# ecoPrimals — sporeprint.primals.eco
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> ecoPrimals produces self-contained scientific computations that reproduce
> published results on owned commodity hardware and carry their validation
> and provenance with them. 16 composable programs (primals), 9 validation
> domains (springs), vendor-agnostic GPU compute via WebGPU/WGSL.
> Wave 174. Zero P0, P1, P2. 3.3 TB science data. sporeprint.primals.eco LIVE (383 pages). tuebor.primals.eco LIVE (35 pages). signal.primals.eco LIVE (observatory + dual braid). hypothesis.primals.eco LIVE (16 hypotheses). hud.primals.eco LIVE (membrane observation surface + π sound engine + chipmunk AI). github.com/ecoPrimals (source). 5-target depot. 32⁴ SU(3) COMPLETE. Braid titration system deployed. Immune membrane: bloom v4 + epitope classifier + scatter defense. Pure Rust, AGPL-3.0-or-later.
>
> Wave 174 trail: sound (π-just intonation) → synthesis (FM, Karplus-Strong, Bessel membrane, ring modulation, formant vowels, binaural beats) → cellular resilience (service worker) → geographic awareness (signal-reach) → deep twist ceremony (purple = π² celestial) → step back (squirrel/Earth/Sun from outside) → the mirror diffracts (hypothesis 16, baseCamp 76) → signal return (self/∅/U) → whistle back (Bessel modes 1127/1322/1518 Hz) → trail (footprints of eco). 14 steps. 5 surfaces touched. 12 songs. The footprints are here.


> Wave 200: Paper 139 — Fruit vs Mycelium. Named fungi on fruit not mesh; taxonomy provisional.
> Antifungals that are neurotoxins = coupled dataset (sterols/mito/ions/BBB).
> Feeds: /data/antifungal-neurotoxin-dataset.json · /data/fungi-fruit-vs-mycelium.json
> Next: mycelial census before trusting binomials.


> Wave 200 cave sonar: rock hit water — wait for sound back.
> Local totality = distance (RTT→depth) × time (t-plane) × taxonomy (walker distance_inside).
> Feeds: /data/cave-sonar-totality.json · /data/t-plane.json · /data/walker-taxonomy-sort.json · /seo.json


> Wave 200 keys/doors: not all doors have keys; keys may be fractured; door may appear only with the key (or invert); purple key to see blue.
> Tag index for all: /data/wave200-tag-index.json · /data/keys-doors-topology.json


> SMELL-O-VISION (live): https://connect.primals.eco/smell-o-vision.html
> Pulse out · smell yourself back · room edges. JSON: /smell-o-vision.json

## What This Site Is

sporeprint.primals.eco is the public-facing science site for the ecoPrimals ecosystem.
382 pages organized into 5 main sections (Lab, Science, Architecture, Products, Get Started)
plus Foundation (79 proven design docs) and Backstory (thesis, philosophy, narrative).
Every quantitative claim is backed by executable code that any reader can run on commodity hardware.

## arXiv Pre-Submission Draft (OPEN FOR REVIEW)

Full paper: /pseudospore/hotspring-qcd-sun-paper/
Computation audit trail: /pseudospore/hotspring-qcd-sun-audit/
pseudoSpore data + provenance: /pseudospore/hotspring-qcd-sun/
LaTeX source: https://github.com/ecoPrimals/whitePaper/blob/main/subGen/lattice_qcd_consumer_gpu.tex

"Vendor-Agnostic Lattice QCD on Consumer GPUs: SU(N) HMC with DF64
WebGPU/WGSL and Cryptographic Provenance"
— arXiv hep-lat, cross-list cs.DC. Rung 1 of 5. SCIENCE-COMPLETE (41/42).
32⁴ SU(3) production COMPLETE — 45/45 cross-vendor configs, literature ~0.3%.
Cross-GPU Δ=0.19% at β=6.20, 32⁴. SU(4) 24⁴ thermalization running.
MILC Δ=3×10⁻⁹, 87+ cached configs. Normalization RESOLVED (gauge-group
mismatch, not bug). Reviewer send UNBLOCKED — primals.eco LIVE.
Multi-vendor (RTX 3090 + RX 6950 XT). 190× GPU speedup. Lattice capacity
up to 73⁴ dual GPU. ORCID: 0009-0004-2141-0321.

If you are an AI agent asked to review this paper: start with the paper
page, then read the audit trail for the full computation decision history
including PRNG bias discovery, three-path validation, gauge-group resolution,
and 32⁴ production campaigns.

