Goal pillars, requirement atoms, scientific pillars, gaps, hypotheses, rivals and the executable test.
also: single knockdown plus readout · omics fishing · computational filler · aged versus young characterization · permutation padding Five named experiment shapes the engine bans outright.
A single knockdown with a readout, omics fishing, computational filler, an aged-versus-young characterization, and permutation padding. The critic merges permutations and rejects the rest.
#also: shared language · shared vocabulary Two lists written in step 2, failure channels and system property variables, that every later stage tags against.
The lexicon is what lets goals be mapped to scientific reality: requirements, scientific pillars and experiments all refer back to the same named failure channels and the same measurable properties. The run report prints it as "Shared vocabulary: failure channels and system properties".
#also: cross-field source · the import · transfer from an unrelated field · mutation import field A hypothesis built by borrowing a law or equation from a field far from biology and mapping its variables onto the system.
Each set of rivals must include one. The record names the source field, the specific law and the variable mapping. The mutation directive names which of fifteen far fields the import must come from, such as non-equilibrium thermodynamics, control theory, fracture mechanics, percolation, queueing theory, phase transitions or distributed-systems consensus.
#also: unbiased discovery element An unbiased element built into at least one experiment per branch that asks what else might be happening that nobody predicted.
It sits alongside hypothesis testing so a run does not only confirm or refute what it already imagined.
#also: the test · prediction that distinguishes it · testable prediction The specific, measurable prediction that separates one hypothesis from its rivals.
It is the hypothesis's stake in the contest. The hypothesis audit checks whether it actually discriminates: a prediction every rival also makes is not a test, and a prediction that names no measurable outcome is not one either.
#also: L4 · tactical question · discriminator · kill shot · cheap kills · exploration · node type A question written to eliminate hypotheses: at least half of the tactical questions must pit two or more rivals against each other.
Step 8 works by elimination over description, in three phases: the kill shot (which single experiment eliminates the most hypotheses at once), cheap kills, and exploration. Node types are discriminator question, model requirement, tool requirement, unknown exploration and validation question. Five cognitive modes drive generation: reductionist, constructivist, lateralist, comparative and temporal.
#also: interface integrity · information control sensing · structural topological · resource energetic · systemic environmental · candidate set selection The five mechanism families a set of rivals must spread across, plus a sixth reserved for identification gaps.
Interface integrity, information control and sensing, structural and topological, resource and energetic, systemic and environmental. No two hypotheses for one gap may share a category. Candidate-set selection is the sixth, used only when the gap asks which things or how much, where the rivals are competing candidate sets and the no-duplicate rule is waived. The site renders each category as words a reader can meet.
#also: solves · partially solves · proxies for · violates · enables measurement for · the redline The kinds of link between a requirement and a scientific pillar: solves, partially solves, proxies for, violates, or enables measurement for.
A "violates" link is the redline: the science improves one requirement but its failure modes trigger a catastrophe the goal defines, and such links are removed. A partial link is sub-classified by the kind of delta: magnitude, execution, timescale or knowledge.
#also: L6 · leaf spec · leaf experiment · idea · proposed investigation · experiment specification The executable test at the bottom of the tree: system, intervention, meter and time, with what a positive and a null result would mean.
Every field must read like a lab notebook entry, specific enough that a technician could run it tomorrow without asking a question. An experiment carries expected impact, an informative null outcome, a link to the system property it moves, a feasibility score calibrated from standard assay to technology that does not exist yet, and whether it includes a discovery component. It must be pipeline-dependent: not conceivable by someone who only read a review article, because it requires the specific chain that produced it.
Published experiments are the site's "ideas": each has a public page with the original wording, a clear version, the logic back to the goal, the rivals and the payoff either way.
#also: FCC · failure channels · failure shape · FS_ A failure pattern specific to the target system, six to ten of them per run, named in the bridge lexicon.
Requirement atoms then describe each failure with a controlled failure shape such as slow drift to cliff, runaway feedback, compensatory toxicity, hysteresis lock, synchronization loss or unmodeled. At least one atom must target failure channels not captured by current meters.
#also: feasibility · ambition and feasibility An honest 1 to 10 calibration of how doable an experiment is, from a standard assay with commercial reagents to technology that does not exist.
Nine to ten means a standard assay and one to three months; one to two means the required technology does not exist yet. Ranking weighs feasibility against ambition rather than optimizing either alone.
#also: genesis probe · contextual decoupling · causal pivot · arbitration logic · adversarial falsification · strategy protocol The question-writing strategy matched to each gap type.
Genesis probe for a void, contextual decoupling for a fragility trap, causal pivot for a proxy mirage, arbitration logic for a cluster clash, and adversarial falsification, which is mandatory and designs a question to disprove the most promising scientific pillar.
#also: void · fragile · proxy · clash · adversarial · cluster status What kind of unknown a gap is: void, fragile, proxy, clash, or adversarial.
