APS Framework Overview

This article provides a simple overview of the APS framework which is described in more detail in the article Agency, Process, Scale (APS), also in its original scientific publication (Spencer, 2025)

Agency, Process, Scale (APS)
The major features of an agency defined, and process-based, understanding of life.
See also biological agency, plant agency, and plant cognition, and APS Frameworl Overview

Schematic produced by AI Co-Pilot

“The APS framework is more than an explanatory model—it’s a compass. It orients biology toward living systems not as machines, but as agents embedded in process and scale, actively maintaining their own existence in dynamic environments.”

What is the APS Framework?

The APS (Agency–Process–Scale) Framework redefines life by emphasizing the active, processual, and multiscale nature of biological systems. It provides a scientifically grounded alternative to mechanistic and reductionist models by focusing on biological agency as the defining feature of life.

A= Agency

Agency is the capacity of a living system to initiate, regulate, and coordinate goal-directed, context-sensitive activity.

Key features of biological agency:

• • • Goal-oriented action: Behavior supports persistence, coherence, and adaptation.
    • Sensorimotor coupling: Organisms sense and respond to internal and external cues.
    • Adaptive behavior: Adjusts based on changing conditions.
    • Systemic autonomy: Maintains internal coherence and viability.
    • Continuity across life: All living systems exhibit agency, not just animals.

Biological agency can be summarized as:

• • • Agent = the organism or acting system
    • Mission = the biological imperative (persistence, adaptation, etc.)
    • Means = biological mechanisms and behaviors used to achieve it

P = Process

Process refers to the ongoing, coordinated activity that sustains a living system.

Key points:

• • • Life is not a static substance but a dynamic process.
    • Living systems are self-producing (autopoietic) and self-regulating.
    • Biological function emerges from process integration, not from isolated parts.
    • Functional evolution is shaped by the behavior of whole agents, not just gene selection.

S = Scale

Scale refers to the multiple, interacting levels at which biological agency and processes occur.

Key distinctions:

• • • APS prefers scale (continuous, dynamic) over traditional levels (rigid, hierarchical).
    • Biological activity is nested: molecules → cells → organisms → ecosystems.
    • Cross-scale interactions are bidirectional: higher scales constrain/enhance lower ones and vice versa.
    • Understanding life requires tracking processes across time and organization.

The Biological Imperative

The biological imperative is the system-level drive of organisms to: persist, cohere, reproduce, adapt, and evolve.

Why it matters:

• • • Replaces vague “survival and reproduction” models with a goal-oriented systems perspective.
    • Emerges from the structure and function of biological agency itself.
    • Explains purpose without invoking mysticism or teleology.

Why the APS Framework Matters in Biology

• • • Replaces mechanistic reductionism with process-based integration.
    • Unifies concepts from evolution, development, cognition, and ecology.
    • Offers a scientifically rigorous account of plant intelligence and non-neural cognition.
    • Centers biology on what organisms do, not just what they’re made of.

Mnemonic to Remember APS

“Agents in Process across Scale pursue a Biological Imperative.”

Agency–Process–Scale (APS) Framework: a new lens on life

Defining the APS Framework
The Agency–Process–Scale (APS) framework explains life as a coordinated, multiscale process driven by biological agency. It unifies structure, function, and purpose in living systems, offering a fresh alternative to reductionist and gene-centric approaches in biology.

What Is the APS Framework?
Biology has long described life in terms of structure, chemistry, and genetic inheritance. While this has delivered powerful insights, it leaves a gap: life is not static—it is active, adaptive, and purpose-driven. The APS framework bridges this gap by focusing on:

Agency: Living systems act on their own behalf, pursuing survival, growth, and reproduction.

Process: Life is continuous activity—self-producing, self-maintaining, and responsive to change.

Scale: Biological systems operate across interacting scales—from molecular networks to ecosystems and evolutionary time.

This triadic view provides a dynamic, processual account of life that highlights function, coordination, and purposive behavior without relying on anthropomorphism or teleological assumptions.

The Three Pillars of APS
1️⃣ Agency: Living Systems as Active Participants
Organisms are not passive machines.

They sense, respond, and adapt to maintain viability.

Biological functions emerge from this goal-directed activity, not merely from biochemical structure.

2️⃣ Process: Life as Ongoing Activity
Living systems are continuous processes, not fixed objects.

They sustain themselves through metabolic, developmental, and ecological interactions.

Processes define what life is, not just what it contains.

