The Identity of Organisms in Scientific Practice: Integrating Historical and Relational Conceptions
Frontiers in Physiology
We address the identity of biological organisms in scientific practices by combining historical and relational, organizational conceptions.
Montévil, Maël, and Matteo Mossio. 2020. “The Identity of Organisms in Scientific Practice: Integrating Historical and Relational Conceptions.” Frontiers in Physiology 11 (June): 611. https://doi.org/10.3389/fphys.2020.00611
The identity of organisms in scientific practice:
integrating historical and relational conceptions∗
Maël Montévil and Matteo Mossio
Abstract
We address the identity of biological organisms at play in experimental
and modeling practices. We first examine the central tenets of two general
conceptions, and we assess their respective strengths and weaknesses. The
historical conception, on the one hand, characterizes organisms’ identity
by looking at their past, and specifically at their genealogical connection
with a common ancestor. The relational conception, on the other hand,
interprets organisms’ identity by referring to a set of distinctive relations
between their parts, and between the organism and its environment. While
the historical and relational conceptions are understood as opposed and
conflicting, we submit that they are also fundamentally complementary.
Accordingly, we put forward a hybrid conception, in which historical and
relational (and more specifically, organizational) aspects of organisms’
identity sustain and justify each other. Moreover, we argue that organisms’
identity is not only hybrid but also bounded, insofar as the compliance
with specific identity criteria tends to vanish as time passes, especially
across generations. We spell out the core conceptual framework of this
conception, and we outline an original formal representation. We contend
that the hybrid and bounded conception of organisms’ identity suits the
epistemological needs of biological practices, particularly with regards to
the generalization and reproducibility of experimental results, and the
integration of mathematical models with experiments.
Scientists often describe biological organisms as exquisitely complex objects. The
adjective ”complex” has various meanings, and one points to a difficulty in providing
an adequate account of their identity, notably in modeling and experimental
practices. What does organisms’ identity refer to? As for any object, the identity of
an organism designates what makes it what it is and, thereby, what makes it different
from something else.
We can understand every conception of organisms’ identity as spanning over a
spectrum going from more stringent to more inclusive interpretations. At one end of
the spectrum, the identity of an organism points to its unicity, i.e., the fact of
possessing a unique set of properties, making it different from any other
organism (and, a fortiori, from any other object). On the other end, the identity
of an organism refers to its individuation, i.e., the fact of possessing those
properties that allow drawing its boundaries and discriminating it from
the surroundings. The reason why we take here individuation as the most
inclusive interpretation of identity (among the many possible ones in the
spectrum) is that even though organisms differ in many respects, we assume
that they share a few (if not the very same) fundamental properties on the
basis of which they can be isolated and recognized as organisms. Identity
as unicity is often referred to as numerical or absolute, while identity as
individuation — as well as for all possible intermediate interpretations — is relative,
in the sense of only holding in relation to specific properties (Noonan and
Curtis, 2018).
Each interpretation of identity in the spectrum provides criteria that generate a
reference class. When understood as unicity, each identity class is supposed to
contain only one organism; when understood as individuation, on the opposite side, a
class should contain the largest number of (if not all) organisms. We understand
more inclusive classes as being presupposed by more restrictive ones: in particular,
the unicity of a given organism presupposes that it also meets the more general
requirements for individuation. Furthermore, as philosophers commonly point out
(see for instance Boniolo and Testa, 2012), the question of identity can be raised
both at a given moment (”synchronic” identity or ”who” question) and through time
(”diachronic” identity or ”persistence” question). Whatever interpretation of identity
is adopted, one can investigate not only whether a given organism meets the criteria
of membership to the reference class here and now, but also whether it keeps
complying with them over time; the more the class is restrictive, the less it tolerates
changes.
The choice of the interpretation of organisms’ identity depends on the aim
pursued. In science, moreover, interpretations and classes are not supposed to be
merely arbitrary or practical groupings of objects: to be relevant, they should stem
from theoretical conceptions and frameworks (Grimaldi and Engel, 2007). In
evolutionary biology, notably, organisms are classified into several taxa, which in turn
form a hierarchy of taxonomic ranks that includes the species, the genus, the family,
up to life as a whole. These taxa are grounded in evolutionary theory (Lecointre and
Le Guyader, 2006), and serve many purposes as eliciting further questions on
evolutionary processes or providing tools for conservation biology (Godfray
et al., 2004).
In this paper, we focus on the concept of organisms’ identity that is relevant to
experimental and modeling practices in Biology. Experimental practices require
observing particular organisms. Yet, the knowledge that biologists usually try to
obtain from their experiments is not supposed to be just about particular organisms
but, instead, to hold for any other organism endowed with the same relevant
properties. In particular, biologists need some theoretical justification for considering
that several organisms are instances of the same experimental object, so as to
distinguish the effects of experimental difference-makers from unrelated, spontaneous
variations (Waters, 2007). In other words, experimental results obtained
about a particular organism, or a few particulars, should apply to any other
organism belonging to the same class. What is at stake is the generalizability of
scientific knowledge and the related reproducibility of experimental results —
the latter facing currently a major crisis, especially in biomedical research
(Baker, 2016).
The complexity of biological organisms vis-à-vis identity is the acknowledged
difficulty of treating particular organisms as instances of the same experimental
object, and of subsuming them under the relevant classes (Agutter and
Wheatley, 2004; Bookstein, 2009; Montévil, 2019a). Several reasons seem to play
a role in explaining such difficulty.
The first reason is that, in both theoretical and empirical practices, scientists can
only take into account a few aspects of biological organizations, understood here as
the whole set of functions and processes constituting each organism. Typically,
mathematical models only focus on some target features while neglecting many
others, although such neglect does not rely on a clear theoretical justification
and a systematic method. The same applies to experimental quantitative
measurements, which are limited to only some aspects of the organisms under
study.
A second reason, related to the previous one, is the strong coupling between
biological organisms and their context. The context should be understood here
in a comprehensive way, so as to include abiotic elements as well as other
organisms, both participating in the determination of organisms’ identity (Gilbert
et al., 2012; Miquel and Hwang, 2016). Disentangling such a network of
interactions requires understanding what matters and what does not when
examining a specific phenomenon. For example, laboratory animals tend to
have immunological properties that are different from those of wild animals
because they usually experience a lower microorganismal biodiversity (Abolins
et al., 2010).
A third reason is that contingent features that appeared throughout historical
processes contribute to determining the properties of current organisms. In
evolutionary theorizing, this idea corresponds to the ”contingency thesis”
(Beatty, 1995). Ontogenesis also conveys contingency, for example, as a
result of developmental plasticity (West-Eberhard, 2003). Organisms are
contingent objects because they undergo continuous variations, and part of these
variations last over time. Distinct individual organisms undergo different
variations and generate new organisms that undergo further variations. Moreover,
variations of organisms can also affect their context. Therefore, each organism
results from such an intra- and cross-generation history of individual and
contextual variations: in a word, organisms are historical objects (Montévil
et al., 2016; Kauffman, 2019).
For all these reasons, an account of organisms’ identity as experimental objects is
a challenging task. Specifically, the challenge consists of adopting a conception of
relative identity that generates one or several classes appropriate for the
generalization and the reproducibility of experimental results. Such a conception
would provide an operational tool for both empirical practices and mathematical
modeling.
