# Bioelectricity and Morphogenesis Source: https://mesmerprism.com/projects/bioelectricity.html Canonical HTML: https://mesmerprism.com/projects/bioelectricity.html Generated: 2026-06-13 Description: Bioelectricity and morphogenesis in Rusty Morphospace: a source-linked educational planarian surface-field model built with Rusty Matter and visualized through Rusty Optics. Markdown: https://mesmerprism.com/projects/bioelectricity.md Plain text: https://mesmerprism.com/projects/bioelectricity.txt BibTeX references: https://mesmerprism.com/projects/bioelectricity.bib CSL JSON references: https://mesmerprism.com/projects/bioelectricity.references.csl.json --- Rusty Morphospace and tissue-scale patterning # Bioelectricity and Morphogenesis Bioelectric morphogenesis asks how voltage-like state, tissue coupling, perturbations, and memory can help shape living form. The Rusty Morphospace version is deliberately modest: it builds inspectable educational models over mesh-surface samples, links each scenario to publication targets, then keeps the simulation, visualization, and public claims in separate layers. [Current slice](https://mesmerprism.com/projects/bioelectricity.html#current-slice) [Showcase export](https://mesmerprism.com/projects/bioelectricity.html#showcase-export) [Source status](https://mesmerprism.com/projects/bioelectricity.html#source-target-status) [Adjacent dynamics](https://mesmerprism.com/projects/bioelectricity.html#cross-project-bridge) [Why planarians](https://mesmerprism.com/projects/bioelectricity.html#planarian) [Reference lanes](https://mesmerprism.com/projects/bioelectricity.html#reference-lanes) [Claim boundary](https://mesmerprism.com/projects/bioelectricity.html#boundary) [Rusty Morphospace](https://mesmerprism.com/projects/rusty-morphospace.html) [References](https://mesmerprism.com/projects/bioelectricity.html#references) Computational medium ## Fields, circuits, and form without overclaiming A planarian fragment does not only carry genes and geometry. It also carries physiological state across tissue: membrane potentials, gap-junction-like communication, wound signals, and downstream patterning responses. The experimental literature around planarian regeneration makes that a useful teaching case, because early bioelectric state can affect anterior/posterior polarity and regenerated head/tail outcomes ([Durant et al., 2019](https://doi.org/10.1016/j.bpj.2019.01.029); [Beane et al., 2011](https://doi.org/10.1016/j.chembiol.2010.11.012)). The Rusty Morphospace model does not try to become a full physiology simulator. It treats bioelectricity as an inspectable layer over a stable surface graph: sample nodes on a body mesh, conductance edges between neighboring samples, normalized voltage state, perturbation bands, memory state, and readout fields. This is enough to teach the architecture of a tissue-scale model while leaving calibrated wet-lab prediction outside the current claim. Current slice ## Rusty Matter owns dynamics; Rusty Optics owns inspection Within Rusty Morphospace, the useful boundary is simple: Matter computes the state; Optics prepares views and browser inspection; Manifold is deferred until commands, sessions, packages, and audit surfaces need to become first-class. Matter now carries compact source/target anchor IDs inside the planarian scenario metadata. Those anchors identify which publication target shaped a scenario; they do not turn the current fixtures into source-fitted physiological predictions. Simulation truth ### [Rusty Matter](https://github.com/MesmerPrism/rusty-matter) Matter owns mesh-surface samples, scalar and vector fields, bioelectric circuit state, deterministic stepping, edit results, schema fixtures, validation, and Wasm runtime exports. Current model Planarian AP bioelectric surface field State Normalized voltage, conductance, memory, readouts Claim Qualitative educational dynamics [Repository](https://github.com/MesmerPrism/rusty-matter) Visual contracts ### [Rusty Optics](https://github.com/MesmerPrism/rusty-optics) Optics owns renderer-neutral frames, color policy, pick/edit-intent contracts, readout panels, activity layers, conductance-edge picking, and browser presentation over Matter-owned payloads. Current view Browser Planarian 3D preview Interaction Node edits, edge gates, neighborhood brush Telemetry Split sim, view, render, and UI timing [Repository](https://github.com/MesmerPrism/rusty-optics) Deferred authority ### [Rusty Manifold](https://github.com/MesmerPrism/rusty-manifold) Manifold is the later lane for commands, sessions, packages, reproducible edit traces, and audit. It should request Matter work; it should not own field arrays or circuit dynamics. Status Deferred for this slice Future use Commands, package descriptors, session audit Boundary Control plane, not simulation state [Repository](https://github.com/MesmerPrism/rusty-manifold) Showcase export ## Validated Planarian 3D surface and graph loops These exports show the current Optics-owned preview/export path over Matter-owned synthetic educational state: a 720-node planarian graph, opaque body material, neon RGB activity/readout color, stable portrait framing, and a seamless reset-activity showcase loop. The animation is a visual teaching mode for surface-field inspection, not a calibrated planarian physiology trace. Both GIFs were generated at the exact export size and decoded after export as 96-frame, 720 x 860 animations at 12 fps. The surface view emphasizes the body field; the graph view exposes the same activity through node and edge structure. The public assets match the latest Optics export smoke outputs. Adjacent dynamics ## A side source for dynamics, not the center of the work Bioelectricity matters to Mesmer Prism because it gives another concrete vocabulary for multi-level patterning: voltage-like fields, conductance, gap-junction-like coupling, perturbation, memory, readout, repair, and target-state change. In Michael Levin's broader framing, cells, tissues, and organs are not passive materials. They are nested problem-solving systems whose physiological networks help navigate anatomical morphospace ([Levin, 2023a](https://doi.org/10.1007/s00018-023-04790-z); [Levin, 2023b](https://doi.org/10.1007/s10071-023-01780-3)). That does not make Plasmatic Multitudes, Mixed-Ability HSI, or Rusty Morphospace biological projects. The useful transfer is more constrained: bioelectric morphogenesis suggests synthetic dynamics for fields, coupling, memory, regeneration-like repair, and multi-scale agency. Those dynamics can inspire virtual swarm bodies or educational prosthetic/biotech questions later, while the current implementation remains a source-linked teaching model rather than a medical, prosthetic, or wet-lab system ([Levin, 2021](https://doi.org/10.1016/j.cell.2021.02.034); [Levin, 2022](https://doi.org/10.3389/fnsys.2022.768201)). DiffeoMorph belongs on this adjacent side too: the paper [DiffeoMorph: Learning to Morph 3D Shapes Using Differentiable Agent-Based Simulations](https://arxiv.org/abs/2512.17129) and the [hormoz-lab/diffeomorph implementation](https://github.com/hormoz-lab/diffeomorph) are useful for target-shape metrics and learned many-agent controllers, but they are not bioelectric or planarian physiology sources. ### Useful transfer - Fields and coupling as dynamic material rules. - Memory and readout as state, not only appearance. - Repair as a system-level process, not only undo. - Target states as navigable morphospace regions. ### Boundary Current public work uses bioelectricity as a qualitative dynamics source and implementation test case for Rusty Matter and Rusty Optics. Any future prosthetic, regenerative, or biotech claim would need a separate evidence, ethics, and validation path. Source status ## Matched to original sources, but not calibrated yet The current implementation is source-linked at the target level. Two source families already have qualitative Matter fixtures, and the derived PlanformDB/metric/taxonomy layer now has a 14-record curated provenance fixture mirrored into Matter. The remaining targets are intentionally planned or open until source figures, tables, categories, or datasets have been extracted into derived, rights-safe artifacts. Target Original sources Current implementation Status ap_transient_memory [Durant et al., 2019](https://doi.org/10.1016/j.bpj.2019.01.029) Matter transient-depolarization memory scenario plus no-memory control; Optics can display the resulting sequence. Qualitative fixture exists; numeric timing/value targets still need source extraction. gap_block_conductance [Oviedo et al., 2010](https://doi.org/10.1016/j.ydbio.2009.12.012); [Emmons-Bell et al., 2015](https://doi.org/10.3390/ijms161126065) Matter gap-block scenario reduces cross-band conductance and records outcome traces. Qualitative fixture exists; figure/table targets still need extraction before thresholds. head_vs_tail_voltage [Beane et al., 2011](https://doi.org/10.1016/j.chembiol.2010.11.012) Represented only as normalized AP voltage and head/tail readout context. Planned annotation layer; no named ion-channel or millivolt claim yet. head_size_scaling [Beane et al., 2013](https://doi.org/10.1242/dev.086900) Normalized region-extent metrics exist for annotation and validation fixtures. No calibrated organ-size or physical morphometry claim yet. species_like_head_labels [Emmons-Bell et al., 2015](https://doi.org/10.3390/ijms161126065) Synthetic species-like head-shape taxonomy fixture exists for educational labeling. Non-calibrated; generated labels avoid paper figure reuse. planformdb_curated_subset [PlanformDB](https://lobolab.umbc.edu/planform/download/); [Lobo