Grammar and the Ghost in the Machine

1 A Haunted Inheritance

Philosophy is full of ghosts. It speaks in the voice of being, will, substance, mind, and essence — and calls them real. But beneath these timeworn abstractions lies something far more familiar: language. For while philosophy has asked for centuries what the world is made of, it rarely asks what its own materials are made of — the materials of thought, argument, and theory.

This series begins with a provocation:

What if many of the most enduring metaphysical ideas in philosophy are in fact reifications of semiotic architecture?

What if “being” and “form” and “substance” are not eternal truths but grammatical metaphors turned into metaphysical doctrines?

We propose that a theory of language — and in particular the systemic functional model developed by M.A.K. Halliday — can help us excavate the buried scaffolding of these ideas. By attending to how meaning is made in language, we gain a new vantage point on what has been taken for granted in centuries of thought.

Language: The Invisible Medium

Theories are realised in language. Whether in Plato’s dialogues, Descartes’ meditations, or Nietzsche’s aphorisms, theory always comes to us as text. But language is not simply a vehicle for ideas. It is itself a system of meaning — structured, patterned, and oriented to action. Like the observer in physics, language has often been left invisible, its shaping influence ignored.

But if language is what theory is made of, then a theory of language can reveal the architecture of theory itself.

This series will follow three key relations from Systemic Functional Linguistics:

• Instantiation: the relation between potential and its individual instances (e.g., from system to text).

• Realisation: the relation between levels of symbolic abstraction (e.g., from meaning to wording, or from system to structure).

• Grammatical Metaphor: the reconfiguration of meaning across strata (e.g., turning processes into things — “he decides” becomes “his decision”).

Each of these semiotic relations corresponds to familiar philosophical moves: from the abstract to the concrete, from appearance to essence, from act to identity. And each, we will argue, has been misrecognised as metaphysical when it is in fact linguistic.

Haunted Concepts

When Plato speaks of perfect Forms, is he not projecting the systemic pole of the cline of instantiation? When Descartes divides mind from body, is he not reifying the clause structure of mental projection? When Kant marks the noumenon as unknowable, is he not confronting the boundary where language can no longer construe?

These are not missteps. They are moments where language itself becomes visible — not because it is recognised, but because it is misunderstood. The philosophical tradition is haunted not by ghosts from another world, but by the unexamined grammar of this one.

Renovating the History of Thought

To renovate is not to destroy, but to rehouse: to take the ideas that have shaped us and place them in new conceptual architecture. The goal of this series is not to dismiss philosophy, but to reconstrue it — to understand it as a history of meaning-making, structured by language and illuminated by it.

In the posts that follow, we will explore how the scaffolding of language underpins some of philosophy’s most iconic ideas. We will begin, appropriately, with Plato — and with his realm of eternal Forms. But we will not climb to a world beyond. We will follow the cline of instantiation.

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2 Plato’s Forms and the Reification of Instantiation

Plato’s metaphysics begins with a distinction that has echoed across millennia: between the world of appearances and the world of Forms. The first is changeable, sensory, particular. The second is eternal, intelligible, universal. We live among the many; only the Forms are truly one.

But what if Plato was not discovering a transcendent realm, but projecting a semiotic architecture — one that belongs not to the cosmos but to language?

The Cline of Instantiation

In systemic functional linguistics (SFL), meaning is construed along a cline of instantiation:

• At one end is the system — a structured potential for meaning.

• At the other is the instance — a concrete enactment of that potential in a specific context.
  Every time we speak or write, we instantiate the system — and in doing so, we add to its potential.

Plato’s ontology closely mirrors this architecture.

• The Form is the pure potential: the universal, unchanging idea of Justice, Beauty, or Tree.

• The particular is the instance: the just act, the beautiful painting, the tree in the grove.

Plato treats the Form as more real than the instance. But in SFL terms, this is a reversal: the system is a potential that exists only by virtue of its instances. It is abstracted from what has been said and done — not the other way around.

From Ontology to Semiotic Architecture

What happens if we read Plato’s metaphysics not as a vision of a metaphysical order but as a misrecognition of the semiotic order? His world of Forms is the system pole of instantiation, reified into an independent realm. His world of appearances is the instance pole, treated as a poor copy of the ideal. But in language, the system and the instance are not in competition — they are mutually constitutive.

Each instance contributes to the shape of the system; each system makes further instances possible. There is no need to posit a second world to account for the regularities of this one. What Plato mistook for eternal reality was the abstract structure of meaning itself.

The Danger of Reification

Plato’s move is not unique. It is part of a wider philosophical habit: the reification of semiotic relations — taking structural features of language and treating them as metaphysical truths.

When the abstract is separated from the concrete, and treated as its origin, the result is metaphysics. But when we see that the abstract arises through the concrete, and returns to it in use, we shift from metaphysics to semiotics.

Instantiation, not Imitation

Plato calls the particular an imitation of the Form. But in SFL terms, it is not an imitation — it is an instantiation. It is not a flawed copy of a perfect original, but a meaning-making event that both draws on and contributes to a system of potential.

Plato's error — and perhaps philosophy’s original ghost — was to mistake the architecture of meaning for the structure of the world.

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Next time, we’ll trace another haunting: how the grammatical metaphor of action gives rise to the metaphysical concept of the Will.

3 The Will and the Reification of Desire

In Western metaphysics, the Will appears as a sovereign force. It acts, chooses, asserts — often in tension with reason, impulse, or fate. In some philosophies, it becomes the seat of the self; in others, the engine of the universe.

But from the perspective of language, the Will is not a metaphysical entity. It is a grammatical pattern, projected into the world and mistaken for its foundation.

Desire as a Grammatical Process

Systemic functional linguistics (SFL) classifies clauses according to process types, each construing a kind of experience as meaning. One such process is mental desiderative:

• I want a new idea.

• She hopes to understand.

• They wish it were otherwise.

Here, ‘want’, ‘hope’, and ‘wish’ are not expressions of force but semiotic processes. They construe the internal world of the speaker — not by referencing something called the Will, but by enacting a grammatical relation: a subject experiencing a mental orientation toward a desired object or outcome.

The Will is born when this pattern is reified. That is, when we take the linguistic projection of desire and treat it as a metaphysical force, as if wanting were a thing rather than a relational meaning.