3️⃣ Scale: Interactions Across Levels of Organization
Life unfolds across nested, interacting scales: molecular, cellular, organismal, ecological, and evolutionary.

Processes at one scale influence and depend on others, creating a coordinated whole.

Recognizing scale prevents oversimplified “one-level” explanations of biology.

Why APS Matters in Biology
Traditional biology often emphasizes structure, genes, and immediate causation, leaving out purpose, coordination, and time-dependent processes. The APS framework:

Explains why living systems behave in agent-like ways.

Integrates evolutionary, ecological, and physiological perspectives.

Offers a foundation for studying plant cognition, non-neural intelligence, and adaptive behavior.

Helps reconnect biology with function and purpose without invoking mysticism or final causes.

APS in more detail

1. Introduction: Why Agency Matters in Biology Now

The APS framework begins with a simple but powerful observation: agency is expressed throughout the living world. Organisms move, grow, adapt, reproduce, and persist in environments that are often unpredictable and hostile. Yet modern biology has long treated this purposive, goal-directed activity as either metaphorical or heuristic—a convenient way to describe living systems, but not something literally real.

This dismissal of agency is historically understandable but conceptually problematic. As biology developed under the influence of Newtonian mechanics, terms like purpose, goal, and function were increasingly viewed with suspicion—tainted by associations with theology, vitalism, and anthropomorphism. In seeking to purify its language and secure its status as a mechanistic science, biology excluded agency and teleology, favoring molecular mechanisms and gene-centered explanations.

But something essential was lost. Organisms are not passive machines assembled by genes. They are active, dynamic systems that engage with their environments, regulate internal conditions, and shape the circumstances of their own persistence. Even evolution, when understood mechanistically, fails to account fully for the purposive behavior of organisms themselves.

This article presents a renewed account of biological agency grounded in the Agency–Process–Scale (APS) framework [Spencer, 2025]. APS reinterprets life as fundamentally agential, processual, and multiscalar. In alliance with the Evolutionary Extended Synthesis (EES) [Pigliucci & Müller, 2010; Laland et al., 2015], it challenges the reductionism of the Modern Synthesis and addresses the fragmentation of contemporary biological disciplines. It proposes a coherent foundation for understanding organisms not as passive products of external forces, but as systems defined by their capacity to act, adapt, and persist.

The following sections trace the historical displacement of agency in biology, identify the philosophical and scientific reasons for its return, and articulate a non-anthropocentric, scientifically grounded theory of life built around agency. The core claim is that biological agency is not an illusion or metaphor, but a real, observable, and necessary feature of life—the central fact around which biological science should be organized [Nicholson, 2014; Walsh, 2015; Levin et al., 2021].

2. Historical Foundations of Agency in Biology

Aristotle: purpose in nature

For Aristotle, biological explanation was inherently teleological. Living things were organized in ways that reflected internal goals: the eye is for seeing, the wing for flying. His concept of final cause grounded life in purpose—not as a supernatural force, but as an intrinsic organizing principle. Form and function were unified in the structure and development of the organism [Aristotle, Physics].

This perspective shaped Western biological thought until the Scientific Revolution, when the success of mechanistic physics prompted biology to reinterpret organisms as machines—systems reducible to physical laws acting on parts.

Kant: Teleology as a Heuristic

Immanuel Kant attempted to reconcile mechanism and purposiveness. He argued that organisms must be treated as if they were purposive systems, because their organization resists reduction to mechanical interactions. However, for Kant, this purposiveness was not in nature but in our mode of cognition [Kant, Critique of Judgment, 1790]. This compromise allowed biology to retain teleological language while denying its ontological status.

Darwin: naturalized purpose

Charles Darwin offered a breakthrough by explaining function, design, and adaptation through natural selection. Purpose no longer required a divine designer but could be explained through descent with modification and differential survival. Organisms appeared purposeful because purposeless processes favored those that behaved as if they had goals [Darwin, 1859].

However, Darwin did not eliminate purpose—he naturalized it. Biological functions were now interpreted in terms of their contribution to survival and reproduction. But over time, this nuanced view was overshadowed by gene-centric and mechanistic interpretations, culminating in the Modern Synthesis—a powerful but incomplete framework that marginalized organismal activity and agency [Walsh, 2015; Noble, 2012].

