However, Carl Woese, who first came up with the universal rRNA phylogeny (also defined the Archaea as a new kingdom and originated the RNA world hypothesis), points out that the origin of life is not so clear cut. Although the rRNA tree gives a nice phylogeny that is agreeable with classical taxonomy, you run into problems when you start to try to compare trees based of sequences of different genes and proteins. For example, the Archaea and Eucarya might have the highest degree of homology when you compare gene A, but the Archaea might be more homologous to the Bacteria with respect to gene B. Apparently the frequency of these conflicts becomes more and more of an issue the further back you go through the tree, to the point where talking about three primitive and distinct cell types and trying to make inferences about their common ancestor doesn't even make any sense. Thus, he writes extensively about the need to develop and test new theories concerning the origins of cellular life. I've been checking out a few of his more recent reviews on the topic and they're pretty provacative and fun to read. Some interesting exerpts regarding the origins of cellular life:
The Annealing Model From The Universal Ancestor:
"A genetic annealing model for the universal ancestor of all extant life is presented; the name of the model derives from its resemblance to physical annealing. The scenario pictured starts when "genetic temperatures" were very high, cellular entities (progenotes) were very simple, and information processing systems were inaccurate. Initially, both mutation rate and lateral gene transfer levels were elevated. The latter was pandemic and pervasive to the extent that it, not vertical inheritance, defined the evolutionary dynamic. As increasingly complex and precise biological structures and processes evolved, both the mutation rate and the scope and level of lateral gene transfer, i.e., evolutionary temperature, dropped, and the evolutionary dynamic gradually became that characteristic of modern cells. The various subsystems of the cell "crystallized," i.e., became refractory to lateral gene transfer, at different stages of "cooling," with the translation apparatus probably crystallizing first. Organismal lineages, and so organisms as we know them, did not exist at these early stages. The universal phylogenetic tree, therefore, is not an organismal tree at its base but gradually becomes one as its peripheral branchings emerge. The universal ancestor is not a discrete entity. It is, rather, a diverse community of cells that survives and evolves as a biological unit. This communal ancestor has a physical history but not a genealogical one. Over time, this ancestor refined into a smaller number of increasingly complex cell types with the ancestors of the three primary groupings of organisms arising as a result."
The Role of Horizontal Gene Transfer (from On The Evolution of Cells):
"A theory for the evolution of cellular organization is presented. The model is based on the (data supported) conjecture that the dynamic of horizontal gene transfer (HGT) is primarily determined by the organization of the recipient cell. Aboriginal cell designs are taken to be simple and loosely organized enough that all cellular componentry can be altered and/or displaced through HGT, making HGT the principal driving force in early cellular evolution. Primitive cells did not carry a stable organismal genealogical trace. Primitive cellular evolution is basically communal. The high level of novelty required to evolve cell designs is a product of communal invention, of the universal HGT field, not intralineage variation. It is the community as a whole, the ecosystem, which evolves. The individual cell designs that evolved in this way are nevertheless fundamentally distinct, because the initial conditions in each case are somewhat different. As a cell design becomes more complex and interconnected a critical point is reached where a more integrated cellular organization emerges, and vertically generated novelty can and does assume greater importance. This critical point is called the "Darwinian Threshold" for the reasons given."
Other Carl Woese papers worth checking out: