A question of ERVs

[mark kennedy]

This is why it's so hard to have a discussion, much less a debate with Mark. Much like Kent Hovind he adopted a script years ago and being immune to correction he sticks to it and repeats it ad nauseum rather than trying to understand why his script is wrong.

So, yes. The EVRs sequenced for the human genome do, axiomatically, represent those found in the human genome. Let's move forward to 2005 and the start of Mark's decade long problem. Everyone remembers what the full title of the chimpanzee genome paper was, right?

Initial sequence of the chimpanzee genome and comparison with the human genome

for Again for emphasis because that really seems to be an issue here - and comparison with the human genome. Comparison. With the human genome. What were the results of the comparison with the human genome?
{snip Table 2}
The results were that we shared the 203,000 ERVs, that the HGP had found because when the comparison took place, only the 361 lineage specific.

Again, because this really seems to be a problem. Table 2 ONLY LISTS LINEAGE SPECIFIC ERVs. The clue to that should be in the headings "chimpanzee lineage" and "human lineage". So when there was a comparison of the two genomes, the human genome was found share 203,000 ERVs with chimpanzee genome and the chimpanzee genome was found to share those same 203,000 ERVs with the only differences being 279 that were only found in the chimpazee lineage and 83 that were only found in the human lineage.



I would suggest we could discuss your years long confusion over nested hierarchies vs. homologies after we finally clear up this simple math problem you can't seem to wrap your head around, but as I've noted, at some point it's an exercise in futility.

What on earth are you talking about, you have numbers flying around all over the place. The lineage specific ERVs are the ones that are the most abundant and the divergence goes through the roof. The Human genome estimation simply lists them, they don't compare them to anything. Your not rooting that in anything specific you are just throwing numbers around like they mean something. No source material just you spouting off numbers, wow, some things never change.

 

[46AND2]

What on earth are you talking about, you have numbers flying around all over the place. The lineage specific ERVs are the ones that are the most abundant and the divergence goes through the roof. The Human genome estimation simply lists them, they don't compare them to anything. Your not rooting that in anything specific you are just throwing numbers around like they mean something. No source material just you spouting off numbers, wow, some things never change.

Yes. Some things never change. Like you claiming that the lineage specific ones are the most abundant, when the paper says nothing of the sort. There are nearly 1000 times as many shared, orthologous ERVS as there are lineage specific.

 

[xianghua]

This is a lie and you know it. I tested your idea and debunked it ages ago.

not realy. are you still claiming that a car isnt more similar to other car then to a trcuk in most cases?

 

[xianghua]

No. I said that common ancestry explains the pattern well. I challenged you all to come up with a better explanation.

no problem. my first explanation is a common designer. since many ervs parts are functional+ the fact that some species cant survive without them= the best explanation is that these ervs were always a part of the genome.

my second explanation is similar target site preference. its important to note that we have evidence for both explanations.

No. There are a couple ways we might find a few at most that contradict the pattern, including sheer dumb luck. What we shouldn't see, however, is a significant percentage of deviation.

this isnt what you said here:

"if we find ERVs which don't match the nested hierarchy, they should not be found at the same location in the pertinent genomes".

you said nothing about "significant percentage".

Indeed, only ONE known example of our 203,000+ ERVs doesn't fit the pattern. I'm asking you to explain the 99.99+% of the hundreds of thousands that do result in the nested hierarchy.

see above me 2 explanations without evolution. do you have any counter evidence?

 

[Jimmy D]

not realy. are you still claiming that a car isnt more similar to other car then to a trcuk in most cases

Wrong again.

 

[xianghua]

Not all trucks are bigger in size or have more wheels than vans.

true. but the majority indeed fit with my "tree" above. especially if we are talking about a single designer\company.

All of these things shatter his supposed nested hierarchy.

remember that its also true for evolution. many traits are shared between far species but not in some species between them. and these cases "solve" by convergent evolution or ils or hgt etc.

 

[Speedwell]

true. but the majority indeed fit with my "tree" above. especially if we are talking about a single designer\company.



remember that its also true for evolution. many traits are shared between far species but not in some species between them. and these cases "solve" by convergent evolution or ils or hgt etc.

Wht do you mean by "species between them???"

