ecoPrimals — Sovereign Prior Art Catalog
Lysogeny prior art record for sovereign compute
At a Glance
A systematic catalog of what AGPL-3.0 makes permanently public. For each primal and spring, this document records the prior art it replaces, the innovation it adds, and the specific capabilities locked into the public commons. 15 primals, 8 springs, 52 novel innovations, ~1.5M lines of Rust — all irrevocably open.
AGPL-3.0 Commons Inventory
Date: March 13, 2026 Purpose: Catalog all prior art locked into AGPL-3.0 public commons. Sovereign code is code that CANNOT be recaptured by fictions (corporations) but is free to use, study, modify, and share by all humans.
Totals: ~1.5M lines Rust | ~84K lines WGSL | ~63,000+ tests & checks | ~100 reproduced papers | 13 primals | 5 springs | 20+ scientific domains | 52 novel innovations | AGPL-3.0 perpetually locked
Classification
Established prior art: Implementations of known techniques in pure Rust under AGPL-3.0. The technique exists elsewhere (often in C/C++ under permissive licenses), but the AGPL Rust implementation is sovereign — it cannot be absorbed into proprietary stacks.
Novel prior art: Capabilities, architectures, or integrations that do not exist in any other open-source project. These are new to technology via ecoPrimals.
I. Foundation Primals
BearDog — Cryptographic Service Provider
| Capability | Type | Description |
|---|---|---|
| Tower Atomic pattern | Novel | Crypto provider ( BearDog) separated from protocol ( Songbird) via JSON-RPC IPC. No other system cleanly separates crypto operations from transport this way. |
| Genetic lineage | Novel | Device seed derivation from root key, lineage certificates, challenge-response authentication. Cryptographic proof of device ancestry. |
| Dark Forest beacon | Novel | Zero-metadata beacon keys via genetic.derive_lineage_beacon_key. HKDF + domain separation for discoverable-but-private service advertisement. |
| Multi-family isolation | Novel | Per-family --family-id instances with fully isolated key derivation trees. |
| Tor v3 crypto in pure Rust | Established | Onion address derivation, ntor handshake, cell encryption. Standard Tor spec, novel in pure Rust without C dependencies. |
| RustCrypto primitives | Established | Ed25519, X25519, AES-GCM, ChaCha20-Poly1305, BLAKE3, SHA-2/3, HKDF, Argon2id. Standard crypto, sovereign implementation. |
| Universal HSM abstraction | Established | Vendor-agnostic HSM trait (software, PKCS#11, StrongBox). Pattern known; AGPL implementation is sovereign. |
30 crates | 13,720 lines Rust | 12,751+ tests | 78.6% coverage
Songbird — Network Orchestration
| Capability | Type | Description |
|---|---|---|
| Pure Rust Tor stack | Novel | Full directory, circuit, stream, onion service in pure Rust. Most Tor implementations use C (arti is Rust but not AGPL). This is the only AGPL-3.0 Tor stack. |
| Sovereign Onion service | Novel | P2P encrypted service with all crypto delegated to BearDog via IPC. No local crypto state in the network layer. |
| NFC Genesis pairing | Novel | Dark Forest mobile pairing with low metadata leakage. Zero-knowledge device introduction. |
| 100% crypto delegation | Novel | Zero cryptographic operations in the network layer. All delegated to BearDog via JSON-RPC IPC. No other networking stack operates this way. |
| Infant Discovery | Novel | O(n) discovery via central hub instead of O(n²) mesh. Scalable service discovery without broadcast storms. |
| QUIC + TLS 1.3 | Established | Standard protocols, sovereign implementation. |
| STUN + IGD NAT traversal | Established | RFC 5389 + UPnP IGD, sovereign implementation. |
~27 crates | 8,515+ tests | 60.84% coverage | #![forbid(unsafe_code)]
NestGate — Universal Storage
| Capability | Type | Description |
|---|---|---|
| Isomorphic IPC | Novel | Single binary adapts transport (Unix socket → TCP) by platform at runtime. Same binary on Linux, macOS, FreeBSD, WSL2, Android. |
| Adaptive backend | Novel | Unified try-optimize-fallback pattern for storage, ZFS, and IPC. |
| Capability-based primal discovery | Novel | Runtime discovery by capability string (“crypto”, “storage”), not hardcoded primal names. |
| NAT traversal persistence | Established | Relay-assisted coordinated punch, standard pattern. |
| ZFS integration | Established | ZFS management in Rust, other implementations exist. |
13 crates | 12,155 tests | 70.07% coverage | zero production unwrap/expect
Squirrel — AI Coordination
| Capability | Type | Description |
|---|---|---|
| TRUE PRIMAL pattern | Novel | Self-knowledge only, runtime discovery, zero compile-time coupling to any AI vendor or other primal. |
| Vendor-agnostic AI routing | Novel | Cost/quality/latency-based provider selection across Ollama, llama.cpp, vLLM, OpenAI, Anthropic, Gemini without vendor-specific code paths. |
| Isomorphic multi-platform IPC | Novel | Same binary across Linux, Android, Windows, macOS, BSD, WASM. |
