200,000 ERVs...

[RichardT]

[post deleted]

 

[Loudmouth]

Just for fun, we could also look at the Alu retrotransposon elements. Out of the 1.09 million Alu insertions found in the human genome only 7,082 are not found in the chimps. This means that 99.4% of Alu retransposon insertins are orthologous

Out of the 516,000 LINE-1 human insertions only 1,814 are not found in chimps, or 99.6% orthology.

The more I look at those tables the worse it gets for Mark.

 

[gamespotter10]

Right around 200,000.

so, there are 200,000 ERVs which are located in both chimps and humans at the same place in the genome?

what about gibbons, orangutans, gorillas, old world monkeys and new world monkeys?

 

[Blayz]

so, there are 200,000 ERVs which are located in both chimps and humans at the same place in the genome?

what about gibbons, orangutans, gorillas, old world monkeys and new world monkeys?

Umm..like...any chance you could wait until we have sequenced those genomes?

 

[Loudmouth]

what about gibbons, orangutans, gorillas, old world monkeys and new world monkeys?

The macaque genome was recently finished. I may have to take a look it in the near future.

Most studies have focused on just a few ERV's here and there, so it's almost impossible to get a feel for the total ERV pools for each primate group.

 

[Pete Harcoff]

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.

Not to get involved in the ERV debate itself, but I find comments like this to be completely bizarre. I've been posting stuff about the use of evolution in modern applied biology for, oh, going on a couple years now. This notion that this is all promoted as part of a conspiracy makes absolutely no sense in light of industry application. For example, is using evolutionary biology as part of AIDS medical research also a part of this so-called "agenda"?

I guess I understand that the only way to explain the acceptance of evolutionary biology make be to invoke some sort of conspiracy, but again, in light of biology-related industries, it makes zero sense.

 

[mark kennedy]

Not to get involved in the ERV debate itself, but I find comments like this to be completely bizarre. I've been posting stuff about the use of evolution in modern applied biology for, oh, going on a couple years now. This notion that this is all promoted as part of a conspiracy makes absolutely no sense in light of industry application. For example, is using evolutionary biology as part of AIDS medical research also a part of this so-called "agenda"?

I guess I understand that the only way to explain the acceptance of evolutionary biology make be to invoke some sort of conspiracy, but again, in light of biology-related industries, it makes zero sense.

It's been a while Pete but you have not changed a bit. This isn't about biology, it's not about genetics, it's not about molecular biology either...heck this isn't even about TOE. This is about religion and the Bible as an historical reference.

There is a big difference between natural science and natural history and I think we do well to recognize it.

 

[mark kennedy]

Just for fun, we could also look at the Alu retrotransposon elements. Out of the 1.09 million Alu insertions found in the human genome only 7,082 are not found in the chimps. This means that 99.4% of Alu retransposon insertins are orthologous

Out of the 516,000 LINE-1 human insertions only 1,814 are not found in chimps, or 99.6% orthology.

The more I look at those tables the worse it gets for Mark.

Funny, you were not interested in tables in our debate, and now you mention one at random. Now I'm interested, cite you source.

 

[Pete Harcoff]

It's been a while Pete but you have not changed a bit. This isn't about biology, it's not about genetics, it's not about molecular biology either...heck this isn't even about TOE. This is about religion and the Bible as an historical reference.

There is a big difference between natural science and natural history and I think we do well to recognize it.

But common descent is part of that applied science. And yes, this includes chimp/human common ancestry.

I know the debate is all about religion, simply because no one else attacks other sciences with the same fervor. I just don't know what those who attack evolutionary biology even expect to accomplish.

You're welcome to whatever religious beliefs you want. But evolutionary biology, especially given it's usefulness in a variety of fields (including common descent), isn't going away. It's not because of conspiracy. It's because of usefulness.

 

[mark kennedy]

But common descent is part of that applied science. And yes, this includes chimp/human common ancestry.

I know the debate is all about religion, simply because no one else attacks other sciences with the same fervor. I just don't know what those who attack evolutionary biology even expect to accomplish.