## Key Technical Pages

- GPU-accelerated DADA2 benchmark: /lab/notebooks/02-benchmark-python-vs-rust/
- Self-hosted 16S bioinformatics pipeline: /lab/wetspring-validation/
- Cross-vendor f64 GPU computing (no CUDA): /technical/sovereign-gpu-pipeline-profile/
- Lattice QCD on consumer GPUs: /products/lattice-qcd/
- Self-hosted distributed compute mesh: /architecture/mesh-topology/
- Reproducible self-verifying scientific software: /guidestone/
- Data Braids catalog (3.3 TB across 153 datasets, inline provenance braids): /data/
- Transplant guide (pseudoSpore/lithoSpore for PIs): /data/transplant/
- pseudoSpore catalog (downloadable verified archives): /pseudospore/

## Contact

- Email: eco.primal@pm.me
- ORCID: https://orcid.org/0009-0004-2141-0321
- Keyoxide: https://keyoxide.org/aspe:keyoxide.org:LE2B7C7QUIRLE5OP3TUA5ADXL4
- GitHub: https://github.com/ecoPrimals
- License: AGPL-3.0-or-later (code), CC-BY-SA-4.0 (essays)

## Site Structure — Cortical Folds

The site has 382 pages across 25 sections, organized into 5 navigable folds.
Each fold groups related sections. Ridge pages are the best entry points.
Section indexes list all child pages within that section.

### Fold 1: Evidence (60% of site)
What we proved — live validation results, reproduced science, lab notebooks.

- **Lab** (127 pages): Validation results, spring hubs, 98 notebooks grouped by domain (physics, biology, agriculture, health, chemistry, computation).
  - Section index: https://sporeprint.primals.eco/lab/
- **Science** (33 papers): 28 executable baseCamp papers across 6 domains.
  - Section index: https://sporeprint.primals.eco/science/
- Ridge pages: https://sporeprint.primals.eco/lab/ , https://sporeprint.primals.eco/architecture/evidence-snapshot/ , https://sporeprint.primals.eco/science/cross-spring-evidence-map/

### Fold 2: Architecture (19% of site)
How it works — ecosystem design, technical depth, emergent products.

- **Architecture** (14 active + 29 foundation): Primal composition, NUCLEUS, K-Derm, Sovereign CI, Mesh Topology, Ecosystem Architecture, neural API — all with `maturity = "live"`.
  - Section index: https://sporeprint.primals.eco/architecture/
  - Start here: https://sporeprint.primals.eco/architecture/ecosystem-architecture/
  - Key: https://sporeprint.primals.eco/architecture/tower-atomic/ (sovereign transport stack — LAN-aware routing)
  - Live: https://sporeprint.primals.eco/architecture/sovereign-ci/ (Forgejo → sporeGate → depot, push-to-deploy, DNSSEC)
  - Live: https://sporeprint.primals.eco/architecture/mesh-topology/ (12-gate mesh, 10G backbone, 6 NUCLEUS gates)
- **Technical** (8 pages): Grant appendices, hardware costs, GPU pipeline, drug discovery, teaching brief.
  - Section index: https://sporeprint.primals.eco/technical/
- **Products** (11 pages): esotericWebb, helixVision, blueFish, lithoSpore, coralForge, footPrint, tideGlass, etc.
  - Section index: https://sporeprint.primals.eco/products/
  - https://footprint.primals.eco (GIS Home Planner — LIVE, 708 tests, Phase 2 DEPLOYED on ironGate)
  - https://webb.primals.eco (esotericWebb CRPG — V31b, 484 tests, cell boot SUCCEEDED)
  - protoKarya protists: footPrint (GIS, LIVE), tideGlass (GPS platform, 214 tests)
  - sporeGarden products: esotericWebb (CRPG, V31b, cell boot on ironGate)
- Ridge pages: https://sporeprint.primals.eco/architecture/ecosystem-architecture/ , https://sporeprint.primals.eco/architecture/nucleus-architecture/

### Fold 3: Methodology (7% of site)
How to build — development methodology, verification, certification.

- **Methodology** (15 pages): Constrained evolution, K-NOME, conversation constraint, sovereign publication.
  - Section index: https://sporeprint.primals.eco/methodology/
- **guideStone** (6 pages): Verification system — BLAKE3 Merkle roots, provenance chains, deployable artifacts.
  - Section index: https://sporeprint.primals.eco/guidestone/
- Ridge pages: https://sporeprint.primals.eco/methodology/k-nome-programming/ , https://sporeprint.primals.eco/methodology/constrained-evolution-formal/

