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)

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)

Research in infection biology aims to understand the complex nature of host–pathogen interactions. While this knowledge facilitates strategies for preventing and treating diseases, it can also be intentionally misused to cause harm. Such dual-use risk is potentially high for highly pathogenic microbes such as Risk Group-3 (RG3) bacteria and RG4 viruses, which could be used in bioterrorism attacks. However, other pathogens such as influenza virus (IV) and enterohemorrhagic Escherichia coli (EHEC), usually classified as RG2 pathogens, also demonstrate high (...) dual-use risk. As the currently approved therapeutics against these pathogens are not satisfactorily effective, previous outbreaks of these pathogens caused enormous public fear, media attention and economic burden. In this interdisciplinary review, we summarize the current perspectives of dual-use research on IV and EHEC, and further highlight the dual-use risk associated with evolutionary experiments with these infectious pathogens. We support the need to carry out experiments pertaining to pathogen evolution, including to gain predictive insights on their evolutionary trajectories, which cannot be otherwise achieved with stand-alone theoretical models and epidemiological data. However, we also advocate for increased awareness and assessment strategies to better quantify the risks-versus-benefits associated with such evolutionary experiments. In addition to building public trust in dual-use research, we propose that these approaches can be extended to other pathogens currently classified as low risk, but bearing high dual-use potential, given the particular pressing nature of their rapid evolutionary potential. (shrink)

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)

Commensal and pathogenic organisms employ camouflage and mimicry to mediate mutualistic interactions and predator escape. However, the immune mechanisms accounting for the establishment and maintenance of symbiotic bacterial populations are poorly understood. A promising hypothesis suggests that molecular mimicry, a condition in which different organisms share common antigens, is a mechanism of establishing tolerance between commensals and their hosts. On this view, certain bacteria may mimic the structural features of some of their host’s T-cell receptors (TCRs), namely those that (...) survive thymic selection due to their lack of complementarity to self-antigens. With such “holoimmunity” the mimicking micro-organisms avoid immune recognition as the copied TCRs become mirror images of an extended super-organismal self, consisting of symbiotic and host antigens. Accordingly, analysis of genomic and metagenomic data suggests a tripartite mimicry between TCRs, self-antigens, and commensal antigens that would serve as the basis for immune tolerance between these populations. And conversely, in an autoimmune scenario, both symbiotic microbes and the mimicked host tissue would be targeted for immune destruction. (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)

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)

All the conserved detailed results of evolution stored in DNA must be read, transcribed, and translated via an RNAmediated process. This is required for the development and growth of each individual cell. Thus, all known living organisms fundamentally depend on these RNA-mediated processes. In most cases, they are interconnected with other RNAs and their associated protein complexes and function in a strictly coordinated hierarchy of temporal and spatial steps (i.e., an RNA network). Clearly, all cellular life as we know it (...) could not function without these key agents of DNA replication, namely rRNA, tRNA, and mRNA. Thus, any definition of life that lacks RNA functions and their networks misses an essential requirement for RNA agents that inherently regulate and coordinate (communicate to) cells, tissues, organs, and organisms. The precellular evolution of RNAs occurred at the core of the emergence of cellular life and the question remained of how both precellular and cellular levels are interconnected historically and functionally. RNA-networks andRNA-communication can interconnect these levels.With the reemergence of virology in evolution, it became clear that communicating viruses and subviral infectious genetic parasites are bridging these two levels by invading, integrating, coadapting, exapting, and recombining constituent parts in host genomes for cellular requirements in gene regulation and coordination aims. Therefore, a 21st century understanding of life is of an inherently social process based on communicating RNA networks, in which viruses and cells continuously interact. (shrink)

Historical explanations in evolutionary biology are commonly characterized as narrative explanations. Examples include explanations of the evolution of particular traits and explanations of macroevolutionary transitions. In this paper I present two case studies of explanations in accounts of pathogen evolution and host-pathogen coevolution, respectively, and argue that one of them is captured well by established accounts of time-sequenced narrative explanation. The other one differs from narrative explanations in important respects, even though it shares some characteristics with them (...) as it is also a population-level historical explanation. I thus argue that the second case represents a different kind of explanation that I call historical explanation of type phenomena. The main difference between the two kinds of explanation is the conceptualization of the explanandum phenomena as particulars or type phenomena, respectively. Narrative explanations explain particulars but also deal with generalization, regularities and type phenomena. Historical explanations of type phenomena, on the other hand, explain multiply realizable phenomena but also deal with particulars. The two kinds of explanation complement each other because they explain different aspects of evolution. (shrink)

