Like you, I used to think the world was this great place where everybody lived by the same standards I did, then some kid with a nail showed me I was living in his world, a world where chaos rules not order, a world where righteousness is not rewarded. That's Cesar's world, and if you're not willing to play by his rules, then you're gonna have to pay the price.
The lysine contingency - it's intended to prevent the spread of the animals is case they ever got off the island. Dr. Wu inserted a gene that makes a single faulty enzyme in protein metabolism. The animals can't manufacture the amino acid lysine. Unless they're continually supplied with lysine by us, they'll slip into a coma and die.