formal-systems-in-biology

formal-systems-in-biology copied to clipboard

• 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

*** [[https://www.cs.cmu.edu/~./epxing/Class/10715/reading/McCulloch.and.Pitts.pdf][A Logical Calculus of the Ideas Immanent in Nervous Activity (1943)]] [[./img/mccullough-pitts.png]]

McCullouch and Pitts study of neurons in biology birthed the pivotal paper that kickstarted A.I., [[https://www.rand.org/content/dam/rand/pubs/research_memoranda/2008/RM704.pdf][regular languages]], and digital computers. It was the only paper included in [[http://abelgo.cn/cs101/papers/Neumann.pdf][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

*** [[https://core.ac.uk/download/pdf/85247309.pdf][Behavioural Model of Man - His Chains Revealed]]

** Stanisław Ulam and Jon Von Neumann

*** [[https://dl.acm.org/doi/book/10.5555/1102024][Theory of Self Reproducing Automata]] [[./img/neumann.png]]

*** [[http://web.mit.edu/6.454/www/papers/pierce_1952.pdf][Probabilistic Logics and the Synthesis of reliable organisms from unreliable components (1952)]] [[./img/neumann-pierce-drawings.png]]

** L Systems

*** [[https://www.sciencedirect.com/science/article/abs/pii/0022519368900799][Mathematical models for cellular interactions in development I (1968)]] [[./img/lsystem-1.png]]

*** [[https://www.sciencedirect.com/science/article/abs/pii/0022519368900805][Mathematical models for cellular interactions in development II (1968)]] [[./img/lsystem-2.png]]

** Karl Sims [[./img/karl-sims.jpg]] *** [[https://www.karlsims.com/evolved-virtual-creatures.html][Evolved Virtual Creatures (1994)]]

** Walter Fontana and Leo Buss (1996)

*** [[https://scholar.harvard.edu/files/walterfontana/files/objects.pdf][The Barrier of Objects From Dynamical Systems to Bounded Organizations]] [[./img/fontana-buss.png]]

** Regev, Silvermann, Shapiro

*** [[https://psb.stanford.edu/psb-online/proceedings/psb01/regev.pdf][Representation and Simulation of Biochemical Process Using the Pi Calculus Process Algebra (2001)]] [[./img/regev-shapiro.png]]

*** [[https://www.nature.com/articles/419343a.pdf][Cell as Computation (2002)]] [[./img/regev-shapiro-2.png]]

*** [[http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.1.4739&rep=rep1&type=pdf][The π-calculus as an abtsraction for biomolecular systems (2004)]]

** Ehud Lamm and Ron Unger

*** [[http://www.ehudlamm.com/biocomputing.html][Biological Computation]] [[./img/ehud-lamm.jpg]]

** P System [[./img/p-system.png]]

** Alan Turing

*** [[https://royalsocietypublishing.org/doi/pdf/10.1098/rstb.1952.0012][The Chemical Basis of Morphogenesis (1952)]] [[./img/reaction-diffusion.png]] Reaction-Diffusion Systems

** Joseph Henry Woodgers

*** [[https://www.amazon.com/axiomatic-method-biology-Joseph-Woodger/dp/B00085P2C8][The Axiomatic Method in Biology (1937)]]

** Louis Kauffman

[[./img/kauffman-magarshak.png]] *** [[http://homepages.math.uic.edu/~kauffman/KauffProteins.pdf][Vassiliev Knot Invariants and the Structure of RNA folding]]

** Marius Buliga

*** [[https://chemlambda.github.io/index.html][Chemlambda]] [[./img/chemlambda.gif]]

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

[[https://mbuliga.github.io/quinegraphs/history-of-chemlambda.html][History of the project]]

** Stefano Maestri and Emaneula Merelli *** [[https://www.nature.com/articles/s41598-018-36965-1][Process calculi may reveal the equivalence lying at the heart of RNA and proteins]] **** Correction to the article: https://www.nature.com/articles/s41598-019-51082-3

** Artem Kaznatcheev *** [[https://www.genetics.org/content/genetics/212/1/245.full.pdf][Computational Complexity as an Ultimate Constraint on Evolution]] **** Tweet thread on it here: https://twitter.com/kaznatcheev/status/1102973539634892800

** Jeffrey Ventrella

*** [[http://ventrella.com/Clusters/][Clusters]] [[./img/clusters.png]]

*** [[http://www.swimbots.com/genepool/][Genepool]] [[./img/genepool.png]]

** Programming Languages

*** [[https://kappalanguage.org/][https://kappalanguage.org/]]

[[./img/kappa.png]]

*** [[http://sbml.org/Main_Page][The Systems Biology Markup Language]]

** Computation with Crabs

[[https://arxiv.org/pdf/1204.1749.pdf][Paper]]

[[./img/crab-or-gate.png]]

[[./img/crab-and-gate.png]]

• Resources to understand the field

** [[https://amzn.to/2UrKeRv][Neurocomics]] (Beginner) [[./img/neurocomics.jpg]]

** [[https://amzn.to/37ft4vD][Introducing Evolution]] (Beginner) [[./img/evolution-graphic-guide.jpg]]

** [[https://amzn.to/2A7pWpH][Introducing Genetics]] (Beginner) [[./img/genetics-graphic-guide.jpg]]

** [[https://amzn.to/2BQ1JEL][Introducing Epigenetics]] (Beginner) [[./img/epigenetics-graphic-guide.jpg]]

** [[https://amzn.to/2XQ39rz][Complexity: A Very Short Introduction]] (Intermediate) [[./img/complexity-a-very-short-introduction.jpg]]

** [[https://amzn.to/3dYA0ja][Games of Life]] (Intermediate) [[./img/games-of-life.jpg]]

• Books

** [[https://link.springer.com/book/10.1007/11885191][Computational Methods in Systems Biology (2006)]]

** [[https://arxiv.org/abs/1112.1440][Complex Systems: A Survey]] A really good survey of books in complexity science here.

