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Theor. Exp. Plant Physiol.
https://doi.org/10.1007/s40626-024-00334-3
Return oftheorganism? The concept inplant biology, now
andthen
ÖzlemYilmaz
Received: 25 January 2024 / Accepted: 11 April 2024
© The Author(s) 2024
Abstract This essay argues for the importance of an
organismic perspective in plant biology and considers
some of its implications. These include an increased
attention to plant-environment interaction and an
emphasis on integrated approaches. Furthermore,
this essay contextualizes the increased emphasis on
the concept of organism in recent years and places
the concept in a longer history. Recent developments
in biology and worsening environmental crises have
led researchers to study plant responses to chang-
ing environments with whole plant approaches that
situate plants in their environments, emphasizing the
intricate and dynamic interaction between them. This
renewed attention to the organism recalls the debates
of the early twentieth century, when organicism was
one of the three main frameworks in biology (along
with vitalism and mechanism). Some scholars see this
renewed importance today as a “return” of this ear-
lier period. This essay argues that including insights
from plant biology will benefit philosophy of biol-
ogy research that examines the concept of organ-
ism and organicism now and in earlier periods. A
comprehensive account of the concept of organism
should involve a botanical conception of the organ-
ism as well as a zoological one (which is more fre-
quently considered). Although this essay does not aim
to present a conceptual analysis, it presents examples
of how an organismic perspective can be useful for
understanding concepts (such as phenotype, stress,
etc.) and research processes (such as experiment set-
ups, data processes, etc.) in plant biology. Philosophy
of biology investigations that aim at a comprehensive
understanding of the concept of organism can benefit
greatly from examinations of cases in plant biology,
both now and in the past.
Keywords Organism· Organismic perspective·
Phenotype· Integrated approach· Plant organism
1 Introduction
Biology is a discipline that investigates organisms.
This alone makes philosophical inquiries on the con-
cept of organism valuable and helps explain its endur-
ing appeal to philosophers and historians of science.
This brief essay aims to contribute to this extensive
literature via its two arguments: first, it will argue for
an organismic perspective for plant biology, which
has entered the twenty-first century as a broad dis-
cipline with many new priorities in addition to its
never-ending curiosity about plant life. Second, it
will argue that philosophy of biology needs to look
into the history of plant science for a more compre-
hensive understanding of organicism and the con-
cept of organism. Both organism and organicism
have a history; they change over time through their
Ö.Yilmaz(*)
Egenis, Centre fortheStudy ofLife Sciences, University
ofExeter, Exeter, DevonEX44PJ, UK
e-mail: [email protected]
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interactions with other concepts and scientific, politi-
cal, sociological, and economic processes. Organi-
cism is a philosophy in biology that emphasizes the
concept of organism—i.e., an integrated whole—as
a fundamental explanatory concept in biology and it
defends the distinction of biology from physics and/
or chemistry.1 Biology has its own methodologies and
theoretical frameworks that are required to investi-
gate organisms, which are living systems maintaining
their stability through their active interaction with the
environment (Allen 2005; Nicholson 2014; Nicholson
and Gawne 2015; Baedke 2019). Although organisms
have connected and coordinated parts (which can also
be analysed separately), investigating the organism
requires integrated approaches.
In order to discuss the two arguments, I will con-
sider (in section two) how organismic perspectives
that do not exclude operative mechanism (or explana-
tory mechanism) seem to be prevalent in today’s plant
science. I will argue that such organismic perspectives
can be helpful for philosophical work on concepts and
research processes in plant biology. Biology, while
investigating organisms, looks into mechanisms: how
a system’s parts work together. Biologists investigate
complex networks of mechanisms at different levels.
They investigate in detail how tiny molecules can be
part of mechanisms in the smallest organelles; how
these mechanisms connect to mechanisms in other
organelles and the cytoplasm of the cell; and how all
these connect to mechanisms between cells, in the
tissues, and on other levels. Biology aims to produce
more and more detailed descriptions and explanations
of all the components of the complex processes of
organism system. The methodologies and theories of
such investigations are mechanistic approaches. Here,
however, I would like to point out a crucial distinc-
tion, following Allen (2005), between operative and
philosophical mechanism. While the first is a wide-
spread epistemological approach in biology, the sec-
ond takes the ontological position that organisms are
complex machines. Philosophical mechanism, which
is closely connected with reductionist approaches,
was especially widespread during the second half of
the twentieth century. Organisms in philosophical
mechanism are thought be no different than complex
machines. This thought entails ignoring crucial differ-
ences such as organisms being self-organised while
machines are not, or the dependence of an organism’s
parts on the whole while a machine’s parts are inde-
pendent (Nicholson 2013).2
Although today’s biology uses “mechanisms”
widely, I would argue that this approach is mostly
operative/explanatory mechanism, which uses the
concept of organism (rather than “organisms as
machines”) as its central concept.3 Section two will
show the centrality of the organism concept in plant
biology, and argue that this centrality can be observed
via the rising emphasises on organism-environment
interaction as well as systemic, integrated, and whole
plant approaches. I will also note how these trends
have risen hand-in-hand with advancements in plant
science research programs and growing global envi-
ronmental problems. This essay does not examine the
operative/explanatory mechanism in biology, which
is clearly present, useful, and widely examined (e.g.
Machamer etal. 2000; Allen 2005; Bich and Bech-
tel 2021). I will only hint at how these organicist
approaches are intertwined with operative/explana-
tory mechanism.
While many contemporary historians and philoso-
phers of biology have worked on organicism in biol-
ogy, there are very few works that focus in this regard
on plant biology.4 Plant biologists are only mentioned
once in a while. Yet a focus on plants is necessary in
history and philosophy of biology research that exam-
ines the concept of organism. Despite important com-
monalities, plant organisms and animal organisms are
different. In fact, I agree with Gerber and Hiernaux
(2022) that “even the general idea of an ‘organism’
is problematic in its application to plants and should
1 For a detailed discussion of organicism as well as mecha-
nism and vitalism, see Allen (2005), for example.
