Where This Article Fits Having introduced APS in What Is APS?, this article explains why such a framework remains worth investigating. It identifies unresolved questions concerning living organisation, asks what an APS organisational perspective might contribute alongside established biological and theoretical approaches, and explains how those possible contributions should be assessed. Readers may wish to read this article immediately after What Is APS? before continuing to the broader orientation pathway.

Section 1 — Introduction. Biology’s Extraordinary Achievement

Modern biology has transformed our understanding of life more profoundly than perhaps any previous scientific discipline. Yet the continuing success of biology has revealed an unexpected consequence: the better we understand living systems, the more clearly we can ask what kind of phenomenon life actually is.

Over little more than a century and a half, biology has revealed the mechanisms of heredity, the dynamics of evolution, the organisation of cells, the molecular basis of development, the complexity of ecological interactions, and the biochemical processes that sustain life. Few scientific disciplines have reshaped both human knowledge and practical life so profoundly.

This achievement has been cumulative rather than dependent upon a single revolutionary discovery. Darwin’s theory of evolution by natural selection unified the diversity of life within a common historical framework. Genetics explained the inheritance of biological traits. Molecular biology uncovered the physical basis of genetic information and cellular function. Physiology, developmental biology, ecology, and systems biology each expanded biology’s explanatory reach by revealing new dimensions of living organisation. Together, these fields have produced an extraordinarily rich understanding of how living systems function, develop, reproduce, adapt, and evolve.

The practical consequences have been equally remarkable. Modern biology underpins contemporary medicine, agriculture, biotechnology, conservation, and public health. It informs responses to infectious disease, guides ecosystem management, enables genetic diagnosis and therapy, and contributes to understanding global environmental change. The explanatory power of biology is therefore measured not only by its theoretical achievements but also by its capacity to improve human life and deepen our understanding of the living world.

Importantly, this success has never depended upon a single explanatory tradition. Biological knowledge has advanced through the interaction of multiple complementary approaches. Mechanistic explanations identify how biological phenomena occur. Evolutionary explanations account for their historical transformation. Developmental biology explains the emergence of organismal form and function throughout the life cycle. Ecology situates organisms within wider environmental relationships. Systems biology investigates the coordinated interactions through which complex biological behaviour emerges. Each perspective illuminates aspects of living systems that cannot be fully understood in isolation from the others. As biology has expanded, its explanatory traditions have become increasingly complementary rather than mutually exclusive, creating opportunities for integrative organisational frameworks alongside continued empirical investigation.

Recognising this diversity is essential. APS does not begin from the claim that modern biology has failed or that its established explanatory traditions are inadequate. On the contrary, the continuing success of modern biology provides the very foundation upon which further conceptual work becomes possible. Mature sciences often discover that their greatest achievements reveal new kinds of foundational questions. Biology is no exception.

Indeed, the history of science suggests that intellectually mature disciplines periodically return to questions lying beneath their expanding body of empirical knowledge. Progress in observation, experimentation, and theory frequently reveals new conceptual issues rather than eliminating them. Physics continues to investigate the foundations of space, time, and quantum reality despite its extraordinary predictive success. Likewise, biology continues to ask what distinguishes living systems, what constitutes biological organisation, and what kinds of explanation are required to understand life as a distinctive natural phenomenon. Such questions do not diminish the achievements of biological science; they arise precisely because those achievements have made deeper forms of understanding possible.

It is within this context that the Agency–Process–Scale (APS) framework should be understood. APS was not developed in opposition to modern biology, nor as a replacement for its established theories. It emerged from the recognition that the continuing success of biological research has brought foundational questions concerning living organisation into increasingly sharp focus. Before considering how APS approaches those questions, it is therefore necessary to understand why successful sciences continue to revisit their conceptual foundations.

Section 2 — Why Success Does Not End Inquiry

Modern biology’s extraordinary achievements do not bring biological inquiry to an end. On the contrary, they make new kinds of questions possible. As knowledge accumulates, sciences often discover that progress reveals deeper conceptual issues rather than eliminating them. The history of science repeatedly shows that explanatory success and foundational inquiry develop together.

