Science itself may be amoral, but various social sciences involve the study or analysis of moral systems, from political science to economics to comparative religious studies.
Science also has something to say about contemporary morality as the result of the evolution of cooperation. By cooperation, I don't merely mean negotiation or compromise. I think that implies that the result of cooperation is ultimately not as good as you would like, if you didn't have to do it. In many cases, I would say that's not true at all.
For example, say there were two people on opposite sides of an island, each building their own house. So each of them climbs on ladders, by themselves, outside each of the houses, doing various things. The problem is that by working alone, they risk injury - the ladder may slip without anyone holding it. They also have nobody to hand them tools when they need it, etc etc.
If they worked together to build the houses (ie. cooperation), then they in fact would have someone to hold the ladder, or hand them tools. Similarly, on an assembly line, everyone works together to produce things much faster than if each of them had to build the whole thing alone.
On the other hand, if the two guys on the island decided to "compete" for the right to control the island, then they might spend their time making spears. When the day the fight comes, one may be killed, and the other may be seriously injured, only to die of an infection a week later. Competition obviously didn't quite work out for either party in this case.
I'm sure some "civilizations" end up like the one in Lord of the Flies, however, the "civilizations" like LotF don't have as much survival advantage as those with more cooperative memes.
The ones that don't have the same survival advantage kill themselves off and therefore their memes don't get propagated to future generations. The civilizations that not only don't kill themselves off, but help the carriers of their memes survive, end up with future generations with similar cooperative memes.
Interestingly enough, this is an amoral explanation for why you shouldn't kill people and why you should help them instead, instead of a moral justification for why you shouldn't kill people... it kind of scares me a bit actually.