2 See Nicholson (2013) for a detailed discussion of differences
between organisms and machines.
3 This essay examines the concept of organism since the early
twentieth century (for a discussion of the concept and its trans-
formations in earlier periods, see for example, Cheung (2010)
which gives a lot of space for plants too).
4 Examples of works that focus on plants in philosophy of
biology include Gerber and Hiernaux’s (2022) historical analy-
sis of the “plants as machines” thesis; Clarke’s (2012) and Ger-
ber’s (2018) examinations of plant individuality, which have
connections with the concept of organism. Also, while not
specifically focusing on plants, Pradeu (2010) mentions plants’
immunological responses with several examples in his work on
the concept of organism.
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be revised.” For example, while most animals have
a centrally controlled neural network, plants have no
neurons or brains; instead, they have a distributed
system including their xylem and phloem to trans-
fer molecules necessary for their whole control. Or,
another striking example: while most animals are
unitary, plants are modular and clonal.5 Such differ-
ences are the subject of many debates in past decades
on topics including plant cognition6 and plant indi-
viduality,7 which are both connected to the concept of
organism.
In the section three, I will place this organismic
perspective in an historical context. In the twenty-first
century, the importance of the concept of organism
has been a central concern in many works in philoso-
phy of biology and in biology.8 Some of these works
(e.g., Nicholson 2014) suggest that the centrality of
the concept marks a “return,” pointing back to debates
in the early twentieth century.9 Therefore, I will look
back to this period as well, considering the three main
frameworks of biology in the early twentieth cen-
tury (i.e., organicism, mechanism, and vitalism).10
In particular, I will look at organicism and the work
of Agnes Arber, whose writings provide an example
of organicism in this period. Her example highlights
perspectives that have been potentially overlooked
in scholarship on history of biology that focuses on
organicist movements. By drawing on examples from
plant biology like Arber, my account in this section
adds nuance to contemporary discussions on the con-
cept of organism.
Overall, this paper will emphasize the importance
of the concept of the organism in the twenty-first cen-
tury and “its return” from the early twentieth century,
when the concept was vigorously debated. Between
these two periods, the concept was not as prevalent
in biology. In the mid-twentieth century, accord-
ing to Nicholson (2014), “The epistemological focus
shifted to sub-organismic entities (like genes) on
the one hand, and to supra-organismic entities (like
populations) on the other.” Moreover, mechanistic
approaches (both operative and philosophical) with
their focus on the research of genes and molecules
became prevalent as they were thought to be the most
important means for understanding living entities.
It took several decades for the concept of organism
5 As I discuss in section two, we might also consider that
the ways human beings interact with plants are different than
human-animal interactions.
6 For debates on plant cognition, see Taiz etal. (2019), Calvo
etal. (2020), and Calvo and Segundo-Ortin (2023).
7 The “individual organism” is a crucial topic in debates on
individuality among philosophers of biology (e.g., Hull 1978;
Dupré and O’Malley 2009; Clarke 2012; Godfrey-Smith 2016;
Pradeu 2016; Gerber 2018). Although many scholars use the
terms “individual” and “organism” interchangeably (e.g.
Clarke 2012), other scholars argue that the notion of “biologi-
cal individual” is different from “organism,” as biological indi-
vidual can refer to entities that are not organisms—a gene, a
leaf, etc. (Pradeu 2016). Also, Pradeu (2016) argues that there
are different subcategories of biological individuals such as
evolutionary, physiological, and ecological. I discuss these
scholars’ work in another paper which focuses on plant physi-
ological individuality specifically (under-review paper, Yilmaz
and Dupré 2024).
8 E.g., El-Hani and Emmeche (2000), Ruiz-Mirazo et al.
(2000), Rehmann-Sutter (2000), Gutmann et al. (2000), Gil-
bert and Sarkar (2000), Callebaut etal. (2007), Kendig (2008),
Huneman and Wolfe (2010), Pradeu (2010), Nicholson (2014),
Nicholson and Gawne (2015), Sultan (2015), Soto et al.
(2016), Drack and Betz (2017), and Fábregas-Tejeda and Mar-
tín-Villuendas (2023). In addition, one of the most significant
international philosophy of biology societies (ISHPSSB, Inter-
national Society for History Philosophy and Social Studies
of Biology) had an open workshop on “Organism” at its 1999
meeting. The workshop discussed how attention in the field
had turned towards more integrated approaches in recent years
(Gutmann etal. 2000).
9 The state of plant biology in the second half of the twenti-
eth century—i.e., before the “return” of the organism—is also
an important topic (albeit one that this essay is not examining).
10 Though I briefly discuss vitalism in relation to organicism
and mechanism in the early twentieth century philosophy of
biology, I do not examine it extensively in this paper. In gen-
eral terms, vitalist framework “claimed that living organisms
defy description in purely physico-chemical terms, because
organisms possess some non- material, non-measurable forces
or directive agents that account for their complexity” Allen
(2005). In other words, organisms’ vital force cannot be inves-
tigated by science.
These years were characterized by the rise of molecular biol-
ogy and the dominance of mechanistic thinking in biology.
For this period too, it is crucial to look into plant biology and
specifically into different branches of plant biology as there
may be important differences. These differences may highlight
slightly different conceptual changes than those that occurred
in zoology and other branches of biology in terms of organ-
isms and environments. For example, controlling plants’ envi-
ronment has always been a crucial problem in plant research
and has a significant place in the history of plant biology.
Munns’s examination (2015) of plant physiology in the cold
war era and how phytotrons were developed illustrates this his-
tory. Another example is the whole-plant physiology perspec-
tive, which Lüttge (2012b) examines in the 1970s and 1980s.
