A question of ERVs

[mark kennedy]

Sure. The BAC method they used only had a resolution down to 100,000 base pairs. The odds that one of those ERVs actually being orthologous, then, is 1 in 100,000. The odds that 2 of them would be orthologous is 1 in 100,000 X 100,000. For all 12, 1 in 100,000 to the 12th power, or 1 in 1,(60 zeroes).

The differences in the genomes of Chimpanzees and humans diverge by 7% based on the differences in the ERVs alone. Ptervs make up a substantial part of the Chimpanzee genome

(Initial Sequence of the Chimpanzee Genome. Nature 2005)

With more than 100 members, CERV 1/PTERV1 is one of the most abundant families of endogenous retroviruses in the chimpanzee genome. (Genome Biol. 2006).

It seems strange that this has transposed itself into a probability argument, considering they mark dramatic differences more then things in common.

 

[46AND2]

The differences in the genomes of Chimpanzees and humans diverge by 7% based on the differences in the ERVs alone. Ptervs make up a substantial part of the Chimpanzee genome

(Initial Sequence of the Chimpanzee Genome. Nature 2005)

With more than 100 members, CERV 1/PTERV1 is one of the most abundant families of endogenous retroviruses in the chimpanzee genome. (Genome Biol. 2006).

It seems strange that this has transposed itself into a probability argument, considering they mark dramatic differences more then things in common.

This has been responded to ad nauseam in other threads. Not going to help you now any more than it did then.

The pattern. Explain the pattern.

 

[In situ]

“Have we actually found and analyzed the genetic material of actual endogenous retro viruses that reflect our ERVs?”

Yes. And they have been carefully documented. E.g. one research team in The Netherlands, and they was heavily crisicized for it, even brought an EVR back to life again. Why do you wonder?

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).

ERV's are per definition insertion of viral DNA into a host genome. If a virus cannot insert its DNA into a host genome it cannot become an ERV. It is, per definition, how retroviruses operates. If you understand this, then I do not see what the problem is with identifying an ERV in a host genome?

intelligently design a complete viral genome

In my opinion the epithet "viral genome" is a misnomer since a virus is not per se an organism, i.e a living thing, but just a collection of big macro molecules interacting in a highly complex way with living things.

 

[xianghua]

ERV's are per definition insertion of viral DNA into a host genome..

how do you know that the opposite isnt true? (that a retrovirus was created from the host genome).

 

[xianghua]

Sure. The BAC method they used only had a resolution down to 100,000 base pairs. The odds that one of those ERVs actually being orthologous, then, is 1 in 100,000. The odds that 2 of them would be orthologous is 1 in 100,000 X 100,000. For all 12, 1 in 100,000 to the 12th power, or 1 in 1,(60 zeroes).

actually its not. this is why they proposed another explanation like several deletions. if this calculation was true then they would not offered such a scenario at all. this is why evolution will not be false even if we will find several ervs that dont fit with the phylogeny.

 

[46AND2]

actually its not. this is why they proposed another explanation like several deletions. if this calculation was true then they would not offered such a scenario at all. this is why evolution will not be false even if we will find several ervs that dont fit with the phylogeny.

What are you talking about? You clearly don't understand what I'm calculating. The paper did not even address what I calculated. I simply used their data to make another point.

If you aren't going to offer an explanation for the nested hierarchical pattern of ERVs we observe, please don't bother replying at all.

 

[46AND2]

We observe:

1. Tens of thousands of orthologous ERVS which form a nested hierarchical pattern shared between the 4 species.

2. And hundreds of shared non-orthologous ERVs which deviate from the pattern.

Both are consistent with, and explained by, the theory of common descent.

My question to creationists: how do YOU explain these observations in such a way that it makes more sense that common ancestry isn't true?

 

[xianghua]

What are you talking about? You clearly don't understand what I'm calculating. The paper did not even address what I calculated. I simply used their data to make another point.

If you aren't going to offer an explanation for the nested hierarchical pattern of ERVs we observe, please don't bother replying at all.

what are you talking about? if your calculation was true then why they offered a scenario of several deletions? this is because they arent sure if these ervs are indeed orthologous. so basically they have no problem if these ervs are indeed orthologous.

 

[46AND2]

what are you talking about? if your calculation was true then why they offered a scenario of several deletions? this is because they arent sure if these ervs are indeed orthologous. so basically they have no problem if these ervs are indeed orthologous.

If that's what you got from what they said, you didn't understand the paper.

So, still no explanation for the pattern we observe?

 

[xianghua]

If that's what you got from what they said, you didn't understand the paper.

you said that it will be almost impossible for these ervs to be orthologous. and yet the paper said that its possible that these ervs are indeed orthologous. so the paper clearly doesnt fit with your calculation.

So, still no explanation for the pattern we observe?

explanation for what? nested hierarchy? we can find it also in designed objects:

so what is your point actually?

 

[46AND2]

you said that it will be almost impossible for these ervs to be orthologous. and yet the paper said that its possible that these ervs are indeed orthologous. so the paper clearly doesnt fit with your calculation.

