The Organism

                                                        The Cicada – Thopha saccata – Double Drummer
                                   Photograph: Roger Spencer, Ulladulla, New South Wales, Australia, 2017.

Biological Agency and the APS Framework: Toward a Unified Theory of Life

This website advances the gathering view of human minded agency as a highly elaborated instance of a more general phenomenon: biological agency. Human cognitive faculties—such as foresight, reasoning, language, and abstract thought—did not arise ex nihilo but emerged through evolutionary elaboration of agential capacities present in simpler life forms. What we call mind evolved from life, not apart from it.

Indeed, many of the capacities attributed to human cognition—learning, memory, decision-making, anticipation, preference, deception—are also observed in non-neural and non-sentient organisms, including plants, fungi, and bacteria. These behaviors are often described using terms that are anthropomorphic because they echo our own faculties. Philosophically, three characteristics treated a deeply and uniquely human can be grouped into three core cognitive domains: epistemology (knowledge, belief), ethics (values, goals), and logic (reasoning)—each is, however, a reflection of deeper biological processes.

The Agency–Process–Scale (APS) framework (Spencer, 2025) offers a theoretical synthesis that places biological agency at the center of our understanding of life. APS does not define life in terms of structural or compositional traits, but as a recursive, purposive organization of function across scale. It proposes that living systems are distinguished by their capacity to regulate, coordinate, and enact functional behaviors that serve the biological imperative: to persist, adapt, transform, and reproduce.

Where traditional theoretical biology often emphasizes mechanistic, hierarchical, bottom-up causation and phylogenetic classification, APS reframes life as a multiscale orchestration of purposive processes. It integrates insights from developmental biology, physiology, ecology, cognition, and evolutionary theory under a unified functional lens. Crucially, APS foregrounds functional equivalence: the idea that different structures or mechanisms can fulfill similar functions across different organisms or scales of organization. This principle allows cognition, for example, to be recognized in bacterial quorum sensing or root foraging behavior, not just in brains.

Three triadic conceptual structures help scaffold the APS framework:

Agency / Process / Scale: Life is understood as the dynamic interaction of agential systems, organized by recursive processes, across multiple nested scales.

Persistence / Inheritance / Transformation: These describe the temporal logic of life—organisms persist through time, inherit structures and behaviors, and transform through development and evolution.

Agent / Cognition / Behavior: These highlight the continuity between being (agency), knowing (cognition), and doing (behavior)—in all life forms, not just sentient ones.

This framing challenges the dominant view in biology that treats living systems as inert matter animated by selection. In that view, life is a result of historical sorting, and agency is often reserved for sentient beings. By contrast, APS treats agency as intrinsic to life at every scale, not as an emergent add-on. The biological imperative—the internal drive of organisms to persist and flourish—manifests through the continuous enactment of behavior, adaptation, and self-organization. From this perspective, matter is not merely acted upon by external forces but participates actively in organizing itself into living form.

In this view, consciousness and human cognition are not radical breaks from biology but its most complex instantiations. Rather than drawing hard boundaries between physics, life, mind, and culture, the APS framework sees these as nested, functionally continuous domains of organized activity, each emerging from and shaped by the demands of agency and context. Biological agency, then, is not only the defining feature of life—it is the foundation for a unified, processual theory of biology.

Related articles

This article is one of a series investigating a 'new biology' that gives full consideration to biological agency and its relationship to human agency. These articles are introduced in the article on biological explanation which considers the forward-looking biological explanatory emphasis on ends, goals, purposes, functions, and agency.  Much of the discussion revolves around the scientific appreciation and accommodation of real (genetically inherited) purposive (teleological, teleonomic) goal-directedness (agency) that is a universal distinguishing feature of life. The series also discusses the nature of biological classification and the way we classify 'everything' in our worldviews and modes of representation.

Human agency is a limited, conscious, and highly evolved form of biological agency. While it is currently conventional to treat biological agency as a human creation - the reading of human intention into nature - this website explores the claim that it was biological agency that gave rise to human bodies and human subjectivity - that, in this temporal sense, biological agency is prior to human agency.

The suite of articles exploring biological agency ranges across topics in theoretical biology and the philosophy of biology, including:

Processes - how biology is more concerned with process than structure or things.
Synthesis and analysis - the biological legacy of analytical reductionism.
What is life? - the crucial role of organisms and their agency agency in determining purpose, values, and what it is to be alive. How agency gives meaning to biological structures, processes, and behavior and must therefore take precedence in biological explanation.
Biological axiom - how this biological principle establishes the necessary behavioral (agential) conditions for all life as the universal, objective, and ultimate biological goals that give organisms - including their structures, processes, and behaviors - biological meaning.
Purpose - the history of the notion of purpose (teleology) including eight potential sources of purpose in biology.
Biological agency - as an account of the nature of biological agency.
Human-talk - the application of human terms, especially cognitive terms, to non-human organisms.
Being like-minded - the way our understanding of the minded agency of human intention is grounded in evolutionary characteristics inherited from biological agency.
Biological values - the grounding of biological values, including human morality, in goal-directed organismal behavioral propensities that express a universal behavioral orientation or perspective on existence (biological normativity).
Evolution of biological agency - the actual evolutionary emergence of human agency out of biological agency.
Plant sense, Plants make sense, and Plant intelligence addressing the rapidly developing research field of pre-cognitive agency in plants.
Biological hierarchy - the explanatory problem of levels, scales, and perspectives in biology.
The organism - the case for an organism-centered biology in which organisms as biological agents are the foundational functional units of biological organization.
Structures, processes, and behaviors - an introduction to biology that avoids the confusion of 'levels of existence'.

