A question of ERVs

pshun2404

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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.

Sorry, there is simply no comparative evidence that most of these sequences are of ancient viral origin and apparently as we see in post 29 there are some scientists beginning to question some of these assumptions as well.

Of course these sequences are passed down by inheritance because they are part of the host-parent genome, but that shows us nothing of the elusive ancestor of the gaps. Also, nested hierarchies are a humanly devised convention of convenience (to group items by similar qualities or characteristics does not demonstrate lineage). The lineal assumptions are not actual truth.

But without diverting into that separate discussion how about demonstrating an actual ancient virus we have analyzed that shows one of these original "insertions" in the ancestor of the gaps creature (even before the mutations that may or may not have happened). Please...if you cannot it is okay to be honest.
 
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pshun2404

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Biologist Dr. Anjeanette Roberts again enlightens us when she reveals “divergence of long terminal repeat sequences (components of ERVs) SOMETIMES VARIES SIGNIFICANTLY from one species to another at shared sites, even when normalized for mutation rates.”

See how different many of these alleged “same ERVs” and “shared sites” actually are? We get the data, but then we INTERPRET the data (filtered through our presuppositions). For those already convinced of a Universal Common Descent, they see the data, and then explain it in light of this hypothesis, but for those who do not, these are simply different segments, and some are insertions. But there is no reason to assume Universal Common Descent. Perhaps there are multiple sources. Perhaps there never were (there certainly are none now) any such thing as “Self-Replicating” organic molecules in nature outside of a living system.

Then there is the question about functionality. By any reasonable conjecture, a virus having once been inserted in the system, after millions of years should no longer possess functionality (save their deleterious effects). Now I know we are told that “our common ancestor” (allegedly 6.5 mya) acquired these retro-viral infections and then they were inherited, but apparently in the opinion of other scientists what are now ERVs still have function in the genome, therefore that premise falls apart. As we just have seen, science has found that in fact many do have essential funvtion. Those that do have function still perform those functions. For example, out of 240,000, the Encode Project has determined that at least 51,195 of them are intimately associated with initiating transcription in the human genome, while 1743 were only found in the UTRs (the untranslated areas of the genome). That is more than 20%.

Their effect, just at p53 (a master gene regulator) helps the body fight cancer, and without their help we would all get cancer and die much more frequently. This alleged ERV is a necessary part of the genome that has served to preserve the species and because of this, it is equally likely it is not just some viral insertion. If it was not a normal and necessary part of us, the human race would have died out epochs ago.

Therefore these section/sequences were essential to the continuation of the human species since the very beginning of humanity. They are and have always been an essential part of who we are. Which means that as much as this may shake the hypothesis, this does not support that they were ever “acquired” into the human genome, but rather an essential part of it. But this does not show they were inherited from some pre- or quasi-human ancestor just that they were always there in humans.

If all these alleged ERVs ARE retroviral insertions then how did they get into the reproductive cells of the ancestor of the gaps without causing major damage? How could we have existed while diverging without their important functions? Why would harmful virus infected reproductive cells be selected as more fit in a natural selection process? These important questions are not even being asked, let alone answered.
 
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mark kennedy

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Sorry, there is simply no comparative evidence that most of these sequences are of ancient viral origin and apparently as we see in post 29 there are some scientists beginning to question some of these assumptions as well.

Of course these sequences are passed down by inheritance because they are part of the host-parent genome, but that shows us nothing of the elusive ancestor of the gaps. Also, nested hierarchies are a humanly devised convention of convenience (to group items by similar qualities or characteristics does not demonstrate lineage). The lineal assumptions are not actual truth.

But without diverting into that separate discussion how about demonstrating an actual ancient virus we have analyzed that shows one of these original "insertions" in the ancestor of the gaps creature (even before the mutations that may or may not have happened). Please...if you cannot it is okay to be honest.
That's a strange argument, the idea that ERVs are the result of germline mutations has always thrown me. They just look like busted protein coding genes to me. Estimates go some 8% of the human genome are the result of these highly dangerous invasions and the chimpanzee apparently has accumulated some million base pairs as the result of them since the split. Meanwhile in the human line only one is actually working and the rest are simply broken protein coding genes. ERVs have go to be the worst homology argument I've ever heard.
 
