The National Center for Biomedical Ontology is a consortium that comprises leading informaticians, biologists, clinicians, and ontologists, funded by the National Institutes of Health (NIH) Roadmap, to develop innovative technology and methods that allow scientists to record, manage, and disseminate biomedical information and knowledge in machine-processable form. The goals of the Center are (1) to help unify the divergent and isolated efforts in ontology development by promoting high quality open-source, standards-based tools to create, manage, and use ontologies, (2) to create (...) new software tools so that scientists can use ontologies to annotate and analyze biomedical data, (3) to provide a national resource for the ongoing evaluation, integration, and evolution of biomedical ontologies and associated tools and theories in the context of driving biomedical projects (DBPs), and (4) to disseminate the tools and resources of the Center and to identify, evaluate, and communicate best practices of ontology development to the biomedical community. Through the research activities within the Center, collaborations with the DBPs, and interactions with the biomedical community, our goal is to help scientists to work more effectively in the e-science paradigm, enhancing experiment design, experiment execution, data analysis, information synthesis, hypothesis generation and testing, and understand human disease. (shrink)

The reproducibility movement in psychology has resulted in numerous highly publicized instances of replication failures. The goal of the present work was to investigate people’s reactions to a psychology replication failure vs. success, and to test whether a failure elicits harsher reactions when the researcher is a woman vs. a man. We examined these questions in a pre-registered experiment with a working adult sample, a conceptual replication of that experiment with a student sample, and an analysis of data compiled and (...) posted by a psychology researcher on their public weblog with the stated goal to improve research replicability by rank-ordering psychology researchers by their “estimated false discovery risk.” Participants in the experiments were randomly assigned to read a news article describing a successful vs. failed replication attempt of original work from a male vs. female psychological scientist, and then completed measures of researcher competence, likability, integrity, perceptions of the research, and behavioral intentions for future interactions with the researcher. In both working adult and student samples, analyses consistently yielded large main effects of replication outcome, but no interaction with researcher gender. Likewise, the coding of weblog data posted in July 2021 indicated that 66.3% of the researchers scrutinized were men and 33.8% were women, and their rank-ordering was not correlated with researcher gender. The lack of support for our pre-registered gender-replication hypothesis is, at first glance, encouraging for women researchers’ careers; however, the substantial effect sizes we observed for replication outcome underscore the tremendous negative impact the reproducibility movement can have on psychologists’ careers. We discuss the implications of such negative perceptions and the possible downstream consequences for women in the field that are essential for future study. (shrink)

The value of any kind of data is greatly enhanced when it exists in a form that allows it to be integrated with other data. One approach to integration is through the annotation of multiple bodies of data using common controlled vocabularies or ‘ontologies’. Unfortunately, the very success of this approach has led to a proliferation of ontologies which itself creates obstacles to integration. The Open Biomedical Ontologies (OBO) consortium has set in train a strategy to overcome this problem. Existing (...) OBO ontologies, including the Gene Ontology, are undergoing a process of coordinated reform and new ontologies being created on the basis of an evolving set of shared principles governing ontology development. The result is an expanding family of ontologies designed to be interoperable, logically well-formed, and to incorporate accurate representations of biological reality. We describe the OBO Foundry initiative, and provide guidelines for those who might wish to become involved. (shrink)

The potential reducibility of chemical entities to their physical bases is a matter of dispute between ontological reductionists on one hand, and emergentists on the other. However, relevant debates typically revolve around the reducibility of so-called ‘higher-level’ chemical entities, such as molecules. Perhaps surprisingly, even committed proponents of emergence for these higher-level chemical entities appear to accept that the ‘lowest-level’ chemical entities – atomic species – are reducible to their physical bases. In particular, the microstructural view of chemical elements, actively (...) developed and defended by emergentists, appears to hold that the explanatory power of nuclear charge justifies being reductionist about atomic species. My first task in this paper is to establish that nuclear charge cannot ultimately provide explanations sufficient to justify a reductionist approach to atomic species, unless we abandon the persuasive intuition that the presence of an element in a substance ought to explain the properties of that substance. The ‘missing piece’ for explaining the properties of substances by way of their elemental constituents is the electronegativity values of participant atoms. But electronegativity is a strikingly disunified concept that appears distinctly unamenable to analysis by way of fundamental physical principles. Through evaluating the uncertain physical identity of electronegativity, as well as its widespread and indispensable epistemic utility in chemical practice, I argue that electronegativity provides compelling grounds to seriously consider emergence for atomic species. (shrink)

