Woese's progenote hypothesis

I thought to help further this topic along I would answer a question so that we could get beyond it. I am not arguing here, merely stating the reason for the progenote concept (why it is necessary according to some rather than a generic amalgum)So the big question is why does Woese believe that a progenote is the only explanation as the common ancestor of the three urkingdoms? I have tried to think of suitable analogies but think it would be better to just explain.Woese makes an assumption that within gene types of the groups studied the change over time is constant. That is, if the distance between two genes is x and that works out to be 10 million years, then a distance of 4x is calculated to be split 40 million years and so on. This molecular clock holds up fairly well and matches known splits within the urkingdoms.So Woese then looks at the differences within the urkingdoms and between them. Looking at the distance within the urkingdoms he extrapolates that they have been evolving since near the origin of life. Assuming a constant rate of change, this would put the common ancestor of the urkingdoms impossibly far back. So if we say in this case that x distance equals 3 billion years (and x is the greatest distance within the urkingdoms) and we see that the difference is between urkingdoms is 2x. That leaves two possibilities. 1) The common ancestor lived 9 billion years ago or 2) x is not a constant or was not a constant in the early days of life.So given this Woese postulates a common ancestor with a mechanism that allows it to change significantly more rapidly than we see today. Whether that is true or not is interesting, and should be the subject of this discussion. I hope this helps illuminate the argument. I found a good number of papers since Woese that discuss this concept. I will read the ones I have and wait for some thers via ILL and hopefully contribute.

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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"

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 explanationI 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.

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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"

Here is the article you quote:
http://www.gps.caltech.edu/...in%2520et%2520al.%25201999.pdfThat line from the article is refering to the exact atmospheric components used in the experiment, meaning that it is now understood that the primitive atmosphere was different then (but still capable of producing organics from inorganic components). You are implying that Scientific American is questioning abiogenesis in that statement.All of that aside, I found something interesting at a site The Miller-Urey Experiement And again: Those seem a little similar to me....Now onto topic. I don't think the origins of life are relevant to the question of progenotes and/or the common ancestry of the urkingdoms. I think it is possible, even likely, that early pre/proto life would have 'tried' different possible configurations. Ultimately only one (as far as we can tell) made it.

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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"