et al., 2013](https://doi.org/10.1093/bioinformatics/btt088) Rights-safe derived fixture records 14 selected Oviedo 2010 source IDs covering octanol crop-position, ventral nerve cord timing, and innexin RNAi crop-position labels, with transform notes, notice text, and use limits. Expanded review fixture exists in Hub and Matter; metadata/annotation only, not runtime dynamics authority or a predictor. Why planarians ## A compact biological teaching case Planarians are useful here because regeneration is spatially legible. A transverse cut gives a wound band, an anterior/posterior axis, and a clear readout problem: head-like and tail-like identity must resolve in the right places. Experimental work gives qualitative constraints for an educational model, including gap-junction-mediated polarity effects and persistent altered morphology after transient perturbations ([Oviedo et al., 2010](https://doi.org/10.1016/j.ydbio.2009.12.012); [Emmons-Bell et al., 2015](https://doi.org/10.3390/ijms161126065)). The first scenarios therefore stay simple: baseline anterior/posterior separation, transverse-cut wound response, conductance-block perturbation, transient depolarization with memory, and a no-memory control. Those scenarios are not meant to predict a real animal. They are checks that the model can express the right kind of tissue-scale relationship before any calibrated source data is introduced. Head size and organ scaling studies add another useful lesson: voltage-like state can be read as an instructive patterning variable, not just a passive byproduct of cell state ([Beane et al., 2013](https://doi.org/10.1242/dev.086900)). In the current model, that idea appears as readout fields driven by normalized voltage and memory state. ### Qualitative checks - Anterior and posterior readouts separate in the baseline state. - Wound response stays localized to the cut band. - Gap-block scenarios change cross-band conductance and field spread. - Transient perturbation persists when memory is enabled. - No-memory controls relax toward baseline. ### Current unit policy Voltage is normalized in the current educational layer. Calibrated millivolt claims require a separate source, unit, and validation gate. Reference lanes ## Legacy projects feed the Morphospace line The older planarian and xenobot work is useful, but it should not become the runtime authority for the Rusty Morphospace implementation. Planarian reference ### Planarian graph and WebXR work The planarian graph project contributes educational region labels, body geometry lessons, outcome labels, and source/provenance habits. Its app code and demo records remain reference material; Matter builds its own computational surface graph and validation fixtures. Use now Region semantics, geometry review, outcome labels Not used as Simulation topology or runtime dynamics Xenobot reference ### Xenobot simulator planning The xenobot planning material frames later body-surface and behavior questions. It is not the first implementation target. The current path builds a generic surface-field substrate first, then leaves locomotion, cilia, hydrodynamics, fabrication, and full xenobot simulation for later. Use now Planning vocabulary and future expansion pressure Not used as First runtime or wet-lab simulator Computational morphogenesis reference ### [DiffeoMorph](https://arxiv.org/abs/2512.17129) DiffeoMorph supplies public reference material for many-agent target-shape learning, shape-matching metrics, and robustness vocabulary. It can inform future Rusty Morphospace validation language without becoming a source for the planarian bioelectric model. Use later Target-shape metrics and many-agent control vocabulary Not used as Bioelectric physiology evidence or planarian runtime authority [Paper](https://arxiv.org/abs/2512.17129) [Official code](https://github.com/hormoz-lab/diffeomorph) Curated metadata source ### [Planform / PlanformDB](https://lobolab.umbc.edu/planform/) PlanformDB is now entering through the source-intake gate as a small, rights-safe metadata fixture: selected experiment/result IDs, normalized labels, source notices, and transform notes. It remains annotation and validation context, not raw runtime authority or a shortcut to calibrated physiology. Use now Traceable source IDs, labels, and review metadata Use later Broader phenotype targets after curated provenance review [Planform page](https://lobolab.umbc.edu/planform/) Discovery map ### [Bioelectricity Nexus](https://bioelectricitynexus.com/) Bioelectricity Nexus is useful for field navigation: papers, tools, researchers, and resource leads such as BETSE and PlanMine. It is a discovery source, not primary evidence for the biological claims on this page. Use now Find source and tool leads Gate needed Primary-source and license review [Nexus](https://bioelectricitynexus.com/) [BETSE](https://github.com/betsee/betse) [PlanMine](https://planmine.mpibpc.mpg.de/) Claim boundary ## What this model does not claim The current implementation is not [BETSE](https://github.com/betsee/betse), a named-ion-channel simulator, a wet-lab planning system, a calibrated PlanformDB predictor, or a full xenobot/anthrobot world model. It uses normalized state and synthetic scenarios to make tissue-scale relationships visible before the project takes on heavier physiology or real-data claims. That boundary is an engineering choice. It keeps the page readable, keeps code ownership clear, and avoids presenting educational dynamics as empirical prediction. The current PlanformDB slice is deliberately metadata-only. More detailed source-derived work can be added later when source IDs, license notices, transformations, and validation targets are explicit; source-paper figures and raw datasets should remain outside the public page unless rights and provenance have been reviewed. ### Next public-safe steps - Expose scenario source/target anchors in the browser-facing teaching UI. - Add a teaching panel for AP separation, wound localization, gap block, and memory controls. - Make voltage-unit policy explicit per preset. - Expand PlanformDB only through small, traceable, rights-safe derived fixtures. - Promote Manifold command/session surfaces only after Matter and Optics contracts settle. References ## Sources and public project surfaces - Levin. "[Bioelectric Signaling: Reprogrammable Circuits Underlying Embryogenesis, Regeneration, and Cancer](https://doi.org/10.1016/j.cell.2021.02.034)." Cell 184(8) (2021). - Levin. "[Technological Approach to Mind Everywhere: An Experimentally-Grounded Framework for Understanding Diverse Bodies and Minds](https://doi.org/10.3389/fnsys.2022.768201)." Frontiers in Systems Neuroscience 16 (2022). - Levin. "[Darwin's Agential Materials: Evolutionary Implications of Multiscale Competency in Developmental Biology](https://doi.org/10.1007/s00018-023-04790-z)." Cellular and Molecular Life Sciences 80 (2023). - Levin. "[Bioelectric Networks: The Cognitive Glue Enabling Evolutionary Scaling from Physiology to Mind](https://doi.org/10.1007/s10071-023-01780-3)." Animal Cognition 26 (2023). - Durant et al. "[The role of early bioelectric signals in the regeneration of planarian anterior/posterior polarity](https://doi.org/10.1016/j.bpj.2019.01.029)." Biophysical Journal 116 (2019). - Beane et al. "[A chemical genetics approach reveals H,K-ATPase-mediated membrane voltage is required for planarian head regeneration](https://doi.org/10.1016/j.chembiol.2010.11.012)." Chemistry & Biology 18 (2011). - Oviedo et al. "[Long-range neural and gap junction protein-mediated cues control polarity during planarian regeneration](https://doi.org/10.1016/j.ydbio.2009.12.012)." Developmental Biology 339 (2010). - Beane et al. "[Bioelectric signaling regulates head and organ size during planarian regeneration](https://doi.org/10.1242/dev.086900)." Development 140 (2013). - Emmons-Bell et al. "[Gap junctional blockade stochastically induces different species-specific head anatomies in genetically wild-type Girardia dorotocephala flatworms](https://doi.org/10.3390/ijms161126065)." International Journal of Molecular Sciences 16 (2015). - Grodstein and Levin. "[A Computational Approach to Explaining Bioelectrically-induced Persistent, Stochastic Changes of Axial Polarity in Planarian Regeneration](https://doi.org/10.1089/bioe.2021.0036)." Bioelectricity 4 (2022). - Lobo, Malone, and Levin. "[Planform: an application and database of graph-encoded planarian regenerative experiments](https://doi.org/10.1093/bioinformatics/btt088)." Bioinformatics 29 (2013). - Lobo Lab. "[PlanformDB download page](https://lobolab.umbc.edu/planform/download/)." University of Maryland, Baltimore County. - Bioelectricity Nexus. "[Bioelectricity Nexus](https://bioelectricitynexus.com/)." Field resource index. - BETSE. "[Bioelectric Tissue Simulation Engine](https://github.com/betsee/betse)." Open-source software repository. - PlanMine. "[PlanMine planarian database](https://planmine.mpibpc.mpg.de/)." Public resource lead. - Pahng et al. "[DiffeoMorph: Learning to Morph 3D Shapes Using Differentiable Agent-Based Simulations](https://arxiv.org/abs/2512.17129)." arXiv 2512.17129 (submitted 2025; revised 2026). - hormoz-lab. "[diffeomorph](https://github.com/hormoz-lab/diffeomorph)." Official implementation repository for the DiffeoMorph paper. - Mesmer Prism. "[Rusty Morphospace](https://mesmerprism.com/projects/rusty-morphospace.html)." Public project page. - MesmerPrism. "[Rusty Matter](https://github.com/MesmerPrism/rusty-matter)." GitHub repository. - MesmerPrism. "[Rusty Optics](https://github.com/MesmerPrism/rusty-optics)." GitHub repository.