{"schema_version":1,"experiment_id":"eoa_inverse_innovation_exp05_complete_proposal_portfolio20_20260803","cell_id":"invariant_mode_decomposition_design__biology_ecology","arm":"COMPLETE_PROPOSAL_PORTFOLIO","candidate_id":"cand_bioeco_founder_balance_mode_gate_004","proposal_index":4,"version":0,"title":"Founder-Contribution Mode Gate for Conservation Breeding Plans","problem":"A conservation breeding program can approve each proposed pairing because it satisfies pairwise kinship and demographic rules while the complete plan still channels future genetic contribution toward a correlated subset of founders. Pair-by-pair metrics do not show how reproduction, offspring retention, aging, and transfers jointly transform founder contributions across breeding classes. A collective lineage-concentration direction can therefore persist or grow even when no individual pairing appears exceptional.","actors":["Conservation breeding program authority","Studbook keeper","Population geneticist","Veterinarians and animal-care teams","Animal-welfare and ethics reviewers","Participating animal-holding institutions","Animals represented in the breeding plan"],"observable_state":"At each breeding-cycle boundary, the program records expected or genotype-informed founder contributions for living animals, organized by reproductive class and participating institution, together with kinship, age, sex, reproductive eligibility, planned pairings, expected offspring allocation, retention, aging, and approved transfers. Conditional on a specified plan and bounded fertility and retention assumptions, an explicit transition matrix maps the current founder-contribution state into the expected next-cycle state. Decision signals include each mode's founder and class loadings, scalar gain, stability class, sensitivity to feasible plan changes, eigenvector conditioning, reconstruction residual against completed cycles, spectral separation, and drift after demographic or pedigree updates.","consequence":"Repeated execution of individually acceptable pairings could amplify a collective contribution imbalance, reduce representation of other founders, or make later demographic and kinship constraints harder to satisfy. Conversely, reacting to a conspicuous rare founder without analyzing the full transformation could shift imbalance into another correlated lineage or reproductive class.","affected_objective":"Authorize a feasible pairing, offspring-retention, and transfer portfolio that meets animal-welfare and demographic requirements while avoiding amplification of reproducible founder-concentration modes and preserving traceability between modal findings and individual breeding decisions.","intervention":"Add a founder-contribution mode gate to breeding-plan authorization. Define the contribution state and target reference distribution; construct the explicit expected transition operator for every feasible plan under fixed welfare, demographic, institutional, and genetic constraints; decompose each operator into invariant modes and gains; and classify deviations from the reference as decaying, marginal, persistent, oscillatory, or growing. A modal sensitivity sweep substitutes one permitted pairing, retention allocation, or transfer at a time and measures the change in action-relevant mode gains, projected contribution balance, demographic feasibility, and protected welfare constraints. The authority may prefer a plan only when its modal distinction is reproducible, adequately conditioned and separated, supported by held-out reconstruction, and not obtained by relaxing non-negotiable constraints. The gate produces an advisory plan and bounded interpretation report; it never authorizes animal actions automatically.","structural_mapping":[{"archetype_element":"Transformation Scope","domain_realization":"The transformation is the expected breeding-cycle update of founder contributions through planned reproduction, retention, aging, and authorized institutional transfers."},{"archetype_element":"State-Vector Definition","domain_realization":"Coordinates represent founder contributions within defined reproductive classes and institutions, rather than treating animals, founders, or pairwise kinship values as independent summaries."},{"archetype_element":"Invariant Mode Basis","domain_realization":"Eigenvectors identify coupled founder-class contribution patterns that a proposed breeding plan approximately preserves as directions over repeated cycles."},{"archetype_element":"Modal Gain Spectrum and Stability Partition","domain_realization":"Eigenvalues estimate whether each contribution imbalance decays, persists, reverses, oscillates, or grows under repeated application of the proposed plan within its validity window."},{"archetype_element":"Dominant Mode Selection Rule","domain_realization":"A contribution mode becomes decision-relevant only if it is reproducible, sufficiently conditioned and separated, consequential for a predefined founder-balance objective, and not merely the neutral total-contribution direction."},{"archetype_element":"Modal Intervention Map and Mode-Coupling Register","domain_realization":"Permitted pairing substitutions, offspring-retention changes, and transfers are mapped to changes in modal gains and coordinates, with cross-effects on other lineages, demographic classes, and institutions recorded."},{"archetype_element":"Reconstruction Residual Check","domain_realization":"Operators fitted before a historical cutoff reconstruct held-out founder-contribution changes from completed cycles; residual magnitude and lineage or class structure determine whether the modal account is usable."},{"archetype_element":"Mode Drift Monitor and Interpretation Scope Contract","domain_realization":"The basis and spectral gap are rechecked after births, deaths, infertility findings, pedigree corrections, genomic updates, eligibility changes, or institutional withdrawal, and every recommendation is limited to the assumptions and candidate set used to construct it."