Gene Assembly in Ciliates – a beautiful sample of Natural Computing

Article type: Research Article

Authors: Rozenberg, G.^{a; b; 1}

Affiliations: [a] Leiden Institute of Advanced Computer Science, Leiden University, The Netherlands | [b] Department of Computer Science, University of Colorado at Boulder, USA

Note: [1] E-mail: rozenber@liacs.nl.

Abstract: Natural Computing is a general term referring to computing going on in nature and computing inspired by nature. When complex phenomena going on in nature are viewed as computational processes, our understanding of these phenomena and of the essence of computation is enhanced. In this way one gains valuable insights into both natural sciences and computer science. Ciliates, a very ancient group of single cell organisms, have evolved extraordinary ways of organizing, manipulating and replicating their DNA. The way that ciliates transform genes from their micronuclear (storage) form into their macronuclear (expression) form, called gene assembly, is very interesting from the computational point of view. Current research in gene assembly is an example of flourishing interdisciplinary research involving computer scientists and molecular biologists. This paper discusses (in tutorial fashion) some central ideas of this research.

Keywords: Natural computing, DNA computing in vivo, sexual reproduction, gene assembly, macronuclear genome, micronuclear genome

DOI: 10.3233/JCM-2002-23-407

Journal: Journal of Computational Methods in Sciences and Engineering, vol. 2, no. 3-4, pp. 343-349, 2002