Introduction

Scientific explanations do not simply report observations. They employ concepts, relations, representations, and explanatory priorities through which phenomena are made intelligible. APS uses the term Explanatory Grammar for the organised conceptual and explanatory relations through which it structures its account of living organisation.

An explanatory grammar influences what an explanatory framework treats as relevant, how it relates phenomena, and what kinds of questions it is organised to answer. It should not be confused with reality itself: its categories remain explanatory commitments whose adequacy must be assessed against the phenomena, evidence, and alternatives concerned.

Within APS, Explanatory Grammar relates viability-oriented organisation, organised persistence, and the analytic projections of Agency, Process, and Scale. Its purpose is to make explicit how APS structures its explanation of living organisation, not to prescribe the necessary form of every biological explanation.

Scientific progress often involves changes in explanatory grammar: new ways of organising phenomena that render previously obscured patterns intelligible. Biology provides a particularly demanding case, because living systems are dynamically organised, historically evolving, and coordinated across interacting spatial and temporal domains.

Explanatory Grammars in Science

Across the sciences, explanatory frameworks organise phenomena through characteristic sets of categories. These are not arbitrary descriptors but determine what is treated as causally relevant.

Newtonian physics: mass – force – motion → mechanical causation

Thermodynamics: energy – entropy – state → transformations of energy

Electromagnetism: field – charge – interaction → distributed physical influence

Darwinian evolution: variation – inheritance – selection → adaptive change

Information theory: signal – code – transmission → informational organisation

Such grammars shape what is measured, what is treated as causal, and what counts as explanation. When explanatory grammars change, scientific understanding changes with them.

Why Biology Is Especially Sensitive to Grammar

Living systems are organisationally complex, self-maintaining, historically evolving, and coordinated across multiple interacting scales. Because of this, biological explanation has developed through multiple partially overlapping grammars, each emphasising different aspects of life.

These grammars capture genuine features of living systems. However, they also tend to privilege particular components or processes as explanatorily primary, generating recurring debates about the “fundamental unit” of biology.

Major Explanatory Grammars in Biology

Gene-centric grammar explains biological change in terms of gene frequencies across generations, enabling precise modelling of evolutionary dynamics while offering a limited account of organismal organisation.

Cell-centric grammar establishes the cell as the fundamental unit of life, grounding development and physiology while remaining less explanatory for evolutionary dynamics.

Organism-centric grammar emphasises integrated regulation and environmental interaction, providing a strong account of functional organisation but weaker formal modelling of evolutionary change.

Systems biology grammar focuses on networks, interactions, and distributed dynamics, enabling multiscale modelling while often under-specifying biological normativity.

Each grammar captures a real aspect of biological organisation. Each also risks treating a particular component or scale as explanatorily primary.

The Problem of Privileged Scale

Some biological explanations have assigned particular explanatory importance to genes, cells, organisms, networks, or other domains of organisation. Such priorities can be scientifically productive when they are appropriate to the question being addressed, but they need not identify a universally privileged basis of biological causation or explanation.

APS approaches this issue differently. It does not assign intrinsic explanatory priority to any particular spatial or temporal scale. Scale identifies where persistence is organised across spatial and temporal extents, while the explanatory importance of particular processes depends upon the biological question and organisation under investigation.

A related distinction concerns analysis and synthesis. Biological inquiry often gains explanatory power by analysing systems into components and processes. Other questions require attention to how those components and processes are organised into functioning systems. APS does not treat either explanatory orientation as universally preferable. Where living organisation and organised persistence are the explanatory targets, however, it gives particular importance to the organisation through which activities, processes, constraints, and interactions jointly contribute to continued viability (see Analysis, Synthesis, and the Direction of Explanation).

Similar care is required in explanations of cognition and behaviour. Concepts such as representation, computation, inference, and decision-making may be useful within appropriate explanatory contexts, but their applicability to biological systems cannot simply be assumed. APS approaches cognition from living organisation, asking how increasingly complex capacities arise from viability-oriented organisational activity rather than taking human cognition as the general model for life.

Human cognition is therefore treated within APS as a specialised development of biological organisation rather than as the starting point for explaining that organisation.

Reductionism should consequently not be identified simply with explanation at smaller scales. The relevant question is whether an explanatory strategy is adequate to the phenomenon and question under investigation. Component-based analysis may sometimes be sufficient; where the target is living organisation and its persistence, APS asks additionally how those components and processes participate in the organisation through which viability is maintained.

Distributed and Reciprocal Causation

IBiological processes occurring across different spatial and temporal extents can influence one another through materially implemented interactions and constraints. Molecular, cellular, organismal, and environmental processes are therefore not explanatory layers exercising abstract upward or downward causation. Their relations are realised through the organisation of the living system itself.

APS treats such cross-scale influence as materially implemented: constraints operating across wider spatial or temporal extents alter the local conditions under which particular processes occur. No scale thereby acquires intrinsic causal or explanatory priority.

