John Dupré
The Centre for the Study of Life Sciences (Egenis), University of Exeter, UK

https://doi.org/10.36866/pn.100.33

Most philosophers, if asked what they took to be the most general way of describing the world, living or otherwise, would refer to an inventory of things and the properties that characterise them. The former may be simple – atoms – or complex, composed of other things. The latter may pertain to individual things, or they may involve relations between things. However the idea that a true description of the world will say what things there are and what their properties are is a natural and plausible one.

This ontology of things and their properties is articulated at a higher level through the concept of mechanism, the arrangement of things into structures that, by virtue of their various properties, interact resulting in overall function. This concept has undergone a resurgence of interest in recent philosophy, reflecting the important role it plays in practitioners’ conceptions of the aims of scientific research. It is open to question, nonetheless, whether the concept of mechanism plays a substantive role in guiding research rather than merely a rhetorical one in promoting it.

There is, at any rate, an alternative ontology, one generally attributed in antiquity to Heraclitus (535 – c. 475 BCE), that takes things themselves to be only temporary manifestations of something more fundamental, change, or process. As Heraclitus put it, ‘There is nothing permanent except change’. On such a view what we think of as things are no more than eddies in the constant flux of process. In the last century, this perspective was forcefully advocated by the philosopher Alfred North Whitehead (1861-1947), and his ideas had a strong influence on a number of biologists including Conrad Waddington (1905-75) and JS Haldane (1860-1936). Despite subsequent decline in interest in process philosophy, I want to claim that an ontology of processes is far better suited to understanding the nature of life and the living than the more standard ontology of things.

What it is that makes something a kinase, a liver, or a turtle? And hence also, what it is that determines whether an entity persists despite changes that it undergoes. Both questions have traditionally been answered by appeal to an essential property or properties, characteristics that are necessary and sufficient for something to be, say, a turtle. But as many philosophers have noted, the fact of evolution makes the postulation of any such properties problematic. Moreover, even if there were some property sufficient to define something as a turtle, could we be confident that the same property would apply to the turtle’s egg? The life cycles of organisms include very different forms; why assume there must be anything common to every stage beyond their participation in a continuous process? The plasticity of development and the robustness of metabolism, its independence of a precise sequence of molecular details, can also raise similar questions for the parts of which organisms are composed.

A central consequence of switching from a thing to a process perspective is the following: When viewing an entity as a thing, what require explanation are the changes that occur to it: the default condition for a thing is stasis; change can raise a question whether the thing has persisted at all. But the default for an organism is not persistence but death. Many thousands of changes must happen every second in every cell for it to persist in a healthy state. This is obvious merely from the familiar observation that life exists far from thermodynamic equilibrium. Physiology does not investigate the properties of a stable object, but the processes that enable a system of some kind to retain its form sufficiently for it to continue to function. Medical science, similarly, concerns the many ways in which these processes can fail. In The Selfish Gene, Richard Dawkins perspicuously described natural selection as a special case of the more obviously tautological survival of the stable. The insight can also mislead, however. The survival of an organism is a very different matter from the survival of an iron atom.

A further advantage of the process perspective is that it sidelines questions about the boundaries of biological entities. Where does the river stop and the eddy begin? Living systems comprise of a hierarchy of deeply intertwined processes, processes that are shaped by both higher and lower level processes with which they are connected. The process perspective enables us to see that answers to such questions are to an important extent matters of convenience rather than of fact.

None of this, of course, is to say that living systems are undifferentiated mush. For an organism to persist, a multitude of discontinuities must be maintained between its parts. The functions of these discontinuous parts provide the central question for physiology. But like the boundaries of a whirlpool, even these discontinuities are very much part of the dynamics of the system. A membrane, for example, is not just a barrier that keeps parts separate one from another. Rather, it is a highly active system or process, expending energy to maintain molecular discontinuities of many kinds between its two sides. The cell itself is maintained as a temporarily stable system both by this dynamic relation to its external environment, and by the countless metabolic and other processes that are happening on its interior.

