confusion and prokaryotes
One of my recurrent interests is confusion, especially in science. The way I understand this concept is as follows: a term or concept is confused = that term or concept takes 2 or more entities to be one entity (where 'entity' covers individual objects, properties, relations, etc.). In other words, a confused concept or term conflates distinct things. I think the phenomenon of confusion is important in science because part of what happens in many scientific revolutions is that, from the point of view of the new scientific framework, the old scientific framework is confused -- or vice versa. (Re: 'vice versa': Einstein's principle of equivalence, for example, would be seen as an unjustified conflation from the viewpoint of a classical physicist: gravitation and inertia are two separate things, and running them together as Einstein does is an unjustified conflation.)
I've recently started looking at another potential case of confusion in science, but I'm a bit uncertain about it, and would like to air it to get reactions.
In high-school biology class, we are told that the highest/ most basic division among life on Earth is between 2 kingdoms: prokaryotes and eukaryotes. Eukaryotes are all those organisms whose genetic material is encapsulated within a nucleus; Prokaryotes are organisms whose genetic material is not. In other words, Prokaryote=df not-Eukaryote.
However, in the last 2-3 decades, the highest taxonomic level has slowly switched to a three-group classification: Eukaryotes, Archaebacteria, and (Eu)bacteria. Why? The short answer is: "on the molecular level, [archaebacteria] resemble other procaryotes, the eubacteria, no more (probably less) than they do the eukaryotes" (C. Woese et al., PNAS 1990 p.4577).
The upshot for present purposes is that there are actually two distinct highest taxa whose genetic material is not enclosed within a nucleus, viz. the archaebacteria and the eubacteria. From this point of view, it appears that 'prokaryote' conflates the archaebacteria and the eubacteria. But if we recall the earlier characterization of 'prokaryote' as simply 'not-eukaryote,' then 'prokaryote' does not appear to be a confused term. So the question is: Is 'prokaryote' confused, or not? (And why?) I'm happy to hear just intuitions, as well as intuitions backed up with some sort of argument or evidence.
P.s. -- For some readers, this discussion will immediately call to mind Quine's solution to the 'grue' paradox in his paper "Natural Kinds" (in Ontological Relativity and other essays). There, Quine notes that if the predicate P picks out a natural kind, then not-P usually doesn't. A hackneyed example: 'gold' picks out a natural kind (any matter with atomic number 79), but 'not-gold' does not, because it covers many, many completely disparate things -- there are too many ways to be not gold for 'not-gold' to refer to a natural kind.
This might make us think that many/ most predicates of the form not-P are, in fact, confused, since such predicates most often apply to many different natural kinds. All I can say at this point is: that sounds counterintuitive to me... it doesn't feel to me like 'not-gold' conflates distinct things.