200,000 ERVs...

[Loudmouth]

You have assumed that and never supported it with the actual evidence. You take your 200,000 orthologue statistic from the HGP that never compared them. It's absurd.

Wrong. I got the total number of human ERV's from the human genome paper. I got the number of human lineage specific ERV's from the chimp genome paper. Subtract the human specific ERV's from the total human ERV's and what you are left with is the number of orthologous ERV's shared between chimps and humans.

I have quoted, cited and linked the source material. The most abundant families of ERVs in the Chimpanzee Genome have rare ortholouges in the Human Genome and you know it.

It is irrelevant. How many orthologous ERV's are found in a comparison of the human and chimp genomes? Is it more or less than the number of PtERV's found in chimps?

Also, could you list the number of ERV families and the number of insertions that belong to each family?

I didn't say there weren't, just that your 200,000 ortholouge ERV thesis is false.

Why? Because chimps have 350 or so ERV's not found in humans? This allows you to ignore the other 200,000?

Let me ask you this, how many genes did they report in that paper? How many do they report now?

How is this relevant to the number of ERV's?

No it's not, particularly when the most abundant families are acquired independently.

What does the family group of the ERV have to do with this? The most abundant group of ERV's are orthologous ERV's when comparing the human and chimp genome. 98-99% of ERV's are orthologous between the two species.

You guys like to emphasize the similarities are such convincing evidence but never admit the inverse logic is intuitively obvious.

I agree with the inverse logic. Non-orthologous ERV's are most likely independently derived. So what? NEARLY ALL OF THE ERV'S SHOULD BE NON-ORTHOLOGOUS IF CHIMPS AND HUMANS DO NOT SHARE A COMMON ANCESTOR. Instead, 98-99% of ERV's are orthologous. Common ancestry is therefore evidenced.

Thanks LM, it was fun but I'm kind of busy right now. I have to move the family before I go back. Your in my prayers.

Grace and peace,
Mark

Your in my thoughts as well. I appreciate your service and wish you the best.

 

[Loudmouth]

You should read Jerry Bergman's "Darwinism and the Deterioration of the Genome", he shows that mutations, the needed mechanism for "new information" (Gitt approach, which is an actual relevant approach for Creation and Evolution) is fatally flawed.

http://www.trueorigin.org/mutations01.asp

How does Bergman explain humans and chimps sharing 200,000 orthologous ERV's?

 

[Loudmouth]

Is this for real? That's extremely dishonest of them if you ask me.
[/SIZE][/COLOR][/FONT]

The comparison of chimp and human ERV's was done in the chimp genome paper. I don't remember reading anything in the HGP paper about how many of the ~200,000 human ERV's were found in the chimp genome other than research that was already available (like the paper I discuss in post #3).

 

[Loudmouth]

Nice find MK.

What is nice about it? All it shows is that the human lineage was not infected by this virus after the chimp and human lineages split. I don't see how 350 non-orthologous ERV's in chimps makes the other 200,000 orthologous ERV's disappear.

It is evolution after all. You know, descent with modificiation? It is expected that each lineage will accrue their own ERV's after they split from the common ancestor.

 

[RichardT]

[post deleted]
http://www.trueorigin.org/virus.asp

 

[notto]

Unfalsifiable much?

The claim is a prediction of the theory of evolution that is supported by the evidence. The evidence could certainly have shown just the opposite of the conclusion.

Suggesting that this is an unfalsifiable conclusion is simply another unsupported claim of yours that is directly contradicted by the evidence in this very thread.

 

[Loudmouth]

That's not the point, the most abundant family of ERVs in the chimpanzee genome were independently acquired.

What point are you making?

You are making this sweeping generality that virtually all of the 200,000 ERVs are identical. That's absurd.

That's exactly what the chimp genome paper states. Only 100 or so human ERV's are specific to the human lineage.

Your begging the question of proof here. The HGP while a landmark publication is none the less outdated. As a matter of fact they simply identified the ERVs in the human genome. There was no comparison to chimpanzee ERVs until the Chimpanzee genome was sequenced.

And what did the comparison in the chimp genome paper state? That out of the 201,000 human ERV's, as established in the human genome paper, only 100 or so were human specific. This means that the number of orthologous ERV's is 201,000 - 100. Instead of calling this 200,900 I round back down to 200,000 because it's easier to type.

As to the chimp genome itself, you have the orthologous ERV's plus the chimp specific ERV's which is around 400. So the total number of chimp ERV's is about 201,300.

