A question of ERVs

[pshun2404]

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

Yes! Which I have done now and then myself. Apparently you are also someone who is able to do this.

 

[pshun2404]

Dogma...healthy skepticism, doubt, and asking reasonable questions are the driving force of good science. If it were not, we would still be stuck in the Ptolemaic model of the Universe.

My insistence that the only way we can demonstrate something has been inserted in anything is by having the original (when it was not there) to compare to (showing it now is). This is born out in many other areas to be the only acceptable evidence of insertion so why should this area get a free pass insisting we (or anybody) must just accept it is because it supports a pre-held belief (that this shows phylogeny). After all, healthy skepticism, doubt, and asking reasonable questions is the basis for most arguments against what many creationists claim (especially the YEC camp).

 

[46AND2]

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.

You know that that's the same exact method scholars use to create accurate translations of the Bible, right?

 

[46AND2]

Dogma...healthy skepticism, doubt, and asking reasonable questions are the driving force of good science. If it were not, we would still be stuck in the Ptolemaic model of the Universe.

My insistence that the only way we can demonstrate something has been inserted in anything is by having the original (when it was not there) to compare to (showing it now is). This is born out in many other areas to be the only acceptable evidence of insertion so why should this area get a free pass insisting we (or anybody) must just accept it is because it supports a pre-held belief (that this shows phylogeny). After all, healthy skepticism, doubt, and asking reasonable questions is the basis for most arguments against what many creationists claim (especially the YEC camp).

It shows phylogenetic patterns regardless of whether it was inserted or not. The phylogeny is observed fact.

 

[46AND2]

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.

HIV does not have a "relative ERV " within our own genome.

 

[pshun2404]

HIV does not have a "relative ERV " within our own genome.

You are right. I stand corrected, thanks. I still have not found any pre-insertion examples to compare our alleged HERVs to (so we can see they were in fact insertions). Not saying that there are no examples, but have not found any.

I realize this may be unrelated to the OP, but perhaps you can help? Were not ERVs originally exogenous at the infection event (even if that happened in the elusive undemonstrated common ancestor with chimps)?

 

[pshun2404]

HIV does not have a "relative ERV " within our own genome.

So then babies born with HIV catch it not inherit it? Correct?

 

[USincognito]

So then babies born with HIV catch it not inherit it? Correct?

They inherit the infection because of exposure to their mothers blood via the placenta, not because the HIV has endogenized into their genome.

 

[pshun2404]

Madalina Barbulescu in, “A HERV-K Provirus in Chimpanzees, Bonobos, and Gorillas, but Not Humans,” Current Biology 11 (May 2001): 779–83, doi:10.1016/S0960-9822(01)00227-5, tells us that SOME of the ERVs found in chimps, bonobos, and gorillas, are not present in humans and many in humans are not found in any of the others (also see Chris T. Yohn et al., “Lineage-Specific Expansions of Retroviral Insertions within the Genomes of African Great Apes but Not Humans and Orangutans,” PLoS Biology 3, April 2005: e110, 10.1371/journal.pbio). So none of these can be used in an argument for common descent and may indicate the exact opposite.

Furthermore, a study done by Catriona M. Macfarlane and Richard M. Badge, (“Genome-Wide Amplification of Proviral Sequences Reveals New Polymorphic HERV-K(HML-2) Proviruses in Humans and Chimpanzees that are Absent from Genome Assemblies,” Retrovirology 12 , April 2015: id. 35, doi:10.1186/s12977-015-0162-8) implies we may need to re-think the time element generally assumed because “mounting evidence indicates a much more recent insertion event for humans than for chimps at shared ERV insertion sites previously thought to confirm common ancestry.”

In light of this, Molecular Biologist, Dr. Anjeanette Roberts believes “the longer I think about ERVs and viral origins, and as I observe scientific reports identifying various critical functions associated with ERVs and other repetitive genomic elements, I believe it may be profitable for driving scientific inquiry to question some of the underlying assumptions that support ERVs as inarguable signs of common descent.”

