I describe Smith's very modest aims and argue that there is an over-expenditure of sophisticated philosophy of language to defend a common sense realism about relatively recent science.

The aim of this volume is to present Kafka not as a writer, or not only as a writer, but as a philosopher. However, even after narrowing the scope of our interest down, there will still be several Kafka’s left on the table. Themes treated in the volume include: the so-called Brentano School in Prague, Kafka’s affiliation to the Louvre Circle, Kafka and existentialist philosophy, Kafka’s Jewish heritage, his love of Nietzsche and Meister Eckhart and—last but not least, since he (...) was such an exceptional writer—his aesthetics. (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)

Philosophy and Phenomenological Research, Volume 104, Issue 3, Page 728-746, May 2022.

Poverty has traditionally been conceived of as a state of deprivation. To be poor is to lack something essential to human flourishing. How that something is understood—in terms of welfare, resources, or capabilities—and how it is measured—in absolute terms or relative to a social standard—has been the subject of much debate within the development literature. In this paper, I put forward an account of poverty rooted in the philosophy of action. I argue that poverty essentially involves being in a context (...) in which a reasonable agent’s future-directed agency is systemically undermined. Centering this dimension of poverty allows us to attend to aspects of poverty that are easily overlooked on existing accounts. (shrink)

This is a reply to de Sousa's 'Emotional Truth', in which he argues that emotions can be objective, as propositional truths are. I say that it is better to distinguish between truth and accuracy, and agree with de Sousa to the extent of arguing that emotions can be more or less accurate, that is, based on the facts as they are.

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

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

Neo-Kantianism is common conceived as a philosophy ‘from above’, excelling in speculative constructions – as opposed to the attitude of patient description which is exemplified by the phenomenological turn ‘to the things themselves’. When we study the work of Emil Lask in its relation to that of Husserl and the phenomenologists, however, and when we examine the influences moving in both directions, then we discover that this idea of a radical opposition is misconceived. Lask himself was influenced especially by Husserl’s (...) Logical Investigations, and Husserl, especially in his later writings, was in some respects closer to Kant than were the Neo-Kantians. The contrast between the two philosophers can be illustrated by looking at their view of the objects of judgment; for Lask, as for Kant, judgment can relate to the thing as such only in an indirect way. The world of judgment is a collection of ‘imitations holding a secondary position’. It is cut apart from the plain world of real things by what Lask calls a ‘chasm of artificiality and imagery’. For Husserl, in contrast, the object of judgment is a ‘Sachverhalt’ or state of affairs, something ontologically ‘positive’ in the sense that it is an entity in its own right and does not point beyond itself in the manner of a mere sign or proxy for something else. (shrink)

I consider Glimcher's claim to have given an account of mental functioning that is at once neurological and decision-theoretical. I am skeptical, but remark on some good ideas of Glimcher's.

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

In manuscripts of 1930-1 Johannes Daubert, principal member of the Munich board of realist phenomenologists, put forward a series of detailed criticisms of the idealism of Husserl’s Ideas I. The paper provides a sketch of these criticisms and of Daubert’s own alternative conceptions of consciousness and reality, as also of Daubert’s views on perception, similar, in many respects, to those of J. J. Gibson.

Johannes Daubert he was an acknowledged leader, and in some respects the founder, of the early phenomenological movement, and was considered – as much by its members as by Husserl himself – the most brilliant member of the group. In Daubert’s unpublished writings we find a series of reflections on Lask, and on Neo-Kantianism, which form the subject-matter of this paper. They range over topics such as the ontology of the ‘Sachverhalt’ or state of affairs, truthvalues (Wahrheitswerte) and the value (...) of truth, negative judgments and the copula, and the relation between perception and judgment. (shrink)

I argue that folk psychology does not serve the purpose of facilitating prediction of others' behaviour but if facilitating cooperative action. (See my subsequent book *The Importance of Being Understood*.

