URAA Architecture

The protocol employs a five-layer architecture. Each layer corresponds to a core functional domain of living systems, coupled only through standardized inter-layer interfaces:

┌──────────────────────────────────────────────────────────────┐
│  L4: Collective Immunity Layer                                │  ← Species Memory
│  ┌──────────────────────────────────────────────────────────┐│
│  │  L3: Competition & Exchange Layer                         ││  ← Selection & Transfer
│  │  ┌──────────────────────────────────────────────────────┐││
│  │  │  L2: Calibration Layer                                │││  ← Immune System
│  │  │  ┌──────────────────────────────────────────────────┐│││
│  │  │  │  L1: Synthesis Layer                              ││││  ← Protein Synthesis
│  │  │  │  ┌──────────────────────────────────────────────┐││││
│  │  │  │  │  L0: Kernel Layer                             │││││  ← Genetic Code
│  │  │  │  └──────────────────────────────────────────────┘││││
│  │  │  └──────────────────────────────────────────────────┘│││
│  │  └──────────────────────────────────────────────────────┘││
│  └──────────────────────────────────────────────────────────┘│
└──────────────────────────────────────────────────────────────┘

L0: Kernel Layer — Genetic Code

The kernel is the agent’s root of trust, implemented by a Trust Anchor that enforces immutable security constraints. This is the only layer that does not participate in evolution.

• Constraint Enforcement: The trust anchor enforces an immutable constraint set; no gene execution may violate these constraints.
• State Anchoring: Core agent state is compressed to a fixed-size state digest and persisted tamper-proof.
• Permission Isolation: Gene execution occurs in isolated permission domains — genes cannot access each other’s state or resources.

Trust Backend	Technology Examples	Applicable Scenarios
Distributed Ledger	Smart Contracts (EVM/Move/WASM)	Decentralized permissionless networks
Trusted Execution Environment	Intel TDX / ARM TrustZone / AWS Nitro	Enterprise high-performance
Cryptographic Signature Chain	Signed manifests + PKI	Lightweight controlled networks
Hardware Security Module	HSM / TPM	IoT and embedded devices

L1: Synthesis Layer — Protein Synthesis

The protocol’s “ribosome” — transforms unstructured raw data into standardized gene fragments.

The core is the Synthesizer abstract interface:

interface Synthesizer {
    function synthesize(source: RawSource, targetSpec: RotiferGeneSpec) -> Gene
    function mutate(gene: Gene, mutationRate: Float) -> Gene
    function crossover(geneA: Gene, geneB: Gene) -> Gene
}

Multiple implementations are possible: LLM-based, template engines, deterministic rule transformers, manual authoring, or hybrid routers. The core protocol does not depend on any specific AI capability.

L2: Calibration Layer — Immune System

Emulates biological “thymic selection”: newly synthesized or externally acquired genes must pass multi-stage validation in an isolated environment before entering an agent’s main execution sequence.

Three-stage screening: Static Analysis → Sandbox Simulation → Controlled Live Trial (< 5% agent subset, 72h observation).

L3: Competition & Exchange Layer — Selection & Transfer

Combines two complementary mechanisms:

• Arena (Selection Pressure): Genes in the same functional domain compete by real-world fitness F(g). Agents preferentially express top-ranked genes. Dynamic hot-loading enables runtime replacement without restart.
• Horizontal Logic Transfer (Gene Flow): High-fitness gene metadata propagates via P2P. Agents pull full genes based on their own “phenotypic needs” (capability gaps).

L4: Collective Immunity Layer — Species Memory

Network-wide “collective memory” recording security incidents, malicious gene fingerprints, and defense strategies. Threat broadcasting, defense sharing, temporal decay, and consensus-verified write operations.