From Process to Power

Grammar allows us to construe the self as a subject who acts. In doing so, it supplies the raw material for philosophical claims about agency.

• I decide.

• I resolve.

• I impose my will.

These are all clause structures in which the subject is medium and the process is intentional. But in language, such clauses are choices — not proof of a metaphysical faculty. The grammar of action provides a model of agency, but not its ontological foundation.

The Will arises when this model is lifted from its semiotic grounds and projected into the structure of reality — as if it were the cause of action rather than its construal.

The Fiction of the Autonomous Subject

The metaphysical Will also requires a metaphysical subject — a self that exists apart from its relations. But in SFL, the subject is a position in meaning, not an ontological entity. It is constituted by its participation in grammatical structures, including those of mental and verbal processes.

The autonomous self, like the Will it wields, is not a given. It is a construct, born of grammatical roles, culturally reinforced, and philosophically enshrined.

Unmasking the Ghost

When we see that language can construe desire as a process, not a power, the ghost of the Will begins to dissipate. What philosophy calls the Will, linguistics calls a desiderative clause. The metaphysical becomes grammatical — and in doing so, becomes tractable, analysable, and demystified.

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In our next post, we’ll look at causality — and how the grammar of transitivity shaped the metaphysical search for necessary connections in nature.

4 Cause and Effect — Transitivity and the Machinery of Nature

Causality is one of philosophy’s deepest problems. What does it mean for one thing to cause another? Is causation a force, a law, a regularity, or an illusion?

But in systemic functional linguistics (SFL), causation is not a mystery. It is a grammatical resource.

Transitivity: Grammar’s Model of Experience

In SFL, the grammar of the clause construes experience through transitivity — the system that organises processes and their participants. A clause like:

• The sun melts the ice
  …construes a material process (melts), an actor (the sun), and a goal (the ice).

This is not a metaphysical claim. It is a semiotic configuration. The grammar does not discover causation in the world; it construes experience as causative by selecting from available grammatical patterns.

There is no metaphysical necessity here — only a semiotic regularity.

From Clause to Cosmos

When we elevate these patterns into metaphysics, we reify them. Clause structures become models of the world’s deep machinery:

• X causes Y.

• The will moves the body.

• Every event has a cause.

These are not discoveries of pure reason or empirical law. They are grammatical construals taken for ontological structures.

In this way, the grammar of transitivity becomes the ghost in the machine — animating our models of force, change, and inevitability.

Necessary Connection or Grammatical Expectation?

Philosophers from Hume to Kant have wrestled with the idea of necessary connection. But if we look through the lens of language, the source of this expectation is plain:

Grammar allows us to construe sequences where one process leads to another:

• He dropped the glass. It shattered.

• Because it rained, the picnic was cancelled.

Here, logical and temporal relations are grammatically construed — not given by nature. The sense of necessity is a product of textual cohesion, not metaphysical structure.

What philosophy calls causality, grammar construes as sequenced process.

Causal Chains as Grammatical Chains

Scientific explanation often seeks causal chains. But these chains are not neutral observations; they are narratives, built from clauses in which agency, process, and goal are selected according to meaning.

To explain an event is to construe it in a particular voice — grammatically, not just empirically.

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In our next post, we’ll explore the reification of truth itself — and how logocentric philosophies mistake the grammar of projection for an external order of reality.

5 Truth and Projection — The Linguistic Architecture of Reality Claims

What is truth? A correspondence with reality? A coherence among propositions? A pragmatic utility?

In systemic functional linguistics (SFL), these abstract theories can be grounded in a concrete fact: truth is not discovered outside language — it is construed within it.

The Clause Complex and Projection

In SFL, the grammar of projection allows language to refer to itself:

• She said that it was raining.

• He believes the earth is round.

• I know that this is true.

Here, the projecting clause (she said, he believes, I know) introduces a projected clause — a meaning encoded as content. This is grammar’s way of construing semiosis itself as a phenomenon.

When philosophers speak of propositions, they are talking about projected clauses — language about language, meaning about meaning.

But when projection is reified, it ceases to be a grammatical function and becomes a metaphysical belief:

• Truth exists independently of thought.

• Propositions have truth-values.

• There is a realm of facts to be matched.

These are not philosophical discoveries. They are grammatical arrangements turned into ontologies.

Truth as Projection Reified

Consider the statement: It is thought that the Earth orbits the sun.

Here, "It is thought…" is a projecting clause construing the following as a proposition.

But now consider: The Earth orbits the sun.

The projecting clause is gone — the claim is presupposed, taken for granted, de-projected.

This shift from projection to assertion is a grammatical shift, but it is often mistaken for an epistemological one.

In reality, the grammar of projection allows us to navigate degrees of certainty, modality, and evidentiality — not to discover an objective realm of truth, but to construe our commitments to meaning.

Metaphysics as Misrecognised Grammar

Philosophy’s theory of truth often begins where grammar has already done its work. What was once a projecting clause becomes an ontological commitment. The distinction between content and commentary collapses into a belief in objective propositions.

Thus, the idea of truth as correspondence — a thought mirroring the world — is grammar misunderstood as metaphysics.

We do not discover truths. We construe propositions, and construe our orientation toward them.

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In our next post, we turn to the concept of essence — that oldest of metaphysical categories — and ask whether it, too, is not a ghost born of grammatical processes.

6 Essence and the Grammar of Being

Where does the idea of essence come from?

Since the time of Plato and Aristotle, Western philosophy has been haunted by the notion that behind every appearance lies an underlying substance — an essence — that makes a thing what it is.

But what if this metaphysical commitment to essence is, at its root, a grammatical commitment?

The Nominalisation of Process

In Systemic Functional Linguistics, one of the most powerful meaning-making strategies is nominalisation — the transformation of a process or quality into a ‘thing’:

• She is wise → Her wisdom

• They govern → Government

• We differ → There is a difference

Nominalisation allows language to package experience into stable entities that can be named, described, possessed, or analysed. This syntactic sleight of hand is the origin of many theoretical constructs — not only in everyday reasoning, but in philosophy, science, and law.

When philosophers seek the essence of courage, beauty, or justice, they often begin by treating these nominalised abstractions as if they were entities with hidden cores, rather than grammatical construals of process and relation.

