Codex — Biology Plan

Drafted 2026-05-17. Per-domain plan for the Biology axis of the five-domain expansion. Sibling of PHYSICS_PLAN.md and CHEMISTRY_PLAN.md. Subordinate to BIBLE_EXPANSION_PLAN.md. Drafted in parallel with chem per the umbrella §6 sequence; both revised after Physics Wave 1 retro.

Status: Draft. Locks the three-section structure (matching the three-tree-DAG biology actually has), hybrid mode, tier anchors per tree, mastery endpoints, the cross-domain prereq cone (heavy: chem + physics + math), exclusions, three-spine coverage scaffold, and the Wave 1 seed slate.

Read before this plan: OVERVIEW.md, BIBLE_EXPANSION_PLAN.md (esp. §2.4 bio exclusions and §3 cross-domain contract), CHEMISTRY_PLAN.md (the densest chem→bio hook surface).

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§1 What this plan does

1. Decomposes biology into three top-level sections §17–19 matching the three weakly-connected entry trees biology actually has: molecular/cellular (§17), organismal/physiological (§18), and ecological/evolutionary (§19). These three are more independent of each other than the five physics branches or the three chemistry sections — a learner can master §19 without ever touching §17, which is not true of physics or chem.
2. Defines hybrid mode for bio — units for mechanisms and specific systems; essays for the higher-level questions ("what is life," "what is consciousness in cellular terms," "evolution as algorithmic process") that span trees and reach into phil.
3. Builds the three-spine coverage scaffold (Alberts MBoC + Campbell + Futuyma) since no single canonical roadmap exists; each spine governs one of the three sections.
4. Names Wave 1 seeds — 3 units + 1 essay, with the §17 unit (action potential) deliberately chosen because it stress-tests the most cross-domain prereqs at once (chem ion channels + physics electrochem + math ODEs).

It does not:

• Produce units (gated on BIBLE_EXPANSION_PLAN.md §10 patches + Physics Wave 1 retro).
• Decide where in v1 vs v2 various excluded subareas (medicine, psych, etc.) land — those are out of v1 per umbrella.
• Lock the question of whether neuroscience eventually splits into a dedicated section (deferred to §8).

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§2 Biology scope

2.1 In scope (v1)

Tree	Topics in scope
§17 Molecular & Cellular	Biomolecule function (proteins, nucleic acids, lipids, carbohydrates — biology side; the chem-side is in §15.12–13); membrane structure and transport; cell structure (organelles); cell division; signaling; gene expression and regulation; molecular genetics; molecular evolution at the sequence level; cellular neuroscience (action potentials, synapses, neural cell biology); immunology mechanism (molecular + cellular); cell-cycle and cancer biology; stem-cell biology basics
§18 Organismal & Physiological	Anatomy of major systems (cardiovascular, nervous, musculoskeletal, respiratory, digestive, endocrine, reproductive, immune); physiology and homeostasis; development (embryology, morphogenesis); physiology of specific organisms (model systems: E. coli, S. cerevisiae, C. elegans, D. melanogaster, M. musculus, A. thaliana, human); comparative physiology; behavior (animal behavior — the ethology side; cognitive aspects defer to phil)
§19 Ecology & Evolution	Population genetics (Hardy-Weinberg, drift, selection coefficients); quantitative genetics; evolutionary theory (natural / sexual / kin selection; neutral theory; molecular evolution); phylogenetics; speciation; macroevolution; ecology (population, community, ecosystem); biogeography; conservation biology basics; coevolution; origin of life (mechanistic side; the philosophical / cosmological side → phil)

2.2 Out of scope (v1) — explicit exclusions

From BIBLE_EXPANSION_PLAN.md §2.4 (restated):

