Could a person ever transcend what it is like to be in the world as a human being? Could we ever know what it is like to be other creatures? Questions about the overcoming of a human perspective are not uncommon in the history of philosophy. In the last century, those very interrogatives were notably raised by American philosopher Thomas Nagel in the context of philosophy of mind. In his 1974 essay What is it Like to Be a Bat?, Nagel (...) offered reflections on human subjectivity and its constraints. Nagel’s insights were elaborated before the social diffusion of computers and could not anticipate the cultural impact of technological artefacts capable of materializing interactive simulated worlds as well as disclosing virtual alternatives to the “self.” In this sense, this article proposes an understanding of computers as epistemological and ontological instruments. The embracing of a phenomenological standpoint entails that philosophical issues are engaged and understood from a fundamentally practical perspective. In terms of philosophical praxis, or “applied philosophy,” I explored the relationship between human phenomenologies and digital mediation through the design and the development of experimental video games. For instance, I have conceptualized the first-person action-adventure video game Haerfest (Technically Finished 2009) as a digital re-formulation of the questions posed in Nagel’s famous essay. Experiencing a bat’s perceptual equipment in Haerfest practically corroborates Nagel’s conclusions: there is no way for humans to map, reproduce, or even experience the consciousness of an actual bat. Although unverifiable in its correspondence to that of bats, Haerfest still grants access to experiences and perceptions that, albeit still inescapably within the boundaries of human kinds of phenomenologies, were inaccessible to humans prior to the advent of computers. Phenomenological alterations and virtual experiences disclosed by interactive digital media cannot take place without a shift in human kinds of ontologies, a shift which this study recognizes as the fundamental ground for the development of a new humanism (I deem it necessary to specify that I am not utilizing the term “humanism” in its common connotation, that is to say the one that emerged from the encounter between the Roman civilization and the late Hellenistic culture. According to this conventional acceptation, humanism indicates the realization of the human essence through “scholarship and training in good conduct” (Heidegger 1998, p. 244). However, Heidegger observed that this understanding of humanism does not truly cater to the original essence of human beings, but rather “is determined with regard to an already established interpretation of nature, history, world, and […] beings as a whole.” (Heidegger 1998, p. 245) The German thinker found this way of embracing humanism reductive: a by-product of Western metaphysics. As Heidegger himself specified in his 1949 essay Letter on Humanism, his opposition to the traditional acceptation of the term humanism does not advocate for the “inhuman” or a return to the “barbaric” but stems instead from the belief that the humanism can only be properly understood and restored in culture as more original way of meditating and caring for humanity and understanding its relationship with Being.). Additionally, this study explicitly proposes and exemplifies the use of interactive digital technology as a medium for testing, developing and disseminating philosophical notions, problems and hypotheses in ways which are alternative to the traditional textual one. Presented as virtual experiences, philosophical concepts can be accessed without the filter of subjective imagination. In a persistent, interactive, simulated environment, I claim that the crafting and the mediation of thought takes a novel, projective (In Martin Heidegger’s 1927 Being and Time, the term “projectivity” indicates the way a Being opens to the world in terms of its possibilities of being (Heidegger 1962, pp. 184–185, BT 145). Inspired by Heidegger’s and Vilem Flusser’s work in the field of philosophy of technology as well as Helmuth Plessner’s anthropological position presented in his 1928 book Die Stufen des Organischen und der Mensch. Einleitung in die philosophische Anthropologie, this study understands the concept of projectivity as the innate openness of human beings to construct themselves and their world by means of technical artefacts. In this sense, this study proposes a fundamental understanding of technology as the materialization of mankind’s tendency to overcome its physical, perceptual and communicative limitations.) dimension which I propose to call “augmented ontology.”. (shrink)

The Plant Ontology (PO) is a community resource consisting of standardized terms, definitions, and logical relations describing plant structures and development stages, augmented by a large database of annotations from genomic and phenomic studies. This paper describes the structure of the ontology and the design principles we used in constructing PO terms for plant development stages. It also provides details of the methodology and rationale behind our revision and expansion of the PO to cover development stages for (...) all plants, particularly the land plants (bryophytes through angiosperms). As a case study to illustrate the general approach, we examine variation in gene expression across embryo development stages in Arabidopsis and maize, demonstrating how the PO can be used to compare patterns of expression across stages and in developmentally different species. Although many genes appear to be active throughout embryo development, we identified a small set of uniquely expressed genes for each stage of embryo development and also between the two species. Evaluating the different sets of genes expressed during embryo development in Arabidopsis or maize may inform future studies of the divergent developmental pathways observed in monocotyledonous versus dicotyledonous species. The PO and its annotation databasemake plant data for any species more discoverable and accessible through common formats, thus providing support for applications in plant pathology, image analysis, and comparative development and evolution. (shrink)

The view of nature we adopt in the natural attitude is determined by common sense, without which we could not survive. Classical physics is modelled on this common-sense view of nature, and uses mathematics to formalise our natural understanding of the causes and effects we observe in time and space when we select subsystems of nature for modelling. But in modern physics, we do not go beyond the realm of common sense by augmenting our knowledge of what is going on (...) in nature. Rather, we have measurements that we do not understand, so we know nothing about the ontology of what we measure. We help ourselves by using entities from mathematics, which we fully understand ontologically. But we have no ontology of the reality of modern physics; we have only what we can assert mathematically. In this paper, we describe the ontology of classical and modern physics against this background and show how it relates to the ontology of common sense and of mathematics. (shrink)

