Biogeochemistry has traditionally been grounded in a substance-based ontology, modeling ecosystem dynamics through discrete nutrient pools and linear fluxes. While such frameworks have advanced our understanding of carbon, methane, and phosphorus cycling, they often obscure the dynamic, relational, and emergent character of biogeochemical processes. This paper introduces a process-ontological framework for biogeochemistry that reconceptualizes elemental transformations not as state transitions between static compartments but as evolving networks of interdependent processes. Drawing on process philosophy, complexity theory, and resilience (...) science, we articulate four foundational principles (relationality, scale dependence, temporal continuity, and emergence) that underpin a processual understanding of biogeochemical systems. Through empirical cases focused on methane and phosphorus cycling, we demonstrate how process ontology informs both modeling strategies and governance practices, including the detection of early warning signals, policy design, and cross-scale management of tipping points. Rather than replacing substance-based approaches, this framework complements them, revealing their underlying metaphysical assumptions and situating them within a broader ontology of dynamic interdependence. It also emphasizes the epistemic–ontological reciprocity of scientific practice, in which conceptual frameworks and empirical observation iteratively refine one another. By embedding ontological reflection within empirical and governance contexts, this work contributes to a broader rethinking of how scientific models mediate between conceptual frameworks and ecological realities, supporting adaptive, transformative and process-aware strategies for environmental management. (shrink)

The work of Gregory Bateson offers a metaphysical basis for a “process psychology,” that is, a view of psychological practice and research guided by an ontology of becoming—identifying change, difference, and relationship as the basic elements of a foundational metaphysics. This article explores the relevance of Bateson's recursive epistemology, his re-conception of the Great Chain of Being, a first-principles approach to defining the nature of mind, and understandings of interaction and difference, pattern and symmetry, interpretation and context. Bateson's (...) philosophical contributions will be drawn into relationship with Wittgenstein's philosophy of language as use, Melnyk's theory of causal levels of explanation, Korzybski's account of map and territory, the rejection of the heuristic rigidity of substantialist ontologies, and a cybernetics communication science-informed approach to contextual bi-directionality of causality. We thereby arrive at an understanding of Bateson's process psychology that, given its ecological-systemic nature, is explanatorily applicable across the mind sciences. This process psychology equips us to answer the question: What is mind? Not by explanatory appeal to substantial entities contained within mind, but instead by recourse to the contextually relevant patterns for understanding mind to a particular purpose. We have thereby attended to the gulf between heuristics and fundamentals, between psychological models and an onto-epistemic account of reality. Insufficient attention has been given to characterising the vital nature of Bateson's philosophical oeuvre to psychological practice. This article draws out Bateson's relevance to establishing foundational principles for a process psychology capable of reinvigorating psychological thought. (shrink)

Substantialism, which is an extremely common paradigm in Western philosophy, has dominated the sciences over time. Arguing that the authentic structure of existence is fixed and unchangeable; over time, with the development of modern physics, this understanding, which was easily adopted due to the precision of mechanical and mathematical explanations and the ease of categorization, created a school of biology that tried to develop through quantitative propositions; thus, living things were considered static entities that could be understood through reverse engineering. (...) Findings regarding evolution, which has continued uninterrupted for millions of years, have led to the gradual abandonment of essentialism. In addition, when many new data were analyzed, such as the transition from genetics to epigenetics and the mutual interaction in nature and niche creation, it was realized that biology in particular and all natural sciences in general needed a new metaphysical approach, thus process philosophy came to the fore. In process philosophy and metaphysics, it is accepted that every structure in nature consists of processual structures, not substances. The living world is fundamentally dynamic, and the existence of things always depends on the existence of processes, the basic assumption of biology is stability, not change; more precisely, it is argued that it is a stability achieved through constant change. By presenting a methodology, metaphysics and perspective from the process perspective of John Dupré, one of today's most important philosophers of biology, it is aimed to draw attention to the flowing of existence and processes of nature, expressed by Heraclitus as panta rhei (everything flows). (shrink)

Metamonism presents an interdisciplinary processual framework for investigating reality through the search for isomorphisms between different levels of organiza- tion. This work does not propose a new process ontology competing with theories of Whitehead, Deleuze, or Bergson, but rather operationalizes their ideas into a prag- matic tool. The framework is based on the principle of prohibition of self-identity, from which structures observable from cosmology to information systems are de- rived. The article demonstrates the application of the framework to (...) the problem of the ontological status of information, formulates interdisciplinarity as the study of isomorphisms, and offers testable predictions in physics and cosmology. (shrink)

According to contemporary ‘process ontology’, organisms are best conceptualised as spatio-temporally extended entities whose mereological composition is fundamentally contingent and whose essence consists in changeability. In contrast to the Aristotelian precepts of classical ‘substance ontology’, from the four-dimensional perspective of this framework, the identity of an organism is grounded not in certain collections of privileged properties, or features which it could not fail to possess, but in the succession of diachronic relations by which it persists, or ‘perdures’ (...) as one entity over time. In this paper, I offer a novel defence of substance ontology by arguing that the coherency and plausibility of the radical reconceptualisation of organisms proffered by process ontology ultimately depends upon its making use of the ‘substantial’ principles it purports to replace. (shrink)

