A question of ERVs

[pshun2404]

Most would say that what we call ERVs are considered Endogenous Viral Elements (EVEs) because they are similar to, or could have been derived from, retroviruses. Now undoubtedly some are or were, but many only might have been or it is likely that this was their source. According to Kim , Battini, Manel, and Sitbon's 2004 article, “Emergence of Vertebrate Retroviruses and Envelope capture” , (Virology. 318 (1): 183–91), these are sub-class Transposons captured and used by the Genome in Gene Expression and Regulation. However the study done by J. Cotton in 2001 titled,. "Retroviruses from retrotransposons" from Genome Biology. 2 (2): 6, shows us that not all ERVs may have originated as an insertion by a retrovirus in fact it may be possible that our genome may have been the source for the genetic code the retrovirus derived or imitates.

Now that being said, as I have read about 50 or more articles and studies on this subject, I am impressed with the number of times the data and conclusions are couched in language in the subjunctive mood (could be, may, we believe that, and so on) which is not the language of known fact, but belief based interpretation, so I must ask, “Have we actually found and analyzed the genetic material of actual endogenous retro viruses that reflect our ERVs?”

 

[Tinker Grey]

are couched in language in the subjunctive mood (could be, may, we believe that, and so on) which is not the language of known fact, but belief based interpretation,

That is not subjunctive mood. Subjuctive mood is for expressing counterfactuals, e.g., "If I were taller..." "Could be, may be, etc." is expressing a hypothesis. That is not "belief base interpretation". It is a proposal of possibility. I often express possibilities that I don't remotely believe in, such as "the fact that the system isn't working could be due to my programming errors."

 

[pshun2404]

I cannot find ANY instances where even a single Endogenous Retro Virus with a relevant sequence has actually ever been found and analyzed. Can you help or direct me to this info?

 

[Tinker Grey]

I'm no expert on this. I'll leave it to our resident biologists such as @sfs

 

[46AND2]

I cannot find ANY instances where even a single Endogenous Retro Virus with a relevant sequence has actually ever been found and analyzed. Can you help or direct me to this info?

I'm not exactly sure what you mean by "relevent sequence has actually ever been found and analyzed."

Because, the simple, straightforward meaning tells me that you must not have looked very hard, cause there are many, many examples.

But here is one, which they analyzed, and resurrected.

 

[DogmaHunter]

Most would say that what we call ERVs are considered Endogenous Viral Elements (EVEs) because they are similar to, or could have been derived from, retroviruses. Now undoubtedly some are or were, but many only might have been or it is likely that this was their source. According to Kim , Battini, Manel, and Sitbon's 2004 article, “Emergence of Vertebrate Retroviruses and Envelope capture” , (Virology. 318 (1): 183–91), these are sub-class Transposons captured and used by the Genome in Gene Expression and Regulation. However the study done by J. Cotton in 2001 titled,. "Retroviruses from retrotransposons" from Genome Biology. 2 (2): 6, shows us that not all ERVs may have originated as an insertion by a retrovirus in fact it may be possible that our genome may have been the source for the genetic code the retrovirus derived or imitates.

Now that being said, as I have read about 50 or more articles and studies on this subject, I am impressed with the number of times the data and conclusions are couched in language in the subjunctive mood (could be, may, we believe that, and so on) which is not the language of known fact, but belief based interpretation, so I must ask, “Have we actually found and analyzed the genetic material of actual endogenous retro viruses that reflect our ERVs?”

Every scientific paper on any subject uses such qualifications.
It's called intellectual honesty.

 

[USincognito]

I cannot find ANY instances where even a single Endogenous Retro Virus with a relevant sequence has actually ever been found and analyzed. Can you help or direct me to this info?

Endogenization is being observed in real time in koalas.

 

[The IbanezerScrooge]

Endogenization is being observed in real time in koalas.

Do you have a link USCog? That sounds super interesting!

 

[whereloveandmercymeet]

I often express possibilities that I don't remotely believe in, such as "the fact that the system isn't working could be due to my programming errors."

This brings back so many memories I had to laugh!

 

[pshun2404]

That is not subjunctive mood. Subjuctive mood is for expressing counterfactuals, e.g., "If I were taller..." "Could be, may be, etc." is expressing a hypothesis. That is not "belief base interpretation". It is a proposal of possibility. I often express possibilities that I don't remotely believe in, such as "the fact that the system isn't working could be due to my programming errors."

You are correct and I was incorrect but this is still not the language of known fact. Do you agree?

 

[pshun2404]

I'm not exactly sure what you mean by "relevent sequence has actually ever been found and analyzed."

Because, the simple, straightforward meaning tells me that you must not have looked very hard, cause there are many, many examples.

But here is one, which they analyzed, and resurrected.

Yes I see that many areas said to be ERVs have been analyzed (I already knew that) but aside from the HIV virus do we have any of the actual viruses that we have analyzed so we can know they actually existed? Can you indicate a source I can look at?

 

[pshun2404]

Every scientific paper on any subject uses such qualifications.
It's called intellectual honesty.

I agree. This language IS intellectual honesty. It suggests possibility not factual reality which might be or could be true (not IS).

 

[46AND2]

Yes I see that many areas said to be ERVs have been analyzed (I already knew that) but aside from the HIV virus do we have any of the actual viruses that we have analyzed so we can know they actually existed? Can you indicate a source I can look at?

