RE: Can ERVs be explained without common descent? (Full Version)

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Method -> RE: Can ERVs be explained without common descent? (5/5/2008 4:40:56 PM)

quote:

ORIGINAL: Jhud
Obviously that is what is in contention, but it would appear that outside aid has been employed.


Let me put it this way. I find it rather juvenile to counter arguments involving the mutation of DNA with "Where did the DNA come from?" diversions. ERV's deal with human evolution and common ancestry with other apes. It does not deal with the origin of DNA or abiogenesis.



Jhud -> RE: Can ERVs be explained without common descent? (5/5/2008 4:45:47 PM)

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But it is strong evidence that chimps and humans share a common ancestor. I have yet to see someone argue that ERV's shared among siblings is due to the actions of an intelligent agent on each genome. Rather, the orthologous ERV's are explained by common descent. I see no reason why this does not extend to humans and chimps, or all primates for that matter.


Well, again, even if we were to assume this (I don’t, but for other reasons), it doesn’t itself do anything to demonstrate the veracity of evolutionary mechanisms.

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Then the ERV was front loaded to cause diabetes, in ID lingo. How does that help?


Proof that this is the case?

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ID fails at telling us why some ERV's are completely neutral and why some are detrimental. Being that the mechanism of ERV insertion is blind to the fitness of the host, random insertion of ERV's through known (non-intelligent) insertion is a much better explanation
.

Actually, what I think is the case is that evolutionists, as they often do, assume certain genetic structures are ‘neutral’ because they haven’t yet discovered a purpose for them.

And if they are ‘detrimental’, why has evolution been allowing them to hang around for 5 million years? Isn’t this rather a failure of natural selection?

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If one person has and ERV and another doesn't, what would ID predict?


I am not sure a ‘prediction’ is warranted – ERVs can be removed from the genome as well as the inherited from an ancestor. It could be either case.



Jhud -> RE: Can ERVs be explained without common descent? (5/5/2008 4:47:39 PM)

quote:

Let me put it this way. I find it rather juvenile to counter arguments involving the mutation of DNA with "Where did the DNA come from?" diversions. ERV's deal with human evolution and common ancestry with other apes. It does not deal with the origin of DNA or abiogenesis.


But the whole point of calling them ERVs is the understanding that the came from a viral infection isn't it? That is obviously a question of the origin of the genetic material.



Method -> RE: Can ERVs be explained without common descent? (5/5/2008 4:53:39 PM)

quote:

ORIGINAL: Jhud
Well, again, even if we were to assume this (I don’t, but for other reasons), it doesn’t itself do anything to demonstrate the veracity of evolutionary mechanisms.


That's why I stated that ERV's are strong evidence for common ancestry but not that great for positive evolution. Most ERV's accumulate mutations as if they are neutral and are often used as benchmarks for positive or negative selection.

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Then the ERV was front loaded to cause diabetes, in ID lingo. How does that help?


Proof that this is the case?


Are mutations random and unguided? If no, then your intelligent designer meant for people to have diabetes.

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Actually, what I think is the case is that evolutionists, as they often do, assume certain genetic structures are ‘neutral’ because they haven’t yet discovered a purpose for them.


I can use a burned out TV as a boat anchor, but that hardly indicates that the burned out TV has a purpose. A vast majority of ERV's have very little, if any, impact on the health or morphology of the host.

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And if they are ‘detrimental’, why has evolution been allowing them to hang around for 5 million years? Isn’t this rather a failure of natural selection?


It may have only recently become detrimental.

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If one person has and ERV and another doesn't, what would ID predict?


I am not sure a ‘prediction’ is warranted – ERVs can be removed from the genome as well as the inherited from an ancestor. It could be either case.


If an ERV is removed, what would ID predict would be the result?



Method -> RE: Can ERVs be explained without common descent? (5/5/2008 5:00:30 PM)

quote:

ORIGINAL: Jhud
But the whole point of calling them ERVs is the understanding that the came from a viral infection isn't it?


But where did the viral DNA come from? WE ARE NOT ROCK APES!!!



