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Cellular computing (Series in Systems Biology)
Amos M., Oxford University Press, 2004. 240 pp. Type: Book (9780195155396)
Date Reviewed: Feb 28 2006

This book is dedicated to an emerging discipline at the intersection of biology, computer science, and engineering: cellular computing. The vital component of this new discipline is engineering, which gives great practical importance to the field, from the development of new biological sensors, to intelligent drug discovery and nanotechnology.

The book is a collection of selected works from authors in the UK, Canada, the US, and Japan. It discusses the theoretical foundations of cellular computing, as well as laboratory experiments.

The most interesting part of the book is Part 1, “Theoretical and Engineering Principles.” The introduction to cellular computing is rather vague, and was obviously created with the goal of introducing the reader to the main terms and dogmas in molecular biology. The other chapters in the same part are on a much higher level, however, so the introduction stays detached from the whole idea of the book. In fact, there are many better formulated, short, and comprehensive texts on computational biology that could serve as an introduction to the foundations of cellular computing, for example, chapter 1 in Setubal and Meidanis’s book [1]. Chapter 3 discusses the issues of enzyme genetic programming, a type of genetic programming that mimics biological representations, with the goal of improving the evolvability (ability of representation) of the program. Chapter 3 also provides an example of the modeling of a single enzyme, based on a simple model. In the model, the enzyme’s functionality is derived on the basis of enzyme activity, and on the shape of its specificities. This cannot describe the enzyme uniquely, but the authors claim that this is a minor problem, since it is unlikely that two enzymes will have the same functionality. Chapter 4 introduces genetic process engineering, a methodology for modifying the DNA of existing genetic elements in order to achieve desired input/output behavior. The chapter also describes BioSpice, a prototype software toolkit for bio-circuit design. Chapter 5 addresses the problems of engineering the information transport between cells, and of modeling information processes in cells. The most interesting parts in the chapter are the discussions of the silicon-mimic approach, and chip-to-cell communication.

Part 2, “Laboratory Experiments,” serves as a practical balance for the theoretical part, discussing some interesting applications in the areas described in Part 1.

Part 3 is particularly interesting, since it is dedicated to ciliates, a class of organisms that encrypt their genomic information. Even without deeper research in this area, an understanding of the assembly of ciliate genes could inspire novel computational implications. Chapter 9 presents the background of the process from a biological point of view, which could serve as a reference for computational modeling.

As a whole, the book provides an excellent introduction to cellular computing. It can motivate researchers from computer science and electronics backgrounds to understand the ideas and technologies underlying the interdisciplinary field of systems biology.

Reviewer:  Alexander Tzanov Review #: CR132500 (0701-0030)
1) Setubal, C.; Meidanis, J. Introduction of computational molecular biology. PWS Publishing, Boston, MA, 1997.
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