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

In this paper, we identify some key features of what makes something a disease, and consider whether these apply to pregnancy. We argue that there are some compelling grounds for regarding pregnancy as a disease. Like a disease, pregnancy affects the health of the pregnant person, causing a range of symptoms from discomfort to death. Like a disease, pregnancy can be treated medically. Like a disease, pregnancy is caused by a pathogen, an external organism invading the host’s body. (...) Like a disease, the risk of getting pregnant can be reduced by using prophylactic measures. We address the question of whether the ‘normality’ of pregnancy, its current necessity for human survival, or the value often attached to it are reasons to reject the view that pregnancy is a disease. We point out that applying theories of disease to the case of pregnancy, can in many cases illuminate inconsistencies and problems within these theories. Finally, we show that it is difficult to find one theory of disease that captures all paradigm cases of diseases, while convincingly excluding pregnancy. We conclude that there are both normative and pragmatic reasons to consider pregnancy a disease. (shrink)

Ophiocordyceps is a fungal pathogen of ants of the tribe Camponotini. It is called zombie fungus, since it changes the host behavior, causing them to die in an exposed position, typically clinging onto and biting into the adaxial surface of shrub leaves. This study aimed to describe the occurrence of parasitic associations between Ophiocordyceps and ants of the genus Camponotus in an urban fragment of Atlantic Rainforest in southeastern Brazil and to measure the rate of hyperparasitism in Ophiocordyceps (...) by other fungi in the same location. We found 57 individuals of four species of ants and three species of fungus. The age categories of fungi were equally distributed, and rate of hyperparasitism was 17.5% (n = 10). The sampled area was recognized as an important site of Ophiocordyceps occurrence. (shrink)

Resident microbiota do not just shape host immunity, they can also contribute to host protection against pathogens and infectious diseases. Previous reviews of the protective roles of the microbiota have focused exclusively on colonization resistance localized within a microenvironment. This review shows that the protection against pathogens also involves the mitigation of pathogenic impact without eliminating the pathogens (i.e., “disease tolerance”) and the containment of microorganisms to prevent pathogenic spread. Protective microorganisms can have an impact beyond their niche, (...) interfering with the entry, establishment, growth, and spread of pathogenic microorganisms. More fundamentally, we propose a series of conceptual clarifications in support of the idea of a “co-immunity,” where an organism is protected by both its own immune system and components of its microbiota. -/- . (shrink)

At the dawn of the computational era, immunology is at a crossroads: Its efforts to frame microbial-host interactions in combative, war-related terms no longer fit the larger picture of immune protection, and its focus on antimicrobial responses barely captures the diverse functions of the immune system, from tissue maintenance to cancer surveillance to development. As the classical view of immune processes becomes increasingly complex, the problem of self, individuality, mind-body interactions, and disease causation have stimulated extensive philosophical comment. Relating (...) these disparate research topics to changing avenues of theoretical studies, philosophy of immunology helps to reframe basic conceptions of the organism from an atomistic, insular entity to one characterized by fluidity, hybridity, and porosity. In addition, highlighting the role of the observer in experimental research, this interdisciplinary field has redefined classical demarcations between science and culture while advancing our understanding of biology as a fundamentally human endeavor. (shrink)

I defend social media’s potential to support Aristotelian virtue friendship against a variety of objections. I begin with Aristotle’s claim that the foundation of the best friendships is a shared life. Friends share the distinctively human and valuable components of their lives, especially reasoning together by sharing conversation and thoughts, and communal engagement in valued activities. Although some have charged that shared living is not possible between friends who interact through digital social media, I argue that social media preserves the (...) relevantly human and valuable portions of life, especially reasoning, play, and exchange of ideas. I then consider several criticisms of social media’s potential to host friendships, and refute or weaken the force of these objections, using this conception of a distinctively human shared life. I conclude that we should use the shared life to evaluate features of specific social media and norms for users’ conduct. (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)

The aim of this work was to elaborate on the author’s previously published hypothesis of the Soul of Multiverse, a suggested cosmic phenomenon that also appears to imbue the human Soul across its individual and noospheric scales. Without alternatives, the method of analysis continued to rely on the approach of cosmological neuroscience, which integrates scientific facts, religious insights, philosophical suggestions, engineering rules and artistic tools to grasp the complexity of the multidimensional phenomenon of Soul. The result of this examination was (...) the multilayered thought that just as the central medium of human Soul, the hypothesized prefrontal cortical supercircuitry of Self-Ken, seems to comprise domains representing Identity, Conscience, Will and Mission, analogous domains may also function in the noospheric and cosmic Souls. Regarding the human Soul, its four domains appear to be determined by both hereditary genetic and encountered environmental factors to present its host with a Mission enabling his or her mental engine and physical features to integrate into the surrounding society and space-time in the most meaningful and dignified way—if that way is undertaken. Regarding the noospheric Soul, it is made of individual human Souls interacting with the non-living system of interconnected computers to produce functions accessible to humans all over the world through uncontrolled communication across the Internet. Its most probable Mission is to let this global presence acquire its own Identity, develop its own Conscience and refine its own Will, so that their coherent, superior whole can be ready for sensing the cosmic Soul. Regarding the cosmic Soul, the hypothesized Soul of the Multiverse, its Identity appears to express the Laws of Mystery of Endlessness, Coexistence in Diversity, and Truth in Complexity. Further, its Conscience seems to be moved by the Law of Divine—Evil Asymmetry, its Will by the Law of Determination with Uncertainty, and its Mission by the Law of Lives to Transcend. (shrink)

