200,000 ERVs...

peteos · Sep 28, 2007

Now, I don't usually trust evolutionists when they make assertions, I am wondering who is right on this issue and why? If it were true that we shared 200,000 ERVs at the same locations, I would have to accept it, but is it not true? Can either MK or LM demonstrate what is reality here?

That was the original intention of my OP! And we are four pages in and still haven't solved it.

Valkhorn · Sep 28, 2007

If a Molecular Biologist themselves came in here with mounds of more evidence for Evolution, Mark would still argue with them.

In fact, he already has before.

Split Rock · Sep 28, 2007

mark kennedy said:
For the third and final time, get the facts straight. These are the facts and stop wasting time with these pointless, outdated Talk Origins arguments that simply don't square with the facts:

A total of 95.8% of these sites were non-orthologous when compared between species. [/CENTER]

"We report here that the chimpanzee genome contains at least 42 separate families of endogenous retroviruses, nine of which were not previously identified. All but two (CERV 1/PTERV1 and CERV 2) of the 42 families of chimpanzee endogenous retroviruses were found to have orthologs in humans. Molecular analysis (PCR and Southern hybridization) of CERV 2 elements demonstrates that this family is present in chimpanzee, bonobo, gorilla and old-world monkeys but absent in human, orangutan and new-world monkeys. A survey of endogenous retroviral positional variation between chimpanzees and humans determined that approximately 7% of all chimpanzee-human INDEL variation is associated with endogenous retroviral sequences." (Identification, characterization and comparative genomics of chimpanzee endogenous retroviruses, Genome Biol. 2006 )

The most abundant family of ERVs in the Chimpanzee do not have ortholouges 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. CERV 1/PTERV1 elements range in size from 5 to 8.8 kb in length, are bordered by inverted terminal repeats (TG and CA) and are characterized by 4 bp TSDs...Phylogenetic analysis of the LTRs from full-length elements of CERV 1/PTERV1 members indicated that this family of LTRs can be grouped into at least two subfamilies (bootstrap value of 99; Figure 3). The age of each subfamily was estimated by calculating the average of the pairwise distances between all sequences in a given subfamily. The estimated ages of the two subfamilies are 5 MY and 7.8 MY, respectively, suggesting that at least one subfamily was present in the lineage prior to the time chimpanzees and humans diverged from a common ancestor (about 6 MYA). This conclusion, however, is inconsistent with the fact that no CERV 1/PTERV1 orthologues were detected in the sequenced human genome. (Identification, characterization and comparative genomics of chimpanzee endogenous retroviruses) Bolded mine

Nice job of cherry-picking from the paper, Mark.

A few little points you neglected to emphasize from the paper:

1. "We report here that the chimpanzee genome contains at least 42 separate families of endogenous retroviruses, nine of which were not previously identified. All but two (CERV 1/PTERV1 and CERV 2) of the 42 families of chimpanzee endogenous retroviruses were found to have orthologs in humans." -- this from your own quote! How do you explain the other 40 families?

2. Here is the rest of the paragraph you neglected to quote with your cherry-picking:

"This conclusion, however, is inconsistent with the fact that no CERV 1/PTERV1 orthologues were detected in the sequenced human genome. Moreover, we were able to detect pre-integration sites at those regions in the human genome orthologous to the CERV 1/PTERV1 insertion sites in chimpanzees, effectively eliminating the possibility that the elements were once present in humans but subsequently excised. 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 [30]. These results suggest that some members of the CERV 1/PTERV1 subfamily entered the chimpanzee genome after the split from humans through exogenous infections from closely related species and subsequently increased in copy number by retrotransposition. The unexpectedly high level of LTR-LTR divergence could be due to variation accumulated during the viral transfer [31] or possibly due to an inter-element recombination or conversion event subsequent to integration. "

You ignored the explanation the authors offered as to why these sequences are present in chimpanzees but not humans.

It is typical of Creationists to pick at the few exceptions, and ignore the preponderance of the evidence, which continues to point to common descent.

