Background: SNOMED CT is a large terminology system designed to represent all aspects of healthcare. Its current form and content result from decades of bottom-up evolution. Due to SNOMED CT’s formal descriptions, it can be considered an ontology. The Basic Formal Ontology (BFO) is a foundational ontology that proposes a small set of disjoint, hierarchically ordered classes, supported by relations and axioms. In contrast, as a typical top-down endeavor, BFO was designed as a foundational framework for domain ontologies in the (...) natural sciences and related disciplines. Whereas it is mostly assumed that domain ontologies should be created as extensions of foundational ontologies, a post-hoc harmonization of consolidated domain ontologies in use, such as SNOMED CT, is known to be challenging. Methods: We explored the feasibility of harmonizing SNOMED CT with BFO, with a focus on the SNOMED CT Clinical Finding hierarchy. With more than 100,000 classes, it accounts for about one third of SNOMED CT’s content. In particular, we represented typical SNOMED CT finding/disorder concepts using description logics under BFO. Three representational patterns were created and the logical entailments analyzed. Results: Under a first scrutiny, the clinical intuition that diseases, disorders, signs and symptoms form a homogeneous ontological upper-level class appeared incompatible with BFO’s upper-level distinction into continuants and occurrents. The Clinical finding class seemed to be an umbrella for all kinds of entities of clinical interest, such as material entities, processes, states, dispositions, and qualities. This suggests the conclusion that Clinical finding would not be a suitable upper-level class from an BFO perspective. On closer inspection of the taxonomic links within this hierarchy and the implicit meaning derived thereof, it became clear that Clinical finding classes do not characterize the entity (e.g. a fracture, allergy, tumor, pain, hemorrhage, seizure, fever) in a literal sense but rather the condition of a patient having that fracture, allergy, pain etc. This gives sense to the current characteristic of the Clinical Finding hierarchy, in which complex classes are modeled as subclasses of their constituents. Most of these taxonomic links are inferred, as the consequence of the ‘role group’ design pattern, which is ubiquitous in SNOMED CT and has often been subject of controversy regarding its semantics. Conclusion: Our analyses resulted in the proposal of (i) equating SNOMED CT’s ‘role group’ property with the reflexive and transitive BFO relation ‘has occurrent part’; and (ii) reinterpreting Clinical Findings as Clinical Occurrents, i.e. temporally extended entities in an organism, having one or more occurrents as temporal parts that occur in continuants. This re-interpretation was corroborated by a manual analysis of classes under Clinical Finding, as well as the identification of similar modeling patterns in other ontologies. As a result, SNOMED CT does not require any content redesign to establish compatibility with BFO, apart from this re-interpretation, and a suggested re-labeling. Regarding the feasibility of harmonizing terminologies with principled foundational ontologies post-hoc, our results provide support to the assumption that this does not necessarily require major redesign efforts, but rather a careful analysis of the implicit assumptions of terminology curators and users. (shrink)

Núñez et al.'s (2019) negative assessment of the field of cognitive science derives from evaluation criteria that fail to reflect the true nature of the field. In reality, the field is thriving on both the research and educational fronts, and it shows great promise for the future.

Over the past 25 years, Graham Priest has ably presented and defended dialetheism, the view that certain sentences are properly characterized as true with true negations. Our goal here is neither to quibble with the tenability of true, assertable contradictions nor, really, with the arguments for dialetheism. Rather, we wish to address the dialetheist's treatment of cases of semantic pathology and to pose a worry for dialetheism that has not been adequately considered. The problem that we present seems to have (...) broader bite, afflicting both consistent and inconsistent proposals for resolving semantic pathology. Thus, while our primary goal is to uncover some important connections between dialetheism, semantic pathology, and other, more general issues, the problem that we pose might be a worry for anyone who aims to resolve semantic pathology - consistently or not. (shrink)

In this paper, we do two things. First, we clarify the notion of deflationism, with special attention to deflationary accounts of truth. Second, we argue that one who endorses a deflationary account of truth (or of semantic notions, generally) should be, or perhaps already is, a pretense theorist regarding truth-talk. In §1 we discuss mathematical fictionalism, where we focus on Yablo’s pretense account of mathematical discourse. §2 briefly introduces the key elements of deflationism and explains deflationism about truth in particular. (...) §3 discusses why deflationary accounts of truth should be construed as pretense accounts and gives a preliminary sketch of a particular pretense account of truth-talk. §4 addresses a main objection to a pretense account, and §5 concludes. (shrink)