What is even more important you dodged the primary point. The most abundant family of ERVs is evidence of independent lineage.

What is your point? Nowhere did I argue you that chimps could not or did not acquire ERV's independently of humans. What I have argued is that these ERV's were acquired after each lineage split away from their common ancestor. Therefore, when comparing ERV's across primate species there should be a nested hierarchy produced by orthologous ERV's, and there is with very, very, very few exceptions (there are 2 ERV-K insertions between chimps, humans, and gorillas that violate the nested hierarchy. We can discuss those if you want).

Splitting hairs won't change that and TOE is littered with false positives. This is just one of them.

There are only 2 that I am aware of (see above).

I understand that 95% of the comparative sequences are the same. As time goes by and the research continues the profound differences are being revealed. I strongly disagree, in fact I have elaborated on this at length.

The chimp and human genome projects have sequenced >98% of each genome. I really don't expect any more surprises at the sequence level.

 

[notto]

Unrelated organisms with similar DNA would tend to get such viruses around the same locations.

Genetic Variability by Design
Gene Hi-Jacking - The Role of Genetic Transformation
Did God Make Pathogenic Viruses?

What evidence presented in these links supports your claim.

Please be specific and quote the appropriate material that specifically supports your claim that we would 'get' such viruses around the same locations.

 

[Atheuz]

Unfalsifiable much?

That's rich coming from a Creationist.

EDIT: Teehee, read it before you deleted the content of the post ...

 

[Loudmouth]

Unfalsifiable much?

No. Orthologous ERV's should fall into a nested hierarchy among all primates, and they do with very, very few exceptions. All primates have lineage specific ERV's.

If chimps and humans did not share common ancestry then they only reason that they should have orthologous ERV's is by pure chance. Even on the best day, I wouln't expect the same retrovirus to insert into the same spot more than once every 1,000 insertions. MK has kindly shown us that the most abundant family of ERV's has about 350 members meaning that it should be extremely rare for two species to share orthologous ERV's through independent insertions.

So what do we see? 98-99% of ERV's found in humans and chimps are found at the exact same spots in each genome.

Special Creation? Unfalsifiable much?

I don't really agree, because if viruses were designed as a DNA transfer system intended to aid adaptability, then this is to be somewhat expected.

It would also be expected if a trickster god created the world last Thursday complete with a false history of evolution.

Also, your explanation does not explain why you and your siblings, parents, and extended family also share these same ERV's.

Unrelated organisms with similar DNA would tend to get such viruses around the same locations.

No, they wouldn't. In the debate that Mark and I participated in I included a chart which mapped about 1,500 HIV insertions into an identical genome. Even when the DNA is exactly the same a retrovirus randomly inserts into thousands of different insertion sites.

Genetic Variability by Design
Gene Hi-Jacking - The Role of Genetic Transformation
Did God Make Pathogenic Viruses?

This doesn't explain why you and your extendend family also share hundreds of thousands of ERV's. I am guessing that you and your family were not magically poofed into existence by an invisible supernatural deity.

 

[Split Rock]

You guys like to emphasize the similarities are such convincing evidence but never admit the inverse logic is intuitively obvious.

What is logical about stressing the <5% sequence difference between chimps and humans and ignoring the >95% similarity?

 

[peteos]

"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 )

Nested Hierarchy
Nested Hierarchy
Nested Hierarchy

All that matters in the Nested Hierarchy of insertions at Orthogonal sites.

So someone help me out with the above. It would appear that it says that 40 of the 42 types have orthogonal sites in humans. It then gives a type CERV 2 and says it is present in "chimpanzee, bonobo, gorilla and old-world monkeys but absent in human, orangutan and new-world monkeys"

Okay, here is the big question, is it in orthogonal sites in all those creatures, (especially chimpanzees and old world monkeys)? If it is, would this not falsify common descent?

A finnally, to return to my OP, after we see LM and MK argue some more, we see they can't agree on the fact of the 200k orthogonal ERVs. So here is a question for Mark. If another study was conducted that demonstrated that LP measurement was correct, that humans and chimps share 200k ERVs at orthogonal sites, would you be convinced off common ancestry, or would it not matter to you?

 

[mark kennedy]

Nested Hierarchy
[/SIZE][/COLOR][/FONT]Nested Hierarchy
Nested Hierarchy

All that matters in the Nested Hierarchy of insertions at Orthogonal sites.

