Agency, Process, Scale (APS)

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The development of the APS (Agency–Process–Scale) framework and the broader philosophical work on biological agency, functional equivalence, process philosophy, and the problem of scale has evolved over many years through independent research, writing, and scholarly reflection, much of which is available on plantspeopleplanet.au.

The recently published preprint (Spencer, 2025), Biological Agency as the Context for Plant Cognition (Available here: https://www.researchgate.net/publication/393418083_Biological_Agency_as_the_Context_for_Plant_Cognition), represents a culmination of this trajectory and includes an explicit acknowledgment of the use of AI tools—specifically ChatGPT, Copilot, and DeepSeek—for drafting, refining, and clarifying scientific language and structure.

AI tools were first incorporated regularly into my writing process around April–May 2024, with ChatGPT serving primarily as a tool for improving clarity, coherence, and expression, rather than as a source of novel scientific hypotheses or conceptual frameworks. All core theoretical contributions, including the formulation of the APS framework and its application to plant cognition, were conceived and developed independently by the author.

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‘The APS framework redefines life as a dynamic interplay of Agency, Process, and Scale, offering theoretical biology a unifying, non-reductionist foundation that integrates function, evolution, and organization across all living systems.

Life is best understood not as a collection of structures, but as the capacity to actively sustain and regulate one’s own existence across time and scale. The APS framework—Agency–Process–Scale—defines biological agency as the intrinsic, multiscale, self-organizing activity by which living systems maintain coherence far from equilibrium. From protocells to ecosystems, this perspective unites evolution, development, and cognition under a single generative principle: to live is to act in the service of continued existence. Agency is not just a feature of life—it is what makes life possible.

Agency, Process, Scale (APS)

The major features of an agency defined, and process-based, understanding of life.

Biology is fundamentally processual: life is not a set of things but a continuous unfolding of activity. Yet, our diagrams are necessarily static, usually 2-dimensional, snapshots. This can mislead us into thinking of living systems as fixed entities with discrete properties. The APS framework explicitly rejects this view:

• Agency is ongoing coordination, not a static trait.
• Processes are flows and feedback loops, not isolated mechanisms.
• Scale is temporal and nested, continuously shifting as living systems persist and evolve.

Static graphics can only hint at these dynamics. Animation, interactive diagrams, or time-based visualizations would more accurately convey the active, self-organizing character of life that APS seeks to foreground. The figure should be read as a conceptual scaffold, not a literal map of living systems.

See also biological agency, plant agency, and plant cognition, and APS Frameworl Overview

Schematic produced by AI Co-Pilot

Introduction

‘The APS framework defines living systems as agential, processual, and scale-dependent—entities that persist and evolve by coordinating internal and environmental processes across time and space.’

What is the APS Framework?

The Agency–Process–Scale (APS) framework (Spencer, 2025) offers a new way of understanding life. At its core is the idea that biological agency—the capacity of living systems to regulate themselves, adapt, and pursue functional outcomes—is the defining feature of life (the biological imperative). Instead of viewing life as a collection of structural traits or static categories, APS sees it as a dynamic, multiscale process organized around purposeful activity.

In this view, living systems—from single cells to ecosystems—are not passive machines or chemical reactions. They are active participants in ongoing processes of self-production, interaction, and transformation.

How is APS different?

Traditional biology has often emphasized structure, classification, and hierarchy. It tends to describe what organisms are made of rather than what they do—prioritizing anatomy over function and relying on checklists of traits like metabolism or reproduction to define life. Biological phenomena are typically explained through mechanistic, hierarchical, bottom-up models that treat agency and purpose as metaphorical or illusory.

These explanations are commonly arranged into rigid hierarchical ‘levels’—from molecules to cells to organisms and ecosystems—implying a linear build-up of complexity. This level-based view can obscure the dynamic, reciprocal interactions that make life coherent and adaptive.

Why Do We Need a New Framework?

Modern biology has produced extraordinary insights, but its disciplines—genetics, physiology, ecology, neuroscience, etc.—often remain siloed, lacking a unifying theoretical foundation. The APS framework addresses this by offering a cohesive lens through which to view life as agential, processual, and multiscale—from molecular networks to evolving ecosystems.

APS reorients biology around what life does to sustain itself over time. It places agency—not as an illusion, but as a biological capacity—at the heart of living systems. These systems act to maintain their own integrity, respond to changing environments, and evolve across generations.

Instead of rigid hierarchies, APS proposes a relational view of scale, where biological organization emerges from interactions across multiple scales simultaneously. It also emphasizes functional integration: the coherence and viability of living systems depend on the coordination of processes that serve the system as a whole.

In doing so, APS highlights the active, purposive, and evolving nature of life—offering a conceptual foundation capable of integrating diverse biological insights.

Why Does APS Matter Now?

As biology expands to explore plant intelligence, microbial communication, and non-neural cognition, the limitations of mechanistic, level-based models become more apparent. APS provides a framework for interpreting these phenomena without reducing them to lower-level mechanisms or dismissing their significance.

By grounding cognition, adaptation, and function in biological agency, APS broadens what counts as meaningful biological activity—opening new possibilities for understanding life in all its complexity.

Defining Life in the APS Framework

The definition of life has long been debated. Some emphasize energy and thermodynamics—life as a “far-from-equilibrium system.” Others stress evolution—life as that which can survive, reproduce, and evolve. Still others focus on autonomy, self-maintenance, or information processing. Each highlights a different facet of a complex phenomenon.

The APS framework helps reconcile these perspectives by integrating them into a coherent picture of what it means to be alive:

Agency refers to the capacity of living systems to organize and sustain their own existence.
Process captures the metabolic, developmental, and regulatory activities that constitute life.
Scale highlights the multilevel organization of living systems, from molecules to organisms to ecosystems.

In this view, life is not defined by a single trait, but by the interplay of three core principles:

The biological axiom defines life in principle—as the capacity to survive, reproduce, adapt, and evolve.
The biological imperative describes how life operates in practice—through the intrinsic tendency of living systems to sustain, regulate, and regenerate their own organized existence.
Biological agency provides the means—through coordinated, multiscale activity that enables organisms to enact this imperative.

Together, these elements reflect the logic of the APS framework: the axiom states what life must achieve; the imperative shows how this is functionally enacted—as what living systems must do, an intrinsic and directional tendency (the “why” of function); and agency explains how living systems organize to do it—the coordinated, multiscale means of fulfilling that propensity.

Rather than offering competing definitions, traditional accounts of life can be understood as emphasizing different aspects of this integrated framework. The APS model draws these together: the biological axiom defines what life must achieve in evolutionary terms, the biological imperative expresses this as a functional, system-internal drive, and biological agency describes how that drive is enacted across scales of organization.

• • • Biological Axiom = formal principle or foundational assumption (what life must do)

    • Biological Imperative = functional tendency, orientation, or expression (how life does it)

    • Biological Agency = system-level capacity or means (how life organizes to do it)

This biological agency is expressed not just in animal activity but across all life forms, including plants. As agents, all organisms embody a unity of purpose—an evolved, functional coherence grounded in their capacity to sense, respond, and adapt to the conditions of existence. This agentive coherence entails internal coordination (e.g., self-regulation, reproduction, adaptation) and interactive engagement with the environment, enabling organisms to persist as historically shaped, self-maintaining systems.

The biological imperative

At the heart of the APS framework is the biological imperative—the intrinsic, self-sustaining orientation of a living system to maintain and regenerate the conditions of its own existence. This imperative is not an externally imposed goal or functional outcome, but the ongoing activity of the system to continue being what it is.

Every living organism, from a single cell to an ecosystem, exhibits this imperative through continuous processes of regulation, adaptation, and functional coordination. It is not simply about surviving or reproducing as outcomes; it is about the ongoing enactment of agency—life as an active, situated, and processual response to changing internal and external conditions.

How the Biological Imperative Relates to APS Principles
Grounded in Agency: The imperative operates because the system is an agent—it has the capacity to sense, respond, and regulate. Agency makes the imperative real and functional, not just abstract.

• • • Realized through Process: The imperative is not possessed but enacted—through metabolism, development, signaling, behavior, and repair. These dynamic processes continuously sustain the system’s organization.
    • Expressed across Scale: From intracellular dynamics to organismal behavior and ecological interaction, the imperative manifests at multiple levels. Its form and function vary by scale, but its role is consistent.

Why It Matters Theoretically
The biological imperative provides a unifying, non-reductive way to explain why living systems behave as they do:

• • • It grounds normativity in biology: living systems “ought” to preserve their own viability, not by prescription, but because disintegration is the consequence of failure.
    • It supersedes trait-based definitions: rather than enumerating features like metabolism or reproduction, the imperative defines life as a dynamic tendency toward self-coordination and persistence.
    • It integrates cognition and behavior: regulation, responsiveness, and coordination are not add-ons but intrinsic to biological agency, linking cognitive capacities to the fundamental dynamics of life.

In sum, the biological imperative is a foundational concept in APS. It links agency (what life is), process (how life works), and scale (where life operates), forming a coherent, descriptive, and explanatory principle. It allows biology to account for life as a self-organizing, purposive, and yet non-teleological phenomenon.

Six Key Principles

The Agency–Process–Scale (APS) framework offers a fresh perspective on what it means to be alive. Rather than defining life by a fixed checklist of traits, APS centers on the capacity of living systems to act purposefully—to sustain themselves through coordinated, adaptive processes that unfold across multiple interacting scales.

The following six principles summarize the core insights of APS, showing how life is an evolving, integrated system of agency that persists through diverse forms and functions. Together, they provide a foundation for understanding biology not as static structure, but as dynamic, self-maintaining activity.

