Where This Article Fits

This article examines APS within the broader tradition of conceptual frameworks for biology. Unlike Agency as the Defining Activity of Life, which establishes APS’s foundational account of living organisation, it is concerned with the organisation of biological knowledge and explanation. It also differs from APS and Contemporary Explanatory Approaches, which distinguishes questions about Life, APS and comparative explanation and guides readers through the relevant articles. The present discussion instead examines established attempts to organise biological theory, particularly those developed by Scheiner, and considers how APS relates to them. Its purpose is to clarify APS’s theoretical position and potential scientific usefulness, not to claim that conceptual integration alone establishes explanatory superiority.

Introduction - Why Conceptual Frameworks Matter

Biology has many successful ways of explaining living systems. A physiologist can identify the mechanisms regulating a cell; a developmental biologist can investigate how tissues form; an ecologist can examine relationships between organisms and environments; and an evolutionary biologist can explain changes across generations. None of these explanations is deficient simply because it addresses only part of biology. Specialisation is indispensable.

Yet the connections among explanations also matter. Regulation depends on material processes; development requires coordinated cellular activity; ecological circumstances affect which activities can be sustained; and evolution changes the organisation that descendants inherit. A question that crosses these fields may require more than several correct answers considered separately. It may require an explicit account of how their assumptions, processes and explanatory dependencies fit together.

A conceptual framework can help organise such questions. Its value is not necessarily to supply a new biological law or replace specialised theories. It may instead clarify concepts, disclose assumptions, relate levels of investigation and indicate where evidence is still needed. The Agency–Process–Scale (APS) framework is one attempt to do this. It belongs, however, to a long and productive history of efforts to understand biology as both a differentiated and a connected science.

A Long History of Biological Integration

Evolution and the coherence of biology

Darwin’s On the Origin of Species (1859) gave biological diversity a powerful historical explanation. Organisms could be understood through descent, variation and natural selection rather than as unrelated forms requiring independent accounts. The subsequent development of evolutionary biology connected inheritance, populations, adaptation and historical change. Mayr’s The Growth of Biological Thought (1982) shows how these ideas emerged through sustained debate and changing scientific practices.

Evolutionary theory remains essential to biological integration, but it does not eliminate the need for physiological, developmental, ecological or molecular explanations. Explaining why a trait spread in a population differs from explaining how an individual organism produces or maintains it. A framework that connects these questions must preserve their differences. APS therefore cannot substitute a general language of viability for the specific evidence required by evolutionary biology.

Systems, organisation and complexity

Systems approaches challenged the idea that complex biological phenomena could always be understood by examining components in isolation. Von Bertalanffy’s General System Theory (1968) foregrounded relationships, open systems and organised wholes. Simon’s account of the architecture of complexity (1962) examined how complex arrangements can be structured into interacting, often hierarchical, subsystems.

These traditions made organisation, interaction and scale familiar subjects of scientific analysis long before APS. They also raise a continuing question: when does describing a system’s organisation improve explanation, and when does it merely rename relationships that specialised research already understands? APS inherits this question rather than resolving it through its terminology.

Mechanisms and explanatory levels

Biologists frequently explain a phenomenon by identifying its component activities, their arrangement and the conditions under which they produce an outcome. Bechtel and Richardson (1993) examined the scientific strategies of decomposition and localisation. Craver (2007) explored how mechanistic explanations can connect different levels of investigation without reducing every question to a single preferred level.

This work matters because a framework spanning scales cannot dispense with the detail of mechanisms. Identifying a viability-relevant outcome is not the same as discovering the processes responsible for it. If APS claims that an organism maintains some condition, it must still identify what does the maintaining, how the relevant activities are organised and which observations could show that the proposed account is mistaken.

Autopoiesis, autonomy and organisational closure

Another influential tradition begins with the question of what makes a living system an organised, self-maintaining system. Maturana and Varela (1980) developed the concept of autopoiesis to characterise living organisation in terms of the production and maintenance of its own components and boundaries. Later work on biological autonomy, including Moreno and Mossio (2015), investigated the conditions under which organised activities sustain the system that makes them possible. Montévil and Mossio (2015) developed an account of biological organisation in terms of closure of constraints.