So someone help me out with the above. It would appear that it says that 40 of the 42 types have orthogonal sites in humans. It then gives a type CERV 2 and says it is present in "chimpanzee, bonobo, gorilla and old-world monkeys but absent in human, orangutan and new-world monkeys"

Okay, here is the big question, is it in orthogonal sites in all those creatures, (especially chimpanzees and old world monkeys)? If it is, would this not falsify common descent?

A finnally, to return to my OP, after we see LM and MK argue some more, we see they can't agree on the fact of the 200k orthogonal ERVs. So here is a question for Mark. If another study was conducted that demonstrated that LP measurement was correct, that humans and chimps share 200k ERVs at orthogonal sites, would you be convinced off common ancestry, or would it not matter to you?

Of course it would matter, he has just failed to produce it. It's pretty cut and dried, if you can't demonstrate your claims your wrong. His 200,000 figure is based on the Human Genome Projects initial sequence figures. I have already demonstrated that the most abundant families of ERVs in the Chimpanzee Genome do not have significant ortholouges.

My question to you is does that make any difference to you at all?

 

[mark kennedy]

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. ​

"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​

 

[peteos]

My question to you is does that make any difference to you at all?

That is not proof against common ancestry. Those are ERVs that are inserted after the split. Proof against common ancestry would be if inserted ERVs at orthogonal sites that broke the nested hierarchy derived by morphology, or by other genetic evidence such as mutations in psudogenes, etc.

So let me be very clear. If chimpanzees share ERVS at orthogonal sites with old world monkeys that are not found in humans or orangutan, that would be proof against common ancestry. And it would matter to me a great deal. That is why I HONESTLY asked it in my last post.

You predict that the ERVs that are orthogonal are somehow being inserted into the same location independently. So there should be no reason we wouldn't find the nested hierarchy broken, and the above scenario might be true. So I ask again, when you posted the above, was that what you thought it was saying?

And you didn't quite answer my question. You claim that LPs argument fails because his measurement is not true (200k ERVs at orthogonal sites). I will grant, that as a non-scientist and getting my information off a webboard, I can not verify if the claim is then true or not. That is why I honestly phased it as a hypothetical that another study was done, redoing the entire human and chimp genome, making all the necessary comparisons, and concluding what LP said was correct, that 200k ERVs have orthogonal locations, would this then be evidence for common ancestry, or do you not think it is evidence one way or another?

 

[mark kennedy]

That is not proof against common ancestry. Those are ERVs that are inserted after the split.

When do you think the split was?

The estimated ages of the two subfamilies are 5 MY and 7.8 MY (cited above)​

Proof against common ancestry would be if inserted ERVs at orthogonal sites that broke the nested hierarchy derived by morphology, or by other genetic evidence such as mutations in psudogenes, etc.

So is the inverse logic intuitively obvious or not?

So let me be very clear. If chimpanzees share ERVS at orthogonal sites with old world monkeys that are not found in humans or [/SIZE][/COLOR][/FONT]orangutan, that would be proof against common ancestry. And it would matter to me a great deal. That is why I HONESTLY asked it in my last post.

The most abundant families of ERVs don't have significant ortholouges. No matter how many times you deny it the facts will speak for themselves and LMs 200,000 orthological ERVs do not exist.

You predict that the ERVs that are orthogonal are somehow being inserted into the same location independently. So there should be no reason we wouldn't find the nested hierarchy broken, and the above scenario might be true. So I ask again, when you posted the above, was that what you thought it was saying?

It shows that the largest group of ERVs were not inherited from a common ancestor. The age of them indicates in entered their genomes well before or right around the split. The lack of ortholouges should be telling you something.

And you didn't quite answer my question. You claim that LPs argument fails because his measurement is not true (200k ERVs at orthogonal sites). I will grant, that as a non-scientist and getting my information off a webboard, I can not verify if the claim is then true or not. That is why I honestly phased it as a hypothetical that another study was done, redoing the entire human and chimp genome, making all the necessary comparisons, and concluding what LP said was correct, that 200k ERVs have orthogonal locations, would this then be evidence for common ancestry, or do you not think it is evidence one way or another?

I think it is yet another false positive that begs the question of proof on it's hands and knees. You have the facts, read the paper I quoted, cited and linked and come to an informed opinion. LM is wrong, there are not that many identical ERVs and he knows it. Believe what you like but the a priori assumption of a common ancestor is either falsified or unfalsifiable.

