A speculative exploration of the distinction between a relational formal ontology and a classical formal ontology for modelling phenomena in nature that exhibit relationally-mediated wholism, such as phenomena from quantum physics and biosemiotics. Whereas a classical formal ontology is based on mathematical objects and classes, a relational formal ontology is based on mathematical signs and categories. A relational formal ontology involves nodal networks (systems of constrained iterative processes) that are dynamically sustained through signalling. The nodal networks are hierarchically ordered and exhibit characteristics of deep learning. Clarifying the distinction between classical and relational formal ontologies may help to clarify the role of interpretative context in physics (eg. the role of the observer in quantum theory) and the role of hierarchical nodal networks in computational models of learning processes in generative AI
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