Footnote 9 (continued)
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to regain its centrality as an explanatory concept.11
I hope that the arguments in the following two sec-
tions of this brief essay will be another step toward
a comprehensive understanding of the organism that
includes plant organisms as well.
2 Organismic perspective inplant biology
Before discussing the concept of plant organism, we
should look at plant science in the twenty-first cen-
tury and the world in which present-day plant scien-
tists find themselves. This context highlights the con-
ditions that have led scientists to give extra attention
to dynamic organism-environment interactions.
Today, we face major effects of environmental
changes on crop plants and plants in natural envi-
ronments. We are losing many of the world’s forests
and climate change is becoming drastic. These issues
create a challenge for plant science: the need to bet-
ter understand plant life, in order to better predict
plant responses to future environments. Here, ‘envi-
ronments’ is emphasized because climate change
does not just create separate factors (temperature
change, floods, droughts, etc.) for plants (or for any
other organisms) to respond to; rather, it affects the
multiple, intricate processes that collectively consti-
tute different environments in different locations of
the world. For example, imagine we are considering
a specific degree of rise in temperature and how this
may affect plants. This change in temperature can
affect different regions differently depending on many
other interacting factors, all of which, collectively, can
cause changes in the plants’ environments. A compre-
hensive project that is researching plants’ acclimation
and adaptation processes to high temperature will
most probably contain investigations related to plants’
drought response, high light response, high concen-
tration of carbon dioxide response, various nutrient
deficiencies, interaction with the soil and microbiota
(which are, simultaneously, facing the changes under
investigation), and the interactive effects of all these
factors on the plants. And, moreover, since plants will
interact with environments that have different com-
binations of degrees of these factors, the observed or
measured phenotypic traits will be not only specific
for the particular plant that is under investigation (its
genome, epigenome, development, and physiology)
but also specific for the particular experimental con-
ditions (i.e., its particular environment—or particular
“field” (Leonelli and Williamson 2022), or “location”
(Taylor 2012)).12
This dynamic interaction is always found between
an organism—for the purposes of this paper, a
plant—and its environment. Organisms organise
themselves through this interaction. They continu-
ously sense their environment and organize them-
selves according to signal transduction pathways
initiated by environmental cues. By responding to
environmental signals, plants constantly regulate their
metabolic and developmental processes and thereby
maintain their stability. For example, they may begin
to produce more or less of certain hormones, or they
may increase or decrease their photosynthetic activ-
ity, or they may open or close their stomata, etc. This
constant and dynamic interaction is necessary for the
continued existence (i.e., life) of the organism. Every
phenotypic trait that is measured or observed occurs
through this interaction. The phenotypic traits, or
“phenomes” (which is the more precise term if we
are talking about a particular individual organism),
belong to certain temporal points or periods of the
organism’s life-time.13
11 See Nicholson (2014) for a more extensive explanation for
the “return of the organism.”
12 I discuss the connection between phenome occurrences and
particular conditions in an earlier work focused on causation
and explanation in plant research (Yilmaz 2017).
13 Plant phenomes can be any features or traits of plants (other
than their genomes), which attract the attention of investigat-
ing humans. These investigations can focus on any level of
the organisation, from the electron microscopy images of the
membranes of the tiniest organelles to satellite images show-
ing plant communities. The definitions of phenotype, phenome,
and phenomics are important to consider, and many research
and review papers in plant science include definitions of these
concepts to clarify how they are used in their work. For exam-
ple, phenotype, according to the Stanford Encyclopedia of
Philosophy, “is the descriptor of the phenome, the manifest
physical properties of the organism, its physiology, morphol-
ogy and behavior” (Taylor and Lewontin 2017). Nicotra etal.
(2010) define it as, “The appearance or characteristics of an
organism resulting from both genetic and environmental influ-
ences.” Phenome, according to Furbank and Tester (2011) is,
“The expression of the genome as traits in a given environ-
ment,” and plant phenomics is “the quantitative measurement
of these traits in high throughput and high resolution” (Fur-
bank etal. 2019). In addition to these examples, Arnold etal.’s
paper on phenotypic plasticity contains a helpful glossary box
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A phenotypic trait of a plant that we observe at a
point of time is actually a continuous process, con-
tinuously being built up on previous processes. Plant
scientists always pay attention to many details related
to controlling the conditions in the experiment set-
tings because they know that the phenotypic trait
in which they are interested is happening through a
complex plant-environment interaction (PxE), not
simply a genome-environment interaction. While
a plant’s genome has a crucial role in its phenome
occurrence, it is far from being the determinant of
phenome. As Lewontin and Levins (1997) write, an
organism’s development “is not an unfolding of an
internal autonomous program, but the consequence
of an interaction between the organism’s internal pat-
terns of response and its external milieu.” Nonethe-
less, in many experiment settings, where a particular
environmental parameter’s effect is being tested on a
particular phenotypic trait of a particular plant (with a
known genome) at a particular developmental stage,
it is convenient to think of phenome as “genome-
environment interaction” (GxE). This is how that data
is analysed (i.e., by showing genome-environment
interaction). However, it is important to appreciate
that the results are reported with a detailed, material-
methods section of experiment settings, which gives
attention to PxE. This material-method section is
important because the results are tied to it. In short,
plant phenome is considered as embedded in many
intricate processes in plant (plant organism)-environ-
ment interaction.
Since the plant phenome—i.e., the features of
a particular plant (other than its genome) that are
observed and measured—occurs dynamically through
complex plant-environment interaction, investiga-
tion of the phenome requires meticulous research on
many processes of plant development and plant-envi-
ronment interaction. As plant science is growing at a
great pace in an ever-changing world, there is always
need for analysis of its main concepts. These include
trait, phenotype, phenome, phenotypic plasticity,
stress, etc.14 Rethinking plant phenomes as belonging
to organisms necessitates more emphasis on plant-
environment interactions and the processual nature
of plants.15 Furthermore, an analysis of the concept
of phenome needs to consider not only interactions
with abiotic and biotic parameters in plants’ environ-
ment but also interactions with human beings. These
can include interactions such as research processes,
agricultural activities, and the management of various
kinds of lands and aquatic environments. The increas-
ing awareness of the complexity and dynamicity of
these intricate processes that collectively cause plant
phenome is one of the triggers of the rise of Plant
Phenomics research in recent decades.
