Endogenous retroviruses

dad · #**371** 20th October 2006, 08:15 PM

Originally Posted by Loudmouth

You use the books of today to tell me that a split happened in the past. Guilty as charged.

You can use no books, past or present to support your same past. I am redeemed.

What living one? Evidence please.

The One that gives evidences to those that seek Him only. The One that has revealed Himself to the world, and rose from the dead.

Not assumed. They are inferred from data.

Same thing. Because the data is interpreted only using an unsupportable same past!

So you accept the mechanism of common ancestry. That's a step forward.

The mechanism is fine, as a created trait. Nowhere will you find evidence to keep going clear past creation with that puppy, though.

Now, as I said before, you and your siblings share hundreds of ERV's that are found at the same spots in your genome. What are the chances that randomly inserting retroviruses infected you and your siblings during your life time and inserted into the same spots in your genome? Extremely, extremely small. I say the shared ERV's are due to common ancestry.

Since the present life processes started our ancestors from the present passed down the ervs. Before that, they came to be apparently quite differently. So, yes, they started to get passed down as the present came to be. The ones that were there already were passed down, and the new ones picked up in the present process also passed down!

I would then sequence your parents' genomes and guess what I would find? Those same exact ERV's. All I am doing is applying the same logic to different species. Please show me why this should not be done.

And I apply the logic in the above post, both which give us exactly what we see today! So, then, to make yours more valid, you need a same past, and past life processes. Too bad you don't have that, eh?

Again, you are telling a lie. The nested hierarchies have nothing to do with beliefs. They are facts. Nested hierarchies, in and of themselves, do not require common ancestry.

Great. Tell you the truth the idea confuses me, and the words just don't mean much to me, nested heirachy. So, where this grouping varies from a garden of Eden start, in a different past, it is a lie! The groupings themselves, however you BELIEVE they should be arranged, don't matter. It is the beliefs and assumptions behind the idea that is a lie. No one argues some grouping may not have ERVs or whatnots.

In fact, nested hierarchies can exist in non-living things as well. For example, matter falls into a nested hierarchy. All molecules are made up of atoms. All atoms are made up of quarks, but not all atoms are molecules. All molecules are made up of quarks. This type of hierarchy is nested where molecules are made up of atoms which are made up of quarks. In the same way, life falls into a nested hierarchy.

Why do you insist on that phrase? I could say that all things in the PO universe fall into a N.H. Even the order in the spirit world, as in the military falls into a N.H. But that really does not crystalize any clear point, or claim, or concept. I sometimes wonder if you are talking about primates, and that grouping, or,...etc? Why not just say what you mean? -Rather than promote a catch phrase?

All primates are mammals, all mammals are vertebrates, and all vertebrates are eukaryotes. Shared ERV's fall into the same pattern. Even Linnaeus, a creationist, noticed that life falls into a nested hierarchy and he did not believe in evolution.

That pattern, precisely is what? That they get carried down now, in this present world? So?

This insistence that nested hierarchies only exist in the minds of evolutionists is perhaps the biggest lie in this thread.

Well, if you talk english, and put your cookies on a lower shelf, people just might take a few.

Again, "knowing" is something that requires ultimate knowledge, something that scientists never claim to have. However, there is very strong evidence that these viruses act just as they do today, and that they evidence common ancestry.

Well, knowing is easy as pie. I know that if I jump off a tall tower, I will fall down. I know if I turn on the lights, the room will get light. No shadow of doubt in my mind at all. I know the sun will rise. I don't know that I'll be here in a physical body to see it, mind you. I do not question laws of physics as applied to where they apply, right in the present. I do not question that viruses are passed down, or dna, or etc etc etc. Nothing at all do I question much, I simply accept what we know.
But that has nothing to do with also accepting that we are, as the bible says, and science is mum about, in a temporary universe! Like a fishbowl, and all we know of this physical only fishbowl applies just here, not outside to the past and future. That has just been assumed. Including how genetics work now. Including how evolution works now. Etc.

It makes testable assumptions, otherwise known as inferrences.