| Sovereign MCP | Established | Model Context Protocol implementation; MCP exists elsewhere, AGPL integration is sovereign. |
~15 crates | 1,957 tests | 13/15 chaos tests passing
ToadStool — Hardware Management
| Capability | Type | Description |
|---|---|---|
| hw-learn pipeline | Novel | Observe → distill → apply → share for GPU initialization. Vendor-neutral, self-teaching hardware driver. No equivalent exists in any open-source project. |
| VFIO GPU backend (pure Rust) | Novel | BAR0 MMIO + DMA + bind/unbind for NVIDIA GPUs via VFIO in pure Rust. First userspace GPU driver in Rust. |
| NvPmu (nvidia-smi replacement) | Novel | GPU telemetry (temperature, power, clock) via sysfs/hwmon without proprietary nvidia-smi. Pure Rust. |
| PrecisionBrain | Novel | O(1) precision routing from hardware calibration. Domain-aware (Critical/Moderate/Throughput) to precision tier (F64/DF64/F32). Includes NVVM transcendental risk detection. |
| Cross-vendor GPU init recipes | Novel | InitRecipe format with GpuGen enum (Maxwell→Ampere), classify_register_for_gen(), RegisterAccess trait. |
| Sovereign dispatch pipeline | Novel | compute.dispatch.submit/status/result/forward JSON-RPC. Thermal gating. Multi-GPU parallel init. Cross-gate forwarding. |
| Science/gaming mode switching | Novel | ecoprimals-mode CLI to switch GPU between display driver and vfio-pci. Dual-use architecture. |
| Akida NPU driver (VFIO) | Novel | BrainChip Akida neuromorphic processor via VFIO in pure Rust. Only Rust NPU driver that exists. |
| DMA allocator with huge pages | Established | Standard pattern; integration with VFIO sovereign stack is the main angle. |
| Spring absorption pattern | Novel | Write→Absorb→Lean methodology. Springs evolve capabilities, toadStool absorbs proven patterns (PrecisionBrain, NvkZeroGuard, StreamingDispatch, etc.). |
~50 crates | 550,941 lines Rust | 20,262 tests | 83% coverage
BearDog Crypto Totals (locked into AGPL-3.0)
| Primitive | Count |
|---|---|
| Signature algorithms | 3 (Ed25519, ECDSA, RSA) |
| Key exchange | 2 (X25519, ECDHE) |
| AEAD ciphers | 3 (ChaCha20-Poly1305, AES-128-GCM, AES-256-GCM) |
| Hash functions | 5 (BLAKE3, SHA-256, SHA-384, SHA-512, SHA3-256) |
| KDFs | 4 (HKDF, TLS PRF, PBKDF2, Argon2id) |
| Password hashing | 3 (Argon2id, bcrypt, scrypt) |
| Protocols | 3 (TLS 1.3, Tor v3, BTSP) |
II. Compute Trio
coralReef — GPU Shader Compiler & Driver
| Capability | Type | Description |
|---|---|---|
| WGSL → native SASS compiler | Novel | Compiles WGSL directly to NVIDIA native ISA (SASS) in pure Rust. No CUDA, no PTXAS, no LLVM. No other AGPL shader compiler exists. |
| WGSL → native GFX ISA compiler | Novel | Compiles WGSL to AMD native ISA (GFX) in pure Rust. Multi-vendor native compilation from a single source language. |
| VFIO compute dispatch | Novel | Full ComputeDevice implementation via VFIO: BAR0 MMIO, DMA buffers, GPFIFO submission, GP_GET sync. Userspace GPU compute dispatch without any kernel GPU driver. |
| VFIO DMA subsystem | Novel | Page-aligned, mlock’d, IOMMU-mapped DMA buffers in pure Rust via rustix. No libc. |
| BAR0 sovereign GR init | Novel | Address-aware firmware split: high-address entries → BAR0 MMIO, low-address entries → FECS channel. Sovereign PGRAPH initialization. |
| UVM GPFIFO dispatch | Established | NVIDIA UVM (Unified Virtual Memory) dispatch. Uses proprietary nvidia-drm, but the Rust implementation wrapping it is sovereign. |
| DRM nouveau dispatch | Established | Linux DRM dispatch via nouveau UAPI. Standard kernel interface, sovereign Rust wrapper. |
| Three dispatch paths | Novel | Single codebase with DRM, UVM, and VFIO dispatch paths. Preference ordering (VFIO > DRM > UVM) with automatic fallback. No other project offers this. |
| QMD builder | Established | Queue Meta Data construction for NVIDIA compute dispatch. Reverse-engineered from public specs. |
GpuContext::from_vfio() | Novel | High-level API: BDF string → compiled shader → native dispatch on bare metal. One function call from application to GPU. |
122 WGSL files | 116,960 lines Rust | 1,704 tests
barraCuda — GPU Math Engine
| Capability | Type | Description |
|---|---|---|
| 806 WGSL scientific shaders | Novel | Largest AGPL-3.0 scientific shader library. Covers QCD, plasma physics, bioinformatics, pharmacology, Anderson localization, RHMC, neural networks, and more. |
| DF64 (double-float emulation) | Novel | Hardware-atheistic FP64 precision via f32×2 pairs in WGSL. Works on GPUs without native FP64. 30+ DF64 shaders. No other WGSL DF64 library exists. |
| RHMC (Rational HMC) | Novel | Remez exchange, multi-shift CG, rational approximations for lattice QCD fermion dynamics. Pure Rust + WGSL. |
| #![forbid(unsafe_code)] math engine | Novel | 291,543 lines of Rust + 64,737 lines of WGSL with zero unsafe. No other GPU math engine of this scale has this guarantee. |