1. Defining Life: imperative and agency in the APS Framework

The APS framework defines life through the interplay of three principles: the biological axiom, imperative, and agency. The biological axiom describes what life must achieve in principle—survival, reproduction, adaptation, and evolution. The biological imperative gives this axiom functional form: it is the intrinsic tendency of living systems to sustain, adapt, and regenerate their own organized existence across time. This imperative distinguishes living from non-living systems by establishing an ongoing, purposive orientation toward self-maintenance and functional continuity. Biological agency is how this imperative becomes observable. It is the capacity of a living system to regulate itself, coordinate internal processes, and respond adaptively to environmental conditions in ways that promote its own persistence.

At the heart of APS is a powerful claim: living systems are agents. They do not merely persist—they take initiative. From single-celled organisms to complex multicellular life, agency marks the ability to act in pursuit of survival and functional viability. This includes sensing, responding, repairing, reproducing, and engaging with the environment in selective, meaningful ways.

In this view, agency is not metaphorical—it is essential. Without some form of purposive regulation oriented toward sustaining itself, no structure, trait, or molecular mechanism alone is sufficient to constitute life. Agency is what makes the biological imperative real in any specific instance (Walsh, 2015; Okasha, 2020, 2023; Levin, 2023a, 2023b; Sultan et al., 2022; Corning et al., 2023; Fulda, 2023; Gilroy & Trewavas, 2023; Virenque & Mossio, 2023; Walsh & Rupik, 2023; DiFrisco & Gawne, 2024; Dodig-Crnkovic & Burgin, 2024; Fábregas-Tejada et al., 2024; Rosslenbroich et al., 2024; Švorcová, 2024).

To define life rigorously, it is necessary to identify the conditions under which agency emerges. In minimal systems—such as protocells, bacteria, and basal multicellular organisms—agency arises through endogenous processes that maintain organizational integrity and enable adaptive interaction with the environment. These systems demonstrate selective environmental engagement, constraint modulation, and an orientation toward persistence grounded in the biological imperative.

This poses several conceptual challenges. Agency must be operationalized without invoking anthropocentric or teleological assumptions, and it must be shown to apply to systems without nervous systems. Organisms like plants, fungi, and microbial communities exhibit adaptive, anticipatory, and context-sensitive behaviors through distributed processes. Their agency shows that purposive organization can precede and operate independently of neural control.

While genes are essential to inheritance and development, they are not themselves the source of agency. Agency is a system-level property—emerging from the coordinated functioning of genetic, epigenetic, physiological, and environmental processes. Life is not defined by the presence of genes, but by the capacity to organize and sustain itself over time. Genes are part of the means; they do not constitute the defining condition of life.

Natural selection plays a crucial role in shaping which forms of agency endure, but it is agency that enables evolution in the first place. Only systems capable of variation, persistence, and reproduction can be subject to selection. Thus, selection and agency are co-defining: evolution shapes agency, and agency provides the foundation for evolutionary dynamics.

In summary, the APS framework holds that life is defined by the biological imperative and realized through biological agency. The imperative provides the criteria for what life must achieve; agency describes how life achieves it. Together, they establish a biologically grounded, non-reductionist, and scalable definition of life that accounts for both the persistence and diversity of living systems.

2. Living Systems as Agents: beyond passive mechanisms

Rather than treating life as a set of static features—organs, molecules, genes—APS sees life as ongoing, adaptive process. Living systems metabolize, develop, interact, and evolve in ways that support their continued viability. These are not arbitrary sequences, but functionally coordinated processes that enact the biological imperative. To understand life, we must understand how these temporal patterns serve the system’s persistence. APS reframes evolution as the transformation of these functional capacities—how organisms adapt their ways of acting and interacting to better sustain themselves. This processual view links domains from molecular biology to cognition, offering an integrated account of life in motion (see the process philosophy of Moreno & Mossio, 2015; Dupré & Nicholson, 2018; Dupré, 2020; Meincke, 2023a; Gómez-Márquez, 2023).

Biological agency is sustained not by static structures but by the dynamic interplay of metabolic, regulatory, developmental, and evolutionary processes. To advance the APS framework, research must operationalize a process ontology—treating organisms as constituted by activity rather than structure—and develop models that explain how these interdependent processes cohere to maintain functional integrity. Central to this is the role of endogenous rhythms, which structure biological time from within and coordinate activity across scales. A theory of biological temporality, grounded in these rhythms, could redefine how time is understood in living systems. Additionally, plasticity—the capacity to reorganize in response to disruption—is key to understanding how organisms adapt, persist, and evolve. Clarifying the mechanisms and limits of plasticity will illuminate how agency is preserved under changing conditions. Together, these efforts will shift biology toward a fully processual understanding of life.

3. Multiscale Organization as a Feature of Life

Life unfolds across multiple, interconnected scales—molecular, cellular, physiological, ecological. These are not isolated levels but dynamically interacting scales through which the biological imperative is expressed and sustained. A shift in one part (like a genetic mutation or an environmental signal) can propagate through the system, altering behavior or function at other scales. APS emphasizes that biological systems are organized not as a hierarchy, but as a web of mutually constraining and enabling processes. To understand how life persists and adapts, we must grasp how these scales co-regulate and co-produce agency.

Plant agency illustrates how functional organization can be distributed across systems lacking centralized control. Plant networks of signal transduction, hormonal coordination, and structural adaptation operate coherently across cellular, organ, and organismal levels. Over generations, these agential processes contribute to evolutionary scale change, such as the emergence of new morphologies or symbiotic relationships. Plants thus provide a living example of how scale and agency are deeply entwined in the persistence and innovation of life.

4. Functional Continuity Through Coordinated Processes

Biological agency is not fixed—it evolves. Living systems inherit not just genes but ways of acting: regulatory strategies, behavioral repertoires, developmental trajectories, and ecological engagements. These inherited forms of agency reflect how past systems met their biological imperatives, and they shape how current systems meet theirs. Evolution, in this view, is the history of viability-preserving capacities—how organisms develop and refine their modes of persistence. Agency is both a product of evolution and a force that shapes it: as organisms evolve new ways of acting, they open new paths for future evolution.

5. Cognition Without Brains: adaptive biological systems

Living systems are not collections of parts—they are functionally integrated wholes. Every part and process works in coordination with others to sustain the system’s viability. A heartbeat matters only in the context of circulation; a receptor only has meaning in guiding behavior. This integration is how the biological imperative is enacted: through dynamic coordination that supports adaptive persistence. Importantly, this coherence is not imposed from outside but arises from the system itself. APS highlights that life is self-organizing and self-maintaining—not because it fits a blueprint, but because its parts work together to keep the system going in a world of constant change.

6. Agency as the Enabler of Evolutionary Change

Living systems sustain themselves not through fixed structures, but through functions that can be achieved in different ways. APS highlights functional equivalence as a core principle: the idea that diverse mechanisms can serve the same viability-preserving role. This allows organisms to adapt, reorganize, and evolve while preserving agency. Functional equivalence explains how different species—or even different parts within a single organism—can perform similar regulatory tasks using distinct means.

For example, plants sense and respond to their environments without neurons. Their cognitive capacities—such as learning, memory, and decision-making—are implemented through cellular and biochemical signaling networks that are structurally unlike animal nervous systems but functionally equivalent in guiding adaptive behavior. These differences in mechanism do not undermine the reality of plant cognition; they reveal how agency can take many forms.

In APS, functional equivalence bridges structural diversity and functional unity. It shows that what matters for life is not what a system is made of, but what it does to stay alive.

From Agency to Cognition

The APS (Agency–Process–Scale) framework gives us a powerful new lens for understanding life. But to fully appreciate its scope, we need to go a little deeper—especially when it comes to concepts like cognition, behavior, and how agency develops across scales. What does it mean to say that even simple cells are cognitive? How do agents evolve, and what distinguishes a bacterium from a brain? This section unpacks these ideas in clear and accessible terms.

1. Cognition Begins with Life

When we hear the word “cognition,” we often think of human thought—reasoning, imagining, making decisions. But in biology, cognition has a much broader meaning. It refers to the capacity of a living system to sense, interpret, and respond to its environment in ways that support its continued existence.

In this light, even the simplest cell displays a basic form of cognition. A bacterium that moves toward food or away from toxins is not just reacting—it is acting to keep itself alive. This is what the APS framework means by agency: the capacity of a system to regulate itself through meaningful interaction with its world.

Cognition, then, is not a special feature added on top of life—it’s part of what life is. And it exists on a continuum: from chemical signaling in cells, to plant growth toward light, to the planning minds of humans. All are examples of systems interpreting and responding to their world.

2. Agents, Cognition, and Behavior: A Living Trio

To understand cognition more clearly, it helps to break things down:

Agents are systems that act to maintain themselves—whether they’re cells, plants, animals, or entire ecosystems.

Cognition is how agents process information about their situation to guide action.

Behavior is the outward expression of that process—the actions an agent takes.

Defining the APS Triad
The APS framework redefines life as the orchestration of three interrelated dimensions:

Agency is the intrinsic capacity to regulate, adapt, and sustain functional integrity through context-sensitive action. It includes even minimal, non-conscious responsiveness (Barandiaran et al., 2009).

Process denotes the ontological substrate of life: the interdependent activities—metabolic, developmental, behavioral—that maintain system identity through transformation and flow (Dupré & Nicholson, 2018; Meincke, 2023a).

Scale provides the context for agency and process. Biological systems operate across spatial and temporal scales, where feedback between scales enables resilience, innovation, and evolution (Gómez-Márquez, 2023).)

These three concepts are tightly linked. Agency gives rise to cognition; cognition shapes behavior; behavior feeds back into agency by influencing future conditions.

A bacterium senses sugar → moves toward it → consumes it.
Agent → Cognition → Behavior.

