Comment on Science, Methodological Naturalism, and Faith by Gene Fortner.

@pauluc: Bacteria did have the digestive function before nylon was invented. The fact that they could not digest nylon before nylon was invented is simply because there wasn’t any nylon to digest.
New evidence shows that the ability was due to plasmids [e.g. K. Kato, et al., ‘A plasmid encoding enzymes for nylon oligomer degradation: Nucleotide sequence analysis of pOAD2’, Microbiology (Reading) 141(10):2585–2590, 1995.] In fact, more than one species of bacteria have the ability, residing on plasmids. This suggests that the information probably already existed, and was just passed between different types of bacteria.
All that would be needed to enable an enzyme to digest nylon is a mutation causing loss of specificity in a proteolytic (protein-degrading) enzyme. This may seem surprising—how would a loss of information create a new ability? Answer: enzymes are usually tuned very precisely to only one type of molecule (the substrate). Loss of information would reduce the effectiveness of its primary function, but would enable it to degrade other substrates, too. Since both nylon and proteins are broken down by breaking amide linkages, a change in a proteolytic enzyme could also allow it to work on nylon. If this process were continued, the result would be a general enzyme with a weakly catalytic effect on the hydrolysis of too many chemicals to be useful where much selectivity is required. To put it into perspective, acids and alkalis also catalyze many hydrolysis reactions, but they also lack specificity. Indeed, an inhibitor of a protein degrading enzyme also inhibits the action of the nylon degrading enzyme.

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