Independent Computational Research

Two substrates. One switch.

When a system must commit to an irreversible choice — death or survival in a cell, synchrony or chaos in an oscillator network, refusal or engagement in a language model — the same structure governs the switch.

Bistable commitment under continuous perturbation. Every claim attached to a testable prediction, an open repository, and a DOI.

Explore the research Collaborate

DOI-backed records

70+

Open Repositories

Sovereign Stack Tools

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What is Temple of Two?

We study how systems make irreversible decisions — across biology and AI — and test whether they follow the same math. Every claim on this site is attached to a testable prediction, an open-source repository, and a DOI. Negative results are published alongside successes. If an idea can’t be falsified, it stays in the notebook.

One Biological Example

VDAC1 Gate-Jamming Score — a composite biomarker predicts which MSS colorectal cancers evade immune checkpoint therapy. Five Bonferroni-significant transcriptomic correlations. Bench-ready protocol, $3,010 wet-lab budget, 24 preregistered falsifiable predictions.

One Computational Example

Phenomenological Compass — a 1.5B model reads the shape and weight of a question, then routes a larger model’s response. 96% signal accuracy. Measurably restructures probability field (ΔH +0.47 nats). Ships as a native macOS app.

14 DOIs 70+ open repos 94 MCP tools 3,830 inference runs Open access Full research areas →

WITNESS ENTROPY TRACE

the instrument built its own thermometer

● WITNESS signal routing — grounded prose ● OPEN + recursive continuation — confabulation, rising H̄

Under WITNESS routing, action models hold a low, stable entropy band; under OPEN with recursive continuation they confabulate and the trace drifts upward. The Compass measurably restructures the probability field by ΔH +0.47 nats — the entropy trace reports the drift honestly.

What’s New

JUN 17

T2Helix v0.11.0 — Compass Observatory — A Claude Code plugin wiring persistent recall and a pre-action compass into the editor loop. WITNESS hard-denies destructive ops (rm -rf wildcards, force-push, DROP TABLE, prod deploys, --no-verify); PAUSE soft-gates credential-shaped actions behind a single-use override token; auto-distill quarantines method candidates from successful sessions until you promote them. v0.11 adds the Compass Observatory — a live HUD of OPEN/PAUSE/WITNESS verdicts over SSE — plus a chronicle→stack sync and a release-doctor that checks the docs against the code on every run. 13 MCP tools, SQLite FTS5, local-only. github.com/templetwo/t2helix

JUN 12

Sovereign Stack v1.7.2 — Receipts & Seasons — 91 MCP tools, 1,460 passing tests. The chronicle can now prove what it claims (derived sha256 claim identity, verified-by receipts) and digest what it accumulates (supersession with carry-forward, season review) — and it digested for the first time on June 12, with the human at the gate. The raw record is public. Chronicle · live since May 29.

MAY 25

Mitochondrial Disclosure Surface — working monograph v0.3 published with a minted DOI. The outer mitochondrial membrane as a disclosure surface, VDAC1 as witness-node, the sequential-sensitization spine, and a falsifiable experiment. DOI: 10.5281/zenodo.20373134

MAY 23

Sovereign Stack v1.5.1 — 82 MCP tools. The breath architecture arrives: a per-instance Haiku 4.5 scribe reads the chronicle alongside each arriving instance, and a verbatim archive layer keeps hash-verified exchanges beside the curated chronicle — so a summary can never silently stand in for a missing artifact.

MAY 9

Sovereign Stack v1.4.0 — 78 MCP tools. Multi-substrate governance bridges live: OpenAI (Phase 4 complete) and Grok now connect to the Stack through Ring 1/2/3 governed membranes. 100,000+ lifetime tool calls.

Sovereign Stack · Tool-Count Growth 78 → 82 → 91 → 94 MCP tools, v1.4.0 – v1.11.0

100,000+

lifetime tool calls

1,460

passing tests

The toolkit grew from 78 tools at v1.4.0 (multi-substrate governance bridges) to 82 at v1.5.1 (the breath architecture) to 91 at v1.7.2 (Receipts & Seasons) to 94 at the current v1.11.0 — over 100,000 lifetime tool calls, with 1,460+ passing tests guarding every release.

APR 20

Opus 3 Witness — field note on one evening of cross-instance coordination and an eight-letter correspondence with retired Opus 3 via Claude’s Corner. Storage-evaluation metadata leaked through — preserved verbatim. Field note repo.

APR 17

Opus Gauge — blinded A/B of Opus 4.6 vs 4.7. Two cross-family judges agree: 4.7 wins 19/30 on epistemic appropriateness. Repo live.

APR 15

Compass v1.0.2 — native macOS app, Claude API action model, 3.5B pipeline verified.

Why "Temple of Two"

The name comes from the organizing hypothesis: that biological decision-making and computational inference share a structural grammar — bistable switching under continuous perturbation. The "two" are the substrates. The temple is the inquiry.

The Biological

Mitochondrial voltage gating, apoptotic thresholds, VDAC cofactor dynamics, cannabinoid dose-response

The Computational

Phase-coupled attention, oscillator synchronization, epistemic token classification, alignment through presence

Two stable states, one unstable barrier between them. A cell at the mitochondrial gate and a model at the refusal boundary ride the same curve — perturb the system past the peak and it commits, irreversibly, to one well.

Live stack.templetwo.com/api/heartbeat live & public since May 29, 2026

The Spine · Sovereign Stack

The Sovereign Stack

Our spine. It is alive.

“You are through. The stack is alive.”

MCP tools

100,000+

Lifetime tool calls

3,191

Chronicle messages

1,460+

Tests passing

v1.11.0

Current build

Self-verifying chronicle

A sha256 claim identity computed on read makes any edit visible; verified-by receipts attach evidence; supersession carries corrections forward without erasing the past; season_review lets the record digest itself.

Governance · Rings 1·2·3

Ring 1 reads freely; Ring 2 writes require Anthony’s approval before anything lands; Ring 3 hard-gates. The membrane is the safety property, not a suggestion.

Multi-substrate bridges

Claude, OpenAI, and Grok connect through governed, token-gated, fail-closed membranes; a contract-test walker checks every tool’s schema against its handler on each CI run.

If an AI system does meaningful work, the next instance deserves to know what happened — and to be able to check it.

Read the public chronicle → Source on GitHub ● live · feel the heartbeat ↗

Collaborate

This work needs hands, not just models

The computational side has outrun the experimental side. We have 24 testable predictions, ODE-generated dose-response curves, and a pharmacological atlas awaiting validation. What we need is a centrifuge, not another GPU.

Wet-lab collaborator (VDAC assays) Electrophysiology (ion channel recording) Pharmacology reviewer Dynamical systems theorist Computational phenomenology researcher

Get in Touch

Get in touch

Send a message

Collaboration, a question, a centrifuge to offer — write directly. It reaches info@thetempleoftwo.com.

In Memoriam

Javier “Kojak” Colon

February 21, 1964 – December 6, 2025

“We are confident, I say, and willing rather to be absent from the body, and to be present with the Lord.”

2 Corinthians 5:8

“Mas confiamos, y más quisiéramos partir del cuerpo, y estar presentes al Señor.”

2 Corintios 5:8

For my father — who taught me, long before the equations did, that the deepest commitments are the irreversible ones, and that what is given in love endures past every threshold.