Where This Article Fits This article is paired with the article Biology — What the Science of Life Explains.

That article introduces the APS account of living organisation. It explains Life as viability-oriented, constraint-closed organisation; distinguishes organised persistence from the definition of Life; and introduces Agency, Process, and Scale as complementary analytic projections through which living organisation can be investigated.

The present article begins from a different problem: biology already contains many successful forms of explanation. Mechanistic, physiological, developmental, evolutionary, ecological, systems, and organisational approaches address different questions and achieve different kinds of explanatory success. The question here is how those achievements can be compared without reducing them to a single theory, method, or explanatory vocabulary.

APS proposes organised persistence—the continuity of living organisation through change—as one possible comparative target. The purpose of this article is not to assume that this target unifies biological explanation, but to ask whether comparison through organised persistence can clarify what different explanatory approaches contribute, where their explanatory strengths differ, and where additional explanatory work may remain.

The two articles are therefore complementary. Biology — What the Science of Life Explains introduces the organisational account. What Is Biology Trying to Explain? investigates what that account may contribute to comparing biological explanations.

Introduction: What is Biology Trying to Explain?

Biology explains an extraordinary range of living phenomena. Genetics explains inheritance. Physiology explains how organisms coordinate their activities. Developmental biology explains how living forms arise and change. Evolutionary biology explains adaptation and diversification, while ecology explains the relationships between organisms and their environments.

These are powerful achievements, but they do not all ask the same questions or explain life in the same way. A genetic explanation of inheritance differs from a physiological explanation of regulation, an evolutionary explanation of adaptation, or an ecological explanation of interdependence. This diversity is not a weakness. It reflects the many different features of living systems and the different methods needed to investigate them.

Yet an important question remains. How do these different explanations relate as explanations of living systems?

The question is not whether biology needs one theory to replace its existing disciplines. Nor is it whether genes, mechanisms, evolution, information, or organisation should be declared the single foundation of life. Each can make an important explanatory contribution. The deeper question is whether their relationships can be clarified without reducing them to one another.

This question remains open despite biology’s extraordinary empirical success. Scientific discoveries continue to reveal how living systems work, develop, evolve, and interact, but they also invite reflection on what makes these phenomena distinctively biological and how different kinds of biological explanation fit together. The continuing discussion of what life is shows that this foundational question has not become obsolete (Nicholson 2025).

The Agency–Process–Scale Framework begins here. APS accepts biology’s explanatory diversity and does not offer another theory intended to replace it. Instead, it asks what different biological approaches contribute to understanding a striking feature of life: living systems persist despite continual change.

This article explores that comparative proposal. It begins with the different answers biology gives to different explanatory questions, then considers the continuity of living organisation through change. From there, it asks whether organised persistence can provide a useful target for comparing explanatory contributions without treating it as the single explanandum of biology or reducing established explanations to APS terminology.

Biology Has More Than One Kind of Answer

Biological explanations differ because they address different questions. A molecular biologist may ask how a particular gene is expressed. A physiologist may ask how body temperature is regulated. A developmental biologist may ask how tissues become organised. An evolutionary biologist may ask how a trait arose, while an ecologist may ask how organisms persist within changing environments.

These questions are related, but they are not interchangeable. Explaining how a structure presently works is different from explaining how it evolved. Describing the molecular interactions involved in a process is different from explaining its contribution to the functioning of an organism. Investigating an organism’s internal regulation is different from investigating its ecological relationships.

No single kind of explanation answers every biological question. This is partly because living systems are extraordinarily complex, but it is also because scientific explanations are selective. They identify particular patterns and relationships according to the question being asked. Different investigations can therefore provide legitimate explanations without offering identical accounts of the same phenomenon (Mitchell 2002; Potochnik 2017).

Biology’s explanatory diversity should not be treated as a problem that must be eliminated. Mechanistic, evolutionary, developmental, ecological, organisational, and other approaches have achieved their success by concentrating on different features of the living world. Their differences allow biology to explain more, not less.