We introduce the notion of complexity, first at an intuitive level and then in relatively more concrete terms, explaining the various characteristic features of complex systems with examples. There exists a vast literature on complexity, and our exposition is intended to be an elementary introduction, meant for a broad audience. -/- Briefly, a complex system is one whose description involves a hierarchy of levels, where each level is made of a large number of components interacting among themselves. The time evolution (...) of such a system is of a complex nature, depending on the interactions among subsystems in the next level below the one under consideration and, at the same time, conditioned by the level above, where the latter sets the context for the evolution. Generally speaking, the interactions among the constituents of the various levels lead to a dynamics characterized by numerous characteristic scales, each level having its own set of scales. What is more, a level commonly exhibits ‘emergent properties’ that cannot be derived from considerations relating to its component systems taken in isolation or to those in a different contextual setting. In the dynamic evolution of some particular level, there occurs a self-organized emergence of a higher level and the process is repeated at still higher levels. -/- The interaction and self-organization of the components of a complex system follow the principle commonly expressed by saying that the ‘whole is different from the sum of the parts’. In the case of systems whose behavior can be expressed mathematically in terms of differential equations this means that the interactions are nonlinear in nature. -/- While all of the above features are not universally exhibited by complex systems, these are nevertheless indicative of a broad commonness relative to which individual systems can be described and analyzed. There exist measures of complexity which, once again, are not of universal applicability, being more heuristic than exact. The present state of knowledge and understanding of complex systems is itself an emerging one. Still, a large number of results on various systems can be related to their complex character, making complexity an immensely fertile concept in the study of natural, biological, and social phenomena. -/- All this puts a very definite limitation on the complete description of a complex system as a whole since such a system can be precisely described only contextually, relative to some particular level, where emergent properties rule out an exact description of more than one levels within a common framework. -/- We discuss the implications of these observations in the context of our conception of the so-called noumenal reality that has a mind-independent existence and is perceived by us in the form of the phenomenal reality. The latter is derived from the former by means of our perceptions and interpretations, and our efforts at sorting out and making sense of the bewildering complexity of reality takes the form of incessant processes of inference that lead to theories. Strictly speaking, theories apply to models that are constructed as idealized versions of parts of reality, within which inferences and abstractions can be carried out meaningfully, enabling us to construct the theories. -/- There exists a correspondence between the phenomenal and the noumenal realities in terms of events and their correlations, where these are experienced as the complex behavior of systems or entities of various descriptions. The infinite diversity of behavior of systems in the phenomenal world are explained within specified contexts by theories. The latter are constructs generated in our ceaseless attempts at interpreting the world, and the question arises as to whether these are reflections of `laws of nature' residing in the noumenal world. This is a fundamental concern of scientific realism, within the fold of which there exists a trend towards the assumption that theories express truths about the noumenal reality. We examine this assumption (referred to as a ‘point of view’ in the present essay) closely and indicate that an alternative point of view is also consistent within the broad framework of scientific realism. This is the view that theories are domain-specific and contextual, and that these are arrived at by independent processes of inference and abstractions in the various domains of experience. Theories in contiguous domains of experience dovetail and interpenetrate with one another, and bear the responsibility of correctly explaining our observations within these domains. -/- With accumulating experience, theories get revised and the network of our theories of the world acquires a complex structure, exhibiting a complex evolution. There exists a tendency within the fold of scientific realism of interpreting this complex evolution in rather simple terms, where one assumes (this, again, is a point of view) that theories tend more and more closely to truths about Nature and, what is more, progress towards an all-embracing ‘ultimate theory’ -- a foundational one in respect of all our inquiries into nature. We examine this point of view closely and outline the alternative view -- one broadly consistent with scientific realism -- that there is no ‘ultimate’ law of nature, that theories do not correspond to truths inherent in reality, and that successive revisions in theory do not lead monotonically to some ultimate truth. Instead, the theories generated in succession are incommensurate with each other, testifying to the fact that a theory gives us a perspective view of some part of reality, arrived at contextually. Instead of resembling a monotonically converging series successive theories are analogous to asymptotic series. -/- Before we summarize all the above considerations, we briefly address the issue of the complexity of the {\it human mind} -- one as pervasive as the complexity of Nature at large. The complexity of the mind is related to the complexity of the underlying neuronal organization in the brain, which operates within a larger biological context, its activities being modulated by other physiological systems, notably the one involving a host of chemical messengers. The mind, with no materiality of its own, is nevertheless emergent from the activity of interacting neuronal assemblies in the brain. As in the case of reality at large, there can be no ultimate theory of the mind, from which one can explain and predict the entire spectrum of human behavior, which is an infinitely rich and diverse one. (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)