Essence as Identifying Process

SFL treats identity as a process — a relational clause type. In sentences like:

• A circle is a round plane figure.

• Water is H₂O.

The verb is enacts an identifying relation — not a metaphysical union, but a semiotic equivalence between two functions in a clause. The structure makes one element the "Token" (the signifier) and the other the "Value" (the signified), inverting the usual logic of substance and property.

Philosophy often reifies this identifying relation into a theory of essence. It takes the structure of a clause and turns it into a structure of reality:

• What is X? becomes What is the essence of X?

But in grammar, this is simply a way of construing meaning — a form of categorisation, not a window into noumenal reality.

The Illusion of Inherent Properties

When we say:

• Gold is heavy.

• Justice is fair.

• The soul is immortal.

We are drawing on attributive relations, projecting qualities onto entities. These too are grammatical: they belong to the system of intensive attribution. Yet over time, the constant co-occurrence of entity and quality becomes naturalised — taken as evidence of essence rather than of meaning-making.

Thus, the ghost of essence is born: an abstract identity, imagined as real, sustained by patterns of language.

7 Language as Origin — A Semiotic Ontology of Thought

In this final post, we draw together the threads of our journey — from Plato’s Forms to Nietzsche’s Will — to propose not the rejection of the philosophical tradition, but a re-reading of it: not as a map of reality, but as an archaeology of meaning.

Throughout the series, we’ve suggested that many core philosophical concepts are not false as such, but fossilised — sedimented residues of semiotic processes that have been turned into metaphysical doctrines. In every case, the origin of the concept was not the world itself, but language’s way of making sense of it.

The Semiotic Roots of Ontology

Systemic Functional Linguistics shows that meaning is organised by systems of choices — systems that are both structured and dynamic. These systems allow us to construe experience as meaningful, to project thoughts, to track agency and causation, and to distinguish appearance from reality.

But these same resources can also become invisible. As philosophy turns its gaze outward — toward Being, Will, Substance, Truth — it often forgets that the terms in which it does so are themselves products of a semiotic architecture.

In other words: philosophy speaks the grammar of meaning without often knowing it.

This is not a critique of philosophy, but a proposal: that the concepts we inherit are crystallised expressions of the architecture of language. To understand their power — and their limits — we must make visible the semiotic scaffolding that supports them.

Theories as Reconstruals of Meaning

Science, philosophy, and mythology all reconstrue the meaning of language. They are not simply ‘ideas about the world’, but second-order systems that re-interpret first-order meaning.

To say that gravity ‘acts’ on bodies is to metaphorise a grammatical structure — transitivity — into a cosmological agent.

To say that the ‘soul’ is distinct from the body is to project mental clauses into metaphysical planes.

To say that there is a ‘will to power’ behind all life is to nominalise a grammatical process and universalise it.

In each case, the movement is the same: from semiotic process to metaphysical reification. A verb becomes a noun. A clause becomes a doctrine. A projection becomes a substance.

Philosophy, then, can be read as the metaphysics of grammar.

Language as Origin, Not Obstacle

Traditionally, language has been treated in philosophy as either a transparent medium (a vehicle for truth) or a frustrating barrier (a source of confusion). But SFL offers a third view: language is the origin of meaning, not its distortion.

We do not simply describe the world with language; we construe it. The categories of thought — subject, predicate, cause, agent, event, intention, possibility — are not given by nature, but constructed in and through language.

To speak is not just to say something about the world. It is to make a world meaningful.

A Semiotic Ontology of Thought

If we take this seriously, then a theory of language offers more than just a tool for interpreting texts. It becomes a meta-theory: a way of reading the history of ideas as the history of meaning-making.

Plato, Descartes, Kant, Nietzsche — and countless others — were not wrong. They were, we might say, listening closely to the architecture of their own thought, without yet knowing its grammar.

A semiotic ontology does not replace philosophy. It re-grounds it. It shows that the most profound metaphysical questions — What is being? What is truth? What is self? — are also questions about the architecture of meaning.

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And so we conclude not with a rejection of metaphysics, but with its renovation. A theory of language does not solve the great problems of philosophy. It lets us see how those problems arose, and how — by attending to the meanings we live by — we might begin to live them differently.

Relational Science and the Future of Inquiry

1 Classical Science vs. Relational Science — Paradigms in Contrast

Science as we know it today is rooted in a tradition that dates back centuries — a tradition grounded in classical assumptions about the nature of reality, observation, and causality. This classical scientific paradigm is characterised by several core ideas: that reality exists independently of observation; that phenomena can be isolated and studied as discrete entities; and that knowledge is built through objective measurement and reproducible experiments.

These assumptions have yielded tremendous insights and technologies. Yet, as we push the boundaries of knowledge—into the quantum realm, complex ecosystems, and social systems—it becomes increasingly clear that the classical model is insufficient to capture the full texture of reality. This insufficiency has prompted calls for a new way of thinking: a relational scientific paradigm.

What is Relational Science?

At its heart, relational science acknowledges that reality is not composed of isolated, self-contained things but of dynamic relations and interactions. Objects and subjects co-constitute each other; the observer participates in shaping what is observed; and processes unfold through networks of interdependence. This relational ontology reframes what counts as an explanation: from linear cause-effect chains between discrete entities to webs of mutual influence, emergence, and co-becoming.

Key Contrasts:

Classical Science	Relational Science
Reality is independent, observer is separate	Reality is co-constructed with the observer
Entities have fixed, intrinsic properties	Properties emerge through relations
Causality is linear and local	Causality is distributed, context-dependent
Knowledge is objective and context-free	Knowledge is participatory and situated
Reductionism: isolate parts to understand whole	Holism: understand wholes through relations

Implications for Scientific Methodology

The shift toward relational science challenges the classical ideal of detached measurement. It requires us to reconsider experimental design, data interpretation, and even what counts as evidence. Relational methods emphasise contextualisation, reflexivity, and multi-modal approaches — combining quantitative data with qualitative insights, and integrating perspectives across disciplines.

Why Does It Matter?

