According to the view of conditionals named 'inferentialism', a conditional holds when its consequent can be inferred from its antecedent. This paper identifies some major challenges that inferentialism has to face, and uses them to assess three accounts of conditionals: one is the classical strict account, the other two have recently been proposed by Douven and Rott. As will be shown, none of the three proposals meets all challenges in a fully satisfactory way. We argue through novel formal results that (...) a variation of the evidential account of conditionals suggested by Crupi and Iacona is the most promising candidate to develop inferentialism in a coherent formal framework. (shrink)

This paper outlines an account of conditionals, the evidential account, which rests on the idea that a conditional is true just in case its antecedent supports its consequent. As we will show, the evidential account exhibits some distinctive logical features that deserve careful consideration. On the one hand, it departs from the material reading of ‘if then’ exactly in the way we would like it to depart from that reading. On the other, it significantly differs from the non-material accounts which (...) hinge on the Ramsey Test, advocated by Adams, Stalnaker, Lewis, and others. (shrink)

To believe that every single scientist ought to be individually engaged in ethical thinking in order for science to be responsible at a collective level may be too demanding, if not plainly unrealistic. In fact, ethical labor is typically distributed across different kinds of scientists within the scientific community. Based on the empirical data collected within the Horizon 2020 ‘RRI-Practice’ project, we propose a classification of the members of the scientific community depending on their engagement in this collective activity. Our (...) classification offers, on the one hand, a model of how the ethical aspects of science are taken into consideration by scientists and, on the other, some indications on how to institutionalize ethics in science. (shrink)

This paper develops a probabilistic analysis of conditionals which hinges on a quantitative measure of evidential support. In order to spell out the interpreta- tion of ‘if’ suggested, we will compare it with two more familiar interpretations, the suppositional interpretation and the strict interpretation, within a formal framework which rests on fairly uncontroversial assumptions. As it will emerge, each of the three interpretations considered exhibits specific logical features that deserve separate consideration.

This paper investigates the logic of reasons. Its aim is to provide an analysis of the sentences of the form ‘p is a reason for q’ that yields a coherent account of their logical properties. The idea that we will develop is that ‘p is a reason for q’ is acceptable just in case a suitably defined relation of incompatibility obtains between p and ¬q. As we will suggest, a theory of reasons based on this idea can solve three challenging (...) puzzles that concern, respectively, contraposing reasons, conflicting reasons, and supererogatory reasons, and opens a new perspective on some classical issues concerning non-deductive inferences. (shrink)

This paper outlines an account of concessive conditionals that rests on two main ideas. One is that the logical form of a sentence as used in a given context is determined by the content expressed by the sentence in that context. The other is that a coherent distinction can be drawn between a reading of ‘if’ according to which a conditional is true when its consequent holds on the supposition that its antecedent holds, and a stronger reading according to which (...) a conditional is true when its antecedent supports its consequent. As we will suggest, the logical form of concessive conditionals can be elucidated by relying on this distinction. (shrink)

Biomedical ontologies are emerging as critical tools in genomic and proteomic research where complex data in disparate resources need to be integrated. A number of ontologies exist that describe the properties that can be attributed to proteins; for example, protein functions are described by Gene Ontology, while human diseases are described by Disease Ontology. There is, however, a gap in the current set of ontologies—one that describes the protein entities themselves and their relationships. We have designed a PRotein Ontology (PRO) (...) to facilitate protein annotation and to guide new experiments. The components of PRO extend from the classification of proteins on the basis of evolutionary relationships to the representation of the multiple protein forms of a gene (products generated by genetic variation, alternative splicing, proteolytic cleavage, and other post-translational modification). PRO will allow the specification of relationships between PRO, GO and other OBO Foundry ontologies. Here we describe the initial development of PRO, illustrated using human proteins from the TGF-beta signaling pathway. (shrink)