The biological axiom establishes the necessary behavioral (agential) conditions for all life. These are the universal, objective, and ultimate biological goals that give structures, processes, and behaviors biological meaning. Without at least an implicit understanding of these goals, biological explanations are an incoherent collection of unrelated facts so, in this sense, agency and function take explanatory precedence in biology. The structures, processes, and behaviors that make up the subject matter of biology may be compared in terms of both their structural-evolutionary history and functional equivalence.

The internal processing required to generate the organismal behavior summarized in the biological axiom can be conceptually framed as biological cognition. On this understanding human cognition^[8] is a species-specific and highly evolved form of biological cognition. Theoretical biology does not have a terminology to distinguish between structurally different but functionally equivalent forms of biological cognition. It therefore resorts to the terminology of human cognition (as cognitive metaphor). Though word meanings cannot be changed at will, in science it is possible to refine categories and concepts to better represent the world.^[73] 

Introduction

For much of the history of science, it was assumed that biology was the ‘study of organisms’ because these were the most evident expressions of life in our environment. While this did not exclude the study of organismal parts, communities, or other biological systems, the organism was generally treated as the unquestioned reference point—the presumed unit of biological description and explanation.

Curiously, and for historical reasons examined in this article, the rationale for treating organisms as foundational has rarely been made explicit, even in contemporary biology.

We recognize other organisms as alive not merely by their structure or composition, but through their patterned, directed activity—their agentive behavior. We intuitively perceive in them the same organizing aims that structure our own existence: the effort to maintain integrity, to persist across time, to buffer against destabilizing forces, to reproduce, and to continuously adjust to changing internal and external conditions. This mode of existence is most coherently understood today in terms of biological agency—understood as the capacity of living systems to initiate and sustain functional, goal-directed activity within their particular contexts.

While most evident in human deliberation and intentional action, agency is not confined to conscious or sentient organisms. It is distributed throughout the living world, from bacteria to flowering plants, as an emergent property of organized, processual systems operating across multiple scales. In this light, agency becomes the distinguishing feature that marks living from non-living systems—what makes even a bacterium or daffodil fundamentally different from a rock.

Beginning in the 18th century, biological inquiry expanded across both microscopic and macroscopic scales, delving into molecular components and ecological collectives. This shift in scale also marked a shift in emphasis—from organisms as wholes to their parts and environmental networks. With the rise of reductionist methodologies and the molecular revolution catalyzed by the discovery of the genetic code in the 1950s, organisms were increasingly regarded as secondary to genes and molecular mechanisms. In this context, the term “organism-centred biology” (OCB), introduced by Koonin and Wolf in 2000, served to reassert the importance of the organismal scale in biological explanation.

Is the organism returning to the center of biology? Within the APS framework, this question takes on renewed significance. Rather than privileging the organism per se, APS recognizes that agency is instantiated through dynamic, multiscale processes—many of which converge at the organismal level. The organism is not the sole locus of biological meaning, but it remains a critical node in the network of agentive processes that constitute life.

This article provides a concise historical account of changing ideas about organismal autonomy, purposiveness, and agency from the 19th century to the present. It includes original insights and reflections from historical figures and contemporary philosophers of biology, drawing primarily on the work of Baedke (2019), Baedke & Fábregas-Tejeda (2023), Baedke et al. (2024), Nicholson and Gawne (2015), and Fábregas-Tejeda (2024).

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Let me know if you’d like it shortened, further clarified, or adapted for a specific section of your paper.

Historical background

Early biology, up to and including the 19th century, was mostly a process of inventory: it was a listing, naming, and description of organisms and their parts – a stocktake of what there was in the world as a basis for the later exploration of other interests and possibilities within the field.

It was largely in the West that systematic scientific thinking had developed out of ancient Greek philosophy. By the end of the 18th century – after an Age of Discovery and Exploration, Enlightenment, and colonial expansion – the world’s boundaries were established by European navigators and a global biological stocktake of biota was well underway. European science looked beyond the local to the universal, establishing universal laws of physics and chemistry and, in biology, the universal system of biological inventory developed by Swedish naturalist Carl Linnaeus (1707-1778).

Biological science at this time was dominated by subjects like taxonomy, nomenclature, description, identification, and anatomy. Having established what there is, in the 19th century work began on determining how these things worked as physiology and developmental biology turned from the study of structures to an investigation of processes. With advances in technology in the 20th century there was a return to structures, but this time at the tiny molecular scale. It was now also possible for biology to expand from the micro to the macro scale of organisms in their totality through an ecology of living communities that would eventually encompass the biosphere.

In the late 20th century biology began to include another dimension, that of behavior and cognitive science as it became more concerned with the mind, brain, nervous system, and consciousness. Biology had now fragmented into many specialized academic disciplines that included, among others, genetics, ecology, evolution, ethology, and physiology, addressing biological structure, function, growth, origin, evolution, behavior, and distribution.

As biologists drilled ever deeper into the minutiae of life and expanded their biological perspective across the globe, research focus moved away from organisms themselves to the sub- and supra-organismic spheres. Now, viewing life from so many scales and perspectives, it was no longer obvious that organisms were at the center of biological things. Perhaps organisms are just one scale or level of biological organization that can be explained and understood from many contexts, so why should organisms be regarded as biologically privileged?

