Hi Philip - sorry about my "enforced absence" during July. Hope you've had a good summer.
Anyway, with reference to your "evolution of proteins/enzymes", I'm afraid you're barking up something of the wrong tree. Not only is there a huge amount of research on-going in this area - with implications for everything from plant breeding to disease - but there are a number of papers outlining precisely that. A simple search on PubMed yielded over 950 citations. A couple of interesting articles include:
Complementary advantageous substitutions in the evolution of an antiviral RNase of higher primates, and
Primitive Protease Discovery May Unlock Mysteries Of Enzyme Evolution, which, although not peer-reviewed, is very interesting.
In any event, there are a couple of points to your argument that merit looking at:
1. A lot (in fact, probably most) existing enzymes evolved via gene duplication, substitution, etc in existing enzymes.
2. It is very difficult (and I'm sure TB can attest to this) to determine the phylogeny of a specific enzyme much beyond a generic "family" (be careful, this term doesn't really correspond to the linnean taxonomic group of the same name). Often different, closely related families, share functional and structural features including enzymes capable of catalyzing similar reactions. Worse still, enzymes within a family may share as little as 10% sequence, even though they have the same 3D structure. Phylogeny may be based on structure or reaction.
3. Some enzymes catalyze completely different reactions. For example, the enzyme chymotrypsine catalyzes both amidase and phosphotriesterase reactions. Even more confusing, carbonic anhydrase II in cows also has a phosphotriesterase action as well as the carbon esterase and CO2 hydratase actions for which it was named.
With all this duplication of effort across gene families, it is fairly easy to see how selection could have caused the evolution of new enzymes using different mechanisms to catalyze the same or different reactions. Anyway, for a more technical discussion, please see
Divergeant Evolution of (beta-alpha)8 Barrel Enzymes. It contains an excellent discussion of the evolution of the enolase enzyme superfamily.
Closing: Even beyond the evolution of specific enzymes, for your argument to hold any validity, you (and TB) are going to have to provide a non-evolutionary explanation for why enzyme families are found in vastly different organisms - some are identical in plants AND animals of various types. All of which leads, if you're an evilutionist, to indications of the common ancestry of ALL life. Of course, you could always just say "goddidit that way". To me, that's begging the question, however.
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