Host-microbiome interactions (HMIs) are critical for the modulation of biological processes and are associated with several diseases, and extensive HMI studies have generated large amounts of data. We propose that the logical representation of the knowledge derived from these data and the standardized representation of experimental variables and processes can foster integration of data and reproducibility of experiments and thereby further HMI knowledge discovery. A community-based Ontology of Host-Microbiome Interactions (OHMI) was developed following (...) the OBO Foundry principles. OHMI leverages established ontologies to create logically structured representations of microbiomes, microbial taxonomy, host species, host anatomical entities, and HMIs under different conditions and associated study protocols and types of data analysis and experimental results. (shrink)

COVID-19 often manifests with different outcomes in different patients, highlighting the complexity of the host-pathogen interactions involved in manifestations of the disease at the molecular and cellular levels. In this paper, we propose a set of postulates and a framework for systematically understanding complex molecular host-pathogen interaction networks. Specifically, we first propose four host-pathogen interaction (HPI) postulates as the basis for understanding molecular and cellular host-pathogen interactions and their relations to disease outcomes. These four (...) postulates cover the evolutionary dispositions involved in HPIs, the dynamic nature of HPI outcomes, roles that HPI components may occupy leading to such outcomes, and HPI checkpoints that are critical for specific disease outcomes. Based on these postulates, an HPI Postulate and Ontology (HPIPO) framework is proposed to apply interoperable ontologies to systematically model and represent various granular details and knowledge within the scope of the HPI postulates, in a way that will support AI-ready data standardization, sharing, integration, and analysis. As a demonstration, the HPI postulates and the HPIPO framework were applied to study COVID-19 with the Coronavirus Infectious Disease Ontology (CIDO), leading to a novel approach to rational design of drug/vaccine cocktails aimed at interrupting processes occurring at critical host-coronavirus interaction checkpoints. Furthermore, the host-coronavirus protein-protein interactions (PPIs) relevant to COVID-19 were predicted and evaluated based on prior knowledge of curated PPIs and domain-domain interactions, and how such studies can be further explored with the HPI postulates and the HPIPO framework is discussed. (shrink)

Plants from a handful of species provide the primary source of food for all people, yet this source is vulnerable to multiple stressors, such as disease, drought, and nutrient deficiency. With rapid population growth and climate uncertainty, the need to produce crops that can tolerate or resist plant stressors is more crucial than ever. Traditional plant breeding methods may not be sufficient to overcome this challenge, and methods such as highOthroughput sequencing and automated scoring of phenotypes can provide significant new (...) insights. Ontologies are essential tools for accessing and analysing the large quantities of data that come with these newer methods. As part of a larger project to develop ontologies that describe plant phenotypes and stresses, we are developing a plant disease extension of the Infectious Disease Ontology (IDOPlant). The IDOPlant is envisioned as a reference ontology designed to cover any plant infectious disease. In addition to novel terms for infectious diseases, IDOPlant includes terms imported from other ontologies that describe plants, pathogens, and vectors, the geographic location and ecology of diseases and hosts, and molecular functions and interactions of hosts and pathogens. To encompass this range of data, we are suggesting inOhouse ontology development complemented with reuse of terms from orthogonal ontologies developed as part of the Open Biomedical Ontologies (OBO) Foundry. The study of plant diseases provides an example of how an ontological framework can be used to model complex biological phenomena such as plant disease, and how plant infectious diseases differ from, and are similar to, infectious diseases in other organism. (shrink)

In this article I try to show that the most deep level ontology can have rich meaning for our understanding of such practical and everyday phenomena as education and interaction. With this deep level ontology I mean the problem of universals. Starting from famous traditional stances of realism and nominalism, which both are for the modern theories of growth and Bildung, I continue to the third and more recently developed ontological theory, trope theory according to which the properties (...) (qualities, relations etc.) are real (unlike in nominalism) but not universal (like in realisms). Then I will take a closer look at the trope theory of CB Martin. According to it every causal event is an interaction event between simple or complex beings in which their existing dispositions may produce manifesting properties. This point of view is radically anti dualistic because that basic level causal interaction has in the simplified forms all the elements of semiotic, meaningful of mental activity of such complex beings likes humans and animals. Ome of the main general conclusions of the article is that all causal affections contain a kind of “interpretation” from the side of affected object. (shrink)

Electromagnetism is usually understood as a theory describing how charged particles and eletromagnetic fields interact. In this paper I argue that a double ontology comprising both particles and fields is problematic. Either we should think of electromagnetism as a theory about charged particles directly interacting with each other, or as theory of fields whose local interactions are manifested as field quanta, called "particles." From a purely theoretical point of view the choice between a particle and a field interpretation (...) does not matter much when it concerns classical electromagnetism; both interpretations are possible and, as shown by Quine, there is a general method for translating a theory about one kind of objects into a theory assuming another kind of objects, provided these theories are empirically equivalent. From an empiricist point of view, however, the particle interpretation is the choice, since some particles are directly observable. Testable predictions of electromagnetism are predictions of the motion of charged bodies, in theory represented as particles, so this must be the empiricists' choice of ontology. In quantum electrodynamics one is however forced to chose a field ontology, since a particle ontology for this theory is impossible. So called "quantum particles" are field quanta, which cannot be treated as individuals making up a domain of quantification. There is thus a tension regarding ontology between classical and quantum electrodynamics. But this tension is nothing else than the much debated measurement problem of quantum mechanics. (shrink)

