Introduction

How should biology explain meaning? Living systems do more than exchange matter and energy with their environments. They also distinguish what matters from what does not, coordinate activity in relation to changing conditions, and maintain their organisation through continual interaction with their surroundings. These capacities have long suggested that biological organisation cannot be understood solely in mechanistic or informational terms. Instead, they invite explanations that account for the organisation through which living systems generate, maintain, and use biologically significant relations.

One of the most influential responses to this challenge has been biosemiotics. Drawing on the semiotic philosophy of Charles Sanders Peirce and the biological insights of Jakob von Uexküll, biosemiotics argues that living systems are fundamentally semiotic. Organisms do not merely react to physical stimuli but inhabit meaningful worlds in which signs are produced, interpreted, and acted upon. Biological organisation is therefore understood as inherently semiotic, and semiosis is regarded as a constitutive feature of life rather than an accidental consequence of biological complexity.

Biosemiotics has made an important contribution to contemporary theoretical biology by demonstrating that biological organisation cannot be adequately understood through purely mechanistic or reductionist accounts. Its emphasis on organisation, interpretation, and meaning has broadened biological explanation beyond the transmission of information or the operation of molecular mechanisms alone. In doing so, it has reopened foundational questions concerning the nature of living systems and the kinds of explanation required to understand them.

The Agency–Process–Scale (APS) framework shares many of these broader commitments. Like biosemiotics, APS rejects the view that life can be fully understood through reduction to molecular mechanisms or informational processes alone. It likewise argues that biological explanation must be organised around the distinctive organisation of living systems rather than around isolated mechanisms, components, or levels of description. Both frameworks therefore seek to naturalise phenomena that have often been regarded as conceptually problematic, including agency, meaning, function, organisation, and cognition.

Despite these shared commitments, the two frameworks differ in their explanatory priorities. Biosemiotics places semiosis at the centre of its explanatory architecture, interpreting living systems as fundamentally organised through the production and interpretation of signs. APS asks a different explanatory question. It understands living systems as viability-oriented organisation and explains biological meaning through agency, biological evaluation, and the generation of biological significance. Within APS, semiosis is neither rejected nor diminished. Rather, it is interpreted as one organisational process through which biologically significant relations may be generated, coordinated, and stabilised. Meaning is therefore explained through the organisation of living activity rather than being treated as originating in semiosis itself.

This difference does not imply that the two frameworks are mutually exclusive or that one replaces the other. The purpose of the present article is not to adjudicate between competing theories of life, nor to argue that one framework should supersede the other. Instead, the article follows the protocol established in Comparative Explanatory Methodology in Theoretical Biology. Biosemiotics and APS are therefore compared through their explanatory targets, organising principles, explanatory priorities, conceptual architectures, domains of strength, and explanatory scope rather than through isolated terminology or theoretical competition.

The comparison is especially significant because both APS and biosemiotics occupy similar positions within contemporary theoretical biology. Each seeks to clarify the conceptual foundations of biological explanation. Each regards organisation as central to understanding living systems. Each challenges reductionist interpretations that identify biological explanation with the description of mechanisms alone. Yet they differ in how they organise the relationship between agency, meaning, information, communication, cognition, and biological organisation. These differences are not merely terminological. They reflect distinct conceptions of what biological explanation should ultimately explain.

Accordingly, this article examines the relationship between APS and biosemiotics as two organisational approaches to biological meaning. It first outlines the principal commitments of biosemiotics before examining the explanatory architecture developed by APS. The subsequent sections compare the two frameworks with respect to semiosis, biological evaluation, significance, information, communication, and cognition. Throughout, the comparison seeks to identify both genuine areas of convergence and important explanatory differences.

The central thesis advanced here is that APS and biosemiotics converge in recognising that biological organisation cannot be adequately explained without accounting for meaning, yet they locate the origin of biological meaning in different organisational phenomena. Biosemiotics explains meaning through semiosis, whereas APS explains meaning as emerging through biological evaluation—the process through which agency generates biological significance—within viability-oriented organisation. The comparison therefore concerns not competing theories, but alternative explanatory priorities within contemporary theoretical biology. Rather than asking which framework is correct, the article examines what each framework explains, where their explanatory priorities converge, where they diverge, and how each contributes to a more comprehensive understanding of biological meaning.

