Significant associations have been found between specific human leukocyte antigen (HLA) alleles and organ transplant rejection, autoimmune disease development, and the response to infection. Traditional searches for disease associations have conventionally measured risk associated with the presence of individual HLA alleles. However, given the high level of HLA polymorphism, the pattern of amino acid variability, and the fact that most of the HLA variation occurs at functionally important sites, it may be that a combination of variable amino acid sites shared (...) by several alleles (shared epitopes) are better descriptors of the actual causative genetic variants. Here we describe a novel approach to genetic association analysis in which genes/proteins are broken down into smaller sequence features and then variant types defined for each feature, allowing for independent analysis of disease association with each sequence feature variant type. We have used this approach to analyze a cohort of systemic sclerosis patients and show that a sequence feature composed of specific amino acid residues in peptide binding pockets 4 and 7 of HLA-DRB1 explains much of the molecular determinant of risk for systemic sclerosis. (shrink)

Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across many key fields in biology, including genomics, systems biology, development, medicine, evolution, ecology, and systematics. Here we survey the current phenomics landscape, including data resources and handling, and the progress that (...) has been made to accurately capture relevant data descriptions for phenotypes. We present an example of the kind of integration across domains that computable phenotypes would enable, and we call upon the broader biology community, publishers, and relevant funding agencies to support efforts to surmount today's data barriers and facilitate analytical reproducibility. (shrink)

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

Taking my cue from Michael Smith, I try to extract a decent argument for non-cognitivism from the text of the Treatise. I argue that the premises are false and that the whole thing rests on a petitio principi. I then re-jig the argument so as to support that conclusion that Hume actually believed (namely that an action is virtuous if it would excite the approbation of a suitably qualified spectator). This argument too rests on false premises and a (...) begged question. Thus the Motivation Argument fails BOTH as an argument for noncognitivism AND as an argument for what Hume actually believed, that moral distinctions are not derived from reason and that moral properties are akin to secondary qualities. So far as the Motivation Argument is concerned, both cognitivists and rationalists can rest easy. Themes: 1) Hume’s Slavery of Reason thesis is only defensible if passions are not only desires but sometimes dispositions to acquire desires (DTADs). 2) A desire for our good on the whole, which Humeans need to posit to fend off apparent counterexamples to the Slavery of Reason Thesis, does not sit well with the Humean theory of how novel desires arise (an objection due originally to Reid). 3) Hume is wrong to suppose that ‘abstract or demonstrative reasoning never influences any of our actions, but only as it directs our judgment concerning causes and effects’ as the examples of Russell and Hobbes convincingly demonstrate. This ironic as both Russell and Hobbes subscribed to the Slavery of Reason Thesis. 4) I critique Michael Smith’s critique of motivational externalism. (shrink)

Hume is widely regarded as the grandfather of emotivism and indeed of non-cognitivism in general. For the chief argument for emotivism - the Argument from Motivation - is derived from him. In my opinion Hume was not an emotivist or proto-emotivist but a moral realist in the modern ‘response-dependent’ style. But my interest in this paper is not the historical Hume but the Hume of legend since the legendary Hume is one of the most influential philosophers of the present age. (...) According to Michael Smith ‘the Moral Problem’ – the central issue in meta-ethics - is that the premises of Hume’s argument appear to be true though the non-cognitivist conclusion appears to be false. Since the argument seems to be valid, something has got to give. Smith struggles to solve the problem by holding on to something like the premises of the argument whilst trying to fend off the conclusion. In my view this is a wasted effort. Hume was not arguing for non-cognitivsm in the first place, and the arguments for non-cognitivism that can be extracted from his writings are no good. Either the premises are false or the inferences are invalid. And this is despite the fact that Hume was substantially right about reason and the passions. Thus ‘the Moral Problem’ is not a problem, and the legendary Hume does not deserve his influence. -/- An important theme in this paper is the concept of a DTAD or a dispositions to acquire desires. These play an important role in motivation but unlike desires (with which they are sometimes confused ) they are NOT propositional attitudes. (shrink)

There may be a limit on our capacity to suppress anthropocentric tendencies toward non-human others. Normally, we do not reach this limit in our dealings with animals, the environment, etc. Thus, continued striving to overcome anthropocentrism when confronted with these non-human others may be justified. Anticipation of super artificial intelligence may force us to face this limit, denying us the ability to free ourselves completely of anthropocentrism. This could be for our own good.