How is organisms’ identity conceived in current biological practice? It seems to
us that two broad theoretical conceptions can be distinguished. The first
conception is historical or genealogical. Accordingly, a bat is a bat because all
bats share a common ancestor, while other life forms do not (Lecointre and
Le Guyader, 2006). Genealogy has here a twofold sense: a narrower one that maps
onto reproductive relations; and a broader one that refers to the role of the past in
determining the identity of a biological organism. In the latter sense, today Alice
is Alice because she has been named so in the past, even though she has
considerably changed over time. The second conception is relational. Biologists
define organisms relative identity by referring to a set of relations between
properties and traits that they possess. Following this strategy, a bat is a
bat because it has the distinctive relations between properties and traits of
bats.
As we will discuss, each conception is open to different interpretations of identity,
going from more restrictive to more inclusive ones. For instance, evolutionary taxa
also stem from a genealogical conception, but these classes are much more inclusive
than the ones which are relevant for most experimental practices, where biologists
deal with strains rather than species or higher ranks (see Montévil, 2019a, for a
discussion and detailed examples). Importantly, the distinction between the
genealogical and relational conceptions does not map onto the distinction between
diachronic and synchronic identity, which means that each conception can
be applied to characterize both the synchronic and diachronic identity of
organisms.
Both conceptions are at work in experimental practices, and each of them has
strengths and weaknesses. Genealogical strategies, we argue, enable scientists to
consider whole organisms as identical without, however, making explicit the
domain of validity of experimental results. In particular, it is unclear how
much variation a set of genealogically connected organisms can undergo
(during ontogenesis and across generations) while maintaining a relevant
identity for a given experimental purpose. Relational strategies, in turn, make
explicit their domain of experimental validity that, however, is restricted to
the properties and relations explicitly taken into account. Organisms are
relationally identical only insofar as it is possible to isolate such properties and to
exclude any other aspects or changes that could (and actually do) make them
different.
We can understand the relations between these two conceptions in different ways.
One could favor the genealogical conception because it matches the historicity of
biological organisms that emanates from the Darwinian theory of evolution.
Alternatively, one could argue that the relational conception is the most fundamental
one; its limited validity would be the mere effect of our (current) lack of theory and
empirical knowledge. An example of the latter attitude (although not specifically
addressing experimental practices) is Goodwin and Webster’s relational theory of
form changes that they take as a requirement to ground phylogenetic reasoning
(Webster and Goodwin, 1996). As in physics’ models of morphogenesis, the authors
argue that genealogical categories (as homology) should stem from relational
descriptions.
We advocate here a different view. We argue that biology requires combining
genealogical and relational conceptions, with the support of an appropriate
theoretical framework. The genealogical conception provides a procedure to select
whole organisms as candidates to be subsumed into relevant identity classes. In turn,
the relational conception – especially in an organizational version – provides explicit
guidelines to understand the stability of biological organisms and, thereby, of the
domain of validity of identity classes, notably in time. The main upshot of our
analysis is a hybrid and bounded conception of organism identity. Organisms can be
subsumed under hybrid identity classes that support the reproducibility and
generalizability of experimental results. Nevertheless, the validity of identity classes
for experimental practices is inevitably limited in time and space, which draws a
fundamental difference between biology and other natural sciences, in particular
physics and chemistry.
2 Contrasting genealogical and relational conceptions of identity
We describe in this section the two conceptions of organisms identity at work in
experimental and modeling practices in biology, and we focus on their background
epistemology. We aim at making explicit their respective strengths and weaknesses
which, because of their complementarity, open the way to the elaboration of an
integrated conception.
2.1 Genealogical identity
A genealogical (or historical) conception of identity may take different forms. For
instance, genealogical identity can be understood as the preservation of properties
having occurred in the past. The version which is at work in biological disciplines
conceives organisms’ identity in terms of a more generic connection with the past.
Several organisms are the same when they have a particular connection with the past
in a historical process.
Historical identity is — unsurprisingly — at work in systematics, the discipline
that elaborates the classification and taxonomy of biological organisms and whose
results are used ubiquitously in biological practice. In systematics, particular
organisms are considered as members of the same class if they belong to a
monophyletic group, which includes only and all the descendants of a last common
ancestor. How do systematics build classes? While the concept of genealogy comes
from Darwin’s theory of evolution, genealogies are usually not observable as such. For
example, it is not possible to ascertain that a given fossil species is an ancestor of a
current species. Instead, it is possible to show that a given specific fossil species is
more closely related to a given current species than to another one. As a result,
unlike the genealogy stricto sensu, phylogenetic groups are defined by their assessed
genealogical proximity, and last common ancestors are theoretical specimens
that biologists do not identify empirically (de Queiroz, 1992; Lecointre and
Le Guyader, 2006; Lecointre, 2015).
The use of the genealogical conception of identity extends to day-to-day
experimental practices across various biological disciplines. Biologists establish
laboratory strains and usually run experiments on organisms coming from
the same strain. By this practice, experimental biologists consider different
individual organisms as hypothetically identical. For example, biologists
assume that the properties of these organisms follow the same probabilistic
distribution in statistical tests. When applying this conception, biologists do not
exhibit a given set of observable properties that the organisms would share;
instead, they build the identity class by referring to their shared recent origin.
The ’Methods’ section of most experimental papers explicitly relies on this
strategy.
Compared to the phylogenetic method of classification, the experimental practice
is, at the same time, less conceptual and more operational. Experimental
biologists do not estimate the genealogy by theoretical arguments based on
similarities and hypotheses on evolutionary processes. Instead, they control
genealogy empirically by letting the ”ancestors” reproduce in laboratory
conditions (Chia et al., 2005). Besides, the relevant identity classes at play in the
experimental practice are often narrower than the taxonomic ranks. The latter often
appear to be inadequate when trying to generalize experimental results. In
the terms used above, we could say that experimental practices adopt a
more restrictive interpretation of genealogical identity when compared to
systematics.
Whatever interpretation is adopted, the genealogical strategy provides
criteria that apply to both synchronic and diachronic identity of organisms.
A group of organisms shares the same synchronic identity if they have a
genealogical connection with a specific common ancestor. Likewise, each organism
remains diachronically a member of the same class whatever difference (due to
variation) appeared — or will appear — between it and the ancestor through
time.
Identity classes built on genealogical conceptions (at least in the version discussed
here) put no principled restrictions on the amount and nature of variations that each
member of the class can undergo. The genealogical conception of identity can
accommodate completely open futures, including the appearance of both structural
and functional novelties, as well as radical changes of already existing structures and
functions (Lecointre, 2015). Accommodating these novelties is a growing concern of
theoretical biology (Montévil et al., 2016; Montévil, 2019b; Kauffman, 2019).
Such inclusiveness is a strength of the genealogical conception of identity that enables
biologists to accommodate the diversity of living organisms. For example, the
’tetrapods’ are organisms that have a common ancestor possessing four skeletal
limbs. While most members of the class do share that trait, sub-classes such as
snakes lost it. However, snakes remain part of the class since the definition refers to
the common ancestor and not to the observable properties of the objects. This
somehow paradoxical lesson can be generalized: no single observable trait or property
has to be shared by a group of organisms being identical only by the reference to the
past.
Let us mention one last aspect concerning genealogical strategies. In principle,
ascribing a relative genealogical identity to a group of organisms requires estimating
their genealogy and their connection to a common ancestor. However, in systematics,
the common ancestor is not directly accessible and cannot be an empirical reference.