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 principle of fair play is widely thought to require simply that costs and benefits be distributed fairly. This gloss on the principle, while not entirely inaccurate, has invited a host of popular objections based on misunderstandings about fair play. Central to many of these objections is a failure to treat the principle of fair play as a transactional principle—one that allocates special obligations and rights among persons as a result of their interactions. I offer an interpretation of the (...) principle of fair play that emphasizes its similarities to another transactional principle: consent. This interpretation reveals that playing fair requires one to reciprocate specifically by following the rules of the cooperative scheme from which one benefits, just as consent requires one to act according to the terms of an agreement. I then draw on the comparison with consent to reply to some popular and persistent objections to the principle. (shrink)

Considerable variation exists not only in the kinds of transposable elements (TEs) occurring within the genomes of different species, but also in their abundance and distribution. Noting a similarity to the assortment of organisms among ecosystems, some researchers have called for an ecological approach to the study of transposon dynamics. However, there are several ways to adopt such an approach, and it is sometimes unclear what an ecological perspective will add to the existing co-evolutionary framework for explaining transposon-host interactions. (...) This review aims to clarify the conceptual foundations of transposon ecology in order to evaluate its explanatory prospects. We begin by identifying three unanswered questions regarding the abundance and distribution of TEs that potentially call for an ecological explanation. We then offer an operational distinction between evolutionary and ecological approaches to these questions. By determining the amount of variance in transposon abundance and distribution that is explained by ecological and evolutionary factors, respectively, it is possible empirically to assess the prospects for each of these explanatory frameworks. To illustrate how this methodology applies to a concrete example, we analyzed whole-genome data for one set of distantly related mammals and another more closely related group of arthropods. Our expectation was that ecological factors are most informative for explaining differences among individual TE lineages, rather than TE families, and for explaining their distribution among closely related as opposed to distantly related host genomes. We found that, in these data sets, ecological factors do in fact explain most of the variation in TE abundance and distribution among TE lineages across less distantly related host organisms. Evolutionary factors were not significant at these levels. However, the explanatory roles of evolution and ecology become inverted at the level of TE families or among more distantly related genomes. Not only does this example demonstrate the utility of our distinction between ecological and evolutionary perspectives, it further suggests an appropriate explanatory domain for the burgeoning discipline of transposon ecology. The fact that ecological processes appear to be impacting TE lineages over relatively short time scales further raises the possibility that transposons might serve as useful model systems for testing more general hypotheses in ecology. (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)

Background: Microbiome biomarker discovery for patient diagnosis, prognosis, and risk evaluation is attracting broad interest. Selected groups of microbial features provide signatures that characterize host disease states such as cancer or cardio-metabolic diseases. Yet, the current predictive models stemming from machine learning still behave as black boxes and seldom generalize well. Their interpretation is challenging for physicians and biologists, which makes them difficult to trust and use routinely in the physician-patient decision-making process. Novel methods that provide interpretability and biological (...) insight are needed. Here, we introduce "predomics", an original machine learning approach inspired by microbial ecosystem interactions that is tailored for metagenomics data. It discovers accurate predictive signatures and provides unprecedented interpretability. The decision provided by the predictive model is based on a simple, yet powerful score computed by adding, subtracting, or dividing cumulative abundance of microbiome measurements. -/- Results: Tested on >100 datasets, we demonstrate that predomics models are simple and highly interpretable. Even with such simplicity, they are at least as accurate as state-of-the-art methods. The family of best models, discovered during the learning process, offers the ability to distil biological information and to decipher the predictability signatures of the studied condition. In a proof-of-concept experiment, we successfully predicted body corpulence and metabolic improvement after bariatric surgery using pre-surgery microbiome data. -/- Conclusions: Predomics is a new algorithm that helps in providing reliable and trustworthy diagnostic decisions in the microbiome field. Predomics is in accord with societal and legal requirements that plead for an explainable artificial intelligence approach in the medical field. (shrink)

The units or levels of selection debate concerns the question of what kind of biological systems are stable enough that part of their evolution is a result of the process of natural selection acting at their level. Traditionally, the debate has concerned at least two different, though related, questions: the question of the level at which interaction with the environment occurs, and the question of the level at which reproduction occurs. In recent years, biologists and philosophers have discussed a (...) new aspect of this debate, namely the possibility that certain multi-species consortia formed by a host and its microbiome may act as a unit of selection. This thesis, however, has not been without criticism, as it is doubtful that such consortia could meet the conditions required to achieve the degree of stability that would allow them to experience natural selection. The purpose of this paper is to systematically examine such criticisms and to defend the thesis that the holobiont/hologenome can act as a genuine level of selection both in the form of an interactor and in the form of a reproducer. To do so, it will be argued that the microbiome should be characterized in functional rather than taxonomic terms. (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)