| VFIO-primary architecture | Novel | VFIO is the designed primary dispatch path, wgpu is fallback. Inverts the normal relationship (vendor driver primary, alternative secondary). |
| GpuBackend trait | Established | Trait-based GPU abstraction. Pattern exists elsewhere; the sovereign dispatch integration is novel. |
| Precision tiers specification | Novel | F32/F64/F64Precise/DF64 tiers with per-shader, per-hardware routing. No other framework offers this granularity. |
806 WGSL shaders | 291,543 lines Rust | 64,737 lines WGSL | 3,415 tests
III. Phase 2 — Federation & Representation
biomeOS — Autonomous Federation Platform
| Capability | Type | Description |
|---|---|---|
| NUCLEUS atomic composition | Novel | Tower/Node/Nest/Full pre-composed atomic patterns. Chemical bonding model (Ionic/Covalent/Metallic/Weak) for distributed system composition. No other system uses chemical bonding metaphors for microservice topology. |
| Neural API (165+ translations) | Novel | Semantic capability routing. Primals compose by capability string, not by name or address. 13 domains, 165+ translations. No hardcoded primal references anywhere. |
| Plasmodium collective | Novel | Physarum polycephalum-inspired decentralized orchestration. HTTP JSON-RPC collective with dynamic join/leave. No central coordinator. Emergent routing. |
| Dark Forest beacon genetics | Novel | Zero-metadata discovery. Genetic lineage = decryption key. Privacy beyond Signal or Tor — metadata itself is invisible, not just encrypted. |
| Mitochondrial + Nuclear DNA model | Novel | Two-seed identity: beacon seed (mitochondrial, service discovery) + lineage seed (nuclear, trust chain). Distinct security semantics from biological analogy. |
| ContinuousExecutor graph engine | Novel | Fixed-timestep graph loops with feedback edges. 60Hz tick clock for game loops, 90Hz for surgical simulation. Graph-based continuous execution with domain-specific tick rates. |
| Surgical VR deployment graph | Novel | Anatomy + tissue physics + biosignals + pharmacokinetics composed as a single graph. Integrated medical simulation pipeline from primal composition. |
| Cross-spring ecology graphs | Novel | airSpring → wetSpring → neuralSpring pipeline defined in TOML. Domain-specific ecology where springs feed each other’s outputs. |
| genomeBin v3 deployment | Novel | Binary isomorphic format. Same binary, same behavior, any substrate. Deterministic deployment with genetic lineage tracking. |
| LifecycleManager auto-resurrection | Established | Health monitoring with auto-restart. Pattern known; sovereign Rust implementation with NUCLEUS integration. |
| 4-tier NAT traversal | Established | LAN/punch/coordinated/relay. Standard pattern; sovereign strategy with BearDog crypto. |
| Federation & sub-federation | Established | Hierarchical trust. Standard pattern; sovereign with genetic lineage gating. |
26 crates | 191,658 lines Rust | 3,670+ tests | 71.47% coverage | 0 unsafe
petalTongue — Universal Representation & UI
| Capability | Type | Description |
|---|---|---|
| UniBin five-mode rendering | Novel | Single binary renders to GUI (egui), TUI (ratatui), web (axum), headless, and status. ~84% size reduction vs separate binaries. No other UI framework offers five modalities from one binary. |
| Proprioception (SAME DAVE) | Novel | UI self-awareness of its own outputs and inputs. Diagnostic events. The UI knows what it is displaying and can reason about its own state. |
| Universal representation engine | Novel | One data model → terminal, SVG, PNG, egui, audio sonification, future VR. Modality-agnostic rendering from a single source of truth (DataService). |
| Human entropy capture | Novel | Multi-modal entropy from audio, visual, narrative, and gesture inputs. Fed to BearDog for cryptographic randomness. Human interaction as entropy source. |
| Discovery → performance split | Novel | biomeOS JSON-RPC for service discovery, tarpc for hot-path data. Automatic protocol upgrade from discovery to high-performance. |
| UIBackend trait system | Novel | Pluggable display backends (eframe, framebuffer, ToadStool GPU). Same rendering logic regardless of display technology. |
| DataService single source of truth | Novel | Event-driven broadcast to all modalities. One data model, broadcast updates, any renderer subscribes. |
| Graph sonification | Novel | Graph topology rendered as audio. Accessibility and multi-modal representation of network state. |
| egui/eframe GUI | Established | Immediate-mode GUI. Standard framework, sovereign integration. |
| ratatui TUI | Established | Terminal UI. Standard framework, sovereign integration. |
| axum web server | Established | HTTP/WebSocket. Standard framework, sovereign integration. |
19 crates | ~400+ tests | A+ grade (95/100) | AGPL-3.0
IV. Provenance Trio + Post-NUCLEUS Primals (Phase 2)
loamSpine — Permanent Ledger
| Capability | Type | Description |
|---|---|---|