What makes this powerful is that it scales. A neuron fires to regulate a heartbeat. A dog anticipates its owner’s return. A forest maintains its internal climate. All involve systems that know something about their world and act accordingly.

3. Why Scale Matters: Cognition Across Scales of Life

Living systems are organized across multiple scales—from molecules to cells, tissues, organisms, and ecosystems. APS emphasizes that these scales are not stacked in a rigid hierarchy. They are interconnected scales of activity that influence and depend on each other.

Cognition is present at each of these scales. A cell processes chemical cues; an organ regulates internal balance; a predator surveys a landscape. As systems grow more complex, their cognitive capacities expand—not because they add something entirely new, but because they evolve new means of coordination (like nervous systems, social structures, or language).

Cognition is scale-sensitive. A tree grows toward light just as a human grows toward understanding—each in its own way.

Understanding life, then, means tracking how cognition is organized differently at each level, and how agency gets distributed, coordinated, and transformed.

4. Principles vs. Operations: How APS Helps Us Think Clearly

As we explore these ideas, it’s important to distinguish between two ways of talking about life:

Principles are the big ideas that explain how life works—like agency, process, and scale.
Operations are what living systems actually do—like metabolizing, sensing, repairing, and evolving. In APS, agency is a principle: it helps us understand why systems behave in coherent, purposeful ways. But it is also visible in real operations—how organisms actually survive and adapt. Likewise, cognition is both a general capacity (principle) and a set of actions (operations) that unfold through time.

Principle = the logic of life.
Operation = the activity of life.

Keeping this distinction clear helps us avoid confusion. It lets us see that the same principles apply whether we’re looking at the behavior of a cell or the deliberations of a conscious mind.

5. Persistence, Inheritance, and Transformation: The Dynamics of Living Cognition

Cognition doesn’t just appear and disappear. It persists, it’s inherited, and it transforms over time:

Persistence: Living systems maintain themselves across time through coordinated behavior.

Inheritance: They pass on not just genes, but entire ways of acting—patterns of regulation, responsiveness, and even learning.

Transformation: Over evolutionary time, agency evolves. Cognition becomes more complex, more reflective, more free.

This is where the APS framework connects beautifully with evolutionary accounts like Kevin Mitchell’s Free Agents (2023), which traces how simple metabolic regulation gives rise—through millions of years—to nervous systems, minds, and eventually to free will.
Life starts by doing the work of staying alive.
Over time, that work becomes the capacity to reflect, imagine, and choose.

This view unifies the physical basis of life with the richness of mind. It shows how agency is not a binary trait but a growing repertoire—rooted in biology, elaborated through history, and flowering into consciousness.

Making sense of life: three triads

The APS framework organizes our understanding of life around three interconnected triads—sets of three key concepts that work together to describe how living systems function, persist, and evolve. These triads are not separate layers, but mutually reinforcing dimensions of biological organization.

The relationship between the triads of agency, process, and scale; persistence, inheritance, and transformation; and agent, cognition, and behavior can be understood as a progression from foundational principles to observable phenomena. The first triad—agency, process, and scale—offers a theoretical framework for understanding life as a dynamic, self-organizing phenomenon that unfolds across multiple levels of biological organization. The second triad—persistence, inheritance, and transformation—translates these abstract principles into operational terms, describing how living systems maintain themselves, transmit continuity across generations, and actively reshape themselves and their environments. The third triad—agent, cognition, and behavior—captures how these dynamics appear in the world: not only in individual organisms, but across nested systems such as cells, collectives, and ecosystems, all of which can exhibit forms of agency, responsiveness, and coordination.

Taken together, these three triads move from theory to function to observation, providing a coherent way to understand life as a process that is at once self-sustaining, historically embedded, and expressed through behavior across scales.

1. Agency – Process – Scale
This is the foundational triad of APS. It reframes biology by asking not just what life is, but how it acts, changes, and spans across different levels of organization.

• Agency refers to the capacity of living systems to regulate themselves—to sense, respond, and act in ways that support their continued existence.

• Process highlights that life is dynamic. Rather than being a collection of static traits, it is made of ongoing, interlinked activities—metabolism, development, evolution.

• Scale recognizes that these processes and forms of agency operate across multiple dimensions: from molecules to ecosystems, from milliseconds to evolutionary epochs.

Together, this triad shifts biology from things to systems-in-action—alive because they are doing something, at every level and every moment.

2. Persistence – Inheritance – Transformation
This second triad unpacks how life continues and changes over time. It gives a functional description of evolution and development without relying solely on gene-centric explanations.

• Persistence is the capacity of a system to maintain itself—to keep functioning as a coherent whole.

• Inheritance allows that persistence to extend across generations, through the transmission of structures, capacities, and patterns of behavior—not only genes but also epigenetic, cellular, ecological, and cultural legacies.

• Transformation is the ongoing modification of these systems—the emergence of new forms, functions, and agents through evolution, learning, or environmental shifts.

This triad captures how life endures, propagates, and adapts. It shows that evolution is not just about changing traits but about modifying the ways agents function.

3. Agent – Cognition – Behavior
The third triad focuses on the individual and collective dynamics of living systems, linking self-regulation, perception, and action.

• An agent is any living system that actively maintains itself through interaction with its environment.

• Cognition is how that agent interprets signals and conditions to guide its actions—not limited to brains, but found in all forms of life, from bacteria to forests.

• Behavior is the visible expression of agency and cognition—the system acting in the world to maintain or enhance its viability.

This triad reveals that cognition is not an optional feature of life—it emerges from agency and underlies all behavior. It scales naturally from simple chemotaxis in microbes to learning in animals and cooperation in ecosystems.

Important Ideas

Biology, as traditionally taught and practiced, has often emphasized form over function, structure over process, and space over time. Living systems have been categorized as if they were stable, spatial objects—organs, species, molecules—while the inherently dynamic, time-bound nature of life has remained under-theorized. With rare exceptions (such as evolutionary theory), biological explanation has largely sidestepped the deep integration of temporality, agency, and scale.

The APS (Agency–Process–Scale) framework offers a transformative response to these limitations. It reconceives life as a dynamic interplay of agentive activity, temporal process, and multiscalar organization, directly addressing foundational problems that conventional biology has long bracketed:

• • • What does it mean for life to persist through time?
    • How do we reconcile teleological behavior with naturalistic explanation?
    • Can we ground biological function and purpose without invoking design?

By integrating agency as the capacity of living systems to initiate and regulate activity, process as the unfolding of life in and through time, and scale as the nested, interacting contexts in which biology operates, APS provides a unified conceptual framework. It enables us to rethink longstanding issues such as the definition of life, the naturalization of purposiveness, and the ontology of biological categories—not as static entities, but as temporally enacted, self-organizing systems.

What follows are some of the most important new ideas that the APS framework brings to light—each addressing a critical blind spot in the foundations of biological theory.

Plants exemplify agency through their autonomous activity: photosynthesizing, growing, healing, reproducing, and adapting without centralized control. Though often underestimated, their biological agency is neither passive nor reactive, but grounded in sophisticated processes of environmental monitoring, communication, and anticipatory adaptation. Over evolutionary time, this agency has enabled plants to flourish across nearly every terrestrial niche, becoming the foundational energy source and ecological context for other life forms.

1. Process & time: neglected dimensions in biology

How is time understood, represented, and integrated into biological categories and explanation?

The Ontological Problem of Time in Biological Categories

Biology, particularly in its historical and educational traditions, has often treated living systems as if they were fixed spatial objects—entities defined by their structural form (e.g. anatomy, morphology, taxonomy). Organisms are described as discrete entities, species as stable classifications, and cells as compartments bounded in space.
This spatial bias has led to an ontological flattening of life, where categories like “organism,” “cell,” or “gene” are taken as temporally static units, despite being dynamically constituted through time.
The philosophical problem arises when we notice that these biological “objects” are not truly stable. They persist only through continuous change:

• Molecules degrade and are replaced.
• Organisms age, grow, reproduce, and die.
• Species emerge, adapt, diverge, and go extinct.

Each of these categories is, in reality, a process through time, not a static thing. Yet biology often treats these as enduring abstract identities—as if there were a stable essence of “frog” or “cell” outside of time. This tension between categorical stability and processual impermanence creates a deep metaphysical challenge:

How can we reconcile the temporality of life with the timelessness of categories?
This echoes philosophical questions raised in the metaphysics of identity and persistence:

• Is a biological entity the same if all its parts change over time?
• What is the ontological status of a species, if it is defined by both its historical continuity and evolutionary divergence?
• Can we have a biological theory that does not reify processes into things?

Biological entities thus present a hybrid ontology—they are temporal processes that we speak of as spatial objects.

Why Biology (Mostly) Ignores Time—Except in Evolution

With the exception of evolutionary theory, biology has often marginalized or simplified time for both epistemic and methodological reasons:

1. Observation Bias Toward Stability
Biology has historically focused on what can be seen, measured, and classified. Time, being intangible and continuous, is harder to observe directly. Early biology emphasized observable structure—organs, bones, cell walls—not the dynamic processes that unfold over minutes, days, or generations.

2. Methodological Reductionism
Laboratory biology has long relied on snapshot methodologies: fixed tissue samples, gel electrophoresis, sequenced genomes. These approaches produce data that is spatially concrete and temporally frozen. Even dynamic systems are often studied under static assumptions or short timescales (e.g. steady-state metabolism).

3. The Legacy of Mechanism
Biological explanation inherited from physics a focus on causal mechanisms, which often assumes time-invariant laws. The mechanistic model tends to subtract time from explanation—focusing on inputs and outputs, rather than emergent dynamics, delays, or histories.

