Biological agency

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.

Shared X-Ray image of a stingray by loctrizzle

Biological Agency: reclaiming a lost cause

Agency, as activity and influence, is everywhere.

Aristotle believed that philosophy must give an account of change—a challenge that remains central to both science and metaphysics. What causes things to happen? What initiates activity in the universe? His answer was the “unmoved mover,” the prime cause that starts everything but is itself unchanged.

Modern science has upended the terms of that question. We now understand the cosmos not as a collection of static substances nudged into motion, but as a field of constant flux. Galaxies, mountains, animals, and atoms alike are transient concentrations in a universe governed by transformation. What was once puzzling was change; now the real mystery is persistence—how anything achieves the fleeting semblance of form, identity, or endurance. What makes a thing a “thing” in a world of processes?

Nature, in its rawest sense, is tumultuous: earthquakes, cyclones, wildfires, plagues. These forces once compelled mythic explanations; we personified them as gods. The instinct to attribute agency is ancient, tied to our need to make sense of change by imagining some hand behind the chaos. Yet the history of science has largely been an exorcism of these unseen forces—stripping nature of its hidden animators and rendering it a system of predictable, measurable causes.

Still, some forces remained oddly intangible. Gravitation, magnetism, and quantum entanglement act invisibly and at a distance. Newton, while quantifying gravity’s effects, resisted explaining its nature. These “spooky” influences remind us that not all causation is mechanical or obvious. Even physics has ghosts of a kind.

Which brings us back to biology—and its own displaced specter: agency. What animates life? What gives living systems their capacity to act, persist, and adapt? Once, this question invited talk of élan vital or soul. But with the rise of mechanism and reductionism, biology learned to avoid such language. The goal-directedness of living systems—their purposive activity—was recast as illusion, a projection of the human mind onto nature. In rejecting metaphysical ghosts, science may have cast out one too many.

The biological notion of agency, especially as it relates to non-cognitive organisms, was long treated as metaphor. Aristotle’s concept of telos, the “that for which” something exists, anchored an ancient understanding of living purpose. In De Anima, he described the soul as the principle of internal organization, a source of immanent activity and form—not separate from the body, but its animating logic. That is strikingly close to what we now call biological agency.

Kant, centuries later, would preserve Aristotle’s insight while neutralizing its ontological bite. For him, purpose in biology was not real, only a necessary way of thinking—a heuristic we must use as if organisms were intrinsically purposive. That as if still governs mainstream biology.

But what if it no longer has to?

Contemporary biology increasingly demands a more integrated framework—one that can acknowledge goal-directedness, processual organization, and multiscale causation without retreating into metaphor. The Agency–Process–Scale (APS) framework emerges from this need: not to return to supernatural teleologies, but to recover the reality of biological agency as a scientifically grounded phenomenon. Life is not defined by what it has (genes, membranes, cells, parts), but by what it does—and the coordinated, purposive, scale-dependent processes that make such doing possible.

The remainder of this account takes seriously the idea that agency is not a fiction, nor an anthropomorphic projection, but a defining and observable property of life itself.

Aristotle

Often regarded as the founder of biological science, Aristotle observed that in biology especially, the structures, processes, and behaviors of organisms became disconnected facts unless framed by the question: What is it for? This question was meaningful precisely because organisms are goal-directed—that is, agential and purposive—in a way that inanimate objects are not. It makes sense to ask what an eye or a wing is for, but the same question asked of a rock or the moon seems nonsensical.

Teleology—the study of ends, purposes, and goals—has an extensive philosophical and scientific literature. The article on purpose provides an introduction to this history, its conceptual evolution, and the diverse views on whether purpose is real, projected, or emergent in the natural world. Historically, at least eight distinct sources for purposiveness in nature have been proposed.

Aristotle’s own teleological framework, particularly his notions of formal and final causes, was eventually rejected during the Scientific Revolution. His view was criticized for implying that future goals could exert causal influence—a mysterious pull from the future—which seemed both philosophically opaque and scientifically illegitimate. These purported goals appeared to resemble supernatural forces, inaccessible to empirical scrutiny. Moreover, such explanations were often dismissed as projections of human intentionality onto non-human organisms—anthropomorphic readings that confused subjective interpretation with objective structure.

These concerns were exacerbated by the prevailing pre-Darwinian worldview, which treated organisms as divinely created, unique entities—a view that Darwin overturned by showing how all life shares common ancestry through descent with modification. This evolutionary perspective reframed teleological talk as potentially misleading, or at least in need of reinterpretation.

While Aristotle’s logical and philosophical rigor laid foundational stones for Western thought, he undervalued empirical observation and controlled experimentation. In contrast, the Scientific Revolution elevated these methods, constructing a new epistemology based on observation, measurement, and repeatability. To gain credibility, early modern science positioned itself against older sources of authority—both the Bible and Aristotelian philosophy. Purging biology of its seemingly mystical teleological language became a kind of scientific purification. Francis Bacon, one of the revolution’s leading voices, famously derided Aristotle’s final causes as “barren virgins dedicated to God”—unproductive, metaphysical remnants of an outdated worldview.

The Scientific Revolution’s reinterpretation of biological agency as a cognitive illusion—a mere projection of human values onto goal-less matter—echoes through modern biology. This stance, comparable to Kant’s heuristic use of teleology (as a useful fiction), remains influential to this day. Its implications—philosophical and scientific—are explored in depth in articles on this website.

What might seem like a semantic issue is, in fact, a metaphysical debate: are purpose and agency real features of living systems, or are they merely convenient constructs?

Over the past few centuries, the principal objections to teleology—its alleged backward causation, theological overtones, anthropomorphic bias, and conceptual vagueness—have been met with increasingly sophisticated responses. The time is now ripe to revisit Aristotle’s original vision of biology: a science permeated by functions and goals, by living systems shaped and sustained by agency—a world in which, as he put it, “nature does nothing in vain.”

Aristotle’s formal and final causes are central to his biology and may be loosely interpreted as follows: formal teleology refers to the intrinsic nature or form of an organism—its defining essence, which guides its development. For example, the acorn’s capacity to become an oak is rooted in its form. Final teleology, by contrast, concerns the end or goal toward which something tends—its function or purpose. For instance, the function of wings is flight.

These two types of explanation are interdependent. An organism’s form contains its purpose; its purpose is realized through its form.

Modern interpretations have found rough parallels: formal teleology is often likened to an organism’s genetic and developmental blueprint, while final teleology maps onto its evolutionary functions—traits that enhance survival and reproduction under selection. In this way, contemporary biology can be seen as recovering Aristotelian insights in updated, empirically grounded language.

Formal teleology aligns with mechanistic or proximate explanations, focusing on internal developmental processes and structures. Final teleology corresponds to holistic or ultimate explanations, which locate traits within broader ecological or evolutionary contexts. Together, they offer an integrated view that links how organisms work (mechanistically) with why they are structured that way (functionally).

Darwin

Enlightenment philosopher Immanuel Kant, like Aristotle, recognized a fundamental distinction between the extrinsic teleology of machines—whose purpose is imposed externally—and the intrinsic purposiveness of living organisms, which arises from within their own self-organizing structures, processes, and behaviors. However, in Kant’s time, it was customary to interpret this apparent goal-directedness in nature as evidence of the divine wisdom of an external Creator. This view informed the natural theology of figures like Carl Linnaeus and was famously elaborated by William Paley, who argued that the design of living beings pointed to a supernatural designer.^[108]

The idea that agency and purpose might be natural, mindless phenomena—rather than cognitive capacities bestowed exclusively upon humans by God—was not yet conceivable within the prevailing theological framework. The possibility of non-cognitive purposiveness remained unconsidered.

Charles Darwin, though reticent on questions of teleology, introduced a causally transparent and naturalistic mechanism for the evolution of life. His theory of natural selection removed the need for supernatural explanations, but it also raised a deeper question: if we can explain the development of species through mechanical processes, does this render concepts like purpose and agency obsolete?

The answer is not so straightforward. While we do not speak of the purposiveness of the planets, we routinely describe the goal-directed behavior of organisms—seeking food, avoiding harm, reproducing—as a central feature of life. In offering a mechanical explanation for evolution, Darwin did not explain away agency and purpose; rather, he naturalized them. Purpose and agency, long associated with divine intention, were now open to scientific investigation as natural properties of living systems.

Still, Darwin’s account lacked a detailed understanding of the mechanism of inheritance. It wasn’t until the emergence of population genetics in the early 20th century and the discovery of the structure of DNA in 1953 that a new synthesis emerged—commonly referred to as the Modern Synthesis or Neo-Darwinism. This gene-centric view emphasized the primacy of genetic information, increasingly casting organisms as mere vehicles for the propagation of genes.

In this conceptual shift, agency and purposiveness were seen as mere illusions, epiphenomena of underlying genetic programs. This perspective reflected a broader reductionist mood in 20th-century science, one increasingly being called into question.

Today, biology faces a lack of conceptual integration, partly due to the fragmentation of the field into increasingly specialized subdisciplines—from microbiology to cognitive science. Each has carved out its own intellectual silo, often without reconciling their findings within a coherent theoretical framework. The need for a renewed synthesis is increasingly recognized.

One response has been the rise of the Extended Evolutionary Synthesis (EES), which expands the Darwinian framework to include processes such as phenotypic plasticity, epigenetic inheritance, niche construction, developmental bias, and inclusive inheritance. Alongside this are philosophical and theoretical efforts that revisit long-neglected ideas: the Agency Perspective, the Philosophy of Organismal Biology, Systems Biology, Complexity Science, Enaction, Field Theory, and others.^{[58,61,62,64,66,72,74,78,86,103,104,110,111]}

Despite the ubiquity of goal-directed behavior in organisms, biology has never fully clarified its status. Teleology, once central to explanations of life, became suspect—too closely associated with supernaturalism. In its place, the term teleonomy was introduced in the mid-20th century to describe evolved purposiveness without invoking external design. Recent work has redefined teleonomy as ‘evolved biological purposiveness,’ a formulation that echoes Aristotle’s natural teleology but is grounded in evolutionary dynamics.^[69,89]

Biological agency, minimally understood as the goal-directedness of living systems, clearly distinguishes life from non-life. Its denial has impoverished our understanding of nature and contributed to a diminished ethical and scientific regard for non-human organisms, which are often interpreted through the lens of physics and chemistry rather than the purposive behavior they display.

A formal scientific recognition of biological agency is overdue. But this requires conceptual clarity: What is a biological agent? What is its goal, and by what means does it pursue that goal? Most importantly, how does biological agency relate to human agency, with its cognitive, intentional, and cultural dimensions?

Meanwhile, evidence is accumulating for non-genetic inheritance, including epigenetic modification, behavioral inheritance, and even some forms of Lamarckian transmission—once ridiculed, now gaining cautious scientific attention. If these findings are to be synthesized meaningfully, biology will require not just more data, but a clarified conceptual vocabulary—definitions, categories, and principles capable of guiding empirical research across diverse domains.

These are the questions now animating both biological science and philosophy as they reconsider the foundations of the study of life.

Before Darwin, no scientific explanation existed for the evident purposiveness in nature. Who or what instilled this directionality into living systems? For most, the only conceivable answer was God.

Darwin, however, proposed a naturalistic account combining heritable variation, differential reproduction, adaptation, selection pressures, and chance events. In doing so, he displaced the need for supernatural design—but he did not eliminate the phenomenon of purpose. The goal-directedness that we see in organisms—present from the first origins of life—remained a persistent feature of biological reality.