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mark kennedy

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If all these alleged ERVs ARE retroviral insertions then how did they get into the reproductive cells of the ancestor of the gaps without causing major damage? How could we have existed while diverging without their important functions? Why would harmful virus infected reproductive cells be selected as more fit in a natural selection process? These important questions are not even being asked, let alone answered.
That's kind of the thing, HIV is pretty dangerous to white blood cells, imagine what it could do to a developing germline. Do they ever take into account the deleterious effects because I'm not seeing that factored in very much.
 
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xianghua

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

no realy. see here:

Lineage-Specific Expansions of Retroviral Insertions within the Genomes of African Great Apes but Not Humans and Orangutans

"First, we examined the distribution of shared sites between species (Table S3). We found that the distribution is inconsistent with the generally accepted phylogeny of catarrhine primates"

"Moreover, the same exact six sites would also have had to have been deleted in the orangutan lineage if the generally accepted phylogeny is correct. Such a series of independent deletion events at the same precise locations in the genome is unlikely
 
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mark kennedy

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no realy. see here:

Lineage-Specific Expansions of Retroviral Insertions within the Genomes of African Great Apes but Not Humans and Orangutans

"First, we examined the distribution of shared sites between species (Table S3). We found that the distribution is inconsistent with the generally accepted phylogeny of catarrhine primates"

"Moreover, the same exact six sites would also have had to have been deleted in the orangutan lineage if the generally accepted phylogeny is correct. Such a series of independent deletion events at the same precise locations in the genome is unlikely
This was apparent in the Chimpanzee Genome paper was well:

Our data are consistent with a retroviral infection that bombarded the genomes of chimpanzees and gorillas independently and concurrently, 3–4 million years ago. We speculate on the potential impact of such recent events on the evolution of humans and great apes. (Lineage-Specific Expansions of Retroviral Insertions within the Genomes of African Great Apes but Not Humans and Orangutans PLOS 2005)

Against this background, it was surprising to find that the chimpanzee genome has two active retroviral elements (PtERV1 and PtERV2) that are unlike any older elements in either genome; these must have been introduced by infection of the chimpanzee germ line. The smaller family (PtERV2) has only a few dozen copies, which nonetheless represent multiple (∼5–8) invasions, because the sequence differences among reconstructed subfamilies are too great (∼8%) to have arisen by mutation since divergence from human...PtERV1-like elements are present in the rhesus monkey, olive baboon and African great apes but not in human, orangutan or gibbon, suggesting separate germline invasions in these species (Initial Sequence of the Chimpanzee Genome)​

nature04072-t2.jpg


Notice the ERV class 1.
 
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pshun2404

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That's kind of the thing, HIV is pretty dangerous to white blood cells, imagine what it could do to a developing germline. Do they ever take into account the deleterious effects because I'm not seeing that factored in very much.

No! I find the issue is selectively excluded in the generally accepted and espoused view. A few have touched on it briefly but generally scoff it off as an insignificant factor.
 
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pshun2404

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no realy. see here:

Lineage-Specific Expansions of Retroviral Insertions within the Genomes of African Great Apes but Not Humans and Orangutans

"First, we examined the distribution of shared sites between species (Table S3). We found that the distribution is inconsistent with the generally accepted phylogeny of catarrhine primates"

"Moreover, the same exact six sites would also have had to have been deleted in the orangutan lineage if the generally accepted phylogeny is correct. Such a series of independent deletion events at the same precise locations in the genome is unlikely

Precisely! Most critics of this view will just blow the study off as too long to read (Why would they? It throws yet another monkey wrench into the generally accepted mantra just as some of the other studies mentioned).
 
