A. Evidence from proteomic dipeptide analyses (JMB study).
B. Genetic code thermostability and protein structure correlations.
C. Current limitations: descriptive/statistical approaches without formal dynamics.
III. Theoretical Foundations
A. Principles of Complex Adaptive Systems.
B. Adaptive landscapes, punctuated equilibria, and coevolution theory.
C. Integration with molecular evolution.
IV. Mathematical Framework
A. Genotype--phenotype mapping (RNA motifs protein domains).
B. Interdependent fitness functions with trade-offs.
C. Replicator--mutator dynamics for coupled populations.
D. Emergent attractors and bifurcations.
V. Results
A. Analytical: stability and bifurcations.
B. Simulation: synchronization and Red Queen cycles.
C. Empirical alignment with proteomic and genomic data.
VI. Discussion
A. Evolution as CAS: novelty and explanatory power.
B. Reconciling RNA-world and protein-first debates.
C. Trade-offs and eco-evolutionary analogues.
D. Implications for the origin of life and systems biology.
VII. Conclusion
A. Summary of contributions.
B. Path forward: empirical calibration and comparative studies.
C. Evolution reframed as CAS across scales.
VIII. References
I. Introduction
A. Limitations of RNA-first and protein-first models
The question of whether RNA or proteins emerged first has long structured debates about the origin of molecular evolution. The RNA World hypothesis argues that RNA came first, serving as both an information carrier and a catalyst before proteins assumed catalytic dominance. Conversely, protein-first models posit that short peptides and proto-proteins, generated through abiotic chemistry, provided early functional advantages and only later became coupled to genetic information systems. Both frameworks have shaped decades of theoretical and experimental research.
Despite their heuristic value, both RNA-first and protein-first models face serious conceptual and empirical limitations:
1. Asymmetry of explanatory scope.
