• Starting today August 7th, 2024, in order to post in the Married Couples, Courting Couples, or Singles forums, you will not be allowed to post if you have your Marital status designated as private. Announcements will be made in the respective forums as well but please note that if yours is currently listed as Private, you will need to submit a ticket in the Support Area to have yours changed.

Endogenous retroviruses

Chalnoth

Senior Contributor
Aug 14, 2006
11,361
384
Italy
✟36,153.00
Faith
Atheist
Marital Status
Single
Meaning what, exactly? Of primates?
Of everything. All life fits into a nested hierarchy.

What is it that it doesn't explain? If wicked pre flood humans infected various primates, and they adapted into other species, etc etc, you really are not saying anything here.
These aren't not independent infections, as independent infections would have existed at different parts of the genome. You're actually suggesting that the interbreeding resulted in children. That is an absurd suggestion on a number of different levels.

And what's more, you haven't explained how such 'relations' could possibly explain a nested hierarchy.
 
Upvote 0

Chalnoth

Senior Contributor
Aug 14, 2006
11,361
384
Italy
✟36,153.00
Faith
Atheist
Marital Status
Single
Devil's advocate:
But if you acknowledge that ERVs are transposable, doesn't that detract credibility from your having ostensibly identified them at the same loci?

Say you claim that ERV-X was found in both chimps and humans at locus A, and that this proves a common origin. But ERV-X might exist at another locus B in the human genome. I claim that God originally created the chimp with ERV-X at locus A in chimps and at locus B in humans, over time ERV-X transposed over to locus A and that's how your ostensible "connection" came about, by a fluke transposition. Who's to say that I'm wrong and you're right?
Any mechanism for creating coincidences like this would randomize the derived phylogenic tree, and, if it were significant, would result in an inability to derive any phylogenic tree. Since we see a very strict phylogenic tree, such coincidences are exceedingly rare.
 
Upvote 0

Loudmouth

Contributor
Aug 26, 2003
51,417
6,143
Visit site
✟98,025.00
Faith
Agnostic
Meaning what, exactly? Of primates? What is it that it doesn't explain?

The pattern of shared ERV's among all primates fits into a nested hierarchy, as do the mutations found in the ERV's themselves. For your "evolution post-flood", this would require a single common ancestor for all primates (apes, old world monkeys, and new world monkeys) including humans.

If wicked pre flood humans infected various primates, and they adapted into other species, etc etc, you really are not saying anything here.

Retroviruses insert randomly among thousands of insertion sites. As I have already shown, the chances of two individuals sharing 20 ERV's through separate infections is highly, highly improbable. The best explanation for shared ERV insertions at orthologous locations in the genome is common ancestry.

If you have siblings you will share hundreds of ERV's at orthologous positions in your genomes. Guess what? Your parents will also have those same insertions at the same spots in their genome. This is exceedingly simple to explain because ERV's are passed down through heredity like any other gene. The same simple, logical explanation is given for ERV's shared by individuals from different species.

True, and what do we observe that is not fantasy here, exactly? Virus infected much of the primate species, and man in the past?

And retroviruses continue to infect us today. The vast majority of the time these viruses infect somatic cells, the cells that make up your functioning body. When viruses insert into these cells it is not inherited by your children. However, on very, very rare occasions a retrovirus will insert into a gamete (egg or sperm). If the retrovirus insertion does not kill the gamete it will become part of that gametes genome. If that gamete is part of creating an offspring, then that retrovirus insertion in the gamete will become part of that offspring's genome, and it will also be found in approx. 50% of that child's offspring. It is not a simple matter of just being infected by the same virus because 1) retroviruses insert randomly into the genome, 2) it is a very rare event.

Or you can rely on your Quixotish fantasies and continue to tilt at windmills.
 
Upvote 0

Schroeder

Veteran
Jun 10, 2005
3,234
69
OHIO. home of THE Ohio State Buckeyes
✟26,248.00
Faith
Anabaptist
Marital Status
Married
Politics
US-Constitution
Whenever you find an object or observation that appears in such a way that it could not have arisen randomly, that is a sign of some sort of process behind that object or observation. Once you find the right process, the unlikely suddenly becomes expected.

Here we have a series of markers that are inherited from parent to child, and exist between species only in a strict hierarchy consistent with the phylogenic tree. The obvious process through which such a thing could become expected is that this is a family tree.

