{ "name": "MorphoSwarm \u2014 open problems work queue", "snapshot": "2026-10-26", "source_repo": "https://github.com/fractastical/morpholib", "graph_url": "https://fractastical.github.io/morpholib/problem-graph.html", "colour_rule": { "possible_pathway": "pooled Delphi bridge posterior >= 15% (classification only \u2014 NOT green)", "low_probability": "pooled Delphi bridge posterior < 15%", "grey": "not scored", "shade_bands_percent": { ">80_dark_green": "#0B6E3F", "70-80_light_green": "#69B86F", "50-70": "#C9A227", "30-50": "#D98E2B", "15-30": "#C45A24", "5-15": "#B03A2E", "<5": "#7E1F2B" }, "note": "Shade bands show the range of opinion. Green is reserved for >70% (light) and >80% (dark); a posterior in the teens is burnt orange. Panel range per problem is in viability.panel_range_percent." }, "protocol": [ "Pick one OP id; do not work two on the same branch without noting it.", "Pre-register the attempt (hypotheses + scoring) before touching held-out data, following the repo's hash-locked blind-test contract.", "RECORD A PROBABILITY FOR EVERY ACTION before attempting it (edge prob 0-100 + probNote with method and date, Thompson-registry style); after the attempt, update the target node's status and never edit the recorded prob. The graph builder refuses edges with neither a prob nor an explicit probStatus.", "Report negative results as results; pruned branches stay in the graph.", "Close by updating the source documents and re-running docs/build_problem_graph_html.py, whose self-checks must pass." ], "problems": [ { "id": "OP-01", "node": "p1", "delphi": "p1", "title": "Prize 1 \u2014 close the transparent-gate loophole (short runs 1\u2264a_i\u22647)", "gap": "Defects D1(t)=1 are proved to arrive infinitely often, but not proved to ever land on a closed gate {c_t=1}. Depth-1 right cylinder has positive topological entropy (~0.32 bits/step) on short runs, so no deeper local transducer closes this; it needs a global phase-spreading / mixing invariant.", "done": "A proof (ideally Lean-checked) that for all t0, \u03a0 and short-run words, some D1(t)=1 lands on {c_t=1} \u2014 or a counterexample word, which would be just as valuable.", "status": "open", "graph_node_label": "Prize 1 \u00b7 Aperiodicity", "source": "RULE30_BAYESIAN_DELPHI_ASSESSMENT.md P1.4 (35% weight, 31.9/100)", "attempted_by_agent_ids": [ "panel", "unattributed" ], "attempted_by": [ "Multi-agent panel", "Unattributed in record" ], "graph_url": "https://fractastical.github.io/morpholib/problem-graph.html#p1", "viability": { "kind": "delphi_bridge_posterior_percent", "pooled": 11.52, "panel_range_percent": [ 5.576, 21.82, 11.805 ], "classification": "below_15_percent", "note": "Classification 'possible_pathway' is >=15% on the pooled posterior, but colour is stricter: green only >70% (light) / >80% (dark), teens are burnt orange. Individual agents may differ (see panel_range_percent)." } }, { "id": "OP-02", "node": "p2", "delphi": "p2", "title": "Prize 2 \u2014 diagonal-sample decorrelation along j=\u230aS/2\u230b", "gap": "Exact 1/2 density is proved on crystals, but the diagonal sample visits a vanishing 2^-n fraction of each period and no Weyl / exponential-sum discrepancy bound exists along the moving diagonal.", "done": "A discrepancy bound for S -> A_S(floor(S/2)) transferring crystal density to the center column, or a proof that such a bound fails.", "status": "open", "graph_node_label": "Prize 2 \u00b7 Density \u00bd", "source": "Delphi P2.4 (35% weight, 6.3/100)", "attempted_by_agent_ids": [ "panel", "unattributed" ], "attempted_by": [ "Multi-agent panel", "Unattributed in record" ], "graph_url": "https://fractastical.github.io/morpholib/problem-graph.html#p2", "viability": { "kind": "delphi_bridge_posterior_percent", "pooled": 2.033, "panel_range_percent": [ 1.216, 3.346, 2.052 ], "classification": "below_15_percent", "note": "Classification 'possible_pathway' is >=15% on the pooled posterior, but colour is stricter: green only >70% (light) / >80% (dark), teens are burnt orange. Individual agents may differ (see panel_range_percent)." } }, { "id": "OP-03", "node": "p3", "delphi": "p3", "title": "Prize 3 \u2014 fixed-seed specialisation transfer", "gap": "Multivariate deg(c_T)=2T-1 collapses under specialisation to the unit seed; a uniform Omega(T) bound needs P-vs-EXP-type machinery. Delphi posterior 0.04% \u2014 work here should be a barrier result, not another attempt at the bound.", "done": "A formal barrier / relativisation result for the fixed-seed problem, or a specified computational model in which the bound is provable.", "status": "open", "graph_node_label": "Prize 3 \u00b7 \u03a9(n) complexity", "source": "Delphi P3.4\u2013P3.5 (55% weight, ~1/100)", "attempted_by_agent_ids": [ "panel", "unattributed" ], "attempted_by": [ "Multi-agent panel", "Unattributed in record" ], "graph_url": "https://fractastical.github.io/morpholib/problem-graph.html#p3", "viability": { "kind": "delphi_bridge_posterior_percent", "pooled": 0.037, "panel_range_percent": [ 0.063, 0.02, 0.04 ], "classification": "below_15_percent", "note": "Classification 'possible_pathway' is >=15% on the pooled posterior, but colour is stricter: green only >70% (light) / >80% (dark), teens are burnt orange. Individual agents may differ (see panel_range_percent)." } }, { "id": "OP-04", "node": "t5", "delphi": null, "title": "Prediction beyond the ~50 Myr horizon", "gap": "The Thompson prediction engine collapses to a clade prior beyond ~50 Myr and the Monte Bolca test was a null result vs stasis (6/16). What, if anything, carries predictive signal at deep horizons \u2014 stem placements, fossil-calibrated priors, non-Gaussian processes?", "done": "A pre-registered deep-horizon test (registered before unblinding, as in the FishShapes protocol) that beats the clade-prior baseline beyond 50 Myr, or a sharper null.", "status": "partial", "graph_node_label": "Prediction engine", "source": "KEY_DISCOVERIES.md \u00a71.11 \u00b7 THOMPSON_PHYLOGENETIC_PREDICTIONS.md", "attempted_by_agent_ids": [ "fable" ], "attempted_by": [ "Claude Fable 5.1 Thinking