Towards a formal description of intracellular biochemical organization (Q1175136)

One of the major drawbacks in the biological sciences is the difficulty of building a precise mathematical foundation on which to build a comprehensive and general framework for the discussion and understanding of biological systems. The biological cell is an immensely complex object, there is a vast amount of biochemical activity occurring at any one time, in general, and in addition there is a great deal of interaction between the cell and its immediate environment, which could be either other cell or the outside world. There is considerable evidence that the true understanding of the behaviour of a cell must be based on a complete, overall formalism that allows us to describe, not only what is happening in a small part of the cellular system, but also the interactions between that system and other influential systems. The approach described here addresses itself to the problem of investigating the organization of metabolism in a cell. We consider the way in which metabolic systems operate by carrying out ``processing'' of a certain type and how this processing relates to other processing in the cell. The two principal themes are this processing of metabolic ``information'' and the communication of this information between metabolic systems. The analysis chosen here reflects some of the recent research carried out in relation to the study of the organization of parallel computer systems and from many points of view the similarities with the metabolism of the cell are quite striking. The main philosophy of the approach is to utilize the thesis that many types of biochemical activity can be modelled using various types of machine at various levels. The most general type of machine involved, the \(X\)-machine, is a generalization of finite state machines, Petri-nets and even Turing machines, and is thus an excellent vehicle for developing a unified structure theory.