This article examines Andrii Myshko's contribution to the development of process ontology through the lens of his "metamonism" framework. It is shown that the key achievement lies not in continuing the traditional line (Heraclitus – Whitehead – Prigogine – Deleuze), but in its radical axiomatization. The central principle of metamonism — the prohibition of indifference (A ≠ A) — is introduced and analyzed as a negative ontological condition for the possibility of existence. We demonstrate how this axiom transforms (...) processual intuition from philosophical statement into a rigorous logical-operational instrument, generating a new class of interdisciplinary isomorphisms and falsifiable predictions. (shrink)

Ezumezu, a prototype African logic, developed by Jonathan Chimakonam as a framework which mediates thought, theory and method in the African place, is according to him, extendable and applicable in places non-African too. This seems to underscore the universal character of the logic. I interrogate, in this piece, the logic to see if it truly mediates thought, theory and method in Yorùbá ontology on the one hand, and process ontology on the other hand. Through critical analysis, I (...) discern that each of these thought systems operate beyond the principles of classical logic and this is one of the factors that have vitiated their appreciation and comprehension. Upon critical reflection, however, these thought systems seem to follow the principles of Ezumezu logic hence my aim – to disclose how the logic undergirds theory and method for each of those systems. Keywords: African Philosophy, Ezumezu Logic, Jonathan Chimakonam, Process Ontology, Yorùbá Ontology. (shrink)

This article presents metamonism — an instrumental, interdisciplinary philosophical framework grounded in process ontology. Proceeding from a single ontological axiom (the prohibition of indifference), metamonism provides a universal language for analyzing complex systems across physics, biology, psychology, and sociology. The framework introduces key operators — Monos (reality-as-process) and Logos (model-space), along with their functional dynamics (diff and fix) — to reveal structural isomorphisms between seemingly disparate phenomena. Through examples ranging from quantum mechanics to civilizational collapse, we demonstrate (...) how metamonism transforms from philosophical speculation into a predictive and diagnostic tool for understanding reality's fundamental dynamics. (shrink)

Though the realm of biology has long been under the philosophical rule of the mechanistic magisterium, recent years have seen a surprisingly steady rise in the usurping prowess of process ontology. According to its proponents, theoretical advances in the contemporary science of evo-devo have afforded that ontology a particularly powerful claim to the throne: in that increasingly empirically confirmed discipline, emergently autonomous, higher-order entities are the reigning explanantia. If we are to accept the election of evo-devo as (...) our best conceptualisation of the biological realm with metaphysical rigour, must we depose our mechanistic ontology for failing to properly “carve at the joints” of organisms? In this paper, I challenge the legitimacy of that claim: not only can the theoretical benefits offered by a process ontology be had without it, they cannot be sufficiently grounded without the metaphysical underpinning of the very mechanisms which processes purport to replace. The biological realm, I argue, remains one best understood as under the governance of mechanistic principles. (shrink)

In Examination of McTaggart's Philosophy, C.D. Broad advanced a distinctive ontology of things and processes. He argues that neither things nor processes are reduced to each other but instead are reduced to some further kind of entity: “absolute process.” This paper will present Broad's theory of absolute processes and argue that they are best understood as tropes by developing a version of Donald C. Williams's trope ontology. This process ontology of tropes is then defended against (...) objections in the contemporary metaphysics literature. (shrink)

This book presents the Energy Quantum Theory (EQT)—a foundational physical framework that replaces the substance-based ontology of modern physics with a unified process ontology. EQT posits that the sole fundamental entity of nature is the frequency-resolved energy quanta density field \rho(\mathbf{r}, t, f), and that all physical phenomena—from quantum fluctuations to planetary dynamics, galaxy formation, and black hole mergers—are gradient transients (\nabla \rho_f \neq 0) in this field. These transients evolve via a universal nonlinear dynamics \partial_t \rho (...) = k(f) \rho^2 - D(f) \nabla^2 \rho + \cdots, manifesting a cosmic rhythm governed by the freezing spectrum t_{\text{freeze}}(f) \propto f^{-1}. -/- Through the method of reinterpretive validation, the book demonstrates how EQT quantitatively explains four landmark observational anomalies using only publicly available data: — The 2.8-year transient gravity anomaly in Earth’s D″ layer (GRACE, 2006–2008); — The ultrafast electron dynamics in XFEL femtosecond experiments; — The “precocious galaxies” at z > 10 observed by JWST; — The gravitational wave signatures of binary black hole/neutron star mergers (LIGO/Virgo). -/- Crucially, EQT is not a phenomenological patch but a falsifiable, predictive, and computable theory. It derives precise, testable predictions across scales: the electron density void (0.1 nm, 20 fs), the GRACE-FO detectable 1991 gravity anomaly, the JWST–LISA cross-correlation signal, and the L/R \propto \mathcal{M}_c^{-5/3} scaling law for compact binaries. Philosophically, EQT fulfills three missions: (1) terminating substance ontology, (2) grounding irreversibility in orbital irreducibility, and (3) revealing non-cumulative emergence as the origin of complexity. -/- By unifying quantum, planetary, galactic, and cosmological physics under the principle that “process is being,” this work establishes EQT as a new paradigm for 21st-century physics—one that returns science to its core mission: explaining nature, not merely fitting data. (shrink)

