7
Reconceptualizing the Organism
From Complex Machine to Flowing Stream
Daniel J. Nicholson
The machine analogy has put us on a wrong scent. . . How long are we to persist in
refusing to look sheer hard facts in the face, merely in the interests of a seventeenthcentury
analogy which by now may well have outgrown its usefulness? Sooner or later
biology will have to take account of them if there is to be any theoretical biology.
—Joseph Henry Woodger (1930: 15–16)
1. Introduction
The greatest intellectual revolutions are those that lead to such a profound reorientation
in our habits of thought that following their occurrence it becomes almost
impossible to comprehend what it was like to think about things in any other way.
They transform our understanding so fundamentally that they come to ground
and guide our inquiries without themselves ever being directly subject to them.
A paradigmatic example is the mechanization of the world picture that took place
during the scientiﬁc revolution (Dijksterhuis 1961). Although there is nothing
inevitable about seeing the world as a vast, ﬁnely tuned machine (indeed, to Aristotle
as to most other ancient thinkers, such a view would have seemed alien and artiﬁcial),
after the seventeenth century it became difﬁcult to think about nature in any other
way. Thereafter, the natural was mechanical and the mechanical was natural.
This radical conceptual transformation, which in many ways precipitated the rise
of modern science, is a testament to the power of metaphors. The critical role that
metaphors play in the conceptualization of phenomena has not always been appreciated
by philosophers. In fact, for much of the twentieth century, metaphors were
dismissed as decorative literary devices, of little relevance to scientiﬁc understanding.
The veriﬁability principle of logical empiricism rendered any appeals to metaphors
meaningless and pushed metaphorical language in general beyond the realm of
cognitive signiﬁcance.¹ Ironically, the idea that metaphors are irrelevant to the
¹ Max Black, probably the ﬁrst analytic philosopher to take metaphors seriously, bitterly complained
about his peers’ reaction to the use of metaphors: ‘To draw attention to a philosopher’s metaphors is to
OUP CORRECTED PROOF – FINAL, 2/5/2018, SPi
pursuit of generating scientiﬁc knowledge emerged during the very same period that
witnessed the reorganization of all of natural philosophy around a single metaphor:
that of the clockwork universe (Collingwood 1945; Dear 2006). Many of the pivotal
ﬁgures of early modern science and philosophy displayed a dismissive—if
not downright hostile—attitude toward metaphors, denouncing them as illegitimate
rhetorical devices that compromise the clarity and objectivity of rational discourse.²
Today such views are rare, as there is widespread recognition of the indispensable
roles that metaphors play in scientiﬁc theory and practice (e.g. Keller 1995; Maasen
et al. 1995; Brown 2003). But out of the endless array of metaphors used in science, it
is difﬁcult to think of one that has been more dominant and has exerted a greater
inﬂuence than the machine metaphor, which provided the basic theoretical foundation
for mechanicist natural philosophy in both physics and biology.
Although the mechanicist worldview, with its emphasis on reductionism and
determinism, collapsed in physics following the quantum revolution of the early
decades of the twentieth century, it somehow managed to survive in biology. For a
time—especially during the interwar years—it seemed as if biology too would
abandon mechanicism, as a collective of biological thinkers known as the organicists
began to articulate a post-mechanicist philosophical foundation for biology that
explicitly rejected the ontological assimilation of organisms to machines (see
Nicholson and Gawne 2015). The organicists were inspired by Alfred North
Whitehead, who had written in 1925 that ‘[t]he appeal to mechanism on behalf of
biology was in its origin an appeal to the well-attested self-consistent physical
concepts as expressing the basis of all natural phenomena. But at present there is
no such system of concepts’ (Whitehead 1925: 129). Nevertheless, in the end
mechanicism not only prevailed but was actually reinvigorated by the meteoric rise
of molecular biology (see e.g. Monod 1971). The neo-Darwinian view of evolution
that became established during the same period also contributed to the consolidation
of mechanicism in biology (see e.g. Williams 1966).
Elsewhere (Nicholson 2013, 2014) I have referred to the central tenet of biological
mechanicism—the metaphorical redescription of the organism as a machine—as the
machine conception of the organism (MCO). The MCO is one of the most pervasive
metaphors in modern biology. Part of its success lies in its remarkable plasticity, as it
is able to take a variety of different forms, depending on the context. To mention only
a few of its contemporary manifestations, in developmental biology it equates the
embryo with a computer that executes a predetermined set of operations in accordance
with a program encoded in its genes (e.g. Jacob 1973); in evolutionary biology it
assimilates organisms to optimally designed artefacts, blindly engineered by natural
belittle him—like praising a logician for his beautiful handwriting. Addiction to metaphor is held to be
illicit, on the principle that whereof one can speak only metaphorically, thereof one ought not to speak at
all . . . [Let us] not accept the commandment, “Thou shalt not commit metaphor”, or assume that metaphor
is incompatible with serious thought’ (Black 1962: 25).
² Thomas Hobbes, for instance, declared that ‘[m]etaphors, and senslesse and ambiguous words, are like
ignes fatui; and reasoning upon them, is wandering amongst innumerable absurdities; and their end,
contention, and sedition, or contempt’ (Hobbes 1996: 36). One cannot help but wonder how Hobbes saw
no inconsistency in decrying the usefulness of metaphors by using one to make his point.
OUP CORRECTED PROOF – FINAL, 2/5/2018, SPi
  . 
selection (e.g. Dawkins 1986); and in molecular biology it identiﬁes the cell as a
factory of highly specialized molecular machines (e.g. Alberts 1998).
In recent years, however, there have been growing voices of dissent from the
mechanicist orthodoxy, as more biologists and philosophers have begun to question
the theoretical legitimacy of the MCO (e.g. Rosen 1991; Lewontin 2000;
Kirschner et al. 2000; Henning and Scarfe 2013). It is becoming clear that the
MCO offers only a partial and rather distorted view of living systems. Most
signiﬁcantly for the purposes of the present volume, the uncritical—and often
tacit—acceptance of the MCO is one of the major reasons for the persistence of
substance metaphysics in biology. This should not be surprising, as mechanicism
has always served as the main vehicle for substance thinking in science. After all, what
are machines if not persistent material things with determinate sets of properties and
which exist independently of the activities they engage in? Demonstrating the
ontological inadequacy of the MCO is a necessary ﬁrst step if we are to come to
terms with the processual nature of life and lay the foundations for a processual
philosophy of biology.
In an earlier paper (Nicholson 2013), I argued that the MCO fails to provide an
appropriate understanding of living systems because organisms and machines differ
from one another in a number of crucial respects. Most fundamentally, I claimed,
organisms are intrinsically purposive (in the sense that their activities and internal
operations are ultimately directed towards the maintenance of their own organization),
whereas machines are extrinsically purposive (given that their workings are
geared towards fulﬁlling the functional ends of external agents).³
The present chapter presents a totally different argument against the MCO: one
based on thermodynamic considerations. As I will show in the next section,
thermodynamics supplies a surprisingly effective means of elucidating the ontological
distinction between organisms and machines.⁴ The thermodynamic character
of life is incompatible with the MCO and calls for the adoption of a
processual view of the organism, which is exempliﬁed by the Heraclitean metaphor
of the stream of life. In section 3 I will examine the intellectual development of this
alternative metaphorical conception and consider the extent to which it captures
the nature of living systems. I will follow this in section 4 by discussing three
speciﬁc ontological lessons that we can draw when we reconceptualize the organism
from complex machine to ﬂowing stream. The ﬁrst relates to questions of
normativity and agency, the second concerns the problem of persistence, and the
third addresses the nature and origins of order. I will conclude by brieﬂy reﬂecting
on the broader consequences of this shift in perspective.
³ Another way of expressing this is that organisms act on their own behalf, while machines serve the
interests of their makers or users (for the full argument, see Nicholson 2013; for various illustrations, see
Nicholson 2014).
⁴ It is a pity that thermodynamics has not played a greater role in the philosophy of biology, especially
given that the implications of thermodynamics for the ﬁeld were explicitly recognized by some of its
earliest practitioners (see Needham 1928: 81–5). The only major exception was the debate—particularly
prominent during the late 1980s—regarding proposals to extend, modify, or even reformulate the neoDarwinian
theory of evolution in accordance with thermodynamic principles (e.g. Brooks and Wiley 1986;
Wicken 1987; Weber et al. 1989).
OUP CORRECTED PROOF – FINAL, 2/5/2018, SPi
   
2. Organisms ≠ Machines: The Argument
from Thermodynamics
Ironically, thermodynamics initially served to vindicate, rather than undermine, the
MCO (understood here as a heat engine rather than a clock). The science of
thermodynamics arose from the desire to understand heat engines, particularly the
relationship between heat and work, and the presumed conformance of organisms to
the ﬁrst law of thermodynamics—a version of the principle of the conservation of
energy—enabled them to be treated as veritable engines. The pioneer in this respect
was Antoine Lavoisier, the father of modern chemistry, who in the late eighteenth
century famously characterized respiration as a form of combustion. Along with
Pierre-Simon Laplace, Lavoisier conducted the ﬁrst calorimetry experiments, comparing
the heat and carbon dioxide produced by a guinea pig with that produced by
the combustion of carbon.⁵
During the nineteenth century, the rise of thermodynamics was so intertwined
with concurrent developments in physiology—united as these disciplines were by
their common interest in ‘engines’, be they technological or biological—that some of
the earliest enunciations of the ﬁrst law, such as those by Hermann von Helmholtz
and Robert von Mayer in the 1840s, were tied to efforts to elucidate the relation
between chemical energy and physiological activity. Helmholtz, a physiologist by
training, was led to his formulation of the ﬁrst law of thermodynamics by his
demonstration of the equivalence between animal heat and energy, as well as by
his discovery that only physico-chemical processes are involved in the generation of
animal heat. And Mayer, a practising physician, gave very explicit consideration to
the bearing of the ﬁrst law on organisms:
In the living body carbon and hydrogen are oxidized and heat and motive power thereby
produced. Applied directly to physiology . . . the oxidative process is the physical condition of
the organism’s capacity to perform mechanical work and provides as well the numerical
relations between [energy] consumption and [physiological] performance.
(Meyer, quoted in Coleman 1977: 123)
At the end of the century, Max Rubner conclusively established that organisms are
subject to the ﬁrst law by showing experimentally that the amount of energy returned to
the environment by an organism (for instance, in the form of excretory products and
heat) is equivalent to the energy taken in, assuming no change in weight. Although this
by itself did not prove that organisms are heat engines—in fact, upon close examination,
the original analogy between combustion and respiration turns out to be rather
problematic⁶—it appeared to offer little reason to question the MCO.