The hologenome concept of evolution is a hypothesis about the evolution of animals and plants. It asserts that the evolution of animals and plants was partially triggered by their interactions with their symbiotic microbiomes. In that vein, the hologenome concept posits that the holobiont (animal host + symbionts of the microbiome) is a unit of selection. -/- The hologenome concept has been severely criticized on the basis that selection on holobionts would only be possible if there were (...) a tight transgenerational host-genotype-to-symbiont-genotype connection. As our current evidence suggests that this is not the case for most of the symbiont species that compose the microbiome of animals and plants, the opportunity for holobiont selection is very low in relation to the opportunity for selection on each of the species that compose the host microbiome. Therefore, holobiont selection will always be disrupted ‘from below’, by selection on each of the species that compose the microbiome. -/- This thesis constitutes a conceptual effort to defend philosophically the hologenome concept. I argue that the criticism according to which holobiont selection requires tight transgenerational host-genotype-to-symbiont-genotype connection is grounded on a metaphysical view of the world according to which the biological hierarchy needs to be nested, such that each new level of selection includes every entity from below. Applied to hologenomes, it entails that the hologenome is a collection of genomes, and selection of hologenomes is assumed to entail cospeciation of the host with the species that constitute its microbiome. -/- Against that interpretation, I propose the ‘stability of traits’ account, according to which hologenome evolution is the result of the action of natural selection in a non-nested hierarchical world. In that vein, hologenome evolution does not entail cospeciation, and thus it does not require tight transgenerational host-genotype-to-symbiont-genotype connection. By embracing a multilevel selection perspective, I argue that hologenome evolution results from the simultaneous action of natural selection on each of the lineages that compose the microbiome, and on the assemblage composed by the host genome plus the functional traits of its microbiome. Hologenome selection occurs when the evolution of the traits of the microbiome result from their effects on the fitness of the host, and it can take the form of multilevel selection 1, or multilevel selection 2. In both cases, hologenome selection entails the evolution of microbiome traits, as well as evolution of the host genome, rather than cospeciation of lineages. (shrink)

The current COVID-19 pandemic and the previous SARS/MERS outbreaks of 2003 and 2012 have resulted in a series of major global public health crises. We argue that in the interest of developing effective and safe vaccines and drugs and to better understand coronaviruses and associated disease mechenisms it is necessary to integrate the large and exponentially growing body of heterogeneous coronavirus data. Ontologies play an important role in standard-based knowledge and data representation, integration, sharing, and analysis. Accordingly, we initiated the (...) development of the community-based Coronavirus Infectious Disease Ontology in early 2020. -/- As an Open Biomedical Ontology (OBO) library ontology, CIDO is open source and interoperable with other existing OBO ontologies. CIDO is aligned with the Basic Formal Ontology and Viral Infectious Disease Ontology. CIDO has imported terms from over 30 OBO ontologies. For example, CIDO imports all SARS-CoV-2 protein terms from the Protein Ontology, COVID-19-related phenotype terms from the Human Phenotype Ontology, and over 100 COVID-19 terms for vaccines (both authorized and in clinical trial) from the Vaccine Ontology. CIDO systematically represents variants of SARS-CoV-2 viruses and over 300 amino acid substitutions therein, along with over 300 diagnostic kits and methods. CIDO also describes hundreds of host-coronavirus protein-protein interactions (PPIs) and the drugs that target proteins in these PPIs. CIDO has been used to model COVID-19 related phenomena in areas such as epidemiology. The scope of CIDO was evaluated by visual analysis supported by a summarization network method. CIDO has been used in various applications such as term standardization, inference, natural language processing (NLP) and clinical data integration. We have applied the amino acid variant knowledge present in CIDO to analyze differences between SARS-CoV-2 Delta and Omicron variants. CIDO's integrative host-coronavirus PPIs and drug-target knowledge has also been used to support drug repurposing for COVID-19 treatment. -/- CIDO represents entities and relations in the domain of coronavirus diseases with a special focus on COVID-19. It supports shared knowledge representation, data and metadata standardization and integration, and has been used in a range of applications. (shrink)

Explaining the behaviour of ecosystems is one of the key challenges for the biological sciences. Since 2000, new-mechanicism has been the main model to account for the nature of scientific explanation in biology. The universality of the new-mechanist view in biology has been however put into question due to the existence of explanations that account for some biological phenomena in terms of their mathematical properties (mathematical explanations). Supporters of mathematical explanation have argued that the explanation of the behaviour of ecosystems (...) is usually provided in terms of their mathematical properties, and not in mechanistic terms. They have intensively studied the explanation of the properties of ecosystems that behave following the rules of a non-random network. However, no attention has been devoted to the study of the nature of the explanation in those that form a random network. In this paper, we cover that gap by analysing the explanation of the stability behaviour of the microbiome recently elaborated by Coyte and colleagues, to determine whether it fits with the model of explanation suggested by the new-mechanist or by the defenders of mathematical explanation. Our analysis of this case study supports three theses: (1) that the explanation is not given solely in terms of mechanisms, as the new-mechanists understand the concept; (2) that the mathematical properties that describe the system play an essential explanatory role, but they do not exhaust the explanation; (3) that a non-previously identified appeal to the type of interactions that the entities in the network can exhibit, as well as their abundance, is also necessary for Coyte and colleagues’ account to be fully explanatory. From the combination of these three theses we argue for the necessity of an integrative pluralist view of the nature of behaviour explanation when this is given by appealing to the existence of a random network. (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)