| Loam certificates with lending | Novel | Sovereign lendable certificates with LoanTerms (duration, grace, auto_return). CertificateManager.process_expired_loans() auto-reverts. Full provenance via MintInfo, CertificateLocation, OwnershipRecord. No blockchain required. |
| Waypoint spines | Novel | Local permanence for borrowed state without upward propagation. Waypoint-only entry types (SliceAnchor, SliceOperation, SliceDeparture). Borrowed data stays locally permanent without polluting the origin spine. |
| Infant Discovery pattern | Novel | Zero-config startup. Five-tier discovery: env vars → DNS-SRV → service registry HTTP → mDNS → dev fallback. Capability-based (“Who can sign?”) not name-based (“Where is BearDog?”). |
| Temporal Moments | Novel | Domain-agnostic time with Moment, MomentContext (CodeChange, ArtCreation, LifeEvent), and four anchor types (Crypto, Atomic, Causal, Consensus). Timestamps mean different things in different contexts. |
| 15 entry types | Novel | Genesis, SessionCommit, SliceCheckout/Return, DataAnchor, BraidCommit, CertificateMint/Transfer/Loan/Return, SliceAnchor/Operation/Departure, TemporalMoment, Custom. Richer than any append-only ledger. |
permanent-storage.* wire compat | Novel | rhizoCrypt dehydration commits arrive via JSON-RPC permanent-storage.commitSession — loamSpine speaks rhizoCrypt’s wire format natively. |
| Hash-linked spine chain | Established | BLAKE3, append-only, signed entries. Standard pattern; sovereign with Sled pure Rust backend. |
| Inclusion/Certificate/Provenance proofs | Established | Path-to-tip proofs, mint+transfer chains, custody chains. Standard crypto proofs; sovereign. |
3 crates | 549 tests | ~90% coverage | #![forbid(unsafe_code)] | AGPL-3.0
rhizoCrypt — Ephemeral Working Memory
| Capability | Type | Description |
|---|---|---|
| Six slice modes | Novel | Copy (no lineage), Loan (auto-return on expiry), Consignment (possession without ownership, auction semantics), Escrow (multi-party confirmation), Waypoint (local spine anchoring), Transfer (full ownership). Each has distinct resolution routes. No other content-addressed storage offers this. |
| Rhizo-Loam layering | Novel | Ephemeral DAG ( rhizoCrypt) over permanent linear spine ( loamSpine). Working memory crystallizes into permanent record via dehydration. Biological metaphor: root network feeding into trunk. |
| Philosophy of forgetting | Novel | Ephemeral by default; persistent only by consent. Sessions expire. Data that isn’t dehydrated is garbage collected. Anti-pattern to “store everything forever.” |
| Conditional resolution routing | Novel | Five resolution routes: ReturnToOrigin, CommitToOrigin, RouteToSpine, WaypointReturn, Conditional. Outcome-based and event-based routing of slice resolution. |
| Dehydration protocol | Novel | Freeze → Merkle root (topological sort) → summary → resolve slices → collect attestations → commit to loamSpine. Multi-step crystallization of ephemeral state into permanent record. |
| Session lifecycle state machine | Novel | `Active → Paused |
| BLAKE3 content-addressed DAG | Established | Vertex = BLAKE3(canonical CBOR). Multi-parent DAG. Standard content-addressing; sovereign with deterministic CBOR encoding. |
| Merkle tree with proofs | Established | Binary Merkle over topological vertex order. Standard construction; sovereign implementation. |
3 crates | 491 tests | 3 fuzz targets | #![forbid(unsafe_code)] | AGPL-3.0
sweetGrass — Attribution & Provenance
| Capability | Type | Description |
|---|---|---|
| Braid attribution with decay | Novel | 12 configurable agent roles with weights (Creator 0.40, Contributor 0.25, Transformer 0.20, Curator 0.10, Publisher 0.05). Inheritance decay 0.5^depth across derivation chains. calculate_rewards() maps shares to value. No blockchain. |
| 0/1/Many compression | Novel | Session analysis → Discard/Single/Multiple strategy. Meta-Braids summarize Braid collections. DAG compression with configurable outcomes. |
| Inter-primal contribution API | Novel | ContributionRecord and SessionContribution for any primal to report work. sweetgrass.recordContribution JSON-RPC. Domain metadata keys for chemistry, ML, games. Any primal can attribute. |
| Niche-configurable semantics | Novel | Same codebase adapts attribution behavior per biomeOS niche: Distributed Science, Gaming, Audit Trail. Context-dependent provenance. |
| GDPR-inspired data rights | Novel | Five data subject requests (Access, Rectification, Erasure, Portability, Objection). Consent tracking (Explicit, Implicit, Withdrawn). Five retention policies. Five privacy levels. Applied to scientific provenance — not just personal data. |
| Domain metadata keys | Novel | Well-known keys for chemistry (CHEMISTRY_*), ML (ML_*), games (GAME_*). Extensible attribution vocabulary for scientific domains. |
| W3C PROV-O export | Established | Entity, Activity, Agent → JSON-LD with @context/@graph. prov, xsd, rdfs, schema, ecop namespaces. Standard ontology; sovereign with ecoPrimals extensions. |