Growing awareness of the ethical implications of neuroscience in the early years of the 21st century led to the emergence of the new academic field of “neuroethics,” which studies the ethical implications of developments in the neurosciences. However, despite the acceleration and evolution of neuroscience research on nonhuman animals, the unique ethical issues connected with neuroscience research involving nonhuman animals remain underdiscussed. This is a significant oversight given the central place of animal models in neuroscience. To respond to these concerns, (...) the Center for Neuroscience and Society and the Center for the Interaction of Animals and Society at the University of Pennsylvania hosted a workshop on the “Neuroethics of Animal Research” in Philadelphia, Pennsylvania. At the workshop, expert speakers and attendees discussed ethical issues arising from neuroscience research involving nonhuman animals, including the use of animal models in the study of pain and psychiatric conditions, animal brain-machine interfaces, animal–animal chimeras, cerebral organoids, and the relevance of neuroscience to debates about personhood. This paper highlights important emerging ethical issues based on the discussions at the workshop. This paper includes recommendations for research in the United States from the authors based on the discussions at the workshop, loosely following the format of the 2 Gray Matters reports on neuroethics published by the Presidential Commission for the Study of Bioethical Issues. (shrink)

What we have learnt in the last six or seven decades about virtual machinery, as a result of a great deal of science and technology, enables us to offer Darwin a new defence against critics who argued that only physical form, not mental capabilities and consciousness could be products of evolution by natural selection. The defence compares the mental phenomena mentioned by Darwin’s opponents with contents of virtual machinery in computing systems. Objects, states, events, and processes in virtual machinery which (...) we have only recently learnt how to design and build, and could not even have been thought about in Darwin’s time, can interact with the physical machinery in which they are implemented, without being identical with their physical implementation, nor mere aggregates of physical structures and processes. The existence of various kinds of virtual machinery (including both “platform” virtual machines that can host other virtual machines, e.g. operating systems, and “application” virtual machines, e.g. spelling checkers, and computer games) depends on complex webs of causal connections involving hardware and software structures, events and processes, where the specification of such causal webs requires concepts that cannot be defined in terms of concepts of the physical sciences. That indefinability, plus the possibility of various kinds of self-monitoring within virtual machinery, seems to explain some of the allegedly mysterious and irreducible features of consciousness that motivated Darwin’s critics and also more recent philosophers criticising AI. There are consequences for philosophy, psychology, neuroscience and robotics. (shrink)

A brief account of epistemological models that try to unfold the intertheoretic context of theory change is proposed. It is stated that all of them has a host of drawbacks, the most salient one being the lack of adequate description of the research traditions interaction process. The epistemological model of mature theory change, eliminating the drawback, is contemplated and illustrated.

In Brazil, the social demand for veterinary expertise is growing. However, there is still a shortage of professionals trained in this area to apply specific knowledge to each case. Studies and research into forensic veterinary medicine are necessary for veterinary experts to assist in investigations and legal proceedings. Veterinary medicine has subjects on its curriculum that cover the knowledge needed to apply in the fields of animal health, public health and the environment. The interaction between human and veterinary medicine, (...) as well as other areas of health, is of great importance in the prevention and control of various diseases, both in animals and humans. Some cases of infectious bovine abortion have a major impact not only on cattle farming and animal health, but also on public and environmental health. The concept of "One Health" integrates human medicine and health professionals. In this context, knowledge of infectious abortive diseases that affect animal, human and environmental health is fundamental. Cattle are affected by specific infectious abortive diseases, caused by pathogens with different forms of presentation and transmission mechanisms. These include brucellosis, leptospirosis and listeriosis, which are potentially zoonotic diseases. Controlling these diseases can contribute to effective public health actions and reduce global health risks. In order to establish the diagnosis of these diseases, it is essential to properly collect specimens from live or dead animals under biosafety and biosecurity conditions, following the chain of custody for each case. These procedures allow for greater success in diagnosing the suspected agent and facilitate the investigation of other causes. Animal health standards for the prophylaxis and control of these diseases are established by specific legislation, including those of the Ministry of Agriculture, Livestock and Supply (MALS). This literature review was based on current knowledge on the Pubmed platform, Google Scholar, articles and textbooks. The aim of this article is to identify, understand and discuss the main infectious abortive diseases of cattle in the legal and forensic context, which have an impact on cattle farming, animal health, food safety, public and environmental health. -/- Referências bibliográficas Abdullah, N. M., Mohammad, W. M. Z. W., Shafei, M. N., Sukeri, S., Idris, Z., Arifin, W. N., Nozmi, N., Saudi, S. N. S., Samsudin, S., & Zainudin, A.-W. (2019). Leptospirosis and its prevention: knowledge, attitude and practice of urban community in Selangor, Malaysia. BMC Public Health, 19(1), 1–8. Agrimani, D. S. R., Rui, B. R., Cruz, I. V, Romano, R. M., & Lopes, H. C. (2011). 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R., Zylbersztajn, A., & Avila-Pires, F. D. (2004). Evolução histórica da medicina veterinária preventiva e saúde pública. Ciência Rural, 34(5), 1661–1668. Pinillos, R. G. (2018). One welfare: A framework to improve animal welfare and human well-being. Cabi. Poester, F. P., Goncalves, V. S. P., & Lage, A. P. (2002). Brucellosis in Brazil. Veterinary Microbiology, 90(1–4), 55–62. Porto, Y. F., Pinto Neto, A., Bernardi, F., Possa, M. G., Mota, M. F., Martinez, A. C., Merlini, L. S., & Berber, R. C. (2018). Occurrence of brucellosis, leptospirosis and neosporosis in cows with retained placenta in Southwest Paraná, Brazil. Pesquisa Veterinária Brasileira, 38(8), 1537–1542. Radostits, O. M., Gay, C. C., Blood, D. C., Hinchcliff, K. W., & McKenzie, R. A. (2010). Clínica Veterinária: um tratado de doenças dos bovinos, ovinos, suínos, caprinos e eqüinos (Vol. 1). Guanabara Koogan. Ramos, T. M. V., Balassiano, I. T., Silva, T. S. M., & Nogueira, J. M. R. (2022). 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A physical model of the electron is suggested according to the basic structures of matter (BSM) hypothesis. BSM is based on an alternative concept about the physical vacuum, assuming that space contains an underlying grid structure of nodes formed of superdense subelementary particles, which are also involved in the structure of the elementary particles. The proposed grid structure is formed of vibrating nodes that possess quantum features and energy well. It is admitted that this hypothetical structure could account for the (...) missing “dark matter” in the universe. The signature of this dark matter is apparent in the galactic rotational curves and in the relation between masses of the supermassive black hole in the galactic center and the host galaxy. The suggested model of the electron possesses oscillation features with anomalous magnetic moment and embedded signatures of the Compton wavelength and the fine-structure constant. The analysis of the interactions between the oscillating electron and the nodes of the vacuum grid structure allows us to obtain physical meaning for some fundamental constants. (shrink)