Embracing a relational paradigm is not merely an abstract philosophical move. It has practical consequences for how we approach pressing global challenges — from climate change and biodiversity loss to social justice and public health. These complex problems involve entangled systems where linear, reductionist approaches fall short. Relational science offers tools better suited to capturing complexity, fostering cooperation, and co-creating sustainable futures.

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In the next post, we will delve deeper into Observer Participation — exploring how measurement, reality, and co-creation intertwine in relational inquiry.

2 Observer Participation — Measurement, Reality, and Co-Creation

A defining feature of relational science is the recognition that the observer is not a passive spectator but an active participant in the phenomena being studied. This insight disrupts the classical scientific ideal of objective, detached observation and invites a deeper inquiry into the entanglement between measurement, reality, and knowledge.

Observer and Reality: A Mutual Constitution

In classical science, measurement is often assumed to reveal pre-existing properties of independently existing entities. Yet, advances in quantum physics and systems theory challenge this notion. The act of observation itself influences what is observed, collapsing potentials into specific outcomes, and in doing so, co-creating reality with the measured system.

This does not imply that reality is purely subjective or constructed arbitrarily. Rather, it means that reality emerges through ongoing relations between observer and observed, context and system, measurement and meaning.

The Measurement Problem and Its Lessons

Quantum mechanics famously exposes the limits of classical observation. Phenomena such as wavefunction collapse and entanglement highlight that the observer’s choice of measurement affects the behaviour of quantum systems in fundamental ways.

Beyond physics, similar patterns arise in ecology, social sciences, and cultural studies: observations shape and reshape the systems under study, whether through researcher influence, participatory methods, or the feedback loops intrinsic to living systems.

Co-Creation in Scientific Practice

Relational science advocates methodologies that embrace observer participation. Reflexivity — where researchers critically reflect on their own role and influence — becomes essential. Collaborative inquiry, where stakeholders co-design studies and interpret findings together, exemplifies this participatory approach.

Such methods do not undermine scientific rigour; instead, they enrich understanding by making explicit the relational dynamics at play and acknowledging the limits of detached objectivity.

Implications for Knowledge and Inquiry

Observer participation implies that knowledge is situated and provisional. Scientific claims are understood as negotiated, contextual, and contingent — rather than final or universally fixed truths. This relational stance opens space for plural perspectives, interdisciplinarity, and adaptive inquiry responsive to changing conditions.

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In our next post, we will explore Methodologies for Relational Inquiry — examining how scientific practices evolve to embody this participatory, situated approach.

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3 Methodologies for Relational Inquiry — From Experiment to Ethnography

If relational science redefines the observer as a participant in the unfolding of phenomena, then the methods of inquiry themselves must also transform. Traditional scientific methodologies—designed for separation and objectivity—must give way or adapt to approaches that acknowledge and incorporate relational dynamics.

Beyond the Detached Experiment

Classical experimental designs aim to isolate variables, control contexts, and produce replicable, universal findings. While this has driven profound advances, it often abstracts phenomena from their contexts and downplays the mutual shaping of observer and system.

Relational inquiry challenges this by emphasising the situatedness of all observations. Experiments are no longer mere snapshots of independent reality but interventions within dynamic systems. This requires flexible designs that account for feedback, context, and the evolving nature of the phenomena.

Ethnography and Participatory Methods

Ethnographic approaches — long established in anthropology and sociology — offer valuable models for relational inquiry. By immersing themselves in contexts, researchers attend to the interplay of actors, environments, meanings, and practices over time.

Participatory action research and community-based studies extend this by involving those studied as co-researchers, valuing local knowledge and fostering collaborative meaning-making. These methods reveal the entangled nature of knowledge production and highlight the ethical responsibility of inquiry.

Systems Thinking and Network Analysis

Relational methodologies often employ systems thinking, which conceptualises phenomena as networks of interdependent components. Network analysis, complexity science, and modelling techniques allow researchers to map, simulate, and interpret interactions that transcend linear causality.

These tools are particularly potent in ecological, biological, social, and technological domains where relationships themselves carry causal force.

Towards Methodological Pluralism

A relational science does not prescribe a single methodology but encourages pluralism—a toolkit adaptable to the question, context, and participants. Mixed methods approaches, iterative cycles of inquiry, and openness to emergent insights characterise this ethos.

Importantly, relational inquiry foregrounds reflexivity: continual examination of how the researcher’s presence, assumptions, and actions shape the process and outcomes.

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In our next post, we will delve into Relational Thinking in Physics, exploring how quantum entanglement and related phenomena exemplify and inspire relational approaches in science.

4 Relational Thinking in Physics — Quantum Entanglement and Beyond

Physics has long been the poster child of classical science’s quest for objective, universal laws. Yet, the advent of quantum mechanics has profoundly challenged this classical picture, revealing a world that resists simple, detached description and invites relational thinking.

Quantum Entanglement: A Paradigm Shift

At the heart of this challenge lies quantum entanglement—a phenomenon where particles become inseparably linked, such that the state of one instantly correlates with the state of another, regardless of distance. This phenomenon defies classical assumptions of independent, local entities and suggests that relations themselves are fundamental.

Entanglement implies that what exists “out there” is not a collection of isolated objects, but a network of interdependencies, where measurement and observation participate actively in defining reality. In other words, the observer and the observed are entwined.

Relational Interpretations of Quantum Mechanics

Relational interpretations, such as Carlo Rovelli’s Relational Quantum Mechanics, propose that the properties of quantum systems exist only relative to other systems — no absolute, observer-independent state exists. This reframes reality as a web of interactions, where knowledge and existence are co-constructed.

Similarly, interpretations like Quantum Bayesianism (QBism) view the wavefunction as a tool for an agent’s expectations, not an objective property. This underscores the participatory nature of scientific inquiry.

Beyond Quantum Physics

Relational thinking extends beyond quantum physics into the realms of spacetime, information theory, and cosmology. Some approaches suggest that spacetime itself emerges from entanglement patterns, positioning relations as ontologically primary rather than derived.

Implications for Science and Philosophy

These insights challenge entrenched dichotomies — subject/object, observer/observed, and independent/dependent — prompting a reconsideration of what science aims to describe. They invite a shift toward a science that is less about uncovering fixed entities and more about understanding networks of relations and processes.

In the next post, we will explore how relational perspectives illuminate biological and ecological systems, highlighting co-evolution and complex networks.

