A question of ERVs

[mark kennedy]

Mark...im comparing apples to apples. The human genome paper lists the number of copies. And the chimp paper lists the number of insertion sites. That's the SAME THING.

200k+ to 200+.

And they BOTH list the number of base pairs in total. 79 million to 1 million. Either way you look at it, orthologous ERVS vastly outnumber non-orthologous ones.

They do list copies, families and subfamilies, I'm talking about the abundance of them. Everything is measured in base pairs, with at least 42 families the 2 most abundant are not in the human genome. What is more the rest of them are not identical, an enormous amount of divergence is due specifically to ERVs being compared. This is the worst homology argument ever. Now what your point is about insertion sites I don't know and I'm not sure you do either.

 

[46AND2]

They do list copies.

Excellent . And how many copies are there (of the cerv/pterv type you are arguing about)??

 

[mark kennedy]

Excellent . And how many copies are there (of the cerv/pterv type you are arguing about)??

Who cares, I thought you were talking apples and apples. This is about what is in the respective genomes, they track the copies I assume because the replicate themselves and keeping track of that is an issue for researchers. This is about sequence identity in a comparison, the first order of business is to measure commonality which isn't no where as great as you would think.

 

[46AND2]

Who cares, I thought you were talking apples and apples. This is about what is in the respective genomes, they track the copies I assume because the replicate themselves and keeping track of that is an issue for researchers. This is about sequence identity in a comparison, the first order of business is to measure commonality which isn't no where as great as you would think.

I am comparing apples to apples. Something you are obviously reticent to do. I wonder why...im comparing number of copies in one paper to number of copies in another.

Why is that so hard to understand?

 

[mark kennedy]

I am comparing apples to apples. Something you are obviously reticent to do. I wonder why...im comparing number of copies in one paper to number of copies in another.

Why is that so hard to understand?

Why do you refuse to measure them in base pairs? When we are talking comparative genomics we should be talking direct comparisons, that means you measure them in base pairs.

 

[46AND2]

Why do you refuse to measure them in base pairs? When we are talking comparative genomics we should be talking direct comparisons, that means you measure them in base pairs.

Because not all ERVS are of the same length. This should be extremely obvious.

Besides, I DID, also, compare total length, to humor you, and orthologous STILL far exceed non-orthologous. 78 million to 1 million.

 

[USincognito]

Mark...im comparing apples to apples. The human genome paper lists the number of copies. And the chimp paper lists the number of insertion sites. That's the SAME THING.

200k+ to 200+.

And they BOTH list the number of base pairs in total. 79 million to 1 million. Either way you look at it, orthologous ERVS vastly outnumber non-orthologous ones.

Multiple people have been explaining it to him including an author of the chimpanzee genome paper, yet he still refused to accept that it might be him instead of everyone else that is wrong.

 

[46AND2]

Why do you refuse to measure them in base pairs? When we are talking comparative genomics we should be talking direct comparisons, that means you measure them in base pairs.

Actually, I should have checked your numbers...the 79 million was only the class 1 ERVs . The total is 126 million to 1 million.

 

[mark kennedy]

Because not all ERVS are of the same length. This should be extremely obvious.

Besides, I DID, also, compare total length, to humor you, and orthologous STILL far exceed non-orthologous. 78 million to 1 million.

I don't know what you think is so significant about the copies but I'm not impressed with selective comparisons.

For almost half a century it was believed that Chimpanzee and Human DNA was virtually identical. This is now known to be false. The Comparison of Human Chromosome 21 and Chimpanzee Chromosome 22 revealed that 83% of the 231 coding sequences, including functionally important genes, show differences at the amino acid sequence level. These included gross structural changes affecting gene products far more common than previously estimated (20.3% of the PTR22 proteins) (Nature, 27 May 2004). Genome wide the differences are now known to include 35 million single base substitutions, and five million indels (with the ~70,000 indels larger than 80 bp comprising 73% of the affected base pairs). This is in addition to 8 chromosomal rearrangements from 2 million base pairs to 4 million base pairs in length coming to more then 20 million base pairs.

Then you look into the direct comparisons in studies like this Phylogenies of seven HERV loci. When 8% of the human genome is made up of ERVs with a 94% nucleotide sequence identity should we really be supprised the seven loci are the same? For HERV-K JML 6.17 they identified 5 substitutions, a couple of them had as many as 10. This is supposed to be some kind of proof?

Here they discuss the probability of the 11 substitutions, assuming they happened by chance:

Although it is possible that any one position may suffer an identical substitution in both LTRs by chance, the probability of 11 positions undergoing identical substitutions in both LTRs is exceedingly low.

And you want to talk about copy numbers based on a table from 2001 when there was no comparison made. I've been down this rabbit hole enough to know your running off on tangents and then running in circles around them.