As scientists target communities for research into the etiology, especially the genetic determinants of common diseases, there have been calls for the protection of communities. This paper identifies the distinct characteristics of aboriginal communities and their implications for research in these communities. It also contends that the framework in the Belmont Report is inadequate in this context and suggests a fourth principle of respect for communities. To explore how such a principle might be specified and operationalized, it reviews existing guidelines (...) for protecting aboriginal communities and points out problems with these guidelines and areas for further work. (shrink)

The principle of compositionality is a statement about the semantics of expressions. It can also be framed slightly differently so that it becomes a principle about the content of complex concepts. This article explains this principle, and the reasons for deviating from it. It will review the psychological research on typicality effects and non-logical reasoning which suggest that explanations can be given for significant phenomena if concepts are understood as prototypes. The evidence suggests that the combination of prototypes follows a (...) principle corresponding to something like PC' rather than PC. PC' states that the content of a complex concept is completely determined by the contents of its parts and their mode of combination, together with general knowledge. A prototype representation of the conjunctive concept is formed by aggregating one feature with another. Any instance is then judged to belong in the conjunction on the basis of its overall similarity to this composite representation. (shrink)

Competing perspectives on the nature of emotion are illustrated with latent and emergent variable models. Latent variable models draw from classical test theory, assuming that the measured indicators of emotion covary by virtue of some common executive, organizing neural circuit or network in the brain. By contrast, emergent variable models draw from a theory-driven, operational definition tradition, positing that emotions do not cause, but rather are caused by, the measured indicators of emotion, assuming no executive neural circuit or network, and (...) requiring no covariation among indicators. I suggest that the emergent variable model may be more compatible with the extant literature on the nature of emotion, especially in the age of affective neuroscience. (shrink)

Izard (2010) did not seek a descriptive definition of emotion—one that describes the concept as it is used by ordinary folk. Instead, he surveyed scientists’ prescriptive definitions—ones that prescribe how the concept should be used in theories of emotion. That survey showed a lack of agreement today and thus raised doubts about emotion as a useful scientific concept.

Previous simulation work on the evolution of communication has not shown how a large signal repertoire could emerge in situated agents. We present an artificial life simulation of agents, situated in a two-dimensional world, that must search for other agents with whom they can trade resources. With strong restrictions on which resources can be traded for others, initially non-communicating agents evolve/learn a signal system that describes the resource they seek and the resource they are willing to offer in return. A (...) large signal repertoire emerges mainly through an evolutionary process. Agents whose production and comprehension abilities rely on a single mechanism fare best, although learning enables agents with separate mechanisms to achieve some measure of success. These results demonstrate that substantial signaling repertoires can evolve in situated multi-agent systems, and suggest that simulated social interactions such as trading may provide a useful context for further computational studies of the evolution of communication. (shrink)

As organizations place greater emphasis on environmental objectives, business educators must produce the next set of leaders who can champion corporate environmental sustainability initiatives. However, environmental sustainability represents a polarizing topic with some students dismissing its importance and legitimacy. Limited research exists to understand student behavioral influences on sustainability education, especially as it translates to environmental sustainability behavior in the workplace. This gap challenges our ability as educators to understand how to best teach environmental sustainability in order to reach diverse (...) student mindsets. We apply the theory of planned behavior (TPB) to address this gap, investigating the influence of student attitudes, subjective norm, and perceived behavioral control on environmental sustainability intention and behavior. A structural model tested with student survey data finds that student attitude represents the strongest influence on environmental sustainability intention. The model also validates that subjective norm affects sustainability intention with students considering professors along with business leaders and politicians as valid references for sustainability knowledge. To tie the results to effective educational interventions, we use the TPB to organize an extensive review of the sustainability pedagogy literature and identify specific teaching recommendations for increasing the effectiveness of environmental sustainability education. (shrink)

Bacteria do many things as organized populations. We have recently learned much about the molecular basis of intercellular communication among prokaryotes. Colonies display bacterial capacities for multicellular coordination which can be useful in nature where bacteria predominantly grow as films, chains, mats and colonies. E. coli colonies are organized into differentiated non-clonal populations and undergo complex morphogenesis. Multicellularity regulates many aspects of bacterial physiology, including DNA rearrangement systems. In some bacterial species, colony development involves swarming (active migration of cell groups). (...) Swarm colony development displays precise geometrical controls and periodic phenomena. Motile E. coli cells in semi-solid media form organized patterns due to chemotactic autoaggregation. On poor media, B. subtilis forms branched colonies using group motility and long-range chemical signalling. The significances of bacterial colony patterns thus reside in a deeper understanding of prokaryotic biology and evolution and in experimental systems for studying self-organization and morphogenesis. (shrink)

An appreciation of the life and word of Barbara McClintock, with special emphasis on what made her a unique and visionary scientist. The obituary indicates unappreciated aspects of her work on biological sensing and how organisms restructure their genomes in response to challenges.