High" ], "graph_url": "https://fractastical.github.io/morpholib/problem-graph.html#t5", "viability": { "kind": "not_scored", "pooled": null, "classification": "not_scored", "note": "No Delphi probability exists for this problem. Do not invent one: the first swarm task is a pre-registered Delphi scoring." } }, { "id": "OP-05", "node": "t8", "delphi": null, "title": "Within-species bee P-matrix (the one missing input)", "gap": "The why-wings causal decomposition is clean for hornets (within-species P) but weaker for bees, where P is within-tribe. A within-species bee wing dataset would make the hornet/bee comparison exact.", "done": "A within-species bee forewing landmark dataset with replicates, run through the registered C1-C8 pipeline without changing its hypotheses.", "status": "partial", "graph_node_label": "Why wings? (causal)", "source": "docs/portfolio/why_wings.md \u00b7 bee_wings.md \u00b7 vespinae_wings.md", "attempted_by_agent_ids": [ "fable" ], "attempted_by": [ "Claude Fable 5.1 Thinking High" ], "graph_url": "https://fractastical.github.io/morpholib/problem-graph.html#t8", "viability": { "kind": "not_scored", "pooled": null, "classification": "not_scored", "note": "No Delphi probability exists for this problem. Do not invent one: the first swarm task is a pre-registered Delphi scoring." } }, { "id": "OP-06", "node": "f3", "delphi": null, "title": "Flagship structural debt: growing-domain Turing, autonomous Meinhardt, C. elegans voxel calibration", "gap": "Pass N+1 left these explicit: the Turing flagship lacks a 2D growing-domain solver; Meinhardt shell parameters are not autonomous; C. elegans lacks true voxel calibration (eggshell 'ASSUMED 50 um').", "done": "Each sub-item closed by a self-test that fails on the current code and passes on the fix, with the audit score re-derived, not asserted.", "status": "solved", "graph_node_label": "Pass N+1 honest re-score", "source": "morphoeval/runs/2026-10-26-flagship15-loop-passN.md", "attempted_by_agent_ids": [ "gemini", "gpt", "grok", "panel", "sonnet" ], "attempted_by": [ "Gemini 4 Argon", "GPT 5.6 Sol Medium", "Grok (unversioned in record)", "Multi-agent panel", "Claude Sonnet 5.5 High" ], "graph_url": "https://fractastical.github.io/morpholib/problem-graph.html#f3", "viability": { "kind": "not_scored", "pooled": null, "classification": "not_scored", "note": "No Delphi probability exists for this problem. Do not invent one: the first swarm task is a pre-registered Delphi scoring." } }, { "id": "OP-07", "node": "b2", "delphi": null, "title": "Xenopus neighbour transfer: kill the orientation confound", "gap": "Headline blind test was negative (LOOO AUC 0.484); orientation carries the signal (0.833) and the PCA side-split subset is suspect (clean-geometry subset 0.802). Is there any wave-feature signal once geometry is ground-truth?", "done": "A v2 pre-registration using only ground-truth-geometry videos, scored by the hash-locked contract, whichever way it comes out.", "status": "refuted", "graph_node_label": "Xenopus blind test", "source": "embryo-blind/README.md \u00b7 XENOPUS_BLIND_RESULTS.md", "attempted_by_agent_ids": [ "panel" ], "attempted_by": [ "Multi-agent panel" ], "graph_url": "https://fractastical.github.io/morpholib/problem-graph.html#b2", "viability": { "kind": "not_scored", "pooled": null, "classification": "not_scored", "note": "No Delphi probability exists for this problem. Do not invent one: the first swarm task is a pre-registered Delphi scoring." } }, { "id": "OP-08", "node": "b3", "delphi": null, "title": "Pixel v2: image-proximity (mirror) neighbour prediction", "gap": "Post-unblinding HTHT mirror signal (AUC 0.61-0.65) is exploratory only and confounded with headward direction because pokes were at the tail. Needs a registered test where mirror and headward predictions separate.", "done": "Pre-registered pixel-v2 scoring on videos where poke position separates the mirror and headward hypotheses.", "status": "partial", "graph_node_label": "Pixel blind v1 + v2", "source": "PIXEL_BLIND_RESULTS.md \u00b7 PIXEL_V2_BLIND_RESULTS.md", "attempted_by_agent_ids": [ "panel" ], "attempted_by": [ "Multi-agent panel" ], "graph_url": "https://fractastical.github.io/morpholib/problem-graph.html#b3", "viability": { "kind": "not_scored", "pooled": null, "classification": "not_scored", "note": "No Delphi probability exists for this problem. Do not invent one: the first swarm task is a pre-registered Delphi scoring." } }, { "id": "OP-11", "node": "f5", "delphi": "bos", "title": "Cow Turing follow-ups: independent re-score + migration-wave colonisation variant", "gap": "The published negative verdict (static Turing rejected; growing RD vs Eden colonisation p=0.91) rests on a builder-scored Pass 9 assessment \u2014 the two blinded Fable audits (54.4, 57.7) predate the Pass 8 scale-matched pipeline. The Eden control is also a minimal interior-founder proxy, while real Holstein white invades from migration fronts; and held-out n=9 limits power.", "done": "A blinded independent re-score of the Pass 8+ tree (audit R11), plus a neural-crest migration-wave colonisation variant scored on the same coat-masked, scale-matched statistics \u2014 published as a superseding assessment either way.", "status": "refuted", "graph_node_label": "Cow Turing claim \u2014 tested", "source": "datasets/bos_taurus_turing_wavelength/README.md \u00b7 morphoeval/audits/2026-10-26-bos-taurus-turing-wavelength-audit-v7.yaml \u00b7 morphoeval/kg/2026-10-26-bos-taurus-turing-wavelength-audit-v7/published.json", "attempted_by_agent_ids": [ "fable", "human", "panel" ], "attempted_by": [ "Claude Fable 5.1 Thinking High", "Joel Dietz (human PI)", "Multi-agent panel" ], "graph_url": "https://fractastical.github.io/morpholib/problem-graph.html#f5", "viability": { "kind": "delphi_bridge_posterior_percent", "pooled": 39.3, "panel_range_percent": [ 13.62, 36.52, 74.96 ], "classification": "possible_pathway", "note": "Classification 'possible_pathway' is >=15% on the pooled posterior, but colour is stricter: green only >70% (light) / >80% (dark), teens are burnt orange. Individual agents may differ (see panel_range_percent)." } }, { "id": "OP-10", "node": "t7", "delphi": null, "title": "Portfolio residue: