Part 1 was an excellent read. Part two was a less excellent read, but deeper. I think the analogy of our universe being like an "embedded system" is a good one. I don't doubt that there's much more to it than we can understand, much like the betta can't understand why he's stuck in a fishbowl, or the hypothetical Mario who can't understand the invisible wall.

On another note, does anyone else find the "big bang" theory incredibly unsatisfying? I have no reason to believe it's not true, but as Yegge points out it seems to bring about more questions than it answers.