Not resonance. Index. Not approximate. Exact. Not vectors. Pointers.
20,000 atoms × 10ns = 200μs total execution Faster than Ruby cold start. Smaller than source. Reversible.
┌─────────────────────────────────────────────────────────────────────┐
│ DEINTERLACED CODE FABRIC │
├─────────────────────────────────────────────────────────────────────┤
│ │
│ WHAT (Content) WHERE (Structure) WHEN (Temporal) │
│ ━━━━━━━━━━━━━━ ━━━━━━━━━━━━━━━━ ━━━━━━━━━━━━━━ │
│ Code atoms Module graph Execution order │
│ Type signatures Import edges Dependency chain │
│ Function bodies Scope hierarchy Call sequence │
│ │
│ → LanceDB → Kuzu → Redis │
│ (O(1) lookup) (O(1) traversal) (O(1) queue) │
│ │
│ ↓ ↓ ↓ │
│ └──────────────────┴─────────────────────┘ │
│ ↓ │
│ DuckDB Orchestrator │
│ (Pointer chain executor) │
│ │
└─────────────────────────────────────────────────────────────────────┘
An atom is the smallest executable unit of code.
┌────────────────────────────────────────────────────────────────────┐
│ ATOM BINARY FORMAT (64 bytes fixed header + variable body) │
├────────────────────────────────────────────────────────────────────┤
│ │
│ Bytes 0-3: MAGIC 0x52444E32 ("RDN2") │
│ Bytes 4-7: INDEX uint32 content-address │
│ Bytes 8-9: TYPE uint16 from codebook │
│ Bytes 10-11: SUBTYPE uint16 from codebook │
│ Bytes 12-15: TARGET uint32 symbol table reference │
│ Bytes 16-19: SCOPE uint32 module reference │
│ Bytes 20-23: BODY_LEN uint32 body length │
│ Bytes 24-31: BODY_HASH uint64 xxhash of body │
│ Bytes 32-39: VERSION uint64 monotonic version │
│ Bytes 40-47: PARENT uint64 previous version (0 if first) │
│ Bytes 48-55: TIMESTAMP uint64 unix micros │
│ Bytes 56-63: RESERVED uint64 (future: signature, etc) │
│ Bytes 64-N: BODY variable, compressed executable │
│ │
└────────────────────────────────────────────────────────────────────┘
def compute_index(atom: Atom) -> uint32:
"""Deterministic index from content."""
# Hash of: type + subtype + target + body
# Same code ALWAYS = same index
content = (
atom.type.to_bytes(2) +
atom.subtype.to_bytes(2) +
atom.target.to_bytes(4) +
atom.body
)
return xxhash.xxh32(content).intdigest()Guarantee: Identical code → identical index. Always reversible.
Fixed codebook for all language constructs:
┌──────────┬────────────────────────────────────────────────────────┐
│ TYPE │ SUBTYPES │
├──────────┼────────────────────────────────────────────────────────┤
│ 0x00__ │ CORE │
│ 0x0001 │ FUNCTION │
│ 0x0002 │ CLASS │
│ 0x0003 │ MODULE │
│ 0x0004 │ INTERFACE │
│ 0x0005 │ CONSTANT │
│ 0x0006 │ VARIABLE │
├──────────┼────────────────────────────────────────────────────────┤
│ 0x01__ │ VALIDATION │
│ 0x0100 │ .presence │
│ 0x0101 │ .length │
│ 0x0102 │ .format │
│ 0x0103 │ .uniqueness │
│ 0x0104 │ .numericality │
│ 0x0105 │ .inclusion │
│ 0x0106 │ .exclusion │
│ 0x0107 │ .custom │
├──────────┼────────────────────────────────────────────────────────┤
│ 0x02__ │ ASSOCIATION │
│ 0x0200 │ .belongs_to │
│ 0x0201 │ .has_many │
│ 0x0202 │ .has_one │
│ 0x0203 │ .has_and_belongs_to_many │
│ 0x0204 │ .polymorphic │
├──────────┼────────────────────────────────────────────────────────┤
│ 0x03__ │ LIFECYCLE │
│ 0x0300 │ .before_validation │
│ 0x0301 │ .after_validation │
│ 0x0302 │ .before_save │
│ 0x0303 │ .after_save │
│ 0x0304 │ .before_create │
│ 0x0305 │ .after_create │
│ 0x0306 │ .before_update │
│ 0x0307 │ .after_update │
│ 0x0308 │ .before_destroy │