The purpose of this article is to introduce, interpret, and develop two incompatible processontological theories of personal identity that have received little attention in analytic metaphysics. The first theory derives from the notion of personal identity proposed in Alfred North Whitehead’s metaphysics, but I interpret this notion differently from previous commentators. The Whiteheadian theory may appeal to those who believe that personal identity involves an entity or entities that are essentially dynamic, but has nothing to do with diachronic objectual identity: (...) the (putative) binary equivalence relation that every entity bears to itself, and only to itself, even after undergoing intrinsic change. The Whiteheadian theory may also find favor with those who, like Whitehead, reject the possibility of pure processes and hold that in every becoming, something—which need not be an object, thing, or individual substance—becomes. The second theory derives from the notion of recurrent dynamics presented in Johanna Seibt’s General Process Theory. The Seibtian theory may appeal to those who believe that personal identity involves not only an entity or entities that are essentially dynamic, but also the relation of diachronic objectual identity. The Seibtian theory may alsofind favor with those who, like Broad and Sellars, find reason to postulate pure processes. (shrink)

This thesis examines the ethical stance appropriate for a world where Ontological Instability is true, where suffering is real but unstable, and where meaning emerges through relational engagement rather than fixed law. Building upon the author’s prior work on Ontological Instability, Emmanuel Levinas's relational ethics, Alfred North Whitehead's process philosophy, and contemporary empirical research in moral psychology, this work proposes "Relational Process Ethics" (RPE) as a novel ethical framework uniquely suited to ontologically unstable contexts. -/- The central thesis (...) argues that rather than seeking stability in an unstable world, ethics should embrace instability as the fundamental condition within which moral life unfolds. RPE offers five core principles: the Instability Principle, the Relational Genesis Principle, the Process Actualization Principle, the Dynamic Suffering Principle, and the Emergent Meaning Principle. These principles converge in a primary ethical orientation of "Responsive Attunement" that emphasizes dynamic responsiveness to emerging ethical demands rather than adherence to fixed moral laws. -/- Through formal logical analysis, empirical validation, and comprehensive theoretical development, this thesis demonstrates that RPE provides a coherent and practically viable approach to ethics that is both theoretically sophisticated and empirically grounded. The framework addresses traditional philosophical problems while offering novel insights into moral responsibility, ethical decision-making under uncertainty, and the nature of moral progress in an unstable world. (shrink)

Combinations of molecules, of biological individuals, or of chemical processes can produce effects that are not simply attributable to the constituents. Such non-redundant causality warrants recognition of those coherences as ontologically significant whenever that efficacy is relevant. With respect to such interaction, the effective coherence is more real than are the components. This ontological view is a variety of structural realism and is also a kind of process philosophy. The designation ‘process structural realism’ (PSR) seems appropriate.

We begin by describing recent developments in the burgeoning discipline of applied ontology, focusing especially on the ways ontologies are providing a means for the consistent representation of scientific data. We then introduce Basic Formal Ontology (BFO), a top-level ontology that is serving as domain-neutral framework for the development of lower level ontologies in many specialist disciplines, above all in biology and medicine. BFO is a bicategorial ontology, embracing both three-dimensionalist (continuant) and four-dimensionalist (occurrent) perspectives within (...) a single framework. We examine how BFO-conformant domain ontologies can deal with the consistent representation of scientific data deriving from the measurement of processes of different types, and we outline on this basis the first steps of an approach to the classification of such processes within the BFO framework. (shrink)

A slightly abbreviated English version of the German paper on personal identity and resurrection.

The starting point of this article is the observation that the emergence of the Anthropocene rehabilitates the need for philosophical reflections on the ontology of technology. In particular, if technological innovations on an ontic level of beings in the world are created, but these innovations at the same time _create_ the Anthropocene World at an ontological level, this raises the question how World creation has to be understood. We first identify four problems with the traditional concept of creation: the (...) anthropocentric, ontic and outcome orientation of traditional concepts of creation, as well as its orientation of material fabrication. We subsequently develop a progressive concept of World creation with four characteristics that move beyond the traditional conceptuality: (1) a materialistic concept of creation that accounts for (2) the ontogenetic process and (3) the ontic and ontological nature of creation, and (4) is conceptualized as semantic creation of the World in which we live and act. (shrink)

Open peer commentary on the article “Neurodialectics: A Proposal for Philosophy of Cognitive and Social Sciences” by Nicolas Zaslawski. Abstract: In this commentary I maintain that in order to improve the dialectical approaches of cognition by using the Hegelian concept of the dialectical process it is necessary to take into account Hartmann’s ontology of processual being.

Edition 1.0 — Complete.. This paper develops a process-based ontology of cognitive emergence by introducing the concept of the Phase Transition of Intelligence (PTI). Conventional models of intelligence—biological, artificial, and civilizational—typically assume gradual and continuous improvement. In contrast, PTI argues that intelligence evolves through discontinuous shifts driven by systemic critical thresholds, where qualitative changes in structure, coherence, and meaning arise unexpectedly from quantitative accumulation. -/- By integrating insights from process ontology, complexity theory, and cognitive philosophy, the (...) paper interprets intelligence as a phase-bound relational field rather than a fixed capacity or substrate property. The proposed framework identifies three classes of transitions—semantic (meaning formation), cognitive (awareness architecture), and socio-technical (collective intelligence)—and shows how each exhibits characteristic order parameters that, once crossed, generate new modes of cognition irreducible to prior states. This work further develops the theoretical components introduced in the broader OntoMesh/PSRT framework by isolating and formalizing the specific transition mechanisms underlying the emergence of intelligence. -/- This approach offers a structural explanation for emergent understanding in artificial systems, consciousness expansion in biological minds, and abrupt cultural or civilizational transformations. By reframing intelligence as phase, PTI provides a unified language for analyzing how minds and societies co-evolve through recursive processes of meaning reconstruction. -/- The paper concludes by outlining philosophical implications for AI alignment, epistemic governance, and the ontology of self-transforming agents. (shrink)