⁵ Lavoisier’s own formulation of the MCO went like this: ‘The animal machine is governed by three
main regulators: respiration, which consumes oxygen and carbon and provides heating power; perspiration,
which increases or decreases according to whether a great deal of heat has to be transported or not;
and ﬁnally digestion, which restores to the blood what it loses in breathing and perspiration’ (Lavoisier,
quoted in Jacob 1973: 43).
⁶ In combustion, the surmounting of the energy of activation—which is necessary for the accomplishment
of oxidative reactions—is achieved by raising the temperature considerably, whereas in respiration
this is not needed. Instead, respiration relies on the enzymatic lowering of the energy of activation. If the
OUP CORRECTED PROOF – FINAL, 2/5/2018, SPi
  . 
The second law of thermodynamics is a completely different matter. Indeed, it is
when we consider how organisms conform to it that the MCO absolutely breaks
down. The second law negates the possibility of a perfectly efﬁcient transformation of
heat into work. It stipulates that the amount of free energy (i.e. energy capable of
performing work) is constantly decreasing, while the amount of dissipated energy
(measured in terms of entropy) is correspondingly increasing. Every natural change,
whether physical or chemical, exhibits this utterly irreversible tendency—pithily
described by Arthur Eddington as the ‘arrow of time’—which results in a net, ever
growing increase in disorder. Such an inexorable trend towards a uniform distribution
of heat and the consequent ‘running down’ of the universe into a state of dead
inertness is diametrically opposed to what we ﬁnd in the living world, where there is a
clear evolutionary tendency for complexity and organization to increase progressively
with time. What are we to make of this paradoxical situation?
The founders of thermodynamics were perfectly aware of this paradox, but instead
of dealing with it they simply ignored it. William Thomson (later Lord Kelvin), who
coined the term ‘thermodynamics’, explicitly excluded living processes in his formulation
of the second law in 1851.⁷ Years later, Helmholtz declared that whether or not
the second law is violated by ‘the ﬁne structure of living organized tissue appears to
me still to be an open question, the importance of which in the economy of nature is
very obvious’ (Helmholtz, quoted in Needham 1928: 81). James Clerk Maxwell
attempted to confront the problem by suggesting how the second law might be
contravened, but his suggestion required postulating a cunning microscopic
being—which Thomson dubbed ‘Maxwell’s Demon’—capable of sorting molecules
according to their speed without the expenditure of work, thereby reducing the
overall level of entropy. Given the total lack of evidence for the existence of such a
fanciful creature, by the early twentieth century biologists—with the exception of a
few neo-vitalists such as James Johnstone (1921)—assumed that organisms do
conform to the second law. The question that remained was how.
The eventual resolution of the paradox came with the realization that the second
law requires only that the universe as a whole exhibits an increase in entropy. Local
eddies of order (or ‘negative entropy’) can be sustained and even propagate, as long
as, overall, there is a global entropic increase. This was lucidly pointed out by Erwin
Schrödinger in his inﬂuential book What Is Life? (Schrödinger 1944). Schrödinger
explained that an organism stays alive in its highly organized condition by importing
matter rich in free energy from outside of itself and degrading it in order to
maintain a relatively low entropic state within its boundaries. The organism thus
preserves its internal organization—thereby eluding (at least for a time) the inert,
time-invariant state of thermodynamic equilibrium we call death—at the expense of
transformation of energy were to take place in organisms in the same way that it does in heat engines, then,
at temperatures at which living systems can exist, the coefﬁcient of their useful activity would fall to an
insigniﬁcant fraction of 1 per cent (see Oparin 1961).
⁷ Thomson’s original enunciation of the law was this: ‘It is impossible by means of inanimate material
agency, to derive mechanical effect from any portion of matter by cooling it below the temperature of the
coldest of surrounding objects’ (Thomson, quoted in Keller 1995: 49, emphasis added).
OUP CORRECTED PROOF – FINAL, 2/5/2018, SPi
   
increasing the entropy (in the form of heat and other waste products) of its external
environment.⁸
Understanding how organisms conform to the second law allows us to see why
they are fundamentally different from machines. Organisms have to constantly
exchange energy and matter with their surroundings in order to maintain themselves
far from thermodynamic equilibrium. Machines, on the other hand, exist in equilibrium
or near-equilibrium conditions, and consequently do not have to constantly
exchange energy and matter with their surroundings. Organisms, in other words, are
necessarily open systems, whereas machines can be open or closed. As a result, they
differ in the kind of stability they exhibit. Machines exhibit a static stability, which
they attain when they reach an equilibrium state that reﬂects the cessation of their
activity. Organisms, in contrast, exhibit a dynamic stability, which is based on their
capacity to actively maintain a low-entropic ‘steady state’ where there is a continuous,
perfectly balanced import and export of materials. The stability of machines at
equilibrium means that they do not require free energy for their preservation,
while the opposite is true for organisms.⁹ A further difference is that, whereas the
activity of a machine is temporary and its onset is reversible (given that a machine
can return to a state of operation after being at rest), the actively maintained steady
state of an organism is ﬁxed and irreversible. An organism must remain permanently
displaced from equilibrium; the moment it yields to it, death inevitably and irrevocably
ensues.
The theoretical distinction between equilibrium and non-equilibrium systems is of
paramount importance. Classical thermodynamics was only ever equipped to deal
with equilibrium systems (which is why the aforementioned paradox concerning life
and the second law arose). The recognition of non-equilibrium systems led to the
development in the mid-twentieth century of what has come to be known as nonequilibrium
thermodynamics, which concerns itself with steady states, irreversible
processes, and non-linear reactions. The subject matter of this relatively new branch
of thermodynamics extends beyond the living realm, as organisms are not the only
far-from-equilibrium open systems found in nature. Whirlpools, ﬂames, and tornadoes
are familiar examples. Less familiar but well-studied cases include Bénard
convection cells and oscillating chemical reactions such as the Belousov–Zhabotinsky
reaction. Ilya Prigogine, whose foundational work in establishing non-equilibrium
thermodynamics earned him a Nobel Prize in 1977, referred to these open systems as
dissipative structures. Perhaps the most signiﬁcant achievement of this new ﬁeld of
physics has been to show how self-organization arises in nature—that is, to explain
how the macroscopic patterns of order displayed by dissipative structures spontaneously
emerge from non-linear interactions and become stabilized in far-fromequilibrium
conditions through an ongoing ﬂux of energy and matter (see Nicolis
⁸ Organisms, then, far from disobeying the second law, help to enact it. Life, with its unassailable
tendency to proliferate, actively contributes to the dissipation of energy by leaving large amounts of
entropic waste in its wake.
⁹ The distinction I draw here between static and dynamic forms of stability corresponds to the
distinction some authors have made between ‘energy-well’ and ‘far-from-equilibrium’ stability (e.g.
Bickhard 2000; Campbell 2009).
OUP CORRECTED PROOF – FINAL, 2/5/2018, SPi
  . 
and Prigogine 1977). Organisms, from this perspective, are the most stable and
complexly differentiated dissipative structures in existence.
In biological theory, the thesis that organisms are dynamically stable open systems
was most systematically articulated by Ludwig von Bertalanffy (1932, 1942, 1950,
1952). However, as Evelyn Fox Keller (2008) has shown, its intellectual roots can be
traced back to the ideas of a number of nineteenth-century authors, including
Herbert Spencer, Gustav Fechner, and especially Claude Bernard, who memorably
asserted that organisms persist in time by keeping their internal environment
constant in the face of external disturbances. Bernard’s conception was the basis
for Walter Cannon’s famous concept of homeostasis, which he coined with the
explicit purpose of accounting for the distinctive thermodynamic character of the
organism:
The highly developed living being is an open system having many relations to its surroundings. . .
The coordinated physiological reactions which maintain most of the steady states in the body are
so complex, and are so peculiar to the living organism, that it has been suggested . . . that a speciﬁc
designation for these states be employed—homeostasis. (Cannon 1929: 400, emphasis added)
The above thermodynamic considerations point to metabolism as the single most
important characteristic of life. Metabolism refers to the balanced coupling of the
energy-releasing processes of catabolism (i.e. the breakdown of organic matter by
means of cellular respiration) with the energy-consuming processes of anabolism (i.e.
the buildup of the macromolecular constituents of cells) that are continuously going
on in an organism. Crucially, metabolism is what maintains the organism in a steady
state far from equilibrium, liberating large amounts of free energy for the organism to
use while simultaneously ‘freeing it from all the entropy it cannot help producing
while alive’ (Schrödinger 1944: 71). It is this emphasis on metabolism, which the
non-equilibrium thermodynamics of organisms prescribes, that enables us to understand
the ontological inadequacy of the MCO.¹⁰
2.1. Addressing potential objections to the argument
Let us now consider a series of objections that may be raised against the preceding
argument. First of all, while some machines (like clocks and computers) are closed
systems, others (like heat engines and water pumps) are decidedly open, as they
exchange matter, and not just energy, with their surroundings. Although the difference
between them and organisms is obvious when they are at rest, do they not
display a dynamic form of stability when they are in operation that is akin to that
shown by organisms? Can we not say, in the case of engines, for example, that they
‘metabolize’ their fuel just as organisms metabolize their food?
The problem of equating fuel with food is that it drastically underestimates the
physiological pervasiveness of metabolism. No matter how dynamic a functioning
¹⁰ Metabolism, incidentally, is also the basis for Humberto Maturana and Francisco Varela’s (1980)
seminal theory of autopoiesis (literally self-production), which has been fruitfully elaborated in recent
decades by a number of philosophers and theoreticians of biology interested in the idea of autonomy (see,
e.g., Moreno and Mossio 2015 and chapter 10 here).
OUP CORRECTED PROOF – FINAL, 2/5/2018, SPi
   
machine may be, it is always possible to distinguish the machine’s physical frame—
which remains ﬁxed—from the materials that ﬂow through it. The actual structure of
the machine does not itself take part in the chemical transformations that the fuel
undergoes as it passes through it. Instead, it serves as a channel that facilitates the
exchange of materials as fuel is converted into waste. An organism, in contrast,
changes wholly and continuously as a result of its metabolizing activity. Organisms
are constantly being reconstituted from the matter they import from their surroundings,
and consequently it is impossible to maintain the distinction between food
materials and bodily constituents. As Hans Jonas phrased it, in an organism ‘[t]he
exchange of matter with the environment is not a peripheral activity engaged by a
persistent core: it is the total mode of continuity (self-continuation) of the subject of
life itself ’ (Jonas 1966: 76, n. 13).¹¹ This is why the fuel–food analogy is so misleading,
and why the stability of a machine—despite its apparent dynamicity—ultimately
resides in an unchanging material structure. In machines there is a speciﬁc ‘inﬂow’
and a speciﬁc ‘outﬂow’. In organisms everything ﬂows.¹²
Even after accepting this, a critic might wish to insist that it is still inappropriate to
characterize the form of machines as ﬁxed. Although machines do not exchange their
material constitution externally in the way organisms do, many do modify their
structure internally to suit their purpose. Windmills, catapults, bicycles, and typewriters
all change their physical conﬁguration in order to accomplish their function.
