Recent work suggests that people predict how objects interact in a manner consistent with Newtonian physics, but with additional uncertainty. However, the sources of uncertainty have not been examined. In this study, we measure perceptual noise in initial conditions and stochasticity in the physical model used to make predictions. Participants predicted the trajectory of a moving object through occluded motion and bounces, and we compared their behavior to an ideal observer model. We found that human judgments cannot be captured by (...) simple heuristics and must incorporate noisy dynamics. Moreover, these judgments are biased consistently with a prior expectation on object destinations, suggesting that people use simple expectations about outcomes to compensate for uncertainty about their physical models. (shrink)

Throughout the Confessions, Augustine repeatedly complains about heresy with a special focus on the heresy he once belonged to, Manicheanism. To those of us who live in a culture in which respectable people rarely, if ever, care about religious orthodoxy to such a degree, these complaints seem rather bizarre. Despite this initial appearance, Augustine presents in the Confessions several plausible reasons for thinking heresy is sinful and, therefore, detrimental to a person’s sanctity and ultimate salvation. In this paper, I argue (...) that Augustine considers heresy sinful because it involves as many as three kinds of idolatry: loving a lie/false conception of God instead of the true God, loving one’s own beliefs more than the Truth, which is God, and loving the worldly praise one receives from developing novel opinions more than God. (shrink)

This article constructively retrieves St. Anselm of Canterbury’s theory of retributive justice and provides a defense of what can be called the retributive model of hell. In the first part of this article, we develop the place of retributive punishment in Anselm’s thinking and discuss how and when retributive punishment is a good thing. In the second part, we apply Anselm’s thinking on retributive justice to the problem of hell and provide a defense of how hell, defined as a state (...) of receiving retributive, damnatory, and irreversible punishment, is good. We then address a series of objections. Despite some criticism that both Anselm and the retributive model of hell receive in the contemporary literature, Anselm’s account of retributive justice can make unique and constructive contributions to the contemporary discussion of hell; by retrieving and applying Anselm’s thought to the problem of hell, we intend to kill two birds with one stone. (shrink)

In this multi-faceted volume, Christian and other religiously committed theorists find themselves at an uneasy point in history—between premodernity, modernity, and postmodernity—where disciplines and methods, cultural and linguistic traditions, and religious commitments tangle and cross. Here, leading theorists explore the state of the art of the contemporary hermeneutical terrain. As they address the work of Gadamer, Ricoeur, and Derrida, the essays collected in this wide-ranging work engage key themes in philosophical hermeneutics, hermeneutics and religion, hermeneutics and the other arts, hermeneutics (...) and literature, and hermeneutics and ethics. Readers will find lively exchanges and reflections that meet the intellectual and philosophical challenges posed by hermeneutics at the crossroads. Contributors are Bruce Ellis Benson, Christina Bieber Lake, John D. Caputo, Eduardo J. Echeverria, Benne Faber, Norman Lillegard, Roger Lundin, Brian McCrea, James K. A. Smith, Michael VanderWeele, Kevin Vanhoozer, and Nicholas Wolterstorff. (shrink)

The paper seeks to develop an account of indexical phenomena based on the highly general theory of structure and dependence set forth by Husserl in his Logical Investigations. Husserl here defends an Aristotelian theory of meaning, viewing meanings as species or universals having as their instances certain sorts of concrete meaning acts. Indexical phenomena are seen to involve the combination of such acts of meaning with acts of perception, a thesis here developed in some detail and contrasted with accounts of (...) indexicals suggested by Frege, Wittgenstein and by the later Husserl himself in his Ideas I. Implications are drawn also for our understanding of the categorial grammar sketched by Husserl in his 4th Logical Investigation, as also for our understanding of the nature of proper names and other candidate indexical expressions. (shrink)