You cannot test the state of the universe in the past, and the life process and atomic and molecular stuctures there! Therefore you can't infer. You can assume it is inferrable!!!

If you can find a virus that inserts at the same spot in the genome time after time then you can cast strong doubt on this evidence.

It doesn't exist any more, if it ever did! Maybe when it did, it was something else than a virus as we know it? Maybe it was useful in the life processes of the day? Any evidence on that, one way or the other? You can't just come up with a missing, what we think was a virus case, and expect that to fly beyond the present, now can you??

Until you do, then we are stuck with the observation that retroviruses insert randomly into a genome among thousands of insertion sites.

They do! But did they, that is the question. Why precisely is it random? Do you even know that much? If not, how would we know why it wasn't random, if it wasn't??

Even genetically identical cells infected by the exact same virus will carry ERV's at different spots in their genome. I can link to that study if you want, but I think it will probably be ignored with the rest of the evidence.

No, I accept that, but it is inadmissable for the past, unless you give us a same past. You can't so you, and your observations, I am afraid, are stuck right here in the present where they apply!!! Get it?

The only assumptions are that those animals have those features. Let's take a look at vertebrates and some gross anatomical structures.

Not too gross, I hope.

Mammals, reptiles, birds, and amphibians are all vertebrates. They fit into the vertebrate hierarchy.

Then that word is too broad! That's like saying God made everything in a week, period. But we know He made birds, and fish the same day. So in that hierarchy, the created one, your order doesn't jive.

Mammals have fur, reptiles have scales, amphibians have permeable skin, and birds have feathers.

Traits of different creature, yes, although the created order doesn't consider that in the way God made it. So it is pretty meaningless, really.

These features are confined to those groups and are not found in any other group. Therefore, each belongs to a separate hierarchy but ALL OF THESE SEPARATE HIERARCHIES ARE NESTED WITHIN THE VERTEBRATE HIERARCHY.

SO WHAT? We could also say, that God created the fish and birds one day, and man and beasts another. But all these seperate HIERARCHIES ARE NESTED WITHIN THE CREATION HIERARCHY. So??? All we do is group things according to our beliefs there, either way!!

All mammals are vertebrates, but not all vertebrates are mammals.

Hey, all men are in the created hierarchy, but not all men are fish. That's fun, guess anyone can play!

Staying with the mammallian group, all primates are mammals, but not all mammals are primates. All apes are primates, but not all primates are apes. All humans are apes, but not all apes are humans. Up and down the animal kingdom all species fit into a nested hierarchy because of the features they have, not because of the imagination of humans.

But all fit into the creation hierarchy! Regardless of how else you desperately try to shuffle the deck here, and get that little phrase in!

I don't care what the Bible says. I care what the evidence says. Again, observation trumps fantasies.

The evidence say things about the observed present, and I don't care what you think the past was like if you can't prove it!

That's what I have done. The distribution of shared ERV's in primates is consistent with common ancestry. If it is not, please show me where the inconsistencies are.

Well, it is now passed down by ancestors, and you simply assume it always and only was in a past that was the same!!!! No can do.

Being infected by the same virus is not the evidence I am presenting. Having the same insertion AT THE SAME SPOT IN THE GENOME is what I am using as evidence. This seems to be ignored by every creationist that is involved in this discussion.

Why is that significant?

I have evidence that the past was the same as today. You have zero evidence that the past was different. I win.

No, you do not have any such thing.

Continuity is evidenced. Discontinuity is not. My case is solid.

No, it is not, not in the state of the universe. We could say that the continuity is a nested heirarchy. It's nest is the present!

I don't need data to ignore something that is unevidenced. Repeat after me. I don't need data to ignore something that is unevidenced. You DO ignore data for the continuity of the physical laws.

Such as??

Then you are doing something other than science. If you want to claim that science is wrong then that is fine. Just don't claim that evolution is wrong in a scientific sense. That is exactly what creationists have been trying to do, force their way into science. This only shows how afraid of science they are.

Evolution in the sense that things evolved, and do evolve is not an issue at all. The 'evolution' that is not science is taking that present observation, and trying to run into the different past they can't prove was a same past with it. Ridiculous.