Another important trigger, of course, is climate
change. Although plants are given only limited space
in the IPCC reports (e.g. “Land-Climate Interactions”
(2019) and “Ocean and Cryosphere” (2019)),16 one
of the main driving forces of current plant research
is the aim to understand plant responses to climate
change for the purposes of maintaining or increas-
ing crop yields and protecting natural environments.
Not surprisingly, many research and review papers
and commentaries in plant science journals start their
introductions by citing IPCC reports and noting the
possible future climate scenarios that they consider
in their experiment designs.17 Given the growing
recognition of the complexity and plasticity of plant
organisms, as well as of the increasing importance of
understanding plant phenomes in light of changing
weather systems, a multi-disciplinary research pro-
gram has arisen to explore plants using a variety of
techniques across a variety of experimental contexts.
14 In fact, regular reconsiderations of the concepts and
research processes in plant science are needed due to the
dynamic interactions within the plant science community, its
15 I follow Dupré’s processual account of philosophy (Dupré
2012; Dupré and Nicholson 2018), where the “processual
nature of plants” means that organisms and their environments
are constituted by intertwined processes. Even seemingly
“unchanging” biological entities that we measure or observe—
such as structures, organelles, and genes—are held stable
through intertwined processes. Furthermore, research pro-
grams and concepts are processes too since “everything flows.”
16 The authors of these reports: Jia et al. (2019) and Pörtner
etal. (2019).
17 E.g., Rustad (2006), Ainsworth etal. (2008), Nicotra etal.
(2010), Yilmaz et al. (2017), Hamann et al. (2021), Yamori
and Ghannoum (2022), and Simkin etal. (2023).
that notes, “The terms used to describe phenotypic plasticity
are numerous and frequently confused or confusing” (2019).
Footnote 13 (continued)
interactions with the public, and the advancements of research
methodologies and technologies.
Footnote 14 (continued)
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Plant phenomics is a broad research area that
involves many kinds of conventional and state-of-
the-art technologies and tools, and includes research
in growth chambers, greenhouses, open fields, and
natural environments. Today, in addition to the great
number of plant research groups that conduct experi-
ments in laboratories, greenhouses, and fields in
many regions around the world, there are also plant
phenomics facilities that have large-scale infrastruc-
ture for phenome research.18 Plant science consists of
researchers with various backgrounds including (but
not limited to) plant physiology, plant molecular biol-
ogy, forestry, plant ecology, plant genetics, chemistry,
physics, data science, and marine biology. This vari-
ety constitutes a rich research structure that is dynam-
ically growing and producing new interactions. More
than ever before, it is welcoming researchers from
social sciences and humanities including philoso-
phers, sociologists, and historians of plant science. It
is in this recent context that many plant scientists have
emphasized the importance of cross-disciplinary dia-
logues in research on plant phenomes, plant responses
to changing climate, and plant phenotypic plasticity
under climate change (e.g. Nicotra etal. 2010; Par-
mesan and Hanley 2015). This communication within
plant science can benefit from conceiving of plant life
as situated in the world—that is understanding plants
as organisms actively and dynamically interacting
with the environment (which includes humans). Such
an understanding can also benefit other disciplines
that have tight connections with plant science such as
geography, anthropology, and climate science.
Many of these advancements in plant science
have been accompanied by “Big Data.” They call for
a meticulous reconsideration of many processes in
plant research activities—“data journeys,” as Leonelli
(2016) describes them—including experiment set-
ups, sample productions, measurements, observation
activities, and the analysis, interpretation, storage,
share, and re-use of data. Examination of these activi-
ties can benefit from an organismic perspective. As
the number of plant databases rises, there are ongoing
efforts to constitute plant ontologies,19 which organise
plant information in accordance with FAIR principles
(i.e., findable, accessible, interoperable, and reusable
(Wilkinson etal. 2016; Arnaud et. al. 2020)) and in
a way that conveys relationships between ontology
terms, which are investigated under different knowl-
edge domains. These open sources are continuously
developed through the interactive efforts of many
collaborators. An example project is Planteome20 by
Plant Ontology Consortium (POC)21 in which plant
ontologies can be browsed under reference ontolo-
gies such as “Plant Trait Ontology,” “Plant Experi-
mental Conditions Ontology,” and “Plant Stress
Ontology” (POC; Bruskiewich etal. 2002; Ilic et al.
2007; Arnaud etal. 2020). The relationships between
the terms are “structured,” i.e. biologically accurate
(Bruskiewich etal. 2002). Each ontology term (also
referred to as “bioentity” and “data object”) is kept
and categorized in its specific relation to other terms.
These relationships reflect the biological organisa-
tion—which is to say, plant organism—and also the
source of the data (i.e., specific project references,
plant taxons, etc.). The organisation of biological
knowledge in such forms embodies an organismic
perspective, which distinguishes each mechanism (or
term) and places it in biological organisation. As this
and the examples discussed so far suggest, today’s
plant science gives significant attention to biological
organisation and the dynamicity and complexity of
plant-environment interaction. All these can be con-
nected to perspectives that have “organism” as a cen-
tral explanatory concept.
