Philosophy in Science

The replication of fermion families is a longstanding structural feature of the Standard Model whose origin remains unexplained. While the gauge structure and interaction content of the theory are highly constrained, the existence and number of fermion generations are introduced as empirical inputs. In this work we revisit the family replication problem from a structural perspective, focusing on the conditions under which multiple fermionic realizations can arise at all. We adopt a general viewpoint in which effective physical descriptions are defined (...) through invariance-preserving projection from an underlying generative structure. Within this setting, fermion families are interpreted as inequivalent realizations associated with different admissible factorizations of such projections. We argue that the requirement of invariance preservation and internal consistency imposes intrinsic constraints on the allowed factorizations, leading to a finite number of non-degenerate realizations. The observed finiteness of fermion families is thus reinterpreted as a consequence of structural saturation rather than as an unexplained numerical coincidence. The analysis does not address the detailed flavor phenomenology of fermion masses or mixing, nor does it require extensions of the Standard Model symmetry content. Instead, it identifies a principled constraint on the existence and multiplicity of fermionic realizations at the level of effective description, illustrating how projection-based classification can yield non-trivial insight into a fundamental open question in particle physics. (shrink)

This article offers a historical-philosophical and methodological clarification of ANAM — a model of the primary act of tensional distinction as the generative ground of distinguishability. ANAM functions as the canonical name of this act, while X is used as its compact symbolic designation in schemes and formal comparisons. The paper examines the problem of the origin of distinguishable order, the status of indistinguishability, and the relation of the whole to its parts. It shows that classical philosophy and related ontological (...) traditions contain stable motifs of a single generative whole, enfolding and unfolding, the part as an expression of the whole, internal self-unfolding, and self-similarity. These motifs can be traced in Plato, Nicholas of Cusa, Giordano Bruno, Spinoza, Leibniz, Hegel, Whitehead, Simondon, the theory of autopoiesis, Spencer-Brown, Deleuze, and Bohm. -/- The specificity of ANAM lies in shifting the explanatory center to the pre-axiomatic level of distinguishability. The primary act of tensional distinction X is understood as a minimal condition of presence in which the distinguishable, the mode of distinguishing, retention, fixation, internal tension, and the possibility of further movement are jointly opened. Indistinguishability in this model receives an actualizational status: it is understood as still enfolded, weakly articulated, and insufficiently localized distinguishability within an already given generative whole. Further multiplicity is considered as a fractal actualization of X, while the regularity of development is understood as the passage of distinguishability through the regimes of retention, fixation, articulation, coordination, localization, and stabilization. -/- The article has the status of a methodological and historical-philosophical comparison. The full derivation of the role-based, regime-based, cosmological, and metric layers belongs to the main corpus of ANAM; in the present work, this corpus is used as a basis for clarifying the place of ANAM within the line of classical philosophical problems of the whole, difference, indistinguishability, substance, self-similarity, and self-unfolding. (shrink)

The Hallmarks of Aging framework has become a widely accepted schema within geroscience, organizing diverse mechanisms of cellular and molecular decline. This article examines whether the Hallmarks function as a scientific paradigm and, beyond that, whether they have enabled genuine scientific progress—an angle largely absents from current literature. Drawing on models from the philosophy of science, the article evaluates the framework’s status and impact from multiple perspectives. From Kuhn, the Hallmarks act as exemplars within the damage paradigm, guiding “normal science” (...) without instigating revolutionary change. From Lakatos, they form part of a protective belt that stabilizes a research programme rather than producing theoretical innovation. From Laudan, they help solve empirical problems but leave conceptual issues unresolved. From Kitcher, their success lies in rhetorical and institutional unification more than inferential structure. From Galison, they are best understood as an instrumental “trading zone” that enables cross-disciplinary coordination. In sum, while the Hallmarks have brought coherence and methodological infrastructure to aging research, they may also constrain conceptual imagination—raising critical questions about the field’s long-term epistemic vitality. (shrink)

