The human brain is a complex organ, and clearly the most capable of any known living organism. The majority of its neurons are contained within the neocortex, a relatively recent addition to evolution's repertoire. While there are many hypotheses as to what allowed for an evolutionary leap in brain complexity – bipedalism being one such theory – it is clear that our species' capacity for abstract thought has given us tremendous power over other animals.
The move towards civilizations began with agriculture and animal domestication thousands of years ago; humans were able to begin accumulating resources and wealth, which eventually led to social stratification.
As the complexity of human civilization grew, so too did our capacity for cruelty. Social hierarchies were constructed in many ways: class systems, slavery and genocide are just a few examples. While some have argued that human nature is inherently good – as evidenced by altruism and selflessness found in many individuals – it is clear that most people will act primarily out of self-interest.
For example, even when people do make sacrifices for others – say, the life of a soldier who dies in battle – they are often motivated to engage in such actions because they have been conditioned to believe that their country is 'good', or at least better than other countries.
You could argue that the human mind is influenced primarily by social conditioning, and thus our behavior reflects our conditioning. But it's important to note that even if we are largely motivated by self-interest and prejudice – in other words, 'free will' is an illusion – we have no choice but to continue existing within this system.
It's also important to note that the world is not as clearly defined as right and wrong. Different people have different perspectives, and often it is difficult for us to understand others when they are so unlike ourselves.
But even if reality is subjective and paradoxical, the human mind has been conditioned to view it as a linear progression of cause-and-effect.