I read your article. It’s an interesting engineer’s perspective. I believe the arrow of time is an illusion, as far as the equations of physics are concerned. It wouldn’t be surprising if that illusion or emergent reality is generated in a confused way, as you suggest, with consciousness and thoughts and feelings going in opposite directions. The brain evolved without intelligent guidance so the brain’s bound to include something akin to kludges.
One problem with the engineering level of explanation is that it can only presuppose the values or ideals that decide which goals the system should pursue. The evolutionary purposes built into the system are pseudo-goals. As you say, they bubble up from ones and zeros or from a host of micro events. If we followed only our most natural goals, such as the ones built into us by our genes, we wouldn’t be the anti-natural, anomalous creatures we are. We wouldn’t have art, religion, science, culture and utopian dreams.
We have irrational faith in our ideals and that sets us against the operational systems and natural cycles and rhythms. Our artificial world is in conflict with the natural environment, because we don’t see ourselves as mere animals. We’re people or “spiritual” beings. We don’t belong in the mere wilderness, we think, with the rest of nature’s dupes. We build new worlds to give us more self-control so that we’re not at the mercy of nature’s mindless, pointless changes. Our apparent dream or ideal is to be gods, which comes across as nonsense from the engineer’s level of explanation, but that’s because there’s no room at that level for any justification of any goal.
A body or a society works “optimally” or efficiently or otherwise, but what does that mean? There’s an optimal way to function for a Nazi society, just as there’s an efficient way to run a socialist utopia. As to which society we should prefer, the engineers alone can’t tell us. Nazis and democratic socialists each have their sets of engineers. It’s like Scotty on the USS Enterprise. The captain decides where to take the ship and Scotty only looks at the system and tells the captain whether the ship can make it here or there. The engineer doesn’t think in terms of values or ideals. Again, if we all thought only in engineering terms, we’d have surrendered to nature’s pseudo-purposes and we’d be content to try to survive as animals. We seem anomalous precisely because we think also as persons, as captains of our ship. If the captain’s level of explanation is illusory, how do we explain the anti-natural tendencies of our artificial environments?