Monoclonal antibodies are essential biomedical research and clinical reagents that are produced by companies and research laboratories. The NIAID ImmPort (Immunology Database and Analysis Portal) resource provides a long-term, sustainable data warehouse for immunological data generated by NIAID, DAIT and DMID funded investigators for data archiving and re-use. A variety of immunological data is generated using techniques that rely upon monoclonal antibody reagents, including flow cytometry, immunofluorescence, and ELISA. In order to facilitate querying, integration, and reuse of data, standardized terminology (...) for describing monoclonal antibody reagents and their targets needs to be used for annotating data submitted to ImmPort. (shrink)

The goal of creating Artificial General Intelligence (AGI) – or in other words of creating Turing machines (modern computers) that can behave in a way that mimics human intelligence – has occupied AI researchers ever since the idea of AI was first proposed. One common theme in these discussions is the thesis that the ability of a machine to conduct convincing dialogues with human beings can serve as at least a sufficient criterion of AGI. We argue that this very ability (...) should be accepted also as a necessary condition of AGI, and we provide a description of the nature of human dialogue in particular and of human language in general against this background. We then argue that it is for mathematical reasons impossible to program a machine in such a way that it could master human dialogue behaviour in its full generality. This is (1) because there are no traditional explicitly designed mathematical models that could be used as a starting point for creating such programs; and (2) because even the sorts of automated models generated by using machine learning, which have been used successfully in areas such as machine translation, cannot be extended to cope with human dialogue. If this is so, then we can conclude that a Turing machine also cannot possess AGI, because it fails to fulfil a necessary condition thereof. At the same time, however, we acknowledge the potential of Turing machines to master dialogue behaviour in highly restricted contexts, where what is called “narrow” AI can still be of considerable utility. (shrink)

In this paper, I challenge the recent consensus that global versions of theological voluntarism—on which all moral facts are explained by God’s action—fail, because only local versions—on which only a proper subset of moral facts are so explained—can successfully avoid the objection that theological voluntarism entails that God’s actions are arbitrary. I argue that global theological voluntarism can equally well avoid such arbitrariness. This does not mean that global theological voluntarism should be accepted, but that the primary advantage philosophers have (...) taken local views to have over global views is, in fact, no advantage at all. (shrink)

We discuss recent progress in the development of cognitive ontologies and summarize three challenges in the coordinated development and application of these resources. Challenge 1 is to adopt a standardized definition for cognitive processes. We describe three possibilities and recommend one that is consistent with the standard view in cognitive and biomedical sciences. Challenge 2 is harmonization. Gaps and conflicts in representation must be resolved so that these resources can be combined for mark-up and interpretation of multi-modal data. Finally, Challenge (...) 3 is to test the utility of these resources for large-scale annotation of data, search and query, and knowledge discovery and integration. As term definitions are tested and revised, harmonization should enable coordinated updates across ontologies. However, the true test of these definitions will be in their community-wide adoption which will test whether they support valid inferences about psychological and neuroscientific data. (shrink)

