SCIENCE AT THE EDGE SEMINAR

QB/GEDD

Friday, November 15 at 11:30am

Room 1400 Biomedical and Physical Sciences Bldg.

Refreshments at 11:15

David Searls

Department of Genetics

 Perelman School of Medicine, University of Pennsylvania

Genome as Literature

Molecular biology is replete with linguistic metaphors, from the language of DNA to the genome as “book of life”. Certainly the organization of genes and other functional modules along the DNA sequence invites a syntactic view, which can be adopted for purposes of pattern-matching search via parsing. It has also been shown that folding of RNA structures is neatly expressed by grammars, and this has led to many novel algorithmic approaches to fold prediction and the like. Grammars and their associated automata have even been adopted to describe evolutionary processes and algorithms for their reconstruction via sequence alignment, and indeed the analogy between the evolution of species and of languages (first noted by Darwin) has been exploited by applying bioinformatics tools to human languages as well. Processive enzymes and other “molecular machines” can also be cast in terms of automata, and thus of grammars, opening up new possibilities for the formal specification, modeling, and simulation of biological processes. This talk will review linguistic approaches to molecular biology, and perspectives on potential future applications of grammars and automata in this field.