Instead, biologists anchor a name to a specific individual organism called
a ’name-bearing type’ that is the ultimate reference for this name (CZN
International, 1999). Name-bearing types are not the common ancestor of a
taxon but, instead, specimens that serve to define a name. The name is then
extended to a group of organisms that includes the type and all the descent of a
common ancestor, assessed by the methods of phylogeny (Lecointre and
Le Guyader, 2006; Grandcolas, 2017). Experimental biologists can also
obtain generations of organisms from an initial controlled group of organisms
(although not necessarily from a specific individual common ancestor). Then
the strain is defined by the reference to this group, often indirectly by the
combination of the strain label and the name of the breeding institution. It
is instructive to contrast these uses of particulars with the definitions in
the International System of Units (Montévil, 2019a). These definitions
rely on the physical theories that define reference units abstractly — they
are invariants of the theory — and not on particular objects (such as the
”prototype meter” that metrologists built afterward to instantiate these abstract
definitions).
Although biologists do not use strains universally, organisms obtained in this way
are widespread in experimental practices. Yet, what justifies the fact of subsuming
them under taxonomic classes, and giving them names coming from systematics? The
implicit hypothesis is that strains under control are subsets of taxonomic ranks: for
instance, the strain “black 6” is supposed to belong to the systematic class of mice
(Mus musculus). It also means that if we estimate the phylogeny of specimens of such
a strain, including the initial group of organisms, they are more closely related to the
member of the intended taxon, especially the name-bearing type, than to other
taxons.
The genealogical conception of biological identity has several strengths. This
conception allows ascribing an identity to organisms as wholes despite their relational
complexity by building on the theoretical genealogies coming from the theory of
evolution (even though it is not reducible to it, as just discussed). Furthermore,
identity classes do not require conservation through time and leave the future open to
indefinite variation. Historical identity is ”invariant by reproduction”: if the parents
are in a class, then the offspring will be in the same class because they share the
same past, used as a reference.
In turn, genealogical identity suffers from significant weaknesses from the
perspective of experimental practices, or applications such as medicine. While
systematics aims at reconstructing the past and describing the present in light of the
past, experimental practices investigate the relations between the parts of organisms,
as well as between organisms and their surroundings. Because of these different
goals, identity classes in systematics can include tetrapods that are such
without having four limbs; in turn, empirical practices need classes that sustain
reproducibility and generalizability of the results over a (hopefully large) group of
organisms.
The source of the problem is the same that generates the strengths of historical
definitions per se, i.e., the fact of being uniquely grounded in genealogical
connections. Experimental biologists try to circumvent the problem by working
mostly on groups of organisms having close ancestors, under the (implicit,
but fundamental) hypothesis that genealogical proximity tends to go with
organizational proximity: the closer individual organisms are in the genealogy, the
less they tend to differ anatomically and functionally (Isaacs, 1986; Mogil
et al., 1999; Montévil, 2019a). The main virtue of this precaution is that it does
work to some extent in practice, which explains why it is widespread in empirical
studies. Yet, no explicit justification of the underlying hypothesis is provided. As a
result, the domain of validity for the experimental practice of genealogical identity
classes is unknown, and there are no specifications about the rate and kind of
variations (and, reciprocally, about the degree of similarity) that would threaten the
membership to a given identity class.
2.2 Relational identity
The relational conception of identity stems from a different epistemological
stance. The description (and, in science, the theoretical determination) of an
object mainly appeals to the relationships between its parts and constituents,
as well as its relationships with other objects. Relations are understood
as more fundamental and meaningful than non-relational aspects, notably
because they have a stable form, amenable to mathematical descriptions
such as equations. Moreover, the relational epistemology emphasizes that
scientists ultimately observe objects via their relations with the measurement
apparatus; therefore, relations can be seen as the starting point of experimental
knowledge.
The relational epistemology pervades most natural sciences and
especially physics. For example, although the electric charge seems to be
an intrinsic property of objects, it is ultimately a quantity that describes
how charged objects exert forces on each other: therefore it is grounded on
relations[1].
According to the relational conception of identity, several objects are identical if
they share the same relationships, and they are different if they do not. For
example, all electrons are identical because they have the same relations
with other objects (i.e., the same interactions), described by equations[2].
Similarly, a group of organisms belongs to the same identity class if they share a
given set of relational properties.
What relations are relevant in the biological domain? After all, one may argue
that genealogy is also a relation. In fact, what matters from a relational perspective
is the form of the relation, the kind of structure linking two or more objects. In this
respect, genealogical relations as such are not relevant, insofar as they would
generate very broad classes: for instance, all humans and mice share the same formal
genealogy (they have all two parents, each of which has two parents...). Accordingly,
more restrictive interpretations of the relational properties of organisms are adopted,
as we discuss below, mainly focusing on their observable functioning and
organization. Moreover, as mentioned, the relational epistemology holds
that the mathematical form of the relations is supposed to remain stable in
time. Relational identity requires, therefore, the stability of the relevant
properties, when considering both the synchronic and diachronic identity of a
group of organisms. The contrast with the genealogical conception, which
characterizes organisms’ identity without relying on stable properties, is
sharp.
In biology, we distinguish two versions of the relational epistemology and the
resulting conception of identity. A first version, adopted in particular by
biophysics and systems biology, consists of studying biological organisms by using
conceptual and mathematical tools common to other natural sciences, as
physics or chemistry. While it relies on well-established and operational
tools, this ”biophysical” version tends to look at biological organisms as
physicochemical systems and, therefore, to emphasize common aspects while
neglecting specifically biological ones. The resulting conception of biological
identity applies to those aspects, and their relations, which are captured by the
models. Different organisms are synchronic instances of the same object
insofar as they possess the same aspects and relations captured by the model,
and they maintain their identity diachronically if they conserve them in
time.
The main strength of the biophysical conception of identity is that, in contrast
with the genealogical one, it makes explicit the conditions of validity of experimental
results. Generalizability and reproducibility of results hold for all organisms
belonging to the same identity class, insofar as they possess the aspects and relations
made explicit by the model or description. At the same time, this definition carries a
crucial weakness: it considers exclusively these aspects. Biophysical identity applies
only by abstracting from any other aspect or property of organisms not
included in the description. By ”abstracting,” we mean that all other aspects of
the organisms are supposed to be negligible for the compliance with the
model.
The problem with this abstraction move is twofold. On the one hand, it implies
dealing with organisms not as wholes, but as circumscribed sub-systems. In fact,
biophysical models used in biology often apply also to abiotic phenomena
(Douady and Couder, 1996; Fleury, 2009). If relational identity is built
upon such a restricted characterization of the organism, one can wonder
whether it constitutes a relevant criterion of organisms’ identity given that,
in a sense, it neglects most of the organism. On the other hand, — and
crucially — the abstraction does not work most of the time. Experimental
biologists and modelers are usually not able to abstract from all other aspects,
which prove to be not negligible and generate observable differences between
organisms (Isaacs, 1986; Mogil et al., 1999; Festing, 2014). As a result,
individual organisms typically exhibit significant variability with respect to a
particular model, and observations contradict their purported relational identity.
Therefore, while its domain of validity is explicit, biophysical identity is seldom
valid.
The second version of the relational epistemology, which we label “organizational”,
places a heavier emphasis on the distinct features of biological organisms. Its
central assumption is that organisms are natural systems endowed with a
distinctive organization. In particular, biologists can analyze organisms (be
them unicellular or multicellular) as constituted of parts that depend on
each other for their continued existence: biological “organization” refers
specifically to such a mutual dependence among parts. Initially advocated by
theoretical biologists like Nicolas Rashevsky (1954) and Robert Rosen (1991), the
organizational epistemology is in a way ”more relational” than the biophysical one
because it focuses on the fact that organisms realize a distinctive regime
of relations between their parts. Classical accounts of the organizational
framework are Varela and Maturana’s autopoiesis (Varela et al., 1974), Rosen’s
systems (Rosen, 1991) and Kauffman’s autocatalytic sets (Kauffman, 1993).
