The time domains of biological adaptations and gene expression. This diagram represents an expanded and supplemented part of the whole p(t)s, but with adaptations more specifically defined as having p(t)s ranges appropriate for prokaryotes.

Homeostasis, the maintenance of a constant internal environment in the face of external changes, is a necessary and fundamental feature of all living systems. I propose to divide the adaptations involved into three categories, here termed "physiological"; "developmental"; and "evolutionary". Other authors have wished to reserve the term "adaptation" for only one of these three kinds of response to the environment. Maynard Smith (1966), for example, reserves "adapted" for "genetically adapted", which is equivalent to "evolutionarily adapted", and, by way of distinction, uses the terms "physiologically versatile or tolerant" and "developmentally flexible". I suggest that the last three adjectives suggest passive properties of systems, and "adaptation", which suggests an active process, is preferable. Furthermore, in plant physiology, a careful distinction is sometimes made between "adaptation", which may be either physiological or evolutionary, and "acclimation", which refers to what a microbiologist would perhaps recognise as a developmental process.

Apart from the idealised arrangement of the three sorts of adaptation along the pts axis, there are further, non-trivial distinctions to be made between them. Firstly, only physiological and developmental adaptations occur within the life-time of an individual organism. The latter depends, of course, very much on the sort of organism being considered. For most microorganisms (especially when grown in a laboratory culture) both physiology and development occur well within the time domain 9 > pt_s > 3. For all living things it is also possible to arrange the three sorts of adaptation according to the level of gene expression at which feedback is exerted as a result of any given environmental change.

Thus physiology concerns largely a feedback control of structure, function, and molecular recognition of macromolecules - for the large part, proteins - that are already in place. Physiological adaptation is a fine-tuning of the machinery you already have. Where such processes as motility are involved, physiological adaptation takes the form of behavioural adaptation, for example, phototaxis (for example, Sprenger et al., 1993).

Development then becomes a matter of influencing transcription, mRNA processing and stability, and translation, in such a way that the environmental signal affects the final composition of the system that interacts with the new environment. Developmental adaptation is usually a matter of choosing a new set of components with which to work, and sometimes one of assembling new components from the old set in a different way. The borderline between physiology and development is perhaps less clear in microbiology than in other fields, but here I wish to propose a line of demarcation, for convenience: any adaptation that occurs within the lifetime of an individual cell or organism can be described as "developmental" if it requires protein synthesis de novo, and "physiological" if it does not. The question of whether protein assembly counts as physiology or development then depends on one's definition of a protein, and becomes semantics.

Evolutionary adaptation, which comes into time domains four and five, arises from the question of whether the new environment can be used at all to make a second set of instructions, however these may be interpreted by development and physiology. The feedback loop from function to DNA replication in the figure is intended to represent this crude, qualitative line of information flow, and not the more subtle, developmental effects seen, for example, in the cell cycle. Evolution is the gradual departure of each succeeding set of instructions from an arbitrarily-chosen original.

Mitochondrion and the "vicious circle" theory of ageing