This paper identifies and diagnoses the collusion of significant figures and integration constants (有効数字と積分定数の談合) as the structural mechanism underlying the historical formation and epistemological limits of falsifiability. The finite precision of any measurement (dx > 0, irremovable) and the underdetermination introduced by integration constants (C in R, free) together constitute a double degree of freedom that structurally facilitates agreement between theory and observation without guaranteeing it. The epistemological novelty lies in treating these two sources of underdetermination not as separate problems (...) -- as the existing literature on measurement theory and philosophy of science has done -- but as a unified dual structure constituting the normal operating condition of quantitative science. Part I traces this collusion through a two-thousand-five-hundred-year genealogy of mathematical languages from the ratio theory originating with Eudoxus to the calculus, establishing its algebraic form. Part II reconstructs falsifiability as a demarcation device erected upon the collusion, examines the Vienna Circle--Popper controversy as an internal dispute that presupposes it, and analyzes the matrix mechanics--wave mechanics episode as a case in which empirical indistinguishability coexists with structural non-equivalence. Part III develops the replacement criterion of translatability within the Operatiology (操作原論) / Cognitional Mechanics (知能力学) framework -- a hierarchically external criterion immune to the collusion -- and articulates the Aufhebung relation: falsifiability is preserved within Tier-3 practice, negated as a warrant for structural claims, and elevated by translatability to the criterion that genuinely reaches Tier-2 operational structure. The deepest contribution is the demonstration that "what makes a theory structurally adequate?" is categorically distinct from "what makes a theory scientific?", and that answering the former requires a criterion external to the collusion that has never previously been identified. The following Python code illustrates the core structural mechanism: as the number of free parameters increases, the absorptive capacity of the model increases monotonically, regardless of the data structure -- the same operation performed by Ptolemy's epicycles.◆◆◆ [PYTHON ILLUSTRATION CODE] ◆◆◆ from numpy import polyfit, polyval, linspace, mean x_obs = linspace(0, 10, 20) y_obs = [7.3, 2.1, 9.4, 0.8, 5.6, 3.2, 8.7, 1.4, 6.9, 4.5, 2.8, 7.1, 0.3, 5.9, 3.6, 8.2, 1.7, 6.4, 4.1, 9.8] delta_x = None for n_params in [1, 2, 3, 5, 10, 15, 19]: coeffs = polyfit(x_obs, y_obs, n_params) y_fit = polyval(coeffs, x_obs) resid = abs(y_fit - y_obs) if delta_x is None: delta_x = max(resid) within = sum(resid < delta_x) / len(resid) print(f"n_params={n_params}: within_delta={within:.1%}") ◆◆◆ [END] ◆◆◆ The replacement criterion of translatability, derived from Operatiology (操作原論) / Cognitional Mechanics (知能力学), is developed as the genuinely external standard for structural adequacy, immune to the collusion. Published on June 25, 2026. DOI: 10.5281/zenodo.20847090. (shrink)

Our universe appears to be fine-tuned for life. But once life emerges, it does not evolve randomly. Evolution has a trajectory. Both evolvability and cooperative integration increase as evolution proceeds. Until now, this trajectory has largely been driven blindly by gene-based natural selection. But humans are developing cognitive capacities that are far superior than natural selection at adapting and evolving humanity. These capacities will enable humanity to use an understanding of evolution's future trajectory to guide its own evolution, avoiding the (...) destructive selection that will otherwise reinforce the trajectory. Humans who help realize this potential will be fulfilling vital evolutionary roles that are meaningful and purposeful in a much larger scheme of things. The paper considers whether these roles remain meaningful when considered in the wider context of possible origins of the universe. But this analysis is faced with a potentially infinite number of origin hypotheses (including innumerable ‘God hypotheses’), which are not falsified by current knowledge. The paper addresses this challenge using methods that enable rational decision-making despite radical uncertainty. Broadly, this approach reinforces the conclusions reached by consideration of the evolutionary trajectory within the universe, and opens some new possibilities. Finally, the paper demonstrates that extending this analysis also largely overcomes Hume's critique of induction, placing scientific methodologies on a firmer footing. It achieves this by recognising that a universe which exhibits a trajectory towards increasing evolvability must contain discoverable regularities that provide adaptive advantages for evolvability. (open access). (shrink)

In light of growing calls to demonstrate the societal relevance of academic work, this paper explores whether peer review can reliably evaluate the societal relevance of humanities research. It also estimates how relevant published journal articles and books from five humanities fields are to society. By modeling two evaluation tasks involving 38 early-career researchers and 885 humanities abstracts in English from Web of Science, we estimate how reviewer characteristics (such as their chauvinism and strictness) and document characteristics (such as field (...) and content) affect societal relevance ratings. We then compare the influence of both reviewer and document characteristics on these ratings and estimate the societal relevance of humanities research where the factors contributing to peer review unreliability are controlled for. Although the study’s design and limited sample size necessitate cautious interpretation, the results of this study do provide tentative evidence that, even according to early-career researchers from the humanities, a substantial portion of published humanities research may not be relevant to society at large. Furthermore, these results also suggest that when using peer review to decide whether a particular piece of research is societally relevant, the selection of reviewers plays a more significant role than the content of the research. (shrink)

This article seeks to interpret how the scientific study of individualization, broadly construed, is conceived from within. It presents and discusses an analysis of qualitative data gained from performing semi-structured expert interviews. By way of a thematic-analytic approach to interpreting this data, this article seeks to investigate the attitudes and opinions of a sample of scientific experts who study individualization, across a wide range of scientific fields, with regard to key concepts, phenomena, motivating factors, and open questions. Centering its analysis (...) on discussion of four themes, this paper (1) emphasizes the importance for science of individuals and individuality, (2) reflects on matters pertaining to language and interdisciplinary communication, (3) distinguishes between nine meanings of the word “individualization,” stressing their significant features, and (4) considers ideas about the consequences of individualization and ongoing methodological concerns. (shrink)