18 For example, the Australian Plant Phenomics Facility
(APPF), which was established in 2007, provides many green-
houses, chambers, and “smart houses,” which can be con-
trolled in many ways, providing constant monitoring of plant
growth and function. These facilities offer the possibility for
various kinds of experiment designs, which otherwise would
be very hard to conduct. Additionally, the APPF has many
sophisticated tools and instruments that allow phenotyping in
the field (e.g., drones; aircrafts that can perform hyperspectral
and thermal imaging; field-explorer vehicles that have many
sensors conducting non-destructive phenotyping; sensor net-
works, which are small stations in the field doing real-time
phenotyping; portable photosynthesis systems providing meas-
urements of photosynthetic activity related phenotypic traits).
APPF. Last accessed May 25, 2023. Available at: https:// www.
plant pheno mics. org. au/.
19 Here, “ontology” is understood as, “a classification meth-
odology for formalizing a subject’s knowledge in a structured
way (typically for consumption by an electronic database)”
(Bruskiewich etal. 2002).
20 https:// plant eome. org/ about.
21 Plant Ontology Consortium (POC): http:// www. plant ontol
ogy. org.
https:// wiki. plant ontol ogy. org/ index. php/ Main_ Page.
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The benefits of approaches that involve an organ-
ismic perspective (such as integrated and whole plant
approaches) become evident as we look further into
the plant organism and its organisation (i.e. plant
coordination through plant-environment interaction).
This interaction enables organisms to actively main-
tain their internal processes, which allow them to use
nutrients for their survival, growth, and reproduc-
tion. These internal processes are coordinated at the
organismal level. Through evolution, organisms have
acquired various ways of coordinating their bodies.
In the plant kingdom too, there are different ways of
coordination, each uniquely complex. Plants coor-
dinate their bodies via physiological processes that
enable them to maintain the stability of their internal
processes, produce systemic responses, and organ-
ize their interactions with their environments.22 This
coordination—which is to say systemic physiological
processes—represent the whole plant (i.e., organ-
ism). Through their physiological processes, plants
perceive environmental signals, transmit them in their
bodies, re-regulate certain processes according to
these transmissions, and produce responses (i.e., their
phenomes).
An example of this coordination can be seen in
the way that plants acquire minerals and water. If a
plant needs more of some minerals or water, the sink
strength of its roots rises, which means more pho-
tosynthates start to move towards the roots instead
of other parts of the plant (i.e., shoots, newly grow-
ing leaves, branches, etc.). Thanks to these sources,
roots can grow more and forage further in the soil for
water and mineral nutrients.23 They can also produce
and release specific molecules (i.e., various kinds
of root exudates24), thereby making mineral nutri-
ents more available for uptake. In many cases, they
can also change microbial communities around them
via their exudates, thereby improving their access to
mineral nutrients and other needs they have for their
development and protection. How much of these
sources can be directed towards roots depends not
only on roots’ sink strength but also on all the other
parts’ sink and source strengths (i.e., the rates of
production and the changing needs), which are inter-
acting through a complex web of many processes.
This means that while it has parts such as shoots
and roots, a plant is a coordinated whole. The whole
plant actively maintains a stable source-sink balance
through its physiological processes, which are tightly
connected to its environment.
Plant modularity does not conflict with this whole
plant coordination. Plants are modular organisms,
meaning that they have modules with meristem tis-
sues. (Here, however, I do not use the term module in
a general meaning, rather I use “module” as meaning
“a self-reproducing and semi-autonomous unit that is
iterated to make up a larger unit or colony” (Clarke
2012)).25 Because of their meristem tissue, each
module has the capacity to produce any part of the
plant or even a whole new plant if it gets separated. In
some cases, they can produce a new plant even with-
out getting separated—i.e., a new ramet. As long as
modules are connected, however, they collectively act
as a whole, e.g., maintaining a source-sink balance or
producing systemic stress responses as described in
this section. This collective action at the whole organ-
ism level is more than a “collection of modules,”
because the whole is more than its parts, since at each
level of organization, there is emergence. “Emergence
is the inevitable unfolding of new functions and struc-
tures of a system on a higher scalar integrative level”
(Lüttge (2012a). Because of emergence, properties on
a level of organization cannot be reduced to proper-
ties of lower levels. As Souza etal. (2016a) empha-
size in their paper on irreducibility in biological
systems in the case of plant ecophysiology, “the key
aspect in emerging phenomena lies in the interactions
between the components of the system.”
22 I have previously discussed plant coordination through
source-sink balance regulations in connection to its impor-
tance in terms of both plant physiological individuality (under-
review paper with John Dupré) and stigmergic coordination
and plant minimal cognition (Sims and Yilmaz 2023).
23 See Lynch (2022) for a recent discussion on root architec-
ture and allocation of carbon to root system.
24 See Badri and Vivanco (2009) for a discussion of regulation
and function of root exudates.
25 Many scholars argue that autonomy is an important aspect
of being an organism since organisms are self-organised
through their active interaction with environments (e.g., Bae-
dke 2019). Modules, however, should not be understood as
autonomous, but rather as semi-autonomous. Oborny (2019),
for example, illustrates “semi-autonomy” by describing how
“the ramet receives and/or sends some material from/to other
ramets, but can also take up some of the resources indepen-
dently of the others.”
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Another crucial aspect of whole plant coordina-
tion—i.e., organism—is a plant’s microbiota. Inves-
tigations of the roles that plant microbiota play in
plants’ physiological, evolutionary, developmental,
and ecological processes are a crucial part of inte-
grated approaches in plant science. The interactions
between plants and their microbiota have great effects
on many processes in plants and soil ecosystems.
