David Searls

College of Science Distinguished Speaker - Thursday December 5, 2013
1:00pm Gosnell Hall 08-A300

Molecules, Languages, and Automata

Abstract:
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. Formal 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.


 

David Searls received undergraduate degrees in Philosophy and in Life Sciences from the Massachusetts Institute of Technology, and a PhD in Biology from the Johns Hopkins University. Following a postdoc at the Wistar Institute he completed a Master's in Computer and Information Science at the University of Pennsylvania. He spent seven years doing artificial intelligence R&D at Unisys, then returned to Penn (where he retains an adjunct appointment) and co-founded the Computational Biology and Informatics Laboratory, with joint faculty appointments in Genetics and Computer and Information Science. He then spent 13 years at GlaxoSmithKline Pharmaceuticals, where he was Senior Vice-President of Computational Biology, and for the last five years has consulted and pursued his own research in molecular linguistics.