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)

Cognitive biases can lead to misinterpretations of human and non-human biology and behavior. The concept of the Umwelt describes phylogenetic contrasts in the sensory realms of different species and has important implications for evolutionary studies of cognition (including biases) and social behavior. It has recently been suggested that the microbiome (the diverse network of microorganisms in a given environment, including those within a host organism such as humans) has an influential role in host behavior and health. In (...) this paper, we discuss the host’s microbiome in relation to cognitive biases and the concept of the Umwelt. Failing to consider the role of host–microbiome (collectively termed a “holobiont”) interactions in a given behavior, may underpin a potentially important cognitive bias – which we refer to as the Holobiont Blindspot. We also suggest that microbially mediated behavioral responses could augment our understanding of the Umwelt. For example, the potential role of the microbiome in perception and action could be an important component of the system that gives rise to the Umwelt. We also discuss whether microbial symbionts could be considered in System 1 thinking – that is, decisions driven by perception, intuition and associative memory. Recognizing Holobiont Blindspots and considering the microbiome as a key factor in the Umwelt and System 1 thinking has the potential to advance studies of cognition. Furthermore, investigating Holobiont Blindspots could have important implications for our understanding of social behaviors and mental health. Indeed, the way we think about how we think may need to be revisited. (shrink)

Current work in experimental biology revolves around a handful of animal species. Studying only a few organisms limits science to the answers that those organisms can provide. Nature has given us an overwhelming diversity of animals to study, and recent technological advances have greatly accelerated the ability to generate genetic and genomic tools to develop model organisms for research on host–microbe interactions. With the help of such models the authors therefore hope to construct a more complete picture of (...) the mechanisms that underlie crucial interactions in a given metaorganism (entity consisting of a eukaryotic host with all its associated microbial partners). As reviewed here, new knowledge of the diversity of host–microbe interactions found across the animal kingdom will provide new insights into how animals develop, evolve, and succumb to the disease. (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)

It is becoming increasingly clear that most, if not all, animals and plants are associated with a diverse array of resident gut microbiota. This symbiosis is regulated by host-microbiome interactions which influence the development, homeostasis, adaptation and evolution of the host. Recent evidence indicated that these interactions can also affect the host germline and have a potential of supporting transgenerational effects, including inheritance of acquired characteristics. Taken together, the influence of gut bacteria on the (...) host soma and germline could potentially give rise to emergent phenotypes, which may be partially inherited by three distinguishable modes of transgenerational influence of gut bacteria: 1) “soma-to-soma” 2) “soma-to-germline” and 3) “soma-germline-soma”. Here, we discuss these possibilities in light of evidence supporting bacterial-mediated modes of transgenerational inheritance. All animals are consortiums of hosts and microbiota. Their interactions influence many aspects of the adaptation and evolution of the Holobiont. The host germline can also be affected which can give rise to new modes of transgenerational influence of gut bacteria: 1) “soma-to-soma” 2) “soma-to-germline,” and 3) “soma-germline-soma.”. (shrink)

The dual role of microbial communities as either beneficial/functional or harmful/pathogenic involves two issues concerning causality in physiology and medicine, etiology of disease, and the notion of function in biology. Causal explanation formulated by the germ theory of disease and the Koch postulates connects the existence of a specifically identified microbe to disease by the isolation and identification of a pathogen from an organism with the disease and the successful infection of a healthy individual. Similarly, microbiome research in medicine (...) centers on taxonomic composition in correlation with physiological conditions and germ-free mice experimentations to establish causal connections. However, because the microbiome is an ecological community, it lacks the specificity of identification assumed in the germ theory. Furthermore, the ecological aspects within and between microbiomes such as background conditions, microbial interactions, and interdependence, are treated as confounding. Looking at ecological studies, the causal explanations are less specific regarding complex systems with their processes of interactions. This article makes the following two points: One is that microbiome causality in the host should be understood similarly to the microbiome causality in an ecosystem. The second is that if considering a microbiome’s causality in the host as an ecosystem, its etiological explanation needs to be revisited to include a heterogeneous and mutual notion of interactions. Finally, according to the second point, the notion of function in ecology with its relevant notion of causality should be considered accordingly. (shrink)