Science as a whole had moved away from the obvious – from the manifest image of our common sense, to a scientific image that revealed an underlying reality very different from the world of appearances.

So, by the 20th century individual organisms were no longer the focus of biological study and theoretical biology was advancing on many different fronts as the number of biological disciplines proliferated. The following is an extremely brief historical synopsis of what has become known as ‘organism-centered biology’.

Definition

Science requires an account, or definition, of what is meant by ‘organism’.

A definition aims to convey the intended meaning of a term in a clear, precise, and comprehensive manner. It considers the context in which the term is used, differentiates it from similar terms, and often provides examples to illustrate its application. Crucially, there are ideal classical terms for which necessary and sufficient conditions apply (e.g. gold is an element with atomic number 79), and fuzzy concepts, which can only articulate necessary conditions (e.g. terms such as beauty, truth, and justice). Fuzzy concepts tend to be more subjective and context-dependent, reflecting a possible diversity of interpretations.

Perspectival definitions might be: biological,  “a living entity that maintains homeostasis, is composed of one or more cells, carries genetic material, and has the ability to grow, reproduce, and adapt to its environment.“^[13]; ecological,  “an individual living entity that interacts with the biotic (living) and abiotic (non-living) components of its environment, influencing ecological systems and contributing to biodiversity.^[14]“; philosophical, “a complex system of interacting parts that exhibits properties of life, such as metabolism, growth, reproduction, and response to stimuli, distinguishing it from inanimate matter.”^[15]

Attempts at definition can learn from Aristotle’s four causes to understand why things exist or happen, and how they are explained. He aimed to provide a comprehensive understanding of objects and change not just in terms of what something is made of (material cause) but also what makes it what it is (formal cause). We think we have explained (definition) of something when we say what it is made of, or describe its unique structure, or design (form), the process or agent that brought it into existence, and its purpose or goal. Aristotle used these four causes to explain change and existence, not just ‘how’ (the processes involved) but also the ‘why’ (the underlying purpose and materials involved). These four approaches moved beyond detached observation and description to a deeper understanding of the ingredients of existence and nature of things. We should not regard this apparent philosophical obscurity as unproductive: it laid the groundwork for future philosophy, science, and ethics.

Specifically, something is an organism if the parts work together for the integrated whole, with high cooperation and low conflict. This means the organism is the largest unit of near-unanimous design. The ‘near’ is required because there can always be some conflict, even within the strongest examples of organisms, such as genetic conflicts within animals

Our understanding of an organism is grounded in its functionally integrated but autonomous agency.

‘An organism has parts that work together for the integrated whole, with high cooperation and low conflict. This means the organism is the largest unit of near-unanimous design. The ‘near’ is required because there can always be some conflict, even within the strongest examples of organisms, such as genetic conflicts within animals‘.^[12]

While life may be understood and explained from many perspectives, and at many scales it is most strongly expressed in the strength of autonomy and goal-directedness found in individual organisms – an individuality and independence that is functionally equivalent to a subject as a biologically cognitive ‘self’.

Organisms are physically bounded autonomous biological agents whole structures (such as cells and tissues), processes (such as metabolism and growth), and behaviors (such as movement and responses to stimuli) are functionally integrated and unified in the propensity to survive, reproduce, adapt (to both external and internal conditions), and evolve (biological axiom). Organisms are therefore the focus of biological study and, since they are goal-directed, biology must necessarily begin with an account of their goals. Without acknowledging the unified and goal-directed functional integration of structures, processes, and behaviors within organisms, biology becomes an incoherent collection of unrelated facts. This is why agency takes precedence over other factors like genes and cells.

Exceptions

Here it is argued that organisms demonstrate a degree of agential individuality that warrants their recognition as paradigmatic biological individuals – to the extent that every biological entity is either (a) an organism, (b) a part of an organism, or (c) a group of organisms – it is either an organism, sub-organismal, or supra-organismal.

Biology is notorious for its gradations and exceptions.

The prioritization of organisms in biology might be contested in the face of more general notions like ‘biological individuals’.^[16] More obvious are the many difficult cases that make the strict definition of ‘organism’ a contentious venture.

Viruses are composed of genetic material (RNA or DNA) surrounded by a protein coat but they  cannot reproduce or carry out metabolic processes independently and require a host cell to replicate; prions are misfolded proteins that can induce misfolding in other proteins – they lack genetic material and do not possess the characteristics of traditional organisms, but they can cause disease in host organisms; bacteria and Archaea as simple unicells but some bacteria can exist in a highly cooperative communal biofilms that hardly differentiate individual organisms from the collective; endosymbiotic organisms like some protists and lichens, exist as symbiotic combinations of different species; sometimes multicellular organisms lose the ability to survive independently (e.g., certain algae) are they single organisms or colonies of individual cells; some giant cells e.g. the syncytium formed from multiple cell fusions (e.g., skeletal muscle fibers) contain multiple nuclei yet function as a single unit; cells that harbor plasmids can exhibit behaviors and traits that are distinct from those of the host cell; hyphal fungi exist in the form of extensive networks made up of connected hyphae, which can blur the line between individual organisms and a single, large organism.

The presence of such exceptions, though complicating the logic of definition, is hardly surprising given the organizational variety expressed throughout the community of life. They do not challenge the utility and scientific applicability of the general concept of an organism. 