The study of the ontology of virtual actions is essentially an examination of the nature of actions in virtual environments directly. This article first examined traditional research on the subject and then showed that these researches ignored findings about the nature of virtual actions. Previous studies have dealt with virtual action mostly from an ethical, psychological, or legal framework and focused on the individual or social effects of virtual action. In addition, these studies discuss not the virtual action itself, (...) but its effect or consequences. Based on these findings, in this study, it was emphasized that a virtual action should be investigated through two different types at a minimum, and an alternative method was developed for studies on virtual actions. According to this method, which is called the Sophisticated Action Model, it has been argued that in virtual action research, firstly the subject performing the action and then the environment in which the action takes place should be analyzed. It is claimed that the difference of virtual subject and environment will also differentiate the ontology of virtual action. In this context, the focus of the article is on the fact that an action augmented by any virtual action has completely different ontologies. The status of augmented actions within virtual actions is considered superior to other virtual actions. The fact that augmented actions, which have such an important status among virtual actions, were ignored in previous studies makes these studies on virtual actions incomplete and flawed. The nature of augmented actions takes virtual actions to a completely different atmosphere. The article concludes by emphasizing this distinctive nature of augmented actions, the ontological separation of virtual actions, and the importance of the Sophisticated Action Model for further studies. (shrink)

As is well known, speech acts such as acts of promising can have ontological consequences. For example an act of promising can give rise to a mutually correlated claim and obligation. Increasingly, speech acts in the narrow sense are being augmented by the use of documents of multiple different sorts. In this paper we analyze the results of this augmenta-tion from the ontological point of view, considering especially the domains of law and com-merce. We show how document acts are (...) not isolated phenomena, but rather form large and complex systems with other entities, including occurrent entities such as acts of signing and inspecting, as well as speech acts for example of instructing people to sign or complete a doc-ument. The paper concludes with a consideration of some of the special problems associated with the use of digital documents, for example as concerns issues of security and provenance. (shrink)

The COVID-19 pandemic has made relevant questions regarding the limits and the justifications of sovereign power as nation states utilize high degrees of power over populations in their strategies of countering the virus. In our article, we analyze a particularly important facet of the strategy of sovereignty in managing the affects caused by a pandemic, which we term the ontology of war. We analyze the way in which war plays a significant role in the political ontology of our (...) societies, through its aiming to produce a unified political subject and an external enemy. Taking our theoretical cue from Butler’s thinking on frames of recognizability we extend her theory through augmenting it with affect theory to argue for how the frame of recognizability produced by the ontology of war fails to guide our understanding of the pandemic as a political problem, a failure that we analyze through looking at the affective register. We argue that the main affect that the nation state tries to manage, in relation to the pandemic, through the ontology of war is anxiety. We show that the nation state tries to alleviate anxiety by framing it through the ontology war, this leads to the appearance of a potentially racist and nationalist affective climate where the “enemy” is no longer felt to be the virus, but members of other nations as well as minorities. We argue that the pandemic reveals both the political ontology of war central to the foundation of our political communities, and how this ontology is used by the nation state to manage feelings of anxiety and insecurity. Ultimately, as we will discuss at the end of this article, this leads to failure. (shrink)

As engineering applications require management of ever larger volumes of data, ontologies offer the potential to capture, manage, and augment data with the capability for automated reasoning and semantic querying. Unfortunately, considerable barriers hinder wider deployment of ontologies in engineering. Key among these is lack of a shared top-level ontology to unify and organise disparate aspects of the field and coordinate co-development of orthogonal ontologies. As a result, many engineering ontologies are limited to their scope, and functionally difficult to (...) extend or interoperate with other engineering ontologies. This paper demonstrates how the use of a top-level ontology, specifically the Basic Formal Ontology (BFO), greatly facilitates interoperability of multiple engineering-related ontologies. We constructed a system of formal linked ontologies by re-engineering legacy ontologies to be conformant with BFO and developing new BFO-conformant ontologies to capture knowledge in the engineering design, enterprise, human factors, manufacturing, and application domain of additive manufacturing. The resulting Integrated Framework for Additively Manufactured Products (IFAMP), including the body knowledge instantiated on its basis, serve as the basis for a proposed Design with Additive Manufacturing Method (DWAM), which we believe can support the design of innovative products with semantically enhanced ideation tools and enhanced access to application domain knowledge. The method and its facilitation through the ontological framework are demonstrated using a case study in medicine. (shrink)

For many employees, ‘work’ is no longer something performed while sitting at a computer in an office. Employees in a growing number of industries are expected to carry mobile devices and be available for work-related interactions even when beyond the workplace and outside of normal business hours. In this article it is argued that a future step will increasingly be to move work-related information and communication technology (ICT) inside the human body through the use of neuroprosthetics, to create employees who (...) are always ‘online’ and connected to their workplace’s digital ecosystems. At present, neural implants are used primarily to restore abilities lost through injury or illness, however their use for augmentative purposes is expected to grow, resulting in populations of human beings who possess technologically altered capacities for perception, memory, imagination, and the manipulation of physical environments and virtual cyberspace. Such workers may exchange thoughts and share knowledge within posthuman cybernetic networks that are inaccessible to unaugmented human beings. Scholars note that despite their potential benefits, such neuroprosthetic devices may create numerous problems for their users, including a sense of alienation, the threat of computer viruses and hacking, financial burdens, and legal questions surrounding ownership of intellectual property produced while using such implants. Moreover, different populations of human beings may eventually come to occupy irreconcilable digital ecosystems as some persons embrace neuroprosthetic technology, others feel coerced into augmenting their brains to compete within the economy, others might reject such technology, and still others will simply be unable to afford it. In this text we propose a model for analyzing how particular neuroprosthetic devices will either facilitate human beings’ participation in new forms of socioeconomic interaction and digital workplace ecosystems – or undermine their mental and physical health, privacy, autonomy, and authenticity. We then show how such a model can be used to create device ontologies and typologies that help us classify and understand different kinds of advanced neuroprosthetic devices according to the impact that they will have on individual human beings. (shrink)