Darwin did not explain away purpose and agency; he opened the door to explaining them scientifically.

This article explores the logical space occupied by the categories of biological agent, biological goal, and the means through which these agents pursue their goals.

The Standard Model

Contemporary biology remains largely shaped by a legacy of skepticism toward concepts of agency and purpose in nature. Coupled with a gene-centered interpretation of evolution known as the Modern Synthesis (or Neo-Darwinism), this outlook constitutes what is here referred to as the Standard Model—a widely accepted, textbook understanding of biology that arose from the mechanistic worldview of the Scientific Revolution and was consolidated through the 20th-century unification of Darwinian evolution with Mendelian genetics.

At the heart of this model lies the belief that agency and purpose are properties uniquely attributable to human minds—products of conscious intention, rational deliberation, and linguistic abstraction. When agency is ascribed to non-human organisms, this is treated not as literal truth but as anthropomorphic shorthand—a convenient metaphorical device used to describe behavior that merely mimics intentionality. Since most organisms lack the neurological complexity necessary for reflective consciousness, it is assumed they cannot possess goals, intentions, or agency in any meaningful sense. Thus, while talk of “foraging strategies,” “signaling,” or “cooperative behavior” may aid communication or pedagogical explanation, such language is understood as heuristic only, with no implication that organisms are genuine agents.

This view, however, rests on a series of questionable assumptions. It obscures the evolutionary continuity of cognition, severing human mentality from its biological roots. It conflates conscious human agency with non-conscious biological agency, thereby excluding functionally coherent organismal behavior from serious causal analysis. It misinterprets metaphorical language (e.g., “plants seek light”) as evidence of anthropomorphic error, rather than recognizing it as a signpost toward under-theorized but real biological capacities. Most critically, it reflects the absence of a precise scientific vocabulary for non-neural, non-human forms of agency, thereby reinforcing a methodological blind spot. These issues are addressed in detail in the articles listed above.

The Gene-Centric View

This suspicion of agency in biology is compounded by the gene-centric interpretation of evolution central to the Modern Synthesis. Although Darwin provided no mechanism of inheritance, the 20th century saw his theory of natural selection integrated with population genetics, producing a powerful framework: the Modern Synthesis, which holds that genetic variation—arising through mutation and recombination—is the raw material on which natural selection acts. Evolution is thereby understood as the change in gene frequencies over time, with genes conceptualized as self-replicating units competing for representation in future generations, usually via the phenotypic traits they influence.

This framework grants primacy to the gene, based on the principle that only genetic information transmitted via germ cells can lead to evolutionary change—thus precluding the inheritance of acquired traits. It casts organisms as vehicles for gene propagation and downplays the causal efficacy of developmental, physiological, ecological, and behavioral processes in shaping evolutionary outcomes.

While the Modern Synthesis has provided a robust account of evolutionary inheritance, its explanatory power is now increasingly called into question. It offers no role for organismal behavior as a driver of evolutionary novelty, and it sidelines phenomena such as epigenetic inheritance, developmental plasticity, niche construction, and systems-level organization. In doing so, it fails to capture the full complexity of how organisms, as integrated and purposive systems, both shape and are shaped by evolutionary processes.

Problems with the Standard Model

1. Inversion of Reasoning: Mistaking Representation for Ontology
The Standard Model often assumes that because agency and purpose are described in human terms, they must be human inventions. This reflects a form of epistemic inversion: the claim that because we represent biological goals in our minds, such goals must only exist in our minds. This conflates epistemology with ontology and overlooks the possibility that agency and goal-directedness are real, evolved features of biological systems—features that precede and give rise to cognitive minds rather than being created by them.

2. Reality of Biological Agency and Purpose
Contrary to assumptions of mind-dependence, agency and purpose are directly observable in the behavior of all living organisms. Goal-directed behavior—e.g., movement toward food, avoidance of harm, reproduction—demonstrates purposiveness independent of cognition. Human agency is an evolved, cognitive elaboration of this biologically grounded purposiveness, not its origin. This demands that agency be treated as a natural, scale-sensitive property of living systems, not merely metaphorical.

3. Behavior and Causation: Subject vs. Object
Reductionist biology often treats organisms as passive objects shaped by genes and environment. However, when studied as subjects, organisms exhibit agential behavior resulting from internal reconciliation between goals (evolved dispositions) and environmental triggers. This reframes causation from a linear, external model to a systems-level, integrative account rooted in the organism’s own activity. Historically supported by Aristotle and Kant, this view affirms the organism as a self-organizing, self-causing agent.

4. The Metaphor Fallacy
When language for describing mindless purposiveness is lacking, we default to cognitive metaphors (e.g., “decision”, “strategy”), which leads to the false inference that purposiveness is not real. This is the metaphor fallacy: dismissing genuine pre-cognitive properties as metaphorical simply because they are described in human-centric terms. The need is not to eliminate such language, but to better distinguish cognitive agency from its biological antecedents.

5. Converse Reasoning and Evolutionary Priority
Human agency should be understood as derivative of biological agency, not as its explanatory foundation. Misreading human agency as primary reverses the evolutionary order and leads to an anthropocentric misinterpretation. A more coherent account sees human cognitive traits as evolutionary refinements of universal biological processes—grounding intelligence in adaptation, reason in decision-like behavior, and values in functional orientation.

6. Mind–No-Mind Confusion
Biological agency and human cognition are not mutually exclusive domains. Evolution produces layered traits, such that unique cognitive capacities (e.g., reasoning) coexist with shared agential traits (e.g., goal-directedness). Treating agency as exclusive to minds imposes a false binary. Mindless organisms exhibit agency in evolved and observable ways, which underlie and inform the later emergence of minded behavior.

7. Conflation of Human and Biological Agency
While human agency is cognitive and reflective, it retains the basic biological imperatives of all life: survival, reproduction, flourishing. This continuity allows us to interpret terms like “knowledge” or “value” as both cognitive and biological, depending on context. Denying this continuity leads to an artificial separation of mind and life, when in fact cognition is a biological phenomenon that evolved out of agential life.

8. Anthropocentrism and the Illusion of Apparent Design
The claim that nature exhibits only “apparent” design relies on a human-centered view of cognition and intention. But biological systems manifest highly structured, functional order—what may reasonably be called design—without conscious intention. Dennett’s insight that concepts like “design,” “purpose,” and “value” can “bubble up from the bottom” reinforces the legitimacy of recognizing real purposiveness in biological systems without invoking intelligent design or human agency.

9. Absence of Technical Terminology
Because we lack a formal vocabulary for non-cognitive agency, we fall back on psychological language. This opens biology to charges of metaphor and undermines the scientific legitimacy of real agential phenomena. Yet devising a wholly new vocabulary is impractical. The challenge is to reclaim existing terms (e.g., goal, function, purpose) with biological precision and processual clarity, rather than abandon them.

10. Reification of Scale and Disciplinary Fragmentation
Modern biology often treats levels of organization (genes, cells, organisms, populations) as ontologically equivalent or hierarchically disconnected. This obscures the special role of the integrated organism as the primary locus of agency, function, and selection. The reification of academic levels (e.g., molecular, cognitive, ecological) fragments biological understanding and falsely pluralizes the agents of evolution. In reality, all processes must converge on the scale of the whole, functionally integrated organism.

11. Neglect of Process in Favor of Substance
The Standard Model, rooted in analytic and reductionist traditions, privileges substance (e.g., genes, molecules) over process (e.g., behavior, adaptation, emergence). This undermines explanation of living systems, which are inherently dynamic and context-sensitive. Process philosophy offers a framework better suited to the complex, self-organizing, and temporally extended phenomena of life and evolution.

12. Gene-Centrism and the Reductive Paradigm
Gene-centric thinking, dominant since the Modern Synthesis, elevates genetic information as the causal and explanatory foundation of life. However, advances in epigenetics, systems biology, and developmental biology show that gene expression is context-sensitive, behaviorally modulated, and embedded within complex systems. Treating genes as the ultimate agents misattributes causality, downplays organismal agency, and confuses part-whole relationships.

13. Mischaracterization of Natural Selection
Contemporary definitions of natural selection focus on changes in gene frequencies, abstracting away the behavioral context in which such changes occur. Darwin, by contrast, understood natural selection as the outcome of organismal struggle. A return to this behavior-centric view would restore agency to its proper place in evolution: organisms, through their purposive behavior, shape the conditions under which traits (and their genetic underpinnings) become evolutionarily significant.

14. Organism-Centric vs. Gene-Centric Evolution
Evolution is best understood as the long-term outcome of short-term, purposive, agential behavior. Organisms, not genes, interact with the environment and determine the contexts of selection. Genes may encode potential, but it is the organism that expresses and enacts this potential in adaptive ways. Evolution, then, is not a gene-level competition but a population-level outcome of organismal behavior.

The objections above highlight the limitations of the Standard Model’s gene-centered, reductionist, and anthropocentric metaphysics. They collectively call for a shift toward an organism-centric, process-oriented, and agency-grounded biology—one that sees life as self-organizing, goal-directed, and evolutionarily continuous from the simplest organism to the most complex mind. The emerging paradigm seeks not to reject the achievements of molecular biology or evolutionary genetics, but to embed them in a richer, more integrated account of living systems.

The Extended Evolutionary Synthesis

The intellectual exploration of biology, once focused firmly on organisms, has broadened out to include populations and ecosystems, and narrowed down to the microscopic detail of genes.  How do we provide explanatory order to this expansion of knowledge and complexity?

In a complex system of interacting and interdependent factors, how do we decide which factor has causal or explanatory priority, or controlling efficacy? How do we rank the different factors and determine the strength and direction of relationships and dependencies? Which factor is a cause, and which a consequence?

As the focus of research shifts from one factor to another, so too does the explanatory emphasis. The ranking of explanatory categories changes in the light of new evidence and our human need to prioritize.

The Modern Synthesis, as an explanation of evolution, was a product of the genetic revolution that occurred between about 1918 and 1942 during an analytic-reductive turn in thinking that was gathering momentum at this time as scientists and logicians looked for the foundations of the world in its smallest discrete constituents.

Dissatisfaction with the main tenets of the Modern Synthesis began to appear from the 1950s (e.g. organicist Waddington) to 1980s (e.g. evolutionary biologist Gould). These ideas were given expression around 2009^[64] and summarized in a 2010 book by Massimo Pigliucci and Gerd B. Müller, Evolution: The Extended Synthesis whose themes have persisted as the Extended Evolutionary Synthesis (EES).

Dissatisfaction with the Modern Synthesis derived from both theoretical objections and the findings of new research concerned with, among other factors, fitness landscapes, multilevel selection, epigenetic inheritance, cultural evolution, organismal development, developmental plasticity, niche construction, evolvability, phenotypic plasticity, reticulate evolution, horizontal gene transfer, symbiogenesis, and more. A recent synthesis of the EES can be viewed here.

In sum, the EES is an expression of disillusionment with the gene-centered analysis of evolution. It is a movement seeking a revision in the emphasis given to the various factors influencing evolution – those underplayed including organisms, agency, ecology, and the inheritance of acquired characteristics.

The revisionist proposals of the EES fall into two broad camps: those concerned with a modification of our understanding of the inheritance of acquired characteristics, and those concerned with biological agency.

The most comprehensive current discussion of the philosophy and principles of agency in biology is Denis Walsh’s Organisms, Agency, and Evolution (2015). Walsh is a member of a team of four biologists concerned with agency in living systems whose objective is  – ‘To develop a scientific theory of organisms as purposive agents and determine the explanatory concepts and structure of an agent theory in relation to conventional scientific object theories‘.

