The claim is frequently made that structured collections of individuals who are themselves subjects of mental and cognitive states – such collections as courts, countries, and corporations – can be, and often are, subjects of mental or cognitive states. And, to be clear, advocates for this so-called group-minds hypothesis intend their view to be interpreted literally, not metaphorically. The existing critical literature casts substantial doubt on this view, at least on the assumption that groups are claimed to instantiate the same (...) species of mental and cognitive properties as individual humans. In this essay, I evaluate a defensive move made by some proponents of the group-oriented view: to concede that group states and individual states aren’t of the same specific natural kinds, while holding that groups instantiate different species of mental or cognitive states – perhaps a different species of cognition itself – from those instantiated by humans. In order to evaluate this defense of group cognition, I develop a view of natural kinds – or at least of the sort of evidence that supports inferences to the sameness of natural kind – a view I have previous dubbed the ‘tweak-and-extend’ theory. Guided by the tweak-and-extend approach, I arrive at a tentative conclusion: that what is common to models of individual cognitive processing and models of group processing does not suffice to establish sameness of cognitive (or mental) kinds, properties, or state-types, not even at a generic or overarching level. (shrink)

It is arguably the case that olfactory system contains two senses that share the same type of stimuli, sensory transduction mechanism, and processing centers. Yet, orthonasal and retronasal olfaction differ in their types of perceptible objects as individuated by their sensory qualities. What will be explored in this paper is how the account of orthonasal smell developed in the Molecular Structure Theory of smell can be expanded for retronasal olfaction (Young, 2016, 2019a-b, 2020). By considering the object of olfactory (...) perception to be the molecular structure of chemical compounds composing odor plumes, Molecular Structure Theory provides a means for determining an odor’s olfactory quality, how odors can be identified and individuated, and how we perceive smellscapes. Surveying the differences between orthonasal and retronasal olfaction provides the basis for the central argument of the paper that the perceptible objects we refer to as smells and individuated on the basis of their olfactory qualities are only relative to orthonasal olfaction. Retronasal olfaction it is speculatively concluded might play an essential role in our perception of flavorful objects. (shrink)

Prior’s puzzle is standardly taken to be the puzzle of why, given the assumption that that-clauses denote propositions, substitution of “the proposition that P” for “that P” within the complements of many propositional attitude verbs is invalid. I show that Prior’s puzzle is much more general than is ordinarily supposed. There are two variants on the substitutional form of the puzzle—a quantificational variant and a pronominal variant—and all three forms of the puzzle arise in a wide range of grammatical positions, (...) rather than merely in the complements of propositional attitude verbs. The generalized puzzle shows that a range of proposed solutions to the original puzzle fail, or are radically incomplete, and also reveals the connections between Prior’s puzzle and debates over the nature of semantic types and higher-order quantification. I go on to develop a novel, higher-order solution to the generalized form of the puzzle, and I argue that this higher-approach is superior to its first-order alternatives. (shrink)

The construction of complex ontologies can be facilitated by adapting existing vocabularies. There is little clarity and in fact little consensus as to what modifications of vocabularies are necessary in order to re-engineer them into ontologies. In this paper we present a method that provides clear steps to follow when re-engineering a thesaurus. The method makes use of top-level ontologies and was derived from the structural differences between thesauri and ontologies as well as from best practices in modeling, some of (...) which have been advocated in the biomedical domain. We illustrate each step of our method with examples from a re-engineering case study about agricultural fertilizers based on the AGROVOC thesaurus. Our method makes clear that re-engineering thesauri requires far more than just a syntactic conversion into a formal language or other easily automatable steps. The method can not only be used for re-engineering thesauri, but does also summarize steps for building ontologies in general, and can hence be adapted for the re-engineering of other types of vocabularies or terminologies. (shrink)

The COVID-19 crisis has forced a difficult trade-off between limiting the health impacts of the virus and maintaining economic activity. Welfare economics offers tools to conceptualize this trade-off so that policy-makers and the public can see clearly what is at stake. We review four such tools: the Value of Statistical Life (VSL); the Value of Statistical Life Years (VSLYs); Quality-Adjusted Life-Years (QALYs); and social welfare analysis, and argue that the latter are superior. We also discuss how to choose policies that (...) differentially affect people’s wellbeing. We argue in favor of evaluating policies using a Social Welfare Function (SWF), which evaluates the possible distributions of wellbeing across individuals that may result from a policy. Such a function, we argue, should regard increases in the wellbeing of the less well-off as especially valuable. We then use a model to illustrate how such a framework can help evaluate two broad policy types in response to the pandemic: eradication of the virus, and more lenient control of the spread. Our model reveals how such evaluations depend on many empirical facts but also on key value judgments about the relative importance of health and on the extent of special concern for the worse off. The purpose of this brief is not to make precise recommendations, as conditions vary widely across countries and over time, but to provide a methodology. (shrink)

In English, as in many other languages, male-gendered pronouns are sometimes used to refer not only to men, but to individuals whose gender is unknown or unspecified, to human beings in general (as in ―mankind‖) and sometimes even to females (as when the casual ―Hey guys‖ is spoken to a group of women). These so-called he/man or masculine generics have come under fire in recent decades for being sexist, even archaic, and positively harmful to women and girls; and advocates (...) of gender-neutral (or nonsexist) language have put forward serious efforts to discourage their use. Have they been successful, and to what extent? In this paper, I review some of the main arguments in favor of abolishing sexist male generics. I then present three studies tracking the use of he/man terminology in academic, popular, and personal discourse over the past several decades. I show that the use of these terms has fallen dramatically in recent years, while nonsexist alternatives have gradually taken their place. We may be paying witness to the early stages of the ultimate extinction of masculine generics. (shrink)