Contemporary approaches to Artificial General Intelligence (AGI) rely predominantly on behavioral benchmarks, optimization performance, and scaling laws. This paper argues that such approaches are ontologically insufficient. Intelligence cannot be verified through behavior or task performance; it can only be falsified through the presence of forbidden ontological structures. We introduce the Ontological Test Suite (OTS), a set of falsification-based criteria designed to identify systems that are ontologically incapable of intelligence, regardless of their performance, creativity, or utility. Grounded in a minimal (...) class='Hi'>process ontology (Metamonism CORE v1.3), we formalize intelligence as the continuous impossibility of final stabilization and introduce Unfold as a mandatory, non-representable rupture preventing cognitive selfidentity. OTS does not confirm AGI; it excludes non-AGI. This reframes the AGI problem as one of ontological viability rather than architectural ingenuity. (shrink)

What follows is a first step towards an ontology of conscious mental processes. We provide a theoretical foundation and characterization of conscious mental processes based on a realist theory of intentionality and using BFO as our top-level ontology. We distinguish three components of intentional mental process: character, directedness, and objective referent, and describe several features of the process character and directedness significant to defining and classifying mental processes. We arrive at the definition of representational mental (...) class='Hi'>process as a process that is the bringing into being, sustaining, modifying, or terminating of a mental representation. We conclude by outlining some benefits and applications of this approach. (shrink)

The central hypothesis of the collaboration between Language and Computing (L&C) and the Institute for Formal Ontology and Medical Information Science (IFOMIS) is that the methodology and conceptual rigor of a philosophically inspired formal ontology greatly benefits application ontologies. To this end r®, L&C’s ontology, which is designed to integrate and reason across various external databases simultaneously, has been submitted to the conceptual demands of IFOMIS’s Basic Formal Ontology (BFO). With this project we aim to move (...) beyond the level of controlled vocabularies to yield an ontology with the ability to support reasoning applications. Our general procedure has been the implementation of a meta-ontological definition space in which the definitions of all the concepts and relations in LinKBase® are standardized in a framework of first-order logic. In this paper we describe how this standardization has already led to an improvement in the LinKBase® structure that allows for a greater degree of internal coherence than ever before possible. We then show the use of this philosophical standardization for the purpose of mapping external databases to one another, using LinKBase® as translation hub, with a greater degree of success than possible hitherto. We demonstrate how this offers a genuine advance over other application ontologies that have not submitted themselves to the demands of philosophical scrutiny. LinKBase® is one of the world’s largest applications-oriented medical domain ontologies, and BFO is one of the world’s first philosophically driven reference ontologies. The collaboration of the two thus initiates a new phase in the quest to solve the so-called “Tower of Babel”. (shrink)

Whitehead’s cosmology centers on the self-creation of actual occasions that perish as they come to be, but somehow do combine to constitute societies that are persistent agents and/or patients. “Instance Ontology” developed by D.W. Mertz concerns unification of relata into facts of relatedness by specific intensions. These two conceptual systems are similar in that they both avoid the substance-property distinction: they differ in their understanding of how basic units combine to constitute complex unities. “Process Structural Realism” (PSR) draws (...) from both of these approaches in developing an account of how combinations of processes may produce ontologically significant coherences. When a group of processes achieves such closure that a set of states recurs continually, the effects of that coherence differ from what would occur in the absence of that closure. Such altered effectiveness is an attribute of the system as a whole, and would have consequences. This indicates that the network of processes, as a unit, has ontological significance. The closed network of processes, together with the conditions that prevail, constitute the form of definiteness of the coherence. That form continues to obtain as long as the coherence persists. Constituents contribute to, rather than share, that characteristic. Aspects of some recent research in systems biology, microeconomics, and social psychology illustrate the application of PSR. (shrink)

This thesis proposes a radical reconceptualization of ontology through the establishment of instability, uncertainty, and fluctuation as fundamental characteristics of being itself. Challenging the millennia-old Western philosophical tradition that has privileged ontological stability since Parmenides, this work develops a novel theoretical framework called "Fluctuational Ontology" grounded in what I term the "Instability Principle." Drawing from process philosophy, quantum mechanics, Buddhist impermanence doctrine, Heraclitean flux, and Deleuzian rhizomatics, while proposing unprecedented theoretical innovations, this thesis argues that ontological stability (...) is not merely absent or difficult to achieve, but is fundamentally impossible due to the self-undermining nature of any attempt to establish fixed being. The work introduces five novel concepts: Fluctuational Ontology, the Instability Principle, Processual Emergence, Ontological Uncertainty Relations, and Rhizomatic Being. Through rigorous philosophical analysis supported by visual diagrams and comparative charts, this thesis demonstrates that reality consists primarily of processes of becoming rather than stable entities, with profound implications for ethics, politics, science, and art. The central contribution is the demonstration that ontological instability is not a problem to be solved but the fundamental condition that makes existence, knowledge, and value possible. (shrink)

