Traditional network architectures suffer from severe protocol ossification and structural fragility due to their reliance on static, human-defined rules that fail to adapt to the emergent edge cases and probabilistic reasoning of modern autonomous agents. To address these limitations, this paper proposes DarwinNet, a bio-inspired, self-evolving network architecture that transitions communication protocols from a \textit{design-time} static paradigm to a \textit{runtime} growth paradigm. DarwinNet utilizes a tri-layered framework-comprising an immutable physical anchor (L0), a WebAssembly-based fluid cortex (L1), and an LLM-driven Darwin cortex (L2)-to synthesize high-level business intents into executable bytecode through a dual-loop \textit{Intent-to-Bytecode} (I2B) mechanism. We introduce the Protocol Solidification Index (PSI) to quantify the evolutionary maturity of the system as it collapses from high-latency intelligent reasoning (Slow Thinking) toward near-native execution (Fast Thinking). Validated through a reliability growth framework based on the Crow-AMSAA model, experimental results demonstrate that DarwinNet achieves anti-fragility by treating environmental anomalies as catalysts for autonomous evolution. Our findings confirm that DarwinNet can effectively converge toward physical performance limits while ensuring endogenous security through zero-trust sandboxing, providing a viable path for the next generation of intelligent, self-optimizing networks.