Glossary

Exploit naturally high quantities to avoid purification.

The coordination substrate for multi-agent research sessions.

A particular version of a gene at a specific position in the genome.

The building blocks of proteins—20 standard types coded by DNA.

Enhance weak signals until they become measurable (↑).

A stable reference to a transcript section (§n format).

Programmed cell death—cells that deliberately kill themselves.

A structured output from a research session (hypotheses, tests, etc.).

Explicit list of load-bearing assumptions and what would break them.

The prior probability of something in a population before specific evidence.

A ratio measuring the evidence for one hypothesis versus another.

Revising beliefs by combining prior probability with new evidence.

The issue tracking system used in BrennerBot development.

A design where the experimenter doesn't know treatment assignments.

A strategic intervention that transforms a stuck problem into a tractable one.

A tiny transparent worm (~1mm) that became a model organism for genetics and neuroscience.

The complete ancestral history of a cell, tracing back to the fertilized egg.

A three-nucleotide sequence that specifies one amino acid.

A hidden variable that varies with treatment and could explain results.

The complete wiring diagram of all neural connections in a nervous system.

The baseline condition an experiment compares against.

The primary source documents in BrennerBot (transcripts + distillations).

Borrow techniques or concepts from other fields (⊕).

An experiment whose result forces a choice between hypotheses.

Deriving specific conclusions from general principles.

A structured update to an artifact from an agent.

Make expensive techniques cheap and accessible (⇓).

Move out of phase with fashion to find open territory (∿).

Discrete, countable markers that make a system tractable.

An experiment designed to distinguish between competing hypotheses.

A processed, structured summary derived from the raw corpus.

Build your own tools when commercial ones don't exist (🔧).

Deoxyribonucleic acid—the molecule that stores genetic information.

An allele whose phenotype shows even when heterozygous.

Neither experimenter nor subject knows treatment assignment.

Ethyl methanesulfonate—a chemical mutagen widely used in genetics.

Data or observations that update beliefs about hypotheses.

Isolate anomalies so they don't corrupt the main theory (ΔE).

A curated selection of corpus sections for a kickoff prompt.

Design tests that rule out hypotheses, not confirm them (✂).

Proving a hypothesis wrong rather than confirming it.

Results that your theory says cannot occur.

Starting with a phenotype and working backward to find the gene.

An imaginary organism designed to think through what's possible.

A segment of DNA that encodes a functional product (usually a protein).

The mapping from DNA triplets (codons) to amino acids.

The genetic makeup (DNA sequence) of an organism.

Have A Look—directly observe before elaborate inference (👁).

An organism with both male and female reproductive organs.

Having two different alleles of a gene.

Having two identical alleles of a gene.

A proposed explanation for phenomena, to be tested by experiment.

A structured list of competing hypotheses to be evaluated.

Generalizing from specific observations to broader principles.

How much an experiment reduces uncertainty about a question.

Find what stays the same across transformations (≡).

The initial prompt that starts a research session.

Measures how different two probability distributions are.

Decompose a problem into distinct levels of organization (⊘).

How much more likely the evidence is under one hypothesis versus another.

Turn abstract theory into concrete, testable predictions (⌂).

A template that generates specific prompts for different research contexts.

A species chosen for study because its properties make experiments tractable.

Messenger RNA—the intermediate that carries genetic information from DNA to ribosomes.

Deliberately inducing mutations to study gene function.

A change in DNA sequence that may alter gene function.

A nerve cell specialized for transmitting electrical and chemical signals.

The default assumption that there's no effect or difference.

Switch which entity you're experimenting on (⟂).

Sweeping inconvenient facts under the rug.

The ratio of probability of an event to probability it doesn't happen.

Defining abstract concepts in terms of measurable procedures.

The collection of Brenner operators defined in the system.

Manipulating analysis until results appear statistically significant.

A framework of assumptions, methods, and problems that defines a scientific field.

Actively seek contradictions—they mark discovery zones (◊).

The observable characteristics of an organism.

Your updated beliefs after seeing new evidence.

An experiment's power to discriminate between hypotheses.

Verify your intervention actually worked before trusting results (🎭).

Your beliefs about a hypothesis before seeing new evidence.

Not knowing the standard approach lets you see alternatives.

A molecular machine made of amino acids that performs cellular functions.

Run a cheap pilot test to de-risk before committing to the full experiment (⚡).

A curated collection of quotable passages from the Brenner corpus.

An allele whose phenotype only shows when homozygous.

Change representation to make patterns visible (𝓛).

Repeating an experiment to verify results are real.

Restate the problem in a domain where constraints are clearer.

Whether results can be obtained again using the same methods.

Starting with a gene and asking what phenotype its mutation causes.

The cellular machine that reads mRNA and builds proteins.

Ribonucleic acid—single-stranded molecule that carries and implements genetic information.

Physics constrains what's possible at each size (⊞).

The probability a test correctly detects a condition when present.

A research interaction between human and AI agents on a specific question.

The probability a test correctly rules out a condition when absent.

A junction where neurons communicate with each other or with muscles.

Deliberately attempt to destroy your own hypothesis (†).

The 'both models are wrong' escape from false dichotomies.

A conversation stream in Agent Mail identified by a unique ID.

The process of copying DNA into RNA.

The process of reading mRNA to build proteins at the ribosome.

Deliberately ignore conventional wisdom to see fresh (⊙).

The normal, non-mutant version of an organism or gene.