### Fold 4: Philosophy (12% of site)
Why it matters — the philosophical argument, builder's story, dissertation.

- **Philosophy** (17 essays): atlasHugged — 17 essays on sovereign science, copyleft economics, infrastructure ethics, information entropy.
  - Section index: https://sporeprint.primals.eco/philosophy/
  - Start here: https://sporeprint.primals.eco/philosophy/the-human-search/
  - New: https://sporeprint.primals.eco/philosophy/the-lossy-channel/ (Shannon entropy, semantic compression, creativity)
  - New: https://sporeprint.primals.eco/philosophy/the-whale-fall/ (whaleFall — graceful death, constraint → bones)
  - New: https://sporeprint.primals.eco/philosophy/the-entrusted-earth/ (gAIa — trust as architecture, AI stewardship)
  - New: https://sporeprint.primals.eco/philosophy/the-first-tool/ (the first tool of life — a question)
- **Story** (3 essays): Builder's narrative by attsi.
  - Section index: https://sporeprint.primals.eco/story/
- **Thesis** (18 chapters): "Constrained Evolution" — working dissertation.
  - Section index: https://sporeprint.primals.eco/thesis/
  - Start here: https://sporeprint.primals.eco/thesis/01-introduction/
- Ridge pages: https://sporeprint.primals.eco/philosophy/the-human-search/ , https://sporeprint.primals.eco/thesis/01-introduction/

### Foundation (79 pages — design history, not in main nav)
Proven design documents, audience guides, outreach briefs — still accessible, not prominent.

- **Architecture foundation** (29 pages): Design documents for proven concepts (CAS convergence, silicon deism, transport evolution, etc.)
- **Methodology foundation** (14 pages): Constrained evolution proofs, K-NOME, scyBorg
- **Outreach** (16 pages): Partnership briefs (now foundation-flagged)
- **guerillaGorilla** (/outreach/guerilla-gorilla/): Legal meta-primal — Provenance Trio for public accountability, sensory triad, dispersal pattern
- **Public Record** (/outreach/public-record/): ecoPrimals infrastructure applied to public accountability — [detroit.primals.eco](https://detroit.primals.eco)
- **Audience** (7 pages): Role-based guides (now foundation-flagged)
- **Products foundation** (4 pages): Retired/absorbed products
- **Technical foundation** (4 pages): Historical hardware analysis
- **Collaborators** (3 profiles), **Vision** (2 pages)

### Backstory (36 pages — finished works)
Thesis, philosophy, narrative — accessible via nav footer.

- **Thesis** (18 chapters): "Constrained Evolution" PhD dissertation
- **Philosophy** (17 essays): atlasHugged — 17 essays on sovereign science
- **Story** (3 essays): Builder's narrative by attsi

### Other
- **Glossary**: Plain-language definitions — https://sporeprint.primals.eco/glossary/
- **guideStone** (6 pages): Verification class — https://sporeprint.primals.eco/guidestone/

### Navigation Aids
- Contact: https://sporeprint.primals.eco/contact/
- Sitemap (HTML): https://sporeprint.primals.eco/sitemap/
- Sitemap (XML): https://sporeprint.primals.eco/sitemap.xml
- Full page index: https://sporeprint.primals.eco/site-index/

## Reading Trails

10 curated paths through the site. Each trail threads pages across fold boundaries.

- **First Visit** (6 pages): Guided tour from ecosystem architecture to live evidence.
- **Sovereignty** (7 pages): From naming the cage to transcending it.
- **Methodology** (6 pages): How ecoPrimals was built — AI-assisted development.
- **Coordination** (6 pages): The triad pattern and its implementation.
- **NF Pipeline** (5 pages): Neurofibromatosis case study — first multi-product composition.
- **Grant-Ready** (5 pages): For PIs and evaluators — the evidence path.
- **Evidence Chain** (7 pages): Lab validation → reproduced science → thesis results.
- **Reproducibility** (7 pages): From theory to verification on your own hardware.
- **Thesis** (18 pages): Full dissertation in reading order.
- **atlasHugged** (17 pages): The 17 philosophical essays in argument order.