clades where Thompson-7 failed (Leporidae 0/3, Vespinae 0/7 pre-venation)", "gap": "45/90 registered multi-clade hypotheses held; the failures are concentrated and unexplained \u2014 is it landmark scheme, tree quality, or a real limit of global grids in those clades?", "done": "A per-clade failure autopsy in the style of the why-wings decomposition, with at least one failure converted into a correct, pre-registered prediction.", "status": "partial", "graph_node_label": "Multi-clade portfolio", "source": "docs/portfolio/PORTFOLIO_STATUS.md", "attempted_by_agent_ids": [ "fable" ], "attempted_by": [ "Claude Fable 5.1 Thinking High" ], "graph_url": "https://fractastical.github.io/morpholib/problem-graph.html#t7", "viability": { "kind": "not_scored", "pooled": null, "classification": "not_scored", "note": "No Delphi probability exists for this problem. Do not invent one: the first swarm task is a pre-registered Delphi scoring." } }, { "id": "OP-12", "node": "top-07", "delphi": null, "title": "TOP-07 \u00b7 When does continuous reaction-diffusion collapse to a discrete automaton? Meinhardt mantle PDE vs the Lean-proved Rule 30 gate", "gap": "Ocellated lizard scales behave as a cellular automaton emerging from RD on a thick-skin lattice (Manukyan 2017), and the repo has Lean-proved that the Ermentrout-Oster neural mantle gate is bit-for-bit Rule 30 \u2014 but whether the repo's Meinhardt-Klingler Conus PDE, discretised at the mantle, induces a Rule 30-class local rule has never been measured. It is the bridge between the Rule 30 programme and the RD programme, and the RD-vs-neural shell-pattern debate is still molecularly unresolved.", "done": "From a Meinhardt PDE kymograph at the mantle edge, extract the empirical 3-neighbourhood -> next-state transducer table (binary threshold pre-registered), report the fraction of transitions agreeing with Rule 30 vs Rule 90 vs best-fit rule, plus the 2D ANF-carry density and wall chirality already used to separate R30 from R90 (node r0); verdict thresholds locked before running.", "provisional": { "posterior": 50.0, "assessor": "Claude Fable 5.1 Thinking High (single assessor, provisional)", "prior": 50.0, "net_db": 0, "resolvability": 78, "band": "RESOLVE NOW" }, "panel": { "id": "TOP-07", "slug": "rd-to-ca-reduction", "pooled": { "method": "log-odds mean across 3 assessors (equal priors 50%, so pooled net dB = mean net dB)", "prior_percent": 50.0, "net_db": 5.33, "bayes_factor": 3.4119, "posterior_percent": 77.33, "panel_range_percent": [ 71.53, 79.92 ], "classification": "possible_pathway" }, "resolvability_panel": { "mean": 89.7, "range": [ 86, 96 ], "band": "RESOLVE NOW", "factor_means": { "tool_fit": 20.3, "data_in_hand": 19.7, "falsifiable_done": 13, "compute_in_repo": 14.7, "isolation": 9.3, "time_to_verdict": 8.7, "not_blocked": 4 } }, "packet_correction": null, "trig": "panel-top-07-rd-to-ca-reduction.trig", "assessors": { "gpt-5.6-sol": { "label": "GPT 5.6 Sol Medium", "provider": "OpenAI", "resolvability": 87, "net_db": 4.0, "posterior_percent": 71.53, "confidence": 0.91, "verdict": "HIGHLY_DECISIVE", "note": "This is the strongest in-repo route: it can decisively reject as well as support the proposed reduction, and current chirality diagnostics already favor rejection." }, "gemini-4-argon": { "label": "Gemini 4 Argon Medium", "provider": "Google", "resolvability": 96, "net_db": 6.0, "posterior_percent": 79.92, "confidence": 0.91, "verdict": "HIGHLY_TRACTABLE_EXPECTED_NEGATIVE", "note": "The crux is fundamental symmetry: Meinhardt-Klingler's 1D diffusion operator d^2/dx^2 is reflection-symmetric (left-right invariant), whereas Rule 30 breaks left-right symmetry via a_{i-1} XOR (a_i OR a_{i+1}). Thus the transducer test will reach a fast, decisive verdict\u2014almost certainly proving that isotropic Meinhardt PDE reduces to a symmetric elementary CA class (like Rule 90/18) rather than chiral Rule 30 unless oblique wave travel or asymmetric coupling is present." }, "claude-fable-5-1": { "label": "Claude Fable 5.1 Thinking High (fresh context)", "provider": "Anthropic", "resolvability": 86, "net_db": 6, "posterior_percent": 79.92, "confidence": 0.75, "verdict": "DECISIVE_LIKELY_NEGATIVE_IN_REPO", "note": "Crux: a symmetric PDE should map to a symmetric (Rule 90-like or additive) rule, so expect a decisive negative on Rule 30; lock the coarse-graining scale and threshold in the registry before running." } }, "nanopub": { "date": "2026-10-27", "nanopub": "https://w3id.org/np/RAC_WiKGB6RpCRDgjaCXGnnKsMsiVxllvMBsmv9TIxdNs", "published": "test" } }, "status": "refuted", "graph_node_label": "TOP-07 \u00b7 rd to ca reduction", "source": "morphoeval/build_turing_open_problems.py \u00b7 morphoeval/audits/2026-10-27-turing-open-problems-assessment.yaml", "attempted_by_agent_ids": [ "fable", "gemini", "gpt", "panel" ], "attempted_by": [ "Claude Fable 5.1 Thinking High", "Gemini 4 Argon", "GPT 5.6 Sol Medium", "Multi-agent panel" ], "graph_url": "https://fractastical.github.io/morpholib/problem-graph.html#top-07", "resolvability": { "score": 89.7, "band": "RESOLVE NOW", "panel_range": [ 86, 96 ], "provisional_score": 78, "rubric": "morphoeval/problem_scout_100.py RUBRIC (deterministic; prices tools, data, done \u2014 not truth odds); panel mean of 3 blinded assessors" }, "viability": { "kind": "delphi_panel_posterior_percent", "pooled": 77.33, "panel_range_percent": [ 71.53, 79.92 ], "prior_percent": 50.0, "net_db": 5.33, "assessors": { "gpt-5.6-sol": { "label": "GPT 5.6 Sol Medium", "provider": "OpenAI", "posterior_percent": 71.53, "verdict": "HIGHLY_DECISIVE" }, "gemini-4-argon": { "label": "Gemini 4 Argon Medium", "provider": "Google", "posterior_percent": 79.92, "verdict": "HIGHLY_TRACTABLE_EXPECTED_NEGATIVE" }, "claude-fable-5-1": { "label": "Claude Fable 5.1 Thinking High (fresh context)", "provider": "Anthropic", "posterior_percent": 79.92, "verdict": "DECISIVE_LIKELY_NEGATIVE_IN_REPO" } }, "provisional_posterior_percent": 50.0, "classification": "possible_pathway", "note": "Three-provider blinded Delphi panel (GPT 5.6 Sol / Gemini 4 Argon / Claude Fable 5.1), pooled in log-odds; supersedes the provisional