In his late years, Thomas Kuhn became interested in the process of scientific specialization, which does not seem to possess the destructive element that is characteristic of scientific revolutions. It therefore makes sense to investigate whether and how Kuhn’s insights about specialization are consistent with, and actually fit, his model of scientific progress through revolutions. In this paper, I argue that the transition toward a new specialty corresponds to a revolutionary change for the group of scientists involved in such a (...) transition. I will clarify the role of the scientific community in revolutionary changes and characterize the incommensurability across specialties as possessing both semantic and methodological aspects. The discussion of the discovery of the structure of DNA will serve both as an illustration of my main argument and as reply to one criticism raised against Kuhn—namely, that his model cannot capture cases of revolutionary yet non-disruptive episodes of scientific progress. Revisiting Kuhn’s ideas on specialization will shed new light on some often overlooked features of scientific change. (shrink)

Thomas Kuhn (1922-1996) is widely considered as one of the most important philosophers of science of the 20th century, while his The Structure of Scientific Revolutions (SSR) is regarded as one of the most influential works in the philosophy ofscience. At the same time, however, his place within philosophy of science remains ambiguous. On the one hand, despite the popularity of SSR, there is no proper ‘Kuhnian school of thought’ in HPS. On the other hand, the interest towards Kuhn does (...) not seem to fade away and the number of publications about his work does not seem to decrease. We suggest that there are at least three different ways to go ‘beyond SSR’: (i) by scrutinising the development of Kuhn’s thought, from his pre- to his post-SSR writings; (ii) by contextualising Kuhn in the philosophical milieu of his time, thus interpreting his view as emerging from the intellectual exchanges he had with contemporary philosophers; (iii) by reinterpreting and developing some of his most known ideas, in ways that perhaps Kuhn himself was not able to contemplate. (shrink)

Once upon a time, some thought that indicative conditionals could be effectively analyzed as material conditionals. Later on, an alternative theoretical construct has prevailed and received wide acceptance, namely, the conditional probability of the consequent given the antecedent. Partly following critical remarks recently ap- peared in the literature, we suggest that evidential support—rather than conditional probability alone—is key to understand indicative conditionals. There have been motivated concerns that a theory of evidential conditionals (unlike their more tra- ditional counterparts) cannot generate (...) a sufficiently interesting logical system. Here, we will describe results dispelling these worries. Happily, and perhaps surprisingly, appropriate technical variations of Ernst Adams’s classical approach allow for the construction of a logic of evidential conditionals with distinctive fea- tures, which is also well-behaved and reasonably strong. (shrink)

In the past few years, social epistemologists have developed several formal models of the social organisation of science. While their robustness and representational adequacy has been analysed at length, the function of these models has begun to be discussed in more general terms only recently. In this article, I will interpret many of the current formal models of the scientific community as representing the latest development of what I will call the ‘Kuhnian project’. These models share with Kuhn a number (...) of questions about the relation between individuals and communities. At the same time, they also inherit some of Kuhn’s problematic characterisations of the scientific community. In particular, current models of the social organisation of science represent the scientific community as essentially value-free. This may put into question both their representational adequacy and their normative ambitions. In the end, it will be shown that the discussion on the formal models of the scientific community may contribute in fruitful ways to the ongoing debates on value judgements in science. (shrink)

The Protein Ontology (PRO) provides a formal, logically-based classification of specific protein classes including structured representations of protein isoforms, variants and modified forms. Initially focused on proteins found in human, mouse and Escherichia coli, PRO now includes representations of protein complexes. The PRO Consortium works in concert with the developers of other biomedical ontologies and protein knowledge bases to provide the ability to formally organize and integrate representations of precise protein forms so as to enhance accessibility to results of protein (...) research. PRO (http://pir.georgetown.edu/pro) is part of the Open Biomedical Ontologies (OBO) Foundry. (shrink)

The Protein Ontology (PRO) web resource provides an integrative framework for protein-centric exploration and enables specific and precise annotation of proteins and protein complexes based on PRO. Functionalities include: browsing, searching and retrieving, terms, displaying selected terms in OBO or OWL format, and supporting URIs. In addition, the PRO website offers multiple ways for the user to request, submit, or modify terms and/or annotation. We will demonstrate the use of these tools for protein research and annotation.

