I'm guessing that what was done was a lot less advanced as far as what is does compared to how it does it. I guarantee there is no complex thought processes going on. All it is, is a simple "stimulus, response!". Straight and level flight? Wow. How do you think this "brain" knows where the plane is going? I'm sure there is a simple input to it that indicates the plane is pitching left, and the super duper brain responds with "pitch right" and vice versa.
And even still, it's only "relatively stable straight and level flight."
What is interesting though are the implications. They are still trying to figure out how this all works, and this is a testbed to do that. The wierd thing is, knowing what I know about computers, it seems pretty far fetched for a program to become "self aware". If we're building computers from neurons, the same ones that run real actual brains, hmm I'm not so sure!!
ETA: Why is my post always the one that bumps over to the next page? It's uncanny!