These approaches are especially important predecessors of APS. They already address maintenance, dependence, constraint and the organisation of living activity. APS’s formulation of life as viability-oriented, constraint-closed organisation should therefore be read in relation to this literature, not as an independent discovery of self-maintenance. Any claimed difference must be specified precisely and assessed against these established accounts.

Integration without a single master explanation

Other approaches have explored how distinct forms of biological explanation can cooperate without collapsing into one universal theory. Mitchell’s Biological Complexity and Integrative Pluralism (2003) argues for taking the diversity of biological explanatory practices seriously while examining how they can be brought into productive relation. Kitano’s work on computational systems biology (2002) shows how models of interacting components can support the investigation of system-level behaviour. Nicholson and Dupré’s edited volume Everything Flows (2018) advances processual perspectives that question overly static pictures of biological entities.

The common lesson is not that all these approaches say the same thing. They address different scientific and philosophical problems. Their significance for APS is that integration, process, interaction and pluralism are already well-developed areas of enquiry. A useful framework must clarify what it adds to this landscape rather than claim ownership of its central concerns.

Scheiner’s Conceptual Framework for Biology

Samuel Scheiner’s Toward a Conceptual Framework for Biology (2010) offers a particularly direct comparison. Scheiner proposes an explicit architecture of general biological principles and associated theories concerned with evolution, ecology, cells, organisms and genetics. The ambition is not to replace detailed biological research but to make the relationships among its theoretical domains more intelligible.

Scheiner’s organismal principles are especially relevant to APS. They address the active maintenance of structural and functional integrity, exchanges of matter and energy, organism–environment relationships and consequences across levels of organisation. These are not concerns newly introduced by APS. A comparison that ignored them would give APS an undeserved advantage.

In The Role of Theory in Biology (2026), Scheiner also emphasises the practical work of theory. His account distinguishes broad theoretical principles, constitutive theories that guide model construction, and models used in relation to evidence. Relationships among models can be recognised or developed through theoretical work. This is a substantive account of scientific integration, not simply a classification of established knowledge.

Scheiner’s work therefore sets a demanding standard. APS cannot establish novelty merely by showing that ideas from physiology, development, ecology and evolution can be discussed together. Nor can it claim scientific gain merely because it makes assumptions or model relationships explicit: these are already recognised aims of biological theory.

What APS Brings to the Discussion

APS begins with a proposed account of living organisation. In its developed formulation, life is viability-oriented, constraint-closed organisation. Living systems persist through materially realised activities and processes that maintain or re-establish the conditions required for their continued organisation. Biological agency denotes this viability-oriented activity; it does not imply that every living system is conscious or deliberates about its goals.

The framework examines one organisation through three complementary analytic projections. Agency concerns viability-oriented activity. Process concerns the material and temporal transformations through which that activity occurs. Scale concerns the spatial, temporal and organisational extent at which relevant dependencies are expressed. These are not three independent forces or three successive levels of life. They are connected perspectives on the same organised phenomenon (Spencer, 2026).

Biological explanation is necessarily plural: physiology, genetics, development, ecology and evolution investigate different but related aspects of living systems. Scientific perspectivism likewise recognises that different investigative standpoints disclose different features of biological organisation. APS does not seek to replace these approaches with a single explanatory method. Rather, it offers an integrative architecture in which agency, process and scale provide complementary perspectives on living organisation, while viability, function and organised persistence help clarify relationships among explanations. Such integration requires careful specification of explanatory targets, attribution conditions and evidential limits. Its purpose is not to eliminate explanatory diversity, but to make the dependencies among legitimate biological explanations more explicit and assessable.

Consider an organism adjusting its physiology under environmental stress. A mechanistic explanation may identify sensory pathways, regulatory processes and energetic costs. An ecological explanation may examine the circumstances in which the response improves persistence. An evolutionary explanation may investigate how the capacity for that response arose and varies among populations. APS asks whether the dependencies among these explanations can be stated clearly: what is being maintained, by which processes, under which conditions, and over which relevant times and scales?

This question can be useful as an organising prompt. It does not, by itself, provide a mechanism, a measurement or an evolutionary explanation. The relevant specialised sciences must supply those. Nor does APS establish that the resulting account is better than an explanation constructed through existing systems, autonomy or mechanistic approaches.