Now, I'm going to assume that you were talking about abiogenesis here, and the probability of abiogenesis calculations. Here again, what we should do is find a process through which abiogenesis can occur, not say that it couldn't. Scientists have done this, and there are currently a large number of abiogenesis theories that are highly plausible. We don't yet know which of them, if any, is correct, but perhaps one day we'll be able to obtain experimental evidence that supports one or the other.
when you ONLY look at it through one IDEA then yes thta is all your consider. the odds are just as good for the other reasons given for it. you just do not wish to accept them because you will not look through a different consideration. meaning if ALL you accept is the theory then they only way you will consider HOW it happens is through the Theory. But math calculations have shown the propability of it is VERY VERY VERY VERY unlikely, YET it is still considered a reasonal chance it did happen. YET given the same chance for our ideas to be correct and it should not even be considered. we are ignorant to think it possible. AS i said ARON RA told me once it only has to happen once no matter what the odds are. this thinking gives you just a little leeway in showing the theory to be true. I do agree that there is nothing wrong with this and that science should studying to find the truth no matter what the odds may be. BUT why does it only apply to one side.
 
Upvote 0

Schroeder

Veteran
Jun 10, 2005
3,234
69
OHIO. home of THE Ohio State Buckeyes
✟26,248.00
Faith
Anabaptist
Marital Status
Married
Politics
US-Constitution
I'm still confused about something, when precisely in a cell's life cycle does this "transposition" occur? And is transposition a rare or common process? Does it happen on an organismal or populational level? (Does that last question actually have any useful answer or does it show that I've misunderstood something?)

Devil's advocate:
But if you acknowledge that ERVs are transposable, doesn't that detract credibility from your having ostensibly identified them at the same loci?

Say you claim that ERV-X was found in both chimps and humans at locus A, and that this proves a common origin. But ERV-X might exist at another locus B in the human genome. I claim that God originally created the chimp with ERV-X at locus A in chimps and at locus B in humans, over time ERV-X transposed over to locus A and that's how your ostensible "connection" came about, by a fluke transposition. Who's to say that I'm wrong and you're right?
but this is not science it is just a reasoning. one that i doubt there try to follow up. there is no point in trying to find a alternative reasoning when they have found one that fits rather nicly into there thinking and has science to back it up. And no real fallback if it is wrong.
 
Upvote 0

JohnR7

Well-Known Member
Feb 9, 2002
25,258
209
Ohio
✟29,532.00
Faith
Pentecostal
Marital Status
Married
The best explanation for shared ERV insertions at orthologous locations in the genome is common ancestry.
Actually ERV's do more to falsify common ancestry, because they just do not show up where they should or where you would expect to find them.
 
Upvote 0

caravelair

Well-Known Member
Mar 22, 2004
2,107
77
46
✟25,119.00
Faith
Atheist
when you ONLY look at it through one IDEA then yes thta is all your consider.

there is only one theory that predicts the nested hierarchy of species, and that's common descent. since it predicts exactly what we find, then that makes this evidence for common descent. since no other theory makes this same prediction, it can only be evidence for evolution.
 
Upvote 0

Schroeder

Veteran
Jun 10, 2005
3,234
69
OHIO. home of THE Ohio State Buckeyes
✟26,248.00
Faith
Anabaptist
Marital Status
Married
Politics
US-Constitution
there is only one theory that predicts the nested hierarchy of species, and that's common descent. since it predicts exactly what we find, then that makes this evidence for common descent. since no other theory makes this same prediction, it can only be evidence for evolution.
see you just made my point. you will not look outside the box of evolution theory. the nested hierarchy of species is wrong or could be wrong. seeing how it was not predicted it was made up to show evidence for the thoery.
 
Upvote 0

caravelair

Well-Known Member
Mar 22, 2004
2,107
77
46
✟25,119.00
Faith
Atheist
see you just made my point. you will not look outside the box of evolution theory.

i am perfectly willing to do that. now please show me an alternate theory that predicts that the nested hierarchy of ERV insertions should match the one predicted by morphology. if you can't then there's nothing "outside the box" for me to look at. as i mentioned above, common descent predicts the nested hierarchy. it is because of the prediction that this is evidence for common ancestry. if you can show me another theory that makes the same prediction, then that would be evidence for that theory too. can you?

the nested hierarchy of species is wrong or could be wrong.

yes it could be, and if we found out that it was, then evolution would be falsified. no one has ever been able to find a species that does not fit in to the nested hierarchy (a horse with bird wings would do, or any other chimera), or a sharing of ERV insertions that violates the nested hierarchy. if they find one of these things, then it will falsify evolution. that's what makes it a scientific theory, it's falsifiable. since no one has been able to falsify it, that makes it good science.

seeing how it was not predicted it was made up to show evidence for the thoery.

nonsense. this proves you have no idea what you're talking about.
 