I did in my previous response. Follow the hyperlink.

But ERVs are highly mutated remnants of retroviruses that are no longer viable viruses. HIV is not endogenous.

 

[Tinker Grey]

You are correct and I was incorrect but this is still not the language of known fact. Do you agree?

Sure. But people who know everything discover nothing. The first step to learning is admitting you don't know.

 

[USincognito]

Do you have a link USCog? That sounds super interesting!

Enjoy.
Koala retrovirus: a genome invasion in real time

 

[DogmaHunter]

I agree. This language IS intellectual honesty. It suggests possibility not factual reality which might be or could be true (not IS).

You're doing your best to downplay any scientific model, as if it isn't something one should take very seriously.

No, you are misrepresenting it.
It's more like this: all the current evidence supports this thing here. It might be wrong, but the current evidence at our disposal suggests that it isn't.

What the language does, is avoid statements of absolute certainty, and that's it.
You'll find such language as well in let's say Germ Theory. You don't seriously doubt that Germ Theory, the idea that micro organism are responsible for plenty of desease to be something that "might be or could be true", right?

There are plenty of scientific theories that you accept as being as good as fact.
Yet they all use such language and qualifiers.

But I get it, you know.... The entire creationist case consists of nothing but casting doubt on the scientific process and make it sound like it's nothing more then some guess or something.

This is why whenever we ask for evidence in support of creationism, all we get are attempts at trying to poke holes in evolution.

 

[mark kennedy]

Most would say that what we call ERVs are considered Endogenous Viral Elements (EVEs) because they are similar to, or could have been derived from, retroviruses. Now undoubtedly some are or were, but many only might have been or it is likely that this was their source. According to Kim , Battini, Manel, and Sitbon's 2004 article, “Emergence of Vertebrate Retroviruses and Envelope capture” , (Virology. 318 (1): 183–91), these are sub-class Transposons captured and used by the Genome in Gene Expression and Regulation. However the study done by J. Cotton in 2001 titled,. "Retroviruses from retrotransposons" from Genome Biology. 2 (2): 6, shows us that not all ERVs may have originated as an insertion by a retrovirus in fact it may be possible that our genome may have been the source for the genetic code the retrovirus derived or imitates.

Now that being said, as I have read about 50 or more articles and studies on this subject, I am impressed with the number of times the data and conclusions are couched in language in the subjunctive mood (could be, may, we believe that, and so on) which is not the language of known fact, but belief based interpretation, so I must ask, “Have we actually found and analyzed the genetic material of actual endogenous retro viruses that reflect our ERVs?”

In all your reading have you found a single human genome invasion of the germline? Was it documented, do you think that 8% of the human genome was the result of these dangerous germline invasions? They look like broken protein coding genes to me, perhaps I'm missing something.

 

[DogmaHunter]

They look like broken protein coding genes to me, perhaps I'm missing something.

Are you a geneticist?

 

[46AND2]

In all your reading have you found a single human genome invasion of the germline? Was it documented, do you think that 8% of the human genome was the result of these dangerous germline invasions? They look like broken protein coding genes to me, perhaps I'm missing something.

Yes, you're missing something, and you've been consistently shown what you are missing for near a decade.

Even if, and that's a huge if, they are nothing but 100% "broken protein coding genes," (they aren't) it does NOTHING for the creationist position. Because it is a PHYLOGENY argument, not a homology argument. Something that you have steadfastly refused to even attempt to address for as long as I have been on this board. Worse, you still consistently claim, nearly every time an ERV thread pops up, that it is a homology argument despite being advised countless times that you are arguing against a position that we don't even hold.

Whether they are viral remnants or broken genes, you still cannot even begin to explain why we observe them in the nested hierarchical pattern we do.

And that goes for the OP as well. Cast all the doubt you want about whether they were ever really viruses. It DOESN'T matter. You are wrong, but it doesn't matter. Because it is purely obfuscation. It completely ignores the single most important part of the ERV argument. The phylogeny.

I was first brought to this forum after doing a google search (or yahoo, or whatever engine was popular at the time) for the ERV argument. I have read virtually every thread on the topic since, and not one creationist has addressed the phylogeny since the first thread I read, here--started in 2007.

 

[pshun2404]

I did in my previous response. Follow the hyperlink.

But ERVs are highly mutated remnants of retroviruses that are no longer viable viruses. HIV is not endogenous.

Glad I did not say HIV was an example of an endogenous virus. Sorry I was not clear, but the point I was getting at was that in this case we have the genetic material of this virus to compare its relevant ERV to within our own genome.

Becasue of that we can then demonstrate and observe that this virus was in fact inserted (it was not there, and then after being infected it is).

Your link referred to an alleged fossilized virus we can not obtain the original genetic material from. The article itself states clearly the modern alleged comparison was created by the researchers (not something actually there in the original).

"the researchers took dozens of known HERV-K(HML2) sequences and aligned them to create a so-called “consensus” sequence. Then they converted this information into a complete viral genome.”

What they did was to assemble what they believed to be a modern representative virus from various (dozens in fact) sequences from modern examples (from many possibly unrelated viral inflictions) and then used these to intelligently design a complete viral genome that they have no original to compare to. That was not an example of what I had hoped or asked for.But thanks it was an interesting article.