The three young philosophers Kevin Mulligan, Peter Simons and Barry Smith have become well-known in the last few years especially in German-speaking analytical philosophy and phenomenology circles. This is on the one hand as a result of their historical and systematic philosophical work; but it is also because of the provocative way in which they represent their philosophy. Because they often appear in threes, they have become known as the "gang of three" or "three musketeers" or even – (...) and this in an admiring sense – "mafiosi" (Rescher). They are known primarily for the small workshops they have been organizing in uncomplicated Anglo-Saxon manner all over Europe. Their goal has been to show that analytic philosophy as it has been pursued up to now is in need of reform and also that the history of scientific philosophizing is not identical to the history of Anglo-Saxon analytic philosophy. Above all, they have tried to make more well known the Austrian tradition of scientific philosophy, and they can be given credit for having done much to promote the current interest in this tradition, which means: the history of Austrian philosophy of the 19th and early 20th centuries and its historical context in the Austro-Hungarian Empire. (shrink)

A realist theory of truth for a class of sentences holds that there are entities in virtue of which these sentences are true or false. We call such entities ‘truthmakers’ and contend that those for a wide range of sentences about the real world are moments (dependent particulars). Since moments are unfamiliar, we provide a definition and a brief philosophical history, anchoring them in our ontology by showing that they are objects of perception. The core of our theory is the (...) account of truthmaking for atomic sentences, in which we expose a pervasive ‘dogma of logical form’, which says that atomic sentences cannot have more than one truthmaker. In contrast to this, we uphold the mutual independence of logical and ontological complexity, and the authors outline formal principles of truthmaking taking account of both kinds of complexity. (shrink)

During the realist revival in the early years of this century, philosophers of various persuasions were concerned to investigate the ontology of truth. That is, whether or not they viewed truth as a correspondence, they were interested in the extent to which one needed to assume the existence of entities serving some role in accounting for the truth of sentences. Certain of these entities, such as the Sätze an sich of Bolzano, the Gedanken of Frege, or the propositions of Russell (...) and Moore, were conceived as the bearers of the properties of truth and falsehood. Some thinkers however, such as Russell, Wittgenstein in the Tractatus, and Husserl in the Logische Untersuchungen, argued that instead of, or in addition to, truth-bearers, one must assume the existence of certain entities in virtue of which sentences and/or propositions are true. Various names were used for these entities, notably 'fact', 'Sachverhalt', and 'state of affairs'. (1) In order not to prejudge the suitability of these words we shall initially employ a more neutral terminology, calling any entities which are candidates for this role truth-makers. (shrink)

Philosophy in the West divides into three parts: Analytic Philosophy (AP), Continental Philosophy (CP), and History of Philosophy (HP). But all three parts are in a bad way. AP is sceptical about the claim that philosophy can be a science, and hence is uninterested in the real world. CP is never pursued in a properly theoretical way, and its practice is tailor-made for particular political and ethical conclusions. HP is mostly developed on a regionalist basis: what is studied is determined (...) by the nation or culture to which a philosopher belongs, rather than by the objective value of that philosopher’s work. Progress in philosophy can only be attained by avoiding these pitfalls. (shrink)

A survey of theories of part, whole and dependence from Aristotle to the Gestalt psychologists, with special attention to Husserl’s Third Logical Investigation “On the Theory of Parts and Wholes”.

‘What is characteristic of every mental activity’, according to Brentano, is ‘the reference to something as an object. In this respect every mental activity seems to be something relational.’ But what sort of a relation, if any, is our cognitive access to the world? This question – which we shall call Brentano’s question – throws a new light on many of the traditional problems of epistemology. The paper defends a view of perceptual acts as real relations of a subject to (...) an object. To make this view coherent, a theory of different types of relations is developed, resting on ideas on formal ontology put forward by Husserl in his Logical Investigations and on the theory of relations sketched in Smith's "Acta cum fundamentis in re". The theory is applied to the notion of a Cambridge change, which proves to have an unforeseen relevance to our understanding of perception. (shrink)

