If you are not familar with my work, it may be best to watch the videos in order.
Title: Molecular Information Theory: From Clinical Applications To Binding Site Evolution
Molecular Information Theory: From Clinical Applications To Binding
Information theory was introduced by Claude Shannon in 1948 to precisely characterize data flows in communications systems. The same mathematics can also be fruitfully applied to molecular biology problems. We start with the problem of understanding how proteins interact with DNA at specific sequences called binding sites. Information theory allows us to make an average picture of the binding sites and this can be shown with a computer graphic called a sequence logo (https://alum.mit.edu/www/toms/glossary.html#sequence_logo).
Sequence logos show how strongly parts of a binding site are conserved in bits of information. They have been used to study a variety of genetic control systems. More recently the same mathematics has been used to look at individual binding sites using another computer graphic called a sequence walker (https://alum.mit.edu/www/toms/glossary.html#sequence_walker). Sequence walkers are being used to predict whether changes in human genes cause mutations or are neutral polymorphisms. It may be possible to predict the degree of colon cancer by this method.
How do genetic systems gain information by evolutionary processes? Information theory was used to observe information gain in the binding sites for an artificial `protein' in a computer model of evolution. The model begins with zero information and, as in naturally occurring genetic systems, the information measured in the fully evolved binding sites is close to that needed to locate the sites in the genome. The transition is rapid, demonstrating that information gain can occur by punctuated equilibrium. (https://alum.mit.edu/www/toms/paper/ev).
Why is the Genetic Code Degenerate? by Tom Schneider at Bits <-> Biology 2014 May 1, Building E14, 6th floor, MIT
Three Principles of Biological States: Ecology and Cancer by Tom Schneider 2014 Oct 29 Wednesday 09:04-10:13 at the meeting Biological and Bio-Inspired Information Theory (14w5170) at the Banff International Research Station (BIRS), Banff, Canada.
I discuss genetic control systems and rhodopsin and the information theory which explains why their isothermal efficiency is often near 69%. This result is explained by understanding the high dimensional coding space that molecular machines function in. Surprisingly, the same theory applies to ecological and developmental systems and leads to a global understanding of cancer incidence in the body. I even can analyze data from the Cambrian Burgess Shale that represents an ecosystem half a billion years ago! Three fundamental principles can be used to understand the reason that the theory has such a wide scope.
Information Theory in Biology
by Tom Schneider
2016 October 19 Wednesday
at the meeting:
at the Indian Institute of Technology, Kanpur India
Celebrates Shannon Centenary
Why Do Restriction Enzymes Prefer 4 and 6 Base DNA Sequences?
by Tom Schneider
2020 Jan 21
at the meeting:
BIOLOGY THROUGH INFORMATION, COMMUNICATION & CODING THEORY
origin: 2014 Nov 03
updated: 2020 Mar 18: lattice talk video bioticc.org2020jan21 my copy