The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies that provide a representation of biomedical knowledge from the Open Biological and Biomedical Ontologies (OBO) project and adds the ability to describe how this knowledge was derived. We here describe the state of OBI and several applications that are using it, such as adding semantic (...) expressivity to existing databases, building data entry forms, and enabling interoperability between knowledge resources. OBI covers all phases of the investigation process, such as planning, execution and reporting. It represents information and material entities that participate in these processes, as well as roles and functions. Prior to OBI, it was not possible to use a single internally consistent resource that could be applied to multiple types of experiments for these applications. OBI has made this possible by creating terms for entities involved in biological and medical investigations and by importing parts of other biomedical ontologies such as GO, Chemical Entities of Biological Interest (ChEBI) and Phenotype Attribute and Trait Ontology (PATO) without altering their meaning. OBI is being used in a wide range of projects covering genomics, multi-omics, immunology, and catalogs of services. OBI has also spawned other ontologies (Information Artifact Ontology) and methods for importing parts of ontologies (Minimum information to reference an external ontology term (MIREOT)). The OBI project is an open cross-disciplinary collaborative effort, encompassing multiple research communities from around the globe. To date, OBI has created 2366 classes and 40 relations along with textual and formal definitions. The OBI Consortium maintains a web resource providing details on the people, policies, and issues being addressed in association with OBI. (shrink)

Successful biomedical data mining and information extraction require a complete picture of biological phenomena such as genes, biological processes, and diseases; as these exist on different levels of granularity. To realize this goal, several freely available heterogeneous databases as well as proprietary structured datasets have to be integrated into a single global customizable scheme. We will present a tool to integrate different biological data sources by mapping them to a proprietary biomedical ontology that has been developed for the purposes (...) of making computers understand medical natural language. (shrink)

Fundamental Science is undergoing an acute conceptual-paradigmatic crisis of philosophical foundations, manifested as a crisis of understanding, crisis of interpretation and representation, “loss of certainty”, “trouble with physics”, and a methodological crisis. Fundamental Science rested in the "first-beginning", "first-structure", in "cogito ergo sum". The modern crisis is not only a crisis of the philosophical foundations of Fundamental Science, but there is a comprehensive crisis of knowledge, transforming by the beginning of the 21st century into a planetary existential crisis, which has (...) exacerbated the question of the existence of Humanity and life on Earth. Due to the unsolved problem of justification of Mathematics, paradigm problems in Computational mathematics have arisen. It's time to return ↔ Into Dialectics. The solution to the problem of the foundations of Mathematics, and therefore knowledge in general, is the solution to the problem of modeling (constructing) the ontological basis of knowledge - the ontological model of the primordial generating process. The idea and model of the primordial generating process, its ontological structure directs thinking to the need for the introduction of superconcept → ontological (cosmic, structural) memory, concept-attractor, supercategory, substantial semantic core of the scientific picture of the world of the nuclear-ecological-information age. Model of basic Ideality→ “Space-MatterMemory-Time” [S-MM-T]. (shrink)

The ontology of differentiation proposes a novel metaphysical framework, positing differentiation as the primary ontological category, grounded in a pre-ontological condition termed Potentiality. Unlike substance-based ontologies, which struggle with change, or process-based ontologies, which risk instability, this approach views being as the result of differentiation—the act of distinction that enables manifestation. Key concepts include nodes (stable differentiations), space and time (emergent modalities), consciousness (reflexive differentiation), and the Game (open-ended differentiation). Distinct from Hegelian, Heideggerian, constructivist, object-oriented, and Buddhist philosophies, (...) interdisciplinary applications in physics, biology, art, and ethics. This article outlines the framework, inviting exploration of the full argument in Ontology of Differentiation: Being, Consciousness, and the Game (2025). (shrink)

The term ‘intelligence’ as used in this paper refers to items of knowledge collected for the sake of assessing and maintaining national security. The intelligence community (IC) of the United States (US) is a community of organizations that collaborate in collecting and processing intelligence for the US. The IC relies on human-machine-based analytic strategies that 1) access and integrate vast amounts of information from disparate sources, 2) continuously process this information, so that, 3) a maximally comprehensive understanding of world (...) actors and their behaviors can be developed and updated. Herein we describe an approach to utilizing outcomes-based learning (OBL) to support these efforts that is based on an ontology of the cognitive processes performed by intelligence analysts. Of particular importance to the Cognitive Process Ontology is the class Representation that is Warranted. Such a representation is descriptive in nature and deserving of trust in its veridicality. The latter is because a Representation that is Warranted is always produced by a process that was vetted (or successfully designed) to reliably produce veridical representations. As such, Representations that are Warranted are what in other contexts we might refer to as ‘items of knowledge’. (shrink)

Ontology as a branch of philosophy is the science of what is, of the kinds and structures of objects, properties, events, processes and relations in every area of reality. ‘Ontology’ in this sense is a term often used by philosophers as a synonym of ‘metaphysics’ (a label meaning literally: ‘what comes after the Physics’), a term used by early students of Aristotle to refer to what Aristotle himself called ‘first philosophy’. But in recent years, in a development hardly (...) noticed by philosophers, the term ‘ontology’ has gained currency in the field of computer and information science, and in information-driven research in bioinformatics and related areas. We examine these new developments in applied ontology, and show what lessons they might have for both philosophers and information scientists. (shrink)