Let us describe in some detail the central tenets of this organizational framework,
by relying on some recent theoretical developments (see also Montévil and
Mossio, 2015; Moreno and Mossio, 2015; Kauffman, 2019, for recent discussions).
One of the central aims of the organizational perspective is to provide a fine-grained
characterization of the mutual dependence between an organism’s parts,
which in turn brings about the idea of circularity. Biological organisms are
understood as natural systems realizing a dual causal regime. On the one hand,
they are thermodynamically open systems: they are traversed by a flow of
energy and matter that enables them to maintain themselves over time in
conformity with the second principle of thermodynamic. On the other hand,
biological organisms control the thermodynamic flow through the action of
structures that, at specific time scales, exert constraints on the ongoing processes
and transformations. In particular, organisms are constituted by a set of
constraints that 1) are generative — they canalize target processes in such a
way to maintain the conditions of existence of other constraints and 2) are
dependent — their existence relies on the action of other constraints (see Figure
1).
The set of constitutive constraints that are both generative and dependent realize
mutual dependence, which is usually referred to as closure. One of the conceptual
strengths of the organizational perspective is that it provides an account for the
concept of biological function, defined as the effect produced by a constraint subject
to closure (Mossio et al., 2009; Nunes-Neto et al., 2014). By realizing closure of
constraints, the organism maintains itself. In turn, the otherwise general idea of
’biological organization’ is defined as closure: for an organism to be organized
means realizing closure of constraints (Montévil and Mossio, 2015, for
details).
Organizational closure provides a specific interpretation of the circularity at work
in biological organisms (Mossio and Bich, 2014). Importantly, the closure principle
provides theoretical guidance to explain the relative stability of biological organisms.
Functional constraints exhibit conservation at the time scale at which they act on
processes: as claimed elsewhere (Montévil and Mossio, 2015), it is precisely their
local conservation that endows them with the capacity to control the thermodynamic
flow. At longer time scales, however, constraints undergo degradation and must
be repaired or replaced: this is where organizational closure steps in and
contributes to explain how organisms as wholes stabilize themselves over
time.
Figure 1:In this diagram, ,
,
,
and
play, ex hypothesi, the role of constraint at
,
,
,
,
and
respectively. Furthermore, ,
,
,
and
are dependent constraints, while ,
,
,
and
are generative constraints. The subset of constraints
that are both generative and dependent is then
(,
,
).
The organization constituted by ,
and
realizes closure (reproduced from Montévil and Mossio, 2015, with permission
from Elsevier.).
With this brief characterization in hand, let us examine how the organizational
framework deals with organisms’ identity. As for any conception of identity, different
interpretations of the organizational one can be adopted. The most restrictive
relative interpretation seems to be that different organisms are instances of the same
object insofar as they share the very same functional organization, i.e., if they realize
(at some given stage of their lifetime) the closure of the same constraints. At the
opposite end, the most inclusive definition would state that different individual
organisms are identical if they merely realize closure, whatever specific set of
functions is involved.
As a matter of fact, Difrisco and Mossio (In press) have recently argued that the
most inclusive interpretation of organizational identity is well suited to account for
organism diachronic identity. A given organism remains the same, despite any kind of
change that it can undergo (especially during development), if it realizes a
continuous succession of regimes of closure, such that each regime depends on
some functional constraints exerted by a previous regime. The connection
between different regimes of closure that grounds diachronic identity is what
DiFrisco and Mossio call organizational continuity. For the purposes of this
paper, which focuses on the conception of organisms’ identity relevant for
modeling and experimental purposes, the most inclusive interpretation of
organizational identity looks inadequate. By hypothesis in the organizational
perspective, all organisms realize closure; therefore, the general criterion of closure
would include a massive number of very diverse organisms, which would
prevent generalizations and reproducibility in most cases. A more restrictive
interpretation, warranting some functional similarity between organisms, seems to be
required.
Let us now consider the most inclusive interpretation, according to which organisms
are identical if they realize the closure of the very same constraints. We consider
here[3]
that two or more constraints are the same in organizational terms if they
perform the same function, which means that they constrain the same kind of
processes by relying on the same kind of mathematical or geometrical structure.
For instance, two constraints are instances of the same vascular system if
the same topological structure of vessels constrains the transport of oxygen
and nutrients to cells, and of wastes afar from them. The emphasis here is
on the qualitative, functional identity between constraints, while limited
quantitative differences are negligible. In contrast, quantitative differences
between functionally identical constraints may be relevant when comparing
whole organizations, insofar as they can lead to a qualitative difference in
some other constraints and, therefore, in the way overall closure is realized[4].
To the extent that organizational closure is a distinctive feature of biological
organisms, this relational conception of organism identity seems to be more suitable
because it avoids the first possible drawback of biophysical ones, i.e., the fact of
leaving aside specifically biological aspects. Indeed, identity grounded on
closure naturally considers organisms as whole entities. As for the biophysical
conception, the organizational one makes explicit its domain of experimental
validity. To be the same, different organisms must share the same organization.
In contrast to the biophysical definition, however, an explicit description
or model of the whole functional organization of an organism appears to
be out of reach for the scientific inquiry. As a result, the criterion is not
directly applicable. One could argue that it constitutes the ”horizon” of a
well-grounded definition of biological identity or, on the opposite, that a
complete description of an organism might also prove impossible to obtain in
principle.
A possible solution to the problem would be to establish descriptions and models
of partial closure, and take them as criteria of identity. By ”partial closure,” we mean
a closure among a subset of all functional constraints constituting a given organism.
For instance, a given model can specifically focus on the reciprocal dependencies
between constraints of the respiratory and vascular systems, under the hypothesis
that these are critical for the cohesion of the whole organization. Accordingly, we
distinguish models of partial closure from local biophysical models: while the
former describe parts of an organism that do realize closure, the latter do
not.
One may object that such a solution would also face the problem of abstracting
most of an organism’s organization, just as the biophysical one. With no theoretical
guidance, partial models would neglect aspects that might actually make a difference
and induce variability between supposedly identical organisms. The objection is
undoubtedly correct. Yet, we submit that the organizational framework
has better prospects than the biophysical one for selecting relevant aspects
of an organism within an adequate theoretical framework. The reason is
that even partial organizational models are nevertheless models of closure
(while biophysical ones are not) and therefore designed to account for the
reciprocal stabilization of functional constraints within whole organisms. As a
result, they can better determine the occurrence and impact of variations
affecting organisms and the extent to which such variations could alter their
identity.
3 An hybrid and bounded conception of organisms identity
The upshot of the previous section is that genealogical and relational conceptions of
organisms’ identity have complementary strengths and weaknesses. In what follows,
we advocate their integration into a hybrid conception that, we hold, is better suited
for taking up the challenge of organisms’ complexity.
The connection with a fixed past allows the genealogical conception to define
organisms’ identity in a way that accommodates biological variations. However,
genealogical identity does not refer to any observable property of organisms, which
leaves unspecified to what extent experimental generalizations are legitimate. In
sharp contrast, relational identity refers to the observable properties of organisms,
which provide specific conditions for scientific generalization and reproducibility.