The comparison developed here builds upon earlier APS analyses of contemporary theoretical biology while extending the comparative methodology to one of the most influential organisational traditions within modern biology. The discussion therefore begins by examining how biosemiotics understands the semiotic character of living systems before considering how APS reconstructs biological meaning through the organisational architecture of agency, biological evaluation, and significance.

Biosemiotics: The Semiotic Interpretation of Life

Biosemiotics seeks to explain how meaning arises within living systems. It approaches this question by proposing that semiosis is a constitutive feature of life itself: it emerged from the recognition that living systems cannot be adequately understood through mechanistic or informational descriptions alone. While molecular biology, genetics, physiology, and systems biology have greatly expanded our understanding of biological processes, biosemiotics argues that these approaches leave unresolved a fundamental question: how do biological interactions become meaningful for the organisms that participate in them? Rather than treating meaning as an exclusively human or linguistic phenomenon, biosemiotics maintains that the production, interpretation, and use of signs are intrinsic features of life itself.

This perspective has developed through the convergence of several intellectual traditions. Charles Sanders Peirce’s general theory of signs provided the philosophical foundation for understanding semiosis as a triadic relation involving a sign, its object, and its interpretant. Jakob von Uexküll demonstrated that organisms inhabit species-specific Umwelten, in which environmental features acquire significance through the organism’s own mode of life. Thomas A. Sebeok subsequently extended semiotic inquiry across the living world, arguing that semiosis characterises biological organisation generally rather than human language alone. Contemporary authors, including Jesper Hoffmeyer, Kalevi Kull, Marcello Barbieri, Donald Favareau, and Claus Emmeche, have developed these ideas into a coherent programme within theoretical biology.

The central claim of biosemiotics is that living systems are fundamentally semiotic systems. Organisms do not merely undergo causal interactions with their environments. They interpret signs that guide their activity in ways that contribute to their continued existence and interaction with the world. A chemical signal, a visual cue, a vocalisation, or a molecular recognition event is therefore understood not simply as a physical event but as part of a semiotic relation through which an organism interprets and responds to its circumstances. Semiosis is consequently regarded as a constitutive feature of living organisation rather than an additional process superimposed upon biological mechanisms.

Within this framework, signs are not confined to symbolic communication or conscious interpretation. Biosemiotics proposes that sign processes occur throughout the living world, from intracellular signalling and developmental regulation to animal communication and human language. Semiotic organisation therefore extends across the full diversity of life. Although the complexity of sign processes differs enormously between bacteria, plants, animals, and humans, the underlying principle remains that biological activity involves the interpretation of signs within organised living systems.

Meaning occupies a central place within this explanatory framework. Biosemiotics rejects the view that meaning emerges only with language or higher cognition. Instead, meaning is understood as arising wherever signs are interpreted within the activities of living organisms. The significance of a chemical gradient for a bacterium, the recognition of a pollinator by a flowering plant, or the interpretation of alarm calls within a social animal population are all regarded as instances of biological meaning because they involve organised sign relations that influence biological activity. Meaning is therefore interpreted as a natural biological phenomenon rather than a uniquely human achievement.

This emphasis on semiosis has important implications for theoretical biology. First, it challenges reductionist accounts that seek to explain biological organisation solely in terms of physical or chemical interactions. Biosemiotics does not deny the necessity of these interactions but argues that they are insufficient, by themselves, to explain how biological interactions acquire meaning within living systems. Second, it broadens biological explanation by recognising that organisms actively interpret and respond to their environments rather than functioning as passive recipients of external causal influences. Third, it provides a unified explanatory perspective through which communication, development, behaviour, ecology, and evolution can be understood as interconnected semiotic processes.

Biosemiotics has therefore become one of the most influential organisational approaches within contemporary theoretical biology. Its importance lies not simply in introducing semiotic terminology into biology, but in proposing that semiosis is indispensable for understanding what distinguishes living systems from non-living systems. By treating meaning as an intrinsic feature of biological organisation, biosemiotics offers a framework that integrates molecular, organismal, ecological, and cognitive phenomena within a common explanatory perspective.

