Multiple studies have demonstrated that traditional homeopathic manufacturing reagents and processes can generate remedy source and silica nanoparticles (NPs). Homeopathically-made NPs would initiate adaptive changes in an organism as a complex adaptive system (CAS) or network. Adaptive changes would emerge from several different endogenous amplification processes that respond to exogenous danger or threat signals that manufactured nanomaterials convey, including (1) stochastic resonance (SR) in sensory neural systems and (2) time-dependent sensitization (TDS)/oscillation. SR is nonlinear coherent amplification of a weak signal by the superposition of a larger magnitude white noise containing within it the same frequencies of the weak signal. TDS is progressive response magnitude amplification and oscillatory reversal in response direction to a given low dose at physiological limits with the passage of time.Hormesis is an overarching adaptive phenomenon that reflects the observed nonlinear adaptive dose–response relationship. Remedies would act as enhanced micro- and nanoscale forms of their source material via direct local ligand-receptor interactions at very low potencies and/or by triggering systemic adaptive network dynamical effects via their NP-based electromagnetic, optical, and quantum mechanical properties at higher potencies.Manufacturing parameters including dilution modify sizes, shapes, and surface charges of nanoparticles, thereby causing differences in physico-chemical properties and biological effects. Based on surface area, size, shape, and charge, nanoparticles adsorb a complex pattern of serum proteins, forming a protein corona on contact that constitutes a unique biological identity. The protein corona may capture individualized dysfunctional biological mediator information of the organism onto the surfaces of the salient, i.e., resonant, remedy nanostructures.SR would amplify this weak signal from the salient remedy NPs with protein corona adsorbed, leading to sensitized nonlinear dynamical modulation of gene expression and associated changes in biological signaling pathways. When the system reaches its physiological limits during a homeopathic aggravation or the natural disease state, the amplified remedy signal triggers a nonlinear reversal in dynamical direction back towards health.