It has become increasingly clear that there is a vast array of microorganisms on and in the human body, known collectively as the human microbiome. Our microbiomes are extraordinarily complex, and this complexity has been linked to human health and well-being. Given the complexity and importance of our microbiomes, we struggle with how to think about them. There is a long list of competing metaphors that we use to refer to our microbiomes, including as an “organ” containing our “second (...) genome,” as a “symbiont” in the human “holobiont,” and as an ecological “community” in the human “ecosystem,” among others. Each of these makes different assumptions about the fundamental biology of the human-microbe system, with important implications for how we choose to study microbiomes, and the therapies we envision for correcting microbiome-linked disorders. We believe that it is time to move beyond metaphors, and we propose a scientifically pluralist approach that focuses on characterizing fundamental biological properties of microbiomes such as heritability, transmission mode, rates of dispersal rates, and strength of local selection. Such an approach will allow us to break out of the confines of narrow conceptual frameworks, and to guide the exploration of our complexity as chimeric beings. (shrink)

Coral reefs have been challenged by the current rate and severity of environmental change that might outpace their ability to adapt and survive. Current research focuses on understanding how microbial communities and epigenetic changes separately affect phenotypes and gene expression of corals. Here, we provide the hypothesis that coral‐associated microorganisms may directly or indirectly affect the coral's phenotypic response through the modulation of its epigenome. Homologs of ankyrin‐repeat protein A and internalin B, which indirectly cause histone modifications in humans, as (...) well as Rv1988 histone methyltransferase, and the DNA methyltransferases Rv2966c, Mhy1, Mhy2, and Mhy3 found in coral‐associated bacteria indicate that there are potential host epigenome‐modifying proteins in the coral microbiome. With the ideas presented here, we suggest that microbiome manipulation may be a means to alter a coral's epigenome, which could aid the current efforts to protect coral reefs. Also see the video abstract here: https://youtu.be/CW9GbChjKM4. (shrink)

Animals exist as biodiverse composite organisms that include microbial residents, eukaryotic cells, and organs that collectively form a human being. Through an interdependent relationship and an inherent ability to transmit and reciprocate stimuli in a bidirectional way, a human body or the holobiont secures growth, health, and reproduction. As such, the survival of a holobiont is dependent on the maintenance of biological order including metabolic homeostasis by tight regulation of the communication between its eukaryotic and prokaryotic residents. In this review (...) an overview and perspective are provided on the bidirectional communication between microbes and their host in mutually nurturing biochemical, biological, and social interconnected relationships between the components of the holobiont. An emphasis is placed on exemplifying microbiome‐mediated effects on host functions—aiming to integrate microbiome functionality to host physiology, be it health or disease. Nutrition, immunology, and sexual dimorphism have been traversed extensively to reflect on health and mind states, social interactions, and urbanization defects/effects. Finally, examples of molecular mechanisms potentially orchestrating these complex transkingdom interactions are provided. (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)

This paper analyzes epistemological and ontological dimensions of Human-Computer Interaction (HCI) through an analysis of the functions of computer systems in relation to their users. It is argued that the primary relation between humans and computer systems has historically been epistemic: computers are used as information-processing and problem-solving tools that extend human cognition, thereby creating hybrid cognitive systems consisting of a human processor and an artificial processor that process information in tandem. In this role, computer systems extend human cognition. Next, (...) it is argued that in recent years, the epistemic relation between humans and computers has been supplemented by an ontic relation. Current computer systems are able to simulate virtual and social environments that extend the interactive possibilities found in the physical environment. This type of relationship is primarily ontic, and extends to objects and places that have a virtual ontology. Increasingly, computers are not just information devices, but portals to worlds that we inhabit. The aforementioned epistemic and ontic relationships are unique to information technology and distinguish human-computer relationships from other human-technology relationships. (shrink)