The explanatory success of biosemiotics naturally raises a further question for theoretical biology. How should the relationship between semiosis and biological organisation be understood? Does semiosis itself provide the fundamental explanatory principle of living systems, or should it be interpreted within a broader account of biological organisation? These alternative explanatory priorities motivate the comparison developed in the remainder of this article. The next section considers how the Agency–Process–Scale framework addresses this explanatory question and how its account of biological meaning compares with that developed by biosemiotics.

APS: Biological Evaluation and the Organisation of Meaning

The Agency–Process–Scale (APS) framework approaches biological meaning from a different explanatory starting point. Whereas biosemiotics begins with semiosis as a constitutive feature of living systems, APS begins with the organisation that makes living systems possible. APS defines life as viability-oriented, constraint-closed organisation: the ongoing modulation of constraints through which living systems maintain and re-establish the conditions of their own persistence. From this perspective, biological meaning is not the point of departure but one consequence of the organisation through which life actively persists.

Within this organisational framework, biological agency is the present-tense activity through which living organisation is enacted and sustained. Agency is not understood as conscious choice, intention, or deliberation. Nor is it treated as an additional property acquired by certain organisms. Rather, it is the viability-oriented organisational activity through which living systems continually regulate their interactions with changing internal and external conditions. Agency therefore expresses the ongoing organisation of life rather than constituting an independent explanatory principle.

The central explanatory concept connecting agency with biological meaning is biological evaluation. APS defines biological evaluation as the process through which agency generates biological significance. Every living system must continuously distinguish conditions that support its continued organisation from those that threaten it. This evaluative activity is neither reflective nor necessarily cognitive. It is an organisational consequence of viability-oriented living systems continually regulating the conditions required for their own persistence. Biological evaluation therefore explains how some aspects of the world become significant for an organism while others remain biologically irrelevant.

Biological significance is the relationally real product of biological evaluation. It does not exist independently of living organisation, nor is it merely a subjective experience or an informational property. Rather, significance arises because living systems continually differentiate environmental conditions according to their contribution to viability-oriented organisation. Nutrients, predators, symbiotic partners, developmental cues, and changing environmental conditions become biologically significant because they are evaluated in relation to the continuing organisation of the organism. Significance is therefore neither imposed upon the world nor extracted from it independently of living activity. It is generated through the ongoing organisation of biological agency.

From this perspective, meaning is not treated as an elementary property of signs. Instead, meaning develops through the organisation of biological significance across increasingly integrated forms of biological activity. Biological evaluation generates significance; significance becomes organised through continuing interactions within the living system; and, in organisms possessing increasingly sophisticated capacities for integration, these organised patterns support progressively richer forms of cognition, representation, communication, and ultimately reflective understanding. Meaning therefore emerges from the organisation of biological significance rather than preceding it.

This explanatory architecture also clarifies the relationship between biological meaning and information. APS does not deny the importance of information in living systems. Information, however, is not intrinsically meaningful. Informational processes become biologically meaningful only insofar as they participate in the organisation through which biological significance is generated, maintained, and integrated. Information therefore contributes to biological organisation, but does not by itself explain why particular informational relations matter for living systems.

APS consequently interprets semiosis differently from biosemiotics. Semiosis is recognised as an important organisational process through which biological significance may be expressed, communicated, stabilised, and elaborated. It is therefore fully compatible with many of the empirical phenomena investigated by biosemiotics. APS differs not in denying semiosis, but in assigning it a different explanatory role. Semiosis is understood as one organisational process within the broader architecture of viability-oriented organisation rather than as the primary explanatory starting point for biological meaning.

