Endogenous retroviruses

[Chalnoth]

If so, then, the underlying assumption is that the past was pretty well the same as now.

No need for that at all. Orthologous endogenous retroviruses, when they only exist within a subset of the species surveyed, always exist in a subset consistent with the phylogenic tree. You can't just wave that away by saying the past was different. If you want to say it's not evidence for common ancestry, then you need to suggest an alternative mechanism. You have failed to do this.

 

[dad]

No need for that at all. Orthologous endogenous retroviruses, when they only exist within a subset of the species surveyed, always exist in a subset consistent with the phylogenic tree.

But isn't that circular reasoning? Here is how phylogenic is defined.
"1. The evolutionary development and history of a species or higher taxonomic grouping of organisms. Also called phylogenesis."
http://www.thefreedictionary.com/phylogenic
So evolution is assumed and then you say that the ERVs only fall in a subset of the evo tree?? I thought I explained that? The trace retrovirus would be passed down along the various animals.
Let's say in a monkey. The various evolved species of the originally affected monkey would all be expected to show the pattern. If ten species evolved from the one, they would all have it.
What precisely are you talking about?

 

[Chalnoth]

But isn't that circular reasoning?

Nope. The chance for all ERV's to form into one single hierarchical structure with no mechanism to form such a structure is essentially zero.

And even if you did find another mechanism for producing a hierarchical structure (any hierarchical structure), then you'd also have to show that other methods of forming the phylogenic tree would naturally give the same result. ERV's are not, after all, the only evidence of common ancestry.

 

[mark kennedy]

Are you?

No, of course not. This kind of speculation about how the ERVs came to be in the human genome subsided after the completion of the Human Genome Project. They found that Retroelements in general made up 47% of the human genome and 8%, for the most part, were these ERVs. This kind of a germline invasion is rare and there are immune systems that fight it. They also are connected to certain diseases so the idea that 8% of the genome is framents of viruses is absurd in the extreme.

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

First of all the ERVs are a large part of the differences between chimpanzees and humans. This whole line of arguement is a way of turning the whole concept of comparing DNA sequences on it's head. They don't want to explain the differences so they emphasis the things that are the same.

I've been tracking down the actual ERVs and it's breathtaking how these are being argued as proof of common ancestry. All I can figure is that they are betting the farm that creationists will go endlessly in circles and never really explore the actual differences.

 

[dad]

Nope. The chance for all ERV's to form into one single hierarchical structure with no mechanism to form such a structure is essentially zero.

I didn't say they formed or any chance at all is required! They were passed down, and the process of evolution was at play in the various species at least. The only difference in the ideas we have, is that the passing down of the ERVs began in a different past, from created creatures. That is where the real trees start and end.

And even if you did find another mechanism for producing a hierarchical structure (any hierarchical structure),

I don't need another explanation. I have evolution from creation. Can't beat that.

then you'd also have to show that other methods of forming the phylogenic tree would naturally give the same result.

Starting with created creatures, and then evolving from there gives us all the trees you can ask for.

ERV's are not, after all, the only evidence of common ancestry.

Ah, readying the retreat already. OK.

 

[Tomk80]

Nope. The chance for all ERV's to form into one single hierarchical structure with no mechanism to form such a structure is essentially zero.

And even if you did find another mechanism for producing a hierarchical structure (any hierarchical structure), then you'd also have to show that other methods of forming the phylogenic tree would naturally give the same result. ERV's are not, after all, the only evidence of common ancestry.

What you basically see here is that the method is it's own check.

If the theory of evolution is correct, we should be able to draw up a (twin-)nested hierarchy. To check this, we build a method (cladisitics) that tries to find this hierarchy. If we find such a hierarchy, the theory is correct.

The method is it's own check, because if common ancestry would not be correct, there would be no reason for the method to work. Indeed, if common ancestry was incorrect, the method should not work. Hence, the fact that the method works shows that common ancestry is correct.

We can further check this by applying the method to things that do not have common ancestors, for example things that we have designed. Eldridge did this on cornets (being an avid cornet player and collector). On cornets, the method does not work, because cornets do not have a common ancestor but rather, are the result of designers.

 

[dad]

No, of course not. This kind of speculation about how the ERVs came to be in the human genome subsided after the completion of the Human Genome Project. They found that Retroelements in general made up 47% of the human genome and 8%, for the most part, were these ERVs. This kind of a germline invasion is rare and there are immune systems that fight it. They also are connected to certain diseases so the idea that 8% of the genome is framents of viruses is absurd in the extreme.

So, you are saying what? That the viruses originally got into the creatures how? Or is it that you feel they are not passed down?