Loudmouth · Sep 28, 2007

RichardT said:
Now, I don't usually trust evolutionists when they make assertions, I am wondering who is right on this issue and why? If it were true that we shared 200,000 ERVs at the same locations, I would have to accept it, but is it not true? Can either MK or LM demonstrate what is reality here?
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You can find the human genome paper here and the chimp genome paper here. Click on the Nature hyperlink to find the full paper. They are both multi-megabyte .pdf files so be prepared.

Table 11 on pg 880 of the human genome paper lists a total of 201,000 ERV's spread between three classes (don't forget that there is a x1,000 multiplier in the column heading). Table 2 in the chimp genome paper looks like this:

Of the 201,000 human ERV's only 82 are human specific, meaning only 82 are non-orthologous. That means the remaining 200,000 or so human ERV's are found at orthologous positions in the chimp genome. I can't see why Mark denies these figures.

Therefore, there are 200,000 ERV's in chimps from the common ancestor of chimps and humans plus the 279 chimp specific ERV's.

I'll try to get a screen capture of Table 11 if it is still in doubt.

peteos · Sep 28, 2007

These results suggest that some members of the CERV 1/PTERV1 subfamily entered the chimpanzee genome after the split from humans through exogenous infections from closely related species and subsequently increased in copy number by retrotransposition. The unexpectedly high level of LTR-LTR divergence could be due to variation accumulated during the viral transfer [31] or possibly due to an inter-element recombination or conversion event subsequent to integration. "

This is worse then Hebrew. Split Rock, maybe you can answer my question. Apparently, there are families of ERVs present in Old World monkeys and Chimpanzees that are not in humans and orangatans. So, ARE THEY IN ORTHOGONAL positions in old world monkeys and chimpanzees?

RichardT · Sep 28, 2007

These results suggest that some members of the CERV 1/PTERV1 subfamily entered the chimpanzee genome after the split from humans through exogenous infections from closely related species and subsequently increased in copy number by retrotransposition.

MK didn't ignore it. We are well aware that evolutionists will say that any ERVs that are not orthologous must have come from after the supposed split.

Loudmouth · Sep 28, 2007

peteos said:
MK claims that the vast majority of "familes" are not found in humans.

Not even that. He is arguing, correctly, that the ERV family with the most members is not found in humans (PtERV's). This is irrelevant to the question of common ancestry. What is relevant is the pattern of orthology between ERV's, not the distribution of ERV families among primates.

Not only that, but of the 42 families of ERV's found in chimps, 40 can be found in humans.

So what is a family?

Hopefully this doesn't confuse things even more. An ERV family is a group of retroviruses that share a more recent common ancestor than they do to other retroviruses. Families are also organized by tRNA binding sites and other features. It's kind of a mixed bag, to tell you the truth.

How does it relate to actual viral insertions in a moment in history.

Viruses mutate faster than their hosts. By studying the change in a virus family over time one can deduce how the virus evolved.

RichardT · Sep 28, 2007

You can find the human genome paper here and the chimp genome paper here.

I don't even know how to navigate this... Is it free? Doesn't seem like I can read it without some kind of subscription.

Loudmouth · Sep 28, 2007

RichardT said:
MK didn't ignore it. We are well aware that evolutionists will say that any ERVs that are not orthologous must have come from after the supposed split.

The actual numbers.

Loudmouth · Sep 28, 2007

RichardT said:
I don't even know how to navigate this... Is it free? Doesn't seem like I can read it without some kind of subscription.

Here is the .pdf file for the human genome paper. Look at table 11 on pg. 880.

Here is the .pdf file for the chimp genome paper. I have a copy of Table 2 in a previous post.

You will need an Adobe Acrobat reader to view the files.

peteos · Sep 28, 2007

MK didn't ignore it. We are well aware that evolutionists will say that any ERVs that are not orthologous must have come from after the supposed split.

Is it your understanding for common descent to be true, all ERVs must be orthologous? Is there some reason, in your understanding, that ERVs can't be added after the split if common descent it true?

mark kennedy · Sep 28, 2007

Again you guys ignored the fact that the most abundant families don't have significant ortholouges in the human genome. You won't acknowledge this and LM just keeps talking in circles about 200,000 orthologues that don't exist.