So based on these and other studies, simple logic tells us that IF the conclusion these scientists have reached is possible or true (in those endogenous samples they examined), THEN it could also be possible or true that the evidence used in these sites no longer can be said to indicate descent. At least questioning the assumption is an equally valid scientific perspective, is it not?

In MacFarlane and Badge we see the alleged same inserted item, located in the same place in the two respective genomes, yet allegedly acquired at two different times in the different creatures (therefore possibly NOT related except via taxonomic convention).

So IMHO it is perfectly reasonable to ask, “Does this evidence really demonstrate a Common Descent or is that merely a POSSIBILITY, based on what was already assumed?” Since the fact that common descent was already assumed can be demonstrated, can't a degree of expectancy bias be assumed in the interpretations of those that hold this presupposition?

Or to paraphrase the possibilities presented by McClintock or Shapiro, perhaps these allegedly similarities in the compared genomes show a sort of biochemical preference as to where such materials would be placed (thus originally having been somewhere else)?

Or is it not plausible to suggest a re-combination of non-ERV material to resemble an ERV for functional purposes is reasonable? Hmmm? In this case, IMHO, maybe the already extant genome (in each respective case) plays a role in selecting or devising sequences that may be useful as well as where this segment will be placed.

 

[pshun2404]

They inherit the infection because of exposure to their mothers blood via the placenta, not because the HIV has endogenized into their genome.

Many thanks. So then it is fair to say that, at least in theory, some retroviruses become endogenized and others do not. Is that a fair assessment?

 

[Steve Petersen]

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?”

I like the fact that when a scientist doesn't know, they say so. But they do try to draw attention to the need for more study. That is what science is supposed to do.

I much prefer it to religious dogma that won't be moved by data (ala Ken Hamm here.)

 

[DogmaHunter]

Please note, if you address someone and either not quote their post or include their name with the @ symbol, then the user doesn't get notified of it. If I hadn't stumbled accross this post by reading the thread, I would have never known that you addressed something to me.

Just a friendly FYI.

Dogma...healthy skepticism, doubt, and asking reasonable questions are the driving force of good science. If it were not, we would still be stuck in the Ptolemaic model of the Universe.

Did I say otherwise somewhere?

The thing is though, there's honest doubt and then there is I don't believe it because I already religion X.

By all means, ask as many question as you want and doubt as much as you want. But your doubt isn't well founded. Your doubt isn't with the specifics of the theory, your doubt is with the entire scientific process and that becomes clear in your posts. This is why you hold up the intellectually honest language one finds in EVERY scientific paper as if it means something concerning the validity of the paper. It doesn't. As I explained. It's standard use of words in any science paper. Science is always provisional, no matter how ridiculously accurate something seems to be, like atomic theory or germ theory or, indeed, evolution theory.

My insistence that the only way we can demonstrate something has been inserted in anything is by having the original (when it was not there) to compare to (showing it now is).

The actual experts of the field don't seem to have any problems with identifying ERV's in genomes. Why would I listen to you over them?

In all honesty here, and without trying to offend you or something, but you are just some random bloke on the internet whose, quite frankly, religion is clouding your judgement of scientific theories that you feel contradict your religious beliefs.

This is born out in many other areas to be the only acceptable evidence of insertion so why should this area get a free pass insisting we (or anybody) must just accept it is because it supports a pre-held belief (that this shows phylogeny). After all, healthy skepticism, doubt, and asking reasonable questions is the basis for most arguments against what many creationists claim (especially the YEC camp).

I'ld be willing to bet nice amounts of money that you're quite wrong about your evaluation here.

Maybe we should ask @sfs for some input on how geneticists can recognise ERV's in a genome, "without having access to the viral DNA". I'm not a geneticist so I don't know. And I'm not arrogant enough to pretend to know better either.

 

[Resha Caner]

"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.

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.

Interesting. Observing similarity without knowing the source of that similarity doesn't seem a very strong argument to me, but still ... interesting.

