To understand Hobbes’s handling of Christian scripture in Part 3 of Leviathan we need to see it in the light of his own radical account of the norms controlling public religious speech and practice as set out in Part 2 and in other works such as De Cive and De Corpore. As these texts make clear, Hobbes holds that we ought rationally to venerate the first cause of all, and that the proper way to venerate this awesome and incomprehensible being (...) is to publicly adopt the local culture’s religious practices, however arbitrary or conventional those practices might be. For the seventeenth-century English subject, the Anglo-Protestant scriptural religion provides the appropriate vehicle to express this rationally mandated religious piety, and thus provides a form of devotion that Hobbes embraces in a spirit of genuine religious reverence. At the same time, he also regards this religion, like all scriptural religions, as a conventional human artifact that, given the ear of the sovereign, he might hope to shape in favor of Hobbesian ideals such as civil obedience, the separation of philosophy from religion, and the extirpation of belief in an immaterial spirit-world. The proposed interpretation dissolves systematic problems facing irreligious readings on the one hand, and more straightforwardly Christian readings on the other. (shrink)

Two senses of ‘ontology’ can be distinguished in the current literature. First is the sense favored by information scientists, who view ontologies as software implementations designed to capture in some formal way the consensus conceptualization shared by those working on information systems or databases in a given domain. [Gruber 1993] Second is the sense favored by philosophers, who regard ontologies as theories of different types of entities (objects, processes, relations, functions) [Smith 2003]. Where information systems ontologists seek to maximize reasoning (...) efficiency even at the price of simplifications on the side of representation, philosophical ontologists argue that representational adequacy can bring benefits for the stability and resistance to error of an ontological framework and also for its extendibility in the future. In bioinformatics, however, a third sense of ‘ontology’ has established itself, above all as a result of the successes of the Gene Ontology (hereafter: GO), which is a tool for the representation and processing of information about gene products and their biological functions [Gene Ontology Consortium 2000]. We show how Basic Formal Ontology (BFO) has established itself as an overarching ontology drawing on all three of the strands distinguished above, and describe applications of BFO especially in the treatment of biological granularity. (shrink)

Contributors: -/- John Beatty (British Columbia); Kelly James Clark (Ibn Haldun, Istanbul); Angela Coventry (Portland State); Thomas Holden (UC Santa Barbara); Willem Lemmens (Antwerp); Robin Le Poidevin (Leeds); Jennifer Marusic (Edinburgh); Kevin Meeker (South Alabama); Amyas Merivale (Oxford); Peter Millican (Oxford); Dan O’Brien (Oxford Brookes); Graham Oppy (Monash); Paul Russell (Lund); Andre C. Willis (Brown).