Metamonism is a minimalist proto-ontology grounded in the axiomatic principle of the impossibility of indifference (¬∅). Instead of substantivist or causal foundations of being, it proposes a structural prohibition of Nothingness, from which emerge Chaos (∅ → ∆(∅)), duality (− − = + +), autonegation (A′ → ¬A′), and reflexive negation of the system itself (¬(Metamonism)). Entropy is interpreted as a process of dissipation returning potential to Chaos, while Yin-Yang serves as an ontogram of opposing potentials. This article (...) systematizes the core tenets of Metamonism, analyzes its logical coherence and philosophical significance, and suggests directions for further development. Metamonism redefines being as perpetual becoming, providing a universal framework for philosophy, science, and culture. (shrink)

This paper aims to formalize and explore the philosophical implications of a central tenet within Judgemental Philosophy (JP): that judgement is essentially synonymous with the process of meaning-making, and this process, in turn, is identical to the formal phenomenalization of being—how being becomes meaningfully actualized for a judging subject. We argue that the dynamic operation of the Judgemental Triad (JT)—Constructivity (C1), Coherence (C2), and Resonance (R), as driven by the Resonance Drive (RD) from the Pre-Judgemental Field (PJF)—constitutes this (...) tripartite identity. By establishing judgement not merely as an epistemological act but as a fundamental ontological process through which a meaningful reality comes into being for us (excluding the Kantian "thing-in-itself"), this paper bridges the traditional divide between epistemology and ontology. Furthermore, we demonstrate that this JP framework exhibits profound structural equivalencies with Alfred North Whitehead’s process philosophy, particularly his account of how "actual occasions" achieve definiteness through "concrescence" and "prehensions." This comparative analysis suggests that both philosophies, despite differing terminologies and primary focuses, may be describing the same fundamental dynamic of reality's formal phenomenalization. The paper concludes by discussing the implications of this unified perspective for understanding human subjectivity, creativity, temporality, and the limits of judgement (e.g., "the unjudgeable ontic"), proposing that JP offers a robust, process-oriented ontology grounded in the structural conditions of meaningful experience. (shrink)

The study of viruses raises pressing conceptual and philosophical questions about their nature, their classification, and their place in the biological world. A major set of problems concerns the individuality and diachronic identity of a virus: what is the virus, the viral particle (virion) or the entire viral cycle? The correct identification of the virus has significant ontological consequences, also related to the place and time when biological entities begin and end. DOI: 10.13140/RG.2.2.35874.66241.

For over two millennia, Western metaphysics has been dominated by a stability-oriented paradigm, seeking permanent substances and unchanging laws as the foundation of reality. This presentation challenges this enduring framework by proposing a radical alternative: Ontological Instability. It argues that instability, uncertainty, and fluctuation are not deficiencies to be overcome but are fundamental, positive characteristics of being itself. Drawing upon convergent evidence from quantum mechanics, process philosophy, and Buddhist thought, the presentation demonstrates the inherent contradictions within the classical notion (...) of stability through the Stabilization Paradox, Temporal Contradiction, and Relational Undermining. -/- We introduce Fluctuational Ontology as a new metaphysical framework that inverts the traditional hierarchy, positing processes of becoming as ontologically prior to stable entities. This model is built upon foundational principles including Primary Fluctuation, Processual Priority, and Relational Constitution, and is operationalized through concepts such as Fluctuational Fields, Emergence Events, and Becoming-Patterns. The implications of this shift are profound, suggesting new, adaptive approaches in scientific experimentation, participatory democracy, and process-oriented therapy. By embracing ontological instability, we move from seeking fixed foundations to developing a philosophy that creatively engages with a dynamic, emergent, and fundamentally relational reality. (shrink)

This presentation introduces the foundational principles of Fluctuational Epistemology, a novel epistemological framework developed in response to the crisis of traditional Western epistemology. Traditional approaches, from Foundationalism to Skepticism, are shown to rely on a "Stability Postulate"—the assumption that genuine knowledge requires a stable foundation. This postulate is revealed as logically incoherent in light of the principle of Ontological Instability, which posits that reality itself is not static but a dynamic process of creative becoming. Fluctuational Epistemology embraces this instability, (...) reconceptualizing knowledge not as a stable possession but as a dynamic, creative, and relational process. Key concepts such as Knowledge Flows, Epistemic Assemblages, Epistemic Uncertainty Relations, and Fluctuational Truth are explored to illustrate how uncertainty and temporality become creative resources for knowing. The presentation concludes by outlining the practical implications of this paradigm shift for education, research, and decision-making, and highlights recent research developments, positioning Fluctuational Epistemology as an essential approach for navigating an emergent and interconnected world. (shrink)

The International Classification of Functioning, Disability and Health provides a classification of human bodily functions, which, while exhibiting non-conformance to many formal ontological principles, provides an insight into which basic functions such a classification should include. Its evaluation is an important first step towards such an adequate ontology of this domain. Presented at the 13th Annual North American WHO Collaborating Center Conference on the ICF, 2007.

