Mini Tour of Tom Schneider's Theory

Banff is an overview video.

paperlist my papers are listed by name.

Below is a suggested reading order of the papers that leads progressively deeper into the theory.

• Basics:
  • primer A short primer on information theory.
  • schneider1986 Using information theory to measure the information at binding sites (Rsequence) and to predict that information from the size of the genome and number of sites (Rfrequency).
  • logo A sequence logo graphically shows for binding sites the average information at each position in the site.
  • walker Sequence walksers graphically show the information of individual binding sites. They are extremely useful!!!
  • ri The math underlying sequence walkers.
  • ev Demonstration of the results of schneider1986 that Rsequence evolves to match Renergy: the ev and evj models. Run the java - complete evolution in a few seconds!
• Advanced theory:
  • ccmm Molecular machines defined, channel capacity for molecular machines, noise, energy dissipation, biological states are high dimensional hyperspheres:
  • edmm Building on ccmm, derive minimum energy per bit (Emin) from channel capacity and second law of thermodynamics:
  • emmgeo Information (in bits) versus energy (converted to bits using Emin) gives efficiency, often 70% for molecular machines. This is the theory I am developing.
  • lattice The efficiency theory depends on high dimensional space. This paper shows how to find the dimensionality for restriction enzymes. 6 base restriction enzymes have apparently discovered the best sphere packing, the 24 dimensional Leech lattice!
  • geneff: Generalized Efficiency. The theory I am working on applies across all biology. When I first discovered this in 2010 I was puzzled - how could a theory built for molecules using thermodynamics apply to entire ecosystems? In the following years I found how to rebuild the theory from scratch so it applies to all levels of biology.

Schneider Lab
origin:    2021 Jun 29
updated: 2023 Oct 07