Inadequacy of the term prokaryote
We have become used to deal with biological organization in the frame of a fundamental distinction between two types of organisms: the prokaryotes and the eukaryotes. This dual partition of the living world has lost much of its appeal with the discovery of the three Domains [5] and it has been proposed recently that the term "prokaryote" should be dropped altogether in favour of "microbes" [25]. Martin and Koonin [26] rightly pointed out the inadequacy of the term "microbes" and argued to maintain a "positive definition of prokaryotes" based on transcription-coupled RNA translation, (TT coupling) in keeping with the lack of a nucleus. However, this definition also is brought into question since the momentous discovery of a nucleus-like structure in some Planctomycetes, with a double membrane and pores [27]. Moreover, Poribacteria and some Archaea-like or ganisms also feature DNA-enclosing compartments [27]. It is not known whether TT coupling also applies in these organisms so that the validity of such a definition awaits confirmation. Nevertheless there are other reasons to relegate the term "prokaryote" to the historical record: (i) the prefix "pro" inappropriately suggests anteriority; (ii) this notion of anteriority of prokaryotes is usually associated with a very common prejudice in favour of an overall directionality in evolution, i.e. from the simple to the complex (a Lamarckian heritage) and, (iii) Bacteria branch off at the lowest position in a popular version of the tree of life [5]. As a result, it is often taken as a matter of course that LUCA must have been "something like a bacterium" and that many eukaryotic attributes evolved by gradual complexification, a notion whose inherent difficulties, however considerable, are often ignored [28-31] and has no compelling basis as a biological principle [32,33]. Indeed, what has increased in the course of evolution is order and its corollary, organization [34], complexity being a rather ill-defined and intuitive concept, except in the very abstract Rosennean definition of being "non-simulable", i.e. Turing incomputable, and in the objective, functional and molecular definitions referred to in the forelast section[35,36]. For example, a biofilm may be more complex than the simplest metazoans but is considerably less ordered. Organismal complexity, when it arises, is contingent on order.
What are the facts and the logic that we can use as a guide to discuss the nature of LUCA, its emergence and its legacy?
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2478661/
