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No, given the information that the virus had attacked chimps and gorillas, but not humans, the prediction was that the ERVs would not be found in the same loci, but rather (as one would suspect from independent infections) at different loci. Of course, if it had attacked humans, but independently of the other apes, one would also expect different loci.

The ERVs that fall into a common descent type phylogeny are those located at identical loci across the hominid family, suggesting a single infection.

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ORIGINAL: Jhud
you have the rather circular argument that the insertion sites both prove, and are the product of, a presumed evolutionary common ancestry.

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ORIGINAL: Jhud

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No, given the information that the virus had attacked chimps and gorillas, but not humans, the prediction was that the ERVs would not be found in the same loci, but rather (as one would suspect from independent infections) at different loci. Of course, if it had attacked humans, but independently of the other apes, one would also expect different loci.

The ERVs that fall into a common descent type phylogeny are those located at identical loci across the hominid family, suggesting a single infection.

What I find to be interesting is if you look at the large number of insertion sites, it seems inevitable that some are going to be identical. Ad so you have this operating assumption that if the insertion sites differ, they occurred after the presumed 'split', and if you look at the ones that are the same, they occurred before the presumed 'split', so that you have the rather circular argument that the insertion sites both prove, and are the product of, a presumed evolutionary common ancestry.

And to top it all off, "Twenty-four locations were ambiguous within the limits of resolution of this study and could, in theory, correspond to 12 orthologous sites", meaning that whether they actually were the same insertion points is really a matter of some debate.

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ORIGINAL: Jhud
What I find to be interesting is if you look at the large number of insertion sites, it seems inevitable that some are going to be identical. Ad so you have this operating assumption that if the insertion sites differ, they occurred after the presumed 'split', and if you look at the ones that are the same, they occurred before the presumed 'split', so that you have the rather circular argument that the insertion sites both prove, and are the product of, a presumed evolutionary common ancestry.

And to top it all off, "Twenty-four locations were ambiguous within the limits of resolution of this study and could, in theory, correspond to 12 orthologous sites", meaning that whether they actually were the same insertion points is really a matter of some debate.

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For someone who keeps emphasizing complexity, you like to avoid it where its convenient. No, it is not as simple as that. For one thing, one must also include the factor of dating when the ERVs originated.

And I am sure you know how to keep an "if X, then Y" prediction in proper sequence.

Case 1: If a virus infects different species independently, the resulting ERVs will probably vary in locus (though one cannot absolutely rule out a coincidental match). Furthermore, any presumed phylogeny based on such ERVs will not correspond to phylogenies based on other data points.

Case 2: If a virus infects the common ancestor of two or more species, the resulting ERV will be inherited by all descendants of the ancestor. It will, of necessity, occur in the same place in the genome and any phylogeny constructed from such orthologous shared ERVs will be consistent with phylogenies based on other data points.


Finally, in both cases, the dating of the origin of these ERVs will be consistent with the timing of the speciations, as deduced from other evidence: independent infections occurring subsequent to speciation (or at least the divisions in the population), and orthologous ERVs originating before speciation.

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ORIGINAL: Jhud

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For someone who keeps emphasizing complexity, you like to avoid it where its convenient. No, it is not as simple as that. For one thing, one must also include the factor of dating when the ERVs originated.

And I am sure you know how to keep an "if X, then Y" prediction in proper sequence.

Case 1: If a virus infects different species independently, the resulting ERVs will probably vary in locus (though one cannot absolutely rule out a coincidental match). Furthermore, any presumed phylogeny based on such ERVs will not correspond to phylogenies based on other data points.

Case 2: If a virus infects the common ancestor of two or more species, the resulting ERV will be inherited by all descendants of the ancestor. It will, of necessity, occur in the same place in the genome and any phylogeny constructed from such orthologous shared ERVs will be consistent with phylogenies based on other data points.


Finally, in both cases, the dating of the origin of these ERVs will be consistent with the timing of the speciations, as deduced from other evidence: independent infections occurring subsequent to speciation (or at least the divisions in the population), and orthologous ERVs originating before speciation.

So you are saying it's impossible for the insertion sites to have been the same across species the result of an incidental occurence?

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ORIGINAL: Jhud
So you are saying it's impossible for the insertion sites to have been the same across species the result of an incidental occurence?

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It is highly improbable that two independent insertions would occur at the same base of the genome in two separate individuals. The overwhelming majority will insert at different spots. This is the overwhelming signal that is observed.

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ORIGINAL: Jhud

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It is highly improbable that two independent insertions would occur at the same base of the genome in two separate individuals. The overwhelming majority will insert at different spots. This is the overwhelming signal that is observed.

But not impossible?

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No, not impossible. We are talking about the same type of odds as the Powerball lottery. Primates carry around 200,000 total ERV's. Out of 200,000 insertions you would expect the same number of independent but orthologous ERV's as you would expect identical lotto numbers from 200,000 Powerball lottery tickets.

The odds may be a little less than that, but still quite steep. There is a much higher probability that an ERV would be lost in a lineage than independent orthologous ERV's. I am aware of a couple HERV-K insertions that seem to have been lost in the human lineage but present in the chimp and gorilla lineage (if memory serves).