3. The Problem with the Standard Model

Modern biology remains shaped by the legacy of gene-centrism, reductionism, and skepticism toward agency. Within this Standard Model:

• • • Genes are treated as the primary causal units; organisms are vehicles.
    • Agency is reserved for human minds; non-human behavior is mechanized.
    • Teleological language persists in practice but is dismissed as metaphor.
    • This has led to enduring conceptual errors:
    • Conflating biological functions with cognitive intentions.
    • Treating goal-directed behavior as merely metaphorical.
    • Neglecting how organisms actively shape their evolutionary environments.

As a result, biology explains how traits are selected, but not how they arise, integrate, or persist within complex living systems. Without a robust theory of agency, biology cannot fully account for what differentiates the living from the non-living.

APS addresses this shortcoming by redefining agency as a real, evolving feature of biological systems—not a cognitive artifact, but a biologically grounded, multiscale phenomenon.

4. The APS Framework: Agency, Process, and Scale as Foundations of Life

The Agency–Process–Scale (APS) framework [Spencer, 2025] presents a unified theoretical model for biology that integrates neglected yet essential concepts: agency, purposiveness, and organismal unity. These principles define life not in terms of what it has, but what it does.

Agency

Agency in APS is defined not by consciousness, but by the system’s capacity to initiate, regulate, and coordinate its activity to support its own persistence. This includes homeostasis, repair, adaptation, reproduction—core features found in all living organisms, from bacteria to humans.

• • • Agency is graded, not binary. It evolves across species and scales:
    • Minimal in bacteria.
    • Integrated in multicellular organisms.
    • Cognitive in animals.
    • Reflective in humans.

This view avoids both mechanistic reductionism and human exceptionalism, situating agency as a natural property of evolving systems [Moreno & Mossio, 2015].

Process

Biological systems are living processes—not static objects composed of parts, but dynamic patterns unfolding in time. Metabolism, movement, reproduction, adaptation—these are ongoing activities. APS aligns biology with process philosophy and systems theory, emphasizing coordinated flows over static structures [Nicholson & Dupré, 2018].

Scale

Life operates across nested, interacting scales—molecular, cellular, organismal, ecological. Causation is multidirectional and recursive: genes affect cells, cells regulate genes; organisms shape ecosystems, ecosystems shape evolution.

APS foregrounds scale as an analytic tool. It replaces static “levels” with dynamically coupled scales, situating the organism as the point where multiple processes converge, integrate, and act coherently [Levin et al., 2021; Bizzarri et al., 2013].

5. Clarifying Biological Agency

To serve as a foundation for biology, agency must be defined in biological, not metaphorical, terms. APS offers a functional definition:

Biological agency is the capacity of a system to sense, respond to, and regulate its conditions to preserve its own functional integrity.

This includes:

• • • Autonomy – regulation not dictated by external forces alone.
    • Goal-directedness – purposive behavior that supports viability.
    • Adaptivity – responsiveness to environmental feedback.
    • Integration – coordination of parts for coherent function.

These properties are evolutionarily distributed across life. APS distinguishes agency by degree:

• • • Minimal agency: bacteria monitoring gradients.
    • Integrated agency: multicellular cooperation.
    • Cognitive agency: learning and choice.
    • Reflective agency: human deliberation and abstraction.

Rejecting the Metaphor Fallacy

Critics often dismiss terms like “want,” “decide,” or “seek” as anthropomorphic metaphors. APS challenges this metaphor fallacy: the assumption that if purposive language sounds human-like, it must be non-literal.

Instead, such language tracks real processual features: goal-oriented activity that evolves, adapts, and supports viability. The challenge is not to eliminate intentional language, but to biologically ground it [Godfrey-Smith, 2009; Levin, 2022].

6. Organisms as Paradigmatic Agents

Within APS, the organism is the paradigmatic agent—the locus where multiscale processes integrate into coherent, purposive activity.

Multiscale Unity

Organisms are not part-collections but functionally integrated wholes. Their components—cells, tissues, organs—cooperate to support persistence. Organisms exist within ecological, developmental, and evolutionary contexts, shaping and being shaped by them [Mossio & Bich, 2017].

APS centers the organism as the processual hub of biological agency.

From Levels to Scales

Traditional biology invokes hierarchical “levels”—genes, cells, organisms. APS reframes this as nested scales of spatiotemporal organization, with recursive causation rather than vertical hierarchy. This avoids reifying levels and better captures the dynamics of biological organization [Love & Brigandt, 2017].

