Currently the only civic for machine intelligence that requires not having biological ships is Exploration Protocols.


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They specifically state organic life in their diplomatic messages though. Personally I think it would make sense that DEs can't use bio ships.I think their major beef (to use an appropriate metaphor) is with sapient life only.
Animals are more like pests or resources to them: used or discarded as needed.
They aren't a threat until they start getting ideas. Ironically, it's exactly the same way organics view synthetics.
OP isn't saying that FP or all genocidals shouldn't be using biological ships though. Just Determined Exterminators (machine inteligence civic) shouldn't, since they explicitly hate every and all biological life, witch makes total sense.Nope, they shouldn't be limited. Because it's on the player to decide such details about your empire.
Do they hate every livign being but themselves? If your fanatical purifying humans wouldn't massacre all dogs and cats on their planet, why would they massacre whatever the Bio ships came from?
Also, if bio ships are artificially created, they are just a machine made of organic material. Why would they care?
Unless you decide that your Purifiers hate every living being but themselves, there is no reason to ban Bio Ships. Purifiers always hate and fear other sentients, not necessarily animals.