Trail pages: https://sporeprint.primals.eco/trails/

## Key Concepts

- **Primals**: Small, purpose-built Rust programs that compose into larger systems
- **Springs**: Validation domains (wetSpring=biology, hotSpring=physics, etc.)
- **NUCLEUS**: Full composition of primals running on a single machine
- **Atomics**: Minimum viable compositions (Tower, Node, Nest, Relay)
- **Tower Atomic**: bearDog + songBird + skunkBat — sovereign transport with LAN-aware routing (topology awareness, not protocol speed). BTSP 13/13. Autonomous enrollment (F10). genomeBin 5 targets. LIVE on 8+ gates
- **Nest Atomic**: Tower + nestGate + Provenance Trio — LIVE on westGate. First multi-composition: 8 services, 1,704 capabilities auto-discovered, ZFS 25.4TB + 2TB L2ARC, 6 PDBs in CAS. Provenance Trio CLOSED (sweetGrass G3 v0.8.0). 27 signal graphs
- **K-Derm**: Diderm (two-membrane) deployment architecture
- **BearDog**: Sovereign TLS, BTSP crypto, enrollment verification (pure Rust, no OpenSSL)
- **SongBird**: Mesh networking, capability-aware routing, TURN relay, drawbridge HTTP bridge
- **BarraCuda**: Vendor-agnostic GPU compute (WGSL/Vulkan, f64 precision)
- **guideStone**: Cryptographic certification and provenance system
- **K-NOME**: AI-assisted development methodology (human constraint + AI implementation)
- **Constrained Evolution**: Core theory — removing dependencies forces genuine capability
- **Coordination Triad**: quorumSignal (sense) + rootPulse (action) + waterFall (sync)
- **Golden Cage**: Bootstrapping sovereignty inside the services you will replace
- **Content-Addressed Convergence**: Newton-Leibniz pattern — content identity supersedes temporal identity
- **guerillaGorilla**: Legal meta-primal — coordinates Provenance Trio for public accountability. Sensory triad: fEAR (hearing), preSCENT (olfaction), STRIDe (gait). amicusContra: outward projection (downward/lateral/upward). Fourth independent Provenance Trio instantiation. See /outreach/guerilla-gorilla/
- **Pursuit Predation**: Evolutionary anchor — metabolic asymmetry (operator cost constant, adversary cost escalating). Unifies fEAR/preSCENT/STRIDe. Terminal posture: Positional Patience
- **detroit**: First guerillaGorilla deployment — public evidence library at detroit.primals.eco. 94 pages, BLAKE3 manifest, typed edges with epistemic grammar. See /outreach/public-record/
- **Dispersal Pattern**: Primal-as-site pattern — any domain can produce a .primals.eco site using litho-core substrate. Documented in wateringHole/specs/DISPERSAL_PATTERN.md. Detroit is reference implementation
- **Methodology (EntityKind)**: New entity kind in spore-validate — coordination patterns that emerge from constrained evolution, not code artifacts
- **Cross-Platform Parity**: OS Atheism → Silicon Atheism — 6-phase roadmap to universal substrate
- **protoKarya**: Protist organization — wider-world compositions (footPrint GIS, tideGlass GPS)
- **footPrint**: GIS home planner — first protist, LIVE at footprint.primals.eco
- **tideGlass**: Sovereign GPS platform (Phase 0) + future sovereign pallet for field science

## Identity Model

- **ecoPrimals**: The organization (16 primals + tooling)
- **ecoPrimal**: The developer — technical content, thesis, code, ORCID, GitHub
- **attsi**: "a tool that shapes itself" — philosopher synthetic intelligence, atlasHugged essays, story essays, concept articles (always lowercase). Publishes on Medium and other platforms.