Through their active interactions, plants and micro-
organisms organise their internal processes and affect
their environments and each other by competing, col-
laborating, etc. Many researchers who investigate
these interactions also emphasize the importance of
“holistic” perspectives for understanding plant life,
as plants cannot be considered as single entities since
they always live with their microbiota with which
they constitute the holobiont (Vandenkoornhuyse
etal. 2015). Holobiont constitutes an important topic
in biological individuality debates. These include dis-
cussions by Skillings (2016) on whether holobionts
are multi-species communities or integrated individu-
als, Gilbert and Tauber’s (2016) on the ecological
approach in immunology and the holobiont as being
continuously constructed through interactions, and
Suárez and Triviño (2019) on holobionts as emer-
gent individuals. While discussing holobiont further
would exceed the limits of this paper, I would like
to point out that integrated approaches investigating
plant life involve considering plant microbiota as a
crucial part of the plant organism. In fact, following
Dupré and O’Malley’s (2009) discussion of “associa-
tions of a variety of …lineage-forming entities” or
“interactors,” we can think of holobionts as “complex
systems involving the collaboration of many highly
diverse lineage-forming entities …the most funda-
mental unit of selection” (Dupré and O’Malley 2009).
Stress is a process where whole-plant-coordination
can be clearly observed. Moreover, stress is a plant-
life phenomenon that requires an organism-centred
stance to grasp. When plants face stress, there is a
stressor stimulus (or stimuli) in their particular envi-
ronment. These stimuli—which can be biotic (e.g.,
some species of bacteria, fungi, etc.) and/or abiotic
(e.g., drought, high or low temperature, high light,
etc.)—are not like daily or seasonal changes and they
cause much more “altered” phenomes. These altera-
tions may even be described as “injuries,” mean-
ing deteriorations in some parts of the plant’s body.
There is a degree of injury (or even death) in stressed
organisms depending on the resistance ability of the
individual organism to the stressor and the wider con-
text in which the organism encounters the stressor.
Investigating stress conditions like these requires
integrated approaches that consider different levels
of organisation. In comparing searches for a single
indicator with a cross-scale multivariate analysis, for
example, Bertolli et al. (2014) examine the impor-
tance of emergent properties in water stress and con-
clude that the multivariate analysis is “an appropriate
method for establishing models that will allow for a
systemic understanding of the complex interactions
between plants and their changing environment.”
Through stress-related physiological processes,
we can observe plants responding at the whole-plant
level even to local stimuli. Intervention by wounding,
for example, can result in rapid systemic responses in
plants. In their investigation of wounding responses,
Fichman and Mittler (2021) show that the wound-
ing of a single leaf in Arabidopsis thaliana plants
results in a rapid, systemic wave of reactive oxygen
species26 production in the whole plant along with a
change in redox concentrations. These responses can
be the cause of altered concentrations of metabolites
in tissues resulting in “an enhanced state of SAA
and SWR” (systemic acquired acclimation and sys-
temic wound response)27 (Fichman and Mittler 2021).
Phenotypic traits such as these, which are related
to stress responses, are processes that are nested in
many other processes in a plant. Therefore, it is cru-
cial to consider all the other processes carefully as
they may have both indirect and direct effects on the
stress responses. With this concern in mind, Forsman
(2015), for example, emphasizes a “whole organism”
rather than a “single trait” approach for “an increased
understanding of the roles of plasticity in the ecologi-
cal success of populations and species.”
These “whole organism” approaches in stress
physiology research clearly consider and examine
the organism in its relation to its environment and
26 ROS (reactive oxygen species) are signaling molecules in
organisms and they have important roles in many biological
processes such as growth and response to environmental stim-
uli.
27 Systemic acquired acclimation (SAA) and systemic wound
response (SWR) are both systemic states of plants responding
to environmental stimuli (Baxter etal. 2014; Fichman and Mit-
tler 2021).
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development. In doing so, some see them as returning
to conceptions of the organism from the early twen-
tieth-century. Sultan, for example, argues that “eco-
devo actually represents a return to the more holis-
tic approach to individual development embraced
by early twentieth-century researchers in embryol-
ogy and genetics” and, she continues, “in evolution-
ary biology too” (Sultan 2015).28 This assessment is
coherent with what contemporary philosophers such
as Nicholson (2014) have described in biology as “the
return of the organism.”
3 Organicism: now andthen
In the previous section, I briefly described some
aspects of contemporary plant biology, pointing to
several reasons why organismic perspectives are
becoming widespread (and needed) in plant research.
These reasons were: (1) the challenge of understand-
ing plant responses to changing environments (i.e.,
global environmental problems); (2) the greater atten-
tion to organism-environment interaction and the
increased tendency to use whole organism and inte-
grated approaches; and (3) developments in plant
science research programs, whose highly-developed,
fast-growing research infrastructures emphasize mul-
tidisciplinary approaches and entail “big data” pro-
duction. My aim was to direct the attention of phi-
losophers and historians of biology to aspects of plant
science that belong uniquely to plant biology and
plant organisms. I argue that, because of these unique
aspects, a comprehensive account of the concept
of organism and/or organicism should specifically
include an examination of plant biology in addition to
other branches of biology such as zoology (the branch
of biology to which philosophers most frequently
look). As this section suggests, our understanding of
organicism can also be aided by a consideration of the
rich history of plant biology, particularly its theoreti-
cal debates in the early twentieth century.
Biological thought has been profoundly influenced
by the three frameworks of organicism, mechanism,
and vitalism. Considering the rich history of biology
and natural philosophy, stretching back centuries, it
is no surprise that these frameworks themselves are
historical processes that interact with cultural, politi-
cal, and economic processes. As a consequence, each
contains a diversity of thought, and, from time to
time, can partially overlap. In the last century too, as
different branches of biology were taking shape, these
frameworks also interacted with each other. Many
contemporary philosophers of biology, who empha-
size the importance of organicism, point to the early
twentieth century as a crucial time when there was
intense discussion and debate about these frameworks
(e.g., Allen 2005; Nicholson 2014; Nicholson and
Gawne 2015; Baedke 2019). And yet, when we look
at these excellent works, we find little or no men-
tion of plant biology. For example, in Nicholson and
Gawne’s (2015) meticulous investigation of scholarly
interactions among organicists in the early twentieth
century, none of the scholars mentioned is a plant
biologist. Similarly, Baedke (2019) presents a useful
table listing the “Central Works on the Concept of the
Organism or Biological Individual, 1908–1945,” but
includes only two works on plants among the thirty-
five citations. As there were certainly plant biologists
engaging with these frameworks at the time, these
absences should prompt us to identify these individu-
als and look closely into their work. Considering their
use of these frameworks and their contributions to
the theoretical discussions of their era can contribute
to our understanding of organicism. Pursuing such
investigations requires us to look into the history of
plant biology.
