to see how these other systems operate within the human mechanism together than go put your precious little HERV's in a box by themselves and see how they operate. I will tell you they do not operate without a relationship between DNA, proteins, and the immuns sytem.

Of course not, noone said that this is what occurs.
????

Jbuza wrote:Before you go attacking and trying to sound intellectually superior perhaps you should look in the mirror and see if you look at all like what you claim others are.

Did you have anything useful to say?

But thanks for all the enlightening input (sheeesh!!!)

I am not trying to sound intellectually superior, I am only pointing out your egregious misunderstandings on this subject.

Do you want me to just let it stand? Is it ok for me to allow others to learn incorrect information from your post on this subject? If so let me know.

Jbuza wrote:You know what is laughable is this smug attitude that since we do not know the function of large parts of the human DNA and RNA that means they have no function. Pompous idiots!!

This has nothing to do with endogenous retroviruses. What we know of DNA is that large parts do not encode for proteins. This we do know.

Jbuza wrote:In addition to the strong link between HERVs and the immune system there are several other roles that these sequences play. Ancient viral remnants my . . .

A retrovirus works in this manor.
It invades a host cell and inserts its genetic material into the host cells DNA. What do you suppose would happen if this process occurred in a cell destined to become a germ cell?

Jbuza wrote:The first suggestion that HERVs play a role in host cell regulation was demonstrated for the amylase gene cluster. Other HERVs have been demonstrated to regulate the HLA-DRB gene, the leptin gene, obese, the HHLA 2 and 3 genes of functions unknown, the apolipoprotein CI gene, and the endothelin B receptor of placental cells. HERVs are also involved in the regulation of human reproduction. Two very specific roles of HERVs in reproduction reveal the depth of co-evolution between the host and the virus. HERV expression is involved in human sperm-egg binding and fusion. It has been demonstrated that HERV-W encodes the adhesion protein, syncytin. This virally encoded protein adheres to the trophoblast forming the syncytiotrophoblast that binds to the endometrium in the early stage of human placental development. To date no human gene has been discovered that encodes this function.
http://shiva.msu.montana.edu/research.html

When a gene is inserted into the genetic code the cell will produce these proteins. It will react with other proteins in the cell.
The information you posted above shows an interesting relationship between mammal evolution and retrovirus evolution. But you focus on one aspect and disregard the rest. Why?

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Jbuza wrote:

BGoodForGoodSake wrote: This article isn't even related! What are you trying to do here!
I hope your not intentionally trying to be dishonest.

Ad hominem deleted. They are in the same sentance not because they are the same but because of a similar trait, transposability! Ad hominem deleted.

So we have some information elements within the genetic structure that allows our immune system to synthesize antibodies. Hmmm lets look around and see if their are any information sequences that could "inform" our immune system about the nature of viruses. hmmm are there any "virus like" sequnces that could aid the immune system? hmmm.

Your trying to suggest that the immune cells known as B cells use endogeneous retroviruses to incite an immune responce.

This is not what occurs.

B cells produce antibodies, antibodies are like markers which attach to proteins. The receptor end of an antibody can take multiple forms simply because of the ability of transposons. Transposons are not endogeneous retroviruses.

This is why the article is unrelated.

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Jbuza wrote:[quote="BGoodForGoodSakeDo you want me to just let it stand?

Can you be more specific about what I said that you are taking such issue with?[/quote]

Sorry,

I didn't mean to get so riled up.

It was as follows.

Endogenous retroviruses are DNA sequences that get activated in the prescense of a virus.
Not necessarily but that's ok because this is true sometimes for those which are active. Although the activation is harmful causing complications and making the viral infection worse than in a normal patient.

It is a communication tool that lets the body know the nature of the virus that has made it past the outer defenses.
Not at all.

It is commonly believed to be left over DNA from a hidden process that never happened.
This is based on your world view not science.

I am quite intrigued by IRs and think little has been done with it because it has been explained by the popularly accepted theory within biology.
How can this be harmonized with,
You know what is laughable is this smug attitude that since we do not know the function of large parts of the human DNA and RNA that means they have no function. Pompous idiots!!

Why put such a spin on this subject, I am willing to leave this alone.

But I want to apologize publicly for my caustic behaviour.
Sorry for loosing my cool.