Incommensurability may be regarded as driving specialisation, on the one hand, and as posing some problems to interdisciplinarity, on the other hand. It may be argued, however, that incommensurability plays no role in either specialisation or interdisciplinarity. Scientific specialties could be defined as simply 'different' (that is, about different things), rather than 'incommensurable' (that is, competing for the explanation of the same phenomena). Interdisciplinarity could be viewed as the co- ordinated effort of scientists possessing complemetary and interlocking skills, and not (...) as the overcoming of some sort of incommensurable divide. This article provides a comprehensive evaluative examination of the relations between specialisation, interdisciplinarity, and incommensurability. Its aim is to defend the relevance of incommensurability to both specialisation and interdisciplinarity. At the same time, it aims at correcting the tendency, common among many philosophers, to regard incommensurability in a restrictive manner - such as, for example, as an almost purely semantic issue. (shrink)

Contemporary interdisciplinary research is often described as bringing some important changes in the structure and aims of the scientific enterprise. Sometimes, it is even characterized as a sort of Kuhnian scientific revolution. In this paper, the analogy between interdisciplinarity and scientific revolutions will be analysed. It will be suggested that the way in which interdisciplinarity is promoted looks similar to how new paradigms were described and defended in some episodes of revolutionary scientific change. However, contrary to what happens during some (...) scientific revolutions, the rhetoric with which interdisciplinarity is promoted does not seem to be accompanied by a strong agreement about what interdisciplinarity actually is. In the end, contemporary interdisciplinarity could be defined as being in a ‘pre-paradigmatic’ phase, with the very talk promoting interdisciplinarity being a possible obstacle to its maturity. (shrink)

Providence, from a philosophical point of view, is a problematic node that runs through much of the history of Western thought. The theme is closely linked to that of necessity, contingency, and causality, and so it can receive a contribution by analysing it starting from Aquinas’ natural philosophy. From the De Principiis Naturae, Aquinas’ youthful text, we witness the development of the theme in this context, which allows us to grasp providence in relation with necessity. The final causality acquires centrality. (...) It is as an “engine” that pushes everything to be according to the proper modality of its nature, and therefore also in the mode of necessity. The rootedness in the natural philosophy allows us to grasp the providence as that modality of divine government capable of holding together the necessity of God’s action and creatural contingency, leaving the rational creature free in its own choices. (shrink)

According to the analysis of concessive conditionals suggested by Crupi and Iacona, a concessive conditional \(p{{\,\mathrm{\hookrightarrow }\,}}q\) is adequately formalized as a conjunction of conditionals. This paper presents a sound and complete axiomatic system for concessive conditionals so understood. The soundness and completeness proofs that will be provided rely on a method that has been employed by Raidl, Iacona, and Crupi to prove the soundness and completeness of an analogous system for evidential conditionals.

A famous passage in Section 64 of Frege’s Grundlagen may be seen as a justification for the truth of abstraction principles. The justification is grounded in the procedureofcontent recarvingwhich Frege describes in the passage. In this paper I argue that Frege’sprocedure of content recarving while possibly correct in the case of first-order equivalencerelations is insufficient to grant the truth of second-order abstractions. Moreover, I propose apossible way of justifying second-order abstractions by referring to the operation of contentrecarving and I show (...) that the proposal relies to a certain extent on the Basic Law V. Therefore,if we are to justify the truth of second-order abstractions by invoking the content recarvingprocedure we are committed to a special status of some instances of the Basic Law V and thusto a special status of extensions of concepts as abstract objects. (shrink)

A miracle is defined as a violation of or intercession in the laws of nature. Some recent reports of UFO phenomena are such that UFOs may satisfy that definition. In this paper, we ask how Hume’s famous argument in “Of Miracles” relates to UFOs. We argue that his critique fails and that some well corroborated UFO reports are such that they justify a belief in miracles (qua violations of laws of nature).

Natural Categories and Human Kinds is a recent and timely contribution to current debate on natural kinds. Because of the growing sophistication of this debate, it is necessary to make careful distinctions in order to appreciate the originality of Khalidi’s position. Khalidi’s view on natural kinds is naturalistic: if we want to know what Nature’s joints really are, we should look at the actual carving job carried out by our best scientific practices. Like LaPorte, Khalidi is a fallibilist: our best (...) scientific theories may be revised or abandoned and so can our current classifications of natural kinds. Unlike LaPorte, however, Khalidi is an anti-essentialist: he argues against the idea that membership in a natural kind is a matter of possessing an essential set of necessary and sufficient properties. Like Dupré, Khalidi is a pluralist and anti-reductionist: he does not believe that there is only one true classification system and that there are natural kinds only at the so-called "fundamental level" of microphysics. Khalidi develops his pluralistic and anti-reductionistic position on the basis of a deep appreciation for the special sciences but, unlike Dupré, he thinks that only the scientific inquiry, which is driven by epistemic purposes, discover natural kinds and that, therefore, there are important differences between scientific and folk classifications. Khalidi’s conception of natural kinds has both an epistemic and a metaphysical component. (shrink)