Why, then, should we not regard these internal structural rearrangements as comparable
to the ones that organisms undergo?
The trouble with this (more restricted) comparison is that it overlooks the fact that
the physical displacements that the parts of a machine undergo conform rigidly to a
precise, predetermined cycle of operations. The successful execution of a function by
a machine implies a periodic restoration of the spatial relations among its parts—a
‘resetting’ of its internal conﬁguration that enables it to perform its function again.
So, although a machine may contain parts that move about, this does not mean that it
goes through a genuine process of transformation. Its physical architecture is still
very much ﬁxed; it is just that this ﬁxity is reﬂected in a recurrent spatio-temporal
pattern rather than in a totally static structure. The only real change that machines
experience is the gradual wearing down of their parts, which eventually leads to their
irrevocable entropic degradation (unless, of course, an external agent intervenes).
The situation with organisms is completely different. Organisms autonomously
modify their structure in response to cues from their environment. When injured,
they are usually able to heal themselves and repair the damage—and this is as true for
bacteria as it is for complex multicellular organisms like trees and vertebrates. Some
organisms (e.g. salamanders) can even regenerate entire body parts, often following
the self-amputation of limbs, in order to avoid predation. The astonishing plasticity
¹¹ Jonas’ insightful analysis of metabolism is also discussed in chapters 8 and 18.
¹² It is rather striking that the organicists were already aware of this fact. For example, John Scott
Haldane, who was heavily inﬂuenced by Claude Bernard, wrote in 1917 that ‘[t]he organs and tissues which
regulate the internal environment . . . are constantly taking up and giving off material of many sorts, and
their “structure” is nothing but the appearance taken by this ﬂow of material through them’ (Haldane 1917:
90; see also Russell 1924 and Woodger 1929).
OUP CORRECTED PROOF – FINAL, 2/5/2018, SPi
  . 
of organisms contrasts with the brittleness of machines, which tend to stop working
when their parts break or are damaged. Of course, redundancy and self-repair can be
built into the design of machines to some extent. Nevertheless, although this can
make their operation more robust and more reliable, the inherent limitations of their
ﬁxed architecture remain.
Not only do organisms modify themselves, but they do so adaptively, in a way
that optimizes their physiological performance. Now a critic could still argue that
servomechanisms—machines controlled by negative feedback with a certain capacity
to self-regulate (e.g. thermostats) or to self-steer (e.g. homing missiles)—also modify
their operation adaptively in response to external inputs; in fact, they are often
described as ‘homeostatic machines’. However, this argument misleadingly conﬂates
the thermodynamic meaning of Cannon’s original use of the word ‘homeostasis’ with
the cybernetic meaning the term acquired after the Second World War. The adaptability
of servomechanisms (measured in terms of input–output adjustments) is of a
very limited kind, its mode and range being deﬁned in advance in accordance to a set
design. Servomechanisms are closed, near-equilibrium systems, and consequently
they are not capable of truly adaptive self-maintenance.¹³
At this point, the most doggedly persistent of critics may take all of the above
considerations on board and simply resort to stretching the concept of machine
sufﬁciently for it to encompass everything that is distinctive about organisms. But in
the end this does not really help the critic’s defense of the MCO, as it undermines
the very properties of machines that make the MCO a heuristically useful idealization
in the ﬁrst place. An instructive illustration of this can be found in a curious paper
titled ‘Living and Lifeless Machines’, in which the distinctive properties of organisms
are forcefully shoehorned into the framework of the MCO. This leads the author
to make a number of exceptionally strange assertions. For example, he notes that
‘[t]he living body is analogous to a motor car in which the chassis, brakes, cylinders,
pistons, connecting rods, valves and bearings all contained combustible material,
some of which was burnt whenever the driver placed his foot on the accelerator’
(Kapp 1954: 101). The question we must ask is this: how is such a bizarre imaginary
motor car still analogous to an actual motor car? Can the causal operation of the
latter really be used to shed light on the causal operation of the former? If not, then
what is the point of clinging on to the MCO, if the price to be paid is that our
understanding of machines has to become completely distorted in order to accommodate
the characteristic attributes of organisms?¹⁴
The far more sensible option is to simply accept the fact that machines are not
good models for coming to terms with the ontology of organisms. The MCO, despite
its obvious heuristic value in biological research, does not provide an adequate
¹³ For more detailed critiques of the cyberneticists’ efforts to assimilate servomechanisms to organisms,
see Taylor 1950, Jonas 1953, Oparin 1961, and Nicholson 2013.
¹⁴ Kapp is by no means the only author to stretch the MCO beyond breaking point. The history of
biology is littered with memorable examples, including Julien Offray de La Mettrie’s clock that winds itself
or Karl Ernst von Baer’s machine that constructs itself, to paraphrase their respective formulations of the
MCO. A more recent example is Richard Dawkins’ (1998: 17) ‘machine that work[s] to keep itself in being,
and to reproduce its kind’.
OUP CORRECTED PROOF – FINAL, 2/5/2018, SPi
   
theoretical understanding of the nature of living systems. As we have seen, the
thermodynamic character of life demands a processual conception of the organism.
Whatever else they may be, living systems are highly stabilized ﬂows of energy and
matter. Machines may take part in various processes, but organisms are themselves
processes. This inescapable fact must constitute the starting point for any theory
of the organism. In the next section we will examine the history of attempts to
develop an alternative conception of living systems that successfully reﬂects their
processual nature.
3. The Stream of Life: A Processual Conception
of the Organism
The MCO has been the most pervasive view of living systems since the seventeenth
century, but it is certainly not the only conception one ﬁnds when surveying the
history of biological thought. In fact, many of those who criticized the MCO in the
past sought alternative metaphors that could highlight the very features of organisms
that the MCO conveniently ignores or inadvertently distorts. A good place to start is
the work of Bertalanffy, who—as we have already mentioned—was responsible for
popularizing the idea that organisms are open systems that maintain themselves in a
steady state far from equilibrium.
In his organicist treatise Problems of Life, Bertalanffy (1952) illustrated the processual
nature of the organism by appealing to the famous aphorism of the Presocratic
philosopher Heraclitus that it is impossible to step into the same river twice
because fresh water is forever ﬂowing through it. A stream is never the same at two
successive temporal points; it is permanently changing. This image encapsulates the
Heraclitean worldview, which emphasized the endless movement and change of all
things. Bertalanffy argued that ‘[w]ith this Heraclitean thought we put our ﬁnger on a
profound characteristic of the living world’ (ibid., 124). Like the river, ever changing
in its waves yet persisting in its ﬂow, an organism only appears to be constant and
invariable, but in reality it is the manifestation of a ceaseless current. As Bertalanffy
put it, ‘living forms are not in being, they are happening; they are the expression of a
perpetual stream of matter and energy which passes the organism and at the same
time constitutes it’. He referred to this processual view of the organism as the stream
of life conception (SLC) and counted it ‘among the most important principles of
modern biology’ (ibid.).
The SLC allows us to grasp, in simple and evocative terms, many of the key
characteristics of organisms that were highlighted in the previous section. The
external form of a stream is stable only because of the constant ﬂow of water
molecules that enter into it and emerge out of it. The moment this ﬂow is interrupted,
the stream itself disappears, as its very existence depends on the steady movement of
water passing through it. In the same way, the physical form of an organism is merely
the visible expression of the constancy of catabolic and anabolic processes going on
within it. Its persistence through time is entirely dependent on the extremely intricate
balancing of these two opposing kinds of reactions. As metabolism proceeds, with the
steady import of nutrients and export of wastes, not much remains at a later time of
OUP CORRECTED PROOF – FINAL, 2/5/2018, SPi
  . 
the matter that once composed the organism. The SLC thus embodies two essential
and complementary aspects of organismic dynamics: the continuous exchange of
matter that lies at the very heart of the concept of metabolism on the one hand,¹⁵ and
the surprising stability of form that is maintained in spite of this material exchange
on the other.¹⁶
Bertalanffy deserves credit for being the ﬁrst to explicitly recognize that the
thermodynamic openness of organisms requires the adoption of a processual perspective.
However, he was by no means the ﬁrst biologist to propose that processual
metaphors offer a more accurate portrayal of the ontology of living systems.
Throughout the nineteenth and the ﬁrst half of the twentieth centuries, a wide
range of authors independently arrived at the conclusion that organisms are best
served by metaphorical conceptions that stress their dynamic, non-equilibrium
qualities. We can explore the versatility of the SLC by considering some of its most
notable historical formulations.
As early as 1817, Georges Cuvier felt compelled to deﬁne life as a vortex—that
most paradigmatic of dissipative structures—using language that clearly preﬁgures
the thermodynamic observations that Schrödinger and others would make more
than a century later:
Life then is a vortex, more or less rapid, more or less complicated, the direction of which is
invariable, and which always carries along molecules of similar kinds, but into which individual
molecules are continually entering, and from which they are continually departing; so that
the form of a living body is more essential to it than its matter. As long as this motion subsists,
the body in which it takes place is living—it lives. When it ﬁnally ceases, it dies.
(Cuvier 1833: 14)
The vortex metaphor enabled Cuvier to make conceptual sense of the persistence of
organismic form coupled with the transience of its constituent materials. This idea
was picked up some years later by William Whewell, who—in the section of The
Philosophy of the Inductive Sciences that dealt with what he was the ﬁrst to call ‘the
philosophy of biology’—paraphrased Cuvier by asserting that ‘life is a constant form
of circulating matter’ (Whewell 1840: 46). Thomas Henry Huxley identiﬁed life more
speciﬁcally with a vortex of water—a whirlpool—remarking that the constituents of an
organism ‘stand to it in the relation of particles of water to a cascade, or a whirlpool’.
Moreover, just as ‘the stoppage of a whirlpool destroys nothing but a form, and leaves
the molecules of the water, with all their inherent activities intact, so what we call the
death . . . of an animal, or of a plant, is merely the breaking up of the form, or manner of
association, of its constituent organic molecules’ (Huxley 1870: 402).
By the early twentieth century, advances in the study of biochemical energetics—
driven by research into the thermodynamics of living systems—had become difﬁcult
¹⁵ The term ‘metabolism’, we should not forget, derives from the Greek word for change. More explicitly
still, the German word for metabolism is Stoffwechsel—literally, ‘material exchange’.