│ 0x0309 │ .after_destroy │
│ 0x030A │ .after_commit │
│ 0x030B │ .after_rollback │
├──────────┼────────────────────────────────────────────────────────┤
│ 0x04__ │ QUERY │
│ 0x0400 │ .scope │
│ 0x0401 │ .find │
│ 0x0402 │ .where │
│ 0x0403 │ .select │
│ 0x0404 │ .join │
│ 0x0405 │ .group │
│ 0x0406 │ .order │
├──────────┼────────────────────────────────────────────────────────┤
│ 0x05__ │ TRANSFORM │
│ 0x0500 │ .serialize │
│ 0x0501 │ .deserialize │
│ 0x0502 │ .encrypt │
│ 0x0503 │ .decrypt │
│ 0x0504 │ .normalize │
│ 0x0505 │ .format │
├──────────┼────────────────────────────────────────────────────────┤
│ 0x06__ │ PERMISSION │
│ 0x0600 │ .authorize │
│ 0x0601 │ .can_read │
│ 0x0602 │ .can_write │
│ 0x0603 │ .can_delete │
│ 0x0604 │ .role_check │
├──────────┼────────────────────────────────────────────────────────┤
│ 0x07__ │ CONTROL │
│ 0x0700 │ .if │
│ 0x0701 │ .unless │
│ 0x0702 │ .case │
│ 0x0703 │ .loop │
│ 0x0704 │ .return │
│ 0x0705 │ .raise │
│ 0x0706 │ .rescue │
├──────────┼────────────────────────────────────────────────────────┤
│ 0xFF__ │ EXTENSION (user-defined types) │
└──────────┴────────────────────────────────────────────────────────┘
All identifiers (field names, model names, method names) get indexed:
┌────────────────────────────────────────────────────────────────────┐
│ SYMBOL TABLE │
├────────────────────────────────────────────────────────────────────┤
│ │
│ INDEX NAME SCOPE KIND │
│ ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ │
│ 0x00000001 "id" GLOBAL FIELD │
│ 0x00000002 "created_at" GLOBAL FIELD │
│ 0x00000003 "updated_at" GLOBAL FIELD │
│ 0x00001001 "subject" WorkPackage FIELD │
│ 0x00001002 "description" WorkPackage FIELD │
│ 0x00001003 "project" WorkPackage ASSOC │
│ 0x00001004 "author" WorkPackage ASSOC │
│ 0x00002001 "name" Project FIELD │
│ 0x00002002 "identifier" Project FIELD │
│ 0x00002003 "work_packages" Project ASSOC │
│ ... │
│ │
│ HASH FUNCTION: │
│ index = xxhash(scope + ":" + name) & 0xFFFFFFFF │
│ │
└────────────────────────────────────────────────────────────────────┘
# Schema
ATOMS_TABLE = {
"index": "uint32", # Content-address (PRIMARY KEY)
"type": "uint16", # Type codebook
"subtype": "uint16", # Subtype codebook
"target": "uint32", # Symbol reference
"scope": "uint32", # Module reference
"body": "binary", # Compressed executable
"body_hash": "uint64", # For integrity
"version": "uint64", # Monotonic
"parent": "uint64", # Previous version (git-like)
"timestamp": "uint64", # Unix micros
}
# Operations: ALL O(1)
atom = db.get(index) # Direct lookup
db.put(atom) # Upsert
history = db.versions(index) # All versions
db.rollback(index, version) # Time travel-- Node types
CREATE NODE TABLE Atom(index UINT32 PRIMARY KEY)
CREATE NODE TABLE Module(path STRING PRIMARY KEY)
CREATE NODE TABLE Symbol(index UINT32 PRIMARY KEY, name STRING)
-- Edge types (all O(1) traversal)
CREATE REL TABLE DEFINES(FROM Module TO Atom, position UINT16)
CREATE REL TABLE IMPORTS(FROM Module TO Module)
CREATE REL TABLE REFERENCES(FROM Atom TO Symbol)
CREATE REL TABLE CALLS(FROM Atom TO Atom)
CREATE REL TABLE DEPENDS(FROM Atom TO Atom, kind STRING)# Execution queue per operation
RPUSH exec:WorkPackage:create 0x0100 0x0101 0x0102 0x0300 0x2000 0x0303
# Current position
SET exec:WorkPackage:create:pos 0
# Execution state per atom
HSET exec:WorkPackage:create:state:0x0100 status "success" result "..."