Reorganization of cell organelle‐deprived host red blood cells by the apicomplexan malaria parasite Plasmodium falciparum enables their cytoadherence to endothelial cells that line the microvasculature. This increases the time red blood cells infected with mature developmental stages remain within selected organs such as the brain to avoid the spleen passage, which can lead to severe complications and cumulate in patient death. The Maurer's clefts are a novel secretory organelle of parasite origin established by the parasite in the cytoplasm of (...) the host red blood cell in order to facilitate the establishment of cytoadherence by conducting the trafficking of immunovariant adhesins to the host cell surface. Another important function of the organelle is the sorting of other proteins the parasite traffics into its host cell. Although the organelle is of high importance for the pathology of malaria, additional putative functions, structure, and genesis remain shrouded in mystery more than a century after its discovery. In this review, we highlight our current knowledge about the Maurer's clefts and other novel secretory organelles established within the host cell cytoplasm by human‐pathogenic malaria parasites and other parasites that reside within human red blood cells. (shrink)

Lopes (2010) offers an account of computer art, which he argues is a new art form. Part of what makes computer art distinctive, according to Lopes, is its interactivity, a quality found in few non-computer artworks. Given the rise in prominence of such artworks, most notably videogames, they are surely worthy of philosophical inquiry. I believe their ontology and properties are particularly worthy of study, as an understanding of these will prove crucial to critical understanding and evaluation of the (...) works themselves. Lopes’ account of interactive art is novel and important, but flawed, and in this essay I will discuss its flaws and suggest a better account of the properties of interactive art that builds on his work, providing a partial account of the ontology of interactive art. In Section 1, I discuss Lopes’ definition and ontology of interactive art; in Section 2, I argue that he only accounts for the properties of displays, neglecting the properties of interactive artworks themselves. In Section 3, I discuss several possible solutions for Lopes and why they are inadequate before Section 4 presents my view, that interactive artworks possess all of the properties of their varying displays because each possible display is part of the artwork. This is compatible with Lopes’ definition of interactive art, and so much of his account can be preserved, but with a refined account of the properties of interactive artworks. What I present is by no means a complete ontological study of interactive art, but hopefully lays the groundwork for future work on this ontology. (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)

Here we evaluate our current understanding of the function of the nervous system in Hydra, a non‐bilaterian animal which is among the first metazoans that contain neurons. We highlight growing evidence that the nervous system, with its rich repertoire of neuropeptides, is involved in controlling resident beneficial microbes. We also review observations that indicate that microbes affect the animal's behavior by directly interfering with neuronal receptors. These findings provide new insight into the original role of the nervous system, and suggest (...) that it emerged to orchestrate multiple functions including host‐microbiome interactions. The excitement of future research in the Hydra model now relies on uncovering the common rules and principles that govern the interaction between neurons and microbes and the extent to which such laws might apply to other and more complex organisms. (shrink)

Human evolution has been punctuated by climate anomalies, structuring environments, deadly infections, and altering landscapes. How well humans adapted to these new circumstances had direct effects on fitness and survival. Here, how the gut microbiome could have contributed to human evolutionary success through contributions to host nutritional buffering and infectious disease resistance is reviewed. How changes in human genetics, diet, disease exposure, and social environments almost certainly altered microbial community composition is also explored. Emerging research points to the (...) microbiome as a key player in host responses to environmental change. Therefore, the reciprocal interactions between humans and their microbes are likely to have shaped human patterns of local adaptation throughout our shared evolutionary history. Recent alterations in human lifestyle, however, are altering human microbiomes in unprecedented ways. The consequences of interrupted host–microbe relationships for human adaptive potential in the future are unknown. (shrink)