This is an updated and expanded version of my book “Our Incorrigible Ontological Relations and Categories of Being”, originally published in 2017. The subject matter of this version includes other innate a priori constituents of knowledge. Among the main conclusions arrived is that reality is para-rational in nature. The work can thus be said to be about the role in cognition of innate information of the sensorial and of the structure of the non-sensorial rational aspect of a para-rational reality. This (...) augmented version preserves the previous content of the former book, but also addresses the innate a priori forms with which the intellect responds to sensorial activation and represents to itself the sensorily given -that is, what acts in our senses- and the forms with which it represents or makes patent to itself the things in the world which do not act on our sensory organs, such as the feeling brought forth by beauty or the emotion of the sublime in mystical experiences, and how these too, constitute a limit to possible knowledge. As the former version it refers to the innate a priori information about reality in itself, with which the intellect makes possible its cognition, yet also constrains our possible knowledge of what there is to the rational aspect of what exists. As shown in this work, the information they provide, no matter the extent of empirical data, does not suffice to explain reality, which makes necessary to presuppose the existence of, either a higher order of reality beyond the rational cognitive reach, or that the nature of what is judged rational reality be a mere aspect of what there is. In other words, that mankind is doomed to have a mere glimpse of what exists and its nature, and totally unable to attain an ultimate explanation of reality. August 16, 2023 . (shrink)

This paper introduces the concept of Adaptive Rooms, which are virtual environments able to dynamically adapt to users’ needs, including ‘physical’ and cognitive workflow requirements, number of users, differing cognitive abilities and skills. Adaptive rooms are collections of virtual objects, many of them self-transforming objects, housed in an architecturally active room with information spaces and tools. An ontology of objects used in adap- tive rooms is presented. Virtual entities are classified as passive, reactive, ac- tive, and information entities, and (...) their sub-categories. Only active objects can be self-transforming. Adaptive Rooms are meant to combine the insights of ubiquitous computing -- that computerization should be everywhere, transpar- ently incorporated -- with the insights of augmented reality -- that everyday ob- jects can be digitally enhanced to carry more information about their use. To display the special potential of adaptive rooms, concrete examples are given to show how the demands of cognitive workflow can be reduced. (shrink)

In their recent paper Bi-facial truth: a case for generalized truth values Zaitsev and Shramko [7] distinguish between an ontological and an epistemic interpretation of classical truth values. By taking the Cartesian product of the two disjoint sets of values thus obtained, they arrive at four generalized truth values and consider two “semi-classical negations” on them. The resulting semantics is used to define three novel logics which are closely related to Belnap’s well-known four valued logic. A syntactic characterization of these (...) logics is left for further work. In this paper, based on our previous work on a functionally complete extension of Belnap’s logic, we present a sound and complete tableau calculus for these logics. It crucially exploits the Cartesian nature of the four values, which is reflected in the fact that each proof consists of two tableaux. The bi-facial notion of truth of Z&S is thus augmented with a bi-facial notion of proof. We also provide translations between the logics for semi-classical negation and classical logic and show that an argument is valid in a logic for semi-classical negation just in case its translation is valid in classical logic. (shrink)

This paper takes as its point of departure recent research into the possibility that human beings can perceive single photons. In order to appreciate what quantum perception may entail, we first explore several of the leading interpretations of quantum mechanics, then consider an alternative view based on the ontological phenomenology of Maurice Merleau-Ponty and Martin Heidegger. Next, the philosophical analysis is brought into sharper focus by employing a perceptual model, the Necker cube, augmented by the topology of the Klein (...) bottle. This paves the way for addressing in greater depth the paper’s central question: Just what would it take to observe the quantum reality of the photon? In formulating an answer, we examine the nature of scientific objectivity itself, along with the paradoxical properties of light. The conclusion reached is that quantum perception requires a new kind of observation, one in which the observer of the photon adopts a concretely self-reflexive observational posture that brings her into close ontological relationship with the observed. (shrink)

This essay examines how Husserl stretches the bounds of his philosophy of meaning, according to which all propositions are categorical, to account for existential propositions, which seem to lack predicates. I examine Husserl’s counterintuitive conclusion that an existential proposition does possess a predicate and I explore his endeavor to pinpoint what that predicate is. This goal is accomplished in three stages. First, I examine Husserl’s standard theory of predication and categorial intuition from his 1901 Logical Investigations. Second, I show how (...) Husserl imposes those 1901 insights to uncover the predicate of the existential proposition in unpublished manuscripts and lectures. He determines that the existential proposition predicates of the subject, that it corresponds to an actual object. This analysis reveals that Husserl’s descriptions of existential propositions from the late 1890s employed both static and genetic methodologies. In those texts, he carefully untangles and clarifies the co-enmeshed passive and active moments of consciousness and shows that the passive givenness of certain circumstances is the condition of possibility for our active verifying of propositions. Finally, I execute a critical assessment of Husserl’s thought to reveal that, while his insights about existential propositions are largely correct, they are augmented by re-construing them within the context of his mature philosophy. Only by renouncing his metaphysical neutrality and by accounting for intersubjectivity, can Husserl properly clarify existential propositions. (shrink)

