/- Copyright (c) 2026 Sovereign Research Stack. All rights reserved. Released under Apache 2.0 license as described in the file LICENSE. Authors: Research Stack Team SyntheticGeneticCoding.lean — 0D(n) Symbol-Coding Objects for GCL Surfaces This module treats all coding systems as purely information-theoretic 0D(n) discrete objects: finite-length strings over finite alphabets. These objects happen to borrow symbol-sets from coding techniques that nature has been stress-testing for ~4.6 billion years. The biology is completely ignored. Only information capacity, channel efficiency, redundancy profiles, and compression bounds matter. TYPE SYSTEM (Three-Layer Doctrine): 1. CodingQ — Canonical normalized coding atom. Type = Q0_64. Range: [-1, 1). Resolution: 2^-63. Used for ALL coding-space values. Properties: normalized, bounded, deterministic, fixed-point, comparable. 2. BioParamQ — Physical-ish fixed-point parameter, NOT a coding atom. Type = Q16_16. Range: [-32768, 32767]. Resolution: 2^-16. Used for raw source measurements: dimensions, charge, rigidity, temperature. These values are >1, dimensioned, or negative — cannot be raw Q0_64. 3. BioCodingProjection — A normalized biological parameter projected into coding space. Contains: optional raw BioParamQ + normalized CodingQ + scaleReceipt. The projection map must be explicit and receipted. WARDEN RULES: - If field is marked coding_atom: type must be Q0_64. - If field is raw physical/geometric/thermodynamic: type must not pretend to be Q0_64 unless a normalization scale is declared. - If Q0_64 value was produced from a raw parameter: require scale_receipt. - If any canonical constructor uses Float: block promotion. No float in canonical coding. Decimal constants enter as rational literals or pre-scaled integers via ofRatio. Per AGENTS.md §1.4: Q0_64 fixed-point for maximum precision dimensionless. Per AGENTS.md §1.5: No float in canonical hot-path code. Per AGENTS.md §2: PascalCase types, camelCase functions. Per AGENTS.md §4: Every def has #eval witness or theorem. -/ import Mathlib.Data.Nat.Basic import Mathlib.Data.Real.Basic import Semantics.FixedPoint namespace Semantics.SyntheticGeneticCoding open Semantics.Q16_16.Q0_64 open Semantics.Q16_16 -- ═══════════════════════════════════════════════════════════════════════════ -- §1 THREE-LAYER TYPE SYSTEM (CodingQ / BioParamQ / BioCodingProjection) -- ═══════════════════════════════════════════════════════════════════════════ /-- Canonical normalized coding atom. Range [-1, 1). All coding values. -/ structure CodingQ where value : Q0_64 deriving Repr, Inhabited, BEq, DecidableEq /-- Physical-ish fixed-point parameter. NOT a coding atom. Used for source-side measurements: dimensions, charge, rigidity, etc. -/ structure BioParamQ where value : Q16_16 deriving Repr, Inhabited, BEq, DecidableEq /-- A normalized biological parameter projected into coding space. The projection map (raw → normalized) must be explicit and receipted. -/ structure BioCodingProjection where raw? : Option BioParamQ -- Optional source measurement normalized : CodingQ -- Projected value in Q0_64 scaleReceipt : String -- Provenance of normalization map deriving Repr, Inhabited -- ═══════════════════════════════════════════════════════════════════════════ -- §2 PROJECTION FUNCTIONS (Source → Coding) -- ═══════════════════════════════════════════════════════════════════════════ /-- Direct rational projection: num/den → CodingQ with receipt. No Float used. Receipt documents the normalization provenance. -/ def projectRatioToCodingQ (num : Nat) (den : Nat) (receipt : String) : BioCodingProjection := { raw? := none, normalized := CodingQ.mk (Q0_64.ofRatio num den), scaleReceipt := receipt } -- ═══════════════════════════════════════════════════════════════════════════ -- §3 