I love love LOVE this thread... I've wondered the same thing Stephen-Aegis...
Protein is such a coveted material in mammalian systems and nothing is wasted from the kidney and organ standpoint - all protein is re-filtered and recovered to prevent excretion. Kidney failure patients cannot retain protein -- and they are j*cked. In the environment, protein (meat/seafood) and omega-3 are relatively scarce and when humans learned to take advantage of these two, their brains emerged with consciousness, art, culture and global domination. Only the 'gut' can sense the abundance of protein and omega-3 in the environment (perhaps the sense of vision/smell in the brain) thus these receptors for amino acids and fatty acids (PPAR) control and regulate the instestines for the overall immunity and health.
Autophagy appears to me like recycling and I think the mitochondria very good at it, since they may be the most important generators of energy and regulators of systemic energy.
This may not address the core of your question but we lose protein and rebuild daily (during sleep...that's when we become BIONIC). If one wears a cast on the arm, the arm muscles will break down. Demand, genetics (myostatin) and perhaps diet control to what degree, I would imagine but I don't know for sure.
What I suspect is what the proteins someone consumes may have a bigger effect than we consider. Methionine -- apparently VERY CRITICAL to health, bowel immunity and antioxidant status. The studies below review it. The first gave a methione-deficient diet and quickly ruined the antioxidant status (glutathione) and gut lining (small instestinal villus atrophy, proliferative crypt cells, etc) and body weight gain decreased in neonatal pigs compared with controls.
Methionine is only find in meat, seafood and dairy in any meaningful amount. Beans and plants have almost none.