In transcriptional regulation, you often find that positive signals proceed by inhibiting or destroying a protein that is in turn inhibiting or destroying the effector protein. This can be seen in the retinoblastoma - E2F signalling pathway, and many others. I was wondering if there was any direct biological utility, and if so what this utility was.
This feels like a my philosophical question...
Direct regulation of proteins would have to have biological utility - such a gene has to be driven by positive selection to adapt that ability. The question is more about learning what might be driving its role.
I would hazard that protein deactivation and degradation would be important to make sure that these inhibitors could be down-regulated fast enough - if they were left to degrade via a general pathway, the specific signal would not be available for too long a time.