Monte Johnson examines one of the most controversial aspects of Aristiotle's natural philosophy: his teleology. Is teleology about causation or explanation? Does it exclude or obviate mechanism, determinism, or materialism? Is it focused on the good of individual organisms, or is god or man the ultimate end of all processes and entities? Is teleology restricted to living things, or does it apply to the cosmos as a whole? Does it identify objectively existent causes in the world, or is it (...) merely a heuristic for our understanding of other causal processes? Johnson argues that Aristotle's aporetic approach drives a middle course between these traditional oppositions, and avoids the dilemma, frequently urged against teleology, between backwards causation and anthropomorphism. Although these issues have been debated with extraordinary depth by Aristotle scholars, and touched upon by many in the wider philosophical and scientific community as well, there has been no comprehensive historical treatment of the issue. Aristotle is commonly considered the inventor of teleology, although the precise term originated in the eighteenth century. But if teleology means the use of ends and goals in natural science, then Aristotle was rather a critical innovator of teleological explanation. Teleological notions were widespread among his predecessors, but Aristotle rejected their conception of extrinsic causes such as mind or god as the primary causes for natural things. Aristotle's radical alternative was to assert nature itself as an internal principle of change and an end, and his teleological explanations focus on the intrinsic ends of natural substances - those ends that benefit the natural thing itself. Aristotle's use of ends was subsequently conflated with incompatible 'teleological' notions, including proofs for the existence of a providential or designer god, vitalism and animism, opposition to mechanism and non-teleological causation, and anthropocentrism. Johnson addresses these misconceptions through an elaboration of Aristotle's methodological statements, as well as an examination of the explanations actually offered in the scientific works. Reviewed in: Notre Dame Philosophical Review 2006.06.15; Bryn Mawr Classical Review 2006.08.37; Il-Sole – 24 Ore 6 Aug. 2006; Philosophy in Review 26 (2006): 360-2; Rhizai 3 (2006): 171-8; Journal of the History of Philosophy 45 (2007): 323-4; Ancient Philosophy 27 (2007): 191-200; Phronesis 52 (2007): 248-9; Isis 98 (2007): 375; Aestimatio 4 (2007) 146-152; The British Journal for the History of Science 41 (2008): 129-130. The European Legacy 14 (2009); La Cultura 47 (2009): 174-175; Sean M. Row, Teleology in Political Contexts: an assessment of Monte Ransome Johnson’s “Aristotle on Teleology”. (A thesis presented to the faculty of the college of arts and sciences of Ohio University, 2009.). (shrink)

Leonidas Montes presents a new reading of Adam Smith's legacy. The classical influences, the meaning of some key concepts, and what other authors were saying at the time, are fundamental to understand what Smith really said. Starting with the famous Das Adam Smith Problem, Montes investigates the causes and the context of the Problem, and proposes the importance of the moral triad of the supposed impartial spectator, propriety and self-command for understanding Smith's broad concept of sympathy. Smith's virtues are fundamental (...) to his moral thought, and the nature of the meaning of self-command and propriety have important philosophical implications, reflecting the relevance of moral autonomy in Smith's thought. The concluding chapter gives an example of the mistake of simply looking at a problem through the eyes of today. It questions the popular version of Smith as a forerunner or founder of general economic equilibrium theory by investigating the real nature of Smith's Newtonianism. (shrink)

