Been a bit since I've read it but: the protomolecule is most likely giving the stem cells the means to communicate with the ring builders' network, as part of their optimization. My understanding is that the protomolecule is a programmable tool for building structures and devices, using bio matter. For example: whatever protomolucule the dogs' have seems to be programed for repairing and optimizing anything that's percieved as broken.
(Of course it's always possible that the protomolecule was never removed from the stem cells)