Organicism

The early 20th century, especially during the 20 interwar years of 1918–1939, was a time of increasing specialization and fragmentation when German-speaking and British biologists called for a revitalization of the foundations of theoretical biology.^[3,4,5,6,7]

This was the organicist movement, whose theoretical ideas, though later stifled by dramatic developments in microbiology in the mid-to-late 20th century, generated ideas that have resurfaced in the Extended Evolutionary Synthesis (EES)^[8,9,10] of the early 21st century. It was a program that lost momentum through lack of institutional support, the rise of molecular biology, ideas of the Modern Synthesis, and other factors in which the organism was no longer an ontological and theoretical challenge to be addressed by evolutionary theory (Walsh 2015).

Baedke & Fábregas-Tejeda (2023) draw attention to the organicist focus on the organism in three ways:

(1) the conceptualization of genes as parts in larger extracellular, organismal and developmental contexts, and the consideration of these contextual wholes in shaping evolutionary trajectories.

(2) the idea that evolution is the result of organism-environment reciprocal interaction (rather than of external environmental factors causing changes in allele frequencies and population dynamics)

(3) that organismal agency is a key explanatory component for understanding how organisms co-construct their evolution.

Organicists considered organisms as dynamic wholes, a unitary functional or dynamical process in which whole and parts are inextricably interconnected, that the whole and its parts are together the expression of the life of the individual. As expressed by German biologist Dürken in 1936 ‘[i]t should not be said that the organism as a whole is built up of parts, but that the organism, which is characterized through a consistent wholeness, develops parts and then, subsequently, has parts.”^[17] In a sense, the whole temporally precedes the differentiation of the parts. Thus, scholars of the organicist movement argued that organismic wholes always have to be investigated first in the study of development and that heredity should be framed as the re-constitution of ontogenetic resources and causal interactions. Against the views of geneticists, it was argued that “the real cause of resemblance is the same factor that creates this organic architecture. Hereditary resemblance is […] a byproduct of development, and will be explained only when we succeed in explaining development”^[18] This followed the teleological pattern of explanation – the whole is first in explanation, last in causation: first in conception, last in realization.

The explanatory significance attributed by the organicist movement to organism-environment reciprocity was diluted in the second half of the twentieth century as, in evolutionary biology and the Modern Synthesis, the organism became increasingly perceived as a passive recipient of environmental influences.^[19,20]

This EES should focus less on genes and more on developing organisms and their active, reciprocal interactions with their environments.

The supremacy and uniqueness of conscious human agency cast doubt on the significance or, indeed, the reality of agency and purpose in other organisms. But the capacity of organisms for self-maintenance, to reproduce, adapt, and survive, suggested they were ‘purposive’ to the point of being authors of their own fate. If, as philosopher of biology Robert Wilson suggested, ‘an agent is an individual entity that is a locus of causation or action’^[21] then organisms seemed to fit the bill. Unlike machines, their causal motivation arose from internal or immanent processes.

This was the ongoing philosophical and semantic struggle between the desire to recognize goal-directedness in biology and uncertainty about the scientific appropriateness of words like ‘agency’ and ‘purpose’ when used in non-human contexts. Besides, organismal agency was widely dismissed as the operation of a genetic program encoding the purpose-like traits that make organisms appear agent-like. (ref) Biology is currently deciding whether biological explanation would benefit from the reinstatement of the organism as causal agent – that constructs its environment, and thus its own development and evolution. Organismal adaptive agency modulates evolutionary selection pressures.

Current evolutionary models often ignore organism-environment reciprocal causation instead focusing on other relata with genes often construed as the agents of development and evolution with organisms primarily the products of genetic programs. This is set against the view that it is more useful to think of whole organisms are centers of causal agency, not products of the agency of genes: that no causally efficacious unit transcends the properties of the interacting parts.^[22]

Evolutionary biology tends to present evolution as the transmission of genes and its effect on populations, rather than on the developing organism and the reciprocal interaction between the environment and the organism’s agential activities. ^{[22, p. 230]}

Organism-centered Biology (OCB)

Baedke (2019) distinguishes between ‘old’ OCB (1910-1940) and its demise in the 1940-1950s and ‘new’ historical phases of this 20th century challenge to the theoretical primacy of organisms in biology.

Old Organism-centered Biology

By the 1930’s new biological disciplines were eroding the autonomy traditionally attributed to organisms. Biological debate during the interwar period has been widely discussed (see, e.g., Nicholson & Gawne, 2015; Esposito, 2016; Peterson, 2016; Baedke, 2019; Donohue & Wolfe, 2023).

In papers published in 1930-31 British biologist and philosopher Joseph Woodger (1894–1981) noted the diminishing interest in organisms despite the many ways they separated themselves from their environments, flexibly integrated environmental components in the process of self-maintenance, actively constructed their intra- and extra-organismic contexts, and formed new collective individuals. These concerns were shared by other leading biologists in Great Britain and the German-speaking world. It was observed that the organism presented the particular form of biological organization from which most (if not all) processes in nature should be understood. Baedke associates this support for organisms with three theoretical trends: organicism, dialectical materialism, and (German) holistic biology.

The organism is a functionally integrated unit whose activities are coordinated and directed towards the development, maintenance and reproduction of the form and modes of action typical of the species to which it belongs (Russell).