In lieu of an abstract, here is a brief excerpt of the content:Reviewed by:Spectres of False Divinity: Hume’s Moral AtheismJohn J. TilleyThomas Holden. Spectres of False Divinity: Hume’s Moral Atheism. Oxford-New York: Oxford University Press, 2010. Pp. xvi + 246. Cloth, $50.00.Thomas Holden argues that a key element of David Hume’s irreligious agenda is his case for moral atheism. According to Holden, Hume defends (conclusively, Hume believes) not merely weak moral atheism, according to which there is (...) no morally praiseworthy deity, but strong moral atheism, according to which there is no deity with any moral characteristics. The idea here is that if any being approximates the traditional notion of God as a first cause or designer, it cannot meet the preconditions for having moral attributes. Holden also discusses arguments that some might expect to be central to Hume’s case but which, according to Holden, are not. For instance, Holden maintains that Hume does not even endorse the evidential argument from evil, let alone use it to support moral atheism. Instead, Hume intends it as a parody of traditional natural theology. Holden closes with several points about the historical and philosophical import of Hume’s moral atheism.Right from the start, Holden faces challenges. How can he square his interpretation of Hume as a moral atheist with Hume’s repeated strictures against theological speculation? And how can he square his interpretation with the fact that Hume never explicitly advocates moral atheism?Holden skillfully meets these challenges. Regarding the first challenge, for example, he distinguishes “core natural theology,” which aims at knowledge of the deity’s distinctive, intrinsic properties, from “liminal natural theology,” which lacks such aims. This distinction, Holden contends, reconciles two elements of Hume’s philosophy that seem to conflict. The first is Hume’s rejection of theological speculation as beyond our cognitive capacities. The second is Hume’s frequent willingness to draw conclusions about divine attributes. Holden argues that although Hume’s strictures against theological speculation pertain to [End Page 297] core natural theology, they are not aimed at liminal natural theology—that is, at speculation about the deity’s non-distinctive or relational properties. Hume’s defense of moral atheism, Holden believes, falls within liminal natural theology.After addressing challenges to his reading of Hume, Holden discusses Hume’s arguments for strong moral atheism. These do not stand out in Hume’s writings (though many of their components do), but Holden finds them there. He does so not through overly imaginative reconstruction but through careful interpretation, with an eye on many texts.Hume’s first argument, the “argument from sentimentalism,” draws on Hume’s theory of the passions and his sentimentalist metaethics. Holden reconstructs it as follows. S1: The deity is not a natural object of any human passion. S2: Moral sentiments are a species of human passion. S3: If a being is not a natural object of the moral sentiments, then it cannot have moral attributes (either virtues or vices). Therefore, S4: The deity cannot have moral attributes. The first premise is the least familiar of the three, and Holden devotes considerable effort to clarifying it, examining Hume’s rationale for it, and addressing objections to it. He performs similar tasks regarding S2, S3, and the argument in general. For instance, he addresses at length three possible objections to the argument, his concern being that if they were sufficiently damaging (he argues that they are not), this might tell against interpreting Hume as advancing the argument.Hume’s second argument, the “argument from motivation,” goes roughly as follows. Although we know nothing about the deity’s distinctive intrinsic properties, we have good reason to think that most likely, the deity (like any unknown being picked out in advance) lacks a sentimental nature anything like ours. But without a sentimental nature akin to ours, a being’s behavior is not intelligible in human terms—for example, it cannot be said to reflect moral concern or such motives as malice and benevolence. And if a being’s behavior is not intelligible in human terms, that being is not morally assessable, which is to say that it lacks moral attributes. Thus, we should conclude that the deity most likely lacks such attributes. Holden... (shrink)

The goal of this short chapter, aimed at philosophers, is to provide an overview and brief explanation of some central concepts involved in predictive processing (PP). Even those who consider themselves experts on the topic may find it helpful to see how the central terms are used in this collection. To keep things simple, we will first informally define a set of features important to predictive processing, supplemented by some short explanations and an alphabetic glossary. -/- The features described here (...) are not shared in all PP accounts. Some may not be necessary for an individual model; others may be contested. Indeed, not even all authors of this collection will accept all of them. To make this transparent, we have encouraged contributors to indicate briefly which of the features are necessary to support the arguments they provide, and which (if any) are incompatible with their account. For the sake of clarity, we provide the complete list here, very roughly ordered by how central we take them to be for “Vanilla PP” (i.e., a formulation of predictive processing that will probably be accepted by most researchers working on this topic). More detailed explanations will be given below. Note that these features do not specify individually necessary and jointly sufficient conditions for the application of the concept of “predictive processing”. All we currently have is a semantic cluster, with perhaps some overlapping sets of jointly sufficient criteria. The framework is still developing, and it is difficult, maybe impossible, to provide theory-neutral explanations of all PP ideas without already introducing strong background assumptions. (shrink)

This three-part paper presents Gordon Pask’s conversation theory (CT) and interaction of actors theory (IA) and outlines ways to apply these cybernetic approaches to designing technologies and scenarios for both formal and informal learning. The first part of the paper covers concepts central to CT and IA, explaining the relationship between conceptual and mechanical operators, and machines mediating informal and formal learning. The second part of the paper applies visual representations of CT and IA to understanding the use of Pask’s (...) course assembly systems (CASTE and THOUGHTSTICKER), created between the late 1960s and the 1980s, and the ThoughtShuffler search interface, created in the 2010s. The third part proposes two pathways for design based on CT and IA: firstly, the potential for designers and observers to reformulate the qualities of tools and learning scenarios to augment human thinking and collective action; and secondly, the possibility to create tools with malleable interfaces that allow users to become intermediaries rather than consumers of knowledge. (shrink)

