A question of ERVs

46AND2 · Dec 17, 2018

xianghua said:
not according to the authors:

"24 sites mapped to similar regions of the human reference genome (approximately 160 kb) and could not be definitively resolved as orthologous or non-orthologous"

so basically they arent sure if these ervs are indeed orthologous or not. and you dont know it either. but the real point here is the fact that these ervs are almost in identical position among primates. this fact alone falsify the claim about nested hierarchy, since there is no real difference between identical site and slmost identical one.

are you sure about that? because even among chimp and human there is about 4% difference. it means that any gene isnt in the same location between chimp and human. so according to this criteria any gene between human and chimp isnt orthologous.

By the way, isn't it the mantra of your side to claim that scientists "discard data that doesn't fit their agenda?"

So why would they include these 12 (out of 287) ERVs which hypothetically COULD be orthologous in their paper?

xianghua · Dec 18, 2018

46AND2 said:
275 of 287 ERVs were not even within 100,000 base pairs of each other...that is unambiguously non-orthologous. So yes, I do know it...and you would, too, if you actually understood what you were reading.

no you dont. this is why they call these specific ervs "ambiguous":

"24 sites mapped to similar regions of the human reference genome (approximately 160 kb) and could not be definitively resolved as orthologous or non-orthologous"

so you probably didnt read the paper or missed that part.

46AND2 said:
There absolutely is a difference between "almost identical" and "identical."

realy?. so there is a big difference between 99% and 98%?

46AND2 said:
Yes, I am sure about that. Because when they found the ERVs in each of the respective genomes, they compared the flanking sequences on either side of the ERVs in both genomes, which indicates that they are inserted at the same spot.

but the ervs cant be in identical position in the genome since chimp and human genomes are different in their length . so it will be near impossible. maybe they refer to the genes order (synteny).

46AND2 said:
No you didn't

are you a thought reader now? thats funny.

46AND2 · Dec 18, 2018

xianghua said:
no you dont. this is why they call these specific ervs "ambiguous":

"24 sites mapped to similar regions of the human reference genome (approximately 160 kb) and could not be definitively resolved as orthologous or non-orthologous"

so you probably didnt read the paper or missed that part.

Yes, those specific sites are ambiguous. So what? I wasn't talking about them. I was talking about the 96% of the sites which were unambiguously non-orthologous. Quit with the red herring, and deal with the issue.

realy?. so there is a big difference between 99% and 98%?

What does this have to do with anything? Another red herring.

I said there is a difference between IDENTICAL and almost identical. Not almost identical and almost identical.

but the ervs cant be in identical position in the genome since chimp and human genomes are different in their length . so it will be near impossible. maybe they refer to the genes order (synteny).

Really grasping at straws now aren't you. Same location as in, hypothetically, right next to the gene for eye color in both species.

pshun2404 · Dec 19, 2018

My apologies to all. My computer died and I am writing this on an old EES netbook (a friends) to say I will not be able to continue participating until the 27th. Still wondering if there are any actual ancient viruses foound and demonstrable that we can compare these alleged insertions/deletions to.

46AND2 · Dec 19, 2018

pshun2404 said:
Still wondering if there are any actual ancient viruses foound and demonstrable that we can compare these alleged insertions/deletions to.

Let's assume that no such ancient virus has been "found," that satisfies your request...because let's face it, no matter what anybody brings forward, you'll have an objection for it. If the Phoenix virus doesn't satisfy it, and a second resurrected virus like this doesn't convince you, then nothing will. And even retroviruses with both endogenous and exogenous versions in other animals like are mentioned here are not good enough, I'm sure.

So let's assume that no such satisfactory comparison exists. Now what?

xianghua · Dec 23, 2018

46AND2 said:
Yes, those specific sites are ambiguous. So what? I wasn't talking about them.

actually you did when you said and prepdicted that we should not find several ervs in the same locations among far species (say in orangutan and human but not in chimp and gorila). but we do find several of them in almost the same location.

46AND2 said:
I said there is a difference between IDENTICAL and almost identical. Not almost identical and almost identical.

sure there is a difference. but only a small one. right?[/QUOTE]

46AND2 · Dec 23, 2018

xianghua said:
actually you did when you said and prepdicted that we should not find several ervs in the same locations among far species (say in orangutan and human but not in chimp and gorila). but we do find several of them in almost the same location.

So what? Almost is the key word. And it makes your post meaningless.

sure there is a difference. but only a small one. right?

No, not right. It's the difference between being passed on through inheritance and not. Pretty big difference.

xianghua · Dec 24, 2018

46AND2 said:
So what? Almost is the key word. And it makes your post meaningless.

again: since there is no big difference between "almost in the same place" and "in the same place" evolution doesnt predict that we will not find ervs in the same place in far species, since there is no big difference between the two from a probability perspective. so evolution predict nothing here actually.

