[Doctor Stochastic]

On the other hand, IF genetic code was being formed by random, natural, unaided processes, then one would expect to see entirely unique instruction sets and absolutely no code re-use.

No, not at all. A randomly generated code with mutation and selection would be expected to show a tree-like structure, which is what we generally observe. Each chunk evolves from earlier chunks. Unique instruction sets could be created separately for each organism but would not be evolved that way.

[Southack]

"Unique instruction sets could [would] be created separately for each organism but would not be evolved that way."

That's the sentence that disagrees with your earlier point and agrees with my own.

[Southack]

"A randomly generated code with mutation and selection would be expected to show a tree-like structure, which is what we generally observe."

Are you claiming that this only happened once? That only one organism was formed purely at random, and that all subsequent organisms were formed due to mutations (and natural selection, of course) in the one?

And if you aren't claiming that, wouldn't we see any number of entirely different organisms created at random without any code re-use among them whatsoever, as well as mutated and selected derivatives of all of the above "original" creations?

I mean, either random natural processes are involved in root/base/first/original species or they aren't (of course, even so one couldn't rule them out for subsequent sub-species/derivations of the above).

But for the original formations, what precisely are you claiming here?