Yet, relational identity faces the problem of abstraction with regards to
most of an organism’s organization, with the result that it seldom proves
valid.
The reason why relational identity fails to apply to organisms easily is not only
that a complete description of their organization is not accessible. Even if a complete
description of an organization were available, we submit that the corresponding
biological organisms would undergo unpredictable variations. Biological variation in
such a ”strong” sense is not merely quantitative; it corresponds to the appearance of
structures, processes, couplings, and functions that are fundamentally new
(Longo, 2018; Montévil, 2019b; Kauffman, 2019). Elsewhere, we have argued that
the appearance of unpredictable variation in biological organisms should be a
fundamental principle of biology — the principle of variation (Montévil
et al., 2016) — which governs biological phenomena together with the principle of
closure.
In this situation, we submit that an adequate conception of organisms’ identity
requires integrating genealogical and relational (organizational) strategies, as Figure
2 illustrates. Organisms are specific objects, which means that each of them can
possess specific features that make it qualitatively different from other organisms to
an extent. Organisms are specific objects because they are the result of a history of
variations, and they continue to undergo further variations over time. Yet, in any
given experimental situation, a group of organisms can also be shown to share some
generic (i.e., common) aspects, typically constraints, captured by a relational
description and supporting generalization. Over time, however, biological variations
may involve a change of these constraints even in controlled laboratory strains.
Such changes would make the identity grounded on the hybrid conception
invalid. Let us discuss in some detail the central tenets of the conception we
advocate.
Figure 2:Integration of genealogical and relational descriptions (reproduced
from Montévil, 2019a, with permission from Springer.). Relational concepts,
constraints here, are insufficient to define specific objects: they are
fundamentally historical. They nevertheless possess relational properties,
constraints, that are valid for some time, and can change over time. This schema
has been designed for biological organisms and is a starting point to integrate
genealogical and relational identities.
3.1 Conceptual tenets
Physicists understand the changes taking place in a given phenomenon by
variables connected by invariant relations, expressed as equations. By contrast,
following the principle of variation, we submit that there is no invariant
mathematical structure (as equations) underlying the behavior and dynamics of
organisms.
A central epistemological implication is that we have to understand the
relative stability of biological phenomena without overarching invariants. As
mentioned in the previous section, organizational closure plays precisely this
epistemological role at the individual scale, by contributing to explain how
functional constraints stabilize each other through their reciprocal relations and
interactions. As recently argued (Mossio and Pontarotti, 2019), closure can
also explain the stability of functional constraints across generations by
providing an organizational understanding of biological heredity. Natural
selection plays a similar role at the evolutionary scale, in that it excludes
some trait variants and, thus, explains the stability of other variants, as
adaptations (Lecointre, 2018). To the extent that both closure and natural
selection are the basis of philosophical accounts of the concept of ’biological
function,’ the ascription of functions is typically understood as a way to explain
the stability of function bearers at the individual and evolutionary scale
(Montévil, submitted).
How should organism identity be characterized in this theoretical framework? We
propose six main tenets. First, organism identity requires elaborating a generic
description of organizational closure, which is supposed to apply to a group of
individual organisms. Such a description aims to capture not only the relations
between functional parts of an individual organism but also, and crucially, its
interactions with the environment as an agent (Barandiaran and Moreno, 2008), as
well as with other organisms (Hernández and Vecchi, 2019).
Second, organizational descriptions are necessarily partial, despite their possible
complexity. This limitation implies that many aspects are neglected, be they other
functional parts, or aspects of the environment, or other organisms. In section 2.2, we
referred to this implication as the abstraction made by relational models. The
ineluctable abstraction of the organizational description means that the neglected
aspects are also uncontrolled and might, therefore, hide relevant differences between
the individual organisms. Because of the complexity of biological organisms discussed
in the Introduction, such differences do exist most of the time and prevents using
explicit organizational descriptions as a sufficient criterion to build identity
classes.
Third, the genealogical strategy steps in and provides a procedure for
dealing with the aspects that the organizational framework does not make
explicit. The procedure considers as candidates for membership to an identity
class those organisms which share the same past. Often, in experimental
biology, organisms have a controlled, recent common ancestor (even though
other aspects of their past may also be controlled, see Montévil (2019a)).
Under the implicit assumption that the closer organisms are to a common
ancestor, the more they tend to share generic aspects, such a procedure
provides indirect control on those aspects neglected by the organizational
description[5].
These neglected aspects include not only parts of organisms but also the environment
of successive generations leading to them, as well as other features that may be
interpreted as belonging either to the former or the to latter, such as the microbiome
of mammals. Since biologists cannot completely describe organisms in relational
terms, they use the genealogical strategy that complements the organizational
description.
To illustrate how the genealogical strategy fills in the gaps of the organizational
one, let us focus on the treatment of specific functional constraints. A constraint is a
relational concept, defined by its mathematical structure and its link with the
constrained process (Montévil and Mossio, 2015). However, the isolated description
of a constraint within an organism is not exhaustive, insofar as it omits other
constraints that may contribute to its stabilization (be it at a higher level or the
same level of organization) or may constitute it at a lower level. For example,
physicists can analyze the camera eyes of mammals and cephalopods with a single
optical model; yet, the details concerning the nerve position, vasculature,
molecules are very different, and so are the possible relations with other
functional constraints, as well as variants, pathological or not. That is why the
genealogical concept of homology enters the picture naturally. Homologous
constraints tend to be constituted by (and articulated with) other constraints
displaying a higher degree of similarity, in comparison to the situation of
analogous constraints. Actually, the genealogical connection that matters here
can be more specific than the one captured by the concept of homology
alone, insofar as relevant constraints would come from specific genealogical
groups, such as specific species or strains. Such genealogical control is a
critical asset when dealing with organizations that have no complete relational
description. As a result, the historical characterization of constraints identity
complements their relational description. Functional constraints are the same
when they have the same historical origin and share the same relational
properties.
Fourth, the organizational conception focuses on constraints closure, which
contributes to explain how biological organisms can maintain themselves over time by
constraining the thermodynamic flow. In particular, closure brings about an inherent
tendency of organisms to stabilize existing functional constraints by removing many
variations and by regenerating them in a fundamentally unaltered form. Such a
tendency to conservation (what we have previously labeled ”organizational inertia” in
Mossio et al. (2016, section 5.1)) would notably apply in those situations in which
variations are circumscribed and do not affect the constraints in charge of
regenerating the one (or set) being affected. In these situations, organizational
closure tends to restore the initial constraints. In other words, organization imposes
theoretical conditions on the kind of variation that is likely to be preserved[6].
Moreover, variations need to be significant for the description in terms of closure of
constraints. The appearance of such functional novelties typically takes time. It
requires the emergence of a specific constraint and its integration to the organization.
Such an outcome is not the result of generic randomness; it requires finding a new
specific functional organization by constituting and exploring new configurations
(Montévil, 2019b).
Fifth, the tendency to conservation emphasized by the organizational framework
provides theoretical support for the hypothesis according to which genealogical
proximity tends to go with organizational proximity. Because of this tendency,
together with the fact that the emergence of functional novelties takes time and
natural selection, the closer genealogically organisms are, the less they tend to differ.
It might be argued that organizational novelties may sometimes be significant over
a relatively short period, for example, within one generation, because of
phenotypic plasticity (West-Eberhard, 2003). The point is certainly right; still, it
seems correct to point out that these changes are quantitatively limited in
comparison to the bulk complexity of biological organizations. The overall result
integrates genealogical and relational conceptions of identity: the former fills in
gaps of the latter, which in turn justifies some implicit assumptions of the
former.
