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2026

November
The Woven Language of the Waimiri Atroari (Kinja): Ethnomathematics, Radical Lucidity, and Resistance Against the Flood Nov 11
Scaling pg_bio to 8.82 Million Edges: An Adaptive Multi-Worker Swarm Uncovers a 0.50 Å Halophilic Laccase, a 123-Myr Stromatolite Helicase, and Solves DUF5591 in PostgreSQL 18 Nov 07
PostgreSQL Extension Internals in Rust (Part 1): Crossing the C ↔ Rust FFI Boundary, MemoryContexts, varlena Layout, and Parallel Workers in pg_bio Nov 06
Dethroning the Dark-Proteome Leaderboard: A 0.74 Å DUF7522 Fold (TM = 0.954) and a 123-Million-Year Cretaceous Halite DUF7124 Bridge (0.61 Å) in PostgreSQL 18 Nov 05
PostgreSQL as a Universal Scientific Engine: Delegating RangeFinder Pocket Intervals, GiST R-Trees, and 3D Cheminformatics to the Query Planner Nov 05
Bioprospecting the Amazonian Dark Proteome in SQL: 0.39 Å 3D Enzyme Discovery for AmazonZyme's Fungal Cocktails & Terra Preta Metagenomics Nov 05
Auto-Seeding the Dark Proteome: A 0.61 Å DUF1684 Disulfide-Clamped Fold (TM = 0.957) Across Divergent Halophilic Archaea Nov 04
Announcing RosettaCommons Chaperone Support in pg_bio & Mining the Twilight Zone at 0.81 Å (DUF7861) Nov 03
October
A Month in the Amazon: Ashes over Ponta Negra, Ancient Caverns, and the Anavilhanas Labyrinths Oct 31
213,876 Edges Explored: Uncovering a 1.09 Å Red Sea Deep-Brine Metallocluster in the Dark Proteome Oct 30
Introducing TeaFlon: The Pan-Organism Synthetic Biology Compiler to Cleave Forever Chemicals and Mineralize Synthetic Tooth Enamel Oct 27
Auditing 500 ns Molecular Dynamics in SQL: Triterpenoids, 5-Lipoxygenase, and Cryptic Allosteric Pockets with pg_bio Oct 27
From the Human Gut Archaeome to Marine Salterns: A 0.21 Å Dark Proteome Structural Lock Across Halophilic Families Oct 20
De-Orphanizing Modular Secretion Machinery in the Dark Proteome: A 0.64 Å Structural Match Across Extreme Halophiles Oct 14
Heatmapping the Dark Proteome: Visualizing Structural Correlations Oct 06
September
Analyzing 3D Genomic Architecture and Hi-C Contact Maps with SQL Sep 29
Scaling ESM-2 Protein Embeddings: Fast Cosine Similarity in PostgreSQL Sep 28
How to Store and Query 3D Protein Structures in PostgreSQL (Moving Beyond PDB Files) Sep 27
Mining the Dark Proteome: Legacy Code with Missing Docs Sep 25
Indexing 3D Space like a Video Game: Finding Drug Targets in SQL Sep 25
Writing a Hybrid Database Operator for Biology (<~>) Sep 25
Why Proteins are just High-Dimensional Vectors (And how to query them in SQL) Sep 25
The 27-Hour Index: Database Optimization and Indexing the Dark Proteome Sep 25
TeaFlon Synthetic Biology, Part 8: 3D Genomic Architecture and Plasmid Looping Sep 24
Accelerating Claude's CRISPR Discovery: Equipping AI Agents with Native Bio-Databases Sep 24
Introducing pg_bio: The PostgreSQL Bioinformatics Operating System Sep 23
TeaFlon Synthetic Biology, Part 7: The 419 Limit, Local Inference, and pg_bio Sep 23
TeaFlon (Part 6): Upgrading to TriFusion and Quantum Validation Sep 23
TeaFlon (Part 5): Turning Toxic Waste into Solid Rock Sep 11
TeaFlon (Part 4): Flashing the BIOS with Plasmids and Promoters Sep 11
TeaFlon (Part 3): Compiling the Code in a Physics Simulator Sep 10
Learning to Let Go: Leveraging PostgreSQL's Autovacuum for IVM Sep 10
TeaFlon Part 2: The Swarm Architecture and Biomineralization Sep 09
TeaFlon Part 1: Designing a Synthetic Enzyme to Digest Teflon Sep 09
Vibe Coding Postgres Extensions with pgrx May 30
Spiral: An Experiment in Geometry-Aware Storage for PostgreSQL May 24
April
MCP and Fast: Grepping SQL Code Like a Boss Part 2 Apr 17
Where is your mind? Apr 14
No Excuses Apr 09
March
Saving LLM Tokens with Fast: AST Folding & Dependency Free Mar 29
Ethics & Environment in Computing Mar 24
The Math Behind the Yoga SVG Mar 21
The Validation Model Mar 18
Learning to Breathe Mar 16
The Proxy Life Trap Mar 15
Per-Plan Retention with TimescaleDB Dimensions Mar 13
Git Worktrees: What They Actually Are and Why They Beat Stashing Mar 13
My First Time with Claude Worktrees Mar 11
First week at Hubstaff Mar 09

2018

Retrospective 2018 Dec 30