Individuation and Persistence

What makes organisms distinct is their ability to maintain identity over time through:

• • • Metabolic closure
    • Normative regulation
    • Adaptive response

This individuated persistence is the hallmark of agency and a defining feature of life.

7. Human Agency as a Case of Biological Agency

Human agency, though complex, is not categorically distinct. APS treats it as a biological elaboration, continuous with evolved agential systems.

Biological Roots of Human Behavior

Cognitive traits such as deliberation and norm formation are built on biological functions:

• • • Decision-making emerges from behavioral plasticity.
    • Values evolve from adaptive preferences.
    • Language and culture extend social agency already present in other species.

Proximate and Ultimate Causes

APS integrates proximate (cognitive, emotional) and ultimate (evolutionary) explanations, showing human action as both biologically grounded and evolutionarily significant [Tinbergen, 1963; Bateson & Laland, 2013].

Mind as an Extension of Agency

Rather than invoking mind to explain agency, APS treats mind as an evolved extension of agency. Cognition becomes one manifestation of life’s general capacity to act in service of persistence [Thompson, 2007; Allen & Bickhard, 2013].

8. The Evolution of Agency

Agency evolves. From minimal self-maintenance to cognitive and reflective systems, life has expanded its capacity to act, adapt, and construct its conditions of persistence.

• • • Enactive Progression
      Minimal agency: basic responsiveness.
    • Sensorimotor: guided movement.
    • Interactive: social coordination.
    • Cognitive: learning, memory, problem-solving.
    • Enactive: niche construction and self-modification [Di Paolo et al., 2017].

This progression reflects diverse evolutionary paths, not a single linear scale.

Organisms as Evolutionary Participants
Organisms shape their own evolution through:

• • • Niche construction
    • Behavioral plasticity
    • Epigenetic inheritance

APS treats organisms as participants, not just substrates of selection [Odling-Smee et al., 2003; Laland et al., 2014].

Functional Evolution

Agency links functional innovation, integration, and inheritance. Traits emerge and stabilize not because they are coded in genes, but because they contribute to persistent, integrated agency [Wouters, 2005].

9. Implications for Biological Theory – Redefining Life

Life is not a list of molecules but a persistent, processual, multiscale agency. A living system is one that:

 Maintains itself through internal processes.

• • • Adapts to environmental change.
    • Integrates parts toward unified function.
    • Evolves by refining agency.

Rethinking Causation

Causality in APS is:

• • • Multiscalar
    • Distributed
    • Bidirectional

Organisms don’t just react; they constrain, generate, and modulate causal flows [Hoel et al., 2013].

Naturalizing Teleology

Biological functions are not mind-imposed; they are roles within agential systems. Teleology becomes a biological reality, not a metaphysical speculation [Cummins, 1975; Mossio et al., 2009].

Biological Agency Without Teleology: The Keystone Argument of APS

1. The Challenge

Biology has long wrestled with the fact that living systems appear purposeful: they grow, repair, reproduce, and act in ways that maintain their own persistence. Yet scientific explanation traditionally rejects teleology—the idea that life acts “for the sake of” future ends—as unscientific or anthropomorphic. The APS framework (Agency–Process–Scale) addresses this by naturalizing purposiveness: grounding agency in the physical and processual organization of living systems, not in conscious intention or external design.

2. Defining Biological Agency

Biological agency is the capacity of a living system to initiate, coordinate, and sustain activity that preserves its own viability, coherence, and functional organization across time and scale.

This is not a mental property but a dynamical one: a product of the system’s self-producing, self-regulating processes (autopoiesis, constraint closure, energy and information flows). Agency is real because it is causally efficacious—the organism actively selects, modifies, and regulates interactions with its environment to maintain itself.

 Non-Teleological Purposiveness

APS rejects external or future-driven purpose. Instead:

Intrinsic Normativity: The “goals” of living systems (e.g., maintaining homeostasis, repairing damage, reproducing) emerge from their material organization. What counts as “success” or “failure” for an organism is defined internally: loss of organization means death.

 Functional Evolution: Evolutionary processes refine and expand these agential capacities without adding intention. Organisms do not act for evolution; rather, evolution acts through organisms’ persistent agency.
 

Causal Closure: Agency arises from real, present-time constraints on flows of matter and energy that keep the system intact. It is this closure of processes—not foresight—that gives rise to biological directionality.

4. Implications for APS

Life as Process: Living is an ongoing coordination of processes aimed at persistence; agency is this coordination in action.

