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)

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)

The purpose of this article is to introduce, interpret, and develop two incompatible process -ontological 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 philosophy, 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 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 also find favor with those who, like Broad and Sellars, find reason to postulate pure processes. (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)

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)

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)

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

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)

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: a materialistic concept of creation that accounts for the ontogenetic process and the ontic and ontological nature of creation, and is conceptualized as semantic creation of the World in which we live and act. (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.

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.

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)

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)

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)

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 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.

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.

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)

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)

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)

Scholars have rejected Wilfrid Sellars’ argument for an ontology of absolute processes on the grounds that it relies on a dubious and dogmatic appeal to the homogeneity of color. Borrowing from Rosenthal’s recent defense, but ultimate rejection of homogeneity, I defend this claim of on Sellarsian/Kantian transcendental grounds, and reconstruct the remainder of his argument. I argue that Sellars has good reason to suppose that homogeneity is a necessary condition of any possible experience, including indirect experience of theoretical-explanatory posits, (...) and therefore good reason to hold that Reductive Materialism, as he conceives it, is an untenable account of color. The remainder of his argument aims to answer the question of what the metaphysical relation is between the state of an experiencing subject that we take color to be and the colorless microphysical particles that we take to constitute that subject. After rejecting Substance Dualism, Epiphenomenalism, and Wholistic or Emergent Materialism as explanatorily inadequate, Sellars proposes that both color-states and micro-physical particles should be understood as manifestations of an underlying ontology on absolute processes. (shrink)

We present some ideas on logical process descriptions, using relations from the DIO (Drug Interaction Ontology) as examples and explaining how these relations can be naturally decomposed in terms of more basic structured logical process descriptions using terms from linear logic. In our view, the process descriptions are able to clarify the usual relational descriptions of DIO. In particular, we discuss the use of logical process descriptions in proving linear logical theorems. Among the types of (...) reasoning supported by DIO one can distinguish both (1) basic reasoning about general structures in reality and (2) the domain-specific reasoning of experts. We here propose a clarification of this important distinction between (realist) reasoning on the basis of an ontology and rule-based inferences on the basis of an expert’s view. (shrink)

Amid the wide variety of interpretations of quantum mechanics, the notion of a fully coherent ontological interpretation has seen a promising evolution over the last few decades. Despite this progress, however, the old dualistic categorical constraints of subjectivity and objectivity, correlate with the metrically restricted definition of local and global, have remained largely in place – a reflection of the broader, persistent inheritance of these comfortable strictures throughout the evolution of modern science. If one traces this inheritance back to its (...) ancient roots in Plato and Aristotle, it is clear that the coherence, scientific utility, and historical durability of the various natural philosophies that followed have been directly proportional to their commitment, tacit or explicit, to object-oriented realism. As Simondon might put it, it is a commitment to the primacy of individuated substance over the process of individuation. For Whitehead, it is the misplaced assimilation of becoming to being, of potentiality to actuality. Quantum mechanics has challenged this commitment with a combined breadth and depth of force that far exceeds any other theory in the history of science. The theory’s objectively demonstrable empirical application is manifest only by way of a fundamentally subjective, context-dependent mechanism of measurement. More compelling still, actual system states are always actualizations of locally contextualized yet globally conditioned potential system states, such that “globally objective” reality is no longer merely the object of local measurement, but also its product. Thus, any coherent, ontological interpretation of quantum theory must include a conceptual framework by which objectivity and subjectivity, actuality and potentiality, global and local, being and becoming, individuated fact and process of individuation, are no longer understood as merely epistemic, mutually exclusive category pairs descriptive of an already extant, closed reality – but rather as mutually implicative ontological categories explicative of an ontogenetic, open reality-in-process. (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)

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 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)

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)

Objective – is to formulate a methodological discourse regarding the place and role of the language interconnected with the process of socialization of a person and develop a systemic idea of the corresponding functional features. -/- Materials & Methods – this discourse is formulated on the basis of a systemic idea of the personality socialization, which, in turn, is realized using the structural-ontological method of studying the subject matter field in interdisciplinary researches. This method involves the construction of special (...) visual-graphic matrices that reflect the interaction of the primary process and the material of the studied system. -/- Results. The work with the structural-ontological matrix made it possible to analyze the functions of the language in the context of such significant factors of socialization as complex psychodynamics, civilization space and the function of reflection. At the same time, reflection is considered at the level of two plans – primary (reflection-bond) and secondary (reflection-splitting). This made it possible to deduce the idea of the role of language beyond the traditional framework of working with text and analyze the place of the language in the context of activities to establish a connection between individuals, which is realized in a specific cooperative situation (Shchedrovitsky). In particular, the look at language as a specific tool of civilizational rationing, the mechanism of which is provided through reflection-communication. Thus, the language is examined through the prism of its systemic influence on the morphology of the psyche. -/- Conclusions – a structural-ontological analysis of the place and role of language in the process of personality socialization has led us to construction of a hypothesis about the phenomenon of language discontentment, as a tendency to distance away ego-consciousness in the process of individuation from linguistic ontology. The arguments were also advanced in favor of the assumption regarding the peculiarities of the influence of language discontentment on cultural activities and the psychodynamic contribution of this phenomenon in the midlife crisis (Jung). (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)