Out of v1	Goes to
Biochemistry mechanism (treated as chemistry of biomolecules in isolation)	Chem §15
Biochemistry as it operates in specific organisms / pathways	Bio (§17) — but the mechanism lives in chem; bio cross-refs
Medicine, pharmacology, clinical applications	Not v1
Psychology, cognitive science (empirical)	Not v1 (phil-of-mind covers conceptual overlap)
Neuroscience: cellular/molecular	Bio §17
Neuroscience: cognitive / computational / consciousness	Phil §20 + v2+
Bioinformatics methods (sequence alignment, phylogenetic inference, statistics of biology)	Math (probability, graph theory, dyn-sys)
Bioinformatics-specific software / tools	Not v1
Public-health / epidemiology models	Math (probability, dyn-sys) for the methods; domain-specific epi → v2+
Detailed clinical anatomy (surgical-detail anatomy)	Not v1 (gross anatomy at the descriptive-physiology level is in scope)

Boundary rules:

• Biochem boundary (cross-references §15.14 chem-side enzyme mechanism): if the question is "what does this enzyme do chemically?" → chem §15.14. If the question is "how does this enzyme function in cellular metabolism / a specific pathway / a specific organism?" → bio §17. The citric-acid-cycle worked example: each individual enzyme's mechanism is chem; the cycle-as-a-cellular-process is bio.
• Neuroscience boundary: action potentials, synaptic transmission, neuroplasticity at the molecular/cellular level → bio §17. Computational neuroscience, theory of cognition, theory of consciousness → phil §20 + v2+.
• Bioinformatics boundary: a unit on "how Bayesian phylogenetic inference works as a method" → math. A unit on "using phylogenetics to test a specific evolutionary hypothesis on a specific clade" → bio §19. Tools (BLAST, Bowtie, etc.) → not v1.
• Origin of life boundary: prebiotic chemistry mechanisms → chem §15 + cross-ref. Plausibility analysis under various cosmological / geological scenarios → bio §19 + phil §20. The fact that life began under particular conditions on Earth → bio §19. The metaphysics of "what does it mean for non-life to become life" → phil.

2.3 What about psychology / cognitive science?

Honest acknowledgment: v1 punts on a contentious boundary. The cellular/molecular substrate of cognition is bio §17. The information-processing / computational / phenomenological aspect is phil §20 (or v2+). Where exactly the line falls between these is genuinely contested in the actual scientific literature, and forcing a clean split is part of why this plan can ship at all. v2 may relax the constraint.

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§3 The three trees (or: why "tree" not "branch")

Physics had five branches with internal ordering each; chem had three sections with softer DAGs each. Bio has three trees, which is structurally weaker than either:

• The molecular/cellular tree descends from atoms → molecules → cells → tissues, with chemistry as the heavy prereq dependency.
• The organismal/physiological tree treats systems and organisms as integrated wholes — it can be entered from cellular biology, but the standard intro-bio undergrad pedagogy starts an organismal student from anatomy/physiology directly without requiring molecular fluency.
• The eco/evo tree is the most independent of the three; it has its own math prereqs (population genetics is its own probability discipline) and minimal direct cellular-biology dependency in most of its content. A learner can master Hardy-Weinberg, drift, selection, and phylogenetics without ever doing a cell-biology unit.

This three-tree structure is not arbitrary — it matches how biology is actually taught at the undergraduate and graduate level (separate molecular-bio, physiology, and ecology curricula at most universities). v1 honors this.

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3.1 §17 Molecular & Cellular Biology

Internal ordering (loose; tree-shaped, multiple entry points):

Chapter	Topic	Entry?
17.01	Biomolecules at the cellular scale — proteins, nucleic acids, lipids, carbs in their biological role	✓
17.02	Membrane structure and dynamics — bilayers, transport, signaling at membranes
17.03	Cellular organization — organelles, cytoskeleton, compartmentalization	✓
17.04	Energy and metabolism in cells — cellular respiration, photosynthesis, lipid + carbohydrate metabolism (the cellular side; chem-side is §15)
17.05	Gene expression — DNA replication, transcription, translation, regulation
17.06	Molecular genetics — mutation, recombination, repair, mobile elements
17.07	Cell signaling — receptors, kinase cascades, GPCRs, second messengers
17.08	Cell cycle and division — mitosis, meiosis, cancer biology basics
17.09	Cellular neuroscience — action potentials, synapses, neural cell biology
17.10	Immunology mechanism — innate + adaptive immunity at the molecular + cellular level
17.11	Stem cells and developmental potency basics
17.12	Molecular evolution — sequence evolution, neutral theory at the molecular level

