{"schema_version":1,"experiment_id":"eoa_inverse_innovation_exp11_mechanism_context_external20_20260804","research_id":"eoa_inverse_innovation_exp11_external_scrutiny_20260804","cell_id":"invariant_mode_decomposition_design__biology_ecology","opaque_id":"invariant_mode_decomposition_design__biology_ecology__B","search_lanes":{"direct_problem":{"queries":["coral reef regime shift eigenvalue eigenmode resilience nutrient grazing macroalgae","coral reef multivariate early warning signals regime shift coral cover conceals resilience","coral macroalgae regime shift nutrient herbivory mesocosm experiment recovery"],"source_ids":["SRC1","SRC2"],"no_result_note":null},"closest_prior_art":{"queries":["dynamic mode decomposition coral reef community resilience eigenmodes","ecological monitoring dynamic mode decomposition eigenvalues regime shift early warning","multivariate autoregressive community matrix eigenvalue early warning ecological resilience intervention","ecosystem intervention aligned leading eigenvector stability experiment community matrix"],"source_ids":["SRC3","SRC4","SRC5"],"no_result_note":null},"historical_terminology":{"queries":["ecology community matrix dominant eigenvector perturbation experimental control resilience return rate","press perturbation community matrix eigenvector management ecosystem stability","coral reef phase shift herbivory nutrients resilience"],"source_ids":["SRC1","SRC2","SRC5"],"no_result_note":null},"products_practices_standards":{"queries":["coral reef resilience indicators management protocol herbivory nutrients coral cover monitoring standard","official coral reef mesocosm facility nutrient herbivory experiment SeaSim AIMS","official permit coral reef research nutrient addition organism removal marine park research permit"],"source_ids":["SRC6","SRC7","SRC8"],"no_result_note":null},"non_english_regional":{"queries":["arrecifes coralinos cambio de régimen macroalgas herbivoría nutrientes resiliencia monitoreo","recifes de coral mudança de regime macroalgas herbivoria nutrientes resiliência monitoramento","récifs coralliens changement de régime macroalgues herbivorie nutriments résilience indicateurs","Caribe manejo arrecifes cobertura coralina macroalgas herbívoros nutrientes protocolo monitoreo"],"source_ids":["SRC6"],"no_result_note":null},"composition_subproblems":{"queries":["ecology dynamic mode decomposition bootstrap spectral gap mode uncertainty","ecological time series eigenmode drift subspace monitoring community transition operator","mesocosm intervention dynamic mode decomposition recovery mediation ecology","mode aligned perturbation dynamic mode decomposition control ecosystem"],"source_ids":["SRC2","SRC3","SRC4","SRC5","SRC7"],"no_result_note":null}},"sources":[{"source_id":"SRC1","title":"Transient dynamics mask the resilience of coral reefs","url":"https://link.springer.com/article/10.1007/s12080-023-00570-4","publisher":"Springer Nature, Theoretical Ecology","date_or_year":"2023","source_type":"PRIMARY_RESEARCH","language":"English","claims_supported":["Apparently stable coral cover over monitoring windows can coexist with a slow trajectory toward collapse.","Common slowing-down metrics and historical coral-cover trends may be unreliable predictors of future reef behavior.","Transient states can create a window for short-term targeted management intervention."]},{"source_id":"SRC2","title":"Effects of herbivory, nutrients, and reef protection on algal proliferation and coral growth on a tropical reef","url":"https://eprints.whiterose.ac.uk/110870/1/nihms380734.pdf","publisher":"Springer, Oecologia; repository copy hosted by White Rose Research Online","date_or_year":"2012","source_type":"PRIMARY_RESEARCH","language":"English","claims_supported":["A 152-day field experiment manipulated herbivory and nutrient enrichment on coral- and macroalgal-dominated reefs.","Herbivore exclusion increased macroalgal cover and biomass substantially, while nutrient enrichment did not have the simple expected positive effect.","The results show why joint pressures require explicit factorial controls rather than assuming nutrient and grazing effects."]