A Worked Example: Predator-Induced Defences in Daphnia

A conceptual framework becomes easier to assess when it is applied to a definite biological problem. Consider the development of defensive traits in Daphnia, small freshwater crustaceans that can respond to chemical cues associated with predators. In suitable species and experimental conditions, exposure to such cues can induce changes in morphology or development. The details vary with the species, predator and environment; the example should not be read as describing a universal Daphnia response.

The developmental question concerns how an environmental cue influences the production of a defensive phenotype. Investigators must establish the cue, the conditions under which it is detected, and the developmental changes that follow. The physiological question concerns the mechanisms and resources involved, including possible energetic or growth costs. Neither question can be answered by saying only that the animal is acting to preserve its viability. The material processes and their effects must be demonstrated.

The ecological question asks whether the induced defence changes outcomes under particular predator conditions. A trait that reduces vulnerability to one predator may carry costs in growth, reproduction or performance under other conditions. The relevant comparison is therefore not simply defended versus undefended morphology, but the consequences of each phenotype in specified environments. A defence may be beneficial in one context and costly in another.

The evolutionary question is different again. It concerns the history, inheritance and population-level consequences of the capacity for an inducible response. Showing that an individual develops a defence does not establish why that capacity evolved or how selection maintains it. Evidence about variation, heritability, fitness and ecological history is required for those claims.

APS can organise these questions around one living system. Agency draws attention to the viability-relevant activity and its conditional consequences. Process directs attention to cue detection, developmental change and the material production of the phenotype. Scale requires the investigator to distinguish changes within an individual from ecological interactions and evolutionary changes across generations. These are different analytical projections of the same case, not three competing causal explanations.

This organisation may help a reader see why an account of defensive development is incomplete if it is mistaken for an account of evolutionary adaptation, or why a survival benefit cannot be assumed from the presence of an apparently protective structure. Yet existing developmental, ecological and evolutionary approaches can already make these distinctions. In the previous APS comparative assessment of this case, the supported outcome was equivalent redescription, not demonstrated explanatory gain. The example therefore illustrates how APS can arrange established dependencies while leaving open the separate question of whether that arrangement offers additional scientific usefulness.

Two Ways of Organising Biological Understanding

A useful initial distinction is that Scheiner principally examines the organisation of biological knowledge—the relationships among broad principles, theories and models—whereas APS principally directs attention to the organisation under investigation: living activity and the material dependencies that sustain it. This is a difference in analytical starting point, not a rigid division between two mutually exclusive enterprises.

Scheiner’s framework addresses real biological organisation, and APS also has implications for the organisation of explanation. Indeed, an APS-inspired account could be expressed as a constitutive theory or model within Scheiner’s architecture. Conversely, an existing constitutive theory may already identify every relationship that APS proposes to highlight. The frameworks may overlap substantially while serving somewhat different immediate purposes.

Suppose a study identifies an environmentally induced defensive response, its developmental costs and its consequences for survival or reproduction. Scheiner’s approach can help locate the theories and models involved and clarify their relations. APS may organise the same evidence around the maintenance of viable organisation across physiological, ecological and evolutionary timescales. If both accounts disclose the same dependencies and support the same investigations, the APS account is an equivalent redescription, not an explanatory advance.

That is a legitimate result. A framework should be allowed to clarify established knowledge without being credited with discoveries it has not made.

What Would Make APS Scientifically Useful?

Several achievements should be distinguished rather than treated as interchangeable.

Conceptual precision requires APS terms to mark definite distinctions. In a particular investigation, viability must refer to specified conditions and outcomes, not simply to the general fact that living systems persist.

Empirical assessability requires proposed dependencies to be connected with observations, interventions or models capable of discriminating among alternatives. Naming an outcome does not establish which measurements or tests will explain it.

Systematic integration requires relationships among concepts and biological domains to be explicit, coherent and appropriately qualified. A shared vocabulary may assist understanding, but does not itself demonstrate a new causal relationship.

Scientific usefulness requires an identifiable contribution to research practice: a better-specified question, an exposed assumption, an overlooked dependency, a more informative comparison or a productive empirical test. Comparative advantage is a further claim, requiring evidence that APS performs better than a strong established alternative addressing the same problem.

