# Concepts and Architecture

Operon is built around the idea that agent reliability depends heavily on structure.

## Core View

The library borrows from biology not as decoration, but as a source of reusable control motifs:

- review bottlenecks
- consensus gates
- bounded resource use
- self-repair and surveillance
- explicit interfaces between stages

## Current Practical Layers

### Pattern-first API

The recommended front door for engineers:

- topology advice
- reviewer gates
- specialist swarms
- skill organisms

### Organelles

Shared infrastructural components such as:

- `Nucleus`
- `Membrane`
- `Mitochondria`
- `Chaperone`
- `Lysosome`

### State and Coordination

Includes:

- ATP / metabolic budgeting
- histone-based memory
- surveillance and healing
- morphogen coordination

### Typed Wiring and Analysis

The lower-level layer models modules, ports, wires, and topology explicitly so the library can reason about architecture instead of treating everything as an opaque chain.

## What Changed Recently

- `v0.17` made the epistemic topology story explicit
- `v0.18` made the practical front door thinner
- `v0.19` added bi-temporal memory with dual time axes
- `v0.20` integrated bi-temporal memory into the SkillOrganism runtime as an auditable substrate, formalizing the three-layer context model (topology, ephemeral, bi-temporal)
- `v0.21` added pattern repository, watcher component, adaptive assembly, and experience pool — the adaptive structure layer
- `v0.22` added cognitive mode annotations (System A/B), sleep consolidation, social learning, and curiosity — the cognitive architecture layer
- `v0.23` added developmental staging with critical periods and capability gating — the developmental layer; release integration with memory adapters and cross-subsystem tests completed the roadmap
- `v0.24` added convergence adapters (Swarms, DeerFlow, AnimaWorks, Ralph, A-Evolve), TLA+ formal verification, co-design composition — the convergence layer (C1–C4)
- `v0.24.1` added Scion adapter, production compilers (organism_to_swarms/deerflow/ralph/scion), distributed watcher, LangGraph node — phase C5
- `v0.25` added evaluation harness (20 tasks, 7 configs), prompt optimization protocols, workflow generation — phases C6–C7
- `v0.25.1` added live LLM evaluation with cross-judging across Gemini API, Claude CLI, and Codex CLI; C8 roadmap
- `v0.26` added meta-evolution (C8 Phase A): evolves organism configurations using biological primitives at the meta-level, with dual stall detection and LLM proposer
- `v0.27` added structural guarantee benchmarks (metabolism, quorum sensing, epiplexity) with 10M+ data points, QuorumSensingBio auto-calibration, MTORScaler, real-embedding confirmation
- `v0.28` added categorical certificate framework (`Certificate`, `certify()`, `verify()`), sequential pipeline validation harness with Gemma 4 local eval, Paper 4 empirical results (error bound validated, rho=+0.751)

The current center of gravity is pattern-first workflows with auditable state.