C.H. Waddington’s concepts of ‘chreods’ (canalized paths of development) and ‘homeorhesis’ (the tendency to return to a path), each associated with ‘morphogenetic fields’, were conceived by him as a contribution to complexity theory. Subsequent developments in complexity theory have largely ignored Waddington’s work and efforts to advance it. Waddington explained the development of the concept of chreod as the influence on his work of Alfred North Whitehead’s process philosophy, notably, the concept of concrescence as a self-causing process. Processes were recognized (...) as having their own dynamics, rather than being explicable through their components or external agents. Whitehead recognized the tendency to think only in terms of such ‘substances’ as a bias of European thought, claiming in his own philosophy ‘to approximate more to some strains of Indian, or Chinese, thought, than to western Asiatic, or European, thought.’ Significantly, the theoretical biologist who comes closest to advancing Waddington’s research program, also marginalized, is Mae-Wan Ho. Noting this bias, and embracing Whitehead’s and Waddington’s efforts to free biology from assumptions dominating Western thought to advance an ontology of creative causal processes, I will show how later developments of complexity theory, most importantly, Goodwin’s work on oscillations, temporality and morphogenesis, Vitiello’s dissipative quantum brain dynamics, Salthe’s work on hierarchy theory, biosemiotics inspired by Peirce and von Uexküll, Robert Rosen’s work on anticipatory systems, together with category theory and biomathics, can augment while being augmented by Waddington’s work, while further advancing Mae-Wan Ho’s radical research program with its quest to understand the reality of consciousness. (shrink)

This paper aims to demonstrate that the ontology of consciousness is consistent with both the modal and the metaphysical versions of Haecceitism. I examine the varieties of Haecceitism, and I specify the intended versions that the arguments will vindicate. I define the property of 'being purely qualitative', and examine its relation to the properties of phenomenal consciousness. I draw, inter alia, on Bayesian perceptual psychology, in order to specify the identity-conditions of phenomenal properties in detail. I provide two, abductive (...) arguments for the claim that the identity-conditions on some individuals are metaphysically haecceitistic, in virtue of the relations that hold between those individuals and the phenomenal properties that they instantiate. The first argument is corroborated by empirical results concerning the phenomenological effects of attention. The second argument is corroborated by empirical results from the study of color in vision science. The arguments vindicate a version of Metaphysical Haecceitism, because the individuals are shown to be typed by the phenomenal properties that they instantiate, although quantification over the individuals is an ineliminable condition on their identity and distinctness. I provide, then, a regimentation of the extant proposals in the ontology of consciousness, using the logic of hyperintensional ground, as augmented by the Bayesian probability calculus. The hyperintensional regimentation vindicates a version of Modal Haecceitism, because the probabilistic ontological dependence of the parts of worlds on other parts thereof provides an ineliminable condition on the identity and distinctness of worlds. (shrink)

Aims: The Research Diagnostic Criteria for Temporomandi¬bular Disorders (RDC/TMD) Axis I diagnostic algorithms were demonstrated to be reliable but below target sensitivity and specificity. Empirical data supported Axis I algorithm revisions that were valid. Axis II instruments were shown to be both reliable and valid. An international consensus workshop was convened to obtain recommendations and finalization of new Axis I diagnostic algorithms and new Axis II instruments. Methods: A comprehensive search of published TMD diagnostic literature was followed by review and (...) consensus via a formal structured process by a panel of experts for revision of the RDC/TMD. Results: The recommended Diagnostic Criteria for TMD (DC/TMD) Axis I protocol includes both a valid screener for pain diagnoses and valid criteria for the most common pain-related TMDs and for one intra-articular disorder. The Axis II protocol retains selected RDC/TMD screening instruments augmented with new instruments to better assess the interactions between pain and psychosocial functioning. A comprehensive classification system is also presented. Conclusion: The recommended evidence-based DC/TMD protocol is appropriate for use in both the clinical and research settings. Simple Axis I and II screening tests augmented by validated Axis I and Axis II instruments allow for identification of simple to complex TMD patients. (shrink)

Defining Artificial Intelligence and Artificial General Intelligence remain controversial and disputed. They stem from a longer-standing controversy of what is the definition of consciousness, which if solved could possibly offer a solution to defining AI and AGI. Central to these problems is the paradox that appraising AI and Consciousness requires epistemological objectivity of domains that are ontologically subjective. I propose that applying the philosophy of art, which also aims to define art through a lens of epistemological objectivity where the domains (...) are ontologically subjective, can further elucidate this unsolved question. In this sense, Art and AI and ultimately consciousness are multifaceted domains where conventional complexity theory and current philosophical approaches may be augmented by aesthetic principles ranging from classical Aristotelian essentialism to Wittgensteinian anti-essentialism. This approach of AI as art may offer novel solutions to characterising and elucidating the ciphers of consciousness and AI. (shrink)

Following an analysis of the state of investigations and clinical outcomes in the Alzheimer's research field, I argue that the widely-accepted 'amyloid cascade' mechanistic explanation of Alzheimer's disease appears to be fundamentally incomplete. In this context, I propose that a framework termed 'principled mechanism' (PM) can help with remedying this problem. First, using a series of five 'tests', PM systematically compares different components of a given mechanistic explanation against a paradigmatic set of criteria, and hints at various ways of making (...) the mechanistic explanation more 'complete'. These steps will be demonstrated using the amyloid explanation, and its missing or problematic mechanistic elements will be highlighted. Second, PM makes an appeal for the discovery and application of 'biological principles' (BPs), which approximate ceteris paribus laws and are operative at the level of a biological cell. As such, although thermodynamic, evolutionary, ecological and other laws or principles from chemistry and the broader life sciences could inform them, BPs should be considered ontologically unique. BPs could augment different facets of the mechanistic explanation but also allow further independent nomological explanation of the phenomenon. Whilst this overall strategy can be complementary to certain 'New Mechanist' approaches, an important distinction of the PM framework is its equal attention to the explanatory utility of biological principles. Lastly, I detail two hypothetical BPs, and show how they could each inform and improve the potentially incomplete mechanistic aspects of the amyloid explanation and also how they could provide independent explanations of the cellular features associated with Alzheimer's disease. (shrink)

This is the formal YACC BNF specification for Minimal Type Theory (MTT). MTT was created by augmenting the syntax of First Order Logic (FOL) to specify Higher Order Logic (HOL) expressions using FOL syntax. Syntax is provided to enable quantifiers to specify type. FOL is a subset of MTT. The ASSIGN_ALIAS operator := enables FOL expressions to be chained together to form HOL expressions.

