Artist Jonathan Mccabe’s interests include theories of biological pattern formation and evolution and their application to computer art. he writes computer programs that measure statistical properties of images for use in artificial evolution of computer art. For more, see www. jonathanmccabe.com/.

 

chemical reactions between them. Proteins may also chemically modify each other by attaching or removing modifying groups, such as phosphate groups, at specific sites. Each such modification may reveal new interaction surfaces. There are tens of thousands of proteins in a cell. At any given moment, each of them has certain available binding sites (which means that they can bind to other proteins, DNA, or membranes), and each of them has modifying groups at specific sites either present or absent. Protein-protein interaction networks are large and complex, and finding a language to describe them is a difficult task. Significant progress in this direction was made by the introduction of Kohn-maps, a graphical notation that resulted in succinct pictures depicting molecular interactions. Other approaches include the textual bio-calcu-lus, or the recent use of existing process calculi (π-calculus), enriched with stochastic features, as the language to describe chemical interactions.

Yet another biological interaction network, and the last that we discuss here, is that of transport networks mediated by lipid membranes. Some lipids can self-assemble into membranes and contribute to the separation and trans-

port of substances, forming transport networks. A biological membrane is more than a container: it consists of a lipid bilayer in which proteins and other molecules, such as glycolipids, are embedded. The membrane structural components, as well as the embedded proteins or glycolipids, can travel along this lipid bilayer. Proteins can interact with free-floating molecules, and some of these interactions trigger signal transduction pathways, leading to gene transcription. Basic operations of membranes include fusion of two membranes into one, and fission of a membrane into two. Other operations involve transport, for example transporting an object to an interior compartment where it can be degraded. Formalisms that depict the transport networks are few, and include membrane systems described earlier, and brane calculi.

The gene regulatory networks, the protein-protein interaction networks, and the transport networks are all interlinked and interdependent. Genes code for proteins which, in turn, can regulate the transcription of other genes, membranes are separators but also embed active proteins in their surfaces. Currently there is no single formal general framework and notation

able to describe all these networks and their interactions. Process calculus has been proposed for this purpose, but a generally accepted common language to describe these biological phenomena is still to be developed and universally accepted. It is indeed believed that one of the possible contributions of computer science to biology could be the development of a suitable language to accurately and succinctly describe, and reason about, biological concepts and phenomena. ¹⁸

While systems biology studies complex biological organisms as integrated wholes, synthetic biology is an effort to engineer artificial biological systems from their constituent parts. The mantra of synthetic biology is that one can understand only what one can construct. Thus, the main focus of synthetic biology is to take parts of natural biological systems and use them to build an artificial biological system for the purpose of understanding natural phenomena, or for a variety of possible applications. In this sense, one can make an analogy between synthetic biology and computer engineering. ³ The history of synthetic biology can be arguably traced back to the discovery in the 1960s, by Jacob and Monod,