This article gives an overview of some of the hypotheses around. The tendentious language is clear, for dr. Martin there is only one theory.
Abstract: Recent findings are summarized in support of the view that mitochondria (including hydrogenosomes) and plastids (including complex ones) descend from symbiotic associations of once free-living organisms. The reasoning behind endosymbiotic hypotheses stems from a comparison of biochemistry and physiology in organelles with that in free-living cells; their strength is shown to lie in the speci¢c testable predictions they generate about expected similarity patterns among genes. Although disdained for many decades, endosymbiotic hypotheses have gradually become very popular. In the wake of that popularity, endosymbiotic hypotheses have been formulated to explain the origins of eukaryotic cell compartments and structures that have no biochemical similarity to free-living cells. In particular, it has become fashionable in recent years to entertain the century-old notion that the nucleus might also descend from an endosymbiotic bacterium. A critique of that hypothesis is formulated and a simple alternative to it is outlined, which derives the nuclear compartment in a mitochondrion-bearing cell.
His opinions of the autogenous hypotheses are not clear, because he seem to claim that autogenous relationships do not lead to an endosymbiotic relationship. This is true and this is the basis of autogenous formation of theory: it is not an endosymbiosis, but the two compartments are interdependent. That is exactly what is needed: interdependence and this can be accomplished by autogenic formation (eg. the ER and the nucleus are interdependent), but not with the endosymbiotic theory because at start there will be no symbiotic relationship.
In addition, in general terms, the alternatives to endosymbiotic hypotheses for the origin of a given cell compartment can be designated collectively as autogenous hypotheses (Doolittle 1980). These posit that the given cell compartment in question arose de novo in the cytosol, usually in response to some specifically formulated selective pressure and, thus, entailed no endosymbiotic relationship.
I don’t have the original articles, but it seems that the autogenic hypotheses at the time work from invaginations of the plasma membrane. I work from the nucleus as the first compartment, followed by the derived ER, followed by the derived (Golgi) vesicles and targeting in which the cytoskeleton existed from very early in the origin of the eukaryotic cell. Moreover, selective advantages are what we needed and, system aspects such as separation of functionalities are a sine qua non for further evolution.
Autogenous hypotheses posit that the nuclear compartment and its membrane results from the reorganization of a pre-existing intracellular membrane system in the common ancestor of eukaryotes. As candidates for such pre-existing intracellular membranes, invaginations of the outer plasma membrane of a primitive phagocytosing cell are by far the most popular (Uzzel & Spolsky 1974; Bogorad 1975; Doolittle 1980; Cavalier-Smith 1987a, 1988), but other alternatives involving thylakoids in a cyanobacterium have also been argued (Cavalier-Smith 1975). Autogenous hypotheses generally demand the existence of a cytoskeleton in the cell which evolved the first nucleus as a mechanism for accounting for such membrane restructuring. This is particularly true for hypotheses that envisage the origin of the nuclear compartment in a phagocytosing prokaryotic (but still `protoeukaryotic’) cell, because the cytoskeleton is a prerequisite for phagocytosis as we know it (De Duve 1969; Stanier 1970; Cavalier-Smith 1987a; Doolittle 1996). Autogenous hypotheses also tend to forward speci¢c selective advantages for the possession of a nuclear envelope, for example the construable advantages of decoupling translation from transcription or other more complex advantages.
Another main problem in dr Martin’s reasoning is that he assumes that the eukaryotic cell evolved from a bacterium, while I pose that a eukaryotic-like genome was the ancestor genome. Then we don’t have the problem of a bacterium evolving a nucleus. So maybe a problem for the original autogenic hypotheses, but not for mine:
In addition, if the nuclear compartment differentiated from a pre-existing endomembrane system in ancient prokaryotes, one would expect to observe evidence for the same process (the origin of a nuclear compartment) in contemporary prokaryotes. Since no prokaryotes are known to possess a structure that can be even vaguely homologized to a nuclear envelope, its pore complexes or the mitotic process with which it is associated, autogenous hypotheses have to come up with a satisfactory explanation for why the nucleus arose in a prokaryote, but only in the one that gave rise to eukaryotes.