2. Partial functionalities as transitional states.
In the weak- and intermediate-coupling regimes, RNA and proteins exist but do not yet stabilize one another fully. These regimes correspond to transitional forms: RNA with limited catalytic capacity or peptides with rudimentary stability functions. Such partial functionalities provide a mechanistic explanation for how RNA-like and protein-like molecules could persist prior to full synchronization.
3. Emergent attractors as a synthesis.
Strong-coupling attractors correspond to ribonucleoprotein complexes---stable, coadapted structures such as ribosomes. The CAS framework predicts that once a system crosses the coupling threshold, a synchronized RNA--protein complex is not only possible but highly robust, explaining the universality of such complexes in modern life.
4. Reinterpretation of empirical evidence.
Observed signatures in proteomic dipeptide correlations and codon reassignment can be understood as "fossils" of intermediate coupling regimes. Rather than privileging RNA-first or protein-first narratives, these data support a coevolutionary trajectory, where both subsystems shaped one another under mutual selective pressures. Thus, the CAS model reconciles the RNA-world and protein-first debates by showing that both contain partial truths. Life's origin may not be the story of one molecule dominating before the other, but of two interdependent codes evolving into synchrony through the dynamics of a complex adaptive system.
C. Trade-offs and eco-evolutionary analogues
A central feature of the CAS model is its ability to capture trade-offs that structure coevolutionary dynamics. In molecular evolution, RNA and proteins do not maximize a single function in isolation; rather, they operate under multi-objective constraints that resemble ecological interactions.
1. Stability versus adaptability.
RNA sequences optimized for rapid replication may sacrifice translational fidelity, while protein domains optimized for thermostability may limit catalytic flexibility. The CAS framework formalizes this as opposing terms in the fitness function, producing equilibria that represent compromises rather than absolute optima. This parallels ecological trade-offs between reproduction and survival in higher organisms.
2. Cooperative dependence and competition.
RNA and proteins are mutually reinforcing yet also impose metabolic and structural costs on one another. This duality is captured in the model by interaction coefficients that are positive at one scale (mutual reinforcement) but negative at another (resource limitation). Such dynamics are directly analogous to mutualism--parasitism continua in ecological systems.
3. Red Queen dynamics.
The oscillatory regime, in which RNA and protein abundances cycle perpetually, embodies a molecular-scale Red Queen effect: continual adaptation is required to maintain functional compatibility. This mirrors host--parasite cycles in ecosystems, suggesting that Red Queen dynamics are not limited to macroscopic organisms but are fundamental to adaptive systems across scales.
4. Attractors as eco-evolutionary niches.
Stable coadapted attractors can be understood as molecular niches, in which RNA motifs and protein domains are tuned to one another's presence. The transition between collapse, oscillatory, and stable regimes reflects niche establishment, competitive instability, and eventual ecological succession. By framing molecular coevolution in terms of trade-offs and eco-evolutionary analogues, the CAS model provides a unified language for understanding adaptation across biological scales. RNA--protein dynamics are no longer an isolated puzzle but part of a continuum of adaptive processes that range from molecules to ecosystems.
D. Implications for broader evolutionary theory, origin of life, and systems biology
The CAS framework for RNA--protein coevolution has implications that extend beyond the molecular level, touching upon fundamental questions in evolutionary theory, the origin of life, and the future of systems biology.
