Woese's progenote hypothesis

I think this is part of the problem. Woese's objection is to the 'Darwinian' form of vertical evolution with novelty arising over succesive generations and spreading though differential reproductive success of progeny.In Woese's world by contrast we have communities of proteinaceous protocells developing from a precellular aggregate of functional and structural nucleic acids. These protocells have no genome as we might recognise it but rather a shifting ensemble of genetic elements. It is like a comunity of bacteria with nothing but short elements of plasmid DNA. So rather than 1 genomic copy of a gene a progenote protocell may have hundreds of copies with highly variable sequence, and these plasmid like sequences can be transferred between protocells leading to massive horizontal gene transfer. Woese himself suggests such an evolutionary scheme might best be described as Lamarkcian.There is no barrier to mechanisms as simple as mutation and natural selection, only to higher order mechanisms associated specifically with 'Darwinian' vertical descent. How does natural selection work in such a world where the metabolism can shift as the genetic community changes and the swapping of characteristics and traits is and everyday occurrence? The obvious answer is of course that natural selection is operating not on the progenote protocell itself but on the various genetic elements being modified and traded around the progenote communities. When the linkage is poor there will be much lower biological specificity and proteins may well be more structural than functional in many cases. Whatever functional proteins there were would need to have more leeway for amino acid changes than we see in many modern highly specific active sites. As long as there remains some linkage between the gene and the protein product there is a target for selection, the better the linkage the more power there will be in selection.Woese himself has some research showing that within such a community there will be a trend to converge on a more universal transcriptional code (Vetsigian et al., 2006), tightening up the loose linkage between gene and protein product and allowing for greatly increased biological specificity. Woese proposes three phases of development of transcription and cellular life.1- A period of weak communal evolution where the transcriptional code is loose.There follows a selection between communities for a common code allowing the rapid sharing of beneficial ensembles of genes by HGT.2- Strong communal evolution: a universal translational code allows for the rapid dissemination of traits, the selection of beneficial ensembles and the production of more complex ensembles due to the potential for improved stability and specificity of the protein products. Eventually the complexity is such that the 2nd communal phase gives way to...3- Individual, vertical or 'Darwinian' evolution much as we are familiar with today.Woese suggests that the origin of each distinct kingdom is the product of such a switch from the communal to the Darwinian types of evolution. That it is not a rudimentary form of the currently extant kingdoms does not mean it was not simpler, just that it was quite different in nature.TTFN,WK

I like woese's theory, it seems to quite elegantly provide a mechanism allowing for the development and optimisation of horizontal gene transmission in concert with refinements in the translational code.I'm not 100% convinced that such a radical solution is neccessarily required to provide a basal common ancestor for the various cellular architectures, but Woese's approach may actually be the most parsimonious in some ways given that the common elements of the 3 kingdoms arguably aren't sufficient to provide a viable ancestral cell architecture.If we accept Woese's argument that the genetic distances between the kingdoms is too great to fit in with a vertical lineage, even one with a moderate degree of HGT as in modern bacteria, then a period with HGT as a prime mover is probably required.As Annafan suggests the communal period of cellular evolution is much akin to a genetic event horizon, with the lineages of many cellular systems being lost in the mix, there are however clearly a number of systems so basal to cellular function that they can be traced beyond what Woese would term the 'Darwinian transition'.I don't think that our not having observed a progenote is particularly relevant to whether Woese is right or not. As others have pointed out we do observe the sort of Lamarckian evolution via HGT which Woese proposes to a limited extent through the swapping of plasmids in bacteria.I certainly don't see any evidence at all to support the idea thay the 3 kingdoms didn't share a common ancestor, although such an ancestor may well have been a pre-cellular genetic community rather than what would be considered a single cell type today. In fact the genetic evidence does point to a common ancestor for a large number of cellular processes as woese's work on the aminoacyl-tRNA synthetases suggests (Woese et al., 2000).TTFN,WKEdited by Wounded King, : No reason given.

Because there is more than one chemical solution to many of the functional structures which suggest a common ancestor.If there were only one possible amino acid sequence for a particular protein or only one possible genetic code then you might have a case for their having arisen independently, but as it is the conservation of these elements when there are alternative possibilities argues for a common ancestor. This could be the case but it would not solve Woese's problem. If we were to accept multiple different abiogenetic events then to fit the progenote scenario or contribute to modern cells they would all need to have been part of the pre-genomic pre-vertical community. The level of commonality between all cells cannot be explained by 3 distinct instance of abiogenesis, even if we were to allow for arguments sake that distinct isolate abiogenetic events would give rise to the same basic genetic elements.So while we might imagine that self replicating RNAs may arise more than once in isolation, or even go as far as to utilise DNA as a more stable genetic medium, there is no way we can go as far as allowing for the genetic code, the transcriptional machinery and many other conserved cellular features to be explained in this way. This doesn't really follow, not without knowing the actual chemistries and circumstances required. This is yet another intuitive estimate of the probability of abiogenesis, only instead of the usual claim that it is too fantastically improbable ever to happen you are claiming that it is so probable that it should be happening all the time. Since humans and cattle are not competing for a common ecological niche this seems like a rather weak argument, especially since man has wiped out so many species. Even if we allow interniche competition if we compare the number of species man maintains domestically with those he has had a hand in 'squeezing out' I think the weight of evidence comes doen heavily on the side of squeezing out.TTFN,WK

