You're using "Isolated DNA" to mean cDNA (a point that I think needs clarifying; you can isolate DNA from cells through other methods). Your metaphor doesn't seem particularly solid to me; it would be more accurate to say that DNA is source code, proteins (and hence enzymes) are object code, and mRNA is code that has been pulled out from disk (the genome), had its comments (introns, as you point out) removed, but is not yet compiled. The computing metaphor obviously breaks down; the best way to characterize cDNA I can think of is as code that's been intercepted on its way to the compiler and placed back into storage - for it to be reverse-engineered object code, it would need to be derived from proteins, which it is not.

We could always call the proteins the binaries, that is to say the output of the linker!

Either way, I was just trying to phrase it in terms familiar to programmers. No metaphor is perfect.

That metaphor really only holds up if your "compiler" does nothing but remove comments (and introduce errors at a low rate).

Obviously DNA is low level. This means it must be assembler- and assembly often is as simple as removing comments and translating "written" code into "machine" code.

Yes, if your "compiler" translates "assembly with comments" to "assembly without comments," then your metaphor is apt.

Update: After reconsidering, I take it back. Introns are important, especially intron boundaries. So, my new assertion: so long as your "compiler" translates "assembly with comments" into "assembly with the same comments intact," then I agree that your metaphor is apt.

So... compiler directives? ;)