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)

In this paper I argue that even the most radical metaphysics of powers (such as that adopted by Mumford & Anjum, Cartwright, or Groff) are compatible with eternalism. I first offer a taxonomy of powers ontologies, and attempt to characterise the difference between moderate and radical powers ontologies – the latter are characterised by an emphasis on production and dynamicity. I consider an argument by C. Friebe to the effect that the productive character of powers is inconsistent with Eternalism and (...) find it wanting. I then elucidate the notion of dynamicity that radical powers theorists employ by making apparent their link with an ontology of irreducible processes. Finally, I respond to an argument by Donatella Donati to the effect that eternalism entails a reductive account of change which is inconsistent with process ontologies, and show that the the two are compatible. I conclude that we have no reason to think that radical powers metaphysics (and, a fortiori, every powers ontology) are not compatible with eternalism. (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)

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)

In conceptual modeling (CM) as a subdiscipline of software engineering, current proposed ontologies (categorical analysis of entities) are typically established through whole adoption of philosophical theories (e.g. Bunge’s). In this paper, we pursue an interdisciplinary research approach to develop a diagrammatic-based ontological foundation for CM using philosophical ontology as a secondary source. It is an endeavor to escape an offshore procurement of ontology from philosophy and implant it in CM. In such an effort, the CM diagrammatic language plays (...) an important role in contrast to dogmatic philosophical languages’ obsession with abstract entities. Specifically, this paper is about developing a descriptive (in contrast to formal) ontology that a modeler accepts as a supplementary account of reality when using thinging machines (TMs; i.e. a reality that uncovers the ontology of things that TM modeling discusses or “talks about,” akin to the ontology of natural language). Although existence is a well-established notion, we defend subsistence (Stoic term) as a supplementary mode of reality (e.g. reflection of event). The aim here is aligned toward developing CM notions and processes that are firm enough. Classical analysis of being per se (e.g. identity, substance, classes, objects) is de-emphasized in this work; nevertheless, philosophical concepts form an acknowledged authority to compare to. As a case study, such a methodology is applied to the notion of information that provides a common-sense understanding of the world. This application would enhance understanding of the TM methodology and clarify some of the issues that shed light on the question of the nature of information as an important concept in software engineering. Information is defined as about events; that is, it is about existing things. It is viewed as having a subsisting nature that exists only through being “carried on” by other things. The results seem to indicate a promising approach to define information and understand its nature. (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)

In a number of papers, Kit Fine introduced a theory of embodiment which distinguishes between rigid and variable embodiments, and has been successfully applied to clarify the ontological nature of entities whose parts may or may not vary in time. In particular, he has applied this theory to describe a process such as the erosion of a cliff, which would be a variable embodiment whose manifestations are the different states of erosion of the cliff. We find this theory very (...) powerful, and especially appropriate to capture the intuition that the same process may go on at different times. However, its formal principles have been subject to some criticisms, mainly concerning the mereological structure of a variable embodiment. Moreover, since the notion of variable embodiment is very general, simply saying that processes are variable embodiments is not enough to understand their ontological nature. To address these concerns, in this paper we proceed in two phases: first, we propose a revised version of Fine’s original theory adapted to the case of processes, which adopts a classical mereology instead of Fine’s hylomorphic mereology, and a temporalized constitution relation in place of Fine’s function of variable embodiment; second, we go deeper into the ontological nature of processes by revisiting the notions of homogeneity, intentionality, and telicity discussed in the literature, and propose an account based on ontological principles and not on semantic properties of predicates. This allows us to organize processes into a novel taxonomy based exclusively on their unity and individuation principles. (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 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)