The whole point of the paper was to demonstrate that it is highly unlikely that any of those PtERVs were orthologous.

So the paper clearly doesn't fit your optimism.

explanation for what? nested hierarchy? we can find it also in designed objects:

View attachment 247886
so what is your point actually?

I've made my point abundantly clear. If you are confused about what I'm asking, I suggest you go back and re-read the thread. Please do so before you respond again.

 

[xianghua]

I've made my point abundantly clear. If you are confused about what I'm asking, I suggest you go back and re-read the thread. Please do so before you respond again.

you said that nested hierarchy of ervs can only be explain by common descent. right? you also predicted that we will not find ervs that dont fit with the species phylogeny. right?

 

[USincognito]

explanation for what? nested hierarchy? we can find it also in designed objects:

View attachment 247886
so what is your point actually?

Not all trucks are bigger in size or have more wheels than vans. A Ford Econoline van is larger than a Ford Ranger or Mazda B-2000. Also the Econoline shared a lot of swapped parts with the F-series pickups.
Ford F-Series - Wikipedia
>> For much of its production life, the Ford E-Series vans shared a high degree of mechanical commonality with the F-Series; in the late 1970s, some body components were shared. <<
Further the very large Ford Super Duty trucks don't have more wheels than vans.

It gets even worse the VW models from the 1980s which I have pointed out repeatedly XH dishonestly keeps ignoring. The Golf hatchback, Scirocco sport coupe and Jetta sedan shared a front end and wheels with the Caddy pickup truck.

All of these things shatter his supposed nested hierarchy.

 

[46AND2]

you said that nested hierarchy of ervs can only be explain by common descent. right?

No. I said that common ancestry explains the pattern well. I challenged you all to come up with a better explanation.

you also predicted that we will not find ervs that dont fit with the species phylogeny. right?

No. There are a couple ways we might find a few at most that contradict the pattern, including sheer dumb luck. What we shouldn't see, however, is a significant percentage of deviation. Indeed, only ONE known example of our 203,000+ ERVs doesn't fit the pattern. I'm asking you to explain the 99.99+% of the hundreds of thousands that do result in the nested hierarchy.

 

[USincognito]

The differences in the genomes of Chimpanzees and humans diverge by 7% based on the differences in the ERVs alone. Ptervs make up a substantial part of the Chimpanzee genome

(Initial Sequence of the Chimpanzee Genome. Nature 2005)

With more than 100 members, CERV 1/PTERV1 is one of the most abundant families of endogenous retroviruses in the chimpanzee genome. (Genome Biol. 2006).

It seems strange that this has transposed itself into a probability argument, considering they mark dramatic differences more then things in common.

Mark has been corrected on this a dozen times over the last at least 5 years. This above table is for lineage specific ERVs. Again, lineage specific ERVs. That means those ERVs found in chimpanzees, but not humans and in humans, but no chimpanzees. During the combined 12 million years of evolution the number of retroviruses both lines have endogenized is 361.

I made this graphic from the Table 11 in the human genome paper, but he still doesn't seem to get it. Again, these are shared elements and in the case of ERVs humans and chimpanzees share 203,000 of them.

203,000 shared
361 lineage specific

 

[mark kennedy]

Mark has been corrected on this a dozen times over the last at least 5 years. This above table is for lineage specific ERVs. Again, lineage specific ERVs. That means those ERVs found in chimpanzees, but not humans and in humans, but no chimpanzees. During the combined 12 million years of evolution the number of retroviruses both lines have endogenized is 361.

I made this graphic from the Table 11 in the human genome paper, but he still doesn't seem to get it. Again, these are shared elements and in the case of ERVs humans and chimpanzees share 203,000 of them.

203,000 shared
361 lineage specific

View attachment 247904

I've been corrected endlessly and you guys never get your facts straight. This was the first entire sequence of the human genome, it simply listed human ERVs, there would be nothing comprehensive regarding a comparison of them until 2005. By 2006 42 families of ERVs were identified, 40 of which had orthologues in the human genome and never are the ERVs described as identical, 2 had no orthologues in the human genome.

With more than 100 members, CERV 1/PTERV1 is one of the most abundant families of endogenous retroviruses in the chimpanzee genome…Consistent with our findings, the results of a previously published Southern hybridization survey indicated that sequences orthologous to CERV 1/PTERV1 elements are present in the African great apes and old world monkeys but not in Asian apes or humans . These results suggest that some members of the CERV 1/PTERV1 subfamily entered the chimpanzee…

…It has been estimated that 3.5% of the sequence differences between chimpanzees and humans is due to INDELs and that this INDEL variation may be of particular evolutionary significance. We have determined that approximately 7% of all chimpanzee-human INDEL variation is attributable to the presence or absence of endogenous retroviral sequences. (Identification, characterization and comparative genomics of chimpanzee endogenous retroviruses. Genome Biol. 2006)
​

The CERV1/PTERV1 is one of the most abundant ERVs in the human genome and does not exist in the human genome. 3.5% of the differences are due to INDELS and 7% of the entire divergence due to INDELS. You call this an argument for common ancestry? ERV class 1 elements simply do not exist in the human genome and compare them to the class II and III elements:

Initial sequence of the chimpanzee genome and comparison with the human genome
Table 2
​

In case you missed it that 234 in the Chimpanzee genome and 5 in the human genome. The class I elements are the PtERV1 and PtERV2 elements making this far and away the worst homology argument I've ever seen.

