I think that the game should add in some ability to ‘turn off’/vestigialise components of your cell. For instance, if your ATP balance is poor, but you don’t want to have to spend all the MP later on to rebuild things you cut for energy, you could mark them as vestigial, which makes them remain in the cell, but be nonfunctional and consume little ATP. Then, later, you can reactivate these components.
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Maybe there should be a feature where a vestigal organ’s reactivation becomes less impactful the longer the vestigial period lasted
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