There is no reason to believe that our conscience is anything other than the name we give to our reasoning process while asking ourselves a moral question. The fact that everyone has a different process and reasoning abilities explains rather nicely the variation in the choices we make.
The way I experience thought is basically talking to myself in my head. I know this is all subjective but I'd be interested to see if/how much our experiences vary in this regard. If my regular thoughts are my own and my thoughts during my 'conscience' reasoning process are not, why do they feel identical? The thoughts that may be attempting to rationalise the the immoral option are depicted as coming from a little devil while the thoughts leading me to the moral option are depicted as coming from an angel.
I would now like to apply the angel/devil theory to a recent dilemma I faced.
I was angered by the arrogance and hypocrisy displayed by Phat and the devil popped up on my shoulder.
"Rip him a new one! Don't hold back" he said.*
I'd had a few beers and I began to reply. My tone was much the same as the condescending tone that Phat had used. I had several unnecessary insults in there. I stopped writing for a moment. The angel popped up now.
"Don't be so harsh. If you really believed in fairy tales, you'd likely get offended on behalf of a supreme being and reject a movement that actually aligns very closely with Jesus' teachings on that basis alone" she said.*
So I went back through and settled with just labelling his fantastical beliefs as fantasy.
* I don't remember the exact thoughts but they were along those lines.
In this scenario, the 'still small voice of god' was telling me to back off a bit and it seemed to feel sorry for Phat, that he wholeheartedly believes something that is almost surely false. I don't mean to pick on Phat, I just thought it was a good way to explain why, to me at least, the idea that god is driving our consicences is silly. Nor are our 'conscience' thoughts anything different from normal thoughts.