Enterprise Risk Management involves the process of identification, evaluation, treatment, and communication regarding risks throughout the enterprise. To support the tasks associated with this process, several frameworks and modeling languages have been proposed, such as the Risk and Security Overlay (RSO) of ArchiMate. An ontological investigation of this artifact would reveal its adequacy, capabilities, and limitations w.r.t. the domain of risk and security. Based on that, a language redesign can be proposed as a refinement. Such analysis and redesign (...) have been executed for the risk elements of the RSO grounded in the Common Ontology of Value and Risk. The next step along this line of research is to address the following research problems: What would be the outcome of an ontological analysis of security-related elements of the RSO? That is, can we identify other semantic deficiencies in the RSO through an ontological analysis? Once such an analysis is provided, can we redesign the security elements of the RSO accordingly, in order to produce an improved artifact? Here, with the aid of the Reference Ontology for Security Engineering (ROSE) and the ontological theory of prevention behind it, we address the remaining gap by proceeding with an ontological analysis of the security-related constructs of the RSO. The outcome of this assessment is an ontology-based redesign of the ArchiMate language regarding security modeling. In a nutshell, we report the following contributions: (1) an ontological analysis of the RSO that identifies six limitations concerning security modeling; (2) because of the key role of the notion of prevention in security modeling, the introduction of the ontological theory of prevention in ArchiMate; (3) a well-founded redesign of security elements of ArchiMate; and (4) ontology-based security modeling patterns that are logical consequences of our proposal of redesign due to its underlying ontology of security. As a form of evaluation, we show that our proposal can describe risk treatment options, according to ISO 31000. Finally, besides presenting multiple examples, we proceed with a real-world illustrative application taken from the cybersecurity domain. (shrink)

Increasingly, the high throughput technologies used by biomedical researchers are bringing about a situation in which large bodies of data are being described using controlled structured vocabularies—also known as ontologies—in order to support the integration and analysis of this data. Annotation of data by means of ontologies is already contributing in significant ways to the cumulation of scientific knowledge and, prospectively, to the applicability of cross-domain algorithmic reasoning in support of scientific advance. This very success, however, has led to a (...) proliferation of ontologies of varying scope and quality. We define one strategy for achieving quality assurance of ontologies—a plan of action already adopted by a large community of collaborating ontologists—which consists in subjecting ontologies to a process of peer review analogous to that which is applied to scientific journal articles. (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)

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)

We propose an ontological theory that is powerful enough to describe both complex spatio-temporal processes (occurrents) and the enduring entities (continuants) that participate in such processes. For this purpose we distinguish between meta-ontology and token ontologies. Token ontologies fall into two major categories: ontologies of type SPAN and ontologies of type SNAP. These represent two complementary perspectives on reality and result in distinct though compatible systems of categories. The meta-ontological level then describes the relationships between the different token ontologies. (...) In a SNAP (snapshot) ontology we have enduring entities such as substances, qualities, roles, functions as these exist to be inventoried at a given moment of time. In a SPAN ontology we have perduring entities such as processes and their parts and aggregates. We argue that both kinds of ontological theory are required, together with the metaontology which joins them together, in order to give a non-reductionistic account of both static and dynamic aspects of the geospatial world. (shrink)

Here we present what we believe is a novel account of what languages are, along with an axiomatically rich representation of languages and language-related data that is based on this account. We propose an account of languages as aggregates of dispositions distributed across aggregates of persons, and in doing so we address linguistic competences and the processes that realize them. This paves the way for representing additional types of language-related entities. Like demographic data of other sorts, data about languages may (...) be of use to researchers in a number of areas, including biomedical research. Data on the languages used in clinical encounters are typically included in medical records, and capture an important factor in patient-provider interactions. Like many types of patient and demographic data, data on a person’s preferred and primary languages are organized in different ways by different systems. This can be a barrier to data integration. We believe that a robust framework for representing language in general and preferred and primary language in particular – which has been lacking in ontologies thus far – can promote more successful integration of language-related data from disparate data sources. (shrink)

Statistics play a critical role in biological and clinical research. However, most reports of scientific results in the published literature make it difficult for the reader to reproduce the statistical analyses performed in achieving those results because they provide inadequate documentation of the statistical tests and algorithms applied. The Ontology of Biological and Clinical Statistics (OBCS) is put forward here as a step towards solving this problem. Terms in OBCS, including ‘data collection’, ‘data transformation in statistics’, ‘data visualization’, ‘statistical (...) data analysis’, and ‘drawing a conclusion based on data’, cover the major types of statistical processes used in basic biological research and clinical outcome studies. OBCS is aligned with the Basic Formal Ontology (BFO) and extends the Ontology of Biomedical Investigations (OBI), an OBO (Open Biological and Biomedical Ontologies) Foundry ontology supported by over 20 research communities. We discuss two examples illustrating how the ontology is being applied. In the first (biological) use case, we describe how OBCS was applied to represent the high throughput microarray data analysis of immunological transcriptional profiles in human subjects vaccinated with an influenza vaccine. In the second (clinical outcomes) use case, we applied OBCS to represent the processing of electronic health care data to determine the associations between hospital staffing levels and patient mortality. Our case studies were designed to show how OBCS can be used for the consistent representation of statistical analysis pipelines under two different research paradigms. By representing statistics-related terms and their relations in a rigorous fashion, OBCS facilitates standard data analysis and integration, and supports reproducible biological and clinical research. (shrink)