Augmented reality (AR) technologies function to ‘augment’ normal perception by superimposing virtual objects onto an agent’s visual field. The philosophy of augmented reality is a small but growing subfield within the philosophy of technology. Existing work in this subfield includes research on the phenomenology of augmented experiences, the metaphysics of virtual objects, and different ethical issues associated with AR systems, including (but not limited to) issues of privacy, property rights, ownership, trust, and informed consent. This paper addresses (...) some epistemological issues posed by AR systems. I focus on a near-future version of AR technology called the Real-World Web, which promises to radically transform the nature of our relationship to digital information by mixing the virtual with the physical. I argue that the Real-World Web (RWW) threatens to exacerbate three existing epistemic problems in the digital age: the problem of digital distraction, the problem of digital deception, and the problem of digital divergence. The RWW is poised to present new versions of these problems in the form of what I call the augmented attention economy, augmented skepticism, and the problem of other augmented minds. The paper draws on a range of empirical research on AR and offers a phenomenological analysis of virtual objects as perceptual affordances to help ground and guide the speculative nature of the discussion. It also considers a few policy-based and designed-based proposals to mitigate the epistemic threats posed by AR technology. (shrink)

In this paper I examine Grace A. de Laguna’s theory of universals in its historical context and in relation to contemporary debates in analytic metaphysics. I explain the central features of her theory, arguing that her theory should be classified as a form of immanent realism and as a powers ontology. I then show in what ways her theory affords a theory of modality in terms of potentialities and discuss some of its consequences along the way.

John Bell proposed an ontology for the GRW modification of quantum mechanics in terms of flashes occurring at space- time points. This article spells out the motivation for this ontology, inquires into the status of the wave function in it, critically examines the claim of its being Lorentz invariant, and considers whether it is a parsimonious but nevertheless physically adequate ontology.

This paper elaborates on relationalism about space and time as motivated by a minimalist ontology of the physical world: there are only matter points that are individuated by the distance relations among them, with these relations changing. We assess two strategies to combine this ontology with physics, using classical mechanics as example: the Humean strategy adopts the standard, non-relationalist physical theories as they stand and interprets their formal apparatus as the means of bookkeeping of the change of the (...) distance relations instead of committing us to additional elements of the ontology. The alternative theory strategy seeks to combine the relationalist ontology with a relationalist physical theory that reproduces the predictions of the standard theory in the domain where these are empirically tested. We show that, as things stand, this strategy cannot be accomplished without compromising a minimalist relationalist ontology. (shrink)

The emerging field of synthetic biology aims to engineer novel biological entities. The envisioned future bio-based economy builds largely on “cell factories”: organisms that have been metabolically engineered to sustainably produce substances for human ends. In this paper, we argue that synthetic biology’s goal of creating efficient production vessels for industrial applications implies a set of ontological assumptions according to which living organisms are machines. Traditionally, a machine is understood as a technological, isolated and controllable production unit consisting of parts. (...) But modified organisms, or hybrids, require us to think beyond the machine paradigm and its associated dichotomies between artificial and natural, organisms and artefacts. We ask: How may we conceptualise hybrids beyond limiting ontological categories? Our main claim is that the hybrids created by synthetic biology should be considered not as machines but as metabolic systems. We shall show how the philosophical account of metabolism can inform an ontology of hybrids that moves beyond what we call the “machine ontology”, considering that metabolism enables thinking beyond the dominant dichotomies and allows us to understand and design lifeforms in a bio-based economy. Thus, the aim of this paper is twofold: first, to develop the philosophical ontology of hybrids, and second, to move synthetic biology beyond the problematically limiting view of hybrids. (shrink)

In this article, the results of conceptualization of the definition of mind as an object of interdisciplinary applied research are described. The purpose of the theoretical analysis is to generate a methodological discourse suitable for a functional understanding of the mind in the context of the problem of natural language processing as one of the components of developments in the field of artificial intelligence. The conceptual discourse was realized with the help of the author's method of structural-ontological analysis, and developed (...) in the mainstream of the system-methodological tradition of the school of G.P. Shchedrovitsky and intended for descriptive research of subject areas of interdisciplinary objects of scientific study. As a result of the structural and ontological analysis of the super-system, the relevant place and role of the directly studied system (mind) are determined, and its primary process and material are localized and structural and functional connections are described. At the basic level, the mind is conceptualized as an energy process unfolding in a spatio-temporal environment and accompanied by archetypal structuring of neural impulses into images. The genesis of the system is separately analyzed by constructing a structural-ontological matrix that reflects the initial stage of the development of the mind. The primary process is concretized with the help of hetero- and homeostatic dichotomy, and also the most significant features of the consistent transformation of the material of the system and its ascent to verbal morphology are described. The structural-ontological comparison of the functioning of the verbal intelligence with the preverbal level has been carried out. The transformation of neural impulses of needs into words, as verbal units fixing semiotic values is analyzed. Structural-ontological connections that determine the reactive and prospective characteristics of the functioning of the system are disclosed. The position of the chronological primacy of "semiotic readiness" for language with respect to the debut of the latter as an information-sign model of the environment is argued. The hypothesis of domination at the initial stage of the development of the mind of exopsychic functions over endopsychic ones is formulated. The theoretical substantiation of the hypothesis of the inevitability of the ontology of language in the functional understanding of the mind is given, corresponding structural and ontological arguments are given, including those based on the ideas about the information relationship between affects and needs, according to the views of P.V. Simonov. The arguments are presented in favor of the non-alternative methodology of A. Turing in studies of artificial intelligence. (shrink)