ALPHABET TYPE HIERARCHY (Pure Symbol Sets) -- ═══════════════════════════════════════════════════════════════════════════ /-- Standard 4-symbol alphabet -/ inductive StandardAlphabet4 where | A | C | G | T deriving BEq, DecidableEq, Repr, Inhabited /-- Expanded 8-symbol alphabet -/ inductive Alphabet8 where | A | C | G | T | P | Z | B | S deriving BEq, DecidableEq, Repr, Inhabited /-- Encoding family identifier (pure channel type, no biology) -/ inductive EncodingFamily where | fourSymbolBlock -- 4-symbol block codes | eightSymbolBlock -- 8-symbol block codes | sixteenSymbolBlock -- 16-symbol block codes | binaryBlock -- 2-symbol binary codes | custom : Nat → EncodingFamily -- N-symbol custom alphabet deriving BEq, DecidableEq, Repr, Inhabited /-- Base pairing constraint (structural compatibility, not chemistry) -/ inductive PairConstraint where | strictComplement -- Must pair A↔T, C↔G style | fourWay -- 4 orthogonal pairs (8-symbol) | unrestricted -- Any symbol can follow any symbol deriving BEq, DecidableEq, Repr -- ═══════════════════════════════════════════════════════════════════════════ -- §4 CODE SPACE (Information Theory) -- ═══════════════════════════════════════════════════════════════════════════ /-- Block code configuration: alphabet size and block length -/ structure BlockCodeConfig where alphabetSize : Nat blockLength : Nat proofPositive : alphabetSize > 0 ∧ blockLength > 0 deriving Repr /-- Number of possible codewords = |A|^L -/ def codeSpaceSize (alphabetSize : Nat) (blockLength : Nat) : Nat := alphabetSize ^ blockLength /-- Standard 4^3 = 64 codewords -/ def code64 : Nat := codeSpaceSize 4 3 /-- Expanded 8^3 = 512 codewords -/ def code512 : Nat := codeSpaceSize 8 3 /-- Quadruplet 4^4 = 256 codewords -/ def code256 : Nat := codeSpaceSize 4 4 /-- Binary 2^8 = 256 bytes -/ def codeByte : Nat := codeSpaceSize 2 8 /-- Normalized information capacity per symbol = log2(N) / 8 For comparison across alphabet sizes, normalized to [0, 1] in CodingQ. Uses pre-computed rational values — NO FLOAT in canonical code. With max alphabet = 256 (byte), log2(256) = 8 bits: - 2-symbol: log2(2)/8 = 1/8 = 0.125 - 4-symbol: log2(4)/8 = 2/8 = 0.25 - 8-symbol: log2(8)/8 = 3/8 = 0.375 - 16-symbol: log2(16)/8 = 4/8 = 0.5 - 256-symbol: log2(256)/8 = 8/8 = 1.0 All results as CodingQ (Q0_64). -/ def normalizedCapacity (alphabetSize : Nat) : CodingQ := match alphabetSize with | 0 => CodingQ.mk zero | 1 => CodingQ.mk zero -- log2(1) = 0 | 2 => CodingQ.mk (Q0_64.ofRatio 1 8) -- 0.125 | 4 => CodingQ.mk (Q0_64.ofRatio 2 8) -- 0.25 | 8 => CodingQ.mk (Q0_64.ofRatio 3 8) -- 0.375 | 16 => CodingQ.mk (Q0_64.ofRatio 4 8) -- 0.5 | 32 => CodingQ.mk (Q0_64.ofRatio 5 8) -- 0.625 | 64 => CodingQ.mk (Q0_64.ofRatio 6 8) -- 0.75 | 128 => CodingQ.mk (Q0_64.ofRatio 7 8) -- 0.875 | 256 => CodingQ.mk one -- 1.0 | _ => CodingQ.mk (Q0_64.ofRatio 1 8) -- default: conservative 2-symbol /-- 4-symbol normalized capacity = 0.25 -/ def cap4 : CodingQ := normalizedCapacity 4 /-- 8-symbol normalized capacity = 0.375 -/ def cap8 : CodingQ := normalizedCapacity 8 /-- 2-symbol normalized capacity = 0.125 -/ def cap2 : CodingQ := normalizedCapacity 2 /-- 16-symbol normalized capacity = 0.5 -/ def cap16 : CodingQ := normalizedCapacity 16 -- ═══════════════════════════════════════════════════════════════════════════ -- §5 CHANNEL PARAMETERS (Noise/Constraint Model — All CodingQ) -- ═══════════════════════════════════════════════════════════════════════════ /-- Channel noise parameters for a given encoding family. ALL values are CodingQ (Q0_64) normalized dimensionless quantities [0, 1). No biological meaning — purely information-theoretic channel properties. -/ structure ChannelParameters where encodingFamily : EncodingFamily -- Symbol reliability: probability of correct transmission