I examine the feminist epistemic values in science, presented by Helen Longino, and their role in framing microbiome causality in the study of inflammatory bowel disease (IBD). In particular, I show how values presented as feminist give an alternative view in scientific theories—focusing on ontological heterogeneity and mutuality of interactions rather than simplicity and one causal direction—when looking at relations between organisms and microorganisms, and between organisms (particularly humans) and their environment. I identify two approaches in microbiome (...) study, an immunological approach that looks at the microbiome pathogenicity and an ecological approach that studies the microbial activity and functions. I show the puzzles stemming from the traditional background beliefs of the immune self and germ theory in the study of IBD causality. Furthermore, I argue for the benefits of a shift to the ecological view of body-microbe interrelations. I conclude with the benefits and advantages of feminist values over traditional ones, both in creating new ways of understanding organisms’ physiology and immune systems and for future biomedical studies involving microbiome causality. (shrink)

During the Nineties, the diffusion of information and communication technologies allowed a dramatic transformation in art practices. Radically new aesthetic experiences, such as tele-presence, immersivity, responsivity, hyper-mediacy and multimediality, emerge in the framework of the digital arts and call into question not only the traditional status of the work of art but also the fundamental relation with the beholder. The aim of this paper is to define a conceptual framework for the ontology of digital arts by identifying some ontological (...) features that are distinctive to digital idioms. Such an analysis tries to outline how aesthetic and technical innovations affect our cognitive and sensorial relationship with technological artifacts. In the first part, the relation between technogenesis and ontology, as well as the key topics of the ontology of digital arts are discussed. The second part deals with the notion of presence. Despite traditional understandings of digital arts, mainly focused on immateriality, simulation and mediation, my analysis demonstrate how the notion of presence can provide an original perspective in order to understand the ontological status of the mediatized artistic practices. In the last three decades the generalisation of information and telecommunication technologies has played a major role in the transformation of the arts, opening the field to important experiments in the domain of computer graphics, digital audio, robotics and motion capture systems… (Dixon 2007). Peculiar forms of aesthetic experience such as tele-presence, immersivity, responsivity, hyper-mediation and multimediality, progressively arise from digital arts and question not only the status of artwork but also, more generally, the foundational relationship between this latter and the recipient. (shrink)

Cognitive control is not only componential, but those components may interact in complicated ways in the service of cognitive control tasks. This complexity poses a challenge for developing an ontological description, because the mapping may not be direct between our task descriptions and true component differences reflected in indicators. To illustrate this point, I discuss two examples: (a) the relationship between adaptive gating and working memory and (b) the recent evidence for a control hierarchy. From these examples, I argue that (...) an ontological program must simultaneously seek to identify component processes and their interactions within a broader processing architecture. (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)

Schistosomes are parasitic blood flukes, responsible for significant human disease in tropical and developing nations. Here we review information on the organization of the cytoskeleton and associated motor proteins of schistosomes, with particular reference to the organization of the syncytial tegument, a unique cellular adaptation of these and other neodermatan flatworms. Extensive EST databases show that the molecular constituents of the cytoskeleton and associated molecular systems are likely to be similar to those of other eukaryotes, although there are potentially some (...) molecules unique to schistosomes and platyhelminths. The biology of some components, particular those contributing to host–parasite interactions as well as chemotherapy and immunotherapy are discussed. Unresolved questions in relation to the structure and function of the tegument relate to dynamic organization of the syncytial layer. BioEssays 26:752–765, 2004. © 2004 Wiley Periodicals, Inc. (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)

The host actin nucleation machinery is subverted by many bacterial pathogens to facilitate their entry, motility, replication, and survival. The majority of research conducted in the past primarily focused on exploitation of a host actin nucleator, the Arp2/3 complex, by bacterial pathogens. Recently, new studies have begun to explore the role of formins, another family of host actin nucleators, in bacterial pathogenesis. This review provides an overview of recent advances in the study of the exploitation of the (...) Arp2/3 complex and formins by bacterial pathogens. Secreted bacterial effector proteins seem to manipulate the regulation of these actin nucleators or functionally mimic them to drive bacterial entry, motility and survival within host cells. An enhanced understanding of how formins are exploited will provide us with greater insight into how a fundamental eurkaryotic cellular process is utilized by bacteria and will also advance our knowledge of host‐pathogen interactions. (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)

