Introduction

Scientific theories do not simply accumulate observations; they organise them through conceptual frameworks that determine what counts as an entity, a cause, and an explanation. These frameworks function as explanatory grammars: structured sets of commitments that define how phenomena become intelligible within a domain.

Just as linguistic grammar structures meaningful sentences, explanatory grammar structures meaningful scientific accounts. It determines which entities appear in explanation, which relations count as causal, and what constitutes an adequate 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 foundational, 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

Despite their differences, these approaches share a common assumption: that biological explanation must identify a privileged scale of causation. At different times, genes, cells, or organisms have been treated as foundational explanatory units.

This assumption reflects patterns familiar from engineered systems, where causal control is hierarchically organised. Living systems, however, do not conform to such structures. Their organisation is distributed, reciprocal, and dynamically maintained.

Distributed and Reciprocal Causation

In living systems, causation is not confined to a single scale but propagates across interacting processes. Molecular dynamics influence cellular organisation; cellular activity reshapes molecular processes; physiological regulation modifies gene expression; organismal activity alters environmental conditions.

Causation is therefore distributed and reciprocal rather than hierarchical. Biological explanation must account for this organisation without reducing it to a single privileged domain.

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.

Biological explanation therefore resolves into three co-constitutive dimensions:

Agency — viability-oriented regulation
Process — the dynamic organisation of activity through time
Scale — the coordination of activity across spatial and temporal domains

These are not independent categories but analytically distinct aspects of a single organisational reality.

This triad 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.

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

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)

Conceptual Symmetry with Evolution

The APS explanatory grammar reveals a structural alignment with evolutionary theory.

Agency corresponds to persistence: systems sustain their own viability
Process corresponds to inheritance: organisation is reproduced through ongoing dynamics
Scale corresponds to transformation: change unfolds across domains

Evolution describes the transformation of organised persistence, while APS specifies the organisational conditions that make such transformation possible.

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 scales, but in viability-oriented organisation sustained through interacting processes across scales.

Explanatory Grammar and Scientific Practice

Scientific explanation necessarily selects conceptual categories to render complex systems intelligible. These categories can become reified, appearing as intrinsic features of nature rather than elements of an explanatory grammar.

In biology, this has led to persistent debates about whether genes, cells, or organisms are fundamental. APS shows that these debates arise from competing grammars rather than from the structure of living systems themselves.

Living systems are not defined by a privileged component but by viability-oriented organisation maintained through distributed, interacting processes. Explanation must therefore track this organisation rather than reduce it to a single scale.

APS provides an explicit grammar capable of doing so.

Where to Go Next

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