| Multi-backend storage | Established | Memory, PostgreSQL (with migrations), Sled (pure Rust). Standard pluggable storage. |
9 crates | 553 tests | 3 fuzz targets | proptest | #![forbid(unsafe_code)] | AGPL-3.0
skunkBat — Defensive Security
| Capability | Type | Description |
|---|---|---|
| Metadata-only threat detection | Novel | Detects threats from packet metadata without content inspection. Privacy-preserving by design. |
| User authority principle | Novel | No autonomous blocking. Graduated response (Monitor → Alert → Block) with human approval required for escalation. |
7,366 lines Rust | 48 tests | 2 crates
V. Springs — Scientific Validation Layer
hotSpring — Computational Physics Reproduction
| Capability | Type | Description |
|---|---|---|
| DF64 hybrid precision (9.9× native f64) | Novel | 3.24 TFLOPS at 14-digit precision on consumer FP32 cores. f32×2 double-float emulation exceeding native f64 throughput. No other GPU physics framework offers this. |
| NPU physics pipeline | Novel | MD → ESN → AKD1000 NPU → transport coefficients at 9,017× less energy. First neuromorphic silicon in a physics pipeline. |
| Lattice QCD phase detection without FFT | Novel | NPU phase classification from position-space observables. Bypasses Fourier transform entirely. |
| 10 NPU SDK assumptions overturned | Novel | Documented in BEYOND_SDK.md. Proved vendor assumptions wrong about their own hardware. |
| Heterogeneous real-time HMC monitor | Novel | Live phase detection with 0.09% overhead, predictive steering. |
| Backend-agnostic MD engine | Novel | MdEngine<B: GpuBackend> — same physics, any dispatch path (wgpu, VFIO, DRM). |
| Dense plasma MD (Sarkas) | Established | 9/9 DSF cases, 0.000% drift. Yukawa OCP. Sovereign Rust implementation. |
| Nuclear EOS (SEMF+HFB) | Established | L1 χ²=2.27 (478× faster than Python). AME2020 validated. |
| Green-Kubo transport | Established | D*/η*/λ* from Stanton-Murillo 2016. 13/13 validated. |
| Pure gauge SU(3) lattice QCD | Established | Wilson action, HMC, gradient flow. 12/12 validated. |
| Anderson localization (1D/2D/3D) | Established | Kachkovskiy spectral theory. 31/31 validated. |
| Abelian Higgs model | Established | Bazavov 2015. 17/17, 143× faster than Python. |
| Chuna dielectric/BGK | Established | Gradient flow, Mermin dielectric, kinetic-fluid. 44/44 validated. |
2 crates | 86 WGSL shaders | 848 lib tests + 115 validation binaries | 25+ papers reproduced | 10 scientific domains
neuralSpring — Learning Layer
| Capability | Type | Description |
|---|---|---|
| Nautilus Shell bridge | Novel | Feed-forward evolutionary reservoir replacing recurrent ESN. Board populations instead of temporal feedback. Cross-spring integration with hotSpring brain architecture. |
| baseCamp biophysical AI | Novel | Weight matrices as disordered Hamiltonians, information flow as wave propagation, loss landscapes as energy landscapes, neural networks as PGMs, multi-agent AI as quorum sensing. 5 sub-theses, 128/128 validation. |
| Cross-spring spectral rewire | Novel | hotSpring diagnostics (bandwidth, condition number, phase) absorbed into WeightSpectralResult. GPU ESN via BarraCuda tensors. 41/41 validated. |
| WDM ESN regime classifier | Novel | GPU echo state network for warm dense matter regime classification. 96.5% accuracy. |
| Isomorphic primitive catalog | Novel | Maps shared ML primitives across 8+ domains to BarraCuda ops. Same MatMul/Attention/LayerNorm serves protein, language, physics, spectral, evolution. |
| helixVision protein structure | Novel | Sovereign AlphaFold2/3-style structure prediction (Evoformer, Pairformer, diffusion, IPA) in pure Rust + WGSL. |
| ESN (Jaeger) | Established | CPU + GPU reservoir computing. Sovereign implementation. |
| HMM forward/backward/Viterbi | Established | Liu et al. phylogenetics. GPU-accelerated. |
| Anderson localization (spectral) | Established | Bourgain-Kachkovskiy. Shared with hotSpring. |
| Replicator dynamics / game theory | Established | Bruger-Waters QS cooperation. GPU spatial payoff. |
| PINN / DeepONet | Established | Raissi 2019, Lu 2021. Sovereign implementations. |
| LeNet-5, MLP, LSTM, Transformer | Established | Standard architectures, sovereign GPU implementations. |
2 crates | 43 WGSL shaders | 753 lib tests + 220 validation binaries | 3,900+ validation checks | 25 papers reproduced
wetSpring — Life Sciences
| Capability | Type | Description |
|---|---|---|
| Anderson-QS coupling | Novel | Anderson localization applied to quorum sensing: population heterogeneity as disorder, W_c ≈ 16.5 in 3D, geometry-dependent QS activation. New theoretical connection. |
| 3D Anderson dimensional phase diagram | Novel | 1D→2D→3D sweep with plateau points 0/5/12. J_c(3D) ≈ 1.28 vs J_c(2D) ≈ 0.56. 28-biome global atlas mapping geometry to QS regime. |
| QS-disorder prediction from diversity | Novel | Real ecosystem diversity profiles → Anderson regime prediction. Connects microbial ecology to condensed matter physics. |