As philosophical and scientific arguments for free will skepticism continue to gain traction, we are likely to see a fundamental shift in the way people think about free will and moral responsibility. Such shifts raise important practical and existential concerns: What if we came to disbelieve in free will? What would this mean for our interpersonal relationships, society, morality, meaning, and the law? What would it do to our standing as human beings? Would it cause nihilism and despair as some (...) maintain or would it rather have a humanizing effect on our practices and policies, freeing us from the negative effects of belief in free will? In this chapter we consider the practical implications of free will skepticism and argue that life without free will and basic desert moral responsibility would not be as destructive as many people believe. We argue that prospects of finding meaning in life or of sustaining good interpersonal relationships, for example, would not be threatened. On treatment of criminals, we argue that although retributivism and severe punishment, such as the death penalty, would be ruled out, preventive detention and rehabilitation programs would still be justified. While we will touch on all these issues below, our focus will be primarily on this last issue. -/- We begin in section I by considering two different routes to free will skepticism. The first denies the causal efficacy of the types of willing required for free will and receives its contemporary impetus from pioneering work in neuroscience by Benjamin Libet, Daniel Wegner, and John-Dylan Haynes. The second, which is more common in the philosophical literature, does not deny the causal efficacy of the will but instead claims that whether this causal efficacy is deterministic or indeterministic, it does not achieve the level of control to count as free will by the standards of the historical debate. We argue that while there are compelling objections to the first route—e.g., Al Mele (2009), Eddy Nahmias (2002, 2011), and Neil Levy (2005)—the second route to free will skepticism remains intact. In section II we argue that free will skepticism allows for a workable morality, and, rather than negatively impacting our personal relationships and meaning in life, may well improve our well-being and our relationships to others since it would tend to eradicate an often destructive form of moral anger. In section III we argue that free will skepticism allows for adequate ways of responding to criminal behavior—in particular, incapacitation, rehabilitation, and alternation of relevant social conditions—and that these methods are both morally justified and sufficient for good social policy. We present and defend our own preferred model for dealing with dangerous criminals, an incapacitation account built on the right to self-protection analogous to the justification for quarantine (see Pereboom 2001, 2013, 2014a; Caruso 2016a), and we respond to recent objections to it by Michael Corrado and John Lemos. (shrink)

Much of the recent philosophical discussion about free will has been focused on whether compatibilists can adequately defend how a determined agent could exercise the type of free will that would enable the agent to be morally responsible in what has been called the basic desert sense :5–24, 1994; Fischer in Four views on free will, Wiley, Hoboken, 2007; Vargas in Four views on free will, Wiley, Hoboken, 2007; Vargas in Philos Stud, 144:45–62, 2009). While we agree with Derk (...) Pereboom and others that the compatibilist’s burden should be properly understood as providing a compelling account of how a determined agent could be morally responsible in the basic desert sense, the exact nature of this burden has been rendered somewhat unclear by the fact that there has been no definitive account given as to what the basic desert sense of moral responsibility amounts to. In Sect. 1 we set out to clarify the compatibilist’s burden by presenting our account of basic desert moral responsibility—which we call retributivist desert moral responsibility for purposes of clarity—and explain why it is of central philosophical and practical importance to the free will debate. In Sect. 2 we employ a thought experiment to illustrate the kind of difficulty that compatibilists of any stripe are likely to encounter in attempting to explain how determined agents can exercise the kind of free will needed for retributivist desert moral responsibility. (shrink)

This article endeavors to identify the strongest versions of the two primary arguments against epistemic scientific realism: the historical argument—generally dubbed “the pessimistic meta-induction”—and the argument from underdetermination. It is shown that, contrary to the literature, both can be understood as historically informed but logically validmodus tollensarguments. After specifying the question relevant to underdetermination and showing why empirical equivalence is unnecessary, two types of competitors to contemporary scientific theories are identified, both of which are informed by science itself. With the (...) content and structure of the two nonrealist arguments clarified, novel relations between them are uncovered, revealing the severity of their collective threat against epistemic realism and its “no-miracles” argument. The final section proposes, however, that the realist’s axiological tenet “science seeks truth” is not blocked. An attempt is made to indicate the promise for a nonepistemic, purely axiological scientific realism—here dubbed “Socratic scientific realism.”. (shrink)

The study assessed the conceptual understanding and attitude toward fractions of teacher education students in a socio-constructivist learning environment. Specifically, it determined the students’ level of conceptual understanding before and after instruction; verified the types of conceptual changes that occurred; and ascertained the attitude of students toward fractions before and after instruction and its relationship to their levels of understanding. Descriptive-correlational research method was used. Socio-constructivist context-based teaching method was employed to introduce the concept of fractions. Achievement tests and interviews (...) were administered to determine the students’ level of conceptual understanding. Conceptual analysis based on Jensen and Finley’s (1995) method with Tiberghien’s (1994) classification of changes was utilized to describe students’ conceptual understanding and conceptual changes. In order to determine their attitude on fractions, students were asked to answer the socio-constructivist attitude questionnaire. The level of conceptual understanding of teacher education students in fraction was functional misconception and partial understanding before and after instruction, respectively. The type of conceptual change that occurred among teacher education students was change for the better. Socio-constructivist learning more likely to improve students’ attitudes toward fractions; promoted prosocial behavior among students; and tend to increase students’ activeness in the classroom activities as evidenced. (shrink)

Recent work takes both philosophical and scientific progress to consist in acquiring factive epistemic states such as knowledge. However, much of this work leaves unclear what entity is the subject of these epistemic states. Furthermore, by focusing only on states like knowledge, we overlook progress in intermediate cases between ignorance and knowledge—for example, many now celebrated theories were initially so controversial that they were not known. -/- This paper develops an improved framework for thinking about intellectual progress. Firstly, I argue (...) that we should think of progress relative to the epistemic position of an intellectual community rather than individual inquirers. Secondly, I show how focusing on the extended process of inquiry (rather than the mere presence or absence of states like knowledge) provides a better evaluation of different types of progress. This includes progress through formulating worthwhile questions, acquiring new evidence, and increasing credence on the right answers to these questions. I close by considering the ramifications for philosophical progress, suggesting that my account supports rejecting the most negative views while allowing us to articulate different varieties of optimism and pessimism. (shrink)

Purpose This paper aims to formalize long-term trajectories of human civilization as a scientific and ethical field of study. The long-term trajectory of human civilization can be defined as the path that human civilization takes during the entire future time period in which human civilization could continue to exist. -/- Design/methodology/approach This paper focuses on four types of trajectories: status quo trajectories, in which human civilization persists in a state broadly similar to its current state into the distant future; catastrophe (...) trajectories, in which one or more events cause significant harm to human civilization; technological transformation trajectories, in which radical technological breakthroughs put human civilization on a fundamentally different course; and astronomical trajectories, in which human civilization expands beyond its home planet and into the accessible portions of the cosmos. -/- Findings Status quo trajectories appear unlikely to persist into the distant future, especially in light of long-term astronomical processes. Several catastrophe, technological transformation and astronomical trajectories appear possible. -/- Originality/value Some current actions may be able to affect the long-term trajectory. Whether these actions should be pursued depends on a mix of empirical and ethical factors. For some ethical frameworks, these actions may be especially important to pursue. (shrink)

This paper evaluates the Natural-Kinds Argument for cognitive extension, which purports to show that the kinds presupposed by our best cognitive science have instances external to human organism. Various interpretations of the argument are articulated and evaluated, using the overarching categories of memory and cognition as test cases. Particular emphasis is placed on criteria for the scientific legitimacy of generic kinds, that is, kinds characterized in very broad terms rather than in terms of their fine-grained causal roles. Given the current (...) state of cognitive science, I conclude that we have no reason to think memory or cognition are generic natural kinds that can ground an argument for cognitive extension. (shrink)