From Explanatory Grammar to Continuity Architecture

APS applies Explanatory Grammar to a foundational question: what organisation characterises living systems, and how is that organisation maintained through change?

Living systems do not merely exhibit activity, process, or coordination across spatial and temporal extents. They persist while continually replacing components, reorganising processes, responding to perturbations, and interacting with changing environments. APS therefore treats organised persistence as a principal explanatory target in its account of life.

APS describes the organisation through which such persistence is maintained as a continuity architecture: viability-oriented organisation that continually maintains and re-establishes the conditions required for its own continuation. Agency, Process, and Scale provide analytic projections of this organisation. Agency concerns what living systems do; Process concerns how continuity is maintained despite change; Scale concerns where persistence is organised across spatial and temporal extents. They are analytic projections rather than independent explanatory domains or components of reality.

The APS Explanatory Grammar therefore organises its account of living systems around viability-oriented organisation and organised persistence rather than assigning intrinsic explanatory priority to genes, cells, organisms, networks, or any particular scale. Biological mechanisms, developmental processes, ecological relations, and evolutionary transformations can be considered in relation to this continuity architecture where doing so contributes to the question being addressed. They do not thereby become subordinate to APS, nor does their explanatory adequacy depend upon incorporation into it.

This gives APS potential foundational generality when living organisation itself is the explanatory target. It does not give APS universal authority over biological explanation. Particular biological phenomena may be adequately explained through other approaches, while APS addresses the more general question of how living organisation is maintained through change.

This revision makes two particularly important corrections to the original.

First, “what kind of organisation biological explanation must ultimately explain” becomes the question APS explicitly addresses. Second, the original final claim that biological phenomena “become intelligible insofar as” they contribute to continuity architecture is removed. That formulation effectively made APS the condition of intelligibility for biology. The replacement preserves APS’s foundational reach without absorbing specialist explanations into APS.

The APS Explanatory Grammar

The Agency–Process–Scale (APS) framework makes explanatory grammar explicit and grounds it in viability-oriented, constraint-closed organisation. Within this grammar, living systems are understood as actively sustaining the conditions of their own persistence through ongoing processes coordinated across interacting scales.

Within the APS Explanatory Grammar, living systems are understood as viability-oriented, constraint-closed organisations that actively maintain and re-establish the conditions of their own persistence.

APS approaches this organisation through three analytic projections:

Agency — what living systems do: viability-oriented organisational activity.

Process — how continuity is maintained despite change.

Scale — where persistence is organised across spatial and temporal extents.

Agency, Process, and Scale are analytic projections rather than components of reality. Organised persistence is not a fourth projection. It identifies the continuity problem around which these projections are brought into explanatory relation.

APS’s Explanatory Grammar therefore organises its account of life around the relationship between viability-oriented organisation and organised persistence without treating any particular component, scale, or projection as independently fundamental.

Living systems regulate because persistence requires regulation. They undergo continual transformation because persistence requires ongoing process. They coordinate activity across scales because persistence depends upon interactions extending beyond any single spatial or temporal domain.

APS therefore replaces the search for a privileged unit with an explanatory grammar grounded in organised persistence.

This framework is not introduced as a classificatory scheme but identified as the minimal structure required for explanatory adequacy. Without agency, normativity disappears; without process, organisation becomes static; without scale, coordination across time and space cannot be explained; without organised persistence, these dimensions remain disconnected and fail to explain what is distinctive about living systems.

APS therefore identifies the organisational conditions that biological explanation must ultimately account for.

Within this framework, biological normativity emerges from the conditions required for continued viability. Living systems do not require externally imposed goals or observer-defined purposes. Conditions become biologically significant because they affect the persistence of organised activity itself. Evaluation, regulation, adaptation, function, and teleonomy therefore arise from the organisational requirements of continuity rather than from standards imposed upon the system from outside.

APS therefore replaces the search for a privileged unit with an explanatory grammar grounded in distributed organisation and continuity-preserving persistence.

It also reframes causation. Rather than treating causation solely as the production of events, APS understands biological causation as the viability-oriented modulation of constraints within organised systems. Mechanistic interactions remain essential, but they are situated within organisation that sustains the conditions under which those interactions remain viable (see Biological Causation — From Mechanism to Organised Persistence).

Mechanisms explain how particular biological activities occur. Within APS, organised persistence provides a wider organisational context for asking whether and how particular activities contribute to continued viability. Mechanistic and organisational explanations can therefore be complementary where the explanatory question requires both.

APS, Evolution, and Organised Persistence

The APS explanatory grammar reveals a complementary relationship between biological organisation and evolutionary theory.

Evolutionary theory explains how populations of organisms change through time through processes such as variation, inheritance, selection, drift, and ecological interaction.

APS addresses a different but equally fundamental question: how viability-oriented organisation is maintained in the first place.

