Binding specificity is a centrally important concept in molecular biology, yet it has received little philosophical attention. Here I aim to remedy this by analyzing binding specificity as a causal property. I focus on the concept’s role in drug design, where it is highly prized and hence directly studied. From a causal perspective, understanding why binding specificity is a valuable property of drugs contributes to an understanding of causal selection—of how and why scientists distinguish between causes, not just causes from (...) noncauses. In particular, the specificity of drugs is precisely what underwrites their value as experimental interventions on biological processes. (shrink)

Empirical philosophers of science aim to base their philosophical theories on observations of scientific practice. But since there is far too much science to observe it all, how can we form and test hypotheses about science that are sufficiently rigorous and broad in scope, while avoiding the pitfalls of bias and subjectivity in our methods? Part of the answer, we claim, lies in the computational tools of the digital humanities, which allow us to analyze large volumes of scientific literature. Here (...) we advocate for the use of these methods by addressing a number of large-scale, justificatory concerns—specifically, about the epistemic value of journal articles as evidence for what happens elsewhere in science, and about the ability of DH tools to extract this evidence. Far from ignoring the gap between scientific literature and the rest of scientific practice, effective use of DH tools requires critical reflection about these relationships. (shrink)

Jacques Monod (1971) argued that certain molecular processes rely critically on the property of chemical arbitrariness, which he claimed allows those processes to “transcend the laws of chemistry”. It seems natural, as some philosophers have done, to interpret this in modal terms: a biological relationship is chemically arbitrary if it is possible, within the constraints of chemical “law”, for that relationship to have been otherwise than it is. But while modality is certainly important for understanding chemical arbitrariness, understanding its biological (...) role also requires an account of the concrete causal-functional features that distinguish arbitrary from non-arbitrary phenomena. In this paper I elaborate on this under-emphasised aspect by offering a general account of these features: arbitrary relations are instantiated by mechanisms that involve molecular adapters, which causally couple two properties or processes which would otherwise be uncorrelated. Additionally, adapters work by acting as intermediate rather than cooperating causes. (shrink)

Throughout the biological and biomedical sciences there is a growing need for, prescriptive ‘minimum information’ (MI) checklists specifying the key information to include when reporting experimental results are beginning to find favor with experimentalists, analysts, publishers and funders alike. Such checklists aim to ensure that methods, data, analyses and results are described to a level sufficient to support the unambiguous interpretation, sophisticated search, reanalysis and experimental corroboration and reuse of data sets, facilitating the extraction of maximum value from data sets (...) them. However, such ‘minimum information’ MI checklists are usually developed independently by groups working within representatives of particular biologically- or technologically-delineated domains. Consequently, an overview of the full range of checklists can be difficult to establish without intensive searching, and even tracking thetheir individual evolution of single checklists may be a non-trivial exercise. Checklists are also inevitably partially redundant when measured one against another, and where they overlap is far from straightforward. Furthermore, conflicts in scope and arbitrary decisions on wording and sub-structuring make integration difficult. This presents inhibit their use in combination. Overall, these issues present significant difficulties for the users of checklists, especially those in areas such as systems biology, who routinely combine information from multiple biological domains and technology platforms. To address all of the above, we present MIBBI (Minimum Information for Biological and Biomedical Investigations); a web-based communal resource for such checklists, designed to act as a ‘one-stop shop’ for those exploring the range of extant checklist projects, and to foster collaborative, integrative development and ultimately promote gradual integration of checklists. (shrink)

Oliver's and Rodriguez-Pereyra's important interpretation of the problem of universals as one concerning truthmakers neglects something crucial: that there is a numerical identity between numerically distinct particulars. The problem of universals is rather how to resolve the apparent contradiction that the same things are both numerically distinct and numerically identical. Baxter's account of instantiation as partial identity resolves the apparent contradiction. A seeming objection to this account is that it appears to make instantiation symmetric, since partial identity is symmetric. (...) Armstrong's standard reply is that the difference between a particular and a universal is what makes instantiation asymmetric. Brown suggests, though, that the instantiation of a universal by a universal is sometimes symmetric. However, the examples on which he relies are not universals. (shrink)