Wilfrid Sellars's "Empiricism and the Philosophy of Mind" begins with an argument against sense-datum epistemology. There is some question about the validity of this attack, stemming in part from the assumption that Sellars is concerned with epistemic foundationalism. This paper recontextualizes Sellars's argument in two ways: by showing how the argument of EPM relates to Sellars's 1940s work, which does not concern foundationalism at all; and by considering the view of H.H. Price, Sellars's teacher at Oxford and the only classical (...) datum theorist to receive substantive comment in EPM. Timm Triplett has claimed that Sellars's discussion simply begs the question against Price, but this depends on the mistaken assumption that Sellars's concern is with foundationalism. On the contrary, Sellars's argument concerns the assumption that the innate capacity for sensory experience counts as "thinking in presence" in the way needed for empiricist accounts of content acquisition. Price's distinction between noticing universals and being aware of them encapsulates the tensions empiricists face here. (shrink)

Tradução para o português do verbete "George Berkeley, de Michael Ayers, retirado de "A Companion to Epistemology", ed. Jonathan Dancy e Ernest Sosa (Oxford: Blackwell, 1997), pp. 261–264. Criticanarede. ISSN 1749-8457.

The neutral and nearly neutral theories of molecular evolution are sometimes characterized as theories about drift alone, where drift is described solely as an outcome, rather than a process. We argue, however, that both selection and drift, as causal processes, are integral parts of both theories. However, the nearly neutral theory explicitly recognizes alleles and/or molecular substitutions that, while engaging in weakly selected causal processes, exhibit outcomes thought to be characteristic of random drift. A narrow focus on outcomes obscures the (...) significant role of weakly selected causal processes in the nearly neutral theory. (shrink)

This paper compares the naturalistic interpretations of religion offered by the Chinese Confucian philosopher Xunzi (c. 310-219 BCE) and the American pragmatist philosopher John Dewey (1859-1952), and shows how each philosopher reconceived the nature of religious life in fundamentally non-supernatural, ethical, and therapeutic terms. While acknowledging that there are important differences between their respective views—especially on such matters as the nature and scope of ethical knowledge, the nature of ethics, and what form an ideal society will take—and that their views (...) were furthermore shaped by very different historical and cultural contexts, the paper argues that both philosophers nevertheless took this naturalized, ethical and therapeutic conception of religion to be the correct and more profound way to understand religious life, and the best way to develop an appropriate sense of oneness with and reverence for the social and natural worlds that we inhabit. For both Xunzi and Dewey, in short, religious attitudes, experiences, and practices are valuable not because they put us into proper relations with something supernatural, but rather because of their capacity to orient and enrich our lives at both the individual and social levels and put us into proper relations with other human beings and the natural world. Overall, the paper argues that a comparative study of Xunzi’s and Dewey’s interpretations of religion not only reveals features of their thought that we might otherwise miss, but also helps us to better understand the range of possible forms that a naturalistic interpretation of religion can take. (shrink)

Grief research in philosophy agrees that one who grieves grieves over the irreversible loss of someone whom the griever loved deeply, and that someone thus factored centrally into the griever’s sense of purpose and meaning in the world. The analytic literature in general tends to focus its treatments on the paradigm case of grief as the death of a loved one. I want to restrict my account to the paradigm case because the paradigm case most persuades the mind that grief (...) is a past-directed emotion. The phenomenological move I propose will enable us to (1) respect the paradigm case of grief and a broader but still legitimate set of grief-generating states of affairs, (2) liberate grief from the view that grief is past directed or about the past, and thus (3) account for grief in a way that separates it from its closest emotion-neighbor, sorrow, without having to rely on the affective quality of those two emotions.If the passing of the beloved causes the grief but is not what the grief is about, then we can get at the nature of grief by saying its temporal orientation is in the past (the event of the passing), but its temporal meaning is the present and future—the new significance of a world with the pervasive absence that is the world without the beloved. The no-longer of grief is a no-longer oriented by a past (that which is no longer) that is referred a present and future (that which is a no-longer understood as not now as it once was). Looking at the griever’s relation to time can tell us much about the pain and the object of grief, then. As the griever puts the past before himself with a certainty about this world “henceforth,” a look at the griever’s lived sense of the fi nality of the irreversibly lost (1) liberates grief from the tendency in the literature to be reduced to a past-directed emotion, (2) accounts for grief ’s intensity, its affective force or poignancy, and thus (3) enables us to separate grief from sorrow according to its intentionalobject in light of the temporal meaning of these emotions. (shrink)