First of all the ERVs are a large part of the differences between chimpanzees and humans. This whole line of arguement is a way of turning the whole concept of comparing DNA sequences on it's head. They don't want to explain the differences so they emphasis the things that are the same.

I think you feel somehow, then, as a believer, that the more differences the better? I take it, that is because you don't like the idea that species evolved, and passed the things down?

I've been tracking down the actual ERVs and it's breathtaking how these are being argued as proof of common ancestry. All I can figure is that they are betting the farm that creationists will go endlessly in circles and never really explore the actual differences.

My idea, of course is that the actual differences were in the past, like when we lived a thousand years, etc. Sure seems like a lot of things with the plant and animal life processes and rates etc were different.
So, if whatever the ERV evolved, or adapted from in that different past was passed down by evolution after that point, from those created creatures, doesn't much matter!

 

[Chalnoth]

They also are connected to certain diseases so the idea that 8% of the genome is framents of viruses is absurd in the extreme.

It would be, if we didn't have billions of years for the ERV's to get inserted into the genome. Since we have observed ERV's inserting themselves into DNA, ERV's are another piece of independent evidence of deep time.

First of all the ERVs are a large part of the differences between chimpanzees and humans.

When measured by number of base pairs, sure. Since each (rare) ERV insertion provides pehraps thousands of base pairs to the genome, and because they have a tendency to make copies of themselves, you don't need many ERV's to make for a lot of difference in the number of base pairs. 5-8 million years is quite enough to explain the differences we do see.

This whole line of arguement is a way of turning the whole concept of comparing DNA sequences on it's head. They don't want to explain the differences so they emphasis the things that are different.

I'm sure there are many evolutionary biologists that are very interested in the mechanisms that drive mutations, as well as any natural selection mechanisms that may affect changes between species. You yourself have posted many papers that are investigating these things as they relate to ERV's.

I've been tracking down the actual ERVs and it's breathtaking how these are being argued as proof of common ancestry. All I can figure is that they are betting the farm that creationists will go endlessly in circles and never really explore the actual differences.

If you could find orthologous ERV's that violate the currently-accepted phylogenic tree to the tune of 32 for every 6 that exist within the accepted phylogenic tree. You would need this many violations for ERV's to be consistent with no phylogenic tree (from my previous calculations here).

 

[dad]

What you basically see here is that the method is it's own check.

If the theory of evolution is correct, we should be able to draw up a (twin-)nested hierarchy. To check this, we build a method (cladisitics) that tries to find this hierarchy. If we find such a hierarchy, the theory is correct.

The method is it's own check, because if common ancestry would not be correct, there would be no reason for the method to work. Indeed, if common ancestry was incorrect, the method should not work. Hence, the fact that the method works shows that common ancestry is correct.

But if common ancestry was only started from created kinds, and the species and whatnots evolved FROM there, then the method does still work, but the concept of common ancestry cannot go back any further than the created ancestors. Therefore the cladistics dreaming goes way way too far, riding the coat tails of a principle that is good, but limited!

 

[Tomk80]

But if common ancestry was only started from created kinds, and the species and whatnots evolved FROM there, then the method does still work, but the concept of common ancestry cannot go back any further than the created ancestors. Therefore the cladistics dreaming goes way way too far, riding the coat tails of a principle that is good, but limited!

Well, if common ancestry was started from created kinds, cladisitics should be able to derive these kinds. The fact that, with cladistics, we can go all the way up to a complete tree of life which includes all life on earth, shows that common ancestry was in fact started from a single organism. Whether that organism was created or not is more for the chemists amongst us to find out.

 

[Chalnoth]

But if common ancestry was only started from created kinds, and the species and whatnots evolved FROM there, then the method does still work,

Then the method would only work up to a point. But we see nested hierarchies all the way back to the simplest animal forms, strongly indicating one single common ancestor, not multiple instances of special creation. For example, all life shares nearly identical genes for performing basic cellular functions such as making proteins from DNA and copying DNA.

 

[mark kennedy]

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.

You are really going to have to come to grips with the fact that this buisness of ERVs being the result of germline invasions is wrong:

I really don't see where they came from as that important, though.

It's simple really, if they were not from a germline invasion then the whole probablity of seperate invasions at the exact same location goes up in smoke.

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.

Normally I would string this along but you are talking in circles. The source is absolutly essential to you arguement, you know what I am talking about right?

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.

Which family of ERVs to you want to talk about because I have yet to see one named. If you tell me which ones you are talking about then I can look them up but argueing in circles around probability statistics is pointless unless you know what the figures used were based on.

I know. I think it's because you don't want to accept that humans evolved.

You don't know how bad I want to know exactly how evolution works, that's your problem. I believe in a very radical version of evolution that does not include apes and humans having a common ancestor.

