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Conscience is an aptitude, faculty, intuition or judgment that assists in distinguishing right from wrong. Moral judgment may derive from values or norms (principles and rules).
Many scientists agree that self-awareness evolved because of the benefits it contributes understanding others and social situations, implying that self-awareness is intrinsically connected to other-awareness. This suggests that there was an advantage for the individual in understanding others, and therefore that competition and cooperation played a pivotal role in how human evolution progressed. Consciousness, then, is an experience, and our capacity for mental construction and time travel allows us to compare current situations with past and future ones. Mental trial and error is much more efficient than actual trial and error, so this part of the decision making process greatly reduces the chance of failure. This extends to our interactions with others – we use our own experiences in order to predict the behavior of others. Mirror neuron experiments in humans and monkeys favor this view.
Animals don't have this, but even atheists have this, and if they do something very wrong the conscience bothers them, since they don't subscribe to biblical principals and rules, why does their conscience still bother them.
[one reviewer's favorite] quote is: "...humans are a species splendid in their array of moral equipment, tragic in their propensity to misuse it, and pathetic in their constitutional ignorance of the misuse."
Science journalist Robert Wright compiled these findings of evolutionary psychology (EP) for the lay reader in 1994 and "Moral Animal" is still a timely treatise. Matt Ridley introduced his excellent "Red Queen" about the same topic around the same year. Wright writes in an engaging manner, intertwining his pearls with biographical sketches of Charles Darwin.
Disclaimer: For those who are offended by the very suggestion that our behavior evolved from apes - and that our behavior is an elaborate, sophisticated manifestation of language and socialization which evolved by natural selection along with a huge brain - you won't like this book.
Animals don't have this, but even atheists have this
Canids (animals in the dog family) learn social codes of conduct at a young age through play. They first invite one another to roughhouse using a "play bow": They lie down on their forelimbs while standing on their hind legs. Even when this is followed by aggressive actions such as growling and snarling, the bow makes their playful intentions clear. During play, dominant members of the pack will engage in role reversal with weaker ones, rolling over on their backs to give low-status playmates a chance at "winning," as well as lessening the force of their bites to prevent injury. If one playmate accidentally bites another too hard, it "apologizes," play-bowing again to show that it is still playing, despite the slip-up.
Breaking these rules of engagement — or other rules, such as taking more than one's fair share of food — is serious business among wolves and coyotes. "There is a consequence of being labeled a cheater," Bekoff said. Others stop bonding with the "immoral" pack member, and eventually it wanders away from the group, usually resulting in an early death because it no longer receives the benefits of pack living. Bekoff believes the rules governing pack behavior offer a glimpse of the moral code that allowed early human societies to function and flourish.
Dogs evolved from wolves, and seem to have maintained a wolfish sense of fairness. "They do have a sense of right and wrong. You see it when they play at the dog park, for example; when a dog asks another dog to play — even if it is larger and may be dominant — it's going to be honest about it. It knows it would be unfair to ask a dog to play and then beat it up or try to mate with it," he said.
Furthermore, experiments at the University of Vienna have also found that dogs become upset by unfair treatment by humans. When asked to shake hands, the dogs in the study were happy to oblige at first regardless of whether they were given treats or not. But the dogs' enthusiasm for the trick waned when they saw other dogs being rewarded with food after a handshake, but received nothing themselves. The ignored dogs also started showing signs of distress, such as licking or scratching. The researchers argued that these stress signifiers proved the dogs were upset about being treated unfairly — not just sad about missing out on a treat.
Ask anyone who has had to kill someone the first time. Conscience does not need to come from god.
Animals killing other animals doesn't make them feel bad. It's instinct, we don't kill another alpha human just because they threaten us within or social circle, but Gorilla's and Lions can and do.