In this retrospective for Ethics, I discuss H.M. Oliver’s “Established Expectations and American Economic Policies.” This article, by a then-modestly-famous economist, has been ignored (no citations) since its 1940 publication. Yet it bears directly on a normative problem at the intersection of ethics and economics that challenges today’s policymakers but has received comparatively little philosophical attention: how should we balance potentially desirable institutional change against the disruption of established expectations? -/- Oliver details how the principle of fulfilling established (...) expectations cuts across political lines. Conservatives, he observes, criticized inflation for disrupting expectations, and demanded the protection of established corporations. New Deal progressives achieved “the safeguarding of the economic positions of certain important sections of the American people” (104) via statutes designed to protect income and homeownership status. And labor leaders lobbied for the preservation of occupational status. Oliver criticizes these demands on two grounds. First, they are noncompossible: they can’t simultaneously be fulfilled. Second, they are economically inefficient. He concludes that “in a modern dynamic economy, the preservation of status is not and cannot be a feasible criterion of economic justice” (107). -/- I argue that Oliver accurately recognizes both the wide endorsement and the moral ill-foundedness of fulfilling expectations. However, I criticize Oliver’s belief in the noncompossibility of expectations. The established expectations of the wealthy, middle-class homeowners and retirees, and current workers can all be maintained, but at the price of constricting the opportunities of new graduates, immigrants, and the poor—all groups yet to develop settled expectations. This insight renders the protection of expectations not merely inefficient but also unjust. (shrink)

In this paper I articulate a view of doxastic control that helps defend the legitimacy of our practice of blaming people for their beliefs. I distinguish between three types of doxastic control: intention-based, reason-based, and influence-based. First I argue that, although we lack direct intention-based control over our beliefs, such control is not necessary for legitimate doxastic blame. Second, I suggest that we distinguish two types of reason-responsiveness: sensitivity to reasons and appreciation of reasons. I argue that while both capacities (...) are necessary for satisfying the control condition, neither is sufficient. Finally, I defend an influence-based view of doxastic control according to which we have the capacity to execute intentions to engage in reflection that causally influences our beliefs in positive epistemic ways. This capacity is both necessary and sufficient for satisfying the control condition for legitimate doxastic blame. I end by defending the view from two objections: that reflection is not necessary for meeting the control condition, and that it is not sufficient. (shrink)

Technological developments have resulted in tremendous increases in the volume and diversity of the data and information that must be processed in the course of biomedical and clinical research and practice. Researchers are at the same time under ever greater pressure to share data and to take steps to ensure that data resources are interoperable. The use of ontologies to annotate data has proven successful in supporting these goals and in providing new possibilities for the automated processing of data and (...) information. In this chapter, we describe different types of vocabulary resources and emphasize those features of formal ontologies that make them most useful for computational applications. We describe current uses of ontologies and discuss future goals for ontology-based computing, focusing on its use in the field of infectious diseases. We review the largest and most widely used vocabulary resources relevant to the study of infectious diseases and conclude with a description of the Infectious Disease Ontology (IDO) suite of interoperable ontology modules that together cover the entire infectious disease domain. (shrink)

In this chapter, we explore whether agents have an epistemic duty to eradicate implicit bias. Recent research shows that implicit biases are widespread and they have a wide variety of epistemic effects on our doxastic attitudes. First, we offer some examples and features of implicit biases. Second, we clarify what it means to have an epistemic duty, and discuss the kind of epistemic duties we might have regarding implicit bias. Third, we argue that we have an epistemic duty to eradicate (...) implicit biases that have negative epistemic impact. Finally, we defend this view against the objection that we lack the relevant control over implicit bias that’s required for such a duty. We argue that we have a kind of reflective control over the implicit biases that we are duty-bound to eradicate. And since, as we show, we have this control over a wide variety of implicit biases, there are a lot of implicit biases that we have epistemic duties to eradicate. (shrink)

