That's the opacity. It's one thing to write a program that solves a specific problem in a specific way. Straightforward IF-THEN-ELSE.
It's quite a different thing to write a starting bit of software and then tell it to keep attacking a problem until it finds a solution. By the time it achieves that solution, it had done so by beating itself into a shape that can find the solution, into "that which knoweth the word".
When the programmer or researcher now dives in to see how the software did what it did, she finds nothing but "spaghetti code," indecipherable yet functional.
What I am saying is that it is actually not that undecipherable. At least in my humble opinion.