This pattern is familiar across the natural sciences. Physics has achieved remarkable predictive power while continuing to investigate the nature of space, time, gravity, and quantum reality. Chemistry successfully explains the composition and transformation of matter while still examining the conceptual foundations of chemical organisation and emergence. Mature sciences do not cease asking fundamental questions because they have become successful; they ask them because success has clarified what remains to be understood.

Biology occupies a similar position. During the past century, enormous advances have illuminated the mechanisms through which living systems develop, reproduce, adapt, communicate, regulate, and evolve. These achievements have transformed our understanding of life at every level of investigation. Yet they have also sharpened several enduring questions. What distinguishes living systems from other organised physical systems? What makes biological organisation a distinctive object of scientific explanation? What, ultimately, is biology attempting to explain?

These questions are sometimes misunderstood as attempts to replace empirical biology with abstract speculation. In fact, they arise from the opposite impulse. The more completely biological mechanisms become understood, the more clearly one can ask what those mechanisms collectively achieve as aspects of living organisation. The issue is not whether molecular biology, physiology, ecology, or evolutionary theory are successful—they demonstrably are—but whether their combined achievements point towards a broader organisational target that deserves explicit investigation.

This distinction is important because it concerns the nature of explanation rather than the accumulation of evidence. Scientific disciplines routinely distinguish between explaining individual phenomena and clarifying the conceptual framework within which those explanations acquire their coherence. Biology explains countless biological processes with extraordinary precision. A different, though complementary, question asks how those diverse explanations relate to one another as explanations of living systems.

For this reason, foundational questions should not be interpreted as signs of disciplinary weakness. They are characteristic of intellectually mature sciences. Every successful explanatory framework eventually raises questions about its own organising concepts, assumptions, and scope. In biology, questions concerning life, organisation, individuality, function, agency, information, and explanation itself remain active precisely because they concern the conceptual organisation of biological knowledge rather than unresolved empirical observations.

Theoretical biology and the philosophy of biology have long recognised the importance of these questions. They investigate not only particular biological phenomena but also the conceptual structures through which biology understands its subject matter. Their aim is not to compete with experimental biology but to clarify the explanatory architecture that allows diverse biological discoveries to form a coherent scientific understanding of life. Within these fields, discussions of organisation, autonomy, mechanism, function, emergence, and individuality reflect an ongoing effort to understand what kinds of explanation are appropriate for living systems.

It is within this continuing conversation that APS should be situated. The framework did not arise because biology lacked evidence, nor because existing theories had ceased to be productive. Rather, it emerged from the recognition that biology’s continuing success has made questions about the organisation of living systems increasingly explicit. Before introducing APS itself, however, one further step is required. We must identify more precisely the nature of the explanatory challenge that these questions reveal.

Section 3 — The Organisational Target of Biological Explanation

The continuing success of modern biology raises a question that is easily overlooked. If biology can already explain heredity, development, metabolism, physiology, behaviour, adaptation, and evolution with remarkable precision, what remains to be explained? At first sight, the answer might appear to be simply “more biology”—more mechanisms, more genes, more pathways, and more interactions. Yet many of the continuing discussions within theoretical biology suggest that the remaining challenge is of a different kind. It concerns not merely the accumulation of additional knowledge, but the clarification of what biological explanation is attempting to explain when living organisation itself becomes the target.

Every biological discipline investigates some aspect of living systems. Molecular biology explains cellular processes through molecular interactions. Physiology explains the coordinated functioning of organisms. Evolutionary biology explains the historical transformation of populations. Developmental biology explains the emergence and maintenance of organised form throughout the life cycle. Ecology explains the relationships between organisms and their environments. Each contributes indispensable knowledge. Their explanatory success is beyond question.

What is striking, however, is that many successful biological explanations concern systems whose activities, development, regulation, reproduction, ecological relations, and evolutionary histories are aspects of living organisation. This raises a further question: when such explanations bear upon the organisation of living systems, can their relationships be investigated without reducing them to a single explanatory vocabulary or assuming that they share one explanandum?

