1 Rethinking the Gene: From Replicator to Developmental Potential
In our recent exploration of memes, we moved beyond the idea of cultural replication and proposed a more relational view: memes are not self-contained replicators but constrained meaning potentials that are instantiated and individuated across social contexts. This shift invites a parallel question: can we rethink genes in the same way?
The gene, like the meme, has often been cast as a replicator—a discrete unit of inheritance, "selfishly striving" to preserve itself across generations. But just as memetics gains depth when we view it through a lens of meaning, context, and selection, genetics too can benefit from a developmental perspective. Rather than treating genes as autonomous agents of replication, we might instead approach them as elements of biological potential, instantiated in the material processes of cellular development and evolution.
From Replication to Instantiation
A gene, in itself, is not a thing that does. It is a sequence of possibilities—a structured potential for participation in processes of growth, differentiation, and adaptation. What a gene becomes in any instance depends on:
The cellular context in which it is transcribed.
The regulatory networks that activate or silence it.
The organismal systems that integrate its effects.
The environmental cues that constrain or afford its activation.
In this view, genes are not replicated in the narrow sense; they are instantiated through a dynamic process of selection, modulation, and integration. Each instance of gene activation is an actualisation of potential—a particular pathway taken among many latent possibilities.
The Ontology of Genetic Potential
We can apply here a relational ontology, in which the gene is not a self-contained unit but a relational entity: its meaning lies not in its internal sequence alone, but in its functional positioning within a larger biological system. In other words:
The genome is a system of biological potential.
Gene activation is instantiation within that system.
Genetic individuation is the variation of instantiations across cells, tissues, and organisms.
This is not to deny the material specificity of genes. Rather, it is to insist that the specificity of DNA sequences does not equate to deterministic agency. Genes make available developmental possibilities; they do not dictate outcomes.
Individuation in the Genetic System
Just as memes are individuated across social users, genes are individuated across biological scales. A single gene may be instantiated differently:
In different cell types within the same organism.
In the same cell type under different developmental stages.
In different organisms sharing a homologous sequence.
This means that genetic potential is not uniformly distributed. The relation between the genome of the cell, the organism, the population, and the species becomes a cline of individuation. The identity of the gene is not fixed by its sequence alone but by the way it participates in meaning-making processes of biological development.
Selection Without Replication
Natural selection still plays a central role—but in this framework, selection acts on instantiations, not on gene sequences abstracted from context. The "fitness" of a gene depends on how its potential is actualised in specific developmental and environmental circumstances. What persists is not a replicator per se, but a pattern of viable instantiations.
Over evolutionary time, certain potentials are reinforced—not because they are selfish, but because they are biologically workable within specific selection landscapes. This parallels our reframing of memes: what spreads is not a unit that copies itself, but a constrained potential whose instantiations prove viable across varied contexts.
Toward a Developmental Gene Ontology
This perspective invites a shift from the gene-as-replicator model to a gene-as-developmental-potential model. It aligns with systems biology, developmental biology, and epigenetics, all of which reveal genes as embedded participants in complex networks of interaction and interpretation.
Such a model opens up new questions:
How do developmental contexts shape the individuation of genetic potential?
How do systemic constraints act as selection pressures on instantiations?
How might this framing help integrate genomic science with organismal and ecological perspectives?
By repositioning the gene within a relational, instantiational ontology, we move toward a richer view of life—not as a battle of replicators, but as a coordinated unfolding of potential across nested systems of meaning and materiality.
2 Epigenetics and the Instantiation of Biological Potential
In our reframing of the gene, we moved from the idea of the gene as a self-replicating unit to a model in which genes are elements of biological potential—instantiated differently across developmental, cellular, and environmental contexts. Nowhere is this more evident than in epigenetics: the study of how gene activity is regulated without altering the DNA sequence itself.
Epigenetics doesn’t just complicate the replicator model; it dismantles it. It shows that what matters is not just what is inherited, but how it is instantiated—and that this instantiation is contextually shaped, dynamically regulated, and in some cases, even heritable across generations.