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.

That is enough, which ERVs are you talking about? I would like to know their location, class and how they have been characterized. I would just love to refute this ridiculas line of argumentation but you are simply arguing in circles.

 

[mark kennedy]

Then the method would only work up to a point. But we see nested hierarchies all the way back to the simplest animal forms, strongly indicating one single common ancestor, not multiple instances of special creation. For example, all life shares nearly identical genes for performing basic cellular functions such as making proteins from DNA and copying DNA.

The tree was made up before there was such a thing as evolututionary biology, did you know that? It's an a priori assumption that cannot predict the level of diversity between closely related taxa. They said for decades that we were 99% ape in our DNA and now they don't want to admit they were wrong. Evolution is not about things that are the same, it's about the change of alleles in populations over time. The burden of proof is on getting a demonstrated mechanism for those changes and you don't have one.

 

[dad]

..For example, all life shares nearly identical genes for performing basic cellular functions such as making proteins from DNA and copying DNA.

So what?? How much life was created with no genes?? What do you think, cells ought to be different in each kind of creature?? Many students use pencils and pens, does this mean they all came from the same parents? Cars use bolts, and wires, do they all come from the same plant? Many creatures have eyes, does that mean they should all be the same creature? How would similar creted building blocks of life not exist from creation, any more or less than evolution from a virus, or lifeform??

 

[Chalnoth]

It's simple really, if they were not from a germline invasion then the whole probablity of seperate invasions at the exact same location goes up in smoke.

No it doesn't, because my probability estimate, as I've explained to you a number of times, assumes nothing about the probability of separate invasions at different locations. My probability estimate assumes that parallel transmission of ERV's at orthologous positions is highly probable (never mind that there is no known process for such transmission). And that estimate comes up with an absurdly miniscule probability for ERV's being consistent with no phylogenic tree existing.

You don't know how bad I want to know exactly how evolution works, that's your problem. I believe in a very radical version of evolution that does not include apes and humans having a common ancestor.

You're welcome to try to find one, but the evidence all points towards a common ancestor. I think your search is just wishful thinking.

That is enough, which ERVs are you talking about? I would like to know their location, class and how they have been characterized. I would just love to refute this ridiculas line of argumentation but you are simply arguing in circles.

Let's just take the ERV's found in the Lebedev et. al. 2000 paper. Those alone are more than enough to show that the phylogenic tree exists.

 

[dad]

Well, if common ancestry was started from created kinds, cladisitics should be able to derive these kinds.

How?

The fact that, with cladistics, we can go all the way up to a complete tree of life which includes all life on earth,

Try not to forget you are only going there in your mind. Cladistics assumes evolution, and doesn't know where to stop.

shows that common ancestry was in fact started from a single organism.

False, in no way does it even begin to show that. How do you claim it does that?

 

[Chalnoth]

The tree was made up before there was such a thing as evolututionary biology, did you know that?

Yes. Because life exhibits a hierarchy of form at every level. The strict hierarchy was obvious to those studying life before the existence of any theory that would explain this hierarchy. As we obtain more and more data about life, particularly genetic data, we modify the tree to keep it consistent with all collected data.

 

[Tomk80]

The tree was made up before there was such a thing as evolututionary biology, did you know that?

Now why would that be?

It's an a priori assumption that cannot predict the level of diversity between closely related taxa. They said for decades that we were 99% ape in our DNA and now they don't want to admit they were wrong.

No Mark, it is not an a priori assumption. It is a conclusion from the evidence, both on a morphological and genetic level. It holds for apes (including us) too. It will be interesting to see what happens when other genomes are fully analyzed though.

Evolution is not about things that are the same, it's about the change of alleles in populations over time. The burden of proof is on getting a demonstrated mechanism for those changes and you don't have one.

Yes we do. That you do not want to accept it does not mean it we don't know it.

 

[dad]

...Evolution is not about things that are the same, it's about the change of alleles in populations over time. The burden of proof is on getting a demonstrated mechanism for those changes and you don't have one.

If there was no adapting and evolving, how do you explain the animals on the ark? They woudn't all fit, if we too, say the thirty some odd species of tigers, etc. So, the mechanism then would be the created mechanism. Obviously something changed, and evolution is slowed to a crawl.

 

[Tomk80]

How?

Because cladistics would then not arrive at a single tree, but at multiple different trees.

Try not to forget you are only going there in your mind. Cladistics assumes evolution, and doesn't know where to stop.

Because common ancestry is true. I've already explained this.

False, in no way does it even begin to show that. How do you claim it does that?

Because we can draw up a single tree. If a universal common ancestor would be correct, there would be no reason why we would be able to arrive at such a tree.