APS therefore arrives at biological meaning through a sequence of organisational concepts beginning with life itself. Viability-oriented organisation gives rise to biological agency; agency generates biological evaluation; biological evaluation generates biological significance; and the continuing organisation and integration of significance makes progressively richer forms of biological meaning possible. Within APS, biological evaluation occupies the explanatory role that semiosis occupies within biosemiotics. Both concepts seek to explain how biological meaning becomes possible, although they identify different organisational processes as explanatorily fundamental. The preceding sections have now presented two organisational approaches to biological meaning on their own terms. The comparison can therefore move beyond description to examine where their explanatory priorities converge, where they diverge, and what each contributes to contemporary theoretical biology.

Comparing Explanatory Priorities

The preceding sections have presented biosemiotics and the Agency–Process–Scale (APS) framework on their own terms. Both seek to explain phenomena that conventional mechanistic accounts have often struggled to accommodate, including biological meaning, organisation, agency, communication, and cognition. Both reject the view that living systems can be adequately understood through reduction to physical mechanisms or informational processes alone. Both instead argue that biological explanation must account for the distinctive organisation of living systems. These substantial areas of agreement provide the foundation for a meaningful comparison. The central question is therefore not whether one framework replaces the other, but how each organises biological explanation and what explanatory priorities each regards as fundamental.

The first point of convergence is methodological. Both biosemiotics and APS seek to naturalise concepts that have frequently been regarded as exceptional or resistant to scientific investigation. Rather than treating meaning, agency, or organisation as phenomena lying outside biology, each framework argues that they are intrinsic features of living systems and therefore legitimate subjects of biological explanation. In doing so, both contribute to a broader movement within theoretical biology that seeks explanations adequate to the distinctive organisation of life rather than explanations derived solely from the physical sciences.

A second area of convergence concerns biological organisation itself. Neither framework understands organisms as passive collections of interacting components. Instead, both regard organisms as organised systems whose activities cannot be understood independently of the organisation that gives those activities biological coherence. Both therefore reject strongly reductionist interpretations in which biological phenomena are regarded as exhaustively explained by molecular or biochemical mechanisms alone. Mechanisms remain indispensable, but they do not exhaust biological explanation.

Despite these shared commitments, the explanatory architectures of the two frameworks differ in their points of departure. Biosemiotics begins with semiosis. It argues that living systems are fundamentally organised through the production, interpretation, and use of signs, and that biological meaning is therefore explained through semiotic organisation. APS begins elsewhere. It begins with viability-oriented, constraint-closed organisation and asks how living systems actively maintain and re-establish the conditions of their own persistence. Within this organisational framework, biological agency, biological evaluation, biological significance, and meaning emerge as successive explanatory developments.

These different starting points lead to different explanatory priorities. For biosemiotics, semiosis occupies the foundational explanatory role because it provides the basis upon which biological meaning becomes possible. The interpretation of signs therefore becomes central to understanding communication, development, behaviour, and cognition. APS assigns this foundational role to viability-oriented organisation and the activity of biological agency. Within APS, biological evaluation explains how living systems generate biological significance, while meaning develops through the continuing organisation and integration of that significance. Semiosis is recognised as an important organisational process, but it is interpreted as one way in which biological significance may be expressed, communicated, and stabilised rather than as the primary explanatory foundation of living organisation.

The difference between the two frameworks is therefore not simply terminological. It concerns the explanatory status assigned to particular biological processes. Biosemiotics asks how sign relations generate biological meaning. APS asks how viability-oriented organisation generates the evaluative relations through which biological significance and, subsequently, biological meaning emerge. These questions are related but not identical. Each framework identifies a different organisational process as explanatorily fundamental, and each consequently organises its conceptual architecture in a different way.

These contrasting explanatory priorities also influence the interpretation of information and communication. Within biosemiotics, information is understood primarily within the context of sign relations and interpretation. Within APS, informational processes acquire biological importance because they contribute to the generation, maintenance, and integration of biological significance within viability-oriented organisation. Communication is likewise interpreted differently. Biosemiotics emphasises communication as an expression of semiotic organisation, whereas APS interprets communication as a mechanism through which biologically significant relations are coordinated between living systems. The empirical phenomena under investigation frequently overlap, but the explanatory emphasis differs.