There is a difference between similar structures arising effectively arising independently in different lineages and the same structures with the same genetic basis arising in distinct lineages. Common placental and mammalian body forms follow function but there is nothing to suggest a common genetic basis for the similarities. In contrast the similarities we are discussing in terms of cellular architecture are either inherently genetic or very tightly coupled to the genetic mechanism. Well, yes! Obviously without knowing every possible chemistry of life we are pretty much in the dark as to the chances of any particular type arising, but there is an awful lot of potential chemical interactions out there and a lot of highly varying environments. So without some compelling evidence that DNA and the genetic code as we see it today are the only possible forms for life it is reasonable to posit a common origin for those elements. This seems a completely unwarranted assumption. There is a capacity within chemistry for abiogenesis to occur that does not mean it is designed to occur. There is a capacity for cars to flip over and kill their drivers, but they are not designed to do so. This assumes your inital unevidenced asserion is true and then compunds it with a similar flight of fancy equally without evidence. Why would it do so? How would it do so? Given that there is life on Earth it seems a given that it must have arisen at least once, by whatever means. That done we have no way of knowing if other possible bases for life have temporarily existed nor what other forms of life might exist beyond Earth.To the best of our ability to determine we only have one example of life arising and 1 is a crappy sample size to derive probabilities from.On the other hand we have a large number of repeatable experiments showing the capability form primitive forms of organic matter associated with life to be generated from inorganic matter in an atmosphere consitent with our best estimates of the atmosphere on pre-biotic Earth. I'm not saying we can't say anything about abiogenesis I'm just saying that we can't say anything about the probability for abiogenesis beyond knowing that it is not impossible as it appears to have occured at least once.Yes this does make a materialist assumption, but then science does that and there is considerably more evidence for the materialist scenario than a supernatural one. Mutation is not rare. Any specific given mutation may be rare but evolution does not rely on specific given mutations. That probability argument does not work unless you insist that the current conformation of life on Earth was the intended goal from the outset.None of these points seem to be new or particularly relevant to Woese's paper, you seem to be drifting back to a familiar set of tropes Randman, we already have threads for discussing morphological and genetic homology and some sort of chemical/genetic frontloading.TTFN,WKEdited by Wounded King, : No reason given.

Way to misrepresent my opinion Randman. What I said was that many structures considered to be analogous at best, such as the forelimbs of vertebrates and the wings of insects share a number of genetic modules regulating pattern and growth. The examples of the morphologies of the marsupials and placentals has absolutely no evidence of a common genetic basis for their morphologies beyond those generally applicable to the growth of tissues such as bone and muscle. Because they are almost always not the same structures, but rather highly morphologically similar and of course because we now have a wealth of genetic evidence suggesting common descent which regulate the development of those similar structures. It does of course place constraints but their extent and their relation to form and function in a genetic rather than gross morphological setting make the degree of those constraints quite distinct from an organismal environment's pressures. Unless there is only one suitable genetic sequence for a function there is no environmental constraint for a specific sequence.In the total absence of any evidence for such a strict environmental constraint there is no reason to needlessly multipy the entities neccessary for particular genetic features to arise. No I didn't say that, I said that we don't know what the products would have been.As to your complaints about Kuresu and PaulK driving you to topic drift, I fail to see what that has to do with our own discussion which has not involved ether of those two, I am not talking about the thread, just our own dialogue.TTFN,WK

I'm not sre where you get that this is the issue from. It is quite clear from Woese's published work that he considers the 'progenote' population from which the 3 kingdoms arose as biotic.The great difference Woese proposes for the progenote is that there are no discrete genetic organisms as is the modern mode, instead there are lots of highly transmissable discrete genetic elements. While they may not constitute life as we know it they are certainly as alive as any of the pseudo biotic form such as viruses.This horizontal transmission dominated community makes tracing discrete genetic lineages beyond a certain point problematic. In theory this could mask some sort of convergence from different abiotic origins, but if we accept Randman's idea that such multiple origins would all produce the same genetic system then the question is totally redundant anyway. Of course it makes Randman's idea completely useless, but there you go.TTFN,WK