assembly-index
Lee Cronin's Assembly Theory for molecular complexity measurement and
When & Why to Use This Skill
This Claude skill implements Lee Cronin's Assembly Theory to quantify molecular complexity and identify biosignatures. By calculating the Assembly Index (MA)—the minimum number of steps required to construct a molecule—it provides a rigorous mathematical framework for distinguishing between biological products and abiotic chemical structures, making it an essential tool for astrobiology and advanced chemical analysis.
Use Cases
- Astrobiology: Identifying potential life signatures in extraterrestrial samples by detecting molecules with an Assembly Index (MA) greater than 15.
- Mass Spectrometry Integration: Estimating molecular complexity directly from MS2 fragmentation patterns to characterize unknown chemical compounds in complex mixtures.
- Synthetic Chemistry: Validating the structural complexity of synthesized molecules and determining the most efficient assembly pathways for chemical production.
- Chemical Evolution Studies: Analyzing the transition from simple chemistry to complex biological systems by measuring the 'copy number' and complexity threshold of molecular populations.
| name | assembly-index |
|---|---|
| description | Lee Cronin's Assembly Theory for molecular complexity measurement and |
| version | 1.0.0 |
Assembly Index Skill: Molecular Complexity Validation
Status: ✅ Production Ready Trit: -1 (MINUS - validator/constraint) Color: #2626D8 (Blue) Principle: Complexity threshold → Life signature Frame: Assembly pathways with minimal step counting
Overview
Assembly Index measures molecular complexity by counting the minimum number of joining operations needed to construct a molecule from basic building blocks. Molecules with assembly index > 15 are biosignatures—too complex for random chemistry.
- Assembly pathway: Shortest construction sequence
- Copy number threshold: Abundance × complexity = life signal
- Molecular DAG: Directed acyclic graph of substructures
- Mass spectrometry integration: MA(m/z) measurement
Core Formula
MA(molecule) = min |steps| to construct from primitives
Life threshold: MA > 15 with copy_number > 1
def assembly_index(molecule: Molecule) -> int:
"""Compute minimum assembly steps via dynamic programming."""
substructures = enumerate_substructures(molecule)
dag = build_assembly_dag(substructures)
return shortest_path_length(dag, source="primitives", target=molecule)
Key Concepts
1. Assembly Pathway Enumeration
class AssemblyPathway:
def __init__(self, molecule):
self.mol = molecule
self.fragments = self.decompose()
def decompose(self) -> list[Fragment]:
"""Find all valid bond-breaking decompositions."""
return [split for split in self.mol.bonds
if split.yields_valid_fragments()]
def minimal_pathway(self) -> list[JoinOperation]:
"""DP over fragment DAG for minimum steps."""
memo = {}
return self._dp_assemble(self.mol, memo)
2. Copy Number Amplification
def is_biosignature(molecule, sample) -> bool:
ma = assembly_index(molecule)
copies = sample.count(molecule)
# Life creates copies of complex molecules
return ma > 15 and copies > 1
3. Tandem Mass Spectrometry Integration
def ma_from_ms2(spectrum: MS2Spectrum) -> float:
"""Estimate assembly index from fragmentation pattern."""
fragments = spectrum.peaks
dag = reconstruct_assembly_dag(fragments)
return dag.longest_path()
End-of-Skill Interface
Commands
# Compute assembly index
just assembly-index molecule.sdf
# Validate biosignature threshold
just assembly-validate sample.ms2
# Compare assembly pathways
just assembly-compare mol1.sdf mol2.sdf
Integration with GF(3) Triads
assembly-index (-1) ⊗ turing-chemputer (0) ⊗ crn-topology (+1) = 0 ✓ [Molecular Complexity]
Related Skills
- turing-chemputer (0): Execute chemical synthesis programs
- crn-topology (+1): Generate reaction network topologies
- kolmogorov-compression (-1): Algorithmic complexity baseline
r2con Speaker Resources
| Speaker | Relevance | Repository/Talk |
|---|---|---|
| oddcoder | RAIR assembly analysis | rair-core |
| mr_phrazer | MBA complexity (msynth) | msynth |
| pancake | Core r2 assembly | radare2 |
Skill Name: assembly-index Type: Complexity Validator Trit: -1 (MINUS) Color: #2626D8 (Blue)