Instantiation in Epigenetic Systems
Epigenetic markers—such as DNA methylation or histone modification—don’t change the underlying genetic code. Instead, they modulate the actualisation of potential. They determine:
Whether a gene is switched on or off.
How strongly a gene is expressed.
When and where in the organism this occurs.
Thus, the genome is not a script to be read linearly but a landscape of potential, with epigenetic mechanisms acting as gates, filters, and signal routers. The same sequence of nucleotides may give rise to radically different outcomes depending on the epigenetic systems that mediate its instantiation.
Epigenetic Individuation
One of the most striking features of epigenetics is how it individuates genetic potential. Every cell in a multicellular organism contains essentially the same genome, yet the epigenetic configuration of those cells diverges widely. This means that:
Epigenetic individuation occurs at the cellular level, enabling differentiation of cell types.
It continues throughout the life course, shaping responses to nutrition, stress, trauma, and environmental cues.
It can be transgenerational, meaning that actualisations of potential may shape the potential available to the next generation—not by altering DNA, but by altering how it is accessed.
From this vantage point, epigenetics is not a supplementary mechanism layered on top of genetics; it is a core dimension of biological actualisation. It embodies the principle that meaning—here, in the form of functional biological outcomes—arises not from isolated sequences but from systems of constrained potential unfolding across time.
Rethinking Heritability
In the traditional gene-as-replicator model, heritability is about the transmission of genetic material. In this alternative model, we might distinguish between:
Genetic inheritance: the transmission of biological potential (i.e., the genome).
Epigenetic inheritance: the transmission of constraints on potential (e.g., methylation patterns).
Developmental inheritance: the ongoing instantiation of potential through interaction with ecological and social environments.
This broader framing allows us to see how heritability is not just about copying, but about the reconstruction of conditions under which potential is realised. This is especially relevant when thinking about how early life conditions, parental experiences, and environmental exposures can shape the developmental trajectory of organisms—sometimes across multiple generations.
Toward a Relational Biology
Epigenetics gives empirical traction to a relational ontology of life. It shows that:
Potential is structured, but never prescriptive.
Context is constitutive, not secondary.
Variation is not noise, but a central feature of biological meaning-making.
Rather than seeing the genome as a stable blueprint over which epigenetics casts a fuzzy shadow, we might say that the genome is a field of potential, and epigenetics is one of the systems through which that field is organised, modulated, and instantiated.
In this way, epigenetics becomes a key locus for thinking about how biological systems are not just self-maintaining, but self-actualising—developing along paths shaped by their history, structure, and situatedness.
3 Embryogenesis and the Unfolding of Developmental Potential
Having reframed genes as structured biological potential—and epigenetics as one of the systems through which that potential is contextually instantiated—we now turn to perhaps the most dramatic theatre of biological actualisation: development. In the unfolding of an organism from a single cell to a complex multicellular individual, we see biological potential not only actualised, but orchestrated, differentiated, and individuated across time and space.
This is the domain of embryogenesis—and it powerfully affirms our model of constrained potential realised in instance.
From Zygote to Organism: A Developmental Trajectory
Every multicellular organism begins as a single cell. That cell contains the full developmental potential of the organism—yet almost nothing of the organism’s structure has been actualised. What unfolds is not a simple execution of a program, but a dynamic cascade of instantiations, each shaped by:
Epigenetic constraints, which modulate access to genetic potential.
Local environments, including the chemical gradients and physical conditions of the embryonic context.
Intercellular signalling, through which developing cells co-regulate one another's differentiation.
Thus, development is not the expression of a code, but the orchestration of a system—a process that is at once internally constrained and environmentally shaped.
Individuation through Differentiation
Each stage of development increases individuation. The fertilised egg is pluripotent, containing the potential for any cell type. But as development proceeds, this potential is progressively constrained. Cells become muscle, skin, neurones—not because they lose genetic information, but because their epigenetic landscape and relational positioning narrows what is possible in each local context.