Both Wilfrid Sellars and John McDowell reject Kant’s conclusion that the world is fundamentally unknowable, and on similar grounds: each invokes conceptual change, what I call the diachronic instability of a conceptual scheme. The similarities end there, though. It is important to Sellars that the world is only knowable at “the end of inquiry” – he rejects a commonsense realism like McDowell’s for its inability to fully appreciate diachronic instability. To evaluate this disagreement, I consider Timothy Williamson’s argument that the (...) knowability thesis, as it rules out “elusive objects”, is problematically idealistic. I argue that McDowell’s insistence on diachronic instability suffices to address Williamson’s worry, and as such that his reply ought to be available to Sellars too. That Sellars would instead invoke the end of inquiry suggests it is he who underestimates the ineliminability of conceptual change. (shrink)

This paper argues that Kant’s most famous objection to the ontological argument -- that existence is not a real predicate -- is not, in fact, his most effective objection, and that his ”neglected objection’ to the argument deserves to be better known. It shows that Kant clearly anticipates William Rowe’s later objection that the argument begs the question, and discusses why Kant himself seems to have overlooked the force of this criticism in his attempt to demolish the traditional proofs for (...) God’s existence. (shrink)

As so often in philosophy, the title not only lays down the battle line but exposes the author’s biases and mistakes, since whether or not we can make sense of the language game ‘Seeing things as they are’ and whether it’s possible to have a ‘philosophical’ ‘theory of perception’ (which can only be about how the language of perception works), as opposed to a scientific one, which is a theory about how the brain works, are exactly the issues. This is (...) classic Searle—superb and probably at least as good as anyone else can produce, but lacking a full understanding of the fundamental insights of the later Wittgenstein and with no grasp of the two systems of thought framework, which could have made it brilliant. As in his previous work, Searle largely avoids scientism but there are frequent lapses and he does not grasp that the issues are always about language games, a failing he shares with nearly everyone. After providing a framework consisting of a Table of Intentionality based on the two systems of thought and thinking and decision research, I give a detailed analysis of the book. -/- Those wishing a comprehensive up to date framework for human behavior from the modern two systems view may consult my book ‘The Logical Structure of Philosophy, Psychology, Mind and Language in Ludwig Wittgenstein and John Searle’ 2nd ed (2019). Those interested in more of my writings may see ‘Talking Monkeys--Philosophy, Psychology, Science, Religion and Politics on a Doomed Planet--Articles and Reviews 2006-2019 3rd ed (2019), The Logical Structure of Human Behavior (2019), and Suicidal Utopian Delusions in the 21st Century 4th ed (2019). (shrink)

This collection of articles was written over the last 10 years and the most important and longest within the last year. Also I have edited them to bring them up to date (2016). All the articles are about human behavior (as are all articles by anyone about anything), and so about the limitations of having a recent monkey ancestry (8 million years or much less depending on viewpoint) and manifest words and deeds within the framework of our innate psychology as (...) presented in the table of intentionality. As famous evolutionist Richard Leakey says, it is critical to keep in mind not that we evolved from apes, but that in every important way, we are apes. If everyone was given a real understanding of this (i.e., human ecology and psychology) in school, maybe civilization would have a chance. In my view these articles and reviews have many novel and highly useful elements, in that they use my own version of the recently (ca. 1980’s) developed dual systems view of our brain and behavior to lay out a logical system of rationality (personality, psychology, mind, language, behavior, thought, reasoning, reality etc.) that is sorely lacking in the behavioral sciences (psychology, philosophy, literature, politics, anthropology, history, economics, sociology etc.). (shrink)