Cross-domain prereq cone:

From	Why
chem §15.12–14	biomolecule structure and mechanism (chem-side)
chem §16.06	metalloenzymes (chem-side)
chem §14.08	kinetics (for enzyme kinetics in cellular metabolism)
chem §14.06	thermodynamics (for bioenergetics)
physics §10	electromagnetism (for 17.09 action potentials)
physics §11	stat mech (for biopolymer physics, 17.02 membrane transport at equilibrium)
physics §11.09	statistical biophysics primer (cross-cited heavily)
physics §12	QM (for photosynthesis at master tier)
math §02	ODEs (for kinetic models), probability (for molecular dynamics, mutation)

Anchor literature:

Tier	Anchor
Beginner	Crash Course Biology; Khan Academy; Why Evolution Is True (Coyne, for the molecular evolution sections); The Vital Question (Lane)
Intermediate	Alberts et al. Molecular Biology of the Cell (textbook tier sections); Lodish Molecular Cell Biology (alt); Karp Cell and Molecular Biology (alt)
Master	Alberts MBoC (advanced sections); Phillips et al. Physical Biology of the Cell; Nelson Biological Physics: Energy, Information, Life; primary lit (Cell, Nature, Science) by subarea

Mastery endpoints:

Tier	Endpoint
Beginner	Explain (with correct causal direction) a mechanism like the action potential, transcription, or muscle contraction; name what's in a cell and what it does at a coarse level
Intermediate	Read experimental figures from MBoC end-of-chapter material and identify the controls / conclusions; predict a mutation's phenotype; work problems on kinetics of metabolism, membrane transport, signaling cascades
Master	Read a primary paper in molecular / cellular biology and (a) identify the methods used, (b) assess confounds, (c) predict what would change under alternative hypotheses; treat a biophysics problem at the Physical Biology of the Cell level

Outbound hooks:

• → Chemistry: most of §17 has heavy inbound chem cites; outbound is rarer (a biological context can sometimes inform chem essay synthesis but units rarely)
• → Philosophy: computation in neural signaling (17.09); information in gene expression (17.05); life as a thermodynamic phenomenon (17.04 + 17.02); origin of life (also §19)

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3.2 §18 Organismal & Physiological Biology

Internal ordering:

Chapter	Topic	Entry?
18.01	Body plans and organization — tissues, organs, integrated systems	✓
18.02	Cardiovascular physiology — heart, vessels, blood, regulation
18.03	Respiratory physiology
18.04	Musculoskeletal — actin-myosin, joint mechanics, locomotion (cross-refs physics §09)
18.05	Nervous system — gross anatomy, brain regions, system-level neuroscience (cellular side in §17.09)
18.06	Digestive physiology and nutrition
18.07	Endocrine — hormones and integrated regulation
18.08	Renal physiology and homeostasis
18.09	Reproductive biology
18.10	Immunology — system-level (cellular/molecular side in §17.10)
18.11	Development — embryology, morphogenesis, organogenesis	✓
18.12	Animal behavior (ethology) — fixed action patterns, instinct, learning at the behavioral level (not cognition)
18.13	Model organism biology — E. coli, yeast, worm, fly, mouse, Arabidopsis, human as integrated wholes
18.14	Plant physiology — photosynthesis at the plant level (cellular side in §17.04); water relations; growth
18.15	Comparative physiology — physiology across taxa; adaptive variation

Cross-domain prereq cone:

From	Why
bio §17 (selected)	cellular substrate (action potential for nervous system, etc.)
physics §09	mechanics (for musculoskeletal, fluid dynamics in cardiovascular)
physics §11	thermodynamics + transport (for renal, respiratory, thermoregulation)
chem §14.06	thermodynamics
chem §15	biochem (for nutrition, metabolism at the organismal level)
math §02	ODEs (for physiological models — compartmental, pharmacokinetic)

Anchor literature:

Tier	Anchor
Beginner	Crash Course Anatomy & Physiology; Campbell Biology (intro chapters)
Intermediate	Campbell Biology (full); Sadava Life: The Science of Biology; Hill Animal Physiology; Knut Schmidt-Nielsen Animal Physiology (alt)
Master	Boron-Boulpaep Medical Physiology (the most rigorous integrated physiology text); Eckert Animal Physiology; Squire et al. Fundamental Neuroscience (for systems neuroscience); primary lit (J. Physiol., Nature Neuroscience, Cell)

Mastery endpoints:

Tier	Endpoint
Beginner	Name the major systems and explain in plain language what each does; predict what happens when one system fails (e.g., what dehydration does at the kidney level)
Intermediate	Work Campbell / Sadava end-of-chapter problems; analyze experimental data (e.g., from a physiology lab) and identify what's being measured; predict how a perturbation propagates across systems
Master	Boron-Boulpaep + Eckert problems; read a J. Physiol. or Nature Neuroscience paper and assess the methodology; integrate cross-system perturbations (e.g., how does a respiratory acidosis propagate through renal, cardiovascular, and nervous responses)

Outbound hooks:

• → Philosophy: agency and goal-directedness in behavior (18.12); free will and the brain (18.05); the unity of an organism — what makes something one biological individual (cross-refs §17 and §19); development as a constructive vs informational process (18.11)
• → Chemistry: nutrition (18.06) cross-refs back into chem §15 metabolism
• → Physics: biomechanics (18.04) cross-refs back into §09

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3.3 §19 Ecology, Evolution & Population Biology

Internal ordering:

Chapter	Topic	Entry?
19.01	Mendelian genetics and inheritance	✓
19.02	Hardy-Weinberg equilibrium and basic population genetics	✓
19.03	Selection — natural, sexual, kin
19.04	Genetic drift and the neutral theory
19.05	Quantitative genetics — heritability, breeder's equation, response to selection
19.06	Speciation — modes (allopatric, sympatric), reproductive isolation
19.07	Phylogenetics — tree reconstruction, molecular clocks, gene-tree vs species-tree
19.08	Macroevolution — clade dynamics, mass extinctions, key innovations
19.09	Population ecology — growth models, Lotka-Volterra, life-history theory
19.10	Community ecology — interactions, food webs, succession
19.11	Ecosystem ecology — energy flow, nutrient cycling
19.12	Biogeography — historical + ecological
19.13	Coevolution — host-parasite, mutualism, sexual conflict
19.14	Conservation biology basics — population viability, extinction risk modeling
19.15	Origin of life — mechanistic + scenario analysis (cross-refs chem prebiotic + phil)

Cross-domain prereq cone:

From	Why
math §02	probability and statistics (heavy: pop gen is essentially applied probability)
math §02	ODEs and dynamical systems (for ecology models, evolutionary game theory)
math (graph theory)	for phylogenetics (location TBD — possibly §03 modern-geometry adjacent or math expansion)
bio §17.12	molecular evolution at the sequence level (for §19.04, §19.07)
chem §15	basic biochem (for origin of life §19.15)

Anchor literature:

Tier	Anchor
Beginner	Why Evolution Is True (Coyne); Crash Course Ecology + Biology evolution episodes; Dawkins The Selfish Gene (popular)
Intermediate	Futuyma Evolution; Begon et al. Ecology: From Individuals to Ecosystems; Hartl-Clark Principles of Population Genetics
Master	Charlesworth Elements of Evolutionary Genetics; Walsh-Lynch Evolution and Selection of Quantitative Traits; Felsenstein Inferring Phylogenies; primary lit (Evolution, Am. Nat., Ecology, Molecular Biology and Evolution)

Mastery endpoints:

Tier	Endpoint
Beginner	Explain natural selection without teleology; recognize what evidence supports evolution; predict qualitatively whether a population is at Hardy-Weinberg
Intermediate	Work Hartl-Clark / Futuyma problems including selection coefficients, drift, F-statistics, fitness landscapes; work Begon ecology problems; interpret a phylogenetic tree (rooted/unrooted, bootstrap, branch length meaning)
Master	Work Charlesworth / Walsh-Lynch problems; assess primary lit on quantitative genetics or molecular evolution; reconstruct a phylogeny computationally and assess methodological choices; treat origin-of-life scenarios rigorously