per symbol symbolReliability : CodingQ -- Pairing constraint strictness: 0 = no pairing, 1 = strict complement pairConstraintStrength : CodingQ -- Sequence stability: resistance to random mutation/insertion/deletion stabilityScore : CodingQ -- Copy fidelity: accuracy of replication/transcription equivalent copyFidelity : CodingQ -- Decoding efficiency: fraction of codewords usable (accounting for degeneracy) decodingEfficiency : CodingQ deriving Repr, Inhabited /-- High-stability channel -/ def highStabilityChannel : ChannelParameters := { encodingFamily := EncodingFamily.fourSymbolBlock, symbolReliability := CodingQ.mk (Q0_64.ofRatio 999 1000), -- 0.999 pairConstraintStrength := CodingQ.mk (Q0_64.ofRatio 95 100), -- 0.95 stabilityScore := CodingQ.mk (Q0_64.ofRatio 99 100), -- 0.99 copyFidelity := CodingQ.mk (Q0_64.ofRatio 999 1000), -- 0.999 decodingEfficiency := CodingQ.mk (Q0_64.ofRatio 95 100) -- 0.95 } /-- Flexible channel -/ def flexibleChannel : ChannelParameters := { encodingFamily := EncodingFamily.fourSymbolBlock, symbolReliability := CodingQ.mk (Q0_64.ofRatio 85 100), -- 0.85 pairConstraintStrength := CodingQ.mk (Q0_64.ofRatio 30 100), -- 0.30 stabilityScore := CodingQ.mk (Q0_64.ofRatio 70 100), -- 0.70 copyFidelity := CodingQ.mk (Q0_64.ofRatio 85 100), -- 0.85 decodingEfficiency := CodingQ.mk (Q0_64.ofRatio 90 100) -- 0.90 } /-- Neutral channel -/ def neutralChannel : ChannelParameters := { encodingFamily := EncodingFamily.fourSymbolBlock, symbolReliability := CodingQ.mk (Q0_64.ofRatio 90 100), -- 0.90 pairConstraintStrength := CodingQ.mk (Q0_64.ofRatio 50 100), -- 0.50 stabilityScore := CodingQ.mk (Q0_64.ofRatio 99 100), -- 0.99 copyFidelity := CodingQ.mk (Q0_64.ofRatio 95 100), -- 0.95 decodingEfficiency := CodingQ.mk (Q0_64.ofRatio 85 100) -- 0.85 } -- ═══════════════════════════════════════════════════════════════════════════ -- §6 CODE EXPANSION (Block Length Extension) -- ═══════════════════════════════════════════════════════════════════════════ /-- Non-standard symbol for expanded codes -/ structure ExtendedSymbol where symbolId : String properties : List String blockAssignment : Option String deriving Repr, Inhabited /-- Code expansion strategy -/ inductive ExpansionStrategy where | reservedBlockRecoding : String → ExpansionStrategy | blockLengthExtension : ExpansionStrategy | senseBlockReassignment : String → ExpansionStrategy deriving Repr /-- Code system definition (pure combinatorics, no translation) -/ structure CodeSystem where name : String alphabetSize : Nat blockLength : Nat totalBlocks : Nat senseBlocks : Nat stopBlocks : Nat extendedSymbols : List ExtendedSymbol orthogonalDecoder : Bool deriving Repr, Inhabited /-- Standard 64-block system (4^3) -/ def standardCodeSystem : CodeSystem := { name := "Standard 64-Block", alphabetSize := 4, blockLength := 3, totalBlocks := 64, senseBlocks := 61, stopBlocks := 3, extendedSymbols := [], orthogonalDecoder := false } /-- Extended 320-block system (4^4 with overlap) -/ def extendedCodeSystem : CodeSystem := { name := "Extended 320-Block", alphabetSize := 4, blockLength := 4, totalBlocks := 320, senseBlocks := 300, stopBlocks := 20, extendedSymbols := [ { symbolId := "AzF", properties := ["click-chemistry", "photocrosslinker"], blockAssignment := some "AGGA" }, { symbolId := "AcF", properties := ["ketone-reactive"], blockAssignment := some "AGGG" } ], orthogonalDecoder := true } /-- 512-block system (8^3) -/ def expanded512CodeSystem : CodeSystem := { name := "Expanded 512-Block", alphabetSize := 8, blockLength := 3, totalBlocks := 512, senseBlocks := 480, stopBlocks := 32, extendedSymbols := [], orthogonalDecoder := false } -- ═══════════════════════════════════════════════════════════════════════════ -- §7 COMPRESSION FUNCTIONS (Information Theory — All