The comparison likewise illuminates differing approaches to cognition. Biosemiotics commonly treats cognition as a highly developed manifestation of semiosis. APS interprets cognition as the organisation of biological significance across time, emerging from earlier organisational processes of agency and biological evaluation. In both frameworks cognition develops within living systems rather than being imposed from outside them. The difference lies in the explanatory pathway through which cognition is understood to arise.

Recognising these differences does not diminish the substantial common ground shared by the two programmes. Both reject reductionism, both regard organisation as central to biological explanation, both seek to naturalise meaning, and both contribute important insights into the nature of living systems. Their differences should therefore be understood primarily as differences in explanatory organisation rather than as incompatible empirical claims. Each framework directs attention towards aspects of living organisation that the other may illuminate less directly, and each therefore contributes valuable perspectives to contemporary theoretical biology.

The comparison developed here consequently suggests that biosemiotics and APS are best understood as complementary organisational approaches rather than mutually exclusive theories. Biosemiotics provides a rich account of the semiotic character of living systems and of the role of signs in biological organisation. APS develops a broader organisational architecture within which biological evaluation, significance, semiosis, information, communication, and cognition are situated according to their respective explanatory roles. The comparison therefore clarifies not which framework should replace the other, but how each contributes to a more comprehensive understanding of biological meaning.

Having established both the substantial convergence and the differing explanatory priorities of the two frameworks, the discussion can now turn to their broader significance for theoretical biology. What does this comparison reveal about the future development of organisational approaches to biological explanation, and what contribution might a comparative explanatory methodology make to that development?

The comparison therefore reveals that APS and biosemiotics differ less in the biological phenomena they seek to explain than in the explanatory priorities through which those phenomena are organised. Recognising this distinction shifts the discussion beyond questions of theoretical competition towards a broader consideration of how organisational frameworks contribute to biological explanation. The implications of this shift extend beyond the relationship between APS and biosemiotics and bear more generally on the future development of theoretical biology.

Implications for Theoretical Biology

The comparison developed in the preceding sections extends beyond the relationship between APS and biosemiotics. Both frameworks seek to explain aspects of biological organisation that have often proved difficult to accommodate within exclusively mechanistic or reductionist accounts of life. Although they differ in their explanatory priorities, they share a commitment to understanding living systems as organised entities whose distinctive properties require explanatory principles appropriate to biological organisation itself. The significance of their comparison therefore lies not only in clarifying two research programmes, but also in illuminating broader questions concerning the nature of biological explanation.

One implication is the increasing importance of organisation as an explanatory target within contemporary theoretical biology. During much of the twentieth century, biological explanation was frequently understood in terms of the identification of mechanisms, molecular pathways, and causal interactions. These achievements remain indispensable. Yet they do not, by themselves, explain how living systems maintain coherent organisation through continual change, generate biological meaning, or regulate their interactions with changing environments. Organisational approaches, including both biosemiotics and APS, reflect a growing recognition that biological explanation must address these questions directly rather than treating them as secondary consequences of mechanistic description.

The comparison also demonstrates the value of distinguishing explanatory priorities from empirical disagreement. Biosemiotics and APS investigate many of the same biological phenomena and frequently draw upon overlapping empirical evidence. Their principal differences arise not because they observe different living systems, but because they organise biological explanation around different explanatory questions. Biosemiotics asks how semiosis makes biological meaning possible. APS asks how viability-oriented organisation generates the evaluative processes through which biological significance and, subsequently, biological meaning emerge. Recognising these distinct explanatory priorities provides a more precise basis for comparison than treating the frameworks as competing theories making incompatible empirical claims.

This distinction suggests a broader methodological principle for theoretical biology. Organisational research programmes need not be evaluated solely according to whether one replaces another. They may also be compared according to the explanatory questions they address, the organisational phenomena they identify as fundamental, the conceptual architectures they develop, and the biological problems they are intended to illuminate. Comparative explanatory methodology therefore complements empirical investigation by providing a systematic way of analysing how different theoretical frameworks organise biological understanding.