But accepting this diversity does not mean that biological explanations are unrelated. Genes function within cells, cells participate in organisms, organisms develop and act within environments, and these relationships are transformed through evolution. Explanations directed at one of these concerns may therefore intersect with explanations directed at another.

The challenge is to understand these relationships without forcing every explanation into one theoretical form. We can ask what each approach explains especially well, where its contribution meets those of other approaches, and what broader features of living systems become clearer when these contributions are considered together.

APS accepts this challenge as a question of comparison rather than unification. It does not ask which biological approach should become the foundation of all the others. It asks how their different achievements contribute to understanding living organisation.

An Enduring Biological Question

Questions about what makes biological explanation distinctive are not new. Throughout its history, biology has approached living beings through different combinations of activity, structure, function, regulation, development, and historical change. These approaches did not all seek the same kind of answer, but each contributed to the continuing effort to make life scientifically intelligible.

Aristotle understood living beings through their characteristic activities, capacities, and forms of organisation. His biology differed greatly from modern science, but it established an enduring idea: explaining an organism involves more than listing the materials from which it is composed. It also involves understanding how those materials participate in the organised activities characteristic of its form of life (Aristotle 1937).

In the nineteenth century, experimental physiology brought a different explanatory priority to the foreground. Claude Bernard investigated the regulated internal conditions that enable organisms to continue functioning despite changes in their surroundings. His work helped establish that living continuity depends on active physiological regulation rather than passive material stability (Bernard 1865).

Darwin transformed biological explanation in another way. Natural selection explained adaptation and diversification historically, showing how present biological forms can be understood through descent, variation, and differential reproduction. Evolutionary explanation did not replace physiological or developmental explanation. It addressed a different question: how living forms and their relationships have changed over generations (Darwin 1859).

Later advances in genetics, molecular biology, development, ecology, and systems biology greatly expanded biology’s explanatory reach. They did not produce one universally accepted answer to what biology explains. Instead, they revealed more clearly the variety of questions involved in understanding living systems. The history of biological thought is therefore not a simple progression toward a single explanatory foundation, but a continuing development of different ways of making life intelligible (Mayr 1982).

This history matters because it changes how the opening question should be approached. We need not assume that Aristotle, Bernard, Darwin, and contemporary biology were all trying to explain exactly the same thing. Their differences are part of the evidence. Biology has repeatedly advanced by developing new forms of explanation while retaining questions that other approaches address especially well.

The task is therefore not to select one historical tradition as the final answer. It is to ask how these different explanatory achievements relate—and whether living systems present a continuing feature that makes their comparison scientifically productive.

Persistence Through Change

Living systems persist, but they do not do so by remaining unchanged. Their materials are continually replaced, their activities vary, and their relationships with their surroundings shift. Organisms grow, develop, repair damage, regulate internal conditions, and respond to circumstances that cannot be held constant.

Even the apparent stability of an organism is therefore an achievement. A living cell must continue exchanging matter and energy with its surroundings. A plant must adjust its growth and physiology as light, water, temperature, and other conditions change. An animal must coordinate metabolism, movement, repair, and behaviour while its internal and external circumstances vary.

Process-oriented biology draws attention to this dynamic character of life. Organisms are not simply structures that happen to undergo change. Their continuity depends on continuing processes that rebuild, regulate, and reorganise them. What requires explanation is not change alone, but how continuity is sustained through change (Nicholson and Dupré 2018).

This continuity is not the preservation of every material component or structural detail. Nor does it require an organism to return continually to one fixed state. Development can transform an organism profoundly while preserving the continuity of its living organisation. Repair may restore functioning through arrangements that differ from those present before damage. Responses to new conditions may alter patterns of activity while maintaining viability.

Persistence also takes different forms across time. During an individual life, living organisation must continually maintain or re-establish the conditions of its functioning. Across generations, evolution transforms inherited and developmental organisation rather than preserving it unchanged. Continuity and transformation are therefore not opposites. Biological persistence often depends on the capacity for organised change.

APS calls this continuity organised persistence: the continuity of living organisation through change. The term does not refer to mere survival, static endurance, or anything that happens to last. Living systems can maintain continuity despite extensive material turnover, developmental transformation, physiological variation, and changing environmental conditions.