Critics have alleged that Democritus’ ethical prescriptions (“gnomai”) are incompatible with his physics, since his atomism seems committed to necessity or chance (or an awkward combination of both) as a universal cause of everything, leaving no room for personal responsibility. I argue that Democritus’ critics, both ancient and contemporary, have misunderstood a fundamental concept of his causality: a cause called “spontaneity”, which Democritus evidently considered a necessary (not chance) cause, compatible with human freedom, of both atomic motion and human actions. (...) Some influential contemporary compatibilists have argued that freedom and responsibility are compatible with causal determinism, but not intentional constraint where some other agent is intentionally manipulating or coercing one’s actions. In line with this, Democritus holds that humans should not blame their actions on other agents like the gods, or agent-like external forces like fate or chance, but should assume ultimate intentional control over their own choices and actions. The famous remark of his associate Leucippus that “everything happens for a reason and out of necessity” is a fitting slogan of their atomistic philosophy, for Democritus pursued what can without anachronism be recognized as a causal theory of freedom. (shrink)

Authenticates approximately 500 lines of Aristotle's lost work the Protrepticus (Exhortation to Philosophy) contained in the circa third century AD work by Iamblichus of Chalcis entitled Protrepticus epi philosophian. Includes a complete English translation of the authenticated material.

An overview of the influence of Lucretius poem On the Nature of Things (De Rerum Natura) on the renaissance and scientific revolution of the seventeenth century, and an examination of its continuing influence over physical atomism in the nineteenth and twentieth centuries.

Faith-based organizations are a key player in major sectors of activity for maintaining the welfare state, including health, education, and social services. This paper uses a multivariate regression model in an attempt to identify the factors that affect the relationship between work engagement and flourishing. The paper also discusses the empirical research gap that has been identified in the literature about the moderated effect of human values on this relationship. This study is based on a sample of 142 nuns of (...) a congregation belonging to a religious organization with an international scope and a Catholic inspiration. The case of religious women who have chosen to live a life consistent with the charism of the congregation constitutes a paradigmatic and unique environment to investigate the potential alignment of personal values with professional activity. Two important conclusions are derived from this work. First, the more engaged nuns are in their work (social action to serve the poorest and most disadvantaged people), the more they flourish in their working environment and in their personal lives. Second, certain personal values reinforce the relationship between the professional role (work engagement) and the personal role (flourishing). (shrink)

For an Aristotelian observer, the halo is a puzzling phenomenon since it is apparently sublunary, and yet perfectly circular. This paper studies Aristotle's explanation of the halo in Meteorology III 2-3 as an optical illusion, as opposed to a substantial thing (like a cloud), as was thought by his predecessors and even many successors. Aristotle's explanation follows the method of explanation of the Posterior Analytics for "subordinate" or "mixed" mathematical-physical sciences. The accompanying diagram described by Aristotle is one of the (...) earliest lettered geometrical diagrams, in particular of a terrestrial phenomenon, and versions of it can still be found in modern textbooks on meteorological optics. (shrink)

Monte Cook - Robert Desgabets's Representation Principle - Journal of the History of Philosophy 40:2 Journal of the History of Philosophy 40.2 189-200 Robert Desgabets's Representation Principle Monte Cook THE CARTESIAN PHILOSOPHER ROBERT DESGABETS'S only philosophical publication is his Critique de la Critique de la Recherche de la vérité , in which he criticizes Simon Foucher's criticism of Malebranche's Search After Truth. This work has never been republished and is now available only in rare book collections. Desgabets also (...) wrote several unpublished works that were widely circulated during his lifetime and in which he developed a unique philosophical system of his own. Fortunately, these were published in 1983 as Robert Desgabets, Oeuvres philosophiques inédites. Drawing particularly on this volume and especially on the longest work in this volume, Supplément à la philosophie de Monsieur Descartes , I give a glimpse of Desgabets's system. I do so by discussing the surprising view of intentionality central to Desgabets's proof of the external world and to Desgabets's system in general. I note some interesting similarities and differences between Desgabets's position and the positions of Descartes and seventeenth-century Cartesians Malebranche and Arnauld. But mainly I clarify and give some needed structure to Desgabets's argument for his view of intentionality. This argument is interesting in itself as a sustained argument.. (shrink)