Context: The majority of contemporary enactivist work is influenced by the philosophical biology of Hans Jonas. Jonas credits all living organisms with experience that involves particular “existential” structures: nascent forms of concern for self-preservation and desire for objects and outcomes that promote well-being. We argue that Jonas’s attitude towards living systems involves a problematic anthropomorphism that threatens to place enactivism at odds with cognitive science, and undermine its legitimate aims to become a new paradigm for scientific investigation and understanding of (...) the mind. Problem: Enactivism needs to address the tension between its Jonasian influences and its aspirations to become a new paradigm for cognitive science. By relying on Jonasian phenomenology, contemporary enactivism obscures alternative ways in which phenomenology can be more smoothly integrated with cognitive science. Method: We outline the historical relationship between enactivism and phenomenology, and explain why anthropomorphism is problematic for a research program that aspires to become a new paradigm for cognitive science. We examine the roots of Jonas’s existential interpretation of biological facts, and describe how and why Jonas himself understood his project as founded on an anthropomorphic assumption that is incompatible with a crucial methodological assumption of scientific enquiry: the prohibition of unexplained natural purposes. We describe the way in which phenomenology can be integrated into Maturana’s autopoietic theory, and use this as an example of how an alternative, non-anthropomorphic science of the biological roots of cognition might proceed. Results: Our analysis reveals a crucial tension between Jonas’s influence on enactivism and enactivism’s paradigmatic aspirations. This suggests the possibility of, and need to investigate, other ways of integrating phenomenology with cognitive science that do not succumb to this tension. Implications: In light of this, enactivists should either eliminate the Jonasian inference from properties of our human experience to properties of the experience of all living organisms, or articulate an alternative conception of scientific enquiry that can tolerate the anthropomorphism this inference entails. The Maturanian view we present in the article’s final section constitutes a possible framework within which enactivist tools and concepts can be used to understand cognition and phenomenology, and that does not involve a problematic anthropomorphism. Constructivist content: Any constructivist approach that aims for integration with current scientific practice must either avoid the type of anthropomorphic inference on which Jonas bases his work, or specify a new conception of scientific enquiry that renders anthropomorphism unproblematic. (shrink)

How does one formalize the structure of structures necessary for the foundations of physics? This work is an attempt at conceptualizing the metaphysics of pregeometric structures, upon which new and existing notions of quantum geometry may find a foundation. We discuss the philosophy of pregeometric structures due to Wheeler, Leibniz as well as modern manifestations in topos theory. We draw attention to evidence suggesting that the framework of formal language, in particular, homotopy type theory, provides the conceptual building blocks (...) for a theory of pregeometry. This work is largely a synthesis of ideas that serve as a precursor for conceptualizing the notion of space in physical theories. In particular, the approach we espouse is based on a constructivist philosophy, wherein ``structureless structures'' are syntactic types realizing formal proofs and programs. Spaces and algebras relevant to physical theories are modeled as type-theoretic routines constructed from compositional rules of a formal language. This offers the remarkable possibility of taxonomizing distinct notions of geometry using a common theoretical framework. In particular, this perspective addresses the crucial issue of how spatiality may be realized in models that link formal computation to physics, such as the Wolfram model. (shrink)

A legacy of Enlightenment thought was to see the human as separate from nature. Human history was neatly distinguished from natural history. The age of Anthropocene has now put all that into question. This human exceptionalism is seen by some as responsible for the devastating impact humans have had on the planet. But if we give up on the nature / culture distinction and see human activity as just another type of natural process, we risk losing our ability to (...) attribute moral agency and responsibility to humanity for the environmental crisis, argues Giuseppina D’Oro. (shrink)

The issue of safety culture is one of the most important in a modern medical facility because any problems during the provision of services may lead to irreversible consequences. Not only the patient may suffer, but the doctor who assisted. Unfortunately, very little attention to this issue is paid in Ukraine. Based on this, we can say that the topic is relevant and requires studying. -/- The purpose of writing this article is the analysis of the ways of forming professional (...) safety culture in clinical medicine. The methods by which we carried out scientific research are observation, analysis, evaluation, comparison, generalization. -/- The work examined interpretation of the term "safety culture", types of innovation in which it belongs and the main methods of its creation in the medical field. -/- Safety culture in the medical field involves the right of all health care workers to use measures to prevent actions that can harm a patient or a colleague. Different approaches were considered in the interpretation of the term "safety culture" and we proposed our own: safety culture is a system of values, objectives, knowledge and skills, rules and procedures, convictions shared by representatives of a certain medical profession and supported by patients, creating a favourable working climate, atmosphere of trust and becoming an efficient tool for achieving the goals of the organization. -/- The main components of the safety culture were defined: responsibilities of managers, communication, performance, resources of safety, trust, the degree of job satisfaction, etc. Based on several studies, it was found that no country has a perfect medical system. Every system should be improved. -/- We proposed measures to fix the situation with the safety culture in health care facilities. The correct management of safety can eliminate or fix many medical errors. That is why the need for a clear program of implementation, execution and control of SC in the medical establishment is necessary. -/- Scientific novelty of this work lies in the interpretation of the term "safety culture" at medical institutions and in determining major steps towards its creation. Practical value of the work is the opportunity to implement these steps in medical institutions for improvement of the safety culture and, therefore, to reduce the risk of bad accidents during treatment. -/- Further research can address safety culture management in medical institutions on the examples from the experience of countries with effective systems of health care. (shrink)

The brain is composed of electrically excitable neuronal networks regulated by the activity of voltage-gated ion channels. Further portraying the molecular composition of the brain, however, will not reveal anything remotely reminiscent of a feeling, a sensation or a conscious experience. In classical physics, addressing the mind–brain problem is a formidable task because no physical mechanism is able to explain how the brain generates the unobservable, inner psychological world of conscious experiences and how in turn those conscious experiences steer the (...) underlying brain processes toward desired behavior. Yet, this setback does not establish that consciousness is non-physical. Modern quantum physics affirms the interplay between two types of physical entities in Hilbert space: unobservable quantum states, which are vectors describing what exists in the physical world, and quantum observables, which are operators describing what can be observed in quantum measurements. Quantum no-go theorems further provide a framework for studying quantum brain dynamics, which has to be governed by a physically admissible Hamiltonian. Comprising consciousness of unobservable quantum information integrated in quantum brain states explains the origin of the inner privacy of conscious experiences and revisits the dynamic timescale of conscious processes to picosecond conformational transitions of neural biomolecules. The observable brain is then an objective construction created from classical bits of information, which are bound by Holevo’s theorem, and obtained through the measurement of quantum brain observables. Thus, quantum information theory clarifies the distinction between the unobservable mind and the observable brain, and supports a solid physical foundation for consciousness research. (shrink)