I provide a critical survey of some of the major findings of Wittgenstein and Searle on the logical structure of intentionality(mind, language, behavior), taking as my starting point Wittgenstein’s fundamental discovery –that all truly ‘philosophical’ problems are the same—confusions about how to use language in a particular context, and so all solutions are the same—looking at how language can be used in the context at issue so that its truth conditions (Conditions of Satisfaction or COS) are clear. The basic problem (...) is that one can say anything but one cannot mean (state clear COS for) any arbitrary utterance and meaning is only possible in a very specific context. I begin with ‘On Certainty’ and continue the analysis of recent writings by and about them from the perspective of the two systems of thought, employing a new table of intentionality and new dual systems nomenclature. -/- Those wishing a comprehensive up to date framework for human behavior from the modern two systems view may consult my book ‘The Logical Structure of Philosophy, Psychology, Mind and Language in Ludwig Wittgenstein and John Searle’ 2nd ed (2019). Those interested in more of my writings may see ‘Talking Monkeys--Philosophy, Psychology, Science, Religion and Politics on a Doomed Planet--Articles and Reviews 2006-2019 3rd ed (2019), The Logical Structure of Human Behavior (2019), and Suicidal Utopian Delusions in the 21st Century 4th ed (2019). (shrink)

I provide a critical survey of some of the major findings of Wittgenstein and Searle on the logical structure of intentionality (mind, language, behavior), taking as my starting point Wittgenstein’s fundamental discovery –that all truly ‘philosophical’ problems are the same—confusions about how to use language in a particular context, and so all solutions are the same—looking at how language can be used in the context at issue so that its truth conditions (Conditions of Satisfaction or COS) are clear. The basic (...) problem is that one can say anything but one cannot mean (state clear COS for) any arbitrary utterance and meaning is only possible in a very specific context. I begin with ‘On Certainty’ and continue the analysis of recent writings by and about them from the perspective of the two systems of thought, employing a new table of intentionality and new dual systems nomenclature. (shrink)

After half a century in oblivion, the nature of consciousness is now the hottest topic in the behavioral sciences and philosophy. Beginning with the pioneering work of Ludwig Wittgenstein in the 1930’s (the Blue and Brown Books) and from the 50’s to the present by his logical successor John Searle, I have created the following table as an heuristic for furthering this study. The rows show various aspects or ways of studying and the columns show the involuntary processes and voluntary (...) behaviors comprising the two systems (dual processes) of the Logical Structure of Consciousness (LSC), which can also be regarded as the Logical Structure of Rationality (LSR-Searle), of behavior (LSB), of personality (LSB), of reality (LSOR), of Intentionality (LSI) -the classical philosophical term, the Descriptive Psychology of Consciousness (DPC) , the Descriptive Psychology of Thought (DPT) –or better, the Language of the Descriptive Psychology of Thought (LDPT), terms introduced here and in my other very recent writings. -/- Those wishing a comprehensive up to date framework for human behavior from the modern two systems view may consult my book ‘The Logical Structure of Philosophy, Psychology, Mind and Language in Ludwig Wittgenstein and John Searle’ 2nd ed (2019). Those interested in more of my writings may see ‘Talking Monkeys--Philosophy, Psychology, Science, Religion and Politics on a Doomed Planet--Articles and Reviews 2006-2019 3rd ed (2019), The Logical Structure of Human Behavior (2019), and Suicidal Utopian Delusions in the 21st Century 4th ed (2019). (shrink)

Machine learning algorithms may radically improve our ability to diagnose and treat disease. For moral, legal, and scientific reasons, it is essential that doctors and patients be able to understand and explain the predictions of these models. Scalable, customisable, and ethical solutions can be achieved by working together with relevant stakeholders, including patients, data scientists, and policy makers.

Recent studies indicate that indicative conditionals like "If people wear masks, the spread of Covid-19 will be diminished" require a probabilistic dependency between their antecedents and consequents to be acceptable (Skovgaard-Olsen et al., 2016). But it is easy to make the slip from this claim to the thesis that indicative conditionals are acceptable only if this probabilistic dependency results from a causal relation between antecedent and consequent. According to Pearl (2009), understanding a causal relation involves multiple, hierarchically organized conceptual dimensions: (...) prediction, intervention, and counterfactual dependence. In a series of experiments, we test the hypothesis that these conceptual dimensions are differentially encoded in indicative and counterfactual conditionals. If this hypothesis holds, then there are limits as to how much of a causal relation is captured by indicative conditionals alone. Our results show that the acceptance of indicative and counterfactual conditionals can become dissociated. Furthermore, it is found that the acceptance of both is needed for accepting a causal relation between two co-occurring events. The implications that these findings have for the hypothesis above, and for recent debates at the intersection of the psychology of reasoning and causal judgment, are critically discussed. Our findings are consistent with viewing indicative conditionals as answering predictive queries requiring evidential relevance (even in the absence of direct causal relations). Counterfactual conditionals in contrast target causal relevance, specifically. Finally, we discuss the implications our results have for the yet unsolved question of how reasoners succeed in constructing causal models from verbal descriptions. (shrink)