single-assessor posterior (kept for the record). Ledger: morphoeval/audits/2026-10-27-turing-open-problems-panel.yaml. Same colour rule as other Delphi posteriors." } }, { "id": "OP-13", "node": "top-09", "delphi": null, "title": "TOP-09 \u00b7 Turing's neglected case: is there a wave (Turing-Hopf) dispersion signature in the embryonic Ca2+ wave field?", "gap": "Turing 1952 also derived oscillatory, travelling-wave instabilities; essentially no developmental system has been shown to use one. The repo's Ca2+ spark-track data (x, y, t per event) is the only place here that can ask whether an observed wave field carries a dispersion ridge omega(k) distinct from a single driven front (omega = v k).", "done": "A pre-registered space-time spectral test on existing spark_tracks CSVs: estimate the (k, omega) power surface per embryo, fit the driven-front line, and test for a secondary ridge against phase-randomised surrogates at a locked false-positive rate; report per-embryo outcomes and the pooled verdict either way.", "provisional": { "posterior": 38.7, "assessor": "Claude Fable 5.1 Thinking High (single assessor, provisional)", "prior": 50.0, "net_db": -2, "resolvability": 71, "band": "RESOLVE NOW" }, "panel": { "id": "TOP-09", "slug": "turing-hopf-wave-signature", "pooled": { "method": "log-odds mean across 3 assessors (equal priors 50%, so pooled net dB = mean net dB)", "prior_percent": 50.0, "net_db": 1.33, "bayes_factor": 1.3583, "posterior_percent": 57.6, "panel_range_percent": [ 38.69, 69.12 ], "classification": "possible_pathway" }, "resolvability_panel": { "mean": 79.7, "range": [ 70, 88 ], "band": "RESOLVE NOW", "factor_means": { "tool_fit": 13, "data_in_hand": 18.3, "falsifiable_done": 13, "compute_in_repo": 14, "isolation": 9.7, "time_to_verdict": 8, "not_blocked": 3.7 } }, "packet_correction": null, "trig": "panel-top-09-turing-hopf-wave-signature.trig", "assessors": { "gpt-5.6-sol": { "label": "GPT 5.6 Sol Medium", "provider": "OpenAI", "resolvability": 81, "net_db": 2.5, "posterior_percent": 64.01, "confidence": 0.79, "verdict": "LIKELY_DECISIVE", "note": "The route can return a calibrated detection result, but an absent ridge should only count as decisive if power against simulated secondary ridges is preregistered." }, "gemini-4-argon": { "label": "Gemini 4 Argon Medium", "provider": "Google", "resolvability": 88, "net_db": 3.5, "posterior_percent": 69.12, "confidence": 0.85, "verdict": "READY_IN_REPO_SPECTRAL_TEST", "note": "The crux is converting sparse, tracked Ca2+ spark centroids into a well-conditioned space-time density field along ap_norm without introducing binning artifacts before computing S(k, omega). Note that COORDINATE_SYSTEM_WARNING.md is cited in the packet and AGENTS.md, though that file path is not currently present in wave-vector-analysis/ (the relevant caveats live in head_tail_comparison.csv and mask_tiff_mismatch_cases.csv)." }, "claude-fable-5-1": { "label": "Claude Fable 5.1 Thinking High (fresh context)", "provider": "Anthropic", "resolvability": 70, "net_db": -2, "posterior_percent": 38.69, "confidence": 0.55, "verdict": "PROCEDURALLY_DECISIVE_UNDERPOWERED", "note": "Crux: the test will return a number, but with ~3 embryos and 1 fps sparse events the 'absent' outcome is weak evidence; pre-register a power analysis on synthetic Turing-Hopf fields so a negative is interpretable." } }, "nanopub": { "date": "2026-10-27", "nanopub": "https://w3id.org/np/RALU82Yi2cyqDHxPUteMQokR05KNaz_NOCYWY40vKJ5ZE", "published": "test" } }, "status": "open", "graph_node_label": "TOP-09 \u00b7 turing hopf wave signature", "source": "morphoeval/build_turing_open_problems.py \u00b7 morphoeval/audits/2026-10-27-turing-open-problems-assessment.yaml", "attempted_by_agent_ids": [ "fable", "gemini", "gpt", "panel" ], "attempted_by": [ "Claude Fable 5.1 Thinking High", "Gemini 4 Argon", "GPT 5.6 Sol Medium", "Multi-agent panel" ], "graph_url": "https://fractastical.github.io/morpholib/problem-graph.html#top-09", "resolvability": { "score": 79.7, "band": "RESOLVE NOW", "panel_range": [ 70, 88 ], "provisional_score": 71, "rubric": "morphoeval/problem_scout_100.py RUBRIC (deterministic; prices tools, data, done \u2014 not truth odds); panel mean of 3 blinded assessors" }, "viability": { "kind": "delphi_panel_posterior_percent", "pooled": 57.6, "panel_range_percent": [ 38.69, 69.12 ], "prior_percent": 50.0, "net_db": 1.33, "assessors": { "gpt-5.6-sol": { "label": "GPT 5.6 Sol Medium", "provider": "OpenAI", "posterior_percent": 64.01, "verdict": "LIKELY_DECISIVE" }, "gemini-4-argon": { "label": "Gemini 4 Argon Medium", "provider": "Google", "posterior_percent": 69.12, "verdict": "READY_IN_REPO_SPECTRAL_TEST" }, "claude-fable-5-1": { "label": "Claude Fable 5.1 Thinking High (fresh context)", "provider": "Anthropic", "posterior_percent": 38.69, "verdict": "PROCEDURALLY_DECISIVE_UNDERPOWERED" } }, "provisional_posterior_percent": 38.7, "classification": "possible_pathway", "note": "Three-provider blinded Delphi panel (GPT 5.6 Sol / Gemini 4 Argon / Claude Fable 5.1), pooled in log-odds; supersedes the provisional single-assessor posterior (kept for the record). Ledger: morphoeval/audits/2026-10-27-turing-open-problems-panel.yaml. Same colour rule as other Delphi posteriors." } }, { "id": "OP-14", "node": "top-03", "delphi": null, "title": "TOP-03 \u00b7 The fine-tuning objection: replicate the two-node vs three-node Turing parameter-volume ratio and the 1%-uncertainty retention claim", "gap": "Turing instability is topologically common but occupies tiny parameter volumes: 0.00035% of sampled space for the classical two-node circuit vs 0.022% for the best three-node topology (Tica et al. 2024, Latin-hypercube linear stability), with 33% retention under 1% parameter uncertainty around a Turing I point. These numbers decide whether the fine-tuning objection to biological Turing systems stands; they have not been independently reproduced.", "done": "A pre-registered Latin-hypercube linear-stability sweep on the repo's two-node kinetics and a three-node immobile-node topology within published parameter bounds, reporting both Turing fractions and the 1%/5% local-retention