Organicism

Organicism, as interpreted by prominent advocate British biologist C.H. Waddington (1905-1975) emphasized the wholeness of the organism (its indivisibility) as critical for investigating and explaining, for example, the causal roles of single genes and the robustness of developmental pathways. The following quotes capture the flavor of this approach:

‘The organism taken alive and whole is as essential to an explanation of its elements as its elements are to an explanation of the organism . . . all attempts to assign explanatory value to the elements in their relation to the whole organism, while at the same time denying either expressly or tacitly, similar values to the entire organism in its relations to the elements, must fail in large degree’. Ritter 1919, p. 1

‘The organism is a system, in which the elements and processes are organized in a particular manner, and in which, in the end, every single part, every single event, depends on all other parts and all other events’. Bertalanffy 1932, p. 2.

‘Every part is functionally related to every other and exists as the servant of the whole’ Henderson

The ‘more’ implied by ‘the whole is greater than the sum of its parts’ is not a physical ‘more’ but one of complex relations. To explain this ‘more’ in less abstract terms requires an understanding of complex dynamics and dependencies.

This led to a ‘levels’ ideation: should explanations proceed ‘top-down’ or ‘bottom-up’ and is the universe organized into a compositional arrangement of parts and wholes?

Organicism reached its peak in the late 1920s and early 1930s^[1].

Today it might be pointed out, for example, that development does not proceed as an inexorable unfolding mechanical process emanating from the genes; it engages feedback from the rest of the organism that guides genetic activity.

Dialectical materialists

Argued that all processes in nature should be thought of as confrontations of antagonists leading to new and qualitatively different forms of order that are in need of their own conceptual framework.

New organism-centered biology

Baedke & Tageda (2023)

Organismic purpose and agency

Fábregas-Tejeda (2024) identifies seven viewpoints on organismal purposiveness and agency prevalent during the two major periods of organism-centered biology. These are briefly summarized below.

Neo- Aristotelian

The coordinated and integrated differentiation of parts when

‘From beginning to end it appears that development is moving toward a goal.’ Conklin, 1929, p. 31

This constitutive purpose was related to Aristotelian philosophy by Conklin and others, notably Canadian entomologist William Robin Thompson.

‘The vital movement, taken as a whole, is essentially adaptive, or, in other words, directed to the attainment of ends advantageous to the organism itself and to its maintenance in existence’. Thompson, 1929, p. 237.

Thompson drew attention to Aristotle’s designation of life as “immanent movement.” Scottish theoretical biologist D’Arcy Thompson who translated Aristotle’s biological writings, commended the centrality of ‘form’, and suggested that final causes should be part of the toolkit of every biologist (see Thompson, 1913).

Drieschianism

It was widely assumed that attribution of purposiveness must entail the supernatural forces of vitalism. Driesch considered organisms to be harmonious- equipotential systems with the capacity to re- produce the whole if disturbed in a plastic, self- regulatory manner that he called ‘equifinality’, that sometimes parts of organisms had the potentiality to become new wholes: the factor facilitating this he called a non-material force or entelechy but not

‘the blueprint of an organism’s organization, nor the creative agent that brings it about, but a kind of a mediator […] that protects the tendency of the system from being disrupted by extraneous factors’

, such as surgical removal.

Eliminativism

Opposition to Drieschian vitalism was often equated to an opposition to the notion of purpose in biology, many biologists choosing to avoid any inference to agency and purposiveness except as related to human conscious intention.

‘[U] ntil purpose can be shown to be effective as a causal factor it is merely an unfortunate expression for the result attained.’

(British plant morphologist W.H. Lang, 1915, p. 784).

‘The analysis of animal conduct only becomes scientific in so far as it drops the question of purpose and reduces the reactions of animals to quantitative laws’.

(physiologist J. Loeb, 1919, pp. 17– 18). British biologist-historian J. Needham agreed that

‘[the neo- mechanistic position] knows teleology to be an unquantitative category, and banishes it from the laboratory to the domain of the philosophers, who are quite capable of dealing with it.’

(1930, p. 192) And so on. This was a widely held position.

Heuristic

While unscientific in principle, purposiveness was regarded as a useful concept to guide research. This was a recognition of the role of teleology in biological explanation as it proceeds by a process of reverse-engineering.

‘We cannot comprehend the specific forms of cleavage without reference to the end- result of the formative process […] Such a conclusion need involve no mystical doctrine of tele ology or of final causes.’

American zoologist E.B. Wilson, 1925, p. 1005. This view had a powerful precedent in Immanuel Kant’s ‘ Critique of the Power of Judgment’ where in organisms are objects ‘in which everything is a purpose and reciprocally also a means’. He recognized an “antinomy of the teleological power of judgment” the paradox of opposition between two assumptions that “All generation of material things and their forms must be judged as possible in accordance with merely mechanical laws” and its antithesis that “[s] ome products of material nature cannot be judged as possible according to merely mechanical laws” (KdU, 5: 387). Kant’s chosen stance was that teleological judgment is valid only for cognitively limited beings like ourselves as a ‘regulative ideal’ for inquiry. This view that, more or less, purposiveness is not constitutive of organisms but transposed into it from the purposiveness of human minds is a widely held position up to the present day and was especially strong in the late 20th century. Ruse

Holistic

In the 1920s biology was still in its theoretical infancy. The eminent brothers Haldane, most notably the biologist J.S. Haldane, believed that the influential Kant was actually mistaken in his conclusions about regulative purposiveness in organisms.