 

[46AND2]

Madalina Barbulescu in, “A HERV-K Provirus in Chimpanzees, Bonobos, and Gorillas, but Not Humans,” Current Biology 11 (May 2001): 779–83, doi:10.1016/S0960-9822(01)00227-5, tells us that SOME of the ERVs found in chimps, bonobos, and gorillas, are not present in humans and many in humans are not found in any of the others (also see Chris T. Yohn et al., “Lineage-Specific Expansions of Retroviral Insertions within the Genomes of African Great Apes but Not Humans and Orangutans,” PLoS Biology 3, April 2005: e110, 10.1371/journal.pbio). So none of these can be used in an argument for common descent and may indicate the exact opposite.

The fact that there are rare (far less than 1%) deviations from the phylogenetic pattern only shows that life is complex, and give us the opportunity to explore mechanisms by which these deviations can occur.

If you have hundreds of thousands of ERVs which fit neatly in the pattern, yet find one that deviates from that pattern, it doesn't negate the fact that the pattern is there. Instead of dismissing the pattern based on one deviation, should we not instead try to find out why the deviation exists? And that the more likely explanation is that the outlier is not indicative of what is actually happening, but rather a unique circumstance?

Furthermore, a study done by Catriona M. Macfarlane and Richard M. Badge, (“Genome-Wide Amplification of Proviral Sequences Reveals New Polymorphic HERV-K(HML-2) Proviruses in Humans and Chimpanzees that are Absent from Genome Assemblies,” Retrovirology 12 , April 2015: id. 35, doi:10.1186/s12977-015-0162-8) implies we may need to re-think the time element generally assumed because “mounting evidence indicates a much more recent insertion event for humans than for chimps at shared ERV insertion sites previously thought to confirm common ancestry.”

Not sure where your underlined quote comes from, because it isn't in the paper you cited. Further, that paper does not seem to imply anything like the "re-thinking" you say it does. In the conclusion, it even says the results were "not unexpected."

In light of this, Molecular Biologist, Dr. Anjeanette Roberts believes “the longer I think about ERVs and viral origins, and as I observe scientific reports identifying various critical functions associated with ERVs and other repetitive genomic elements, I believe it may be profitable for driving scientific inquiry to question some of the underlying assumptions that support ERVs as inarguable signs of common descent.”

Dr. Roberts is a creationist. In the article from which your quote comes, she also says, " Some elements are found in chimps, bonobos, and gorillas, but are absent in humans."

1. The ERV you mentioned in the first paper you cited is the ONLY KNOWN EXAMPLE OF THIS. So her statement is misleading.

2. The source she cites for this statement has nothing to do with ERVs.

She goes on to say: "Others are present in chimps and great apes but not in humans and orangutans."

1. She gives no source for this claim.

2. The footnote for this claim talks about something OTHER than ERVs.

Notice the wording she uses in a paragraph that is purportedly about ERVs. She says "ELEMENTS are found in chimps...." not "ERVs are found in chimps..." This leaves her free to be technically correct when she supports her statements in her footnotes, despite the fact that, you know, it's a bait and switch, cause the footnotes have nothing to do with ERVs.

So based on these and other studies, simple logic tells us that IF the conclusion these scientists have reached is possible or true (in those endogenous samples they examined), THEN it could also be possible or true that the evidence used in these sites no longer can be said to indicate descent. At least questioning the assumption is an equally valid scientific perspective, is it not?

No, it is not. You don't throw the baby out with the bathwater. Outliers do not refute the profound preponderance of evidence.

In MacFarlane and Badge we see the alleged same inserted item, located in the same place in the two respective genomes, yet allegedly acquired at two different times in the different creatures (therefore possibly NOT related except via taxonomic convention).

Can you provide the part of the paper which says this--quote a couple sentences? It's a long paper and haven't had time to read it all, so this would be helpful for the sake of the discussion.

Regardless, why would this be a problem? It is unlikely that two ERVs are independently obtained orthologously by chance, but not impossible. For it to happen hundreds of thousands of times at a 99.9+% clip, though? Not so much.

