> ## Documentation Index
> Fetch the complete documentation index at: https://docs.zookooree.ai/llms.txt
> Use this file to discover all available pages before exploring further.

# Thesis 5: Germline and Soma

> The recursion needs change control: changes to what makes agents are held to a stricter standard than changes to agents.

Toyota's cars do not build cars. This factory's outputs staff the factory — its products are also its workers. That recursion is the plant's compounding advantage and its most dangerous failure mode: a bad specification can cause agents to produce coherent-looking garbage at scale.

The answer borrows the biological firewall. Everything in the factory splits into two classes:

* **Germline:** the templates, base protocol, station gates, validators, work-order schemas, the standard work itself — anything that shapes *future units*. Changes here are congenital: a defect propagates into every unit ever produced afterward. Germline changes get the strictest control in the plant — PR-only, human sign-off, versioned with a changelog, evals re-run against fixture units before merge.
* **Soma:** deployed unit instances and their run-state. Faster iteration, lighter gates, recoverable by recall and re-issue.

The asymmetry is deliberate. A somatic defect costs one unit; a germline defect costs every future unit and hides while it compounds. So the review weight follows the blast radius, not the diff size — a one-line edit to a template outranks a hundred-line edit to a deployed instance.

## The compiled form

This thesis runs as code. The germline path list lives in a machine-readable manifest; `germline/check-changelog.py` fails any change to a germline path that does not carry a dated changelog entry in the same diff — and it reads the manifest at both ends of the range, so a change cannot ungate itself by deleting its own listing. Fail closed: a range the gate cannot evaluate is a FAIL, never a pass. The gate runs on every pull request as one of the four CI gates ([Gates](/gates)). The standard work itself carries the changelog this gate demands; the discipline is documented in [Standard Work](/standard-work).

The founding wound this heals: the factory's most important document — the standard work — once had no changelog. The document that shapes every unit could not show its own history. Under this thesis that is not an oversight; it is a germline violation, and it is fixed.

Self-improvement without change control is self-corruption on a delay. The firewall is what lets the factory improve itself and stay itself.

## Self-audit

| Claim                                                                                                                                  | Source                                         |
| -------------------------------------------------------------------------------------------------------------------------------------- | ---------------------------------------------- |
| Outputs staff the factory; recursion is the compounding advantage and most dangerous failure mode; "coherent-looking garbage at scale" | docs/factory-design.md:60                      |
| Germline definition and strictest controls: PR-only, human sign-off, changelog, fixture evals                                          | docs/factory-design.md:64                      |
| Soma definition: lighter gates, recoverable by recall and re-issue                                                                     | docs/factory-design.md:65                      |
| The standard work's missing changelog was a germline violation                                                                         | docs/factory-design.md:67                      |
| Changelog now exists and is enforced                                                                                                   | workflows/production-line.md:95–99             |
| Gate mechanics: manifest-driven, both-ends read, fail closed                                                                           | germline/check-changelog.py (module docstring) |