As great strides have been made in understanding the function of the brain and how to treat certain diseases or the effects of injury, there is still quite a bit more to learn. And for certain higher level functions, it may be a very long time before the true manner in which the brain processes and controls them is well understood. And it may very well be that there will always be certain aspects which are simply beyond our grasp to fully understand.
Why people react to different situations and how we gain things like emotion, compassion, etc. is not entirely understood.
CogniFit's blog: Brain – What We Know And What We Don’t