Given one conception of biological individuality (evolutionary, physiological, etc.), can a holobiont – that is the host + its symbiotic (mutualistic, commensalist and parasitic) microbiome – be simultaneously a biological individual and an ecological community? Herein, we support this possibility by arguing that the notion of biological individuality is part‐dependent. In our account, the individuality of a biological ensemble should not only be determined by the conception of biological individuality in use, but also by the biological characteristics of (...) the part of the ensemble under investigation. In the specific case of holobionts, evaluations of their individuality should be made either host‐relative or microbe‐relative. We support the claim that biological individuality is part‐dependent by drawing upon recent empirical evidence regarding the physiology of hosts and microbes, and the recent characterization of the ‘demibiont’. Our account shows that contemporary disagreements about the individuality of the holobiont derive from an incorrect understanding of the ontology of biological individuality. We show that collaboration between philosophers and biologists can be very fruitful in attempts to solve some contemporary biological debates. (shrink)

The expression of products encoded by the major histocompatibility complex (MHC) on tumor cells has recently been studied extensively. It has been found that many malignant tumor cells have their MHC antigens ‘switched‐off’ but that these antigens are re‐expressed following DNA‐mediated gene transfer, with increased tumor immunogenicity as a result and the consequence that these ‘transformed’ tumor cells are rejected in vivo.: This review will discuss approaches that have been taken to induce strong tumor‐specific immunity by the manipulation of MHC (...) expression on tumor cells. (shrink)

The ontology of Ortega y Gasset crystallized slowly between the years of 1934 and 1945. These were years of exile, years of war and financial insecurity that forced him to move from country to country. His health too was sorely tested on various occasions during this period. Remoteness from intellectual resources, familiar libraries, co-laborers, were doubtlessly disturbing obstacles to his progress. Ortega was fifty in 1933; yet for all these hindrances the next decade of his life was his most (...) ambitiously productive. (shrink)

This paper argues that Spinoza's notions of “conatus” and “power of acting” are derived by means of generalization from the notions of “force of motion” and “force of determination” that Spinoza discussed in his Principles of Cartesian Philosophy to account for interactions among bodies on the basis of their degrees of contrariety. I argue that in the Ethics, Spinoza's ontology entails that interactions must always be accounted for in terms of degrees of “agreement or disagreement in nature” (...) among interacting things. The notion of “power of acting” is used to express the extent to which a thing's conatus is aided or restrained by external causes on the basis of its degree of agreement or disagreement in nature with them. “Power of acting” generalizes the same approach and method of resolution at the basis of the notion of “force of determination” in order to account for causal interactions not only among the simplest bodies but also among more complex individuals. (shrink)

Jeffrey E. Brower presents and explains the hylomorphic conception of the material world developed by Thomas Aquinas, according to which material objects are composed of both matter and form. In addition to presenting and explaining Aquinas's views, Brower seeks wherever possible to bring them into dialogue with the best recent literature on related topics. Along the way, he highlights the contribution that Aquinas's views make to a host of contemporary metaphysical debates, including the nature of change, composition, material constitution, (...) the ontology of stuff vs. things, the proper analysis of ordinary objects, the truthmakers for essential vs. accidental predication, and the metaphysics of property possession. (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)

Parallel lives is an ontological model of nature in which quantum mechanics and special relativity are unified in a single universe with a single space-time. Point-like objects called lives are the only fundamental objects in this space-time, and they propagate at or below c, and interact with one another only locally at point-like events in space-time, very much like classical point particles. Lives are not alive in any sense, nor do they possess consciousness or any agency to make decisions—they are (...) simply point objects which encode memory at events in space-time. The only causes and effects in the universe occur when lives meet locally, and thus the causal structure of interaction events in space-time is Lorentz invariant. Each life traces a continuous world-line through space-time, and experiences its own relative world, fully defined by the outcomes of past events along its world-line, which are encoded in its external memory. A quantum field comprises a continuum of lives throughout space-time, and familiar physical systems like particles each comprise a sub-continuum of the lives of the field. Each life carries a hidden internal memory containing a local relative wavefunction, which is a local piece of a pure universal wavefunction, but it is the relative wavefunctions in the local memories throughout space-time which are physically real in PL, and not the universal wavefunction in configuration space. Furthermore, while the universal wavefunction tracks the average behavior of the lives of a system, it fails to track their individual dynamics and trajectories. There is always a preferred separable basis, and for an irreducible physical system, each orthogonal term in this basis is a different relative world—each containing some fraction of the lives of the system. The relative wavefunctions in the lives’ internal memories govern which lives of different systems can meet during future local interactions, and thereby enforce entanglement correlations—including Bell inequality violations. These, and many other details, are explored here, but several aspects of this framework are not yet fleshed out, and work is ongoing. (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)