¹⁶ An interesting implication of the dynamic stability of form is that, as Nicholas Rescher (1996: 52–3)
has acutely observed, Heraclitus was only half-right when he declared that we cannot step into the same
river twice. We may not be able to step twice into the same waters, but we can certainly step twice into the
same river (that is, of course, assuming we also stayed the same!).
OUP CORRECTED PROOF – FINAL, 2/5/2018, SPi
   
to ignore, and this is reﬂected in the SLC formulations of the time (cf. Gilbert 1982).
Lawrence Henderson (1913: 23–4), for instance, argued that ‘[l]iving things preserve,
or tend to preserve, an ideal form, while through them ﬂows a steady stream of energy
and matter which is ever changing’. John Scott Haldane (1919: 49) also stressed the
energetic and material ﬂux taking place in the organism, declaring that ‘organic
structure is nothing but a molecular stream’. Charles Sherrington (1940: 82), for his
part, described the cell as ‘an eddy in a stream of energy’ and as ‘a stream of movement
which has to fulﬁl a particular pattern in order to maintain itself’ (ibid., 83).
While some of those who adopted the SLC drew quite generically on dissipative
structures like vortices in the way that Cuvier had done—such as Ralph Stayner Lillie
(1945: 28), who emphasized ‘the “vortex-life” feature of the vital constitution’—the
majority were captivated speciﬁcally by the ﬂuidity of water, ﬁnding in streams,
waterfalls, and rivers the most suitable analogues for the organism. Edward Stuart
Russell (1924: 6) observed that, ‘[j]ust as in a stream a ripple of constant shape and
position is formed by the water ﬂowing over a pebble, so the apparently static form
and composition of organic substance are merely the expression of continuous . . .
activity’. A similar assertion was made by Edmund Sinnott (1955: 117), who wrote
that ‘[a]n organism has a sort of ﬂuid form like a waterfall, through which water
ceaselessly is pouring but which keeps in its descent a deﬁnite pattern’. Conrad Hal
Waddington pointed out in The Strategy of the Genes (Waddington 1957: 2) that
organismic form ‘is more nearly comparable to a river than to a mass of solid rock’,
and Alexander Oparin (1961: 9) stated—echoing Bertalanffy and alluding to
Heraclitus—that ‘[o]ur bodies ﬂow like rivulets, their material is renewed like
water in a stream. This is what the ancient Greek dialectician Heraclitus taught’.
Water, however, was not the only resource available to those wanting to underscore
the dynamic stability of living systems. Some biologists resorted to ﬁre in their articulation
of the SLC, identifying the organism with a ﬂame. John Burdon Sanderson
Haldane (son of John Scott Haldane) claimed that ‘a man is as much more complicated
than a ﬂame as a grand opera is more complicated than a blast on a whistle. Nevertheless,
the analogy is real’ (Haldane 1940: 57). This is not such a far-fetched analogy as it
may seem. When a candle is lit, the ﬂame ﬂares up but almost immediately settles into a
stable dynamic form that represents the attainment of a steady state. As long as it is
continuously supplied with wax and oxygen, the ﬂame is able to maintain itself far from
equilibrium. It achieves this by keeping its temperature above the combustion threshold
and vaporizing the wax, which induces convection that pulls in oxygen and removes
combustion products. For Haldane, the ﬂame analogy depicted the inherent dynamicity
of life in ways that accentuated the inadequacy of the MCO. He indicated, among other
things, that ‘a ﬂame is like an animal in that you cannot stop it, examine the parts, and
start it again, like a machine. Change is part of its very being’ (ibid.).¹⁷
Nevertheless, by the mid-twentieth century the SLC was rapidly losing ground to
the MCO. This was partly a consequence of the shift in the biological agenda that
took place during this period. The focus on metabolism and energetics that had
¹⁷ For additional ﬂame-based formulations of the SLC, see Brillouin 1949 and Bertalanffy 1967. The
thermodynamic character of ﬂames and its relevance for understanding organisms is also examined in
chapter 10.
OUP CORRECTED PROOF – FINAL, 2/5/2018, SPi
  . 
shaped physiological and biochemical research in earlier decades gave way to
molecular biology’s intense preoccupation with the structure and speciﬁcity of
macromolecules, especially nucleic acids and proteins. As interests shifted from the
plasticity and adaptability of biological form to the coding, replication, and expression
of genetic information, so did the metaphorical conceptions used to characterize
living systems. In the last third of the twentieth century, the MCO regained its place
at the centre of biological theory and the SLC almost completely disappeared from
the biological discourse.
Only in recent years—as the explanatory limits of molecular biology have become
apparent—have we begun to witness the ﬁrst signs of a revival of the SLC. In an
inﬂuential article titled ‘A New Biology for a New Century’, Carl Woese speciﬁcally
singled out the MCO as one of the major obstacles impeding further progress in
biology. In place of the MCO, Woese invoked the SLC as a more appropriate
metaphor with which to think about organisms:
If they are not machines, then what are organisms? A metaphor far more to my liking is this.
Imagine a child playing in a woodland stream, poking a stick into an eddy in the ﬂowing
current, thereby disrupting it. But the eddy quickly reforms. The child disperses it again. Again
it reforms, and the fascinating game goes on. There you have it! Organisms are resilient
patterns in a turbulent ﬂow—patterns in an energy ﬂow. A simple ﬂow metaphor, of course,
fails to capture much of what the organism is. None of our representations of [the] organism
capture [sic] it in its entirety. But the ﬂow metaphor does begin to show us the organism’s (and
biology’s) essence. And it is becoming increasingly clear that to understand living systems in
any deep sense, we must come to see them not materialistically, as machines, but as (stable)
complex, dynamic organization[s]. (Woese 2004: 176)
Woese is, of course, right to point out that the SLC does not capture every aspect of
living systems. Even different versions of the SLC vary in their capacity to portray
particular features of organisms. For example, a ﬂame depicts metabolism more
accurately than a whirlpool in that metabolism is essentially a series of chemical
reactions; and, while the steady state of a ﬂame is similarly sustained by continuous
chemical changes, the steady state of a whirlpool is not.
At a more general level, however, it is obvious that organisms differ from ﬂames,
whirlpools, and other dissipative structures in a number of ways. For a start,
organisms exhibit a far greater degree of stability, being able to maintain themselves
for much longer periods of time. The key to their extraordinary stability lies in their
ability to store energy, which enables them to manage their metabolic needs without
having to rely on a constant supply of external energy, like other dissipative structures.
In addition, organisms are distinctive in that they are demarcated by a physical
boundary—a semi-permeable membrane—which helps regulate the intake and outtake
of materials ﬂowing through them. It is also evident that organisms display
much higher levels of internal complexity, as they are functionally differentiated and
hierarchically organized. Most dissipative structures lack these features because they
spontaneously self-organize under appropriate conditions—a phenomenon that
Stuart Kauffman (1995) memorably called ‘order for free’—and this results in a
single ordered macroscopic structure within which it is difﬁcult to differentiate
distinct functional contributions to the maintenance of the overall system.
OUP CORRECTED PROOF – FINAL, 2/5/2018, SPi
   
Organisms, on the other hand, do not arise spontaneously but instead derive from
previous organisms, and their structure reﬂects the gradual consolidation, through
the eons of evolution, of an intricate ‘higher-order self-organizing dynamic among
component self-organizing processes’ (Haag et al. 2011: 329).
Some authors have seen in these differences an unbridgeable gap separating
organisms from all other dissipative structures—a gap that undermines any attempts
to elucidate the former by examining the latter. For instance, Alvaro Moreno and
Matteo Mossio have recently argued in their book-length treatment of autonomy
(which they regard as the deﬁning characteristic of living systems) that non-living
dissipative structures ‘are not relevant for understanding autonomy, not only because
they are “too simple” . . . but also because they cannot be taken as a “starting point”
for the emergence of closure and autonomy’ (Moreno and Mossio 2015: 18). This
seems a rather excessive (not to mention premature) conclusion. Inanimate selforganizing
systems are undoubtedly simpler than animate ones, but there is a clear
continuity between the two, as the latter must have emerged from the former at
some point in the distant past. So, if there is anything that non-living dissipative
structures offer biology, it is precisely a starting point from which one may investigate
life’s origins.
But, even more importantly, organisms and other dissipative structures are fundamentally
isomorphic from a purely physical point of view. As we saw in the
previous section, they can be understood by means of the same thermodynamic
principles. Even Moreno and Mossio admit that autonomy ‘is essentially grounded in
thermodynamics’ (ibid., 6) and that many of the autonomous features of organisms
‘in fact derive from the fact that they are thermodynamically open systems, in farfrom-equilibrium
conditions’ (ibid., xxviii). It is therefore difﬁcult to see what exactly
the problem is, if there really is one, with invoking the SLC and drawing on simple
dissipative structures to shed light on aspects of more complex ones—provided, of
course, that one recognizes that knowledge of the former cannot by itself sufﬁce to
explain the latter.
4. Organisms as Streams: Three Lessons
for Biological Ontology
The SLC constitutes a promising point of departure for thinking about the ontology
of organisms. In direct contrast to the MCO, it correctly identiﬁes and accurately
portrays the speciﬁc thermodynamic character of living systems. It supplies a ﬁrm
physical foundation upon which we can begin to articulate a theory of the organism
that does justice to its thoroughly processual nature. Although undoubtedly not
sufﬁcient, the SLC does show us a path through which we can ultimately arrive at
a fully ﬂedged biological understanding of organisms that is simply beyond the reach
of the MCO. In this respect, the SLC can act as a ladder that can eventually be kicked
away after it has served its purpose. After centuries of dominance of the MCO, the
question in front of us is simple: what does biological ontology look like when
we reject the mechanical and adopt the processual? In this section I will examine
three concrete ontological lessons that we can draw from reconceptualizing the
OUP CORRECTED PROOF – FINAL, 2/5/2018, SPi
  . 
organism from complex machine to ﬂowing stream. The ﬁrst relates to questions of
normativity and agency, the second concerns the problem of persistence, and the
third addresses the nature and origins of order.
4.1. First ontological lesson: ‘Activity is a necessary condition for existence’
Perhaps most evidently, using the SLC to shed light on the ontology of organisms
allows us to make sense of their peculiar existential predicament. Owing to their
thermodynamic condition, organisms—like all other dissipative structures—can only
exist insofar as they are able to maintain themselves in a steady state far from
equilibrium, and this requires a constant expenditure of free energy. The existence
of a whirlpool, for instance, is a direct consequence of its own unremitting activity,
which is what enables it to maintain itself through time. In the same way, if an
organism is to stay alive, it has to keep acting (‘working’, in the thermodynamic
sense) to avoid the ever present threat of equilibrium. To stop acting is to stop
existing. As far as any living system is concerned, to be is to act. We can draw from
this our ﬁrst ontological lesson, which is that, for an organism, activity is a necessary
condition for existence.