Jhud -> RE: Can ERVs be explained without common descent? (5/5/2008 5:08:32 PM)

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But where did the viral DNA come from? WE ARE NOT ROCK APES!!!


I am not even sure what the heck this is supposed to mean.



Jhud -> RE: Can ERVs be explained without common descent? (5/5/2008 5:15:45 PM)

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That's why I stated that ERV's are strong evidence for common ancestry but not that great for positive evolution. Most ERV's accumulate mutations as if they are neutral and are often used as benchmarks for positive or negative selection.


So you weren't disagreeing then; good enough.

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Are mutations random and unguided? If no, then your intelligent designer meant for people to have diabetes.


Actually I have no problem as an IDist with the idea that unguided changes to the genome cause disease. In fact that is what I would expect them to do.

I can use a burned out TV as a boat anchor, but that hardly indicates that the burned out TV has a purpose. A vast majority of ERV's have very little, if any, impact on the health or morphology of the host.

Well, again, I would say that this understanding is regularly undergoing revision, just as it did with 'junk DNA'.

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It may have only recently become detrimental.


Seems to be a lot of guesswork going on here.

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If an ERV is removed, what would ID predict would be the result?


It could certainly effect a loss of functionality; though such a loss may only be apparent under certain circumstances.



Method -> RE: Can ERVs be explained without common descent? (5/5/2008 6:07:35 PM)

quote:

ORIGINAL: Jhud
Actually I have no problem as an IDist with the idea that unguided changes to the genome cause disease. In fact that is what I would expect them to do.


So if a disease is caused by the conversion of an adenine to a guanine it is unguided, but if a beneficial allele is created by the conversion of an adenine to a guanine then it is front loaded and guided. Is that correct?

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Well, again, I would say that this understanding is regularly undergoing revision, just as it did with 'junk DNA'.


Can cars in a junk yard be used for beneficial purposes? Yep. But it's still a car in a junk yard. That is what ERV's are, tossed away sequences that no longer serve their original function. Like cars in a junkyard, ERV's may play a small role but it is a far cry from their original function.

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It could certainly effect a loss of functionality; though such a loss may only be apparent under certain circumstances.


And if there is no loss of functionality? What then? Is ID falsified?



Jhud -> RE: Can ERVs be explained without common descent? (5/5/2008 6:19:18 PM)

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So if a disease is caused by the conversion of an adenine to a guanine it is unguided, but if a beneficial allele is created by the conversion of an adenine to a guanine then it is front loaded and guided. Is that correct?


Not at all.

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Can cars in a junk yard be used for beneficial purposes? Yep. But it's still a car in a junk yard. That is what ERV's are, tossed away sequences that no longer serve their original function. Like cars in a junkyard, ERV's may play a small role but it is a far cry from their original function.


Actually, ERVs have been shown to play some fairly critical functions; I wouldn't continually use a car from the junk yard for highly critical functions.

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And if there is no loss of functionality? What then? Is ID falsified?


You mean if they deledted the gene and the organism didn't immediately die? No, I would think not, not anymore than if it was shown to have essential function would falsify Ievolution.

Plus, such functionality may be of the sort that is demonstrated over the course of generations in various circumstances, not simply something that is immediately expressed.



gluadys -> RE: Can ERVs be explained without common descent? (5/5/2008 7:23:27 PM)

quote:

ORIGINAL: Jhud

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I didn't notice this until Method responded to your post.

What makes you say that the rewriting of DNA by an "external entity" is not part of the evolutionary process in the neo-Darwinian sense of the word?

The neo-Darwinian definition of evolution is a change in the distribution of alleles in the gene pool over generations. How new alleles originate--whether the originating agent is internal or external-- is irrelevant to that definition.


Well, if 'neo-Darwinism' is indifferent to the origin of genetic information, then it certainly has no reason to discount ID.



If ID was only about rewriting DNA that would be true. Given the unpredictability of mutations, there is no way we can exclude the possibility of a direct, though undetectable, manipulation of a DNA sequence by the creator. However, mutations per se only set the stage for evolution. My impression of ID is that it also sees the elimination of natural selection or at least considers natural selection an insufficient agent in marshalling genetic information toward the formation of ---what is that list again?--body plans, organs, structures systems? It is also my impression of ID that it is not content with the notion of undetectable action by an intelligent agent.