Successful therapies to combat microbial diseases and cancers require incorporating ecological and evolutionary principles. Drawing upon the fields of ecology and evolutionary biology, we present a systems‐based approach in which host and disease‐causing factors are considered as part of a complex network of interactions, analogous to studies of “classical” ecosystems. Centering this approach around empirical examples of disease treatment, we present evidence that successful therapies invariably engage multiple interactions with other components of the host ecosystem. Many (...) of these factors interact nonlinearly to yield synergistic benefits and curative outcomes. We argue that these synergies and nonlinear feedbacks must be leveraged to improve the study of pathogenesis in situ and to develop more effective therapies. An eco‐evolutionary systems perspective has surprising and important consequences, and we use it to articulate areas of high research priority for improving treatment strategies. (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)

Praxis is the identifying signature of the most prevalent contemporary versions of the reception and interpretation of Marx and of the movements of thought inspired or provoked by him. This view seems to accord well with the early “Theses on Feuerbach” and is frequently mobilized in support of the further claim that the “mature” or “scientific” Marx, the Marx of Das Kapital, above all had left behind his former preoccupations with philosophy in anything like a traditional sense, in order to (...) pursue single-mindedly and whole-heartedly his critical diagnosis of bourgeois political economy, the opening wedge in his “practical” campaign to establish first socialism and then communism. In this essay, I want to call into question some of the central commitments of this consensus. In particular, I shall suggest that Marx’s understanding of praxis, of human activity and interaction, is pervasively shaped by his conception of poiesis, the production of hitherto non-existing objects and, therewith, the ongoing transformation of external Nature. Accordingly, appreciations of Marx’s supposedly revolutionary transfiguration of the relation between theoria and praxis need to be recast and reconstrued in light of his reduction of praxis to technical production. Poiesis is the cardinal, indeed the unique, category in the ontological vocabulary Marx adopted in his earliest works and never abandoned afterwards, even when he went on to treat ontological issues much more economically. This monochromatic vocabulary so colored Marx’s analysis of the nature and civic places of labor and human interrelations, that both tended to lose the variegated contours by which pre-modern, if not all pre-Marxist, thinkers recognized them. Marx’s elliptical, not to say sibylline, allusions to the condition and the telos of “socialized humanity” in the Grundrisse and in the final volume of Das Kapital prove so perplexing exactly because ‘labor’ itself has become paradoxical—does it figure with equal prominence in both the ‘realm of necessity’ and the ‘realm of freedom’?—while praxis, once it seems finally set free from the spell cast on it by the presumptive ultimacy of poiesis, appears to lose its bearings, its pre-modern orientation to a goal such as achieved and mutually-acknowledged human excellence. The claims and promises of praxis turn out to be deeply enigmatic. (shrink)

This paper offers an account of the social foundations of a theory of democracy. It purports to show that a social ontology of democracy is the necessary counterpart of a political theory of democracy. It notably contends that decisions concerning basic social ontological assumptions are relevant not only for empirical research, but bear a significant impact also on normative theorizing. The paper then explains why interactionist rather than substantialist social ontologies provide the most promising starting point for building a (...) social ontology of democracy. It then introduces and examines the three notions of habits, patterns of interaction, and forms of social organization, conceived as the main pillars of an interactionist social ontology of democracy and briefly discusses some major implications of this approach for democratic theory. (shrink)

