Introduction

The history of science can be read as a history of naturalisation: the gradual transformation of phenomena once treated as metaphysical, theological, or irreducibly subjective into empirically tractable objects of scientific inquiry.

This process is not simply empirical. It is conceptual. Scientific progress repeatedly requires that familiar terms be reinterpreted so that they can function within explanatory frameworks grounded in the natural world. Concepts such as motion, force, life, heredity, and information have all undergone profound shifts in meaning as they moved from philosophical speculation into scientific explanation.

The Agency–Process–Scale (APS) framework situates agency, purpose, normativity, and cognition within this historical trajectory. APS does not eliminate these concepts or treat them as metaphorical residues. Instead, it reconceptualises them as organisational features of living systems—continuous with life itself.

To understand this move, it is helpful to examine the broader pattern through which science has repeatedly expanded its explanatory scope.

The Historical Expansion of Scientific Explanation

Across the history of science, phenomena once explained through metaphysical or theological frameworks have gradually been reinterpreted through empirical investigation and theoretical refinement.

This expansion can be understood as a sequence of transformations:

  • Ancient and early philosophy
    Motion explained through purpose or intrinsic tendencies

  • Scientific Revolution
    Motion explained through universal physical laws

  • Nineteenth-century biology
    Life explained through physiology and metabolism rather than vital forces

  • Twentieth-century molecular biology
    Heredity explained through DNA and regulatory systems

  • Contemporary cognitive science
    Mind studied through neural, behavioural, and dynamical processes

  • APS
    Agency, purpose, and biological normativity grounded in viability-oriented organisation

This progression illustrates a recurring pattern: phenomena once considered metaphysical gradually become empirically tractable as scientific understanding deepens.

Scientific progress therefore involves more than discovering new facts. It requires redefining what counts as part of the natural world.

Conceptual Drift and Scientific Maturation

A striking feature of scientific development is that familiar words often acquire new meanings as understanding deepens.

Consider the concept of force. In Aristotelian physics, force was closely linked to intention and purpose: objects moved because they sought their natural place. In Newtonian mechanics, force became a mathematically defined relation between mass and acceleration.

The word remained the same, but its explanatory role changed entirely.

A similar transformation occurred with energy, which evolved from a philosophical notion of activity into a rigorously conserved quantity in physics.

Scientific progress often proceeds through this kind of conceptual refinement. Terms inherited from earlier traditions are retained but disciplined: their meaning is constrained by empirical investigation and theoretical integration.

Biology has followed a similar path, though more slowly. Concepts such as life, function, and purpose resisted straightforward mechanistic treatment. Attempts to eliminate teleological language entirely proved unsatisfactory because living systems appear organised for persistence, regulation, and reproduction.

The challenge was therefore not simply empirical but conceptual: how to naturalise purposive organisation without reintroducing metaphysics.

The Pattern of Naturalisation

Across the history of science, naturalisation tends to follow a recurring pattern:

  • Metaphysical framing
    The phenomenon is treated as special or irreducible

  • Scientific exclusion
    Early science brackets the phenomenon to focus on simpler domains

  • Functional re-entry
    The phenomenon reappears as an organisational or functional property

  • Conceptual refinement
    Scientific concepts are reshaped to align with empirical constraints

  • Integration
    The phenomenon becomes part of standard scientific explanation

This pattern can be seen in the treatment of motion, life, heredity, and information, and increasingly in the scientific study of cognition and agency.

Naturalisation does not eliminate phenomena. It reorganises them.

Life and the Limits of Mechanism

The naturalisation of life marked a crucial stage in the development of modern biology.

Early biological thought often relied on vital forces or special life principles to explain the apparent autonomy of organisms. These ideas were eventually abandoned, but their replacement was not simple reductionism.

With Darwin, biology acquired a historical dimension: biological organisation could be understood as the outcome of cumulative evolutionary processes. Later developments in physiology, biochemistry, and systems biology reinforced the view that life is not defined by a particular substance but by a distinctive organisation of processes.

Yet this shift left unresolved questions about agency, normativity, and meaning. Organisms do not merely persist; they regulate themselves, respond selectively to environmental conditions, and maintain their own organisation over time.

Something matters to a living system in a way that it does not matter to a rock or a flame.

These features require conceptual tools capable of describing organised activity without invoking external design or metaphysical forces.

The Remaining Frontier: Agency, Purpose, and Meaning

Despite centuries of naturalisation, several concepts remain difficult to integrate fully into biological explanation:

  • purpose
  • function
  • agency
  • normativity
  • meaning

These terms appear constantly in biological discourse. Organisms regulate their internal states, respond selectively to environmental conditions, repair damage, and sustain their own organisation over time.

Yet traditional theoretical frameworks often treat such language as metaphorical or historically inherited rather than as scientifically grounded.

This tension reveals an unresolved problem: how should science understand the organised activity of living systems themselves?

APS and the Naturalisation of Agency

The APS framework addresses this problem by grounding these concepts in the organisation of living systems.

In APS:

  • Life is the organisation of biological agency—the viability-oriented activity by which systems sustain their own persistence
  • Purpose refers to the organisation of activity toward continued viability
  • Function describes how particular processes contribute to that persistence
  • Normativity arises because some conditions support viability while others undermine it

These features are not metaphysical additions to biology. They arise from the organisational properties of systems that must actively sustain themselves in changing environments.

APS begins with biological agency rather than with cognition or representation. Agency is not primarily psychological; it is a property of systems that regulate their own persistence.

Within this framework, cognition emerges as an extension of agency rather than its foundation. Cognitive systems are those whose regulatory activity exhibits temporal depth—allowing present behaviour to be shaped by absent or anticipated conditions.

This perspective naturalises cognition without reducing it to mechanism or representation. Human minds remain distinctive, but they are situated within a broader continuum of biological organisation.

APS as the Next Stage of Naturalisation

Seen in historical perspective, APS continues a long scientific trajectory in which phenomena once treated as philosophical problems become subjects of empirical investigation.

  • Physics naturalised motion
  • Chemistry naturalised matter and reaction
  • Biology naturalised life processes
  • Neuroscience naturalised cognition
  • APS naturalises agency and biological normativity

APS therefore extends the empirical reach of biology by clarifying the organisational conditions under which living systems regulate, adapt, and persist.

It does not introduce metaphysics into science. It resolves the residual metaphysics already present in biological language by grounding it in observable organisation.

Conclusion: Naturalisation Without Reduction

The progressive naturalisation of science is not a story of elimination but of conceptual maturation. Phenomena once treated as metaphysical are not discarded; they are reinterpreted.

Scientific explanation advances by learning how to use familiar language in new ways—ways that connect words to observable organisation and testable processes.

Mind, long regarded as the final frontier of metaphysics, is now undergoing this transformation. The challenge is not to discard mentalistic vocabulary but to refine it so that it tracks real features of the natural world.

APS contributes to this effort by providing an explanatory grammar grounded in agency, process, and scale. By situating purpose, normativity, and cognition within the organisational dynamics of living systems, it extends one of science’s oldest and most powerful trajectories:

the steady expansion of what counts as part of the natural world.

Key Point

APS situates agency, purpose, and biological normativity within the long scientific process of naturalisation—reinterpreting phenomena once treated as metaphysical as features of viability-oriented, constraint-closed organisation.