200,000 ERVs...

[peteos]

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

You answered the first question as if it was the second. The first question was not what percent between humans and chimps. The first question is, again, the ERV family CERV 2 that old world monkeys share with Chimps (but not humans or Oranatuans), is that in orthogonal positions or not.

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.

I didn't ask about the most abundant families. I have tried to make it clear that that could mean or could not mean anything depending on what family means in the first place. What matters is actual viral insertions, one at a time, into our (and the chimp) genome. Now, you seem to sort of hint that perhaps 95% of the ERVs are indeed shared. That is what I will take "Now in answer to your question, my guess would be that it's 95% since that is the sequence identity.", if I am wrong, correct me now. I used to argue that a similar DNA showed a common designer. But ERVs inserted into the exact same region for 95% of the virus (between humans and chimps that is) and a nested hierarchy with all ERVs common to all apes shows common descent. Of course there are some differences, anything after the split. If 95% of the virus were NOT orthogonal (instead of being orthogonal) I would agree with you that it seems VERY unlikely that ALL of them happened after the split. But 95% are indeed Orthogonal, as you SEEM to just admit (once again, correct me if that is not what you mean).

I honestly could care less if we evolved from apes or not,

Wow, I'm surprised to hear you say that. I care a great deal. As a born again Christian, who believes completly and trusts my very salvation in the super natural act of Jesus death and resurrection, I care a great deal whether we are evolved from apes and wish beyond doubt we could prove that we did not.

 

[Split Rock]

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 This is about religion and the Bible as an historical reference.

Quoted for Truth!

 

[Split Rock]

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.

The paper you cite says otherwise.

1. "The most abundant family of EVRs" in the Chimp genome does not equal "the most ERVs" in the Chimp genome.

2, Most of the ERVs in Chimps that are not in Humans apperared after the split, or have been deleted in humans.

3. Only a small minority of these ERVs cannot not accounted for and there is an explanation provided by the authors you continue to ignore.

How does cherry-picking from papers provide a "slam-dunk" that topples common descent?

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.

No, it is not. Why is it then that you cannot get the facts straight?

 

[Loudmouth]

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

I am referencing the same tables we used in our debates: Table 11 from the human genome paper and Table 2 from the chimp genome paper. Both of those tables can be found in posts in this very thread.

Again, you get the total number of human ERV's from the HGP, subtract the number of human specific ERV's, and what remains are the ERV's shared by humans and chimps at orthogonal sites which is about 200,000. Where is the flaw in my math Mark?

I have done the very same thing with Alu elements and LINE-1 elements because lineage specific elements were listed in the chimp genome paper. I applied the same math as I did with the ERV's.

 

[Loudmouth]

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 totally agree that the most abundant family of chimp ERV's (CERV) are rarely found in the human genome. But guess what, there are 103 families of human ERV's listed in the HGP, not to mention 194 subfamilies. Why are you harping on CERV's? What are you trying to prove? That 1-2% of the chimp ERV's can not be found in humans? What does this prove?

I stated from the very first part of my OP in our debate that evolution predicted a NESTED HIERARCHY. I offered ERV's as evidence of this fact, being that ORTHOLOGOUS ERV's fall into a nested hierarchy in primates. The reverse logic would be that ORTHOLOGOUS ERV's WHICH VIOLATE THE NESTED HIERARCHY WOULD FALSIFY COMMON DESCENT. That is the true reverse logic Mark, not humans and chimps having lineage specific ERV's. You tried to offer PtERV's as a refutation but none of them can be shown to be unambiguously orthogonal, and you know it.

Why not stop with the distractions and actually focus on the data THAT YOU FIRST PRESENTED, such as Table 2 from the CGP and Table 11 from the HPG.

BTW, how do you explain humans and chimps sharing over 1 million orthologous Alu retrotransposon elements? I guess we can tackle this one next.

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.

You are ignoring the fact that human have 203,000 ERV's. It has been shown in black and white and yet you are incapable of seeing it. Why is that?

 

[RichardT]

I shall be waiting for MKs reply, although he's serving now. It will be a pain to research this for myself.

 

[Loudmouth]

I shall be waiting for MKs reply. But I think he's serving now, I might have to research this myself. It will be a pain.

If you give us an idea of what you are looking for we might be able to point you in the right direction.

 

[RichardT]

If you give us an idea of what you are looking for we might be able to point you in the right direction.

I want to see the 200,000 orthologous ERVs for myself.

 

[Loudmouth]

I want to see the 200,000 orthologous ERVs for myself.

The first place to start is http://www.ncbi.nlm.nih.gov/sites/entrez?db=Genome

Click on the Eukaryotae hyperlink and then find Pan troglodytes and Homo Sapiens. After going through a few screens you will have a box on the right hand side that includes "Genome Projects". Click on that and you can enter several genomic databases for each species. A search for erv, env, ltr, and pol. Start with the "erv" search. It doesn't return 200,000 hits but I think this is a matter of annotation. That is, they haven't gotten around to naming them yet.

sfs would be the best person to ask. I would venture a guess that they used a search function that looked for LTR's and compared flanking sequences.

I will get back to you with more info once I get some more info.

 

[RichardT]

. Click on that and you can enter several genomic databases for each species. A search for erv, env, ltr, and pol. Start with the "erv" search. It doesn't return 200,000 hits but I think this is a matter of annotation.

I got zero results when I ran a search for "ERV" for some reason.

 

[RichardT]

LoudMouth, are you a trained geneticist (I thought I heard that you were from somewhere)?

 

[RichardT]

sfs would be the best person to ask.

sfs doesn't like me.

 

[notto]

I got zero results when I ran a search for "ERV" for some reason.

Here's your start.
http://www.ncbi.nlm.nih.gov/mapview/map_search.cgi?taxid=9606&query=erv


Have fun!

 

[RichardT]

Here's your start.
http://www.ncbi.nlm.nih.gov/mapview/map_search.cgi?taxid=9606&query=erv


Have fun!

Can you give me a link to the chimp genome as well? So that I can compare? Thanks.

 

[notto]

Can you give me a link to the chimp genome as well? So that I can compare? Thanks.

How are you going to do your comparison? Can you explain in your own words what you are looking at in the first link?

 

[RichardT]

How are you going to do your comparison? Can you explain in your own words what you are looking at in the first link?

Retroviral insertions. If you give me the other link I'll look for orthologous ones between the chimp and human genomes.

 

[notto]

Retroviral insertions. If you give me the other link I'll look for orthologous ones between the chimp and human genomes.

I followed the instructions you were given before and it worked just fine for me. Why don't you give the tool another try. It will help you in your comparison to do the steps yourself.

Have Fun!

 

[Loudmouth]

LoudMouth, are you a trained geneticist (I thought I heard that you were from somewhere)?

I work on stuff further down the line (i.e. protein chemistry), mostly in prokaryotes.

 

[RichardT]

I followed the instructions you were given before and it worked just fine for me. Why don't you give the tool another try. It will help you in your comparison to do the steps yourself.

Have Fun!

If it doesn't work this time, can you give me the link to the chimp genome? I just want to go through the whole thing, it doesn't matter to me how long it takes, I'll have fun taking note of every single orthologous retroviral insertions.

 

[Loudmouth]

Agh... If it doesn't work this time, can you give me the link to the chimp genome? I just want to go through the whole thing, it doesn't matter to me how long it takes, I'll have fun taking note of every single orthologous retroviral insertions.

The Pan troglodytes genome can be found here:

http://www.ncbi.nlm.nih.gov/sites/entrez?Db=genomeprj&cmd=ShowDetailView&TermToSearch=13184