Agahnim -> RE: Can ERVs be explained without common descent? (5/6/2008 8:02:21 AM)

I’m kind of dissatisfied with the way this thread has gone. I was having an interesting discussion with DanJames, and then somehow Method’s posts caused Betta to post one of his off-topic rants that’s going to cause him to say in future threads that he refuted the OP, even though he didn’t address most of the points in it. Past experience has shown that I won’t be able to reply to him directly without causing him to post a dozen or so of off-topic quips that will each take several paragraphs to address, so that allowing him to hijack the thread in this manner is the only alternative to letting him claim he’s refuted it. Jhud, since you complain pretty often about me bringing up off-topic stuff in other threads, I hope you can understand why I have a problem with the discussion here. The essay in this thread was not intended to prove a specific mechanism of evolution—it’s only intended to be proof of common descent, and debating whether a specific mechanism can be inferred from this is off-topic here.

For now, I’m just going to reply to what DanJames posted.

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I think you're getting this a bit backwards. You're saying that because our science books claim that the earth is a gazillion years old and that all life originated from one ancestor, therefore the Bible is demonstrated to be untrue because it disagrees. I used reason to conclude that your essay describes ERVs in a way that would lead me to conclude that there is evidence of a common ancestor between apes and humans. I use reason to conclude that the Bible must be true apart from our observations in nature, which are always incomplete and notoriously mis-understandable. The Bible disagrees with my conclusion based on your essay, and naturally the Bible must be the higher authority, therefore the conclusion I reached based on your essay must be wrong. I don't know how I am wrong, so I must assume that everything in your essay is true until proven wrong scientifically.

This is an oversimplification of what I’m saying; I think you should read the essay I linked to. But for now, I guess we can just discuss it in these terms anyway.

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The Bible is demonstrated to be divinely inspired because it says things that only God can know. For instance, the way to tell if a prophet is from God is that he or she would make a prediction and, if it came true, the prophet was known to speak for God. I think the Bible as a whole can be demonstrated to be divine as well, in that the history of the middle-east was given before any of it ever happened. A very compact version of this is shown in Nebuchadnezzar's statue dream. (wow, I totally just spelled that guy's name correctly on the first try!) Babylon, Medo-Persia, Greece, Rome, and even the countries that came from Rome's fall were pictured in this statue. (Daniel 2) Today, we can't even get tomorrow's weather correct, but here we see the next 400+ years of history recorded in scripture. Even the amount of time that Syria would control and oppress Israel (2300 days) and the manner in which the oppressive king would die is recorded in Daniel 8. Very unlikely indeed that a king would die an ill-timed death due to disease. Other prophecy that Daniel gives is so specific that it is thought that the book was written afterwards. Ezekiel, also gives a very unlikely prediction of the future and fall of the powerful city of Tyre. (Ezekiel 26-28) Any fortune cookie can predict bad times, but to say that a mighty nation will fall when it's still in its prime... that takes divinity.

OK, so the way in which you determined that you think the Bible is divinely inspired is because it accurately predicted certain historical events in a way that people living at the time when it was written couldn’t have done on their own. Now, how exactly do you know that these predictions were accurate? You obviously have to research historical information recorded outside of the Bible, make sure you’re interpreting it correctly, and then see whether it lines up with the predictions in the Bible. (In this case, it apparently does.) So in other words, the way in which you were able to conclude that the Bible is divinely inspired depends on researching and interpreting information in the world itself, and then determining that the Bible is consistent with it.

What I’m saying is that if these sorts of observations are what the authority of the Bible is based on, it doesn’t make sense to turn around and say that when the Bible appears to be inconsistent with what can be concluded from the physical world, that means the conclusions drawn from physical evidence need to be rejected. It isn’t just that the conclusions drawn from the Bible and the conclusions drawn from physical evidence are both based on reason; the authority of the Bible itself is based on the conclusions drawn from physical evidence. So if there are situations in which the two truly contradict each other and cannot be reconciled, the only possible thing this can mean is that the Bible has less authority than you previously assumed.