In lieu of an abstract, here is a brief excerpt of the content:Philosophy, Psychiatry, & Psychology 12.3 (2005) 257-259 [Access article in PDF] Atrocity, Banality, Self-Deception Adam Morton Keywords evil, self-deception, banality, atrocity, motivation When talking about evil we must make a fundamental choice about how we are to use the term. We may use it as half of the contrast "good versus evil," in which case it covers everything that is not good. That includes moral incompetence, lack of (...) imagination, willingness to follow orders, overreactions, and a host of other reasons why people who do not have personalities that we would call evil do things that are wrong, often very wrong. Call this the weak reading of evil: evil as wrongdoing. Or we may use it with the meaning suggested by "evil person," "really evil act," "the evil lurking in all of us," and other such idioms. If we do this, we focus on a particular class of actions, and the motives and people that produce them, that arouse a particular moral revulsion in us. Call this the strong reading of evil: evil as atrocity (for more on this contrast see Morton [2004] and Card [2002]).Kubarych, following Peck, thinks of evil in the strong way. Most of the time at any rate: Some of the philosophers, such as Kant, that he draws on are thinking of evil in the weak way, and some of his quotations are from the German, where good/bad/evil distinctions are not drawn in the same way as in English. He explores a general explanation of evil that seems to be targeted at the psychology of extremely abhorrent actions. But, I argue, his account is in danger of collapse in either of two directions. Depending on how we interpret Kubarych's account, it could turn out that it describes all wrongdoing as evil, or, making some different choices, it could turn out that there are no really evil people.The strong reading of evil is definitely the most interesting and potentially fruitful. After all, we have no shortage of satisfying explanations of why people lie to get out of unwelcome appointments, steal to support their children or their drug habits, or defraud investors to become rich. But we do feel deeply puzzled by those who commit torture, serial murder, or genocide. We ask of these people not so much "Why did he do it?" as "How could he do it?" We feel the need of a philosophical or psychological theory that can give us even a slight handle of these people and their deeds. There are two risks associated with the project of explaining atrocity, though. The first is the risk of accepting unsatisfactory accounts, just because they purport to explain what we desperately want to understand. The second is the risk of supposing that there is a single explanation when the causes of the phenomenon are in fact too varied. On other topics these two risks have often combined to make people believe what seem to us now to be evident falsehoods. Humans have often for example wanted to know the causes of disease, and as a result have accepted blanket explanations, in terms of [End Page 257] evil spirits or lack of faith, that seem ludicrous to us now that we have a better grasp of the variety of factors that can cause our bodies to misfunction. So before asking naively "Why and how can people do these awful things?" we should ask "Is there a deeper causal unity here, beyond the fact that we react to these acts with horror?"My suspicion is that there is not much unity, that it is asking too much to want a common profile to the psychology of serial killers, or of proponents of genocide, let alone a profile that applies across these and other categories. What we can do, I believe, is describe our concept of evil in such a way that we can leave some parameters to be filled in by a large variety of objective psychological factors. Even this runs the risk that the really relevant factors cannot be forced into the role that the philosophical account requires. In... (shrink)

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

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

As health systems around the world turn towards highly distributed, specialized and cooperative structures to increase quality and safety of care as well as efficiency and efficacy of delivery processes, there is a growing need for supporting communication and collaboration of all parties involved with advanced ICT solutions. The Electronic Health Record (EHR) provides the information platform which is maturing towards the eHealth core application. To meet the requirements for sustainable, semantically interoperable, and trustworthy EHR solutions, different standards and different (...) national strategies have been established. The workshop summarizes the requirements for such advanced EHR systems and their underlying architecture, presents different strategies and solutions advocated by corresponding protagonists, discusses pros and cons as well as harmonization and migration strategies for those approaches. It particularly highlights a turn towards ontology-driven architectures. (shrink)

I compare our idioms for quantifying into belief contexts to our idioms for quantifying into intention contexts. The latter is complicated by the fact that there is always a discrepancy between the action as intended and the action as performed. The article contains - this is written long after it appeared - an early version of a tracking or sensitivity analysis of the relation between a thought and its object.

According to Marr's theory of vision, computational processes of early vision rely for their success on certain "natural constraints" in the physical environment. I examine the implications of this feature of Marr's theory for the question whether psychological states supervene on neural states. It is reasonable to hold that Marr's theory is nonindividualistic in that, given the role of natural constraints, distinct computational theories of the same neural processes may be justified in different environments. But to avoid trivializing computational explanations, (...) theories must respect methodological solipsism in the sense that within a theory there cannot be differences in content without a corresponding difference in neural states. (shrink)

A critical exposition of plans to colonize other planets , especially Mars, and their costs. The final chapter links with issues about the value and future of human life. See the extended summary uploaded to this site.

The pivotal role of the relation part-of in the description of living organisms is widely acknowledged. Organisms are open systems, which means that in contradistinction to mechanical artifacts they are characterized by a continuous flow and exchange of matter. A closer analysis of the spatial relations in biological organisms reveals that the decision as to whether a given particular is part-of a second particular or whether it is only contained-in the second particular is often controversial. We here propose a rule-based (...) approach which allows us to decide on the basis of well-defined criteria which of the two relations holds between two anatomical objects, given that one spatially includes the other. We discuss the advantages and limitations of this approach, using concrete examples from human anatomy. (shrink)

I assess Churchland's views on folk psychology and conceptual thinking, with particular emphasis on the connection between these topics.