Scalability: Agency is not binary but distributed across scales (molecular → cellular → organismal → ecological), each level contributing to persistence.

Cognition and Meaning: Sense-making, responsiveness, and information use are natural consequences of agency; cognition is life acting with agential meaning, not mental representation.

Biological Imperative: Every living system embodies a built-in imperative to continue living, a dynamical fact of its organization, not a teleological “goal.”

Keystone Claim:

Biological agency is the necessary and sufficient condition for life, fully explainable as a process of self-sustaining organization that generates apparent purposiveness without appeal to final causes. APS builds from this principle to unify biological theory around agency, process, and scale.

Unifying the Life Sciences

APS provides conceptual coherence across fields:

• • • Genetics: situates genes within dynamic systems.
    • Development: sees form as emerging from agential processes.
    • Ecology: emphasizes reciprocal organism–environment agency.
    • Evolution: reframes selection as a dialogue, not a filter.

10. Conclusion: A New Paradigm for the Life Sciences

The Agency–Process–Scale framework offers a robust alternative to reductionist biology. It shifts emphasis:

• • • From structure to process.
    • From parts to whole-system coordination.
    • From levels to interacting scales.
    • From passive objects to active agents.

APS does not reject molecular or evolutionary insights—it recontextualizes them within a richer ontology. At a time when biology must grapple with complexity—from cognition to ecosystems to climate change—APS provides a theoretically integrated, organism-centered, and dynamical account of life.

To study life, under APS, is to study what it means to act, persist, and evolve in a changing world.

The APS framework acknowledges that agency is everywhere in the natural world—organisms move, grow, adapt, reproduce, and persist in environments that are often unpredictable and hostile. Yet modern biology has long treated this purposive, goal-directed activity as either metaphorical or heuristic—a convenient way to speak about living systems, but not something literally true.

This dismissal of agency is both historically understandable and conceptually problematic. As biology grew into a mechanistic science in the shadow of Newtonian physics, concepts such as purpose, goal, and function came under suspicion for their associations with theology, vitalism, and anthropomorphism. In an effort to purify its language, biology cast out teleology and agency—seeking instead explanations rooted in molecular mechanisms and gene-centered inheritance.

But something vital was lost. Organisms are not passive machines assembled by genes; they are active systems that engage their environments, regulate their internal processes, and shape the conditions of their own persistence. Evolution itself, understood mechanistically, cannot be fully explained without accounting for the purposive behavior of organisms.

This article presents a renewed account of biological agency, grounded in a contemporary theoretical framework: Agency–Process–Scale (APS) (Spencer, 2025). The APS framework reinterprets life as fundamentally agential, processual, and multiscalar—along with the Evolutionarily Extended Synthesis (EES) it challenges the reductionism of the Modern Synthesis and the fragmentation of current biological disciplines. It offers a new foundation for understanding organisms not as objects moved by external forces, but as systems defined by their capacity to act, adapt, and persist.

This article traces the historical displacement of agency from biological thought, identifies the philosophical and scientific challenges that demand its return, and articulate a scientifically grounded, non-anthropocentric theory of life built around agency. It argues that biological agency is a real, observable, and necessary feature of life—not an illusion or metaphor, but the central fact around which biological science should be organized.

APS Glossary – Key Terms

Agency – The capacity of a living system to initiate, coordinate, and sustain goal-directed activity in response to internal and external conditions. In the APS framework, agency is biologically grounded—emerging from the system’s functional organization and expressed through processes such as sensing, regulating, adapting, and persisting across scales.

Agent – A system that exhibits agency. In biology, this is typically an organism—an integrated, multiscale unity capable of context-sensitive, goal-directed behavior that serves its own persistence and coherence. Agents regulate their own activity in accordance with the biological imperative.

Agential Realism (in Biology) – The view that agency is not limited to conscious minds but is an intrinsic, observable property of living systems. APS supports this naturalized version of agential realism, grounding purposiveness in the functional and organizational properties of life rather than anthropocentric metaphors.

APS (Agency–Process–Scale) – A theoretical framework that places agency at the center of biological explanation, recognizes process as the fundamental substrate of living systems, and treats scale as essential for understanding multilevel coordination. APS offers a non-reductionist alternative to the Standard Model by emphasizing the dynamic, purposive, and self-organizing nature of life.

Autopoiesis – The self-producing, self-maintaining process by which living systems generate and sustain their own boundaries and internal organization. A foundational concept that complements agency and process in APS by explaining biological selfhood.