This paper seeks to answer the question: Can contemporary forms of artificial intelligence be creative? To answer this question, I consider three conditions that are commonly taken to be necessary for creativity. These are novelty, value, and agency. I argue that while contemporary AI models may have a claim to novelty and value, they cannot satisfy the kind of agency condition required for creativity. From this discussion, a new condition for creativity emerges. Creativity requires curiosity, a motivation to pursue epistemic (...) goods. I argue that contemporary AI models do not satisfy this new condition. Because they lack both agency and curiosity, it is a mistake to attribute the same sort of creativity to AI that we prize in humans. Finally, I consider the question of whether these AI models stand to make human creativity in the arts and sciences obsolete, despite not being creative themselves. I argue, optimistically, that this is unlikely. (shrink)

In this paper, I solve a puzzle generated by three conflicting claims about the relationship between faith, belief, and control: according to the Identity Thesis, faith is a type of belief, and according to Fideistic Voluntarism, we sometimes have control over whether or not we have faith, but according to Doxastic Involuntarism, we never have control over what we believe. To solve the puzzle, I argue that the Identity Thesis is true, but that either Fideistic Voluntarism or Doxastic Voluntarism is (...) false, depending on how we understand "control." I distinguish two notions of control: direct intention-based control and indirect reflective control. I argue that though we have direct intention-based control over neither belief nor faith, we have indirect reflective control over each of them. Moreover, indirect reflective control helps explain how we can be held accountable for each. (shrink)

This paper reviews the hole argument as an argument against spacetime substantivalism. After a careful presentation of the argument itself, I critically review possible responses.

We make some remarks on the mathematics and metaphysics of the hole argument, in response to a recent article in this journal by Weatherall ([2018]). Broadly speaking, we defend the mainstream philosophical literature from the claim that correct usage of the mathematics of general relativity `blocks' the argument.

This paper uses a schema for infinite regress arguments to provide a solution to the problem of the infinite regress of justification. The solution turns on the falsity of two claims: that a belief is justified only if some belief is a reason for it, and that the reason relation is transitive.

In this paper I offer an argument against one important version of panentheism, that is, mereological panentheism. Although panentheism has proven difficult to define, I provide a working definition of the view, and proceed to argue that given this way of thinking about the doctrine, mereological accounts of panentheism have serious theological drawbacks. I then explore some of these theological drawbacks. In a concluding section I give some reasons for thinking that the classical theistic alternative to panentheism is preferable, all (...) things considered. (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)

I argue that notions of relative fundamentality need to be invoked if there is to be something substantive at stake in the debate between proponents of Harvey Brown's dynamical approach to relativity and defenders of a more traditional interpretation of spacetime. I will review some problems that stand in the way of the advocate of the dynamical approach making good on their claim that dynamical symmetries are more fundamental than spacetime symmetries.

Eleonore Stump insightfully develops Aquinas’s theodicy to account for a significant source of human suffering, namely the undermining of desires of the heart. Stump argues that what justifies God in allowing such suffering are benefits made available to the sufferer through her suffering that can defeat the suffering by contributing to the fulfillment of her heart’s desires. We summarize Stump’s arguments for why such suffering requires defeat and how it is defeated. We identify three problems with Stump’s account of how (...) such suffering is defeated and offer solutions to each. We defend and strengthen Stump’s response to the hardest cases for her view, and explain what her view demands of God. (shrink)

In this paper I argue, based on a comparison of Spinoza's and Descartes‟s discussion of error, that beliefs are affirmations of the content of imagination that is not false in itself, only in relation to the object. This interpretation is an improvement both on the winning ideas reading and on the interpretation reading of beliefs. Contrary to the winning ideas reading it is able to explain belief revision concerning the same representation. Also, it does not need the assumption that I (...) misinterpret my otherwise correct ideas as the interpretation reading would have it. In the first section I will provide a brief overview of the notion of inherence and its role in Spinoza‟s discussion of the status of finite minds. Then by examining the relation between Spinoza‟s and Descartes‟ distinction of representations and attitudes, I show that affirmation can be identified with beliefs in Spinoza. Next, I will take a closer look at the identification of intellect and will and argue that Spinoza's identification of the two is based on the fact that Spinoza sees both as the active aspect of the mind. After that, I analyze Spinoza‟s comments on the different scopes of will and intellect, and argue that beliefs are affirmations of the imaginative content of the idea. Finally, through Spinoza‟s example of the utterance of mathematical error, I present my solution to the problem of inherence of false beliefs. (shrink)

