Three platforms (among others) for genetic medicine have become standard in recent years: the adeno-associated virus (AAV), nanolipoprotein particles (NLPs), and the Nissle E. coli chassis.
All three platforms are programmable, the first two via plasmids such as the Nanoplasmid, the last through general reprogramming of the E. coli genome. The foundational AAV vector patents have now expired and the leading biologic molecules are inexpensive to produce: what was once gated by intellectual property is increasingly gated only by understanding.
With standardized programmable platforms available, the decisive work has moved to the software of gene programming rather than the optimization of the wetware. That software problem is what this site is about.
Our research program, Cognimed — Cognitive Biology, assembles the themes introduced on these pages — TERRA RNAs, the HOX clusters, the Polycomb complex, and the bioelectric layer — into a single computable model of development: the genome read as a large model, the tissue as a neural cellular automaton, and the bioelectric field as the map on which anatomy is written. Nine papers are published open-access, with code.
The program’s results are collected in a slide deck covering all nine papers: view the deck (PDF, 4 MB) or download the PowerPoint (10 MB).
The trained model itself — the complete NCA+LGM parameter set — is published on Hugging Face: huggingface.co/jacobsme/cognimed-nca-lgm (37 MB, CC-BY).
The age of programmable biology has begun.
Projects
Cognimed — Cognitive Biology is the flagship project: a computable model of vertebrate development, trained on real spatial transcriptomic atlases of the mouse and zebrafish embryo, published as nine open-access papers with open code. Its long-range aim is in-silico medicine — designing and validating interventions against the model before the wet lab.
Application areas under study:
- Aging and partial epigenetic reprogramming — the telomere/TERRA–PRC2 clock
- Regenerative medicine and the bioelectric control of anatomy
- Gene therapy on the now-open AAV platform
Earlier focus areas — the genetics of alcoholism, methamphetamine addiction, schizophrenia, and clinical depression — remain target indications for the platform once the modelling foundation is complete.