},{"source_id":"SRC3","title":"Spatial early warning signals for tipping points using dynamic mode decomposition","url":"https://www.math.auckland.ac.nz/~gdon030/papers/DMDEWS.pdf","publisher":"Elsevier, Physica A; author-hosted copy","date_or_year":"2022","source_type":"PRIMARY_RESEARCH","language":"English","claims_supported":["Dynamic mode decomposition can extract a leading mode and associated eigenvalue as an early-warning signal.","The method was demonstrated on an ecological tipping-point model as well as a physiological model.","The work is predictive and model-based; it does not validate a coral-reef intervention aligned to the inferred mode."]},{"source_id":"SRC4","title":"Dynamic Mode Decomposition with Control","url":"https://epubs.siam.org/doi/10.1137/15M1013857","publisher":"Society for Industrial and Applied Mathematics","date_or_year":"2016","source_type":"PRIMARY_RESEARCH","language":"English","claims_supported":["DMD with control estimates a transition operator and input effects from state and actuation snapshots.","It separates underlying dynamics from external forcing and produces reduced input-output models.","The general transition-decomposition-with-intervention mechanism substantially overlaps the proposal, but the paper does not test coral nutrient-grazer treatments or the proposed causal contrasts."]},{"source_id":"SRC5","title":"How ecosystems recover from pulse perturbations: A theory of short- to long-term responses","url":"https://sete-moulis-cnrs.fr/fr/component/flexicontent/download/215/204/30","publisher":"Elsevier, Journal of Theoretical Biology; manuscript hosted by CNRS","date_or_year":"2018","source_type":"PRIMARY_RESEARCH","language":"English","claims_supported":["Ecological return rates depend on perturbation direction at finite times.","Long-term asymptotic resilience is determined by a dominant community-matrix eigenvalue.","Rare species can determine the dominant eigenvalue while contributing little to observable short-term recovery, warning against uncritical mode-based interpretation."]},{"source_id":"SRC6","title":"Protocolo de Monitoreo de la Biodiversidad Marina en Áreas Naturales Protegidas del Caribe Mexicano","url":"https://simar.conabio.gob.mx/explorer/libroprotocolosmarinos/index2.html","publisher":"CONABIO, Mexico","date_or_year":"2020-era protocol; page undated","source_type":"OFFICIAL_STANDARD","language":"Spanish","claims_supported":["The official regional protocol monitors live coral cover, algal functional groups, sea-urchin density, coral recruitment, substrate complexity, and other indicators.","Operational reef monitoring already extends beyond coral cover to multiple biological dimensions.","CONABIO and protected-area monitoring programs are identifiable potential adopters or data partners."]},{"source_id":"SRC7","title":"What we do: National Sea Simulator","url":"https://www.aims.gov.au/about-us/what-we-do","publisher":"Australian Institute of Marine Science","date_or_year":"Undated; accessed 2026-08-04","source_type":"FIRST_PARTY_PRODUCT","language":"English","claims_supported":["SeaSim supports complex, long-term aquarium experiments on tropical marine organisms.","The facility can precisely control environmental variables and develop bespoke experimental systems.","It provides husbandry and continuous system monitoring, making a bounded controlled reef mesocosm study operationally plausible."]},{"source_id":"SRC8","title":"Permit Information","url":"https://ausseabed.gov.au/resources/permit","publisher":"AusSeabed, Australian Government-supported national seabed program","date_or_year":"Undated; accessed 2026-08-04","source_type":"OFFICIAL_GUIDANCE","language":"English","claims_supported":["Marine research permissions depend on jurisdiction and must be confirmed before research begins.","Research in the Great Barrier Reef Marine Park requires authorization from the Great Barrier Reef Marine Park Authority.","Extractive or potentially destructive work involving marine biota may require additional approval."]}],"problem_evidence":{"status":"PARTLY_SUPPORTED","finding":"The broader problem is supported: apparently stable coral cover can mask a slow decline trajectory, official programs monitor coral, algae, herbivores, recruitment, and other dimensions, and experimental evidence shows that grazing and nutrient effects are context-dependent. No retained source empirically establishes the proposal's specific hidden, repeatable coral–algae–grazer–nutrient–oxygen eigenmode in a reef census series.","source_ids":["SRC1","SRC2","SRC6"],"uncertainty":"The exact weakly damped coupled mode remains hypothetical, and transient nonlinear dynamics or direct herbivory effects could explain the observations without a stable local mode."