Intelligent Design

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Mutation does not increase complexity. Point mutations just change existing DNA leading to a decrease in function (which can be advantageous in certain environments, but it is still degrading the information). Gene duplication is the evolutionist way of explaining increasing complexity, but duplicated genes are silenced in the offspring, and because natural selection can only work on expressed phenotypes from the protein product of the gene, there is no way for a duplicated gene to eventually settle into a new function if it is not being expressed. The only point mutation that can actually add new nucleotides to the genome are insertion mutations, which are always harmful considering that they push each following codon back one nucleotide, which changes EVERY following amino acid in the protein.
Bacteria have the capability to acquire new genes from the environment or from conjugation, but the genes they acquire were already in existence and are not the result of mutation. I would suspect that this is the case with nylonase. I am skeptical of new digestive structures being produced through mutation. I could see existing structures altering, which is still well within the parameters of the variation I would expect based on how genes are regulated.

As one who has walked into at least one scientific field with the presumption that everything which exists owes its existence to a designing creator, why do you think your god would bother with any sort of automatic coding system at all, much less one which could only degrade and never, ever improve? Keep in mind that if said god is all-powerful and perfect then he is also tireless, therefore he really could design each individual with as much thought that went into the first. You'd better not try and chalk this up to that "curse of sin" nonsense, not if you want to play at science.

a-HIDEY-HO!!!

Why does God create a genome that can't improve? Well if He created one that was in need of improving, then you would be asking why didn't He make it better? Why bother with a coding system? because the fact that there is an intelligible system that we can observe allows us to conclude the designer's existence. If God designed each being individually, then there would be no observable coding system that demonstrates an intelligent creator. Why does the genome degrade? It has amazing capacities to maintain DNA's original structure. There are many enzymes whose purpose is to fix mistakes and mutations. It degrades when we stray from natural environmental conditions. We eat carcinogenic foods and don't exercise. Proper nutrition and physical activity increases the transcription of many enzymes and helps our cells to take care of their genome.