 

[46AND2]

I've been corrected endlessly and you guys never get your facts straight. This was the first entire sequence of the human genome, it simply listed human ERVs, there would be nothing comprehensive regarding a comparison of them until 2005. By 2006 42 families of ERVs were identified, 40 of which had orthologues in the human genome and never are the ERVs described as identical, 2 had no orthologues in the human genome.

With more than 100 members, CERV 1/PTERV1 is one of the most abundant families of endogenous retroviruses in the chimpanzee genome…Consistent with our findings, the results of a previously published Southern hybridization survey indicated that sequences orthologous to CERV 1/PTERV1 elements are present in the African great apes and old world monkeys but not in Asian apes or humans . These results suggest that some members of the CERV 1/PTERV1 subfamily entered the chimpanzee…

…It has been estimated that 3.5% of the sequence differences between chimpanzees and humans is due to INDELs and that this INDEL variation may be of particular evolutionary significance. We have determined that approximately 7% of all chimpanzee-human INDEL variation is attributable to the presence or absence of endogenous retroviral sequences. (Identification, characterization and comparative genomics of chimpanzee endogenous retroviruses. Genome Biol. 2006)
​

The CERV1/PTERV1 is one of the most abundant ERVs in the human genome and does not exist in the human genome. 3.5% of the differences are due to INDELS and 7% of the entire divergence due to INDELS. You call this an argument for common ancestry? ERV class 1 elements simply do not exist in the human genome and compare them to the class II and III elements:

Initial sequence of the chimpanzee genome and comparison with the human genome
Table 2
​

In case you missed it that 234 in the Chimpanzee genome and 5 in the human genome. The class I elements are the PtERV1 and PtERV2 elements making this far and away the worst homology argument I've ever seen.

Why is this a problem, Mark? There would have been separate endogenization events in the 7 million years since the lineages diverged.

 

[mark kennedy]

Why is this a problem, Mark? There would have been separate endogenization events in the 7 million years since the lineages diverged.

It's the nature of the argument that drives me up the wall. The most abundant families of ERVs aren't even in the human genome, what kind of an argument is that? Then there is the fact that these are transposable elements, highly vulnerable to mutations till there are very few in the human genome that actually function. What's more do you know where evolution was with the hominid line 7 mya because the actual hominids don't actually appear in the fossil record until 2 mya.

What's the problem? There's no argument here, that's the problem. What's truly amazing here is that there is a premise that cannot be proven, namely that 8% of the human genome is the result of germline invasions.

Retroelements and the human genome: New perspectives on an old relation

Just over 8% actually, they can't tell you how the human brain nearly tripled in size over night but can elaborate endlessly on some convoluted germline invasions no one even bothers to qualify. That's the problem.

 

[pitabread]

explanation for what? nested hierarchy? we can find it also in designed objects:

This is a lie and you know it. I tested your idea and debunked it ages ago.

 

[USincognito]

I've been corrected endlessly and you guys never get your facts straight. This was the first entire sequence of the human genome, it simply listed human ERVs, there would be nothing comprehensive regarding a comparison of them until 2005.

This is why it's so hard to have a discussion, much less a debate with Mark. Much like Kent Hovind he adopted a script years ago and being immune to correction he sticks to it and repeats it ad nauseum rather than trying to understand why his script is wrong.

So, yes. The EVRs sequenced for the human genome do, axiomatically, represent those found in the human genome. Let's move forward to 2005 and the start of Mark's decade long problem. Everyone remembers what the full title of the chimpanzee genome paper was, right?

Initial sequence of the chimpanzee genome and comparison with the human genome

for Again for emphasis because that really seems to be an issue here - and comparison with the human genome. Comparison. With the human genome. What were the results of the comparison with the human genome?
{snip Table 2}
The results were that we shared the 203,000 ERVs, that the HGP had found because when the comparison took place, only the 361 lineage specific.

Again, because this really seems to be a problem. Table 2 ONLY LISTS LINEAGE SPECIFIC ERVs. The clue to that should be in the headings "chimpanzee lineage" and "human lineage". So when there was a comparison of the two genomes, the human genome was found share 203,000 ERVs with chimpanzee genome and the chimpanzee genome was found to share those same 203,000 ERVs with the only differences being 279 that were only found in the chimpazee lineage and 83 that were only found in the human lineage.

...making this far and away the worst homology argument I've ever seen.

I would suggest we could discuss your years long confusion over nested hierarchies vs. homologies after we finally clear up this simple math problem you can't seem to wrap your head around, but as I've noted, at some point it's an exercise in futility.