{"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_seedbank_escape_mode_002","proposal_index":2,"version":0,"title":"Seedbank Escape-Mode Suppression for Invasive Annual Plants","problem":"A land manager treats an invasive annual plant according to visible seedling density or adult cover, but the population moves through coupled seedbank, emergence, growth, reproduction, and dispersal states across different habitat zones. Adult removal can make standing cover fall while a combined deep-seedbank–late-emergence–seed-rain direction remains weakly damped or grows. Acting on the most visible life stage can therefore leave the transformation that replenishes future cohorts substantially intact.","actors":["Protected-area land manager","Invasive-plant control crew","Plant population ecologist","Seed-testing laboratory","Facility biosafety officer for contained trials","Native plants and soil biota in prospective treatment areas"],"observable_state":"At fixed intervals, measurements form a state vector comprising viable shallow and deep seedbank density, early and late emerged seedlings, vegetative plants, reproductive stems, captured seed rain, and movement among edge, disturbed, and intact habitat zones. Within a declared density, moisture, temperature, and phenological window, an estimated transition matrix maps one interval's deviations from a reference state to the next. Observable decision signals include each mode's stage-zone composition, scalar gain, stability class, sensitivity to permitted treatments, eigenvector conditioning, retained-mode reconstruction residual, spectral gap, and drift across blocks or seasons.","consequence":"A treatment chosen from adult cover alone could remove current stems while failing to interrupt the coupled direction that transfers viable seeds through late emergence and edge-zone reproduction into the next seedbank. The manager could then repeat labor-intensive treatment, expand disturbance, or declare control prematurely without evidence that the action-relevant population trajectory was damped.","affected_objective":"Allocate a fixed manual-control budget across life stages, treatment times, and habitat zones so that the action-relevant replenishment mode is opposed while native-plant disturbance, soil disturbance, seed escape, worker exposure, and model-invalidity safeguards remain within preset limits.","intervention":"Adopt a mode-gated treatment-scheduling protocol. Define the stage-by-zone state and local transition window; estimate an explicit transition matrix from securely contained plant microcosms; compute its full eigenbasis and gain spectrum; classify growing, decaying, marginal, and oscillatory modes; and identify any reproducible mode that carries viable seedbank mass toward renewed reproduction. Represent permitted controls—surface seed capture, early seedling removal, and pre-seed-set stem clipping with bagged material—as timed inputs. A modal sensitivity sweep compares equal-effort treatment schedules by their predicted influence on the targeted mode and records cross-effects on other modes. Only the lowest-disturbance schedule that opposes the targeted mode without amplifying a protected native-plant or dispersal mode advances to contained validation. No field recommendation is issued when the basis is ill-conditioned, the relevant mode lacks adequate spectral separation, held-out residuals are excessive or structured, mode identity drifts, or observations leave the interpretation window.","structural_mapping":[{"archetype_element":"Transformation Scope","domain_realization":"The transformation is the fixed-interval movement of an invasive annual plant through seedbank, emergence, vegetative, reproductive, and seed-dispersal states across defined habitat zones."},{"archetype_element":"State-Vector Definition","domain_realization":"Every coordinate identifies both a biological stage and a spatial zone, preventing adult cover or total abundance from standing in for the full population state."},{"archetype_element":"Invariant Mode Basis","domain_realization":"Eigenvectors represent coupled stage-zone patterns that the fitted local transition approximately preserves as directions, such as a pattern linking late emergence at edges to seed rain and shallow-seedbank replenishment."},{"archetype_element":"Modal Gain Spectrum","domain_realization":"Eigenvalues estimate whether each coupled pattern grows, decays, persists, reverses, or oscillates from one sampling interval to the next within the declared regime."},{"archetype_element":"Stable/Unstable Mode Partition","domain_realization":"Modes are classified relative to the discrete-time stability boundary, with near-boundary estimates retained as marginal and uncertainty reported."},{"archetype_element":"Modal Intervention Map and Mode-Coupling Register","domain_realization":"Each timed manual treatment is projected into modal coordinates, and unintended movement of non-target stage-zone patterns is recorded rather than assuming that treatments act independently."},{"archetype_element":"Reconstruction Residual Check","domain_realization":"Independent microcosm trajectories are reconstructed from retained modes; both residual magnitude and remaining phenological or spatial structure determine fitness for use."},{"archetype_element":"Mode Drift Monitor, Spectral Gap Threshold, and Interpretation Scope Contract","domain_realization":"The protocol tracks mode rotation, reordering, and retained-versus-omitted spectral separation, while binding every interpretation to the tested density, soil, moisture, temperature, and treatment ranges."