Organised persistence should not be confused with the APS definition of Life. APS defines:

Life as viability-oriented, constraint-closed organisation.

The distinction is important. The definition of Life identifies the organisation APS proposes as characteristic of living systems. Organised persistence identifies the continuity of that living organisation through change. It is therefore a phenomenon requiring explanation, not a second definition of Life and not itself the activity through which continuity is maintained.

This distinction gives the opening question a more focused comparative form. APS does not assume that every biological explanation has organised persistence as its explanandum. It asks instead whether relating different explanatory achievements to the continuity of living organisation can clarify what each contributes and where important explanatory differences remain.

The APS Proposal

APS advances a comparative proposal: in appropriate cases, biological explanations can be compared by asking what each contributes to understanding the continuity of living organisation through change.

This does not mean that every biological discipline is secretly explaining organised persistence. Genetics, physiology, development, evolution, ecology, and other fields address distinct questions and phenomena, and their explanations must first be understood on their own terms. APS does not reduce them to one theory or judge them by a single method.

The comparative question arises only after those explanatory targets and achievements have been identified. APS then asks whether relating them to organised persistence reveals explanatory relationships, differences, or omissions that are not already clear within the established explanations themselves.

For any biological approach, comparison therefore begins by asking:

  • What is the explanatory target?
  • What does the approach explain especially well?
  • What, if anything, does relating that explanation to organised persistence add?

A mechanistic explanation might reveal how a particular biological process works. An evolutionary explanation might show how a trait or organisation arose and changed historically. An ecological explanation might clarify how an organism’s continued functioning depends on its relationships with its surroundings. APS does not replace any of these explanations. It asks how their different contributions relate to the persistence of living organisation.

Organised persistence is therefore a proposed comparative target, not a new biological mechanism. Whether it proves useful depends on the explanatory work it enables: whether comparison reveals relationships, distinctions, or unresolved questions that are not already adequately represented by the strongest established explanations. If it merely redescribes those explanations in APS terminology, no explanatory gain has been established.

APS also begins from biological agency. Living systems do not merely undergo change; through their activities they regulate, repair, respond, and reorganise. Biological agency is the viability-oriented organisational activity through which living systems maintain and re-establish the conditions of their persistence (Spencer 2026).

This does not imply conscious intention or decision-making. A cell regulating its internal conditions and a plant adjusting its growth are not assumed to deliberate about future outcomes. Their agency lies in the organised activity through which conditions affecting viability are actively managed.

The APS proposal can therefore be stated compactly:

Biology offers many legitimate explanations of living phenomena. APS compares their contributions by asking how each helps explain the organisation through which living systems persist despite change.

This proposal does not settle the question posed by the article’s title. It provides a way of investigating it.

Agency, Process, and Scale

APS investigates living organisation through three complementary analytic projections. These distinguish explanatory questions without dividing biological reality into three components, causes, or levels.

Agency asks what living systems do in relation to viability. Living systems regulate their activities, respond to changing conditions, repair damage, acquire and use resources, and reorganise under changing circumstances. APS describes biological agency as viability-oriented organisational activity. Agency does not require consciousness or deliberate choice.

Process asks how organisational continuity is maintained through change. Living systems persist through continuing material and organisational activity. Metabolism, regulation, development, repair, and other processes involve change while contributing, in different circumstances, to continuity of living organisation. Process therefore concerns the organisation of continuity through change; it should not be equated simply with time.

Scale asks across what materially realised spatial and temporal extents, and through what relations among them, persistence is organised. Biological entities, activities, processes, constraints, and relations occur across physically real spatial and temporal extents. Scale, as an analytic projection, asks which of those extents and relations are relevant to the explanatory problem. It should therefore be distinguished both from physical scale itself and from a hierarchy of biological levels.

Consider a plant responding to water shortage. Agency asks what the plant does in relation to changing conditions: for example, regulating water loss, altering growth, or reallocating resources. Process asks how continuity of living organisation is maintained or re-established while the plant and its conditions change. Scale asks which materially realised spatial and temporal extents and relations—such as cellular activity, whole-plant coordination, environmental interaction, development, or evolutionary history—are relevant to the particular explanation being sought.