Biological Agency – The intrinsic capacity of living systems to act on their own behalf to sustain coherence, regulate activity, adapt to change, and pursue continued existence. Biological agency is enacted through dynamic internal processes and is grounded in the system’s organization, not imposed externally.

Biological Axiom – The biological axiom has traditionally been expressed as the principle that living systems survive and reproduce. While accurate as a summary of observable outcomes, this formulation is limited in scope and fails to capture the full dynamics of life. Within the APS framework, the axiom is broadened to include not only survival and reproduction but also adaptation and evolution. This expanded formulation enhances the axiom’s explanatory power by accounting for the system’s capacity to respond flexibly to changing conditions and to generate long-term functional innovation. It also aligns the axiom more closely with both proximate and ultimate causation, bridging developmental and evolutionary perspectives. Nevertheless, the biological axiom, even in its expanded form, remains descriptively inert unless interpreted through the purposive activity of agents acting on the biological imperative. In this view, the outcomes summarized by the axiom result from the internal organization and self-regulatory capacities of living systems, not from external imposition or metaphorical projection.

Biological Cognition – The capacity of living systems to sense, evaluate, and respond to relevant conditions in ways that support survival and functional integration. In APS, cognition is not limited to brains or minds but is a property of biological organization—observable in processes such as perception, memory, signaling, and adaptive behavior.

Biological Imperative – The biological imperative refers to the intrinsic drive of living systems to sustain, adapt, and regenerate their own organized existence over time. Unlike the biological axiom, which summarizes outcomes like survival and reproduction, the biological imperative focuses on the purposive activity of organisms—their active striving to maintain viability in changing environments. This imperative is not imposed from outside but emerges from within: it is expressed through the system’s capacity for self-regulation, responsiveness, and functional integration. It underpins all forms of biological agency, shaping behavior, development, and evolution. In the APS framework, the biological imperative serves as the guiding principle that links agency with process and scale, giving purpose a naturalized and observable basis in the dynamics of living systems.

Developmental Agency – The capacity of an organism to actively guide its own development through internal regulatory processes, rather than being passively shaped by genes or environment.

Extended Evolutionary Synthesis (EES) – A contemporary framework that extends the Modern Synthesis by integrating developmental systems, plasticity, niche construction, epigenetics, and organism–environment feedbacks. It aligns with APS in emphasizing reciprocal causation, active organisms, and non-genetic inheritance mechanisms.

Functional Equivalence – Functional equivalence refers to the capacity of structurally different components or processes to perform the same biological function. For example, different organisms may evolve distinct mechanisms to achieve similar outcomes, such as nutrient absorption or locomotion. Within the APS framework, functional equivalence highlights the adaptive flexibility of life: what matters biologically is not how a function is achieved, but that it is achieved in a way that supports the organism’s continued existence. This principle helps explain the diversity of life while reinforcing the unity of its functional aims. It also reveals how agency can be expressed in different material forms, and why similar purposive behaviors can emerge from very different biological architectures. Recognizing functional equivalence strengthens the case for a multiscale and processual understanding of life.

Functional Evolution – Functional evolution refers to evolutionary change understood through the lens of biological function rather than genetic variation alone. It emphasizes the continuity of function across generations, focusing on how traits, processes, and strategies that support coherence, adaptability, and persistence are conserved, transformed, or repurposed over time. By integrating adaptation and evolution into a unified account, this perspective highlights how internal regulatory processes and agentive behavior shape evolutionary trajectories. Within the APS framework, functional evolution connects proximate functions—such as homeostasis, sensing, or regeneration—with their evolutionary consequences, offering a more integrated view of development, behavior, and selection. It underscores that evolution is not merely a product of external pressures but is actively constrained and directed by the functional organization of living systems.

Functional Organization – The dynamic pattern of processes and constraints by which a system maintains its integrity, coordinates internal regulation, and enacts agency. It underlies biological functions and allows for purposeful responses across changing contexts and scales.

Homeostasis – The active maintenance of internal stability and functional coherence despite external or internal perturbations. Central to agency and internal regulation.

Internal Regulation – Processes by which living systems monitor and adjust their internal states to maintain functional organization, enabling agency across scales.

Internalism (Biological) – The perspective that explanation in biology must begin from within the system—from its organization, agency, and internal regulatory dynamics. APS emphasizes internalism as a corrective to externalist accounts that over-rely on genes, selection, or environment to explain living activity.