Upvote 0

sfs

Senior Member
Jun 30, 2003
10,839
7,861
65
Massachusetts
✟394,207.00
Country
United States
Gender
Male
Faith
Non-Denom
Marital Status
Married
I'm still confused about something, when precisely in a cell's life cycle does this "transposition" occur? And is transposition a rare or common process? Does it happen on an organismal or populational level? (Does that last question actually have any useful answer or does it show that I've misunderstood something?)
As far as I know, transposition can occur anytime the ERV is transcribed. The transcript is read back into DNA by reverse transcriptase (produced by the local gene in the ERV, if that is functioning, or produced elsewhere in the genome), and the resulting DNA is integrated into a chromosome. (How and when the integration takes place I don't know.) If the cell in question happens to be a germ cell, the result is a germ-line mutation.

Transposition (of all sorts, not just ERV transposition) is quite rare in humans, more common in mice and very common in fruit flies, where it causes more than 50% of mutations. Like any mutation, a transposition occurs in a single germ cell of a single individual. Thereafter it may spread through the population or it may disappear due to random genetic drift.


Devil's advocate:
But if you acknowledge that ERVs are transposable, doesn't that detract credibility from your having ostensibly identified them at the same loci?

Say you claim that ERV-X was found in both chimps and humans at locus A, and that this proves a common origin. But ERV-X might exist at another locus B in the human genome. I claim that God originally created the chimp with ERV-X at locus A in chimps and at locus B in humans, over time ERV-X transposed over to locus A and that's how your ostensible "connection" came about, by a fluke transposition. Who's to say that I'm wrong and you're right?
When doing any phylogenetic reconstruction, you have to be aware of the possibility that a diagnostic trait you're using could have occurred independently in two different lineages, and you'd better be able to show that the frequency of this event (which is called "homoplasy", by the way) is low enough that it will not fatally damage your analysis.

In humans and near relatives, transposition is rare and this is not a significant concern. There are something like a few hundred thousand copies (mostly truncated) of ERVs in our genome, which has 3 billion base pairs. If humans have ERV-X at locus A, the probability that chimpanzees have some ERV at exactly the same locus (that is, between the same base pairs) is not that small -- perhaps 1 in a few thousand, if you assume ERVs insert at random, perhaps as high as 1% if you take into account biases in the insertion process. Start comparing multiple species, and the probability of finding something at that spot for spurious reasons should be a real concern.

But a sane analysis won't look for any old ERV at the same locus; it will look for an ERV from the same sub-family. There may only be a couple of hundred copies of that particular subfamily around, and the odds that one inserted in the chimpanzee lineage at exactly the same point are a few hundred out of 3 billion, or something like 1 in ten million.
 
Upvote 0

Chalnoth

Senior Contributor
Aug 14, 2006
11,361
384
Italy
✟36,153.00
Faith
Atheist
Marital Status
Single
But a sane analysis won't look for any old ERV at the same locus; it will look for an ERV from the same sub-family. There may only be a couple of hundred copies of that particular subfamily around, and the odds that one inserted in the chimpanzee lineage at exactly the same point are a few hundred out of 3 billion, or something like 1 in ten million.
Let alone a dozen of them, which brings us into the absurd probability region.
 
Upvote 0

Loudmouth

Contributor
Aug 26, 2003
51,417
6,143
Visit site
✟98,025.00
Faith
Agnostic
Actually ERV's do more to falsify common ancestry, because they just do not show up where they should or where you would expect to find them.

Examples please? I know of a select few in the human/chimp/gorilla lineage, but these are easily explained by heterozygosity in the ancestral group. This would be expected in cases where species divergence occurs in a brief amount of time, as is the case in the human/chimp/gorilla lineage. IOW, the common ancestor was heterozygotic for the ERV, and it was bred out of the human lineage while it became fixed in the chimp and gorilla lineages. If this was common I would agree that ERV's are evidence against common ancestry, but these occurences are extremely rare.
 
Upvote 0

Loudmouth

Contributor
Aug 26, 2003
51,417
6,143
Visit site
✟98,025.00
Faith
Agnostic
when you ONLY look at it through one IDEA then yes thta is all your consider.