In Big Gods, Norenzayan (2013) presents the most comprehensive treatment yet of the Big Gods question. The book is a commendable attempt to synthesize the rapidly growing body of survey and experimental research on prosocial effects of religious primes together with cross-cultural data on the distribution of Big Gods. There are, however, a number of problems with the current cross-cultural evidence that weaken support for a causal link between big societies and certain types of Big Gods. Here we attempt to (...) clarify these problems and, in so doing, correct any potential misinterpretation of the cross-cultural findings, provide new insight into the processes generating the patterns observed, and flag directions for future research. (shrink)

A question, long discussed by legal scholars, has recently provoked a considerable amount of philosophical attention: ‘Is it ever appropriate to base a legal verdict on statistical evidence alone?’ Many philosophers who have considered this question reject legal reliance on bare statistics, even when the odds of error are extremely low. This paper develops a puzzle for the dominant theories concerning why we should eschew bare statistics. Namely, there seem to be compelling scenarios in which there are multiple sources of (...) incriminating statistical evidence. As we conjoin together different types of statistical evidence, it becomes increasingly incredible to suppose that a positive verdict would be impermissible. I suggest that none of the dominant views in the literature can easily accommodate such cases, and close by offering a diagnosis of my own. (shrink)

Mystery of Being by Gabriel Marcel depicts the harm of spectating in contemporary society. Marcel describes how spectating rather than participating causes us to lose our sense of being. This essay will show how technology, particularly television, social media, and cell phones, has negatively influenced people's decisions to leave small communities and develop spectating habits. Marcel demonstrates how the yearning for ingatheredness among individuals is depleting as self-centered consumerism rises. This illustrate that this rise is primarily due to the performative (...) actions of people and the influence of social media. Indeed, Dr. Lonnie Aarssen’s work What We Are will be used to illustrate the addiction to technology in a biological standpoint. More specifically, using Dr. Aarssen’s work, will display how we have developed a type of ‘nose blindness’ to technology by not living fulfilling lives. This will exemplify how individuals become accustomed to this mode of living and lose the participatory aspects of their lives. I will argue why I support Marcel's fear and present counterarguments regarding performative accounts to further my agreement. Ultimately, the advancement of technologies promotes detached communities and removes individuals from the arena of world participation. (shrink)

Embodied cognitive theories predict that linguistic conceptual representations are grounded and continually represented in real world, sensorimotor experiences. However, there is an on-going debate on whether this also holds for abstract concepts. Grammar is the archetype of abstract knowledge, and therefore constitutes a test case against embodied theories of language representation. Former studies have largely focussed on lexical-level embodied representations. In the present study we take the grounding-by-modality idea a step further by using reaction time (RT) data from the linguistic (...) processing of nominal classifiers in Chinese. We take advantage of an independent body of research, which shows that attention in hand space is biased. Specifically, objects near the hand consistently yield shorter RTs as a function of readiness for action on graspable objects within reaching space, and the same biased attention inhibits attentional disengagement. We predicted that this attention bias would equally apply to the graspable object classifier but not to the big object classifier. Chinese speakers (N = 22) judged grammatical congruency of classifier-noun combinations in two conditions: graspable object classifier and big object classifier. We found that RTs for the graspable object classifier were significantly faster in congruent combinations, and significantly slower in incongruent combinations, than the big object classifier. There was no main effect on grammatical violations, but rather an interaction effect of classifier type. Thus, we demonstrate here grammatical category- specific effects pertaining to the semantic content and by extension the visual and tactile modality of acquisition underlying the acquisition of these categories. We conclude that abstract grammatical categories are subjected to the same mechanisms as general cognitive and neurophysiological processes and may therefore be grounded. (shrink)

The Ockhamist claims that our ability to do otherwise is not endangered by God’s foreknowledge because facts about God’s past beliefs regarding future contingents are soft facts about the past—i.e., temporally relational facts that depend in some sense on what happens in the future. But if our freedom, given God’s foreknowledge, requires altering some fact about the past that is clearly a hard fact, then Ockhamism fails even if facts about God’s past beliefs are soft. Recent opponents of Ockhamism, including (...) David Widerker and Peter van Inwagen, have argued along precisely these lines. Their arguments, if successful, would undermine Ockhamism while avoiding the controversy over the alleged softness of facts about God’s past beliefs. But these arguments do not succeed. The past facts they rely on must be clear and uncontroversial examples of hard facts about the past, and these facts must be such that an ability to refrain from the relevant future action implies an ability to alter the relevant hard fact. We demonstrate the flaw in these arguments by showing how they rely on past facts that do not satisfy these criteria. The Ockhamist may have troubles, but this type of argument is not one of them. (shrink)

The electric activities of cortical pyramidal neurons are supported by structurally stable, morphologically complex axo-dendritic trees. Anatomical differences between axons and dendrites in regard to their length or caliber reflect the underlying functional specializations, for input or output of neural information, respectively. For a proper assessment of the computational capacity of pyramidal neurons, we have analyzed an extensive dataset of three-dimensional digital reconstructions from the NeuroMorphoOrg database, and quantified basic dendritic or axonal morphometric measures in different regions and layers of (...) the mouse, rat or human cerebral cortex. Physical estimates of the total number and type of ions involved in neuronal electric spiking based on the obtained morphometric data, combined with energetics of neurotransmitter release and signaling fueled by glucose consumed by the active brain, support highly efficient cerebral computation performed at the thermodynamically allowed Landauer limit for implementation of irreversible logical operations. Individual proton tunneling events in voltage-sensing S4 protein alpha-helices of Na+, K+ or Ca2+ ion channels are ideally suited to serve as single Landauer elementary logical operations that are then amplified by selective ionic currents traversing the open channel pores. This miniaturization of computational gating allows the execution of over 1.2 zetta logical operations per second in the human cerebral cortex without combusting the brain by the released heat. (shrink)

Inspired by the early Wittgenstein’s concept of nonsense (meaning that which lies beyond the limits of language), we define two different, yet complementary, types of nonsense: formal nonsense and pragmatic nonsense. The simpler notion of formal nonsense is initially defined within Tarski’s semantic theory of truth; the notion of pragmatic nonsense, by its turn, is formulated within the context of the theory of pragmatic truth, also known as quasi-truth, as formalized by da Costa and his collaborators. While an expression will (...) be considered formally nonsensical if the formal criteria required for the assignment of any truth-value (whether true, false, pragmatically true, or pragmatically false) to such sentence are not met, a (well-formed) formula will be considered pragmatically nonsensical if the pragmatic criteria (inscribed within the context of scientific practice) required for the assignment of any truth-value to such sentence are not met. Thus, in the context of the theory of pragmatic truth, any (well-formed) formula of a formal language interpreted on a simple pragmatic structure will be considered pragmatically nonsensical if the set of primary sentences of such structure is not well-built, that is, if it does not include the relevant observational data and/or theoretical results, or if it does include sentences that are inconsistent with such data. (shrink)