Vaccine research, as well as the development, testing, clinical trials, and commercial uses of vaccines involve complex processes with various biological data that include gene and protein expression, analysis of molecular and cellular interactions, study of tissue and whole body responses, and extensive epidemiological modeling. Although many data resources are available to meet different aspects of vaccine needs, it remains a challenge how we are to standardize vaccine annotation, integrate data about varied vaccine types and resources, and support advanced (...) vaccine data analysis and inference. To address these problems, the community-based Vaccine Ontology (VO) has been developed through collaboration with vaccine researchers and many national and international centers and programs, including the National Center for Biomedical Ontology (NCBO), the Infectious Disease Ontology (IDO) Initiative, and the Ontology for Biomedical Investigations (OBI). VO utilizes the Basic Formal Ontology (BFO) as the top ontology and the Relation Ontology (RO) for definition of term relationships. VO is represented in the Web Ontology Language (OWL) and edited using the Protégé-OWL. Currently VO contains more than 2000 terms and relationships. VO emphasizes on classification of vaccines and vaccine components, vaccine quality and phenotypes, and host immune response to vaccines. These reflect different aspects of vaccine composition and biology and can thus be used to model individual vaccines. More than 200 licensed vaccines and many vaccine candidates in research or clinical trials have been modeled in VO. VO is being used for vaccine literature mining through collaboration with the National Center for Integrative Biomedical Informatics (NCIBI). Multiple VO applications will be presented. (shrink)

This paper investigates how reticulate evolution contributes to a better understanding of human sociocultural evolution in general, and community formation in particular. Reticulate evolution is evolution as it occurs by means of symbiosis, symbiogenesis, lateral gene transfer, infective heredity, and hybridization. From these mechanisms and processes, we mainly zoom in on symbiosis and we investigate how it underlies the rise of (1) human, plant, animal, and machine interactions typical of agriculture, animal husbandry, farming, and industrialization; (2) diet-microbiome relationships; (...) and (3) host-virome and other pathogen interactions that underlie human health and disease. We demonstrate that reticulate evolution necessitates an understanding of behavioral and cultural evolution at a community level, where reticulate causal processes underlie the rise of synergistic organizational traits. (shrink)

The basic kinds of physical causality that are foundational for other kinds of causality involve objects and the causal relations between them. These interactions do not involve events. If events were ontologically significant entities for causality in general, then they would play a role in simple mechanical interactions. But arguments about simple collisions looked at from different frames of reference show that events cannot play a role in simple mechanical interactions, and neither can the entirely hypothetical causal (...) relations between events. These arguments show that physics, which should be authoritative when it comes to the metaphysics of causality, gives no reasons to believe that events are causal agents. Force relations and some cases of energy-momentum transfer are examples of causal relations, with forces being paradigmatic in the macroscopic world, though it is conceivable that there are other kinds of causal relation. A relation between two objects is a causal relation if and only if when it is instantiated by the two objects there is a possibility that the objects that are the terms of the relation could change. The basic metaphysics of causality is about objects, causal relations, changes in objects, and a causal primitive. The paper also includes a discussion of the metaphysics of forces and a discussion of the metaphysics of energy and momentum exchanges. (shrink)

Patient-centered care (PCC) is an approach to healthcare that values patients’ preference, need, and autonomy. The estimation of healthcare partly depends on how well PCC is implemented. In addition, the result of clinical research can inform the assessment of the implementation of PCC. In clinical research, health-related quality of life (HRQL) theoretical models offer a conceptual toolbox that informs clinical research and guides the hypotheses generation. Wilson and Cleary (1995) developed the most widely used HRQL theoretical model (Bakas et al., (...) 2012). Ontological assumptions about causation in Wilson and Cleary’s model will influence which kind of hypotheses will be generated. I will argue that Wilson and Cleary’s model instilled a kind of causal bias into hypothesis generation in clinical research on HRQL. Causation from biomedical factors to non-biomedical factors is frequently hypothesized while causation from non-biomedical factors to biomedical factors is rarely hypothesized. It leads to that the interdependence and interaction between constituent parts of patients are ignored, which is an obstacle to the implementation of PCC. In addition, I will propose a revised HRQL theoretical model which avoids the causal bias brought by Wilson and Cleary’s model. By doing so, I leave room for the improvement of the practice of healthcare by analyzing the ontological assumptions about causation. (shrink)

Intellectual property law tends to be viewed as the only (or most significant) mechanism for achieving policy goals relating to innovation assets. Yet more creative and effective solutions are often available. When analysed from a transdisciplinary perspective, relying on the cooperative efforts of researchers from fields other than law, innovation governance is characterized not simply as the product of legal rules, but as a function of the interaction of legal rules, practices and institutions. When policy-makers seek to identify conditions under (...) which the creation, use and exchange of innovation assets flourishes, care should be taken to focus on this combination of factors. This article describes the development of an ontology—a computerized method of representing knowledge as concepts and relations between concepts—to convey such understanding. Policy makers (and researchers) are provided with an organized, accessible representation of innovation governance that enriches their understanding and improves their decision-making. (shrink)

Research on the human microbiome has gen- erated a staggering amount of sequence data, revealing variation in microbial diversity at the community, species (or phylotype), and genomic levels. In order to make this complexity more manageable and easier to interpret, new units—the metagenome, core microbiome, and entero- type—have been introduced in the scientific literature. Here, I argue that analytical tools and exploratory statisti- cal methods, coupled with a translational imperative, are the primary drivers of this new ontology. (...) By reducing the dimensionality of variation in the human microbiome, these new units render it more tractable and easier to interpret, and hence serve an important heuristic role. Nonetheless, there are several reasons to be cautious about these new categories prematurely ‘‘hardening’’ into natural units: a lack of constraints on what can be sequenced metagenomically, freedom of choice in taxonomic level in defining a ‘‘core microbiome,’’ typological framing of some of the concepts, and possible reification of statistical constructs. Finally, lessons from the Human Genome Project have led to a translational imperative: a drive to derive results from the exploration of microbiome variation that can help to articulate the emerging paradigm of per- sonalized genomic medicine (PGM). There is a tension between the typologizing inherent in much of this research and the personal in PGM. (shrink)