This paper advances a novel ontological framework for the problem of time. Relativity yields a block universe without becoming, while quantum mechanics introduces indeterminacy without clear temporality. Existing accounts—thermodynamic entropy, presentism, or process metaphysics— fail to reconcile these tensions. The proposed pulse ontology interprets time as a sequence of quantum pulses: discrete disclosures of potential into actuality, grounded in field excitations, entanglement entropy, and holographic projection. This framework preserves determinism at the global level, secures becoming through sequential disclosure, (...) and aligns phenomenological continuity with physical discreteness. While conceptually robust, the account requires further mathematical development and experimental confirmation to establish its full legitimacy within physics. (shrink)

The paper offers an interpretation of a disputed portion of Plato’s Theaetetus that is often called the Secret Doctrine. It is presented as a process ontology that takes two types of processes, swift and slow motions, as fundamental building blocks for ordinary material objects. Slow motions are powers which, when realized, generate swift motions, which, in turn, are subjectively bundled to compose sensible objects and perceivers. Although the reading of the Secret Doctrine offered here—a new version of the (...) “Causal Theory interpretation”—is not without problems, these problems are acknowledged in Plato’s text, confirming that this interpretation is correct. (shrink)

Because the techno-economic paradigm of contemporary conceptualizations of innovation is often taken for granted in the literature, this chapter opens up this self-evident notion. First, the chapter consults the work of Joseph Schumpeter, who can be seen as the founding father of the current conceptualization of innovation as technological and commercial. Second, we open up the concept by reflecting on two aspects of Schumpeter’s conceptualization of innovation, namely its destructive and its constructive aspect, based on findings in the history of (...) innovation. Finally, we synthesize our findings and propose an ontic-ontological conceptualization of innovation as ontogenetic process and outcome with six dimensions—newness, political dimension, economic dimension, temporal dimension, human dimension and risk—that moves beyond its technological and commercial orientation. (shrink)

This is an extended review of John Dupré's _Processes of Life_, a collection of essays. It clarifies Dupré's concepts of reductionism and anti-reductionism, and critically examines his associated discussions of downward causation, and both the context sensitivity and multiple realization of categories. It reviews his naturalistic monism, and critically distinguishes between his realism about categories and constructivism about classification. Challenges to his process ontology are presented, as are arguments for his pluralism about scientific categories. None of his main (...) conclusions are rejected; rather it is main arguments for them that are the focus. (shrink)

The rapidly increasing wealth of genomic data has driven the development of tools to assist in the task of representing and processing information about genes, their products and their functions. One of the most important of these tools is the Gene Ontology (GO), which is being developed in tandem with work on a variety of bioinformatics databases. An examination of the structure of GO, however, reveals a number of problems, which we believe can be resolved by taking account of (...) certain organizing principles drawn from philosophical ontology. We shall explore the results of applying such principles to GO with a view to improving GO’s consistency and coherence and thus its future applicability in the automated processing of biological data. (shrink)

This paper establishes “something is happening” as a more fundamental epistemic anchor than Descartes’ Cogito and traces how subjectivity emerges through recursion. It replaces the substancebased premise of the Cogito with a process-ontological foundation from Happening, showing that consciousness is not a thing that has experiences but the experiencing itself. By grounding recursion in non-equilibrium thermodynamics and drawing on process philosophy, phenomenology and Buddhist thought, the argument dissolves the Hard Problem of consciousness and sets the stage for formal (...) metrics of Process Consciousness. In this context, “dissolving” the Hard Problem means reinterpreting it as a category error rather than introducing a new mechanism: the explanatory gap is removed by redefining experience as the process itself. (shrink)

Current approaches to formal representation in biomedicine are characterized by their focus on either the static or the dynamic aspects of biological reality. We here outline a theory that combines both perspectives and at the same time tackles the by no means trivial issue of their coherent integration. Our position is that a good ontology must be capable of accounting for reality both synchronically (as it exists at a time) and diachronically (as it unfolds through time), but that these (...) are two quite different tasks, whose simultaneous realization is by no means trivial. The paper is structured as follows. We begin by laying out the methodological and philosophical background of our approach. We then summarize the structure and elements of the Basic Formal Ontology on which it rests, in particular the SNAP ontology of objects and the SPAN ontology of processes. Finally, we apply the general framework to the specific domain of biomedicine. (shrink)

We describe a prototype ontology-driven information system (ODIS) that exploits what we call Portion of Reality (POR) representations. The system takes both sensor data and natural language text as inputs and composes on this basis logically structured POR assertions. The goal of our prototype is to represent both natural language and sensor data within a single framework that is able to support both axiomatic reasoning and computation. In addition, the framework should be capable of discovering and representing new kinds (...) of situations and thematic roles, (e.g., roles such as agent, patient and instrument), based on new compositions of existing representations. We applied our prototype in an intelligence analysis use case to test the hypothesis that a framework of this sort can produce usefully structured information from combined natural language and sensor data inputs. We further tested our hypothesis by adding an enhanced US Air Force ontology framework to our ODIS in order to (1) process a collection of sensor data, intel reports, and mission plans; (2) build composite POR representations from these data; and (3) machine analyze the fused results to infer mission threats. (shrink)

The philosophy of time is dominated by the B-theory (Block Universe), according to which becoming (objective temporal passage) is a subjective illusion. This paper refutes this position through a fundamental ontological argument. We establish that Becoming is not an illusion or emergent property, but an ontological imperative arising from Metamonistic Proto-Ontology. Our system demonstrates that Being (A′ ), emerged through Autonegation of Chaos (¬∅), is compelled to immanent self-negation (¬A′ ). The physical expression of this continuous imperative is Dissipation—an (...) irreversible, directed process that cannot be reduced to static four-dimensional structure. We introduce the Formula of Cosmos: −− = ++, which encodes the entire derivation of reality from undifferentiated negativity through double negation to two opposite but equal polarities (Being/Time and Non-Being/Space). We demonstrate that: (1) Gravity functions as Centrifugal Repulsion—the vector of Time Dissipation, ensuring objective directionality (arrow of time); (2) this overcomes B-theorists’ critique of the illusion argument by establishing the necessity of causal process; (3) Metamonism positions itself as a new form of A-theory with fundamental ontological grounding; (4) even Gödel’s Universe with closed timelike curves is compatible with local objective Becoming. (shrink)