46AND2 said:
No, not right.

so there is no small difference between almost in the same place and in the same place?

46AND2 said:
It's the difference between being passed on through inheritance and not. Pretty big difference.

are you saying that if a gene is in a different place in the genome (say a different chromosome) between 2 species its not the result of common descent?

Justatruthseeker · Dec 24, 2018

And then you all keep ignoring that we use virus to alter genomes in genomic alteration. Virus that target specific types of cells. So why would we not expect virus to invade two separate species that have similar cellular structure?????

46AND2 · Dec 24, 2018

Justatruthseeker said:
And then you all keep ignoring that we use virus to alter genomes in genomic alteration. Virus that target specific types of cells. So why would we not expect virus to invade two separate species that have similar cellular structure?????

Um...what? :scratch:

46AND2 · Dec 24, 2018

xianghua said:
again: since there is no big difference between "almost in the same place" and "in the same place" evolution doesnt predict that we will not find ervs in the same place in far species, since there is no big difference between the two from a probability perspective. so evolution predict nothing here actually.

1. You know that your "almost the same place" that you are trying to argue here is not really very close, right? For those 12 ambiguous viruses, according to that paper, to all have orthologous matches, it's a 1 in 1,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000 chance.

2. If you think evolution predicts "nothing" here, you don't understand the prediction.

so there is no small difference between almost in the same place and in the same place?

No there is more than a small difference, as explained to you several different ways now.

are you saying that if a gene is in a different place in the genome (say a different chromosome) between 2 species its not the result of common descent?

If they are not in orthologous positions, then they are not passed down through inheritance. The reason you have the same 200,000+ ERVs, in the same position, as your parents, is because you inherited them.

Justatruthseeker · Dec 24, 2018

46AND2 said:
1. You know that your "almost the same place" that you are trying to argue here is not really very close, right? For those 12 ambiguous viruses, according to that paper, to all be located in the same spot, it's a 1 in 1,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000 chance.

2. If you think evolution predicts "nothing" here, you don't understand the prediction.

Because you keep ignoring that virus attack the same cells that they have attack mechanisms designed for..... it is what makes genomic alteration possible. Which would not be the case if your propaganda of randomness was anything close to the reality......

If they are not in orthologous positions, then they are not passed down through inheritance. The reason you have the same 200,000+ ERVs, in the same position, as your parents, is because you inherited them.

AFTER they were inserted way back when, correct?

that you confuse the fact that virus attack similar cells in different creatures, and are then passed down as meaning those creatures share common descent, is your confusion about the reality..... not the reality.....

46AND2 · Dec 24, 2018

Justatruthseeker said:
Because you keep ignoring that virus attack the same cells that they have attack mechanisms designed for..... it is what makes genomic alteration possible. Which would not be the case if your propaganda of randomness was anything close to the reality......

AFTER they were inserted way back when, correct?

that you confuse the fact that virus attack similar cells in different creatures, and are then passed down as meaning those creatures share common descent, is your confusion about the reality..... not the reality.....

I ignore it because it is entirely unsupported, and indeed contrary to actual observation.

And it is also irrelevant.

For if what you say is true, there would still be no reason for the pattern of shared ERVs to form a nested hierarchy. Out of tens of thousands of ERVs, for example, there are zero which infected just humans and gorillas, or just orangutans and chimps, nor any other of the many ways that the nested hierarchy can be violated.

The pattern. Explain the pattern. Evolution does so beautifully.

Justatruthseeker · Dec 24, 2018

46AND2 said:
I ignore it because it is entirely unsupported, and indeed contrary to actual observation.

Lol, actual observation shows we use virus for genomic alteration because they tend to target specific cells..... That's why you avoided it.....

And it is also irrelevant.

Because you want to believe that virus which target specific cells would instead be random so you can keep your flawed beliefs that it must mean shared ancestry....

For if what you say is true, there would still be no reason for the pattern of shared ERVs to form a nested hierarchy. Out of tens of thousands of ERVs, for example, there are zero which infected just humans and gorillas, or just orangutans and chimps, nor any other of the many ways that the nested hierarchy can be violated.

The pattern. Explain the pattern. Evolution does so beautifully.

The pattern is explained, they infect cells which are similar to which they have already adapted an attack routine for.

If it was random insertion, then their would be no pattern.... The pattern is perfectly explainable without using the false belief of shared ancestry, but instead the laboratory proven FACT that virus attack specific cells, which is what makes genomic alteration possible.....

Stop ignoring that we use virus in genomic alteration because they attack specific cells, not because their invasion is random......

46AND2 · Dec 24, 2018

Justatruthseeker said:
Lol, actual observation shows we use virus for genomic alteration because they tend to target specific cells..... That's why you avoided it.....

Because you want to believe that virus which target specific cells would instead be random so you can keep your flawed beliefs that it must mean shared ancestry....