Anthropomorphism, the attribution of human-like qualities to non-human entities, can influence comprehension of the surrounding world. Going beyond previous research on the general assessment of anthropomorphism, the current study aimed to explore how anthropomorphising a specific animal species influences public acceptance of livestock keeping practices. Specifically, we focused on welfare-infringing practices that limit animals’ freedom, describe disruptive procedures, social isolation, or other stressful situations. Lacking experience in livestock keeping, it is likely that people project their own preferences to animals when (...) judging livestock keeping practices. Questionnaire data from a sample of the Swiss German public (N = 1232) were analysed regarding their acceptance of livestock keeping practices, as well as anthropomorphism for three animals: cattle, pigs, and poultry. We showed that judgement of livestock keeping was related to an anthropomorphic view of animals. This takes two opposite directions: (1) anthropomorphising was connected to a more critical view of livestock keeping practices and (2) the attribution of more cognitive capabilities to cattle and poultry was associated with a higher acceptance of welfare-infringing livestock keeping practices. The tendency to anthropomorphise was species-dependent, with the two mammals eliciting a higher tendency to anthropomorphise than poultry. The results suggest that the tendency to anthropomorphise plays a significant role in shaping the public’s opinion on livestock keeping. We argue that, when activating the tendency to anthropomorphise in the media, advertisements, or political publicity (e.g. by highlighting human-like features), a certain level of caution should be taken to avoid undesirable outcomes. (shrink)

This fieldnotes article documents the design and implementation of a Philosophy for Children (P4C) lesson aimed at introducing children aged 8–12 to the ethical dimensions of Artificial Intelligence (AI), with a particular focus on data privacy. Drawing on the Community of Philosophical Inquiry (CoPI) methodology— specifically the “Plain Vanilla” model associated with Thomas Jackson and disseminated by the IAPC (Yarmel & Gregory, 2023)—the session employed an illustrated narrative stimulus, “Liam’s Secret Base,” followed by student-generated dialogue and a collaborative “Safe Sharing (...) Scenario” activity. These components were designed to foster critical, creative, and caring thinking (Lipman, 2003) about digital life. This article demonstrates that engaging young learners in ethical inquiry about AI technologies is both timely—given the global call for age-appropriate AI-ethics education (UNICEF, 2021; Dabbagh et al., 2025)—and feasible, since most children already interact with AI-mediated platforms. Classroom reflections showed that the lesson supported higher-order reasoning, metacognitive awareness, and collaborative dialogue in a supportive environment, outcomes consistent with reported benefits of P4C (Adams et al., 2023; Ab Wahab et al., 2022). Rather than prescribing a list of “don’ts,” educators used open-ended questions and realistic digital-life scenarios to nurture children’s autonomy in ethical decision-making, echoing participatory design approaches from the MIT Media Lab’s AI + Ethics curriculum (Wu, 2020; Williams et al., 2022). We conclude that P4C—co-founded by Matthew Lipman and Ann Margaret Sharp (Gregory & Laverty, 2017)—provides an effective pedagogical framework for integrating digital-ethics learning into childhood education, enabling students to become thoughtful, informed, and responsible digital citizens capable of navigating an increasingly data-driven world (Floridi, 2023/2024; Turner, 2019). (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)

Recent efforts in a range of scientific fields have emphasised research and methods concerning individual differences and individualisation. This article brings together various scientific disciplines—ecology, evolution, and animal behaviour; medicine and psychiatry; public health and sport/exercise science; sociology; psychology; economics and management science—and presents their research on individualisation. We then clarify the concept of individualisation as it appears in the disciplinary casework by distinguishing three kinds of individualisation studied in and across these disciplines: Individualisation ONE as creating/changing individual differences (the (...) process that generates differences between individuals: intrapopulation or intraspecific variation/heterogeneity); Individualisation TWO as individualising applications (the tailoring or customising of something—information, treatment, a product or service, etc.—for an individual or specific group of individuals); and Individualisation THREE as social changes influencing autonomy, risk, and responsibilities (the process discussed under the rubric of sociological individualisation theory). Moreover, we analyse conceptual links between individualisation and individuality, and characterise different sorts of individuality that the disciplines study. This paper aims to promote interdisciplinary research concerning individualisation by establishing a common conceptual-theoretical basis, while leaving room for disciplinary differences. (shrink)

When an empirical prediction E of hypothesis H is observed to be true, such observation is said to confirm, i.e., support (although not prove) the truth of the hypothesis. But why? What justifies the claim that such evidence supports the hypothesis? The widely accepted answer is that it is justified by induction. More specifically, it is commonly held that the following argument, (1) If H then E; (2) E; (3) Therefore, (probably) H (here referred to as ‘hypothetico-deductive confirmation argument’), is (...) inductively strong. Yet this argument looks nothing like an inductive generalization, i.e., it does not seem inductive in the term’s traditional, enumerative sense. If anything, it has the form of the fallacy of affirming the consequent. This paper aims to solve this puzzle. True, in recent decades, ‘induction’ has been sometimes used more broadly to encompass any non-deductive, i.e., ampliative, argument. Applying Bayesian confirmation theory has famously demonstrated that hypothetico-deductive confirmation is indeed inductive in this broader, ampliative sense. Nonetheless, it will be argued here that, despite appearance, hypothetico-deductive confirmation can also be recast as enumerative induction. Hence, by being enumeratively inductive, the scientific method of hypothetico-deductive confirmation is justified through this traditional, more restrictive type of induction rather than merely by ampliative induction. (shrink)

This short paper seeks to throw light on the sense in which the prior knowledge used by AlphaFold is to be understood in ontological terms. The paper is a comment on the 2022 ICBO presentation by Jobst Landgrebe entitled “What AlphaFold teaches us about deep learning with prior knowledge”.