The magisterial analyses of logic and meaning advanced in Husserl's Logical Investigations of 1900/01 have for a number of reasons been neglected by analytical philosophers in subsequent decades. This state of affairs has to do, in part, with the history of the editions and translations of Husserl's writings. Findlay's readable but imperfect translation appeared seventy years after the work itself was first published, and the editors and translators and expositors of Husserl's works have reflected the prevailing philosophical atmosphere on the (...) Continent by concentration their energies on Husserl's later writings. Now, however, over eighty years after the appearance of Husserl's one true masterpiece, a critical edition of the work is at last available in completed form. We here analyze the structure and content of this new edition, published as part of the Husserliana series by the Husserl Archive in Louvain. (shrink)

The discussions which follow rest on a distinction, first expounded by Husserl, between formal logic and formal ontology. The former concerns itself with (formal) meaning-structures; the latter with formal structures amongst objects and their parts. The paper attempts to show how, when formal ontological considerations are brought into play, contemporary extensionalist theories of part and whole, and above all the mereology of Leniewski, can be generalised to embrace not only relations between concrete objects and object-pieces, but also relations between what (...) we shall call dependent parts or moments. A two-dimensional formal language is canvassed for the resultant ontological theory, a language which owes more to the tradition of Euler, Boole and Venn than to the quantifier-centred languages which have predominated amongst analytic philosophers since the time of Frege and Russell. Analytic philosophical arguments against moments, and against the entire project of a formal ontology, are considered and rejected. The paper concludes with a brief account of some applications of the theory presented. (shrink)

The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies that provide a representation of biomedical knowledge from the Open Biological and Biomedical Ontologies (OBO) project and adds the ability to describe how this knowledge was derived. We here describe the state of OBI and several applications that are using it, such as adding semantic expressivity to (...) existing databases, building data entry forms, and enabling interoperability between knowledge resources. OBI covers all phases of the investigation process, such as planning, execution and reporting. It represents information and material entities that participate in these processes, as well as roles and functions. Prior to OBI, it was not possible to use a single internally consistent resource that could be applied to multiple types of experiments for these applications. OBI has made this possible by creating terms for entities involved in biological and medical investigations and by importing parts of other biomedical ontologies such as GO, Chemical Entities of Biological Interest (ChEBI) and Phenotype Attribute and Trait Ontology (PATO) without altering their meaning. OBI is being used in a wide range of projects covering genomics, multi-omics, immunology, and catalogs of services. OBI has also spawned other ontologies (Information Artifact Ontology) and methods for importing parts of ontologies (Minimum information to reference an external ontology term (MIREOT)). The OBI project is an open cross-disciplinary collaborative effort, encompassing multiple research communities from around the globe. To date, OBI has created 2366 classes and 40 relations along with textual and formal definitions. The OBI Consortium maintains a web resource providing details on the people, policies, and issues being addressed in association with OBI. (shrink)

This is a review article on Franz Brentano’s Descriptive Psychology published in 1982. We provide a detailed exposition of Brentano’s work on this topic, focusing on the unity of consciousness, the modes of connection and the types of part, including separable parts, distinctive parts, logical parts and what Brentano calls modificational quasi-parts. We also deal with Brentano’s account of the objects of sensation and the experience of time.

French translation of "Truth-Makers" (1984). A realist theory of truth for a class of sentence holds that there are entities in virtue of which these sentences are true or false. We call such entities ‘truthmakers’ and contend that those for a wide range of sentences about the real world are moments (dependent particulars). Since moments are unfamiliar we provide a definition and a brief philosophical history, anchoring them in our ontology by showing that they are objects of perception. The core (...) of our theory is the account of truthmaking for atomic sentences, in which we expose a pervasive ‘dogma of logical form’, which says that atomic sentences cannot have more than one truthmaker. The authors uphold the mutual independence of logical and ontological complexity. The theory is compared with that of Wittgenstein’s Tractatus, and the authors outline formal principles of truthmaking taking account of both kinds of complexity and suggesting how to overcome Wittgenstein’s problem of negation. (shrink)