In this sense:
Development is individuation through instantiation. Each differentiation is a move from general potential toward specific actualisation.
The organism as a whole is not simply a sum of cells, but a self-organising instantiation of its own potential.
Crucially, individuation happens within a system—the developing embryo. Each part's identity is shaped not only by its internal potential, but by its relation to the whole.
Developmental Potential Is Not Destiny
It is tempting to think of developmental potential as deterministic—but this is an artefact of the replicator metaphor. In reality, developmental pathways are robust but flexible. They are regulated through feedback, sensitive to environmental cues, and open to multiple pathways of actualisation.
Temperature can affect sex determination in reptiles.
Nutritional signals can shift metabolic development.
In humans, early relational environments can shape neurobiological development well into adulthood.
Such variability is not a bug in the system—it is part of its design. Developmental potential is not a script, but a field of affordances, structured yet responsive.
The developing organism is not only making a body; it is making a self—an individuated system capable of perception, action, and interaction.
Development Is Ongoing
Embryogenesis may seem like a contained process, but in truth, development never ends. The same principles that guide early development continue throughout life:
Neural plasticity enables ongoing individuation of experience.
Immune development continues into adulthood, shaped by environmental exposure.
Social and symbolic environments modulate biological systems across the lifespan.
Thus, the developmental potential of an organism is not confined to the womb. It is lifelong—and always embedded in contexts of meaning.
In this light, development is not merely biological engineering—it is living semiosis: the ongoing instantiation of a structured potential shaped by internal dynamics, environmental contexts, and the organism's own unfolding history.
4 From Development to Evolution: Populations as Potentials in Motion
If development is the instantiation of biological potential within the life of a single organism, then evolution is the restructuring of biological potential across the life of a population. What changes over generations is not just what is actualised, but what is possible—what a given lineage can become, given its structured constraints and environmental affordances.
In reframing genes not as replicators but as structured potential, we unlock a view of evolution not as the competition of discrete entities, but as a history of shifting constraints—a dynamic dance between potential and instance, between lineage and environment, between what can be and what is.
Populations as Biological Potentials
A population is not merely a group of individuals, but a field of potential variation—a set of structured possibilities instantiated in different ways across members, environments, and time. Variation arises not simply from mutation, but from:
Epigenetic modulation across generations,
Developmental plasticity within individuals,
Ecological relationships that shape both potential and selection.
Thus, we can treat the population itself as a system of biological possibility.
Each individual organism is an individuation of the population’s developmental potential, shaped by the constraints of its genotype, the regulation of its epigenome, and the specificity of its environment. And just as meaning systems evolve through repeated instantiations, biological systems evolve as the systemic structure of potential itself shifts—through drift, selection, and developmental constraint.
Selection Without Replication
Selection, in this view, does not act on replicators—it acts on instances. That is, it acts on the actualisations of potential. What persists over time is not an individual gene, but the viability of certain instantiations under prevailing environmental constraints.
This view shifts the question from "What replicates best?" to:
What is repeatedly actualisable under given conditions?
What constraints on potential prove adaptive or maladaptive over time?
How do developmental systems bias the direction of future variation?
Crucially, this opens a door to understanding the role of developmental bias—the idea that not all variation is equally likely, and that some pathways of change are more readily accessible than others. Evolutionary change, then, is not an arbitrary shuffle of genotypes, but the reconfiguration of structured possibilities, constrained by past actualisations and future affordances.
Evolution as the Individuation of Lineages
If individual development is a process of individuation—where pluripotent cells become differentiated tissues—then we might say that evolution is the individuation of lineages. Over time, a lineage becomes more distinct, more constrained, and more specialised in how it instantiates biological potential.
Speciation, in this light, is not the splitting of a replicating entity, but the differentiation of developmental trajectories—a point at which systems of potential have diverged far enough that they no longer instantiate into mutually recognisable forms.
And just as in meaning systems, individuation always unfolds within an ecology—of other organisms, of niches, of symbolic or environmental pressures. It is always relational.