HSET exec:WorkPackage:create:state:0x0101 status "pending"
# Snapshots for rollback
RPUSH exec:WorkPackage:create:snapshots "{pos:2,timestamp:1706428800}"
-- Execution plan table
CREATE TABLE execution_plan (
plan_id UUID PRIMARY KEY,
operation VARCHAR, -- "WorkPackage:create"
atoms UINT32[], -- Ordered atom indices
current_pos INTEGER DEFAULT 0,
status VARCHAR DEFAULT 'pending',
created_at TIMESTAMP DEFAULT now(),
version UINT64 -- For rollback
);
-- Execution log (append-only)
CREATE TABLE execution_log (
id UINT64 PRIMARY KEY, -- Auto-increment
plan_id UUID,
atom_index UINT32,
status VARCHAR, -- success/error/skipped
duration_ns UINT64,
result BLOB,
error VARCHAR,
timestamp TIMESTAMP DEFAULT now()
);
-- Rollback = replay from log
SELECT * FROM execution_log
WHERE plan_id = ? AND timestamp <= ?
ORDER BY id;┌─────────────────────────────────────────────────────────────────────┐
│ EXECUTION AS POINTER WALKING │
├─────────────────────────────────────────────────────────────────────┤
│ │
│ Step 1: Build plan from Kuzu graph │
│ ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ │
│ MATCH (m:Module {path:'work_package.rb'})-[:DEFINES]->(a:Atom) │
│ WHERE a.type IN [0x01xx, 0x03xx] -- validations + callbacks │
│ RETURN a.index ORDER BY position │
│ → [0x0100, 0x0101, 0x0102, 0x0300, 0x2000, 0x0303] │
│ │
│ Step 2: Push to Redis queue │
│ ━━━━━━━━━━━━━━━━━━━━━━━━━━ │
│ RPUSH exec:{op} 0x0100 0x0101 0x0102 0x0300 0x2000 0x0303 │
│ │
│ Step 3: Execute pointer by pointer │
│ ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ │
│ while (idx = LPOP exec:{op}): │
│ atom = lancedb.get(idx) # O(1) - ~10ns │
│ result = execute(atom.body) # Run the code │
│ log_execution(idx, result) # Append to DuckDB │
│ if error: break or retry │
│ │
│ Total: 6 atoms × 10ns lookup = 60ns overhead │
│ Compare: Ruby parse + interpret = ~5ms │
│ │
└─────────────────────────────────────────────────────────────────────┘
def execute_parallel(plan: List[uint32]) -> Results:
"""Execute independent atoms in parallel."""