I examine the positive and negative features of homeopathy from an ethical perspective. I consider: (a) several potentially beneficial features of homeopathy, including non-invasiveness, cost-effectiveness, holism, placebo benefits and agent autonomy; and (b) several potentially negative features of homeopathy, including failure to seek effective healthcare, wastage of resources, promulgation of false beliefs and a weakening of commitment to scientific medicine. A utilitarian analysis of the utilities and disutilities leads to the conclusion that homeopathy is ethically unacceptable and ought to be (...) actively rejected by healthcare professionals. (shrink)

Proponents of empirically supported treatment have argued that psychotherapists have an ethical obligation to make an EST the first choice in clinical practice. This paper challenges this idea. The EST program assumes a model of therapy as technology or applied science that poorly fits the reality of psychotherapeutic practice. The problems brought to therapy implicate fundamental questions regarding what constitutes a good life. A therapeutic response to such problems is not a technical means to change a circumscribed disorder, but an (...) engagement with the client that has relevance to broader moral concerns. Further, the picture of therapy as technology of change implicitly proposes views of a good life, while not acknowledging that it is doing so. 2012 APA, all rights reserved). (shrink)

Focusing on present‐day possibilities raised by existing technology, I consider the normative aspects of genetically modifying the human germline from a utilitarian standpoint. With reference to a hypothetical case, I examine the probable consequences of permitting a well‐conceived attempt to correct a disease‐associated gene in the human germline using current CRISPR gene‐editing technology. I consider inter alia the likely effects on utility of creating healthy new lives, of discouraging adoption, and of kickstarting a revolution in human germline genetic modification (HGGM). (...) I reject various objections to HGGM, including claims that the risks of genetic harm outweigh the likely benefits. From this utilitarian analysis, I conclude that strong grounds exist to support intervening in the human germline using current technology. Delay in commencing such work will impose a utility cost, because the longer we wait until commencing the HGGM revolution and moving towards a world of increased utility, the greater will be the quantity of suffering accrued meantime through genetically influenced disease. Nevertheless, considering residual safety concerns and the negative publicity engendered by an ethically problematic recent (2018) first attempt at HGGM, it seems prudent—and ultimately generative of the greatest amount of utility—to delay implementing HGGM for a modest period of time, in the order of 1–2 years. (shrink)

I examine the positive and negative features of synthetic biology (‘SynBio’) from a utilitarian ethical perspective. The potential beneficial outcomes from SynBio in the context of medicine are substantial; however it is not presently possible to predict precise outcomes due to the nascent state of the field. Potential negative outcomes from SynBio also exist, including iatrogenesis and bioterrorism; however it is not yet possible to quantify these risks. I argue that the application of a ‘precautionary’ approach to SynBio is ethically (...) fraught, as is the notion that SynBio-associated knowledge ought to be restricted. I conclude that utilitarians ought to support a broadly laissez-faire stance in respect of SynBio. (shrink)

In opposition to the premises of Against Homeopathy – a Utilitarian Perspective, all four respondents base their objections on the central claims that homeopathy is in fact scientifically plausible and is supported by empirical evidence. Despite ethical aspects forming the main thrust of Against Homeopathy, the respondents’ focus on scientific aspects represents sound strategy, since the ethical case against homeopathy would be weakened concomitant with the extent to which any plausibility for homeopathy could be demonstrated. The trouble here is that (...) the respondents are attempting to perpetuate a sterile debate. The notion that homeopathic preparations could have any biological effects represents a fringe viewpoint, one not entertained by serious scientists nor supported by reason and evidence.In the present article, I shall endeavour to explain why the respondents do not have a valid case. I will deal firstly with their general approach to scientific plausibility and evidence, and then consider some of the specific claims they have made. Finally, I will answer the philosophical arguments some of the respondents have raised. (shrink)

A letter to The Times of London, May 9, 1992 protesting the Cambridge University proposal to award an honorary degree to M. Jacques Derrida.