In this article I offer an explicating interpretation of the procedure of content recarving as described by Frege in §64 of the Foundations of Arithmetic. I argue that the procedure of content recarving may be interpreted as an operation that while restricting the subject matter of a sentence, performs a generalization on what the sentence says about its subject matter. The characterization of the recarving operation is given in the setting of Yablo’s theory of subject matter and it is based (...) on the relation of determination between properties. The main advantage of the proposal is its generality, for it is applicable not just to the case of abstraction principles. (shrink)

The enormous increasing of connections between people and the noteworthy enlargement of domains and methods in sciences have augmented extraordinarily the cardinality of the set of meaningful human symbols. We know that complexity is always on the way to become complication, i.e. a non-tractable topic. For this reason scholars engage themselves more and more in attempting to tame plurality and chaos. In this book distinguished scientists, philosophers and historians of science reflect on the topic from a multidisciplinary point of view. (...) Is it possible to dominate complexity through reductionism? Are there other conceptual instruments useful to take account of complexity? What is complexity in biology, mathematics, physics and philosophy of mind? These are some of the questions which are faced in this volume. (shrink)

The Protein Ontology (PRO; http://proconsortium.org) formally defines protein entities and explicitly represents their major forms and interrelations. Protein entities represented in PRO corresponding to single amino acid chains are categorized by level of specificity into family, gene, sequence and modification metaclasses, and there is a separate metaclass for protein complexes. All metaclasses also have organism-specific derivatives. PRO complements established sequence databases such as UniProtKB, and interoperates with other biomedical and biological ontologies such as the Gene Ontology (GO). PRO relates to (...) UniProtKB in that PRO’s organism-specific classes of proteins encoded by a specific gene correspond to entities documented in UniProtKB entries. PRO relates to the GO in that PRO’s representations of organism-specific protein complexes are subclasses of the organism-agnostic protein complex terms in the GO Cellular Component Ontology. The past few years have seen growth and changes to the PRO, as well as new points of access to the data and new applications of PRO in immunology and proteomics. Here we describe some of these developments. (shrink)

This study thoroughly investigates the financial behaviors of financially independent, young, single professionals aged 24 to 35 in Balayan, Batangas, amidst a period of global inflation. Focusing on five industries—education, finance, government, healthcare, and retail—the research employs a mixed-methods approach. Quantitative analysis, involving 75 respondents through a 4-point Likert scale survey, is complemented by qualitative insights from in-depth interviews with 5 participants from each industry. The findings from numerical values revealed that demographics did not impact working professionals' saving habits and (...) buying behaviors during the global inflation surge. This suggests that despite differences in age, gender, industry, employment status, and monthly income or salary, all professionals prioritized robust, strong savings and reduced spending to ensure financial stability. The research underscores the significance for professionals in various industries to prioritize specific aspects of personal financial management during the prevailing global inflation surge. The study suggests that, irrespective of industry, working professionals should prioritize specific aspects of personal financial management during the global inflation surge. (shrink)

Secularism is a condition of the times when we live in today. It gives awareness to the global community that in reality there is only the immanent—there is no God. So, theism is seen as just one of the many available options: atheism becomes even more attractive to embrace. Generally, a theist will respond by demonstrating the theism plausibility through positive arguments about the existence of God. The author rejects this and offers an approach from Reformed epistemology on the problem, (...) as it is a thesis on how one knows God. Through Reformed epistemology, the author views secularism as what he considers as a cognitive environment. A cognitive environment prevents the “knowing subject” from knowing God, as the authors point out that the appropriate response to secularism is involving the “knowing subject” into the liturgy. Thus, liturgy can also be understood as an act that has an epistemic dimension which enables a person knowing God. (shrink)