The pattern is explained, they infect cells which are similar to which they have already adapted an attack routine for.

If it was random insertion, then their would be no pattern.... The pattern is perfectly explainable without using the false belief of shared ancestry, but instead the laboratory proven FACT that virus attack specific cells, which is what makes genomic alteration possible.....

Stop ignoring that we use virus in genomic alteration because they attack specific cells, not because their invasion is random......

Retroviruses are continuously shown to attack any location in the genome. Whatever engineered example you have is entirely irrelevant to retroviruses.

And the pattern is not explained by your claim. Why aren't there any examples of one that infected orangutans and humans, but not chimps and gorillas? Why are there examples of the same virus at different locations in multiple species, despite your claim that they target specific sites?

Your explanation is as absurd as it is false. In addition to not explaining the pattern at all.

xianghua · Dec 24, 2018

46AND2 said:
1. You know that your "almost the same place" that you are trying to argue here is not really very close, right? For those 12 ambiguous viruses, according to that paper, to all have orthologous matches, it's a 1 in 1,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000 chance.

before i will continue, can i see your calculation please?

46AND2 said:
No there is more than a small difference, as explained to you several different ways now.

so there is a big different between 99% and 100% then? fine. i dont think so.

46AND2 said:
If they are not in orthologous positions, then they are not passed down through inheritance

but many genes arent in the same place and scientists still claims that they are the result of common descent. for instance: some globin genes are on different chromosomes in different creatures. but of course that scientists dont say that all of these genes are the result of convergent evolution (see fig 2):

Evolution of Hemoglobin and Its Genes

so even according to evolution the same gene can be found in non orthologous position. even if it had a common descent.

Justatruthseeker · Dec 24, 2018

46AND2 said:
Retroviruses are continuously shown to attack any location in the genome. Whatever engineered example you have is entirely irrelevant to retroviruses.

Not true at all for any virus from the HIV virus to the flu virus.....

Once again, stop with the propaganda and face the facts that they use virus in genomic alteration because they target specific cells, otherwise the purpose of changing specific cells would be useless...

And the pattern is not explained by your claim. Why aren't there any examples of one that infected orangutans and humans, but not chimps and gorillas? Why are there examples of the same virus at different locations in multiple species, despite your claim that they target specific sites?

Your explanation is as absurd as it is false. In addition to not explaining the pattern at all.

Because those multiple species all share similar cells...... not that those multiple species all share a common ancestor......

It's why flu and cold virus attack only the respiratory cells. Why HIV only attack the T-cells. Neither insert randomly into random cells throughout the body..... despite your claims to the contrary, reality shows those claims to be false....

46AND2 · Dec 24, 2018

xianghua said:
before i will continue, can i see your calculation please?

so there is a big different between 99% and 100% then? fine. i dont think so.

but many genes arent in the same place and scientists still claims that they are the result of common descent. for instance: some globin genes are on different chromosomes in different creatures. but of course that scientists dont say that all of these genes are the result of convergent evolution (see fig 2):

Evolution of Hemoglobin and Its Genes

so even according to evolution the same gene can be found in non orthologous position. even if it had a common descent.

Sure. The BAC method they used only had a resolution down to 100,000 base pairs. The odds that one of those ERVs actually being orthologous, then, is 1 in 100,000. The odds that 2 of them would be orthologous is 1 in 100,000 X 100,000. For all 12, 1 in 100,000 to the 12th power, or 1 in 1,(60 zeroes).

46AND2 · Dec 24, 2018

Justatruthseeker said:
Not true at all for any virus from the HIV virus to the flu virus.....

Once again, stop with the propaganda and face the facts that they use virus in genomic alteration because they target specific cells, otherwise the purpose of changing specific cells would be useless...

Because those multiple species all share similar cells...... not that those multiple species all share a common ancestor......

It's why flu and cold virus attack only the respiratory cells. Why HIV only attack the T-cells. Neither insert randomly into random cells throughout the body..... despite your claims to the contrary, reality shows those claims to be false....

What does cell targeting have to do with anything? You know that nearly every cell contains our entire DNA, right?

When we say that ERVS are in orthologous positions, we mean that they are at the same base pair location within each species, IN EVERY CELL OF OUR BODY.

46AND2 · Dec 24, 2018

Justatruthseeker said:
Because those multiple species all share similar cells...... not that those multiple species all share a common ancestor......

.

Explain the pattern, justa, instead of avoiding it. Yes, they all have similar cells, how does that explain the pattern? Why are there no ERVs which are shared between orangutans and humans, but not chimps and gorillas, despite the fact that all 4 species have similar cells?

Why do virtually all orthologous ERVS form a pattern of nested hierarchy? and why is it that the only times the nested hierarchy is violated is when the ERVs are not orthologous-exactly as we would expect?

A question of ERVs

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