Psychotherapy helps one enact ideas about a good life, and therapists practice orientations rooted in their chosen approach. A 'good life' can therefore mean different things depending on the therapy. Building on the philosophy of Charles Taylor, Smith examines the link between therapy, ethics and the root of therapeutic views in comparison to modern, Western ideas about 'living well'. This is one of two complementary volumes. This volume builds on the last to explore what it means to engage the (...) different ethics of different therapies by offering a deeper explication of therapeutic ethics. Utilizing Taylor's work on practical reasoning, Smith explores topics like the nature of the ethical argument, the role of ethical intuitions and the value of framing ethical debate as ongoing dialogue. He applies this to therapeutics ethics to show how vital it is to consider the ethical proposals that are present in current theories and practices in order to understand the psychotherapies. A key text for upper level undergraduate, postgraduate students and professionals in the field of psychotherapy, psychoanalysis, theoretical psychology and philosophy of the mind. (shrink)

Psychotherapy helps one enact ideas about a good life, and therapists practice orientations rooted in their chosen approach. A 'good life' can therefore mean different things depending on the therapy. Building on the philosophy of Charles Taylor, Smith examines the link between therapy, ethics and the root of therapeutic views in comparison to modern, Western ideas about 'living well'. This is one of two complementary volumes. This volume explores the links between therapeutic aims and conceptions of wellbeing. It examines (...) three schools of psychoanalysis to show how similar therapies can be distinguished by their ethics. Smith argues that research shows little distinction ethical visions of psychotherapies and challenges the conception of therapy as a technical intervention for the treatment of circumscribed disorders. A key text for upper level undergraduate, postgraduate students and professionals in the field of psychotherapy, psychoanalysis, theoretical psychology and philosophy of the mind. (shrink)

In this short note, we discuss several aspectsof “dimensions” and the related constructof “factors”. We concentrate on those aspectsthat are relevant to articles in this specialissue, especially those dealing with the analysisof the wild animal cases discussed inBerman and Hafner's 1993 ICAIL article. We reviewthe basic ideas about dimensions,as used in HYPO, and point out differences withfactors, as used in subsequent systemslike CATO. Our goal is to correct certainmisconceptions that have arisen over the years.

I examine the process and outcomes of animal genetic manipulation (‘transgenesis’) with reference to its morally salient features. I consider several objections to transgenesis. I examine and reject the alleged intrinsic wrongness of ‘deliberate genetic sequence alteration’, as I do the notion that transgenesis may lead to human genetic manipulation. I examine the alleged wrongness of killing inherent in transgenesis, and suggest that the concept of ‘replaceability’ successfully justifies such killing, although not for entities deemed to possess ‘personhood’. I examine (...) ‘significant suffering’ associated with transgenesis and propose the radical conclusion that, although it would be wrong to prohibit animal genetic manipulation per se, utilitarians ought to support a ‘default prohibition’ on transgenic experiments that entail significant suffering. (shrink)

Two prominent theoretical frameworks in moral psychology, Moral Foundations and Dual Process Theory, share a broad foundational assumption that individual differences in human morality are dispositional and in part due to genetic variation. The only published direct test of heritability, however, found little evidence of genetic influences on moral judgments using instrumentation approaches associated with Moral Foundations Theory. This raised questions about one of the core assumptions underpinning intuitionist theories of moral psychology. Here we examine the heritability of moral psychology (...) using the moral dilemmas approach commonly used in Dual Process Theory research. Using such measures, we find consistent and significant evidence of heritability. These findings have important implications not only for understanding which measures do, or do not, tap into the genetically influenced aspects of moral decision-making, but in better establishing the utility and validity of different intuitionist theoretical frameworks and the source of why people differ in those frameworks. (shrink)