I argue, through appeal to the distinction between analysis and decomposition described by Dummett, that Wittgenstein employs both of those notions in the Tractatus. I then bring this interpretation to bear upon the issue of propositional unity, where I formulate an objection to the views of both Leonard Linksy and José Zalabardo. I show that both Linsky and Zalabardo fail to acknowledge the distinction between analysis and decomposition present in the Tractatus, and that they consequently mischaracterise Wittgenstein’s position with respect (...) to propositional unity. (shrink)

A repository of clinically associated Staphylococcus aureus (Sa) isolates is used to semi‐automatically generate a set of application ontologies for specific subfamilies of Sa‐related disease. Each such application ontology is compatible with the Infectious Disease Ontology (IDO) and uses resources from the Open Biomedical Ontology (OBO) Foundry. The set of application ontologies forms a lattice structure beneath the IDO‐Core and IDO‐extension reference ontologies. We show how this lattice can be used to define a strategy for the construction of a new (...) taxonomy of infectious disease incorporating genetic, molecular, and clinical data. We also outline how faceted browsing and query of annotated data is supported using a lattice application ontology. (shrink)

Two extremely detailed accounts of temporal experience can be found in the work of C. D. Broad. These accounts have been subject to considerable criticism. I argue that, when we look more carefully at Broad’s work, we find that much of this criticism fails to find its target. I show that the objection that ultimately proves troubling for Broad stems from his commitment to two principles: i) the Thin-PSA, and ii) the ‘Overlap’ claim. I use this result to demonstrate that (...) we can learn two extremely important lessons from Broad’s work on temporal experience. -/- The first lesson is that there is a structural problem facing any account that commits to these two principles. This is significant given that a number of recent accounts of temporal experience are so committed. The second lesson is that the problem facing these accounts stems only from commitment to the Thin-PSA and ‘Overlap’, rather than to commitment to a particular conception of how experiences are to be individuated. This, I argue, gives us reason to reject Tye’s recent claim that the problems facing accounts of temporal experience can be dissolved simply by making stipulations about how experiences are to be individuated. (shrink)

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

In the following article I intend to examine the problem of the unity of the proposition in Russell, Frege, and Wittgenstein. My chief aim will be to draw attention to the distinction between Russell’s conception of propositional constituents, on the one hand, with Frege and Wittgenstein’s on the other. My focus will be on Russell’s view of terms as independent, propositions being built up out of these building blocks, compared with Frege and Wittgenstein’s ‘top down’ approach. Furthermore, I will argue (...) that, contra certain other commentators, Frege’s metaphor of saturation and unsaturation does not serve as a solution to the problem of unity, and that the extension of this metaphorical language to Wittgenstein is, therefore, inappropriate. (shrink)

An accurate classification of bacteria is essential for the proper identification of patient infections and subsequent treatment decisions. Multi-Locus Sequence Typing (MLST) is a genetic technique for bacterial classification. MLST classifications are used to cluster bacteria into clonal complexes. Importantly, clonal complexes can serve as a biological species concept for bacteria, facilitating an otherwise difficult taxonomic classification. In this paper, we argue for the inclusion of terms relating to clonal complexes in biomedical ontologies.

The following four theses all have some intuitive appeal: (I) There are valid norms. (II) A norm is valid only if justified by a valid norm. (III) Justification, on the class of norms, has an irreflexive proper ancestral. (IV) There is no infinite sequence of valid norms each of which is justified by its successor. However, at least one must be false, for (I)--(III) together entail the denial of (IV). There is thus a conflict between intuition and logical possibility. This (...) paper, after distinguishing various conceptions of a norm, of validity and of justification, argues for the following position. (I) is true. (II) is false for legislative justification and true for epistemic justification. (III) is true for legislative and false for epistemic justification. (IV) is true for legislative justification; for epistemic justification (IV) is true or false depending on the conception taken of a norm. Our intuition in favour of (II) must therefore be abandoned where justification is conceived legislatively. Our intuition in favour of (III) must be abandoned, and our intuition in favour of (IV) qualified, where justification is conceived epistemically. (shrink)