‘. . . the distinguishing feature of vital activity is self- preservation [. . . ]; and this is just as true of the most complicated actions of the human body as of the movement of the amoeba towards a source of nourishment. […] The fact is that every part of the organism must be conceived as actually or potentially acting on and being acted on by the other parts and by the environment, so as to form with them a self- conserving system.’ Haldane & Haldane, 1883, pp. 54– 55

This emphasis on wholes was referred to as holism which, the Haldane brothers argued precluded any need for the language of ‘function,’ ‘purpose,’ ‘means,’ and ‘ends’ .

‘. . . we are looking at the organism, not as acted on by things outside it, but as in teleological connection with that which is different from, but not existent independently of it” (Haldane & Haldane, 1883, p. 58) . . . It seems to me that as mere biologists we have no need to make use of the concepts of either memory or purpose. What we observe in all lives is simply their tendency to maintain and reproduce themselves as co-ordinated wholes.‘ Haldane, 1931, p. 161

This view was endorsed by influential German botanist and philosopher Emil Ungerer and the Dutch ecologist Cornelis van der Klaauw.

The flavor of the debate comes through in discussion at the Seventh International Congress of Philosophy held at Oxford in 1930 wnen a whole session was devoted to the topic of organismal purposiveness and the holistic stance that dominated there. Biologists and philosophers, such as Haldane, Ungerer, Wildon Carr, Alfred Hoernlé, and others, agreed that self- maintenance could not be described as purposive. In his summary of this session, Hoernlé expressed a biological weariness with the mechanism vs purpose debate noting the replacement of the concept of purpose by that of the whole [the implication is that purpose is a ‘human’ term’ while whole applies to all organisms] Protagonists of agency and purpose in biology argued primarily on methodological, not on metaphysical, grounds – that the most profitable technique of investigation in biology is to assume that biological processes must be holistically conceived, in order to be mechanistically studied. Hoernlé, 1931, p. 44.
This amounted to a form of purpose eliminativism expressed by German neurologist Kurt Goldstein as follows:

‘The idea of an intended task is superfluous for an understanding of the organism, but that of a definite end [. . . ] may be very fruitful [. . .] Yet the idea of “end” must also be taken only as a guiding notion for the procedure of knowledge rather than in a metaphysical sense [. . . ]. In this sense, one can describe the concept of wholeness, as a category, as the category that substantiates and encompasses the subject matter of biology.’ Goldstein, 1995, p. 324

Explananda for Dynamic Equilibria-Related Research

The notion of purpose in biology has long been treated as fundamentally unscientific and therefore to be ignored, eliminated, replaced or reduced to authentic science. This view was expressed by the Canadian physiologist R. S. Lillie who addressed the problem as follows:

‘Apparently, the general “purpose” of most animal actions is to take some advantage of conditions existing in the environment, or to modify the relations between the individual and the environment in some way favorable to the species. [. . .]. This is why they impress us as “purposive.” The “teleological” characteristic of living beings appears most conspicuously in this aspect of their life. But from the physiological point of view it is necessary to reach some purely objective or physicochemical definition of the term “purposive” as applied to such actions. Lillie, 1915, p. 589

And that:

‘[. . .] My procedure and methods of reasoning will be those of objective natural science purely; and 50 Alejandro Fábregas-Tejeda purposive actions […] will be considered simply as events in external nature, disregarding their possible conscious or psychic accompaniment’ Lillie, 1915, p. 590.

‘[T] he organism is to be regarded as a physicochemical system of a special kind, exhibiting a dynamic equilibrium with its surroundings, i. e., an equilibrium in which two sets of processes, one constructive or constitutive, the other destructive or dissipative, balance each other. Many other so- called “stationary” systems— characterized by a continual and balanced interchange of material and energy with the surroundings— exist in nature; […] hence, the comparison of a living organism with a vortex or candle- flame is traditional, and serves to make clear certain fundamental peculiarities of the living condition. One of the most interesting general properties of such systems is a certain power of regulatory adjustment to changes of condition.’ Lillie, 1915, p. 593.

Thus so-called purposive actions secure an energy supply for the future. Any action that facilitates the continued existence of an organism can be called purposive. From a physicochemical perspective, all instances of adaptation represent organic equilibria of varying complexity. In effect, purposive actions are the result of a dynamic equilibrium between the organism and its changing environment. This was a physiological interpretation of purpose as “the reattainment of a condition of equilibrium which has been overthrown” and supported by other scientists.

‘. . . every system in equilibrium is teleological. The means that produce the reaction are directed to a definite end, to overcome the constraint, and the reaction might be said to take place in order that the system may be preserved. This is evidently the source of the “purposefulness,” that has occasioned endless biological discussion.’ Hooker, 1919, p. 509

While open systems could never be absolutely, but internal forces could nevertheless be directed towards an equilibrium or ‘steady state’. As Bertalanffy expressed it:

‘We can, however, suppose that the “purposefulness” and “striving towards a goal” of organic processes is nothing else than the outcome of communicating systems of causally determined processes, the inner dynamical conditions of which tend towards equilibrium.’ Bertalanffy, 1933, pp. 103– 104

Noetic

Scottish philosopher-biologist E.S. Russell,^[11] in 1916, published a book on Form and Function, his ideas at first distinctly Neo-Aristotelian:

‘We need to look at living things with new eyes and a truer sympathy. We shall then see them as active, living, passionate beings like ourselves, and we shall seek in our morphology to interpret as far as may be their form in terms of their activity. This is what Aristotle tried to do, and a succession of master- minds after him. We shall do well to get all the help from them we can.’ Russell, 1916, p. 364

Fábregas-Tejeda claims that Russell changed his opinion somewhat over the years, believing that we must view the world from the dynamic perspective of the organism (its umwelt).

