So, when a planet's generated it also generates 3-9 creatures to populate it. There's a 10% chance (more if you have factories/use some form of radiation field?) of a creature mutating, with all the benefits/disadvantages it brings. Each body part has a 3% chance of mutating. The mutation would choose a DIFFERENT PART TO REPLACE IT. For example, if they have "left front leg 6" and "wings 4" and both get mutated, it could suddenly have "left front leg 4" and "no wings"
