Molecules as Automata

Molecular biology investigates the structure and function of biochemical systems starting from their basic building blocks: macromolecules. A macromolecule is a large, complex molecule (a protein or a nucleic acid) that usually has inner mutable state and external activity. Informal explanations of biochemical events trace individual macromolecules through their state changes and their interaction histories: a macromolecule is endowed with an identity that is retained through its transformations, even through changes in molecular energy and mass. A macromolecule, therefore, is qualitatively different from the small molecules of inorganic chemistry. Such molecules are stateless: in the standard notation for chemical reactions they are seemingly created and destroyed, and their atomic structure is used mainly for the bookkeeping required by the conservation of mass. Attributing identity and state transitions to molecules provides more than just a different way of looking at a chemical event: it solves a fundamental difficulty with chemical-style descriptions. Each macromolecule can have a huge number of internal states, exponentially with respect to its size, and can join with other macromolecules to from even larger state configurations, corresponding to the product of their states. If each molecular state is to be represented as a stateless chemical species, transformed by chemical reactions, then we have a huge explosion in the number of species and reactions with respect to the number of different macromolecules that actually, physically, exist. Moreover, macromolecules can join to each other indefinitely, resulting in situations corresponding to infinite sets of chemical reactions among infinite sets of different chemical species. In contrast, the description of a biochemical system at the level of macromolecular states and transitions remains finite: the unbounded complexity of the system is implicit in the potential molecular interactions, but does not have to be written down explicitly. Molecular biology textbooks widely adopt this finite description style, at least for the purpose of illustration. Many proposal now exist that aim to formalize the combinatorial complexity of biological systems without a corresponding explosion in the notation. Macromolecules, in particular, are seen as stateful concurrent agents that interact with each other through a dynamic interface. While this style of descriptions is (like many others) not quite accurate at the atomic level, it forms the basis of a formalized and growing body of biological knowledge. The complex chemical structure of a macromolecule is thus commonly abstracted into just internal states and potential interactions with the environment.