Researchers of non-human animal emotions tend to defend some forms of anthropomorphism and seek ways to make it more critical, self-aware, and useful for scientific purposes. I propose that to achieve this goal, we need first to conduct a Kantian investigation into the deeper structure of anthropomorphism. I argue that we can distinguish at least three levels of anthropomorphising: a narrative level, a cognitive level and an in-between, metatheoretical level which is the deeper structure determining how we anthropomorphise. Because the (...) current debate tends to focus either on the narrative level or on the cognitive level, this paper concentrates on the metatheoretical level, discusses its role in emotion research, the possible errors it may cause, and how we can work on it, drawing on predictive processing-based theories of emotions and an evolutionary approach. The key to being critical in anthropomorphism is to be aware of the complexity of this whole structure, as well as to be able to challenge and put into question all and any of its elements. (shrink)

Research and engineering in the quantum domain involve long chains of activity involving theory development, hypothesis formation, experimentation, device prototyping, device testing, and many more. At each stage multiple paths become possible, and of the paths pursued, the majority will lead nowhere. Our quantum metascience approach provides a strategy which enables all stakeholders to gain an overview of those developments along these tracks, that are relevant to their specific concerns. It provides a controlled vocabulary, built out of terms that are (...) designed to be maximally comprehensible to all groups of stakeholders and across all the sub-fields of the quantum domain. (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)

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

The translational research community, in general, and the Clinical and Translational Science Awards (CTSA) community, in particular, share the vision of repurposing EHRs for research that will improve the quality of clinical practice. Many members of these communities are also aware that electronic health records (EHRs) suffer limitations of data becoming poorly structured, biased, and unusable out of original context. This creates obstacles to the continuity of care, utility, quality improvement, and translational research. Analogous limitations to sharing objective data in (...) other areas of the natural sciences have been successfully overcome by developing and using common ontologies. This White Paper presents the authors’ rationale for the use of ontologies with computable semantics for the improvement of clinical data quality and EHR usability formulated for researchers with a stake in clinical and translational science and who are advocates for the use of information technology in medicine but at the same time are concerned by current major shortfalls. This White Paper outlines pitfalls, opportunities, and solutions and recommends increased investment in research and development of ontologies with computable semantics for a new generation of EHRs. (shrink)

We have now reached the point at which cloud computing and other types of advanced infrastructure are bringing about a situation in which knowledge objects can be delivered in an efficient manner to hose who need to consume them. And just as highways were the infrastructure necessary for a manufacturing economy, serving as the arteries along which raw materials and manufactured goods coming in from all directions could flow, so we believe that ontologies will in the future provide an important (...) pillar in the infrastructure that is necessary for the accurate and safe delivery of all varieties of knowledge. (shrink)

We begin at the beginning, with an outline of Aristotle’s views on ontology and with a discussion of the influence of these views on Linnaeus. We move from there to consider the data standardization initiatives launched in the 19th century, and then turn to investigate how the idea of computational ontologies developed in the AI and knowledge representation communities in the closing decades of the 20th century. We show how aspects of this idea, particularly those relating to the use of (...) the term 'concept' in ontology development, influenced SNOMED CT and other medical terminologies. Against this background we then show how the Foundational Model of Anatomy, the Gene Ontology, Basic Formal Ontology and other OBO Foundry ontologies came into existence and discuss their role in the development of contemporary biomedical informatics. (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)

Plant biologists widely accept plants demonstrate capacities for intelligence. However, they disagree over the interpretive, ethical and nomenclatural questions arising from these findings: how to frame the issue and how to signify the implications. Through the trope of ‘plant neurobiology’ describing plant root systems as analogous to animal brains and nervous systems, plant intelligence is mobilised to raise the status of plants. In doing so, however, plant neurobiology accepts an anthropocentric moral extensionist framework requiring plants to anthropomorphically meet animal standards (...) to be deserving of moral respect. I argue this strategy is misguided because moral extensionism is an erroneous ontological foundation for ethics. (shrink)

The evolutionary origin of consciousness has been a growing area of study in recent years. Nevertheless, there is intense debate on whether the existence of phenomenal consciousness without the cerebral cortex is possible. The corticocentrists have an empirical advantage because we are quasi-confident that we humans are conscious and have the well-developed cortex as the site of our consciousness. However, their prejudice can be an anthropic bias similar to the anthropocentric prejudice in pre-Darwinian natural history. In this paper, I propose (...) three basic principles to provide a conceptual basis for evolutionary studies of consciousness: the non-solipsistic principle, the evolution principle, and the anthropic principle. These principles collectively help us to avoid solipsism, anthropocentrism, and anthropomorphism to some degree, although we cannot be completely free from them. Also, the landscape metaphor associated with the anthropic principle provides an image of how different forms of consciousness can be acquired. (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)