The problem for you is that there is no barrier between the nested hierarchies at what are supposed to be the created kinds.

All depends on how we group them, and organize them into hierarchies! Boy you sure like that phrase, nested hierarchies!

All mammals fit into a nested hierarchy. All eukaryotes fit into a single nested hierarchy. What you are telling me is that Noah only needed a single prokaryote and a single eukaryote, which is a little different than what I was taught in Sunday School.

He needed just the one kind, yes. They then engaged in a little prokaryote! But, true, I never learned that either, it took some creative deduction, and matching of facts and evidence with the bible record.

I do, as does the rest of science which are using these phylogenies in comparative genomics to search for the cause of disease and potential medications.

So what? I go beyond just looking at the present genome, and look at the eternal sequence coming, and that Adam originally had. I look at the new universe genome that has no disease, or death or sickess, or pain!!!!! Do not presume you can one up me. Science is like a tot playing with little blocks, compared to the knowledge of God.

But there are chimeras in the fossil record. Archaeopteryx is both reptile and bird, for example. It has features of both.

So what? Maybe a repltile or a bird evolved to adapt to the changing planet here, maybe God made a few strange creatures!! I really don't get why that turns your crank.

The whole thing is that we only see the chimeras that are predicted by the ToE. There is no reason that an omnipotent Creator would create in a way that mirrors a theory constructed by a 19th century naturalist. That is, unless that creator used evolution from the very start and a universal common ancestor.

Now don't make too much of a little bird that looked like a reptile, or whatever it was. After all, there is adapting that went on, so it is possible the original kinds are quite hard to distinguish now.

I find it strange that the vocal diatribe of "there are no intermediate fossils" has been replaced by "who cares" in the creationist argument.

Well, not all creationists have evolved as I have in their positions. But from my perspective, there had to be hyper evolution in the past, to explain the species that could not fit on the ark. Still, that does not mean your little bird reptile thingie was not from either a created bird, or a created reptile. Birds did not evolve, they were created. Finding a few strange ones does not mean that the creation nested heirarchy is affected.

Why does creationism not predict a mammal/bird chimera? Please enlighten me.

Birds were created, and beasts were created. They are seperate. If some things were created that look a bit like both, or did some evolving, it does not change a thing as to what was created. Our nested creation heirarchy stands!

Perfect, you agree that evolution is falsifiable. If evolution is false then these intermediates should exist.

I simply said I wouldn't be surprised that bats may have adapted from what they once may have been.

What Eden? Evidence please.

The Eden that created things were made in, and which you have no evidence against, no matter how many times you say your little buzz phrase.

mark kennedy · #**372** 21st October 2006, 03:37 PM

Woah! Miss a couple of days on here and you miss a lot. It was a little supprising to see how much attention this thread got but no matter, let's see if we can get back on subject.

I would like to take another look at these ERVs and so much is buried in the thread I really don't want to have to go back through them. First of all, are you guys seriously on board with the prevailing view that all the ERVs are really the result of germline invasions?

I don't know why the ERVs seem so convincing but it's not the simularities that are so stricking, it's the differences. I posted some things to the formal debate I am having with EA. If you guys want to take a look and bring some of the details up here I would be interested in what you have to say.

dad · #**373** 21st October 2006, 04:27 PM

Originally Posted by mark kennedy

I would like to take another look at these ERVs and so much is buried in the thread I really don't want to have to go back through them. First of all, are you guys seriously on board with the prevailing view that all the ERVs are really the result of germline invasions?

Are you?

I don't know why the ERVs seem so convincing but it's not the simularities that are so stricking, it's the differences.

Bottom line there, what's the point, precisely either way?

Chalnoth · #**374** 21st October 2006, 04:34 PM

Originally Posted by mark kennedy

I would like to take another look at these ERVs and so much is buried in the thread I really don't want to have to go back through them. First of all, are you guys seriously on board with the prevailing view that all the ERVs are really the result of germline invasions?

All ERV families are originally from germline invasions. But germline retranspositions are certainly going to be a mechanism for many ERV's to copy themselves to different places in the genome.