When you require evidence for a proposed mechanism all you are left with is common ancestry. Occam's Razor cuts off unevidenced deities from the explanation. As soon as you offer observed instances of a deity inserting ERV's into the genomes of living species I will grant that explanation plausibility.

the odds are just as good for the other reasons given for it. you just do not wish to accept them because you will not look through a different consideration. meaning if ALL you accept is the theory then they only way you will consider HOW it happens is through the Theory.

Actually, it's straight Mendellian genetics. It has nothing to do with the ToE. It just so happens that the ToE predicts the pattern observed.

But math calculations have shown the propability of it is VERY VERY VERY VERY unlikely, YET it is still considered a reasonal chance it did happen.

If there is another OBSERVED MECHANISM (Mendellian genetics) that is MUCH MUCH MUCH MUCH MORE likely, then that is the better explanation. Again, you and your siblings (if you have any) share hundreds and hundreds of ERV's at the same position in your genomes. If you sequenced your parents genomes those same ERV's would be found at the same spot in their genomes. The chances that all of those shared ERV's are due to separate infections between your parents, your siblings, and you is frighteningly small. The best explanation is simple Mendellian genetics. The same logic is applied to individuals from different species.

AS i said ARON RA told me once it only has to happen once no matter what the odds are.

We are talking about more than one occurrence, we are talking about multiple occurrences.

I do agree that there is nothing wrong with this and that science should studying to find the truth no matter what the odds may be. BUT why does it only apply to one side.

Why does one side (evolution) have to provide evidence while the other side (creationists) have no other evidence than their faith in a literal interpretation of a holy book? If you were truly being fair you would supply us with observations of this deity inserting ERV's into the genomes of living species. If you can't, then there is no reason why we should consider it given the ample observations of viral insertion in the field and lab.
 
Upvote 0

dad

Undefeated!
Site Supporter
Jan 17, 2005
44,905
1,259
✟25,524.00
Country
Canada
Gender
Male
Faith
Christian
Marital Status
Private
Of everything. All life fits into a nested hierarchy.
In other words, we can group it a certain way, which really is neither here no there. As for the virus traces in primates, do you claim some pattern that what I said could not account for in a different past or not???

These aren't not independent infections, as independent infections would have existed at different parts of the genome. You're actually suggesting that the interbreeding resulted in children. That is an absurd suggestion on a number of different levels.
Now, yes, but not in a different past, perhaps, where the molecular level changes mean that the present is not the standard it is to be measured.

And what's more, you haven't explained how such 'relations' could possibly explain a nested hierarchy.
Well, perhaps you could explain what is unexplained? If a man and a monkey had an offspring, would not some of that viral trace stuff be passed down?
 
Upvote 0

dad

Undefeated!
Site Supporter
Jan 17, 2005
44,905
1,259
✟25,524.00
Country
Canada
Gender
Male
Faith
Christian
Marital Status
Private
The pattern of shared ERV's among all primates fits into a nested hierarchy, as do the mutations found in the ERV's themselves. For your "evolution post-flood", this would require a single common ancestor for all primates (apes, old world monkeys, and new world monkeys) including humans.
No the wicked pre flood people could have ritually mated with many kinds of primates. Then, the hyper adaption, still possible then, may have branched it out furhter, just exactly the way we see it, no?



Retroviruses insert randomly among thousands of insertion sites. As I have already shown, the chances of two individuals sharing 20 ERV's through separate infections is highly, highly improbable. The best explanation for shared ERV insertions at orthologous locations in the genome is common ancestry.
I just gave you that, so now what's the problem???

If you have siblings you will share hundreds of ERV's at orthologous positions in your genomes. Guess what? Your parents will also have those same insertions at the same spots in their genome. This is exceedingly simple to explain because ERV's are passed down through heredity like any other gene. The same simple, logical explanation is given for ERV's shared by individuals from different species.
OK, then the wicked pre flood explains things. Anything else you need a little help on??


And retroviruses continue to infect us today. The vast majority of the time these viruses infect somatic cells, the cells that make up your functioning body. When viruses insert into these cells it is not inherited by your children. However, on very, very rare occasions a retrovirus will insert into a gamete (egg or sperm). If the retrovirus insertion does not kill the gamete it will become part of that gametes genome. If that gamete is part of creating an offspring, then that retrovirus insertion in the gamete will become part of that offspring's genome, and it will also be found in approx. 50% of that child's offspring. It is not a simple matter of just being infected by the same virus because 1) retroviruses insert randomly into the genome, 2) it is a very rare event.
Very rare now, yes, but why would it be rare in a different past????! I mean living a thousand years is pretty rare now, no? Ha. So, this means there was a huge difference in the way things worked. Case solved, it seems. Unless you want to try to relegate the past to the present state. But you can't do that, so all we can look for is the best and simplist explanation.