This question does not ask biology to abandon mechanisms in favour of organisational explanation. Mechanistic explanation remains indispensable because living systems are materially realised through physical and chemical processes. Nor does it seek a master theory capable of replacing evolutionary, developmental, physiological, ecological, or other biological explanations. Different explananda can legitimately require different explanatory approaches.

The issue is therefore conditional rather than universal. Where living organisation itself, or its continuity through change, is the explanatory target, it may be useful to ask how different findings bear upon that target. Where the explananda differ, no such integration should be assumed.

Organisation is already a major subject within theoretical biology. General systems theory, relational biology, autopoiesis, autonomy theory, constraint-based approaches, and organisational accounts of function have all developed substantive ways of investigating it. APS enters this established field rather than claiming to introduce organisation as a previously missing object of inquiry.

Its particular proposal is to investigate whether viability-oriented, constraint-closed organisation and organised persistence clarify some biological explananda, expose useful relationships among established explanations, or generate assessable questions that existing approaches do not already supply. Whether they do so must be established rather than inferred from APS architecture.

The Agency–Process–Scale framework therefore enters theoretical biology as one candidate organisational perspective. It asks what explanatory work its formulation of living organisation can perform and where, if anywhere, that work differs consequentially from the strongest relevant alternatives.

Modern Biology
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Continuing Explanatory Success
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Increasingly Explicit
Foundational Questions
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Organisation as the
Target of Explanation
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Agency–Process–Scale

The continuing success of modern biology progressively reveals questions concerning the organisation of living systems. APS is presented as one methodological response to those questions.

Organisation Is Not an Alternative to Biology

APS does not argue that biological mechanisms, evolutionary history, development, or ecology are insufficient. It asks whether their explanatory achievements sometimes raise further questions about the organisation of the living systems concerned, and whether an APS analysis contributes anything to answering those questions.

Section 4 — Why APS Was Developed

The Agency–Process–Scale (APS) framework was developed in response to the explanatory question identified in the preceding section. It does not begin by proposing a new biological mechanism, a new evolutionary theory, or a new account of molecular function. Instead, it begins by asking whether living organisation can be more clearly specified as an explanatory target and what follows if it can.

APS therefore begins from an organisational proposal rather than a new biological mechanism. It asks whether living systems can usefully be investigated as viability-oriented, constraint-closed organisation whose activity maintains and re-establishes conditions of persistence. This proposal does not imply that the diverse phenomena studied throughout biology are merely expressions of one explanatory process. It provides a candidate organisational target against which relevant relationships among those phenomena can be investigated.

This perspective distinguishes two complementary tasks that can arise within biological explanation. The first is to explain particular biological phenomena through the appropriate empirical sciences, including molecular biology, physiology, developmental biology, ecology, and evolutionary biology. The second, where living organisation itself is explanatorily relevant, is to ask how those explanations bear upon the organisation and continuity of the living system. APS addresses this second task without assuming that it is required for every biological explanandum.

This orientation also explains why APS is organised around three complementary analytic projections:

Agency, Process, and Scale. These are neither separate components of reality nor independent causal forces. They are complementary analytic projections of one and the same living organisation.

Agency asks what living systems do. It investigates the viability-oriented activity through which organisms maintain and re-establish the conditions of their own persistence.

Process asks how continuity is maintained despite ongoing material turnover, developmental change, and environmental variation. It examines the dynamic organisation through which organised persistence is sustained.

Scale asks across what spatial and temporal extents, and through what materially implemented relations among them, persistence is organised. It does not treat those extents as explanatory hierarchies.

Taken together, these analytic projections provide a framework for investigating living organisation while preserving the specialised explanatory methods of biology. Evolutionary theory continues to explain historical transformation. Molecular biology continues to investigate biochemical mechanisms. Ecology continues to explain organism–environment relationships. APS asks how such explanations bear upon viability-oriented, constraint-closed organisation where that relationship is relevant to the explanandum.

The framework therefore makes a deliberately bounded claim. It does not propose that Agency, Process, and Scale answer every biological question. Rather, they provide complementary analytic projections through which a particular class of questions concerning living organisation can be formulated and investigated. Whether doing so provides explanatory value cannot be determined by the architecture alone.

