Showing posts with label context. Show all posts
Showing posts with label context. Show all posts

20 June 2025

Grammar and the Ghost in the Machine

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.


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.


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

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.


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

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.


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.

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.


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.

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 wiseHer wisdom

  • They governGovernment

  • We differThere 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.


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.

18 June 2025

Relational Biology: Applying SFL’s Semiotic Architecture to Life

1 Not Meaning Systems, but Meaningful Distinctions

Biology is not a meaning system. Cells do not speak. Genes do not form clauses. Proteins do not interpret messages. Yet it may still be possible — and indeed clarifying — to use semiotic distinctions to understand biological processes.

In this series, we propose that certain core concepts from systemic functional linguistics (SFL), especially the distinctions of instantiation, realisation, and individuation, offer powerful tools for describing how biological systems are organised. These concepts arise in the study of meaning-making in language, but they are not confined to language. They are structural distinctions that help us understand how potential becomes actual, how different levels of organisation interact, and how differentiation emerges within systems. And these are precisely the kinds of questions that biology must ask.

Importantly, we are not claiming that biology is a semiotic system. Rather, we are asking: what if we treat certain biological relations as if they instantiate the same kinds of structural distinctions found in meaning-making? Might this approach allow us to see familiar processes — such as gene expression, cell differentiation, or organismal development — in a new and more integrated way?

Distinctions, Not Analogies

This is not an exercise in metaphor. We are not likening the genome to a text or reading language into molecules. Instead, we are proposing that the SFL architecture of meaning provides analytical distinctions that help us map relations within any complex system, including biological ones.

To be clear:

  • We are not saying that genes mean proteins.

  • We are saying that the relation between a gene and the protein it specifies has a similar structural form to the semiotic relation between content and expression.

By distinguishing between potential, instance, and realisation — and between system-wide potential and individual differentiation — we gain tools to describe biological organisation without reducing it to code or chemistry.

Why Use SFL?

Systemic functional linguistics is unique in offering a mature, explicit theory of how meaning is structured across multiple levels. Crucially, it distinguishes:

  • Instantiation: the relation between a system of potential and its individual instances;

  • Realisation: the relation between levels of symbolic abstraction (e.g., content and expression);

  • Individuation: the relation between collective systems and the differentiated potential of individuals.

These are not merely linguistic constructs. They are ways of mapping relations in complex systems. And because biological systems are rich in layered organisation, these distinctions may help illuminate the logic of developmental and evolutionary processes — in a way that avoids both mechanistic determinism and vague holism.

A Shift in Perspective

This approach invites us to move away from thinking of biological parts as discrete units with fixed meanings (e.g., the gene as a blueprint or programme) and toward viewing them as participants in patterned systems, whose behaviour depends on how they are instantiated, realised, and individuated in context.

It’s a shift from static substance to dynamic relation. From code to configuration. From inheritance as replication to inheritance as potential.

What’s to Come

In the posts that follow, we will explore:

  • how the concept of instantiation helps us rethink gene activation and cellular development;

  • how realisation clarifies the layered structure of biological processes;

  • how individuation sheds light on differentiation within organisms and populations;

  • and how these distinctions, when integrated, allow us to describe living systems with new precision.

This is not a metaphorical import from linguistics into biology. It is an attempt to test whether semiotic distinctions, developed to model complex meaning systems, can do useful analytical work in another domain of systemic complexity: life itself.


2 Instantiation — From Genetic Potential to Cellular Actuality

One of the foundational distinctions in systemic functional linguistics is that between meaning potential and meaning instance — linked by the process of instantiation. The system of language offers a structured potential for meaning, but each text (or utterance) is an instance: a particular actualisation of that potential in context. This same structural logic can help us understand how biological potential becomes biological actuality.

In this post, we explore how instantiation can illuminate biological processes — particularly the activation of genes and the development of cells — by distinguishing between what can happen and what does happen, and how the one becomes the other.


Gene Activation as Instantiation

At the molecular level, the genome does not operate like a program that runs from start to finish. It provides a potential — a structured, constrained field of possibilities — but only some genes are activated in any given context. This process of activation is deeply contingent: it depends on environmental cues, cellular conditions, regulatory signals, and epigenetic marks.