Walsh outlines his philosophical position as follows:

The ‘Aristotelian purge’ was seen as a pivotal achievement of early modern science. As a consequence of the scientific revolution, the natural sciences learned to live without teleology. Current evolutionary biology, I contend, demonstrates that quite the opposite lesson needs now to be learned. The understanding of how evolution can be adaptive requires us to incorporate teleology – issuing from the goal-directed, adaptive plasticity of organisms – as a legitimate scientific form of explanation. The natural sciences must, once again, learn to live with teleology.^[53]

. . . the capacity of a system to pursue goals, to respond to the conditions of its environment and its internal constitution in ways that promote the attainment, and maintenance of its goals states^[56]

Walsh points out that the purposive activities of organisms have a strong influence on evolutionary outcomes – that evolution is, in this sense, a by-product of organisms’ pursuit of their intrinsic purposes. Evolution is not a product of four discrete and independent processes – inheritance, development, innovations, and biased change. Rather, each of the component processes of evolution—like adaptive evolution itself— is a consequence of what organisms as agents do.

A new biological paradigm

If biology has managed to ignore agency—for centuries, if not millennia—why do we need it now, and how can it be integrated into science as a relevant, practical, and operational concept?

We must study agency because it is a real feature of living systems, not a philosophical illusion. Its historical dismissal reflects conceptual inertia rather than empirical invalidity. If, as some argue, “evolution is a by-product of organisms’ pursuit of their intrinsic purposes,” then excluding agency and purpose from biology has been a major philosophical and scientific error of judgement.

Just as biology once resisted the idea that humans are animals—until growing understanding of evolutionary continuity forced a semantic and conceptual shift—so too must we now reassess the status of agency and purposiveness in organisms. As the science of life deepens, it reveals that biological agency is not an anthropocentric projection, but a general property of living systems, with human agency representing a specialized form of this broader capacity.

Agency has never been absent from biology—it has been implicit, often hidden behind technical terms like “adaptation,” “fitness,” and “selection.” While scientifically legitimate, this language can obscure the real-time, goal-directed behavior of organisms. The evolutionary process, understood through the APS (Agency–Process–Scale) framework, requires that we make agency explicit: as a system’s capacity to persist, coordinate, and transform across multiple scales through goal-directed interactions with its environment.

In this light, it becomes scientifically legitimate to ask: “What is this trait or behavior for?” and “What is this organism trying to do?” Far from semantic error, this reframing helps biology reconnect with the reality of organisms as active, self-regulating participants in evolution—not passive entities shaped solely by external forces.

Philosopher Samir Okasha, in Agents and Goals in Evolution (2020), contributes to this emerging perspective. He affirms that organisms can be treated as agent-like if they are well-adapted to their environments—a condition he calls the “unity of purpose.” In Biological Agency and Evolution (2023), he clarifies two key uses of the term “agency”: (1) as a thesis—that organisms are agents (OAT), and (2) as a heuristic—that we can interpret organisms as if they were agents (OAH). He further distinguishes four senses of agency: minimal (behavioral responsiveness), intelligent (adaptive, AI-like), rational (goal-maximizing), and intentional (psychological state-driven).

This website affirms the organism-as-agent thesis (OAT). While metaphor and human-centered language are often used in discussions of biological agency, we argue that it is more scientifically productive to interpret human agency as a refinement of biological agency, rather than treating biological agency as a metaphor for human psychology.

The anthropocentric impulse often leads to questions like, “Why do organisms behave as if they have beliefs or desires?” But such questions reverse the empirical relationship. It is human intention and cognition that emerge from deeper, evolutionarily grounded forms of agential behavior—not the reverse.

This view invites empirically tractable questions: What are the mechanisms by which non-neural organisms display goal-directed behavior? How is coordination achieved without cognition? Why does cognitive metaphor persist in scientific discourse if it is merely heuristic?

Dismissing such questions as metaphorical misses the point. When we say a plant “wants” water, the metaphor is not the issue—the issue is the real biological capacity for agency. Plants lack cognition in the human sense, but this does not mean they lack purposive behavior or self-directed function. The so-called “metaphor fallacy” arises when we confuse linguistic form with biological function.

This website explores three core themes:

The reality of biological agency—beyond heuristic models and anthropomorphic metaphor.

The relationship between human and biological agency—including evolutionary continuity.

The intersection of agency, cognition, and goal-directedness—across the scales of life.

Situated within the APS framework, agency is a multiscale, processual capacity that grounds life’s continuity, transformation, and evolutionary relevance. The scientific and philosophical implications extend far beyond biology—reaching into AI, robotics, biomedicine, and cognitive science. Most importantly, recognizing real agency in organisms reorients biology toward a deeper understanding of what it means to be alive.

The Biological Imperative in the APS Framework

The biological imperative refers to the inherent, self-sustaining drive of living systems to maintain, adapt, and regenerate their organized functional structure across time. It expresses the agential orientation of organisms toward preserving their viability under changing conditions through coordinated processes such as metabolism, repair, regulation, reproduction, and adaptive behavior.

In the APS framework, the biological imperative is not reducible to any single mechanism or structure but emerges from multiscale, processual integration—the dynamic coordination of nested biological processes acting in service of the organism’s continued existence as an agent. It reflects not only what life does but what life is in functional terms: a system that persists by acting to preserve itself.

Theoretical Significance

Definition of Life:
The biological imperative is proposed as the most scientifically robust and inclusive definition of life because it captures what unites all living systems—not through structural features alone, but through their shared functional orientation. It refers to the intrinsic tendency of living systems to sustain, adapt, and regenerate their own organized existence across time. While agency explains how this is achieved—through context-sensitive activity and coordination—the imperative explains why such capacities arise. Unlike agency, which varies in complexity, the biological imperative is expressed universally, making it a more fundamental and unifying criterion for life. Operationally, this imperative is manifested through interdependent, context-sensitive processes that continuously regenerate the system’s structure and function in opposition to thermodynamic decay.

Alternative to Gene-Centrism:
It offers a robust alternative to the reductionist gene-centered view of biology, by foregrounding function, agency, and process over static material components. Genes are recontextualized as tools within broader agentive dynamics rather than as drivers.

Bridge Across Disciplines:
As a unifying concept, the biological imperative links physiology, evolution, cognition, and ecology under a single, non-teleological but purposive framework, compatible with contemporary process biology, systems theory, and enactivist cognitive science.

Paradigm Shift in Biology:
By re-centering biology on the imperative to survive and functionally persist, the APS framework reframes evolutionary theory, organismal biology, and definitions of agency and cognition, offering a conceptually coherent and operational basis for studying life as inherently purposive without invoking vitalism or anthropocentrism.

The APS and the Naturalization of Metaphysical Concepts

The Agency–Process–Scale (APS) framework offers a systematic and scientifically grounded approach to the longstanding task of naturalizing concepts traditionally confined to metaphysics or philosophy.

Just as Darwin reframed biological purpose as the outcome of natural selection rather than divine design, the APS extends this naturalization by embedding agency, normativity, and intention within the dynamic organization of living systems. Biological agents, in this view, are not passive aggregates of mechanism but self-regulating, purposive systems whose activities are directed toward maintaining their own persistence, coherence, and functional integration across scales. Normativity arises not from external moral systems but from the internal logic of self-maintenance and adaptability; intentions are not reducible to conscious representations but emerge from the directedness of organismic behavior toward biologically salient ends.

This framework thus provides a coherent biological grounding for a wide range of cognitive and evaluative terms—such as intelligence, reason, value, sentience, and even consciousness—by reframing them as natural outcomes of multiscale agentive processes. In doing so, the APS does not eliminate these concepts but repositions them as essential components of a scientifically tractable theory of life, unifying philosophical insight with empirical investigation.

Agency

What exactly do we mean by agency, and what are the most effective ways to investigate its relevance to biology? If biological agency is real, then what is its role in evolution?

This overview begins with our general understanding of agency before turning to its manifestation in nature, the characteristics of human agency, and the relationship between human and biological agency. It then focuses on how the concept can be applied within biological science.

‘Agency’ is a loosely defined idea with applications across many disciplines, giving it a broad semantic compass. Dictionaries typically define an agent as something that acts—so, in a highly abstract and general sense, an agent can be understood as a cause that brings about an effect. Yet, in everyday usage, we are more inclined to associate agency with the intentional behavior characteristic of human activity.

Agency involves at least a degree of autonomy and self-determination directed toward specific goals or objectives. An agent initiates or influences events such that its actions produce changes not entirely governed by external conditions. At the same time, we can imagine computer programs—such as those of AI—that exhibit a non-living form of agency, one that is autonomous in some sense, though ultimately rooted in or overlaid by human input.

The goals or objectives of cognitive agents are typically referred to as purposes. We often speak of the purposes (or goals) of inanimate objects like chairs, knives, or guided missiles, but in such cases we are usually projecting the human intentions behind their design. We do not regard these objects themselves as independent agents.

This conceptual terrain may seem ambiguous at first. But as we move from general notions to biological specifics, a more precise and operational understanding of agency begins to take shape—one that can be meaningfully integrated into the scientific study of life.

Natural agency

Though rarely foregrounded as a crucial philosophical idea, the notion of agency lies at the heart of both religious and scientific understandings of the world. What initiates activity in the universe? What causes change? What has causal efficacy? Such questions cut to the core of how we explain the world—yet their answers often remain elusive. Change itself can imply the presence of some mysterious, possibly supernatural force—an unseen influence that resists our senses and defies easy explanation.

More specifically: what animates living things—what gives them ‘life’? What is the vitality that so obviously departs from a body when it dies?

Nature, in its broadest sense, is filled with powerful, sometimes terrifying non-biological agencies: earthquakes, tsunamis, lightning storms, wildfires, floods, plagues, and famines. Why do these calamities occur, and why must humans suffer them? Who—or what—is the agency behind them? It is no wonder that across cultures and centuries, we have personified nature with gods who punish or reward, gods who control events and demand interpretation.

The history of science can be seen as a gradual exorcism of these agential spirits. From its inception, science has grappled with the problem of invisible forces. Even in physics, some of the most foundational forces act at a distance, without apparent mechanism. Newton famously described gravitational attraction but refused to speculate on its cause. Only much later did we begin to map the strange and invisible agencies of electromagnetism—and even now, phenomena like quantum entanglement continue to stretch our grasp of what a force or cause might be.

Biological agency poses a similarly stubborn mystery. The goal-directedness of living systems—their apparent will, their responsiveness, and their vitality—seem to imply some animating principle, a kind of life force or inner motivation. We may attempt to remain scientifically neutral by describing such tendencies in terms of propensities or dispositions to act. But such terms often fall short of capturing the immediacy and intensity of lived agency: the felt momentum of being alive.

These reflections are rarely taken seriously today. The myriad ‘pushes’ and ‘pulls’ of life—our needs, drives, and desires—are regarded as familiar and unremarkable, and thus unworthy of deeper inquiry. Yet they remain forces, nonetheless.

Organisms survive, reproduce, and flourish. But none of this is logically necessary. We do not have to feed, to breed, or to continue living. And yet something—some internal drive or organizing force—keeps most organisms going most of the time. This applies especially to organisms without minds, whose behavior is no less purposeful for being automatic. In fact, when humans consciously interrupt these life-affirming drives, it is seen as abnormal or pathological: something has gone wrong and needs correction.