Outbound hooks:

• → Philosophy: teleology vs evolution (the canonical phil-of-bio question); design inference and its failures; the unit-of-selection problem (gene vs individual vs group); the nature of fitness; species as natural kinds vs nominalist; origin of life as scientific vs metaphysical question
• → Chemistry: origin of life (19.15) cross-refs prebiotic chem
• → Math: dynamical systems applied to ecology / coevolution

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§4 Hybrid mode — units vs essays in biology

Bio has a higher essay-to-unit ratio than chem because of the synthesis-heavy questions at the boundary with philosophy:

4.1 Tiered units (majority)

Units cover: specific mechanisms (action potential, transcription), specific systems (cardiovascular, immune), specific principles (Hardy-Weinberg, selection coefficients), specific organisms (model systems).

4.2 Synthesis essays (more here than in chem)

Candidate essay	Why an essay
"What life is — the biology between physics and intentionality"	Spans §17 + §18 + §19; interpretive; pairs with phil
"Information in biology — gene as message, gene as switch, gene as nothing-of-the-kind"	The DNA-as-information question is one of the most contested in phil-of-bio; cuts across §17 + phil
"Evolution as algorithmic process — what does and doesn't reduce to a search algorithm"	Cross-disciplinary; touches §19, computer-science / algorithms questions, phil
"Agency at biological scales — from chemotaxis to behavior"	§17.07 + §18.12 + phil; what does it mean for a cell, an organism, a colony, to do something
"Consciousness from the brain stem up"	§17.09 + §18.05 + phil; the cellular substrate side of the consciousness question
"Reductionism in biology — what counts as a biological explanation"	Phil-of-bio meta; pairs with phil-of-science
"Origin of life as scientific question — the necessary vs the contingent"	§19.15 + chem prebiotic + phil; how do we know we'd recognize it if we found it elsewhere

Initial essay budget: ≤ 7 across the bio axis (slightly higher than chem's 5 because bio→phil hook surface is denser).

4.3 Where they live

Locked (per UNIT_SPEC.md §2.2):

• Tiered bio units live at content/17-mol-cell-bio/, content/18-organismal-bio/, content/19-eco-evo-bio/.
• Essays live at site/src/content/biology/NN-slug.md with frontmatter:

  id: <17|18|19>.essays.NN
  applies_to: [<section-numbers>]
  

• Primary-section rule applies (cf. CHEMISTRY_PLAN.md §4.3): essay's id uses its primary section's prefix, applies_to: lists every section it spans. E.g., a "What life is" essay spanning §17/§18/§19 + phil §20 might carry id: 17.essays.01, applies_to: [17, 18, 19, 20].

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§5 Coverage scaffold — three spines

Bio has no Fast-Track-style canonical roadmap; even more than chem, the field is heterogeneous. Three spines combine to scaffold coverage:

5.1 Spine 1 — Alberts Molecular Biology of the Cell (drives §17)

MBoC is the gold-standard molecular/cellular biology reference at intermediate and master. Its chapter list defines the molecular/cellular coverage. v1 maps every MBoC chapter (or coherent chapter-cluster) to at least one §17 unit at intermediate tier; master tier follows where MBoC depth merits.

5.2 Spine 2 — Campbell Biology + Boron-Boulpaep Medical Physiology (drives §18)

Campbell defines the organismal intermediate-tier coverage; Boron-Boulpaep defines the master-tier integrated physiology. The Campbell + Boron-Boulpaep chapter unions provide the §18 coverage spec.

5.3 Spine 3 — Futuyma Evolution + Begon Ecology + Hartl-Clark Pop Gen (drives §19)

Three smaller spines compose into §19. Futuyma covers evolutionary theory; Begon covers ecological theory; Hartl-Clark covers the quantitative population-genetics core. Their unions provide §19 coverage.

5.4 Reference archive expansion

Like chem, bio needs reference/ expansion. Candidate license-permissive sources: OpenStax Biology / Anatomy & Physiology / Microbiology; iBiology lectures (where licensable); NCBI Bookshelf for some primary references. Sourcing is a Wave 1 deliverable.