The Infectious Disease Ontology (IDO) is a suite of interoperable ontology modules that aims to provide coverage of all aspects of the infectious disease domain, including biomedical research, clinical care, and public health. IDO Core is designed to be a disease and pathogen neutral ontology, covering just those types of entities and relations that are relevant to infectious diseases generally. IDO Core is then extended by a collection of ontology modules focusing on specific diseases and pathogens. In this paper we (...) present applications of IDO Core within various areas of infectious disease research, together with an overview of all IDO extension ontologies and the methodology on the basis of which they are built. We also survey recent developments involving IDO, including the creation of IDO Virus; the Coronaviruses Infectious Disease Ontology (CIDO); and an extension of CIDO focused on COVID-19 (IDO-CovID-19).We also discuss how these ontologies might assist in information-driven efforts to deal with the ongoing COVID-19 pandemic, to accelerate data discovery in the early stages of future pandemics, and to promote reproducibility of infectious disease research. (shrink)

The overall goal of the approach developed in this paper is to estimate the likelihood of a given kinetic kill scenario between hostile spacebased adversaries using the mathematical framework of Complex Conceptual Spaces Single Observation. Conceptual spaces are a cognitive model that provide a method for systematically and automatically mimicking human decision making. For accurate decisions to be made, the fusion of both hard and soft data into a single decision framework is required. This presents several challenges to this data (...) fusion framework. The first is the challenge involved in handling multiple complex terminologies, which is addressed by drawing on a set of Space Domain Ontologies. Another challenge is the complex combinatorics involved when considering all possible feature combinations. This can be mitigated by using integer linear programming optimization that is outlined by the Complex Conceptual Spaces Single Observation mathematical model framework. A third challenge is the complicated physics that is involved in a spacecraft collision that must be addressed to obtain a better understanding of threat assessment. Overcoming these various challenges allows for a quantitative ranking for the potential of a kinetic kill collision across multiple spacecraft pairs. In addition to overcoming these challenges this paper will break down threat assessment into four domains and identify a ranking of threat both for each individual domain and for the four domains combined. Simulation results are shown to verify the developed concepts. (shrink)

This paper describes an AFOSR-supported basic research program that focuses on developing a new framework for combining hard with soft data in order to improve space situational awareness. The goal is to provide, in an automatic and near real-time fashion, a ranking of possible threats to blue assets (assets trying to be protected) from red assets (assets with hostile intentions). The approach is based on Conceptual Spaces models, which combine features from traditional associative and symbolic cognitive models. While Conceptual Spaces (...) are revolutionary, they lack an underlying mathematical framework. Several such frameworks have attempted to represent Conceptual Spaces, but by far the most robust is the model developed by Holender. His model utilizes integer linear programming in order to obtain an overall similarity value between observations and concepts that support the formation of hypotheses. This paper will describe a method for building Conceptual Spaces models for threats that utilizes ontologies as a means to provide a clear semantic foundation for this inferencing process; in particular threat ontologies and space domain ontologies are developed and employed in this approach. A space situational awareness use-case is presented involving a kinetic kill scenario and results are shown to assess the performance of this fusion-based inferencing framework. (shrink)

Achieving space situational awareness requires, at a minimum, the identification, characterization, and tracking of space objects. Leveraging the resultant space object data for purposes such as hostile threat assessment, object identification, and conjunction assessment presents major challenges. This is in part because in characterizing space objects we reference a variety of identifiers, components, subsystems, capabilities, vulnerabilities, origins, missions, orbital elements, patterns of life, operational processes, operational statuses, and so forth, which tend to be defined in highly heterogeneous and sometimes inconsistent (...) ways. The Space Domain Ontologies are designed to provide a consensus-based realist framework for formulating such characterizations in a way that is both consistent and computable. Space object data are aligned with classes and relations in a suite of ontologies built around the existing Space Object Ontology. They are stored in a dynamically updated Resource Description Framework triple store, which can be queried to support space situational awareness and the needs of spacecraft operators and analysts. This paper provides an overview of the Space Domain Ontologies and their development and use. It presents the motivation for and advantages of the Space Domain Ontologies, including the benefits they provide for enhancing and maintaining long-term space situational awareness. (shrink)

Current COVID-19 pandemic and previous SARS/MERS outbreaks have caused a series of major crises to global public health. We must integrate the large and exponentially growing amount of heterogeneous coronavirus data to better understand coronaviruses and associated disease mechanisms, in the interest of developing effective and safe vaccines and drugs. Ontologies have emerged to play an important role in standard knowledge and data representation, integration, sharing, and analysis. We have initiated the development of the community-based Coronavirus Infectious Disease Ontology (CIDO). (...) As an Open Biomedical Ontology (OBO) library ontology, CIDO is an open source and interoperable with other existing OBO ontologies. In this article, the general architecture and the design patterns of the CIDO are introduced, CIDO representation of coronaviruses, phenotypes, anti-coronavirus drugs and medical devices (e.g. ventilators) are illustrated, and an application of CIDO implemented to identify repurposable drug candidates for effective and safe COVID-19 treatment is presented. (shrink)