4. Educational and Taxonomic Constraints
School and textbook biology is organized around classification systems, which rely on stable categories. Development, physiology, and ecology are often presented as if they occur in stages rather than as continuous flows. There is little emphasis on temporal integration across systems.

5. Evolution as the “Temporal Exception”
Evolutionary theory is the one branch of biology where time is indispensable. It deals explicitly with change over generations, deep time, and the historical contingency of life. But even here, the focus is often on phylogenetic branching or population-level change—leaving out the lived temporalities of organisms (e.g., rhythms, development, senescence, learning).

The Missing Dimension in Biology

Biology remains incomplete without a full account of time. Organisms are not just things that exist in time; they are constituted by time—by rhythms, development, memory, anticipation, and evolution. To treat biological entities as static objects is to miss the essence of life itself.
This philosophical problem demands a reformulation of biological categories not as fixed containers, but as time-bound processes. It invites a shift from an ontology of things to an ontology of becomings—in which form is secondary to function, and function is inseparable from time.

Time & the APS framework

The APS (Agency–Process–Scale) framework directly addresses these longstanding anomalies by reframing life not as a static collection of structural objects, but as a dynamic coordination of agentive, temporally extended processes operating across multiple nested scales. Where traditional biology abstracts entities from time, APS embeds agency within time, recognizing that organisms are not passive objects but active agents continually negotiating their existence through sensing, responding, and adapting. Processes, not forms, become primary: development, metabolism, cognition, reproduction, and evolution are treated as temporally structured patterns of activity rather than outcomes frozen in space. Scale, too, is reconceived—not as a set of fixed levels, but as the interplay of temporal and organizational gradients through which life maintains coherence. In doing so, the APS framework resolves the philosophical contradictions between spatial representation and temporal reality, offering a unified ontology in which biological categories are understood as time-bound, functionally integrated, and contextually enacted phenomena.

2. Rethinking Teleology

For much of modern science, teleology—the idea that life is guided by purpose or end-directedness—was treated with suspicion. To avoid associations with mysticism or vitalism, biologists focused on mechanism, structure, and physical causation, often sidelining the purposive nature of living systems. This fear of teleology led to an overly narrow view of life, where agency and function were described as metaphors rather than real, explanatory features. But today, this view is changing.

Contemporary biology increasingly recognizes that living systems are inherently goal-directed—not because of external design, but because they organize, sustain, and adapt themselves in ways that serve their continued existence (Lennox, 2024; García-Valdecasas & Deacon, 2024; McShea & Babcock, 2024; Levesley, 2025; Levin & Resnik, 2025). These ideas have been strongly supported through the popular writings of philosopher Dan Dennett.^[1]

As the APS framework shows, purpose in biology can be fully naturalized: agency and functional behavior emerge from physical processes, evolve over time, and operate across scales. Far from being unscientific, teleology—properly understood—is now essential to explaining what life is and how it works.

Goal-directed behavior

Biological systems exhibit goal-directed (and therefore purposive) behavior—plants grow toward light, animals seek food, and cells repair damage. These outcomes are real, functional, and often consistent, which historically invited teleological interpretations. The APS offers a naturalized description of this goal-directedness: purposiveness and agency are not imposed from outside or derived from conscious intention but emerge from the dynamic, self-organizing processes of living systems.

In this view, biological agency is not driven by foresight or centralized control but unfolds through embedded responsiveness and internal regulation. Organisms maintain themselves through continual interaction across multiple scales—molecular, cellular, behavioral, and ecological. Their actions are structured by viability constraints, which give rise to stable patterns of activity. These patterns, while directional and adaptive, do not imply that organisms are aiming at predefined ends. Rather, they reflect attractor dynamics—tendencies that emerge from how systems are organized and how they respond to their environments.

This reframing aligns with the concept of teleonomy: organisms display functionally directed behavior not because they intend outcomes, but because such outcomes have been shaped and stabilized by evolutionary processes. Purpose, in this context, is not metaphysical—it is an observable and measurable feature of organized living matter. Traits such as thorns, eyes, or wings exhibit functional coherence because they support the persistence of the organism within its adaptive landscape.

APS thus avoids the pitfalls of classical teleology—such as appeals to final causes or mind-like intention—while preserving the explanatory value of purpose-like behavior. It shows that purposiveness can be understood as emergent normativity: the capacity of living systems to regulate themselves in context-sensitive ways to sustain their organization. Survival, repair, reproduction, and adaptation are not externally imposed ends but internally enacted tendencies grounded in the system’s organization.

Rather than eliminating purpose from biology, APS redefines it. Teleological language remains useful, not as a projection or metaphor, but as a recognition of how living systems operate. Functional outcomes are not illusions; they are real patterns shaped by history (natural selection) and enacted in real time through regulatory dynamics. Purpose and agency, in this sense, are intrinsic properties of life—not exceptions to be explained away, but core features of biological systems.
This account supports a continuum of purposiveness across scales and complexities, from the gradient-following behavior of bacteria to the symbolic reasoning of humans. What unites them is not a shared mind or intention, but a shared logic: the self-organized, scale-dependent regulation of activity in the service of viability. In this light, APS does not deny purpose—it naturalizes it. Biological systems are purposive not because they think, but because they persist.

While common usage equates purpose with conscious intent, in biology, purposiveness refers to the reliable production of functional outcomes by systems that regulate themselves in response to internal and external conditions. What appears to be goal-directed is not an illusion—but a real, emergent property of how living systems are organized.

3. Hierarchy: ladders to networks

Biology has long described life using hierarchical metaphors, invoking “levels of organization”—with genes at the “bottom,” organisms in the “middle,” and ecosystems at the “top.” This language often brings with it notions of “top-down,” “bottom-up,” or “horizontal” causation. But such stacking can be misleading. It suggests a unidirectional flow of causation and obscures the fact that living systems operate as dynamic, multiscale processes.

The APS framework offers a conceptual alternative. Rather than viewing biological organization as a linear hierarchy, APS emphasizes reciprocal interactions across scales. Life is not layered like a cake—it is more like a woven web of interactions that span time, space, and function. Instead of rigid levels, APS foregrounds recursive networks and context-sensitive, distributed causation (Nicholson & Dupré, 2018; Baedke et al., 2021).

For example:

• • • A mutation may influence behavior.
    • Behavior reshapes selection pressures.
    • Selection, in turn, feeds back to influence genomic architecture.

These entangled feedback loops are better captured by dynamic coordination than by linear causation (Nuño de la Rosa & Müller, 2020).

APS shifts biological understanding from hierarchy to coordination:

• • • From static levels → to dynamic scales
    • From ontological layering → to functional interrelation
    • From hierarchical causation → to context-sensitive coordination

This conceptual reorientation is essential for a modern account of multiscale biological agency—one that avoids the pitfalls of outdated hierarchical models and embraces the complexity, processuality, and relationality of life.

Scale and Level in the APS Framework

APS calls for a more precise, philosophically grounded use of the terms scale and level, especially regarding how biological processes unfold across space and time. While both terms are widely used in biology, they are often conflated or applied inconsistently.

What Is Scale?
In APS, scale refers to the relational dimensions along which biological activity is observed and coordinated. These include:

• • • Spatial and temporal extents
    • Degrees of complexity
    • Functional integration
    • Causal interdependence
    • Organizational depth

Crucially, scale is not reducible to physical size or clock time. Biological scales encompass emergent properties, recursive feedback, and integrative coordination across domains. Thus, APS treats scale as a pluralistic, process-oriented concept, not a linear continuum.

What Is Level?
By contrast, level in traditional biology is often a spatial metaphor used to define zones of analysis (e.g., molecular, cellular, organismal). However, this framing risks reifying arbitrary distinctions and suggesting ontologically discrete layers.

In APS, levels are better understood as epistemic tools: heuristic perspectives for focusing analysis within a continuous, interacting system. Levels are not structures in nature, but analytical lenses on nature.

Scale – refers to relational dimensions—such as time, space, complexity, and function—along which processes interact. It highlights continuity, integration, and multiscale coordination.

Level – refers to localized zones of analysis—e.g., the “cellular level”—used as heuristic foci. It emphasizes focal perspectives within a system, not ontological separations.

Describes processual relations across systems. Provides analytical framing, not a literal structure of reality.

The APS framework clarifies the confusion between levels and scales by redefining them in terms of process and perspective. It replaces rigid hierarchies with interactive coordination across dynamic scales, providing a richer and more accurate way to understand biological organization, agency, and causation.

4. Reductionism: the limits of “nothing but” thinking

Many scientists and philosophers still assume that biology is best explained by reducing it to physics and chemistry. This “nothing but” view—life is nothing but molecules, cognition nothing but neurons—can lead to the mistaken belief that broader frameworks like APS are unnecessary.

Beyond Reductionism: uderstanding life as organized process
Reductionism has been a powerful tool in biology. By breaking organisms into genes, cells, and molecules, it has yielded major insights. But it also creates serious blind spots. Living systems are not just collections of parts—they are functionally integrated wholes. Their properties emerge not from the parts alone, but from the organization, interaction, and coordination of those parts over time.

The APS framework doesn’t reject physics or chemistry—it builds on them. But it shows that life cannot be fully explained at the molecular level. Agency, cognition, and evolution are not incidental byproducts of chemical reactions; they are core properties of how living systems regulate themselves, adapt, and persist.

APS offers a scientifically grounded, non-reductionist framework that recognizes the causal power of organization, process, and scale. It explains how cells coordinate, how organisms sense and act, and how ecosystems self-regulate—without invoking mystical forces or abandoning empirical rigor. In doing so, it reveals why life cannot be understood by parts alone: it must be seen in terms of the dynamic, purposive systems those parts create.

