The brain's file system for morale is interesting (especially if you are a backyard nero surgeon) but it doesn't explain the origins nor does it cover the parts of the topic that Amerikanse asks about.
What I read is that some of you subscribe to a group selection theory - that the survival of the group meant they had to become moral. This might be true to a certain extent, but I believe Richard Dawkins more when he says that it could also have been on an individual basis. A person who practiced good morales probably found it easier to build alliances and benefit from co-operation to the extent that his survival benefited.
To a certain degree morality has to do with conflict management. It dictates how we deal with conflicts of our believes between each other. Some people will see you as a lower being for having different believes or viewpoints simply because they think they are as inerrant as their scriptures.
All in all morality is a positive by product of the development of our intellect and subsequent development of social structure.
As for who or why we have certain morales, they are a reflection of our world view. For many people religion and morales are one and the same thing, for these individuals it usually turns out pretty bad. Most religions tend to have a deterministic strict outlook on morales, you should do X and not Y to expect Z - no exceptions or negotiations. Morality based purely on religion is stagnate and ignores the simple fact that life today is different than what it was two thousand years ago.
Morality, like the rest of our software has to be constantly re-evaluated against the face of a changing world.
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