Encourages parsimony by penalizing:
Disruptive or destabilizing mutations (e.g., introduction of charged residues in hydrophobic core)
Over-mutation leading to function loss
Loss of allosteric pathways or domain modularity
4.C.4. Systemic Scoring as an Adaptive Utility Function
This composite score is not static---it evolves as the system interacts with changing environments or substrate analogs. For example:
If a substrate mutates (e.g., new plastic polymer), SaffS_{\text{aff}} becomes dominant.
Under thermal stress, SstabS_{\text{stab}} takes precedence.
In co-evolving simulations, SdynS_{\text{dyn}} rises in importance as enzymes must adapt to moving fitness landscapes.
This flexibility renders the system context-aware, enabling a level of adaptive evolution that approximates natural molecular learning.
4.C.5. Practical Implementation