Civic engagement requires individuals to have both knowledge of democratic principles and the skills for enacting change. Acquiring the knowledge and skills necessary for a productive civic life can be difficult for students if they are not provided conceptual scaffolds and opportunities to practice citizenship. We implemented and studied an activity using Westheimer and Kahne's (2004) citizenship typology during a summer civics institute to help students grapple with their understandings of “good” citizenship. We found (1) students appropriated the language of (...) Westheimer and Kahne's citizenship typology by using it to describe their expanding understandings of citizenship; and (2) students used the citizenship typology to name and make sense of their civic identity. We discuss these findings and reflect on our use of Westheimer and Kahne's citizenship typology as a cognitive scaffold. (shrink)

Recent developments in studies of sperm‐mediated gene transfer (SMGT) now provide solid ground for the notion that sperm cells can act as vectors for exogenous genetic sequences. A substantive body of evidence indicates that SMGT is potentially useable in animal transgenesis, but also suggests that the final fate of the exogenous sequences transferred by sperm is not always predictable. The analysis of SMGT‐derived offspring has shown the existence of integrated foreign sequences in some cases, while in others stable modifications of (...) the genome are difficult to detect. The appearance of SMGT‐derived modified offspring on the one hand and, on the other hand, the rarity of actual modification of the genome, suggest inheritance as extrachromosomal structures. Several specific factors have been identified that mediate distinct steps in SMGT. Among those, a prominent role is played by an endogenous reverse transcriptase of retrotransposon origin. Mature spermatozoa are naturally protected against the intrusion of foreign nucleic acid molecules; however, particular environmental conditions, such as those occurring during human assisted reproduction, can abolish this protection. The possibility that sperm cells under these conditions carry genetic sequences affecting the integrity or identity of the host genome should be critically considered. These considerations further suggest the possibility that SMGT events may occasionally take place in nature, with profound implications for evolutionary processes. BioEssays 27: 551–562, 2005. © 2005 Wiley periodicals, Inc. (shrink)

Like most domains of science, the study of the mind has been tackled at many scales of analysis, from the behavior of large groups of people, to the diffusion of ions across cellular membranes. At each of these scales, researchers often believe that the critical phenomena of interest, and the most powerful explanatory constructs and mechanisms, reside at their scale of analysis, with finer scales argued to be incapable of predicting the interesting phenomena, while coarser scales are purported to miss (...) critical mechanistic subtleties. Here we argue by analogy that, for better or worse, researchers at all scales are correct: phenomena at each scale of analysis are intractable from other scales; thus, while reductionism is a useful scientific goal, it will not obviate the need for macroscopic research, constructs, and formalisms. (shrink)

In his critique of the therapeutic, Taylor argues that therapy fails to engage with the ethical and spiritual significance of human suffering. Therapy’s denial of ethics is representative of a wide...

Establishing reasonable, prior distributions remains a significant obstacle for the construction of probabilistic expert systems. Human assessment of chance is often relied upon for this purpose, but this has the drawback of being inconsistent with axioms of probability. This article advances a method for extracting a coherent distribution of probability from human judgment. The method is based on a psychological model of probabilistic reasoning, followed by a correction phase using linear programming.

This book reveals the numerous ways in which moral, ethical and legal principles are being violated by those who provide, recommend or sell ‘complementary and alternative medicine’. The book analyses both academic literature and internet sources that promote CAM. Additionally the book presents a number of brief scenarios, both hypothetical and real-life, about individuals who use CAM or who fall prey to ethically dubious CAM practitioners. The events and conundrums described in these scenarios could happen to almost anyone. Professor emeritus (...) of complementary medicine Edzard Ernst together with bioethicist Kevin Smith provide a thorough and authoritative ethical analysis of a range of CAM modalities, including acupuncture, chiropractic, herbalism, and homeopathy. This book could and should interest all medical professionals who have contact to complementary medicine and will be an invaluable reference for patients deliberating which course of treatment to adopt. (shrink)

We provide a detailed exposition of Brentano’s descriptive psychology, focusing on the unity of consciousness, the modes of connection and the types of part, including separable parts, distinctive parts, logical parts and what Brentano calls modificational quasi-parts. We also deal with Brentano’s account of the objects of sensation and the experience of time.