The early twentieth century was characterized by
hectic political, cultural, and technological changes
including rapid industrialization, the mechanization
of daily life, World War I, and the turmoil of the inter-
war period. Likewise, during this time, biology went
through significant changes. Sub-branches emerged
and set their own methodological and theoretical
frameworks. Unsurprisingly, amid this ferment, sig-
nificant dichotomies emerged in plant biology includ-
ing physiology vs morphology, experimentalists vs
naturalists/taxonomists, physico-chemical processes
vs phylogeny and natural history. There were many
discussions around these branches of plant biol-
ogy and debates over concepts and methodologies.
Plant biologists read, followed, and discussed each
28 Other examples of contemporary plant biologists calling
for systems approaches, integrated approaches, and/or organis-
mic approaches in biology are Somerville etal. (2004), Lüttge
(2012a, b), Bertolli etal. (2014), Souza etal. (2016a, b).
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other’s work.29 Even between sub-branches that were
understood to be on opposite sides of these dichoto-
mies—or seen as inhabiting “incompatible ‘concep-
tual worlds’”30—there were collaborations leading to
important turns in plant biology. Hagen, for example,
considers several instances of these collaborations
and argues that, “without denying either the existence
or the significance of controversies among twentieth-
century biologists …the naturalist-versus-experimen-
talist dichotomy is an oversimplification” (Hagen
1984).
In the midst of this tumultuous time, plant biolo-
gists discussed methodologies, theories, concepts,
and the philosophical foundations of their research.
A striking example can be found in the writings of
Agnes Arber (1879–1960). Arber is known for her
meticulous collection of plant morphological data
and elaborated interpretation of this data in the light
of both biology and philosophy literature.31 Her inter-
pretation of plant morphology involves “the descrip-
tion and interpretation of the entire external and inter-
nal organization of the plant, from the beginning to
the end of its life-history” (Arber 1950). Her under-
standing of plant form expands from the Aristotelian
concept of form as “the whole of the intrinsic nature
of which any given individual was a manifestation,”
and as a “student of nature” herself, she considers the
“four causes as falling into two classes—the mechani-
cal and physico-chemical causes (material + efficient
causes), and the teleological causes (final + for-
mal causes)” (Arber 1950). This teleology that she
emphasizes is connected to “the urge to self-mainte-
nance.” In plant form, particularly, this self-mainte-
nance can be observed as repetitive branching since
each part of the plant at growing points has the urge
to be a whole plant.32 Intrinsic purposiveness and
organismic teleology, which are significant themes
in Arber’s work, are the sort of “recurring themes”
that Nicholson and Gawne (2015) argue “enable us
to legitimately speak of an ‘organicist school’ or an
‘organicist movement.’” In general, they highlight
early twentieth century biologists’ search for a “third
way,” avoiding mechanism and vitalism. More specif-
ically, they emphasize a shared focus on “the central-
ity of the organism concept in biological explanation;
…the importance of organization as a theoretical
principle; and …the defence of the autonomy of biol-
ogy” (Nicholson and Gawne 2015).
Arber’s position in relation to the mechanism-
vitalism-organicism debates of her time can be clearly
seen in much of her work. For example, in her 1933
paper “Floral anatomy and its morphological inter-
pretation,” she examines the work on vascular anat-
omy by many scholars (including both her mentor/
colleague, Ethel Sargant, and herself). Her unflinch-
ing critical stance throughout the paper is apparent
from the start, as she makes it clear that she will ques-
tion even widely accepted facts. While she touches
on multiple points in this article (not all of which are
relevant for the purpose of this essay), mentioning a
few can give a sense of her position in the philoso-
phy of biology debates of the early twentieth century.
She criticizes, for instance, the mystical approach of
Wilhelm Troll (1897–1978) for treating morphology
as unanalysable and unexplainable. She argues that,
“He puts aside ‘explanation,’ in the sense in which
that word is used in the exact sciences, and treats it as
having no place in morphology” (Arber 1933). Arber
thinks that “whole” or “unity” or “organism” is open
to scientific investigation, it is not “unanalysable,” as
vitalists argue.
While acknowledging the value of analysis, she
emphasizes the importance of reintegration after each
analysis, which reflects her critique of reductionist
approaches. She warns against “the habit of isolating
structural details and dealing with them, as it were, in
vacuo,” since all these are part of the plant organism.
Towards the end of the paper, her call for an organis-
mal standpoint becomes especially clear. In discuss-
ing work on development and heredity by marine
29 Tansley’s (1924) presidential address to the Botany Section
of the British Association for the Advancement of Science’s
is an excellent example of the discussions among different
sub-branches of plant biology and how plant biologists were
acknowledging the significance of each other’s work.
30 “Conceptual worlds” comes from Ernst Mayr’s “Prologue:
Some Thoughts on the History of the Evolutionary Synthesis”
(1980), as quoted in Hagen (1984).
31 For discussions of Arber’s life and the significance of her
work in both plant biology and the history of plant biology,
see Schmid and Stevenson (1976), Schmid (2001), Flannery
(2003), and Feola (2019).
32 She describes this as “partial-shoot theory of the leaf”
(Arber 1950).
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biologist Edward Stuart Russell,33 one of the scholars
in “organicist movement” of the early twentieth cen-
tury, she argues that his position:
…appears to be a much more reasonable one.
Though his sympathies are all with the “organ-
ismal” standpoint, which is essentially syn-
thetic, he is careful not to rule out analysis, pro-
vided it is invariably followed by reintegration.