Drawing from Arjen Kleinherenbrink's recent book, Against Continuity: Gilles Deleuze's Speculative Realism (2019), this paper undertakes a detailed review of Kleinherenbrink's fourfold "externality thesis" vis-à-vis Deleuze's machine ontology. Reading Deleuze as a philosopher of the actual, this paper renders Deleuzean syntheses as passive contemplations, pulling other (passive) entities into an (active) experience and designating relations as expressed through contraction. In addition to reviewing Kleinherenbrink's book (which argues that the machine ontology is a guiding current that emerges in Deleuze's (...) work after Difference and Repetition) alongside much of Deleuze's oeuvre, we relate and juxtapose Deleuze's machine ontology to positions concerning externality held by a host of speculative realists. Arguing that the machine ontology has its own account of interaction, change, and novelty, we ultimately set to prove that positing an ontological "cut" on behalf of the virtual realm is unwarranted because, unlike the realm of actualities, it is extraneous to the structure of becoming-that is, because it cannot be homogenous, any theory of change vis-à-vis the virtual makes it impossible to explain how and why qualitatively different actualities are produced. (shrink)

In this paper recognition is taken to be a question of social ontology, regarding the very constitution of the social space of interaction. I concentrate on the question of whether certain aspects of the theory of recognition can be translated into the terms of a socio-ontological paradigm: to do so, I make reference to some conceptual tools derived from John Searle's social ontology and Robert Brandom's normative pragmatics. My strategy consists in showing that recognitive phenomena cannot be isolated (...) at the level of human interaction, and are, rather, in part proper to animal interaction as well. Furthermore, it is argued that recognitive powers are constitutive powers more basic than deontic ones and play a role much broader than the one they in fact assume in Searle and in Brandom. (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)

The arguments are exhibited in favour of the necessity to modify the history of the genesis and advancement of general relativity (GR). I demonstrate that the dynamic creation of GR had been continually governed by internal tensions between two research traditions, that of special relativity and Newton’s gravity. The encounter of the traditions and their interpenetration entailed construction of the hybrid domain at first with an irregular set of theoretical models. Step by step, on eliminating the contradictions between the models (...) contrived, the hybrid set was put into order. It is contended that the main reason of the GR victory over the rival programmes of Abraham and Nordström was a synthetic character of Einstein’s programme. Einstein had put forward as a basic synthetic principle the principle of equivalence that radically differed from that of rival approaches by its open, flexible and contra-ontological character. (shrink)

As the international genomic research community moves from the tool-making efforts of the Human Genome Project into biomedical applications of those tools, new metaphors are being suggested as useful to understanding how our genes work – and for understanding who we are as biological organisms. In this essay we focus on the Human Microbiome Project as one such translational initiative. The HMP is a new ‘metagenomic’ research effort to sequence the genomes of human microbiological flora, in order to pursue (...) the interesting hypothesis that our ‘microbiome’ plays a vital and interactive role with our human genome in normal human physiology. Rather than describing the human genome as the ‘blueprint’ for human nature, the promoters of the HMP stress the ways in which our primate lineage DNA is interdependent with the genomes of our microbiological flora. They argue that the human body should be understood as an ecosystem with multiple ecological niches and habitats in which a variety of cellular species collaborate and compete, and that human beings should be understood as ‘superorganisms’ that incorporate multiple symbiotic cell species into a single individual with very blurry boundaries. These metaphors carry interesting philosophical messages, but their inspiration is not entirely ideological. Instead, part of their cachet within genome science stems from the ways in which they are rooted in genomic research techniques, in what philosophers of science have called a ‘tools-to-theory’ heuristic. Their emergence within genome science illustrates the complexity of conceptual change in translational research, by showing how it reflects both aspirational and methodological influences. (shrink)

Human nature has always been a foundational issue for philosophy. What does it mean to have a human nature? Is the concept the relic of a bygone age? What is the use of such a concept? What are the epistemic and ontological commitments people make when they use the concept? In What’s Left of Human Nature? Maria Kronfeldner offers a philosophical account of human nature that defends the concept against contemporary criticism. In particular, she takes on challenges related to social (...) misuse of the concept that dehumanizes those regarded as lacking human nature (the dehumanization challenge); the conflict between Darwinian thinking and essentialist concepts of human nature (the Darwinian challenge); and the consensus that evolution, heredity, and ontogenetic development results from nurture and nature. After answering each of these challenges, Kronfeldner presents a revisionist account of human nature that minimizes dehumanization and does not fall back on outdated biological ideas. Her account is post-essentialist because it eliminates the concept of an essence of being human; pluralist in that it argues that there are different things in the world that correspond to three different post-essentialist concepts of human nature; and interactive because it understands nature and nurture as interacting at the developmental, epigenetic, and evolutionary levels. On the basis of this, she introduces a dialectical concept of an ever-changing and “looping” human nature. Finally, noting the essentially contested character of the concept and the ambiguity and redundancy of the terminology, she wonders if we should simply eliminate the term “human nature” altogether. (shrink)

