Woese's progenote hypothesis

Could someone please explain succinctly what the fuss on this thread is about? Woese's hypothesis appears to only counter the simplistic LUCA idea - something that I personally always felt was problematic, given precisely the incredible amount of lateral gene transfer (or HGT - the terms are synonomous and interchangeable) that has gone on and is going on at the unicellular level. All the paper seems to be talking about is the fact that the deepest roots of life were extraordinarily intertwined. He certainly doesn't discount the possibility of something like a "last eukaryote common ancestor" or a "last prokaryote common ancestor" as far as I can see. Even there, it could be problematic to identify one common ancestor, again because of gene transfer, etc.So could someone explain what the issue is here? Thanks.

I'm not sure I read it the same way. Woese claimed that there was no way that one or more of the urkingdoms could have evolved from any of the others (the prokaryote to eukaryote idea, for instance). This pretty much puts paid to the LUCA idea. On the other hand, whether or not he's proposing a "radically different form of evolution" isn't clear from the article or subsequent discussion. Would you mind expanding on that part?In any event, whether the progenote idea is true or not, there's been quite a bit of evidence amassed since that paper was published concerning the origin of the different domains. For instance, it appears that eukaryotes are the result of genomic fusion of different prokaryote clades (see, for instance, Rivera MC, Lake JA, 2004, "The Ring of Life Provides Evidence for a Genome Fusion Origin of Eukaryotes", Nature 431:134-137). Fusion is one of the methods for gene transfer between unicellular organisms. It is, in a way, sort of Lamarckian. Like you hugged a tree and woke up one morning with the ability to photosynthesize, and were able to pass it on to your lineage. That's why more recent analogies of the "tree of life" resemble a mangrove with lots of intertwining roots, rather than Darwin's model of an oak tree. It's also why it's so difficult for anyone to point to a "last common ancestor" - because unicellular organisms are so promiscuous with their genetic material. However, that doesn't mean the mechanisms of natural selection, etc, don't apply. In fact, several studies seem to indicate that selection can favor stability in operons and functional protein sequences, regardless of genome or lack thereof (see, for example, Omlechenko MV, et al, 2003, "Evolution of mosaic operons by horizontal gene transfer and gene displacement in situ", Genome Biology, 4:R55).In short, rand, I'm sorry but I still don't understand where the problem lies. You seem to be arguing about a paper where parts have been largely superceded and parts of it confirmed. Fill me in, here, please.

Thanks for the summary. Isn't that what I said?

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Q writes:
Woese claimed that there was no way that one or more of the urkingdoms could have evolved from any of the others (the prokaryote to eukaryote idea, for instance).

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I did recognize what Woese's point was. I was trying (and still am) to figure out what yours is.WK has done a great job pointing out some key points in the paper. I agree that the progenote hypothesis provides an "elegant" solution to the question of precursers. On the other hand, I don't necessarily agree with Woese that there's something - a progenote - that necessarily has to be the ancestor of all three domains. More likely WK's precursor "community", where a single lineage is either indetectable or non-existent. On the other (other) hand, it is obvious that there was something that preceeded the rise of the three domains. However, the Rivera paper I cited clearly indicates that at least the earliest eukaryotes may have been chimerae. A hypothesis, btw, which supports Woese's idea that none of the three domains evolved into any of the others, but concurrently refutes his hypothesis about an identifiable "progenote", at least as far as eukaryotes go.When we get down to the faint, fine line between the RNA world and the cellular world, there's very little hard evidence available, and speculation/data interpretation is relatively open. Given lateral gene transfer, genomic fusion, etc, at that level, and a much larger database today on genome sequences than Woese had available, we can even trace some specific inter-domain transfers. At the level Woese is talking about, these transfers relate to swapping operons and functional protein sequences among a group of non-genetic (as we understand the term) "organisms". These critters may not even be "life-as-we-know-it".Be that as it may, the primary mechanisms of evolution - random changes and natural selection (especially purifying or stabilizing selection on functionality - see the Omlechenko paper I cited previously) would of necessity be operant. Thus you're going to have to be patient and explain why you think Woese's paper provides some kind of refutation or challenge to evolution. The ToE appears to be operating even at that pre-genetic level. Just not lineal descent, although even there we aren't sure what was going on down in the mud.I still don't see what the fuss is about. Edited by Quetzal, : eliminating "actually"s - three in a row was too much

I think the Woese paper does in fact make the claim that there is no "universal common ancestor" when you get down to the pre-genetic line between an RNA world and the domains as we know them today. Obviously, that doesn't refute or even challenge the idea of common descent. It just means that the "last universal common ancestor" may in some sense be ancestors, plural. When we get down to that level, there's so much noise-to-signal that it is difficult to separate out what is going on from what isn't.If rand is trying to make a case that descent with modification is bogus, he's going to need to come up with a different paper. That particular paper of Woese's doesn't provide the support he needs. It is, after all, a theoretical (read "speculative") scientific paper. Like all good speculative scientific papers, the hypothesis is based on solid data/observations (in this case, the differences in functional sequences between the domains). Beyond that, the paper simply discusses Woese's explanation for the data - his interpretation, if you will. Given his standing, it's obviously speculation that should be taken seriously. On the other hand, as you well know, just because Woese wrote it doesn't mean it's right...and parts have been shown to be to a degree incorrect by subsequent research. As is to be expected. Rand doesn't seem to get that part. Edited by Quetzal, : Deleted another "actually" - bad habits are hard to break

As I tried to point out to rand, Woese doesn't postulate any new "mechanisms". LGT is an observed phenomena. We can even trace some of the inter-domain transfers back into the distant past. However, it's still all evolution by natural selection. There's really no better explanation for the differentiation, after all. It's just NS working on a different class of critters - but still working exactly the same as today. The ToE isn't affected at all, that I can see. Indeed.Edited by Quetzal, : murdered the final "actually"