Echi--I am with you 100%--I do think every one of us is built with an inner guiding system that works as both what can be considered conscience and also, I have no doubt that it also functions as that inerrant 'gut instinct' that I also think we all have but don't listen to. It's an untraceable immediate and immediate thought-response that I think many of us learn to shut out at an early age, and I think more operate sans gut than they do conscience.
Also, it has been my experience that often-times that gut instinct is dissuaded by one's religious upbringing. I have heard it said that we should not trust that voice, because it our self and we are supposed to trust God.
Where is God supposed to be? That what I don't get--they say don't listen to yourself, listen to us--because you should listen to God.
Well, if you can't help me out with a multiple choice Algebra test
(you know, the your-first-answer-is-always-right thing?) then I'm betting on moi. Because I feel that if 'the answer is always right' then it certainly is not me, but something else.
And my experiences, with the gut instinct theory are where the theory comes from, actually. In my early 20's I started noticing that the more I heeded it, the less trouble I had, in all parts of life, and the louder and clearer it became. I'm 37 now and I pretty much operate on that 'gut instinct' thing--and I know for sure, at this point, that it is something far more alive than even my own self. In fact, at some point about 3 years ago, my life changed in a way I really have to describe as a transformation. And I never saw it coming nor did I search for it in the various ways many people seek that kind of thing--whether it be through church and western type religions or eastern philosophies. I have learned about all sorts of things, but never adopted any one discipline or philosophy for myself. I did, however, find truth in everything, but nothing that was 'all truth' that was outside of myself.
My conscience used to 'prick me' and I could often ignore it and not really be bothered with lingering pricks, but these days I cannot. It isn't really a pricking anymore, either. I just know what is the thing I should do and I do it. That may not sound like a big deal, but I've always had a life that allowed me to be all about me. I've never been vain or arrogant, but I was definitely self-oriented in a very big way and had no idea.
I think self-orientation is essentially 'sin.' It is a sort of state of isolation that causes harm and slights to others in ignorance and oblivion. Even when I thought I was doing the right thing for someone else, looking back I can see what my motivation was, without exception. I also see that I truly didn't know. And I think that's our biggest problem, as humans--even though we are born equipped with what we need as far as God goes, we look for God outside of ourselves and don't understand God isn't about us--God is love and paying attention to others so that the illusion of motivational isolation eventually dissolves.
Conscience is a word known to all, and many think it is their motivation, but I think there is much confusion between that and morality. I see them as opposites, with conscience being of the unity factor and morality being of the ego. We do what is right or wrong, based on what those around us, society, and all those who expect us to be what they have grown used to us being, and it is that duty that is not always correct. It seems like giving of one's self but it is taking, in a sense, by all involved. It is not freedom and it doesn't really benefit anyone in the long run. But we think that what is 'right' and 'wrong' on the outside is the same on the inside. We know there is conflict when we have guilt, discomfort, that strange out-of-place feeling, and resentment.
I have found that the bible is not at all contradictory to this ideas--maybe no expressed just so, but actually more than most realize. Religion does a pretty good job of hiding the truth, any religion, IMO.
Paul especially mentions the conscience many times:
Romans 9:1 I say the truth in Christ, I lie not, my conscience also bearing me witness in the Holy Ghost,
1 Corinthians 8:8-13, 10:23-33
2 Corinthians 1:12, 4:1-7
1 Timothy 1:5-11, 3:9, 4:1-5
Titus 1:1-16--and v15 is really significant, IMO:
all things, indeed, are pure to the pure, and to the defiled and unstedfast is nothing pure, but of them defiled are even the mind and the conscience;
Hebrews 9:14, 10:2, 10:22, 13:18
Peter also uses that word in the same fashion Paul does.
1 Peter 2:19, 3:16, 21
I think, from all those passages, that what you say about conscience is not only solid understanding, but just what you believe it to be--the Holy Spirit.
It seems, also, that the problem with those who either don't seem to have it or else have denied it until it clammed up and withdrew--this seems to be the cause of the absence, that is, the denying of it's worth or application in the first place.
Many prefer morality--it usually nets gains that are tangible in one way or another such as wealth or the esteem of other people. It's basically 'serving mammon' as opposed to 'serving God.' Now when I say that, about morality, I'm speaking of what I define morality as, but many use the word instead of conscience. Regardless, the fruit is still the trustworthy indicator.
I know, too, from observing others, that if one declines one's gut instinct and/or conscience in favor of theologies and doctrines that they feel to be more accurate of a spiritual compass, no matter how much they aimed on God in the beginning, they lose touch rapidly and don't even realize it amidst the din of all the outward goings-on and ritual, and they lose their ears that hear when they start listening with their external ears more, as far as for guidance.
I believe that the biggest 'leap of faith' in regard to God is the leap away from tradition and society, for most people. It is probably the scariest thing most people face and therefore, most don't. I never had to leap away, since I never jumped in, in the first place, for whatever reason. No indoctrination to get over, and for that I am infinitely grateful, every day.