The emergence of signaling systems has been observed in numerous experimental and real-world contexts, but there is no consensus on which shared mechanisms underlie such phenomena. A number of explanatory mechanisms have been proposed within several disciplines, all of which have been instantiated as credible working models. However, they are usually framed as being mutually incompatible. Using an exemplar-based framework, we replicate these models in a minimal configuration which allows us to directly compare them. This reveals that the development of (...) optimal signaling is driven by similar mechanisms in each model, which leads us to propose three requirements for the emergence of conventional signaling. These are the creation and transmission of referential information, a systemic bias against ambiguity, and finally some form of information loss. Considering this, we then discuss some implications for theoretical and experimental approaches to the emergence of learned communication. (shrink)

The emergence of signaling systems has been observed in numerous experimental and real‐world contexts, but there is no consensus on which (if any) shared mechanisms underlie such phenomena. A number of explanatory mechanisms have been proposed within several disciplines, all of which have been instantiated as credible working models. However, they are usually framed as being mutually incompatible. Using an exemplar‐based framework, we replicate these models in a minimal configuration which allows us to directly compare them. This reveals that the (...) development of optimal signaling is driven by similar mechanisms in each model, which leads us to propose three requirements for the emergence of conventional signaling. These are the creation and transmission of referential information, a systemic bias against ambiguity, and finally some form of information loss. Considering this, we then discuss some implications for theoretical and experimental approaches to the emergence of learned communication. (shrink)

Mental and behavioral disorders represent a significant portion of the public health burden in all countries. The human cost of these disorders is immense, yet treatment options for sufferers are currently limited, with many patients failing to respond sufficiently to available interventions and drugs. High quality ontologies facilitate data aggregation and comparison across different disciplines, and may therefore speed up the translation of primary research into novel therapeutics. Realism-based ontologies describe entities in reality and the relationships between them in such (...) a way that – once formulated in a suitable formal language – the ontologies can be used for sophisticated automated reasoning applications. Reference ontologies can be applied across different contexts in which different, and often mutually incompatible, domain-specific vocabularies have traditionally been used. In this contribution we describe the Mental Functioning Ontology (MF) and Mental Disease Ontology (MD), two realism-based ontologies currently under development for the description of humanmental functioning and disease. We describe the structure and upper levels of the ontologies and preliminary application scenarios, and identify some open questions. (shrink)

Ontologies are being developed throughout the biomedical sciences to address standardization, integration, classification and reasoning needs against the background of an increasingly data-driven research paradigm. In particular, ontologies facilitate the translation of basic research into benefits for the patient by making research results more discoverable and by facilitating knowledge transfer across disciplinary boundaries. Addressing and adequately treating mental illness is one of our most pressing public health challenges. Primary research across multiple disciplines such as psychology, psychiatry, biology, neuroscience and pharmacology (...) needs to be integrated in order to promote a more comprehensive understanding of underlying processes and mechanisms, and this need for integration only becomes more pressing with our increase in understanding of differences among individuals and populations at the molecular level concerning susceptibility to specific illnesses. Substance addiction is a particularly relevant public health challenge in the developed world, affecting a substantial percentage of the population, often co-morbid with other illnesses such as mood disorders. Currently, however, there is no straightforward automated method to combine data of relevance to the study of substance addiction across multiple disciplines and populations. In this contribution, we describe a framework of interlinked, interoperable bio-ontologies for the annotation of primary research data relating to substance addiction, and discuss how this framework enables easy integration of results across disciplinary boundaries. We describe entities and relationships relevant for the description of addiction within the Mental Functioning Ontology, Chemical Entities of Biological Interest Ontology, Protein Ontology, Gene Ontology and the Neuroscience Information Framework ontologies. (shrink)

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