Biological ontologies are used to organize, curate, and interpret the vast quantities of data arising from biological experiments. While this works well when using a single ontology, integrating multiple ontologies can be problematic, as they are developed independently, which can lead to incompatibilities. The Open Biological and Biomedical Ontologies Foundry was created to address this by facilitating the development, harmonization, application, and sharing of ontologies, guided by a set of overarching principles. One challenge in reaching these goals was that the (...) OBO principles were not originally encoded in a precise fashion, and interpretation was subjective. Here we show how we have addressed this by formally encoding the OBO principles as operational rules and implementing a suite of automated validation checks and a dashboard for objectively evaluating each ontology’s compliance with each principle. This entailed a substantial effort to curate metadata across all ontologies and to coordinate with individual stakeholders. We have applied these checks across the full OBO suite of ontologies, revealing areas where individual ontologies require changes to conform to our principles. Our work demonstrates how a sizable federated community can be organized and evaluated on objective criteria that help improve overall quality and interoperability, which is vital for the sustenance of the OBO project and towards the overall goals of making data FAIR. Competing Interest StatementThe authors have declared no competing interest. (shrink)

In the present review we focus on what we take to be some remaining issues with the Behaviour Change Intervention Ontology (BCIO). We are in full agreement with the authors’ endorsement of the principles of best practice for ontology development In particular, we agree that an ontology should be “logically consistent and having a clear structures [sic], preferably a well-organised hierarchical structure,” and that “Maximising the new ontology’s interoperability with existing ontologies by reusing entities from existing ontologies where appropriate” is (...) critically important (Wright et al., 2020, p. 17). Our remaining concerns with BCIO relate directly to these two principles. First, we identify a number of issues with some of the classifications and definitions in BCIO that seem to be in tension with the just-mentioned principle . Second, we note some reservations about the reuse of certain classes in BCIO, namely from the Gazetteer (GAZ), the Ontology of Medically Related Social Entities (OMRSE), and the Information Artifact Ontology (IAO). While the latter principle of “reuse” is important, it is also important not to let the reuse of existing classes (or their corresponding definitions) compromise the logical integrity or the realist nature of one’s ontology. (shrink)

My aim in this paper is to investigate Hegel’s relation to Spinoza’s account of teleology by discussing Spinoza and Hegel’s stance to two straightforward objections against teleological views of reality: the anthropomorphism objection and the backward causation objection. I show that both argue against a teleological account that would be committed to the anthropomorphism objection by raising the same argument: such a divine intelligence would lack what it desires to realize. I then argue that their dealing with the backward causation (...) objection differs. Whereas Spinoza finds the backward causation objection against natural purposiveness to be valid, Hegel uses this objection to build his own case: natural purposiveness obtains to a different aspect of reality than effective causality. In contrast, Spinoza defends the backward causation objection because he believes there is only one fundamental principle that reality is subject to. Not only has the issue of Spinoza and Hegel’s relationship on teleology been neglected, I also argue that such a discussion can prove illuminating with respect to Hegel’s stance to monism, as, in contrast to Spinoza, Hegel must assume that there are different fundamental principles governing reality and not merely one. (shrink)

Driven by the use cases of PubChemRDF and SCAIView, we have developed a first community-based clinical trial ontology (CTO) by following the OBO Foundry principles. CTO uses the Basic Formal Ontology (BFO) as the top level ontology and reuses many terms from existing ontologies. CTO has also defined many clinical trial-specific terms. The general CTO design pattern is based on the PICO framework together with two applications. First, the PubChemRDF use case demonstrates how a drug Gleevec is linked to multiple (...) clinical trials investigating Gleevec’s related chemical compounds. Second, the SCAIView text mining engine shows how the use of CTO terms in its search algorithm can identify publications referring to COVID-19-related clinical trials. Future opportunities and challenges are discussed. (shrink)

In “Toward an Ontology of Commercial Exchange” [11], we proposed human readable definitions for terms that are central to an ontology of commercial exchange. This paper furthers that project in two ways. First, the definitions have been modified to be compatible with the Common Core Ontologies (CCO). CCO is used in a wide variety of domains including the industrial and military domains. Having a commerce ontology compatible with CCO allows data about the exchange of goods relevant to those domains to (...) be tagged with compatible ontologies. Second, we propose preliminary formalizations of these definitions, with the aim of informing the creation of an ontology which can be used to assist in reasoning over businessrelated data. (shrink)

Applied ontologies have been used more and more frequently to enhance systems engineering. In this paper, we argue that adopting principles of ontological realism can increase the benefits that ontologies have already been shown to provide to the systems engineering process. Moreover, adopting Basic Formal Ontology (BFO), an ISO standard for top-level ontologies from which more domain specific ontologies are constructed, can lead to benefits in four distinct areas of systems engineering: (1) interoperability, (2) standardization, (3) testing, and (4) data (...) exploitation. Reaping these benefits in a model-based systems engineering (MBSE) context requires utilizing an ontology’s vocabulary when modeling systems and entities within those systems. If the chosen ontology abides by the principles of ontological realism, a semantic standard capable of uniting distinct domains, using BFO as a hub, can be leveraged to promote greater interoperability among systems. As interoperability and standardization increase, so does the ability to collect data during the testing and implementation of systems. These data can then be reasoned over by computational reasoners using the logical axioms within the ontology. This, in turn, generates new data that would have been impossible or too inefficient to generate without the aid of computational reasoners. (shrink)

This essay is a response to Luis M. Augusto’s intriguing paper on the rift between mainstream and formal ontology. I will show that there are in fact two questions at issue here: 1. concerning the links between mainstream and formal approaches within philosophy, and 2. concerning the application of philosophy (and especially philosophical ontology) in support of information-driven research for example in the life sciences.

