I can't believe that I've spent a Friday evening (Good Friday at that) doing literature searches and Entrez and Blast searches on this blasted bug!!! Also on Pseudomonas. Ho hum, what fun!!! Anyway, first thing to say is that some of the information in the AIG article and some of the interpretations don't make a lot of sense. I had intended to disect it, but my DNA analysis software has led me a merry dance on the sequence alignments and translations in all three reading frames and I don't have time tonight. Hopefully I'll get back to it tomorrow (toddler and his disease permitting).
One thing I will say with regards to the genes in question residing on plasmids and not the Chromosome is that the effects of selection pressure on plasmids in bugs are so much more readily seen. Carrying a plasmid is a bioburden on a bug - it has to use valuable resources copying the pasmid as well as the chromosome when it divides. In an environment devoid of nylon, those bugswhich have the nylon digesting enzyme gene on a plasmid are at a distinct reproductive disadvantage and so become less numerous in the population. However, possession of the pasmid in these conditions is not lethal and so the odd one or two will still carry copies. If all other carbon and nitrogen sources run out and only nylon remains, these very few are now at a distinct advantage, even with their bioburden and so they become more numerous. Under these conditions the non-possession of the plasmid IS lethal because the bugs will starve. Eventually, the entire population in the given environment will contain the plasmid. So, although the bug doesn't change into another species or become extinct, evolution can be seen in the behaviour of the plasmid withn the bugs, even although the plasmid doesn't change its DNA sequence. There is no mutation involved, as no offspring will contain information that the parent didn't, since the parent MUST have the plasmid for the offspring to have it (I believe this plasmid is non-conjugative). The whole thing is population dynamics.
To complicate matters, the presence of a number of transposons on the plasmid CAN cause DNA rearrangements. These jumping genes can jump to new locations in the plasmid, possibly inactivating genes that they jump into and leaving a copy of themselves in the original position. They can also jump into the chromosome under certain circumstances.
The bottom line is that I'm going to have to do a lot more reading before I can explain this in a less garbled manner, but my opinion is that the behaviour of this plasmid and its nylon-digesting gene is a wonderful example of selection pressures acting on a population and demonstrates perfectly the mechanisms behind the ToE.