• Further Research

• Rashevsky and Rosen

[[https://en.wikipedia.org/wiki/Nicolas_Rashevsky][Rashevsky]] devised the [[https://doi.org/10.1002%2Fjhbs.1094][primary model of neural networks]] which was interpreted using the boolean language by McCullough/Pitts. His student [[https://en.wikipedia.org/wiki/Robert_Rosen_(theoretical_biologist)][Robert Rosen]] went on to work on using Category Theory to model biology. These works need to be catalogued here. [[https://en.wikipedia.org/wiki/Herbert_A._Simon][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

*** [[https://link.springer.com/article/10.1007%2FBF02484495][Topology and life: In search of general mathematical principles in biology and sociology]] *** [[https://link.springer.com/article/10.1007%2FBF02476737][On relation between sets — 1961]] *** [[https://link.springer.com/article/10.1007%2FBF02476851][The representation of organisms in terms of predicates — 1965]] *** [[https://link.springer.com/article/10.1007%2FBF02476395][On relations between sets: II - 1966]] *** [[https://link.springer.com/article/10.1007%2FBF02477001][A note on relations between sets – 1966]] *** [[https://link.springer.com/article/10.1007%2FBF02476967][Organismic sets: Outline of a general theory of biological and social organisms - 1967]] *** [[https://link.springer.com/article/10.1007%2FBF02476947][Organismic sets: II. Some general considerations - 1968]] *** [[https://link.springer.com/article/10.1007/BF02477842][The Geometrization of Biology]] *** [[https://link.springer.com/article/10.1007%2FBF02478215][Outline of a unified approach to physics, biology and sociology]]

** Sampling of Rosen’s work:

*** [[https://link.springer.com/chapter/10.1007/978-94-009-2975-3_35][Pattern Generation in Cellular Spaces]] *** [[https://link.springer.com/chapter/10.1007/978-1-4684-4640-1_31][Relational Biology and the Origin of Life]] *** [[https://link.springer.com/article/10.1007/BF02459437][On a unified approach to pattern generation]] *** [[https://link.springer.com/chapter/10.1007/978-94-010-1239-3_9][Complexity and System Description]] *** [[https://link.springer.com/article/10.1007/BF02459555][The Chief Abstractions of Biology]] *** [[https://link.springer.com/chapter/10.1007/978-1-4899-6419-9_8][Input-Output Systems]] *** [[https://link.springer.com/article/10.1007/BF02477959][The derivation of D’Arcy Thompson’s theory of transformations from the theory of optimal design]] *** [[https://link.springer.com/article/10.1007/BF02477897][A logical paradox implicit in the notion of a self-reproducing automaton]] *** [[https://link.springer.com/article/10.1007/BF02478302][A relational theory of biology]] *** [[https://link.springer.com/article/10.1007/BF02477890][The representation of biological systems from the standpoint of the theory of categories]]

• Ilya Pregorine’s Work

• Gregory Chaitin’s work

• Stochastic CFG for RNA

• Zuse-Fredkin thesis / [[https://en.wikipedia.org/wiki/Digital_philosophy][Digital Philosophy]] Think I need to mention the work of Zuse-Fredkin thesis along with Ulam-Neumann model.

• Knot Theory for Protein Molecules

• Wang Tiles and DNA

• [[https://www.sciencedirect.com/science/article/pii/B9780128140666000064][Molecular Networks and Monomial Ideals]]

• [[https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004591][Computational Modeling, Formal Analysis, and Tools for Systems Biology: Survey]]

• Luca Cardelli

• [[https://dx.doi.org/10.1186/1752-0509-8-84][Morphism of reaction networks that couple structure to function]]

** Tools

*** [[https://github.com/GollyGang/ready][Ready]] Ready is a program for exploring continuous and discrete cellular automata, including reaction-diffusion systems, on grids and arbitrary meshes.

** Blogs

*** [[https://jsomers.net/i-should-have-loved-biology/][I should have loved biology]]

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.

*** [[http://jackterwilliger.com/biological-neural-networks-part-i-spiking-neurons/][(A Bit of) Biological Neural Networks (2018)]] A really nice series of articles on the biological aspects of neural networks by Jack Terwilliger

** Talks

*** [[https://www.hkw.de/en/app/mediathek/video/69773][Giuseppe Longo: Alphabets, Axioms, DNA: On Human Knowledge and the Myth of Alphanumeric Coding]]

** Prior Art

*** [[https://en.wikipedia.org/wiki/Santiago_Ram%C3%B3n_y_Cajal][Ramón y Cajal]] *** [[https://en.wikipedia.org/wiki/Camillo_Golgi][Camillo Golgi]]