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:]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).
"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."
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.