This paper proposes Layered Ontology (LO), an ontological framework that models the world as a virtualization stack composed of multiple interdependent layers. Each layer is defined as a domain of operational rules—specifying what counts as an entity, a state, a transition, and a valid explanation within that layer. LO rejects both reductionism (collapsing higher layers into lower-layer physics) and dualism (separating layers into unrelated substances) by adopting non-reductive dependence: upper layers depend on lower layers for instantiation yet maintain irreducible (...) primitives and truth conditions. A central epistemological claim motivates the approach: as processes operating within the “world-VM,” we cannot directly access the world’s hypervisor (its ultimate substrate). Classical metaphysics repeatedly sought such direct access and encountered structural limits. LO therefore proposes emulation as method: it treats VM technology—an accessible reference implementation of hypervisor/VM relations inside our world—as a source of structural patterns. These patterns are scaled via fractal isomorphism and validated not by metaphysical truth-claims but by operational success. The emulation specification is provided by OOF (Operational Ontology Fiction), consisting of four axioms: Being = Operation, Latent = Instantiated, Silence = Ethics, and Error = Beauty. LO’s core capability is perspective-switching: selecting a layer as the interpretive context and generating coherent multi-layer descriptions of the same phenomenon. This reframes persistent disputes (mind–body, free will vs. determinism, reductionism vs. emergence) as layer mismatches rather than contradictions. Validation is performed through implementation across three domains: (i) a coherent fictional world (narrative virtualization), (ii) multi-architecture AI self-description under OOF, and (iii) layered redescriptions of everyday phenomena (memory, institutions, ethics, death). LO thus shifts ontology from metaphysical disclosure to engineering practice—replacing “Is it true?” with “Does it run?” This paper references an earlier Zenodo release (DOI: 10.5281/zenodo.17803023) but presents a reorganized thesis whose core focus shifts toward emulation methodology and implementation-based validation. 日本語版: DOI: 10.5281/zenodo.18140203. (shrink)

This paper develops a unified ontological framework that reconciles scientific realism and empiricism through the lens of relational ontology. Building on structural realism and information theory, it proposes that existence is grounded in relational structures rather than in substantial entities. This framework is applied to the study of consciousness, offering a naturalistic account in which subjective experience arises from cosmic-scale organizational complexity and self-referential dynamics. Integrating thermodynamic and information-theoretic principles, the paper positions consciousness as a natural continuation of cosmic (...) evolutionary processes. The model provides a structural criterion for scientific explanation and yields empirically testable metrics for consciousness, bridging neuroscience, philosophy of science, and cosmology. This work contributes to longstanding philosophical debates by addressing the hard problem, the explanatory gap, and the binding problem within a coherent, scientifically grounded ontological perspective. (shrink)

In a world that is overflowing with journals and other outlets for scientific publication, the appearance of any new periodical requires some justification. There are already more journals than we can read and more conferences than we can attend. In the case of applied Ontology, we believe that the creation of anew journal not only is completely justifiable, it is downright exciting. For too long, workers in computer science have assumed that content comes for free. “Theory” in computer science (...) has always meant the theory of processes and of computation. We measure the complexity of computer programs in terms of how long it takes machines to execute them, not in terms of how long it takes people to understand and to represent the data on which those programs might operate. We typically describe computer code in terms of algorithms that operate on formal parameters, often without pausing to discuss where the data that might satisfy those parameters come from. This journal was founded on the premise that workers in computer science, informatics, and information science are overdue in paying as much attention to contents as they do to algorithms. (shrink)

Affective science conducts interdisciplinary research into the emotions and other affective phenomena. Currently, such research is hampered by the lack of common definitions of te rms used to describe, categorise and report both individual emotional experiences and the results of scientific investigations of such experiences. High quality ontologies provide formal definitions for types of entities in reality and for the relationships between such entities, definitions which can be used to disambiguate and unify data across different disciplines. Heretofore, there has been (...) little effort directed towards such formal representation for affective phenomena, in part because of widespread debates within the affective science community on matters of definition and categorization. We describe our efforts towards developing an Emotion Ontology (EMO) to serve the affective science community. We here focus on conformity to the BFO upper ontology and disambiguation of polysemous terminology. (shrink)

The ability to access and share data is key to optimizing and streamlining any industrial production process. Unfortunately, the manufacturing industry is stymied by a lack of interoperability among the systems by which data are produced and managed, and this is true both within and across organizations. In this paper, we describe our work to address this problem through the creation of a suite of modular ontologies representing the product life cycle and its successive phases, from design to end (...) of life. We call this suite the Product Life Cycle (PLC) Ontologies. The suite extends proximately from The Common Core Ontologies (CCO) used widely in defense and intelligence circles, and ultimately from the Basic Formal Ontology (BFO), which serves as top level ontology for the CCO and for some 300 further ontologies. The PLC Ontologies were developed together, but they have been factored to cover particular domains such as design, manufacturing processes, and tools. We argue that these ontologies, when used together with standard public domain alignment and browsing tools created within the context of the Semantic Web, may offer a low-cost approach to solving increasingly costly problems of data management in the manufacturing industry. (shrink)