In a recent study, we found a negative association between psychopathy and violence against genetic relatives. We interpreted this result as a form of nepotism and argued that it failed to support the hypothesis that psychopathy is a mental disorder, suggesting instead that it supports the hypothesis that psychopathy is an evolved life history strategy. This interpretation and subsequent arguments have been challenged in a number of ways. Here, we identify several misunderstandings regarding the harmful dysfunction definition of mental disorder (...) as it applies to psychopathy and regarding the meaning of nepotism. Furthermore, we examine the evidence provided by our critics that psychopathy is associated with other disorders, and we offer a comment on their alternative model of psychopathy. We conclude that there remains little evidence that psychopathy is the product of dysfunctional mechanisms. (shrink)

In this paper, I investigate whether Spinoza theory of intellect can be considered as an Averroistic, Themistian or Alexandrian theory of intellect. I identify key doctrines of these theories that are argumentatively and theoretically independent from Aristotelian hylomorphism and thus can be accepted by someone rejecting hylomorphism. Next, I argue that the textual evidence is inconclusive: depending on the reading of Spinoza's philosophy accepted, Spinoza's theory of intellect can or cannot be considered as an Averroistic theory.

In this paper I examine the question whether Spinoza can account for the necessity of death. I argue that he cannot because within his ethical intellectualist system the subject cannot understand the cause of her death, since by understanding it renders it harmless. Then, I argue that Spinoza could not solve this difficulties because of deeper commitments of his system. At the end I draw a historical parallel to the problem from medieval philosophy.

In this paper, through a close reading of Spinoza's use of common notions I argue for the role of experiential and experimental knowledge in Spinoza's epistemology.

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)

Spinoza’s account of memory has not received enough attention, even though it is relevant for his theory of consciousness. Recent literature has studied the “pancreas problem.” This paper argues that there is an analogous problem for memories: if memories are in the mind, why is the mind not conscious of them? I argue that Spinoza’s account of memory can be better reconstructed in the context of Descartes’s account to show that Spinoza responded to these views. Descartes accounted for the preservation (...) of memories by holding that they are brain states without corresponding mental states, and that the mind is able to interpret perception either as new experience or as memory. Spinoza has none of these conceptual resources because of his substance monism. Spinoza accounts for memories as the mind’s ability to generate ideas according to the order of images. This ability consists in the connection of ideas, which is not an actual property, but only a dispositional one and thus not conscious. It is, however, grounded in the actual property of parts of the body, of which ideas are conscious. (shrink)

The immediate occasion for this special issue was Christia Mercer’s influential paper “The Contextualist Revolution in Early Modern Philosophy”. In her paper, Mercer clearly demarcates two methodologies of the history of early modern philosophy. She argues that there has been a silent contextualist revolution in the past decades, and the reconstructivist methodology has been abandoned. One can easily get the impression that ‘reconstructivist’ has become a pejorative label that everyone outright rejects. Mercer’s examples of reconstructivist historians of philosophy are deceased (...) (P. F. Strawson, Margaret J. Osler, Richard Watson, and Bernard Williams), anonymous (the fans of philosopher* mentioned by Lisa Downing), or authors whose more recent work followed a contextualist methodology (Jonathan Bennett). The reconstructivist camp seems to have turned into a shadowy group, largely extinct by now, not unlike the Death Eaters in the fictional universe of Harry Potter. There are some figures who previously belonged to this group, but they have since reformed their ways – or so it seems. Sometimes it is rumoured that certain people may still have secret allegiance to it, but no one dares to fly its banner openly. We decided to create this special issue because we believe that reconstructivist methodology does not deserve this shadowy existence. (shrink)

Lack of consent is valorized within popular culture to the point that sexual assault has become a spectator sport and creepshot entertainment on social media. Indeed, the valorization of nonconsensual sex has reached the extreme where sex with unconscious girls, especially accompanied by photographs as trophies, has become a goal of some boys and men.