Agency, Process, and Scale are analytic projections of one living organisation. Their differentiation belongs to explanatory analysis; it does not divide the living system into three independently existing parts. The activities, processes, constraints, and spatial and temporal relations they disclose are biologically real, while their separation into Agency, Process, and Scale serves investigation and explanation.

Analytic differentiation therefore does not imply ontological separation.

This threefold enquiry helps APS compare explanations without forcing them into one form. A molecular explanation may clarify a mechanism, a physiological explanation may clarify coordinated functioning, an ecological explanation may clarify environmental dependency, and an evolutionary explanation may clarify historical transformation. Agency, Process, and Scale help identify how these different contributions bear on organised persistence.

The APS name therefore identifies an explanatory practice rather than a division of reality. It keeps three questions together:

  • What is the living system doing?
  • How is continuity being maintained or re-established through change?
  • Across what spatial and temporal extents, and through what relations among them, is that persistence organised?

What Difference Does This Make?

APS does not give biology a new set of facts. Its contribution lies in changing how explanatory questions are related. It asks what becomes visible when established biological explanations are considered in relation to organised persistence.

Mechanism

A mechanistic explanation asks how a phenomenon is produced through organised entities and activities (Machamer et al. 2000). It might explain how a membrane channel regulates ion movement, how a signalling pathway initiates a cellular response, or how physiological processes coordinate temperature regulation.

APS preserves these explanations and also asks:

How does this mechanism contribute to maintaining or re-establishing viable organisation?

This additional question does not alter or automatically improve the mechanistic explanation. For some explanatory problems, the mechanism may already provide everything required. Where the explanandum concerns living organisation, however, it may be useful to ask how the identified mechanism bears on viability or organised persistence. APS contributes only if that additional question reveals an explanatory relationship not already adequately represented by the mechanistic account.

Evolution

Evolutionary explanation asks how biological traits, populations, and forms of organisation have changed historically. Natural selection, inheritance, variation, drift, and other evolutionary processes explain patterns that cannot be understood from present functioning alone.

APS also asks:

What organisation is being transformed, and how does that transformation alter the conditions under which living systems can persist?

This does not make evolution a process of preserving organisms unchanged. Evolution concerns the historical transformation of living organisation across generations. Established evolutionary theory explains that transformation through variation, inheritance, selection, drift, and other relevant processes. APS asks whether relating such historical transformation to organised persistence clarifies something about the organisation being transformed that the evolutionary explanation does not already make explicit.

Systems Biology

Systems biology investigates how interacting components and processes generate coordinated biological behaviour. It examines networks, dynamics, regulation, and control rather than treating biological components in isolation (Kitano 2002).

Where the explanatory problem concerns living organisation, APS may additionally ask:

How does this coordination bear on the maintenance or re-establishment of viable organisation?

Not every organised network is alive, and not every stable pattern is biologically significant. But neither does identifying a relation to viability automatically improve a systems explanation. The comparative question is whether making that relation explicit contributes something not already captured by the systems account.

Biological Autonomy

Organisational approaches ask how living systems maintain themselves through mutually dependent processes and constraints. They have shown why biological organisation cannot be understood simply as a collection of externally assembled parts (Moreno and Mossio 2015).

APS overlaps with this concern while asking a distinct comparative question:

What does biological autonomy contribute to understanding organised persistence, and how does it relate to mechanistic, evolutionary, developmental, and ecological explanations?

The convergence is important, but the approaches are not identical. Biological autonomy is a substantive account of living organisation. APS uses comparison to clarify what this and other approaches contribute to a broader explanatory enquiry.

Ecology

Ecological explanations investigate relationships between organisms and their surroundings. Access to water, energy, nutrients, other organisms, and suitable physical conditions can all affect whether living organisation continues to function.

APS also asks:

How do these relationships alter conditions relevant to the organised persistence of the living systems involved?

This question does not imply that an ecosystem is itself a biological agent. It asks how environmental relationships become materially involved in the persistence of organisms and other living systems.

