At present, there are only a couple of mobs that really interact with the environment or other mobs. Endermen will pollinate cacti by moving one block and placing it somewhere else, and wolves will attack sheep. I think it would be cool if there were more self-interaction in the minecraft world. It would also be interesting if player actions altered the ecology. For example, players tend to cut down forests. If the players cut down enough trees, will the area change to a new biome, and have different mobs spawn? Perhaps (through player interaction) it could be made more difficult for wolves to catch sheep, and the sheep population would rise over time. Adding some sort of evolutionary A.I. (as mentioned in a previous post) could also change how the world interacts with itself and adapts to what the player does.
That would be a much more complicated addition to an already very complex game. Hence, I'm not sure this would work (or how it would turn out if actually programmed). Excellent idea though.
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Minecraft Ecology