How different neural crest derivatives differentiate in distinct embryonic locations in the vertebrate embryo is an intriguing issue. Many attempts have been made to understand the underlying mechanism of specific pathway choices made by migrating neural crest cells. In this speculative review we suggest a new mechanism for the regulation of neural crest cell migration patterns in avian and mammalian embryos, based on recent progress in understanding the expression and activity of receptor tyrosine kinases during embryogenesis. Distinct subpopulations of crest‐derived (...) cells express specific receptor tyrosine kinases while residing in a migration staging area. We postulate that the differential expression of receptor tyrosine kinases by specific subpopulations of neural crest cells allows them to respond to localized growth factor ligand activity in the embryo. Thus, the migration pathway taken by neural crest subpopulations is determined by their receptor tyrosine kinase response to the differential localization of their cognate ligand. (shrink)

In this article I respond to commentaries of my review of latent versus emergent variable models of emotion. I note that Ross Buck’s view of emotion as stated in his commentary largely endorses an emergent variable model. Drawing from Dynamical Systems Theory, Camras frames the emergent variable model as softly-assembled attractor states. This implies that emotions are “fuzzy sets” of indicators that vary in the degree to which they indicate an emergent emotional state. Calvo offers affective computing as a method (...) of evaluating indicators according to their incremental contribution to predicting human emotional responses. This innovative perspective holds a great deal of promise. Ultimately, I hope that this discussion has contributed to the field's understanding of emotion and emotional processes. (shrink)

Christian theology and ethics are largely inadequate to confront the ecological crisis of today. They are in need of reformation. At the center of Christian faith, we shall not find a mandate to pollute, plunder, and prey on the rest of nature. Instead, we shall discover that the core affirmations endow all life with a moral significance that entails human responsibility toward the whole of nature.

Cellular differentiation and multicellular development require the programmed expression of coregulated suites of genetic loci dispersed throughout the genome. How do functionally diverse loci come to share common regulatory motifs? A new paper finds that retrotransposons (RTEs) may play a role in providing common regulation to a group of functions expressed during the development of oocytes and preimplantation embryos. Examining cDNA libraries, Peaston et al.1 find that 13% of all processed transcripts in full-grown mouse oocytes contain RTE sequences, mostly from (...) the MT family of retroviral-like elements. Smaller but still significant percentages of RTE sequences are found in cDNA libraries from 2-cell embryos and blastocysts. A quarter of these RTE sequences are at the 5′ ends of chimeric transcripts that also contain exons from endogenous mouse loci. These chimeric transcripts display restricted expression in oocytes and preimplantation embryos and presumably originate from developmentally regulated LTR promoters. Some, but not all, chimeric transcripts encode novel protein products. BioEssays 27:122–125, 2005. © 2005 Wiley Periodicals, Inc. (shrink)

There is no mistaking the fact that the narrative traditions of the Old Testament expect to find a hearing among people prepared to recognize their own story in what is told and to see their own times as a direct extension of the same story.

G. W. F. Hegel is stuck between a rock and a hard place in the history of moral philosophy. On one hand, he is frequently regarded as an infamous critic of Kantian moral individualism. From the standpoint of Kierkegaard’s Socratic revival, Hegel is seen as ignoring or even suppressing the individual in favor of a ‘systematic’ form of philosophy. This paper addresses both criticisms by reconstructing Hegel’s unique contribution to the history of moral philosophy. Refusing to reduce Hegel to a (...) foil for either Kant or Kierkegaard reveals his own inheritance of a Socratic ethic. I argue that Hegel revives a long-suppressed form of moral and practical philosophy: the Bildung of one’s self-understanding that involves both self-knowledge and self-transformation. Understanding the way in which Hegel resurrects and reinterprets this conception of moral philosophy requires that one pay attention to the close connection between his systematic method and his unique version of skepticism. (shrink)