The ‘will to live’ is not a supernatural concept. It is an evolved, biologically inherited orientation—a basic expression of life’s agency. So why should talk of agency or goal-directedness in organisms be dismissed as unscientific, mystical, or obsolete?

Minded humans evolved from mindless organisms. Human agency—reflective, deliberative, and richly symbolic—emerged from the simpler, mindless agency of biological systems. Our purposiveness is not an anomaly; it is a continuation. Human agency evolved out of biological agency.

Human agency

We understand agency primarily through our own human agency. While human agency is strongly associated with rational considerations and deliberate intention, it is not expressed exclusively through the medium of conscious mental representations.

Human bodies demonstrate biological goals in several additional ways, including the mindless but integrated and goal-directed biological processes of self-maintenance—such as growth, metabolism, homeostasis, and homeorhesis. These processes do not require reflective thought but are nevertheless adaptive, norm-sensitive, and organized toward the preservation of life. Then there are the minded but unconscious goals associated with our instincts and intuitions, including our inherited, objective, universal, and ultimate biological propensity to survive, reproduce, and flourish—reconfigured in terms of the APS as the biological imperative.

Like all organisms, we are engaged in a constant process of adjustment (adaptation) to what is going on both inside and outside our bodies—especially to those conditions that are relevant to our continued existence, as shaped by our human biology. These salient conditions define our commonsense reality or umwelt (see manifest image), which refers to the organism-specific world of significance constructed through perception and function.

Key adaptive ingredients of the human cognitive agential umwelt include:

Intentionality – our goal-directedness as the purposive focus of our mental activity, which we describe using the agential language of intentional psychology. In contemporary biology and philosophy, intentionality can be naturalized through evolutionary function (Millikan, 1984), predictive processing (Friston, 2010), and biosemiotic responsiveness (Thompson, 2007), which ground purposive behavior in organismic norm-sensitivity and functional relevance rather than supernatural teleology.

Conscious self-awareness of our actions and their consequences, enabling us to reflect on our thoughts, choices, actions, and motivations. This includes an awareness of our capacity for independent (autonomous) decision-making through rational deliberation.

Capacity for self-regulation based on both individual and collective societal principles, values, norms, and ethical precepts. These normative dimensions, often considered distinctively human, can also be traced to the value-laden structure of biological life itself, where normativity arises from the needs and organizational logic of living systems (Jonas, 1966; Di Paolo et al., 2018).

Creativity and the ability to learn from experience and acquire new skills in adjusting to our environments—properties that build on and extend the adaptive plasticity found throughout the biological domain.

Providing a concise summary of our human mental life is a tall order, but when well-founded, succinct statements—like principles and laws—have great explanatory power. From at least the time of the ancient Greek philosophers, our mental life has been subsumed under three useful categories: knowledge (epistemology), values (ethics), and reason (logic). These three drivers of human behavior will be re-visited at the end of this article.

Human & biological agency

This website argues that human agency is best understood biologically—as a specialized, highly evolved, and minded form of biological agency.

While evolution implies transformation, it also entails elaboration on existing traits. Darwin viewed evolution as the gradual modification of inherited forms, not radical departure. In this light, the complexity of human agency can be seen as an extension of basic biological processes.

The necessity for organisms to survive and reproduce constitutes a biological imperative—a foundational condition uniting all life. This imperative underpins the vast continuum of living forms and explains the functions of their structures, behaviors, and physiological processes.

All organisms, including humans, are subject to this imperative. But because human agency is mediated through advanced cognitive capacities, the evolutionary roots of our actions are often masked by proximate experiences. We eat not only to survive, but because food tastes good and satisfies hunger. We engage in sex not only to reproduce, but for pleasure, intimacy, and bonding. These proximate motives obscure the deeper, ultimate functions that biology selects for.

Such examples illustrate how distinctively human mental life remains grounded in general biological functions. They also reveal the anthropocentric bias that isolates human cognition from its evolutionary context. We accept that our physical traits evolved from other animals, yet often resist the idea that our cognitive traits did too. But human-minded agency is just one expression of a broader biological agency: an evolved capacity for functional self-regulation in response to environmental demands.

The distinctive features of human agency emerge from the universal, objective characteristics shared by all living agents. This is why we intuitively treat animals—and even plants—as agents, unlike rocks or rivers. And it is why human cognitive states often resemble the functional behaviors observed in organisms that lack nervous systems: there is a continuity of function that bridges these apparent differences.

There are scientifically grounded—not merely metaphorical—reasons to recognize analogues of purpose, agency, value, and even knowledge in non-human organisms.

Skeptics often point to the specialized vocabulary of human psychology as a barrier to recognizing non-human agency. But while dogs and oak trees behave purposively, they lack the means to describe their agency. What language, then, can we use to characterize real, non-cognitive forms of agency?

In practice, we borrow terms from human intentional psychology because there is no species-specific vocabulary for non-human agency. This creates tension: we wish to acknowledge biological agency, but risk anthropomorphism when we use cognitive terms. The danger is not that the agency is unreal, but that the language used to describe it is misleading (see metaphor fallacy).

These issues are explored further in the articles human-talk, being-like-minded, and biological values.

Suffice it to say that intentional language is typically used to highlight real, shared features of biological agency—not to imply that non-human organisms possess minds like ours. When we say a plant “wants” water, we are describing a persistent, goal-directed behavior essential to its survival—not attributing conscious desire.

Categorizing Biological Agency: a multiscale, multiform phenomenon

Biological agency resists simple classification. It spans from minimal, self-maintaining systems to highly elaborated, cognitive forms. To make sense of this diversity, we need a framework that accommodates degrees, types, and contexts of agency across biological scales.

A useful starting point is to distinguish kinds of biological agency based on the functional capacities organisms exhibit:

• • • Proto-agency: Seen in minimal autopoietic systems, such as protocells, that sustain themselves through metabolic closure and boundary maintenance. These systems exhibit basic forms of self-production and environmental interaction.

    • Functional agency: Expressed in physiological regulation and behavioral responsiveness—e.g., thermoregulation, chemotaxis, immune responses. Here, systems actively maintain internal conditions in relation to external changes.

    • Developmental agency: Found in morphogenetic processes where coordinated cell activities construct, repair, and regulate organismal form over time. This involves both constraint-based organization and environmental responsiveness.

    • Evolutionary agency: Characterizes entities capable of heritable variation and differential persistence, enabling open-ended evolution. Evolutionary agents contribute not just to their own survival, but to lineage-level trajectories shaped by selection and adaptation.

These categories are not mutually exclusive but rather reflect overlapping and nested capacities. For example, developmental agency presupposes functional agency, and evolutionary agency often builds upon both.

Ambiguous cases—such as viruses, ecosystems, or holobionts—highlight that agency is not an essence but a context-sensitive achievement, grounded in the capacity for functional integration and coordination across scales.

Transient and Embedded Agency

Not all forms of biological agency are evolutionarily individuated. Systems such as immune networks, cellular collectives, or microbial communities may express transient or embedded agency—forms of agential behavior that contribute to the adaptability of higher-level systems without themselves being stable evolutionary units. These cases complicate simple organism-based taxonomies but emphasize the distributed and processual nature of biological agency.

This multiscale perspective links proximate mechanisms (metabolism, homeostasis, perception) to ultimate outcomes (evolutionary persistence) through organizational closure—the recursive interdependence of constraints that sustain a system’s identity (Moreno & Mossio, 2015). Such closure is not cognitive, yet it is constitutively agential in a biological sense.

Four Philosophical Senses of Agency

Philosopher Samir Okasha (2018) identifies four broad senses of agency:

1. Minimal agency: The capacity to do or behave—rudimentary responsiveness.

2. Intelligent agency: Adaptivity or goal-seeking behavior, as seen in AI systems.

3. Rational agency: Utility-maximizing behavior guided by preferences and constraints.

4. Intentional agency: Acting on beliefs and desires, typical of human psychology.

These senses reflect different levels of complexity and are tied to distinct disciplinary assumptions. Rational and intentional agency often presuppose internal representations and mental states, while minimal agency refers simply to directed behavior.

When applied to biology, these categories raise important questions. Should agency be defined in cognitive or psychological terms? Or can it be grounded in biological organization and function, independent of mental content?

Toward a Biological Understanding of Agency

A more fruitful path is to naturalize agency—treating it as a general feature of living systems. This “bottom-up” approach views agency as rooted in biological functions such as self-maintenance, regulation, adaptive response, and coordination, rather than in mental representation.

From this standpoint:

• • • Human agency becomes a specialized, evolved form of biological agency.

    • Cognition, reason, and intention emerge from fundamental agential processes shared across life.

    • Agency precedes mind, rather than requiring it.

This perspective reframes the scientific inquiry: rather than projecting human intentionality onto life (a top-down heuristic), we can study how general features of living systems give rise to more complex forms of agency (a bottom-up investigation).

Ontological vs Instrumental Views

Okasha (2018) further distinguishes between two stances:

• • • OAT (Organisms As Agents Thesis): Organisms are agents in an ontological sense.

    • OAH (Organisms As If Agents Hypothesis): Organisms can be treated as if they are agents, for explanatory convenience.

The former treats agency as a real biological property, the latter as a modeling tool. This website adopts the ontological view: organisms are genuinely agential beings, a position gaining increasing traction in both philosophy and theoretical biology.

Summary Framework: Dimensions of Biological Agency

The language of agency

In both biology and philosophy, terms like function, goal, purpose, intention, and reason are often used to describe directed activity, but each carries distinct explanatory weight. In biology, a function refers to the role or contribution a trait, structure, or process makes to the organism’s operation—typically described mechanistically and often without implying agency. Philosophical theories such as the Selected Effects Theory define functions in terms of evolutionary history (i.e. what a trait was selected for), but these views risk overlooking the dynamic, present-time role that functions play in sustaining a living system.

By contrast, a goal introduces a stronger sense of directionality and normativity. It represents an outcome that a system is actively oriented toward—like survival, reproduction, or homeostasis. While goals can be mindless (as in bacterial chemotaxis), they imply a form of biological agency. Purpose deepens this further, referring to the system-level reason-for-being of a structure or behavior. Though often avoided in scientific contexts due to its teleological overtones, purpose can be naturalized—as in the APS (Agency–Process–Scale) framework—as the internal coordination and coherence that drives an organism’s activity. In this view, the purpose of the whole system grounds the functions of its parts.

Intention and reason are reserved for agents with cognitive sophistication. Intentions involve mental representation and commitment to a course of action, and are typically associated with conscious organisms. Reasons go further, referring to the justifications an agent might offer for actions or beliefs, and are central to human-level rationality and ethics. These distinctions clarify that while all organisms may exhibit goal-directedness and functional coherence, only a subset (like humans) engage in intentional and reason-based behavior.

The APS framework accommodates these distinctions by linking them to biological scale and complexity. Functions describe the contributions of parts; goals and purposes describe system-level coherence; and intentions and reasons emerge in more advanced forms of biological agency. This layered view allows for a scientifically grounded yet philosophically coherent understanding of directed activity across the living world.

Biological Agency & APS Framework

The Agency–Process–Scale (APS) framework offers a rigorous, scientifically grounded approach to understanding agency as a constitutive property of life. In contrast to views that treat agency as a philosophical relic or a metaphor for human mental activity, APS holds that agency is not an optional overlay but an intrinsic, processual property of living systems. Organisms are not passive entities shaped solely by external forces; they are active systems that regulate, repair, reproduce, and adapt themselves through continuous engagement with their environments.