You're welcome to whatever religious beliefs you want. But evolutionary biology, especially given it's usefulness in a variety of fields (including common descent), isn't going away. It's not because of conspiracy. It's because of usefulness.

Did you notice that the facts in the OP are flawed, do you care? I pointed out the the most abundant family of ERVs in the chimpanzee genome have very rare orthologues in the human genome. It's a straight forward point with peer reviewed scientific literature backing it. It does not even get a passing remark.

Yea, this is about an antitheistic agenda and it makes no sense to pass it off as science. You can't ignore the science and then pretend to be a protector of it. It makes no sense at all.

 

[mark kennedy]

Another one bites the dust...

 

[Pete Harcoff]

Did you notice that the facts in the OP are flawed, do you care? I pointed out the the most abundant family of ERVs in the chimpanzee genome have very rare orthologues in the human genome. It's a straight forward point with peer reviewed scientific literature backing it. It does not even get a passing remark.

I read the thread, but like I said, I'm not looking into getting into a debate about ERVs at this point. It's completely besides the point.

The point I was raising is that evolutionary biology, including common descent, is an applied science. In industry. Not theory, not academia, not atheistic conspiracies designed to smote the religious. Applied science.

Do you not get the implication of that? If evolutionary biology, again including common descent, is being applied by real-world companies looking to solve issues, develop products, etc, etc, then claiming all this is part of some sort of conspiracy is just ludicrous to the extreme. I mean, really, do you really think the pharmaceutical industry is in on it? A 600 billion dollar industry with nothing better to do than promote an atheistic agenda by secretly applying evolutionary biology in their quest for new drugs to treat illness?

I'm sorry, but I'm just not *that* paranoid.

Yea, this is about an antitheistic agenda and it makes no sense to pass it off as science. You can't ignore the science and then pretend to be a protector of it. It makes no sense at all.

I think someone is ignoring science here, but I don't think it's me. Do you have anything to comment on the way modern evolutionary biology is applied? Do you even care?

 

[peteos]

Mark, could you please answer my two simple questions posed on post #56 on page 6 of this thread.

Thank you.

 

[notto]

It does not even get a passing remark.

This is simply not true and I'm sorry Mark but it is intellectually dishonest for you to suggest that your (continuously repeated) comment has not been addressed. It was addressed immediately and repeatedly. You seem to be ignoring that it has been addresses and it has been shown that it is not outside the predictions of common descent and is nothing more than a distraction you are using to avoid addressing the damning evidence that demonstrates common descent.

 

[mark kennedy]

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?

I know for a fact that at least 95% are not.

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

Already answered in detail with source material backing it to the hilt.

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.

Believe me when I tell you, I am not shy about saying I don't know. In this case I do.

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.

It's not true, the most abundant family of ERVs in the chimpanzee genome are not represented in the human genome. Now in answer to your question, my guess would be that it's 95% since that is the sequence identity. You are thinking in terms of identical regions, you have to seriously look at the differences.

Hang in there, this is a tough issue to deal with. I'm a creationist in hostile territory and I get a lot out of it. Just be patient and above all, check the source material.

Grace and peace,
Mark

 

[mark kennedy]

This is simply not true and I'm sorry Mark but it is intellectually dishonest for you to suggest that your (continuously repeated) comment has not been addressed. It was addressed immediately and repeatedly. You seem to be ignoring that it has been addresses and it has been shown that it is not outside the predictions of common descent and is nothing more than a distraction you are using to avoid addressing the damning evidence that demonstrates common descent.

The most abundant family of ERVs in the Chimpanzee genome are not represented in the human genome. That is a slam dunk on another false positive that begs the question of proof on it's hands and knees. I honestly could care less if we evolved from apes or not, the evidence is saying we did not. My religion is not about molecular biology, it's about a relationship I encountered because God insisted.

If the evidence persuades you contrary to my beliefs, go in peace I have no problem with you. I ask only one thing, in these debates and discussions get the facts straight and then we can honestly agree to disagree. I don't think that is unreasonable.