In this paper, I present two crucial problems for Wolff’s metaphysics of quantities: 1) The structural identification problem and 2) the Pythagorean problem. The former is the problem of uniquely defining a general algebraic structure for all quantities; the latter is the problem of distinguishing physical quantitative structure from mathematical quantities. While Wolff seems to have a consistent and elegant solution to the first problem, the second problem may put in jeopardy his metaphysical view on quantities as spaces. After drawing (...) a parallelism between Wolff’s treatment of quantitative structures and Frege’s conception of quantitative domain, I propose a solution to the Pythagorean problem based on the idea that mathematical structures are the result of applying an abstraction principle on physical quantitative structures. In particular, I propose the view that abstraction may be seen as the operation of structure determination which transforms concrete physical quantities (i.e. undetermined structures) into abstract mathematical quantities (fully determined structures of thin and shallow objects). (shrink)

We provide a 'verisimilitudinarian' analysis of the well-known Linda paradox or conjunction fallacy, i.e., the fact that most people judge the probability of the conjunctive statement "Linda is a bank teller and is active in the feminist movement" (B & F) as more probable than the isolated statement "Linda is a bank teller" (B), contrary to an uncontroversial principle of probability theory. The basic idea is that experimental participants may judge B & F a better hypothesis about Linda as compared (...) to B because they evaluate B & F as more verisimilar than B. In fact, the hypothesis "feminist bank teller", while less likely to be true than "bank teller", may well be a better approximation to the truth about Linda. (shrink)

According to the Bad Company objection, the fact that Frege’s infamous Basic Law V instantiates the general definitional pattern of higher-order abstraction principles is a good reason to doubt the soundness of this sort of definitions. In this paper I argue against this objection by showing that the definitional pattern of abstraction principles – as extrapolated from §64 of Frege’s Grundlagen– includes an additional requirement (which I call the specificity condition) that is not satisfied by the Basic Law V while (...) is satisfied by other higher-order abstractions such as Hume’s Principle. I also show that the failure of this additional requirement in the case of Basic Law V is engendered by an essential feature of Frege’s conception of logic and thus that Frege himself should not have regarded the Basic Law V as a definition by abstraction. (shrink)

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

In some recent works, Crupi and Iacona have outlined an analysis of ‘if’ based on Chrysippus’ idea that a conditional holds whenever the negation of its consequent is incompatible with its antecedent. This paper presents a sound and complete system of conditional logic that accommodates their analysis. The soundness and completeness proofs that will be provided rely on a general method elaborated by Raidl, which applies to a wide range of systems of conditional logic.

The Protein Ontology provides terms for and supports annotation of species-specific protein complexes in an ontology framework that relates them both to their components and to species-independent families of complexes. Comprehensive curation of experimentally known forms and annotations thereof is expected to expose discrepancies, differences, and gaps in our knowledge. We have annotated the early events of innate immune signaling mediated by Toll-Like Receptor 3 and 4 complexes in human, mouse, and chicken. The resulting ontology and annotation data set has (...) allowed us to identify species-specific gaps in experimental data and possible functional differences between species, and to employ inferred structural and functional relationships to suggest plausible resolutions of these discrepancies and gaps. (shrink)

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

The Linda paradox is a key topic in current debates on the rationality of human reasoning and its limitations. We present a novel analysis of this paradox, based on the notion of verisimilitude as studied in the philosophy of science. The comparison with an alternative analysis based on probabilistic confirmation suggests how to overcome some problems of our account by introducing an adequately defined notion of verisimilitudinarian confirmation.

Identification of non-coding RNAs (ncRNAs) has been significantly enhanced due to the rapid advancement in sequencing technologies. On the other hand, semantic annotation of ncRNA data lag behind their identification, and there is a great need to effectively integrate discovery from relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a precisely defined ncRNA controlled vocabulary, which can fill a specific and highly needed niche in unification of ncRNA biology.

Review of the book "Paraconsistent Logic: Consistency, Contradiction, and Negation by Water Carnielli and Marcelo Coniglio.

