Terrible things happen in the world. Wonderful things happen in the real world. The rest is in between. Attributing "evil" to the natural order and "goodness" to something supernatural doesn't offer much help, unless one is just attempting to justify a concept of the supernatural or is dependent on invoking the supernatural to explain things. In fact, many people wonder and ask how God can allow such terrible things to occur as really do occur in reality.
For those who see science as a belief system (rather than a set of methods for obtaining and evaluating evidence), I must suggest that there is a very well demonstrated capacity in science for self-criticism, change, and refinement. It will come as no surprise that I think science fares rather well according to that standard alongside all faith traditions.
There are many scientists who attempt to explain how "empathy" and "altruism" and other prosocial behaviors could evolve. Others of us wonder how such patterns could NOT develop, given the fundamental requirement of nature that humans and other animals get along well enough to procreate and survive without killing each other or becoming prey.
Some people believe that "agape" love exists only in humans is worth thinking carefully about. Perhaps mother love (abundantly apparent among mammals) and parental care (widespread among animals--but certainly not perfect in humans) do not qualify as "agape." Such affectional attachments that have biological utility do seem, at least to be related to the agape concept.