5.5 Coverage manifest

manifests/production/bio-coverage.json (analog of chem-coverage.json, per CHEMISTRY_PLAN.md §11) maps the three-spine chapter unions to (eventually) Codex unit IDs. Empty initially.

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§6 First wave — three seed units + one synthesis essay

Purpose: stress-test the cross-domain link contract on the densest cross-domain prereq node in any of the five domains — biology's action-potential unit cites chem, physics, AND math simultaneously.

Tree	Seed	Why this one
§17 mol/cell	17.09.02 The action potential — ionic basis	Maximum cross-domain prereq density: chem §15 (ion channels = proteins), physics §10 (electrochemical potentials), physics §11 (Nernst equation from stat mech), math §02 (Hodgkin-Huxley = coupled ODEs). Hooks out to phil §20 (information processing in neurons). Anchored in Hille Ion Channels of Excitable Membranes + MBoC ch. 11. Single best test of the link contract on bio.
§18 organismal	18.04.02 Muscle contraction — actin-myosin cycle	Cross-domain prereqs: physics §09 mechanics, chem §15 ATP-driven catalysis. Hooks out to phil §20 (mechanism vs purposive action). Anchored in Boron-Boulpaep ch. on muscle + MBoC ch. 16.
§19 eco/evo	19.02.01 Hardy-Weinberg equilibrium	Cleanest math-side dependence on bio's axis (probability §02); minimal chem/physics cross-deps; hooks out to phil (chance, contingency, fitness as latent variable). Anchored in Hartl-Clark ch. 2 + Futuyma ch. on selection.
Essay	"What life is — biology between physics and intentionality" (17.essays.01 or pan-bio essay slot)	Spans all three trees, pairs with phil §20; exercises essay-mode with cross-tree references

Sequence: 19.02.01 → 18.04.02 → 17.09.02 → essay.

Rationale for order:

• Hardy-Weinberg first because it has the fewest cross-domain prereqs (essentially just math probability). Establishes the bio production pattern on the lightest cross-deps so we can isolate bio-specific friction before piling on cross-domain complexity.
• Muscle contraction second because it brings in physics §09 and chem §15 — two cross-domain prereqs, not yet the maximum.
• Action potential third because it's the hardest test case: chem + physics + math + bio-internal prereqs simultaneously. If the link contract survives the action potential, it survives anything bio will throw at it.
• Essay last because it can reference the three units already shipped.

6.1 Success criteria (Wave 1 bio)

• All 3 units exist in content/1{7,8,9}-<slug>/ per spec, with hooks_out.
• The essay exists at site/src/content/biology/01-what-life-is.md with ID 17.essays.01 (or pan-bio scheme TBD).
• The action potential unit declares cross-domain prereqs to chem §15 (ion channels), physics §10 (electromagnetism), physics §11 (Nernst from stat mech), math §02 (ODEs). At least 3 of these are cross-domain pending if the targets don't exist yet.
• All hooks_out to phil land on either 20.essays.NN or 20.NN.NN analytic-phil unit targets, with kind: proposed until the phil-side reviewer attests them (no special 20.pending placeholder — the proposed state in the umbrella §3.2 contract is the "target may not exist yet" mechanism).
• At least one hooks_out → chem exists somewhere in the wave (the cellular biology side does cite into chem-mechanism units; cross-direction hook for the bidirectional graph).
• Reviewer attestation logged; bio-side reviewer recruited or flagged.
• Retro into docs/pilot-lessons.md — explicitly diagnose whether action-potential's cross-domain prereqs strained the contract.

The wave fails if:

• Action potential ships with fewer than 3 cross-domain prereqs (cells-only treatment would defeat the stress-test purpose).
• Any pending_prereqs edge into chem or physics fails to resolve to a planned future unit (would mean the chem/physics plans don't actually cover what bio needs).
• The essay's cross-refs across the three bio sections don't resolve.
• Reviewer recruitment for bio has zero progress by wave end.