‘A living thing must be able to follow and counter by appropriate response the changes in its environment which [. . .] have a vital meaning for it. Now this can be achieved only through perception. I use the word here [. . .] in a broad way [i.e., not related to conscious states], to cover all degrees of the receptive side of vital activity.’ Russell, 1924, p. 57; text inside brackets added.

Fábregas-Tejeda notes that for Russell,

‘Separation from the environment is needed by the organism to have agency, or phrased differently, that individuality is a precondition for agency. “The living thing can have, no more than the machine, an internal or self- existent purposiveness,” he stated, “unless it has at the same time real individuality and persistence’ Russell, 1924, pp. 16– 17.

Russell sought to carve out organisms as subjects, as agents in the world that act on their own behalf.

‘[I]t is mainly through perception that life becomes individualized and separates itself out from the environing flux. Through perception the organism clears, as it were, a space around it in which to live […]. The living individual is then a subject, or better— if we lay emphasis on action rather than on presentation or representation—an agent; and there is necessarily implied an object, or more generally, something sensed to which the individual responds. Individuality has therefore as its necessary complement a sensed environment, an objective world however dimly presented. Russell, 1924, p. 59

Fábregas-Tejeda interprets this mode of ‘scientific understanding’ as a noetic principle.

‘In the physical sciences and to a large extent in physiology we are concerned primarily with causal explanations […]. We do not get this sort of knowledge by using the direct or descriptive method. What we get may be better described as an understanding of behaviour. When you see a wasp, for example, standing on a gate post and busily chewing at the wood, you do not understand this action until you follow the wasp up and find out that it uses this material to construct its nest; you go on then to discover what the nest is used for— the care and upbringing of the young. In a word, to understand the action of the wasp on the gate post you have to integrate this action into the whole directive cycle of activity […]. This is the sort of knowledge which we get by studying animals from the [agential] point of view, and it is extremely valuable knowledge too. Without this knowledge we simply cannot make sense of behaviour; even the most extreme believer in mechanism must use this sort of knowledge to make behaviour intelligible at all.’ Russell, 1934, p. 15

‘If we . . . consider [the parts of organisms] separately, without relation to the life of the organism as a living, developing, reproducing whole, we shall never understand them, even though we succeed in working out their physico- chemical “mechanism” or mode of action. We shall acquire […] a vast mass of unrelated facts of biochemistry and biophysics, but we shall never build up a real biology.’ Russell, 1945, p. 9

This was asserting that the goal-directed character of behavior is absolutely necessary for understanding it scientifically and this noetic standpoint was extended to physiological processes that only “become intelligible” when scientists link them “with one of the main biological ends which the organisms blindly pursues” Russell, 1945, p. 9.

For Russell it was simply impossible for practicing scientists to investigate developing, behaving organisms without the presumption of agency and purposiveness. Also, Russell, like Aristotle, emphasized a simple point – that in teleological explanation the end must always come first. We cannot infer a house from a pile of building materials. Thus, ends are necessarily first in explanation and last in causal sequence: first in conception, last in realization. Further, these ends are not mysterious, supernatural, from the future, or heuristic. They are transparently uncomplicated natural ends, like a mature organism, or a completely constructed house.

New organism-centered biology

Commentary

During the late 20th-century the organism was swallowed by genetics and ecology.

Still, it never really went away, it just became lost in the exuberance of biological discoveries, especially those of genetics and its applications in biotechnology, and the wider concerns of environments and ecology. Biology proliferated into narrow specializations within academic silos each, like the parts of an organism, critical to the broader picture and convinced of its special significance. As with the organism itself, these were parts of biology that needed to recognize their place within a greater whole, and to capture the earlier spirit of organicism as an attempt to bring some harmony and unity into biological theory.

Today’s 21st-century biology investigates life at many scales, and from many perspectives, and it is still in the thrall of the ground-breaking genetic discoveries of the mid-20th century and their spin-offs into biotechnology.

Do we still think that the organism is special in some way, or is it just one level of biological organization – one scale, perspective, or context of explanation?

We can, for example, now provide a compelling account of life from genetic, physiological, behavioral or other points of view. The list of life’s necessary structures, processes, and behaviors is now so long that it is considered foolish to single out any particular one as special. Finding the necessary and sufficient conditions for life is a holy grail that is beyond our grasp. And yet the primacy of the organism in biology remains strong.

While parts of organisms – their structures, processes, and behaviors (including genes) – often demonstrate a high degree of independence, self-maintenance, and goal-directed activity, they are ultimately subordinate to the goals of the functionally integrated and self-determining adaptive agency of whole organisms. Organisms thus express a greater degree of agential autonomy than their parts or communities and act as causal hubs within the biological network of causal connection.

Emphasis on reductive molecular-genetic and other explanatory ‘levels’ results from misplaced hierarchical thinking (see biological hierarchy).

