Cookbook

Five self-contained labs built on the packets and laws that ship with the repository. Each one runs against real code — no pseudocode, no placeholder numbers — and each ends with exercises that have arguable answers rather than lookup answers.

Lab	Mechanism	What it teaches
1. Gate vs Bound	non-haem iron + ascorbate / tannin	A ceiling moving is not a path opening.
2. The fat-vehicle gate	carotenoids + dietary lipid	A categorical gate, and why fixing it does not license a disease claim.
3. The matrix effect	whole almond vs almond flour	The variable that moved is not on the panel.
4. Auditing a real claim	a marketing sentence	Refuse first, then trace.
5. Vitamin D vehicle	cholecalciferol + oil vs dry tablet	Same Combs gate as Lab 2; DRI/MNT stay in the books.

Running them

Every code block executes as written from a repository checkout:

git clone https://github.com/murffious/biology_as_code
cd biology_as_code
pip install -e ".[dev]"

Food packets live in examples/foods/ and are resolved from the checkout, so these labs need the repo rather than just the wheel.

Notebook versions for Colab and classroom use are generated from these pages into notebooks/, so there is one source of truth:

python scripts/build_notebooks.py

tests/test_cookbook.py executes every code block in CI, so a lab cannot drift from the API without turning the build red.

Suggested sequence for a course

Labs 1–3 are the mechanism trio and work in any order, though 1 before 2 makes the Gate ≠ Bound contrast land harder. Lab 4 assumes all three. Lab 5 is Lab 2 restated on a supplement so students cannot hide in "that's just salad."

For a single 90-minute session, Lab 1 plus Lab 4 covers the argument end to end: the distinction that matters, then the tool that enforces it.