6.2 Production strategy

Item	Strategy	Notes
19.02.01 Hardy-Weinberg	Manual	Pattern-setter for bio; lightest cross-deps
18.04.02 Muscle contraction	Agent-drafted + editorial pass	Standard textbook content
17.09.02 Action potential	Manual	Densest cross-domain prereq node; benefits from human-author judgment on cross-cite choices
Essay	Manual	Synthesis-mode; spans trees

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§7 Reviewer roster

Bio reviewer recruitment is even harder than chem because:

1. Tyler's bio background is not assumed at expert level (cf. PHYSICS_PLAN where gauge-theory expertise grounds the math/physics side).
2. Bio sub-fields are more siloed than chem — a Hodgkin-Huxley reviewer is not the same person as a population-genetics reviewer.
3. Three trees → at least three reviewer specialties needed.

Tree	Tyler-solo?	Outside reviewers needed
§17 mol/cell	Yellow at beginner; Red at intermediate/master	Mol-bio / biochem PhD (general 17.01–07); cellular neuroscientist (17.09); cell-cycle/cancer specialist (17.08); immunologist (17.10) — likely overlapping with one reviewer covering 17.01–07
§18 organismal	Yellow at beginner; Red at intermediate/master	Physiologist (general); developmental biologist (18.11); animal behavior researcher (18.12)
§19 eco/evo	Yellow with math-probability grounding from math §02; Red at master	Evolutionary biologist (pop gen + quantitative); ecologist; phylogeneticist

Recruitment priority:

1. Molecular / cellular biologist — covers most of §17 and the cellular sides of §18. Single highest-leverage hire.
2. Evolutionary biologist — covers §19, has lightest overlap with other domains so requires a dedicated hire.
3. Physiologist — covers §18 and the system-level side.

Three reviewers minimum before Wave 2 ships any master-tier unit. (Chem needed three reviewers also; bio likely needs the same number but with different specialties.)

LLM-augmented review is even more relied-on for bio than for chem at intermediate tier. Master tier requires named human review without exception — "predict a mutation phenotype" and "assess a primary paper's methods" are not LLM-checkable mastery endpoints.

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§8 Open questions (deferred)

Question	Deferred to	Why now is wrong
Does neuroscience eventually split out into its own section (e.g., §21 if expanded) given how much it spans §17 + §18 + phil?	After v1 ships; v2+ scope discussion	Premature; v1 distributes neuroscience across §17.09, §18.05, phil §20
Does v1 include any computational / systems biology as a coherent subsection, or remain distributed?	After Wave 2	Treat as distributed for now (Boolean networks, dynamical-systems models live in §17 / §19 chapters as application material)
How are the increasingly important AI-and-biology topics handled (protein folding via deep learning, AlphaFold-class results, ML for genomics)?	Per-unit; default no until clearly load-bearing	The underlying biology is in scope; the AI methods are not v1 chem/bio
What happens to "synthetic biology" as a discipline — distributed across §17 + §18 + chem, or its own subsection?	After Wave 2	Premature; treat as application chapters in §17
Does v1 include any sociobiology / evolutionary psychology?	Per-unit; default no	Contested; defer rather than commit to a take

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§9 Risks

Risk	Mitigation
The action-potential seed unit fails because the prereqs in chem / physics / math aren't yet shipped, and the cross-domain pending machinery isn't ready	Action potential is sequenced third in Wave 1 specifically so that Hardy-Weinberg and muscle contraction can debug the cross-domain pending machinery first
Reviewer recruitment for bio takes longer than for chem (it likely will), delaying Master-tier production	Restrict bio to Beginner+Intermediate until ≥ 1 reviewer of each specialty is named
The bio→phil hook surface is so dense that the essay budget (7) is exceeded by Wave 2	Hard cap at 7 enforced via reviewer rejection unless a strong "couldn't be a unit because X" justification
Boundary creep: pharm / clinical / cognitive content sneaks into bio because authors don't enforce exclusions	Reviewers check §2.2 boundary rules per unit; the test case for §17 is "is this about how the cell does it, or about how the drug fixes it" — only the first is bio v1
Three-spine coverage scaffold has more gaps than ACS / Fast Track because the three spines don't intersect cleanly	Coverage manifest (bio-coverage.json) tracks each spine's chapter coverage independently. Gap audit happens after Wave 2.
Origin-of-life unit (19.15) becomes a magnet for philosophical controversy that doesn't belong in a science curriculum	The unit covers mechanistic scenarios (RNA world, hydrothermal vents, lipid worlds, etc.) and explicit evidential standards; the metaphysical question lives in phil §20 with cross-ref