 

[46AND2]

Multiple people have been explaining it to him including an author of the chimpanzee genome paper, yet he still refused to accept that it might be him instead of everyone else that is wrong.

Yeah, I've seen it over and over since I first came to the site. I'm only responding for the benefit of others who have not seen those discussions.

 

[46AND2]

I don't know what you think is so significant about the copies but I'm not impressed with selective comparisons.

For almost half a century it was believed that Chimpanzee and Human DNA was virtually identical. This is now known to be false. The Comparison of Human Chromosome 21 and Chimpanzee Chromosome 22 revealed that 83% of the 231 coding sequences, including functionally important genes, show differences at the amino acid sequence level. These included gross structural changes affecting gene products far more common than previously estimated (20.3% of the PTR22 proteins) (Nature, 27 May 2004). Genome wide the differences are now known to include 35 million single base substitutions, and five million indels (with the ~70,000 indels larger than 80 bp comprising 73% of the affected base pairs). This is in addition to 8 chromosomal rearrangements from 2 million base pairs to 4 million base pairs in length coming to more then 20 million base pairs.

Then you look into the direct comparisons in studies like this Phylogenies of seven HERV loci. When 8% of the human genome is made up of ERVs with a 94% nucleotide sequence identity should we really be supprised the seven loci are the same? For HERV-K JML 6.17 they identified 5 substitutions, a couple of them had as many as 10. This is supposed to be some kind of proof?

Here they discuss the probability of the 11 substitutions, assuming they happened by chance:

Although it is possible that any one position may suffer an identical substitution in both LTRs by chance, the probability of 11 positions undergoing identical substitutions in both LTRs is exceedingly low.

And you want to talk about copy numbers based on a table from 2001 when there was no comparison made. I've been down this rabbit hole enough to know your running off on tangents and then running in circles around them.

Because "copies" are a direct comparison, mark. As is total base pairs. Both of which show vastly more orthologous sequences than non.

 

[mark kennedy]

Multiple people have been explaining it to him including an author of the chimpanzee genome paper, yet he still refused to accept that it might be him instead of everyone else that is wrong.

Nonsense, you have argued in circles around the actual evidence and make corrections that do not correspond to actual errors. Your making it up as you go along and have no patience for actual evidence when by now you should be an expert on the facts, you don't even manage basic insights. I have no problem being wrong, I don't appreciated being corrected when I'm not, especially by someone who hasn't bothered to do the reading.

 

[mark kennedy]

Because "copies" are a direct comparison, mark. As is total base pairs. Both of which show vastly more orthologous sequences than non.

That's not the point, the point is the ERVs are a lousy homology argument and these pedantic details are a diversion.

 

[pitabread]

I have no problem being wrong

 

[46AND2]

That's not the point, the point is the ERVs are a lousy homology argument and these pedantic details are a diversion.

The point is that you utterly fail to support your assertion that the non-orthologous ERVs are the most abundant. And I've shown that to be the case using 2 metrics, including your preferred base pair comparison--126 million base pairs (total ERV base pairs from human genome paper) to 1 million (non-orthologous ERVs from chimp comparison paper).

Unless you can somehow show that 1 is greater than 126, I'd say your claim is pretty busted.

 

[USincognito]

That's not the point, the point is the ERVs are a lousy homology argument and these pedantic details are a diversion.

Here's another thing he's been corrected on for years - ERVs are not a homology argument. They are evidence of nested hierarchy and technically are molecular vestiges of common ancestry.

 

[mark kennedy]

Here's another thing he's been corrected on for years - ERVs are not a homology argument. They are evidence of nested hierarchy and technically are molecular vestiges of common ancestry.

Here is another argument you ignored over the years, yes it is, and you never did the reading.

 

[46AND2]

.

 

[xianghua]

I'm claiming that vehicles don't fall into nested hierarchies the way you keep saying they do.

Go back to the thread I linked. Here are links to the relevant posts:

the self replicating watch argument - post #1510

the self replicating watch argument - post #1533

the self replicating watch argument - post #1552

the self replicating watch argument - post #1610

You made a bunch of claims about vehicles falling into nested hierarchies. I tested those claims. Those claims you made turned out to be false.

There's not much else to say.

i actually refute this claim here:

the self replicating watch argument

 

[xianghua]

No it isn't. As you said yourself, PART of some ERVs have function. The rest is highly mutated junk.

the rest were degenerated by natural mutations. like many other pseudogenes in the genome. so at their initial condition they were functional. you also need too deal with the problem of creatures that cant live without some of these ervs. how they lived in the first place? and how the virus itself evolved at the first place without a host?

We don't have nearly the evidence necessary to support your position.

yes we do. from the paper:

"This apparent independent clustering of retroviral insertions at similar locations may be a consequence of preferential integration bias or the effect of selection pressure against gene regions, limiting the number of effective sites that are tolerated for fixation"

and we are talking about resolution of about 1\30000 of the genome. far from a random event.