White progressives in the U.S. are currently experiencing two profound reckonings that typically are assumed to be unrelated. On the one hand, the Dobbs verdict overturned the assumption that the right to choose with respect to abortion is too socially entrenched, juridically settled, or politically sacred to be denied. On the other hand, climatological conditions of possibility for comfortable existence are increasingly under threat in locales in which residents have come to expect to enjoy secure lives and livelihoods. This essay (...) highlights what Indigenous communities across the U.S. already know well. Namely, threats to reproductive freedom and climate crisis are neither new nor separable. Both phenomena have common colonial roots that continue to proliferate. Each is a result of the disruption and destruction of Indigenous kinship assemblages. Indeed, in aiming to remediate their current reckonings, white progressives routinely (if unthinkingly) support forms of settler state violence that perpetuate reproductive and climate injustice in Indigenous communities. We appeal to white progressives, notably including white feminists, to embrace the proposition that their reckonings cannot be properly understood, nor successfully addressed without prioritizing Indigenous futurity. We call for centering forms of Indigenous feminist praxis that facilitate robust Indigenous coalitions of anti-colonial resistance. (shrink)

This paper, while neutral on questions about the minimality of truth, argues for the non-minimality of truth-aptness.

The God Experiment – Let there be Light -/- The question “What is real?” can be traced back to the shadows in Plato’s cave. Two thousand years later, Rene Descartes lacked knowledge about arguing against an evil´ deceiver feeding us the illusion of sensation. Descartes’ epistemological concept later led to various theories of what our sensory experiences actually are. The concept of ”illusionism”, proposing that even the very conscious experience we have – our qualia – is an illusion, is not (...) only a red-pill scenario found in the 1999 science fiction movie ”The Matrix” but is also a philosophical concept promoted by modern tinkers, most prominently by Daniel Dennett. He describes his argument against qualia as materialistic and scientific. Reflection upon a possible simulation and our perceived reality was beautifully visualized in “The Matrix”, bringing the old ideas of Descartes to coffee houses around the world. Irish philosopher Bishop Berkeley was the father of what has later been coined as “subjective idealism”, basically stating that “what you perceive is real” (e.g., ”The Matrix” is real because its population perceives it). Berkeley then argued against Isaac Newton’s absolutism of space, time, and motion in 1721, ultimately leading to Ernst Mach and Albert Einstein’s respective views. Several neuroscientists have rejected Dennetts’ perspective on the illusion of consciousness, and idealism is often dismissed as the notion that people want to pick and choose the tenets of reality. Even Einstein ended his life on a philosophical note, pondering the very foundations of reality. With the advent of quantum technologies based on the control of individual fundamental particles, the question of whether our universe is a simulation isn’t just intriguing. Our ever-advancing understanding of fundamental physical processes will likely lead us to build quantum computers utilizing quantum effects for simulating nature quantum-mechanically in all complexity, as famously envisioned by Richard Feynman. Finding an answer to the simulation question will potentially alter our very definition and understanding of life, reshape theories on the evolution and fate of the universe, and impact theology. No direct observations provide evidence in favor or against the simulation hypothesis, and experiments are needed to verify or refute it. In this paper, we outline several constraints on the limits of computability and predictability in/of the universe, which we then use to design experiments allowing for first conclusions as to whether we participate in a simulation chain. We elaborate on how the currently understood laws of physics in both complete and small-scale universe simulations prevent us from making predictions relating to the future states of a universe, as well as how every physically accurate simulation will increase in complexity and exhaust computational resources as global thermodynamic entropy increases. Eventually, in a simulation in which the computer simulating a universe is governed by the same physical laws as the simulation and is smaller than the universe it simulates, the exhaustion of computational resources will halt all simulations down the simulation chain unless an external programmer intervenes or isn’t limited by the simulation’s physical laws, which we may be able to observe. By creating a simulation chain and observing the evolution of simulation behavior throughout the hierarchy taking stock of statistical relevance, as well as comparing various least complex simulations under computability and predictability constraints, we can gain insight into whether our universe is part of a simulation chain. -/- Index Terms—Simulation, simulation hypothesis, quantum computing, universe, life, intelligence. (shrink)

