Similar to DNA that has evolved to create living organisms. Each evolutionary step was selected because it worked, but the result is in no way optimized to be understood by human brains.

There's a hierarchy of systems:

* non-working, random, chaotic

* working, but not understood/understandable

* working, and clearly understood by at least 1 human brain

Clearly, each step in the hierarchy is less primitive than its predecessors. Also, since human brains are the greatest intelligence we know of, the 3rd bullet point seems like the pinnacle.