Populations as Semiotic Systems?
Without pressing too hard on terminology, we might say that populations—like meaning systems—are structured orders of potential instantiated in context. They carry the marks of previous actualisations, and they reshape what is possible in the future. They evolve, not through simple replication, but through the ongoing negotiation of constraint and possibility.
In this way, the model we built for memes now illuminates the biology of evolution—not by collapsing one domain into the other, but by showing how both operate through the patterned interplay of:
Structured potential
Contextual instantiation
Constraint and variation
Emergent individuation
With this, we've extended our model across ontogeny and phylogeny—across individual development and population-level evolution.
5 Ecology as the Field of Co-Instantiation: Completing the Arc from Genes to Meaning
If we reframe genes not as replicators but as structured potentials, and view development as the process of biological instantiation, then evolution becomes not the survival of replicators, but the historical transformation of what can be instantiated. Throughout this reconceptualisation, we have moved from the level of genes to cells, to organisms, and to developmental systems. To complete the arc, we must now turn to the ecological systems in which these potentials are always embedded, and through which they are actualised.
Ecology as Instantiating Context
In traditional evolutionary narratives, the environment plays the role of selector: it rewards or punishes organisms based on how well their inherited traits suit current conditions. But if we adopt a relational ontology, the ecological environment is not just a backdrop for selection. It is the dynamic and co-evolving field of instantiation for biological potential.
This means:
The environment does not merely select from a fixed pool of variations.
It co-participates in shaping what can be varied, developed, and sustained.
Ecological systems are not external filters but semi-structured potentials that enter into relation with genetic, cellular, and organismic potentials.
From this perspective, an ecological system is not a static stage but a co-instantiating partner. It is:
Material: composed of energy flows, chemical gradients, food webs, and climate systems.
Historical: shaped by previous instantiations, including those of other organisms.
Potential-laden: offering affordances and constraints for future instantiation.
Development in Ecological Context
Developmental systems theory already emphasises that development is not pre-programmed but context-sensitive. Ecology is the name we give to that broader context in which development unfolds:
Genes are expressed differently depending on environmental signals.
Phenotypes emerge through interactions with both physical and social surroundings.
Behaviour, morphology, and life strategies are co-shaped by conditions that are themselves shaped by other organisms.
This makes the ecological system a participant in instantiation at every level. An ecological niche is not a container; it is an interface of mutual shaping. A beaver does not simply inhabit a stream—it co-instantiates a wetland system through dam building. Coral reefs emerge not just from the genes of coral polyps, but from their interactions with water temperature, symbiotic algae, nutrient flows, and other species.
Evolution as Ecological Reconfiguration
When ecological systems are seen as co-instantiating fields, evolution becomes not just a shift in gene frequencies, but a reconfiguration of the possible. Ecological changes—whether slow or abrupt—reshape what can be biologically instantiated. For example:
Climate change alters developmental thresholds and reproductive timing.
Species invasions open or close off relational pathways.
Habitat loss collapses the relational scaffolds that sustain some phenotypes.
So evolution is not just adaptation to a fixed environment. It is the co-adaptive transformation of organisms and environments—what some theorists call niche construction, and what we might now call the mutual shaping of potential across levels of biological and ecological organisation.
From Meaning to Matter, and Back Again
Throughout our exploration of memes, genes, and ecology, we have used the model of potential and instantiation to bridge meaning and biology. The logic that holds across them is neither metaphorical nor mechanical. It is ontological:
Meaning is semiotic potential instantiated in context.
Development is biological potential instantiated in context.
Ecology is the relational context through which both are co-instantiated.
We end where we began: not with discrete units that replicate, but with structured potentials that are actualised in relation. The world is not made of things that persist. It is made of potentials that unfold through relation, in the strata of meaning and matter, mind and life, individual and collective, organism and ecology.
And this is what it means to think ecologically: to see not just systems, but instantiating fields—spaces of unfolding, negotiation, and co-emergence. Ecology is not just the context in which life happens. It is the relational grammar of life itself.
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