Movement sonification can improve motor control in both healthy subjects (e.g., learning or refining a sport skill) and those with sensorimotor deficits (e.g., stroke patients and deafferented individuals). It is not known whether improved motor control and learning from movement sonification are driven by feedback-based real-time (“online”) trajectory adjustments, adjustments to internal models over multiple trials, or both. We searched for evidence of online trajectory adjustments (muscle twitches) in response to movement sonification feedback by comparing the kinematics and error of (...) reaches made with online (i.e., real-time) and terminal sonification feedback. We found that reaches made with online feedback were significantly more jerky than reaches made with terminal feedback, indicating increased muscle twitching (i.e., online trajectory adjustment). Using a between-subject design, we found that online feedback was associated with improved motor learning of a reach path and target over terminal feedback; however, using a within-subjects design, we found that switching participants who had learned with online sonification feedback to terminal feedback was associated with a decrease in error. Thus, our results suggest that, with our task and sonification, movement sonification leads to online trajectory adjustments which improve internal models over multiple trials, but which themselves are not helpful online corrections. (shrink)

Risk Management Strategies and Investment Behaviors are considered important factors in the investing activities of the retail investors. This study seeks to determine the relationship between Risk Management Strategies and Investment Behavior of Generation Z retail investors. The study is a correlational research and purposive sampling was used to select the respondents for this study. Cochran’s formula was utilized to determine the total sample size or total number of respondents. Spearman’s Rank-Order Correlation was employed to assess the significant relationship of (...) Risk Management Strategies and Investment Behaviors. Based on the results, it showed that risk management strategies have a significant relationship with one or more of the investment behaviors. Risk avoidance has a significant relationship with confirmation bias. Risk reduction has a significant relationship with all of the investment behaviors such as overconfidence, loss-aversion, recency bias, and confirmation bias. Risk transfer shows a significant relationship with only loss-aversion and confirmation bias. And lastly, risk acceptance also has a significant relationship with all of the investment behaviors. This study recommends exploring other types of behavioral biases under cognitive bias and emotional bias to determine their correlation with risk management strategies. Also, broadening the sample size, demographic scope, and geographic scope of the study can improve the generalizability of the study and provide a more comprehensive understanding of the relationship between investment behavior and risk management strategies. The researchers also recommend to utilize interviews and focus group discussions to gain an in-depth understanding of the underlying values and attitudes concerning investment behavior. (shrink)

How do we find what is clinically significant in the swarms of data being generated by today’s diagnostic technologies? As electronic records become ever more prevalent – and digital imaging and genomic, proteomic, salivaomics, metabalomics, pharmacogenomics, phenomics and transcriptomics techniques become commonplace – fdifferent clinical and biological disciplines are facing up to the need to put their data houses in order to avoid the consequences of an uncontrolled explosion of different ways of describing information. We describe a new strategy to (...) advance the consistency of data in the dental research community. The strategy is based on the idea that existing systems for data collection in dental research will continue to be used, but proposes a methodology in which past, present and future data will be described using a consensus-based controlled structured vocabulary called the Ontology for Dental Research (ODR). (shrink)

Volume 19, Issue 9, September 2019, Page 64-66.

Ontology is one strategy for promoting interoperability of heterogeneous data through consistent tagging. An ontology is a controlled structured vocabulary consisting of general terms (such as “cell” or “image” or “tissue” or “microscope”) that form the basis for such tagging. These terms are designed to represent the types of entities in the domain of reality that the ontology has been devised to capture; the terms are provided with logical defi nitions thereby also supporting reasoning over the tagged data. Aim: This (...) paper provides a survey of the biomedical imaging ontologies that have been developed thus far. It outlines the challenges, particularly faced by ontologies in the fields of histopathological imaging and image analysis, and suggests a strategy for addressing these challenges in the example domain of quantitative histopathology imaging. The ultimate goal is to support the multiscale understanding of disease that comes from using interoperable ontologies to integrate imaging data with clinical and genomics data. (shrink)

Letter commenting on the paper Barry Smith, Louis J. Goldberg, Alan Ruttenberg & Michael Glick, "Ontology and the Future of Dental Research Informatics", Journal of the American Dental Association 141 2010;(10):1173-75 with responses by the authors of the paper.