I’m not saying this is necessarily the case; I think Genesis can probably interpreted in a way that’s consistent with evolution. But do you understand what I’m saying about how you can’t use the authority of the Bible to reject what can be concluded from physical evidence, when the former is completely dependent on the latter?



Method -> RE: Can ERVs be explained without common descent? (5/6/2008 12:35:44 PM)

quote:

ORIGINAL: DanJames
I used reason to conclude that your essay describes ERVs in a way that would lead me to conclude that there is evidence of a common ancestor between apes and humans. I use reason to conclude that the Bible must be true apart from our observations in nature, which are always incomplete and notoriously mis-understandable. The Bible disagrees with my conclusion based on your essay, and naturally the Bible must be the higher authority, therefore the conclusion I reached based on your essay must be wrong. I don't know how I am wrong, so I must assume that everything in your essay is true until proven wrong scientifically.


Science does not state the Truth(tm) unequivocably. Science is always tentative in it's conclusions. The best any theory can do is make accurate predictions, and ERV's are a great example of a theory doing just that.

The theory of evolution states that if species share a common ancestor then you should observe two nested hierarchies, the nested hierarchy of morphology and the nested hierarchy of genetics. ERV's fall into the latter category.

From the genetic sequence of ERV's it is an unavoidable conclusion that they resemble modern day retroviruses, viruses that insert themselves into the host DNA and use the host mechanisms to produce new viral particles. Endogenous retroviruses (ERV's) are viral sequences that have become a permanent part of the host genome. We also observe that retroviruses insert randomly among thousands of insertion sites in each genome. Therefore, the chances of a single retrovirus inserting into the same spot in two different organisms is 1 in several thousand. The chances of numerous retroviruses inserting into the same spots in two different genomes is astronomical. In the case of chimps and humans we are talking about hundreds of thousands of ERV's. Therefore, ERV's make for strong markers for shared ancestry in that an ERV found at the same position in two genomes is best explained by a single event that occurred in a common ancestor.

From this information the theory of evolution predicts that orthologous ERV's (ERV's found in the same genomic position) should form a nested hierarchy among species who share a common ancestor. For primates (including humans and chimps) this is true with very, very few exceptions. For example, if humans and orangutans share an ERV at the same position then one should also find that same ERV in chimps. This is what is observed.

You can discount common ancestry if you want, but you must also admit that it makes very accurate predictions. If the theory of evolution is wrong, why is it able to make such accurate predictions?



DanJames -> RE: Can ERVs be explained without common descent? (5/9/2008 10:55:09 AM)

quote:

ORIGINAL: Agahnim

OK, so the way in which you determined that you think the Bible is divinely inspired is because it accurately predicted certain historical events in a way that people living at the time when it was written couldn’t have done on their own. Now, how exactly do you know that these predictions were accurate? You obviously have to research historical information recorded outside of the Bible, make sure you’re interpreting it correctly, and then see whether it lines up with the predictions in the Bible. (In this case, it apparently does.) So in other words, the way in which you were able to conclude that the Bible is divinely inspired depends on researching and interpreting information in the world itself, and then determining that the Bible is consistent with it.

What I’m saying is that if these sorts of observations are what the authority of the Bible is based on, it doesn’t make sense to turn around and say that when the Bible appears to be inconsistent with what can be concluded from the physical world, that means the conclusions drawn from physical evidence need to be rejected. It isn’t just that the conclusions drawn from the Bible and the conclusions drawn from physical evidence are both based on reason; the authority of the Bible itself is based on the conclusions drawn from physical evidence. So if there are situations in which the two truly contradict each other and cannot be reconciled, the only possible thing this can mean is that the Bible has less authority than you previously assumed.

