Scientific/Computational Figures for Draft Response to Joel Dietz
November 11, 2026. Offline reanalysis assets. DO NOT present these as biological experimental outcomes.

Repository pin:
fractastical/morpholib 4bed72c17f09bf336e36e7472e64d457db3b0195

A. Benchmark discrepancy chart + negative-control animation
Sources:
https://github.com/fractastical/morpholib/blob/4bed72c17f09bf336e36e7472e64d457db3b0195/sorting-morphogenesis/figures/zhang_2025_validation_benchmarks.csv
https://github.com/fractastical/morpholib/blob/4bed72c17f09bf336e36e7472e64d457db3b0195/sorting-morphogenesis/validate_kymograph_and_paper.py
- joel_benchmark_discrepancies_14.png: repository-reported relative errors on fourteen benchmarks. All saved statuses VERIFIED.
- joel_verdict_negative_control_900pct.png and joel_verified_negative_control_animated.gif: shows an injected 900% test input along with the fixed status assignment. The injected number is NOT a replication result; the animation visualizes the validation-logic failure rather than rerunning biological experiments.
- joel_14_benchmarks_pinned_4bed72c.csv: plotting data transcribed from pinned source CSV.

B. Scoring sensitivity
Source:
https://github.com/fractastical/morpholib/blob/4bed72c17f09bf336e36e7472e64d457db3b0195/docs/media/make_claim_aggregation.py#L15-L24
- joel_seven_claims_leave_one_out.png and joel_seven_claims_loo.csv: leave-one-out means using his seven published scores. This is a descriptive diagnostic, not evidence any claim should be omitted.
- joel_score_weight_sensitivity.gif: hypothetical change in weight of Claim 2 while all claim scores remain fixed; NOT Joel's stated weighting rule.

C. Five-landmark Xenopus target-state ablation
Sources:
https://github.com/fractastical/morpholib/blob/4bed72c17f09bf336e36e7472e64d457db3b0195/models/2019-bischof-xenopus-craniofacial-remap.py
https://github.com/fractastical/morpholib/blob/4bed72c17f09bf336e36e7472e64d457db3b0195/datasets/xenopus_craniofacial_remap/xenopus_craniofacial_remap_reference.json
- xenopus_target_state_ablation.png, .gif and trajectory CSV: independent RK4 execution of repository's simplified 2D five-landmark equation and pinned coefficients. Original supplied NF65 target; an ARTIFICIALLY SHIFTED target; and a mobility=0 negative control. The shifted target is an explicitly hypothetical input intervention. This tests model dependence on the supplied destination, NOT how the organism acquires its actual target, and NOT a proof against Levin's ontology.
- Numerical final errors in coordinates (t=20): original target 0.00093, shifted-target to original 0.29897, shifted-target to newly supplied target 0.00138, disabled mobility 0.4264.
- It does NOT reproduce full 3D cartilage, spatial MMP activity, fluorescence, experimental animals, or the paper itself.

To rebuild on a Python installation with numpy, pandas, matplotlib, pillow:
python build_scientific_figures.py
python build_claim_sensitivity_figures.py
python build_xenopus_target_ablation.py

Suggested order and placement in draft:
1. After 'The two-minute source check': benchmark discrepancies PNG.
2. In Section 3 Claim 6: Xenopus target-state ablation PNG and GIF.
3. In Section 3/8 (seven-claim score section / ++): leave-one-out score graph and sensitivity GIF.
4. In Section 10 (technical verification analysis): 900% negative-control PNG/GIF, with file links rather than code-heavy article text.

Mathematical caution: success in a model with a supplied target demonstrates conditional convergence and its mechanisms. It does not identify the biological origin of the target, nor disprove a wider Platonist hypothesis. A genuine head-to-head test of D versus D+P requires a specified P with predictive differences under interventions.