Level – A traditional descriptive category in biology (e.g., molecule, cell, organism, ecosystem). Although useful, “levels” imply fixed hierarchies and one-way causation. APS replaces this with a multiscale perspective that emphasizes dynamic coordination across interacting scales.

Metaphor Fallacy – The mistaken belief that language of purpose, agency, or cognition in biology is purely metaphorical. APS rejects this fallacy, insisting that purposive activity is a real and observable aspect of living systems and should be treated as scientifically legitimate.

Multiscale Causation – The principle that biological causation operates reciprocally and dynamically across multiple temporal, spatial, and functional scales.

Multiscale coordination – is the process by which living systems integrate activities across different levels of organization—molecular, cellular, physiological, ecological, and evolutionary. No level acts in isolation; instead, biological systems sustain themselves by coordinating processes across time and space. For example, a plant’s response to drought involves molecular signaling, changes in cell behavior, systemic water regulation, and developmental adaptation over time. In the APS framework, multiscale coordination is essential to agency: it allows a living system to act as a coherent whole despite being composed of many interacting parts. It also grounds purposive behavior in real, observable mechanisms that link proximate regulation with ultimate evolutionary outcomes. Without multiscale coordination, agency would fragment and the organism would fail to maintain its identity over time.

Naturalized Purpose – Purpose understood as an intrinsic, functional orientation of living systems, not as an imposed or mental construct. In APS, purpose is expressed through the biological imperative, enacted through agency, and grounded in the system’s internal organization and continuity.

Non-Neural Cognition – Cognitive processes occurring without a nervous system, such as in plants or microbial communities, supporting the idea of cognition as a biological capacity rather than a mental state.

Organizational Closure – A network of mutually dependent processes and constraints in living systems that form a self-sustaining organization, fundamental to biological agency.

Organism – The paradigmatic biological agent: a self-producing, self-regulating, and self-maintaining unity of interdependent processes. Organisms are not passive outcomes of genes or selection but active, adaptive participants in their own development and evolution.

Process – The continuous, dynamic activity by which living systems generate and sustain themselves. In APS, processes are both the medium of biological function and the vehicle of agency. They operate across molecular, physiological, behavioral, and ecological domains and are coordinated through internal regulation.

Reciprocal Causation – Two-way causal interactions between organism and environment or among biological scales, contrasting with one-way mechanistic causation.

Scale – A dimension of biological organization (spatial, temporal, energetic, or functional) through which systems regulate activity and coordinate function. APS treats scale as multivariate and continuous, not hierarchical. Agents integrate across scales to maintain coherence and respond adaptively to change. cf. level.

Self-Regulation – The ongoing adjustment of an organism’s internal processes to maintain coherence, pursue goals, and adapt.

Standard Model (of Modern Biology) – A shorthand for the dominant 20th-century biological paradigm that explains life in terms of molecular causation, gene-centered evolution, and mechanistic processes. The Standard Model tends to exclude purposive, organizational, or agentive explanations, which APS seeks to reintegrate into biological science.

Teleonomy – The apparent purposefulness or goal-directedness of biological functions and structures as explained by evolutionary and organizational processes.

Teleology (Naturalized) – An explanation of goal-directedness grounded in biological organization and agency, not invoking metaphysical or mentalistic assumptions.

Threshold of Life –The threshold of life defines the minimal set of conditions a system must satisfy to be considered alive within the APS framework. First, the system must demonstrate autonomy by producing and maintaining itself over time. It must show biological agency, meaning it actively regulates and adapts its internal and external interactions to sustain its existence. Functional integration is essential, with parts working together to maintain coherence and enable adaptive responses. Life also requires processual continuity, where the system continuously engages in dynamic activities that build and modify its own structure and function. Moreover, the system operates across multiple scales—temporal, spatial, and organizational—coordinating activities to maintain viability. The capacity for adaptation allows the system to adjust behavior and internal states in response to environmental changes. Crucially, the system must be capable of reproduction to ensure persistence across generations, and it participates in evolutionary processes that allow functional and structural changes over time. Together, these conditions place a system above the threshold of life, distinguishing living agents from non-living matter. The APS framework emphasizes that this threshold is not defined by any single criterion but emerges from the integration of agency, ongoing process, and multiscale organization.

Vitality – The qualitative aspect of living systems characterized by continuous self-generation, adaptive responsiveness, and purposive activity.