In the exploratory study reported here, we tested the efficacy of an intervention designed to train teenagers with Möbius syndrome (MS) to increase the use of alternative communication strategies (e.g., gestures) to compensate for their lack of facial expressivity. Specifically, we expected the intervention to increase the level of rapport experienced in social interactions by our participants. In addition, we aimed to identify the mechanisms responsible for any such increase in rapport. In the study, five teenagers with MS interacted with (...) three naïve participants without MS before the intervention, and with three different naïve participants without MS after the intervention. Rapport was assessed by self-report and by behavioral coders who rated videos of the interactions. Individual non-verbal behavior was assessed via behavioral coders, whereas verbal behavior was automatically extracted from the sound files. Alignment was assessed using cross recurrence quantification analysis and mixed-effects models. The results showed that observer-coded rapport was greater after the intervention, whereas self-reported rapport did not change significantly. Observer-coded gesture and expressivity increased in participants with and without MS, whereas overall linguistic alignment decreased. Fidgeting and repetitiveness of verbal behavior also decreased in both groups. In sum, the intervention may impact non-verbal and verbal behavior in participants with and without MS, increasing rapport as well as overall gesturing, while decreasing alignment. (shrink)

Last year saw the 20th anniversary edition of JECP, and in the introduction to the philosophy section of that landmark edition, we posed the question: apart from ethics, what is the role of philosophy ‘at the bedside’? The purpose of this question was not to downplay the significance of ethics to clinical practice. Rather, we raised it as part of a broader argument to the effect that ethical questions – about what we should do in any given situation – are (...) embedded within whole understandings of the situation, inseparable from our beliefs about what is the case, what it is that we feel we can claim to know, as well as the meaning we ascribe to different aspects of the situation or to our perception of it. Philosophy concerns fundamental questions: it is a discipline requiring us to examine the underlying assumptions we bring with us to our thinking about practical problems. Traditional academic philosophers divide their discipline into distinct areas that typically include logic: questions about meaning, truth and validity; ontology: questions about the nature of reality, what exists; epistemology: concerning knowledge; and ethics: how we should live and practice, the nature of value. Any credible attempt to analyse clinical reasoning will require us to think carefully about these types of question and the relationships between them, as they influence our thinking about specific situations and problems. So, the answers to the question we posed, about the role of philosophy at the bedside, are numerous and diverse, and that diversity is illustrated in the contributions to this thematic edition. (shrink)

We often talk and behave as if being a man required more than just being male, and being a woman required more than just being female. There are expectations that need to be met if someone wants to fully qualify as a man or a woman in their social environment, expectations regarding their behaviour as well as character. It is, however, not entirely obvious what ‘being a man’ or ‘being a woman’ actually means and in what way and to what (...) extent it defines our identity, making us who we are. Would I be a different person if I were a woman? And what would it take for me to be a woman? Could I conceivably be neither? Or both? If gender were nothing but sex, telling a man to ‘be a man’ would make little sense. We may have different ideas about what it means to be a man or woman and how we need to behave in order to secure or maintain our manhood or womanhood, but we are all likely to have some deeply ingrained understanding of what makes a man a man and a woman a woman that goes beyond mere biology. Does it, however, follow that gender can, if necessary or desired, be completely detached from sex, that I can be a woman despite having all the physical attributes of a male member of my species, or a man despite being biologically female? If so, on what grounds exactly would we decide who is what? (shrink)

Here we present what we believe is a novel account of what languages are, along with an axiomatically rich representation of languages and language-related data that is based on this account. We propose an account of languages as aggregates of dispositions distributed across aggregates of persons, and in doing so we address linguistic competences and the processes that realize them. This paves the way for representing additional types of language-related entities. Like demographic data of other sorts, data about languages may (...) be of use to researchers in a number of areas, including biomedical research. Data on the languages used in clinical encounters are typically included in medical records, and capture an important factor in patient-provider interactions. Like many types of patient and demographic data, data on a person’s preferred and primary languages are organized in different ways by different systems. This can be a barrier to data integration. We believe that a robust framework for representing language in general and preferred and primary language in particular – which has been lacking in ontologies thus far – can promote more successful integration of language-related data from disparate data sources. (shrink)