This assertion constitutes a radical departure from the conventional ontological
stance of the western philosophical tradition, which is ﬁrmly rooted in substance
metaphysics. A great deal of philosophical thought throughout history has been
tacitly committed to the scholastic principle operari sequitur esse (Rescher 1996)—
that is, activity is subordinated to being and thus follows from it; there can be no
activity if there is no being to begin with. The processual nature of organisms requires
that we relinquish this principle, given that—in the biological world, at least—activity
and being necessarily presuppose one another. Being is neither ontologically nor
temporally prior to activity, as the very existence of a living being is only possible by
means of continuous activity.
Unsurprisingly, the MCO perfectly encapsulates the traditional substanceontological
position. The existence of a machine is totally independent of whether or
not the machine happens to be performing its function. Machines have two modes of
being: they can be active (‘on’) or they can be at rest (‘off’). They can move back and
forth between these two states without jeopardizing their structural integrity, and
this is due to the fact that they exist in reversible, near-equilibrium conditions. The
problem is that organisms, much like waterfalls or tornadoes, do not have an ‘off’
switch.¹⁸ Metabolic processes can be slowed down, for example during sleep or hibernation,
but they cannot be stopped completely. Even organisms in extremely dormant
states, such as seeds or spores, exhibit basal levels of metabolic activity. Absolute stasis
¹⁸ It should not escape anyone’s attention that the ability to study machines successfully when they are
turned off is the key to the enormous methodological appeal of the MCO. If organisms are machines, then
we are justiﬁed in believing that they can be fruitfully investigated in abstraction from time. It is only when
we adopt the SLC and are confronted with their processual nature that we realize that studying organisms
atemporally is not to study them as they actually exist. It becomes apparent that using methods that strip
organisms of their temporal extension (methods such as anatomical techniques that involve the desiccation,
pickling, ﬁxing, or freezing of biological samples) means resigning ourselves to characterizing static
snapshots of an inherently dynamic reality.
OUP CORRECTED PROOF – FINAL, 2/5/2018, SPi
   
signiﬁes death, not inactivity, as it implies the irreversible attainment of thermodynamic
equilibrium.
The indissoluble bond linking existence to activity in organisms and other dissipative
structures obtains because their operation is directed inwardly, towards the
generation and maintenance of their own organization. The operation of machines,
by contrast, is directed outwardly, towards the production of something external to
themselves. Organisms, unlike machines, are autopoietic; they persist as a result of
their own activity. This ongoing self-producing activity is not optional—not undergoing
constant metabolic regeneration is not a possibility. The thermodynamically
grounded fact that organisms need to keep acting in order to keep existing helps to
account for the emergence of a rudimentary form of normativity in nature (cf.
Mossio et al. 2009; Christensen 2012). It is because its existence depends on its
own activity that an organism must act in accordance to the operational norms
that enable it to persist through time. If the organism stops following these norms, it
ceases to exist. What this means is that it is in principle possible to objectively specify
what is intrinsically ‘good’ or ‘bad’ for an organism (that is to say, what is and what is
not in an organism’s ‘interest’) by evaluating its activities according to the contribution
they make towards the preservation of its organization in far-from-equilibrium
conditions.¹⁹
Attributing intrinsic normativity to the behaviour of organisms implies ascribing
agency to them in some minimal (i.e. non-intentional) sense. Fortunately, the
ontological interdependence of activity and existence also helps us come to terms
with this elusive notion (cf. Barandiaran et al. 2009; Barham 2012). It is generally
assumed that, in order to be an agent, an entity must be able to distinguish itself from
its surroundings and, in doing so, delineate an external world with which it can
maintain causal interactions. Organisms demarcate themselves from their surroundings
through their metabolic activities, by taking in and pumping out energy and
matter from outside of themselves. Importantly, the capacity of organisms to individuate
themselves and interact with their environment is a direct consequence of
their thermodynamic exigency to regulate their exchanges with it in order to ensure
their continued viability.
As agents, organisms are inherently active, as opposed to machines, which are
typically reactive. The former are primary sources of activity, whereas the latter must
be activated by external means. A clock has to be wound up, a computer has to be
turned on, a car has to be started, the keys of an organ have to be pressed, and so on.
This crucial difference—already highlighted by Bertalanffy (1952), among others—
reﬂects yet another respect in which the MCO distorts biological ontology. According
to the MCO, the organism is essentially a passive system, being set into action
through outside inﬂuences. Just as a vending machine, by virtue of an internal
mechanism, delivers an article after a coin is inserted, so an organism performs a
¹⁹ Of course, it is also possible to make normative claims about the operation of machines, but there is
an essential difference. Whereas in the organism the norms of its operation are endogenously generated
and are intrinsically relevant to its own continued existence, in the machine they are imposed by an
external agent (usually the machine’s maker or user), who monitors the machine’s operation and evaluates
its performance according to his or her own needs or interests.
OUP CORRECTED PROOF – FINAL, 2/5/2018, SPi
  . 
preset operation upon receiving a stimulus from its environment.²⁰ In actual fact,
because activity is a necessary condition for existence, a stimulus never really triggers
the onset of activity in a hitherto inactive organism, but rather modiﬁes the preexisting
network of processes that are already occurring within it.²¹
This leads to the important conclusion that, more often than not, it is not so much
the nature of the external stimuli as the organism’s internal physiological state that
determines its reactions and behaviour. And as an organism’s current physiological
state is a product of the sequence of past events that led to it, it follows that the
history of an organism fundamentally shapes its behaviour. Again, the contrast with
machines is instructive. The operation of a machine is not signiﬁcantly inﬂuenced by
its history. After a machine executes its function, its conﬁguration is reset to its
default inactive state, and every time this happens the particular historical record of
its operation—beyond the gradual wearing down of its parts—is erased. However,
because an organism never stops functioning during its lifetime (as we have seen, it
cannot do so), it never returns to the same exact state. The upshot of all of this is that
organisms cannot be fully accounted for without affording careful consideration to
their individual historical (i.e. developmental) trajectories.
One last implication of this ﬁrst lesson is that it explains why organisms are
inextricably intertwined with their environment. After all, the incessant activity of
organisms that guarantees their continued existence is an activity of exchange with
their environment. Organisms are totally dependent on their environment for the
energy they need to maintain themselves far from equilibrium. In addition, they are
quite literally composed of the materials they import from it. It is therefore misleading
to presume that an organism can be understood in isolation from the environment
in which it is always embedded. This assumption, like so much of what we have
discussed, has its basis in the MCO. Although a machine requires energy from outside
of itself to carry out its function, its existence does not rely on the fact that it has
permanent access to environmental resources. A machine is placed in an environment
and reacts to the stimuli it receives from it. An organism, by comparison, is made from
its environment, and at the same time helps to construct it through its activities (which
include its metabolic exchanges with it). This process is known as niche construction,
and it has recently been recognized to have profound consequences for evolution (see
Odling-Smee et al. 2003).
4.2. Second ontological lesson: ‘Persistence is grounded in the continuous
self-maintenance of form’
Our second lesson concerns the conundrum of diachronic identity, often referred to
as ‘the problem of persistence’. As we will see in what follows, taking the SLC as the
²⁰ This problematic conception has found its way not only into the study of physiology and animal
behaviour but also into molecular biology. As Robert Rosen wryly remarked, ‘[g]enetic engineers, who are
the molecular biologists turned technologues, habitually regard their favorite organism, E. coli, as a simple
vending machine; insert the right token, press the right button, and the desired product is automatically
delivered, neatly packaged and ready for harvest’ (Rosen 1991: 21).
²¹ Chapter 17 illustrates this claim in the context of olfaction.
OUP CORRECTED PROOF – FINAL, 2/5/2018, SPi
   
starting point for our biological ontology forces us to rethink how we individuate and
reidentify a particular organism over time. Ordinary physical objects are usually
reidentiﬁable by means of their material constitution, which tends to remain invariant.
The problem with streams, ﬂames, and hurricanes is that their identity over time
does not coincide with the identity of the materials that compose them. In the same
way, the material content of an organism is in constant ﬂux throughout its lifetime.
As a result, no two ‘time slices’ of it are materially identical. Only in death, when the
organism ﬁnally succumbs to thermodynamic equilibrium, does its material constitution
stop changing.
The challenge that this poses for understanding biological persistence was carefully
examined by Jonas (1966), who concluded, very much in line with the biologists who
have advocated the SLC, that in an organism form is emancipated from matter.
Organismic form exhibits a degree of independence that enables it to continue to
exist despite incessant material exchange—indeed because of it.²² For Jonas, organisms
invert the ontological relation between matter and form found in inanimate
objects like a stone or a lump of iron. Whereas in the latter form is subordinated to
matter (as form in such instances reﬂects nothing more than the contingent spatial
conﬁguration of a physical body), in the former it is matter that is subordinated to
form (as form here speciﬁes a uniﬁed, causally efﬁcacious whole).
Machines, however, are considerably different from stones and lumps of iron in
that their form is not merely accidental. As with organisms, their matter is arranged
into a speciﬁc organization that allows them to perform their function. The relevant
difference with regard to organisms, as we noted earlier in the chapter, is that their
form is manifested as a ﬁxed structure rather than as a persisting ﬂow. But suppose
that a machine kept its form intact despite changes to all of its material parts. What
then? The famous ‘ship of Theseus’ of antiquity serves as a convenient example to
explore this scenario. According to Greek legend, for centuries this ship performed
an annual voyage from Athens to the island of Delos. Over time, the ship underwent
numerous repairs and replacements of worn-out parts, until eventually it contained
none of its original planks, ropes, or sails. In spite of this, Athenians continued to
regard it as the same venerable ship. One could imagine the same situation applying
to a number of machines today, such as a medieval cathedral clock still in operation,
or a painstakingly restored steam locomotive. The question is: do such machines—let
us call them ‘Thesian machines’—exhibit the sort of diachronic identity that
characterizes organisms?²³
²² Note, however, that the independence of form from matter is not absolute. Form never totally
transcends the domain of matter altogether, as it can only emancipate itself from a speciﬁc material
constitution by adopting another material constitution. One should therefore be sceptical of claims by
proponents of so-called ‘artiﬁcial life’ research that the living form can be logically decoupled from any
concrete material instantiation and re-created in a computer medium (for an in-depth examination of this
issue, see the essays in Boden 1996).
²³ John Locke, in the second edition of his Essay Concerning Human Understanding (published in 1694),
already considered a version of this question, noting, in relation to the identity of animals compared to that
of machines, that, ‘[i]f we would suppose [a] Machine one continued Body, all whose organized Parts were
repair’d, increas’d or diminish’d, by a constant Addition or Separation of insensible Parts, with one
Common Life, we should have something very much like the Body of an Animal’ (Locke, quoted in
McLaughlin 2001: 177).