So IMHO it is perfectly reasonable to ask, “Does this evidence really demonstrate a Common Descent or is that merely a POSSIBILITY, based on what was already assumed?” Since the fact that common descent was already assumed can be demonstrated, can't a degree of expectancy bias be assumed in the interpretations of those that hold this presupposition?

It is, by far, the best explanation for the data we see. Rare deviations from the pattern notwithstanding.

Or to paraphrase the possibilities presented by McClintock or Shapiro, perhaps these allegedly similarities in the compared genomes show a sort of biochemical preference as to where such materials would be placed (thus originally having been somewhere else)?

I'm not sure what you mean here.

Or is it not plausible to suggest a re-combination of non-ERV material to resemble an ERV for functional purposes is reasonable? Hmmm? In this case, IMHO, maybe the already extant genome (in each respective case) plays a role in selecting or devising sequences that may be useful as well as where this segment will be placed.

The sites look exactly like mutated remnants of retroviruses, with every indication that they behaved the same way that current retroviruses do. And indeed, as I showed you, we even revived one of these viruses, and it functioned as a virus. The parsimonious explanation is that they ARE retroviral remnants.

It is not plausible to suggest that non-ERV material recombines to resemble an ERV for functional purposes, because...they don't function. They are highly mutated junk DNA, with the rare exception of PARTS of a few ERVs have developed some functionality. No full ERV sequence has been shown to be active.

 

[46AND2]

Interesting. Observing similarity without knowing the source of that similarity doesn't seem a very strong argument to me, but still ... interesting.

The source of the similarity [more accurately, the pattern of similarity] is most easily explained by heredity. This would be true even if the ERVs were originally obtained by some mechanism other than viral insertion.

 

[Resha Caner]

The source of the similarity [more accurately, the pattern of similarity] is most easily explained by heredity. This would be true even if the ERVs were originally obtained by some mechanism other than viral insertion.

Well, no. You can't conclude heredity is the most likely without comparing it to other possibilities. If there's no comparison, it's merely an assumption.

I always thought biologists felt heredity was the only known (reasonable) possibility. I've proposed a few alternatives, but I'm not a biologist, and my proposals were rejected as ridiculous. Are there other possibilities I'm not aware of that have been studied?

 

[46AND2]

Well, no. You can't conclude heredity is the most likely without comparing it to other possibilities. If there's no comparison, it's merely an assumption.

I always thought biologists felt heredity was the only known (reasonable) possibility. I've proposed a few alternatives, but I'm not a biologist, and my proposals were rejected as ridiculous. Are there other possibilities I'm not aware of that have been studied?

But it is compared. To chance, to special creation (not scientifically, of course), to present day observations, etc. And of course there were early proposed alternatives to evolution by natural selection when proposed by Darwin. Which was before genetics, naturally, but the cause for the pattern of similarities in other areas (morphology, biodiversity, etc.) was certainly debated.

And I've read enough of your posts to know that you recognize that when I say it is "most easily explained" it is provisional, and that the "of all explanations we currently have" is implied. And science is always open to considering alternative explanations, even if it leads to discounting one long held true.

But I'd be happy if you presented an alternative explanation. As intimated earlier in this thread, I've been waiting for someone to do that for a long time. With the exception of presenting rare diversions from the pattern, I've yet to see anybody confront the issue.

 

[Resha Caner]

And of course there were early proposed alternatives to evolution by natural selection when proposed by Darwin. Which was before genetics, naturally, but the cause for the pattern of similarities in other areas (morphology, biodiversity, etc.) was certainly debated.

I was hoping for something recent. Something that wasn't dismissed 100+ years ago.

And I've read enough of your posts to know that you recognize that when I say it is "most easily explained" it is provisional, and that the "of all explanations we currently have" is implied. And science is always open to considering alternative explanations, even if it leads to discounting one long held true.

Sorry, but no, I didn't know you meant that. Does that mean you're not aware of any plausible alternative explanations? I'm not trying to bait you or set you up. I'm honestly curious if you're aware of something.

But I'd be happy if you presented an alternative explanation. As intimated earlier in this thread, I've been waiting for someone to do that for a long time. With the exception of presenting rare diversions from the pattern, I've yet to see anybody confront the issue.