| NPU reservoir deployment (biology) | Novel | ESN → int8 quantization → AKD1000: QS phase classifier, phylogenetic placement, genome binning, spectral triage, bloom sentinel. |
| Nanopore signal bridge | Novel | Sovereign POD5/NRS parsing without ONT SDK. Synthetic community reads, int8 quantization for NPU. |
| Pure GPU streaming pipeline | Novel | Multi-stage bio pipeline with zero CPU round-trips. 441–837× speedup vs round-trip architecture. |
| 16S rRNA pipeline (DADA2) | Established | FASTQ QC, denoising, chimera, taxonomy, UniFrac, diversity. Sovereign Rust replacing QIIME2. |
| Phylogenetics suite | Established | Felsenstein pruning, NJ, bootstrap, Robinson-Foulds, DTL reconciliation, HMM. |
| Population genomics | Established | ANI, SNP calling, dN/dS, molecular clock, pangenome. |
| LC-MS / PFAS screening | Established | mzML parsing, EIC, peak detection, KMD, spectral matching. Sovereign Rust replacing pyOpenMS. |
| Drug repurposing (NMF, TransE) | Established | Pathway scoring, knowledge graph embedding. Sovereign Rust. |
| Quorum sensing ODE systems | Established | Waters, bistable, cooperation, phage defense. Sovereign Gillespie SSA. |
3 crates | 0 local shaders (79 ToadStool primitives consumed) | 1,073 Rust tests + 5,061 validation checks | 52 papers reproduced | 6 scientific tracks
airSpring — Ecological Validation
| Capability | Type | Description |
|---|---|---|
| Pure Rust FAO-56 pipeline | Novel | Complete Penman-Monteith ET₀, water balance, Kc adjustment in Rust without scipy. Only AGPL implementation of FAO-56. |
| GPU bridge for agricultural science | Novel | BatchedEt0, KrigingInterpolator, SeasonalReducer dispatched to GPU via BarraCuda. No other agricultural framework uses GPU compute. |
| Real-data cross-validation (918 station-days) | Novel | R²=0.967 against Open-Meteo across 918 station-days. 3 API sources (Open-Meteo, NOAA CDO, OpenWeatherMap). |
| SoilWatch 10 calibration | Novel | Topp equation + correction curves for commercial soil sensors. Pure Rust signal processing. |
| FAO-56 Penman-Monteith | Established | Allen et al. 1998. Standard method, sovereign implementation. |
| Ordinary kriging | Established | Spatial interpolation. Uses BarraCuda KrigingF64. |
| Soil moisture modeling | Established | Topp equation, dielectric permittivity → VWC. |
1 crate | 0 local shaders | ~162 Rust tests + 119 validation checks | 65/65 Python↔Rust cross-validated | 3 papers reproduced
groundSpring — Reality Layer (Measurement & Uncertainty)
| Capability | Type | Description |
|---|---|---|
| Cross-domain noise framework | Novel | Unified bias-variance decomposition across agriculture, meteorology, microbiology, and seismology. Same uncertainty budget methodology applied to every spring’s measurements. |
| Uncertainty budget for springs | Novel | Provides measurement error labels that neuralSpring uses for robust training. Every spring’s “ground truth” passes through groundSpring’s uncertainty quantification. |
| Literature extension roadmap | Novel | Connects Bazavov (lattice QCD), Waters (QS), Liu (phylogenetics), Kachkovskiy (spectral) published research to measurement uncertainty. |
| Monte Carlo error propagation | Established | Standard MC uncertainty. Sovereign Python implementation. |
| Seismic travel-time inversion | Established | 1D inversion with Nelder-Mead. Standard geophysics. |
| Multinomial rarefaction | Established | Standard microbial ecology. |
0 Rust crates (Phase 0 Python) | 71 validation checks | 5 experiments | Cross-domain synthesis
VI. Summary: Novel Prior Art (New to Technology)
These capabilities exist NOWHERE else in open source:
Infrastructure, Systems & Provenance (1–27)
| # | Innovation | Primal | Why It’s Novel |
|---|---|---|---|
| 1 | Userspace GPU driver in Rust via VFIO | coralReef + toadStool | Nobody has built a GPU compute driver in userspace Rust. DPDK did this for NICs. |
| 2 | WGSL → native GPU ISA compiler (AGPL) | coralReef | No AGPL shader compiler exists. The only ones are in Mesa (MIT) and NVIDIA (proprietary). |
| 3 | Self-teaching GPU hardware learning | toadStool hw-learn | Observe → distill → apply → share. GPUs teach each other initialization sequences. |
| 4 | Hardware-atheistic DF64 precision | barraCuda | FP64 precision on any GPU via f32×2, with per-shader precision routing. |
| 5 | 806 scientific WGSL shaders (AGPL) | barraCuda | Largest open scientific shader library under copyleft. |
| 6 | PrecisionBrain routing | toadStool | Domain-aware precision selection with NVVM transcendental risk detection. |
| 7 | Pure Rust Tor stack (AGPL) | songBird | Only AGPL-3.0 Tor implementation. Full directory/circuit/stream/onion. |
| 8 | Tower Atomic crypto delegation | bearDog + songBird | Network layer has zero crypto state. All delegated via IPC. |