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mark kennedy

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No! I find the issue is selectively excluded in the generally accepted and espoused view.
It depends on what you mean, ERVs are a big deal with regards to HIV, a lot of research has been done simply because of AIDs. I thought the Phoenix virus was especially interesting because they were trying to figure out out how they get inserted. I'm just incredulous that all of them are the result of germline invasions, I think such a thing would be devastating. I find very few documented cases of this being known to occur but it usually is associated with deleterious effects.
 
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46AND2

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It depends on what you mean, ERVs are a big deal with regards to HIV, a lot of research has been done simply because of AIDs. I thought the Phoenix virus was especially interesting because they were trying to figure out out how they get inserted. I'm just incredulous that all of them are the result of germline invasions, I think such a thing would be devastating. I find very few documented cases of this being known to occur but it usually is associated with deleterious effects.

You only think it would be devastating because you assume that all retroviruses are as devastating as HIV. They are not.

This paper discusses HTLV virues. HTLV-1 is associated with Adult T-cell Leukemia (ATL). However most people who obtain the virus are asymptomatic. Only 2-4% of those infected actually develop ATL, and even when they do, it can be 30-40 years after infection. Additionally, with the HTLV-2 and HTLV-5 viruses, it's unclear what they even do with regard to disease.
 
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46AND2

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This was apparent in the Chimpanzee Genome paper was well:

Our data are consistent with a retroviral infection that bombarded the genomes of chimpanzees and gorillas independently and concurrently, 3–4 million years ago. We speculate on the potential impact of such recent events on the evolution of humans and great apes. (Lineage-Specific Expansions of Retroviral Insertions within the Genomes of African Great Apes but Not Humans and Orangutans PLOS 2005)

Against this background, it was surprising to find that the chimpanzee genome has two active retroviral elements (PtERV1 and PtERV2) that are unlike any older elements in either genome; these must have been introduced by infection of the chimpanzee germ line. The smaller family (PtERV2) has only a few dozen copies, which nonetheless represent multiple (∼5–8) invasions, because the sequence differences among reconstructed subfamilies are too great (∼8%) to have arisen by mutation since divergence from human...PtERV1-like elements are present in the rhesus monkey, olive baboon and African great apes but not in human, orangutan or gibbon, suggesting separate germline invasions in these species (Initial Sequence of the Chimpanzee Genome)​

nature04072-t2.jpg


Notice the ERV class 1.

I know that it has been explained to you that these viruses are found at NON-orthologous locations. And the fact that they are found at different locations SUPPORTS the pattern that is the argument for evolution. Put simply, if we find ERVs which don't match the nested hierarchy, they should not be found at the same location in the pertinent genomes, indicating each of the species obtained them in separate events....and this is exactly what we see.

You and I both know that this has been explained to you by @Loudmouth many times. Why do you continue to mislead others here who may not have read those discussions?
 
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46AND2

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no realy. see here:

Lineage-Specific Expansions of Retroviral Insertions within the Genomes of African Great Apes but Not Humans and Orangutans

"First, we examined the distribution of shared sites between species (Table S3). We found that the distribution is inconsistent with the generally accepted phylogeny of catarrhine primates"

"Moreover, the same exact six sites would also have had to have been deleted in the orangutan lineage if the generally accepted phylogeny is correct. Such a series of independent deletion events at the same precise locations in the genome is unlikely

You, sir, do not have any idea what you are talking about.

The apes which have these insertions have them at different parts of their genomes. This indicates that they were obtained by separate events in each of the species, and not passed down through common ancestry (they would be in the same location if due to ancestry).

In other words, it actually provides MORE support for evolution, not less. These viruses which go against the nested hierarchy should be found at different locations if common ancestry is correct...and they are. Just like we expect.
 
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46AND2

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Precisely! Most critics of this view will just blow the study off as too long to read (Why would they? It throws yet another monkey wrench into the generally accepted mantra just as some of the other studies mentioned).

