2.C. Discussion on Emergence, Bifurcation, and Phase Transitions in Biomolecular Systems
The complexity inherent in protein evolution---especially under synthetic constraints such as anti-plastic functionality---requires a departure from linear cause-effect frameworks. In line with the Complex Adaptive Systems (CAS) perspective, emergence, bifurcation, and phase transitions become not only useful metaphors but formal tools for understanding and simulating how molecular novelty arises, stabilizes, or collapses.
This section articulates how these nonlinear dynamics can be identified, modeled, and applied in the design of next-generation enzymes through CAS-guided simulation engines.
1. Emergence in Biomolecular Systems
Emergence refers to novel patterns or functions that arise from interactions among simpler components, which cannot be predicted solely by examining those components in isolation. In protein systems, this may manifest as:
The sudden acquisition of a new catalytic mechanism from seemingly neutral mutations,
The appearance of allosteric regulation from secondary structure rearrangement,
Or cooperative binding behavior due to subtle changes in protein-protein interfaces.
In the CAS model, emergence is formalized through the transition of the system from low-order (weakly interacting substructures) to high-order (coherently functioning entities) via increasing interaction density II and fitness-weighted structure-function coupling WW.
This emergence is not manually engineered but arises probabilistically, often from parameter regimes near criticality, where interaction and instability are finely balanced.
2. Bifurcation as a Mechanism of Molecular Decision
