You have quite a marvelous story-telling voice Luke. I find myself entranced by your "dream sequences" (although I guess they would technically be flashbacks) and greatly enjoy the use of multiple characters with seemingly extreme depth in juxtaposition to others that seem to be only foils.
Your history and philosophy are very interesting to read. They bring the reader to the edge of their seat as they wish to learn more of why all this is occurring, what led to the rise of the "Humanist" movement, and why facilities like the one portrayed are even allowed (or perhaps they are not and its very existence is a "dirty little secret"). Your dialogue is still wonderful and very flavorful. The diction and syntax modifies for each person so that it's not only easy, but natural to imagine a different voice for each character (for example, it may be me, but I imagined Benjamin [the Alpha] to have a deep, confident voice that rang with easy strength).
Having said that, I still think you are moving too fast. Within the space of two paragraphs Luke was taken from his cell and deep into a medical procedure. Now, that may be purposeful to show the reader how fast it is, but you skip a lot of details when you move that quickly that can emphasize the fear and suspicion that is paramount in that situation.
Overall, this is a great work. Two thumbs up.