Organisms are biological agents that act on, and respond to, their conditions of existence in a flexible adaptive way. While agency, in a narrow sense, is associated with sentient organisms, notably the consciousness, intention, and deliberation we associate with human subjectivity, it has its evolutionary origins in the goal-directed behavior of all organisms – their universal, objective, and ultimate propensity to survive, reproduce, adapt, and evolve. Human agency is therefore a highly evolved and limited instance of biological agency.

Adaptation entails both short-term access, storage, and processing (interpretation) of information as a form of universal biological cognition driving behavior, ultimately leading to long-term genetic change. Human cognition is a highly evolved and limited conscious form of biological cognition.

The organism provides an empirically justified and prioritized scale for the biological explanation as grounded in the agential process that defines all life.

Biology is the study of organisms, their parts, and their communities. This is the foundational principle of organism centered biology (OCB).The organism is a fundamental analytical, methodological, epistemic, and ontological biological category. It is the basic unit of biological classification (the species is a group of similar organisms), of ecology, and of evolution. The organism is always, therefore, a reference point for biological description and explanation.

What makes organisms stand out as units of biological study is their agency. Aristotle’s dictum, often translated as ‘the whole is more than the sum of its parts‘, remains as true and compelling today as it was in his times. Every aspect of their biology is crucial – their DNA, their physiology, their life processes of metabolism and homeostasis, and many more necessary factors. However, what really stands out is that each organism has an autonomy that is expressed through its integrated functional organization; it has structures, processes, and behavior that combine to express a goal-directed unity of purpose – the universal, objective, and ultimate propensity of the whole organism to survive, reproduce, adapt, and evolve (the biological axiom). These are the characteristics that most obviously distinguish every organism from inanimate objects and the dead.

Biological explanation presupposes agency; biology does not make sense unless we know what its objects are ‘for’, and that is because nature mindlessly designed all its objects for a purpose, including the human brain and human subjectivity. Without the universal and purposive goals of biological agents, life assumes the same character as inanimate matter – of purposeless physics and chemistry, and biological science becomes a collection of unrelated facts.

Much of the nuanced historical debate about purpose and teleology in biology (and less so agency) can be understood as a simple and understandable resistance to the generalization of the word ‘purpose’ from humans to other organisms. Historically – perhaps even more than now – ‘purpose’ was a word tied to the domain of human subjectivity. To make its meaning acceptable to science it would have to be either removed altogether or translated into something less scientifically controversial.

Formal historical resistance to purpose was traditionally based on its perceived inference to the supernatural, impossible backward causation (goals from the future determining means), and the reading of human intuitions into nature. The simple and objective reality of organismal goal-directed behavior precluded all these reservations. The only remaining substantial difficulty was the reconciliation of mindless purpose in non-human organisms with the minded purpose of humans.

Theoretical biology is yet to provide a non-controversial account of the relationship between real (empirically verifiable) goal-directed behavior and human purpose. The problem has, over the last decade or so, gathered momentum with the realization that there is a strong functional equivalence of human cognition and the behavior of organisms. So, for example, both goal-directed behavior and human cognition involve the generalized access, storage, processing, and prioritization of information as a guide behavior. This striking similarity has resulted in an increasing acknowledgment of ‘biological cognition’. This is, however, further complicated by the additional recognition that strictly mental properties, long treated as uniquely human – reason, knowledge, value, learning, memory, communication, and much more, including the experience, sentience, and subjectivity itself – also have biological functional equivalents. So, for example, if subjectivity involves our experience of the world then this is a property of all organisms has that therefore have their own ‘reality’ or umwelt, it is just that the human subjective experience has a uniquely mental component.

So, how are we to speak in a scientifically meaningful way about plant cognition, plant sentience, or plant intelligence when these terms are associated uniquely with human mental states?

In recent years a compromise has been reached through the less confronting notion of agency. It is possible to treat goal-directed behavior as a demonstration of agency, even though the word ‘purpose’ may seem inappropriate.

But this goes only part way to resolving the problem. For example, there are real properties inherent in goal-directed behavior that are functionally equivalent to reason and yet we do not have the technical scientific vocabulary for these real traits. This leaves a limited number of options:

1. We can continue, business as usual, with current ambiguities. However, the increasing awareness of cognitive equivalence across the community of life is only likely to increase, leading to further ambiguity and controversy.

2. We develop a new technical vocabulary denoting the real traits of biological cognition. This draws attention to the fact that the vocabulary of human cognition and intentional psychology is actually a species-specific terminology. In an ideal world, then, each species would have its own lexicon of agential terms. Realistically neither of these options is practical and therefore extremely unlikely to be accepted by the general biological community,

3. We extend the current language of human cognition to all organisms. This too would be resisted, but it appears to be the only possible solution to gathering theoretical problem. The major advantage is that it would accept the reality of these traits in all organisms and acknowledge uniquely human cognitive traits as limited and highly evolved functional evolutionary adaptations. Our restriction of the meaning of these terms to human mental states was probably a form of anthropocentrism anyway. At present, the application of the language of human intentional psychology to other organisms is treated unsatisfactorily as cognitive metaphor – mistakenly treating these real traits in nature as figurative, the reading of human subjective states into nature. This would provide a more scientific account of the biological world. The need to then distinguish between, on the one hand, universal biological agency and universal cognitive terms and, on the on the other, uniquely human terms seems the the least disruptive. Any of these paths entail disruption with 2 and 3 involving a substantial revision of biological theory.