"... sometimes there are illogical reasons for things being in place too."

More often than not, it's just that we haven't worked out the proper logic/connections yet.

I think the term 'counter-intuitive' is what you may be thinking of...like the guy who 'proved' that bumblebees shouldn't be able to fly. *grin*

The first people who saw bread dough 'rise' didn't understand it either...I'd wager they prayed and made 'offerings' before they learned about yeast. To this day there are Belgian breweries who allow 'natural' yeast to settle into open kettles to create Lambic beer, and NO ONE is allowed to clean the room where the kettles are, for fear of messing up the formula. They know THAT it works, and they have some idea 'how' it works...but......