First of all it's 8% and you should have acknowledged that by now LM:

he human genome is littered by endogenous retrovirus sequences (HERVs), which constitute up to 8% of the total genomic sequence. (Divergent Patterns of Recent Retroviral Integrations in the Human and Chimpanzee Genomes: Probable Transmissions between Other Primates and Chimpanzees. Patric Jern, Göran O. Sperber, and Jonas Blomberg1 Journal of Virology February 2006)

For another thing this is typical of evolutionist arguments. You guys skew the facts and pretend it's proof.

With more than 100 members, CERV 1/PTERV1 is one of the most abundant families of endogenous retroviruses in the chimpanzee genome. CERV 1/PTERV1 elements range in size from 5 to 8.8 kb in length, are bordered by inverted terminal repeats (TG and CA) and are characterized by 4 bp TSDs...Phylogenetic analysis of the LTRs from full-length elements of CERV 1/PTERV1 members indicated that this family of LTRs can be grouped into at least two subfamilies (bootstrap value of 99; Figure 3). The age of each subfamily was estimated by calculating the average of the pairwise distances between all sequences in a given subfamily. The estimated ages of the two subfamilies are 5 MY and 7.8 MY, respectively, suggesting that at least one subfamily was present in the lineage prior to the time chimpanzees and humans diverged from a common ancestor (about 6 MYA). This conclusion, however, is inconsistent with the fact that no CERV 1/PTERV1 orthologues were detected in the sequenced human genome. (Identification, characterization and comparative genomics of chimpanzee endogenous retroviruses)

The ERVs are proof of the lengths to which evolutionists will go to to promote their secular agenda. It doesn't matter whether or not it's true, as long as it promotes this humanistic philosophy.

gamespotter10 · Sep 28, 2007

wait, exactly how many orthologus ERVs do humans and chimps share?

notto · Sep 28, 2007

peteos said:
I will await to see you explain what a "family" of ERVs are or let LP or others dispute your claim.

That is all a distraction from the argument. That is the only tactic Mark has left in this one. The more he avoids answering your questions the more you should realize that he has something to hide.

He is basically saying 'Look! Over There!' to try to distract people from the clear evidence that leads to the conclusion of common descent. Mark cannot explain this evidence so he needs to distract you to evidence he thinks he can explain.

Go ahead, ask him again. You'll get a repeat of his same information and you will be no closer to him explaining the data that leads to the conclusion of common descent and he will start to spout off about conspiracy and nonsense instead of addressing the evidence in an intellectually honest and direct way.

That is his MO.

Loudmouth · Sep 28, 2007

gamespotter10 said:
wait, exactly how many orthologus ERVs do humans and chimps share?

Right around 200,000.

peteos · Sep 28, 2007

Before you restate you facts again, which I will discuss in a moment, could you PLEASE answer this question. I don't care what you would think the fact would suggest. I don't care if it is evidence that God created us in 6 days, 6 months, over 1 billion years, or if aliens created us in 6 days or last Thursday. All I want to know, to the best of your knowledge, are the CERV 2 that are found in old world monkeys and chimpanzees but not in humans or orangutans found at orthogonal sites?

Acceptable answers would be
1) yes
2) no
3) I don't know.

There is no shame in the last answer. I know pretty much nothing about molecular genetics, which is why I am asking the question in the first place. It is not a trick question. I do not know what the answer is.

Here is the second question. And once again, I don't care for an interpretation on what it means. You keep asserting that the most abundant families are not shared. LP defines families as viruses with recent common ancestors. That does not however, tell us how many there are of each family in our actual genome. LP does make the assertion. This is LP assertion.

1) Of all the ERVs in the human genome, 99% are shared with chimpanzees are orthogonal sites. The remaining 1% are not shared at orthogonal sites.

Without any reference to families, in other words, how you wish to group seperate ERVs together, could you please assert that this fact is either

1) true. 99% of ERVs in humans are found in orthogonal locations in chimps.
2) false. It is not 99%. It is a) 98%, b)50% c) < X
3) I don't know the answer.

Once again, no shame in the last one if that is the truth.