From a relational perspective, we can say:

  • The genome constitutes the meaning potential of the organism.

  • A gene activation event is an instance of that potential.

  • The process of instantiation selects particular elements from the potential and actualises them in response to contextual conditions.

This allows us to shift from a static view of the genome as a code to a dynamic view of genetic potential as something instantiated in context — not unlike how a speaker selects meanings from the system of language to produce a specific utterance in a specific situation.


Development as a Cascade of Instantiations

Instantiation does not occur once. It unfolds over time, with each instance influencing future selections. In multicellular organisms, early instantiations (e.g. in embryogenesis) set the stage for subsequent ones. Gene expression patterns become increasingly specialised, as certain potentials are actualised while others are held in reserve or excluded.

This gives us a way to understand:

  • Development not as the execution of a predetermined plan, but as a progressive, branching cascade of instantiations;

  • Contextual modulation as central to development, since each instantiation reconfigures the context for the next;

  • Plasticity and constraint as two poles of potential — with instantiation navigating between them.

Seen this way, development is not a pipeline but a dialogue between genetic potential and environmental context, where meaning emerges through use.


Instantiation Across Levels

Although we’ve focused on gene activation, the logic of instantiation applies at many levels in biology:

  • In cellular signalling, where potential responses are instantiated in actual behaviour;

  • In immune systems, where a structured potential for recognition is instantiated in particular antigen responses;

  • In neural plasticity, where learning instantiates specific patterns of connectivity within a system of latent affordances.

In each case, we can distinguish the system of potential from the instance, and the process that links them: instantiation as contextually contingent actualisation.


Not Just Activation — But Selection in Context

This perspective also clarifies that instantiation is not mere activation or triggering. It is selection in context, shaped by the system’s internal architecture and by its ongoing relations with its environment. It always implies:

  • an internal structuring of potential;

  • a contingent actualisation;

  • a shaping role for context.

It is this structural clarity that the concept of instantiation provides. It invites us to describe biological processes not only in terms of mechanism, but in terms of potential, constraint, and the pathways from one to the other.


In the next post, we turn to realisation, the second of our semiotic distinctions, to explore how different levels of biological organisation are linked — not by cause-and-effect, but by relations of symbolic abstraction.


3 Realisation — Linking Levels of Biological Meaning

In systemic functional linguistics (SFL), realisation is the relation that links levels of symbolic abstraction. Semantics is realised by lexicogrammar, which is in turn realised by phonology or graphology. Realisation is not a causal process but an identifying one: a relation of symbolic mapping between strata of meaning.

This post explores how the concept of realisation can illuminate biological systems — especially the relationship between genetic sequences and their functional products, and between different levels of organisation in living systems.


Realisation Is Not Mechanism

In everyday language, we might say that a gene "produces" a protein, or that DNA "codes for" traits. But these are mechanistic metaphors that often obscure the symbolic nature of biological systems. What if we instead treated these relations as analogous to realisation?

In this frame:

  • A gene is not simply a physical molecule but a structured unit of symbolic potential;

  • A protein is not simply a material effect, but the realisation of a genetic sequence at a lower level of abstraction;

  • The process of transcription and translation is not itself the realisation — it is the material mediation of the realisation relation.

This distinction is subtle but powerful. It allows us to describe biology not just as a set of causes and effects, but as a layered system of symbolic relations: a meaning architecture that can be clarified by tools developed for understanding language.


Codons and Amino Acids: A Symbolic Mapping

The most direct example of realisation in biology is the relation between codons (triplets of nucleotide bases) and amino acids. This mapping is not intrinsic — it is historically contingent and mediated by a translation system. It is a convention established by evolutionary processes, maintained by tRNA and ribosomal machinery.

In SFL terms, we might say:

  • A codon is a unit of content;

  • An amino acid is its realised form at the level of expression;

  • The genetic code is a structured system of realisation relations — mapping symbolic potential onto material outcomes.

This analogy helps us see that what matters is not just the substance of the elements, but their patterned relations across levels. It is the structure of realisation that makes biological semiosis possible.