We offer a sceptical examination of a thesis recently advanced in a monograph published by Princeton University Press, entitled Greek Buddha: Pyrrho’s Encounter with Early Buddhism in Central Asia. In this dense and probing work, Christopher I. Beckwith, a professor of Central Eurasian studies at Indiana University, Bloomington, argues that Pyrrho of Elis adopted a form of early Buddhism during his years in Bactria and Gandhāra, and that early Pyrrhonism must be understood as a sect of early Buddhism. In making (...) his case Beckwith claims that virtually all scholars of Greek, Indian, and Chinese philosophy have been operating under flawed assumptions and with flawed methodologies, and so have failed to notice obvious and undeniable correspondences between the philosophical views of the Buddha and of Pyrrho. In this study we take Beckwith’s proposal and challenge seriously, and we examine his textual basis and techniques of translation, his methods of examining passages, his construal of problems and his reconstruction of arguments. We find that his presuppositions are contentious and doubtful, his own methods are extremely flawed, and that he draws unreasonable conclusions. Although the result of our study is almost entirely negative, we think it illustrates some important general points about the methodology of comparative philosophy. (shrink)

In some influential histories of ancient philosophy, teleological explanation and mechanistic explanation are assumed to be directly opposed and mutually exclusive alternatives. I contend that this assumption is deeply flawed, and distorts our understanding both of teleological and mechanistic explanation, and of the history of mechanistic philosophy. To prove this point, I shall provide an overview of the first systematic treatise on mechanics, the short and neglected work Mechanical Problems, written either by Aristotle or by a very early member of (...) his school. I will argue that the work is thoroughly Aristotelian in methodology, and that taking it seriously can deepen our understanding of Aristotle’s discussion of animal and human self-motion in the Physics and On the Movement of Animals. (shrink)

I develop a positive interpretation of Democritus' theory of agency and responsibility, building on previous studies that have already gone far in demonstrating his innovativeness and importance to the history and philosophy of these concepts. The interpretation will be defended by a synthesis of several familiar ethical fragments and maxims presented in the framework of an ancient problem that, unlike the problem of free will and determinism, Democritus almost certainly did confront: the problem of the causes of human goodness and (...) success. I will argue that Democritus' account of the virtues and success is naturally interpreted as an intellectualist one. His focus on our intellectual powers as the source of our own agency and cause of our success led him to remarkable breakthroughs in moral psychology, including the development of a kind of cognitive-behavioral therapy for stress and anxiety, and the proposal of an autonomous source of moral sanction. (shrink)

Nowadays decision making is strongly supported by the high-confident point estimations produced by deep learning algorithms. In many activities, they are sufficient for the decision-making process. However, in some other cases, confidence intervals are required too for an appropriate decision-making process. In this work, a first attempt to generate point estimations with confidence intervals for the $^{222}$Rn radiation level time series at Canfranc Underground Laboratory is presented. To predict the low-radiation periods allows correctly scheduling the unshielded periods for maintenance operations (...) in the experiments hosted in this facility. This should minimize the deposition of radioactive dust on the exposed surfaces during these unshielded periods. An approach based on deep learning with stochastic regulation is evaluated in the forecasting of point estimations and confidence intervals of the $^{222}$Rn time series and compared with a second approach based on Gaussian processes. As a consequence of this work, an evaluation of the capacity of Gaussian process and deep learning with stochastic regularization for generating point estimations and their confidence intervals for this time series is stated. (shrink)

We hope to show that the overall protreptic plan of Aristotle's ethical writings is based on the plan he used in his published work Protrepticus (Exhortation to Philosophy), by highlighting those passages that primarily offer hortatory or protreptic motivation rather than dialectical argumentation and analysis, and by illustrating several ways that Aristotle adapts certain arguments and examples from his Protrepticus. In this essay we confine our attention to the books definitely attributable to the Nicomachean Ethics (thus excluding the common books).