These criteria need not succeed together. APS might clarify a cross-disciplinary question without improving the resulting model. It might support teaching or conceptual orientation without producing new empirical predictions. It might also impose an unnecessary terminological burden. Such possibilities should remain open to assessment.

A demanding test would begin with a narrowly specified biological problem, reconstruct the strongest existing explanation independently of APS, and only then examine whether APS identifies an additional material dependency or scientifically useful distinction. Positive, equivalent and adverse results would all be informative. Applying APS vocabulary to many examples, without such comparisons, cannot establish explanatory gain.

Conceptual Frameworks and Scientific Progress

Scientific progress does not always consist in discovering a new mechanism or formulating a new law. It can also involve identifying an ambiguity, distinguishing questions that have been conflated, bringing separate bodies of evidence into a productive relationship, or showing precisely where a proposed explanation remains unsupported. These achievements matter because they can change what investigators ask, measure and compare. They are nevertheless different from demonstrating a new causal dependency.

A conceptual framework may assist such work by making its assumptions inspectable. In the Daphnia example, a clear separation of developmental production, ecological consequences and evolutionary history helps prevent evidence for one claim from being treated as evidence for another. APS provides one vocabulary for organising those distinctions. The relevant test is whether its vocabulary makes a real difference to the formulation or conduct of an investigation, rather than merely restating distinctions already available to researchers.

The distinction between integration and superiority is therefore essential. A framework can make a complex subject more accessible to students or researchers crossing disciplinary boundaries without outperforming an established theory on a matched explanatory task. Such communicative or organisational value should be investigated on its own terms. It should not be converted automatically into a claim of explanatory gain; nor should the possibility of additional terminology imposing a burden be ignored.

The most informative evaluation would identify a specific audience or research task, establish a strong comparison using existing approaches, and define in advance what would count as success. Does APS help readers identify relevant dependencies more accurately? Does it expose an assumption that would otherwise be missed? Does it lead to a better-defined empirical question? Or does the comparator perform equally well with fewer conceptual demands? Each outcome would tell us something useful about the framework’s practical role.

In this sense, the scientific promise of APS is a research question, not a conclusion built into its architecture. Its contribution will be better established through bounded demonstrations of precision, assessability and usefulness than through declarations that biology needs a single unifying language.

Integration Without Replacement

APS belongs within a substantial history of attempts to understand biology through evolution, systems, mechanisms, autonomy, processes and relations among theories. Its orientation towards viability, organised persistence and connected scales offers a particular way of arranging biological questions. It should not be presented as replacing those traditions or as having demonstrated a superior general theory.

The present comparison supports a bounded conclusion. Scheiner has already developed an explicit account of biological theory and model relationships, while organisational and autonomy approaches already investigate much of the biological territory central to APS. APS may still contribute by making certain viability-relevant dependencies more precise, accessible or assessable across domains. Whether it does so beyond the strongest existing alternatives remains an empirical and methodological research question.

The constructive aim is therefore not a unified vocabulary for its own sake. It is clearer biological enquiry: explanations that preserve the strengths of specialised research while making important relationships open to examination, comparison and revision.

Explanatory Architecture

Central Question

How can APS organise relationships among biological explanations without replacing specialised theories or presuming comparative explanatory gain?

Architectural Role

This Synthesis article in the Methodology and Explanation cluster places APS within the history of biological conceptual frameworks, especially Scheiner’s account of principles, theories and models. It distinguishes a framework’s conceptual organisation from evidence of its scientific usefulness.

Explanatory Dependencies

APS asks how viability-relevant activity is materially realised and how its dependencies are investigated at appropriate spatial, temporal and organisational scales. These questions guide enquiry; they are not a universal causal sequence or an alternative to mechanistic, ecological, developmental or evolutionary evidence.

Position within APS

Agency, Process and Scale are complementary analytic projections of one viability-oriented, constraint-closed organisation, not independent causes or hierarchical levels. Their application to a biological problem requires specified explananda, empirical warrant and fair comparison with established approaches.

Corpus Significance

This article locates APS among existing integrative frameworks and distinguishes conceptual precision, empirical assessability, systematic integration, scientific usefulness and comparative advantage. Equivalent redescription remains an admissible outcome; architectural difference alone establishes no explanatory superiority.