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§10 Decision log entries (to be added to OVERVIEW.md §12 on the same date)

Date	Decision	Rationale
2026-05-17	Bio decomposes into three sections §17 (mol/cell), §18 (organismal/physiological), §19 (eco/evo), matching the three independent trees biology actually has at the curricular level	The three trees are more independent than physics branches or chem sections — a learner can master §19 without §17; pretending otherwise would force false dependencies
2026-05-17	Three-spine coverage scaffold: Alberts MBoC drives §17; Campbell + Boron-Boulpaep drive §18; Futuyma + Begon + Hartl-Clark drive §19	No single canonical roadmap exists; three spines covering three trees keeps coverage decidable
2026-05-17	Boundary rules: biochem mechanism → chem §15.14, biochem-in-organism → bio §17. Action potentials → bio §17.09; computational/cognitive neuroscience → phil + v2+. Bioinformatics methods → math; tools → not v1. Origin-of-life mechanism → bio §19.15; metaphysics of life-emergence → phil	Without explicit boundaries, bio scope balloons (medicine, psych, bioinfo, etc. all try to enter); explicit rules prevent it
2026-05-17	Hybrid-mode essay budget ≤ 7 across bio v1 (vs ≤ 5 for chem)	Bio→phil hook surface is denser than chem→phil; explicit higher budget reflects this
2026-05-17	Wave 1 bio: 3 units + 1 essay, sequenced 19.02.01 Hardy-Weinberg → 18.04.02 muscle contraction → 17.09.02 action potential → essay. Action potential is the densest cross-domain prereq node in any domain	Sequencing escalates cross-domain prereq density; action potential is the link-contract stress test for bio
2026-05-17	Bio reviewer recruitment is gated as a Wave-2 blocker for master tier; three reviewer specialties needed minimum (mol/cell, evo, physiology)	Three independent trees → three reviewer specialties; no overlap possible
2026-05-17	v1 punts on the cog-sci / phil-of-mind boundary; cellular and systems neuroscience are bio, cognition is phil + v2+. Honest acknowledgment that this is a forced split contested in real research	Forcing a clean split is part of why v1 can ship; v2 may relax

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§11 Next immediate actions

Gated on BIBLE_EXPANSION_PLAN.md §10 patches AND Physics Wave 1 retro:

1. Sourcing pass — populate reference/_meta/SOURCES.md extensions for bio; identify license-permissive sources for the first units.
2. Coverage-scaffold manifest — create manifests/production/bio-coverage.json with three-spine chapter lists; empty unit-IDs until Wave 1 ships.
3. Reviewer recruitment — start outreach for three specialties (mol-cell, evo, physiology). Bandwidth target: ≥ 1 hire of each kind before Wave 2 master-tier production.
4. Produce 19.02.01 Hardy-Weinberg manually — the lightest-cross-deps seed; establishes the bio production pattern on bio-internal content first.
5. Retro on Hardy-Weinberg — diagnose bio-specific spec gaps before scaling.
6. Produce 18.04.02 muscle contraction agent-drafted with editorial pass.
7. Produce 17.09.02 action potential manually — the densest cross-domain prereq node; human author judgment on cross-cite choices.
8. Cross-domain audit on action potential specifically: did the link contract survive? Any pending edges fail to resolve? Any essential cross-domain dependencies missed? This is the wave-defining test.
9. Produce the essay manually after the three units ship; cross-references the trees.
10. Coordinate with chem plan — bio's chem prereqs (§15.14 enzyme mechanism, §15.12–13 biomolecules) need to be in chem's near-term backlog; revisit CHEMISTRY_PLAN.md §11 to align.

This plan is the canonical reference for the biology axis. When uncertain about bio section structure, tree boundaries, or coverage spines, check here. When updating, propagate to OVERVIEW.md §12 and BIBLE_EXPANSION_PLAN.md §6 the same day.