In the era of “big data,” science is increasingly information driven, and the potential for computers to store, manage, and integrate massive amounts of data has given rise to such new disciplinary fields as biomedical informatics. Applied ontology offers a strategy for the organization of scientific information in computer-tractable form, drawing on concepts not only from computer and information science but also from linguistics, logic, and philosophy. This book provides an introduction to the field of applied ontology that is of (...) particular relevance to biomedicine, covering theoretical components of ontologies, best practices for ontology design, and examples of biomedical ontologies in use. After defining an ontology as a representation of the types of entities in a given domain, the book distinguishes between different kinds of ontologies and taxonomies, and shows how applied ontology draws on more traditional ideas from metaphysics. It presents the core features of the Basic Formal Ontology (BFO), now used by over one hundred ontology projects around the world, and offers examples of domain ontologies that utilize BFO. The book also describes Web Ontology Language (OWL), a common framework for Semantic Web technologies. Throughout, the book provides concrete recommendations for the design and construction of domain ontologies. (shrink)

This paper provides a method for characterizing space events using the framework of conceptual spaces. We focus specifically on estimating and ranking the likelihood of collisions between space objects. The objective is to design an approach for anticipatory decision support for space operators who can take preventive actions on the basis of assessments of relative risk. To make this possible our approach draws on the fusion of both hard and soft data within a single decision support framework. Contextual data is (...) also taken into account, for example data about space weather effects, by drawing on the Space Domain Ontologies, a large system of ontologies designed to support all aspects of space situational awareness. The framework is coupled with a mathematical programming scheme that frames a mathematically optimal approach for decision support, providing a quantitative basis for ranking potential for collision across multiple satellite pairs. The goal is to provide the broadest possible information foundation for critical assessments of collision likelihood. (shrink)

Ontologies, as the term is used in informatics, are structured vocabularies comprised of human- and computer-interpretable terms and relations that represent entities and relationships. Within informatics fields, ontologies play an important role in knowledge and data standardization, representation, integra- tion, sharing and analysis. They have also become a foundation of artificial intelligence (AI) research. In what follows, we outline the Coronavirus Infectious Disease Ontology (CIDO), which covers multiple areas in the domain of coronavirus diseases, including etiology, transmission, epidemiology, pathogenesis, diagnosis, (...) prevention, and treatment. We emphasize CIDO development relevant to COVID-19. (shrink)

We will survey a range of ontologies relevant to space and ground system domains. The ontologies form part of the Common Core Ontology ecosystem (CCO) developed under the IARPA KDD initiative. We focus specifically on the Space Domain Ontologies, a suite of ontologies to support space situational awareness, including the Spacecraft Mission Ontology, Spacecraft Ontology, Space Event Ontology and Space Object Ontology.

This article investigates the deep-rooted logical structures underlying our thinking about other animals with a particular focus on topics relevant for cognitive primate research. We begin with a philosophical propaedeutic that makes perspicuous how we are to differentiate ontological from epistemological considerations regarding primates, while also accounting for the many perplexities that will undoubtedly be encountered upon applying this difference to concrete phenomena. Following this, we give an account of what is to be understood by the assertion of a thesis (...) of anthropological difference, identifying, inter alia, a property that fulfils the exclusivity, universality, and constitution criteria and demarcates the differentia specifica between humans and other animals. Also, we systematically develop how such theses can be formulated more moderately. Furthermore, we account for different theoretical frameworks, argumentative schemes, and sociological factors whose employment is associated with theses as such. This endeavor is carried out under the guise of anthropomorphism and anthropodenial. Doing so, we show that both are favored by the logic of cognitive primate research. Put briefly, concepts like cladistic parsimony and arguments by analogy favor anthropomorphism whereas concepts like traditional parsimony and Morgan’s canon favor anthropodenial. We close by framing these topics in the light of the self-other category mistake that lies in ascribing exclusive self-properties to some other. Lastly, we probe this category mistake for potency and scope of implications and find it to be central to and unavoidably ingrained in our thinking about other animals. (shrink)

