A question of ERVs

[pitabread]

i actually refute this claim here:

the self replicating watch argument

Did you just link to a random post?

Nothing in that post addresses anything I said.

 

[46AND2]

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?





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.

Dude, even if insertion points were limited to just 2 spots out of the 3 billion in our genome, it would be like flipping a coin and getting heads 99.9+% of the time in 203,000 attempts. But target sites are only preferential, not exclusive, so it's not even THAT good for you.

Not only that, many of the ERVs are copies from replicating themselves...so not only would the viruses have to ALWAYS target a specific site at infection, the copies would also have to target their specific site. Your explanation is ludicrous, and shows that you simply don't grasp the magnitude of what orthologous ERVS mean.

So like I said, you don't have near the evidence necessary to support your claim.

And as for the parts of ERVs that are functional, the answer is the same as any other symbiotic relationship...our ancestors developed a need for them. It's not like the ERV inserted itself and then, bam, we couldn't live without it from then on. Don't be silly.

 

[46AND2]

the rest were degenerated by natural mutations. like many other pseudogenes in the genome. so at their initial condition they were functional.

Oh, and this...yes they are mutated from the originals (which functioned as viruses)...in such a way that it forms yet another nested hierarchy. Why is it that ERVS we share with orangutans, gorillas, and chimps have a much higher degree of mutation, than the ones we only share with chimps?

Common ancestry explains this easily. The ones we share with all the species have been in the genome for much longer (since our common ancestor with orangutans, rather than our common ancestor with chimps), and therefore accumulated more mutations.

 

[xianghua]

Did you just link to a random post?

Nothing in that post addresses anything I said.

yes it does: "since in general a bicylce is more similar to other bicylce than we do have here statistically significant."

something you said that doesnt exist in vehicles.

 

[xianghua]

Dude, even if insertion points were limited to just 2 spots out of the 3 billion in our genome, it would be like flipping a coin and getting heads 99.9+% of the time in 203,000 attempts. But target sites are only preferential, not exclusive, so it's not even THAT good for you.

when we are talking about a spot of about 1/30000 of the genome its a very specific target.

And as for the parts of ERVs that are functional, the answer is the same as any other symbiotic relationship...our ancestors developed a need for them

so we need to believe in evolution to accept it. isnt it the point you suppose to prove? the evidence show that a creature x cant live without it. you on the other hand believe against this evidence. so who is going by the evidence and who doesnt?

Oh, and this...yes they are mutated from the originals (which functioned as viruses)...in such a way that it forms yet another nested hierarchy. Why is it that ERVS we share with orangutans, gorillas, and chimps have a much higher degree of mutation, than the ones we only share with chimps?

not a ccording to these papers:

Human Endogenous Retroviral Elements as Indicators of Ectopic Recombination Events in the Primate Genome

"The tree for HERV-K10p14 deviates from the predicted topology because, although the sequences of the two LTRs form separate clusters, each cluster gives a different estimate of host phylogeny."

or:

"The analysis of the HERV-K(II) sequences deviated quite strikingly from the predicted topology"

and: "Examination of the LTR sequences at the HERV-K9q34.3 locus, which also gave an underestimated integration time estimate indicating sequence homogenization"

and: "However, its relatively low level of LTR divergence suggested that it represents a much more recent integration even"

or:


Cross-Species Transmission and Differential Fate of an Endogenous Retrovirus in Three Mammal Lineages


"Thus, estimates of the age of proviruses based on LTR divergence should be interpreted with caution, as they are likely to be underestimates"[/QUOTE]

 

[pitabread]

yes it does: "since in general a bicylce is more similar to other bicylce than we do have here statistically significant."

something you said that doesnt exist in vehicles.

That quote from you about bicycles doesn't refute anything. It's just an unsupported claim, no different than your claim about cars and trucks.

In order to demonstrate this claim, you'd need to first construct a data set based on bicycle characteristics, then create phylogenetic trees from that data set (I recommend the software Mesquite) and then do the calculations to test for statistical significance between different trees constructed from different characteristic subsets.

Have you done any of this?

Until you do all of that, all you have is an unsupported claim.

I already tested your claims about cars and trucks and it turns out your claims are false. Why would we assume your claim about bicycles will be any different?

 

[46AND2]

when we are talking about a spot of about 1/30000 of the genome its a very specific target.

Um. No it isn't. 1/30,000th of the genome is still 10,000 possible locations. I just showed you that even if there were only TWO possible spots in the genome a virus could go, it still would not be specific enough.

Besides, they aren't "target spots" they are more like "hot spots" where the viruses insert more frequently. It isn't the ONLY spots they insert, just more frequent; they still insert all over the genome.

You should just give up the target site argument. It's really, really bad.

so we need to believe in evolution to accept it. isnt it the point you suppose to prove? the evidence show that a creature x cant live without it. you on the other hand believe against this evidence. so who is going by the evidence and who doesnt?

You believe in a magical super being, who zaps creatures with viruses that allow them to survive, in order to tinker with his creations, because he didn't quite get it right the first time.