Seen from this perspective, explanatory pluralism need not imply conceptual fragmentation. Different organisational frameworks may contribute complementary insights into the complexity of living systems while remaining open to critical comparison. Biosemiotics provides a sophisticated account of semiosis, sign relations, and the naturalisation of meaning. APS develops an organisational architecture centred on viability-oriented organisation, agency, biological evaluation, and biological significance. Appreciating these different explanatory contributions allows theoretical biology to benefit from conceptual diversity without abandoning the search for greater explanatory coherence.

The methodological implications extend beyond the present comparison. The same comparative approach may be applied to other organisational research programmes, including autopoiesis, autonomy theory, organisational biology, process biology, and related approaches concerned with the nature of living organisation. In each case, the central question is not simply whether a framework is correct, but what explanatory questions it asks, what organisational phenomena it privileges, and how its explanatory architecture contributes to understanding living systems. Comparative explanatory methodology therefore provides a common basis for analysing diverse theoretical programmes while respecting their distinctive explanatory contributions.

The comparison developed in this article consequently suggests that progress in theoretical biology depends not only upon accumulating new empirical knowledge but also upon improving the ways in which biological explanation itself is organised. Comparing explanatory architectures makes it possible to identify shared commitments, clarify genuine differences, and understand how alternative organisational perspectives contribute to a richer and more coherent account of life. The concluding section therefore returns to the question with which this article began: how should biology explain biological meaning, and what does the comparison between APS and biosemiotics contribute to answering that question?

Conclusion

This article began by asking how biology should explain biological meaning. The comparison between biosemiotics and the Agency–Process–Scale (APS) framework has shown that this question cannot be answered simply by identifying the biological phenomena to be explained. It also requires consideration of the explanatory priorities through which those phenomena are organised. Although both frameworks seek to naturalise biological meaning and understand living systems as organised entities, they differ in the organisational processes they regard as explanatorily fundamental.

Biosemiotics approaches biological meaning through semiosis. It interprets living systems as inherently semiotic and explains meaning through the production, interpretation, and organisation of signs. APS begins from a different explanatory question. It investigates how viability-oriented, constraint-closed organisation gives rise to biological agency, biological evaluation, and biological significance, from which biological meaning progressively develops. These differences do not reflect disagreement concerning the existence of meaning within living systems. Rather, they express different ways of organising biological explanation.

The comparison has also shown that these frameworks share substantial common ground. Both reject reductionist accounts that seek to explain living systems solely through physical mechanisms or informational processes. Both recognise organisation as indispensable to biological explanation. Both seek to naturalise phenomena that have often been regarded as resistant to scientific investigation, including meaning, agency, communication, and cognition. These shared commitments suggest that the comparison is most productively understood not as a contest between incompatible theories, but as an analysis of different organisational approaches to understanding life.

The principal contribution of this article therefore lies not only in clarifying the relationship between APS and biosemiotics, but also in demonstrating the value of comparative explanatory methodology. Organisational research programmes need not be compared solely according to whether one supersedes another or whether they make conflicting empirical claims. They may also be compared according to the explanatory questions they ask, the organisational phenomena they identify as fundamental, the conceptual architectures they construct, and the explanatory priorities through which they organise biological understanding. Such comparisons provide a more precise account of both commonality and difference while respecting the distinctive contributions of individual research programmes.

This methodological perspective has implications extending beyond the present comparison. Contemporary theoretical biology encompasses a growing diversity of organisational approaches, each seeking to illuminate different aspects of living systems. Comparative explanatory methodology provides a systematic means of analysing these approaches without reducing them to isolated concepts or treating them as mutually exclusive alternatives. By comparing explanatory architectures rather than theoretical labels, it becomes possible to identify shared concerns, clarify genuine points of divergence, and understand how different frameworks contribute to biological explanation.

The comparison developed here therefore suggests that progress in theoretical biology depends not only upon continued empirical investigation but also upon increasing clarity concerning the organisation of biological explanation itself. As organisational approaches continue to develop, the ability to compare their explanatory architectures may become an important component of theoretical inquiry. Within this broader context, the relationship between APS and biosemiotics is significant not simply because it compares two frameworks concerned with biological meaning, but because it illustrates how comparative explanatory methodology can contribute to a more coherent and integrative understanding of living organisation.