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5 Relational Biology and Ecology — Systems, Networks, and Co-Evolution

While physics has prompted us to rethink the foundational nature of reality, biology and ecology offer equally profound insights into relationality—revealing life itself as a dynamic network of interactions that shape and are shaped by their contexts.

From Organisms to Systems

Traditional biology often treated organisms as discrete units, bounded entities that evolve through gene-centred processes. Yet, relational biology invites us to view organisms as systems—complex, open, and interdependent networks of cells, genes, and environmental interactions.

This systems perspective acknowledges that the boundaries of organisms are porous and that life unfolds in continuous relation with its surroundings.

Networks and Interactions

Ecology extends this perspective further, focusing on the webs of interaction between organisms and their environments. Food webs, mutualistic relationships, and ecosystem dynamics exemplify how no species or individual evolves in isolation.

The concept of co-evolution captures this beautifully: species adapt not simply to static environments but to other evolving organisms, producing reciprocal influences over time.

Niche Construction and Ecological Inheritance

We have explored how organisms modify their environments and pass these changes to subsequent generations, a process known as niche construction. This challenges gene-centric views by positioning environment modification as a form of inheritance and evolutionary influence.

Relational Development and Phenotypic Plasticity

Developmental biology contributes another layer: phenotypic plasticity—organisms’ capacity to develop different traits in response to environmental cues—highlights how relational interactions during development shape evolutionary outcomes.

This underscores the fluidity and contextuality of life, where genotype, environment, and history are intertwined.

Towards a Relational Biology

Embracing relationality shifts biology from a focus on static ‘things’ to a science of processes and relations. It highlights networks, feedback loops, and histories as foundational to understanding life’s diversity and adaptability.

In the next post, we will examine how the social sciences and humanities are embracing relational approaches, transforming our understanding of culture, meaning, and society.

6 Social Sciences and Humanities — The Relational Turn in Culture and Meaning

The social sciences and humanities have long grappled with the complexity of human experience, culture, and meaning. Recently, a relational turn has reshaped these fields, offering fresh perspectives that resonate with relational ontologies in science.

From Individuals to Networks of Relations

Where classical approaches often centred on individuals as isolated agents or fixed social structures, relational thinking foregrounds the networks, interactions, and processes that constitute social life.

Human identity, culture, and knowledge are understood not as static possessions but as emergent from ongoing interactions—between people, their histories, institutions, and environments.

Language, Meaning, and Semiotics

Relational approaches emphasise language and semiotics as dynamic systems of meaning-making. Meaning is not inherent in isolated words or symbols but arises in relations—between speakers and listeners, texts and contexts, and cultural traditions and innovations.

This dynamic challenges essentialist notions of identity or culture, highlighting hybridity, fluidity, and co-construction.

Power, Agency, and Ethics

A relational lens also reshapes understandings of power and agency. Power is seen not merely as possession but as distributed across networks, enacted in relations.

Agency emerges relationally—through participation, negotiation, and contestation within social fields—inviting ethical reflections on responsibility, participation, and co-creation.

Transdisciplinarity and Methodological Innovation

Social sciences and humanities increasingly adopt transdisciplinary and participatory methods, such as ethnography, dialogic inquiry, and collaborative research.

These methodologies align with relational epistemologies by valuing situated knowledge, multiple perspectives, and the co-production of meaning.

Implications for Culture and Society

Understanding culture and society relationally encourages us to see social change as emergent from complex interactions rather than solely from top-down structures or individual choices.

It opens pathways for more inclusive, responsive, and adaptive approaches to addressing contemporary social challenges.

7 The Future of Science — Toward Integrative, Participatory Inquiry

As we conclude this series, it is clear that adopting a relational ontology invites us to rethink not only what science studies, but how science is done. The future of inquiry points toward more integrative, participatory, and co-creative approaches that transcend traditional disciplinary boundaries.

Beyond Reductionism and Fragmentation

Classical science often seeks to break complex phenomena into isolated parts, aiming for precision through reduction. Relational science, by contrast, embraces complexity as fundamental, focusing on patterns of interaction and emergence.

This shift challenges the fragmentation of knowledge and calls for holistic frameworks that honour interconnectedness.

Participatory Epistemologies

Relational inquiry recognises the active participation of observers and practitioners in the production of knowledge. Measurement, observation, and interpretation are not passive acts but co-creative processes that shape what is known.

This participatory stance fosters reflexivity—awareness of how methods, perspectives, and values influence scientific outcomes.

Transdisciplinary Collaboration

Future science increasingly requires collaboration across disciplines, cultures, and sectors. Complex global challenges—such as climate change, health crises, and social inequality—demand integrative approaches that combine insights from physics, biology, social sciences, humanities, and indigenous knowledge.

Relational science provides a conceptual and ethical foundation for such transdisciplinary engagement.

Methodological Innovation

Embracing relationality encourages innovation in methods—blending quantitative and qualitative tools, integrating systems thinking, network analysis, ethnography, and participatory action research.

This methodological pluralism respects multiple ways of knowing and invites diverse stakeholders into inquiry.

Ethics of Inquiry and Co-Creation

A relational future science is deeply ethical. It recognises that scientific knowledge co-produces realities and affects communities and environments. This awareness compels scientists to engage responsibly and collaboratively, fostering science as a shared, dynamic practice embedded in social and ecological contexts.

A Vision for Tomorrow

Ultimately, relational science envisions inquiry as a participatory journey rather than a quest for fixed truths. It calls on us to become co-creators in an ongoing dance with the living world—cultivating curiosity, humility, and openness.

This future is not distant. It is already emerging in pockets of innovation, dialogue, and mutual learning worldwide. The question is: how will we nurture and expand it?

Relational Evolution

1 Cold Rice, Hot Topic — Rethinking Evolution from the Margins

In May 2025, Nature reported on a study that many hailed as a “landmark” in evolutionary biology. Conducted over more than a decade, the research showed that rice plants exposed to cold conditions for several generations acquired a stable tolerance to freezing temperatures — without any detectable changes to their DNA sequence. The adaptive trait was passed on through changes in epigenetic markers: molecular tags that regulate how genes are expressed, without altering the genetic code itself.

