Joint Penn-UDel Colloquium on the Nature of Computing

Computing with Biomolecules:
The Meaning of Truth in an Interdisciplinary World

Lila Kari
Department of Computer Science, University of Western Ontario

Biomolecular computation is a field situated at the intersection of disciplines as diverse as computer science, mathematics, molecular biology, biotechnology, biochemistry and physics. As a result, one of the obstacles that hinder the progress in this area is the lack of common standards for notions like input, output, data, computation, correctness and solution.

To illustrate these ``cultural'' differences, I will present the DNA computing research project currently under way at The University of Western Ontario. The purpose of our experimental project is to solve an instance of a hard computational problem, The Shortest Common Superstring Problem, by sole means of DNA manipulation.

In this context, I will discuss the different meanings that terms like ``truth'', ``solution'', ``answer'', ``proof'', ``exactness'' have in mathematics, computer science and molecular biology, and the stringent necessity for reaching a consensus. I will then argue that these differences, far from being detrimental, have the potential to forward the progress in biomolecular computing, while at the same time enriching the originating fields.