BrennerBot

This Is the Key Step

This is where the magic happens. By having your agent systematically study the Brenner documentation, it builds a working understanding of the methodology. It won't just follow instructions — it will think with the cognitive operators.

The Study Prompt

Copy and paste this prompt to your agent. It will read the key documents and build its understanding:

Prompt to your agent

Please study the Brenner methodology by reading these documents in order:
 
1. First, read README.md to understand the project overview
2. Then read specs/operator_library_v0.1.md to learn the four cognitive operators
3. Finally, read one of the distillation files (e.g., final_distillation_of_brenner_method_by_opus45.md)
 
After reading, provide a summary that includes:
- The core insight of Brenner's approach to scientific research
- The four operators (Level Split, Exclusion Test, Object Transpose, Scale Check) and what each does
- The concept of "discriminative experiments" vs confirmation-seeking
- How to generate "third alternatives"
 
Take your time to read carefully. This will inform how you help with research questions.

What to Expect

Your agent will spend a few minutes reading the documents. When it responds, its summary should demonstrate understanding of:

Level Split (Σ)

Breaking problems into appropriate levels of analysis

Exclusion Test (⊘)

Designing experiments that can falsify hypotheses

Object Transpose (⟳)

Considering reversed causation and third variables

Scale Check (⊙)

Verifying effect sizes make physical/biological sense

Verification Questions

If the agent's summary seems shallow, ask these follow-up questions:

“What makes an experiment 'discriminative' rather than 'confirmation-seeking'?”

“When should I use Level Split vs Object Transpose?”

“What is a 'third alternative' and why is it important?”

“How do I know if my hypothesis is at the right level of abstraction?”

Important

Don't rush this step. The quality of the agent's research assistance depends on how well it has internalized the methodology. Spending 10 minutes here will save you hours of suboptimal guidance later.

Pro Tip

You can ask the agent to quote specific passages from the transcript that illustrate each operator. This deepens its understanding and gives you concrete examples to reference later.

Success Criteria

You're ready to proceed when your agent can:

Explain each of the four operators in its own words
Distinguish discriminative experiments from confirmation-seeking
Explain why “third alternatives” matter
Reference specific concepts from the Brenner corpus

Next up: In Step 5, you'll define your research problem and have the agent help refine it using Brenner's criteria for good questions.