In questo lavoro si presenta un nuovo esperimento mentale che solleva un particolare problema per quello che possiamo chiamare “fisicalismo minimale” in filosofia della mente. In particolare si argomenta che il fisicalismo minimale o i) non è in grado di fornirne un resoconto adeguato dell’esperimento mentale presentato, o ii) viene costretto a fornire un resoconto che è fortemente in contrasto con la nostra immagine scientifica del mondo. Il problema sollevato è un particolare esempio di quelli che Chalmers (1996) definisce hard (...) problems in filosofia della mente. Questa è la struttura del lavoro. Nella sezione 2. si presenta l’esperimento mentale, che chiameremo di Shem-Shaun1. Nella sezione 3. illustriamo il nostro argomento principale contro il fisicalismo minimale a partire dall’esperimento mentale della sezione precedente. Nella sezione conclusiva si discutono diversi modi di controbattere all’argomento principale e le sue conseguenze per il fisicalismo. (shrink)

Representing species-specific proteins and protein complexes in ontologies that are both human and machine-readable facilitates the retrieval, analysis, and interpretation of genome-scale data sets. Although existing protin-centric informatics resources provide the biomedical research community with well-curated compendia of protein sequence and structure, these resources lack formal ontological representations of the relationships among the proteins themselves. The Protein Ontology (PRO) Consortium is filling this informatics resource gap by developing ontological representations and relationships among proteins and their variants and modified forms. Because (...) proteins are often functional only as members of stable protein complexes, the PRO Consortium, in collaboration with existing protein and pathway databases, has launched a new initiative to implement logical and consistent representation of protein complexes. We describe here how the PRO Consortium is meeting the challenge of representing species-specific protein complexes, how protein complex representation in PRO supports annotation of protein complexes and comparative biology, and how PRO is being integrated into existing community bioinformatics resources. The PRO resource is accessible at http://pir.georgetown.edu/pro/. (shrink)

The Protein Ontology (PRO) is designed as a formal and principled Open Biomedical Ontologies (OBO) Foundry ontology for proteins. The components of PRO extend from a classification of proteins on the basis of evolutionary relationships at the homeomorphic level to the representation of the multiple protein forms of a gene, including those resulting from alternative splicing, cleavage and/or posttranslational modifications. Focusing specifically on the TGF-beta signaling proteins, we describe the building, curation, usage and dissemination of PRO. PRO provides a framework (...) for the formal representation of protein classes and protein forms in the OBO Foundry. It is designed to enable data retrieval and integration and machine reasoning at the molecular level of proteins, thereby facilitating cross-species comparisons, pathway analysis, disease modeling and the generation of new hypotheses. (shrink)

We investigate a recently devised polyhedral semantics for intermediate logics, in which formulas are interpreted in n-dimensional polyhedra. An intermediate logic is polyhedrally complete if it is complete with respect to some class of polyhedra. The first main result of this paper is a necessary and sufficient condition for the polyhedral completeness of a logic. This condition, which we call the Nerve Criterion, is expressed in terms of Alexandrov’s notion of the nerve of a poset. It affords a purely combinatorial (...) characterisation of polyhedrally complete logics. Using the Nerve Criterion we show, easily, that there are continuum many intermediate logics that are not polyhedrally complete but which have the finite model property. We also provide, at considerable combinatorial labour, a countably infinite class of logics axiomatised by the Jankov–Fine formulas of ‘starlike trees’ all of which are polyhedrally complete. The polyhedral completeness theorem for these ‘starlike logics’ is the second main result of this paper. (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)

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)

This work, in English "Struggle for power, organic crisis and judicial independence", has its origin in research academics of the IAEN carried out to provide expert advise to the Inter American Court of Human Rights in the case Quintana and others (Supreme Court of Justice) vs the State of Ecuador. The research is about the nature of the evolution of the ecuadorian state, the dynamics of its institutions, its players, parties, laws, its factors of instability, the way rights have been (...) deployed since the return to democracy in 1979, those who have benefited from neoliberal democracy and those who have paid the costs, and where in all this was the Supreme Court of Justice. The Introduction takes a look at this origin of the work and its intellectual import, provides a brief characterization of the Inter American Sistem of Human Rights Protection, how the Quintana Case fits within it, and an overview of the chapters and their logic. The first chapter analyzes the institutional and sociological factors that have contributed to Ecuador's historically unstable state, based primarily in an antagonistic struggle for power between the Executive and Legislative branches. The second chapter analyzes the economic and political factors that provoked an organic crisis, or crisis of hegemony, between 1997 and 2007 in Ecuador. The third chapter analyzes the evolution of the way in which judges are selected in Europe, the outcomes they have generated, and how they compare with the ecuadorian systems of judge selection in terms of securing judicial independence. The fourth chapter develops a theory of judicial independence in democracy and analyzes how Ecuador measures up to that standard, from when it became a neoliberal minimal democracy in 1981, to when it became a neoliberal false democracy as a consequence of instalation of a system evidently lacking in the people's support under the guise of the 1998 Constitution and its system of judge selection, and the new democratic horizons set by the 2008 Constitution, and the judicial system that springs from it. (shrink)

