The TGD based model for biological self-organization relies on the hierarchy heff=nh0 of effective Planck constants labelling dark phases of ordinary particles residing at magnetic flux quanta. This model generalizes and suggests the replacement of non-equilibrium thermodynamics as basis of self-organization with its quantum variant based on dark matter hierarchy. The challenge is to formulate basic thermodynamical notions like work in terms TGD based quantum theory.
The basic mechanism would be a phase transition creating dark matter phase as a Bose-Einstein condensate like state with particles having identical conserved quantum numbers. Conservation laws would force the ordinary matter to have opposite total charges. For instance, in the case of work one has momentum or angular momentum as a conserved charge. In the case of charge separation and high Tc superconductivity it would be em charge. Even color charges can correspond to conserved charges in TGD framework allowing scaled variants of strong interaction physics.
Basic biological functions involving the notion of work and also the formation of sensory percepts would rely on this mechanism. Also the ZEO based theory of consciousness predicting the change the arrow of time in ordinary state function reduction plays a central role and a model of nerve pulse is discussed as an example.
See the chapter Quantum Theory of Self-Organization or the article Quantum self-organization by heff changing phase transitions.