Freedom, liberty and rights are terms that long have suffered from vagueness that allows a host of differing interpretations, most of them ideological and overly simplistic. Good, serious modeling descriptions of those terms would not overlook the necessary complexity involved in these social interactions. MacCallum’s idea of (political and social) triadic freedom is here extended to include resources, ability, externalities, benefits to the exerciser, and reasons for non-interference. Interference is described as a subset of freedoms with significant externalities. A (...) right is then described as a compound of a freedom protected by interferences. This provides a basis for the analysis of the game-theoretic economics of rights and when they will be produced. (shrink)

This paper concerns the Black Box. It is not the engineer’s black box that can be opened to reveal its mechanism, but rather one whose operations are inferred through input from (and output to) a companion observer. We are observers ourselves, and we attempt to understand minds through interactions with their host organisms. To this end, Ranulph Glanville followed W. Ross Ashby in elaborating the Black Box. The Black Box and its observer together form a system having different properties (...) than either component alone, making it a greater Black Box to any further-external observer. How far into this greater box can a further-external observer probe? The answer is crucial to understanding Black Boxes, and so an answer is offered here. It employs von Foerster’s machines, abstract entities having mechano-electrical bases, just like putative Black Boxes. Von Foerster follows Turing, Ashby, E. F. Moore, and G. H. Mealy in recognizing archetype machines that he calls trivial (predictable) and non-trivial (non-predictable). It is argued here that non-trivial machines are the only true Black Boxes. But non-trivial machines can be concatenated from trivial machines. Hence, the utter core of any greater Black Box (a non-trivial machine) may involve two (or more) White Boxes (trivial machines). This is how an unpredictable thing emerges from predictable parts. Interactions of White Boxes—of trivial machines—may be the ultimate source of the mind. Keywords: . (shrink)

Wikipedia is a goldmine of information; not just for its many readers, but also for the growing community of researchers who recognize it as a resource of exceptional scale and utility. It represents a vast investment of manual effort and judgment: a huge, constantly evolving tapestry of concepts and relations that is being applied to a host of tasks. This article provides a comprehensive description of this work. It focuses on research that extracts and makes use of the concepts, (...) relations, facts and descriptions found in Wikipedia, and organizes the work into four broad categories: applying Wikipedia to natural language processing; using it to facilitate information retrieval and information extraction; and as a resource for ontology building. The article addresses how Wikipedia is being used as is, how it is being improved and adapted, and how it is being combined with other structures to create entirely new resources. We identify the research groups and individuals involved, and how their work has developed in the last few years. We provide a comprehensive list of the open-source software they have produced. (shrink)