OUP CORRECTED PROOF – FINAL, 2/5/2018, SPi
  . 
On the face of it, organisms and Thesian machines display the same dynamic
stability of form. Nevertheless, upon closer examination, we are able to see that they
differ in three key respects (cf. Jonas 1968). First, the replacements of the material
parts of a Thesian machine are caused from the outside, that is, by an agent other
than the machine itself. This is by virtue of the fact that machines are extrinsically
purposive. In an organism, on the other hand, the material exchange is caused from
within, which means that the organism, being intrinsically purposive, is its own agent
of change. Organisms thus persist actively, by maintaining themselves, whereas
Thesian machines persist passively, by means of external interventions. Second, the
replacement of parts in a Thesian machine does not take place continuously, as a
matter of course, but is rather a consequence of contingent events. For example, the
ship of Theseus would have required repairs after incurring damage during a
thunderstorm or after an accidental collision with rocks near the shore, but it
could well have not required such repairs, if those particular circumstances had
been different. In contrast, the material exchange in an organism is—as we have
already discussed—a constant, inviolable feature of its persistence through time; it is
neither contingent nor accidental. And, third, the form of an organism does not stay
ﬁxed during its lifetime. Organisms grow and develop. Some undergo major morphological
changes, such as metamorphosis. Nothing comparable happens to a
machine (Thesian or otherwise), given that the ﬁxity of its internal structure is
precisely what allows it to perform the function it was designed for.
These differences prevent us from straightforwardly concluding that the maintenance
of form, coupled with the exchange of matter, is a sufﬁcient condition for the
persistence of organisms—even if it might be for Thesian machines. The maintenance
of form in an organism is actually a type of self-maintenance. This selfmaintenance,
moreover, is a necessary rather than a contingent occurrence, and it
takes place continuously, in an uninterrupted sequence of causal events that collectively
lead to the progressive modiﬁcation of the form that is being maintained, as
the organism grows and develops. It is clear, then, that, in order to comprehend
the persistence of organisms, we must ﬁrst let go of the MCO in all of its possible
manifestations—including hypothetical Thesian ones—and take fully on board their
processual nature.
As processes, organisms are extended and differentiated not only in space but also
in time. It is wrong to speak of an organism and its history as if the two were
somehow separable. Strictly speaking, an organism does not have a temporal trajectory;
it is itself a temporal trajectory. What we perceive as an organism at any point in
time represents only a cross section (or a time slice) in the unfolding of the process it
instantiates. And it is this entire four-dimensional process, rather than any of its
momentary three-dimensional manifestations, that constitutes the actual living
entity (cf. Woodger 1930; Torrey 1939).²⁴ These perdurantist considerations signal
²⁴ From this perspective, the process of metabolism could be said to take ontological precedence over
the organism that undergoes it, given that what appears as an organism at a given time derives its existence
from the metabolic process it embodies. This is, I think, what Jonas had in mind when he cryptically
remarked that ‘the organism must appear as a function of metabolism rather than metabolism as a function
of the organism’ (Jonas 1966: 78).
OUP CORRECTED PROOF – FINAL, 2/5/2018, SPi
   
the importance of causal continuity in biological persistence. This criterion of
diachronic identity—which indexes the continuous interlinking of temporal states
that an entity undergoes—was termed ‘genidentity’ by Kurt Lewin in the 1920s, and it
has recently been defended by several philosophers of biology (see Boniolo and
Carrara 2004; Guay and Pradeu 2016; and chapters 2, 4, 5, and 11 here).
Let me now try to come to some sort of conclusion. We have seen that it makes no
sense to identify an organism over time with the materials that compose it, given that
these are constantly being replenished by the whole. The constituents of an organism
at any particular instant are only the temporary realization of the self-producing
organizational unity of the whole. Unlike the MCO, the SLC accurately reﬂects the
fact that the matter of an organism is necessarily and continuously exchanged while
its form is actively maintained. Bringing together the autonomous maintenance of
form with the causal continuity of process that makes up a living entity over time, we
can draw our second ontological lesson, which is that, as far as organisms are
concerned, persistence is grounded in the continuous self-maintenance of form.
Two issues require further clariﬁcation in relation to this lesson. The ﬁrst is that, as
we have indicated above, to speak of the maintenance of form is not to say that it
remains totally ﬁxed over time; form does change gradually as the organism develops.
It is rather to emphasize that form is stabilized sufﬁciently to be reidentiﬁable as an
uninterrupted steady state in spite of the constant turnover of matter that realizes it.
The second clariﬁcation is that the relentless ﬂux of matter entering and leaving the
organism does not prevent us from identifying parts within it over time.²⁵ It is
important in this context not to confuse material constituents with architectural
components. The former are ephemeral and accidental (as they are constantly being
exchanged), whereas the latter are persistent and necessary, inasmuch as they
contribute—physiologically and morphologically—to the preservation of the organism
as a whole.²⁶
Before moving on, I wish to draw attention to one more aspect of the diachronic
identity of organisms that the SLC can help elucidate, and that is the issue of what may
be called ‘cross-generational identity’. If we take seriously the processual idea that the
organism is ontologically subsidiary to the self-maintaining metabolic stream that
instantiates it at any given moment, then it follows that the identity of this stream can
be maintained across generations of organisms. Reproduction, in this view, can be
reinterpreted as the means by which a self-maintaining metabolic stream perpetuates
itself beyond the lifespan of individual organisms (cf. Hardy 1965; Griesemer 2000;
Saborido et al. 2011). A key advantage of conceptualizing reproduction in this way is
²⁵ Part decompositions do not lose their explanatory power when we adopt a processual conception of
the organism. Making the case for this epistemological claim, however, would take me beyond the scope of
the present discussion.
²⁶ The organicists drew attention to the contrast between the maintenance of form (both of the whole
and of the parts) and the ﬂuidity of matter by distinguishing between the ‘biological’ and the ‘physicochemical’
viewpoints of the organism. Haldane, for instance, wrote that ‘when we have observed the shape
of a friend’s nose we can predict from the biological standpoint that it will be the same a year hence, though
from a physical and chemical standpoint a very small portion of the same atoms or molecules may be
present in the nose after the year’ (Haldane 1931: 140–1, emphasis added; similar claims can be found in
Ritter 1909, Russell 1924, Woodger 1929, and Bertalanffy 1933).
OUP CORRECTED PROOF – FINAL, 2/5/2018, SPi
  . 
that it is better able to account for epigenetic inheritance, as it assumes a far greater
degree of continuity between parent and offspring. It is worth elaborating on this
point a little. If reproduction essentially boils down to the replication of the genetic
material of the parent(s), which—in accordance with the MCO—supplies the blueprint
for the de novo programmatic construction of the offspring, then epigenetically
inherited traits can only be treated as oddities or anomalies. But, if the offspring is
construed—in accordance with the SLC—as the offshoot of a self-maintaining metabolic
stream (or, in the case of sexual reproduction, as the ‘intersection’ of two such
streams), then it is evident that the genetic material is only going to constitute a part
(albeit a very important part) of what gets transmitted during reproduction. The
essential point is that, within the process-ontological framework of the SLC, the
detection of epigenetically inherited traits ceases to be a strange and surprising
discovery and comes to be something we would actually expect to ﬁnd.
4.3. Third ontological lesson: ‘Order does not entail design’
We turn now to a third area of biological ontology that can be illuminated by
rejecting the MCO and adopting the SLC: the nature and origins of biological
order. Organisms and machines are both, to be sure, highly ordered systems. In
abstraction from time, their hierarchical structure is quite comparable, which is one
of the reasons why the MCO is such a useful heuristic tool. However, when they are
considered in time, it becomes apparent that their mode of organization is fundamentally
different. Machines exhibit a static organization, in the sense that their
physical architecture—as well as the degrees of freedom of their parts—is ﬁxed upon
manufacture. Organisms, on the other hand, exhibit a dynamic organization in the
sense that their form, as we have discussed above, reﬂects a stabilized pattern of
continuous material exchange with their environment. Organismic organization, is
dynamic in a further respect, namely in its capacity to modify itself so as to
compensate against external perturbations—a feature we have also discussed.
The ontological chasm separating organisms from machines widens even more
when we consider the origins of the order they each display. The order of a machine
invariably reﬂects a particular design—a preexisting plan, usually in the form of a
blueprint or a diagram, which has been implemented by an external agent (i.e. the
machine’s creator). The striking thing about the order of all dissipative structures,
including organisms, is that it arises in the absence of design. As we noted earlier in
the chapter, the recognition that natural systems can spontaneously self-organize
from non-linear interactions and become stabilized in far-from-equilibrium conditions
through a constant ﬂux of energy and matter is probably the most momentous
discovery of non-equilibrium thermodynamics. Nevertheless, it has proven remarkably
difﬁcult to incorporate this insight into our biological understanding of organismic
order. One reason is undoubtedly that biologists today are more accustomed to thinking
about organisms mechanically (in accordance with the MCO) than thermodynamically
(in accordance with the SLC).
It is rather ironic that Schrödinger’s What Is Life?, which helped to shed light on
how life conforms to the second law of thermodynamics, was simultaneously
responsible for spawning the modern mechanicist conception of organismic order.
Schrödinger argued that the source of all biological order is to be found in the
OUP CORRECTED PROOF – FINAL, 2/5/2018, SPi
   
chemical structure of a single molecule, the self-replicating chromosome, which he
conceived as an ‘aperiodic crystal’ in order to account for its stability in the face of
thermal ﬂuctuations. In this respect, organisms are no different from machines,
which also exhibit rigid, solid-state structures capable of withstanding thermal
agitation that enable them to operate in a regular, orderly way. In Schrödinger’s
own words, ‘the clue to the understanding of life is that it is based on a pure
mechanism, a “clock-work” . . . [that] also hinges upon a solid—the aperiodic crystal
forming the hereditary substance, largely withdrawn from the disorder of heat
motion’ (Schrödinger 1944: 82, 85).
According to Schrödinger, organisms and machines are both subject to the same
preformationist ‘order-from-order’ principle. Just as the order of a clock derives from
the preexisting plan of a clockmaker, so the order of an organism derives from the
‘hereditary code-script’ contained in its genome, which speciﬁes ‘the entire pattern of
the individual’s future development and . . . its functioning in the mature state’ (ibid.,
21). But genes, for Schrödinger, do not just store the information for development;
they are also ‘instrumental in bringing about the development they foreshadow. They
are law-code and executive power—or, to use another simile, they are architect’s plan
and builder’s craft—in one’ (ibid., 22). These provocative ideas served as the basis for
the metaphor of the genetic program, which came to dominate late twentieth-century
developmental biology (see Keller 2000). This incarnation of the MCO equates the
embryo with a computer that executes a predetermined set of operations in accordance
with a program encoded in its genes. The genetic program model is fraught with
problems but, since I have examined them in detail elsewhere (Nicholson 2014), I will
refrain from doing so again here. Sufﬁce it to say that it has taken biology decades to
remove the misconceptions that resulted from it; indeed they still linger.