5. Grounding cognition in biology

Cognition is often equated with the presence of a brain or nervous system, but this assumption reflects a narrow, anthropocentric view. In the context of biology, cognition can be more broadly understood as the capacity of living systems to sense, evaluate, and respond to their environments in ways that support their continued existence. From this perspective, cognition is not limited to neural activity—it is a fundamental feature of biological agency. All organisms, to persist, must interpret signals, make functional decisions, and regulate their internal processes in context-sensitive ways.

This broader conception—what we might call biological cognition—opens the door to recognizing forms of intelligence in organisms that lack brains entirely. Plants offer a particularly striking example. They perceive light, gravity, moisture, mechanical disturbance, and chemical signals from competitors and kin. They integrate this information to regulate growth, resource allocation, defense, and reproduction in adaptive ways. If cognition involves goal-directed regulation in response to environmental stimuli, then plant behavior is not only complex but unmistakably cognitive.

The APS framework provides the theoretical language needed to recognize plant cognition as real, not metaphorical. It locates cognition within a continuum of biological agency—defined not by the presence of neurons, but by the organism’s capacity to act meaningfully within its conditions of existence. In this view, intelligence in nature is not confined to humans or animals; it is distributed across the living world, expressed through diverse strategies that emerge from the interaction of agency, process, and scale.

6. Biological Causation

Biological causation is relational, reciprocal, recursive, dynamic, and multiscale.

In physics, causes often appear simple and direct: a ball rolls because it’s pushed. But in biology, causation is far more complex. The same molecule can have different effects depending on the cell it’s in, the state of the system, or the timing of its activation. The APS (Agency–Process–Scale) framework helps make sense of this complexity by emphasizing that biological causation is relational—it doesn’t just depend on isolated components, but on how those components participate in dynamic, evolving systems.

Modern biology increasingly supports this view. Research in epigenetics, systems biology, and evolutionary developmental biology (evo-devo) shows that biological outcomes arise through nonlinear feedback across genes, physiology, behavior, and environment (Noble, 2016; Walsh, 2015). Organisms are not just shaped by their environments—they also shape them, through development, behavior, and niche construction (Odling-Smee et al., 2003; Emirbayer & Mische, 1998.

From this perspective, causality in living systems is not linear or one-directional. It is networked and distributed, unfolding through the interactions of living agents whose dynamic activity gives rise to emergent properties (Boucher, 2015; Meincke, 2023a; Shan, 2025). Evolution itself is not simply the result of external pressures, but the cumulative trace of these embedded, agent-driven histories.

The APS framework introduces two complementary forms of causation: reciprocal and recursive. Reciprocal causation refers to mutual influence among components of a system, where changes in one part affect others in ongoing, bidirectional interactions—such as between genes and environments or organisms and niches. Recursive causation, by contrast, involves feedback that re-enters a system over time, allowing it to iteratively modify its own operation—such as in development or learning. These forms of causation are central to APS because they show how biological systems are not merely reactive but actively regulate and restructure themselves across multiple scales to maintain coherence and adapt to change.

By reframing causation as relational and context-sensitive, APS allows us to model life not as a chain of events, but as a mesh of interacting constraints, affordances, and functions (Gibson, 1979; Rietveld & Kiverstein, 2014). This approach helps explain functional equivalence: how different biological structures can serve similar regulatory roles, maintaining system integrity in diverse ways (Noble, 2016).

In biology, the conventional use of spatial metaphors—such as “bottom-up,” “top-down,” or “nested”—can misrepresent the complex, dynamic nature of causation. These directional terms suggest linear flows or fixed hierarchies, whereas biological causation often unfolds through feedback, mutual influence, and temporal coordination. Concepts like reciprocal causation are better expressed without invoking spatial directionality. While metaphors like nesting may still serve to describe relational structure, they should be used cautiously and clarified to avoid implying unidirectional or static models of control.

7. The Natural Basis of Meaning

We intuitively recognize that the activities of living systems—seeking, sensing, adapting, persisting—are rich with purpose and significance in a way that mechanical interactions among rocks or gases are not. The Agency–Process–Scale (APS) framework provides a scientific foundation for this intuition by placing biological agency at the center of life and meaning.

In APS, meaning is not imposed from outside, nor is it merely a human construct. It emerges intrinsically from the organization and activity of living systems. When a bacterium moves toward nutrients, it is not just obeying physical laws—it is acting to sustain its own existence. This is a meaningful action, grounded in the system’s structure, history, and self-generated goals.

APS shows how meaning arises through three interwoven dimensions:

Agency: Living systems generate goals, maintain identity, and act purposefully in relation to their environment.

Process: Meaning unfolds over time—through development, adaptation, and evolution.

Scale: Meaning is distributed and transformed across levels of organization, from molecular sensing to human intention to ecosystem regulation.

This perspective shows that meaning is not confined to minds or language. It is present wherever life organizes itself to act in the world. APS thus bridges science and philosophy by grounding the phenomenon of meaning in the natural, evolving activity of life itself.

Rather than asking Where does meaning come from? APS reframes the question in biological terms: How does life generate, sustain, and transform meaning through its own activity—across time, scale, and context?

8. Uniting Proximate and Ultimate Causes

Traditional biology divides explanation into “proximate” causes (how something works now) and “ultimate” causes (why it evolved that way). This split has been useful but can obscure how life actually operates. The APS framework dissolves this divide by showing that agency operates across time: the same functional processes that maintain a system in the present also shape its evolutionary future. Persistence, inheritance, and transformation are not separate stories—they are different aspects of one continuous biological logic.

The classical distinction between proximate and ultimate causes—explaining how traits work versus why they evolved (Mayr, 1961, 1965a, 1965b; Tinbergen, 1963)—has been foundational for biological inquiry. However, this temporal hierarchy often reinforces a linear view of causation, separating short-term mechanisms from long-term evolutionary processes. It obscures the recursive interplay among development, behavior, and evolution (Walsh, 2015; Baedke et al., 2021), and can misrepresent the organism’s active role in shaping its own history.

APS dissolves this divide by reconceiving causation as temporally recursive and co-constructed. Developmental and behavioral processes influence, and are influenced by, evolutionary dynamics. Rather than separate domains, proximate and ultimate causes are dynamically entangled within living systems.

9. Avoiding Trait-Based Definitions of Life

The APS framework avoids defining life by a checklist of static traits—such as metabolism, homeostasis, or reproduction—because these traits describe outcomes or manifestations rather than the underlying dynamics that generate and sustain living systems. Trait-based definitions risk treating life as a set of passive properties rather than a system of active, coordinated processes.

In contrast, APS defines life in terms of biological agency—the capacity of a system to sustain itself, regulate its internal conditions, and respond adaptively to its environment. This approach emphasizes process over parts and views traits like metabolism or reproduction as emergent expressions of deeper organizational patterns, not as defining features in themselves.

The APS framework does not reject trait-based language—terms like “cell wall,” “nephron,” or “photosynthesis” remain essential to communication and teaching. These named traits offer a practical shorthand that allows us to talk about the complex, coordinated activities of living systems. In this way, they are indispensable tools for exposition and understanding.

However, APS invites us to see beyond the trait—to recognize that what we name as a “thing” is often a snapshot of a slower or stabilized process. Even seemingly solid structures, like bones or leaves, are constantly maintained by underlying metabolic and developmental activity. In this sense, all biological objects are processes extended in space and time. Rather than condemning trait-based descriptions, APS reframes them: it encourages us to ask not just what something is, but how it participates in the system’s agency. For example, instead of seeing the heart as merely a pump, APS views it as part of a distributed coordination of oxygen delivery, energy regulation, and behavioral adaptability. This perspective enriches—not replaces—our traditional understanding.

The shift from traits to processes does not make prior knowledge obsolete. Instead, APS grounds biological knowledge in a more coherent and explanatory framework, offering deeper insight into how life works and how its parts interrelate across scale.

10. Reframing Biological Imperatives

APS retains the core biological imperatives—survival, reproduction, adaptation, and evolution—but reframes them as emergent, agent-driven processes rather than fixed goals or teleological ends:

• Survival becomes a continuous process of self-maintenance and internal regulation, not merely persistence over time.
• Reproduction is understood as the propagation of functional organization, not just the transfer of genetic material.
• Adaptation includes learning, plasticity, and niche construction, emphasizing an organism’s active role in modifying its own conditions.
• Evolution is reconceived as the recursive outcome of organism–environment interactions, not a detached population-level mechanism.

This shift dissolves the traditional opposition between proximate and ultimate causes, framing biological activity instead as a recursive system of interdependent processes unfolding across time and scale.

APS moves beyond trait-based definitions by grounding life in dynamic agency rather than static features. It reframes biological imperatives as emergent outcomes of self-organizing, multiscale processes, offering a more integrated, processual understanding of what it means to be alive.

In traditional biology, survival and reproduction are treated as the ultimate goals of life—often invoked as explanatory endpoints. But in doing so, they are assigned a kind of external teleology, as if life exists in order to survive and reproduce. The APS framework challenges this assumption by reinterpreting these outcomes not as goals imposed from outside, but as emergent tendencies of the organizational dynamics that constitute living systems.

APS is fundamentally processual and non-teleological in the classical sense. It does not attribute purpose to life in the form of final causes. Instead, it locates teleological-like behavior—such as persistence, adaptation, repair, and self-production—as arising internally, from the system’s own organization and constraints. This is what APS refers to as the biological imperative: the intrinsic orientation of living systems to sustain themselves through coordinated, context-sensitive activity across multiple scales.

From this perspective, survival and reproduction are not the aims of life, but reliable outcomes of organisms acting in accordance with this imperative. They are signatures of viability, not explanatory foundations. When an organism grows, repairs, or reproduces, it is not obeying a fixed teleological law; it is enacting a set of processes that preserve coherence under changing conditions. APS naturalizes purpose by grounding it in real-time regulation, not abstract goals.