Numerous studies of the beliefs of people with anorexia nervosa (AN) suggest that a subset of such individuals may experience delusions. We first describe what makes a belief delusional and conclude that such characteristics can be appropriately applied to some beliefs of people with AN. Next, we outline how delusional beliefs may relate to the broader psychopathological process in AN, including: (1) they may be epiphenomenal; (2) they may be an initial partial cause of AN; (3) they may be caused (...) by aspects of AN; or (4) they may be sustaining causes, possibly involved in reciprocal causal relations with aspects of AN. We argue that there is good reason to believe that delusional beliefs of people with AN are not merely epiphenomenal, but rather that they’re causally connected to AN. Because of this, empirical studies can be designed to test for the presence of causal relations. We describe how these studies should be designed. The results of such studies have important implications for understanding the experience of individuals with AN and for the treatment of AN. We outline these implications. (shrink)

This article argues that we can construct a complex interpretation of the nature of time by linking Aciman’s gnostic thread to aspects of twentieth century theory, from philosophy and psychoanalysis. In brief, it attempts to demonstrate the roles of dislocation, deferral, and Otherness in constituting human temporality. The essay begins by surmising the conceptual history of time, touching on key ideas put forward by Augustine and Bergson. The second section takes a psychoanalytic turn after exploring Homo Irrealis to describe the (...) significance of desire and fantasy. Thirdly, we develop a unique and temporal application of difference and deferral, building off of Deleuze and Derrida. The fourth section will consider how the psychoanalytic concept of the Other is inhered within time. We conclude that an Acimanic analysis of time is the means by which we can understand existence not as a series of moments, but a rich progression of dissimilitude and Otherness defined moreso by its lack of cohesion and directness of being than by a unified and self-identifying subject. (shrink)

Scalability, efficiency, and security had been a persistent problem over the years in data mining, several techniques had been proposed and implemented but none had been able to solve the problem of scalability, efficiency and security from cloud computing. In this research, we solve the problem scalability, efficiency and security in data mining over cloud computing by using a restful web services and combination of different technologies and tools, our model was trained by using different machine learning algorithm, and finally (...) using different validation and cross-validation methods to compare and validate our results. We build, train, test and deploy our model by restful API services which can be called through an endpoint, and with very high accuracy and huge success. (shrink)

This paper addresses a family of issues surrounding the biological phenomenon of resistance and its representation in realist ontologies. The treatments of resistance terms in various existing ontologies are examined and found to be either overly narrow, internally inconsistent, or otherwise problematic. We propose a more coherent characterization of resistance in terms of what we shall call blocking dispositions, which are collections of mutually coordinated dispositions which are of such a sort that they cannot undergo simultaneous realization within a single (...) bearer. A definition of ‘protective resistance’ is proposed for use in the Infectious Disease Ontology (IDO) and we show how this definition can be used to characterize the antibiotic resistance in Methicillin-Resistant Staphylococcus aureus (MRSA). The ontological relations between entities in our MRSA case study are used alongside a series of logical inference rules to illustrate logical reasoning about resistance. A description logic representation of blocking dispositions is also provided. We demonstrate that our characterization of resistance is sufficiently general to cover two other cases of resistance in the infectious disease domain involving HIV and malaria. (shrink)

On 25 December 1991 Alaa Hamed must for his literary work to the "Emergency Court for National Security" in Cairo. The judge read out the verdict: 2,300 egyptian pounds fine and eight years in prison for violating of state security and social peace. - A shock not only for egyptian intellectuals! The Arabic Department of BBC London placed the sentence in second place in the news, immediately after the notification of the resignation of Michail Gorbachev. Even in Germany the message (...) arrived in the media (FAZ, 30 December 1991). The egyptian journalist Jusif El Kaid spoke of the "most dangerous convicted of the 20 century" (Almussawar. No. 3508, 3 January 1992). The human rights organization of Egypt criticized the verdict as a violation of the right to freedom of expression and artistic innovation. It was the first time in modern history (after the 1952 revolution), that an author should because of his literary work in prison. (shrink)