From this perspective, agency emerges from the dynamic organization of living matter across multiple biological scales. It is graded and evolutionary, not all-or-nothing, and increases in complexity as systems evolve new forms of control, communication, and integration. This makes it possible to trace a non-reductive continuity from the basic life processes of microbes to the reflective deliberations of humans.

Historically, the concept of agency has been marginalized in biology—either excluded as unscientific or reduced to anthropocentric terms like intention and rational choice. The dominance of molecular and genetic explanations contributed to displacing the organism from theoretical centrality, obscuring its role as a multiscale biological agent. APS restores the organism as a primary locus of agency—situated within nested processual and evolutionary dynamics—and reasserts agency as a defining feature of life.

Conventional understandings of agency, especially in popular discourse, often limit the term to deliberate human action. For example, the Wikipedia entry for “biological agent” (as of 28 April 2023) refers primarily to pathogens used in bioterrorism, revealing a stark disconnection from the concept’s broader biological significance. Such misrepresentations underscore the need for a systematic account of biological agency rooted in empirical and theoretical biology rather than metaphor or mentalistic analogy.

The APS framework addresses this by identifying agency not with human-like minds, but with the goal-directed capacities inherent in all living systems. Organisms exhibit autonomous behavior based on their ability to sense, respond to, and modify their environments in ways that support their own viability. These non-cognitive agential capacities—sometimes referred to as pre-cognitive—include biologically grounded, purposive processes that do not require conscious awareness or representational thought.

In this view, the question is not whether organisms think, but whether they do. Agency is defined not by reflective intention, but by the capacity for coordinated activity that maintains the organism’s functional integrity. Thus, agency becomes recognizable in the structured behavior of bacteria, plants, and animals alike—not as metaphor, but as an explanatory category that distinguishes the living from the non-living.

Biological agency can be understood as the system’s capacity to coordinate internal and external processes toward the maintenance of its own viability. This includes core biological features: homeostasis, stimulus–response behavior, adaptive plasticity, reproduction, energy processing, autonomy, environmental modulation, and information processing. Rather than being treated as a checklist of traits, APS integrates these under a unified conception of agency as multiscale, functional integration.

APS further differentiates agency dynamically along a continuum:

Minimal agents exhibit self-regulation and responsiveness to environmental conditions.

Adaptive agents add functional plasticity, memory, and predictive capacity.

Cognitive or rational agents (e.g., humans) further incorporate symbolic representation, reflective reasoning, and deliberate planning.

These distinctions reflect differences in scale and complexity, not differences in fundamental kind. All are variations on the same underlying agential architecture.

Importantly, APS rejects the view of evolution as a purely passive process. Organisms do not merely endure selection; they participate in shaping their own evolutionary trajectories. Through homeostasis, behavior, niche construction, and dynamic coupling with their environments, they modify the conditions under which selection operates—both for themselves and for other species. This agent-driven co-construction of evolutionary dynamics is a central principle of the APS framework: evolution is not blind adaptation alone, but a feedback-rich process embedded in the ongoing activity of living systems.

By situating human cognition as one elaborated form of agency among many, APS provides a biologically inclusive understanding of mind and purpose. It shows that what appears “mindless” may still be purposive, and that goal-directedness in life need not imply consciousness or rationality. Non-cognitive agency is not a metaphor—it is a biological reality.

In short, agency is the necessary and sufficient condition for life. It provides the conceptual foundation for understanding how living systems function, persist, and evolve. The APS framework redefines agency as a scalable, evolutionary, and processual property of life, inviting new approaches to biology that are capable of integrating the full range of living systems—from microbes to minds—within a unified theoretical model.

Agency – The capacity of living systems to act in ways that support their own continued existence.

Biological Imperative – The underlying drive or purpose of that action: to survive, adapt, and maintain organization.

Process – The coordinated biological activities that carry out this goal (e.g. metabolism, development, behavior).

Scale – The levels and timescales at which life operates, from molecules to ecosystems, and from moments to generations.

APS = Agency + Process + Scale

Agency = who or what acts
Biological Imperative = why it acts
Process = how it acts
Scale = where and when it acts

Our intuitive approach to agency engages an Agent, is Mission (goals), and its Means. Each of these factors is treated separately in what follows.

The agent, mission, & means

We understand agency in human terms as an agent carrying out a mission using particular means. Within the APS, this familiar triad is reinterpreted in biological terms without invoking intention or consciousness.

The biological agent is typically the organism—an autonomous system capable of initiating and coordinating context-sensitive activity in support of its own continued existence.

Its ‘mission’ is not a fixed goal but the biological imperative: an intrinsic orientation toward persistence, functional coherence, reproduction, and adaptive responsiveness. This imperative gives direction to agency, shaping the organism’s activity without requiring foresight or planning.

The ‘means’ by which this mission is enacted are the dynamic processes of life—physiological, behavioral, developmental, and evolutionary mechanisms—that operate across scales. These processes are not static routines but flexible, feedback-sensitive patterns of activity, enabling the organism to respond appropriately to changing internal and external conditions. Scale plays a critical role by determining not only where and when these processes unfold, but also what is relevant or functional in a given context. It reveals how fast, local processes integrate with slower, broader ones to sustain the agent as a whole.

In this way, the APS framework preserves the coherence of the agent–mission–means structure, while grounding it fully in biological terms.

The Biological Agent

To understand life through the lens of the APS (Agency–Process–Scale) framework, we begin with the concept of the biological agent—the paradigmatic unit of autonomous, purposive activity in living systems. Intuitively, we treat organisms as the primary agents of life, and indeed, biology has traditionally been defined as the study of organisms. This intuition is grounded in empirical reality: organisms are discrete, bounded, self-maintaining systems that engage with their environments through goal-directed behavior. They are born, grow, adapt, reproduce, and die—manifesting the full biological cycle.

However, this traditional view has been challenged by developments in molecular biology, genetics, microbiology, and systems ecology, which expose the complexity of life’s organization across multiple levels and contexts. Cells, genes, collectives (e.g., swarms, colonies), and ecosystems have each been proposed as alternate or supplementary loci of agency. Biology today exhibits existential pluralism, with different subdisciplines adopting different operational units depending on their investigative aims.

Despite this, the organism remains the most coherent and explanatory focal point for biological agency. Organisms exhibit a unique combination of:

Physical boundary and integration – they are cohesive, functionally integrated entities.

Autonomy – they initiate and regulate internal processes in pursuit of their own viability.

Self-maintenance and reproduction – they preserve their structure and lineage across time.

Behavioral orientation – they act in accordance with internal needs in relation to external conditions.

Evolutionary participation – they actively shape, not just endure, their environments of evolutionary adaptation.

Organisms do not merely contain agency in their parts (e.g., genes, cells) or contribute to collective agency (e.g., in colonies); rather, they instantiate biological agency in the most integrated and evolutionarily consequential form. While genes may guide developmental potentials, it is the organism that enacts behavior, navigates its umwelt, and determines survival outcomes. Agency, therefore, is not solely located in parts or collectives, but in the whole organism as an adaptive, emergent entity.

Agency in organisms exists independent of cognition, as organisms without nervous systems still demonstrate clear behavioral dispositions. These non-cognitive expressions of agency—termed pre-cognitive—include tropisms, homeostasis, immune responses, and other purposive behaviors grounded in evolved biological structure and function. They reflect a minimal but real perspective: the capacity of the organism to register and respond to circumstances in ways that further its biological aims.

From an APS perspective, agency is not binary (present or absent) but graded and processual. The degree of agency exhibited by an entity corresponds to its level of functional integration and behavioral flexibility:

A minimal agent self-regulates and responds to its environment.

An adaptive agent modifies its internal state and behavior through learning or plasticity.

A cognitive agent deliberates and plans using symbolic representation.

Yet all are variants of the same underlying phenomenon: goal-directed behavior embedded in functional systems.
In sum, to be a biological agent is to be a materially grounded, physically bounded, functionally integrated system capable of maintaining itself in the face of entropic pressures through internal regulation, adaptive interaction, and participation in evolutionary processes. Among all biological entities, the organism most clearly exemplifies this unity of purpose, and thus stands as the canonical agent in biology.

The Organism

In the APS framework, evolutionary selection operates across multiple spatiotemporal and organizational scales, but most integratively and consequentially through the organism. While genes contribute to trait variation, it is the organism’s behavior and context-sensitive engagement with its environment that plays a decisive role in shaping evolutionary outcomes.

Organisms are not passive vehicles of genetic expression but active agents that modulate their own evolutionary trajectories through sensing, acting, and adapting. As autonomous, self-producing, and functionally integrated systems, organisms uniquely exhibit the full suite of characteristics associated with life, positioning them as the primary biological agents and central loci of natural selection.

Agent’s Mission: the goals of biological agency

Within the APS (Agency–Process–Scale) framework, the mission of a biological agent refers to its intrinsic, functional orientation toward certain objective, evolutionarily grounded ends.

We have traditionally framed these goals in ultimate terms – typically survival and reproduction (referred to as the here as the biological axiom) – risking teleological interpretations. In contrast, the biological imperative interprets these outcomes as emergent attractor behaviors of self-organizing, and persisting processual systems.

From the perspective of the APS (Agency–Process–Scale) framework, a biological goal can be defined as:

A dynamically maintained end-state or functional condition that an organism or biological system tends toward through internally regulated activity, arising from its capacity as an agent embedded in multiscale biological processes.

 And goal-directedness may be defined as:

The coordinated, adaptive pursuit of a biological goal through processes that are organized and sustained across multiple scales of biological organization, reflecting the system’s capacity to monitor, regulate, and respond to conditions in ways that promote persistence, viability, or functional continuity.

Clarifying these features in APS terms:

Agency: The goal exists only insofar as it is enacted by an agent that is capable of sensing, evaluating, and acting in relation to its internal and external conditions.

Process: Goal-directedness is not a fixed property but a continuous, self-organizing activity embedded in metabolic, behavioral, developmental, and ecological processes.

Scale: Goals are neither reducible to molecular mechanisms nor purely emergent at the population level—they are maintained through coordination across organizational scales (e.g., gene regulation, cellular signaling, whole-organism behavior).

This naturalizes biological purposiveness: biological goals are not imposed externally but emerge from the living system’s own operational coherence and functional orientation within its environment. 

The Biological Axiom: life’s core orientation

Organisms behave in ways that consistently promote survival, reproduction, adaptation, and evolution. These interrelated capacities define the biological axiom: a unifying principle that captures the objective, universal, and ultimate conditions of life.

Objective, because they do not require consciousness to operate.

Universal, because all life depends on them.

Ultimate, because they organize and integrate all proximate structures, processes, and behaviors.

These goals are evident in even the simplest organisms and are functionally equivalent to what, in humans, are described as intentions, values, or interests. On this view, human cognitive agency is a sophisticated elaboration of the same foundational orientation exhibited by all living systems. 

The Biological Imperative: a processual interpretation

Whereas the biological axiom emphasizes life’s outcomes—what it appears to be for—the biological imperative reframes this mission in strictly processual terms. It describes not a pursuit of fixed ends, but a continuous, system-internal imperative: the dynamic capacity to maintain viability through integrated interactions across multiple levels and timescales.

Organisms do not pursue survival and reproduction as abstract goals, but enact them through ongoing processes of self-organization. Their persistence is not driven by foresight but sustained by the functional coherence of systems that remain viable in fluctuating environments.

This imperative is:

Agential, because it arises only in systems with autonomous, integrated organization.

