Dequantizing Complexity: A High-Fidelity Computational Audit of Assembly Theory vs. Recursive LZW Compression in Biological Macromolecules

The Sovereign Audit of Complexity. This work presents the first exact, high-fidelity computational audit of the "Assembly Theory vs. LZW Compression" debate in astrobiology. Utilizing the "God-Stack"—a custom heterogeneous cluster comprising Apple Silicon (M3 Ultra) and NVIDIA (DGX Spark) nodes—we transitioned from stochastic approximation to Exact Causal Enumeration. Key Deliverables: The Resolution: We demonstrate that LZW (Compression) and Assembly Index (Construction) are orthogonal metrics. LZW filters thermodynamic noise; Assembly Index identifies causal history. The Benchmark: We release the Sovereign-1K Dataset (sovereign_benchmark_1k.csv), containing exact Assembly Indices for 5,652 FDA-approved small molecules. The Speed: The audit achieved a throughput of >3,400 molecules per second, dequantizing the computational barrier previously cited as a limitation of Assembly Theory. This repository contains the full manuscript, the Python kernels (sovereign_audit_ultra.py), and the verified datasets.