So, once teleology is naturalized within APS, biological explanation no longer needs to default to “survival and reproduction” as its ultimate ends. Instead, it can appeal to:

The organizational closure of systems maintaining themselves (autopoiesis),

• • • The context-sensitive regulation of activity (agency),
    • The integration of internal and external conditions over time (process),
    • And the emergence of functional stability across scales (scale).

In short: organisms do not survive and reproduce because that is their purpose; rather, they survive and reproduce because these are the emergent consequences of being organized as living systems. APS enables us to see this not as metaphor or heuristic, but as a scientifically grounded account of life as coordinated, purposive process.

11. Organisms as Canonical Agents

In the APS framework, organisms occupy a distinctive but not ontologically privileged position. The APS treats the organism as ontologically processual, rather than a container of processes.

APS rejects any fixed “level” as primary, recognizing instead that agency is distributed across scales—from molecular pathways to ecosystems. Yet organisms play a focal role because they are uniquely positioned at the intersection of internal regulation and environmental engagement. As adaptive agents, organisms interpret cues, modulate behavior, and enact changes—such as niche construction or developmental reprogramming—that shape both their own futures and the selective landscapes they inhabit (Odling-Smee et al., 2003; Shan, 2025).

This means organisms are not simply products of evolution but participants in its ongoing dynamics. Their agency is exercised through plasticity, sensory integration, and functionally coherent behavior, enabling them to sustain viability under changing conditions. Importantly, this functional and causal efficacy does not grant organisms special status as a “level” of reality. Rather, it highlights their strategic importance as loci of coordination, where multiscale processes—genetic, physiological, ecological—converge and interact. In this way, APS reframes the organism not as a hierarchical unit, but as a context-sensitive hub of agency within an evolving web of biological processes.

Definition
Traditionally, organisms have been defined as individual living entities composed of one or more cells that exhibit a suite of life functions—metabolism, growth, reproduction, response to stimuli, and homeostasis. These traits-based definitions reflect a long-standing view in biology that treats organisms as discrete, bounded units whose properties can be catalogued and classified. In this view, the organism serves as a central reference point for biological analysis, both as a unit of structure and as a bearer of evolutionary fitness.

However, within the  (APS) framework, the organism is redefined in more dynamic and integrative terms. Rather than focusing on fixed traits or cellular composition, APS conceptualizes the organism as a multiscale, processual system that enacts biological agency. Organisms are understood not merely as things that have life, but as systems that do life—actively sustaining their own integrity through ongoing, coordinated interactions across nested levels of organization. They sense and respond to their environments, regulate their internal conditions, and adapt over time in ways that reflect a purposive orientation toward maintaining viability. This agentive behavior is not incidental but constitutive: to be an organism, in APS terms, is to be a system that persistently reconstitutes itself in the face of perturbation.

Moreover, the APS perspective situates organisms as emergent agents of scale-dependent processes. From molecular pathways and cellular signaling to behavior and ecological participation, organismal identity is forged and maintained through interactions that span biological levels. Crucially, these interactions are not merely hierarchical but functionally integrated, meaning that changes at one scale (e.g., genetic expression) can have consequences for, and be shaped by, dynamics at others (e.g., behavioral or ecological responses). The organism, then, is not simply a structural level between genes and populations but a site of coherence, coordination, and causal integration across scales.

In this light, the organism is best described as a functionally integrated agentive system: one that emerges from and contributes to biological processes in ways that support its continued existence. This processual and scale-sensitive account allows us to move beyond rigid classifications and instead recognize the organism as a dynamic, self-maintaining locus of biological purpose. It also opens the door to more inclusive and generalized understandings of life, applicable not only to familiar multicellular animals and plants but also to unicellular entities, symbiotic collectives, and other complex agents that meet the same criteria of agentive coherence.

12. Biological Normativity & Human Morality

The Agency–Process–Scale (APS) framework grounds biological phenomena not in static traits or structural forms, but in the dynamic, self-organizing activity of multiscale processes. Life, in this view, is defined by the capacity of living systems to regulate and sustain themselves in a changing environment—a capacity rooted in agency (Moreno & Mossio, 2015; Spencer, 2025). This agentive organization underpins biological normativity: the inherent capacity of living beings to evaluate internal and external conditions in terms of their contribution to viability.

Unlike inert systems, which are governed solely by external forces, living systems impose constraints on themselves to maintain coherence and persistence. This active regulation enables organisms to distinguish functional from dysfunctional states, adaptively responding to perturbations in ways that promote continued existence (Di Paolo, 2005; Bich & Mossio, 2019). Biological normativity thus emerges from within the system. A state is “good” insofar as it supports the organism’s capacity for autopoiesis, regulation, and adaptive engagement with its environment (Varela, 1979; Jonas, 1966). As Thompson (2007) puts it, such systems enact “immanent normativity”—a normative orientation arising from within the living process itself.

The APS framework extends this insight by demonstrating that biological normativity is scale-dependent. At higher levels of organization—such as in multicellular organisms, ecosystems, and human societies—new forms of norm-enactment arise through coordination across parts and processes. Normativity scales upward, becoming more complex and context-sensitive, yet always remains grounded in the core logic of viability and self-regulation.
This multiscale perspective is particularly significant for understanding human morality. According to traditional moral philosophy, nature is not normative and cannot yield moral claims. This position is rooted in David Hume’s is–ought distinction (1739/2000), which warns against deriving moral imperatives from empirical facts. Building on this, G.E. Moore (1903) coined the term naturalistic fallacy to critique attempts to define moral goodness in terms of natural properties such as pleasure or survival. On this view, morality belongs to the domain of rational agents, not natural systems: only humans can judge, deliberate, and act from reasons.

The APS framework acknowledges the power of this objection but offers a reframing rather than a refutation. It does not collapse morality into biology or attempt to deduce “ought” from “is.” Instead, APS contends that normativity is an emergent feature of living systems—one that is enacted rather than inferred, and that becomes increasingly complex through evolutionary and organizational elaboration (Canguilhem, 1991; Jonas, 1966; Mossio & Moreno, 2020). The normativity of simple organisms is not moral in the reflective human sense, but it is no less real. A bacterium, for example, does not reason, but it evaluates—orienting toward nutrient gradients and away from toxins. This orientation reflects an agentive stance: a primitive “concern” for maintaining its own organization (Di Paolo, 2005).

What distinguishes human morality is its reflective and symbolic elaboration. Through language, culture, memory, and recursive self-modeling, humans are able to abstract and generalize the norms that govern their actions. Moral systems, in this light, are not alien to biology, but are cognitive and social extensions of the norm-enacted dynamics found in all living systems (De Jaegher & Di Paolo, 2007; Froese & Di Paolo, 2011). They represent a scaling-up of agency across longer timescales and broader social ecologies.

Human norms—such as fairness, reciprocity, empathy, or justice—can thus be understood as adaptive strategies for maintaining viability not only at the level of individual bodies, but at the level of groups, institutions, and entire cultures (Sterelny, 2012; Churchland, 2011). Emotional processes like empathy, shame, and guilt are biological mechanisms evolved to facilitate cooperative action, social cohesion, and collective viability (Zahavi, 2014; Tomasello, 2016). These mechanisms are not mere byproducts of reason; they are bio-cognitive regulatory capacities evolved within complex agentive systems.

The APS framework therefore bridges the gap between biological and ethical normativity. It avoids the reductionism of equating morality with fitness, while also rejecting the dualism that would sever human values from the natural world. Morality, in the APS view, is a reflective reorganization of the same fundamental logic that governs all living systems: the logic of agentive regulation, enacted across nested temporal and spatial scales. Norms are not imposed from without, nor do they emerge ex nihilo from reason; they are refined expressions of the value-laden structure of life itself (Spencer, 2025).

This naturalized but non-reductive approach preserves the insight of Hume’s is–ought distinction: moral judgments are not mechanical extensions of facts. But it challenges the assumption that nature is devoid of normativity. Living systems are not passive; they care, in a biological sense, about their own persistence. Reason, reflection, and ethical deliberation do not invent normativity; they expand and deepen it, making explicit the stakes that were always already present in the biological condition.

14. Reframing Evolution

The APS (Agency–Process–Scale) framework builds on the Extended Evolutionary Synthesis (EES) by deepening its emphasis on organismal activity, developmental dynamics, and multilevel causation. While the EES expands evolutionary theory beyond gene-centric models to include processes like niche construction, plasticity, and developmental bias, APS further reframes evolution through the lens of biological agency.

In APS, evolution is not merely a population-level outcome of selection pressures but a consequence of the agential, processual activity of living systems acting across scales. Organisms are seen as active participants in their own evolution, not passive recipients of genetic variation. This reframing highlights:

• • • Agency: Organisms modify their developmental pathways and environments in ways that influence evolutionary outcomes.
    • Process: Evolution is shaped by dynamic, interdependent processes—developmental, ecological, and behavioral—that unfold over time.
    • Scale: Evolution operates across nested temporal and organizational scales, from molecular to ecological systems.

By integrating these dimensions, APS provides a unified framework in which evolution is driven by the ongoing, coordinated activity of living systems to maintain and adapt their functional organization. This reframing situates evolution within a broader understanding of life as an emergent, self-organizing process.

15. Necessary & Sufficient Conditions for Life

Providing the necessary and sufficient conditions for life has long been considered an unlikely and foolhardy enterprise, but the APS framework brings us closer to such a goal.

Life is a bounded, far-from-equilibrium system capable of self-construction, maintenance, and adaptive response through intrinsically coordinated, multiscale processes. It enacts a biological imperative: to sustain its own viability by metabolically regenerating its components and organizational states, thereby enabling open-ended evolution.