},"adopter_evidence":{"status":"SUPPORTED","finding":"Identifiable adopters and authorizers exist: CONABIO and protected-area reef-monitoring programs collect relevant multivariate indicators; AIMS operates a controlled tropical-marine experimental facility; and marine-park authorities such as GBRMPA authorize relevant research.","source_ids":["SRC6","SRC7","SRC8"],"uncertainty":"The eventual jurisdiction, facility, organism-collection permissions, institutional animal-care requirements, and responsible manager would need to be named before execution."},"implementation_evidence":{"status":"PARTLY_SUPPORTED","finding":"The components are individually feasible: reef nutrient-by-herbivory experiments exist, DMD extracts leading ecological modes, DMD with control estimates state and input operators, recovery theory treats perturbation direction explicitly, and controlled marine mesocosm infrastructure exists. The full package—bootstrap-separated coral community modes followed by projection-matched randomized interventions and mediation through gain reduction—was not found as an implemented reef study.","source_ids":["SRC2","SRC3","SRC4","SRC5","SRC7"],"uncertainty":"Compositional constraints, limited replication, observation noise, nonlinear recruitment, rare-species dynamics, seasonal drift, and weak spectral separation may prevent reliable mode estimation or causal interpretation."},"prior_art":{"disposition":"ADJACENT_PRIOR_ART","closest_analogues":[{"name":"Transient-dynamics models of hidden coral-reef resilience loss","source_ids":["SRC1"],"same_problem":true,"same_causal_lever":false,"overlap":"Shows that stable-looking coral cover can mask a slow collapse trajectory and motivates targeted intervention during a transient window.","remaining_difference":"Does not infer multivariate census transition modes, estimate modal gain, or test mode-aligned nutrient-grazer treatments."},{"name":"Dynamic-mode early warning for ecological tipping models","source_ids":["SRC3"],"same_problem":false,"same_causal_lever":true,"overlap":"Uses a fitted leading dynamic mode and eigenvalue as a warning of slowing near an ecological tipping point.","remaining_difference":"It is not a coral community study and does not link the inferred mode to randomized control inputs or recovery mediation."},{"name":"Dynamic Mode Decomposition with Control","source_ids":["SRC4"],"same_problem":false,"same_causal_lever":true,"overlap":"Already provides the general state-transition-plus-control decomposition needed to distinguish autonomous modes from actuation effects.","remaining_difference":"It does not supply the coral state vector, ecological validity checks, mode-projection treatment contrast, or causal recovery estimand."},{"name":"Perturbation-direction and dominant-eigenvalue theory for ecological recovery","source_ids":["SRC5"],"same_problem":false,"same_causal_lever":true,"overlap":"Establishes that recovery depends on perturbation direction and connects long-term recovery to community-matrix eigenvalues.","remaining_difference":"It analyzes response after displacement rather than testing whether a mode-aligned intervention selectively damps a risky mode; it also warns that dominant eigenvalues can be controlled by practically unobservable rare species."},{"name":"Factorial herbivory-by-nutrient coral-reef experiments","source_ids":["SRC2"],"same_problem":true,"same_causal_lever":false,"overlap":"Directly manipulates the proposed pressure family and measures coral and algal responses with interaction controls.","remaining_difference":"Treatments are defined by ecological variables, not by projection onto a fitted transition mode, and no modal-gain mediation test is performed."