Actually I just got to one of those small... nuanced moments you guys have been talking about. And I think the only reason I caught it is because it involved Amos, my favorite character. In the middle of S2 E3 the "important players" are discussing why the scientists they just captured researching the extra-solar bio-weapon seem to be sociopathic lunatics and the doctor they are consulting gives them a thorough explanation that they are still human, and still have empathy, just don't seem to recognize it due to "orders" or some other trigger. At which point Amos perks up and asks if there is any way to cure it.
This is why I love that character and the way that actor portrays it. He nailed that scene and let me, as a viewer, know that the conversation was apropos and that my feelings towards his character were grounded. With one, simple line. Just in the way he delivered it. Yea Amos... buddy, we know you're fucked up and just want a little love. But maybe someone did that to you on purpose, to keep you subservient.
A lot like religion... hrmm... there's been some mention of Mormons though not too much to this point in the show so far.