Ultimately, Schrödinger was right to suppose that genes are material carriers of
information. There really is a code connecting DNA to RNA to the primary structure
of proteins—a fact that has become enshrined in every biology textbook as ‘the
central dogma of molecular biology’. But he was wrong to localize in the genome all
the information required to specify the adult organism, and even more so to invest it
with the causal power to initiate, control, and direct the developmental process.
Ontogeny, it turns out, is a highly heterogeneous process involving the conﬂuence of
numerous intersecting causal factors, only some of which have their physical basis in
the DNA. Replacing the MCO with the SLC enables us to make sense of this
empirical ﬁnding. Once we internalize the notion that the organism is a thermodynamically
open dissipative structure, we are able to see that its order cannot
possibly derive from any one of its material constituents, and that it must instead
be construed as a systemic property emerging from the collective dynamics of the
complex web of chemical reactions that underlie it.
Organisms are, of course, rather peculiar dissipative structures in that they do not
spontaneously self-organize, like whirlpools or tornadoes. This is precisely where
genes come into the picture. Genes can be said to encode a historical record of
successful modes of self-organization—a record that liberates organisms from the
burden of having to ‘reinvent’ the metabolic pathways of chemical transformation
they need to survive every time they undergo a reproductive cycle (cf. Schneider and
Kay 1995; Weber and Depew 2001). From the perspective of the SLC, the role of
OUP CORRECTED PROOF – FINAL, 2/5/2018, SPi
  . 
genes is not to initiate, control, or direct development, but rather to constrain the
possible paths of dynamically stable forms of self-organization to those with the
highest probability of producing a viable, structurally and functionally differentiated
adult. The genome, in this view, constitutes a sort of catalogue or database of effective
self-organization strategies that is transmitted from one generation to the next in a
given lineage. What follows from this empirically motivated reconceptualization is
the conclusion that biological order does not come preformed in a static ‘order-fromorder’
structure (as Schrödinger famously conjectured), but rather emerges progressively,
through an epigenetic ‘order-from-disorder’ process.²⁷ By restating this thesis
in simpler, more straightforward terms, we arrive at our third and ﬁnal ontological
lesson, which is that, in biology, order does not entail design.
5. Conclusions
After the scientiﬁc revolution, the notion that nature is a well-oiled machine proved
irresistible. The machine metaphor conforms to our naïve, pre-theoretical expectations
about the world, which are grounded in good old-fashioned substance metaphysics;
and the proﬁtable deployment of this metaphor in different areas of scientiﬁc
inquiry historically served to reafﬁrm such preconceptions. This, in turn, helped to
legitimize the ontological adequacy of the metaphor, and it vindicated the mechanicist
conviction that nature is lawful, deterministic, and totally explainable in reductionistic
terms. Over the past century, however, we have slowly been coming to the realization
that that this view of nature simply does not work (cf. Whitehead 1925; Prigogine and
Stengers 1984; Dupré 1993). Physicists ﬁrst, and biologists more recently, have begun
to challenge the substantialist assumptions that underlie the mechanicist worldview,
which emerged with the rise of modern science.
As far as the living world is concerned, non-equilibrium thermodynamics demonstrates
with piercing clarity that organisms are not ﬁxed things with predeﬁned
sets of unchanging properties, but resilient processes exhibiting dynamic stabilities
relative to particular timescales. What I have sought to convey in this chapter is that
the ﬁndings of thermodynamics render elaborate philosophical arguments in support
of a processual view of life almost unnecessary. The idea that an organism is an open
system which must constantly exchange energy and matter with its environment in
order to keep itself far from equilibrium is not a metaphysical claim but a scientiﬁc
fact. Of course, a great deal needs to be said philosophically about what kind of
processes organisms are and what exactly follows from their processual nature.
But the crucial point is that, if we want an ontology of life that is grounded and
informed by natural science, then a processual account is unavoidable. Whatever else
²⁷ Interestingly, Schrödinger actually discussed an ‘order from disorder’ principle in What Is Life?, but
he took it to apply exclusively to the sort of order described by statistical mechanics, which arises from the
statistical averaging of vast numbers of molecules that, taken together, display regular, law-like patterns of
behaviour (e.g. diffusion). The very possibility of order spontaneously emerging in far-from-equilibrium
conditions did not even occur to him.
OUP CORRECTED PROOF – FINAL, 2/5/2018, SPi
   
organisms may be, what cannot be denied is that they are stable metabolic ﬂows of
energy and matter.
As the MCO is the perfect biological embodiment of the commitments of substance
metaphysics, in order to come to terms with the processual nature of life we
require a different theoretical conception of the organism. We have seen that the
history of biological thought already furnishes us with one such alternative, the SLC,
which, although harking back to Heraclitus, only became fully articulated in the
nineteenth and twentieth centuries—often in explicit opposition to the MCO. By
metaphorically appealing to familiar non-living dissipative structures, the SLC
enables us to grasp, in simple and evocative terms, the dynamic, far-from-equilibrium
features of organisms that a thermodynamic perspective compels us to consider.
And, just as the MCO has an impressive range of incarnations (the organism
has been variously construed as a clock, a steam engine, a chemical factory, or a
computer, depending on context and historical period), so does the SLC prove to be
remarkably versatile in its manifestations, invoking as it does streams, vortices,
whirlpools, or ﬂames, depending on the aspects of the organism being highlighted.
Of course, organisms are quite different from all of these entities, and consequently
their correspondence with them is necessarily incomplete. But the SLC is still a
considerable improvement on the MCO, as it accurately portrays the physical
conditions of life and provides the foundation for a scientiﬁcally grounded understanding
of the organism capable of making sense of its processual nature.
Taking the SLC as the cornerstone of our biological ontology has a number of
interesting philosophical consequences. We have had the opportunity to explore in
some depth three such consequences, which we have formulated as ‘lessons’ in order
to underscore the pedagogical payoff of reconceptualizing the organism from complex
machine to ﬂowing stream. Importantly, this process of reconceptualization
does not render the MCO useless or irrelevant; on the contrary, it highlights its
enormous heuristic value. We should not underestimate the fact that it is only by
uncovering how the MCO fails to truthfully capture the organism that we have
managed to elucidate its processual nature and derive our three ontological lessons.
Bertalanffy was quite right to remark that ‘we cannot speak of a machine “theory” of
the organism, but at most of a machine ﬁction’ (Bertalanffy 1933: 38). It remains,
nevertheless, an extremely useful ﬁction.
With regard to the SLC itself, our discussion has shown that it displays a number
of features that we tend to look for in a scientiﬁc theory: it is able to organize a large
body of facts, establish connections between seemingly disparate concepts, and make
sense of unexpected empirical ﬁndings. By adopting the SLC we have found a way to
think naturalistically about normativity and agency, we have grasped the ineliminable
role that history plays in shaping biological behaviour, and we have accounted
for the inextricable link between organism and environment. The SLC has also given
us a new handle on the problem of persistence, and it has allowed us to understand
why organismic order needs to be construed as a systemic property. In addition, it
has helped us come to terms with certain phenomena, such as niche construction and
epigenetic inheritance, which seem perplexing and intractable when viewed from the
perspective of the MCO. Finally, at a most general level, we have seen how the
SLC brings biological principles into closer contact with physical ones by means of
OUP CORRECTED PROOF – FINAL, 2/5/2018, SPi
  . 
non-equilibrium thermodynamics, thereby paving the way for a non-reductionist,
non-mechanicist reconciliation of biology with physics.
Acknowledgements
I have beneﬁtted greatly from the comments I received on earlier versions of this chapter by
John Dupré, David Depew, Alvaro Moreno, James DiFrisco, Stephan Guttinger, Sune Holm,
Jan Baedke, Laurent Loison, Richard Gawne, and Andrea Raimondi. I am also grateful to the
audiences at the HOPOS meeting in Halifax, the PBUK workshop in Cambridge, the ISHPSSB
meeting in Montréal, and the EPSA conference in Dusseldorf for valuable feedback on
presentations of this material. Finally, I am pleased to acknowledge ﬁnancial support from
the European Research Council under the European Union’s Seventh Framework Program
(FP7/2007-2013)/ERC grant agreement nº 324186.
References
Alberts, B. (1998). The Cell as a Collection of Protein Machines: Preparing the Next Generation
of Molecular Biologists. Cell 92: 291–4.
Barandiaran, X., Di Paolo, E., and Rohde, M. (2009). Deﬁning Agency: Individuality,
Normativity, Asymmetry and Spatio-Temporality in Action. Journal of Adaptive Behavior
17: 367–86.
Barham, J. (2012). Normativity, Agency, and Life. Studies in History and Philosophy of
Biological and Biomedical Sciences 43: 92–103.
Bertalanffy, L. von. (1932). Theoretische Biologie, vol. 1: Allgemeine Theorie, Physikochemie,
Aufbau und Entwicklung des Organismus. Berlin: Gebrüder Borntraeger.
Bertalanffy, L. von. (1933). Modern Theories of Development: An Introduction to Theoretical
Biology. Oxford: Oxford University Press.
Bertalanffy, L. von. (1942). Theoretische Biologie, vol. 2: Stoffwechsel, Wachstum. Berlin:
Gebrüder Borntraeger.
Bertalanffy, L. von. (1950). The Theory of Open Systems in Physics and Biology. Science
111: 23–9.
Bertalanffy, L. von. (1952). Problems of Life: An Evaluation of Modern Biological and Scientiﬁc
Thought. New York: Harper & Brothers.
Bertalanffy, L. von. (1967). Robots, Men, and Minds: Psychology in the Modern World.
New York: George Braziller.
Bickhard, M. H. (2000). Autonomy, Function and Representation. Communication and
Cognition (Special issue) 17: 111–31.
Black, M. (1962). Models and Metaphors: Studies in Language and Philosophy. Ithaca, NY:
Cornell University Press.
Boden, M. A. (ed.). (1996). The Philosophy of Artiﬁcial Life. Oxford: Oxford University Press.
Boniolo, G. and Carrara, M. (2004). On Biological Identity. Biology & Philosophy 19: 443–57.
Brillouin, L. (1949). Life, Thermodynamics, and Cybernetics. American Scientist 37: 554–68.
