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‘Isomorphogenesis No.2’ © Gemma Anderson, 2014.
Watercolour on paper.
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
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
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.),
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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Since the last decades of the twentieth and the beginning of the twenty-first century, the use of metaphysics by philosophers when approaching conceptual problems in biology has increased. Some philosophers call this tendency in philosophy of biology ‘Metaphysics of Biology’ (Guay and Pradeu in Synthese 1–20, 2017). In this paper, I aim at characterizing Metaphysics of Biology by paying attention to the diverse ways philosophers use metaphysics when addressing conceptual problems in biology. I will claim that there are two different modes of doing Metaphysics of Biology, namely Metaphysics for Biology and Metaphysics in Biology.
... Often it is difficult for students and pupils to perform a scientific method and therefore, to simplify it, several authors suggested the use of ontological systems [10,7,11,12,13,14,15,16,17,18,19,20,21]. But they did not use on all stages of scientific methods used during educational researches. ...
... Besides, a common disadvantage of all considered systems [7,10,11,13,14,20,21,12,15,16,17,18,19] is unsuitability for use by pupils and novice researchers due to the complexity of using. For example, "Open proVenance" requires using both nodes and classes, which requires additional specific knowledge and additional time to create an ontology. ...
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Providing complex digital support for scientific research is an urgent problem that requires the creation of useful tools. Cognitive IT-platform Polyhedron has used to collect both existing informational ontology-based tools, and specially designed to complement a full-stack of instruments for digital support for scientific research. Ontological tools have generated using the Polyhedron converter using data from Google sheets. Tools "Search systems", "Hypothesis test system", "Centre for collective use", "The selection of methods", "The selection of research equipment", "Sources recommended by Ministry of Education and Science of Ukraine", "Scopus sources", "The promising developments of The National Academy of Sciences of Ukraine" were created and structured in the centralized ontology. A comparison of each tool to existing classic web-based analogue provided and described.
... The derision of descriptive science has been argued to be more of a prejudice [10,11]. Biology and astronomy were both descriptive sciences [12,13]; today, calls have been made to return descriptive work into the purview of biological sciences in general [14,15], and descriptive approaches have become the gold standard in genetics [16]. A broader defense of descriptive sciences is beyond the scope of this article. ...
... The derision of descriptive science has been argued to be more of a prejudice [10,11]. Biology and astronomy were both descriptive sciences [12,13]; today, calls have been made to return descriptive work into the purview of biological sciences in general [14,15], and descriptive approaches have become the gold standard in genetics [16]. A broader defense of descriptive sciences is beyond the scope of this article. ...
We propose a method of consensually validating phenomenal data. We believe such a method is necessary due to underreporting of explicit validation procedures in empirical phenomenological literature. We argue that descriptive science, exemplified by phenomenology and natural history, rely on nominalization for construction of intersubjectively accessible knowledge. We compare the epistemologies of phenomenology and natural history, pointing out that they differ in their attitudes towards the interpretation of texts and visual epistemology, however, they both rely on eidetic intuition of experts for knowledge construction. In developing our method, we started out with the prismatic approach, a method of researching embodied social dynamics. We then used debriefings on the experience of consensual validation to further refine the method. Importantly, we suggest that for a nominalization of experiential world to be intersubjectively accessible, a group of co-researchers has to independently construct said vocabulary. We therefore propose that during consensual validation, co-researchers be presented with composite descriptions of experiential categories, compare them with their experience, attempt to falsify them, and finally jointly name them. Our approach does not yield a single vocabulary for description of experience, but a number of commensurable vocabularies, contingent on a specific research setting
... But it seems that times may be changing. Recently, a growing number of philosophers of science, first and foremost John Dupré and coworkers (see Dupré, 2014Dupré, , 2015Dupré & Guttinger, 2016;Nicholson & Dupré, 2018), have emphasized the need to adopt a processual perspective for studying the complex dynamics and close connectedness of living systems. Usually, process ontology includes a holistic perspective according to which every state of a process can only be defined in a fully relational manner (Whitehead, 1929). ...
This paper addresses the role of time scales in conceptualizing biological hierarchies. So far, the concept of hierarchies in philosophy of science has been dominated by the idea of composition and parthood, respectively. However, this view does not exhaust the diversity of hierarchical descriptions in the biosciences. Therefore, we highlight a type of hierarchy usually overlooked by philosophers of science. It distinguishes processes based on the different time scales (i.e. rates, frequencies, and rhythms) on which they occur. These time scale hierarchies often are connected with assumptions defended in process ontology. Due to their ability to describe interlevel dynamics of various kinds, we call these hierarchies ‘dynamic hierarchies.’ In order to highlight and discuss their organization, explanatory roles, and epistemic virtues we focus on dynamic hierarchies in developmental biology and evolutionary developmental biology (evo-devo). In these fields, dynamic hierarchies offer crucial complementary information to descriptions of compositional hierarchies.
... In closing, we briefly discuss our agenda of situating biologies in comparison with recent process ontological thinking (Bapteste and Dupré, 2013;Dupré, 2014) and epidemiological ecosocial theory, addressing the emergent embodied phenotype (Krieger, 2005(Krieger, , 2012. The philosopher of biology John Dupré makes the point that recent biological research casts doubt on the basic Aristotelian assumption that living things might best be understood as substances. ...