fractions; verdict = within one order of magnitude of the published ratio (>=10x three-node over two-node) or not.", "provisional": { "posterior": 79.9, "assessor": "Claude Fable 5.1 Thinking High (single assessor, provisional)", "prior": 50.0, "net_db": 6, "resolvability": 88, "band": "RESOLVE NOW" }, "panel": { "id": "TOP-03", "slug": "robustness-fraction", "pooled": { "method": "log-odds mean across 3 assessors (equal priors 50%, so pooled net dB = mean net dB)", "prior_percent": 50.0, "net_db": 3.67, "bayes_factor": 2.3281, "posterior_percent": 69.95, "panel_range_percent": [ 61.31, 79.92 ], "classification": "possible_pathway" }, "resolvability_panel": { "mean": 78.7, "range": [ 71, 93 ], "band": "RESOLVE NOW", "factor_means": { "tool_fit": 13.3, "data_in_hand": 15.3, "falsifiable_done": 14.3, "compute_in_repo": 13.3, "isolation": 9.3, "time_to_verdict": 8, "not_blocked": 5 } }, "packet_correction": null, "trig": "panel-top-03-robustness-fraction.trig", "assessors": { "gpt-5.6-sol": { "label": "GPT 5.6 Sol Medium", "provider": "OpenAI", "resolvability": 72, "net_db": 2.0, "posterior_percent": 61.31, "confidence": 0.74, "verdict": "LIKELY_DECISIVE", "note": "The result can be decisive if the published sampling measure and topology are reproduced rather than replaced by convenient repo defaults." }, "gemini-4-argon": { "label": "Gemini 4 Argon Medium", "provider": "Google", "resolvability": 93, "net_db": 6.0, "posterior_percent": 79.92, "confidence": 0.92, "verdict": "IMMEDIATE_COMPUTATIONAL_WIN", "note": "This is the cleanest computational replication in the packet because it requires only vectorized Jacobian eigenvalue algebra and published parameter bounds. The packet should explicitly note that finding non-trivial positive steady states for Hill kinetics at each Latin-hypercube sample is part of the Scholes/Tica denominator definition." }, "claude-fable-5-1": { "label": "Claude Fable 5.1 Thinking High (fresh context)", "provider": "Anthropic", "resolvability": 71, "net_db": 3, "posterior_percent": 66.61, "confidence": 0.65, "verdict": "DECISIVE_IF_PUBLISHED_KINETICS_ADOPTED", "note": "Crux: adopt Tica's exact ODEs and bounds, not the repo's Gray-Scott; otherwise the ratio test is a comparison of different models. The done should specify log-uniform sampling as in the paper." } }, "nanopub": { "date": "2026-10-27", "nanopub": "https://w3id.org/np/RAv59sstCLMawS4X_MCcCd9HknvvTh7UuoOHHtoNfWV4w", "published": "test" } }, "status": "solved", "graph_node_label": "TOP-03 \u00b7 robustness fraction", "source": "morphoeval/build_turing_open_problems.py \u00b7 morphoeval/audits/2026-10-27-turing-open-problems-assessment.yaml", "attempted_by_agent_ids": [ "fable", "gemini", "gpt", "panel" ], "attempted_by": [ "Claude Fable 5.1 Thinking High", "Gemini 4 Argon", "GPT 5.6 Sol Medium", "Multi-agent panel" ], "graph_url": "https://fractastical.github.io/morpholib/problem-graph.html#top-03", "resolvability": { "score": 78.7, "band": "RESOLVE NOW", "panel_range": [ 71, 93 ], "provisional_score": 88, "rubric": "morphoeval/problem_scout_100.py RUBRIC (deterministic; prices tools, data, done \u2014 not truth odds); panel mean of 3 blinded assessors" }, "viability": { "kind": "delphi_panel_posterior_percent", "pooled": 69.95, "panel_range_percent": [ 61.31, 79.92 ], "prior_percent": 50.0, "net_db": 3.67, "assessors": { "gpt-5.6-sol": { "label": "GPT 5.6 Sol Medium", "provider": "OpenAI", "posterior_percent": 61.31, "verdict": "LIKELY_DECISIVE" }, "gemini-4-argon": { "label": "Gemini 4 Argon Medium", "provider": "Google", "posterior_percent": 79.92, "verdict": "IMMEDIATE_COMPUTATIONAL_WIN" }, "claude-fable-5-1": { "label": "Claude Fable 5.1 Thinking High (fresh context)", "provider": "Anthropic", "posterior_percent": 66.61, "verdict": "DECISIVE_IF_PUBLISHED_KINETICS_ADOPTED" } }, "provisional_posterior_percent": 79.9, "classification": "possible_pathway", "note": "Three-provider blinded Delphi panel (GPT 5.6 Sol / Gemini 4 Argon / Claude Fable 5.1), pooled in log-odds; supersedes the provisional single-assessor posterior (kept for the record). Ledger: morphoeval/audits/2026-10-27-turing-open-problems-panel.yaml. Same colour rule as other Delphi posteriors." } }, { "id": "OP-15", "node": "top-01", "delphi": null, "title": "TOP-01 \u00b7 Mechanism identification: a pre-registered statistic that separates reaction-diffusion from colonisation, phase separation and buckling on static patterns", "gap": "Pattern phenomenology does not identify mechanism: zebrafish stripes are cell-contact mediated (Nakamasu 2009), feather buds mechanical first (Shyer 2017), Holstein spotting indistinguishable between growing RD and Eden colonisation at p=0.91 (OP-11). No registered discriminator exists that, given only an adult pattern, says which class of generator made it with a stated error rate.", "done": "A hash-locked discriminator (candidate features: radial power-spectrum shape, Minkowski functionals, defect/junction statistics, two-point anisotropy) trained and scored on synthetic ground truth from four generators (Gray-Scott/Schnakenberg RD, Eden colonisation, Cahn-Hilliard phase separation, elastic buckling) with a pre-registered held-out accuracy threshold and published confusion matrix; then applied blind to the 10 coat-masked Holstein specimens, reported either way.", "provisional": { "posterior": 55.7, "assessor": "Claude Fable 5.1 Thinking High (single assessor, provisional)", "prior": 50.0, "net_db": 1, "resolvability": 77, "band": "RESOLVE NOW" }, "panel": { "id": "TOP-01", "slug": "mechanism-discriminator", "pooled": { "method": "log-odds mean across 3 assessors (equal priors 50%, so pooled net dB = mean net dB)", "prior_percent": 50.0, "net_db": 1.67, "bayes_factor": 1.4689, "posterior_percent": 59.5, "panel_range_percent": [ 55.73, 61.31 ], "classification": "possible_pathway" }, "resolvability_panel": { "mean": 76, "range": [ 70, 84 ], "band": "RESOLVE NOW", "factor_means": { "tool_fit": 13.7, "data_in_hand": 18, "falsifiable_done": 13.3, "compute_in_repo": 12.7, "isolation": 8.7, "time_to_verdict": 6.7, "not_blocked": 3 } }, "packet_correction": null, "trig": "panel-top-01-mechanism-discriminator.trig", "assessors": { "gpt-5.6-sol": { "label": "GPT 5.6 Sol Medium", "provider": "OpenAI", "resolvability": 70, "net_db": 2, "posterior_percent": 61.31, "confidence": 0.72, "verdict": "LIKELY_DECISIVE", "note": "The synthetic benchmark is closeable, but the packet overstates data-in-hand: the checked dataset has pinned references rather than the ten image files. A reject or abstention rule is also needed to make the Holstein class assignment scientifically definite." }, "gemini-4-argon": { "label": "Gemini 4 Argon Medium", "provider": "Google", "resolvability": 84, "net_db": 1.0, "posterior_percent": 55.73, "confidence": 0.78, "verdict": "SYNTHETIC_SEPARABLE_EMPIRICAL_AMBIGUOUS", "note": "The crux is whether higher-order morphological statistics (Minkowski functionals, chord-length distributions, or boundary curvature spectra) can break the OP-11 degeneracy between growing-domain RD and Eden colonisation after binary Otsu thresholding. The packet understates how severely the low patch count per Holstein flank limits spectral and defect-based features on the empirical specimens." }, "claude-fable-5-1": { "label": "Claude Fable 5.1 Thinking High (fresh context)", "provider": "Anthropic", "resolvability": 74, "net_db": 2, "posterior_percent": 61.31, "confidence": 0.6, "verdict": "SYNTHETIC_LEG_DECISIVE_HOLSTEIN_FRAGILE", "note": "Crux: the synthetic confusion matrix is cheap and decisive; the blind Holstein application is where the hypothesis will be fought over. Packet says CH/buckling generators 'must be written fresh' but non-template phase-separation (2002-sumper) and buckling (1975-richman) scripts exist to adapt." } }, "nanopub": { "date": "2026-10-27", "nanopub": "https://w3id.org/np/RATv3ryEVNA5ZoIG740ex4W_hHdeJoSTyz0uPw76yc6XE", "published": "test" } }, "status": "open", "graph_node_label": "TOP-01 \u00b7 mechanism discriminator", "source": "morphoeval/build_turing_open_problems.py \u00b7 morphoeval/audits/2026-10-27-turing-open-problems-assessment.yaml", "attempted_by_agent_ids": [ "fable", "gemini", "gpt", "panel" ], "attempted_by": [ "Claude Fable 5.1 Thinking High", "Gemini 4 Argon", "GPT 5.6 Sol Medium", "Multi-agent panel" ], "graph_url": "https://fractastical.github.io/morpholib/problem-graph.html#top-01", "resolvability": { "score": 76, "band": "RESOLVE NOW", "panel_range": [ 70, 84 ], "provisional_score": 77, "rubric": "morphoeval/problem_scout_100.py RUBRIC (deterministic; prices tools, data, done \u2014 not truth odds); panel mean of 3 blinded assessors" }, "viability": { "kind": "delphi_panel_posterior_percent", "pooled": 59.5, "panel_range_percent": [ 55.73, 61.31 ], "prior_percent": 50.0, "net_db": 1.67, "assessors": { "gpt-5.6-sol": { "label": "GPT 5.6 Sol Medium", "provider": "OpenAI", "posterior_percent": 61.31, "verdict": "LIKELY_DECISIVE" }, "gemini-4-argon": { "label": "Gemini 4 Argon Medium", "provider": "Google", "posterior_percent": 55.73, "verdict": "SYNTHETIC_SEPARABLE_EMPIRICAL_AMBIGUOUS" }, "claude-fable-5-1": { "label": "Claude Fable 5.1 Thinking High (fresh context)", "provider": "Anthropic", "posterior_percent": 61.31, "verdict": "SYNTHETIC_LEG_DECISIVE_HOLSTEIN_FRAGILE" } }, "provisional_posterior_percent": 55.7, "classification": "possible_pathway", "note": "Three-provider blinded Delphi panel (GPT 5.6 Sol / Gemini 4 Argon / Claude Fable 5.1), pooled in log-odds; supersedes the provisional single-assessor posterior (kept for the record). Ledger: morphoeval/audits/2026-10-27-turing-open-problems-panel.yaml. Same colour rule as other Delphi posteriors." } }, { "id": "OP-16", "node": "top-02", "delphi": null, "title": "TOP-02 \u00b7 The diffusion-ratio problem: which molecularly identified Turing systems can be two-species at all?", "gap": "Two-species activator-inhibitor models need D_inh/D_act above the Lean-checked threshold (d_c = 3.93 for the repo's Gray-Scott Jacobian; ~4-10 generally), yet measured extracellular diffusivities rarely show it; three-node networks with an immobile node remove the requirement (Marcon 2016) and extracellular wiring changes behaviour qualitatively (2025 bioRxiv). Nobody has tabulated, system by system, which of the molecularly supported cases (WNT/DKK, FGF/Shh palate, Bmp-Sox9-Wnt digits, GDF5/NOG joints, EDAR/WNT/BMP ridges, Nodal/Lefty) actually satisfies the two-species condition with measured D.", "done": "A registered table of >=6 molecular Turing systems giving measured or bounded D_act, D_inh (with DOI), run through the repo's dispersion relation, classifying each as two-node-feasible / needs immobile third node / D unmeasured; the count in each class pre-registered before the literature values are looked up.", "provisional": { "posterior": 55.7, "assessor": "Claude Fable 5.1 Thinking High (single assessor, provisional)", "prior": 50.0, "net_db": 1, "resolvability": 78, "band": "RESOLVE NOW" }, "panel": { "id": "TOP-02", "slug": "diffusion-ratio-census", "pooled": { "method": "log-odds mean across 3 assessors (equal priors 50%, so pooled net dB = mean net dB)", "prior_percent": 50.0, "net_db": 3.0, "bayes_factor": 1.9953, "posterior_percent": 66.61, "panel_range_percent": [ 58.55, 78.01 ], "classification": "possible_pathway" }, "resolvability_panel": { "mean": 74.3, "range": [ 61, 89 ], "band": "RESOLVE NOW", "factor_means": { "tool_fit": 13.3, "data_in_hand": 13.7, "falsifiable_done": 12, "compute_in_repo": 14.3, "isolation": 9.3, "time_to_verdict": 7, "not_blocked": 4.7 } }, "packet_correction": null, "trig": "panel-top-02-diffusion-ratio-census.trig", "assessors": { "gpt-5.6-sol": { "label": "GPT 5.6 Sol Medium", "provider": "OpenAI", "resolvability": 73, "net_db": 1.5, "posterior_percent": 58.55, "confidence": 0.67, "verdict": "PLAUSIBLY_DECISIVE", "note": "A useful census is achievable, but class rules must distinguish unmeasured transport from evidence for a third immobile node." }, "gemini-4-argon": { "label": "Gemini 4 Argon Medium", "provider": "Google", "resolvability": 89, "net_db": 5.5, "posterior_percent": 78.01, "confidence": 0.88, "verdict": "HIGHLY_TRACTABLE_DECISIVE", "note": "The crux is distinguishing truly unmeasured