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:
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We are not saying that genes mean proteins.
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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:
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Instantiation: the relation between a system of potential and its individual instances;
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Realisation: the relation between levels of symbolic abstraction (e.g., content and expression);
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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:
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how the concept of instantiation helps us rethink gene activation and cellular development;
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how realisation clarifies the layered structure of biological processes;
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how individuation sheds light on differentiation within organisms and populations;
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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:
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The genome constitutes the meaning potential of the organism.
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A gene activation event is an instance of that potential.
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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:
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Development not as the execution of a predetermined plan, but as a progressive, branching cascade of instantiations;
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Contextual modulation as central to development, since each instantiation reconfigures the context for the next;
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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:
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In cellular signalling, where potential responses are instantiated in actual behaviour;
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In immune systems, where a structured potential for recognition is instantiated in particular antigen responses;
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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:
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an internal structuring of potential;
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a contingent actualisation;
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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:
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A gene is not simply a physical molecule but a structured unit of symbolic potential;
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A protein is not simply a material effect, but the realisation of a genetic sequence at a lower level of abstraction;
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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:
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A codon is a unit of content;
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An amino acid is its realised form at the level of expression;
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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:
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Genes are realised as proteins;
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Regulatory networks are realised as cellular behaviours;
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Cellular activities are realised in tissue morphologies;
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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:
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A gene does not intend to be expressed;
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A codon does not mean an amino acid in the semantic sense;
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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.
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Stem cells represent undifferentiated potential — pluripotency.
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Differentiated cells are individuated instances of that potential — distinct profiles of gene expression, morphology, and function.
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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.
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Clonal organisms (e.g. genetically identical plants or insects) may exhibit diverse phenotypes based on micro-environmental cues.
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Phenotypic plasticity shows how the same genotype can give rise to different outcomes — depending on what aspects of potential are made actual.
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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:
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The system provides structured potential;
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The instance actualises a distinctive realisation of that potential;
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And both are shaped by participation in a larger ecology of meaning.
This means:
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A cell does not simply “become” a neuron; it participates in a network that makes being-a-neuron meaningful;
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An organism does not simply express traits; it joins an ecosystemic conversation in which those traits matter;
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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:
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Instantiation helps us see how potential becomes actual — from gene activation to trait development;
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Realisation reveals the layered symbolic mappings that structure biological systems — from codons to amino acids, regulatory networks to organismal functions;
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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:
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Instantiation as the actualisation of biological potential, from gene activation to trait development.
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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.
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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:
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A genome is not just a code, but a system of potential biological meanings.
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A developmental trajectory is not just an outcome, but a patterned actualisation of that potential.
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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:
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The distinction between activation (instantiation) and expression (realisation) helps disentangle the logic of gene regulation from the material processes it directs.
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Recognising individuation allows us to describe not just diversity, but the structuring of diversity — how variation becomes meaningful within the system as a whole.
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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.
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In developmental systems theory, we already see recognition that traits are not “in” the genes, but arise from dynamic interactions across levels of organisation.
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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.
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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.