This definition is functional, operational, and sufficient, unifying biological agency, thermodynamic openness, and evolutionary continuity across material and organizational scales.

1. Agency Without Anthropomorphism
Doesn’t the use of “agency” invoke intentionality or cognition? In APS, agency is naturalized: it refers to the capacity of a system to act on its own behalf by maintaining its viability through internally coordinated processes. It does not require consciousness or goal-directedness in a mental sense. Instead, agency is defined functionally, as the emergent outcome of self-regulation, responsiveness, and integration—observable in all living systems, from cells to ecosystems.

2. Multiscale Validity
Doesn’t invoking “scale” introduce ambiguity? APS responds by explicitly linking process to structure and causation across organizational levels—from molecular mechanisms and cellular interactions to organismal behavior and ecological dynamics. This ensures that agential coherence is evaluated relative to the system’s organizational integrity, not arbitrary levels of description.

3. Borderline Cases (e.g., Viruses)
A persistent challenge in defining life is how to handle edge cases. APS excludes viruses as living in isolation, as they lack the capacity to enact the biological imperative independently—failing to metabolize, self-organize, or regulate internal conditions. However, APS adopts a relational view: viruses may contribute to agential dynamics within broader, host-dependent systems, without qualifying as living entities themselves.

More broadly, APS accommodates edge cases like lichens, the Portuguese Man-of-War, biofilms, holobionts, and endobionts by prioritizing functional integration and the enactment of the biological imperative over rigid individual boundaries. Systems are considered living when they exhibit internally coordinated, self-sustaining activity across scales, whether as single organisms or cooperative consortia. This allows APS to treat composite entities as biological agents when they function as coherent, self-regulating systems, while excluding uncoordinated or purely dependent aggregations. In doing so, APS offers a scalable, process-based criterion capable of resolving longstanding definitional ambiguities.

4. Universality vs. Earth-Centrism
By focusing on carbon–water chemistry and metabolic regeneration, some may argue the definition is Earth-biased. APS avoids overcommitment to biochemical particulars by centering on functional organization and endogenous processual activity. While rooted in empirical life, the definition remains sufficiently abstract to allow extension to novel or hypothetical life forms, provided they enact the biological imperative through intrinsic, scale-integrated coordination.

5. Distinguishing Life from Complexity
Finally, APS distinguishes life from non-living complex systems (e.g., crystals, fire, artificial intelligence) by requiring that functional organization is maintained from within—through processes that serve the system’s own continued existence. Complexity alone does not imply life; it is the recursive, self-sustaining orchestration of function that defines living systems.

The APS definition of life, grounded in agency, is designed to be scientifically rigorous, theoretically integrative, and empirically applicable. It avoids reductionism while maintaining clarity, distinguishing life from non-life without relying on arbitrary trait lists. By grounding life in the biological imperative, APS provides a unified framework capable of addressing known life, supporting astrobiological inquiry, and accommodating future discoveries.

16. Life: Principle & Practice

Life, in principle, is defined by a system’s capacity to survive, reproduce, adapt, and evolve—a set of minimal conditions referred to here as the biological axiom. These criteria mark the threshold between living and non-living systems by identifying what is required for persistence across generations under evolutionary dynamics.

In practice, these abstract conditions are realized through the biological imperative: the intrinsic tendency of living systems to sustain, adapt, and regenerate their own organized existence over time. Where the axiom defines what life must achieve to count as living, the imperative describes how life actually achieves it—through self-organizing, internally coordinated processes that maintain viability.

This distinction is critical. The axiom sets the theoretical boundary of life; the imperative reveals its lived dynamics. Considered separately, each has limits: the axiom can appear static and formal, the imperative open-ended and descriptive. But taken together, they offer an integrated account of biological agency: the capacity of a system to act on its own behalf, guided by internal norms aimed at continued existence.

Biological agency arises from this coupling. Organisms enact the imperative because they fulfill the axiom; they are self-regulating systems shaped by evolutionary necessity. Agency is not imposed from outside, but emerges from the need to remain viable, adaptive, and self-renewing in a changing world.

This framework reveals three interrelated conceptual layers: the ontological (what life is), the functional (what life does), and the theoretical (how life is explained). Evolution, while not enacted by individual organisms, remains a core part of the axiom, ensuring continuity between organismal activity and long-term evolutionary outcomes.

Philosophy of Structure & Function

Traditionally, biology has treated structure and function as mutually dependent: the structure of a biological entity (a cell, organ, protein, etc.) enables its function, and function is realized through structure. In this view, neither has clear priority—form and action are co-defined.

However, APS departs from this symmetry by elevating function—especially processual, agential function—as primary. This shift is philosophically and empirically justified in several ways:

1. Function Grounds Biological Identity Over Time
Structure is often transient or replaceable; what persists across time is the organization of functions. A cell, for example, can regenerate or replace many of its structural components, but it maintains its identity only through the continuity of its self-regulating functions. This insight underlies autopoietic and processual accounts of life (e.g., Maturana & Varela, 1980; Nicholson & Dupre, 2018).

⚬ The organism is not defined by its structure but by its capacity to maintain structure through ongoing processes.

2. Function Explains Agency and Purpose
APS defines life as an agentive system—one that regulates itself in ways that preserve its own viability. This regulatory function is what distinguishes living from non-living systems. Structural configurations may correlate with agency, but they do not explain it. Function, not form, is what makes a system purposeful in the biological sense.

⚬ Agency and purposiveness are not features of physical structure, but of functional organization.

3. Evolution Selects for Function, Not Structure
In evolution, natural selection does not preserve structures for their own sake but for the functions they perform. Structures may change dramatically across lineages (e.g., homologous limbs, divergent morphologies), yet perform functionally equivalent roles. This justifies APS’s emphasis on functional continuity over structural similarity—and supports its approach to cognition, inheritance, and behavior as functionally grounded across scales.

4. Structure Emerges From and Serves Function
In a dynamic, multiscale system, structure is not static but emergent from underlying processes. APS thus treats structure as a temporary configuration of functionally coordinated processes. From this view, structure is not ontologically prior—it is a stabilized outcome of life’s ongoing activity.

⚬ Life is not built from static parts upward, but from dynamic regulation outward.

5. Historical Parallels
The APS emphasis on function resonates with organicism, process philosophy, and systems biology, but it goes further by embedding function in the concept of agency. Historically, 20th-century biology (especially molecular biology) favored structural explanations. APS joins a newer lineage (e.g., Rosen, Kauffman, Moreno, Gánti, and enactivist thinkers) that reasserts the centrality of function, process, and system autonomy.

Thus:
The APS framework justifies its prioritization of function over structure by:

• • grounding biological identity in process, not form
  • recognizing agency and purposiveness as functional properties
  • emphasizing evolution as selection for functional coherence
  • interpreting structure as emergent from functionally integrated processes
  • building on a philosophical tradition that treats life as activity, not architecture

This is not a denial of structure, but a reframing: structure is meaningful only insofar as it supports the functional persistence of the living system.

Extending APS: Evolution & Development

The Agency–Process–Scale (APS) framework offers a powerful theoretical lens for understanding life as a self-organizing coordination of processes guided by biological agency across multiple scales. It models agency as a capacity emergent from thermodynamically sustained, structurally grounded processes of regulation, viability maintenance, and adaptive responsiveness. Yet, for all its strengths in providing a processual, multiscale alternative to static, part-based models of life, APS presents certain limitations—both in scope and in explanatory depth—which Mitchell’s Free Agents (2023) helps to address.

1. Theoretical Limitations of APS

While the APS framework excels in capturing the organizational dynamics that constitute biological agency, it remains relatively neutral—or underdeveloped—with respect to:

Phylogenetic deepening: APS is largely synchronic in focus. It gives an account of what life is (an agentive process system) but does not, in itself, provide a detailed evolutionary account of how agency arises, diversifies, or transforms across evolutionary time.

Developmental and cognitive transitions: APS accommodates cognition as an emergent property of agency, but it does not provide a graded account of how simple forms of sensorimotor responsiveness evolve into complex forms of learning, representation, and abstract thought.

Neural architectures and symbolic capacity: The role of nervous systems, memory, prediction, and symbolic reasoning in reshaping agency—especially in humans—is only tangentially addressed in the basic APS model. It provides a substrate-neutral account of agency, but not an elaborated view of its qualitative transformation through neurological and cognitive evolution.

Reflexivity and normativity: APS grounds normativity in the biological imperative of self-maintenance. However, it stops short of exploring how agentive systems come to represent their own goals, evaluate alternatives, or construct normative frameworks—features central to moral and deliberative cognition.

2. Mitchell’s Contributions: A Dynamic Extension of APS

Kevin Mitchell’s Free Agents enriches and extends APS by embedding agency within an explicitly evolutionary-developmental narrative. This extension proceeds in several crucial ways:

From proto-agency to predictive modeling: Mitchell begins with the foundational dynamics already central to APS—homeostasis, metabolic regulation, environmental responsiveness—and traces their elaboration through natural selection. He shows how agency begins not as a mystery, but as the functional logic of life’s persistence. Importantly, this aligns with APS’s grounding in viability and functional integration.

Nervous systems as amplifiers of agency: Where APS emphasizes organizational closure and processual coherence, Mitchell highlights how nervous systems enable agents to go beyond immediate responsiveness: to simulate future scenarios, integrate information across contexts, and inhibit impulsive reactions. Nervous systems do not create agency ex nihilo; they reorganize and scale it, expanding the temporal and spatial range over which agents can operate. This reinforces the APS view that agency is not a binary (present/absent) but a spectrum.