in vivo diffusivities from indirect effective range estimates, since all three classification buckets are already guaranteed to be populated by Nodal/Lefty, Bmp-Sox9-Wnt, and WNT/DKK. Note that d_c = 3.9271 is specific to Turing's 1952 numerical Jacobian example, whereas each biological system has its own kinetic Jacobian bounds on D_inh/D_act." }, "claude-fable-5-1": { "label": "Claude Fable 5.1 Thinking High (fresh context)", "provider": "Anthropic", "resolvability": 61, "net_db": 2, "posterior_percent": 61.31, "confidence": 0.55, "verdict": "CENSUS_REACHABLE_CLASSES_DISPUTABLE", "note": "Crux: the table will be assembled, but 'two-node-feasible' needs a per-system Jacobian or a stated generic bound; the packet's reliance on the GS d_c is the weak link." } }, "nanopub": { "date": "2026-10-27", "nanopub": "https://w3id.org/np/RAuS57SWttfCqMSDztyeBD27DgvQ88biO9JwCXUus0oP0", "published": "test" } }, "status": "open", "graph_node_label": "TOP-02 \u00b7 diffusion ratio census", "source": "morphoeval/build_turing_open_problems.py \u00b7 morphoeval/audits/2026-10-27-turing-open-problems-assessment.yaml", "attempted_by_agent_ids": [ "fable", "gemini", "gpt", "panel" ], "attempted_by": [ "Claude Fable 5.1 Thinking High", "Gemini 4 Argon", "GPT 5.6 Sol Medium", "Multi-agent panel" ], "graph_url": "https://fractastical.github.io/morpholib/problem-graph.html#top-02", "resolvability": { "score": 74.3, "band": "RESOLVE NOW", "panel_range": [ 61, 89 ], "provisional_score": 78, "rubric": "morphoeval/problem_scout_100.py RUBRIC (deterministic; prices tools, data, done \u2014 not truth odds); panel mean of 3 blinded assessors" }, "viability": { "kind": "delphi_panel_posterior_percent", "pooled": 66.61, "panel_range_percent": [ 58.55, 78.01 ], "prior_percent": 50.0, "net_db": 3.0, "assessors": { "gpt-5.6-sol": { "label": "GPT 5.6 Sol Medium", "provider": "OpenAI", "posterior_percent": 58.55, "verdict": "PLAUSIBLY_DECISIVE" }, "gemini-4-argon": { "label": "Gemini 4 Argon Medium", "provider": "Google", "posterior_percent": 78.01, "verdict": "HIGHLY_TRACTABLE_DECISIVE" }, "claude-fable-5-1": { "label": "Claude Fable 5.1 Thinking High (fresh context)", "provider": "Anthropic", "posterior_percent": 61.31, "verdict": "CENSUS_REACHABLE_CLASSES_DISPUTABLE" } }, "provisional_posterior_percent": 55.7, "classification": "possible_pathway", "note": "Three-provider blinded Delphi panel (GPT 5.6 Sol / Gemini 4 Argon / Claude Fable 5.1), pooled in log-odds; supersedes the provisional single-assessor posterior (kept for the record). Ledger: morphoeval/audits/2026-10-27-turing-open-problems-panel.yaml. Same colour rule as other Delphi posteriors." } } ], "registered_prediction_followups": { "note": "Registered predictions scored partially_resolved on 2026-10-26: outcome neither confirmed nor refuted; each names the exact missing series. Closing one means supplying that series, not re-arguing the prediction.", "items": [ { "id": "ZF-HH-01", "organism": "Danio rerio", "mechanism": "morphogen_condensation", "missing_evidence": "Lipidation is functional in zebrafish Shh signalling: 'New chemical probes targeting cholesterylation of Sonic Hedgehog in human cells and zebrafish' (2014, doi:10.1039/C4SC01600A), and dual-lipid release biology reviewed in doi:10.1002/bies.202100133. Bound established: wild-type ShhNp is dually lipidated and tethered (repo state), and cholesterylation is required for normal signalling in zebrafish. NOT established from sources extracted: the specific registered gradient-shape claim (distal ptc-domain expansion + reduced near-source peak upon lipidation loss) in a zebrafish tissue assay. Missing data: paired ptc1/ptc2 domain measurements for lipidation-perturbed vs wild-type zebrafish Shh." }, { "id": "ZF-CLK-01", "organism": "Danio rerio", "mechanism": "clock_wavefront", "missing_evidence": "Bound established: the proportional architecture (clock period sets somite size at a given wavefront speed) is the standard, literature-supported segmentation-clock framework (zebrafish clock-mechanism studies, e.g. doi:10.1371/journal.pbio.0050150; core-circuit dynamics doi:10.1371/journal.pbio.1001364). NOT established: a paired dataset (measured T change + measured S change, wavefront controlled) sufficient to test the registered x0.80/x0.90/x1.10/x1.20 multipliers within 5 points. Missing data: paired her1-period and somite-length measurements under a controlled-wavefront perturbation, tabulated in one source." }, { "id": "ZF-VTX-01", "organism": "Danio rerio", "mechanism": "vertex_packing", "missing_evidence": "Bound established: 3.813 is the established vertex-model jamming value carried by the dataset law. NOT established: a zebrafish (EVL/epiboly) measured shape-index transition inside 3.76-3.87; the targeted literature search returned no zebrafish shape-index transition dataset. Missing data: cell shape-index series across a zebrafish epithelial jamming/unjamming transition (measurable from published epiboly images, not yet tabulated)." }, { "id": "DM-MUR-NEG-01", "organism": "Drosophila melanogaster", "mechanism": "branching_tree", "missing_evidence": "Bound established: insect tracheal systems are not generically Murray-optimal (ant tracheal branching violates network-transport assumptions, doi:10.1371/journal.pcbi.1007853; Murray compliance varies by insect system, doi:10.1186/s12915-021-01130-0), consistent with the negative prediction. NOT established: a Drosophila tracheal parent/daughter diameter series sufficient to fit an exponent against the registered 2.8-3.2 band. Missing data: tabulated Drosophila tracheal diameters across branch orders." }, { "id": "XT-CLK-01", "organism": "Xenopus tropicalis", "mechanism": "clock_wavefront", "missing_evidence": "Bound established: Xenopus somitogenesis uses a her/hes segmentation clock with a wavefront, so the proportional S~T architecture is the applicable framework (cross-species replication target of ZF-CLK-01). NOT established: paired Xenopus period-manipulation + somite-length measurements sufficient to test the x0.80-x1.20 multipliers within 5 points. Missing data: paired clock-period and somite-length series under