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Well I guess that just goes to show you, Professor, that among the population of monoclonal (genetically identical) bacteria, for whatever reason, perhaps some of these "critturs" were more successful information processors than others.

Monoclonal means they were descended from one cell by asexual reproduction; it doesn't imply cloning. You plate out bacteria on a petri dish, thinly enough so each single bacterium grows into a single, non overlapping colony, and then grow a culture from that colony. The bacteria are different only in respect of the number of spontaneous mutations they happen to pick up in 30 generations (say) of doubling. That rate is very small and quantifiable.

We know this because we've been doing microbiological experiments of this sort since long before I did them myself as a young lad. Microbial genetics is simpler and better understood than mammalian genetics - the genome is much smaller.

There is a simple and parsimonious explanation for the phenomenon - we expose the bugs to something that causes point mutations in their DNA. We find some develop resistance. We isolate the DNA, and find the ones that have the resistance have a point mutation in the penicillinase gene. We do a crystal structure of the expressed penicillinase, and find the enzyme from those bacteria with resistance has a binding pocket which has been enlarged by the mutation to accomodate the different antibiotic, which we can show using molecular modelling.

In other words, there's a direct chain of evidence, from a mutagen that causes a known chemical change in the DNA, to the mutant protein whose amino acid sequence is completely determined by the changed DNA, to the folded protein whose three dimensional structure is completely determined by the amino-acid seqeunce, to the enzyme activity which depends on the three dimensional structure, to the improved survival of the modified organism, which is a result of the new enzyme activity. You have mutation followed by natural selection, understood on a molecular level.

The new functionality does come at the expense of the old functionality, if you remove the selective pressure to retain the old functionality. However, as I mentioned toward the end of my post, if you maintain the selective pressure (if you expose the bugs to penicillin in addition) a double mutation occurs that retains the first functionality while adding the second.