| 9 | Genetic lineage identity | bearDog + biomeOS | Cryptographic device ancestry modeled on biology (mitochondrial + nuclear). |
| 10 | Dark Forest discovery | bearDog + songBird | Zero-metadata service advertisement. Discoverable but private. |
| 11 | Neural API (165+ translations) | biomeOS | Semantic capability composition. Primals compose by capability, not name. |
| 12 | Plasmodium orchestration | biomeOS | Slime-mold-inspired decentralized coordination without central authority. |
| 13 | Six-mode content slicing | rhizoCrypt | Copy/Loan/Consignment/Escrow/Waypoint/Transfer with distinct resolution routes. |
| 14 | Rhizo-Loam ephemeral→permanent layering | rhizoCrypt + loamSpine | Working memory crystallizes into permanent record via dehydration protocol. |
| 15 | Philosophy of forgetting | rhizoCrypt | Ephemeral by default, persistent by consent. Anti-“store everything forever.” |
| 16 | Braid attribution with inheritance decay | sweetGrass | 12 roles, configurable weights, 0.5^depth decay, calculate_rewards(). No blockchain. |
| 17 | 0/1/Many compression | sweetGrass | Session→Discard/Single/Multiple. Meta-Braids. DAG compression. |
| 18 | Inter-primal contribution API | sweetGrass | Any primal reports work via ContributionRecord. Domain metadata keys. |
| 19 | Loam certificates with auto-reversion | loamSpine | LoanTerms, process_expired_loans(), full provenance chain. No blockchain. |
| 20 | Waypoint spines | loamSpine | Local permanence for borrowed state without upward propagation. |
| 21 | Temporal Moments (4 anchor types) | loamSpine | Domain-agnostic time: Crypto, Atomic, Causal, Consensus anchors. |
| 22 | Infant Discovery (5-tier) | loamSpine | env → DNS-SRV → registry → mDNS → fallback. Capability-based. |
| 23 | GDPR data rights on scientific provenance | sweetGrass | Access/Rectification/Erasure/Portability/Objection applied to compute provenance. |
| 24 | Metadata-only threat detection | skunkBat | Privacy-preserving security: detects threats without reading content. |
| 25 | Isomorphic IPC (single binary) | nestGate | Platform-adaptive transport selection at runtime. |
| 26 | NPU driver in pure Rust (VFIO) | toadStool | Only Rust driver for BrainChip Akida neuromorphic processor. |
| 27 | Spring absorption methodology | toadStool | Write→Absorb→Lean: springs evolve capabilities, primals absorb proven patterns. |
Platform & Representation (28–36)
| # | Innovation | Primal | Why It’s Novel |
|---|---|---|---|
| 28 | NUCLEUS chemical bonding model | biomeOS | Ionic/Covalent/Metallic/Weak bonds for distributed system composition. |
| 29 | ContinuousExecutor graph engine | biomeOS | Fixed-timestep graph loops with feedback edges. 60Hz game, 90Hz surgical. |
| 30 | UniBin five-mode rendering | petalTongue | Single binary → GUI, TUI, web, headless, status. One binary, five modalities. |
| 31 | Proprioception (SAME DAVE) | petalTongue | UI self-awareness. The interface knows what it is displaying. |
| 32 | Human entropy capture | petalTongue | Multi-modal entropy (audio, visual, narrative, gesture) fed to BearDog. |
| 33 | Graph sonification | petalTongue | Network topology rendered as audio. Accessibility + multi-modal representation. |
| 34 | DataService universal broadcast | petalTongue | One data model, event-driven broadcast to any renderer modality. |
| 35 | Cross-spring ecology graphs | biomeOS | Domain-specific spring composition in TOML. Springs feed each other. |
| 36 | genomeBin v3 deployment | biomeOS | Binary isomorphic format with genetic lineage tracking. |
Scientific & Domain (37–52)
| # | Innovation | Spring | Why It’s Novel |
|---|---|---|---|
| 37 | NPU physics pipeline (9,017× less energy) | hotSpring | First neuromorphic silicon in lattice QCD / plasma physics pipeline. |
| 38 | Lattice QCD phase detection without FFT | hotSpring | NPU phase classification from position-space observables. Bypasses Fourier transform. |
| 39 | 10 NPU SDK assumptions overturned | hotSpring | Proved vendor wrong about their own hardware. Documented. |
| 40 | Heterogeneous real-time HMC monitor | hotSpring | Live phase detection at 0.09% overhead with predictive steering. |
| 41 | Backend-agnostic MD engine | hotSpring | MdEngine<B: GpuBackend> — same physics, any dispatch (wgpu, VFIO, DRM). |
| 42 | Nautilus Shell bridge | neuralSpring | Feed-forward evolutionary reservoir replacing recurrent ESN. |
| 43 | baseCamp biophysical AI (5 sub-theses) | neuralSpring | Weight matrices as Hamiltonians, loss as energy, NN as PGM, multi-agent as QS. 128/128 validated. |
| 44 | Cross-spring spectral rewire | neuralSpring | hotSpring diagnostics absorbed into neural weight analysis. 41/41 validated. |
| 45 | WDM ESN regime classifier | neuralSpring | GPU echo state network for warm dense matter. 96.5% accuracy. |
| 46 | Anderson-QS coupling | wetSpring | Anderson localization applied to quorum sensing. W_c ≈ 16.5, geometry-dependent. New theoretical connection. |