The richness of the term “unsettling” has made it readily employable for phenomenological accounts of racism in philosophy of race literature; yet, the term has been left largely under-theorized. Here, I argue that unsettling encounters can be said to occur when the unfamiliar other has come into contact with the boundary of one’s existential home. For many white people, interracial interactions produce an (often unwarranted) feeling of physical danger, but as I hope to show, this habitual (mis)perception of such (...) encounters is not merely a conditioned response; it also functions to subvert situations that might unsettle white identifies partially constituted by phenomenological demarcations of space along racial lines. Drawing on empirical literature and recent developments in critical phenomenology, I suggest that by exercising habitual, racist gestures and perceptions, white people (mis)perceive ontological threats to their worldview—e.g., a bookish Black student or a masculine gay man—as ontically threatening so as to avoid the kind of work and existential anguish that altering one’s normative expectations would require. (shrink)

The aim of this thesis is to propose a deflationary approach towards the ontological analysis of physical theories. Such an approach sustains that the development of ontologies for physical theories must be neutral relatively to the debate between realists and anti-realists in philosophy of physics. Mainly, our attention will be oriented towards what we called "quantum domain", which includes the non-relativistic Quantum Mechanics and variants of the Quantum Field Theory. This meta-ontological approach consists in an attempt to provide a methodology (...) for the development of specific ontologies for physical theories. With this aim we suggest the separation between physical phenomena and physical theories on one side, and physical theories and ontologies on the other side. This separation intends to endorse the idea that physical theories can provide all the informative contents required for the development of the ontologies associated with them. The result is a defense of the idea that physical theories can positively contribute for the constitution of the ontologies in physics. Additionally, we present a critical analysis of four different ontological approaches to QM and QFT. Each one of these interpretations deals with a different ontological category (tropes, events and processes). At the end of the thesis we will analyze the concepts of interaction and commutation in QFT in order to exemplify the main lines of the deflationary approach suggested here. (shrink)

The suggestion of Logical Quanta (LQ) is a bidirectional synthesis of the theory of logos of Maximus the Confessor and the philosophical interpretation of quantum mechanics. The result of such a synthesis is enrichment to the ontology of classical mechanics that enable us to have a unified view and an explanatory frame of the whole cosmos. It also enables us to overcome the Cartesian duality both on biology and the interaction of body and mind. Finally, one can reconstruct a (...) new understanding of religion. (shrink)

Statements about the behavior of biochemical entities (e.g., about the interaction between two proteins) abound in the literature on molecular biology and are increasingly becoming the targets of information extraction and text mining techniques. We show that an accurate analysis of the semantics of such statements reveals a number of ambiguities that have to be taken into account in the practice of biomedical ontology engineering: Such statements can not only be understood as event reporting statements, but also as ascriptions (...) of dispositions or tendencies that may or may not refer to collectives of interacting molecules or even to collectives of interaction events. (shrink)

Over the last three decades, studies in microbiology have exposed a world of diverse and dynamic interactions. Through metagenomic sequencing, complex bacterial communities became visible and proved important for many biological phenomena. As a result of discovering the connection between microorganisms and organisms’ survival, the notion of the holobiont has become prominent and has been suggested as a biological individual. The view of the holobiont as an individual, commonly known as the Hologenome Theory, focuses on the interactions and (...) relations between the host and its symbionts in the host’s development and evolution. Today, the holobiont is at the heart of the debate on the nature of the biological individual, a debate which is connected to the same question about the nature of the individual organism. (shrink)

Holobionts are symbiotic assemblages composed by a macrobe host plus its symbiotic microbiota. In recent years, the ontological status of holobionts has created a great amount of controversy among philosophers and biologists: are holobionts biological individuals or are they rather ecological communities of independent individuals that interact together? Chiu and Eberl have recently developed an eco-immunity account of the holobiont wherein holobionts are neither biological individuals nor ecological communities, but hybrids between a host and its microbiota. According to (...) their account, the microbiota is not a proper part of the holobiont. Yet, it should be regarded as a set of scaffolds that support the individuality of the host. In this paper, we approach Chiu and Eberl’s account from a metaphysical perspective and argue that, contrary to what the authors claim, the eco-immunity account entails that the microorganisms that compose the host’s microbiota are proper parts of the holobiont. Second, we argue that by claiming that holobionts are hybrids, and therefore, not biological individuals, the authors seem to be assuming a controversial position about the ontology of hybrids, which are conventionally characterized as a type of biological individual. In doing so, our paper aligns with the contemporary tendency to incorporate metaphysical resources to shed light on current biological debates and builds on that to provide additional support to the consideration of holobionts as biological individuals from an eco-immunity perspective. (shrink)

Winner of the 2020 Essay Competition of the International Social Ontology Society. -/- Ian Hacking uses the looping effect to describe how classificatory practices in the human sciences interact with the classified people. While arguably this interaction renders the affected human kinds unstable and hence different from natural kinds, realists argue that also some prototypical natural kinds are interactive and human kinds in general are stable enough to support explanations and predictions. I defend a more fine-grained realist interpretation of (...) interactive human kinds by arguing for an explanatory domain account of the looping effect. First, I argue that knowledge of the feedback mechanisms that mediate the looping effect can supplement, and help to identify, the applicability domain over which a kind and its property variations are stably explainable. Second, by applying this account to cross-cultural case studies of psychiatric disorders, I distinguish between congruent feedback mechanisms that explain matches between classifications and kinds, and incongruent feedback mecha- nisms that explain mismatches. For example, congruent mechanisms maintain Western auditory experiences in schizophrenia, whereas exporting diagnostic labels inflicts incongruence by influencing local experiences. Knowledge of the mechanisms can strengthen explanatory domains, and thereby facilitate classificatory adjustments and possible interventions on psychiatric disorders. (shrink)

