Published May 19, 2026 | Version 0.1.0
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itu-kdev: ITU Pass-2 Development Toolkit #29 (Developmental Biology Information Theory K_dev)

Authors/Creators

  • 1. Roboken

Description

Copyright (C) 2026 Munehiro Terada. Licensed under CC-BY-4.0.

ITU Pass-2 Development Research artifact #29. Python toolkit implementing K_dev modular Hamiltonian on H_dev = H_egg ⊗ H_morphogen ⊗ H_genome ⊗ H_celltype ⊗ H_body, with four operational pillars:

  • Turing 1952 reaction-diffusion morphogenesis: Phil. Trans. R. Soc. B 237:37 last major paper before Turing's 1954 death; 1-D Gierer-Meinhardt activator-inhibitor simulator (D_h/D_a > threshold for Turing instability); biological realisations include zebrafish stripes, mouse hair-follicle spacing, digit patterning (Kondo-Miura 2010); ⭐ UK posthumous royal pardon 2013.12.24 after Gordon Brown 2009 PM apology.
  • Hox genes + Drosophila segmentation: Lewis 1978 Nature 276:565 bithorax complex + Nüsslein-Volhard-Wieschaus 1980 Nature 287:795 Heidelberg EMS screen; Drosophila Antennapedia + Bithorax complexes; vertebrate Hox-A/B/C/D paralogues; 5-level cascade (maternal → gap → pair-rule → segment-polarity → Hox); ⭐ Nobel 1995.10.9 Lewis + Nüsslein-Volhard + Wieschaus.
  • Yamanaka iPS cells: 4 transcription factors Oct3/4 + Sox2 + Klf4 + c-Myc; ⭐ Takahashi-Yamanaka 2006 Cell 126:663 mouse + Takahashi 2007 Cell 131:861 human; competing Yu-Thomson 2007 Science 318:1917 alternative cocktail; ⭐ Nobel 2012.10.8 Yamanaka + Gurdon; 2014 RIKEN Takahashi first iPS retinal transplant.
  • Organoids: ⭐ Sasai eye-cup 2008-2012 (Eiraku 2011 Nature 472:51 + Nakano 2012 Cell Stem Cell 10:771) at RIKEN CDB Kobe; ⭐ Clevers-Sato 2009 Nature 459:262 gut Lgr5+ organoid at Hubrecht; ⭐ Knoblich-Lancaster 2013.8.28 Nature 501:373 cerebral organoid at IMBA Vienna (microcephaly + Zika models); FDA Modernization Act 2.0 (2022.12.29) allows organoids as non-animal alternative.

Software metadata
  Repository URL: https://github.com/munehiroterada/quantum_gravity_info
  Programming Language: Python 3.9+
  Development Status: 3 - Alpha
  Tests: 32 unit tests (pytest), all passing in 0.29 s

Numerical validation: ITU axiom δS = δ⟨K⟩ verified at rel_err = 0 (machine precision) on 32-dim K_dev state. Reaction-diffusion concentrations remain positive (a ≥ 0, h > 0). Yamanaka 4 factors include Oct, Sox2, Klf4, c-Myc with Oct4 marked essential.

Companion theory paper: ITU Tier 1+ #29 K_dev, DOI 10.5281/zenodo.20273748.

Notes

Copyright (C) 2026 Munehiro Terada Licensed under CC-BY-4.0. === SOFTWARE METADATA === Repository URL: https://github.com/munehiroterada/quantum_gravity_info Programming Language: Python 3.9+ Development Status: 3 - Alpha Build System: setuptools / pyproject.toml Core Dependencies: numpy >= 1.23 Optional: matplotlib >= 3.5 (viz), pytest >= 7.0 (test) OS Support: Cross-platform Tests: 32 unit tests (pytest), all passing in 0.29 s === ITU PROGRAMME === Twenty-ninth software artifact of the ITU Pass-2 Development Research phase (2026-). Companion: ITU Tier 1+ #29 K_dev, DOI 10.5281/zenodo.20273748

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Additional details

Continues
Software: 10.5281/zenodo.20305798 (DOI)
Is derived from
Software: https://github.com/munehiroterada/quantum_gravity_info (URL)
Is part of
Preprint: 10.5281/zenodo.20109209 (DOI)
Preprint: 10.5281/zenodo.20284787 (DOI)
Is supplement to
Preprint: 10.5281/zenodo.20273748 (DOI)
Is supplemented by
Software: https://github.com/munehiroterada/quantum_gravity_info (URL)

References

  • Faulkner T., Leigh A., Parrikar O., Wang H. (2014). Modular Hamiltonians. JHEP 09:038.
  • Witten E. (2018). Notes on QFT entanglement. Rev. Mod. Phys. 90:045003.
  • Chandrasekaran V., Longo R., Penington G., Witten E. (2023). Type II crossed-product. JHEP 02:082.
  • Turing A. M. (1952). The chemical basis of morphogenesis. Phil. Trans. R. Soc. B 237:37.
  • Lewis E. B. (1978). Bithorax complex. Nature 276:565.
  • Nüsslein-Volhard C., Wieschaus E. (1980). Heidelberg EMS screen. Nature 287:795.
  • Takahashi K., Yamanaka S. (2006). Mouse iPS. Cell 126:663.
  • Eiraku M. et al. / Sasai (2011). Self-organising eye-cup. Nature 472:51.
  • Sato T. et al. / Clevers (2009). Lgr5+ gut organoid. Nature 459:262.
  • Lancaster M. A. et al. / Knoblich (2013). Cerebral organoid. Nature 501:373.
  • Nobel 1995: Lewis + Nüsslein-Volhard + Wieschaus.
  • Nobel 2012: Yamanaka + Gurdon.
  • Terada M. (2026). ITU Tier 1+ #29: Developmental Biology Information Theory (K_dev). Zenodo 10.5281/zenodo.20273748.
  • Terada M. (2024-2026). ITU Pass-0/1/1.5 series. Zenodo, 45 deposits.

Subjects

Programming Language :: Python :: 3
https://pypi.org/classifiers/
Development Status :: 3 - Alpha
https://pypi.org/classifiers/
Topic :: Scientific/Engineering :: Bio-Informatics
https://pypi.org/classifiers/
Topic :: Scientific/Engineering :: Medical Science Apps.
https://pypi.org/classifiers/
Intended Audience :: Science/Research
https://pypi.org/classifiers/
License :: CC-BY-4.0
https://creativecommons.org/licenses/by/4.0/