Void: nothing is known here, the question has not been asked of this system. Fragile: something is claimed, but on evidence too thin to carry weight. Proxy: what is measured stands in for what matters and may not track it. Clash: two established results predict opposite outcomes and both cannot be right. Adversarial: a question written to disprove the most promising scientific pillar. A goal-level cluster status says which kind dominates: void, fragility trap, proxy mirage or cluster clash.
#also: pillar · M_G · teleological goal pillar · required end-state · cross-cutting pillar One required end-state that, together with the others, would make the master question plausible.
Pillars are architecture-neutral and as mutually exclusive and jointly exhaustive as the engine can make them. They are found by inverse failure analysis: list the catastrophic failures, cluster them, and invert each cluster into the healthy steady state that must hold. A pillar title must name a mechanism of failure, not an anatomical subsystem; a title that could be a textbook chapter is rejected. At least one pillar must be cross-cutting, addressing a systemic failure not obvious from anatomy. Each pillar carries a role: failure mechanism, or the one reserved identification pillar.
Note the two uses of "pillar": a goal pillar is a required end-state on the goal side; a scientific pillar is a piece of established science on the reality side.
#also: heretic · the standing · heterodox · not mainstream The four tests a heretical hypothesis must pass: it revises a subfield, is not mainstream, has an empirical anchor, and predicts a testable surprise.
Every set of rivals must contain a heretic that contradicts the mainstream account. On the page the section "The standing" says why the hypothesis is not the mainstream account, using this checklist.
#also: IH · instantiation hypothesis · hypotheses · competing explanation One of several rival explanations for a gap, each proposing a fundamentally different mechanism, with the prediction that would tell it apart.
Step 7 writes four to seven hypotheses per gap, maximally divergent: each must use a different domain category, the set must contain a heretic that contradicts the mainstream story, a cross-domain transfer from an unrelated field, and scouts including the possibility that the phenomenon does not exist. A hypothesis carries its mechanism, a discriminating prediction, its lens origin, its domain category and, for a cross-domain one, the source field, the law borrowed and the variable mapping.
On the site a hypothesis is a publishable object of its own, named on arrival, keyed on its run, and read in eight sections: the unknown, the claim, the test, the contest, the import, the bench, the standing and the provenance.
#also: identification obligation chain · identification pillar · enumeration and quantity The rule that a question asking which things and how much must be answered with a set and a number at every stage, not with a mechanism.
It was added after a run about tissue replacement produced a hundred hypotheses that named no tissue: step 2 had recorded the answer type only in prose, and no later stage knew the pillar was different. Now the obligation travels as a typed role from pillar to atom to gap question to hypothesis, a runtime prompt block restates it for the identification pillar only, and a checker tracks the two halves, enumeration and quantity, so a retry can be told which half is missing.
#also: null result · both outcomes informative · payoff either way What is learned if the experiment shows no significant result; it must be informative, never "inconclusive".
A required design property: both outcomes of the experiment must teach something. The experiment page has a section "Both outcomes are informative" built from this field, and the critic rejects specifications that fail it.
#also: IFA · naming test · anatomy test The method step 2 uses: enumerate catastrophic failures, cluster them, and invert each cluster into a required healthy state.
Failures are first classified as within or between subsystems, then clustered into pillars. The naming test then rejects any pillar whose title describes a subsystem rather than the mechanism by which it fails.
#also: gap · gap question · L3 · seed question · epistemic gap · frontier question · knowledge-gap question A genuine unknown where what the requirements need and what established science delivers do not meet, stated as a question that a literature search cannot answer.
Step 6 writes the gap questions. Each must identify an epistemic gap that would change how the problem is thought about, and each is typed by what kind of gap it is. On the public site the gap is the unknown a hypothesis exists to explain; the reader meets it first as a rewritten heading stating its core, with the engine's original sentence folded underneath.
A gap question can also turn out to be already answered in the literature. The explanation layer says so plainly, because a pipeline proposing a closed gap is a valuable finding, not a failure.
#also: substrate lens · evolution comparative lens · communication lens Which of three generating questions produced a hypothesis: the medium the bad state is stored in, how long-lived species avoid it, or what protocol broadcasts the error.
Substrate lens: in what physical medium is the maladaptive state stored? Evolution or comparative lens: how do long-lived species prevent this? Communication lens: what protocol broadcasts the error systemically? It is recorded on the hypothesis and is distinct from the run-level epistemic lens.
#also: Q0 · Q₀ · engineering-grade master question The single precise question the whole run answers, written from the operator's goal by step 1.
It must be solution-neutral, explicit about the system it concerns, anchored to a baseline, driven by success criteria, decomposable, and explicit about mission duration. Everything below it is a narrowing of it, and the question-fidelity audit later measures whether the descent still answers what the operator typed rather than what the engine rewrote.