Nihilism is the thesis that no composite objects exist. Some ontologists have advocated abandoning nihilism in favor of deep nihilism, the thesis that composites do not existO, where to existO is to be in the domain of the most fundamental quantifier. By shifting from an existential to an existentialO thesis, the deep nihilist seems to secure all the benefits of a composite-free ontology without running afoul of ordinary belief in the existence of composites. I argue that, while there are (...) well-known reasons for accepting nihilism, there appears to be no reason at all to accept deep nihilism. In particular, deep nihilism draws no support either from the usual arguments for nihilism or from considerations of parsimony. (shrink)

This paper examines the need for static dispositions within the basic ontology of the powers view of properties. To lend some focus, Neil Williams’s well developed case for static dispositions is considered. While his arguments are not necessarily intended to address fundamental ontology, they still provide a useful starting point, a springboard for diving into the deeper metaphysical waters of the dispositionalist approach. Within that ontological context, this paper contends that Williams’s arguments fail to establish the need to (...) posit static dispositions, or at least any sort not already well appreciated by advocates of the powers view. The paper then proceeds to suggest an alternative motivation for positing static dispositions, the success of which depends greatly on which ontological approach to objects is paired with the powers view. (shrink)

For much of the first fifty years of its existence, analytic philosophy shunned discussions of normativity and ethics. Ethical statements were considered as pseudo-propositions, or as expressions of pro- or con-attitudes of minor theoretical significance. Nowadays, in contrast, prominent analytic philosophers pay close attention to normative problems. Here we focus our attention on the work of Searle, at the same time drawing out an important connection between Searle’s work and that of two other seminal figures in this development: H.L.A. Hart (...) and John Rawls. We show that all three thinkers tend to assume that there is but one type of normativity within the realm of social institutions – roughly, the sort of normativity that is involved in following the results of chess – and that they thereby neglect features that are of crucial significance for an adequate understanding of social reality. (shrink)

The automatic integration of information resources in the life sciences is one of the most challenging goals facing biomedical informatics today. Controlled vocabularies have played an important role in realizing this goal, by making it possible to draw together information from heterogeneous sources secure in the knowledge that the same terms will also represent the same entities on all occasions of use. One of the most impressive achievements in this regard is the Gene Ontology (GO), which is rapidly acquiring (...) the status of a de facto standard in the field of gene and gene product annotations, and whose methodology has been much intimated in attempts to develop controlled vocabularies for shared use in different domains of biology. The GO Consortium has recognized, however, that its controlled vocabulary as currently constituted is marked by several problematic features - features which are characteristic of much recent work in bioinformatics and which are destined to raise increasingly serious obstacles to the automatic integration of biomedical information in the future. Here, we survey some of these problematic features, focusing especially on issues of compositionality and syntactic regimentation. (shrink)

This paper investigates the connection between temporal attitudes (attitudes characterised by a concern (or lack thereof) about future and past events), beliefs about temporal ontology (beliefs about the existence of future and past events) and temporal preferences (preferences regarding where in time events are located). Our aim is to probe the connection between these preferences, attitudes, and beliefs, in order to better evaluate the normative status of these preferences. We investigate the hypothesis that there is a three-way association between (...) (a) being present-biased (that is, preferring that positive events are located in the present, and negative events are located in the non-present), (b) believing that past and future events do not exist and (c) tending to have present-focused rather than non-present-focused temporal attitudes. We find no such association. This suggests that insofar as temporal preferences and temporal attitudes are connected to the ways we represent time, they are not connected to the ways we represent temporal ontology; rather, they are more likely connected to the ways we represent relative movement in, or of, time. This has important consequences for, first, explaining why we exhibit these preferences and, second, for their normative evaluation. (shrink)

Monoclonal antibodies are essential biomedical research and clinical reagents that are produced by companies and research laboratories. The NIAID ImmPort (Immunology Database and Analysis Portal) resource provides a long-term, sustainable data warehouse for immunological data generated by NIAID, DAIT and DMID funded investigators for data archiving and re-use. A variety of immunological data is generated using techniques that rely upon monoclonal antibody reagents, including flow cytometry, immunofluorescence, and ELISA. In order to facilitate querying, integration, and reuse of data, standardized terminology (...) for describing monoclonal antibody reagents and their targets needs to be used for annotating data submitted to ImmPort. (shrink)

The COVID-19 pandemic prompted immense work on the investigation of the SARS-CoV-2 virus. Rapid, accurate, and consistent interpretation of generated data is thereby of fundamental concern. Ontologies––structured, controlled, vocabularies––are designed to support consistency of interpretation, and thereby to prevent the development of data silos. This paper describes how ontologies are serving this purpose in the COVID-19 research domain, by following principles of the Open Biological and Biomedical Ontology (OBO) Foundry and by reusing existing ontologies such as the Infectious Disease (...) Ontology (IDO) Core, which provides terminological content common to investigations of all infectious diseases. We report here on the development of an IDO extension, the Virus Infectious Disease Ontology (VIDO), a reference ontology covering viral infectious diseases. We motivate term and definition choices, showcase reuse of terms from existing OBO ontologies, illustrate how ontological decisions were motivated by relevant life science research, and connect VIDO to the Coronavirus Infectious Disease Ontology (CIDO). We next use terms from these ontologies to annotate selections from life science research on SARS-CoV-2, highlighting how ontologies employing a common upper-level vocabulary may be seamlessly interwoven. Finally, we outline future work, including bacteria and fungus infectious disease reference ontologies currently under development, then cite uses of VIDO and CIDO in host-pathogen data analytics, electronic health record annotation, and ontology conflict-resolution projects. (shrink)