RichardT · Sep 28, 2007

Here is the .pdf file for the human genome paper. Look at table 11 on pg. 880.

peteos · Sep 28, 2007

All I want to know, to the best of your knowledge, are the CERV 2 that are found in old world monkeys and chimpanzees but not in humans or orangutans found at orthogonal sites?

BTW, anyone can answer this question. I really wish to know the answer. I only ask Mark because he is the one who posted the original source, and I wanted him to clarify.

Loudmouth · Sep 28, 2007

mark kennedy said:
Again you guys ignored the fact that the most abundant families don't have significant ortholouges in the human genome. You won't acknowledge this . . .

I have acknowledged it. It is in Table 2 of the chimp genome paper. Now, how many ERV's do humans have? Of those, how many are human specific? How did the authors of the chimp genome paper determine which ERV's are specific to each lineage?

and LM just keeps talking in circles about 200,000 orthologues that don't exist.

Do you reject both the human and chimp genome papers?

First of all it's 8% and you should have acknowledged that by now LM:

8% of the human genome is made up of retroviral associate seqeuences, but not all of that 8% are ERV's. That 8% is made up of solo LTR's, ERV's, and MaLR's (mammalian assocated LTR retrotransposons). ERV's comprise 4.5% of the human genome and about another 4% is made up of solo LTR's and MaLR's. Is this correct Mark? (reference table 11 in the human genome paper)

Solo LTR's and MaLR's are not ERV's, but all three are retrovirus related.

he human genome is littered by endogenous retrovirus sequences (HERVs), which constitute up to 8% of the total genomic sequence. (Divergent Patterns of Recent Retroviral Integrations in the Human and Chimpanzee Genomes: Probable Transmissions between Other Primates and Chimpanzees. Patric Jern, Göran O. Sperber, and Jonas Blomberg1 Journal of Virology February 2006)

They obviously, and incorrectly, lump ERV's in with LTR's and MaLR's.

For another thing this is typical of evolutionist arguments. You guys skew the facts and pretend it's proof.

So how many human ERV's are there and how many are found in orthologous positions in the chimp genome?

With more than 100 members, CERV 1/PTERV1 is one of the most abundant families of endogenous retroviruses in the chimpanzee genome. CERV 1/PTERV1 elements range in size from 5 to 8.8 kb in length, are bordered by inverted terminal repeats (TG and CA) and are characterized by 4 bp TSDs...Phylogenetic analysis of the LTRs from full-length elements of CERV 1/PTERV1 members indicated that this family of LTRs can be grouped into at least two subfamilies (bootstrap value of 99; Figure 3). The age of each subfamily was estimated by calculating the average of the pairwise distances between all sequences in a given subfamily. The estimated ages of the two subfamilies are 5 MY and 7.8 MY, respectively, suggesting that at least one subfamily was present in the lineage prior to the time chimpanzees and humans diverged from a common ancestor (about 6 MYA). This conclusion, however, is inconsistent with the fact that no CERV 1/PTERV1 orthologues were detected in the sequenced human genome. (Identification, characterization and comparative genomics of chimpanzee endogenous retroviruses)

And their explanation was

These results suggest that some members of the CERV 1/PTERV1 subfamily entered the chimpanzee genome after the split from humans through exogenous infections from closely related species and subsequently increased in copy number by retrotransposition. The unexpectedly high level of LTR-LTR divergence could be due to variation accumulated during the viral transfer [31] or possibly due to an inter-element recombination or conversion event subsequent to integration.

Also, there are no uambiguously orthologous ERV's that break the nested hierarchy. We have gone over this before. It's in our debate.

The ERVs are proof of the lengths to which evolutionists will go to to promote their secular agenda. It doesn't matter whether or not it's true, as long as it promotes this humanistic philosophy.

And the conspiracy theory is complete.

Loudmouth · Sep 28, 2007

Captured a print screen for table 11 from the human genome paper. It is attached below.

My memory was a little off. Solo LTR's are not listed separately, but ERV's still make up about 4.5% of the human genome and there are 203,000 of them. The first column lists the number of copies (x 1,000).

200,000 ERVs...

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