The Quantum Thief, 2010, by Hannu Rajaniemi is set in a universe of “embodied cognition” where souls can have many minds and many bodies.  Mentioned at the beginning, one of the super-powers in the story, the Archon, is tasked with turning the matter of the physical universe into a Prison, “to increase the purity of the Universe.  This is what their Father, the Engineer of Souls, taught them to love.  This is the way the world is made right.”  There is much religion and philosophy within this book to ponder, but you’ll never have time to do that on a first reading because you will be too involved with following the Thief, Jean le Flambeau, as he struggles to escape this prison during a very exciting sci-fi mystery story.