The essay constructs an ontological theory designed to capture the categories instantiated in those portions or levels of reality which are captured in our common sense conceptual scheme. It takes as its starting point an Aristotelian ontology of “substances” and “accidents”, which are treated via the instruments of mereology and topology. The theory recognizes not only individual parts of substances and accidents, including the internal and external boundaries of these, but also universal parts, such as the “humanity” which is (...) an essential part of both Tom and Dick, and also “individual relations”, such as Tom’s promise to Dick, or their current handshake. (shrink)

Notions such as śūnyatā, catuṣkoṭi, and Indra's net, which figure prominently in Buddhist philosophy, are difficult to readily accommodate within our ordinary thinking about everyday objects. Famous Buddhist scholar Nāgārjuna considered two levels of reality: one called conventional reality, and the other ultimate reality. Within this framework, śūnyatā refers to the claim that at the ultimate level objects are devoid of essence or "intrinsic properties", but are interdependent by virtue of their relations to other objects. Catuṣkoṭi refers to the claim (...) that four truth values, including contradiction, are admissible in reasoning. Indra's net refers to the claim that every part of a whole is reflective of the whole. Here we present category theoretic constructions that are reminiscent of these Buddhist concepts. The universal mapping property definition of mathematical objects, wherein objects of a universe of discourse are defined not in terms of their content, but in terms of their relations to all objects of the universe is reminiscent of śūnyatā. The objective logic of perception, with perception modeled as [a category of] two sequential processes (sensation followed by interpretation), and with its truth value object of four truth values, is reminiscent of the Buddhist logic of catuṣkoṭi. The category of categories, wherein every category has a subcategory of sets with zero structure within which every category can be modeled, is reminiscent of Indra's net. Our thorough elaboration of the parallels between Buddhist philosophy and category theory can facilitate better understanding of Buddhist philosophy, and bring out the broader philosophical import of category theory beyond mathematics. (shrink)

The ontology of marketing, particularly the question of what products and brands are, is still largely unexplored. The ontological status of brands hinges on their relationship with products. Idealists about brands see perceptual or cognitive acts of consumers grouped under the heading ‘brand awareness’ or ‘brand image’ as constitutive for the existence of brands so that, in their view, tools of the marketing mix can influence relevant mental dispositions and attitudes. Brand realists, on the other hand, reject the view (...) of brands as mere marks or names and interpret them as emergent products with properties that afford branding in the sense of Gibson’s ecological psychology. Brand strength is a function of the degree to which brands occupy defensible niches in product space. Branding as a process involves changing external or internal boundaries of products. Several arguments are proposed in favor of brand realism. The fragments of an ontology of marketing are developed in a broadly Aristotelian framework. Brand realism has significant implications for a new understanding of issues ranging from the effects of advertising to financial brand valuation, the nature of trademarks, and marketing strategy in general. It permits one to treat brand equity as a real phenomenon not dependent on associations, attitudinal states such as brand loyalty, or spurious constructs such as brand character or personality. (shrink)

The identity "relation" is misconceived since the syntax of "=" is misconceived as a relative term. Actually, "=" is syncategorematic; it forms (true) sentences with a nonpredicative syntax from pairs of (coreferring) flanking names, much as "&" forms (true) conjunctive sentences from pairs of (true) flanking sentences. In the conaming structure, nothing is predicated of the subject, other than, implicitly, its being so conamed. An identity sentence has both an objectual reading as a necessity about what is named, and also (...) a metalinguistic reading as a contingency about the names. Either way the claim about the subject referent has no extralinguistic content. The necessity of alteridentity (non-self-identity) statements is "lexical", due to contingencies of the names' reference, much like the necessity of analytic statements, due to contingencies of the predicates' sense, and unlike the necessity of logical truths (e.g., self-identities) whose truth is secured by syntax alone. Both alter-identity and analytic sentences are readable as objectual necessities and metalinguistic contingencies. Epistemically, alter-identity statements are not essentially unlike analyticities. "Greece is Hellas"/"g=h" and "Greeks are Hellenes"/"(x)(Gx<=>Hx)" are equally (un)informative; so too for "Azure is cobalt"/"a=c" and "Everything azure is cobalt"/"(x)(Ax<=>Cx)". The real epistemic contrast is between proper names (terms without predicative sense) and terms with a predicative sense (names and predicates of properties). Proper names refer to concrete objects, property names refer to abstract objects. That contrast is metaphysical and thus epistemic. (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)

This review article offers a discussion of some aspects of the historical and conceptual context when the term “ontology” (Lat. ontologia) was first introduced in the scholarly circles of the early 17th century. In particular, Barry Smith's (2022) analysis of the birth of ontology provides a springboard for some further remarks on the author of the work with the first known occurrence of the word “ontologia”, Jacob Lorhard, including an analysis of his relationship with earlier philosophers Petrus Ramus (...) and Clemens Timpler. (shrink)

Local food projects are steadily becoming a part of contemporary food systems and take on many forms. They are typically analyzed using an ethical, or sociopolitical, lens. Food focused initiatives can be understood as strategies to achieve ethical change in food systems and, as such, ethics play a guiding role. But local food is also a social movement and, thus social and political theories provide unique insights during analysis. This paper begins with the position that ontology should play a (...) more prominent part in the analysis of local food movements, as this lens could provide unique insights into basic commitments guiding such initiatives. The paper presents the argument that ontological analyses are imperative for fully understanding local food movements. It then provides an overview of the justice frameworks and ontological orientations that guide two dominant types of initiatives: Those committed to increasing food security and those committed to food sovereignty. The paper ends with the argument that food sovereignty projects are revolutionary, not only because they challenge us to change industrial food practices, but also because they are built on a radical new political ontology, and co-constitutive food-focused orientation, that forms the foundation for alternative social and political structures. (shrink)