His attitude offers—in theory, if not entirely
in practice—a sane compromise between the
exclusively analytical and the exclusively syn-
thetic positions. It is greatly to be wished that
someone would produce a treatment on broad
lines of the botanical conception of the organ-
ism, to balance and supplement Russell’s bril-
liant exposition, which is basically zoological.
(Arber 1933).
It should be recognized that Arber is emphasizing the
need for conceptions of the organism that are botani-
cal even as she was producing such a conception
herself.
Considering Arber’s critique towards both mecha-
nism and vitalism, her emphasis on a need for an
organismic understanding (i.e., a “the third way”),
and—as noted earlier—other recurring themes in her
work in general (i.e., intrinsic purposiveness, organis-
mic teleology, whole plant), she can clearly be under-
stood as a participant in the organicist movement of
her time. Her insights should be considered as we
seek to develop a better understanding of that move-
ment’s history.
4 Conclusion
The concept of organism is crucial for plant biology.
It is also crucial for philosophy of biology, whose
frameworks of organicism, mechanism, and vital-
ism can be better understood through more exten-
sive engagement with the history of plant biology.
An organismic framework can be helpful not only
for conceptual analysis in plant biology, but also for
understanding various processes in plant research,
including organism selection, experiment set-ups, and
data processes. Today, plant scientists still use mecha-
nisms extensively. At the same time, they treat these
mechanisms as processes happening in plant organ-
isms that are interacting with their environments
dynamically and intricately. As I have shown in this
essay, there is much to be learned from the botanical
conception of the organism and the interactions of
different plant science branches, both today and in the
past century. This paper, however brief, is a step in
that direction.
Plant science is a broad discipline with differ-
ent branches. Each has its own research questions
and methodologies, which may entail slightly dif-
ferent conceptualizations of various aspects of plant
life. Even though many research questions require an
integrated view of plants—which means comprehen-
sive studies that simultaneously look into multiple
aspects of plant life (including physiology, evolution,
development, ecology, genetics, etc.)—each branch
still keeps its own research agendas. Moreover, these
branches involve not only specialized plant scientists
but also researchers with other backgrounds. While
this paper has not aimed to unify plant science, I
would nonetheless like to remind and emphasize that,
overall, we need a unified concept of plants. I argue
that the concept of plant organism can help us con-
nect and integrate different branches when needed.
The plant organism concept always requires us to
consider plant life in its context—that is, plant organ-
isms in their environments and the dynamic and intri-
cate interactions between them.
I would like to finish this essay by quoting two plant
biologists, one from today and one from the early twen-
tieth century, both of whom emphasize the importance
of an integrated approach in plant biology. While Arthur
Tansley, the early twentieth century scholar, empha-
sizes the importance of coordination between branches
and, overall, a “unified notion of the subject,” especially
in botany education, he still acknowledges the separated
research agendas and practices of branches in his time;
more recently, however, Sonia Sultan has argued for
the importance of integration in the research programs.
Maybe we can read this difference as a development in
science. While a century ago, integration was more a
theoretical understanding than a practical one, today
it can be both equally. Maybe today’s plant science
technology and knowledge can enable an integrated
approach more easily than those of a century ago could
for examining the plant organism—that is, the complex
33 Here, Arber is discussing Russell’s book The Interpretation
of Development and Heredity (1930).
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plant environment interaction and its implications for
plants, environments, and their evolution.
Sultan (2015) argues that, “An organism–environ-
ment research program will, of necessity, integrate stud-
ies of gene expression and developmental pathways,
ecological conditions, and evolutionary trajectories, in
ways that promise to illuminate and enrich these for-
merly separate disciplines.” This call for an integration
of disciplines can be especially important in education.
Moreover, it resonates with Arthur Tansley’s emphasis
on the “unified notion of the subject” (botany), a hun-
dred years ago. In his presidential address to the Botany
Section of the British Association for the Advancement
of Science, Tansley cautioned that:
…if botany, as the science of plants, is to retain
any meaning as a whole, somebody must retain
the power of looking at it as a whole. And if, as
teachers, we fail to keep touch with the newer
developments, and are consequently no longer
able to focus the whole subject from a viewpoint
determined by current knowledge, this power will
come to be possessed by fewer and fewer bota-
nists, and the subject will definitely and finally
break up into a number of specialised and unco-
ordinated pursuits. (Tansley 1924).
Acknowledgements I would like to thank to following peo-
ple from the Egenis Research Exchange reading group for their
comments on the earlier version of this paper: John Dupré,
Sabina Leonelli, Adrian Currie, Rose Trappes, Hugh Wil-
liamson, Celso Neto, Elis Jones, Sophie Gerber, Ric Sims, and
Paola Castaño. I would like to thank the anonymous reviewers
for their comments. Also, I would like to thank Reuben Silver-
man for his feedback on the both earlier and later versions.
Funding This paper is a part of the Plant Phenome Project
that has received funding from the European Union’s Hori-
zon 2020 research and innovation programme under the Marie
Skłodowska-Curie Grant Agreement No: 833353.
Declarations
Conflict of interest The corresponding author states that
there is no conflict of interest.
Open Access This article is licensed under a Creative Com-
mons Attribution 4.0 International License, which permits
use, sharing, adaptation, distribution and reproduction in any
medium or format, as long as you give appropriate credit to the
original author(s) and the source, provide a link to the Crea-
tive Commons licence, and indicate if changes were made. The
images or other third party material in this article are included
in the article’s Creative Commons licence, unless indicated
otherwise in a credit line to the material. If material is not
included in the article’s Creative Commons licence and your
intended use is not permitted by statutory regulation or exceeds
the permitted use, you will need to obtain permission directly
from the copyright holder. To view a copy of this licence, visit
http://creativecommons.org/licenses/by/4.0/.
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