Im Jahre 1870, da Garibaldis Truppen in Rom den Kirchenstaat auflösten, gelangte in Europa die Grenznutzen-Schule in der Ökonomie zum Durchbruch. Die Wertlehre nicht nur der klassischen englischen, auch der marxistischen Ökonomie, war objektivistisch. Die subjektivistische Wertlehre hingegen verlieh der unvollständig ausgebildeten klassischen konkurrenzwirtschaftlichen Theorie ein Fundament, wurde später zum Ausgangspunkt der Wohlfahrtsökonomie wie im 20. Jh. der Spieltheorie. Zugleich der Günstlinge und Priester einer rentenabhängigen Staatsklasse höhnend wie die Existenz von Armut im Kapitalismus als dysfunktional anprangernd, stellt Nietzsche in (...) MA fast ironisch Grenznutzen-Überlegungen an: „ein ganz Armer richtet sich gewöhnlich durch Vornehmheit der Gesinnung zu Grunde, er kommt nicht vorwärts und erwirbt Nichts […] – Dabei ist aber zu bedenken, daß der Reichtum fast die gleichen Wirkungen ausübt, wenn Einer dreihundert Thaler oder dreissigtausend jährlich verbrauchen darf: es giebt nachher keine wesentliche Progression der begünstigenden Umstände mehr. Aber weniger zu haben, als Knabe zu betteln und sich zu erniedrigen, ist furchtbar: obwohl für Solche, welche ihr Glück im Glanze der Höfe, in der Unterordnung unter Mächtige und Einflussreiche suchen oder welche Kirchenhäupter werden wollen, es der rechte Ausgangspunct sein mag (– Es lehrt, gebückt sich in die Höhlengänge der Gunst einzuschleichen.)” (MA I, 479, KSA 2, 313). (shrink)

Methodological critique of the sociological theory "spontaneous cooperation" to explain the revolution in Germany in 1989. This approach represented the german sociologists Dieter Opp and Detlef Pollack. The author reconstructs the two statements. Opp's approach is logically inconsistent. This approach is also unfit for scientific prediction, but Opp says the possibility of prediction is a necessary criterion for a scientific theory. Pollack's systemtheoretical approach ignores the really existing organized resistance of the subversive groups in Leipzig, for example the "Working group (...) for human rights" or the "Working group for Justice". Miracle or surprise chance are scientifically anacceptable models to explain a revolution. Both economically and politically offered the capitalist welfare state more for the workers than the socialism. So people noticed socialism as a system with more work for less prosperity and without civil rights, as a system of "exploitation by inefficiency" (Elsenhans). The author describes the revolution as a result of very effective collaboration between people, who willing to take risks and wanted to emigrate from the GDR to West, and the subversive groups, that could organize the revolutionary resistance. - This is a possible interpretation of the revolution from the interaction of transition-theory and voice-and-exit-theory (Hirschman). (shrink)

1. Kulturkomparatistik / 2. Physis als Gewissheit / 3. Kultur und Wertungskriterium / 4. Genealogie als Methode der Entbindung aus Tradition / 5. Genealogie der Ahnenkultur am Beispiel der Inuit / 6. Zwei Errungenschaften Europas: Liberaler Universalismus und individualistische Vernunftkritik / 7. Theorie der Notgemeinschaft und die Psychologie des Ressentiments zur Lösung von Isaiah Berlins "Paradoxon kollektiver Selbstbestimmung" / 8. Konflikt-Transformationen nach Albert O. Hirschman / 9. Der Wille zur Anthropodiversität übersteigt die Toleranz.

We introduce a family of operators to combine Description Logic concepts. They aim to characterise complex concepts that apply to instances that satisfy \enough" of the concept descriptions given. For instance, an individual might not have any tusks, but still be considered an elephant. To formalise the meaning of "enough", the operators take a list of weighted concepts as arguments, and a certain threshold to be met. We commence a study of the formal properties of these operators, and study some (...) variations. The intended applications concern the representation of cognitive aspects of classi cation tasks: the interdependencies among the attributes that de ne a concept, the prototype of a concept, and the typicality of the instances. (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)

This paper addresses the use of dispositions in the Infectious Disease Ontology (IDO). IDO is an ontology constructed according to the principles of the Open Biomedical Ontology (OBO) Foundry and uses the Basic Formal Ontology (BFO) as an upper ontology. After providing a brief introduction to disposition types in BFO and IDO, we discuss three general techniques for representing combinations of dispositions under the headings blocking dispositions, complementary dispositions, and collective dispositions. Motivating examples for each combination of dispositions is given (...) along with a specific use case in IDO. Description logic restrictions are used to formalize statements relating to these combinations. (shrink)