In lieu of an abstract, here is a brief excerpt of the content:Reviewed by:Picturing Hegel: An Illustrated Guide to Hegel’s Encyclopaedia LogicJames A. Dunson IIIJulie E. Maybee. Picturing Hegel: An Illustrated Guide to Hegel’s Encyclopaedia Logic. Lanham, MD: Lexington Books, 2009. Pp. xxvii + 639. Paper, $56.95.If Hegel were alive to read an illustrated guide to his Encyclopaedia Logic, he might not immediately appreciate the project. Not only did he consider “picture-thinking” deficient in comparison to conceptual thinking, but he regarded (...) the Encyclopaedia Logic as a text suitable for German students. In her recent book, Picturing Hegel, Julie Maybee acknowledges these ironies and proceeds to guide those of us who need a little extra help in understanding Hegel’s speculative logic.What results is a significant contribution to the literature, a step-by-step commentary [End Page 536] through one of Hegel’s most underappreciated works. Using diagrams to cut through the often-difficult prose proves to be an excellent strategy. Maybee’s exquisitely detailed and admirably clear exposition makes her a suitable Virgil to guide us through the Inferno of Hegel’s logic.Maybee’s task is to show how Hegel’s logic is, actually, logical, and not, as she puts it, “A jumble of random moves from one step to the next” (xiii). She distinguishes Hegel’s speculative logic from the logic we teach nowadays by emphasizing Hegel’s concern to generate and develop the concepts he employs. That is, he is concerned not merely with the rules connecting the logical terms (i.e. syntax), but also the meanings of the terms themselves (i.e. semantics).As one might expect, these concepts are developed dialectically: two elements that are ordinarily opposed to one another are revealed to be mutually defining and interdependent. Readers already familiar with Hegel’s work will appreciate the way in which Maybee explains complicated ideas like “Actuality” and “spurious infinity.” Maybee has a talent for inventive examples, some of which she carefully carries through the entire work. Also, she has an eye for Hegel’s own examples (see, for instance, the comparison of the Absolute Idea and an old man on 580–82).One of the chief merits of her detailed account is its balanced approach. Instead of perpetuating prevalent but superficial interpretations, she explains the different senses in which something is true. For instance, she distinguishes the different meanings of idealism and shows how Hegel retains some materialist elements in his logic (302). Her knowledge of the history of philosophy helps her to put Hegel’s logic in its proper context. The asides to the Pre-Socratic philosophers and the repeated references to Kant are especially useful.Maybee’s approach to the logic, especially the way in which she frames Hegel’s project, raises interesting philosophical questions. She portrays Hegel as attempting to overcome Kant’s skepticism regarding the unity of thought and being. The question is whether reality is fundamentally accessible to reason, or whether the categories we employ to understand the world are limited to our phenomenal experience.But if Hegel’s logic is supposed to refute the Kantian “thing-in-itself,” we can ask whether this is an intelligible philosophical goal. First, Maybee points out that critics like Nietzsche would ask whether we have to be “committed to logical or conceptual necessity” (130). Perhaps Hegel exhibits a rather typical philosophical bias toward conceptual stability and even necessity. Second, any investigation into logical semantics that is biased in this way inevitably opens Pandora’s Box. Determining the meaning of logical terms is a messy business, and Hegel sometimes seems to stipulate meanings instead of genuinely deriving them. For instance, as Maybee writes, a crucial part of Hegel’s definition of existence is that something is “capable of being experienced” (204). But this simply begs the question against Kant’s “thing-in-itself,” since clearly Kant does not think it exists in this way.Third, given that Maybee points out Hegel’s anthropocentric language, we can ask whether his casual and frequent references to human experience are innocent or self-undermining. For instance, what are we to make of Hegel’s use of ethical examples to explain logical concepts like actuality, necessity, and possibility? A Kantian might... (shrink)

The eighteenth century was a time of brilliant philosophical innovation in Britain. In Of Liberty and Necessity James A. Harris presents the first comprehensive account of the period's discussion of what remains a central problem of philosophy, the question of the freedom of the will. He offers new interpretations of contributions to the free will debate made by canonical figures such as Locke, Hume, Edwards, and Reid, and also discusses in detail the arguments of some less familiar writers. Harris (...) puts the eighteenth-century debate about the will and its freedom in the context of the period's concern with applying what Hume calls the "experimental method of reasoning" to the human mind. His book will be of substantial interest to historians of philosophy and anyone concerned with the free will problem. (shrink)

Quantum mechanics tells us that states involving indistinguishable fermions must be antisymmetrized. This is often taken to mean that indistinguishable fermions are always entangled. We consider several notions of entanglement and argue that on the best of them, indistinguishable fermions are not always entangled. We also present a simple but unconventional way of representing fermionic states that allows us to maintain a link between entanglement and non-factorizability.