The short monograph Creative Nature (Francisco Javier Novo, Rubén Pereda, and Javier Sánchez-Cañizares. 2018. Naturaleza Creativa. Madrid: Rialp. ISBN: 978-84-321-4916-0. 196 pp. Paperback, €14.25) is a welcome contribution to the philosophy of nature that arose from interdisciplinary conversations between authors who are both up-to-date in the scientific literature and deeply grounded in the Western intellectual tradition. In this third and final part of the review essay, I take Creative Nature as a point of departure and develop a theological synthesis of (...) our relationship with the natural world. My approach to making sense of natural evil draws on the Aristotelian-Thomistic metaphysical tradition. I emphasize the wisdom of viewing nature as a whole and avoiding anthropomorphisms, in order to both come to peace with our common home and feel like we belong in a welcoming world. I draw from St. Paul’s teaching on cosmic redemption in his letters to the Colossians and Ephesians to shine the light of supernatural faith on our relationship with the natural world. This approach illustrates how a sound philosophy of nature and biblical interpretation are pivotal for faith–science dialogue.The short monograph Creative Nature (Francisco Javier Novo, Rubén Pereda, and Javier Sánchez-Cañizares. 2018. Naturaleza Creativa. Madrid: Rialp. ISBN: 978-84-321-4916-0. 196 pp. Paperback, €14.25) is a welcome contribution to the philosophy of nature that arose from interdisciplinary conversations between authors who are both up-to-date in the scientific literature and deeply grounded in the Western intellectual tradition. In this third and final part of the review essay, I take Creative Nature as a point of departure and develop a theological synthesis of our relationship with the natural world. My approach to making sense of natural evil draws on the Aristotelian-Thomistic metaphysical tradition. I emphasize the wisdom of viewing nature as a whole and avoiding anthropomorphisms, in order to both come to peace with our common home and feel like we belong in a welcoming world. I draw from St. Paul’s teaching on cosmic redemption in his letters to the Colossians and Ephesians to shine the light of supernatural faith on our relationship with the natural world. This approach illustrates how a sound philosophy of nature and biblical interpretation are pivotal for faith–science dialogue. (shrink)

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

The growing body of research on interdisciplinarity has encouraged a more in depth analysis of the relations that hold among academic disciplines. In particular, the incursion of one scientific discipline into another discipline’s traditional domain, also known as scientific imperialism, has been a matter of increasing debate. Following this trend, Scientific Imperialism aims to bring together philosophers of science and historians of science interested in the topic of scientific imperialism and, in particular, interested in the conceptual clarification, empirical identification, and (...) normative assessment of the idea of scientific imperialism. Thus, this innovative volume has two main goals. Indeed, the authors first seek to understand interdisciplinary relations emerging from the incursion of one scientific discipline into one or more other disciplines, such as in cases in which the conventions and procedures of one discipline or field are imposed on other fields; or more weakly when a scientific discipline seeks to explain phenomena that are traditionally considered proper of another discipline’s domain. Secondly, the authors explore ways of distinguishing imperialistic from non-imperialistic interactions between disciplines and research fields. (shrink)

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

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)

A diagnostic process is an investigative process that takes a clinical picture as input and outputs a diagnosis. We propose a method for distinguishing diagnoses that are warranted from those that are not, based on the cognitive processes of which they are the outputs. Processes designed and vetted to reliably produce correct diagnoses will output what we shall call ‘warranted diagnoses’. The latter are diagnoses that should be trusted even if they later turn out to have been wrong. Our work (...) is based on the recently developed Cognitive Process Ontology and further develops the Ontology of General Medical Science. It also has applications in fields such as intelligence, forensics, and predictive maintenance, all of which rely on vetted processes designed to secure the reliability of their outputs. (shrink)

We propose capability as a universal or type intermediate between function and disposition. A capability is, broadly speaking, a disposition that is of a type whose instances can be evaluated on the basis of how well they are realized. A function, on the view we are proposing, is a capability the possession of which is the rationale for the existence of its bearer. To say for example that a water pump has the function to pump water is to say that (...) the pump exists because something was needed that would pump water. A water pump may have many capabilities, including: to be weatherproof, to run without lubricant, to be transportable, and so forth. But its function is to pump water. We focus here on capabilities possessed by humans – such as piano playing or language using – and we explore the relation between capabilities of these sorts and structures in the brain. (shrink)

The ability to access and share data is key to optimizing and streamlining any industrial production process. Unfortunately, the manufacturing industry is stymied by a lack of interoperability among the systems by which data are produced and managed, and this is true both within and across organizations. In this paper, we describe our work to address this problem through the creation of a suite of modular ontologies representing the product life cycle and its successive phases, from design to end of (...) life. We call this suite the Product Life Cycle (PLC) Ontologies. The suite extends proximately from The Common Core Ontologies (CCO) used widely in defense and intelligence circles, and ultimately from the Basic Formal Ontology (BFO), which serves as top level ontology for the CCO and for some 300 further ontologies. The PLC Ontologies were developed together, but they have been factored to cover particular domains such as design, manufacturing processes, and tools. We argue that these ontologies, when used together with standard public domain alignment and browsing tools created within the context of the Semantic Web, may offer a low-cost approach to solving increasingly costly problems of data management in the manufacturing industry. (shrink)

In the Soviet scientific literature of 1920‒30 the concept of probability was holly debated. The frequency concept which was proposed by R. von Mises became popular among Soviet physicists belonging to the L.I. Mandelstam community. Landau and Lifshitz were also close to this concept in their famous course of theoretical physics. A.Khinchin, a mathematician who cooperated with Kolmogorov, opposed to the frequency conception. In this paper we try to demonstrate that the frequency position was connected with the anthropomorphous approach to (...) physics, whereas Khinchin’s positions implied the criticism of anthropomorphism and put forward the ideal of objective knowledge. (shrink)