I really don't see where they came from as that important, though. The original source of the ERV's is interesting, to be sure, and provides an explanation for their usefulness in using them to examine the phylogenic tree. But it's not important to the argument of ERV's for common descent. It's sort of like how the theory of gravity explains how gravity works, but the theory is not necessary to know that things fall when you drop them. Similarly, it's not necessary to know where ERV's came from to know that they are tracers of common descent.

The important aspect of ERV's as evidence for common descent is the strict hierarchy that they form. Here we have a heritable genetic marker that exists in a strict hierarchy, with very few exceptions to that hierarchy that are easily explained through known genetic mechanisms. The most obvious way to explain a strict hierarchy of heritable markers is common descent. That's all there is to it.

Originally Posted by mark kennedy

I don't know why the ERVs seem so convincing but it's not the simularities that are so stricking, it's the differences. I posted some things to the formal debate I am having with EA. If you guys want to take a look and bring some of the details up here I would be interested in what you have to say.

I know. I think it's because you don't want to accept that humans evolved. But in order to push ERV's away as support for common descent, you need to explain the strict hierarchy that ERV's form in some other manner. Pointing out methods by which ERV's might be in common between organisms without common descent doesn't help, because any such methods aren't going to result in a strict hierarchy of commonality, and could thus be easily accounted for by just observing where ERV's are found in various species.

Tomk80 · #**375** 21st October 2006, 06:01 PM

Originally Posted by Chalnoth

I know. I think it's because you don't want to accept that humans evolved. But in order to push ERV's away as support for common descent, you need to explain the strict hierarchy that ERV's form in some other manner. Pointing out methods by which ERV's might be in common between organisms without common descent doesn't help, because any such methods aren't going to result in a strict hierarchy of commonality, and could thus be easily accounted for by just observing where ERV's are found in various species.

The differences would be interesting though. Because these should follow the exact same pattern as the ERV's themselves do.

If an ERV was inserted and fully fixed in the genome of the common ancestor of chmips, gorillas and humans, the mutations in the ERV should more or less follow the pattern of common ancestry. For example, a mutation occurring in the gorilla lineage after gorillas split of from humans and chimps, would not be found in the chimp/human lineage. So the differences would this way provide additional evidence for lineages. (this is a bit simplistic of course, there is still the problem of crossing over and not fully fixed mutations, but that would also show in the analysis).

Ondoher · #**376** 21st October 2006, 06:39 PM

Originally Posted by mark kennedy

Woah! Miss a couple of days on here and you miss a lot. It was a little supprising to see how much attention this thread got but no matter, let's see if we can get back on subject.

I would like to take another look at these ERVs and so much is buried in the thread I really don't want to have to go back through them. First of all, are you guys seriously on board with the prevailing view that all the ERVs are really the result of germline invasions?

This is pretty well established, given that we can determine the retroviral families many ERV's belong to, and because they contain what looks like a retroviral genome, or at least parts of one.

Originally Posted by mark kennedy

I don't know why the ERVs seem so convincing but it's not the simularities that are so stricking, it's the differences.

This is actually, true. But probably not in the way you mean. What is striking about the differences in ERV orthologues is how they can be used to infer a phylogeny.

Now, if each identified ERV orthologue present in multiple species implied a different phylogeny, then we'd have to seriously reconsider common ancestry. This is because common ancestry demands that there is a single, true phylogeny of species. This is the phylogeny that results from descent with modification: the true family tree of life. That cladistic analysis of ERV's produce consistent phylogenies is the expected outcome of common ancestry. As far as I can tell, no form of creationism can naturally deduce this pattern.

Originally Posted by mark kennedy

I posted some things to the formal debate I am having with EA. If you guys want to take a look and bring some of the details up here I would be interested in what you have to say.

One thing I noticed about that debate is that when discussing shared pseudogenes, you neglected to address the fact that pseudogenes, like ERV's, can be used to infer phylogenies.