Before variation can be inherited or selected, there must already exist systems capable of maintaining organised persistence across time. Organisms must sustain viability long enough to reproduce. Developmental systems must regenerate organisational structure across generations. Ecological conditions must support the continuation of living organisation.

APS is not proposed as an alternative to evolutionary theory. It addresses questions about the organisation whose historical transformation evolutionary explanations investigate. The explanatory relationship between them depends upon the question being asked. Rather, it provides an explanatory framework for understanding the organised systems upon which evolutionary processes operate.

APS explains the organisation that persists.

Evolution explains the transformation of that organised persistence through time.

The two frameworks therefore address complementary dimensions of biological explanation: one concerned with the maintenance of viability-oriented organisation, the other with its historical transformation.

Foundational Generality without Explanatory Monopoly

APS makes living organisation itself an explicit explanatory target. In this restricted sense, its Explanatory Grammar has potential foundational generality: it proposes an account intended to apply to the organisation characteristic of living systems across the biological domain.

Foundational generality does not mean that APS is causally prior, hierarchically deeper, or obligatory for every biological explanation. Particular mechanisms, developmental processes, evolutionary transformations, ecological relations, and other biological phenomena may be adequately explained without reconstructing them through APS.

The claim is instead that APS addresses a question that bears upon the identity of the biological domain itself: what distinguishes living organisation and how is that organisation maintained through change? Whether APS provides the preferred general account of this target cannot be inferred from the breadth or coherence of its grammar. It requires comparison with the strongest alternative accounts addressing the same question and a demonstration of explanatory gain.

Why This Grammar Matters

By making explanatory grammar explicit, APS clarifies core biological questions. It specifies what counts as a biological individual, how organisms regulate their internal conditions, how evolution transforms organised systems, and how cognition emerges from biological activity.

Explanation is thereby grounded not in isolated components or privileged scales, but in viability-oriented organisation sustained through interacting processes across scales.

This shift has important consequences.

Biological individuality becomes a question of continuity-preserving organisation rather than static material composition.

Biological causation becomes a question of how constraints are organised and modulated within viable systems.

Function becomes a question of contribution to organised persistence rather than externally assigned purpose.

Cognition becomes a specialised elaboration of biological organisation rather than the conceptual foundation from which biological explanation must begin.

Across these domains, APS seeks to explain life in terms of the organisational conditions that allow living systems to maintain themselves despite continual change.

Explanatory Grammar and Scientific Practice

Scientific explanation necessarily employs conceptual categories that render complex phenomena intelligible. These categories are indispensable, yet they can also become invisible. When this occurs, elements of an explanatory grammar may come to appear as intrinsic features of reality itself rather than as components of a particular explanatory framework.

In biology, this tendency has repeatedly generated debates concerning the fundamental units and causes of life. Genes, cells, organisms, populations, networks, developmental systems, and ecological communities have each been proposed as privileged explanatory centres. Yet these disputes often persist not because of conflicting evidence, but because different explanatory grammars prioritise different aspects of biological organisation.

APS suggests that many long-standing controversies in biology are therefore best understood as disagreements about explanatory grammar rather than disagreements about empirical facts. Different traditions frequently illuminate genuine features of living systems while simultaneously elevating particular explanatory categories to positions of explanatory priority.

This insight also helps clarify a number of familiar philosophical debates. Reductionism, emergence, mechanism, holism, and organicism need not be understood as mutually exclusive accounts of life. Each highlights important aspects of biological organisation while operating within a particular explanatory orientation. Their apparent incompatibilities often arise from differences in explanatory grammar, explanatory direction, or explanatory scale.

APS does not seek to eliminate or absorb these perspectives. Its comparative role is to clarify their explanatory targets, priorities, relations, strengths, and limits and, where appropriate, to identify ways in which independently successful explanations can contribute to understanding living organisation. Integration therefore means relating explanatory contributions where this produces gain, not subordinating all biological explanation to APS.

The central question therefore shifts. Instead of asking which entity, mechanism, process, or scale is fundamentally responsible for life, APS asks how organised persistence is achieved and maintained. Within APS, the foundational explanatory question becomes how living systems achieve and maintain organised persistence through continual transformation.

Living systems are not defined by a privileged component. They are continuity-preserving organisations maintained through distributed and interacting processes. Explanation must therefore track this organisation rather than reduce it to any single explanatory domain.

APS provides an explicit explanatory grammar for investigating that question.

Where to Go Next

To see how this explanatory grammar is developed within the APS framework:

Explanatory Grammar is not an additional component of biological reality. In APS, it names the organised conceptual and explanatory relations through which living organisation and organised persistence are made intelligible. By making this grammar explicit, APS seeks to explain living systems as viability-oriented, constraint-closed organisations that persist, transform, and evolve through time. Its potential foundational generality derives from that explanatory target; its adequacy and any comparative superiority remain matters for evidence and target-matched assessment.