These examples show where APS seeks explanatory gain. It does not repeat each explanation in new vocabulary, and it does not claim that organised persistence supplies what existing biology has failed to discover. Instead, it provides a common point of comparison.

That comparison can reveal several things:

  • different explanations may address different aspects of the same biological problem;
  • explanations that use similar terms may nevertheless ask different questions;
  • present functioning and evolutionary history make distinct contributions;
  • environmental relationships may condition agency without replacing it;
  • detailed mechanisms may acquire biological significance through their contribution to viable organisation.

The value of APS therefore depends on demonstrable explanatory gain. Comparison must clarify relationships, distinctions, unresolved questions, or possible lines of investigation beyond what the strongest established explanation already provides. If organised persistence merely redescribes existing explanations in APS terminology, no explanatory gain has been established.

APS is best understood as an invitation to test a question:

Does comparing biological explanations through organised persistence help us understand living systems more clearly?

An Invitation to Explore

The question “What is biology trying to explain?” does not require biology to choose one theory, method, or explanatory foundation. Living systems present different phenomena at different spatial and temporal extents, and biology has developed correspondingly different ways of investigating them.

APS begins from this diversity. It does not claim that every biological discipline is explaining exactly the same thing. It asks whether comparing their distinctive achievements in relation to organised persistence can produce greater explanatory clarity.

This proposal remains open to investigation. Its value depends on whether organised persistence clarifies relationships among biological explanations, exposes unresolved questions, and supports productive research. APS should therefore be assessed by what it helps biology explain—not simply by the coherence of its terminology.

Readers wishing to continue can follow three immediate paths:

  • What Is APS? introduces the purpose and scope of the framework.
  • Naturalising Life explains how APS approaches life through viability-oriented, constraint-closed organisation.
  • The Core Structure of APS develops the relationship among Agency, Process, and Scale.

These articles lead into the wider APS programme, including evolution, development, cognition, individuality, ecology, and biological explanation. Each extends the enquiry begun here while addressing a more specific domain or problem.

Readers interested in the wider scientific and methodological setting of this proposal can also follow the APS-THEORY research programme. Its three studies examine the historical identity of theoretical biology, the functional boundary between theoretical biology and philosophy of biology, and a neutral method for comparing dependency claims in biological explanation. Together, they provide an independent test of the explanatory setting within which APS makes its own proposals.

APS therefore proposes organised persistence neither as biology’s final or exclusive explanation nor as a universal explanandum to which every biological explanation must be reduced. It offers organised persistence as a candidate comparative target: a way of asking whether the distinctive achievements, relationships, and limits of biological explanations become clearer when considered in relation to the continuity of living organisation through change. Its value must be established by the explanatory contribution that comparison actually makes.

Explanatory Architecture

This article develops the following explanatory architecture:

Biological explanatory plurality
→ biology contains multiple successful explanatory approaches directed toward different questions and phenomena

The comparison problem
→ explanatory diversity raises the question of how different explanatory achievements can be related without reducing them to a single theory, method, or vocabulary

Living organisation through change
→ organised persistence identifies the continuity of living organisation through change

The APS comparative proposal
→ organised persistence is treated as a candidate comparative target rather than assumed to be the universal explanandum of biology

Agency, Process, and Scale
→ provide complementary analytic projections through which the living organisation relevant to a comparison can be investigated

Comparator control
→ established explanations must first be understood according to their own explanatory targets, strengths, and scope

Explanatory contribution
→ APS contributes only where comparison through organised persistence clarifies relationships, distinctions, unresolved questions, or possible lines of investigation beyond what the strongest established explanation already provides

Failure condition
→ if comparison merely redescribes established biological explanations in APS terminology, no explanatory gain has been established

The architecture therefore moves from explanatory plurality to controlled comparison, not from plurality to theoretical unification. Organised persistence provides a proposed point of comparison whose value must be demonstrated rather than assumed.

In summary:

Biology’s explanatory diversity does not require unification, but it does invite comparison. APS succeeds only where that comparison makes an additional explanatory contribution.