The ascorbic acid pseudogene in question is similarly damaged in primates, and differently damaged in guinea pigs. And in the primate version, the accumulated differences in this pseudogene can be used to infer a phylogeny that matches understood primate relationships. Again, this is the expected, and necessary outcome of common ancestry. I have seen no other explanation put forward to explain the nested hierachy of life as a necessary consequence of that explanation

Chalnoth · #**377** 21st October 2006, 06:44 PM

Originally Posted by Tomk80

The differences would be interesting though. Because these should follow the exact same pattern as the ERV's themselves do.

If an ERV was inserted and fully fixed in the genome of the common ancestor of chmips, gorillas and humans, the mutations in the ERV should more or less follow the pattern of common ancestry. For example, a mutation occurring in the gorilla lineage after gorillas split of from humans and chimps, would not be found in the chimp/human lineage. So the differences would this way provide additional evidence for lineages. (this is a bit simplistic of course, there is still the problem of crossing over and not fully fixed mutations, but that would also show in the analysis).

Well, sure, and that adds even more weight to the idea that ERV's are evidence of ancient germline infections. However, genetic dating is quite inaccurate, due to a large number of factors that can influence mutation rates, so it's not terribly strong evidence, in my opinion. I like ERV homology because it's totally binary evidence: either it's there, or it's not. The uncertainty is almost zero.

Tomk80 · #**378** 21st October 2006, 07:01 PM

Originally Posted by Chalnoth

Well, sure, and that adds even more weight to the idea that ERV's are evidence of ancient germline infections. However, genetic dating is quite inaccurate, due to a large number of factors that can influence mutation rates, so it's not terribly strong evidence, in my opinion. I like ERV homology because it's totally binary evidence: either it's there, or it's not. The uncertainty is almost zero.

I wasn't talking about genetic dating specifically, although the mutations might also give rough estimates in that direction. My main point is that, if common ancestry is correct, not only will the ERV's show a nested hierarchy, but the mutations of ERV's should also show their own, independent nested hierarchy.

dad · #**379** 21st October 2006, 08:13 PM

Originally Posted by Ondoher

Now, if each identified ERV orthologue present in multiple species implied a different phylogeny, then we'd have to seriously reconsider common ancestry. This is because common ancestry demands that there is a single, true phylogeny of species. This is the phylogeny that results from descent with modification: the true family tree of life. That cladistic analysis of ERV's produce consistent phylogenies is the expected outcome of common ancestry. As far as I can tell, no form of creationism can naturally deduce this pattern.

Well, I think I may do just that. I think what is being said here, is that the ERV orthologue ("orthologs are genes in different species which evolved from a common ancestral gene. " Wikopedia) are similar in different creatures. The interpretation being that it was passed down from a common ancestor?
If so, what is it we actually see here? That an ancient virus, or retrovirus, or something similar that evolved down to it's present form, and was in amny species, and kinds of animals.
Because of the way viruses are now transferred, or come to be in an animal, it is assumed it was also this same way in the past. Then, as an explanation, a common ancestor is needed to pass it on down?

If so, then, the underlying assumption is that the past was pretty well the same as now.
If it was drastically different, and the viruses were able to get around in ways they cannot now do, doing whatever different thing they used to do then, they would end up residing in a wide swath of creatures. Therefore, as the processes changed, and the present came to be, we simply see how it is now passed down. All assumptions of common ancestry become nothing more than assumptions that the past was the same. How we doing here so far?
I'll just float that, before driving home the conclusion.

Chalnoth · #**380** 21st October 2006, 08:15 PM

Originally Posted by Tomk80

I wasn't talking about genetic dating specifically, although the mutations might also give rough estimates in that direction. My main point is that, if common ancestry is correct, not only will the ERV's show a nested hierarchy, but the mutations of ERV's should also show their own, independent nested hierarchy.

Well, that's what I meant. The frequency of mutations in the ERV's themselves will be dependent upon the individual biology of the different species, which includes the amount of time between generations. It will also depend upon whether or not specific ERV's become active and selected (which could both increase and decrease the observed mutation rate). There may also be environmental changes that affect mutation rates.

Anyway, I think it's an interesting thing to look at, for sure, but will be much more prone to uncertainties.