I completely agree with everything balyons said, except that no mutation can be beneficial. Mutations can be beneficial - depending on what criteria you're using - but they can't add information.
Explain how a new open reading frame whose product digests material only around since the early part of this century is not new information.
Although that may have looked like new genetic information, or macroevolution, at first, it's more likely to have been a loss of information in that the enzyme catalysis processes became less specific. By a loss of information, the enzymes would be less effective but more general in what they digested, allowing the enzymes to remove any inbuilt inhibition they may have had against chewing up nylon.
You are switching from one gene product to a "catalysis process". The old catalysis process, a complete glycolysis pathway, has been turned off due to lack of carbohydrates. The genes for the glycolytic pathway are still there. What has been produced, by a single mutation, is a novel pathway that supplies energy to the cell from a substrate that was up until this time unused.
Also, explain how the flavobacterium was inhibited in its ability to digest nylon. You seem to be suggesting that the bacteria had the ability to digest nylon before but another protein/chemical was preventing this.
Proteins and nylon are digested in a very similar manner (which is why nylon is the first substance you'd notice being catalysed if these mutations began).
Is there another example of a protein digesting enzyme that also digests nylon? I haven't heard of any, but I could be wrong. Could you please cite any examples.
Degeneration again - beneficial for the moment, mind you, depending on whether nylon is good for bacteria, but such losses of information would eventually create an enzyme that is permitted to digest a wide range of substances but is not good at it.
Explain how taking advantage of an unused niche is bad for a bacterium. Also explain how further mutation will cause the enzyme to be less specific, citing examples of other mutations to nylonase genes. Explain how digesting nylon is bad on principle alone.
Such bacteria would not survive when pitted against bacteria with substrate-specific very efficient enzymes.
In a solution of nylon, the new flavobacterium will kick the butt of any other bacteria out there. If you don't think so, cite another bacterium that can survive on nylon alone. Also, cite any other nylonase genes that are more nylon specific than that found in the flavobacterium.
But new evidence actually suggests plasmids may be responsible for the nylon digestion. Other bacteria have the same property and could have passed this information to the flavobacteria. See 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.
The nylC gene on the plasmid has been known from the start. What you are missing is that the identical plasmid, minus the frameshift mutation, is present in the wild-type carbohydrate only flavobacterium. Horizontal gene transfer may have contributed the plasmid in the past, but gene mutation that occurred could have been in the chromosomal genome as easily as in the plasmid. Frameshift mutations can occur in the chromosome as easily as in the plasmids.
If you think there is a disctinction, please explain how mutation to extrachromosomal DNA does not count as being beneficial or an increase in information.
In general, could you also explain what new information, in a genetic sense, would look like? Before you can explain away a negative, I think it would only be fair to define a positive as well. To simply say new information can not arise through mutation is a priori dismissing it without first defining what new information would look like.