Lockheed Martin Corp. has funded research to generate a framework and methodology for developing semantic reasoning applications to support the discipline oflntelligence Analysis. This chapter outlines that framework, discusses how it may be used to advance the information sharing and integrated analytic needs of the Intelligence Community, and suggests a system I software architecture for such applications.

This paper presents the Obstetric and Neonatal Ontology (OntONeo). This ontology has been created to provide a consensus representation of salient electronic health record (EHR) data and to serve interoperability of the associated data and information systems. More generally, it will serve interoperability of clinical and translational data, for example deriving from genomics disciplines and from clinical trials. Interoperability of EHR data is important to ensuring continuity of care during the prenatal and postnatal periods for both mother and child. As (...) a strategy to advance such interoperability we use an approach based on ontological realism and on the ontology development principles of the Open Biomedical Ontologies Foundry, including reuse of reference ontologies wherever possible. We describe the structure and coverage domain of OntONeo and the process of creating and maintaining the ontology. (shrink)

The current informal practice of pharmacometrics as a combination art and science makes it hard to appreciate the role that informatics can and should play in the future of the discipline and to comprehend the gaps that exist because of its absence. The development of pharmacometric informatics has important implications for expediting decision making and for improving the reliability of decisions made in model-based development. We argue that well-defined informatics for pharmacometrics can lead to much needed improvements in the efficiency, (...) effectiveness, and reliability of the pharmacometrics process. The purpose of this paper is to provide a description of the pervasive yet often poorly appreciated role of informatics in improving the process of data assembly, a critical task in the delivery of pharmacometric analysis results. First, we provide a brief description of the pharmacometric analysis process. Second, we describe the business processes required to create analysis-ready data sets for the pharmacometrician. Third, we describe selected informatic elements required to support the pharmacometrics and data assembly processes. Finally, we offer specific suggestions for performing a systematic analysis of existing challenges as an approach to defi ning the next generation of pharmacometric informatics. (shrink)

Ontological principles are needed in order to bridge the gap between medical and biological information in a robust and computable fashion. This is essential in order to draw inferences across the levels of granularity which span medicine and biology, an example of which include the understanding of the roles of tumor markers in the development and progress of carcinoma. Such information integration is also important for the integration of genomics information with the information contained in the electronic patient records in (...) such a way that real time conclusions can be drawn. In this paper we describe a large multi-granular datasource built by using ontological principles and focusing on the case of colon carcinoma. (shrink)

One way to detect, monitor and prevent adverse events with the help of Information Technology is by using ontologies capable of representing three levels of reality: what is the case, what is believed about reality, and what is represented. We report on how Basic Formal Ontology and Referent Tracking exhibit this capability and how they are used to develop an adverse event ontology and related data annotation scheme for the European ReMINE project.

Interoperability across data sets is a key challenge for quantitative histopathological imaging. There is a need for an ontology that can support effective merging of pathological image data with associated clinical and demographic data. To foster organized, cross-disciplinary, information-driven collaborations in the pathological imaging field, we propose to develop an ontology to represent imaging data and methods used in pathological imaging and analysis, and call it Quantitative Histopathological Imaging Ontology – QHIO. We apply QHIO to breast cancer hot-spot detection with (...) the goal of enhancing reliability of detection by promoting the sharing of data between image analysts. (shrink)

BioéthiqueOnline was launched in March 2012 as a non-peer reviewed journal with the aim of providing a platform to facilitate and encourage the development of a bilingual bioethics community in Canada and internationally. In light of discussions amongst the Editorial Committee over the past few months regarding the growth of the journal, we have decided to move to a peer-reviewed process for articles submitted to the journal.