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In this paper, we posit the notion of ‘situated biologies’ as a conceptual contribution to the often-polarised debate over the material human body as being either local or universal. To argue our case, we briefly recapitulate the medical anthropological concept of ‘local biologies’ before highlighting current molecular biological research on epigenetics and its implications. We discuss how different forms of ‘local’ arise in environment/human entanglements and how material agency becomes situated and contingent through various knowledge practices. We conclude by developing the overarching concept of ‘situated biologies’ to further a collaborative ethnographic agenda that explores the multiple effects of particularising or universalising material agency in research on environment/human entanglements.
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This collection of essays explores the metaphysical thesis that the living world is not ontologically made up of substantial particles or things, as has often been assumed, but is rather constituted by processes. The biological domain is organized as an interdependent hierarchy of processes, which are stabilized and actively maintained at different timescales. Even entities that intuitively appear to be paradigms of things, such as organisms, are actually better understood as processes. Unlike previous attempts to articulate processual views of biology, which have tended to use Alfred North Whitehead’s panpsychist metaphysics as a foundation, this book takes a naturalistic approach to metaphysics. It submits that the main motivations for replacing an ontology of substances with one of processes are to be looked for in the empirical findings of science. Biology provides compelling reasons for thinking that the living realm is fundamentally dynamic and that the existence of things is always conditional on the existence of processes. The phenomenon of life cries out for theories that prioritize processes over things, and it suggests that the central explanandum of biology is not change but rather stability—or, more precisely, stability attained through constant change. This multicontributor volume brings together philosophers of science and metaphysicians interested in exploring the consequences of a processual philosophy of biology. The contributors draw on an extremely wide range of biological case studies and employ a process perspective to cast new light on a number of traditional philosophical problems such as identity, persistence, and individuality.
Recent research uncovering extraordinary organismal complexity (e.g., extent of symbiotic associations, genetic exchange between organisms) has led to empirical challenges concerning the recognition of individuality in biological organisms. Our ability to distinguish between organisms, parts of organisms, and groups of organisms is now more problematic. Further, this has led to philosophical challenges concerning the concept of biological individuality. The holobiont, or metaorganism, can be characterized as a host organism having important associations with numerous species of organismal exo- and endosymbionts, many of which are required for the proper function of the complex whole. The holobiont (indeed, all organisms) are also exposed to potential horizontal gene exchange throughout their life cycle. The blurring of organismality continues to the level of colonial organisms and other socially cooperating entities. Epistemologically, we recognize the metaorganism as a processual system subject to continuous change in itself and in relation to its environment. Whereas the metaorganism resists individuation in terms of its intrinsic properties of mixed origin, it acts as an individual by engaging in causal interactions that are predicated on its integrative nature and emergent properties. In terms of the biological individuality debate, the question is not “is the metaorganism a biological individual?” The question is rather “what individuating processes does the metaorganism (or any organism) engage in?” When explained in terms of the causal properties and propensities of its parts (which are of potentially mixed origin), the underlying conception of the metaorganism is that of a homeostatic property cluster. Thus, for metaorganisms, a hierarchical dialectic between natural kindness and individuality exists, depending on the epistemic project being pursued. A process ontology of organisms recognizes their fuzzy boundaries and life’s dynamic nature while preserving the organism as a fundamental explanatory concept in biology.
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The term 'information' is used extensively in biology, cognitive science and the philosophy of consciousness in relation to the concepts of 'meaning' and 'causation'. While 'information' is a term that serves a useful purpose in specific disciplines, there is much to the concept that is problematic. Part 1 is a critique of the stance that information is an independently existing entity. On this view, and in biological contexts, systems transmit, acquire, assimilate, decode and manipulate it, and in so doing, generate meaning. I provide a detailed proposal in Part 2 that supports the claim that it is the dynamic form of a system that qualifies the informational nature of meaningful interactive engagement, that is, that information is dependent on dynamic form rather than that it exists independently. In Part 3, I reflect on the importance of the distinction between the independent and dependent stances by looking specifically at the implications for how we might better interpret causation and emergence. In relation to causation, Hume (1748) talks of a power or force that is entirely concealed from us, describing this power as 'the secret connexion' which induces one causal impetus to follow another in an uninterrupted succession: We only learn the influence of our will from experience. And experience only teaches us, how one event constantly follows another, without instructing us in Biosemiotics https://doi.
Shaun Gallagher [2019 Gallagher, S. 2019. Rethinking Nature: Phenomenology and a Non-reductionist Cognitive Science, Australasian Philosophical Review 2/2: 125–37. [Google Scholar]] argues for a ‘non-classical’ conception of nature, which includes subjects as irreducible constituents. As such, first-person phenomenology can be naturalised and at the same time resist reduction to the third-person. In the first part of this paper, I raise three concerns for the claim that nature is irreducibly subject-involving. In the second part of the paper, I suggest that embracing a process ontology could help strengthen Gallagher’s proposal.
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