Processual, because it is sustained through ongoing negotiation of internal and external conditions.

Scaled, because it manifests at molecular, cellular, organismal, and ecological levels.

Thus, the mission of biological agents is not reducible to outward behavior alone but is embedded in their capacity to sustain coherence through organized activity across time and scale.

Proximate and Ultimate Goals

Biological agents act in the short term to meet immediate needs (proximate goals), such as acquiring nutrients, avoiding harm, or engaging in reproduction. These behaviors are not random but are organized around long-term functional ends—adaptation and evolutionary continuity (ultimate goals). This unity of purpose does not stem from intention but from inherited structure: organisms behave as if they value continued existence because those that did not failed to persist. The APS framework dissolves the proximate–ultimate binary by showing that immediate biological processes (proximate causes) and long-term evolutionary outcomes (ultimate causes) are dynamically entangled across scales, with each shaping and constraining the other in the continuous organization of living systems.

Natural Ends, Not Metaphors

This account resists the view that talk of goals, values, or purposes in biology is merely metaphorical or anthropomorphic. The ends pursued by organisms are natural ends: real outcomes of causal, observable biological processes. They do not imply backward causation or external design, but instead reflect the organizational logic of living systems. Goals are last in causal sequence—as the outcomes of system dynamics—but first in explanation, because they reveal what the system is organized to sustain or achieve.

Means: how agents achieve goals

In the APS (Agency–Process–Scale) framework, a complete account of biological agency must explain not only what a biological agent is and what goals (mission) it pursues, but also how it pursues those goals. The means of biological agency are the internal capacities and external behaviors that enable organisms to adaptively maintain their existence—namely, the structural, processual, and behavioral mechanisms by which life achieves survival, reproduction, adaptation, and flourishing.

Adaptation as a Foundational Means

At the heart of biological means lies adaptation, broadly construed. Adaptation is not just a genetic outcome of natural selection; it is a processual expression of agency. Organisms are not passively shaped by their environments but engage in goal-directed adjustment to their conditions of existence. This continuous feedback loop between organism and environment—described as the biological condition—is a defining trait of agency.

Adaptation can be:

Short-term and behavioral, driven by immediate internal and external cues.

Long-term and genetic, shaped by selective pressures over generations.

Yet even long-term adaptations emerge from the capacity of organisms to act in the present. Agency, therefore, plays a causal role in evolution by influencing the conditions under which genetic change occurs.

Core Means of Agency

To pursue their mission, biological agents employ several interrelated capacities:

Behavioral Orientation
Organismal behavior is directed toward particular outcomes—it has directionality. This “mindless mission” is not metaphorical. Even non-cognitive organisms exhibit preferences and avoidances, which constitute a real behavioral orientation or perspective on the world. These orientations are observable, repeatable, and causally significant: they define what the organism values.

Functional Integration
All behavior emerges from the internal coordination of structure and function. Organisms integrate internal processes with external cues to resolve tension between their biological goals and the constraints of their conditions. This reconciliation of internal propensities with external triggers is what generates real-time, goal-directed behavior.

Information Processing
To behave meaningfully, organisms must gather, store, process, and retrieve information about both internal states and environmental conditions. Functional integration relies on this information flow to coordinate behavior across the system. Information, here, is not metaphorical: it describes the real interconnection between components of a system in a goal-directed whole.

Behavioral Flexibility (Plasticity)
A key marker of agency is the ability to respond adaptively to varied conditions. Organisms vary in their degrees of behavioral freedom—the range of responses available within the constraints of their genotype and physiology. This phenotypic plasticity allows agents to explore, learn, and modify behaviors in ways that enhance persistence. Flexible organisms are better equipped to shape their own evolutionary futures.

Environmental Coupling and Niche Construction
Agents not only react to environments but also modify them. This mutual shaping is seen in niche construction, where organismal behavior feeds back into the environment, altering the selective landscape. Behavior, therefore, is not just a response—it is a means of evolutionary participation.

Biological Behavior as the Expression of Agency

While functional integration is the internal engine of agency, behavior is its outward manifestation. Observable behavior reflects the internal logic of adaptation and is the primary means by which agency is expressed, recognized, and communicated—especially in social organisms and humans via symbolic language.

Behavior has both:

Proximate causes (immediate physiological or situational triggers), and

Ultimate causes (long-term evolutionary and agential rationales).

In biology, to say that behavior is goal-directed is to claim that it is not random but oriented toward maintaining viability—whether through feeding, mating, defending, or navigating.

From Mindless Means to Human Mind

Though most life forms are non-cognitive, the means they employ prefigure the cognitive traits of humans. Our capacities for:

Knowledge arise from evolved mechanisms of information processing.

Values stem from biological goals and behavioral orientation.

Reason emerges from evolved abilities to coordinate action in response to complex environmental demands.

In this light, human cognitive agency is a highly elaborated case of more general biological means, not a categorical exception. Our minds extend, rather than replace, the biological logic of goal-directed adaptation.

Aristotle to Agency: theoretical biology

Biology began as a reflection on the complexity and apparent purposiveness of living systems. Aristotle, in his foundational biological work, identified four types of causes: material, efficient, formal, and final. Modern science, shaped by the Scientific Revolution, retained the material and efficient—what things are made of and how they come to be—but largely discarded formal and final causes as metaphysical or unscientific. Explanation shifted away from wholes to parts, from purposiveness to mechanism, and from synthesis to analysis.

In this mechanistic worldview, organisms were no longer treated as unified agents pursuing ends, but as assemblages of parts governed by impersonal laws. Yet Aristotle’s central insight—that living systems exhibit telos, a directedness or purposefulness intrinsic to their organization—remained unresolved. His conviction that “nothing in nature is accidental” pointed to a biological order that could not be fully captured by physics or chemistry alone.

Darwin’s theory of evolution by natural selection marked a pivotal shift. Although careful to avoid overt teleology, Darwin nonetheless reintroduced natural purpose by showing how traits evolve through their contribution to survival and reproduction. Adaptation implied functionality; traits were “for” something, even if not designed. Darwin thus naturalized teleological language—but cautiously, never fully confronting the implications of agency in non-human life.

The 20th century brought a renewed push toward reductionism with the rise of molecular biology and genetics. The gene became the locus of explanation, and organisms were often portrayed as mere vehicles for gene replication. The organism as an integrated, purposive system was sidelined. Function, behavior, and development were increasingly treated as downstream consequences of molecular mechanisms, culminating in the gene-centric vision popularized by the “selfish gene” metaphor.

Yet this model proved insufficient. Living systems are not passive outcomes of genetic programs—they actively maintain, regulate, and transform themselves across multiple scales of organization. Organisms shape their environments, construct niches, and influence their own evolutionary trajectories. They are not just products of evolution but participants in it. This capacity—expressed in persistent, goal-directed, and adaptive behavior—is what we now recognize as biological agency.

The limitations of strict reductionism have led to a conceptual shift. The Extended Evolutionary Synthesis acknowledges developmental processes, phenotypic plasticity, and niche construction as evolutionary forces. These perspectives affirm that life cannot be fully understood without reference to the biological imperative—the evolved, emergent drive of organisms to persist, adapt, and flourish within complex ecological and developmental contexts.

Crucially, agency is not an all-or-nothing property tied to consciousness, but a biological capacity distributed across the living world. Whether through microbial chemotaxis, plant tropisms, or animal cognition, organisms exhibit functional autonomy and behavioral flexibility oriented toward survival and reproduction. These are not metaphorical “goals”—they are real, evolutionarily grounded constraints and dispositions that organize living activity.

To make sense of life as life, biology must move beyond mechanism alone and recover a framework capable of integrating agency, function, and multiscale organization. The Agency–Process–Scale (APS) framework offers such a synthesis. APS reframes living systems as agentive, self-organizing processes embedded in dynamic contexts across biological scales. It captures the way organisms enact their goals through coordinated, multilevel interactions—where function explains structure, and purposive behavior arises from integrated processes.

In this light, APS is not a return to premodern teleology, but a natural progression in theoretical biology. It draws a through-line from Aristotle’s purposiveness, through Darwin’s naturalized function, to today’s recognition of life as goal-directed, processual, and scale-dependent. APS clarifies how biological systems sustain themselves: not by design, but by evolving the means to realize their biological imperative—the active pursuit of persistence, reproduction, and transformation in a contingent world.

Summary: integrative processual biology

The explanatory categories used in biology often depend on the specific nature of the question being asked—whether mechanistic, developmental, ecological, or evolutionary. However, the philosophy of biology also faces a deeper and more enduring challenge: to identify categories of the broadest generality—those that reveal not only how living systems operate under particular conditions but what distinguishes life itself from non-life across all scales of organization.
In this context, a shift from substance-based to processual and integrative thinking has gained increasing philosophical and scientific traction. The APS framework offers a coherent synthesis of this emerging perspective by grounding biological theory in six foundational features of living systems.

1. Biological Agency

At the heart of life is not passivity, but activity. Organisms do not merely react to stimuli—they initiate, regulate, and coordinate their actions in ways that promote persistence, reproduction, and adaptation. This capacity to act in context-sensitive and self-sustaining ways is what we call biological agency.
Why fundamental? Because without agency, there is no basis for purposiveness, goal-directedness, or functional coherence in living systems. Agency underwrites autonomy, coordination, and the teleological character of biological activity—without invoking external design or consciousness.

Agency is reflected across several categorical triads:
Agent / Mission / Means frames agency in terms of what is acting, why, and how.
Agency / Process / Scale positions agency as the central organizing feature of life.
Agent / Cognition / Behavior emphasizes the sensing-acting loop through which agency is expressed.

2. Processual Organization

Living systems are not defined by static structures but by organized processes—metabolism, growth, development, reproduction, repair, adaptation. Organisms persist not through fixed substance but through dynamic patterns of interaction maintained over time.
Why fundamental? Because biological persistence is process-based. Life is always in the making—an ongoing set of coordinated transformations.

This is reflected in:
Process / Transformation / Inheritance, which highlights continuity through change.
Agency / Process / Scale, where process links intention-like activity to multilevel coordination.

3. Multiscale Structure and Causation

Biological systems are deeply hierarchical. Processes at the molecular level influence cells; cells shape tissues; organisms inhabit ecosystems. Causality is not linear or unidirectional but reciprocal and distributed across scales.
Why fundamental? Because no biological phenomenon is fully intelligible at a single level. Emergent properties and downward causation are hallmarks of living systems.

This is captured in:
Scale as a core APS category.
Supplementary triads such as Signal / Response / Feedback, which emphasize cross-level regulatory interactions.

4. Functional Integration

Organisms are not collections of parts loosely joined—they are coherent wholes. Functional integration is the principle by which different parts and processes are coordinated to sustain the organism as an organized unity.
Why fundamental? Because coherence, regulation, and robustness are essential for survival and adaptation in changing environments.
This underlies categories like:

Agent / Means, focusing on how functionality is deployed.
Persistence / Inheritance / Transformation, where integration supports both continuity and change.

Related systems-biological categories such as Structure / Function / Organization.

5. Open-ended Evolution

Living systems are not static: they are the product of, and continue to undergo, open-ended evolutionary processes. Variation, selection, inheritance, and historical contingency ensure that life continually explores and transforms the space of functional possibilities.
Why fundamental? Because life is not just what it is—it is what it becomes. Evolutionary potential is intrinsic to life.
This connects directly to:

Transformation / Inheritance / Persistence as the triad of evolutionary continuity.
Evolutionary logic expressed in Variation / Selection / Heredity.