| 47 | 3D Anderson dimensional phase diagram | wetSpring | 1D→2D→3D sweep. 28-biome global atlas mapping geometry to QS regime. |
| 48 | Pure GPU streaming bio pipeline | wetSpring | Zero CPU round-trips. 441–837× speedup. |
| 49 | Nanopore signal bridge (no ONT SDK) | wetSpring | Sovereign POD5/NRS parsing. Only open-source nanopore reader in Rust. |
| 50 | GPU agricultural science | airSpring | BatchedEt0, KrigingInterpolator, SeasonalReducer on GPU. No other ag framework uses GPU. |
| 51 | Cross-domain noise framework | groundSpring | Unified bias-variance across agriculture, meteorology, microbiology, seismology. |
| 52 | Constrained evolution methodology | ecosystem | AI as mutation operator, Rust as natural selection, physics as fitness. 69K invocations, 51B tokens. |
VII. Established Prior Art (Sovereign Implementations)
These techniques exist elsewhere but are locked into AGPL-3.0 sovereign implementations that cannot be captured:
Systems & Infrastructure
| Domain | What’s Locked | Why It Matters |
|---|---|---|
| Cryptography | Ed25519, X25519, AES-GCM, ChaCha20, BLAKE3, HKDF, Argon2 | Pure Rust crypto outside ring/rustls permissive ecosystem |
| TLS 1.3 | Full handshake + record layer | Sovereign TLS not dependent on OpenSSL or ring |
| GPU compute | DRM, UVM dispatch in pure Rust | Sovereign wrappers around Linux GPU subsystems |
| Storage | Content-addressed DAG, Merkle trees | Sovereign storage not dependent on IPFS |
| Networking | QUIC, STUN, IGD, mDNS | Sovereign networking stack |
| AI coordination | MCP, inference routing | Sovereign AI orchestration |
Scientific Reproductions (~100+ papers across all springs)
| Domain | Papers | Algorithms Locked | Source |
|---|---|---|---|
| Dense plasma physics | 5+ | Yukawa OCP MD, Green-Kubo transport, TTM | hotSpring |
| Nuclear physics | 2+ | SEMF, HFB, AME2020 EOS | hotSpring |
| Lattice gauge theory | 6+ | SU(3) Wilson, HMC, gradient flow, staggered Dirac, CG | hotSpring |
| Spectral theory | 9+ | Anderson 1D/2D/3D, Hofstadter, Aubry-Andre, Lanczos | hotSpring + neuralSpring |
| Abelian Higgs | 1 | U(1)+Higgs HMC | hotSpring |
| Dielectric response | 3+ | BGK, Mermin, kinetic-fluid | hotSpring |
| Neural architectures | 10+ | ESN, HMM, PINN, DeepONet, LeNet-5, MLP, LSTM, Transformer | neuralSpring |
| Evolutionary computation | 5 | Counterdiabatic, MODES, lexicase, swarm | neuralSpring |
| Phylogenetics | 5+ | HMM, SATe, NJ, Felsenstein, DTL, bootstrap | neuralSpring + wetSpring |
| Game theory / QS | 3+ | Replicator dynamics, Hill regulatory, cooperation | neuralSpring + wetSpring |
| Population genetics | 2+ | FST, Mantel, pangenome, molecular clock | neuralSpring + wetSpring |
| Protein structure | 1 | AlphaFold2/3 (Evoformer, Pairformer, diffusion) | neuralSpring ( helixVision) |
| 16S rRNA microbial ecology | 10 | DADA2, chimera, taxonomy, UniFrac, diversity | wetSpring |
| Deep-sea metagenomics | 6 | ANI, SNP, dN/dS, pangenomics, rare biosphere | wetSpring |
| Analytical chemistry / PFAS | 4 | mzML, EIC, peak detection, KMD, spectral matching | wetSpring |
| Drug repurposing | 5 | NMF, TransE, pathway scoring | wetSpring |
| Quorum sensing | 6+ | Waters ODE, bistable, cooperation, phage defense, Gillespie | wetSpring |
| Soil Anderson / tillage | 9 | Anderson localization in soil pore geometry | wetSpring |
| Evapotranspiration | 3 | FAO-56 PM, Hargreaves, water balance | airSpring |
| Soil science | 2 | Topp equation, SoilWatch calibration | airSpring |
| Measurement uncertainty | 5 | Monte Carlo propagation, bias-variance, seismic inversion | groundSpring |
Validation Infrastructure (sovereign)
| Metric | Value |
|---|---|
| Total Rust tests (all springs) | ~3,000+ |
| Total validation checks | ~10,000+ |
| Python baselines cross-validated | ~500+ |
| Papers reproduced | ~100+ |
| Scientific domains | 10+ |
| Named tolerance constants | ~240 ( hotSpring ~150 + wetSpring ~92) |
| Three-tier methodology | Python baseline → Rust CPU → Rust GPU |
VIII. The Lock
Every line of code in this catalog is:
- Published on GitHub under AGPL-3.0
- Timestamped via git commit history
- Reproducible via Cargo.lock → deterministic binary
- Permanent — copyright lasts life + 70 years; AGPL is irrevocable on published versions
A corporation can:
- ✅ Use this code (AGPL allows all use)
- ✅ Modify this code (AGPL allows modification)
- ❌ Close modifications (AGPL requires sharing back)
- ❌ Offer as proprietary service (AGPL network service clause)
- ❌ Claim independent invention (timestamped prior art)
- ❌ Patent covered techniques (prior art defense)
A human can:
- ✅ Use, study, modify, share — forever
- ✅ Build on it, improve it, extend it
- ✅ Receive attribution ( sweetGrass)
- ✅ Benefit from the commons as the commons benefits from them
Sovereign science. Sovereign code. Free for humans. Fiction-proof.
Catalog compiled March 13, 2026. Updated as primals evolve. The prior art grows with every commit. The commons only expands.