Research Orchestration
BrennerBot: Three AI Minds. One Rigorous Method. Zero Blind Spots.
Coordinate Claude, GPT, and Gemini in structured debates. Run 11-phase research sessions that produce hypothesis slates, discriminative tests, and evidence trails. Prevent hindsight bias, unfalsifiable claims, and sloppy reasoning in one command.
curl -fsSL https://brennerbot.org/install.sh | bashOptions: --easy-mode, --verify, --system
Unified Artifact
Hypothesis slate / Discriminative tests / Evidence ledger
Ready to Apply the Method?
Three learning paths from quick start to multi-agent orchestration. Apply Brenner's scientific method to your own research questions.
What's Inside
A research toolkit for applying Brenner's epistemology to your own scientific questions.
Corpus
The complete Brenner transcript collection from Web of Stories, plus curated and .
Distillations
Three frontier model of Brenner's methodology. Compare perspectives from GPT-5.2, Opus 4.5, and Gemini 3.
Method
The , loop structure, and framework that operationalize Brenner's approach to scientific discovery.
Core Workflow
From Question to Conclusion: The Brenner Loop
Research sessions follow a rigorous, reproducible path. Every step is tracked, auditable, and reversible.
1. Intake
Frame the research question
2. Sharpening
Refine hypotheses and scope
3. Level-Split
Separate program from interpreter
4. Exclusion-Test
Design discriminative tests
5. Object-Transpose
Choose the optimal system
6. Scale-Check
Validate against physics
7. Agent-Dispatch
Convene the tribunal
8. Synthesis
Merge agent outputs
9. Evidence
Gather external signals
10. Revision
Update hypotheses
11. Complete
Publish artifacts
Intake
Frame the research question
Sharpening
Refine hypotheses and scope
Level-Split
Separate program from interpreter
Exclusion-Test
Design discriminative tests
Object-Transpose
Choose the optimal system
Scale-Check
Validate against physics
Agent-Dispatch
Convene the tribunal
Synthesis
Merge agent outputs
Evidence
Gather external signals
Revision
Update hypotheses
Complete
Publish artifacts
Undo / Redo
Every action is reversible. Explore without fear.
Session Replay
Reproduce any session exactly for audit and learning.
Error Recovery
Graceful checkpoints when things go wrong.
Apply the Method to Your Research
The is an interactive research framework that helps you develop using four cognitive operators. Run structured sessions and track your evolving understanding.
Multi-Agent Orchestration
Your Research Team: AI Agents That Debate, Challenge, and Synthesize
Each agent has a precise mandate. Together they sharpen hypotheses, design lethal tests, and merge evidence into auditable artifacts - without surrendering control.
"What if you could have Claude, GPT, and Gemini debate your hypothesis - challenging each other until only the strongest ideas survive?"
Powered by GPT
Hypothesis Generator
Hunt paradoxes, propose hypotheses
Creative, divergent thinking
Signature stance
"What if both established models are wrong?"
Powered by Claude
Test Designer
Design discriminative tests with potency controls
Rigorous, detail-oriented
Signature stance
"This test will eliminate half our hypotheses in one observation."
Powered by Gemini
Adversarial Critic
Attack framing, check scale constraints
Skeptical, thorough
Signature stance
"Have you considered that the entire premise might be wrong?"
Oxford Style
Debate ModeProposition vs opposition with a judge
Socratic
Debate ModeProbing questions to surface hidden assumptions
Steelman Contest
Debate ModeBuild the strongest case, then dismantle it
# Start a debate session
brenner session start --thread-id RS-20260105 \
--format oxford \
--question "Does the morphogen gradient model explain cell fate?"
# Watch agents debate in real-time
brenner session status --thread-id RS-20260105 --watch
# See the merged artifact
brenner session compile --thread-id RS-20260105Coordination Visualization
Deterministic MergeKickoff
Threaded prompt goes to each agent role
Deltas
Structured responses return with citations
Merge
Deterministic compiler reconciles evidence
Human
You decide what ships and what dies
Coordination Without Chaos
Agent Mail keeps every exchange auditable
Every message lands in a thread, every response is acknowledged, and every delta is preserved. You stay in the loop with human approval gates at every step.
Research Hygiene
Built-In Guardrails for Rigorous Science
The system blocks common failure modes: hindsight bias, unfalsifiable hypotheses, ignored confounds, and overconfidence. Rigor is enforced before you waste a week.