}],"mechanism_mapping":[{"mechanism_slug":"eigendecomposition_workflow","role":"Factor the explicit stage-by-zone transition matrix into a complete local mode basis and gain spectrum traceable to measured plant states.","counterfactual_removal":"Without the decomposition, treatment planning would remain organized around separate life-stage counts and could not identify the coupled replenishment direction."},{"mechanism_slug":"modal_stability_analysis","role":"Classify each mode as growing, decaying, marginal, or oscillatory within the declared phenological and environmental window.","counterfactual_removal":"Without stability classification, the analysis could describe coupled patterns but could not distinguish a fading pattern from one requiring control attention."},{"mechanism_slug":"modal_sensitivity_sweep","role":"Perturb the timing and allocation of equal-effort manual controls in the fitted model, rank their leverage on the targeted mode, and register cross-mode effects.","counterfactual_removal":"Without the sweep, the mode with the largest gain would not be connected to an actionable schedule, and a treatment that transfers pressure into another stage or zone could appear attractive."},{"mechanism_slug":"residual_reconstruction_test","role":"Reconstruct held-out stage-zone trajectories using the retained modes and inspect the leftover error for magnitude and biological structure.","counterfactual_removal":"Without this test, a low-amplitude late-emergence or dispersal pattern could be omitted even if it materially replenishes the seedbank."},{"mechanism_slug":"spectral_gap_monitor","role":"Track separation between retained and omitted modes and changes in mode direction or ordering across replicate blocks and subsequent estimation windows.","counterfactual_removal":"Without gap and drift monitoring, a treatment schedule could remain attached to a mode after that mode becomes an unstable mixture or loses decision relevance."},{"mechanism_slug":"spectral_decomposition_report","role":"Document mode composition, gains, treatment sensitivities, couplings, residuals, conditioning, guardrails, and prohibited interpretations for control crews and authorizers.","counterfactual_removal":"Without a bounded report, descriptive local modes could be communicated as independent biological causes or as prescriptions valid across untested soils and seasons."}],"causal_chain":["Seeds, seedlings, vegetative plants, reproductive stems, and seed rain transition jointly across habitat zones rather than changing as independent counts.","A locally estimated transition matrix encodes those coupled stage and spatial transfers over a fixed interval.","Decomposition exposes stage-zone combinations that approximately retain their direction while growing, decaying, persisting, or oscillating.","Stability, conditioning, and spectral-separation checks determine whether a replenishment mode is sufficiently interpretable to support a bounded decision.","Sensitivity sweeps show how equal-effort treatment schedules project onto that mode and whether suppressing it moves other protected or dispersal modes.","A contained mode-aligned sequence applies controls at the stages and zones whose combined leverage opposes replenishment, rather than concentrating effort on visible adults.","Held-out modal amplitude, viable-seed production, residual structure, mode drift, native-plant proxies, and containment checks determine whether the schedule is rejected, revised, or eligible for a separately authorized field test."],"baseline":"The operational baseline is visible-stage control: survey adult cover, clip or pull dense patches before seed set, and revisit locations whose cover exceeds a threshold. Timing and location follow current standing abundance; shallow and deep seedbank states, late emergence, cross-zone transfer, modal gain, residual reconstruction, and basis drift do not gate the decision.","nearest_rivals":["A stage-structured population matrix analyzed only through the dominant growth rate and single-transition elasticities, without decomposing multiple action-relevant modes or checking reconstruction residuals.","A habitat-suitability map that directs crews toward high-scoring patches but does not model transfers among biological stages and zones.","A seedbank-depletion model that optimizes treatment duration from aggregate viable-seed counts without representing spatially coupled replenishment modes.","A factorial control trial comparing endpoint adult cover or seed production across schedules without testing which invariant stage-zone direction each schedule excites.","A network-centrality ranking of dispersal zones that ignores within-zone seedbank, emergence, and reproduction transitions."],"remaining_contrastive_claim":"The candidate's bounded contrast is that it selects an equal-effort treatment sequence from its leverage on a reproducible stage-zone replenishment mode and conditions use on modal stability, coupling, reconstruction, spectral-gap, and drift checks. Rivals select from visible abundance, isolated transition elasticity, habitat score, aggregate seedbank forecasts, or endpoint treatment averages. This contrast does not establish that the mode-gated sequence will perform better.","authority_safety":{"decision_authority":"The protected-area land manager owns treatment decisions. The facility biosafety officer controls possession, propagation, containment, and destruction of invasive plant material during the first evidence step. Any later field test requires separate land-management and regulatory authorization.","authorized_first_step":"Run one securely contained, randomized microcosm study