So why have the Cylon "scream" if it wasn't in pain? They even asked what it was doing and she said it was screaming. No offense Yong but I think you're analyzing it too deeply. The scene was clearly showing us that Cylons have the ability to feel pain. Whether or not Bekka is sympathetic to the Cylon's plight in that moment is irrelevant. She was simply used as a way to convey this point (that of Cylons feeling pain) to the viewers.
No matter how you slice it though it's a stupid plot device. I get that they want us to believe that the Cylons were working on a way to become human essentially, but equipping robot combat soldiers in the field (on a desolate ice planet no less) feel pain is just plain dumb. If anything they would make it so that these soldiers didn't feel any physical pain. Besides, if they can feel pain from physical abuse (bullets, metal pipes) why don't they feel pain from sub-zero temps?
Again, it's all just crap that Moore/Eick have thrown into the mix to muddle the story and, in their eyes, make it "deeper".
BTW -- did anyone else read the original Glen Larson BSG story? I did as a kid and it was very interesting. They Cylons weren't robots (and they sure as hell weren't proto-humans). They were an alien species that humans got into a war with. I remember in Adama's journal how he talked about the supreme leader getting his third brain. At any rate, the original story was about a war between humans and an alien race, not a war with creatures we had made ourselves. Shame that the current PTB have mucked it up so much.
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I wish I could ignore the fact that the Cylon warriors feel pain but it's just too stupid to ignore. In a lab setting and in non-combat models it would make sense to work on developing a sensory network within those "bodies", but for the Centurions guarding the gate it makes little sense.
Now, if they took the time to explain that the Cylons on that ice planet were all part of the experiment then fine, I could understand that. They could come up with some lame excuse as to why they fitted the Centurions who guard the place with pain sensors (a lack of test subjects, etc.) but they haven't done that. All they've done is showed us a Cylon screaming on the floor and told us it feels pain. Bad writing is what it is, simply that and nothing more (or should I say "Moore"?).