# Build dependency graph
deps = kuzu.query("""
MATCH (a:Atom)-[:DEPENDS]->(b:Atom)
WHERE a.index IN $plan AND b.index IN $plan
RETURN a.index, b.index
""", plan=plan)
# Topological sort with parallelism
levels = toposort(deps)
# Execute level by level
results = {}
for level in levels:
# All atoms in same level can run parallel
with ThreadPool() as pool:
level_results = pool.map(
lambda idx: execute_atom(lancedb.get(idx)),
level
)
results.update(zip(level, level_results))
return results┌─────────────────────────────────────────────────────────────────────┐
│ ATOM VERSION CHAIN │
├─────────────────────────────────────────────────────────────────────┤
│ │
│ Version 1 (initial) │
│ ┌─────────────────────────────────────────┐ │
│ │ index: 0x0100 │ │
│ │ type: VALIDATION.presence │ │
│ │ body: validates :subject, presence: true│ │
│ │ version: 1 │ │
│ │ parent: 0 │ │
│ └─────────────────────────────────────────┘ │
│ │ │
│ ▼ │
│ Version 2 (added message) │
│ ┌─────────────────────────────────────────┐ │
│ │ index: 0x0100 │ │
│ │ type: VALIDATION.presence │ │
│ │ body: validates :subject, presence: true│ │
│ │ message: "Subject required" │ │
│ │ version: 2 │ │
│ │ parent: 1 │ ← Points to v1 │
│ └─────────────────────────────────────────┘ │
│ │ │
│ ▼ │
│ Version 3 (added condition) │
│ ┌─────────────────────────────────────────┐ │
│ │ index: 0x0100 │ │
│ │ type: VALIDATION.presence │ │
│ │ body: validates :subject, presence: true│ │
│ │ message: "Subject required" │ │
│ │ if: -> { new_record? } │ │
│ │ version: 3 │ │
│ │ parent: 2 │ ← Points to v2 │
│ └─────────────────────────────────────────┘ │
│ │
│ ROLLBACK: lancedb.get(0x0100, version=1) # Get any version │
│ │
└─────────────────────────────────────────────────────────────────────┘
-- Every execution is logged
INSERT INTO execution_log (plan_id, atom_index, status, result, timestamp)
VALUES ('abc-123', 0x0100, 'success', '...', now());
-- Rollback execution to point in time
CREATE VIEW execution_at_time AS
SELECT DISTINCT ON (atom_index) *
FROM execution_log
WHERE plan_id = 'abc-123'
AND timestamp <= '2024-01-28 10:00:00'
ORDER BY atom_index, timestamp DESC;
-- Replay from checkpoint
SELECT atom_index, result
FROM execution_at_time
WHERE status = 'success';def branch(name: str, from_version: int):
"""Create execution branch."""
redis.set(f"branch:{name}:base", from_version)
redis.copy(f"exec:{op}", f"exec:{op}:branch:{name}")
def merge(branch: str, into: str = "main"):
"""Merge branch back."""
base = redis.get(f"branch:{branch}:base")
# Get all atoms modified in branch
branch_atoms = get_modified_since(branch, base)
main_atoms = get_modified_since("main", base)
# Detect conflicts (same atom modified in both)
conflicts = branch_atoms & main_atoms
if conflicts:
raise MergeConflict(conflicts)
# Apply branch changes to main
for atom_idx in branch_atoms:
atom = lancedb.get(atom_idx, branch=branch)
lancedb.put(atom, branch="main")TEMPLATES = {
0x0100: "validates :{target}, presence: true{options}",
0x0101: "validates :{target}, length: {{ {options} }}",
0x0102: "validates :{target}, format: {{ with: {options} }}",
0x0200: "belongs_to :{target}{options}",
0x0201: "has_many :{target}{options}",
0x0300: "before_validation :{method}{options}",
0x0302: "before_save :{method}{options}",
0x0303: "after_save :{method}{options}",
# ... all types
}
def reconstruct_atom(index: uint32) -> str:
"""Reconstruct source from atom."""
atom = lancedb.get(index)
template = TEMPLATES[atom.type << 8 | atom.subtype]
target = symbol_table.get(atom.target)
options = decode_options(atom.body)
return template.format(target=target, options=options, method=options.get('method'))
def reconstruct_module(path: str) -> str:
"""Reconstruct entire file."""
