Randman writes:
The molecular clock angle is interesting because it does suggest that the 3 kingdoms could not have arisen via present processes we observe today
This is essentially the gist of Woese's argument for a progenote. It would be better to state ... "via processes known in the mid 1980's" as I know there have been some advances since then. As I mentioned before, I have a few refs on ILL, they might have some more recent info.
Just to put my two cents in, I don't see how the progenote concept, as Woese defines, contains any explanatory power to the origin of the urkingdoms. I mean by definition (if you accept abiogenesis) something called a progenote had to have existed, but it doesn't explain very much about subsequent division of life. I agree with Rand on this, we should exhaust possibilities within what we do know before appealing to a hypothetical unknown, if that makes sense. Science is not served by putting forth unknowables as the explanation
I spoke briefly last week with a geneticist about the Woese paper (not about this aspect) and she commented that the paper was written before alot of new higher-rank taxonomy had been sorted out although it is generally still the same. One difference is that the hypothesis of multiple origins has pretty much died, as more genes are mapped we find too many similarities in too many places to be coincidence or even gene transfer. So if we accept abiogenesis, the ToE, and not the progenote we cannot consider multiple origin as a tenable hypothesis.
It is my suspicion that the issue lies (or formerly so) in our inability to see the whole picture. We are looking at three ancient lineages that seem very far apart. In all probability the differences wouldn't seem so great if we could look at a genetic sample from 3.5 bya.
Doctor Bashir: "Of all the stories you told me, which were true and which weren't?"
Elim Garak: "My dear Doctor, they're all true"
Doctor Bashir: "Even the lies?"
Elim Garak: "Especially the lies"