I discuss how Aristotle’s formulation of the problem of moral luck relates to his natural philosophy. I review well-known passages from Nicomachean Ethics I/X and Eudemian Ethics I/VII and Physics II, but in the main focus on EE VII 14 (= VIII 2). I argue that Aristotle’s position there (rejecting the elimination of luck, but reducing luck so far as possible to incidental natural and intelligent causes) is not only consistent with his treatment of luck in Physics II, but is (...) to be expected, given that the dialectical path of EE VII 14 runs exactly parallel to that of Physics II 4-6. Although Aristotle resolves some issues that he raises, he cannot avoid the problem of constitutive moral luck that, as Thomas Nagel puts it, pertains to ‘the kind of person you are, where this is not just a question of what you deliberately do, but of your inclinations, capacities, and temperament’. The problem for Aristotle follows not only from his ethical positions, but also directly from his more general physical and political principles and assumptions. Furthermore, the problem touches the very essence of Aristotle’s moral theory. (shrink)

A long tradition regards Robert Desgabets as a Cartesian empiricist. He says things that sound strikingly like Locke, and he argues against anti-empiricist reasoning in Descartes, Malebranche, and Arnauld. Moreover, throughout his writings he endorses the empiricist principle that nothing is in the intellect except what was previously in the senses. Since the Cartesians are generally supposed to be prototypical non -empiricists, Desgabets’s being a Cartesian empiricist would make him a particularly interesting specimen. In this paper, however, I challenge the (...) case for taking Desgabets to be an empiricist. (shrink)

Aristotle is the first philosopher on record to subject the meaning of life to systematic philosophical examination: he approaches the issue from logical, psychological, biological, and anthropological perspectives in some of the central passages in the Corpus Aristotelicum and, it turns out, in some fragments from his (lost) early popular work the Protrepticus (Exhortation to Philosophy). From an Aristotelian perspective, in asking about life’s “meaning”, we may be asking either a theoretical question about the definition of the term life (and (...) this either generically or with specific reference to human life), or a practical question about the final end or purpose of life (or human life). Aristotle carefully considered both questions, and in his view answering the theoretical question is the key to answering the practical question. In brief, his theoretical view is that humans are distinguished from all other living things, and thus defined by their ability to use reason; thus his practical view is that the end or purpose of human existence is intellectual activity, especially doing philosophy. (shrink)

This work investigates some of the most important logical limits of scientific knowledge. We argue that scientific knowledge is based on different logicalforms and paradigms. The logical forms, which represent the rational structure of scientific knowledge, show their limits through logical antinomies. The paradigms, which represent the scientific points of view on the world, show their limits through the theoretical anomalies. When these limits arise in science and when scientists become fully and deeply aware of them, they can determine logical (...) or paradigmatic revolutions. These are different in their respective courses, although the logical forms and the paradigms are parts of the same type of knowledge. In the end, science can avoid or can integrate its different limits. In fact, the limits of science can become new opportunities for its growth and development. (shrink)

The key term of Aristotle’s teleology is “the cause for the sake of which”. Aristotle discusses in several key texts the fact that this has two different senses: aim and beneficiary. The aim of a knife is cutting, but the beneficiary is the person who does, or orders, the cutting. Aristotle uses this distinction to show how natural things have both aims and are beneficiaries of their functions. He also shows how non-natural things, such as god, can operate as causes (...) for the sake of which, but not as beneficiaries. Eternal things cannot be beneficiaries, because they cannot undergo change. Thus, the beneficiaries of Aristotle’s teleology are the elements, plants, and animals that can both undergo change and have functional aims. A survey of other terms of Aristotle’s teleology, such as “nature does nothing in vain”, the terms “complete” or “perfect”, as well as “end” and “entelechy” further show the specific orientation of Aristotle’s teleology, as do his use of axiological terms such as “better” and “fine”. (shrink)

