I would be very amused if modern science discovered souls (your "operating system") and the spiritual realm exist. Much like dragons/monsters were discovered (but renamed Dinosaurs). I already believe this so I am biased, but I do firmly believe that modern humans overestimate not only what they know but what they are capable of knowing and undetstanding. I think the realm of reality you interact with originated from elsewhere.

This and some of the topics I am learning about in quantum mechanics (like virtual particles) remind me of this:

"By faith we understand that the universe was formed at God’s command, so that what is seen was not made out of what was visible." -- Hebrews 11:3 NIV

Just sharing an opinion and an observation.