Hint: not you.

not a ccording to these papers:

Human Endogenous Retroviral Elements as Indicators of Ectopic Recombination Events in the Primate Genome

"The tree for HERV-K10p14 deviates from the predicted topology because, although the sequences of the two LTRs form separate clusters, each cluster gives a different estimate of host phylogeny."

or:

"The analysis of the HERV-K(II) sequences deviated quite strikingly from the predicted topology"

and: "Examination of the LTR sequences at the HERV-K9q34.3 locus, which also gave an underestimated integration time estimate indicating sequence homogenization"

and: "However, its relatively low level of LTR divergence suggested that it represents a much more recent integration even"

There you go trying to find anomalies again. While scientists try to find out the complexities to explain atypical results, you just throw out the typical results.

or:


Cross-Species Transmission and Differential Fate of an Endogenous Retrovirus in Three Mammal Lineages


"Thus, estimates of the age of proviruses based on LTR divergence should be interpreted with caution, as they are likely to be underestimates"

If millions of years is likely an UNDERestimate, how does that help your young earth view, exactly?

 

[xianghua]

I already tested your claims about cars and trucks and it turns out your claims are false. Why would we assume your claim about bicycles will be any different?

so according to you this:

is more similar to this:

then to this:

what can i say... make sense.

(all images from wiki).

 

[pitabread]

so according to you

<snip>

No, I didn't make any claims about the similarities of bicycles.

What I am saying is that if you want to make claims about creating phylogenetic trees with bicycles, then you need to test those claims. This is something you've never bothered to do.

And given that your claims about trucks and cars didn't work out, I don't know why you'd think that changing it to bicycles is going to make a difference here.

Furthermore, phylogenetic trees are not strictly about similarities or differences. Rather they are about specific nested patterns based on inferred hereditary relationships. Which is why constructing trees based on inanimate objects makes no sense. And I already demonstrated this with the cars/trucks trees.

 

[xianghua]

1/30,000th of the genome is still 10,000 possible locations.

if we got these viruses even if the chance of it by a random event is about 30,000 (at least 6 times) , then its also possible to get it more specific.

I just showed you that even if there were only TWO possible spots in the genome a virus could go, it still would not be specific enough.

see above. it can be even more specific. unless you can show me a barrier.

There you go trying to find anomalies again

i will call it "evidence against evolutionery predictions" but you are welcome to call it anything you want.

If millions of years is likely an UNDERestimate, how does that help your young earth view, exactly?

who is talking about young earth here? i dont. and its also base on evolutionery assumptions here anyway. so lets stick with the ervs.

in summary:

1) we have evidence that viruses can be insert into very specific spots in the genome. up to 1/30,000th of the genome. and it can be even more specific.

2) we have evidence that creatures cant live without some ervs. therefore the logical conclusion is that these ervs were always been a part of the genome.

3) we have evidence that a retrovirus can be created from genome parts.

4) some ervs have no homologous and therefore this is another evidence that viruses were created from the host and not the opposite.

5) a tipical retrovirus contain only about 3-4 genes. again: it make sense if the virus created from the host genome.

6) the virus itself cant survive without a host. another evidence that the virus created from the host genome.

to continue?

 

[46AND2]

if we got these viruses even if the chance of it by a random event is about 30,000 (at least 6 times) , then its also possible to get it more specific.



see above. it can be even more specific. unless you can show me a barrier.





i will call it "evidence against evolutionery predictions" but you are welcome to call it anything you want.




who is talking about young earth here? i dont. and its also base on evolutionery assumptions here anyway. so lets stick with the ervs.

in summary:

1) we have evidence that viruses can be insert into very specific spots in the genome. up to 1/30,000th of the genome. and it can be even more specific.

2) we have evidence that creatures cant live without some ervs. therefore the logical conclusion is that these ervs were always been a part of the genome.

3) we have evidence that a retrovirus can be created from genome parts.

4) some ervs have no homologous and therefore this is another evidence that viruses were created from the host and not the opposite.

5) a tipical retrovirus contain only about 3-4 genes. again: it make sense if the virus created from the host genome.

6) the virus itself cant survive without a host. another evidence that the virus created from the host genome.

to continue?

No, in summary, you have completely failed to explain the pattern of ERVs we see. Even if all 6 of your summary points were true (they are not), they still don't explain, or even attempt to explain the nested hierarchical pattern we see, which was my original challenge. They are all evasion, so that you don't have to actually address the problem.

By the way, do you even know what a summary is? You've included things in your summary which haven't even been discussed.

 

[xianghua]

No, in summary, you have completely failed to explain the pattern of ERVs we see. Even if all 6 of your summary points were true (they are not), they still don't explain, or even attempt to explain the nested hierarchical pattern we see, which was my original challenge.

what is the problem? first: if we accpet these 6 ervs then we do find evidence against this hierarchy. and inseatd of falsify evolution these scientists actually admit that at best we need to change the primate phylogeny. so in any case they will believe in evolution. with nested hierarchy and without. second: i already showed that we can find nested hierarchy in d esigned objects too. so nested hierarchy doesnt prove non design:

 

[Speedwell]

second: i already showed that we can find nested hierarchy in d esigned objects too.