6. Adaptive Cognition (Sense–Respond Capacity)

Even the simplest organisms are not blind automatons. They sense, interpret, and respond to their environments in ways that are structured by their internal states and history. This basic form of biological cognition is essential to autonomy and survival.
Why fundamental? Because agency requires more than movement—it requires sensitivity, interpretation, and adaptive response. Cognition is not exclusive to minds but is grounded in the capacities of living systems.
This feature is expressed in:

Agent / Cognition / Behavior, where cognition mediates the relationship between sensing and acting.
Signal / Response / Feedback, which highlights dynamic environmental coupling.

The Integrative Strength of the APS Framework

The Agency–Process–Scale (APS) triad stands out because it does not isolate these features—it integrates them. It:

Grounds agency in naturalistic, functional, and evolutionarily selected capacities;

Frames life as a dynamic interplay of processes, unfolding in time and capable of transformation;
Locates action across nested biological scales, allowing for multi-level analysis and coordination.

Rather than selecting between mechanism and teleology, structure and function, or proximate and ultimate causation, the APS framework shows how these dimensions are unified in the living system itself. It thus supports a non-reductionist, multiscale, and process-centered understanding of life that meets both philosophical and scientific demands for generality, coherence, and explanatory depth.

Energy, Negentropy, and Life

Life has long challenged scientists to explain how complex order persists in a universe governed by the Second Law of Thermodynamics. In the early 20th century, Alfred Lotka (1922) framed evolution as a fundamentally physical process, where organisms that most effectively capture and transform energy have a selective advantage. This energy-based perspective became central to later ecological theory.

Erwin Schrödinger (1944) provided a seminal insight by introducing the concept of negentropy: living systems maintain their intricate structure by importing free energy and exporting entropy to their surroundings. Life is therefore not an exception to thermodynamics but an open, dissipative process that locally defies disorder while contributing to its overall increase in the universe. This concept bridged biology, physics, and information theory, inspiring Brillouin’s (1953) treatment of biological order as information sustained by energy flow.

Building on these foundations, Eugene and Howard Odum (1953, 1971) developed ecological energetics, quantifying how energy moves through ecosystems and demonstrating that biological communities self-organize to maximize energy capture, transfer, and efficiency. Howard Odum formalized this principle in his Maximum Power Principle, proposing that ecological and even societal systems evolve to optimize power use over time.

Later advances in non-equilibrium thermodynamics (Prigogine & Nicolis, 1977) described life as a network of dissipative structures—self-organizing processes that persist by consuming energy gradients. Modern frameworks extend these ideas, linking energy to information processing and agency. Theories such as constraint closure (Mossio & Montévil, 2013) and the Free Energy Principle (Friston, 2010) treat organisms as autonomous systems actively directing energy flow to maintain structure, adapt, and evolve.

Across this historical trajectory, one theme persists: life is a process of organizing energy against entropy, creating the conditions for persistence, adaptation, and complexity at all scales of biology.

References
Brillouin, L. (1953). Negentropy principle of information. Journal of Applied Physics, 24(9), 1152–1163. https://doi.org/10.1063/1.1721463

Friston, K. (2010). The free-energy principle: A unified brain theory? Nature Reviews Neuroscience, 11(2), 127–138. https://doi.org/10.1038/nrn2787

Lotka, A. J. (1922). Contribution to the energetics of evolution. Proceedings of the National Academy of Sciences, 8(6), 147–151. https://doi.org/10.1073/pnas.8.6.147

Mossio, M., & Montévil, M. (2013). Closure of constraints: A theoretical framework for autonomy in biology. Journal of Theoretical Biology, 354, 110–118. https://doi.org/10.1016/j.jtbi.2013.05.012

Odum, H. T. (1971). Environment, power, and society. Wiley-Interscience.

Prigogine, I., & Nicolis, G. (1977). Self-organization in non-equilibrium systems: From dissipative structures to order through fluctuations. Wiley.

Schrödinger, E. (1944). What is life? The physical aspect of the living cell. Cambridge University Press.

Glossary - Biological Agency

Adaptation - biological – the dynamic, multiscale means by which biological agents persist, flourish, and reproduce in changing environments. Within the APS (Agency–Process–Scale) framework, adaptation is understood as an agentive process that operates across temporal and spatial scales: from immediate behavioral responses to environmental challenges, to physiological and developmental plasticity, and ultimately to evolutionary change via natural selection. Adaptations may manifest as traits—structures, processes, or behaviors—that functionally contribute to the agent’s continued viability. As both outcome and process, adaptation reflects the biological imperative: the tendency of living systems to maintain functional coherence and achieve context-sensitive goals through inherited, enacted, and emergent means.
Agency - general - the capacity of a system to initiate and regulate actions in response to conditions of existence, typically involving goal-directed behavior. biological - the intrinsic capacity of living systems to sense, respond to, and adaptively regulate their internal and external conditions in ways that support persistence, coherence, and functional continuity across scales. Biological agency involves context-sensitive activity that promotes the organism’s own viability. human - biological agency extended and transformed by the evolved capacities of the human mind, including language, self-awareness, conscious deliberation, abstract reasoning, and temporal projection (hindsight and foresight).
Agent - general - an entity that acts or brings about effects; a source or instrument of activity through which a function, goal, or change is realized. Inanimate or mindless agents (e.g., missiles, machines, or software) may act without awareness or autonomy, as instruments of external design or control.biological - a living system—typically an organism—that exhibits semi-autonomous, goal-directed activity in pursuit of continued existence. As a biological agent, the organism actively regulates internal processes and interacts with its environment through energy, material, and information exchange. It senses, processes, and responds to conditions in ways that support its functional integration and persistence, consistent with the biological imperative. While agency may be distributed across scales (e.g., genes, cells, collectives), the organism remains the paradigmatic biological agent. Goals need not be consciously held to be real—they emerge from the system’s organized, adaptive constitution.
Agential realism - a philosophical position—central to the APS framework—that affirms the real, causal efficacy of agency in the natural world, including in non-human and non-cognitive organisms. biological that biological systems exhibit genuine, mindless agency grounded in their capacity to initiate, regulate, and coordinate context-sensitive activity in support of their own continued existence. Agential realism rejects the view that agency requires consciousness or intentionality, instead rooting goal-directedness and purposiveness in the organized dynamics of living processes. In this view, human agency integrates both mindless biological agency and evolved capacities for reflection, abstraction, and self-aware deliberation. Agential realism thus grounds cognitive metaphors in real biological functions, rather than projecting human-like minds onto non-human life.
Algorithm of life - life is autonomous and agential matter that self-replicates with variation that, by a process of evolutionary selection, incorporates feedback from the environment thus facilitating its persistence.

1. Endow units of matter with agency as a capacity to adapt to conditions of existence (i.e. to survive, reproduce, adapt, and evolve).
2. Combine the behavioral orientation of 1 with genetic modifications arising in each new generation
3. Expose 2 to evolutionary selection pressures resulting in differential survival
4. Surviving forms return to step 2

