[gore3000]

But, as these people show, evolution as the only input to how natural programs are organized is also probably wrong.

So what is supposedly this other input? Also can you give some examples of these simple systems that give supposedly complex results?

[eno_]

At www.wolframscience.com you can browse cample pages from his book, and, if you have Mathematica, you can download and run the code that actually conducts his experiments.

That "other input" to how genetics works are the laws of complexity theory. In other words, random mutation and evolution do not have a free hand in modifying genomes. There are more basic laws of complexity, information theory, expressive power of systems, etc. at work. Biochemistry meets information theory.