The viewpoint that consciousness, including feeling, could be fully expressed by a computational device is known as strong artificial intelligence or strong AI. Here I offer a defense of strong AI based on machine-state functionalism at the quantum level, or quantum-state functionalism. I consider arguments against strong AI, then summarize some counterarguments I find compelling, including Torkel Franzén’s work which challenges Roger Penrose’s claim, based on Gödel incompleteness, that mathematicians have nonalgorithmic levels of “certainty.” Some consequences of strong AI are (...) then considered. A resolution is offered of some problems including John Searle’s Chinese Room problem and the problem of consciousness propagation under isomorphism. (shrink)

Die bahnbrechenden wissenschaftlichen Ergebnisse der letzten Jahre erzwingen eine neue philosophische Auseinandersetzung mit den Grundkategorien der Biologie und der benachbarten Disziplinen. Insbesondere die Anwendung neuer informationstechnischer Mittel in der biomedizinischen Forschung und die damit verbundene, kontinuierlich zunehmende Datenflut sowie die Notwendigkeit, ihrer Herr zu werden, erfordern ein konsequentes Nachdenken darüber, wie biologische Daten systematisiert und klassifiziert werden können. Dafür wiederum bedarf es robuster Theorien von Grundbegriffen wie Art, Spezies, Teil, Ganzes, Funktion, Prozess, Fragment, Sequenz, Expression, Grenze, Locus, Umwelt, System usw. (...) Solche Begriffe gehören zum impliziten Wissen jedes Biologen. Sie spiegeln einerseits eine Dimension der biologischen Wirklichkeit wider, die auch vor dem Hintergrund der biologischen Evolution unverändert bleibt. Andererseits verlangt deren theoretische Behandlung nach zeitgemäßen Analoga der in der traditionellen aristotelischen Metaphysik entwickelten Methoden. Zugleich können so die explizit formulierten Theorien und Definitionen bereitgestellt werden, die für computergestützte Informationssysteme unabdingbar sind. Das Entwickeln derartiger Theorien und Definitionen ist eine Aufgabe der Philosophie, die in diesem Sinne herausgefordert ist, zwischen Biologie und Informatik zu vermitteln. (shrink)

This paper provides a method for characterizing space events using the framework of conceptual spaces. We focus specifically on estimating and ranking the likelihood of collisions between space objects. The objective is to design an approach for anticipatory decision support for space operators who can take preventive actions on the basis of assessments of relative risk. To make this possible our approach draws on the fusion of both hard and soft data within a single decision support framework. Contextual data is (...) also taken into account, for example data about space weather effects, by drawing on the Space Domain Ontologies, a large system of ontologies designed to support all aspects of space situational awareness. The framework is coupled with a mathematical programming scheme that frames a mathematically optimal approach for decision support, providing a quantitative basis for ranking potential for collision across multiple satellite pairs. The goal is to provide the broadest possible information foundation for critical assessments of collision likelihood. (shrink)

As well as disagreeing about how much one should donate to charity, moral theories also disagree about where one should donate. In light of this disagreement, how should the morally uncertain philanthropist allocate her donations? In many cases, one intuitively attractive option is for the philanthropist to split her donations across all of the charities that are recommended by moral views in which she has positive credence, with each charity’s share being proportional to her credence in the moral theories that (...) recommend that particular charity. Despite the fact that something like this approach is already being used by real-world philanthropists to distribute billions of dollars of donations, it is not supported by any of the approaches to moral uncertainty that have been proposed thus-far in the philosophical literature. In this paper, we will develop a bargaining-based approach to moral uncertainty that honors the proportionality intuition in favor of splitting one’s donations. We also show how this bargaining-based approach has several further advantages over the best alternative proposals. (shrink)

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)

This paper investigates the role of visual experience in Wittgenstein's work. The specific thesis is that visual experience provides not only diverse illustrative examples of what could be an explanation of meaning, but that it also provides a recurrent metaphor for the whole process of meaning and understanding. Wittgenstein uses a great number of visual examples in his texts. Their diversity may be accounted for by the great diversity of ways in which he attempts to describe the relationship between a (...) word and its meaning. The resultant variety of visual examples may be summarised by what I call the Visual Discontinuity Thesis. However, beneath this diversity there lies a thread of continuity. This is provided by the persistent use of visual experience in the description of the word-meaning relation. This use underlies the projection relationship of the Tractatus and the "seeing-as" relationship of the Investigations. This recurrent visual metaphor may be summarised by what I call the Visual Continuity Thesis. This paper presents the latter thesis in the context of a description of the former. (shrink)