Sometimes, maybe, if you arrange them without any regard at all for their actual developmental history.

so nested hierarchy doesnt prove non design:

NOTHING CAN PROVE NON-DESIGN. DESIGN IS AN UNFALSIFIABLE PROPOSITION AND CAN NEVER BE RULED OUT.

 

[pitabread]

second: i already showed that we can find nested hierarchy in d esigned objects too. so nested hierarchy doesnt prove non design:

View attachment 248442

Did you already forget that we just talked about how your claims about vehicles and nested hierarchies were already debunked?

This was only a week ago. What is your deal?

 

[46AND2]

what is the problem? first: if we accpet these 6 ervs then we do find evidence against this hierarchy. and inseatd of falsify evolution these scientists actually admit that at best we need to change the primate phylogeny. so in any case they will believe in evolution. with nested hierarchy and without. second: i already showed that we can find nested hierarchy in d esigned objects too. so nested hierarchy doesnt prove non design:

View attachment 248442

The problem, as pitabread and others have repeatedly shown you, is that designed things DON'T fit into nested hierarchies. Please learn what this pattern requires, as you clearly don't understand the concept.

When you finally understand what the pattern we are talking about requires, feel free to actually respond to what I have challenged. You can reread the challenge in post #91.

 

[xianghua]

And given that your claims about trucks and cars didn't work out, I don't know why you'd think that changing it to bicycles is going to make a difference here.

so lets try it again. for start: do you agree that in general a bicycle is more similar to other bicycle then to a say a car?

 

[xianghua]

The problem, as pitabread and others have repeatedly shown you, is that designed things DON'T fit into nested hierarchies. Please learn what this pattern requires, as you clearly don't understand the concept.

When you finally understand what the pattern we are talking about requires, feel free to actually respond to what I have challenged. You can reread the challenge in post #91.

again, like this one:

 

[46AND2]

again, like this one:

View attachment 248639

Again, not a nested hierarchy.

 

[mark kennedy]

The problem, as pitabread and others have repeatedly shown you, is that designed things DON'T fit into nested hierarchies. Please learn what this pattern requires, as you clearly don't understand the concept.

When you finally understand what the pattern we are talking about requires, feel free to actually respond to what I have challenged. You can reread the challenge in post #91.

Again, not a nested hierarchy.

again, like this one:

View attachment 248639

Notice the nature of the argument, @xianghua. The nested hierarchy doesn't allow for design, so the pattern requires a naturalistic explanation. The thing is, there is no rational, let alone empirical evidence that ERVs can invade a germline on the scale required. These germline invasions are exceedingly rare and yet they will tell us that 8% of the human genome is composed of them, that's the power of supposition. At least a million base pairs have been added to the Chimpanzee genome since the split, supposedly, from these highly deleterious invasions yet with no ill effects, which is ludicrous. Not only that the most abundant families of ERVs in the Chimpanzee genome are absent in the human genome and they do not intend to answer that once, just run it endlessly in circles.

It's not an argument, it's a diversion. The question of how the human brain could have evolved from that of apes 2 million years ago is never going to be addressed to say nothing of the other 40,000 genes that would have had to underwent major changes.

But it's fun to watch you go toe to toe with them, just saying, they don't have a real argument.

Grace and peace,
Mark

 

[46AND2]

Notice the nature of the argument, @xianghua. The nested hierarchy doesn't allow for design, so the pattern requires a naturalistic explanation. The thing is, there is no rational, let alone empirical evidence that ERVs can invade a germline on the scale required. These germline invasions are exceedingly rare and yet they will tell us that 8% of the human genome is composed of them, that's the power of supposition. At least a million base pairs have been added to the Chimpanzee genome since the split, supposedly, from these highly deleterious invasions yet with no ill effects, which is ludicrous. Not only that the most abundant families of ERVs in the Chimpanzee genome are absent in the human genome and they do not intend to answer that once, just run it endlessly in circles.

It's not an argument, it's a diversion. The question of how the human brain could have evolved from that of apes 2 million years ago is never going to be addressed to say nothing of the other 40,000 genes that would have had to underwent major changes.

But it's fun to watch you go toe to toe with them, just saying, they don't have a real argument.

Grace and peace,
Mark

Still can't explain why we don't see ERVs shared orthologously between orangutans and humans, but missing from gorilla and chimp, eh mark? Or why the ERVs which do deviate from the nested hierarchy are non-orthologous, as expected by common ancestry?

Why are the ERVs which are shared by all 4 species among the most mutated? Why are the ones shared only by chimps and humans among the least mutated? Why does this also hold true with LTR divergence?

Your incredulity is the real diversion here. Because you fail to offer an alternative explanation for the pattern. You simply can't believe, for some reason, that ERVs can be inserted in the germline...despite the fact that USCognito has presented a paper where we are witnessing it happening in REAL TIME with Koalas. And have also been shown examples of ERVs where the mutations were reversed, and resulted in viable viruses.