Nah. I don't need more people telling me what they think is wrong with my ideas. I've got plenty of that.

 

[46AND2]

I was hoping for something recent. Something that wasn't dismissed 100+ years ago.



Sorry, but no, I didn't know you meant that. Does that mean you're not aware of any plausible alternative explanations? I'm not trying to bait you or set you up. I'm honestly curious if you're aware of something.



Nah. I don't need more people telling me what they think is wrong with my ideas. I've got plenty of that.

Not that I'm aware of, but somebody like tas, or sfs would be more up to speed on competing ideas.

But if there aren't any plausible alternatives, it isn't for lack of trying. TOE faces more opposition than pretty much any other theory in science.

The fact that has withstood 150 years of intense scrutiny says a lot about the explanatory power it possesses.

Ultimately, we know that these ERVS are passed down through inheritance because we observe that they are. And IF they were similarly passed down between species through common ancestry, a nested hierarchy is expected and required. And we observe that, too.

 

[USincognito]

Madalina Barbulescu in, “A HERV-K Provirus in Chimpanzees, Bonobos, and Gorillas, but Not Humans,” Current Biology 11 (May 2001): 779–83, doi:10.1016/S0960-9822(01)00227-5, tells us that SOME of the ERVs found in chimps, bonobos, and gorillas, are not present in humans and many in humans are not found in any of the others (also see Chris T. Yohn et al., “Lineage-Specific Expansions of Retroviral Insertions within the Genomes of African Great Apes but Not Humans and Orangutans,” PLoS Biology 3, April 2005: e110, 10.1371/journal.pbio). So none of these can be used in an argument for common descent and may indicate the exact opposite.

Furthermore, a study done by Catriona M. Macfarlane and Richard M. Badge, (“Genome-Wide Amplification of Proviral Sequences Reveals New Polymorphic HERV-K(HML-2) Proviruses in Humans and Chimpanzees that are Absent from Genome Assemblies,” Retrovirology 12 , April 2015: id. 35, doi:10.1186/s12977-015-0162-8) implies we may need to re-think the time element generally assumed because “mounting evidence indicates a much more recent insertion event for humans than for chimps at shared ERV insertion sites previously thought to confirm common ancestry.”

In light of this, Molecular Biologist, Dr. Anjeanette Roberts believes “the longer I think about ERVs and viral origins, and as I observe scientific reports identifying various critical functions associated with ERVs and other repetitive genomic elements, I believe it may be profitable for driving scientific inquiry to question some of the underlying assumptions that support ERVs as inarguable signs of common descent.”

So based on these and other studies, simple logic tells us that IF the conclusion these scientists have reached is possible or true (in those endogenous samples they examined), THEN it could also be possible or true that the evidence used in these sites no longer can be said to indicate descent. At least questioning the assumption is an equally valid scientific perspective, is it not?

In MacFarlane and Badge we see the alleged same inserted item, located in the same place in the two respective genomes, yet allegedly acquired at two different times in the different creatures (therefore possibly NOT related except via taxonomic convention).

So IMHO it is perfectly reasonable to ask, “Does this evidence really demonstrate a Common Descent or is that merely a POSSIBILITY, based on what was already assumed?” Since the fact that common descent was already assumed can be demonstrated, can't a degree of expectancy bias be assumed in the interpretations of those that hold this presupposition?

Or to paraphrase the possibilities presented by McClintock or Shapiro, perhaps these allegedly similarities in the compared genomes show a sort of biochemical preference as to where such materials would be placed (thus originally having been somewhere else)?

Or is it not plausible to suggest a re-combination of non-ERV material to resemble an ERV for functional purposes is reasonable? Hmmm? In this case, IMHO, maybe the already extant genome (in each respective case) plays a role in selecting or devising sequences that may be useful as well as where this segment will be placed.

It's very dishonest not only to plagiarize several paragraphs from a webpage and not cite it, but to do so apparently to hide the fact that the person making the assertion is an Old Earth Creationist.
A Common Design View of ERVs Encourages Scientific Investigation