 

[notto]

It's not true, the most abundant family of ERVs in the chimpanzee genome are not represented in the human genome.

What percentage of all ERV's in the chimp genome are represented by those groups?

 

[notto]

The most abundant family of ERVs in the Chimpanzee genome are not represented in the human genome. That is a slam dunk on another false positive that begs the question of proof on it's hands and knees..

Nested Hierarchy.

What you are claiming is a false positive is not when taken in the context of a nested hierarchy.

You are cherry picking Mark. You keep repeating this over and over and you have ignored that it has been addressed and instead of addressing the rebuttal's, you simply repeat again.

All but two (CERV 1/PTERV1 and CERV 2) of the 42 families of chimpanzee endogenous retroviruses were found to have orthologs in humans.

 

[Pete Harcoff]

The most abundant family of ERVs in the Chimpanzee genome are not represented in the human genome. That is a slam dunk on another false positive that begs the question of proof on it's hands and knees. I honestly could care less if we evolved from apes or not, the evidence is saying we did not.

I decided to read in full the paper you had linked to earlier in this thread (and where you are getting your material). And after looking at this paper, I really don't understand how you are arriving at this conclusion.

So two ERV families (of 42) are not represented in the human lineage. This is a problem because...?

 

[notto]

I decided to read in full the paper you had linked to earlier in this thread (and where you are getting your material). And after looking at this paper, I really don't understand how you are arriving at this conclusion.

So two ERV families (of 42) are not represented in the human lineage. This is a problem because...?

That paper really is not supportive of Marks position. It is hard to think of how the following can be valid if common descent is not responsible for the shared ERV's

The presence of an endogenous retroviral sequence in chimpanzees that is missing at an orthologous genomic position in humans can be due to a novel insertion in chimpanzees or deletion of the element in humans. Similarly, the presence of an endogenous retroviral sequence in humans that is missing at an orthologous genomic position in chimpanzees can be due to novel insertion in humans or due to deletion of the element in chimpanzees. Because endogenous retroviruses do not precisely excise from insertion sites [4], it is possible to distinguish between these two possibilities. If a region in humans orthologous to the position of an endogenous retroviral insertion in chimpanzees contains a remnant of endogenous retroviral sequence (for example, fragmented element or solo LTR), we score the gap as a deletion in humans. If the orthologous region contains no remnant of the endogenous retrovirus but the pre-integration genomic sequence can be clearly identified, we score the gap as an insertion in chimpanzees. The same rules apply for the analogous dataset of the endogenous retroviral sequences present in humans but absent in chimpanzees.


Of the 41 instances where an endogenous retroviral sequence is present in chimpanzees but lacking in humans, 29 were due to novel insertions in chimpanzees while 12 were deletions in humans (Tables 3 and 4; Figure 6a). Of the 31 instances where an endogenous retrovirus is present in humans but absent in chimpanzees, we found that 8 were due to novel insertions in humans while 23 were deletions in chimpanzees (Table 4; Figure 6b). Of the 29 novel insertions in chimpanzees, 25 belong to the CERV 1/PTERV1 family, 2 to the CERV 2 family, 1 to the CERV 3 (HERVS7 1) family and 1 to the CERV 30 (HERVK10) family whereas all the 8 novel insertions in humans belong to the CERV 30 (HERVK10) family (Tables 3 and 4). Thus, four families of endogenous retroviruses have been transpositionally active in the chimpanzee lineage, resulting in full-length insertions, since chimpanzees and humans diverged from a common ancestor while only one of these families (CERV 30 (HERVK10)) has been active in humans (Tables 3 and 4). However, the family that is active in both humans and chimpanzees (CERV 30 (HERVK10)) generated eight novel full-length insertions in humans as opposed to only one novel insertion in chimpanzees since they diverged from the common ancestor (Tables 3 and 4).


This additional analysis is consistent with common descent and shows even more congruity between the genomes. Basically, we can predict accurately where we would expect to see a deletion in the genome if common descent was correct and what do you know! When we look, it is there.