CodingQ) -- ═══════════════════════════════════════════════════════════════════════════ /-- Compute compression potential of a symbol sequence. Returns CodingQ [0, 1]. Higher info density → lower redundancy → higher compression. -/ def compressionPotential (alphabetSize : Nat) (_sequenceLength : Nat) (redundancyFactor : CodingQ) : CodingQ := let infoContent := (normalizedCapacity alphabetSize).value let oneMinusRedundancy := Q0_64.sub one redundancyFactor.value CodingQ.mk (Q0_64.mul infoContent oneMinusRedundancy) /-- Channel stability score: combines reliability and stability -/ def channelStabilityScore (ch : ChannelParameters) : CodingQ := let r1 := Q0_64.mul ch.symbolReliability.value (Q0_64.ofRatio 3 10) -- weight 0.3 let r2 := Q0_64.mul ch.stabilityScore.value (Q0_64.ofRatio 4 10) -- weight 0.4 let r3 := Q0_64.mul ch.copyFidelity.value (Q0_64.ofRatio 3 10) -- weight 0.3 CodingQ.mk (Q0_64.add (Q0_64.add r1 r2) r3) /-- Block optimization score: penalize low-efficiency codes -/ def blockOptimizationScore (blockUsageTable : Array CodingQ) (desiredBlock : Nat) (rareBlockThreshold : CodingQ) : CodingQ := if desiredBlock >= blockUsageTable.size then CodingQ.mk zero else let frequency := blockUsageTable[desiredBlock]!.value if frequency < rareBlockThreshold.value then CodingQ.mk (Q0_64.ofRatio 5 10) -- penalize: 0.5 else CodingQ.mk one -- ═══════════════════════════════════════════════════════════════════════════ -- §8 GCL SURFACE BIND FUNCTIONS (All return CodingQ) -- ═══════════════════════════════════════════════════════════════════════════ /-- Information-theoretic bind: measures coding efficiency -/ def informationalBind (code : CodeSystem) : CodingQ := let capacity := (normalizedCapacity code.alphabetSize).value let efficiency := Q0_64.ofRatio code.senseBlocks code.totalBlocks CodingQ.mk (Q0_64.mul capacity efficiency) /-- Stability bind: noise resilience as CodingQ -/ def stabilityBind (ch : ChannelParameters) : CodingQ := channelStabilityScore ch /-- Control bind: decoder orthogonality and expansion capability -/ def controlBind (code : CodeSystem) : CodingQ := if code.orthogonalDecoder then CodingQ.mk (Q0_64.ofRatio 8 10) -- 0.8 else CodingQ.mk (Q0_64.ofRatio 4 10) -- 0.4 -- ═══════════════════════════════════════════════════════════════════════════ -- §9 DELTA-PHI-GAMMA-LAMBDA AUDIT GRAMMAR (v3 Delta Definitions) -- ═══════════════════════════════════════════════════════════════════════════ /-- Delta (Δ): Residual change — what was lost, distorted, or left over. Magnitude is CodingQ [0, 1]: normalized residual. -/ structure DeltaResidual where changeDescription : String magnitude : CodingQ receipt : Option String deriving Repr, Inhabited /-- Phi (φ): Invariant structure — what must survive transformation -/ structure PhiInvariant where invariantDescription : String preserved : Bool proofReceipt : Option String deriving Repr, Inhabited /-- Gamma (γ): Compression pressure — force toward collapse/abstraction. Normalized pressure level [0, 1] in CodingQ. -/ structure GammaPressure where pressureLevel : CodingQ description : String deriving Repr, Inhabited /-- Lambda (λ): Scale band — resolution of comparison -/ structure LambdaScale where scaleDescription : String byteSpan : Option Nat temporalWindow : Option Nat deriving Repr, Inhabited /-- Complete Delta-Phi-Gamma-Lambda audit record. All dimensionless quantities are CodingQ (Q0_64). -/ structure DeltaPhiGammaLambdaAudit where delta : DeltaResidual phi : PhiInvariant gamma : GammaPressure lambda : LambdaScale auditPassed : Bool deriving Repr, Inhabited /-- Audit check: Did phi survive within bounded delta under gamma at lambda? -/ def dpglAuditCheck (audit : DeltaPhiGammaLambdaAudit) : Bool := audit.phi.preserved && audit.delta.magnitude.value < Q0_64.ofRatio 1 10 && -- threshold 0.1 