The widespread mistrust of metaphysics-the main obstacle to the unification of physics and philosophy-is based on the myth that metaphysical claims cannot be falsified or verified, because they are supposedly true independently of empirical knowledge. This is not true of metaphysical naturalism, whose approach is to critically reflect on the theories and findings of all the empirical disciplines and abstract from them a theory about such general features of reality that no single empirical discipline can be the authority on. Causation (...) is such a feature, since its instances include anything from planetary motions to particle interactions, chemical reactions, biological functions, and closing a door. Consequently, a general account of causation is beyond any particular empirical discipline. Metaphysical naturalism takes a meta-perspective on the results of the empirical sciences and attempts to figure out how it fits together in a coherent whole, e.g. by offering a general account of causation. General accounts of this kind are falsifiable in so far as the theories are falsifiable from which they are generalizations. The paper also discusses some fundamental metaphysical principles implicitly assumed by the sciences generally, and why they imply that unification is methodologically virtuous. (shrink)

This essay presents an alternative to contemporary substantivalist and relationist interpretations of quantum gravity hypotheses by means of an historical comparison with the ontology of space in the seventeenth century. Utilizing differences in the spatial geometry between the foundational theory and the theory derived from the foundational, in conjunction with nominalism and platonism, it will be argued that there are crucial similarities between seventeenth century and contemporary theories of space, and that these similarities reveal a host of underlying (...) conceptual issues that the substantival/relational dichotomy fails to distinguish. (shrink)

The Protein Ontology (PRO; http://purl.obolibrary.org/obo/pr) formally defines and describes taxon-specific and taxon-neutral protein-related entities in three major areas: proteins related by evolution; proteins produced from a given gene; and protein-containing complexes. PRO thus serves as a tool for referencing protein entities at any level of specificity. To enhance this ability, and to facilitate the comparison of such entities described in different resources, we developed a standardized representation of proteoforms using UniProtKB as a sequence reference and PSI-MOD as a post-translational (...) modification reference. We illustrate its use in facilitating an alignment between PRO and Reactome protein entities. We also address issues of scalability, describing our first steps into the use of text mining to identify protein-related entities, the large-scale import of proteoform information from expert curated resources, and our ability to dynamically generate PRO terms. Web views for individual terms are now more informative about closely-related terms, including for example an interactive multiple sequence alignment. Finally, we describe recent improvement in semantic utility, with PRO now represented in OWL and as a SPARQL endpoint. These developments will further support the anticipated growth of PRO and facilitate discoverability of and allow aggregation of data relating to protein entities. (shrink)

The National Center for Biomedical Ontology is a consortium that comprises leading informaticians, biologists, clinicians, and ontologists, funded by the National Institutes of Health (NIH) Roadmap, to develop innovative technology and methods that allow scientists to record, manage, and disseminate biomedical information and knowledge in machine-processable form. The goals of the Center are (1) to help unify the divergent and isolated efforts in ontology development by promoting high quality open-source, standards-based tools to create, manage, and use ontologies, (2) (...) to create new software tools so that scientists can use ontologies to annotate and analyze biomedical data, (3) to provide a national resource for the ongoing evaluation, integration, and evolution of biomedical ontologies and associated tools and theories in the context of driving biomedical projects (DBPs), and (4) to disseminate the tools and resources of the Center and to identify, evaluate, and communicate best practices of ontology development to the biomedical community. Through the research activities within the Center, collaborations with the DBPs, and interactions with the biomedical community, our goal is to help scientists to work more effectively in the e-science paradigm, enhancing experiment design, experiment execution, data analysis, information synthesis, hypothesis generation and testing, and understand human disease. (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)

In this paper, I propose a framework that supports both free will and anomalous mind-matter interaction (psychokinesis). I begin by considering the argument by the physicist Sean Carroll that the laws of physics as we understand them rule out psychokinesis (and other modes of psi). I find Carroll’s claims problematic, in part due to what I believe are misunderstandings of arguments borrowed from David Hume. I proceed to consider a more dispositional notion of causality (in contrast to one characterized by (...) universal and necessary laws) which I argue is more hospitable to both psychokinesis and free will. I then incorporate recent work from the philosophy of mind and science to arrive at a framework that supports both real volition and psychokinesis, which I argue are intimately linked. This approach is fundamentally dispositional, but grounded in an ontologically prior field of awareness and potentiality. I also consider that the regularities (or causal natures) we observe in our physical world are ultimately supported by what we might term teleological “intentions” within a nonlocal, mind-like quantum ground. (shrink)

Recent research about the microbiome points to a picture in which we, humans, are ‘living through’ nature, and nature itself is living in us. Our bodies are hosting—and depend on—the multiple species that constitute human microbiota. This article will discuss current research on the microbiome through the ideas of Japanese ecologist Imanishi Kinji (1902–1992). First, some of Imanishi’s key ideas regarding the world of living beings and multispecies societies are presented. Second, seven types of relationships concerning the human (...) microbiome, human beings, and the environment are explored. Third, inspired by Imanishi’s work, this paper develops the idea of dynamic, porous, and complex multispecies societies in which different living beings or species are codependent on others, including microbiota and human beings. (shrink)