}],"contrastive_claim_remaining":"Within a preregistered, locally bounded coral-community mesocosm, a reproducible and spectrally separated census-derived mode predicts risk beyond single indicators and a non-modal multivariate rival, and an equal-magnitude joint nutrient-by-grazer treatment aligned with that mode reduces its gain more than matched single-variable treatments and a low-projection multivariate treatment; the gain reduction then mediates faster recovery after adjustment for treatment assignment.","contrastive_claim_falsifier":"The claim fails if the mode is not reproducible or spectrally separated, held-out residuals exceed the preregistered budget, a single indicator or non-modal rival matches prediction, the aligned joint arm has no gain-reduction advantage over matched controls and direct treatment terms, or estimated gain reduction does not predict recovery after treatment adjustment.","confidence":"MODERATE","search_limitations":"The bounded search retained exactly eight opened public sources and covered six adversarial lanes, including Spanish regional terminology, older community-matrix language, official protocols, facilities, permits, and component combinations. It did not exhaust subscription databases, citation graphs, theses, patents, unpublished protocols, or every jurisdiction and therefore cannot establish world novelty."},"researchability_gates":{"externally_supported_problem":{"status":"PASS","rationale":"Primary reef research shows that stable-looking coral cover can mask slow decline, while experiments and official protocols show that herbivory, algae, nutrients, and other state variables matter beyond coral cover alone.","source_ids":["SRC1","SRC2","SRC6"]},"identifiable_adopter_or_authorizer":{"status":"PASS","rationale":"CONABIO/protected-area monitoring programs and AIMS are identifiable research adopters, and marine-park authorities are identifiable authorizers for regulated research.","source_ids":["SRC6","SRC7","SRC8"]},"distinct_testable_incremental_claim":{"status":"PASS","rationale":"Although mode-based early warning, DMD with control, ecological eigenvalue theory, and nutrient-herbivory experiments already exist, none of the retained sources combines them into the specified projection-matched randomized reef experiment and gain-mediated recovery test.","source_ids":["SRC2","SRC3","SRC4","SRC5"]},"bounded_next_evidence_step":{"status":"PASS","rationale":"A small replicated controlled-aquarium study can compare the aligned joint arm with control, matched single-variable arms, and an equal-magnitude low-projection arm while applying preregistered residual, drift, and spectral-separation criteria.","source_ids":["SRC2","SRC4","SRC7"]},"no_unresolved_safety_or_authority_stop":{"status":"PASS","rationale":"The proposed first step excludes wild-reef manipulation and is compatible with controlled aquarium infrastructure. Execution must remain conditional on facility review, organism-care requirements, collection permissions, and relevant marine authority approval; these are authorizable conditions rather than an intrinsic stop.","source_ids":["SRC7","SRC8"]},"adequate_search_evidence":{"status":"PASS","rationale":"All six required lanes were searched adversarially using direct, historical, technical, official, product, regional non-English, and component-combination terminology. Eight opened sources from independent publishers include primary studies, official standards/guidance, and a first-party facility source.","source_ids":["SRC1","SRC2","SRC3","SRC4","SRC5","SRC6","SRC7","SRC8"]}},"strict_success":true,"screen_survival":true,"remaining_research_value":"HIGH","recommended_next_step":"Preregister a power-checked pilot using an existing controlled marine facility. First use untreated repeated censuses to test mode resampling stability, spectral separation, held-out prediction, compositional handling, and drift. Proceed to randomized treatments only if those gates pass; estimate the aligned joint arm's gain reduction against control, matched single-variable arms, and an equal-magnitude low-projection arm, then test whether gain reduction mediates recovery. Stop on mortality, water-quality, containment, residual, or mode-instability thresholds.","world_novelty_boundary":"This result identifies adjacent prior art and a remaining falsifiable incremental claim within a bounded eight-source search. It does not establish world novelty, patentability, freedom to operate, market size, realized impact, or absence of undiscovered prior art."}