I don't think you are stupid at all, On My Way. You ask very interesting questions!
I have just written a bit about guilt. I hope I'm not boring you all with this:
INTRO
It has been established before that we are social animals. We have a hierarchy with one or several leaders. We continually struggle to reach this top: We all dream of being famous singers, the president, a princess, the leader of a ‘clan’ in a computer game, a better job with more influence etc.: We want to climb the social ladder. What good does it do us to reach for the top? Fame and fortune, admiration of fans, a high standard of living and the first choice at picking your mate. Even noticed that actors and singers tend to have very pretty boy/girl friends? In short: Social status is GOOD. We see the same behaviour in other social animals: Dominant males have to ward off other males that try to get higher up on the social ladder, because the higher you get, the higher the chance that you get to pass on your genes (which seems to be one of the main drives, if not THE main drive behind the existence of life forms).
Hypothesis on the evolutionary origin of guilt
I think guilt is realising that you have done something, which has led to loss of status. A compliment makes you feel good: someone realised your strong points and acknowledged it. An insult is pointing out a weakness and has the opposite effect on your mood. In the eyes of the person that made the insult, your status is lower than his/hers. (We ‘measure’ status by the praise of others.)
Feeling guilt is the result of an action, and I think this action is something that leads to loss of status. Committing a crime can lead to feelings of guilt afterwards. Criminals are generally not praised in our hierarchy. If you know that someone murdered a person or stole something, you are less likely to date that person. Guilt has evolved to warn us that status-reducing behaviour does not benefit your offspring. To be more precise: Individuals that could identify status-increasing behaviour from status-decreasing behaviour had a greater chance of passing on their genes, and this trait was passed along as well.
EXAMPLE
I’ll give an example that is probably going to sound familiar. I have seen that a lot of christians seem to think that masturbation is a bad thing. I’ll use that example to demonstrate the relation between status and guilt.
First of all, status depends on your frame of reference: Every social ladder has ‘do’s and ‘don’t’s. Starting a fight is not going to give you more status if you are in politics, but it might give you status among friends. Being a very good football player does not increase your status as a painter. Status depends on the rules (written or unwritten) within your social group.
With this in mind, imagine an adolescent christian boy. Living your live according to the christian morality will increase your status within that group. This also means that deviating from those rules results in lower status. If masturbation is considered something bad, the boy’s status will drop if anyone were to find out. He is now a sinner and the other members of the social group are not too fond of sinners. The boy realises the status-decreasing thing he did. He knows ‘the rules’ and he broke them. Guilt is (in my opinion) a painful response that reminds you that you are reducing your chances of passing on your genes (within your social group), because you are reducing your position in the social hierarchy.
If someone grows up in (and feels part of) a social group that does not think of masturbation as a bad thing, the deed will not result in feelings of guilt, because you are not doing something that causes your social position in your group to decline.
EXAMPLE IN NATURE
You asked for this behaviour in nature. The problem is that we can not ASK animals about this and it is difficult to point out what ‘rules’ animals have in their social group. Your dog will not feel guilty if you yell at him, because he does not comprehend why playing in the trash is bad.
I have seen a form of guilt in our cats. It is in an evolutionary way not a good thing to urinate or poop in your own den/layer/burrow/nest etc. (Though some penguins form an exception to this)
Our cats will hold it in and go outside to do this. It is a ‘rule’ and they are aware of this rule within the social group. In this case the social group consists of people and cats in the house. When a cat gets locked in at night and can’t go outside, it is sometimes forced to poop/urinate in the house. When I come into the room next morning and I discover a puddle of urine, I can SEE that the cat knows it broke a rule (it will actually hide or run out of the house when he the door is opened). The chances of the cat mating with me are not reduced (lol) but its social status drops: It will not be petted by me, for example. One of our cats has a tendency to throw up a lot in the house, and is openly attacked by an other (somewhat more aggressive) cat of ours.
CONCLUSION
In conclusion: I think we can see a clear relation between guilt and reducing your social status. Guilt is a logical trait that helps us to go up the social ladder, towards success and pretty girlfriends.
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On My Way: My point is that we can explain a lot of supposedly 'divine' characteristics of the human mind. There is no indication 'guilt' was put into our heads by any god, because we can see that 'guilt' is a logical thing in social animals: It is a drive that stimulates behaviour that increases your chances of mating, and delivers a 'painful' response when we consciously are aware we are reducing/have reduced our status.
Consequently: the ability to feel guilt is favoured over the lack of this ability in natural selection.