}],"mechanism_mapping":[{"mechanism_slug":"eigendecomposition_workflow","role":"Factor each explicit breeding-plan transition operator into its complete invariant contribution modes and scalar gains.","counterfactual_removal":"Without decomposition, the program could compare pairwise or aggregate genetic metrics but could not see collective founder-class directions preserved and amplified by the full plan."},{"mechanism_slug":"modal_stability_analysis","role":"Classify contribution-imbalance modes relative to the discrete-cycle stability boundary while separating them from the neutral total-contribution direction.","counterfactual_removal":"Without stability classification, the analysis would not distinguish an imbalance expected to fade from one that persists or grows under repeated planning."},{"mechanism_slug":"modal_sensitivity_sweep","role":"Substitute feasible pairings, retention allocations, and transfers one at a time to rank their leverage on targeted modes and reveal cross-effects on other constraints.","counterfactual_removal":"Without the sweep, a concerning mode would remain descriptive and planners could not identify which permissible decision changes it or what collateral shifts those changes create."},{"mechanism_slug":"residual_reconstruction_test","role":"Compare contribution changes reconstructed from retained modes with held-out completed-cycle records and inspect lineage- and class-structured residuals.","counterfactual_removal":"Without reconstruction testing, expected inheritance and retention assumptions could make a compact modal plan appear reliable despite systematic mismatch with realized breeding cycles."},{"mechanism_slug":"spectral_gap_monitor","role":"Track separation and identity of action-relevant modes as the candidate population, pedigree, reproductive eligibility, and institutional commitments change.","counterfactual_removal":"Without gap and drift monitoring, an advisory plan could remain attached to a mode that has rotated, exchanged order, or ceased to be distinguishable."},{"mechanism_slug":"spectral_decomposition_report","role":"Document mode composition, gains, sensitivities, couplings, reconstruction error, welfare constraints, demographic assumptions, and prohibited interpretations for the authorization body.","counterfactual_removal":"Without the report, expected contribution modes could be mistaken for deterministic offspring outcomes or used to obscure welfare and institutional judgments behind a mathematical ranking."}],"causal_chain":["Reproduction transmits combinations of parental founder contributions into offspring, while retention, aging, and transfers determine which combinations enter the next breeding state.","Taken together, the planned decisions form a repeated transformation that is not represented by inspecting each pairing separately.","Decomposition exposes collective founder-class directions that the plan is expected to damp, preserve, reverse, or amplify.","Stability, conditioning, consequence, and spectral-gap rules distinguish an action-relevant concentration mode from neutral conservation of total contribution or numerical artifacts.","Sensitivity sweeps identify feasible pairing, retention, or transfer substitutions that oppose the selected mode and disclose their effects on other lineages and demographic classes.","A plan may pass the modal gate only after all animal-welfare, veterinary, demographic, and institutional constraints have been applied independently of its modal score.","Held-out reconstruction and post-update drift checks determine whether the advisory plan remains interpretable or must be withdrawn and recomputed."],"baseline":"The baseline is sequential breeding-plan construction using pairwise mean kinship, demographic compatibility, reproductive eligibility, rare-founder priorities, and institutional feasibility. Planners review aggregate projected diversity, but authorization is not conditioned on the invariant modes, gains, conditioning, residual reconstruction, or drift of the complete breeding-cycle transformation.","nearest_rivals":["Minimum-mean-kinship pairing that ranks candidate mates from pairwise relatedness without decomposing the repeated full-plan transformation.","Optimal-contribution selection that allocates reproductive contributions under an aggregate coancestry objective without an explicit modal stability and residual gate.","Rare-founder quotas that reserve breeding opportunities for underrepresented lineages without modeling correlated founder-class directions.","Demographic population-viability simulation that tests population size and age structure but does not expose genetic-contribution modes.","Monte Carlo pedigree or genomic simulation that compares endpoint distributions across plans without producing traceable invariant directions and scalar gains."],"remaining_contrastive_claim":"The candidate's bounded contrast is procedural: it evaluates the complete repeated breeding-plan operator, identifies reproducible founder-contribution modes, and conditions any advisory preference on mode gain, feasible decision sensitivity, reconstruction residual, spectral separation, drift, and independently enforced welfare constraints. Rivals rank pairings, optimize aggregate coancestry, impose founder quotas, or compare simulated endpoints. This contrast does not establish superior genetic or demographic outcomes.","authority_safety":{"decision_authority":"The multi-institution conservation breeding authority owns the advisory comparison, but each holding institution and its veterinarian retain authority over animals in their care. Welfare and ethics reviewers may reject any plan regardless of its modal score.","authorized_first_step":"Perform a non-operative retrospective replay using pedigree, genomic, demographic, and completed breeding-cycle records available under existing governance. Fit operators using records before a declared cutoff, test reconstruction on a held-out completed cycle, and generate a shadow plan for the next cycle that has no operational force.","excluded_actions":["No pairing, separation, transfer, contraception, gamete collection, assisted reproduction, offspring-retention decision, or