over a complete plant life cycle. Use an identification set to estimate the stage-zone transition and freeze the modal decision rule, then compare untreated, visible-adult clipping, the best equal-effort single-stage treatment, and the mode-aligned treatment sequence in an independent validation set.","excluded_actions":["No landscape-scale pulling, clipping, seedbank disturbance, herbicide use, or habitat-zone modification from this first study.","No release of viable seed, soil, plant fragments, or reproductive material outside the containment facility.","No use of above-window seed densities merely to force clearer modal separation.","No extrapolation to other species, soils, climates, seasons, or disturbance regimes.","No concealment of ill-conditioning, near-degenerate modes, structured residuals, containment failures, native-plant damage, or null results.","No automatic conversion of model rankings into crew assignments."],"halt_rollback":"Stop handling and isolate the affected unit after any containment breach, unaccounted reproductive material, worker-safety event, or unauthorized germination outside a designated vessel; recover material where safe and sterilize it under the facility protocol. Return the analysis to observation-only status if eigenvectors are ill-conditioned, the targeted mode is not reproducible, the spectral gap crosses its preregistered minimum, mode direction drifts beyond tolerance, held-out residuals exceed their budget or retain stage-zone structure, or measurements leave the local validity window."},"negative_tests":{"strongest_counterevidence":"Across independent validation microcosms and resampled identification sets, the inferred replenishment mode is unstable or non-reproducible, and its coordinates provide no useful held-out trajectory discrimination beyond adult cover, total viable seed count, or a direct multivariate predictor.","problem_falsifier":"Future viable-seed production and seedbank carryover are adequately determined by one directly observed stage within the tested regime, with no reproducible coupled stage-zone mode contributing additional trajectory structure.","intervention_falsifier":"The preregistered mode-aligned sequence does not move the targeted modal coordinate in the predicted direction relative to untreated units, or it provides no advantage over the equal-effort visible-stage or best single-stage rival while increasing viable seed escape, protected-state disturbance, or structured residual error.","risks":["Transition estimates may be unstable when some life stages are rare or imperfectly detected.","The annual life cycle may be nonlinear across density, moisture, temperature, or germination thresholds.","A non-normal transition can produce consequential transient growth even when eigenvalues indicate eventual decay.","Closely spaced eigenvalues can rotate or exchange mode identity across replicate blocks.","Contained microcosms may alter dispersal, seed burial, competition, microbial interactions, and field transferability.","Manual treatments can disturb soil or native-plant proxies in ways omitted from the state vector.","The schedule may suppress the measured mode while an unmeasured dormancy or dispersal pathway replenishes the population.","Propagation of invasive reproductive material creates a containment hazard even when intended only for evidence generation."]},"next_evidence_step":"Conduct a preregistered two-stage experiment in a secure growth facility using sterilizable vessels, captured seed rain, and accountable reproductive material. Randomized identification microcosms span only the declared soil-moisture and density window and receive permitted downward controls; their fixed-interval observations estimate the transition operator. Before validation outcomes are inspected, freeze the state vector, scaling, mode-matching method, conditioning limit, stability boundary, spectral-gap threshold, residual budget, targeted mode, equal-effort treatment schedules, containment rules, and native-plant disturbance measures. Apply the four validation arms in independent randomized blocks for one life cycle. The first evidence question is whether the targeted mode is reproducible and moves in the predicted direction under the mode-aligned sequence without containment or safeguard failure; the study does not authorize a field-effectiveness claim.","prior_art_status":"UNSEARCHED","diversity_from_prior_proposals":"Earlier proposal 1 addresses coupled bloom and hypoxia dynamics in a shallow lake and gates nutrient-input reduction and mechanical mixing using physicochemical and food-web modes. This proposal addresses persistence of an invasive annual plant through coupled life stages and habitat zones, and reallocates manual seed capture, seedling removal, and pre-seed-set clipping to oppose a replenishment mode. Its managed object, actors, state variables, transition timescale, control authority, intervention hardware, causal path, safeguards, evidence system, and failure consequences are distinct. It is independently adoptable by an invasive-plant management unit and neither extends nor supplies a feature of the lake-management protocol.","revision_record":{"parent_version":null,"progress_targets_addressed":["Created a second complete candidate for a materially different biological and ecological problem.","Specified an independently adoptable intervention and causal path distinct from proposal 1.","Added operational authority, containment safeguards, rivals, falsifiers, and a bounded first evidence step."],"conceptual_changes":[],"operational_changes":[],"evidence_changes":[],"claim_changes":[]}}