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Formal Systems in Biology

A collection of resources that apply formal systems to model biological processes. Some easily accessible books to understand the general approaches in this field are also included.

McCulloch-Pitts Work

./img/mccullough-pitts.png

McCullouch and Pitts study of neurons in biology birthed the pivotal paper that kickstarted A.I., regular languages, and digital computers. It was the only paper included in the EDVAC report by John Von Neumann.

An interactive demo of their model is available here: https://justinmeiners.github.io/neural-nets-sim/

Arthur Iberall / Warren McCulloch

Stanisław Ulam and Jon Von Neumann

./img/neumann.png

./img/neumann-pierce-drawings.png

L Systems

./img/lsystem-1.png

./img/lsystem-2.png

Karl Sims

./img/karl-sims.jpg

Walter Fontana and Leo Buss (1996)

./img/fontana-buss.png

Regev, Silvermann, Shapiro

./img/regev-shapiro.png

./img/regev-shapiro-2.png

Ehud Lamm and Ron Unger

./img/ehud-lamm.jpg

P System

./img/p-system.png

Alan Turing

./img/reaction-diffusion.png Reaction-Diffusion Systems

Joseph Henry Woodgers

Louis Kauffman

./img/kauffman-magarshak.png

Marius Buliga

./img/chemlambda.gif

For animations, checkout: https://chemlambda.github.io/collection.html

History of the project

Stefano Maestri and Emaneula Merelli

Artem Kaznatcheev

Jeffrey Ventrella

./img/clusters.png

./img/genepool.png

Programming Languages

./img/kappa.png

Computation with Crabs

Paper

./img/crab-or-gate.png

./img/crab-and-gate.png

Resources to understand the field

Neurocomics (Beginner)

./img/neurocomics.jpg

./img/evolution-graphic-guide.jpg

./img/genetics-graphic-guide.jpg

./img/epigenetics-graphic-guide.jpg

./img/complexity-a-very-short-introduction.jpg

Games of Life (Intermediate)

./img/games-of-life.jpg

Books

A really good survey of books in complexity science here.

Further Research

  • Rashevsky and Rosen

Rashevsky devised the primary model of neural networks which was interpreted using the boolean language by McCullough/Pitts. His student Robert Rosen went on to work on using Category Theory to model biology. These works need to be catalogued here. Herbert Simon was also his student.

There could also be more possible works from the conference where McCullough presented his work and met Pitts.

Sampling of Rashevsky’s work

Sampling of Rosen’s work:

  • Ilya Pregorine’s Work
  • Gregory Chaitin’s work
  • Stochastic CFG for RNA
  • Zuse-Fredkin thesis / Digital Philosophy

Think I need to mention the work of Zuse-Fredkin thesis along with Ulam-Neumann model.

Tools

Ready is a program for exploring continuous and discrete cellular automata, including reaction-diffusion systems, on grids and arbitrary meshes.

Blogs

A beautiful piece of writing from James Somers on the rich tapestry of the field of biology and what user interface design might have to offer the field.

A really nice series of articles on the biological aspects of neural networks by Jack Terwilliger

Talks

Prior Art

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Application of formal systems to model biological systems

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