I don't just blow it off, I explain exactly why (see my previous two posts) the paper on PtERVs is even MORE compelling for evolution.
 
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46AND2

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Sorry, there is simply no comparative evidence that most of these sequences are of ancient viral origin and apparently as we see in post 29 there are some scientists beginning to question some of these assumptions as well.

Of course these sequences are passed down by inheritance because they are part of the host-parent genome, but that shows us nothing of the elusive ancestor of the gaps. Also, nested hierarchies are a humanly devised convention of convenience (to group items by similar qualities or characteristics does not demonstrate lineage). The lineal assumptions are not actual truth.

But without diverting into that separate discussion how about demonstrating an actual ancient virus we have analyzed that shows one of these original "insertions" in the ancestor of the gaps creature (even before the mutations that may or may not have happened). Please...if you cannot it is okay to be honest.

I don't know what to tell you, man. If the Phoenix virus, in which we determined its original structure using the same exact method we use to translate the Bible, and resulted in a viable virus, is not relevent enough for you, then your request is unreasonable. It's simply your version of Ken Ham's "were you there?"
 
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mark kennedy

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I know that it has been explained to you that these viruses are found at NON-orthologous locations. And the fact that they are found at different locations SUPPORTS the pattern that is the argument for evolution. Put simply, if we find ERVs which don't match the nested hierarchy, they should not be found at the same location in the pertinent genomes, indicating each of the species obtained them in separate events....and this is exactly what we see.

You and I both know that this has been explained to you by @Loudmouth many times. Why do you continue to mislead others here who may not have read those discussions?
Loudmouth mimicked what he read on a blog and never made a substantive argument. Non-orthologous simply means homology isn't an issue, his arguments were largely pedantic.
 
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mark kennedy

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You only think it would be devastating because you assume that all retroviruses are as devastating as HIV. They are not.

This paper discusses HTLV virues. HTLV-1 is associated with Adult T-cell Leukemia (ATL). However most people who obtain the virus are asymptomatic. Only 2-4% of those infected actually develop ATL, and even when they do, it can be 30-40 years after infection. Additionally, with the HTLV-2 and HTLV-5 viruses, it's unclear what they even do with regard to disease.
Those are horizontally transferred viruses, the germline invasions are another issue entirely.
 
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46AND2

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Loudmouth mimicked what he read on a blog and never made a substantive argument. Non-orthologous simply means homology isn't an issue, his arguments were largely pedantic.

Orthologous viruses: Fit nested hierarchy
non-orthologous viruses: deviate from nested hierarchy

Orthologous viruses: passed down through inheritance
non-ortholgous viruses: separate invasion events

And 99+% percent of the data supports this, and it all supports common ancestry. Try to deal with it.
 
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46AND2

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Those are horizontally transferred viruses, the germline invasions are another issue entirely.

Why? If the virus inserts in the X or Y chromosome, it makes it more dangerous somehow?
 
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mark kennedy

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Orthologous viruses: Fit nested hierarchy
non-orthologous viruses: deviate from nested hierarchy

Orthologous viruses: passed down through inheritance
non-ortholgous viruses: separate invasion events

And 99+% percent of the data supports this, and it all supports common ancestry. Try to deal with it.
I have dealt with it and there isn't anything there but a criteria that is hopelessly biased. I've seen the evidence and it's anecdotal at best. You take a handful of mutations and make them into a homology argument which abandons all real evidence for or against.
 
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Why? If the virus inserts in the gametes, it makes it more dangerous somehow?
That's when they are the most vulnerable:

Given the hierarchical, step-wise logic or "architecture" of animal development, early stages such as cleavage and gastrulation lay the groundwork for all that follows. Body plan structures in the adult, for example, trace their cellular lineage to these early stages. Thus, if macroevolution is going to occur, it must begin in early development. Yet it is precisely here, in early development, that organisms are least tolerant of mutations. (Homology, a Concept in Crisis)​
 
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