I don't think it's necessary to equate a study of history, such as the fall of the great city of Tyre, and the fall of Babylon, and the death of Alexander the Great by disease, is the same as an interpretation of a fossilized bone. You can't reinterpret history, it already happened, and you either have a contradictory account or you don't. Even if you do, it seems highly coincidental that the Bible happens to line up with these accounts even though it was told in advance, so we can take the Historian at his word.
But about the conclusions from the physical world; even if we were dead certain about what we think we know, that doesn't change the fact that we've gotten things heinously wrong about the physical world in the past, even the recent past. Ernst Haeckel went on tour with his drawings of the embryos and we know he was a fraud, yet it was sure-fire evidence of evolution for the time. Vestigial organs was flaunted as sure-fire evidence for evolution, yet we've found a purpose for almost every single one of them. Want to make a prediction based on that last statement? And now we've found that the most recent sure-fire evidence of evolution, bacterial resistance, is also not all it was cracked up to be. You want me to trade the account recorded in the Bible, which has never been shown to be mistaken, for the next sure-fire evidence for evolution? You want me to be one of the evolutionists that jump ship from evidence to evidence?
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I’m not saying this is necessarily the case; I think Genesis can probably interpreted in a way that’s consistent with evolution. But do you understand what I’m saying about how you can’t use the authority of the Bible to reject what can be concluded from physical evidence, when the former is completely dependent on the latter?

Genesis cannot be interpreted in a way that is consistent with evolution. It states, among other things, that flowering plants arrived before the sun. Angiosperms are a younger taxon then vertebrates, which arrived long after the sun. In fact, they arrived after the earth, which itself arrived after the sun.
And I do understand your point, but I don't think that history and natural science is the same thing.



DanJames -> RE: Can ERVs be explained without common descent? (5/9/2008 11:00:39 AM)

quote:

ORIGINAL: Method

From this information the theory of evolution predicts that orthologous ERV's (ERV's found in the same genomic position) should form a nested hierarchy among species who share a common ancestor.


Keep this statement in mind because some day some dingle-berry is going to say that nobody ever said it.



Bettawrekonize -> RE: Can ERVs be explained without common descent? (5/12/2008 10:53:37 PM)

quote:

ORIGINAL: DanJames

quote:

ORIGINAL: Method

From this information the theory of evolution predicts that orthologous ERV's (ERV's found in the same genomic position) should form a nested hierarchy among species who share a common ancestor.


Keep this statement in mind because some day some dingle-berry is going to say that nobody ever said it.


I refute Method's statement (the quote that you quoted) in post 3 (the link). Again, if you have questions, feel free to ask. There is no reason for UCD to predict any such "hierarchy," it's more like a postdiction. People have been claiming that there is a hierarchy before Darwin and Darwin merely accommodated what was thought to be true at the time into his hypothesis. It's not that evolution predicts any of it.

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Vestigial organs was flaunted as sure-fire evidence for evolution, yet we've found a purpose for almost every single one of them.


This is another example of the postdictive power of evolution. It was thought that these organs were vestigial (which, at the time, meant useless or so close to useless such that they are no longer subject to natural selection) at the time and evolutionists merely accommodated what was thought to be true into their hypothesis. It's not that evolution predicts this, and evolution is glad to change what evolution should predict if we find that what was thought to be true is false. Likewise is true with this alleged hierarchy. It was thought that there is a hierarchy before Darwin and Darwin merely accommodates what was thought into his hypothesis. It's not that evolution predicts any such thing, and in fact, I explain in the link I referred you to why it's actually a problem for evolution. Evolution just says, "whatever the evidence is is what I predict," but it doesn't actually predict anything.



Method -> RE: Can ERVs be explained without common descent? (5/14/2008 3:45:47 PM)

quote:

ORIGINAL: Bettawrekonize
I refute Method's statement (the quote that you quoted) in post 3 (the link).


Your refutation treated humans as asexually reproducing individuals. I would hardly call that a refutation. Not only that, but your refutation could not even explain why you and your siblings share hundreds of thousands of ERV's.

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Again, if you have questions, feel free to ask. There is no reason for UCD to predict any such "hierarchy," it's more like a postdiction.


A nested hierarchy was predicted before DNA was even discovered. It was predicted by Darwin himself.

And you have yet to approach the topic of the thread. How do you explain the pattern of orthologous ERV's among primates without common descent?

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People have been claiming that there is a hierarchy before Darwin and Darwin merely accommodated what was thought to be true at the time into his hypothesis. It's not that evolution predicts any of it.