Sixth, the integration between genealogical and relational conceptions leads us to
advocate a hybrid conception of organism identity. Individual organisms are members
of the same identity class if they have a high degree of genealogical proximity
and they share a distinctive, specific regime of organizational closure. Let
us assume, for instance, that biologists want to study the flight of bats.
Two organisms are experimentally identical bats if they descend from a
close common ancestor and they share a specific set of organized, functional
constraints as those involving flight, which include (among other things) the
anatomy of their wings. Biologists would also exclude bats with congenital
abnormalities affecting wings and other variations impacting the relevant
properties involved in bat flight. We submit that such a hybrid definition
of organism identity keeps the benefits of both genealogical and relational
conceptions while avoiding — or at least mitigating — some of their central
drawbacks.
Yet, the hybrid nature of the definition is not the end of the story. Indeed, our
theoretical framework relies on the principle of variation, according to which
individual organisms do undergo variation over time. The main implication here is
that, even though an individual organism satisfies the hybrid conception at a given
moment, there is no guarantee that it will do so as time passes. Consequently,
although a population of organisms shares the same hybrid identity during several
generations, sooner or later, some of these organisms will undergo variations
that will contravene their membership to that identity class. As a result,
our conception of organism identity is not only hybrid but also bounded in
time.
3.2 Towards a theoretical characterization
The conceptual framework outlined above would gain clarity if it were expressed by
an adequate formal language, which, to our knowledge, is currently lacking. Let us
take some preliminary steps in this direction.
We first introduce a new symbol,
,
which represents the historical aspects of organism identity.
relies
on a genealogical connection with an ancestor, or more generally with the past, and
complements relational descriptions of organisms. Accordingly, it includes all those
aspects of identity which are not made explicit by the relational part of
any given description. In conformity to the features of genealogical identity,
accommodates
past variations and contexts that have shaped the present (group of) organism(s) in
evolutionary and ontogenetic time. As such, theoretical and relational invariants do not
define
,
although it might include stable relations that have remained implicit or neglected
(voluntarily or not, see also below) in the relational description.
In any characterization or model complying with the hybrid conception of organisms’
identity,
realizes organizational closure in combination with the constraints
explicitly represented in relational terms. The overall characterization
does not make the closure entirely explicit, precisely because it contains
.
A group of organisms that meet the hybrid model — and would,
therefore, share the same explicit relational description and the same — would share
the same identity, even though they could nevertheless hide some differences, because of the very
nature of
. At
the same time,
can also contain some implicit stable relations due to the organizational
tendency to conservation, as mentioned in the fourth tenet. Genealogical
strategies of symmetrization exploit this tendency and provide some control over
(typically, by selecting different organisms having a close common ancestor).
Together, the explicit relational description of the constraints and
generate an identity class adequate for experimental work.
Since there is no theoretical invariant specified by
,
its status is fundamentally different from that of a variable, as used
in physics. Variables are defined through formal relations, while
refers
to a genealogical connection with a specific object, a particular. As a result, it is
ultimately a symbol in the etymological sense of the word, bridging the formal
description and the part of the world under study.
How is
formally integrated into an organizational model or diagram? The general idea is to
represent
as a sui generis constraint subject to organizational closure. As such,
is understood as being both dependent and generative for some
other constraints of the diagram. Yet, the specific nature of
implies that its relations with the rest of the system have a special
meaning. To a first approximation, we submit that the integration of
to
organizational closure, rather than representing actual relational knowledge, consists
of a background assumption that requires a conceptual justification and a formal
representation. Let us discuss these issues in some details.
(a)(b)
Figure 3:Integration of a historical symbol and organizational closure. Since
and the relational constraints have a different epistemological nature,
we use different arrows for constraints and processes related to
.
Zigzag arrows are relational constraints; straight arrows are
processes; spring arrows represent constraining effects that relate to
and are therefore not entirely relational; dashed arrows
indicate hypothetical processes constrained by spring
arrows. Constraints are defined in relational terms while
is defined genealogically, by reference to the past. In
diagram 3a, there is a global closure that involves
,
while diagram 3b includes an additional partial closure of constraint in
relational terms.
Figure 3 shows two kinds of diagrams that realize organizational closure by integrating
.
Figure 3a provides the most general version, in which there is only
one global closed path of constraint dependencies, which includes
. In
turn, Figure 3b describes a situation in which, in addition to the global
closure, a partial closure is realized among the constraints, independently from
. Because of the
specific nature of
,
the global closure that includes it has a hypothetical status and does not count as a
legitimate model of an organism. Hence, the kind of diagram depicted in Figure 3a
requires a justification within an organizational framework, typically by exhibiting
empirically relevant examples that satisfy the diagram and also realize partial
closure. In a nutshell, we can justify Figure 3a if it has concrete instances like in
Figure 3b. With this justification, biologists can legitimately use a diagram with no
partial closure, insofar as it is not always necessary to explicitly represent the
latter in a model, and some aspects of organizational knowledge can be left
implicit[7].
With these clarifications in hand, we can use diagrams of both Figure 3a
and 3b to build hybrid identity classes for groups of organisms in the
context of modeling and experimental practices. The more constraints are
included, the more the interpretation of identity (and the resulting classes) is
restrictive, and the more stringent empirical checking has to be. Similarly,
the more strict the tentative experimental, genealogical control exerted on
is,
the more restrictive the class is.
Diagrams integrating
to organizational closure raise the question of the connection between
and the explicit relational part. Depending on what the modeler knows
and ignores about the organisms, the diagram has a different meaning
and form, in particular with regards to the dependencies between
and other
constraints. Besides, if the diagram does contain a partial closure, specific organizational
patterns become visible, and further general challenges arise. For instance, as one can see
in Figure 3b, the coexistence between global and partial closure seems possible only if
depends
on, and maintains, at least one constraint (not necessarily the same) that is also part
of the partial closure. This situation implies — among other things — that at least
one constraint in the diagram must perform multiple functions. Understanding how
this organizational pattern can be realized (or how another pattern can produce the
junction) is a typical example of a general scientific question raised by the inclusion
of
to
closure.
When considering the relations between
and
the constraints in a diagram, we can distinguish several cases. Without trying
to be exhaustive, let us mention a few significant ones. It is worth noting
that these cases are not supposed to be mutually exclusive: the very same
in
the same diagram can carry aspects that are relevant for several of these
cases.
The first case is a generalization of the situation that we
discussed earlier for Figure 3a. In a given diagram and situation
,
might refer
to organisms where other aspects could be made explicit in relational terms in a different
diagram
.
So to speak, there is some knowledge that can be ”unpacked,” if required.
This operation can imply a transition from a model with no partial closure
to a model with partial closure (as discussed above) or from a model
with partial closure to a model with an enriched partial closure. The
central idea, here, is that part of the situation described by the initial
can
be described by a set of organizational features that are, at least to some extent,
known to be generic, i.e., common to several organisms sharing the initial
hybrid identity. Accordingly, these features could be explicitly integrated
into a new model determining a more restrictive hybrid identity formally,
. The
latter may exclude some concrete organisms which were previously included by
. The choice
between
and
ultimately depends on the specific epistemological, experimental, and modeling
objectives pursued. For example, the constraints involved in cellular respiration are
mostly generic in the sense of being relatively common to, say, all mammals and,
therefore, could be left implicit in models focusing on other aspects unless
the model is explicitly aiming at providing a relational characterization of
oxygen transport. Formally, there are two ways to link the initial diagram
and the
new one
.