With the present paper I maintain that the group field theory (GFT) approach to quantum gravity can help us clarify and distinguish the problems of spacetime emergence from the questions about the nature of the quanta of space. I will show that the mechanism of phase transition suggests a form of indifference between scales (or phases) and that such an indifference allows us to black-box questions about the nature of the ontology of the fundamental levels of the theory. I (...) consider the GFT approach to quantum gravity which derives spacetime as an emergent property from abstract non-geometrical tetrahedra through a processes of phase transition. Because the physical interpretation of the tetrahedra is problematic in view of their (non)-spatiotemporal nature, I will apply the considerations about phase transitions to GFT and conclude that the fundamental ontology of the theory and the mechanism of spacetime emergence can and should be treated separately. (shrink)

My topic is the materialist appropriation of empiricism – as conveyed in the ‘minimal credo’ nihil est in intellectu quod non fuerit in sensu (which interestingly is not just a phrase repeated from Hobbes and Locke to Diderot, but is also a medical phrase, used by Harvey, Mandeville and others). That is, canonical empiricists like Locke go out of their way to state that their project to investigate and articulate the ‘logic of ideas’ is not a scientific project: “I shall (...) not at present meddle with the Physical consideration of the Mind” (Essay, I.i.2, in Locke 1975; which Kant gets exactly wrong in his reading of Locke, in the Preface to the A edition of the first Critique). Indeed, I have suggested elsewhere, contrary to a prevalent reading of Locke, that the Essay is not the extension to the study of the mind of the methods of natural philosophy; that he is actually not the “underlabourer” of Newton and Boyle he claims politely to be in the Epistle to the Reader (Wolfe and Salter 2009, Wolfe 2010). Rather, Locke says quite directly if we pay heed to such passages, “Our Business here is not to know all things, but those which concern our Conduct” (Essay, I.i.6). There would be more to say here about what this implies for our understanding of empiricism (see Norton 1981 and Gaukroger 2005), but instead I shall focus on a different aspect of this episode: how a non-naturalistic claim which falls under what we now call epistemology (a claim about the senses as the source of knowledge) becomes an ontology – materialism. That is, how an empiricist claim could shift from being about the sources of knowledge to being about the nature of reality (and/or the mind, in which case it needs, as David Hartley saw and Denis Diderot proclaimed more overtly, an account of the relation between mental processes and the brain). (David Armstrong, for one, denied that there could be an identification between empiricism and materialism on this point: eighteenth-century history of science seems to prove him wrong: see Armstrong 1968 and 1978.) Put differently, I want to examine the shift from the logic of ideas in the seventeenth century (Locke) to an eighteenth-century focus on what kind of ‘world’ the senses give us (Condillac), to an assertion that there is only one substance in the universe (Diderot, giving a materialist cast to Spinozism), and that we need an account of the material substrate of mental life. This is neither a ‘scientific empiricism’ nor a linear developmental process from philosophical empiricism to natural science, but something else again: the unpredictable emergence of an ontology on empiricist grounds. (shrink)

In this paper, I critically assess different interpretations of Bohmian mechanics that are not committed to an ontology based on the wave function being an actual physical object that inhabits configuration space. More specifically, my aim is to explore the connection between the denial of configuration space realism and another interpretive debate that is specific to Bohmian mechanics: the quantum potential versus guidance approaches. Whereas defenders of the quantum potential approach to the theory claim that Bohmian mechanics is better (...) formulated as quasi-Newtonian, via the postulation of forces proportional to acceleration; advocates of the guidance approach defend the notion that the theory is essentially first-order and incorporates some concepts akin to those of Aristotelian physics. Here I analyze whether the desideratum of an interpretation of Bohmian mechanics that is both explanatorily adequate and not committed to configuration space realism favors one of these two approaches to the theory over the other. Contrary to some recent claims in the literature, I argue that the quasi-Newtonian approach based on the idea of a quantum potential does not come out the winner. (shrink)

In recent decades, theories of representation have undergone a constructivist turn, as many theorists no longer view the represented subject as prior to but rather as an effect of representation. Whereas some critics have claimed that lacking an ontologically pre-given subject undermines the theory of representation, many democratic theorists have sought to reconceptualize representation and its democratic possibilities by turning away from ontological questions altogether. By focusing instead on how representatives come to know the public interest, many scholars now contend (...) that an epistemological account best explains how political representation can foster democratic participation. Yet, theorists of representation have not assessed whether this turn to epistemology has overcome the ontological problems that initially motivated it. This article tracks epistemological defenses of representation to outline two models of political representation that attempt to tackle the epistemological problem of constituent interest without positing a foundational ontology of the subject. I argue that both theoretical tendencies ultimately remain caught in the problems of ontology, thereby undercutting their normative aspirations to foster political participation. Turning to Hannah Arendt’s comments on public interest and her writings on council democracy, the article retheorizes the concept of political representation to avoid the ontological problems that beset current accounts. (shrink)

Response to the paper “The Biomedical Ethics Ontology Proposal: Excellent Aims, Questionable Methods" by James DuBois, published in the Journal of Empirical Research on Human Research Ethics.

Many philosophers of science are ontologically committed to a lush rainforest of special science entities ), but are often reticent about the criteria that determine which entities count as real. On the other hand, the metaphysics literature is much more forthcoming about such criteria, but often links ontological commitment to irreducibility. We argue that the irreducibility criteria are in tension with scientific realism: for example, they would exclude viruses, which are plausibly theoretically reducible and yet play a sufficiently important role (...) in scientific accounts of the world that they should be included in our ontology. In this paper, we show how the inhabitants of the rainforest can be inoculated against the eliminative threat of reduction: by demonstrating that they are emergent. According to our account, emergence involves a screening off condition as well as novelty. We go on to demonstrate that this account of emergence, which is compatible with theoretical reducibility, satisfies common intuitions concerning what should and shouldn't count as real: viruses are emergent, as are trouts and turkeys, but philosophically gerrymandered objects like trout-turkeys do not qualify. (shrink)