Morphogenesis

2011-01-19 — 2024-02-27

agents
compsci
distributed
dynamical systems
extended self
game theory
generative art
hidden variables
incentive mechanisms
life
photon choreography
self similar
spatial
statmech
Figure 1

On instructing cells to grow into differentiated bodies. This notebook has been resurrected from the trash bin years after I deleted it because of my great enjoyment of Mordvintsev et al. (2020) on differentiable cellular automata.

1 Differentiable Cellular Automata

See learning automata.

2 Actual Biologically-Plausible Morphogenesis

I know nothing of that.

3 Abstracted Morphogenesis, mathetmatical tools for

Plum and Serra (2025) looks interesting:

Developmental biology has long drawn on dynamical systems to understand the diverging fates and the emerging form of the developing embryo. Cell differentiation and morphogenesis unfold in high-dimensional geneexpression spaces and position spaces. Yet, their stable and reproducible outcomes suggest low-dimensional geometric structures—e.g., fixed points, manifolds, and dynamic attracting and repelling structures—that organize cell trajectories in both spaces. This review surveys the history and recent advances in dynamical systems frameworks for development. We focus on techniques for extracting the organizing geometric structures of cell fate decisions and morphogenetic movements from experiments, as well as their interconnections. This unifying, dynamical systems perspective aids in rationalizing increasingly complex experimental datasets, facilitating principled dimensionality reduction and an integrated understanding of development, bridging typically distinct domains.

Figure 2: Plum and Serra (2025) figure 1: Geometric structures in cell fate decisions and morphogenetic movements.

4 References

Hussein, Maselko, and Pantaleone. 2016. Growing a Chemical Garden at the Air–Fluid Interface.” Langmuir.
Kücken, Rinkevich, Shaish, et al. 2011. Nutritional resources as positional information for morphogenesis in the stony coral Stylophora pistillata.” Journal of Theoretical Biology.
Kuffner, and LaValle. 2009. “Space-Filling Trees.”
Lee, Shin, and Park. 2007. Computational Morphogenesis Based Structural Design by Using Material Topology Optimization.” Mechanics Based Design of Structures and Machines.
Mordvintsev, and Niklasson. 2021. μNCA: Texture Generation with Ultra-Compact Neural Cellular Automata.”
Mordvintsev, Randazzo, Niklasson, et al. 2020. Growing Neural Cellular Automata.” Distill.
Pajouheshgar, Xu, Mordvintsev, et al. 2023. Mesh Neural Cellular Automata.”
Pearce. 1980. Structure in nature is a strategy for design.
Plum, and Serra. 2025. Dynamical Systems of Fate and Form in Development.” Seminars in Cell & Developmental Biology.
Randazzo, Mordvintsev, and Fouts. 2023. Growing Steerable Neural Cellular Automata.” In.
Tang, Kumar, De Lorenzis, et al. 2023. Neural Cellular Automata for Solidification Microstructure Modelling.” Computer Methods in Applied Mechanics and Engineering.
Thompson, and Bonner. 1997. On growth and form.
Turing. 1952. The Chemical Basis of Morphogenesis.” Philosophical Transactions of the Royal Society B: Biological Sciences.