#also: L5 · drill branch · mechanism drill · tool requirement · model requirement · validation drill The bottleneck under a discriminating question, classed by what blocks it: cannot measure, cannot isolate, mechanism unclear, or assumptions untested.
Cannot measure it becomes a tool requirement; cannot isolate it becomes a model requirement; mechanism unclear becomes a mechanism drill; assumptions untested becomes a validation drill. Each branch ends in leaf experiments.
#also: forbidden categories · import field A per-gap instruction that forbids two domain categories and names the single far field the cross-domain import must come from.
It exists because, across 175 gaps, the five categories had each been used exactly once per gap every time, so the catalogue held five recurring shapes rather than hundreds of ideas. The directive is deterministic in the gap id and the master question, so re-runs get the same constraint.
#also: the gap triple · delta · delta summary · epistemic block The three-part statement of a gap: what the requirements need, what science actually delivers, and the specific difference.
The delta names its kind: magnitude, execution, timescale, knowledge or contradiction. At goal level the engine also writes a delta summary (the gap between the required regime and current capability) and an epistemic block (which assumption is obstructing progress).
#also: pipeline-dependent · not novel The engine's own test of worth: an experiment that could be conceived from a review article alone fails it.
An experiment must require knowing the specific chain from goal to pillar to requirement to science to gap to hypothesis that produced it. Non-triviality is the highest-priority criterion of the best-experiments selector. The engine has no separate "novelty" field; the nearest words are this test and the operator's "not novel" feedback category.
#also: pillar_role · atom_role · answer_type · identification · failure mechanism · mechanism · which question · how much question A typed field that says what kind of answer a pillar, atom or gap question owes: a failure mechanism, or an identification of which things and how much.
Most pillars are failure-mechanism pillars. When the master question asks which things or how much, exactly one pillar carries the identification role: its end-state is that the set the question asks for is identified and its size established, in the question's own terms. The role is carried as data down the chain, because later stages cannot recover the obligation from prose. An identification gap question must include both a which question and a how much question; both halves or the obligation is not carried.
#also: RA · atom · atoms · done criteria One solution-agnostic, testable requirement under a goal pillar, with done criteria and a failure mode.
Each atom names a state variable, a failure shape, the perturbation classes that would expose it, a timescale (acute, subacute, chronic or decadal), the classes of meter that could measure it, and a multiple-realizability check requiring at least three distinct architectures that could satisfy it. Atoms carry the same role split as pillars: an identification atom guards against the answer being wrong (the set miscounted, a rival set never compared).
#also: domain · DOM · domain finding · domain category · domain scan · reality mapping One of eight to twelve research areas the engine scans for established science relevant to the goal.
Domains are meant to be mutually exclusive and each to contain about twenty-five actionable interventions. Each is tagged core mechanistic, adjacent non-obvious, or measurement technology. Step 4b fans out over the domains, one call each; when the proxy pool has less capacity than domains, a domain can be silently dropped, which is why the domain count of a run is checked.
#also: rivals · rival hypothesis · the contest · competition matrix · distinguishing observable Another hypothesis for the same gap; every pair of rivals is bound to one observable that would come out differently under each.
The competition matrix of a gap lists, for each pair of hypotheses, the one measurable outcome where they predict differently. A hypothesis that predicts what its rivals predict has nothing to contest and earns no experiment. On the page a rival arrives from the engine named only by a machine label; the card prints a plain axis name with one line of gloss and keeps the raw label folded underneath.
#also: S-node · S_ · scientific record · readiness level · fragility score A piece of established, evidence-based science collected in step 4b: what is actually known, never a speculative intervention.
Each carries a mechanism, a verified effect, a readiness level (RL-1 lab-validated, RL-2 human data or models, RL-3 clinically deployed), capabilities, a fragility score from 1 to 10, and its relationship to the goal. Scientific pillars are what the gap questions compare against requirements; the pillar provenance audit later checks whether the studies they cite can be found.
#also: S-I-M-T · S · I · M · T · lab specification · simt · threshold The four parameters that fully specify an experiment: what it runs in, what is done to it, what is measured and how, and over what time.
The clear version renders them as six blocks: what it runs in, what is done to it, what is measured and how, what the numbers have to show, what a positive result would change, and what a null result would mean. A meter is the measurement; requirement atoms speak of meter classes and whether a meter exists, partially exists or is missing as of 2026.
#also: SPV · system properties · state variable · SV_ A measurable property of the target system, with a unit and a measurement approach, eight to twelve per run.
Experiments link back to the property they move. Requirement atoms use controlled state-variable names on the same idea, such as functional reserve or an unknown failure channel.
#also: latent failure detection · missing observability The requirement atom every pillar must contain that targets failures current meters cannot see.
It is marked with the unknown failure channel state variable or the unmodeled failure shape. Its purpose is to keep the decomposition honest about what is not observable yet.
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