euthanasia based on the pilot output.","No relaxation of welfare, veterinary, demographic, legal, institutional, or species-management constraints to improve a modal score.","No treatment of expected founder contributions as deterministic inheritance outcomes.","No exclusion of an animal solely because it loads strongly on an unfavorable mode.","No use of genomic or institutional data beyond its approved purpose or access boundary.","No automated ranking presented without the feasible alternatives, residuals, conditioning, couplings, and interpretation limits.","No extrapolation beyond the represented candidate population, institutions, reproductive assumptions, or planning horizon."],"halt_rollback":"Withdraw the shadow plan and revert to the existing authorization process if pedigree or genotype provenance fails review, candidate eligibility changes, a participating institution withdraws, a welfare constraint is incompletely encoded, the operator is defective or ill-conditioned, the action-relevant spectral gap falls below its preregistered threshold, held-out residuals exceed budget or retain lineage structure, or mode identity drifts beyond tolerance. Because the first step is non-operative, rollback consists of discarding the advisory ranking, correcting inputs or scope, and documenting why no animal action was authorized."},"negative_tests":{"strongest_counterevidence":"Across held-out completed cycles and reasonable uncertainty ranges, modal identities and plan rankings are unstable, and the mode gate supplies no reliable distinction beyond minimum-mean-kinship, optimal-contribution, or Monte Carlo planning under the same welfare and demographic constraints.","problem_falsifier":"All feasible plans have only neutral or adequately decaying contribution-imbalance modes within the planning window, or aggregate contribution and pairwise criteria fully determine the next-cycle trajectory without any reproducible collective founder-class direction.","intervention_falsifier":"The preregistered shadow plan does not reduce the targeted mode's predicted or held-out realized coordinate relative to a matched rival plan, or any apparent reduction depends on violating welfare, demographic, institutional, data-governance, or founder-representation safeguards.","risks":["Expected transmission operators can underrepresent Mendelian segregation, uncertain fertility, offspring survival, and unplanned retention decisions.","Small candidate populations can produce repeated or closely spaced eigenvalues and unstable mode identities.","A non-normal operator can create transient concentration not summarized by asymptotic eigenvalue stability.","Pedigree errors, missing founders, genomic uncertainty, or changing reproductive eligibility can rotate the inferred basis.","An aggregate founder-balance target may conflict with demographic viability or species-specific management priorities.","Mathematical rankings can exert undue authority over veterinary, welfare, and institutional judgments.","Individuals or institutions could be stigmatized through careless interpretation of high modal loadings.","A locally favorable plan can reduce future flexibility outside the modeled planning horizon." ]},"next_evidence_step":"Predeclare a historical cutoff and use only earlier records to define the founder-class state, reference distribution, feasible-plan constraints, fertility and retention ranges, operator construction, mode-matching rule, conditioning limit, stability boundary, spectral-gap threshold, residual budget, and rival planning methods. Reconstruct one or more completed post-cutoff cycles without refitting and compare predicted modal coordinates with recorded founder-contribution changes. Then construct a non-operative shadow plan for the upcoming cycle and record whether the modal gate changes any pairing, retention, or transfer preference after identical welfare and demographic constraints are imposed. The first evidence question is whether the modes are reproducible, reconstruct realized contribution changes within the stated budget, and distinguish feasible plans without overriding protected constraints; no live breeding action follows.","prior_art_status":"UNSEARCHED","diversity_from_prior_proposals":"Proposal 1 changes nutrient loading and mechanical mixing to oppose coupled bloom–hypoxia dynamics in a shallow lake. Proposal 2 schedules seed capture, seedling removal, and clipping to suppress an invasive annual plant's stage-zone replenishment mode. Proposal 3 reallocates pathogen assays to improve observability of a wildlife host-stage–reservoir mode without changing the underlying disease process. This proposal governs conservation breeding by comparing how complete pairing, offspring-retention, aging, and transfer portfolios transform founder genetic contributions. Relative to proposal 1, it manages inheritance and reproductive planning rather than physicochemical ecosystem dynamics. Relative to proposal 2, it preserves representation within a managed conservation population rather than suppressing an invasive population, and its controls are pairings and retention decisions rather than removal treatments. Relative to proposal 3, it changes the biological transition itself through a separately authorized breeding plan rather than reallocating measurements. Its actors, managed object, state representation, intervention, authority structure, ethical safeguards, evidence source, and causal path are distinct, making it independently adoptable rather than a feature or population variant of any earlier proposal.","revision_record":{"parent_version":null,"progress_targets_addressed":["Created a fourth complete candidate for a distinct conservation-breeding problem.","Specified a breeding-plan authorization intervention based on founder-contribution modes.","Distinguished the candidate explicitly from proposals 1, 2, and 3.","Included non-operative first evidence, animal-welfare authority boundaries, rivals, safeguards, residual checks, and falsifiers."],"conceptual_changes":[],"operational_changes":[],"evidence_changes":[],"claim_changes":[]}}