We are all immersed in a sea of social norms, but they are sometimes tricky to observe with any clarity. They are often invisible to us and emerge only when they are not observed. Social norms are important to understand because they are both limiting of our freedom, such as gendered and racialized norms, and at the same time the very conditions of our agency. Social Goodness presents an original, externalist answer to the question of the source or origin of (...) social role normativity. Rather than grounding social normativity in the attitudes of persons, the book argues for an externalism that roots social role normativity in the social world itself: in its positions, institutions, and larger architecture. The core insight of externalism is that the function or structural feature of an enterprise or activity can bring with it normative demands quite independently of the attitudes of those who engage with it. According to the artisanal model, just as a carpenter, ceramicist, or chef is responsive to and evaluable under a set of artisanal norms or techniques, so too is a mother and or an academic or a President. The source of normativity is this technique or expertise, independent of the preferences, endorsements, or recognitive attitudes of individuals. The artisanal model for social role normativity has resources to explain both the "stickiness" or persistence of social norms and our ability to criticize existing norms and to engage in normative self-creation--to create new normative selves. The artisanal model also has resources to capture and express the social situatedness, locality, and materiality of social roles. The relational ontology of social roles, implicit in the artisanal model, provides a useful frame to consider both hierarchical and oppressive social relations. (shrink)

Discrimination is a social phenomenon which seems to be widespread across different societies and cultures. Examples of discrimination concerning race, class, gender, and sexual orientation are not difficult to find in contemporary western societies. In this article, the author focus on the ontological ground of this phenomenon, with particular attention to its diffuse and institutionalised forms. The author defends a broadly speaking reductionist approach, according to which the various manifestations of discrimination are grounded on the existence of the effects of (...) “discriminatory stances” in social contexts. Discrimination may become part of the institutional sphere, either by way of bottom-up “crystallisation” of discriminatory practices, or by top-down “dilution” of institutional defaults into ordinary interactions. (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)

The concept of digital culture defines a set of values, practices, and expectations regarding the format of human interaction in today’s online society. Predictions of digital culture describe the specifics of the online environment and the general context of social life. The range of interpretations of digital culture varies between two poles: from the recognition of digital technologies as a way of presenting libraries, museums, historical monuments, etc., to the concepts of digital culture as a new socio-anthropological reality, the content (...) of which is not limited to ICT. Culture as a phenomenon means the semantic unity of human activity, the desire to format social life following ideas and values, the movement from existing to obligatory, from actual to potential, and digital culture is an adequate response to the demands and challenges. People worldwide change their placement of everyday activity, and we could admit such huge transformation in the Chinese People’s Republic exactly obvious. (shrink)

In the past half century, the theory of the firm has become a specific and prolific research field. However, the social ontology of this central institution of capitalism has never truly been the subject of investigation. I consider this negligence harmful for organizational economics and management and, more broadly, for the social sciences, notably because the first and central question raised by the theory of the firm relates to its nature: What is a firm? For this reason, I propose (...) some novel considerations for a social ontology of the firm by focusing on social emergence, reconstitution, the two-level institutional logic of the firm, complex organizational dynamics and interacting mechanisms, and power. (shrink)

The microbiome of human hair follicles (HFs) has emerged as an important player in different HF and skin pathologies, yet awaits in‐depth exploration. This raises questions regarding the tightly linked interactions between host environment, nutrient dependency of host‐associated microbes, microbial metabolism, microbe‐microbe interactions and host immunity. The use of simple model systems facilitates addressing generally important questions and testing overarching, therapeutically relevant principles that likely transcend obvious interspecies differences. Here, we evaluate the potential of (...) the freshwater polyp Hydra, to dissect fundamental principles of microbiome regulation by the host, that is the human HF. In particular, we focus on therapeutically targetable host‐microbiome interactions, such as nutrient dependency, microbial interactions and host defence. Offering a new lens into the study of HF – microbiota interactions, we argue that general principles of how Hydra manages its microbiota can inform the development of novel, microbiome‐targeting therapeutic interventions in human skin disease. (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)

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)