In recent years, sequencing technologies have enabled the identification of a wide range of non-coding RNAs (ncRNAs). Unfortunately, annotation and integration of ncRNA data has lagged behind their identification. Given the large quantity of information being obtained in this area, there emerges an urgent need to integrate what is being discovered by a broad range of relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a systematically structured and precisely defined controlled vocabulary for (...) the domain of ncRNAs, thereby facilitating the discovery, curation, analysis, exchange, and reasoning of data about structures of ncRNAs, their molecular and cellular functions, and their impacts upon phenotypes. The goal of NCRO is to serve as a common resource for annotations of diverse research in a way that will significantly enhance integrative and comparative analysis of the myriad resources currently housed in disparate sources. It is our belief that the NCRO ontology can perform an important role in the comprehensive unification of ncRNA biology and, indeed, fill a critical gap in both the Open Biological and Biomedical Ontologies (OBO) Library and the National Center for Biomedical Ontology (NCBO) BioPortal. Our initial focus is on the ontological representation of small regulatory ncRNAs, which we see as the first step in providing a resource for the annotation of data about all forms of ncRNAs. (shrink)

A holobiont is a composite organism consisting of a host together with its microbiome, such as a coral with its zooxanthellae. To explain the often intimate integration between hosts and their microbiomes, some investigators contend that selection operates on holobionts as a unit and view the microbiome’s genes as extending the host’s nuclear genome to jointly comprise a hologenome. Because vertical transmission of microbiomes is uncommon, other investigators contend that holobiont selection cannot be effective because a (...) holobiont’s microbiome is an acquired condition rather than an inherited trait. This disagreement invites a simple mathematical model to see how holobiont selection might operate and to assess its plausibility as an evolutionary force. This paper presents two variants of such a model. In one variant, juvenile hosts obtain microbiomes from their parents (vertical transmission). In the other variant, microbiomes of juvenile hosts are assembled from source pools containing the combined microbiomes of all parents (horizontal transmission). According to both variants, holobiont selection indeed causes evolutionary change in holobiont traits. Therefore, holobiont selection is plausibly an effective evolutionary force with either mode of microbiome transmission. The modeling employs two distinct concepts of inheritance, depending on the mode of microbiome transmission: collective inheritance whereby juveniles inherit a sample of the collected genomes from all parents, as contrasted with lineal inheritance whereby juveniles inherit the genomes from only their own parents. A distinction between collective and lineal inheritance also features in theories of multilevel selection. (shrink)

Statements about the behavior of biological entities, e.g. about the interaction between two proteins, abound in the literature on molecular biology and are increasingly becoming the targets of information extraction and text mining techniques. We show that an accurate analysis of the semantics of such statements reveals a number of ambiguities that is necessary to take into account in the practice of biomedical ontology engineering. Several concurring formalizations are proposed. Emphasis is laid on the discussion of biological dispositions.

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)

A crucial philosophical problem of social robots is how much they perform a kind of sociality in interacting with humans. Scholarship diverges between those who sustain that humans and social robots cannot by default have social interactions and those who argue for the possibility of an asymmetric sociality. Against this dichotomy, we argue in this paper for a holistic approach called “Δ phenomenology” of HSRI. In the first part of the paper, we will analyse the semantics of an HSRI. (...) This is what leads a human being to assign or receive a meaning of sociality by interacting with a social robot. Hence, we will question the ontological structure underlying HSRIs, suggesting that HSRIs may lead to a peculiar kind of user alienation. By combining all these variables, we will formulate some final recommendations for an ethics of social robots. (shrink)

Following the proposal of a new kind of selective structural realism that uses as a basis the distinction between framework and interaction theories, this work discusses relevant applications in fundamental physics. An ontology for the different entities and properties of well-known theories is thus consistently built. The case of classical field theories—including general relativity as a classical theory of gravitation—is examined in detail, as well as the implications of the classification scheme for issues of realism in quantum mechanics. These (...) applications also shed light on the different range of applicability of the ontic and epistemic versions of structural realism. (shrink)

The paper argues that digital ontology (the ultimate nature of reality is digital, and the universe is a computational system equivalent to a Turing Machine) should be carefully distinguished from informational ontology (the ultimate nature of reality is structural), in order to abandon the former and retain only the latter as a promising line of research. Digital vs. analogue is a Boolean dichotomy typical of our computational paradigm, but digital and analogue are only “modes of presentation” of Being (...) (to paraphrase Kant), that is, ways in which reality is experienced or conceptualised by an epistemic agent at a given level of abstraction. A preferable alternative is provided by an informational approach to structural realism, according to which knowledge of the world is knowledge of its structures. The most reasonable ontological commitment turns out to be in favour of an interpretation of reality as the totality of structures dynamically interacting with each other. The paper is the first part (the pars destruens) of a two-part piece of research. The pars construens, entitled “A Defence of Informational Structural Realism”, is developed in a separate article, also published in this journal. (shrink)

Holobionts are symbiotic assemblages composed by a host plus its microbiome. The status of holobionts as individuals has recently been a subject of continuous controversy, which has given rise to two main positions: on the one hand, holobiont advocates argue that holobionts are biological individuals; on the other, holobiont detractors argue that they are just mere chimeras or ecological communities, but not individuals. Both parties in the dispute develop their arguments from the framework of the philosophy of biology, (...) in terms of what it takes for a “conglomerate” to be considered an interesting individual from a biological point of view. However, the debates about holobiont individuality have important ontological implications that have remained vaguely explored from a metaphysical framework. The purpose of this paper is to cover that gap by presenting a metaphysical approach to holobionts individuality. Drawing upon a conception of natural selection that puts the focus on the transgenerational recurrence of the traits and that supports the thesis that holobionts are units of selection, we argue that holobionts bear emergent traits and exert downward powers over the entities that compose them. In this vein, we argue, a reasonable argument can be made for conceiving holobionts as emergent biological individuals. (shrink)

