A diversity of export systems of varying complexity exist, and there is a functional continuum of membrane complexes ranging from single proteins and passive pores through to active, gated export systems, indicating that there are no major evolutionary puzzles to solve. The cataloguing and categorizing of transport proteins is already yielding insights into their origin (Saier, 2003).No assessment is made throughout the paper of exactly how likely the evolution of a membrane complex is. And yet the observation is made that the fact that there is a continuum of membrane complexes indicates that there are "no major evolutionary puzzles to solve".
But this statement is made having presumed that the membrane complexes can evolve. It is assumed that the answer to the key question - whether membrane complexes are likely evolve - is "yes" - and the evidence is then circularly interpreted in the light of this assumption.
Now let's suppose that we discover that, in fact, the likelihood of a membrane transport system arising is below the universal probability boundary. Does the evidence then suggest that there are no major evolutionary puzzles to solve? No. Instead, the evidence suggests now either that we have determined the likelihood incorrectly, or that intelligent design was responsible for the abundance of such systems.
Okay, now consider the actual state of knowledge - that is, we don't really know what the likelihood is of a membrane transport system arising. What does the fact that we have a continuum of such systems suggest? Well, if we assume that the likelihood is high, then Matzke is right - there are evidently no evolutionary problems here. If we assume that the likelihood is low, then the fact that there are a whole range of membrane transport options would appear to be evidence of design.
I am aware of the fact that membrane transport isn't considered an irreducibly complex system - not even, I would hazard, by the most ardent creationist, let alone by the ID camp. The point I am making is that the conclusion drawn by Matzke is dependent upon, but also conceals, his presuppositions.