A. Evolution as CAS: novelty and explanatory power
The modeling results demonstrate that framing molecular evolution as a Complex Adaptive System (CAS) provides explanatory leverage beyond that offered by traditional linear or reductionist models. Whereas classical evolutionary theory often emphasizes stepwise mutation and selection acting independently on sequences, the CAS perspective captures the nonlinear, interdependent, and emergent properties that are intrinsic to RNA--protein coevolution.
Several dimensions of novelty emerge from this framing:
1. Coevolution as emergent synchronization.
In conventional accounts, the relationship between RNA coding rules and protein structures is treated as sequential: one evolves first, the other follows. By contrast, the CAS model reveals that synchronization can emerge spontaneously from feedback dynamics, producing attractors where RNA motifs and protein domains co-stabilize. This shifts the explanatory narrative from "which came first" to "how mutual dependence produces stable evolutionary outcomes."
2. Red Queen dynamics at the molecular scale.
The model predicts oscillatory regimes in which neither RNA nor protein evolution reaches a static endpoint. This introduces the concept of a molecular Red Queen race, extending ecological Red Queen theory to the biochemical substrate of life. Empirical signatures such as continual tRNA--synthetase adjustments align with this prediction, suggesting that perpetual coevolution is a fundamental property of molecular codes.
3. Bifurcations as evolutionary punctuation.
CAS analysis demonstrates that small parameter shifts can induce bifurcations, leading to sudden transitions in coevolutionary dynamics. This provides a mechanistic basis for punctuated patterns observed in codon reassignment and amino acid usage. Rather than invoking historical contingency alone, the model identifies mathematical conditions under which discontinuities naturally arise.
4. Integration across scales.
By situating molecular evolution within a CAS framework, the model integrates micro-level biochemical interactions with macro-level evolutionary phenomena such as convergence, divergence, and adaptive radiation. This cross-scale explanatory power marks a significant advance over siloed approaches that separately analyze genetic, proteomic, and ecological data. In summary, treating evolution as a CAS reframes long-standing paradoxes and aligns theoretical predictions with empirical regularities. It introduces novel explanatory categories---such as emergent synchronization, molecular Red Queen cycles, and attractor landscapes---that are not easily captured within the traditional mutation--selection framework.
B. Reconciling RNA-world and protein-first debates
The origin of life debate has long been polarized between two competing hypotheses: the RNA-world model, in which RNA served both as genetic material and catalyst before proteins emerged, and the protein-first model, which emphasizes the primordial role of peptides in catalysis with genetic coding appearing later. Each framework captures part of the evolutionary logic but struggles to account for the coevolutionary interdependence between nucleic acids and proteins observed in extant biology.
The CAS framework provides a resolution by reframing the debate not as a binary "first-mover" problem, but as an issue of emergent synchronization across coupled adaptive systems:
1. Simultaneity over precedence.
Our simulations reveal that RNA and protein populations can co-adapt through feedback loops, producing attractor states where each stabilizes the other. In this perspective, the question "which came first?" becomes less relevant than identifying the parameter regimes that enable stable coevolutionary attractors.