Realisation and Functional Integration

Realisation also helps us think about integration across scales:

  • Genes are realised as proteins;

  • Regulatory networks are realised as cellular behaviours;

  • Cellular activities are realised in tissue morphologies;

  • Organ functions are realised in organismal capacities.

Each level construes the level above and is construed by the level below — not in a one-to-one fashion, but through complex many-to-many mappings. These mappings are not just material but symbolic: structured, patterned, and functional.

Realisation allows us to see how form and function co-emerge — not as mechanical outputs of a code, but as levels of biological meaning in relation.


Realisation Without Teleology

One might worry that talking about realisation introduces a teleological bias — as if genes intend to become proteins. But this is not the case. In SFL, realisation is not about purpose but about structured dependency. One stratum construes another, and the relation between them is both enabling and constraining.

Similarly in biology:

  • A gene does not intend to be expressed;

  • A codon does not mean an amino acid in the semantic sense;

  • But these symbolic correspondences are nonetheless real and consequential.

Recognising this allows us to talk about biological structure and function without reducing either to mere chemistry or to anthropomorphic metaphor.


In the next post, we turn to the third pillar of our framework: individuation — the process by which systems of potential are distributed, differentiated, and developed across populations of cells, organisms, and lineages.


4 Individuation — Differentiating Biological Meaning Potential

In systemic functional linguistics (SFL), individuation refers to how a shared meaning potential becomes differently available to individuals or subgroups within a community. It addresses how each speaker draws upon and contributes to the collective semiotic system, developing a distinct “voice” or meaning potential of their own.

In this post, we explore how individuation provides insight into biological differentiation — from cell specialisation to developmental pathways and ecological divergence — wherever a shared biological potential becomes particularised in actual living systems.


From Genetic Potential to Developmental Differentiation

Every cell in a multicellular organism typically contains the same genome. Yet liver cells, neurons, and muscle cells look and behave differently. Why?

Because what is shared as potential (the genome) becomes individuated through differential activation and interpretation — shaped by context, interaction, and developmental history.

  • Stem cells represent undifferentiated potential — pluripotency.

  • Differentiated cells are individuated instances of that potential — distinct profiles of gene expression, morphology, and function.

  • This individuation is mediated by systems of epigenetic regulation, signalling gradients, and tissue contexts that act like semiotic environments — modulating what gets activated, when, and how.

We might say: a liver cell is not just a cell with a certain identity, but a cell with a particular instantiation of the shared meaning potential — its own way of being a cell, shaped by the system it participates in.


Biological Systems as Individuated Meaning Systems

This individuation does not end with cells. Whole organisms, populations, and ecosystems also participate in the differentiation of shared biological potentials.

  • Clonal organisms (e.g. genetically identical plants or insects) may exhibit diverse phenotypes based on micro-environmental cues.

  • Phenotypic plasticity shows how the same genotype can give rise to different outcomes — depending on what aspects of potential are made actual.

  • Niche specialisation in ecosystems reflects long-term processes of individuation — as lineages come to occupy different roles and enact different functions within a shared evolutionary potential.

Just as in language, where each speaker’s repertoire is a patterned subset of the language system, each organism enacts a distinctive subset of the biological system — a particular way of being alive within a field of possibilities.


Not Just Variation — Participation

Individuation is not merely variation. It is a relational process: a system–instance dynamic in which:

  • The system provides structured potential;

  • The instance actualises a distinctive realisation of that potential;

  • And both are shaped by participation in a larger ecology of meaning.

This means:

  • A cell does not simply “become” a neuron; it participates in a network that makes being-a-neuron meaningful;

  • An organism does not simply express traits; it joins an ecosystemic conversation in which those traits matter;

  • A species does not merely diverge; it individuates a lineage-level potential into a new role or identity.

Individuation helps us understand not only what is inherited or expressed, but how difference itself is made meaningful in living systems.