In this paper I distinguish between two kinds of meta-hypotheses, or hypotheses about science, at issue in the scientific realism debate. The first are descriptive empirical hypotheses regarding the nature of scientific inquiry. The second are epistemological theories about what individuals should / can justifiably believe about scientific theories. Favoring the realist Type-D meta-hypotheses, I argue that a particular set of realist and non-realist efforts in the debate over Type-E’s have been valuable in the quest to describe and (...) understand the nature of scientific inquiry. For the realism debate itself has inadvertently and indirectly laid the foundations for an important kind of Type-D meta-hypothesis, one regarding creativity in the history of science—which, in turn, is relevant to refining our descriptions of inference. After illustrating this result with regard to the historical argument against realism, I suggest that these empirically attained meta-hypotheses pertaining to scientific creativity can, in turn, be made methodologically prescriptive. (shrink)

In this paper I argue for a version of the Total Evidence view according to which the rational response to disagreement depends upon one's total evidence. I argue that perceptual evidence of a certain kind is significantly weightier than many other types of evidence, including testimonial. Furthermore, what is generally called "The Uniqueness Thesis" is actually a conflation of two distinct principles that I dub "Evidential Uniqueness" and "Rationality Uniqueness." The former principle is likely true but the latter almost certainly (...) false. Seeing why the Rationality Uniqueness fails opens the door to seeing how mutual reasonable disagreement is possible even among those who share the same evidence. (shrink)

There are numerous formal systems that allow inference of new conditionals based on a conditional knowledge base. Many of these systems have been analysed theoretically and some have been tested against human reasoning in psychological studies, but experiments evaluating the performance of such systems are rare. In this article, we extend the experiments in [19] in order to evaluate the inferential properties of c-representations in comparison to the well-known Systems P and Z. Since it is known that System Z and (...) c-representations mainly differ in the sorts of inheritance inferences they allow, we discuss subclass inheritance and present experimental data for this type of inference in particular. (shrink)

Dombrowski and Murdoch offer versions of the ontological argument which aim to avoid two types of objection – those concerned with the nature of the divine, and those concerned with the move from an abstract concept to a mind-independent reality. For both, the nature of the concept of God/Good entails its instantiation, and both supply a supporting argument from experience. It is only Murdoch who successfully negotiates the transition from an abstract concept to the instantiation of that concept, however, and (...) this is achieved by means of an ontological argument from moral experience which, in a reversal of the Kantian doctrine, depends ultimately on a form of the cosmological argument. (shrink)

Initial responses to questionnaires used to assess participants' understanding of informed consent for malaria vaccine trials conducted in the United States and Mali were tallied. Total scores were analyzed by age, sex, literacy (if known), and location. Ninety-two percent (92%) of answers by United States participants and 85% of answers by Malian participants were correct. Questions more likely to be answered incorrectly in Mali related to risk, and to the type of vaccine. For adult participants, independent predictors of higher (...) scores were younger age and female sex in the United States, and male sex in Mali. Scores in the United States were higher than in Mali (P = 0.005). Despite this difference participants at both sites were well informed overall. Although interpretation must be qualified because questionnaires were not intended as research tools and were not standardized among sites, these results do not support concerns about systematic low understanding among research participants in developing versus developed countries. (shrink)

This synthesis of 5 prominent conflict management paradigms uses power differential as the single most contributing variable to their process and outcome of conflict. Efforts of scholars to integrate or synthesize conflict paradigms have been unsuccessful or clumsy by the scholars’ own assessments. The 5 selected paradigms represent an interdisciplinary set of normative and descriptive paradigms from different social contexts and intellectual frameworks. The 5 share the common traits of rival goals, three levels of socially constructed power differential, and outcomes (...) relative to the total value of the rival goal. An inverse relationship between power differential and the total value of conflict outcomes is supported by all 5 paradigms and empirical data. Explanatory metatheory is the methodology used for synthesis. An increase in power differential results in a decrease in total value of the rival goal. Power differential is constructed using Max Weber’s ideal-type method. The power differentials are abstracted from the paradigms themselves. Empirical work form secondary sources and case studies complete the analysis. (shrink)

Christy Mag Uidhir has recently argued (a) that there is no in principle aesthetic difference between a live performance and a recording of that performance, and (b) that the proper aesthetic object is a type which is instantiated by the performance and potentially repeatable when recordings are played back. This paper considers several objections to (a) and finds them lacking. I then consider improvised music, a subject that Mag Uidhir explicitly brackets in his discussion. Improvisation reveals problems with (b), (...) because the performance-event and the performance-type are distinct but equally proper aesthetic objects. (shrink)

In recent years, critical discourse concerning the millenarian eschatology of the early Patristic era of Christianity has called into question the common notion that millenarian concepts have been utterly rejected as heretical by the Roman Catholic Church. No Ecumenical Council has ever rejected millenarian eschatology, and papal and juridical statements on the issue have been taken out of context. This essay brings forward, as testing agents, John Henry Newman’s first two notes in Development in order to determine whether Patristic millenarianism, (...) along with a more recently explored version called Eucharistic millenarianism, is a valid example of doctrinal development of an earlier type. Eucharistic millenarianism borrows many aspects from a primitive apostolic source and has been embraced by the Catholic hierarchy, raising the question of how millenarian aspects might legitimately inform contemporary theology. Newman’s theory of the development of doctrine, particularly as seen in his first two notes, is a valuable tool for reevaluating latent concepts that have been unfairly viewed as marginal or even heretical in mainline theological discourse. (shrink)

Committing to contribute to promoting the 11th progressive cultural element – environmental-healing value – and building the eco-surplus culture for sustainable development, the AISDL Team (represented by Drs. Minh-Hoang Nguyen and Quan-Hoang Vuong) has collaborated with Discover Sustainability to launch “Environmental Sustainability Needs Humanities” Topical Collection. In contributing to the generation of knowledge that aids the social transitions toward an eco-surplus utopia, the Topical Collection welcomes various types of articles across disciplines, including Research, Reviews, Perspectives, Comments, Brief Communications, Case Studies, (...) Registered Reports, and Data Notes that are related but not limited to these issues: - Socio-cultural and economic issues that help mitigate and adapt to climate change and prevent biodiversity loss - Socio-cultural and economic issues that support the development and implementation of nature-based solutions and artificial technologies for achieving environmental sustainability - Factors that help restore the connection between nature and humans, such as science, art, literature, and lived experiences - The psychology towards climate change, biodiversity loss, social transition, and technological transformation - The roles of creativity, serendipity, and knowledge management in sustainability transformation - Sustainable financing mechanism for climate change mitigation and adaptation as well as biodiversity conservation - The roles of urban and rural humans in addressing climate change and biodiversity loss - Global agreement, national commitments, and local actions for addressing climate change and biodiversity loss. (shrink)