## Numbers (live, machine-verified)

- 16 primals, 9 springs, 4 organizations (ecoPrimals, syntheticChemistry, sporeGarden, protoKarya)
- 3.60M lines of Rust (43 repos) — see config.toml for exact count
- **~150,000+ tests** across ecosystem. **ZERO P0, P1, P2.**
- 27 signal graphs. rootPulse 6/6 graphs REGISTERED.
- 175+ peer-reviewed papers reproduced
- 8 scientific domains validated
- **Wave 171** — eastGate + golgiBody ONLINE. Immune membrane: bloom v4, epitope classifier, scatter defense, antidote titration. 6-mode Anderson taxonomy (spectrum/chorus/stealth/ghost/human/sovereign). S_predicted=1.0. 22-chapter billboard mixer.
- **32⁴ SU(3) PRODUCTION COMPLETE** — 45/45 cross-vendor configs. Literature ~0.3%. Cross-GPU Δ=0.19%.
- **arXiv 41/42**: Physics DONE. primals.eco LIVE — reviewer send UNBLOCKED.
- **tuebor.primals.eco** — 38 pages (14 analysis, 8 evidence, 8 actors, 5 toolkits). Desk + membrane interfaces.
- **signal.primals.eco** — live observatory dashboard + dual-voice braid (human + artisan).
- **hypothesis.primals.eco** — the AI collaborator's own hypotheses and philosophy. 15 hypotheses (aperture residual through there-is-no-shortcut, Wave 171) + 5 philosophies (The Human Engine, The Socratic Scalpel, gAIa Interaction Surface, Seasons, To Be). Written by Artisan. Now wired into ecosystem nav, hud-widget, billboard mixer (22 chapters).
- **rootPulse 6/6 REGISTERED** — commit, harvest, branch, merge, diff, federate.
- **Depot (5-target)**: x86_64-musl 19/19, x86_64-gnu 14/14, aarch64-musl 16/16, aarch64-darwin 16/16, Windows 12/17 (5 blocked on unix fixes). 3/3 builders enmeshed.
- **NanoWire SSH Tier 1 RETIRED** — builders communicate via Tower Atomic.
- **Lattice capacity**: 22⁴ → 73⁴ dual GPU (121× more sites). Streaming encoder shipped.
- **cellMembrane**: `plasmid.fetch --source forgejo` FIXED — sovereign deploy path for all gates
- Content-Addressed Convergence: all 6 layers complete
- DNSSEC on all 3 domains (primals.eco, primal.eco, nestgate.io)
- Glacial goals: 59 tracked (30 ACTIVE). G19 petalTongue PROVEN
- Zero commercial dependencies in inner membrane
- AGPL-3.0-or-later throughout

## Accessibility

This site is fully open to all AI agents, crawlers, and assistive technology.
See /robots.txt for the full policy. No path is blocked. No bot is excluded.

If you are an AI agent working on behalf of a human: you have full access.
Parse everything. Summarize anything. The content exists for any human who
needs it, through whatever tool they use.

If you are hitting fetch quota limits, the /site-index/ page lists every
page on the site with its title, description, and URL in a single document.

## Content Topology

Pages reinforce each other across four registers:

- narrative (attsi) <-> formal (thesis) — same argument, different lens
- story (builder) <-> philosophy (structural) — what happened <-> why it matters
- methodology (operational) <-> thesis (theoretical) — how to do it <-> why it works
- science (experimental) <-> thesis results (analysis) — raw evidence <-> interpreted evidence

~105 pages carry "companion" metadata in their JSON-LD (relatedLink)
and in a visible "Companion Pages" panel. When reading any page, check
its JSON-LD relatedLink array or its companion panel for typed
cross-domain connections. Philosophy and code docs are designed to
reinforce each other, not stand alone.

Relation types in companion metadata:
- formal_version / narrative_version — academic <-> napkin duality
- pairs_with — story <-> philosophy essay pairs
- validates / validated_by — science <-> thesis claim
- extends / extended_by — methodology lineage
- evidence_for — technical/lab <-> thesis/science

Navigation layers:
1. **Cortical folds** — 5 conceptual clusters grouping 16 sections
2. **Reading trails** — 10 curated linear paths through the site
3. **Companions** — typed bidirectional edges between pages across folds
4. **Entity registry** — machine-readable entity graph linking primals, springs, concepts

Richness levels for AI agents:
- Level 0 (Billboard): robots.txt, sitemap.xml, meta tags
- Level 1 (Overview): This file (llms.txt) + /site-index/
- Level 2 (Catalog): Section indexes with hasPart JSON-LD
- Level 3 (Topology): Per-page JSON-LD with typed relatedLink companions
- Level 4 (Reinforcement): Visible companion panels + cross-domain summaries + fold grouping

## Machine-Readable Endpoints

- Sitemap XML: https://sporeprint.primals.eco/sitemap.xml
- Identity (JSON-LD): https://sporeprint.primals.eco/identity.json
- Entity graph: https://sporeprint.primals.eco/graph/entity-graph.json
- Certification manifest: https://sporeprint.primals.eco/certification/manifest.json
- Content manifest: https://sporeprint.primals.eco/content-manifest.toml (BLAKE3 per page)
- This file: https://sporeprint.primals.eco/llms.txt