I think the conscience is the general alarm in your spirit that tries to tell you when you are doing wrong. I don't think the conscience is the holy spirit, though I do think the holy spirit tries to influence the conscience.

I believe that our conscience can be imperfect. For example, if we learn that smoking cigarettes is a sin we may, in our conscience come to believe that anyone who smokes is guilty.

However, when we read Jesus teaching that nothing which goes into the mouth defiles us, but that which comes out of the mouth, then we may realize that we were wrong to believe all those smokers to be guilty of sin because of smoking in itself. While it is definitely more healthy NOT to smoke, not smoking is still just a health rule and not a moral rule.

Our conscience learns something new.

The same is true if we believe smoking is wrong and yet we ourselves are smokers. The Bible also says


1jn 3:20 For if our heart condemn us, God is greater than our heart, and knoweth all things.

I believe this is a reference to a guilty conscience which really should not feel guilty.