Conscience is based on the ability to tell right from wrong and to make moral decisions thereupon. When we choose rightly, we feel good, even if the only good result is the feeling that we acted with integrity. When we make the wrong choice, we feel guilty or ashamed. We live in fear of the consequences of what we have done, and often we lie to cover it up.
Conscience is probably like language: the capability is hard-wired into the human brain, but not the specifics. Just as I can speak English and you can speak Spanish and she can speak Chinese, different cultures can have different opinions on what is or is not wrong, evil, or sinful. Some cultures see nothing wrong with cannibalism in everyday life, for example, while others reserve it to religious ritual. Some cultures believe that "thou shalt not kill" covers war, capital punishment, euthanasia, and killing animals for food; in the U.S., "Christian" leaders tell citizens that there is no disconnect between Christianity and preemptive warfare. (But whom WOULD Jesus bomb, if his finger were on the button?) Some cultures insist that only their values are approved by God, and anything else is "moral relativism" — despite the fact that their "God's Housekeeping Seal of Approval" values invariably include misogyny, inequality, hypocrisy, exclusiveness, and oppression of minorities.
Nevertheless, having a conscience is vital in moral decision-making. A moral decision is needed when you are trying to distinguish between right and wrong. Moral values are generally shared values. For example: public drunkenness is disgusting; torture is both useless and contemptible; helping people in need is good; pedophilia should be punished — unless the pervert is a Roman Catholic priest, in which case he should be reassigned to a different diocese and his crimes should be covered up. (You say you disagree with that last point, as I do. If you are a member of the Roman Catholic Church, your actions contradict you.)
Most cultures share certain fundamental moral values: truthfulness is good. Murder is bad. Loyalty, justice, and promise-keeping are good. Doing harm to someone unnecessarily is bad. Problems tend to arise when different cultures, or even different people within a culture, disagree as to the scope of their values. For example, when is removing a piece of tissue the size of a grain of rice okay, and when is it "murder"? Is truthfulness more important than preventing a terrible crime? Is spanking "necessary injury," or is it abuse? Should you break a promise to save a life? When is it ending terrible suffering and when is it murder?
Having a conscience requires you to be able to see from some other person's point of view. Narcissists, sociopaths, and psychopaths, lacking this ability, are capable of sleeping soundly after committing horrendous crimes.
Most of morality is about relationships — with family, friends, coworkers, students/teachers, community, region, state, nation, religion. Having a conscience requires you to understand these social relationships, and to understand that when any given groups are in conflict, there is some overarching group that can, or ought to, unite them. The Hatfields and the McCoys might agree that murder is wrong and go right on shooting each other, unless they can be brought to understand they need to fight together against the dreaded "revenooers." You may have seen nothing wrong with fur coats until you saw a video of an animal suffering horribly in an evil trap and you understood you were both members of the overarching group "beings loved by God."
There is no one right or wrong way to make a moral decision. There are some basic considerations that most moral decisions share, however:
* You need to identify the "interested parties" — people who have a stake in the outcome of your decision. Often there are more people affected than you might think at first glance. When Michael Schiavo wanted to pursue an act of compassion, self-righteous fundamentalist leaders whipped the faithful into such a froth of outrage at what was falsely portrayed as "murder" that Congress went into special session, and the president interrupted his vacation to fly to Washington and sign the bill!
* You need to identify the relationships between the interested parties. Does one of them have some special status, for example, that might influence your decision? (Perhaps you don't care what Mom thinks, but you quail in terror of what Grandmother is going to think.)
* You need to look for similar situations. What decisions were made? Do you approve of those decisions? What happened next? Do you approve of what happened next?
* You need to consider the potential outcomes, both good AND bad. This involves talking over the decision with someone you trust and respect as well as with everyone who will be affected by it.
* You need to identify the moral issues involved in your decision. Is it a question of fairness? Will anyone be hurt or helped? Is it a question of autonomy? Is it a question of trust?
This is where having a conscience comes in handy. It is your conscience that says to you, "Yes, but Mom would cry herself to sleep every night for the rest of her life." It is your conscience that says, "Everyone would treat you as if you were a child molester." It is your conscience that says, "Everyone would be disgusted with me and hold me in contempt."
If you have no conscience, the only person you care about is yourself. You'll rape, rob, and murder without a care in the world; you'll lie cheerfully on any subject; in short, you'll pee in the great swimming pool of life. People who have no conscience are mentally ill, although they may LOOK completely normal.
In making any moral decision, your conscience is, and should be, the first thing you consult. Who will be hurt if I do X? Who will be angry? Who will be disappointed? Will they want to punish me? If I do this, SHOULD I be punished? Will I feel guilty or ashamed? SHOULD I feel guilty or ashamed?
As the cliché has it, let your conscience be your guide!