Higher-Order Epistasis Is Generated by Dynamics
Higher-order knockout epistasis is generated by dynamics, not molecular rules, in 28 Boolean gene regulatory networks
Exhaustive combinatorial knockout sweeps across 28 published Boolean gene regulatory networks (7–18 genes) show that the network’s dynamics create higher-order epistasis three times more often than they destroy it (19 of 25 non-null networks). A Walsh–Hadamard decomposition measures the composition gap between the interaction spectra of the local regulatory rules and of the attractors, with gaps from under 1 to +83 percentage points. No joint model of standard topological features predicts the gap (cross-validated R² = −0.27). Converting the networks to Hill-function ODEs preserves the sign of the gap in all 25 non-null networks, and size- and degree-matched random networks produce markedly smaller gaps, so the effect requires the specific regulatory rules and their wiring. Creation dominance is specific to complete knockout and inverts by half-strength knockdown.