 

[46AND2]

no problem. my first explanation is a common designer. since many ervs parts are functional+ the fact that some species cant survive without them= the best explanation is that these ervs were always a part of the genome.

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

So then you have to wonder why this designer would place so much worthless DNA that looks exactly like remnants of retroviruses (and indeed can be resurrected into functional viruses), in a pattern consistent with what we would expect of common ancestry.

my second explanation is similar target site preference. its important to note that we have evidence for both explanations.

We don't have nearly the evidence necessary to support your position. Target site preference only shows that some sites are infected more frequently than others. It does not exclude the rest of the genome. In other words, HIV, for example, doesn't always insert at the same spot, which you would need to be true for the 200k identical insertions at a 99.9+% clip we observe.

And the paper YOU cited refutes your claim anyway, because it discusses shared ERVs between several species which inserted at different sites.

this isnt what you said here:

"if we find ERVs which don't match the nested hierarchy, they should not be found at the same location in the pertinent genomes".

you said nothing about "significant percentage".

Yup, and 99.9+% of the time, we don't see it. The problem with creationist arguments is that you think if you find one outlier, you can ignore the hundreds of thousands of good data points, instead of taking the obvious approach and try to figure out the reason for the anomaly.

see above me 2 explanations without evolution. do you have any counter evidence?

Funny thing is that your 2 explanations contradict each other.

 

[pitabread]

not realy. are you still claiming that a car isnt more similar to other car then to a trcuk in most cases?

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.

 

[USincognito]

The problem with creationist arguments is that you think if you find one outlier, you can ignore the hundreds of thousands of good data points, instead of taking the obvious approach and try to figure out the reason for the anomaly.

They do this all the time. A Jurassic horse would falsify evolution. The secondary burial of a Holocene horse in Jurassic strata would not, but Creationists would demand that it did despite the fact that we have an explanation for why it was there.

 

[mark kennedy]

Yes. Some things never change. Like you claiming that the lineage specific ones are the most abundant, when the paper says nothing of the sort. There are nearly 1000 times as many shared, orthologous ERVS as there are lineage specific.

That's exactly what the paper says and the 1000 times is a number you made up. The hundreds of ERV class 1 add up to over a million base pairs, a thousand million orthologous ERVs? You think using some convoluted term and making crazy hyperbolic statements is an argument. What is more, not that any of you care, the ERVs are pretty much a protein coding gene grave yard, most of them are riddled with mutations. All they really do is replicate themselves and find a new insertion site, so if the two genomes were identical with these viral reading frames all over the place that would be astonishing. It doesn't bother me that you guys disagree with me, I always come away with more interesting information then I came in with. But for a group that considers itself a defender of science I would think you would spend a little time actually enjoying some of the research that is out there. Running in circles, waving your hands in the air and shouting thousands of orthologous ERVs is just silly.

Every now and then I try to look up ERV invasions into germline cells, you know that is actually pretty rare highly deleterious. You never give any thought to the devastating consequences of these viruses inserting themselves at such a vulnerable time of development.

Thousands of times more orthologous ERVs!!! I can't think of a more pointless argument then the ones surrounding ERVs.

 

[46AND2]

That's exactly what the paper says and the 1000 times is a number you made up. The hundreds of ERV class 1 add up to over a million base pairs, a thousand million orthologous ERVs?

No mark, it doesn't. You misread. Again.

And where the heck do you get a thousand million orthologous ERVs? It's like if I say there are 1760 yards in a mile, and you scoff and say, each yard contains 3 feet, 5280 yards in a mile? You aren't counting the same thing.

You've been shown where the 203k comes from many times. Your own post says that 40 of 42 families are orthologous, with the PtERVs being the remaining two. And you think the non-orthologous ones are the most abundant? Your numbers dont make any sense.

 

[mark kennedy]

No mark, it doesn't. You misread. Again.

And where the heck do you get a thousand million orthologous ERVs? It's like if I say there are 1760 yards in a mile, and you scoff and say, each yard contains 3 feet, 5280 yards in a mile? You aren't counting the same thing.

You've been shown where the 203k comes from many times. Your own post says that 40 of 42 families are orthologous, with the PtERVs being the remaining two. And you think the non-orthologous ones are the most abundant? Your numbers dont make any sense.

I've been shown nothing, just the pedantic beating of a rug. At least 7% of the divergence due to Indels is in the ERVs and the Ptervs 1 and 2 don't even exist in the human genome.