Emergence of self-models and reflexive control: Mitchell’s account helps address the reflexivity gap in APS by showing how internal models allow agents to simulate themselves within potential futures, evaluate imagined outcomes, and act toward abstract or deferred goals. This shift from reactive to reflective agency is pivotal for understanding the evolution of human cognition, language, and culture.

Normativity through evolution and learning: While APS grounds normativity biologically, Mitchell enriches this by showing how internal representations of value—goals, preferences, ideals—can evolve and be learned, giving rise to subjective normativity. This opens the door to a richer, naturalized account of moral cognition and deliberation, in which agency becomes not just regulatory but evaluative.

3. Toward a Synthesis: APS Plus Evolutionary Cognition

Kevin Mitchell’s Free Agents offers a powerful evolutionary deepening of the Agency–Process–Scale (APS) framework by supplying a developmental and neurobiological context for the emergence of biological agency. Where APS models agency as a multiscale, process-based capacity for adaptive self-regulation, Mitchell adds an evolutionary scaffold that traces how such agency becomes increasingly complex over time. This historical trajectory helps address a key limitation in APS: its relative abstraction from evolutionary lineage. Mitchell’s account shows how agency emerges in graded fashion—from basic reactivity to sophisticated reasoning—thereby offering a more detailed and developmentally grounded theory of cognition. While APS adopts a substrate-neutral stance toward intelligence, treating cognitive functions as realizable in any sufficiently integrated agentive system, Mitchell anchors intelligence in the structural and dynamical constraints of neural architectures and predictive control. Finally, his emphasis on internal models, learning mechanisms, and biologically instantiated value systems enriches the APS account of normativity, rooting it not just in self-maintenance but in evolved systems of meaning and evaluation. Taken together, Mitchell’s contribution complements APS by embedding its abstract principles within the concrete realities of evolutionary, developmental, and neural processes.

Together, APS and Free Agents yield a more complete picture of life as an evolving spectrum of agency—from metabolic maintenance to reflexive deliberation. APS supplies the structural and processual logic of biological agency, while Mitchell offers the historical and cognitive dynamics by which this logic is amplified and transformed. In this integrated view, cognition is not an add-on to life but its deepening: a temporally extended mode of agency shaped by evolutionary history and realized through complex functional architectures.

Addressing APS Concerns

The Agency–Process–Scale (APS) framework reorients biological explanation around the principles of agency, multiscale coordination, and processual causation. While it offers a robust alternative to reductionist models, several conceptual objections are likely to arise. Below is a brief summary of common concerns and how APS addresses them.

1. On Vagueness and Inflation
Agency and cognition are functionally and scalably defined through criteria like environmental responsiveness and regulatory closure, drawing on minimal cognition (Godfrey-Smith, 2001) and process-based agency (Barandiaran et al., 2009).

2. On Empirical Tractability
APS is empirically anchored through systems biology, evo-devo, and dynamic modeling, supporting predictions about distributed regulation, niche construction, and adaptive feedback (Laland et al., 2016; Schaffer & Ideker, 2021).

3. On Mechanistic Compatibility
Rather than rejecting mechanistic models, APS embeds them within broader processual architectures, aligning with mechanistic contextualism and extended causal analysis (Burnston, 2022).

4. On Multiscale Causation
The framework relies on causal dynamics across molecular to ecological scales, supported by systems biology tools for modeling hierarchical and reciprocal interactions (Schaffer & Ideker, 2021).

5. On Metaphor
Terms like “feedback” and “self-organization” refer to operationally defined, observable processes (e.g., morphogenesis, homeostasis), not vague or rhetorical constructs (Muñoz et al., 2020).

6. On Teleology
APS naturalizes purposiveness by grounding it in biological agency—goal-directedness arises from self-sustaining regulatory dynamics, not external design or final causes. This approach avoids metaphysical teleology while retaining explanatory power for function and normativity (Moreno & Mossio, 2015; Walsh, 2020).

The Biological Condition

At the heart of biology lies an existential challenge: the biological condition. This condition is the existential correlate of the biological axiom—a minimal, universal statement of what life is in principle. It asserts that all living systems are necessarily organized to survive, reproduce, and adapt. These are not merely observed tendencies but the necessary conditions without which life cannot be sustained or recognized as such.

Yet these principles are not abstract ideals: they are enacted concretely by organisms embedded in time, matter, and contingency. This enactment—life in practice—is what we call the biological imperative. It expresses the demand placed upon every organism to realize, under actual conditions, the goals set by life in principle. The biological condition, then, is the lived tension between what life must be and what life must do to remain.

Just as the human condition reflects the burden and possibility of self-awareness within a finite life, the biological condition marks the deeper substrate from which this burden arises—the universal demand to persist through autonomous, embodied striving.

From this perspective, the problem of existence is not merely to be alive, but to remain alive by continuously fulfilling the terms of the biological axiom through adaptive and purposeful activity. Failure to meet these terms leads not just to dysfunction, but to the dissolution of the very status of being alive.

Evolution, in this light, is not random change but the historical unfolding of life’s search for viable solutions to the problem of existence. It is the exploration of those configurations—of structure, process, and behavior—that can satisfy the biological axiom under the ever-changing conditions of reality.

Each organism is thus a situated realization of life’s general possibility. Life in principle defines what must be true of any living system; life in practice reveals the countless forms through which organisms attempt to satisfy that truth. The diversity of life is testimony to the many ways this universal condition has been met, embodied, and sustained.

Plant Agency and the Human Relationship

Plants are not just background scenery but active participants in Earth’s evolutionary story. Their long-standing evolutionary success—accounting for 99.7% of terrestrial biomass—has shaped the biosphere and human civilization. Recognizing plant agency highlights our deep interdependence with these quiet, enduring agents of life. We depend entirely on their photosynthetic productivity, yet our cultural narratives have long marginalized them. Addressing this “plant awareness disparity” invites a more inclusive understanding of agency in nature.

Life

From Biological Agency to Consciousness: A Continuum of Life’s Purposeful Organization

All living organisms, plants and animals alike, are composed of the same fundamental substance as the non-living universe. We are, quite literally, made of stardust. What sets living beings apart from inert matter is not their ingredients, but the way these ingredients are organized. Life is matter arranged to metabolize—to draw energy from its surroundings, build and repair itself, and sustain a fragile individuality against the constant drift toward entropy.

Life did not begin with intention or foresight. It began as organized processes capable of self-maintenance and replication, processes that introduced variation into a challenging and changeable environment. Variations that enhanced the ability to persist—to fit with the conditions of existence—tended to endure, while less effective configurations disappeared. This was natural selection: a non-conscious, non-teleological process that shaped function through differential survival. So far as we know, this origin of life was singular, meaning that all living beings share descent from a common ancestral stock. Evolution connects humans not only to other animals, but to plants and all organisms, through a continuous history of functional adaptation and shared biological heritage.

The APS (Agency–Process–Scale) framework builds on this evolutionary foundation, understanding agency as the defining property of life itself: the ability of living systems to initiate, coordinate, and sustain activity in pursuit of their own persistence. Agency precedes cognition and consciousness. It is expressed whenever a living system senses conditions, evaluates possibilities (biochemically or physiologically), and acts in ways that secure its ongoing viability.

Over evolutionary time, agency has diversified and become more elaborate. Early life forms enacted agency through simple feedback loops, adjusting internal chemistry to match external conditions. Plants embody a distributed form of agency, sensing light, water, pressure, and chemical signals, integrating this information across tissues, and modulating growth and behavior accordingly. These purposive responses occur without neural networks, mental images, or subjective awareness, yet they are meaningfully directed toward the organism’s own flourishing.

Cognition can be understood as a refined elaboration of agency: the ability to process information, evaluate options, and coordinate increasingly complex responses. Cognition emerges wherever living systems link sensing to functional action in adaptive ways. Plants, for instance, exhibit memory of past stress, communication with neighbors, and anticipatory behavior. These capacities represent biological intelligence—not thought in the human sense, but the ability to act on meaningful differences in the environment.

Consciousness, in this view, is not the starting point of meaning or value, but a late evolutionary development, an enriched layer of cognitive agency made possible by the vast neural architectures of certain animals. Subjective experience builds upon deep biological processes that already carried intrinsic purposiveness, long before minds appeared. Consciousness expands the reach of agency, allowing complex organisms to model their world, plan across time, and reflect on their own actions—but it is a specialization of a more ancient, universal capacity for self-directed, purposeful living.

The APS framework thus reverses the traditional anthropocentric narrative that treats meaning, purpose, and intelligence as unique human achievements. Instead, it sees them as graded properties of life, emerging from fundamental biological organization. Plants do not need consciousness to act with purpose, select between alternatives, or shape their futures. Their agency is naturalized purposiveness, grounded in the physics, chemistry, and evolution of living systems. Consciousness is one branch on this evolutionary tree—a late-blooming phenomenon, not the root from which biological meaning springs.

Metaphysics

Metaphysics makes progress by refining our understanding of core concepts like causality, agency, process, and identity—each of which is central to the APS (Agency–Process–Scale) framework. APS draws on this progress by redefining agency not as a mental or supernatural property but as an embodied capacity of living systems to initiate, regulate, and sustain themselves. It aligns with a process-based metaphysics that treats life as dynamic organization rather than static substance, reflecting a broader shift away from entity-based thinking. The APS emphasis on scale—understood as the spatial and temporal extent and resolution of biological activity—also reflects metaphysical advances in understanding the layered, continuous nature of reality. Moreover, APS incorporates recent insights into reciprocal and recursive causation, offering an alternative to reductive, linear models. In this way, APS exemplifies metaphysical progress: it provides a coherent, scientifically grounded account of life, agency, and function that both draws from and contributes to contemporary metaphysical thought.