As an alternative to using the concepts of emotion, fear, anger, and the like as scientific tools, this article advocates an approach based on the concepts of core affect and psychological construction, expanding the domain of inquiry beyond “emotion”. Core affect is a neurophysiological state that underlies simply feeling good or bad, drowsy or energised. Psychological construction is not one process but an umbrella term for the various processes that produce: (a) a particular emotional episode's “components” (such as facial movement, (...) vocal tone, peripheral nervous system change, appraisal, attribution, behaviour, subjective experience, and emotion regulation); (b) associations among the components; and (c) the categorisation of the pattern of components as a specific emotion. (shrink)

Feeling bad is one thing, judging something to be bad another. This hot/cold distinction helps resolve the debate between bipolar and bivariate accounts of affect. A typical affective reaction includes both core affect and judgments of the affective qualities of various aspects of the stimulus situation. Core affect is described by a bipolar valence dimension in which feeling good precludes simultaneously feeling bad and vice versa. Judgments of affective quality of opposite valence can occur simultaneously because the stimulus situation has (...) many aspects. Affective reaction can also include an emotional meta-experience, which can, but rarely does, embrace simultaneous emotion categories of opposite valence. (shrink)

The lack of concrete guidance provided by managerial moral standards and the ambiguity of the expectations they create are discussed in terms of the moral stress experienced by many managers. It is argued that requisite clarity and feelings of obligation with respect to moral standards derive ultimately from public discussion of moral issues within organizations and from shared public agreement about appropriate behavior. Suggestions are made about ways in which the moral dimension of an organization's culture can be more effectively (...) managed. This is the third in a research series of three papers. (shrink)

It has been claimed that (1) computer professionals should be held responsible for an undisclosed list of “undesirable events” associated with their work and (2) most if not all computer disasters can be avoided by truly understanding responsibility. Programmers, software developers, and other computer professionals should be defended against such vague, counterproductive, and impossible ideals because these imply the mandatory satisfaction of social needs and the equation of ethics with a kind of altruism. The concept of social needs is debatable (...) with no one possessing the authority to impose their version of them. Similarly, the notion of “positive responsibility” is difficult to apply, does not effectively change computing practice, and confuses good (i.e., efficient) computer engineering with good (i.e. moral) computer engineering. (shrink)

Comment on an article by Peter Zachar An account of emotion must include categories and dimensions. Categories because humans categorize reality, and a person's categorization of their own state influences aspects of that state. Dimensions because humans are always in some state of Core Affect, which varies by degree along dimensions of valence and activation . In Psychological Construction, Core Affect and a host of other "components" are separate on-going processes, always in some pattern. Occasionally the pattern resembles a prototype (...) of a category of emotion sufficiently to count as an instance of that category. 2012 APA, all rights reserved). (shrink)

The Self We Live By confronts the serious challenges facing the self in postmodern times. Taking issue with contemporary trivializations of the self, the book traces a course of development from the early pragmatists who formulated what they called the 'empirical self', to contemporary constructionist views of the storied self. Presenting an institutional context for the increasing complexity and ubiquity of narrative identity, the authors illustrate the 'everyday technology of self construction' and idscuss the resulting moral climate. The book is (...) suitable for advanced undergraduates and graduate students in courses such as Individual in Society, Contemporary American Society, Social Psychology, Social Interaction and Culture & Personality. (shrink)

This paper raises the question of how a history of the philosophy of eighteenth-century Britain should be written. First, it describes the usual answer to this question, which divides the period into what happened before Hume, then Hume, then responses to Hume. It notes that this answer does not correspond well with how the period saw itself. It then considers how ‘philosophy’ is defined in Britain in the eighteenth century, taking into account dictionary definitions, book titles, and university syllabi. Obvious (...) differences between eighteenth-century and twenty-first-century philosophy are explored, including the idea that ‘natural philosophy’ is as much part of philosophy as moral philosophy, metaphysics, and logic, and the difficulty of making a distinction between philosophy and what we now call psychology. In the final section of the paper some difficulties are raised regarding the hypothesis that ‘enlightenment’ might provide an organizing concept for a more historically sensitive account of eighteenth-century British philosophy. (shrink)