 

[Loudmouth]

Of course it would matter, he has just failed to produce it. It's pretty cut and dried, if you can't demonstrate your claims your wrong. His 200,000 figure is based on the Human Genome Projects initial sequence figures.

No, it is based on BOTH the chimp and human genome papers, for the thousandth time. I got the number of total human ERV's from the human genome paper and the total number of human SPECIFIC ERV's from the chimp genome paper. Subtract the human specific ERV's from the total ERV's and you get the number of orthologous ERV's. It's that simple. I have demonstrated it in spades.

Let me give you a few true or false questions so we can at least agree on a few things.

True or false, the human genome paper lists 201,000 ERV's spread over three classes.

True or false, the chimp genome lists about 100 human specific ERV's (mostly ERV-K) and about 400 chimp specific ERV's (mostly PtERV and some ERV-K).

Out of the PtERV insertions found in primates, how many have been shown to be orthologous at one base resolution?

I asked before and you totally dogded the question. How did they determine which ERV's were chimp and human specific in the chimp genome paper? I know how it's done, but you seem to run away from this question every time I ask. I'll give you a hint. It has nothing to do with which family the ERV is from. There are both orthologous and lineage specific ERV-K insertions.

I have already demonstrated that the most abundant families of ERVs in the Chimpanzee Genome do not have significant ortholouges.

Which is more abundant, non-orthologous or orthologous ERV's when comparing the human and chimp genome?

And what makes the PtERV the most significant family? Why not the ERV-W insertions?

My question to you is does that make any difference to you at all?

That 1% of chimp ERV's are not found in humans? Not when 99% are found at orthologous positions in the human genome.

 

[peteos]

When do you think the split was?

I don't know when the split was.

So is the inverse logic intuitively obvious or not?

WHAT?!?!

Mark, is the nested hierarchy broken or not? Do you know what an nested hierarchy is? Perhaps a yes or no answer. Can, lets say, all 2007 Ford models of cars and trucks be put into a nested hierarchy?

The most abundant families of ERVs don't have significant ortholouges. No matter how many times you deny it the facts will speak for themselves and LMs 200,000 orthological ERVs do not exist.

You continue to not answer the simple question. Your own source stated CERV 2 was present in "chimpanzee, bonobo, gorilla and old-world monkeys but absent in human, orangutan and new-world monkeys". However you would interpret this data, can you please answer this simple question, because for me, common descent is FALSIFIABLE and WOULD BE FALSIFIED if the following is true, are these CERV 2 present in ORTHOGONAL sites in chimpanzee and old world monkeys?

But, to return to your statement. You are saying the most abundant families of ERVs are non orthogonal. LP seems to differ. I don't know what a family refers to. I think what would matter would be individual virus insertions at different points in times. So are you saying that 95% of whatever your exact number was of viral insertions into our genome our non-orthogonal? If they are not breaking the nested hierarchy patter, it would not be the smoking gun I was looking for, but it would be HIGHLY suspicious and need some serious explaining.

It shows that the largest group of ERVs were not inherited from a common ancestor. The age of them indicates in entered their genomes well before or right around the split. The lack of ortholouges should be telling you something.

Strange, you admit it is possible from estimated age that it happened right after the split. So why would that be falsifying common descent? But I agree with you, if the vast majority of viral insertions into chimpanzee and human genomes are not in orthogonal sites, that is indeed telling us something. I will await to see you explain what a "family" of ERVs are or let LP or others dispute your claim.

I think it is yet another false positive

Don't know what you mean. Do you mean it would be a HUGE coincidence? Listen I know you dispute the 200k ERV deal. I know you think you have a paper that disputes it, LP seems to disagree. But what I am saying is, pretend that it was shown to be true for a moment, is it or is it not evidence for common descent, !!IF!! it is true (notice the IF).

 

[RichardT]

LMs 200,000 orthological ERVs do not exist.

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?

 

[peteos]

After reading LP's response, I think are argueing from two different angles.

LP claims 1% of chimp ERVs are not found in humans. 99% of them are found and in orthogonal sites.

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

Perhaps they are both right, maybe the majority of families are in that 1%. What matters to me is actual viral insertions. Perhaps a one or two families make up almost all of the insertions and hence why 99% can be orthogonal while the majority of families are not?

So what is a family? How does it relate to actual viral insertions in a moment in history. And Mark, do you agree at all that 99% of chimp ERVs are found in humans in orthogonal sites. Not percentage of families, but percentage of total ERVs? Or is this also disputed?