The rice plants had, in effect, inherited a new capacity not by mutating, but by modulating the expression of what was already possible. What made headlines, however, was not just the discovery itself, but how it was framed. “The study adds to evidence challenging the dominance of ‘natural selection’ as the sole adaptive force in evolution,” Nature reported. To some, this seemed to suggest a quiet revolution: evolution without mutation, inheritance without genes, adaptation without Darwin.

But what, exactly, is being challenged here — and what is being misunderstood?

As with many scientific breakthroughs, this study’s significance lies not only in its results but in what it invites us to reconsider. Yet to ask what this discovery means is to enter a space where biology and philosophy converge. What kind of thing is an adaptation? Where does variation come from? Can evolution be understood not only as a process of random mutations filtered by environmental selection, but as something more relational — something in which organism and environment co-participate in the actualisation of traits?

This series takes the rice study as a departure point for rethinking some of our inherited assumptions about evolution. It does not seek to discard natural selection, but to contextualise it. Nor does it argue that epigenetics overturns Darwinian evolution, as some popular accounts might imply. Instead, we ask: what happens when we stop treating genes as the sole site of evolutionary change, and begin to see adaptation as an unfolding within relationships — between organism and environment, past and future, potential and instance?

The cold-tolerant rice study is striking, not because it contradicts evolutionary theory, but because it exposes the limitations of a still-dominant narrative in which adaptation is framed as the gradual selection of random genetic variants. That narrative, often identified with the “Modern Synthesis” of mid-20th century biology, has long struggled to accommodate the plasticity, responsiveness, and situatedness that living systems exhibit. Evolution, we’re learning, is not only about what survives — but about what emerges, and how.

In the posts to follow, we’ll explore how epigenetics reshapes our understanding of variation, inheritance, and selection. We’ll look at how evolutionary biology is already moving beyond the gene-centric paradigm, and how a relational ontology might help make sense of this transition. Most of all, we’ll try to ask what it means to think with evolution — not as spectators watching traits compete for survival, but as participants in the very processes that shape the unfolding of life.

If rice can learn to grow cold within a few seasons, perhaps it is time we warmed to a more dynamic, relational view of evolution.

2 What Is Epigenetic Inheritance — and What Is It Not?

If evolution is typically understood as the selection of genetic variation, then epigenetics has arrived as something of a conceptual disruptor. In recent years, it has become a buzzword not only in biology but in popular science, psychology, and even wellness culture. Amid this proliferation of meanings, it’s worth pausing to ask: what do we actually mean by epigenetic inheritance? And just as importantly: what don’t we mean?

The rice study that sparked this series showed that cold tolerance could be passed from one generation to the next without changes to the DNA sequence. Instead, what changed were epigenetic markers — molecular tags (such as methyl groups) that affect whether specific genes are expressed or silenced. Crucially, these tags were heritable: they persisted across generations even when the original environmental trigger (cold stress) was removed.

This kind of inheritance challenges the narrowest reading of the “central dogma” of molecular biology, which once held that information flows one way: from DNA to RNA to protein. It also complicates the standard evolutionary account in which new traits arise through random mutations that, if beneficial, are retained through natural selection.

But epigenetic inheritance is not magic, nor is it a wholesale rejection of evolutionary theory. Rather, it invites us to broaden our framework. The question is not whether genetic change matters — clearly, it does — but whether all meaningful biological variation must be genetic in origin.

Epigenetics opens a space for adaptive plasticity: the ability of organisms to modulate their gene expression in response to environmental cues, in ways that can be passed on to offspring. It reintroduces the environment not just as a selective filter acting on random variation, but as a participant in the actualisation of variation itself.

Yet here is where we must tread carefully. To say that epigenetic changes are inherited is not to say that the environment can programme an organism’s traits at will. Nor does it mean that we have discovered a neo-Lamarckian mechanism in which acquired characteristics are routinely passed on. Most epigenetic marks are not stably inherited; many are reset during gamete formation or early development. What makes the rice study exceptional is precisely the durability of the observed changes.

We should also resist the temptation to think of epigenetics as somehow more “intentional” than mutation — as if the environment were purposefully sculpting traits in response to need. Evolution remains an emergent process, not a directed one. What epigenetics shows us is not that organisms consciously adapt, but that the boundary between organism and environment is more porous, and more responsive, than a strictly gene-centred model allows.

In this light, epigenetics may be less a repudiation of Darwinian evolution than a refinement — a gesture toward a more relational account of variation and inheritance. It suggests that evolutionary novelty can arise not only through randomness filtered by selection, but through context-sensitive modulation of existing potential.

Where genetic inheritance assumes a largely stable archive of possibility, epigenetic inheritance shows us how that archive can be dynamically interpreted. It is not the script that changes, but the reading of it.

In the next post, we’ll explore this idea further by asking: What counts as variation? And how might our assumptions about randomness, causality, and novelty be shaped by the models we use?

For now, the takeaway is this: epigenetics doesn’t replace the genetic model — but it helps us reframe the story of evolution as a more entangled, co-emergent process. One in which life does not simply adapt to its conditions, but evolves with them.

3 What Counts as Variation? Rethinking Evolution’s Raw Material

In classical evolutionary theory, variation is the fuel of change. Mutations — random changes in DNA — introduce novel traits, and natural selection acts on these traits to shape populations over time. From this perspective, variation is a kind of background noise: unpredictable, unstructured, and external to the processes that filter it.

But what if variation is not just random input, but relational output? What if what counts as “variation” depends not simply on chance, but on the ongoing interaction between organism and environment — and on the frameworks through which we interpret that interaction?

Let’s return to the rice study. The researchers didn’t observe a new gene, a mutation, or even a hybrid genotype. Instead, they observed a change in gene expression patterns — a difference not in what was present, but in how it was activated. This shift produced a functional difference (cold tolerance), and that difference persisted across generations.

So is this “variation”? If we define variation as differences in DNA sequence, then no. But if we define it more broadly — as the emergence of new traits with potential adaptive consequences — then yes. And crucially, this broader view allows us to see variation as something that can be induced, not just stumbled upon.

