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‘Isomorphogenesis No.2’ © Gemma Anderson, 2014.
Watercolour on paper. www.gemma-anderson.co.uk
This artwork is part of a series created through interaction with a drawing
based algorithm. Anderson is an artist and researcher who has been
collaborating with John Dupré since 2012 and this series has been inspired
by Dupré’s ‘Process Philosophy for Biology’ ERC project
Features
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.
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.
A process ontology for biology
Functions are just fast processes and structures are (relatively) slow processes
John Dupré
The Centre for the Study of Life
Sciences (Egenis),
University of Exeter, UK
© Guido Castagnoli
33
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/>
Physiology News / Autumn 2015 / Issue 100
... positivists. 2 Philosophers have tended to widely acknowledge the usefulness of metaphysics when dealing with conceptual and theoretical problems in different biological disciplines such as evolutionary biology, evolutionary and developmental biology (evo-devo), developmental biology, and molecular biology (see Boogerd et al., 2005;Dupré, 2012Dupré, , 2015Austin, 2016aAustin, , 2016bWaters, 2017;Nicholson & Dupré, 2018). Some authors have used the term 'Metaphysics of Biology' to name this increasing tendency in philosophy of biology (Guay & Pradeu, 2017). ...
... 7 In this regard, the debate on whether biological entities are better understood as processes or substances has become a core concern among philosophers of biology in the last few years. Although substance ontology, according to which substances are the primary units of reality, has been the predominant one in Western philosophy (Seibt, 2016), advances in evolutionary and developmental biology (Bapteste & Dupré, 2013;Nuño de la Rosa, 2013;Austin, 2016a), as well as the study of some aspects of biological entities, such as developmental plasticity, robustness, or the different forms and properties that characterize organisms during the different stages of their life cycle, have recently been used to claim that biological entities are not ontologically substances but processes (Dupré, 2012(Dupré, , 2015Nicholson & Dupré, 2018), that is, dynamic entities that are continuously 7 In this regard, a reviewer asked me to clarify the notion of 'implications' since it is rare to claim that biological phenomena have ontological implications. The reviewer is right in considering that 'implications' seem to be a notion mainly associated with propositions. ...
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