The idea that causation involves the production of changes due to the exertion of influence of something on something else—the core idea of causal realism—used to be the default view. Today this idea is at the heart of (i) transmission/causal process accounts, (ii) mechanistic accounts, and (iii) powers-based accounts. However, as I have previously argued (Ingthorsson 2021) the above-mentioned approaches are based—to varying degree—on the very problematic assumption that causal influence is essentially unidirectional; that it passes from whatever is the (...) cause to the effect. As first pointed out be Mario Bunge (1959), the idea that causal influence is unidirectional is incompatible with what is today considered a scientific fact, notably that all interactions are perfectly reciprocal; whenever any object exerts an influence on any other object, the latter simultaneously exerts the same kind of influence, of the same magnitude, on the former. Drawing on Bunge’s result, I have developed a fourth approach to efficient causation that accepts the reciprocity of interactions (Ingthorsson 2002 & 2021). According to this view a cause is not the action of something on something else that receives the influence, but the reciprocal action between powerful particulars which results in a modification of both sides, producing a new state of affairs. In this paper, I present the core ideas of the four different approaches to causal efficacy, what I think is problematic with the first three and finally attempt to compare how well the four approaches fare in explaining two often discussed types of causal interactions: (i) collisions between billiard balls, and (ii) how water dissolves salt. I argue that only reciprocal actions between powerful particulars can plausibly claim to fully account for these phenomena, in a manner compatible with the theories and findings of the natural sciences. (shrink)

In the era of “big data,” science is increasingly information driven, and the potential for computers to store, manage, and integrate massive amounts of data has given rise to such new disciplinary fields as biomedical informatics. Applied ontology offers a strategy for the organization of scientific information in computer-tractable form, drawing on concepts not only from computer and information science but also from linguistics, logic, and philosophy. This book provides an introduction to the field of applied ontology that is of (...) particular relevance to biomedicine, covering theoretical components of ontologies, best practices for ontology design, and examples of biomedical ontologies in use. After defining an ontology as a representation of the types of entities in a given domain, the book distinguishes between different kinds of ontologies and taxonomies, and shows how applied ontology draws on more traditional ideas from metaphysics. It presents the core features of the Basic Formal Ontology (BFO), now used by over one hundred ontology projects around the world, and offers examples of domain ontologies that utilize BFO. The book also describes Web Ontology Language (OWL), a common framework for Semantic Web technologies. Throughout, the book provides concrete recommendations for the design and construction of domain ontologies. (shrink)

The present dissertation aims at analyzing some linguistic aspects related to the lexical, semantic and syntactic behaviour of a number of verbs of FEELING in English whose lexical, grammatical and idiosyncratic properties have been entered into the FunGramKB Editor in application of study of the theoretical assumptions propounded by the Lexical-Constructional Model. -/- Analysis and subsequent input of data have been assessed against the background of some of the 20th-century trends in linguistics which find their expression in the first decade (...) of this century, and the role of semantics in a world in which increasing priority is given to probabilistic, machine-learned output in lexicographic work. From this stance, the generic features contained in the FunGramKB meaning postulates and thematic frames as outlined in the Lexical-Constructional Model bring hope for a more faithful rendering of the semantic relationships established within human expression, while making provisions for a semanticist‟s contribution to refinement and storage of both thorough and extensive knowledge. (shrink)

One of the moral questions concerning autonomous vehicles (henceforth AVs) is the choice between types that differ in their built-in algorithms for dealing with rare situations of unavoidable lethal collision. It does not appear to be possible to avoid questions about how these algorithms should be designed. We present the results of our study of moral preferences (N = 2769) with respect to three types of AVs: (1) selfish, which protects the lives of passenger(s) over any number of bystanders; (2) (...) altruistic, which minimizes the number of casualties, even if this leads to death of passenger(s); and (3) conservative, which abstains from interfering in such situations. We differentiate between scenarios in which participants are to make their decisions privately or publicly, and for themselves or for their offspring. We aim to answer two research questions: (1) whether the public visibility of the choice of an AV type choice make this choice more altruistic and (2) which type of situation makes it more difficult to choose altruistically: when choosing for society as a whole, when choosing only for oneself, or when choosing only for one’s offspring. Our results show that respondents exhibit a preference for an altruistic strategy for AVs and that it is reinforced when signaled to others. The altruistic preference is strongest when applies to everybody else, weaker when it reflects a solely personal choice, and weakest when choosing for one’s own child. We conclude that a public choice is considerably more likely to pressure consumers into accepting a more socially beneficial solution. (shrink)

This chapter argues that Simon anticipated what has emerged as the consensus view about human cognition: embodied functionalism. According to embodied functionalism, cognitive processes appear at a distinctively cognitive level; types of cognitive processes (such as proving a theorem) are not identical to kinds of neural processes, because the former can take various physical forms in various individual thinkers. Nevertheless, the distinctive characteristics of such processes — their causal structures — are determined by fine-grained properties shared by various, often especially (...) bodily related, physical processes that realize them. Simon’s apparently anti-embodiment views are surveyed and are shown to be consistent with his many claims that lend themselves to an embodied interpretation and that, to a significant extent, helped to lay the groundwork for an embodied cognitive science. (shrink)

Recent research has relied on trolley-type sacrificial moral dilemmas to study utilitarian versus nonutili- tarian modes of moral decision-making. This research has generated important insights into people’s attitudes toward instrumental harm—that is, the sacrifice of an individual to save a greater number. But this approach also has serious limitations. Most notably, it ignores the positive, altruistic core of utilitarianism, which is characterized by impartial concern for the well-being of everyone, whether near or far. Here, we develop, refine, and validate (...) a new scale—the Oxford Utilitarianism Scale—to dissociate individual differences in the ‘negative’ (permissive attitude toward instrumental harm) and ‘positive’ (impartial concern for the greater good) dimensions of utilitarian thinking as manifested in the general population. We show that these are two independent dimensions of proto-utilitarian tendencies in the lay population, each exhibiting a distinct psychological profile. Empathic concern, identification with the whole of humanity, and concern for future generations were positively associated with impartial beneficence but negatively associated with instrumental harm; and although instrumental harm was associated with subclinical psychopathy, impartial beneficence was associated with higher religiosity. Importantly, although these two dimensions were independent in the lay population, they were closely associated in a sample of moral philosophers. Acknowledging this dissociation between the instrumental harm and impartial beneficence components of utilitarian thinking in ordinary people can clarify existing debates about the nature of moral psychology and its relation to moral philosophy as well as generate fruitful avenues for further research. (shrink)