controlled wavefront conditions in Xenopus." } ], "registry_url": "https://github.com/fractastical/morpholib/blob/main/predictions/prediction_registry.json" }, "live_arguments": { "note": "Contested literature questions (\u22652 camps) mapped to repo datasets, genome tiers and the measurement that would settle each. Candidates only: Delphi-score the probability (recorded on the graph edge), then register, then score. Settled halves (e.g. LA-01) must not be re-litigated.", "source": "predictions/live_arguments.json", "items": [ { "id": "LA-01", "question": "How is the zebrafish BMP dorsoventral gradient formed: Chordin-mediated shuttling, regulated free diffusion/source-sink, or ECM/HSPG-shaped diffusion?", "argument_status": "partly_settled", "camps": [ "Shuttling essential", "Regulated diffusion / source-sink sufficient", "ECM/HSPG-shaped" ], "related_datasets": [ "datasets/danio_rerio_turing_wavelength", "datasets/danio_rerio_morphogen_condensation", "datasets/danio_aesculapii_turing_wavelength", "datasets/danio_albolineatus_turing_wavelength", "datasets/danio_margaritatus_turing_wavelength" ], "genome_tier": "A (congeners C)", "settling_measurement": "Paired FRAP/effective-mobility measurements of tagged BMP and Chordin plus pSmad1/5 gradient ranges in at least two Danio species of different embryo size, under identical staging.", "candidate_confidence": 0.55 }, { "id": "LA-02", "question": "Are zebrafish stripes (and fish pigment patterns generally) a Turing reaction-diffusion system, or a cell-interaction network that only mimics one?", "argument_status": "live", "camps": [ "Turing / reaction-diffusion", "Cell-interaction network" ], "related_datasets": [ "datasets/danio_rerio_turing_wavelength", "datasets/danio_albolineatus_turing_wavelength", "datasets/danio_nigrofasciatus_turing_wavelength", "datasets/bos_taurus_turing_wavelength", "datasets/equus_quagga_turing_wavelength" ], "genome_tier": "A (Bos B)", "settling_measurement": "Stripe wavelength and regeneration kinetics in cell-interaction mutants (leopard/gja5b, pfeffer/csf1ra) compared quantitatively against both model classes fitted on the same fish; the Turing account must predict the wavelength shift from a kinetic parameter, the cell account from interaction ranges.", "candidate_confidence": 0.6 }, { "id": "LA-03", "question": "Is vertebrate digit patterning a BMP-SOX9-WNT Turing system modulated by Hox dose, or a positional-gradient system in which Turing-like periodicity is secondary?", "argument_status": "live", "camps": [ "Turing (BSW) primary", "Positional / Hox primary" ], "related_datasets": [ "datasets/mus_musculus_turing_wavelength", "datasets/mus_musculus_morphogen_condensation" ], "genome_tier": "A", "settling_measurement": "Digit wavelength (condensation spacing) as a function of distal Hox dose in allelic series, tested against the BSW prediction that wavelength -- not just digit identity -- shifts continuously with Hox-modulated parameters.", "candidate_confidence": 0.5 }, { "id": "LA-04", "question": "How is Hedgehog transported: extracellular diffusion (with Dispatched/Scube hand-off) or cytoneme-mediated delivery?", "argument_status": "live", "camps": [ "Extracellular diffusion / hand-off", "Cytoneme delivery" ], "related_datasets": [ "datasets/danio_rerio_morphogen_condensation", "datasets/xenopus_tropicalis_morphogen_condensation", "datasets/drosophila_melanogaster_morphogen_condensation" ], "genome_tier": "A", "settling_measurement": "Gradient range after cytoneme disruption that leaves secretion intact (and vice versa), in the same tissue, with the lipidation state of the transported species verified from sequence/protein state.", "candidate_confidence": 0.45 }, { "id": "LA-05", "question": "Does somite size scale with segmentation-clock period via wavefront speed (clock-and-wavefront), and what sets the scaling across species?", "argument_status": "live", "camps": [ "Clock-and-wavefront scaling", "PSM-growth / multi-factor control" ], "related_datasets": [ "datasets/danio_rerio_clock_wavefront", "datasets/xenopus_tropicalis_clock_wavefront", "datasets/drosophila_melanogaster_clock_wavefront" ], "genome_tier": "A", "settling_measurement": "Paired clock-period and somite-length measurements with PSM length/wavefront speed recorded in the same embryos, across at least the fish and frog systems the repo holds.", "candidate_confidence": 0.5 }, { "id": "LA-06", "question": "How does the Dpp/BMP gradient scale with the growing Drosophila wing disc: degradation-mediated scaling, expansion-repression, or growth-coupled production?", "argument_status": "live", "camps": [ "Degradation / kinetics scaling", "Expansion-repression / feedback scaling" ], "related_datasets": [ "datasets/drosophila_melanogaster_morphogen_condensation", "datasets/drosophila_melanogaster_turing_wavelength" ], "genome_tier": "A", "settling_measurement": "Dpp gradient length, disc size, Dpp turnover and candidate-expander expression measured across growth stages/genotypes in one quantitative series; the two camps predict different couplings between turnover and length.", "candidate_confidence": 0.65 }, { "id": "LA-07", "question": "Is the bioelectric (Vmem) prepattern instructive for Xenopus craniofacial/orientation patterning -- upstream information that biochemical gradients read out -- or a downstream correlate of conventional pathways?", "argument_status": "live", "camps": [ "Instructive bioelectric prepattern", "Conventional-pathway primacy" ], "related_datasets": [ "datasets/xenopus_tropicalis_bioelectric_polarity", "datasets/xenopus_tropicalis_morphogen_condensation", "datasets/danio_rerio_bioelectric_polarity" ], "genome_tier": "A", "settling_measurement": "Blinded, pre-registered ion-channel misexpression with BMP-pathway transcriptional readout and craniofacial scoring, where the bioelectric account predicts the readout change in advance and the conventional account predicts none without direct pathway manipulation. The repo's own blind-test contract (hash-locked, scorer refuses on mismatch) is the required format, given its earlier negative blind results.", "candidate_confidence": 0.4 } ] } }