Anthropocentric - to view and interpret circumstances in terms of human experience and values
Anthropomorphism - the attribution of human traits, emotions, or intentions to non-human entities
Apomorphy - a specialized trait or character that is unique to a group or species: a character state (such as the presence of feathers) that is not present in an ancestral form
Autopoiesis - self-replication combined with self-maintenance and modification is sometimes referred to as autopoiesis
Behavior (biology) - the outward expression of the internal processes of biological cognition; actions performed by a biological agent (or, more loosely, its parts); the internally coordinated but externally observable response of whole organisms to internal and external stimuli. Behaviour may be: mindless or minded; conscious, unconscious, or subconscious; overt or covert; innate or learned; voluntary or involuntary. Learning capacity is graded in complexity
Behavioral ecology – the study of the evolution of animal behavior in response to environmental pressures
Biological agency - the capacity of autonomous living organisms as biological agents to act on, and respond to, their conditions of existence in a flexible way and with a unity of adaptive purpose - the goal-directed behavioral propensity to survive, reproduce, and flourish; the capacity of living organisms to act with intentionality; a life-defining property of living organisms; the motivation for biological activity as described by the biological axiom; the capacity of organisms to act with purpose and intentionality; the biological principle that has generated the entire community of life; the capacity organisms act intentionally in the sense that their behavior is purposeful and adaptive i.e. directed towards objects, properties, or states of affairs. Externally observable biological agency is generated by the internal processing of biological cognition.
Biological agent - while biological agency, in a broad sense. can be ascribed to almost any biological structure, process, or behavior, it is the organism that best serves as its exemplar, standard, or prototype cf. organism, biological agency. an organism as an autonomous unit of matter with a flexible and adaptive propensity to survive, reproduce, and flourish (the universal, objective, and ultimate unity of purpose shared by all life); biological agents, organisms are self-replicating units that regulate the internal and external exchange of energy, materials, and information that is required for their autonomous pursuit of goals
Biological axiom – The biological axiom refers to the universal and objective pattern of behavior exhibited by all living organisms: the persistent tendency to survive, reproduce, adapt, and evolve. These core capacities represent the ultimate outcomes toward which all proximate biological activities are directed. The axiom is universal (shared across all life), objective (independent of cognition or perspective), and ultimate (serving as the summative orientation of biological function). It expresses the foundational behavioral logic of life, often approximated in evolutionary terms as ‘fitness maximization.’ This axiom defines the constraints to which biological structures, processes, and behaviors are ultimately subordinate. It is descriptive of what organisms do across evolutionary time, outlining the pattern by which life operates at its most general. Biological Imperative (contrast)—central to the APS framework—refers to the intrinsic, present-tense drive or orientation of living systems toward continued viability. It captures the agential tendency of organisms to initiate, coordinate, and adapt their activity in real time, across multiple scales, in ways that sustain coherence and functionality. While the axiom is a retrospective summary of biological outcomes, the imperative is an ongoing process enacted by agents in context. In short, the biological axiom expresses what life does in evolutionary terms; the biological imperative expresses how life persists through active, organized agency.
Biological cognition - the accession, storage, interpretation, and processing of information necessary for biological agents to adapt to their conditions of existence. In its highly evolved sentient form, this entails the mental processes of perceiving, interpreting, and responding to stimuli that encompasses learning, memory, problem-solving, and decision-making, all grounded in the brain's structure and function as shaped by evolution cf. basal cognition, cognition. Biological cognition is manifested externally as biological agency.
Biological goal - the object towards which the behavior of a biological agent is directed. Biological goals are the natural ends or limits of internally generated biological processes that follow transparent causal pathways - the development of a structure, maturation of an organism etc. Their sources may be mindless, minded but unconscious, or conscious. Short-term proximate goals serve long-term ultimate ends. Goal-directedness confers both purpose and agency. Biological goals are usually observed and studied as the behavioral outcomes of internal processes.
Biological object - something from the living world that can be studied scientifically; taken to be either a structure (whole or part), process, or behavior
Biological Imperative - a foundational principle of life that refers to the intrinsic, evolved orientation of living systems toward persistence, functional integration, reproduction, and adaptive self-maintenance. The biological imperative is not a conscious drive but a systemic tendency, expressed through the coordinated processes that sustain an organism’s viability over time. While not itself one of the core categories of the APS framework, it underlies and motivates biological agency, shaping the processes through which agents act and adapt across scales. The biological imperative provides a naturalistic grounding for concepts such as function, normativity, and purposiveness in biology, distinguishing living systems from inert matter and enabling a coherent, non-reductive account of life’s organizational logic. It is a key unifying concept for theoretical biology, linking evolution, development, behavior, and cognition through a shared commitment to survival and functional coherence
Biological normativity - the mostly mindless, universal, objective, and ultimate behavioral rules and standards (conditions) essential to sustain life as the survival, reproduction, adaptation, and evolution of organisms (the biological axiom). The biological axiom is, in effect, a code of behavior for life - the conditions that constrain the possibilities of the structures, processes, and behaviors of organisms and grounding human morality.
Biological norms - the physiological, genetic, developmental, and behavioral ranges and standards of healthy functioning in organisms. The organismal propensity to persist is both a biological necessity driven by evolutionary pressures and a logical necessity contingent on the empirical premise that the goal of life is to continue existing. However, the notion that existence is ‘better’ than non-existence is shaped by subjective human values and the ethical reasoning that is an aspect of our human species-specific form of normativity. The universality of biological normativity and its functional equivalence across species demonstrates how uniquely human values and ethical considerations are grounded in our biological nature.
Biological principle - an underlying regularity of a biological system e.g. evolutionary principles (like natural selection), agential principles (survival, reproduction, adaptation, evolution), biochemical laws (like the laws of thermodynamics), or ecological principles (like the cycles of matter and energy flow). By understanding these principles, scientists can make predictions about biological outcomes and develop theoretical frameworks that explain how and why organisms behave and evolve in particular ways.
Biological process - refers to the dynamic, integrated mechanisms—physiological, behavioral, developmental, and evolutionary—through which agency is enacted. These are not static routines but flexible, feedback-sensitive patterns of activity.
Biological simile – a comparison (likeness) of biological phenomena that is based on real evolutionary connection
Bioteleological realism - the claim that purposes exist in nature and that most cognitive metaphors used in science are grounded in non-cognitive biological facts
Biosemiotics - the study of the production, interpretation, and communication of signs and meanings in living systems
Bioteleology - purpose resides in the fact that there are natural ends or limits to biological processes (e.g. the maturing of an acorn into an oak tree; the termination of a mating ritual in copulation), that these ends are objectively  goal-directed and therefore purposive. Teleonomy controversially interprets teleology as implying a metaphysically questionable source of purpose. The word teleonomy attempts to replace this purported implication with a naturalistic explanation. The distinction between teleology and teleonomy, and whether that distinction is warranted, remains unclear
Cognition - the internal processing that precedes and guides the behavior of biological agents; the goal-directed and adaptive process of acquiring and interpreting information about the conditions of biological existence;  the acquiring, processing, storing, organizing, prioritizing, and communication of information. In its highly evolved and limited human form, it involves perception, memory, reasoning, and problem-solving, allowing individuals to understand their environment, make decisions, and establish knowledge through experiences and interactions with the world cf. basal cognition, biological cognition
Cognitive ethology – the study of the influence of conscious awareness and intention on the behavior of an animal
Cognitive metaphor - a metaphor used in the context of human intentional psychology. When we have no words to describe real pre-cognitive agential traits, we resort to the language of human cognition, thus condemning these traits to the figurative world of metaphor
Complementary properties – the properties instantiated by the relata of a biological simile
Conditions of existence (biology) - those factors influencing the inner processing of organisms including triggers arising from both inside and outside the organism.
Derived concept – a concept with a narrow semantic range
Emergence - as used here - the origin of novel objects, properties, or relations in the universe that warrant human categorization
Environmental factors - the external factors impacting on the existence of an organism
Evolutionary biology – the study of evolutionary processes (notably natural selection, common descent, speciation) that created the community of life
Fitness - a measure of reproductive success (survival) in relation to both the genotype and phenotype in a given environment
Function - In the APS framework, a function is the role a biological structure, process, or behavior plays in supporting the persistence, coherence, or reproduction of a biological agent. Functions are not merely effects, but contributions to the organized activity of the whole system, understood in relation to biological agency. They may be viewed both as evolutionary outcomes (etiological functions) and as current systemic contributions. In APS, function is naturalized—grounded in agency, realized through processes, and distributed across scales.
Functional equivalence - performing the same function through the unique structures, processes, and behaviors of different organisms and species
Genotype - the genetic constitution of an individual organism, encoded in the nucleus of every cell
Goal - (biological) a dynamically maintained end-state or functional condition that an organism or biological system tends toward through internally regulated activity, arising from its capacity as an agent embedded in multiscale biological processes.
Grounding concept – the general ideas that underpin more specific (derived) concepts
Heuristic – stimulating interest and investigation
Holobiont – an aggregation of the host and all of its symbiotic microorganisms
Homeorhesis - (Gk - similar flow) a term applied to dynamic systems that return to a specific path or trajectory, in contrast with systems that return to a particular state (homeostasis). Homeostasis refers to the maintenance of a stable internal environment in response to external changes (e.g. body temperature in mammals) while homeorhesis is the adjustment, sometimes changing over time, to meet particular organismal functions or goals (e.g. changes in blood composition that support the fetus during pregnancy).
Homology – a similarity in the structure, physiology, or development of different species of organisms based upon their descent from a common evolutionary ancestor
Human agency - behavior motivated by conscious intention; the uniquely human specialized form of biological agency that is described using the human agential language of intentional psychology; the capacity to act based on reasons as cognitive and motivational states (beliefs, desires, attitudes) (philosopher Kim)
Human-talk - the language of humanization - the attribution of human characteristics to non-human organisms, objects, and ideas. (Biology) the description of non-human organisms using language that is usually restricted to humans and human intentional psychology; the use of cognitive metaphor to describe non-cognitive but real biological agency; the psychologizing of adaptive explanations
Intention - a cognitive goal, or pre-cognitive behavior that is directed towards objects, properties, or states of affairs
Intentional idiom - the use of intentional language in a wide range of contexts including those relating to non-human organisms
Life – units of matter with the agential capacity to survive, reproduce, and flourish (cf. biological axiom) as best exemplified by autonomous organisms. Life processes, such as growth, reproduction, response to stimuli, and metabolism are subordinate to the organismal wholes of which they are a part
Metabolism - the set of processes that sustains an organism (or, more generally, any biological system)
Metaphor - figurative language as ‘nonliteral comparisons in which a word or phrase from one domain of experience is applied to another domain’. An 'as if' direct (not a 'like') comparison that is not grounded in reality e.g. 'You are a rat'.
Natural agency - any agency in the natural world
Natural purpose - the natural goals, ends, or limits of biological agents, both cognitive and non-cognitive
Normative realism - the view that normativity has its origin in biology through the mindless and mindful ultimate goals of survival and reproduction, and proximate goal of flourishing
Organism - unicellular to multicellular life forms that include fungi, plants, and animals. The mostly physically bounded and functionally organized basic unit of life and evolution. As a mostly autonomous biological agent the organism acts on, and responds to, its conditions of existence with flexible but unified and goal-directed behavior that demonstrates the objective, ultimate, and universal propensity of organisms to survive, reproduce, and flourish. While life can be described at many scales and from many perspectives (and the structures, processes, and behaviors of organisms all demonstrate a degree of autonomy), it is the entire organism that provides the agential reference point of life - whose autonomy is both intuitively and scientifically most discrete. Exceptional cases such as lichens, Portuguese Men-o-War, the Great Barrier Reef, sexually aberrant variants etc., do not erode these core characteristics.
Organismal factors - the internal factors impacting the existence of an organism
Personification - the representation of something in the form of a person
Phenotype - the set of observable characteristics of an individual resulting from the interaction of its genotype with the environment
Physical reductionism - the view that biological phenomena can be adequately explained in terms of physico-chemical entities
Process ontology – it is processes that create phenomena including emergent and ephemeral ‘things’ which are derived from processes as transient and cohesive patterns of stability within the general flux. Thus, things are derivative of processes. In practical terms this does not mean that things do not exist or are not useful concepts. However, instead of thinking of processes as belonging to things, it is more scientifically informative to think of things as derived from processes. Organisms are prime examples of transient things in process
Proximate explanation - an explanation dealing with immediate circumstances: the immediate mechanisms and processes behind biological phenomena, including genetic, developmental, and physiological factors specific to individuals or species
Purpose – the n the APS framework, purpose refers to the context-sensitive, adaptive orientation of biological agents—typically organisms—toward outcomes that support their persistence, coherence, reproduction, or flourishing. It is not externally imposed but emerges from the intrinsic, multiscale activity of living systems as they regulate and coordinate themselves. Biological purpose is grounded in agency and expressed through structures, processes, and behaviors that contribute to an organism’s continued existence—that is, what they are for in functional terms. While function often applies to parts (e.g. a heart pumps blood), purpose refers to the integrated role such functions play in sustaining the whole organism as an agent. Purpose thus precedes cognition and is evident in all living systems. Human purposes, involving intention and mental representation, are a specialized cognitive form of this broader biological purposiveness. Though historically linked to Aristotle’s telos, purpose in the APS view is not metaphysical but explanatory. Darwin naturalized it, showing how purpose and agency arise through evolution. Purpose names the organized, goal-directed orientation of life—not eliminated by causal explanations, but understood as the coordination of means to ends across biological scales.
Reduction - - a mode of explanation that explains a ‘whole’ by breaking it down into its constituent parts, focusing on the components themselves. Saying ‘A house is an assemblage of bricks’ is an example of reduction, as it emphasizes the individual elements that make up the structure cf. synthesis
Relata – the objects being compared
Semantic range – the degree of generality or abstraction encompassed in the meaning of a word - range of objects and ideas encompassed by its meaning
Synapomorphy - a characteristic present in an ancestral species and shared exclusively (in more or less modified form) by its evolutionary descendants
Synthesis - a mode of explanation that explains a ‘part’ in terms of its role, function, or purpose within a greater whole. This approach considers how parts contribute to and interact within a broader context. Saying ‘A house, as an aggregation of bricks that provides shelter and a space for living’ emphasizes the function and relationship of parts to the whole cf. reduction
Teleology - the philosophical concept of purpose and design in the natural world. The claim that natural phenomena occur for reasons as natural ends or purposes that are neither necessitated by human or supernatural intention nor implying backward causation or foresight. For teleology in biology see bioteleology. The article on bioteleology discusses 8 senses of 'teleology'
Teleonomy - see bioteleology
Temporal scale - in the APS framework, temporal scale refers to the duration, frequency, and timing of biological processes. Just as spatial scale ranges from molecules to organisms to ecosystems, temporal scale ranges from milliseconds (e.g., neural firing) to years (e.g., development) to millennia (e.g., evolution). Biological functions often depend on precise timing and multiscale coordination, making temporal scale essential to understanding agency and process.
Trait - a unit of the phenotype (physical or behavioral)
Ultimate explanation - a long-term, often evolutionary, explanation (e.g. in biology the purpose or measure of fitness of a particular trait); the reasons or adaptive significance behind biological phenomena, focusing on universal principles that apply across species and contexts
Umwelt - an agent-centric orientation to the world; the environment of adaptive significance for a particular organism - its unique perspective or 'point of view': those factors important for its survival, reproduction, adaptation, and evolution: its mode of experience or 'reality'. For humans, this is the commonsense world of everyday experience (cf. manifest image) that is mostly a consequence of our innate mental processing which is, in turn, a consequence of our uniquely human evolutionary history
Values – (biological agency) that which ultimately motivates the behavior of biological agents (living organisms), namely the universal and objective goals of the biological axiom. Human agency - the proximate and subjective attitudes, beliefs, and inclinations that guide human behavior