Or you can rely on your Quixotish fantasies and continue to tilt at windmills.
Sancho, my steed!
 
Upvote 0

Tomk80

Titleless
Apr 27, 2004
11,570
429
45
Maastricht
Visit site
✟36,582.00
Faith
Agnostic
see you just made my point. you will not look outside the box of evolution theory. the nested hierarchy of species is wrong or could be wrong. seeing how it was not predicted it was made up to show evidence for the thoery.
It could be wrong, yes. But it is not wrong, or at least not shown wrong up to this point.
 
Upvote 0

Chalnoth

Senior Contributor
Aug 14, 2006
11,361
384
Italy
✟36,153.00
Faith
Atheist
Marital Status
Single
In other words, we can group it a certain way, which really is neither here no there. As for the virus traces in primates, do you claim some pattern that what I said could not account for in a different past or not???
Yes, I claim that you cannot account for ERVs in any other way than humans and other apes once were one single species that diverged. You simply cannot explain why the ERV's stay within a strict tree formation. Your laughable bestiality explanation predicts the furthest thing from a strict tree, and doesn't come close to explaining how we have ERV's in common with species much more different than us. Furthermore, your bestiality explanation would predict that we would see 'half breeds' which are not only completely impossible, but would be incredibly obvious.
 
Upvote 0

dad

Undefeated!
Site Supporter
Jan 17, 2005
44,905
1,259
✟25,524.00
Country
Canada
Gender
Male
Faith
Christian
Marital Status
Private
Yes, I claim that you cannot account for ERVs in any other way than humans and other apes once were one single species that diverged. You simply cannot explain why the ERV's stay within a strict tree formation. Your laughable bestiality explanation predicts the furthest thing from a strict tree,
First of all the tree is imagined, if I recall, just a grouping of certain creations, as if they evolved from one another. The issue at hand is the primates, and the ervs. I could see ruling out some ideas if you had a good case. I can't see that at all yet. Precisely what ervs are in what apes chimps, or monkeys, that could not be explained as wicked pre flood contact, some offspring, and a mess of adapted or 'evolved' species from them?? (For example, there are some thirty five or something like that, species of tigers, all coming from the one on the ark)

and doesn't come close to explaining how we have ERV's in common with species much more different than us.
That, likely would have to be a different past's different way of dealing with virii. After all, if we look at bible documentation, and the long lifespans recorded there, we can assume that disease was dealt with far differently, as well as any virus, germs, etc.
As a curiousity, I might ask what we know of the ervs, to where the virus was identical to today's or not!?? After all they do mutate, and a flu changes. etc.
Nowthen, if the virus of the past were benefitial, why that might change the whole picture! So, we need to look at precisely what we actually KNOW, and seperate that from the things we assume.


Furthermore, your bestiality explanation would predict that we would see 'half breeds' which are not only completely impossible, but would be incredibly obvious.
Good point. But, how do we know, say, chimps are not half breeds? Or, some original primate 'kind' that adapted to chimps?
I would like to rule this one out. One would think that God would have had some barriers there that would have prevented that sort of thing, like today.

I am starting to like the other idea more.

EDIT:
" Typically, ancient proviruses have sustained numerous point mutations, deletions, and insertions, rendering them incapable of expressing virus. No biologically active viruses have been associated with the ancient proviruses. .."
http://www.pnas.org/cgi/content/full/96/18/10254
Sounds like they really don't know whether the leftovers really were not something used in another process than we know. The bad virus we might know today, that evolved from possibly a good one, or less bad one, then, seems beyond our ability to determine?! Therefore, we can toss out assumptions of how things are now spread, and some such things!?
". HERV-KC4, HERV-KHML6.17, and RTVL-Ia are found in both OWMs and hominoids, ..... By contrast, HERV-K18, RTVL-Ha, and RTVL-Hb are found only in humans, chimpanzees, and gorillas"
Seems we might then have some chance of looking at why some things are, such as the pattern mentioned above. Offspring are no longer needed to account for things! Wow.
 
Upvote 0