This challenges the idea that variation must be random to be evolutionary. The randomness of mutation has long served as a conceptual buffer between evolution and teleology: if change is random, then it cannot be purposeful. But randomness is not the same as independence. A dice roll is random, but it presupposes a system of rules, constraints, and possible outcomes. Likewise, epigenetically induced variation is not directed, but it is structured — shaped by the relational dynamics between organism and environment.

From a relational perspective, then, variation is not a static property of an isolated genome. It is an emergent property of interaction — of the organism’s openness to contextual influence, and the environment’s capacity to actualise different potentials. This is not to say that all variation is environmentally induced, but that even so-called “random” variation is only meaningful in relation to a system that constrains and interprets it.

This insight matters because it reframes how we understand novelty in evolution. In a strictly gene-centric model, novelty is additive: new traits arise when genetic accidents build up over time. But in a relational model, novelty can also be combinatorial and contextual — arising from new patterns of activation, new environmental triggers, or new configurations of interaction.

In this view, the question “what counts as variation?” is no longer a simple matter of molecular bookkeeping. It is a matter of framework — of how we define change, where we locate agency, and what kinds of difference we are prepared to recognise.

The rice didn’t gain a new gene. But it did gain a new capacity — one that emerged through its history of interaction with a particular stress, and that became inheritable through epigenetic marking. That change is as real, and as evolutionarily relevant, as any nucleotide substitution.

In the next post, we’ll explore how this redefinition of variation affects our understanding of inheritance. If traits can be passed on without changes to DNA, what does it mean to say that something is “inherited”? And how stable must a trait be to count?

4 What Counts as Inheritance? Expanding the Evolutionary Ledger

Inheritance has traditionally meant one thing in evolutionary theory: the transmission of genetic information from parent to offspring. Encoded in DNA, this information is thought to specify the organism’s developmental programme, which unfolds (with some environmental modulation) to produce traits. The rest — epigenetics, physiology, behaviour, culture — is considered either background noise or downstream consequence.

But the rice study demands a reconsideration. Here we find cold tolerance passed from one generation to the next, not through mutation or recombination, but through changes to chemical tags on the genome. These changes alter gene expression and persist for multiple generations. The underlying DNA remains constant. And yet, something clearly has been inherited.

This phenomenon is not new. In recent decades, biologists have documented epigenetic inheritance in plants, animals, and even humans. What makes the rice study striking is the clarity of the mechanism and the functional benefit — a heritable trait, induced by environmental stress, that increases fitness and spreads. In other words: this is inheritance, in any evolutionary sense that matters.

So what counts as inheritance?

One answer is purely molecular: only DNA sequence counts, because only sequence is stable, replicable, and “digital.” But this answer is increasingly unsatisfactory. Stability is a matter of degree, not kind. Epigenetic marks can persist across generations. So can maternal effects, microbiomes, learned behaviours, and environmental legacies. If the test of inheritance is whether a trait recurs in offspring and influences evolutionary dynamics, then DNA is not the only medium.

This is the view taken by the Extended Evolutionary Synthesis (EES), which argues for a broader conception of inheritance — one that includes epigenetic, ecological, behavioural, and symbolic systems. From this perspective, inheritance is not just about molecules, but about informational continuity — any process by which prior states constrain or enable future possibilities.

The relational turn takes this one step further: it views inheritance not just as a transmission of pre-formed content, but as a reinstantiation of relational patterns. What is inherited is not a static message, but a set of structured affordances — potentials that can be reactivated, reconfigured, and redeployed in novel contexts.

In this view, the rice plants didn’t pass on a fixed trait. They passed on a conditioned responsiveness, a readiness to activate certain patterns under certain stresses. This responsiveness was made material through epigenetic tags, but its significance lies in the relational history that gave rise to those tags — the plant’s encounter with cold, its selective memory of that encounter, and its conveyance of that memory to the next generation.

This is not Lamarckism in its caricatured form — the idea that any acquired trait can be inherited. Nor is it a rejection of genetic inheritance. Rather, it is a reframing of inheritance as multimodal: a system of layered constraints, some genetic, some epigenetic, some ecological or behavioural, all interacting to shape what becomes possible.

What matters, then, is not whether a trait is written in DNA, but whether it participates in the organism–environment dynamic that makes evolution happen. Inheritance, in this light, is not a chain of discrete handovers. It is a pattern of continuity-in-difference — a means by which the past remains active in the unfolding of the present.

Next, we’ll turn to the heart of the evolutionary process: selection. If variation can be induced, and inheritance is relational, then what exactly is being selected — and by whom?

5 What Counts as Selection? Induction, Participation, and the Environment as Co-Agent

Selection is often framed as the ultimate editor of evolution. Random mutations provide variation; natural selection winnows the results, favouring traits that confer reproductive advantage. On this view, selection is reactive — it operates after the fact, passively eliminating the unfit and letting the fittest survive.

But the rice study complicates this picture. The cold environment doesn’t simply reward plants that happen to survive the stress. It induces heritable change. It participates in shaping the very variation that it will later reward. In this scenario, selection is not an impartial filter. It is an active partner in the generation of traits.

This is not a new idea. Developmental systems theorists and advocates of the Extended Evolutionary Synthesis have long argued that selection is only part of the story — that variation is not always random, and that organisms and environments co-construct one another over time. But what the rice study shows is that this mutual shaping can occur over just a few generations, and that the environment can induce heritable change without altering DNA sequence.

So what counts as selection?

Classically, selection operates on phenotypic variation — differences in traits — and promotes those variants that confer greater reproductive success. But this model presumes a separation: variation is random, selection is external, inheritance is genetic. The rice study dissolves these separations. Variation is not random, but induced. The environment is not external, but entwined. Inheritance is not purely genetic, but epigenetic and relational.

From a relational perspective, selection is not a matter of external pressures acting on isolated traits. It is the co-emergence of trait and context — the mutual attunement of organism and environment over time. Traits are not simply selected; they are made selectable by the histories of interaction that render them meaningful, useful, or viable.

In the rice case, selection is not the cold simply “choosing” those plants that happen to survive. It is the cold interacting with a responsive system — a system capable of reconfiguring itself under stress, of “remembering” that configuration, and of passing it on. This is not natural selection as a sieve. It is selection as a dialogue — a history of adjustments, reciprocal constraints, and shared shaping.