Against this background, it was surprising to find that the chimpanzee genome has two active retroviral elements (PtERV1 and PtERV2) that are unlike any older elements in either genome…PtERV1-like elements are present in the rhesus monkey, olive baboon and African great apes but not in human, orangutan or gibbon, suggesting separate germline invasions in these species (Nature 2005)
​

I know why you guys obsess over this, there is nothing at stake and you can chase it in circles endlessly. That distracts from the actual evidence that may or may not shed some light on the universal common ancestry myth.

 

[46AND2]

I've been shown nothing, just the pedantic beating of a rug. At least 7% of the divergence due to Indels is in the ERVs and the Ptervs 1 and 2 don't even exist in the human genome.

Against this background, it was surprising to find that the chimpanzee genome has two active retroviral elements (PtERV1 and PtERV2) that are unlike any older elements in either genome…PtERV1-like elements are present in the rhesus monkey, olive baboon and African great apes but not in human, orangutan or gibbon, suggesting separate germline invasions in these species (Nature 2005)
​

I know why you guys obsess over this, there is nothing at stake and you can chase it in circles endlessly. That distracts from the actual evidence that may or may not shed some light on the universal common ancestry myth.

You've even been shown in this very thread:

Notice at the top of the column it says:

Number of copies (X 1,000)

Those are the orthologous ones. 203,000 of them. Compared to a couple hundred non-orthologous PtERVs you claim are most abundant.. Get where my "nearly 1000 times as many" comes from now?

 

[mark kennedy]

You've even been shown in this very thread:

View attachment 247934

Notice at the top of the column it says:

Number of copies (X 1,000)

Those are the orthologous ones. 203,000 of them. Compared to a couple hundred non-orthologous PtERVs you claim are most abundant.. Get where my "nearly 1000 times as many" comes from now?

The base pairs are 79 mbp and the ERV class 1 listed in the Chimpanzee Genome paper is over a million. That's not thousands of times, do a little basic math and you do know that genomes are measured in base pairs right?

 

[46AND2]

The base pairs are 79 mbp and the ERV class 1 listed in the Chimpanzee Genome paper is over a million. That's not thousands of times, do a little basic math and you do know that genomes are measured in base pairs right?

Yes, because all ERVS must be the same size, right?

 

[mark kennedy]

Yes, because all ERVS must be the same size, right?

That is the number of base pairs collectively, you are looking at the number of copies, try the next column. I mean are you guys serious, this is about as basic as it gets.

 

[46AND2]

That is the number of base pairs collectively, you are looking at the number of copies, try the next column. I mean are you guys serious, this is about as basic as it gets.

Yes, Mark. I have always been talking about the number of copies. You are the one changing what is being counted. It really is basic. 203k to 250+. Nearly 1000 to one.

But let's go with your numbers. 1 million base pairs for the PTERVS, and 79 million for the rest. Please explain to me how 1 million is more abundant than 79 million.

 

[mark kennedy]

Yes, Mark. I have always been talking about the number of copies. You are the one changing what is being counted. It really is basic. 203k to 250+. Nearly 1000 to one.

But let's go with your numbers. 1 million base pairs for the PTERVS, and 79 million for the rest. Please explain to me how 1 million is more abundant than 79 million.

I didn't change anything, what I said was:

With more than 100 members, CERV 1/PTERV1 is one of the most abundant families of endogenous retroviruses in the chimpanzee genome. (Genome Biol. 2006).​

They can be found in African great apes but not in humans. That's a direct quote and an often repeated observation. You guys keep correcting something by rephrasing and shifting the emphasis to copies rather then members and the size overall as being measured in based pairs. It is really basic, the most abundant families of ERVs in the chimpanzee genome are absent in the human genome.

 

[46AND2]

I didn't change anything, what I said was:

With more than 100 members, CERV 1/PTERV1 is one of the most abundant families of endogenous retroviruses in the chimpanzee genome. (Genome Biol. 2006).​

They can be found in African great apes but not in humans. That's a direct quote and an often repeated observation. You guys keep correcting something by rephrasing and shifting the emphasis to copies rather then members and the size overall as being measured in based pairs. It is really basic, the most abundant families of ERVs in the chimpanzee genome are absent in the human genome.

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.