The central hypothesis of the collaboration between Language and Computing (L&C) and the Institute for Formal Ontology and Medical Information Science (IFOMIS) is that the methodology and conceptual rigor of a philosophically inspired formal ontology will greatly benefit software application ontologies. To this end LinKBase®, L&C’s ontology, which is designed to integrate and reason across various external databases simultaneously, has been submitted to the conceptual demands of IFOMIS’s Basic Formal Ontology (BFO). With this, we aim to move beyond the level (...) of controlled vocabularies to yield an ontology with the ability to support reasoning applications. (shrink)

I discuss Quine's claim that anyone denying what we now take to be a logical truth would be using logical words in a novel way. I trace this to a confusions between outright denial and failure to assert, and assertion of a negation. (This abstract is written from memory decades after the article.).

There are a number of existing classifications and staging schemes for carcinomas, one of the most frequently used being the TNM classification. Such classifications represent classes of entities which exist at various anatomical levels of granularity. We argue that in order to apply such representations to the Electronic Health Records one needs sound ontologies which take into consideration the diversity of the domains which are involved in clinical bioinformatics. Here we outline a formal theory for addressing these issues in a (...) way that the ontologies can be used to support inferences relating to entities which exist at different anatomical levels of granularity. Our case study is the colon carcinoma, one of the most common carcinomas prevalent within the European population. (shrink)

Many of our most important goals require months or even years of effort to achieve, and some never get achieved at all. As social psychologists have lately emphasized, success in pursuing such goals requires the capacity for perseverance, or "grit." Philosophers have had little to say about grit, however, insofar as it differs from more familiar notions of willpower or continence. This leaves us ill-equipped to assess the social and moral implications of promoting grit. We propose that grit has an (...) important epistemic component, in that failures of perseverance are often caused by a significant loss of confidence that one will succeed if one continues to try. Correspondingly, successful exercises of grit often involve a kind of epistemic resilience in the face of failure, injury, rejection, and other setbacks that constitute genuine evidence that success is not forthcoming. Given this, we discuss whether and to what extent displays of grit can be epistemically as well as practically rational. We conclude that they can be (although many are not), and that the rationality of grit will depend partly on features of the context the agent normally finds herself in. In particular, grit-friendly norms of deliberation might be irrational to use in contexts of severe material scarcity or oppression. (shrink)

Epistemological objections to moral realism allege that realism entails moral skepticism. Many philosophers have assumed that theistic moral realists can easily avoid such objections. In this article, I argue that things are not so easy: theists run the risk of violating an important constraint on replies to epistemological objections, according to which replies to such objections may not rely on substantive moral claims of a certain kind. Yet after presenting this challenge, I then argue that theists can meet it, successfully (...) replying to the objections without relying on the problematic kinds of substantive moral claims. Theists have a distinctive and plausible reply to epistemological objections to moral realism. (shrink)

Experiments are actions, performed in order to gain information. Like other acts, there are virtues of performing them well. I discuss one virtue of experimentation, that of knowing how to trade its information-gaining potential against other goods.

A criticism of Dorothy Edgington's attempt to make Gibbard's problem for indicative conditionals apply to counterfactuals.

I classify emotions in the family of regret, remorse, and so on, in such a way that it is easy to see how there can be further emotions in this family, for which we happened not to have names in English. I describe some of these emotions.

Suppose some person 'A' sets out to accomplish a difficult, long-term goal such as writing a passable Ph.D. thesis. What should you believe about whether A will succeed? The default answer is that you should believe whatever the total accessible evidence concerning A's abilities, circumstances, capacity for self-discipline, and so forth supports. But could it be that what you should believe depends in part on the relationship you have with A? We argue that it does, in the case where A (...) is yourself. The capacity for "grit" involves a kind of epistemic resilience in the face of evidence suggesting that one might fail, and this makes it rational to respond to the relevant evidence differently when you are the agent in question. We then explore whether similar arguments extend to the case of "believing in" our significant others -- our friends, lovers, family members, colleagues, patients, and students. (shrink)