[Ichneumon]

[Junior:] The paper is on lineage specific retroviral insertions in the genus pan (chimps and bonobos). As far as I can tell, it has nothing to do with tracing the overall tree of life using fossil retroviral insertions within the genome. Now, I could be wrong because I'm a computer geek, not a working biologist. That's why I've pinged someone with a lot more experience in this than me when it comes to reading these things.

Correct, mostly. It is lineage-specific, but it also includes gorillas, not just the chimpanzee family.

so_real makes a number of errors in his commentary about this topic in general, and the linked paper in particular:

[so_real:] I understand that you made a quick summary for the sake of brevity in your post, but I think you are jumping the gun a little bit drawing conclusions from retroviral insertion points -- at least at this time.

Not at all. The DNA evidence which allows the reconstruction of evolutionary lineages is extremely strong, and allows multiple independent cross-checks. Even the paper which so_real himself links makes clear that the molecular evidence is strong, vast, and unlikely to be found wrong at this point, as for example when it writes:

This seems unlikely in light of the extensive molecular evolutionary data that have been collected over the last few years [5,25] that clearly place orangutan as the outgroup species to the human–chimpanzee–gorilla clade and Old World monkeys as an outgroup to the human/ape lineage.

It's also clear that contrary to so_real's implication, the authors of this study do not feel that their own results challenge the validity or findings of the existing evidence.

[so_real:] You are making assumptions that the source viruses do not assert an insertion point bias,

No, he is not making such an assumption, and neither do the researchers who use endogenous retroviruses (and other forms of DNA evidence) to uncover evolutionary relationships.

[so_real:] that the source viruses endogenous markers do not wane and cannot be re-introduced exogenously,

No one makes this assumption either. Clearly they can. But also as clearly, there are methods which allow us to determine if a particular case of a shared retrovirus is, or is not, the result of an ancestral event, or due to horizontal transmission. The paper which so_real himself links demonstrates several of those methods.

[so_real:] and that the source viruses are not capable of zoonosis or other cross-species transmission.

See above -- same answer. The results of such events can be distinguished from ancestral events.

[so_real:] Without these assumptions, there is no guarantee that the "critters ... will be related".

No such assumptions are made, so your conclusion is faulty. Instead, such potentially confounding cases are recognized by their characteristic features, and are excluded from phylogenetic analyses. That's what this paper *does* -- employs methods which distinguish the PTERV retroviral cases from ancestral retroviruses. How could you link the paper and not see that it already answers your potential objections?

[so_real:] Here is an interesting study that speaks to some of these issues, if you are interested. Note that this is not a creationist or ID'ist study -- it speaks only to a better understanding of evolution and raises questions regarding the validity of those assumptions from an evolutionist point of view.

...and it only *confirms* that non-ancestral retroviruses (such as the one examined by the paper) can indeed be distinguished, via several different characteristics, from ancestral cases.

[so_real:] The bottom line is that the jury is still out on what information can be inferred from retroviral insertions within genomes.

No, the "bottom line" is that non-ancestral retroviruses can and are distinguished from ancestral retroviruses, and that the inferrences reached via examination of endogenous retroviruses are still valid, and not subject to the kind of undetected error which you assert.

We are still in the data collection phase and I'd not hasten to insult a dissenting interpretation of that data until more is known.

We are *well* beyond the "data collection phase", and it is perfectly appropriate to laugh at someone who makes such *enormously* ignorant and incorrect claims as:

[Petrosius:]
"naturalistic evolution itself is untestable"

"... it is but mere speculation."

"The genome project can only tell you what the genes do today. It cannot tell you how they became so arranged."

"Morphology only show [sic] similarity in design, not how that similarity came about."

"...natural evolution is untestable until you can demonstrate a test that will repoduce the creation of a new species."

These are all statements that show an absolute and complete ignorance of the subject (as well as an arrogance which allows one to "lecture" on a topic without even the most elementary knowledge of it).

What really earns extra helpings of scorn, however, is the hilarious assertion that, despite these clear expressions of near total ignorance, "I know more about the the subject than you think."

No, actually, he doesn't. He doesn't even know enough to realize how very little he knows about it.

This is, unfortunately, pretty typical of anti-evolution creationists.

[Petrosius]

I never rejected the fact of a linear sequence of species. My complaint has been that as of yet no mechanism has been shown to explain the appearance of new species. I accept the evidence that shows genetic relationships between the species but you are jumping the gun if you insist that there must therefore be a natural causality for it. I also want to state that I am not denying the possibility for such a natural cause either, only that it has yet to be shown. I can easily accept that God might have use the natural laws as the instrumental cause of his design. I am a skeptic either way.

I stand by my statements that natural evolution is untestable. If there is any ignorance it is with the doctrinaire evolutionists who do not understand basic logic and assume that the limitations inherent in the methodology of the natural sciences demands that the truth can only accept natural causality. Present the theory of evolution (it might even be true) but have the humility and honesty to say that it is only a theory and that others have serious and legitimate objections to it.

[so_real]

PTERV1 was not found in humans, orangutans, siamangs, or gibbons. But it was found in chimpanzees, gorillas, baboons, and macaques.

This contradicts the accepted phylogenetic evolutionary tree established through observing differences in HERV insertions five years ago. An ancient infection in a common ancestor within the Old World monkeys could not have skipped human, orangutan, and gibbon decendents while leaving markers in chimpanzees and gorillas. It didn't add up -- the jury was still out -- data collection continued. Hence the need for research.

Two possible solutions: the primate phylogeny is incorrect "as has been proposed by a minority of anthropologists", or PTERV1 emerged from an exogenous source having cross-species transmission ability, exhibiting strong integration location bias, being endemic in multiple continents, leaving a marker 4 million years ago in gorillas and chimps and a subsequent marker 2 million years ago in baboons and macaques, but being unknown today. Had anyone suggested this of the HERV study, I suspect they would have met with a good deal of ridicule.

The study I linked, *proposes* the feasibility of the second solution -- and it is an entirely realistic proposal, I do not argue against their findings -- but it *confirms* nothing. The authors themselves speak in terms of speculation, possibilities, and scenarios. You do them a dis-service by establishing they have made a definitive "confirmation" where they have not. The point they make is that their data is consistent with the possibility of such events. I linked the study because they are redefining the realm of possibility in what we know about retroviruses.

It is possible the researchers have successfully distinguished contemporary exogeneous PTERV1 markers from ancestral markers. The formula for this research has not yet, at least to my knowledge, been re-applied to the HERV study. (If you know otherwise, I would be extremely interested in a link.) What if, once it is re-applied, similar conditions are found? That's exciting. As such, the jury is still out and data collection continues. As it should be - there is much more regarding retroviruses to be learned.

I listen to all sides of the debate (including those who question the primate phylogeny) with equinamity and civility. Anything less is close-minded and irrational -- and it encourages the same from those across the table. I don't want that.

In the words of Bill O'Reilly "I'll give you the last word." :-)