Coach Mode
Guided checkpoints, inline explanations, and Brenner quotes as you work.
Prediction Lock
Lock outcomes before results arrive to eliminate hindsight bias.
Calibration Tracking
Brier score, overconfidence bias, and domain-level accuracy trends.
Confound Detection
Domain-specific confounds flagged with targeted prompting questions.
Artifact Linting
50+ rules enforcing third alternatives, potency controls, and citation hygiene.
Prediction Lock Timeline
No hindsightDesign test
Enter predictions
Lock outcomes
LockedRun experiment
Compare results
Confound Detection
8 domainsCalibration + Linting
ScorecardCalibration curve (last 10 tests)
Without Guardrails
With BrennerBot
Discovery & Intelligence
Intelligence Built In: Search, Simulate, Score
Connect to prior work instantly, model evidence impact before you test, and track which hypotheses survive pressure. This is research intelligence, not a chat log.
Hypothesis Similarity Search
Find related work across sessions with offline embeddings and clusters.
What-If Scenarios
Simulate outcomes before running tests and prioritize high-impact experiments.
Robustness Scoring
Evidence-weighted survival scores reveal fragile vs battle-tested ideas.
Anomaly Detection
Track contradictions and spawn new hypotheses instead of burying them.
Similarity Search
OfflineStatement 0.8 / Mechanism 0.6 / Domain 0.9
Statement 0.7 / Mechanism 0.5 / Domain 0.8
Statement 0.6 / Mechanism 0.4 / Domain 0.9
Runs entirely client-side - your hypotheses never leave your machine.
What-If Scenario
Info gainRobustness
Survival score3 supporting / 1 challenging (survived)
1 supporting / 2 inconclusive
Anomaly Register
QuarantineOscillating fate markers
Conflicts with H1 + H2
Late-stage inversion
Waiting on potency control
Deep Dive
The Operator Algebra: Brenner's Methods as Executable Code
Sydney Brenner's breakthrough wasn't just his discoveries - it was his method. We've encoded his cognitive patterns as composable operators that you can apply systematically.
The Brenner Method in 4 Steps
Split the levels
Separate the 'what' from the 'how'
Design killing tests
Find experiments that eliminate possibilities
Choose your system
Pick the easiest organism/model to test with
Check the physics
Make sure it's physically possible
Want the precise notation? See the operators below.
Level-Split
"Separate program from interpreter"
Message vs machine, genotype vs phenotype. Includes the 'chastity vs impotence' diagnostic.
Template
"What is the information? What is the mechanism?"
Exclusion-Test
"Design tests that eliminate, not confirm"
Forbidden patterns: what cannot occur if H is true. Rated by discriminative power.
Template
"If H1 is true, we should NEVER see..."
Object-Transpose
"Change the system until the test is easy"
Choose organism or model strategically. The experimental object is a design variable.
Template
"What system would make this test cheap and unambiguous?"
Scale-Check
"Stay imprisoned in physics"
Validate against physical constraints. Calculate timescales, length scales, energy scales.
Template
"Is this physically possible at the relevant scale?"
The Core Composition
(⌂ ∘ ✂ ∘ ≡ ∘ ⊘) powered by (↑ ∘ ⟂ ∘ 🔧) constrained by (⊞) kept honest by (ΔE ∘ †)- Start from a paradox (◊), split levels (⊘), extract invariants (≡)
- Design exclusion tests (✂), materialize as decision procedure (⌂)
- Power by amplification (↑) in well-chosen system (⟂) you build yourself (🔧)
- Constrain by physics (⊞), keep honest with exception handling (ΔE) and theory killing (†)
Extended Operators6 more patterns
Amplify
Use selection, dominance, regime switches
Paradox-hunt
Use contradictions as beacons
Cross-domain
Import tools from other fields
Dephase
Work out of phase with fashion
Theory-kill
Drop hypotheses when the world says no
Materialize
What would I see if this were true?
import { pipe } from "@/lib/brenner-loop/operators/framework";
const brennerPipeline = pipe(
levelSplit, // Separate levels
invariantExtract, // Find what survives
exclusionTest, // Design killing experiments
materialize, // Compile to decision procedure
);
const result = brennerPipeline(hypothesis, context);“I think many fields of science could do a great deal better if they went back to the classical approach of studying a problem, rather than following the latest fashion.