Computational Biology: A Programming Perspective

Abstract

Abstract. Computation via biological devices has been the subject of close scrutiny since von Neumann's early work some 60 years ago. In spite of the many relevant works in this field, the notion of programming biological devices seems to be, at best, ill-defined. While many devices are claimed or proved to be computationally universal in some sense, the full step to a bona fide programming language is rarely taken, and one question is noticeable by its absence: If the device is universal, where are the programs?We begin with an extensive review of the literature on programmingrelated biocomputing; and briefly identify some strengths and shortcomings from a programming perspective. To show concretely what one could see as programming in biocomputing, we outline (from recent work) a computation model and a small programming language that are biologically more plausible than existing silicon-inspired models. Whether or not the model is biologically plausible in an absolute sense, we believe it sets a standard for a biological device that can be both universal and programmable. ContextThe terms "biocomputing" and "systems biology", taken in their broadest senses, span many fields and areas of research: biology, chemistry, physics, mathematics, electrical engineering and computer science among others. Two major subareas:-Computer modeling of biological and biomolecular processes -Biological hardware for computationThe terms "biomolecular computation" and "biomolecular computational model" occur with both meanings in the literature (see Section 4), sometimes referring to the one and sometimes the other subarea. This paper emphasises the second. More precisely: we take a synthetic viewpoint, concerned with building things as in the engineering and computer sciences. This is in contrast to the inevitable and ubiquitous analytic viewpoint common to the natural sciences, concerned with finding out how naturally evolved things work. We ask: What can be done or built or constructed; and not: how does nature work? (Caveat: just as in engineering, one will need to understand nature's cause-and-effect sufficiently well to be able to modulate it, i.e., to use nature to effectively serve our purposes.) A Theme: Biological Problem-SolvingOur main aim is thus to use the biological world as a computational medium. From a programming perspective, the main goal is problem-solving by writing programs. This section thus refers to solving problems by biology, not solving problems about biology or in biology.Given: a computational problem. To find: a biological solution. Further, problem-solving by a program means finding a general solution (and not just one run of one algorithm on one input data instance).A top-down approach is to devise a model of computation that -satisfies requirements for computer science/engineering -that could conceivably be realised in a biological medium -in which programs are clearly visible, and programming can be done -is a framework in which it is possible, at least in principle, to say when a problem has be...