Without horizontal genetic transfer a nested hierarchy is the only pattern that the mechanisms of evolution can produce. This is a known and testable fact.

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This is another example of the postdictive power of evolution. It was thought that these organs were vestigial (which, at the time, meant useless or so close to useless such that they are no longer subject to natural selection) at the time and evolutionists merely accommodated what was thought to be true into their hypothesis.


I can use a burned out TV as a boat anchor, but guess what? A burned out TV is still vestigial even though it has a use. In the same way, the human vermiform appendix is vestigial given the fact that it has a rudimentary function compared to the same organ in other species. The HVA is just as vestigial today as it was 150 years ago.

ERV's are also vestigial. They no longer code for active and infectious viral particles as they do in retroviruses themselves. Whatever function they may or may not serve now is a rudimentary function compared to their original function.

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It was thought that there is a hierarchy before Darwin and Darwin merely accommodates what was thought into his hypothesis.


Darwin provided the mechanism by which a nested hierarchy is produced. That was the importance of his work.

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Evolution just says, "whatever the evidence is is what I predict," but it doesn't actually predict anything.


That's not true, and you know it.



BVZ -> RE: Can ERVs be explained without common descent? (6/5/2008 4:04:08 AM)

quote:

ORIGINAL: Bettawrekonize

quote:

ORIGINAL: DanJames

quote:

ORIGINAL: Method

From this information the theory of evolution predicts that orthologous ERV's (ERV's found in the same genomic position) should form a nested hierarchy among species who share a common ancestor.


Keep this statement in mind because some day some dingle-berry is going to say that nobody ever said it.


I refute Method's statement (the quote that you quoted) in post 3 (the link). Again, if you have questions, feel free to ask. There is no reason for UCD to predict any such "hierarchy," it's more like a postdiction.


Actually, in creatures with no horizontal gene transfer, there is only one thing that is CAN POSSIBLY form, and that is a nested hierarchy. If you disagree, please show me an example (you can make one up) that complies with the following:

1) There is no horizontal gene transfer. (Like humans and chimps.)
2) They form something OTHER than a nested hierarchy.

Since this is impossible, you will fail. But since you think it IS possible, feel feel to try.

quote:


People have been claiming that there is a hierarchy before Darwin and Darwin merely accommodated what was thought to be true at the time into his hypothesis. It's not that evolution predicts any of it.


Actually... the current theory of evolution DOES predict common ancestry, and common ancestry predicts a nested hierarchy. Also, the hierarchy is OBSERVABLE TODAY. Directly.

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quote:


Vestigial organs was flaunted as sure-fire evidence for evolution, yet we've found a purpose for almost every single one of them.


This is another example of the postdictive power of evolution. It was thought that these organs were vestigial (which, at the time, meant useless or so close to useless such that they are no longer subject to natural selection) at the time and evolutionists merely accommodated what was thought to be true into their hypothesis.


That is still what vestigial means. An organ that does not serve it's original purpose to a degree to be selected for that purpose is a vestigial organ. Any current use it may or may not have is completely irrelevant.

Now that you have been corrected on this, answer the following question: Are wings on a penguin vestigial?

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It's not that evolution predicts this, and evolution is glad to change what evolution should predict if we find that what was thought to be true is false.


If a prediction is false, there must be something wrong with the theory that produced it. If there is something wrong with the theory, then it must be changed. Were you SERIOUSLY expecting scientists NOT to adjust scientific theories as new evidence is found?

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Likewise is true with this alleged hierarchy. It was thought that there is a hierarchy before Darwin and Darwin merely accommodates what was thought into his hypothesis.


Okay lets assume that he did. So what? The nested hierarchy is still observable.

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It's not that evolution predicts any such thing, and in fact, I explain in the link I referred you to why it's actually a problem for evolution. Evolution just says, "whatever the evidence is is what I predict," but it doesn't actually predict anything.


If what you say is true, then the ToE would have no use.

Since the ToE has a use, you are wrong.

The ToE predicts that in any situation where you have imperfect replicators competing with each other, these replicators will adapt in such a way that thier own genetic material becomes more widespread.



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