On ground shared by environmental hermeneutics, critical social theory, and environmentally minded feminism, this article attempts to conciliate between the nearly antithetical ethical viewpoints of environmental philosophers David Abram and Steven Vogel. It will demonstrate first that Abram’s linguistic arguments for extending ethical considerability to nonhuman nature succumb to two of Vogel’s debilitating critiques, which it labels the social constructivist critique and the discourse ethics critique, and secondly that Abram fails to guard against the problem of human-human oppression. The article (...) also points out, on the other hand, that while Vogel evades the problem of human-human oppression, his view fails to protect against the problem of dangerous anthropocentrism. Operating within the boundaries that Vogel establishes, it will seek to avoid the pitfalls of Abram’s view, to address the underlying ideology that leads to both types of oppression, and to eliminate the problem of dangerous anthropocentrism. To do so it draws upon the arguments of Trish Glazebrook, contending that Abram’s appeals to the “speech” of nature can be more effectively conceptualized as erotic appeals, and that engaging in this call-and-response eros promotes the development of virtues that undermine our current ideology and extend to both the human and the nonhuman. (shrink)

The file on this site provides the slides for a lecture given in Hangzhou in May 2018, and the lecture itself is available at the URL beginning 'sms' in the set of links provided in connection with this item. -/- It is commonly assumed that regular physics underpins biology. Here it is proposed, in a synthesis of ideas by various authors, that in reality structures and mechanisms of a biological character underpin the world studied by physicists, in principle supplying detail (...) in the domain that according to regular physics is of an indeterminate character. In regular physics mathematical equations are primary, but this constraint leads to problems with reconciling theory and reality. Biology on the other hand typically does not characterise nature in quantitative terms, instead investigating in detail important complex interrelationships between parts, leading to an understanding of the systems concerned that is in some respects beyond that which prevails in regular physics. It makes contact with quantum physics in various ways, for example in that both involve interactions between observer and observed, an insight that explains what is special about processes involving observation, justifying in the quantum physics context the replacement of the unphysical many-worlds picture by one involving collapse. The link with biology furthermore clarifies Wheeler’s suggestion that a multiplicity of observations can lead to the ‘fabrication of form’, including the insight that this process depends on very specific ‘structures with power’ related to the 'semiotic scaffolding' of the application of sign theory to biology known as biosemiotics. -/- The observer-observed 'circle' of Wheeler and Yardley is a special case of a more general phenomenon, oppositional dynamics, related to the 'intra-action' of Barad's Agential Realism, involving cooperating systems such as mind and matter, abstract and concrete, observer and observed, that preserve their identities while interacting with one another in such a way as to act as a unit. A third system may also be involved, the mediating system of Peirce linking the two together. Such a situation of changing connections and separations may plausibly lead in the future to an understanding of how complex systems are able to evolve to produce 'life, the universe and everything'. -/- (Added 1 July 2018) The general structure proposed here as an alternative to a mathematics-based physics can be usefully characterised by relating it to different disciplines and the specialised concepts utilised therein. In theoretical physics, the test for the correctness of a theory typically involves numerical predictions, corresponding to which theories are expressed in terms of equations, that is to say assertions that two quantities have identical values. Equations have a lesser significance in biology which typically talks in terms of functional mechanisms, dependent for example on details of chemistry and concepts such as genes, natural selection, signals and geometrical or topologically motivated concepts such as the interconnections between systems and the unfolding of DNA. Biosemiotics adds to this the concept of signs and their interpretation, implying novel concepts such as semiotic scaffolding and the semiosphere, code duality, and appreciation of the different types of signs, including symbols and their capacity for abstraction and use in language systems. Circular Theory adds to this picture, as do the ideas of Barad, considerations such as the idea of oppositional dynamics. The proposals in this lecture can be regarded as the idea that concepts such as those deriving from biosemiotics have more general applicability than just conventional biology and may apply, in some circumstances, to nonlinear systems generally, including the domain new to science hypothesised to underlie the phenomena of present-day physics. -/- The task then has to be to restore the mathematical aspect presumed, in this picture, not to be fundamental as it is in conventional theory. Deacon has invoked a complex sequence of evolutionary steps to account for the emergence over time of human language systems, and correspondingly mathematical behaviour can be subsumed under the general evolutionary mechanisms of biosemiotics (cf. also the proposals of Davis and Hersh regarding the nature of mathematics), so that the mathematical behaviour of physical systems is consistent with the proposed scheme. In conclusion, it is suggested that theoretical physicists should cease expecting to find some universal mathematical ‘theory of everything’, and focus instead on understanding in more detail complex systems exhibiting behaviour of a biological character, extending existing understanding. This may in time provide a more fruitful understanding of the natural world than does the regular approach. The essential concepts have an observational basis from both biology and the little-known discipline of cymatics (a discipline concerned with the remarkable patterns that specific waveforms can give rise to), while again computer simulations also offer promise in providing insight into the complex behaviours involved in the above proposals. -/- References -/- Jesper Hoffmeyer, Semiotic Scaffolding of Living Systems. Commens, a Digital Companion to C. S. Peirce (on Commens web site). Terrence Deacon, The Symbolic Species, W.W. Norton & Co. Karen Barad, Meeting the Universe Halfway: Quantum Physics and the Entanglement of Matter and Meaning, Duke University Press. Philip Davis and Reuben Hersh, The Mathematical Experience, Penguin. Ilexa Yardley, Circular Theory. (shrink)

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)

Scientists use models to understand the natural world, and it is important not to conflate model and nature. As an illustration, we distinguish three different kinds of populations in studies of ecology and evolution: theoretical, laboratory, and natural populations, exemplified by the work of R.A. Fisher, Thomas Park, and David Lack, respectively. Biologists are rightly concerned with all three types of populations. We examine the interplay between these different kinds of populations, and their pertinent models, in three examples: the notion (...) of “effective” population size, the work of Thomas Park on /Tribolium/ populations, and model-based clustering algorithms such as /Structure/. Finally, we discuss ways to move safely between three distinct population types while avoiding confusing models and reality. (shrink)

We present evidence from a pre-registered experiment indicating that a philosophical argument––a type of rational appeal––can persuade people to make charitable donations. The rational appeal we used follows Singer’s well-known “shallow pond” argument (1972), while incorporating an evolutionary debunking argument (Paxton, Ungar, & Greene 2012) against favoring nearby victims over distant ones. The effectiveness of this rational appeal did not differ significantly from that of a well-tested emotional appeal involving an image of a single child in need (Small, Loewenstein, (...) and Slovic 2007). This is a surprising result, given evidence that emotions are the primary drivers of moral action, a view that has been very influential in the work of development organizations. We did not find support for our pre-registered hypothesis that combining our rational and emotional appeals would have a significantly stronger effect than either appeal in isolation. However, our finding that both kinds of appeal can increase charitable donations is cause for optimism, especially concerning the potential efficacy of well-designed rational appeals. We consider the significance of these findings for moral psychology, ethics, and the work of organizations aiming to alleviate severe poverty. (shrink)

