Logical thoughts generated by a brain; a brain that may perhaps (as it's said to often do) distort reality. So he claims that we can't trust our senses, but ultimately he trusts his logic and reasoning.
I think of logic as something of a flashlight and reality as a maze. We often bump into walls and get lost (faulty theory) until a bright light (Einstein, Feynman, Witten, what have you...) points us in the right direction again. So we learn more and more about the maze (reality) as all historical accounts of our journey (previous theories that are modified or thrown out (dead ends)) are documented (science texts). What gets me is that you have to put your complete faith and trust in logic (or a human brain) so that as Dick confronts the problems of sensory bias (and inherited faulty assumptions, passed on like a baton in a relay race) he fails to confront logic itself. How can he trust his human mind, and how can he trust his theory created by his human mind?
If he breaks down reality to a set of cold, hard, unbiased numbers... and sidesteps (or confronts) the problem of sensory distortion of facts (or truths), then how can he take that foundation and build on it with a human brain? Sure the foundation is sturdy, but what of the structure he built on top of it? If we trust his human mind to build this theory, we arrive right back at square one: the problem of distortion of facts. Whether it be biases inherited through biological evolution, faulty assumptions, or we do away with those problems and have to confront yet another (trusting logic), we never really accomplished anything. It's like his theory contradicts itself simply by definition of one of its postulates. If we can't trust our eyes and ears, why trust our brain (and logic)? Reasoning with numbers (mathematics), even though they seemingly have external properties of their own, devoid of the possibilty of human tampering and mistakes (math seems to take on a life of its own), we ultimately deal with math on the basis of logical reasoning. They seemingly have external/platonic properties, but as we learn over and over nothing is as it seems.
How can he trust the "flashlight" to not distort the "real picture"? (ever wear colored sunglasses?) He eliminates our dependence on our senses to tell us the truth, but we find ourselves still lost in the maze questioning the illusions projected by the flashlight (logic, numbers, math, whatever).
After all this I have a couple of final "what-ifs". What if the journey through the maze (the process of learning) turns out to be in vain, as the maze turns out to be a cruel self-contained prison with no exit point. We'll never truly know reality; we can wonder around forever to no avail. All theories will forever be improved upon but never really accurate. In fact, with no exit (exit = last step in learning: final truth and complete knowledge of everything) there really is no correct direction to walk (which would naturaly be the "right path" leading to the exit). In that case, any and every philosophy of reality was, is, and will always be correct.
What if there is an exit but the route leading to it is akin to a dog taking a key, unlocking a lock, turning a doorknob, and stepping into a room to hit the light switch (and actualy understanding why he did this, rather than robotically). In other words, us knowing reality as it is... is as impossible as a simple creature knowing what to do, how to do, and why to do, to get in the next room. The capacity to understand simply isn't there, and all knowledge is nothing more impressive than a dog knowing where his food dish is and to scratch at the door to get out. Our logic is on the level of a stupid dog when it comes to "actual reality". Knowledge of the truth is as beyond our grasp as quantum physics is to a genius 2 year old.
Sorry for all the analogies.