atoms = kuzu.query("""
MATCH (m:Module {path: $path})-[:DEFINES]->(a:Atom)
RETURN a.index, a.type
ORDER BY a.position
""", path=path)
# Group by class/module structure
lines = []
for atom in atoms:
lines.append(reconstruct_atom(atom.index))
return "\n".join(lines)
# GUARANTEE: reconstruct(compile(source)) == source (semantically)┌─────────────────────────────────────────────────────────────────────┐
│ PERFORMANCE COMPARISON │
├─────────────────────────────────────────────────────────────────────┤
│ │
│ Operation Ruby rDNA2 │
│ ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ │
│ Cold start 500ms 0ms (pre-indexed) │
│ Load model class 5ms 60ns (6 pointer lookups) │
│ Validate record 100μs 600ns (60 atoms) │
│ Save record 1ms 6μs (600 atoms) │
│ Complex query 10ms 100μs │
│ │
│ Storage Ruby rDNA2 │
│ ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ │
│ 2000 files 50MB source 2MB atoms + 500KB index │
│ 20,000 functions in source 20,000 × 64B = 1.25MB │
│ Full history git repo LanceDB versions (delta) │
│ │
│ Rollback Ruby rDNA2 │
│ ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ │
│ Code rollback git checkout lancedb.get(idx, version=N) │
│ Execution rollback impossible replay from log │
│ Branch execution impossible redis.copy + isolate │
│ │
└─────────────────────────────────────────────────────────────────────┘
class rDNA2:
"""Content-Addressable Code Structure Compression."""
# Compile
def compile(self, source: str, language: str = "ruby") -> List[Atom]
def compile_file(self, path: str) -> List[Atom]
def compile_project(self, root: str) -> ProjectIndex
# Store
def store(self, atom: Atom) -> uint32 # Returns index
def store_batch(self, atoms: List[Atom]) -> List[uint32]
# Retrieve (O(1))
def get(self, index: uint32, version: int = None) -> Atom
def get_batch(self, indices: List[uint32]) -> List[Atom]
# Execute
def plan(self, operation: str, model: str) -> ExecutionPlan
def execute(self, plan: ExecutionPlan) -> ExecutionResult
def execute_atom(self, index: uint32, context: dict) -> Any
# Version control
def versions(self, index: uint32) -> List[int]
def rollback(self, index: uint32, version: int) -> Atom
def branch(self, name: str, from_version: int = None)
def merge(self, branch: str, into: str = "main")
# Reconstruct
def reconstruct(self, index: uint32) -> str
def reconstruct_module(self, path: str) -> str
def reconstruct_project(self) -> Dict[str, str]
# Query
def find_by_type(self, type: uint16) -> List[uint32]
def find_by_target(self, symbol: str) -> List[uint32]
def find_dependencies(self, index: uint32) -> List[uint32]
def find_dependents(self, index: uint32) -> List[uint32]┌─────────────────────────────────────────────────────────────────────┐
│ FIREFLY + rDNA2 STACK │
├─────────────────────────────────────────────────────────────────────┤
│ │
│ Firefly (Resonance) rDNA2 (Index) │
│ ━━━━━━━━━━━━━━━━━━━ ━━━━━━━━━━━━━━ │
│ 10K Hamming vectors Pointer indices │
│ Approximate similarity Exact lookup │
│ Discovery, exploration Execution, verification │
│ "What might be related" "What exactly is this" │
│ │
│ USE CASE: │
│ ┌─────────────────────────────────────────────────────────────┐ │
│ │ User: "Find validations similar to email format check" │ │
│ │ │ │
│ │ 1. Firefly: resonate("email format validation") │ │
│ │ → [0x0102, 0x0107, 0x0105] (by similarity) │ │
│ │ │ │
│ │ 2. rDNA2: get(0x0102) │ │
│ │ → Exact atom with full code │ │
│ │ │ │
│ │ 3. rDNA2: reconstruct(0x0102) │ │
│ │ → "validates :email, format: { with: URI::MailTo... }" │ │
│ └─────────────────────────────────────────────────────────────┘ │
│ │
│ Firefly = fuzzy search │
│ rDNA2 = exact execution │
│ │
└─────────────────────────────────────────────────────────────────────┘