El emergente paradigma educativo del aprendizaje ubicuo está dando lugar a nuevos entornos virtuales de aprendizaje. El objetivo de este estudio es contribuir a esta transformación en los procesos de aprendizaje para avanzar en el dominio del inglés, con un diseño didáctico innovador inspirado en el concepto de ‘entorno personal de aprendizaje’, con el uso de vídeos de YouTube. Los resultados demuestran el potencial pedagógico de los PLE, su eficacia no sólo a nivel cognitivo sino también como experiencia emocional. Este (...) diseño también se ha mostrado de utilidad para promover la autonomía y la motivación intrínseca del estudiante. (shrink)

In lieu of an abstract, here is a brief excerpt of the content:Journal of the History of Philosophy 43.1 (2005) 21-36 [Access article in PDF] Desgabets on the Creation of Eternal Truths Monte Cook For many philosophers Robert Desgabets's1 doctrine of the creation of eternal truths will be of interest for the light it throws on Descartes's doctrine of the creation of eternal truths, a doctrine receiving considerable scrutiny the past several years.2 Desgabets was one of the few followers (...) of Descartes to defend this doctrine; and he not only defended it, he made it central to his philosophy.3 He spoke of the [End Page 21] doctrine as "being of the greatest importance and having great and incomparable consequences;" and he referred to it as being "so lofty, so fine, so saintly and so worthy of God" that Descartes ought never to have departed from it (RD 208, 209).4 But, Desgabets thinks, Descartes sometimes forgets his own doctrine and says things incompatible with it. More important, he thinks, Descartes fails to realize how important the doctrine is and fails to extend it to its full consequences. In Desgabets we get from a Cartesian and a near contemporary of Descartes: an interpretation of Descartes's doctrine of the creation of eternal truths, a criticism of Descartes's version of the doctrine purportedly based on Descartes's own principles, and the development of the supposedly correct version of the doctrine that Descartes would have advocated had he been truer to his own principles.5Recent discussions have brought to the fore several controversies about how to interpret Descartes's comments on the creation of the eternal truths. I piece together both where Desgabets's own doctrine stands on these controversies and how Desgabets interprets Descartes's position on them, and I note some consequences that Desgabets draws from the doctrine that are clearly opposed to Descartes's explicit views. 1. Desgabets's Interpretation of Descartes In Critique de la Critique, Desgabets first states Descartes's doctrine of the creation of eternal truths as follows: That the Whole is greater than its part, that the circle has its diameters equal, that man is a rational animal, that two & two are four, etc., are not such of themselves but... God has made & established them with a sovereign indifference being able not to establish them so that what is now true & necessary should not be so if he had not established it. (CdC 73) This states the core of Descartes's doctrine of the creation of eternal truths, and I doubt that anyone would deny that it is in Descartes.In the next paragraph, however, Desgabets both expands and limits the scope of what he takes to be Descartes's doctrine: Descartes claims that there is neither nature, nor essence, nor reality, nor conceivability, nor truth among created things that God has not made or established with a sovereign indifference, so that before we conceive that he has freely resolved to make & establish things & truths there is nothing conceivable except his unique Essence. And we must not listen to those who say that before his free decrees & before his [End Page 22] indifferent action he already necessarily saw natures & determined essences that had by themselves a real possibility that they did not owe to him & that distinguished them from chimeras & beings of reason. (CdC 74) Whether or not Descartes subscribes to the views expressed in this paragraph, they clearly go beyond the core doctrine of the creation of eternal truths expressed in the previous paragraph.First, Desgabets expands Descartes's doctrine to include opposition not just to the view that the eternal truths exist independently of God, but also to the view that God creates by giving actual existence to pre-existent essences that determine what is possible. Desgabets believes that for Descartes God does not create by contemplating pre-existent essences, to some of which he gives actual existence. Rather, God creates the essences themselves (cf. RD 32-33, 232). Moreover, Desgabets believes that for Descartes God gives existence not just to essences but also to possibilities. God does not confront... (shrink)