> For the complete documentation index, see [llms.txt](https://docs.holons.io/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://docs.holons.io/software/dna.md).

# DNA

How a holon's identity is composed from chromosomes

A holon's **DNA** is its identity, expressed as an ordered sequence of chromosomes. Each chromosome captures one element of what the holon is or does—a value it holds, a tool it uses, a practice it observes. The DNA sequence is what makes a holon recognizable as itself: distinct from the holons around it, even when they share members or resources.

The `@holons/core/dna` domain provides the canonical model—the same chromosomes, sequences, and validation rules used by every interface in the [Harvest](/software/harvest-dashboard.md) monorepo.

## Concepts

### Chromosome

A single element of identity:

```ts
interface Chromosome {
  id: string;
  holonId: string;
  name: string;
  type: 'value' | 'tool' | 'practice';
  description: string;
  createdAt: number;
  updatedAt: number;
  icon?: string;
  color?: string;
}
```

Three types, by design:

* **Value** — what the holon cares about (e.g. "regeneration", "transparency", "care").
* **Tool** — what it uses (e.g. "Telegram", "sociocracy", "permaculture").
* **Practice** — what it does regularly (e.g. "weekly check-in", "rotating stewardship", "consent-based decisions").

Each chromosome lives in the holon's **ChromosomeLibrary**—the set of available pieces. Not every chromosome in the library is part of the DNA; the DNA is a curated, ordered subset.

### DNA Sequence

```ts
interface DNASequence {
  holonId: string;
  chromosomeIds: string[]; // Ordered, unique, max 20
  createdAt: number;
  updatedAt: number;
  version: number;
}
```

Constraints enforced by validation:

* **Ordered.** Sequence order matters—earlier chromosomes are more defining.
* **Unique.** No chromosome appears twice in a sequence.
* **Bounded.** `MAX_CHROMOSOMES_PER_DNA` caps the sequence at 20.
* **Referentially valid.** Every ID in the sequence must point to a real chromosome in the library.
* **Versioned.** The sequence carries a version counter for optimistic concurrency.

## Seed data

`@holons/core/dna/seed-data` ships default chromosomes so a new holon doesn't start from a blank slate:

* `defaultValues` — common starting values
* `defaultTools` — typical tools
* `defaultPractices` — frequently useful practices
* `getAllDefaultChromosomes()` / `getDefaultChromosomesByType(type)` — accessors

A newly created holon usually has its library seeded with these (`seedChromosomeLibrary`) and then evolves over time.

## Operations

The public functions exported by `@holons/core/dna`:

| Function                                    | Purpose                                              |
| ------------------------------------------- | ---------------------------------------------------- |
| `getChromosomeLibrary(holonId)`             | Load the full library for a holon                    |
| `getChromosome(holonId, id)`                | Read a single chromosome                             |
| `addChromosome(holonId, chromosome)`        | Add a new chromosome to the library                  |
| `updateChromosome(holonId, id, patch)`      | Modify an existing chromosome                        |
| `removeChromosome(holonId, id)`             | Remove a chromosome (with sequence-reference checks) |
| `getDNASequence(holonId)`                   | Load the current DNA sequence                        |
| `saveDNASequence(holonId, sequence)`        | Persist a new sequence (validated first)             |
| `seedChromosomeLibrary(holonId)`            | Initialize a library with defaults                   |
| `subscribeToChromosomeLibrary(holonId, cb)` | Live updates                                         |
| `subscribeToDNASequence(holonId, cb)`       | Live updates                                         |

And the pure validation helpers:

| Function                                                                | Purpose                                              |
| ----------------------------------------------------------------------- | ---------------------------------------------------- |
| `validateChromosome(chromosome)`                                        | Field-level validation                               |
| `validateDNA(sequence, library)`                                        | Whole-sequence validation against a library          |
| `validateDNASequence(sequence)`                                         | Structural validation (ordering, uniqueness, bounds) |
| `findDuplicates(sequence)` / `findInvalidReferences(sequence, library)` | Diagnostics for `validateDNA`                        |
| `createDNAError(type, message)`                                         | Construct a typed `DNAValidationError`               |

`DNAValidationError` distinguishes between `duplicate`, `max_length`, `invalid_reference`, and `missing_required` failures, so UIs can surface specific feedback rather than a generic "invalid."

## Governance interplay

DNA changes are typically not made unilaterally. The common pattern:

1. A member opens a [Council](/software/council.md) proposal: "Add chromosome *consent-based decisions* to our practices."
2. Members vote.
3. On agreement, the chromosome is added (`addChromosome`) and the sequence updated (`saveDNASequence`).

This binds DNA to the holon's governance: identity drifts only when the holon consents to it.

## MCP tool surface

The [MCP server](/software/mcp-server.md) exposes **12 tools** in the `dna` domain — full chromosome and sequence management, validation, and library seeding. An AI agent connected via MCP can propose, validate, and (if its actor has standing) commit DNA changes directly.

## See also

* [Council](/software/council.md) — the proposal lifecycle that governs DNA changes
* [Glossary: shared DNA](/getting-started/glossary.md#shared-dna) — the protocol-level concept this domain operationalizes
* [Glossary: membrane](/getting-started/glossary.md#membrane) — the identity boundary that DNA fills


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