As I've said before, I'll continue to discuss the biological basis of morality.
To reiterate, these are the five pillars of human morality elucidated by Dr Jonathan Haidt:
3) In-Group Loyalty
4) Respect for Authority/Elders
As I said, the first two form the basis for reciprocal altruism. The third reinforces that by forming an us vs them mentality; those on the inside are fully human (or chimp, for our chimp cousins), those on the outside are not. We can see this among ourselves today and in history. Our close family is incredibly important, our more distant family/friends come next, and so on, until we come to strangers who are also foreigners of a different religion who dress funny who barely qualify as human. Yes, that's an increasingly outdated concept, but it's still out there.
How does identifying someone as not being worthy of altruism reinforce altruism? Because we can't be indiscriminate. Resources are scarce and we can't share all the time with everyone. Identifying some people as more important than others helps decide who we share our limited resources with, who we fight for and who we abandon. From the standpoint of the gene, we need to defend those closely related to us and help them because they share our genes. From the game theory point of view, cooperation, whether among kin or strangers, leads to a greater degree of success.
The fourth I believe started as respect for authority, a way to sort the group into a less egalitarian family band, with certain individuals in charge and others following. Think on this, the origin of the "moot point". "Moot" is an old English word, originally meaning, essentially, "a democratic assembly to discuss important points", hearkening to the democracies that were Germanic English villages. Important things had to be discussed before the moot (you may recall the term showing up in the _Lord of the Rings_ trilogy, as Treebeard [AKA Fangorn] called for the Ent-Moot), thus a 'moot point' was something too important for one person to decide. However, the nature of democratic assemblages is that the larger the population, the more untenable direct democracy becomes, and thus the moot got sidelined in favor of more autocratic processes and a 'moot point' gradually became something so unimportant that it could be put before the moot without any harm. To put it another way, "A committee is the only animal with twenty stomachs and no brain".
When one person is in charge, things get done (not necessarily for the best, see my explanation, forthcoming, for why democratic-republics are the most awesome form of government). Although our ancestors were apparently largely egalitarian while living in small family groups (according to anthropology), they segued into pseudo-chiefdoms, followed by chiefdoms, followed by increasingly stratified, rigidly defined hierarchical religious kingdoms. Respect for authority started as a way to organize small, flexible group relationships and was reinforced as a method for organizing large, inflexible group relationships.
However, I believe that number four became, for humans at least, respect for elders as a method of education. We're not the only animal that teaches their young, but we may be unique in that we educate through language. Our young are credulous to a fault and respect for elders reinforces that. It's not just among children, though; think about the last time you were the new guy in the workplace. How respectfully did you listen to the guy who showed you around? How long did it take for you to stop being the new guy? And when the next new guy came in, how easy was it to assume an air of authority as the guy who knows what's up? It works.
In short, I feel that these first four pillars of human morality shape our interactions among a group, for short- and long-term benefit through mutual cooperation and reciprocal altruism.
What of sanctity/purity? That's the notion that the body can be harmed/made impure through immoral behavior, which notion isn't restricted to religion (vegans, anyone?). I believe it started as a simple biological compulsion to avoid eating things like poop that was repurposed. Our hierarchical/authoritarian bent was repurposed by our need to educate our offspring, and I think our disgust imperative was repurposed for a social function. I'll get into that more later.
For now, I think I've discussed where our moral sense comes from enough to provide a good argument that, although the god hypothesis does not explain either good or evil, evolution certainly explains good as the result of game theory and gene theory.