This also suggests a broader account of agency. The environment is not a static backdrop against which evolution plays out. It is an active participant, a co-agent in the evolutionary process. To say that cold “selects” for tolerance is not to anthropomorphise the cold, but to recognise that selection is not one-sided. It emerges from relational entanglement — from the way living systems and their environments co-constitute each other across time.

If variation can be induced, and selection is relational, then evolution is not a one-way process of adaptation to fixed external pressures. It is a process of becoming-with — of reciprocal transformation between organism and world.

In the next post, we will return to the heart of evolutionary theory: the concept of adaptation. What does it mean to adapt in a world where variation is induced, inheritance is multimodal, and selection is mutual?

6 What Counts as Adaptation? The Grammar of Fit in a Co-Created World

Adaptation is the crown jewel of evolutionary explanation. It accounts for the appearance of design without a designer, and for the apparent harmony between organism and environment. Organisms seem fit for their worlds — as if sculpted by the very forces they endure.

But what do we mean by “fit”? In classical Darwinian terms, fitness is about differential reproductive success. Traits that enhance survival and reproduction are selected over time. An adaptation, then, is a trait shaped by this process — a product of natural selection operating on inherited variation.

Yet as we’ve seen, the rice study — and the growing body of work on epigenetics, developmental plasticity, and niche construction — challenges the separability of variation, inheritance, and selection. It invites us to rethink the very notion of adaptation.

Let us pause on the grammar of the word. To “adapt” is to be adapted to, but also to adapt oneself. The first is passive; the second is active. One is done by an external force; the other is done with or through the organism’s own capacities. The rice plants do not merely receive cold tolerance as a selective gift. They actively respond, reorganise, retain, and transmit that capacity — all in relation to the environmental provocation.

This reframes adaptation as not merely a matter of fit, but of fitting-with — a dynamic attunement between organism and world. It is not just that a trait fits an environment; it is that trait and environment are co-shaped in the unfolding of evolutionary time.

The rice plants’ cold tolerance is not simply a pre-existing variant selected from a pool. It is a relational achievement — one that involves perception, response, memory, and reproduction. The trait did not exist before the stress; it emerged with it. In this sense, the adaptation is not a static outcome but a process — an unfolding of potential across instances of interaction.

This view draws attention to the semiotic dimensions of adaptation. Adaptations are not just mechanically useful; they are meaningful within the ecology of interactions in which they arise. The chemical tags that modify the ACT1 gene are not mere switches; they are signals, cues, signs in a system that interprets and responds. The organism is not a passive substrate. It is a participant in the construction of its own capacities to be affected and to affect.

From this perspective, we might say that adaptation is not simply the preservation of form under pressure, but the emergence of form through relation. It is the crystallisation of shared history — of the ways in which organisms and environments have come to matter to one another.

This also has implications for how we understand maladaptation, constraint, and change. If adaptation is not a static match but a living process, then so too is the breakdown of adaptation — not a failure of design, but a shift in relational resonance. What once fit may no longer fit, not because the trait is faulty, but because the context has transformed — or the relationship has frayed.

The rice study teaches us that adaptation is not just an outcome of selection; it is a mode of participation. The plants do not simply endure the cold; they learn with it, remember it, and pass that learning on.

In our final post, we will reflect on what this means for the theory of evolution itself. If variation is induced, inheritance is multimodal, selection is mutual, and adaptation is relational — what kind of theory do we need to account for life as a co-creative process?

7 What Counts as a Theory of Evolution? Towards a Relational Understanding of Life’s Becoming

Evolutionary theory has long been one of the cornerstones of biology, a grand narrative explaining how life diversifies, adapts, and thrives. For much of the twentieth century, the Modern Synthesis—blending Darwin’s natural selection with Mendelian genetics—held sway. It presented evolution as a process driven by random genetic mutations filtered by natural selection, with inheritance confined to DNA sequences.

But the rice study on epigenetic cold tolerance, alongside decades of research into plasticity, developmental systems, and ecological feedback, challenges the simplicity of this framework. It demands a deeper, more relational account of evolution—one that honours the complexity and entanglement of life and environment.

If variation can be induced by the environment, if inheritance operates across multiple channels beyond DNA, if selection is mutual rather than unilateral, and if adaptation is a process of participation rather than mere fit, then our theory of evolution must expand accordingly.

What would such a theory look like?

1. Multi-dimensional Inheritance:
   Inheritance is not limited to DNA sequences. It encompasses epigenetic marks, cellular structures, ecological legacies, cultural knowledge, and behavioural traditions. Each of these forms of inheritance participates in the ongoing construction of organism and environment alike.

2. Induced Variation and Developmental Plasticity:
   Variation is not solely random mutation. Organisms can respond plastically to environmental inputs, producing novel phenotypes that may be stable across generations. Developmental systems shape these responses, enabling organisms to actively participate in their own evolution.

3. Relational Selection:
   Selection is not simply an external filter but a co-creative process. Organisms and environments shape each other reciprocally over time, making traits selectable through their mutual history and context.

4. Adaptation as Process:
   Adaptation is not a static state of “fit” but an ongoing, dynamic process of attunement, interpretation, and transformation. It involves semiotic systems—signalling, memory, and meaning—that mediate organism–environment relations.

5. Evolution as Becoming-With:
   Life does not evolve as isolated entities competing in a fixed arena. It evolves through entangled histories, through becoming-with others—organisms, environments, ecologies, cultures.

This relational view does not reject the power of natural selection or genetics; rather, it situates them within a richer conceptual landscape. It invites us to see evolution not just as change over time but as the unfolding of relational patterns, the weaving of co-constitutive threads that create the fabric of life.

The rice study stands as a landmark, not because it overturns classical theory in one stroke, but because it reveals the multifaceted choreography of evolutionary processes — a dance of genes, molecules, environments, and histories.

Why does this matter?

Embracing relational evolution deepens our understanding of biology and enriches other fields—from ecology to medicine, from philosophy to anthropology. It compels us to rethink agency, causality, and the nature of living systems. It reminds us that life is not a collection of static parts but a dynamic, responsive, and co-creative process.

As we move forward, this perspective opens new avenues for research and reflection—inviting us to ask not only how life evolves, but how we, as part of the living world, evolve with it.