Monists and pluralists disagree concerning how many ordinary objects there are in a single situation. For instance, pluralists argue that a statue and the clay it is made of have different properties, and thereby are different. The standard monist’s response is to hold that there is just a single object, and that, under the description “being a statue”, this object is, e.g., aesthetically valuable, and that, under the description “being a piece of clay”, it is not aesthetically valuable. However, Fine (...) provided an ontological reading of the expression “an object under a description”: the theory of rigid embodiments. The debate between monists and pluralists reduplicates in the domain of ordinary occurrences, like walks and conferences. Specifically, they disagree whether an occurrence in progress (also called “process”) like John’s walk that is happening at tn is identical to some completed occurrence (also called “event”) like John’s walk that happened between, e.g., t1 and tn. Under the adoption of the pluralist’s position, the article aims to provide a novel theory of ordinary occurrences that develops the ontological reading of “under a description” to account for occurrences in progress and completed occurrences. As a first result, we formulate a theory according to which both occurrences in progress and completed occurrences are rigid embodiments. As a second result, we argue that the suggested theory is explanatorily powerful to the extent it solves two puzzles that we call “the Puzzle from the Completion of a Process” and “the Metaphysical-cum-Semantical Puzzle”. (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’ is often used by philosophers as a synonym for ‘metaphysics’ (literally: ‘what comes after the Physics’), a term which was used by early students of Aristotle to refer to what Aristotle himself called ‘first philosophy’. The term ‘ontology’ (or ontologia) was itself coined in 1613, independently, by two (...) philosophers, Rudolf Göckel (Goclenius), in his Lexicon philosophicum and Jacob Lorhard (Lorhardus), in his Theatrum philosophicum. The first occurrence in English recorded by the OED appears in Bailey’s dictionary of 1721, which defines ontology as ‘an Account of being in the Abstract’. (shrink)

Abstract: The following is an outline of an emerging foundation for science that begins to explain living forms and their patterns of movement beyond the sphere of mechanistic interactions. Employing an event ontology based on a convergence of quantum physics and Alfred North Whitehead’s process philosophy, coupled with the controversial yet promising theory of formative causation, this development will explore possible influences on the outcomes of events beyond any combination of external forces, laws of Nature, and chance. If (...) it turns out there are no such additional influences--beyond mechanistic causes--it is difficult to see how agency or free will could exist. Assuming agency exists, as Whitehead apparently does, while committing to an event ontology in which process is fundamental leads to interesting questions about the natures of any entities that might participate in events. Furthermore, what might the purposes and agendas of such entities be based upon, beyond memory traces or DNA code? This ontological model, recognizing processes as fundamental, leads to a revised cosmology where the trajectory of a series of events may be due to more than rearrangement of material bits according to external forces and where goal-directed, recurring processes and the emergence of mind are not so surprising. Just as special relativity reduces to classical treatment when speeds slow down, this scientific model for a living world reduces to mechanistic materialism whenever conditions are more limited. Though this development is based on a philosophy of process, there are some dissimilarities with respect to Whitehead’s particular version. (shrink)

Common sense is on the one hand a certain set of processes of natural cognition - of speaking, reasoning, seeing, and so on. On the other hand common sense is a system of beliefs (of folk physics, folk psychology and so on). Over against both of these is the world of common sense, the world of objects to which the processes of natural cognition and the corresponding belief-contents standardly relate. What are the structures of this world? How does the scientific (...) treatment of this world relate to traditional and contemporary metaphysics and formal ontology? Can we embrace a thesis of common-sense realism to the effect that the world of common sense exists uniquely? Or must we adopt instead a position of cultural relativism which would assign distinct worlds of common sense to each group and epoch? The present paper draws on recent work in computer science (especially in the fields of naive and qualitative physics), in perceptual and developmental psychology, and in cognitive anthropology, in order to consider in a new light these and related questions and to draw conclusions for the methodology and philosophical foundations of the cognitive sciences. (shrink)

The paper proposes a novel solution to the problem of the time of a killing (ToK), which persistently besets theories of act-individuation. The solution proposed claims to expose a crucial wrong-headed assumption in the debate, according to which ToK is essentially a problem of locating some event that corresponds to the killing. The alternative proposal put forward here turns on recognizing a separate category of dynamic occurents, viz. processes. The paper does not aim to mount a comprehensive defense of (...) class='Hi'>process ontology, relying instead on extant defenses. The primary aim is rather to put process ontology to work in diagnosing the current state of play over ToK, and indeed in solving it. (shrink)