Interactive social cognition theory and approaches of developmental psychology widely agree that central aspects of emotional and social experience arise in the unfolding of processes of embodied social interaction. Bi-directional dynamical couplings of bodily displays such as facial expressions, gestures, and vocalizations have repeatedly been described in terms of coordination, synchrony, mimesis, or attunement. In this paper, I propose conceptualizing such dynamics rather as processes of affective resonance. Starting from the immediate phenomenal experience of being immersed in interaction, (...) I develop the philosophical notion of affective resonance to refer to a dynamic entanglement of moving and being-moved in relation. The concept of affective resonance makes visible that the interaction dynamic itself creates an affective experience rather than transmitting internal feeling states between pre-existent individuals. This leads to a philosophical framework in which relationality and ontogeny are primary over separate individuals, and in which the naturalistic distinction of a fundamental physical level versus an emerging level of social processes has to be given up. (shrink)

People's attitude to animals is similar to the attitude Westworld has people adopt vis‐a‐vis the hosts: People often deem animal suffering acceptable because it improves their well‐being but still feel upset when an animal is mistreated just for the sake of it. Speciesism is the view that human well‐being matters more than that of other creatures. One justification for this view attempts to ground human beings’ special moral status in their membership in the human species itself. Some of Westworld's characters (...) are visibly tempted by this kind of justification. Logan is a prime example. One common argument in defense of speciesism is that non‐human animals are far less intelligent than human beings. Westworld's characters have interesting discussions about free will. In Westworld, all dialogues about free will focus on whether the hosts are determined or whether they could act otherwise. (shrink)

Luminance and color are strong and self-sufficient cues to pictorial depth in visual scenes and images. The present study investigates the conditions Under which luminance or color either strengthens or overrides geometric depth cues. We investigated how luminance contrasts associated with color contrast interact with relative height in the visual field, partial occlusion, and interposition in determining the probability that a given figure is perceived as ‘‘nearer’’ than another. Latencies of ‘‘near’’ responses were analyzed to test for effects of attentional (...) selection. Figures in a pair were supported by luminance contrast or isoluminant color contrast and combined with one of the three geometric cues. The results of Experiment 1 show that luminance contrasts associated with hue, when it does not interact with other hues, produces the same effects as achromatic luminance contrasts: The probability of‘‘near’’ increases with luminance contrast while the latencies for ‘‘near’’ responses decrease. Partial occlusion is found to be a strong enough pictorial cue to support a weaker red luminance contrast. Interposition cues lose out against cues of spatial position and partial occlusion. The results of Experiment 2, with isoluminant displays of varying color contrast, reveal that red color contrast on a light background supported by any of the three geometric cues wins over green or white supported by any of the three geometric cues. On a dark background, red color contrast supported by the interposition cue loses out against green or white color contrast supported by partial occlusion. These findings reveal that color is not an independent depth cue, but is strongly influenced by luminance contrast and stimulus geometry. Systematically shorter response latencies for stronger ‘‘near’’ percepts demonstrate that selective visual attention reliably detects the most likely depth cue combination in a given configuration. (shrink)

Could interacting mindreaders be in a position to know things which they would be unable to know if they were manifestly passive observers? This paper argues that they could. Mindreading is sometimes reciprocal: the mindreader’s target reciprocates by taking the mindreader as a target for mindreading. The paper explains how such reciprocity can significantly narrow the range of possible interpretations of behaviour where mindreaders are, or appear to be, in a position to interact. A consequence is that revisions and extensions (...) are needed to standard theories of the evidential basis of mindreading. The view also has consequences for understanding how abilities to interact combined with comparatively simple forms of mindreading may explain the emergence, in evolution or development, of sophisticated forms of social cognition. (shrink)

A recent study suggests that value and quantum states seem to be governed by the same underlying mechanisms. In our recent book titled "Better economics for the Earth: A lesson from quantum and information theories," specifically Chapter 5, we have proposed an informational entropy-based notion of value, drawing on the granular worldview and primary features of quantum mechanics, Shannon’s information theory, and the mindsponge theory. Specifically, the notion suggests that values are created through the interactions of information. But how do (...) information and its interactions lead to values? This research note aims to contribute to the answer to this question. (shrink)

In recent years, a number of philosophers and cognitive scientists have advocated for an ‘interactive turn’ in the methodology of social-cognition research: to become more ecologically valid, we must design experiments that are interactive, rather than merely observational. While the practical aim of improving ecological validity in the study of social cognition is laudable, we think that the notion of ‘interaction’ is not suitable for this task: as it is currently deployed in the social cognition literature, this notion leads (...) to serious conceptual and methodological confusion. In this paper, we tackle this confusion on three fronts: 1) we revise the ‘interactionist’ definition of interaction; 2) we demonstrate a number of potential methodological confounds that arise in interactive experimental designs; and 3) we show that ersatz interactivity works just as well as the real thing. We conclude that the notion of ‘interaction’, as it is currently being deployed in this literature, obscures an accurate understanding of human social cognition. (shrink)