Brooks, D. R. and Wiley, E. O. (1986). Evolution as Entropy: Toward a Uniﬁed Theory of
Biology. Chicago: University of Chicago Press.
Brown, T. L. (2003). Making Truth: Metaphor in Science. Urbana: University of Illinois Press.
Campbell, R. J. (2009). A Process-Based Model for an Interactive Ontology. Synthese
166: 453–77.
Cannon, W. B. (1929). Organization for Physiological Homeostasis. Physiological Reviews
9: 399–431.
OUP CORRECTED PROOF – FINAL, 2/5/2018, SPi
   
Christensen, W. (2012). Natural Sources of Normativity. Studies in History and Philosophy of
Biological and Biomedical Sciences 43: 104–12.
Coleman, W. (1977). Biology in the Nineteenth Century: Problems of Form, Function, and
Transformation. Cambridge: Cambridge University Press.
Collingwood, R. G. (1945). The Idea of Nature. Oxford: Oxford University Press.
Cuvier, G. (1833). The Animal Kingdom, Arranged in Conformity with Its Organization.
New York: G. & C. & H. Carvill.
Dawkins, R. (1986). The Blind Watchmaker. New York: Norton.
Dawkins, R. (1998). Universal Darwinism. In D. L. Hull and M. Ruse (eds), The Philosophy of
Biology (pp. 15–37). Oxford: Oxford University Press.
Dear, P. (2006). The Intelligibility of Nature: How Science Makes Sense of the World. Chicago:
Chicago University Press.
Dijksterhuis, E. J. (1961). The Mechanization of the World Picture. New York: Oxford
University Press.
Dupré, J. (1993). The Disorder of Things: Metaphysical Foundations of the Disunity of Science.
Cambridge, MA: Harvard University Press.
Gilbert, S. F. (1982). Intellectual Traditions in the Life Sciences: Molecular Biology and
Biochemistry. Perspectives in Biology and Medicine 26: 151–62.
Griesemer, J. (2000). Reproduction and the Reduction of Genetics. In P. Beurton, R. Falk, and
H.-J. Rheinberger (eds), The Concept of the Gene in Development and Evolution: Historical
and Epistemological Perspectives (pp. 240–85). Cambridge: Cambridge University Press.
Guay, A. and Pradeu, T. (2016). To Be Continued: The Genidentity of Physical and Biological
Processes. In A. Guay and T. Pradeu (eds), Individuals Across the Sciences (pp. 317–47).
New York: Oxford University Press.
Haag, J. W., Deacon, T. W., and Ogilvy, J. (2011). The Emergence of Self. In J. W. van
Huyssteen and E. P. Wiebe (eds), In Search of Self (pp. 319–37). Grand Rapids: William
B. Eerdmans.
Haldane, J. B. S. (1940). Keeping Cool and Other Essays. London: Chatto & Windus.
Haldane, J. S. (1917). Organism and Environment, as Illustrated by the Physiology of Breathing.
New Haven: Yale University Press.
Haldane, J. S. (1919). The New Physiology and Other Addresses. London: Charles Grifﬁn.
Haldane, J. S. (1931). The Philosophical Basis of Biology. London: Hodder & Stoughton.
Hardy, A. C. (1965). The Living Stream: A Restatement of Evolution Theory and Its Relation to
the Spirit of Man. London: Collins.
Henderson, L. J. (1913). The Fitness of the Environment. New York: Macmillan.
Henning, B. G. and Scarfe, A. C. (eds). (2013). Beyond Mechanism: Putting Life Back into
Biology. Lanham: Lexington Books.
Hobbes, T. (1996). Leviathan, ed. by R. Tuck. Cambridge: Cambridge University Press.
Huxley, T. H. (1870). Address to the British Association: Liverpool Meeting, 1870. Nature
2: 400–6.
Jacob, F. (1973). The Logic of Life: A History of Heredity. New York: Pantheon.
Johnstone, J. (1921). The Mechanism of Life in Relation to Modern Physical Theory. London:
Edward Arnold.
Jonas, H. (1953). A Critique of Cybernetics. Social Research 20: 172–92.
Jonas, H. (1966). The Phenomenon of Life: Toward a Philosophical Biology. Evanston: Northwestern
University Press.
Jonas, H. (1968). Biological Foundations of Individuality. International Philosophical Quarterly
8: 231–51.
Kapp, R. O. (1954). Living and Lifeless Machines. British Journal for the Philosophy of Science
5: 91–103.
OUP CORRECTED PROOF – FINAL, 2/5/2018, SPi
  . 
Kauffman, S. (1995). At Home in the Universe: The Search for Laws of Self-Organization and
Complexity. Oxford: Oxford University Press.
Keller, E. F. (1995). Reﬁguring Life: Metaphors of Twentieth-Century Biology. New York:
Columbia University Press.
Keller, E. F. (2000). The Century of the Gene. Cambridge, MA: Harvard University Press.
Keller, E. F. (2008). Organisms, Machines, and Thunderstorms: A History of SelfOrganization,
Part One. Historical Studies in the Natural Sciences 38: 45–75.
Kirschner, M., Gerhart, M., and Mitchison, T. (2000). Molecular ‘Vitalism’. Cell 100: 79–88.
Lewontin, R. C. (2000). The Triple Helix: Gene, Organism, and Environment. Cambridge,
MA: Harvard University Press.
Lillie, R. S. (1945). General Biology and Philosophy of Organism. Chicago: University of
Chicago Press.
Maasen, S., Mendelsohn, E., and Weingart, P. (eds). (1995). Biology as Society, Society as
Biology: Metaphors. Dordrecht: Kluwer.
Maturana, H. R. and Varela, F. J. (1980). Autopoiesis and Cognition: The Realization of the
Living. Dordrecht: Reidel.
McLaughlin, P. (2001). What Functions Explain: Functional Explanation and Self-Reproducing
Systems. Cambridge: Cambridge University Press.
Monod, J. (1971). Chance and Necessity: An Essay on the Natural Philosophy of Modern
Biology. Glasgow: Williams Collins Sons.
Moreno, A. and Mossio, M. (2015). Biological Autonomy: A Philosophical and Theoretical
Enquiry. Dordrecht: Springer.
Mossio, M., Saborido, C., and Moreno, A. (2009). An Organizational Account of Biological
Functions. British Journal for the Philosophy of Science 60: 813–41.
Needham, J. (1928). Recent Developments in the Philosophy of Biology. Quarterly Review of
Biology 3: 77–91.
Nicholson, D. J. (2013). Organisms 6¼ Machines. Studies in History and Philosophy of Biological
and Biomedical Sciences 44: 669–78.
Nicholson, D. J. (2014). The Machine Conception of the Organism in Development and
Evolution: A Critical Analysis. Studies in History and Philosophy of Biological and Biomedical
Sciences 48: 162–74.
Nicholson, D. J. and Gawne, R. (2015). Neither Logical Empiricism nor Vitalism, but Organicism:
What the Philosophy of Biology Was. History and Philosophy of the Life Sciences
37: 345–81.
Nicolis, G. and Prigogine, I. (1977). Self-Organization in Non-Equilibrium Systems: From
Dissipative Structures to Order through Fluctuations. New York: J. Wiley & Sons.
Odling-Smee, J., Laland, L., and Feldman, M. (2003). Niche Construction: The Neglected Process
in Evolution. Princeton: Princeton University Press.
Oparin, A. I. (1961). Life: Its Nature, Origin and Development. Edinburgh: Oliver & Boyd.
Prigogine, I. and Stengers, I. (1984). Order Out of Chaos: Man’s New Dialogue with Nature.
Toronto: Bantam Books.
Rescher, N. (1996). Process Metaphysics: An Introduction to Process Philosophy. Albany: SUNY
Press.
Ritter, W. E. (1909). Life from the Biologist’s Standpoint. Popular Science Monthly 75: 174–90.
Rosen, R. (1991). Life Itself: A Comprehensive Inquiry into the Nature, Origin, and Fabrication
of Life. New York: Columbia University Press.
Russell, E. S. (1924). The Study of Living Things: Prolegomena to a Functional Biology. London:
Methuen.
Saborido, C., Mossio, M., and Moreno, A. (2011). Biological Organization and CrossGeneration
Functions. British Journal for the Philosophy of Science 62: 583–606.
OUP CORRECTED PROOF – FINAL, 2/5/2018, SPi
   
Schneider, E. D. and Kay, J. J. (1995). Order from Disorder: The Thermodynamics of
Complexity in Biology. In M. P. Murphy and L. A. J. O’Neill (eds), What Is Life? The
Next Fifty Years (pp. 161–73). Cambridge: Cambridge University Press.
Schrödinger, E. (1944). What Is Life? The Physical Aspect of the Living Cell. New York:
Macmillan.
Sherrington, C. S. (1940). Man on His Nature. Cambridge: Cambridge University Press.
Sinnott, E. W. (1955). The Biology of the Spirit. New York: Viking Press.
Taylor, R. (1950). Comments on a Mechanistic Conception of Purposefulness. Philosophy of
Science 17: 310–17.
Torrey, T. W. (1939). Organisms in Time. Quarterly Review of Biology 14: 275–88.
Waddington, C. H. (1957). The Strategy of the Genes. London: George Allen & Unwin.
Weber, B. H. and Depew, D. J. (2001). Developmental Systems, Darwinian Evolution, and the
Unity of Science. In S. Oyama, P. E. Grifﬁths, and R. D. Gray (eds), Cycles of Contingency:
Developmental Systems and Evolution (pp. 239–53). Cambridge, MA: MIT Press.
Weber, B. H., Depew, D. J., Dyke, C., Salthe, S. N., Schneider, E. D., Ulanowicz, R. E., and
Wicken, J. S. (1989). Evolution in Thermodynamic Perspective: An Ecological Approach.
Biology & Philosophy 4: 373–405.
Whewell, W. (1840). The Philosophy of the Inductive Sciences, vol. 2. London: John W. Parker.
Whitehead, A. N. (1925). Science and the Modern World. Cambridge: Cambridge University
Press.
Wicken, J. S. (1987). Evolution, Thermodynamics, and Information: Extending the Darwinian
Program. Oxford: Oxford University Press.
Williams, G. C. (1966). Adaptation and Natural Selection. Princeton: Princeton University
Press.
Woese, C. R. (2004). A New Biology for a New Century. Microbiology and Molecular Biology
Reviews 68: 173–86.
Woodger, J. H. (1929). Biological Principles: A Critical Study. London: Routledge & Kegan
Paul.
Woodger, J. H. (1930). The ‘Concept of Organism’ and the Relation between Embryology and
Genetics, Part I. The Quarterly Review of Biology 5: 1–22.
OUP CORRECTED PROOF – FINAL, 2/5/2018, SPi
  . 