If we use
instead of
,
the diagram change corresponds to a change of identity. Alternatively, one may keep
the initial identity and justify the articulation between the constraints and
by the
subclass
describing a partial closure that includes the constraints explicit in
. In this case,
is complemented by a
special case,
, that justifies
the articulation between
and constraints in
.
This justification does not guarantee that the constraints under study are always functional
in
;
however, it guarantees that they are in some cases. We can thus see
as an ”organizational
type” of
, and write
this concept as
.
In a given situation, when the constraints involved are largely conserved, we can argue
that
is representative of most cases, then other situations will be exceptions.
In the second case, we postulate that some aspects of
are
equivalent to aspects explicitly described in relational terms. The underlying hypothesis
is that a constraint may have a single generic effect on a class of processes having
different roles in the organizational diagrams. For example, cell membranes constrain
the diffusion of a broad class of molecules similarly, or ribosomes constrain the
translation of most RNAm similarly. In particular, a constraint can act in the same,
generic manner on a process contributing to the partial closure and have an effect on
in
the global closure. Figure 3b somehow captures this situation: constraint
acts on the process
maintaining
and on
a process acting on
.
The critical point is that the way such a constraint acts does not require
us to specify the process constrained; instead, this process just needs
to be in the target class, and we need to assume that maintaining
requires such processes — a valid assumption for the membrane and the ribosomes.
Let us take another biological example. In a mammal, the constraints involved in
oxygen transport (among others, and roughly speaking, those of the vascular systems
and the lungs) lead to oxygen distribution to all organism’s cells. Cells depending on
oxygen distribution include those of the vascular systems and the lungs themselves,
which allows drawing a partial closure among them. Moreover, we can safely claim
that almost all other cells in the organisms depend on these constraints. This claim
justifies the assumption that the constraints are also involved in the global
closure[8].
The way this dependence is materialized is, however, extremely diverse because oxygen,
and respiration, enable cells and organisms to perform all kinds of processes: there is
a generic dependence on respiration. Under the assumption that the constraints involved
in respiration are generic, a theoretical connection can, therefore, be established between
and
the relational description (which can include or not an explicit partial closure)
without needing an explicit relational description of the purportedly relevant aspects
of
.
The third case refers to a situation in which, although
could be ”unpacked,” as discussed above, the resulting organizational model
would be extremely specific, and therefore unfit to sustain generalization
and reproducibility. In other words, the transition from an initial diagram
to a
new, more complex one would tend to make specific relational aspects explicit rather
than generic ones. As a result, the identity class would become extremely restrictive,
and only a small subgroup of organisms (if not just one) would meet the criteria. For
example, the regulatory effects of thyroid hormones can be radically diverse, as
shown by examples like frog metamorphosis or mammal hibernation, among many
others. Trying to elaborate an organizational model which would include the various
effects of these hormones and, at the same time, would apply to a broad
group of organisms, would presumably be a dead-end initiative. In this case,
accommodates a diversity coming from past novelties that is irreducible to an
organizational model that would aim to generate an inclusive identity class. Let us call
the initial
diagram and
,
,
,..., other more specific diagrams where a relational closure is
explicit[9]. Then,
like in the previous case, one may choose to work with a different object, having a different
identity, say
.
Again like before, one may instead consider the
as organizational
types of
, written
. Then, we make explicit
that the constraints of
may be functional in a diversity of ways. The fact that organizational models
do
not possess an acceptable degree of generality does not imply that they have no
epistemological role. They increase biological knowledge by showing that specific
constraints can have functions in a given class, even though in a diversity of
ways.
The fourth and last case that we discuss here concerns the situation in which
includes intrinsically diachronic constraints. As such, these constraints may involve
novelties that have not appeared yet and whose nature may be unprestatable
(Longo et al., 2012; Montévil, 2019b). Consequently, these constraints
are only potentially functional in relational terms, and their position in the
organizational diagram can be assessed only ex-post. One notable example is the
”propulsive constraints” described by Miquel and Hwang (2016) following
previous analyses by Canguilhem (1972). Propulsive constraints promote the
appearance of novelties that are unpredictable and even unprestatable. For
example, the ”mutator system” is a regulation of the mutation rate of DNA
exerted by specific molecular constraints. Bacteria under stress can reduce
mutation corrections, which increases mutation rates and allows exploring new
organizational possibilities (Miquel and Hwang, 2016). The emerging capacities
and constraints can be functional, but the mutator system itself , as well as
other relational properties of the initial organization, do not specify the
features of these new constraints. As a result, the mutator system cannot be
located into an organizational diagram, insofar as its functional contribution
is unknown a priori. As for the previous case, we can use organizational
types to justify that the constraints of the mutator system are functional
, with
. However,
there are two critical differences with the previous case. First, the organizational types
are not at the same time point. Second, it is not possible to avoid using types and only
study
because the latter does not make the function of the propulsive constraints explicit.
The fact that the mutator system cannot be included in a general organizational
model does not imply that relational descriptions are not useful. In all those
cases in which the increased rate of mutations triggers the emergence of
functional changes in organisms, specific organizational models can account for
the new functional role, and therefore justify the function of the mutator
constraints.
The integration of
within organizational models covers a variety of situations. Following the specific
scientific objectives and depending on the available knowledge, the relational
part of the diagram can be more or less detailed, and generate more or less
restrictive hybrid classes of identity (together with the genealogical control on
). Yet,
it is worth underscoring that, as we discussed in section 2.2, we maintain that an
organizational description is never complete (be it for contingent or principled
reasons), which means that whatever model of an organism does include
.
Organisms’ historical identity possesses irreducibility that cannot be captured by any
given organizational model.
By characterizing the identity of organisms for modeling
and experimental practices, organizational diagrams integrating
can also
represent a typical experiment. Before concluding this section, let us have a brief look at
this application of the framework (Figure 4). In a a typical experiment, several organisms
(
,
,
and
)
are candidates as a support to enquiry on the properties of some target
relational capacities and features (represented in Figure 4 as the constraints
-
).
Each organism is characterized by a diagram including both the constraints under scrutiny and
the symbol
.
Being the offspring of the same common ancestor, specimens
,
,
share the
same
(i.e.,
)
and are therefore genealogically identical. Moreover,
and
also
share the same relational description of the target functional constraints. Consequently,
and
share
the same hybrid identity as defined by the model, and they can be tentatively defined
as two instances of the same experimental object. In contrast, specimen
does not share the same identity because it exhibits significant
variations in its relational description: despite having the same
than its relatives, its relational difference breaks the criteria
for membership in this specific hybrid identity class. Specimen
,
in turn, shares the same relational description than
and
with respect to the target constraints, but it does not share the same
genealogical connection with the past. This difference excludes it
from the same identity class (for opposite reasons when compared to
).
Although this case may seem paradoxical since it looks identical in relational
terms, its exclusion from the identity class is theoretically justified precisely
because historical identity is taken into account: accordingly, a different
may,
and will, carry hidden differences.
Figure 4:Theoretical representation of a typical experiment. Top:
is a specimen that is a common ancestor to the organisms studied in
the experiment. This specimen may be identified, or its existence may
be theoretical, in which case another particular serves as a reference,
like in systematics. Accordingly, the existence of the specific constraints,
,
for this specimen may be an empirical observation or a hypothesis.