The article investigates how the use of extended reality technologies and interactive digital interfaces have affected the design of exhibition spaces. Its main objective is to shed light on how these technologies have influenced the ways in which immersive art installations are conceived and experienced. Particular emphasis is placed on the impact of interactive technologies on how visitors experience exhibition spaces. The article examines an ensemble of immersive art cases, paying special attention to the distinction between immersion and interactivity. Two (...) concepts that are pivotal for understanding the transformations concerning the subjectivity of the exhibition visitor those of the “imagineer” and the “ultra-technologist”, which are analysed in the article. The intention is to render explicit how extended reality technologies have contributed to the design of immersive experiences, significantly influencing the interrelations between the technical, aesthetic and institutional aspects concerning exhibition design and the methods of dissemination of art. (shrink)

Leibniz has almost universally been represented as denying that created substances, including human minds and the souls of animals, can causally interact either with one another or with bodies. Yet he frequently claims that such substances are capable of interacting in the special sense of what he calls 'ideal' interaction. In order to reconcile these claims with their favored interpretation, proponents of the traditional reading often suppose that ideal action is not in fact a genuine form of causation but (...) instead a merely apparent influence which serves to 'save the appearances.' I argue that this traditional reading distorts Leibniz's thought and that he actually considers ideal action a genuine (though non-standard) form of causation. (shrink)

Interactions between an intelligent software agent and a human user are ubiquitous in everyday situations such as access to information, entertainment, and purchases. In such interactions, the ISA mediates the user’s access to the content, or controls some other aspect of the user experience, and is not designed to be neutral about outcomes of user choices. Like human users, ISAs are driven by goals, make autonomous decisions, and can learn from experience. Using ideas from bounded rationality, we frame these interactions (...) as instances of an ISA whose reward depends on actions performed by the user. Such agents benefit by steering the user’s behaviour towards outcomes that maximise the ISA’s utility, which may or may not be aligned with that of the user. Video games, news recommendation aggregation engines, and fitness trackers can all be instances of this general case. Our analysis facilitates distinguishing various subcases of interaction, as well as second-order effects that might include the possibility for adaptive interfaces to induce behavioural addiction, and/or change in user belief. We present these types of interaction within a conceptual framework, and review current examples of persuasive technologies and the issues that arise from their use. We argue that the nature of the feedback commonly used by learning agents to update their models and subsequent decisions could steer the behaviour of human users away from what benefits them, and in a direction that can undermine autonomy and cause further disparity between actions and goals as exemplified by addictive and compulsive behaviour. We discuss some of the ethical, social and legal implications of this technology and argue that it can sometimes exploit and reinforce weaknesses in human beings. (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)

In 2006 we awoke, in Europe at least, to the odd situation in which twitchers – obsessive birdwatchers who spend much of their leisure time on the far-flung edges of countries – are being reinvented as the eyes and ears of the state, helping warn of new border incursions. These incursions are posited as taking an avian form that may bring with it very unwelcome pathogens. Everyday avian observations and knowledges of migratory routes are being reinvented as a kind of (...) border patrol, a first line of veterinary surveillance. (shrink)

This paper examines the ways in which social scientific discourse and classification interact with the objects of social scientific investigation. I examine this interaction in the context of the traditional philosophical project of demarcating the social sciences from the natural sciences. I begin by reviewing Ian Hacking’s work on interactive classification and argue that there are additional forms of interaction that must be treated.

Rejection is an essential part of the scholarly publishing process, acting as a filter to distinguish between robust and less credible scientific works. This study examines the advantages and limitations of the rejection mechanism through the lens of Shannon’s information theory and the theory of granular interactions thinking. We argue that while rejection helps reduce entropy and increase the likelihood of disseminating useful knowledge, the process is not devoid of subjectivity. We propose two recommendations to improve the rejection mechanism: providing (...) more informative rejection letters to guide authors and encouraging humility among editors and reviewers to minimize bias against novel ideas. These steps could enhance the efficiency of knowledge production by ensuring that valuable scientific contributions are not overlooked. (shrink)

This study aimed to identify the interactive justice and its impact on the organizational loyalty of the Faculty Staff in the Technical University of Palestine-(Kadoorei). In order to achieve this, the researchers used a questionnaire consisting of (22) paragraphs where the first area (10) paragraphs looking at interactive justice, while the second area (12) in the area of organizational loyalty to the Faculty Staff at the university, where it was distributed to (105) individuals from the study sample, and after the (...) process of distribution of the questionnaire was collected and coded and entered into the computer and processed statistically using the statistical package of social sciences. The results of the study indicated that there is a statistically significant effect at the level of significance (α = 0.05) between the interactive justice at the Technical University of Palestine (Kadoorei) at the level of organizational loyalty among the teaching staff of the university. In light of the results of the previous study, the researchers recommended several recommendations, namely, the need for the university to pay attention to the level of interactive justice at department heads and to show more democracy in the decision-making mechanisms of Faculty Staff. (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)