That's probably where you lost him. In the genetic algorithm/ simulated evolutionary work, you have a known, constant goal the entire time; ecosystems do not suddenly appear and vanish; there is no predation nor disease; and there is never any extinction.
Not to mention that it begs the questions about "origins" etc. The sample code from which you start, the computer, the kernel of the algorithm which keeps the "best" solutions and discards the others, the very parameters used in the scoring function, did not spontaneously appear.
Perhaps a better illustration would be to start with a blank slate of memory, or random 1's and 0's, and not even a compiled program to start as the basis for your mutations. [Pre-amino acids, you know. ;-) ]
So as an illustrative example to point the capabilities, or a "thought experiment" put into practice, it's just dandy.
But the degree of similarity to biological systems might not be as close as you want for a well-formed simulation...
Cheers!
Chemistry is not a blank slate. The trick in building computer simulations of evolution is to model the crucial features of chemistry with available computer resources.
That's one of the things the Santa Fe Institute was established to study. If they had "the" solution we'd have heard about it.