Seen in this way, APS belongs within the continuing development of theoretical biology. It emerges from biology’s existing achievements, engages with established questions concerning organisation and explanation, and seeks to provide a systematic way of investigating them. Its purpose is not to replace biology’s explanatory traditions or to assume that they form parts of a single APS explanation, but to determine where an organisational perspective clarifies their relationships, generates useful questions, or identifies additional explanatory work.

Section 5 — What APS May Contribute

The reason to investigate APS is not that biology lacks successful explanations of mechanisms, evolution, development, regulation, ecology, autonomy, or organisation. Nor is APS justified simply because established biological results can be redescribed using the language of Agency, Process, Scale, viability, or organised persistence.

APS may make several different kinds of contribution, and they should not be conflated.

First, APS may make a conceptual contribution. It may help specify biological explananda, distinguish questions that are easily conflated, or clarify relationships among concepts concerned with living organisation. Its distinction between Life as viability-oriented, constraint-closed organisation and organised persistence as the continuity of that organisation through change is one such proposal. Conceptual clarification can be scientifically useful, but it does not by itself establish that APS explains a biological phenomenon better than existing approaches.

Second, APS may make a methodological contribution. It can provide ways of asking how biological explanations relate without assuming that different vocabularies represent competing theories or that conceptual integration constitutes explanatory gain. APS therefore emphasises specification of the explanandum, comparison with the strongest relevant alternatives, identification of materially implemented dependencies, and explicit allowance for redundancy, complementarity, comparator advantage, or null results. It can also generate questions about living organisation that are open to further investigation.

Third, APS may in some cases make a biological explanatory contribution. This is the strongest claim and carries the greatest evidential burden. Such a contribution is established only where, for a specified explanandum, APS identifies explanatory relationships, dependencies, consequences, or discriminating expectations not already supplied by the strongest relevant established explanation.

These three forms of contribution do not entail one another. A useful concept need not produce a better method. A useful method need not produce new biological explanation. And conceptual coherence, integrative scope, accessibility, or the ability to redescribe many biological phenomena in APS terminology does not establish explanatory superiority.

This distinction also clarifies how APS should be tested. Illustrating APS is not testing APS. Showing that a biological system can be described in terms of viability, agency, process, scale, constraints, or organised persistence demonstrates applicability of the vocabulary. Testing a biologically consequential APS claim requires a specified explanandum, an adequate comparator, an identifiable difference in explanatory dependency or expectation, and some condition under which the APS claim could fail.

APS should therefore be understood as both an organisational proposal and a research programme for determining what, if anything, follows explanatorily from that proposal. Its value may lie in clarification, methodological organisation, hypothesis generation, or demonstrated biological explanatory gain. Where none of these survives comparison with established alternatives, APS adds no corresponding scientific contribution.

The wider APS corpus develops these questions across life, biological agency, organised persistence, constraint closure, cognition, individuality, development, evolution, social organisation, morality, and biological explanation. Each domain must carry its own evidential burden rather than deriving its scientific status merely from membership in the APS architecture.

Concluding Reflection

Modern biology continues to expand our understanding of living systems through increasingly sophisticated empirical investigation. At the same time, its continuing success leaves legitimate questions concerning how living organisation should be conceptualised, investigated, and related to the many successful explanations biology already provides. APS represents one attempt to address those questions through an organisational framework centred on viability-oriented, constraint-closed organisation.

Whether APS proves scientifically valuable cannot be settled by the coherence or breadth of its architecture. Its contribution must be assessed by whether it clarifies important explananda, improves explanatory comparison, generates productive and assessable biological questions, or—where stronger claims are made—identifies explanatory dependencies or consequences not already supplied by the strongest relevant alternatives. Where it merely redescribes established biology in APS terminology, no additional explanatory gain has been demonstrated.

The purpose of this article is therefore not to establish that biology needs APS in advance. It is to explain why APS poses questions worth investigating and to make clear what the framework would have to contribute for that investigation to succeed.