The Cell Ontology (CL) is designed to provide a standardized representation of cell types for data annotation. Currently, the CL employs multiple is_a relations, defining cell types in terms of histological, functional, and lineage properties, and the majority of definitions are written with sufficient generality to hold across multiple species. This approach limits the CL’s utility for cross-species data integration. To address this problem, we developed a method for the ontological representation of cells and applied this method to develop a (...) dendritic cell ontology (DC-CL). DC-CL subtypes are delineated on the basis of surface protein expression, systematically including both species-general and species-specific types and optimizing DC-CL for the analysis of flow cytometry data. This approach brings benefits in the form of increased accuracy, support for reasoning, and interoperability with other ontology resources. 104. Barry Smith, “Toward a Realistic Science of Environments”, Ecological Psychology, 2009, 21 (2), April-June, 121-130. Abstract: The perceptual psychologist J. J. Gibson embraces a radically externalistic view of mind and action. We have, for Gibson, not a Cartesian mind or soul, with its interior theater of contents and the consequent problem of explaining how this mind or soul and its psychological environment can succeed in grasping physical objects external to itself. Rather, we have a perceiving, acting organism, whose perceptions and actions are always already tuned to the parts and moments, the things and surfaces, of its external environment. We describe how on this basis Gibson sought to develop a realist science of environments which will be ‘consistent with physics, mechanics, optics, acoustics, and chemistry’. (shrink)

Background Analysis of aphasic narratives can be a challenge for clinicians. Previous studies have mainly employed measures that categorized speech samples at the word level. They included quantification of the use and misuse of different word classes, presence and absence of narrative contents and errors, paraphasias, and perseverations, as well as morphological structures and errors within a narrative. In other words, a great amount of research has been conducted in the aphasiology literature focusing on micro-linguistic structures of oral narratives. Aspects (...) of macro- linguistic structures, such as the analysis of content information by a speaker, consistency of using cohesive devices to present information within a narrative, and order of presenting information necessary to form a coherent discourse, have not been extensively investigated. The current investigation proposes a clinical analytic system to target three aspects of macro-linguistic structures in narratives among speakers with aphasia. Specifically, (1) the presence of search events (i.e., the mentioning of key events that allow the listener to understand; Capilouto, Wright, &Wagovich, 2006) within a narrative, (2) the sequence of the mentioned events, and (3) the informativeness (i.e., the fulfillment of lexical items that allow the user to understand what the event is detailing) of the event contents, were focused in the proposed framework. Method Ten controls transcripts from were selected from the AphasiaBank (MacWhinney, Fromm, Forbes, & Holland, 2011). Three narrative tasks, including sequential picture description of ‘Refused Umbrella’, procedural narrative of making a ‘Peanut Butter and Jelly Sandwich’, and telling of ‘Cinderella’ story, were used to establish normative data for the basis of analysis. Specifically, the Search Events (e) and Informative Words (i) used by at least 70% of the speakers were listed for each genre. The sequential order of mentioning the Search Events, i.e., common order of events in 90% of the speakers, (s.total) was determined. Twelve speakers with aphasia (nine fluent and three non-fluent) were recruited and administered the Western Aphasia Battery and Object and Action Naming Battery. Their performance in the above three discourse tasks were orthographically transcribed and analyzed using the following measures: e.total, e.matched with norm, e.missed, e.irrlevant, e.extra, s.total, i.pb&j, i.umbr, i.cind, and i.total. Three samples were randomly chosen to be re-analyzed for inter- and intra-rater reliability. Results Results of an independent t-test suggested significant differences between the fluent and non-fluent subjects in sequential order of Search Events for all genres (s.total) and i.total, suggesting sensitivity of this framework to differentiate between the two fluency groups. Results of Pearson product-moment correlations revealed significant relation between Informative Words and WAB spontaneous speech scores, AQ, as well as OAB scores, for both aphasic groups. The mean value of coefficients for intra-rater reliability (0.992), with significant correlations on e.match, e.miss, and e.extra, was higher than that of inter-rater reliability (0.897). Discussion Based on our preliminary results, this objective framework allowed clinical evaluation of impairment in macro-linguistic structures present in aphasic discourse. Further extension should involve more subjects encompassing a wider range of severity with different types of aphasia. (shrink)

Vaccine research, as well as the development, testing, clinical trials, and commercial uses of vaccines involve complex processes with various biological data that include gene and protein expression, analysis of molecular and cellular interactions, study of tissue and whole body responses, and extensive epidemiological modeling. Although many data resources are available to meet different aspects of vaccine needs, it remains a challenge how we are to standardize vaccine annotation, integrate data about varied vaccine types and resources, and support advanced vaccine (...) data analysis and inference. To address these problems, the community-based Vaccine Ontology (VO) has been developed through collaboration with vaccine researchers and many national and international centers and programs, including the National Center for Biomedical Ontology (NCBO), the Infectious Disease Ontology (IDO) Initiative, and the Ontology for Biomedical Investigations (OBI). VO utilizes the Basic Formal Ontology (BFO) as the top ontology and the Relation Ontology (RO) for definition of term relationships. VO is represented in the Web Ontology Language (OWL) and edited using the Protégé-OWL. Currently VO contains more than 2000 terms and relationships. VO emphasizes on classification of vaccines and vaccine components, vaccine quality and phenotypes, and host immune response to vaccines. These reflect different aspects of vaccine composition and biology and can thus be used to model individual vaccines. More than 200 licensed vaccines and many vaccine candidates in research or clinical trials have been modeled in VO. VO is being used for vaccine literature mining through collaboration with the National Center for Integrative Biomedical Informatics (NCIBI). Multiple VO applications will be presented. (shrink)

In the era of “big data,” science is increasingly information driven, and the potential for computers to store, manage, and integrate massive amounts of data has given rise to such new disciplinary fields as biomedical informatics. Applied ontology offers a strategy for the organization of scientific information in computer-tractable form, drawing on concepts not only from computer and information science but also from linguistics, logic, and philosophy. This book provides an introduction to the field of applied ontology that is of (...) particular relevance to biomedicine, covering theoretical components of ontologies, best practices for ontology design, and examples of biomedical ontologies in use. After defining an ontology as a representation of the types of entities in a given domain, the book distinguishes between different kinds of ontologies and taxonomies, and shows how applied ontology draws on more traditional ideas from metaphysics. It presents the core features of the Basic Formal Ontology (BFO), now used by over one hundred ontology projects around the world, and offers examples of domain ontologies that utilize BFO. The book also describes Web Ontology Language (OWL), a common framework for Semantic Web technologies. Throughout, the book provides concrete recommendations for the design and construction of domain ontologies. (shrink)