The study of active matter systems demonstrates how interactions might co-constitute agential dynamics. Active matter systems are comprised of self-propelled independent entities which, en masse, take part in complex and interesting collective group behaviors at a far-from-equilibrium state (Menon, 2010 ; Takatori & Brady, 2015 ). These systems are modelled using very simple rules (Vicsek at al. 1995), which reveal the interactive nature of the collective behaviors seen from humble to highly complex entities. Here I show how the study (...) of active matter systems supports two related proposals regarding interaction and agency. First, I argue that the study of interactive dynamics in these systems evidences the utility of treating interaction as an ontological category (Longino, 2021 ) and challenges methodological individualism as the received explanatory primitive in the study of agency. Second, the methods used to research active matter systems demonstrate how a minimal approach to agency can scale up in studying interactive agential dynamics in more complex systems. The examples of coordination dynamics (Kelso, 2001 ) and participatory sense-making (De Jaegher & Di Paolo, 2007 ) are provided to show how understanding agency requires us to look beyond the individuals to the interactive agential dynamics that can guide, scaffold, or constrain their activity. (shrink)

Research has indicated that microRNAs (miRNAs), a special class of non-coding RNAs (ncRNAs), can perform important roles in different biological and pathological processes. miRNAs’ functions are realized by regulating their respective target genes (targets). It is thus critical to identify and analyze miRNA-target interactions for a better understanding and delineation of miRNAs’ functions. However, conventional knowledge discovery and acquisition methods have many limitations. Fortunately, semantic technologies that are based on domain ontologies can render great assistance in this regard. In (...) our previous investigations, we developed a miRNA domain-specific application ontology, Ontology for MIcroRNA Target (OMIT), to provide the community with common data elements and data exchange standards in the miRNA research. This paper describes (1) our continuing efforts in the OMIT ontology development and (2) the application of the OMIT to enable a semantic approach for knowledge capture of miRNA-target interactions. (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.

In order to re-contextualize the otherwise ontologically privileged meaning of metaphysical debates into a more insubstantial form, metaphysical deflationism runs the risk of having to adopt potentially unwanted anti-realist tendencies. This tension between deflationism and anti-realism can be expressed as follows: in order to claim truthfully that something exists, how can deflationism avoid the anti-realist feature of construing such claims singularly in an analytical fashion? One may choose to adopt a Yablovian fallibilism about existential claims, but other approaches can be (...) appealed to as well. Amie Thomasson's Easy Ontology is one such approach, whereby the interaction of empirical as well as analytic features within the construction of its ontological theory affords a role for analytical rules without forsaking a link with empirical reality. The development of these analytical and empirical features has resulted in significant critiques regarding, one, potential reference failure of easy-ontological claims, and two, a circularity in how easy ontology explains the relation between its analytical rules and existential claims. This essay offers a response by showcasing how an easy ontological deflationism can reject these criticisms without succumbing to, one, the anti-realism of pure analyticism, and two, a further critique of wholesale referential indeterminacy in its referring terms. (shrink)

The manufacturing industry is evolving rapidly, becoming more complex, more interconnected, and more geographically distributed. Competitive pressure and diversity of consumer demand are driving manufacturing companies to rely more and more on improved knowledge management practices. As a result, multiple software systems are being created to support the integration of data across the product life cycle. Unfortunately, these systems manifest a low degree of interoperability, and this creates problems, for instance when different enterprises or different branches of an enterprise interact. (...) Common ontologies (consensus-based controlled vocabularies) have proved themselves in various domains as a valuable tool for solving such problems. In this paper, we present a consensus-based Additive Manufacturing Ontology (AMO) and illustrate its application in promoting re-usability in the field of dentistry product manufacturing. (shrink)

Medical terminology collects and organizes the many different kinds of terms employed in the biomedical domain both by practitioners and also in the course of biomedical research. In addition to serving as labels for biomedical classes, these names reflect the organizational principles of biomedical vocabularies and ontologies. Some names represent invariant features (classes, universals) of biomedical reality (i.e., they are a matter for ontology). Other names, however, convey also how this reality is perceived, measured, and understood by health professionals (...) (i.e., they belong to the domain of epistemology). We analyze terms from several biomedical vocabularies in order to throw light on the interactions between ontological and epistemological components of these terminologies. We identify four cases: 1) terms containing classification criteria, 2) terms reflecting detectability, modality, uncertainty, and vagueness, 3) terms created in order to obtain a complete partition of a given domain, and 4) terms reflecting mere fiat boundaries. We show that epistemology-loaded terms are pervasive in biomedical vocabularies, that the “classes” they name often do not comply with sound classification principles, and that they are therefore likely to cause problems in the evolution and alignment of terminologies and associated ontologies. (shrink)

This paper examines the phenomenon of ‘interactive kinds’ first identified by Ian Hacking. An interactive kind is one that is created or significantly modified once a concept of it has been formulated and acted upon in certain ways. Interactive kinds may also ‘loop back’ to influence our concepts and classifications. According to Hacking, interactive kinds are found exclusively in the human domain. After providing a general account of interactive kinds and outlining their philosophical significance, I argue that they are not (...) confined to the human realm, but that they can also occur elsewhere. Hence, I conclude by arguing that interactive kinds pose a challenge to scientific realism about kinds by making it difficult to make a distinction between real and non-real kinds. (shrink)