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I don't think the goal of departmental lathes is to make it so everyone has absolutely anything they could ever want. If we wanted to do that, we'd just give everyone autolathes that produce everything. For things somewhat out of your department's specialization you need to go to another department. But that's fine, departmental teamwork and all that. If there is an item a department really needs and consistently doesn't get it can just be added to their own autolathe. Under the current system no one gets anything unless they go through science, so even assuming there will sometimes be issues, it's still a vast improvement.

Departmental lathes would solve this problem. Instead of the protolathe being one all in one machine to all the best stuff, each department gets it's own protolathe that can only print things relevant to their department. Each lathe would be locked to an ID of that department, so even if engineering builds a science protolathe it won't do them any good without a science ID. It has the added bonus of decentralizing power away from science. Part of the reason departments do this is because sometimes getting science to actually give other departments stuff is pulling teeth. Half of science is usually traitors and you're lucky if you can find someone who will be nice enough to actually man the RnD window and not just print all the best stuff for themselves and go wander off blow up monkeys or something.