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ORIGINAL: Jhud

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No, not impossible. We are talking about the same type of odds as the Powerball lottery. Primates carry around 200,000 total ERV's. Out of 200,000 insertions you would expect the same number of independent but orthologous ERV's as you would expect identical lotto numbers from 200,000 Powerball lottery tickets.

The odds may be a little less than that, but still quite steep. There is a much higher probability that an ERV would be lost in a lineage than independent orthologous ERV's. I am aware of a couple HERV-K insertions that seem to have been lost in the human lineage but present in the chimp and gorilla lineage (if memory serves).

So, you argument is 'the odds against similar insertions points are high, so common decent is a more reasonable explanation'?

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ORIGINAL: Jhud
So, you argument is 'the odds against similar insertions points are high, so common decent is a more reasonable explanation'?

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Sure, since common descent is observed to produce this very pattern. You and your siblings (or cousins) are a perfect example.

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ORIGINAL: Jhud
So a 'common descent of the gaps' argument then it is.

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Not so. The results of genetic studies are consistent with what one would expect from common ancestry. It is the same concept that is used for DNA paternity tests. The only difference is that STR's (short tandem repeats) are used for paternity tests instead of ERV's, but the same methodology applies.

Actually, DNA paternity tests make for a good example. Each one of us has thousands of STR's in our genomes. For a known set of STR's we may have 4 repeats for one while 8 repeats in another. The distribution of STR alleles is more or less uniform in the human population. Therefore, the number of repeats in each STR makes for an individual identifier like a social security number. If one picks enough STR's it is highly improbable (greater than 1 in 3 billion) that a child and prospective father would share these identifiers without being child and father. Are you saying that paternity tests are bad and innacurate simply because no one was there to observe the father's sperm fertilizing the mother's egg?

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ORIGINAL: Jhud
You already made the argument; because the possibility of ERVs inserting in similar locations is considered to remote to have occured by some other unknown method, evolutionists assume common descent. It's the classic 'CD of the gaps' argument.

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You are referring to an unknown method that for an unknown reason imitates common descent. Why reach for that when we know that common descent would produce the pattern observed without bringing unknowns into the picture?

I am sure you've heard of Occam's razor.

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ORIGINAL: Jhud

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You are referring to an unknown method that for an unknown reason imitates common descent. Why reach for that when we know that common descent would produce the pattern observed without bringing unknowns into the picture?

I am sure you've heard of Occam's razor.

Common descent is not a method.

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rrelevant. We know what sort of genetic pattern will be the result of common descent and why that is the pattern associated with common descent. We also observe that pattern in actual species genomes.

Any unknown method, to be considered at all, would have to produce the same observed pattern. Since it is a pattern with a known cause, why introduce an unknown imitator?

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ORIGINAL: Jhud

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rrelevant. We know what sort of genetic pattern will be the result of common descent and why that is the pattern associated with common descent. We also observe that pattern in actual species genomes.

Any unknown method, to be considered at all, would have to produce the same observed pattern. Since it is a pattern with a known cause, why introduce an unknown imitator?

The genetic pattern is not the 'result of common descent' - common descent is a result. A genetic pattern might be evidence for common descent, but it's not the result of common descent - common descent would be the result of generation of organisms enduring slight genetic changes over a period of millions of generations leading to the all the sorts of organisms that ever existed and currently exist. The mechanisms that allow for this are what are in question - if they don't work, then common descent as evolutionist understand it could not have occurred, whatever the activity of ERVs.

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Wow, I've never seen anything so backward in my life. Usually you are pretty coherent, but this is ridiculous.

My siblings and I share a common genetic pattern because we have common ancestors. Those common ancestors are not the result of our genetic patterns. The fact that we share certain unique derived characters is indeed a result of our common descent from these ancestors.


Therefore, because we know that common descent necessarily results in the shared inheritance of traits, the observation of such a pattern where ancestry is unknown is a legitimate reason to infer common ancestry as the source of the pattern. Common descent from a common ancestor is a known producer of shared inheritable traits in the unique pattern of a nested hierarchy.

And the mechanisms that allow for this are very well known. Imperfect replication of DNA. Reproduction, both sexual and asexual. Natural selection and speciation.

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ORIGINAL: Jhud
Common descdent is neither the cause nor mechanism of you or your ancestors, it is the description of your relationship, which was my simple point.

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That relationship is defined by inheritance via reproduction. Reproduction is a mechanism of inheritance. Inheritance of similar genetic material in a particular pattern from a common ancestor is what common descent is about.

It seems to me you are just playing with semantics here.

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ORIGINAL: Jhud

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That relationship is defined by inheritance via reproduction. Reproduction is a mechanism of inheritance. Inheritance of similar genetic material in a particular pattern from a common ancestor is what common descent is about.

It seems to me you are just playing with semantics here.

No, I am simply trying to clarify that common descent is neither a method nor mechanism.

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Well common descent is nothing without reproduction and reproduction is certainly a mechanism for transferring genetic information from parent to offspring. So I don't know what the purpose of your clarification is. It is still splitting hairs as far as I can see.