The question of boundaries has recently surfaced in intense philosophical debate about the nature of biological individuals, or organisms. It has become increasingly clear that symbiosis is omnipresent in the living world. Are mutualistic bacteria in the human gut parts of the human system or just fellow travellers? Given that many of them seem essential for our well-being, what is the criterion by which we deny that they are parts of the human organism? Are there sharp distinctions between mutualism, commensalism, and parasitism? From the point of view of intertwined and interdependent processes, no obvious importance attaches to these labels, though of course we will often want to know whether a particular associated organism is necessary for or harmful to our well-being.

I mentioned the traditional association of physiology with the analysis of function. However, a further issue that is potentially transformed by a processual perspective on living systems is the distinction between structure and function. It is common to think of biological objects having particular structures that enable them to perform particular functions. But if these ‘objects’ are in fact constantly fluid and evolving processes, this perspective can be misleading. Structure and function are intertwined aspects of process. Or perhaps, as was suggested by the founder of General Systems Theory, Ludwig von Bertalanffy (1901-1972), functions are just fast processes and structures are (relatively) slow processes.

Good illustrations of such a view come from plant development. The growing meristem of a plant is typically an opportunistic growth process capable of producing a variety of structures – leaves, flowers, roots – in response to the environment it encounters. These putative structures are traditionally understood as distinguished in virtue of their particular functions – photosynthesis, attraction of pollinators, absorption of nutrients, etc. – they serve. But the attempt to distinguish sharply between these traditional morphological elements is often problematic. One often encounters claims such as that the colourful bracts of Bougainvillea, or the spines of a cactus, are really leaves. But given the totally unrelated functions and structures of these entities, and the general plasticity of plant development, it is hard to make sense of such claims. Better, perhaps, to say with JS Haldane in his 1931 book, The Philosophical Basis of Biology, ‘structure and functional relation to environment cannot be separated in the serious scientific study of life, since structure expresses the maintenance of function, and function expresses the maintenance of structure’, it should be unsurprising, I suppose, that physiology and morphology are in the end just different perspectives on the same underlying phenomena.

Or consider proteins, the paradigmatic examples of biological entities for which structure has been assumed to determine function. This simple structure/function analysis has been increasing stretched as it has been found that many proteins serve a range of functions (‘moonlighting’ proteins); that many or most proteins do not have a fully determinate structure (‘intrinsically disordered’ proteins); and that the interaction between an enzyme and the molecule with which it interacts, does not really fit the traditional ‘lock and key’ model, but rather involves a considerable amount of mutual configuration. All of these phenomena fit better into the view of the protein molecule as a dynamic entity, the causal powers of which are constantly being reconfigured in relation to the processes in which it participates, than into the classical model of a thing with a fixed nature that determines once and for all what it is and what it can do.

I would summarise much of the foregoing discussion by claiming that both structure and function are ultimately best seen as abstractions from underlying process. Descriptions in terms of structure abstract from the crucial temporal dimension of living processes, as well as selecting non-arbitrary but underdetermined spatial limits for the objects of interest. Function brings back the time dimension, but at a cost of focus on an increasingly specific set of properties of the entities under review. Distinguishing biological mechanisms involves abstractions of both kinds.

Does this kind of broad philosophical analysis matter much for practising scientists? In the end I must leave it for them to answer. I would suggest, however, that it may have the potential virtue of replacing a certain kind of excessive concern with realism with a more defensible pragmatism. No one has any prospect of providing the complete truth about a living system; particular models are provided with particular goals for insight or intervention. It is vital to be aware of the limitations imposed by particular abstractions in model building, but equally important not to mistake limitations for objections. This may be a particular important reminder for the emerging field of systems biology.

Further reading

Dupré J (2012). Processes of Life: Essays in the Philosophy of Biology, OUP

Seibt J (Fall 2013 Edn). ‘Process Philosophy’, The Stanford Encyclopedia of Philosophy, Edward N. Zalta (ed.), http://plato.stanford.edu/archives/fall2013/entries/process-philosophy/