In this article I interpret resilience and evolution in view of the philosophy of Leibniz. First, I discuss resilience as a substance’s or a monad’s “quantity of essence” — its “degree of perfection” — which I express as the quality of the Whole with respect to the sum of the qualities of the Parts. Then I discuss evolution, which I interpret here as the autopoietic Principle that sets Itself in motion and creates all reality, including Itself. This Principle may be (...) considered as a sort of ante-litteram metaphysical Darwinian Selection. My interpretations provide a different formulation for questions such as “why natural evolution evolves?” and “why is this the best of all possible worlds?” In this article I also provide a geometrical interpretation of a key aspect behind the “divine mathematics” of the autopoietic Principle. (shrink)

Identification of non-coding RNAs (ncRNAs) has been significantly improved over the past decade. On the other hand, semantic annotation of ncRNA data is facing critical challenges due to the lack of a comprehensive ontology to serve as common data elements and data exchange standards in the field. We developed the Non-Coding RNA Ontology (NCRO) to handle this situation. By providing a formally defined ncRNA controlled vocabulary, the NCRO aims to fill a specific and highly needed niche in semantic annotation of (...) large amounts of ncRNA biological and clinical data. (shrink)

The term gestalt, when used in the context of general systems theory, assumes the value of “systemic touchstone”, namely a figure of reference useful to categorize the properties or qualities of a set of systems. Typical gestalts used, e.g., in biology, are those based on anatomical or physiological characteristics, which correspond respectively to architectural and organizational design choices in natural and artificial systems. In this paper we discuss three gestalts of general systems theory: behavior, organization, and substance, which refer respectively (...) to the works of Wiener, Boulding, and Leibniz. Our major focus here is the system introduced by the latter. Through a discussion of some of the elements of the Leibnitian System, and by means of several novel interpretations of those elements in terms of today’s computer science, we highlight the debt that contemporary research still has with this Giant among the giant scholars of the past. (shrink)

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

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

Nella sua straordinaria opera scientifica, Franco Selleri si è sempre opposto alla rinuncia alla comprensione della struttura della realtà e della natura degli oggetti fisici, che egli considera come l’elemento caratterizzante delle principali teorie della fisica del Novecento e che è stata stigmatizzata da Karl Popper come tesi della “fine della strada in fisica”. Sin dalla fine degli anni ’60, egli ha sviluppato quella riflessione critica nei confronti delle teorie fondamentali della fisica moderna, in particolar modo della teoria delle particelle (...) elementari e della meccanica quantistica, e in un secondo tempo delle teorie relativistiche, che contraddistingue il suo programma di ricerca. Nel corso della sua intensa e infaticabile attività scientifica, Selleri è entrato in proficuo contatto con molti grandi fisici e filosofi della scienza, instaurando un intenso dialogo critico con Louis de Broglie, John Bell e Karl Popper. Le sue originali e non convenzionali ricerche lo hanno portato a risultati significativi non solo nell’ambito dei fondamenti della fisica, ma anche della storia e della filosofia della fisica. Per questo abbiamo voluto dedicare un numero speciale di Isonomia al nostro impareggiabile amico e collega, sia per la sua passione instancabile e la sua profonda conoscenza dei fondamenti formali, concettuali e filosofici delle teorie della fisica contemporanea, sia e forse ancor più come maestro di una prospettiva perennemente critica che egli ha sempre seguito e proposto con particolare rigore ed estrema determinazione. (shrink)