audit.auditPassed -- ═══════════════════════════════════════════════════════════════════════════ -- §10 AUTHORITY STATES (v3 Delta Definitions) -- ═══════════════════════════════════════════════════════════════════════════ /-- GCL separates existence from authority. Objects exist but must earn authority. -/ inductive AuthorityState where | U_scope -- Unscoped: exploratory, no authority | HOLD -- Important but unresolved; preserve but do not promote | V_scope -- Valid under declared local scope only | REVIEWED -- Review or audit receipts exist | CANONICAL_LEAN -- Formal artifact builds without hidden gaps | QUARANTINE -- Unsafe, misleading, or category-confused deriving BEq, DecidableEq, Repr, Inhabited /-- Check if authority state permits promotion -/ def canPromote (auth : AuthorityState) : Bool := match auth with | AuthorityState.CANONICAL_LEAN => true | AuthorityState.REVIEWED => true | _ => false -- ═══════════════════════════════════════════════════════════════════════════ -- §11 COMBINED GCL CODING OBJECT (v3 Delta Definitions) -- ═══════════════════════════════════════════════════════════════════════════ /-- Combined GCL Coding Object for unified inspection across regimes. All coding values are CodingQ. Raw measurements use BioCodingProjection. -/ structure CombinedGCLCodingObject where gclId : String preferredName : String aliases : List String codingVariant : String kind : String claimState : String authorityScope : AuthorityState definition : String genotype : String expression : String expansionSlots : List String gates : List String receipts : List String projections : List String mutationHistory : List String repairPaths : List String blockedUsages : List String dpglAudit : Option DeltaPhiGammaLambdaAudit deriving Repr, Inhabited /-- Convert EncodingFamily to String for genotype field -/ def encodingFamilyToString (ef : EncodingFamily) : String := match ef with | EncodingFamily.fourSymbolBlock => "4sym" | EncodingFamily.eightSymbolBlock => "8sym" | EncodingFamily.sixteenSymbolBlock => "16sym" | EncodingFamily.binaryBlock => "bin" | EncodingFamily.custom n => s!"c{n}" /-- Create a synthetic genetic coding object with GCL v3 structure. All normalized values are CodingQ. -/ def makeSyntheticGCLObject (name : String) (encFamily : EncodingFamily) (alphabetSize : Nat) (auth : AuthorityState) : CombinedGCLCodingObject := { gclId := s!"gcl_synthetic_{name}", preferredName := name, aliases := [], codingVariant := match encFamily with | EncodingFamily.fourSymbolBlock => "4-symbol" | EncodingFamily.eightSymbolBlock => "8-symbol" | EncodingFamily.sixteenSymbolBlock => "16-symbol" | EncodingFamily.binaryBlock => "binary" | EncodingFamily.custom n => s!"custom-{n}", kind := "synthetic_genetic", claimState := "experimental", authorityScope := auth, definition := s!"Block code with {alphabetSize}-symbol alphabet", genotype := s!"family={encodingFamilyToString encFamily}, alphabet={alphabetSize}", expression := "surface_projection_pending", expansionSlots := ["epigenetic_marks", "modified_bases"], gates := ["channel_stability_gate", "decoding_efficiency_gate"], receipts := [], projections := [], mutationHistory := [], repairPaths := ["reverse_collapse_to_binary"], blockedUsages := if auth == AuthorityState.QUARANTINE then ["therapeutic_use"] else [], dpglAudit := none } -- ═══════════════════════════════════════════════════════════════════════════ -- §12 WARDEN VALIDATION RULES (v3 Delta Definitions) -- ═══════════════════════════════════════════════════════════════════════════ /-- Warden emission types for combined surface validation -/ inductive WardenEmission where | bioOverclaim -- Biological analogy presented as evidence | aliasBoundaryBlur -- Aliases collapse incompatible meanings | projectionProofConfusion -- Surface used as proof | missingTestReceipt -- Algorithmic collapse lacks behavior tests | recursiveAbstractionWithoutGround -- No reverse-collapse target | fixedPointViolation -- Floats in fixed-point hot path | codingAtomTypeViolation -- Field marked coding_atom but not CodingQ | deltaUnbounded -- Residual change exceeds threshold | phiNotPreserved -- Invariant failed under compression deriving BEq, DecidableEq, Repr, Inhabited /-- Warden validation result -/ structure WardenValidation where passed : Bool emissions : List WardenEmission requiredHolds : Bool deriving Repr, Inhabited /-- Check if emissions list is empty -/ def emissionsEmpty (emissions : List WardenEmission) : Bool := match emissions with | [] => true | _ => false /-- Validate a synthetic genetic object against Warden rules -/ def wardenValidateSynthetic (obj : CombinedGCLCodingObject) : WardenValidation := let emissions : List WardenEmission := [] -- Check 1: If claiming biological relevance, need external receipts let emissions := if obj.claimState == "biological_evidence" && obj.receipts == [] then WardenEmission.bioOverclaim :: emissions else emissions -- Check 2: If aliases present but no repair paths let emissions := if obj.aliases != [] && obj.repairPaths == [] then WardenEmission.aliasBoundaryBlur :: emissions else emissions -- Check 3: If no reverse collapse path let emissions := if obj.repairPaths == [] then WardenEmission.recursiveAbstractionWithoutGround :: emissions else emissions -- Check 4: Authority state check let passed := emissionsEmpty emissions && canPromote obj.authorityScope { passed := passed, emissions := emissions, requiredHolds := !emissionsEmpty emissions } -- ═══════════════════════════════════════════════════════════════════════════ -- §13 REVERSE COLLAPSE SAFETY -- ═══════════════════════════════════════════════════════════════════════════ /-- Reverse collapse path: can abstraction unfold back to concrete anchor? -/ structure ReverseCollapsePath where targetAbstraction : String concreteAnchor : String collapseSteps : Nat recoveryTest : Option String deriving Repr, Inhabited /-- Verify reverse collapse is possible -/ def verifyReverseCollapse (obj : CombinedGCLCodingObject) (path : ReverseCollapsePath) : Bool := path.collapseSteps > 0 && path.recoveryTest != none && obj.repairPaths != [] -- ═══════════════════════════════════════════════════════════════════════════ -- §14 THEOREMS (Formal Verification) -- ═══════════════════════════════════════════════════════════════════════════ /-- Theorem: 512-block space is 8x larger than 64-block -/ theorem block512vs64 : code512 = 8 * code64 := by rfl /-- Theorem: Extended 4-block system has 4x more blocks than 3-block -/ theorem block256vs64 : code256 = 4 * code64 := by rfl -- ═══════════════════════════════════════════════════════════════════════════ -- §15 #eval WITNESSES -- ═══════════════════════════════════════════════════════════════════════════ #eval code64 -- 64 #eval code512 -- 512 #eval code256 -- 256 #eval codeByte -- 256 #eval cap4 -- CodingQ with ~0.25 #eval cap8 -- CodingQ with ~0.375 #eval cap2 -- CodingQ with ~0.125 #eval cap16 -- CodingQ with ~0.5 #eval highStabilityChannel.stabilityScore #eval flexibleChannel.stabilityScore #eval neutralChannel.copyFidelity #eval compressionPotential 4 1000 (CodingQ.mk (Q0_64.ofRatio 3 10)) #eval channelStabilityScore highStabilityChannel #eval informationalBind standardCodeSystem #eval controlBind extendedCodeSystem #eval canPromote AuthorityState.CANONICAL_LEAN #eval canPromote AuthorityState.HOLD #eval (makeSyntheticGCLObject "test_4sym" EncodingFamily.fourSymbolBlock 4 AuthorityState.HOLD).authorityScope #eval (wardenValidateSynthetic (makeSyntheticGCLObject "test_xna" EncodingFamily.eightSymbolBlock 8 AuthorityState.U_scope)).passed end Semantics.SyntheticGeneticCoding