A process that provides protective therapy for biological tissues or fluids includes applying a pulsed energy source to a target tissue or a target fluid having a chronic progressive disease or a risk of having a chronic progressive disease to therapeutically or prophylactically treat the target tissue or target fluid. A pulsed energy source having selected energy parameters may be applied to a brain of an individual who has Alzheimer's or other neurodegenerative disease or is at risk of developing such a neurodegenerative disease so as to prevent or treat the neurodegenerative disease.