The Semiotic Architecture of Life

Across the first four posts, we’ve proposed that three key SFL concepts — instantiation, realisation, and individuation — offer a clarifying semiotic lens on biology:

  • Instantiation helps us see how potential becomes actual — from gene activation to trait development;

  • Realisation reveals the layered symbolic mappings that structure biological systems — from codons to amino acids, regulatory networks to organismal functions;

  • Individuation highlights the differentiation of shared potential into particular pathways, forms, and identities.

Together, these concepts offer more than metaphor. They provide a principled way of describing life as a system of meaning — one that unfolds not just through chemical interactions, but through structured relations of potential, actualisation, and differentiation.

In our final post, we’ll reflect on what this perspective contributes to biological understanding — and how it might open up new ways of thinking across the boundaries of language, life, and meaning.


5 Biology as a Semiotic System — Rethinking Life Through Meaning

What happens when we look at life not just as a set of chemical and physical processes, but as a meaning system — one that can be better understood using the semiotic architecture of systemic functional linguistics?

Over the last four posts, we’ve explored how three foundational SFL concepts — instantiation, realisation, and individuation — offer deep insight into biological organisation:

  • Instantiation as the actualisation of biological potential, from gene activation to trait development.

  • Realisation as the symbolic mapping that connects genetic codes with the material forms they specify — codons realised as amino acids, regulatory patterns realised as cell types.

  • Individuation as the differentiation of shared potential into distinct developmental paths, functional roles, or ecological identities.

In this concluding post, we step back to consider the broader implications of this perspective — and what it contributes to the study of life.


A Shift in Ontology: From Matter to Meaning

At first glance, applying semiotic theory to biology might seem like a stretch. Isn’t meaning something humans do with language, not something cells or genes are involved in?

But meaning, in the SFL tradition, is not confined to words. It is about structured potential — and how that potential is selectively activated, expressed, and differentiated in context.

From this perspective:

  • A genome is not just a code, but a system of potential biological meanings.

  • A developmental trajectory is not just an outcome, but a patterned actualisation of that potential.

  • A differentiated cell type or ecological niche is not just a form, but an individuation of shared possibility.

Biology, in this sense, is not a closed mechanism but an open system of meaning — one that unfolds dynamically through layered semiotic relations.


Clarifying Complexity: What This Model Offers

Why use semiotic concepts to talk about life? Because they offer clarifying distinctions that are often blurred in current biological discourse.

For example:

  • The distinction between activation (instantiation) and expression (realisation) helps disentangle the logic of gene regulation from the material processes it directs.

  • Recognising individuation allows us to describe not just diversity, but the structuring of diversity — how variation becomes meaningful within the system as a whole.

  • Framing biological processes in terms of meaning enables us to speak more clearly about function, interpretation, and responsiveness — without reducing everything to chemistry or computation.

This is not about replacing existing biological models. It’s about supplementing them with a relational semiotic perspective — one that foregrounds how life means as well as how it works.


An Invitation to Transdisciplinary Thinking

Applying SFL’s semiotic architecture to biology opens up more than a novel interpretation. It invites transdisciplinary thinking across the sciences and humanities.

  • In developmental systems theory, we already see recognition that traits are not “in” the genes, but arise from dynamic interactions across levels of organisation.

  • In evolutionary biology, concepts like niche construction and ecological inheritance show that meaning-making is part of how organisms shape and are shaped by their environments.

  • In philosophy of biology, there is growing interest in how agency, interpretation, and signification figure into life processes.

A semiotic view can bridge these insights, offering a formal vocabulary for understanding life as a system of relations — not just of cause and effect, but of potential and instance, symbol and realisation, difference and identity.


Life, Differently Understood

To say that biology is a meaning system is not to anthropomorphise it. It is to recognise that meaning — in the sense of structured, actualisable potential — is not exclusive to language, but intrinsic to life.

Cells interpret signals. Genes map to outcomes. Organisms differentiate shared codes into diverse forms. All this is not merely information processing; it is semiotic activity — patterned, relational, and meaningful.

By bringing the distinctions of instantiation, realisation, and individuation into biological thought, we do not impose a linguistic model onto life. We allow life’s own complexity to become more intelligible — by attending to the kinds of relations that make systems, and systems that make meaning.

This is not the end of a story, but the beginning of a question:
What else becomes visible when we think of life semiotically?