Bottom: several specimens are generated, possibly after multiple
generations. Their genealogical identity (including their context)
is considered equivalent; therefore, we use a single symbol,
.
and
have the same hybrid identity because both their
genealogical and relational components coincide. Of course,
if we were to investigate other aspects accommodated by
,
we would find qualitative differences between these two specimens:
is defined genealogically and is compatible
with such variations. In the case of specimen
,
the variations lead to a change in the constraints described; here,
becomes ,
and there is a new constraint .
As a result, this specimen escapes the relational part of the hybrid identity class
of
and .
Note that, for ,
the symbol
remains the same as for
and
because the genealogical identity remains the same. If a biologist wants
to investigate the nature of the variations leading to the change of
constraints observed, then other constraints have to be made explicit.
This operation would lead to a different definition of the class of
.
Last,
possesses a different .
The corresponding constraints may be analogous, or
may correspond to a different strain or species where the constraints described
are homologies. Consequently, it does not belong to the same identity class of
and ,
but the reason is contrary than for .
Overall, the diagrams represented in Figure 3 and 4 build hybrid identity classes of
organisms. In a nutshell, a hybrid identity class integrates genealogical aspects represented
by
and relational ones represented by all the constraints. Organisms may violate the
relational description in time, which is why the hybrid identity is also bounded. In
some cases, as mentioned, the proper justification of such diagrams requires the use
of organizational types, which are more restrictive classes than the initial
one.
4 Conclusions
Biological organisms are a very peculiar kind of natural systems. They are familiar to
us and, at the same time, resistant to a comprehensive scientific understanding. As
claimed in the Introduction, they are complex objects.
The characterization of organisms’ identity faces their complexity. It is a
notoriously difficult task to tell whether a group of organisms that look similar at
first sight does not hide substantial differences, which may be revealed after
in-depth scrutiny. Similarly, it is difficult to make explicit the conditions at
which it is legitimate to claim that an organism remains the same over time.
Despite these challenges, a workable notion of organisms’ identity is required,
because of its pivotal role in grounding generalization and reproducibility in
science.
In this paper, we have discussed the strengths and weaknesses of two broad
conceptions on identity. The genealogical conception builds identity classes by
reference to the past, especially by linking individual organisms to a common
ancestor. Experimental biologists routinely use this strategy to work on
hypothetically equivalent organisms. While it tends to work, genealogical identity
does not provide its conditions of validity for experimental purposes. The relational
conception, in turn, defines identity by referring to a set of relations possessed by
individual organisms. While its conditions of validity are explicit, it faces the
widespread problem of biological variability.
To overcome this situation, we have put forward a hybrid conception of
organisms’ identity. We have argued that the identity of biological organisms should
be construed by integrating both genealogical and relational conceptions. In short, we
suggest that individual organisms belong to the same identity class when they share
the same specific organization of functional constraints and they are the
offspring of the same close common ancestor. The two poles of the definition are
complementary, in the sense that they provide mutual support and contribute
to filling in their reciprocal gaps. The genealogical conception provides an
operational procedure to subsume whole organisms to the same identity class, even
though no complete relational description is available; in turn, the relational
conception – in particular in its organizational version, that we adopt –
provides a theoretical justification of the implicit hypotheses underlying
the genealogical one. In the last section, we have provided a preliminary
formal representation of biological hybrid identity, by introducing a symbol,
,
that accommodates the contribution of the genealogical conception of
identity, within an organizational description of an organism. The formal
representation of history within a relational diagram is a stimulating
challenge that future studies should take up. Our discussion suggested that
allows
describing different possible connections between the historical and organizational
dimensions of organisms, as well as their implications for experimental and modeling
practices.
Even though the hybrid definition of identity was deemed to be useful and fecund
in the biological domain, we have also underscored that the validity of identity classes
cannot be but limited in time. Because of their inherent tendency to vary, individual
organisms that meet the criteria of an identity class at some moment may contravene
these criteria as time passes, and their offspring will presumably do the same after
some generations. Therefore, organisms’ identity is not only hybrid but also bounded:
both aspects draw a fundamental difference between biology and other natural
sciences.
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∗Maël Montévil and Matteo Mossio. “The identity of organisms in scientific
practice: integrating historical and relational conceptions.” Frontiers in physiology.
doi: 10.3389/fphys.2020.00611.
1By contrast, properties that do not stem from relations are arbitrary. For example, in
classical mechanics, both stillness and uniform movement correspond to no force, thus ultimately to
the same situation. In Galilean relativity, the difference between the two situations stems only from
the arbitrary choice of a reference frame; choosing a different reference frame can transform the
stillness of an object into uniform motion.
2Current debates in physics concern the alternative between the possible use of absolute
concepts (such as the absolute time of Newton) or the adoption of a purely relational epistemology.
However, both positions acknowledge that physics relies mostly on a relational conception (Huggett
and Hoefer, 2018).
3A full-fledged discussion of constraints identity goes beyond the scope of this paper. As
detailed in Montévil and Mossio (2015), the formal definition of constraints appeals to
conserved properties, which enable them to produce a causal effect on a target process.
A precise characterization of their identity should, therefore, take into account these
aspects.
4Let us mention that the issue is complex since mathematical descriptions, especially
equations, precisely subsume a diversity of situations under the umbrella of a single mathematical
frame. As a result, different views coexist. Two systems may be considered different on quantitative
bases, either by their states (different positions) or their parameters (different mass). On the
opposite, they may also be different if the overall equation representing them is different. Last, there
are situations in between. For example, physical morphogenesis or bifurcation are situations where a
change of state corresponds to a qualitative change of the trajectory or structure of the
object.
5The idea behind genealogical proximity can be understood from a more general perspective
in terms of symmetrizations (Montévil, 2019a). Symmetrization refers to all methods
adopted to handle the historicity of living organisms, so as to make them tentatively
identical, and to enable biologists to perform reproducible experiments. In addition to
genealogical strategies, biologists can also apply symmetrization procedures to organisms
that are not genealogically close, as, for instance, the fact of considering the allometric
relationships among mammals, choose experimental conditions that reduce the effects of their
diversity.
6There are several theoretical scenarios in which such functionally significant variations can
appear. One possibility consists of a significant geometrical change (as neovasculogenesis in the case
of the vascular system) or a mutation (in the case of DNA) affecting a constraint. There are other
scenarios, which include more general changes of organization (Montévil, 2019b), or the
accumulation of small variations generating a massive and irreversible change. In all these situations,
and under the hypothesis that they are not lethal, variations would induce a shift toward a different
functional regime.
7The necessity of this justification makes a principled difference from biophysical
relational models discussed above. While the latter can focus on some local constraints or
constraints dependencies and could acknowledge that, ”somehow,” these local phenomena
are connected to the global organization, organizational models cannot focus on local
phenomena if they cannot exhibit and justify the connection between the parts and the
whole.
8Note that we write that ”almost” all other cells depend on oxygen transport.
refers
here to the historical identity of organisms (they are mammals), and, as discussed, it can
include variations. In cancers, for example, cells switch to the glycolytic metabolism that
does not require oxygen, a phenomenon called ”the Warburg effect” (Vander Heiden
et al., 2009).
9Note that the genealogical specification of
may
also be more restrictive.
Today we discussed the paper “The Identity of Organisms in Scientific Practice: Integrating Historical and Relational Conceptions” by Maël Montévil and Matteo Mossio (published in @FrontPhysiol). Thanks to everyone for joining! www.frontiersin.org/articles/10.3389/fphys.2020.00611/full