There are three theories in the epistemology of modality that have received sustained attention over the past 20 years: conceivability-theory, counterfactual-theory, and deduction-theory. In this paper we argue that all three face what we call the problem of modal epistemic friction. One consequence of the problem is that for any of the three accounts to yield modal knowledge, the account must provide an epistemology of essence. We discuss an attempt to fend off the problem within the context of the internalism (...) versus externalism debate about epistemic justification. We then investigate the effects that the PMEF has on reductive and non-reductive theories of the relation between essence and modality. (shrink)

A central tenet of medical ethics holds that it is permissible to perform a medical intervention on a competent individual only if that individual has given informed consent to the intervention. However, in some circumstances it is tempting to say that the moral reason to obtain informed consent prior to administering a medical intervention is outweighed. For example, if an individual’s refusal to undergo a medical intervention would lead to the transmission of a dangerous infectious disease to other members of (...) the community, one might claim that it would be morally permissible to administer the intervention even in the absence of consent. Indeed, as we shall discuss below, there are a number of examples of public health authorities implementing compulsory or coercive measures for the purposes of infectious disease control (IDC). The plausibility of the thought that non-consensual medical interventions might be justified when performed for the purpose of IDC raises the question of whether such interventions might permissibly be used to realize other public goods. In this article we focus on one possibility: whether it could be permissible to non-consensually impose certain interventions that alter brain states or processes through chemical or physical means on serious criminal offenders. We shall suggest that some such interventions might be permissible if they safely and effectively serve to facilitate the offender’s rehabilitation and thereby prevent criminal recidivism. (shrink)

In a paper recently published in this journal, Navin and Largent argue in favour of a type of policy to regulate non-medical exemptions from childhood vaccination which they call ‘Inconvenience’. This policy makes it burdensome for parents to obtain an exemption to child vaccination, for example, by requiring parents to attend immunization education sessions and to complete an application form to receive a waiver. Navin and Largent argue that this policy is preferable to ‘Eliminationism’, i.e. to policies that do not (...) allow non-medical exemptions, because Inconvenience has been shown to maintain exemption rates low while not harming parents by forcing them to do something that goes against their beliefs. We argue that it is at least doubtful that Inconvenience is ethically preferable to Eliminationism: while the latter disregards the value of liberty, Inconvenience disregards the value of fairness in the distribution of the burdens entailed by the preservation of a public good like herd immunity. We propose a variant of Inconvenience, which we call ‘Contribution’, which we think is preferable to the versions of Inconvenience discussed by Navin and Largent in that it successfully strikes a balance between the values of parents’ liberty, fairness and expected utility. (shrink)

We provide conditions under which an incomplete strongly independent preorder on a convex set X can be represented by a set of mixture preserving real-valued functions. We allow X to be infi nite dimensional. The main continuity condition we focus on is mixture continuity. This is sufficient for such a representation provided X has countable dimension or satisfi es a condition that we call Polarization.

Reproductive genetic technologies allow parents to decide whether their future children will have or lack certain genetic predispositions. A popular model that has been proposed for regulating access to RGTs is the ‘genetic supermarket’. In the genetic supermarket, parents are free to make decisions about which genes to select for their children with little state interference. One possible consequence of the genetic supermarket is that collective action problems will arise: if rational individuals use the genetic supermarket in isolation from one (...) another, this may have a negative effect on society as a whole, including future generations. In this article we argue that RGTs targeting height, innate immunity, and certain cognitive traits could lead to collective action problems. We then discuss whether this risk could in principle justify state intervention in the genetic supermarket. We argue that there is a plausible prima facie case for the view that such state intervention would be justified and respond to a number of arguments that might be adduced against that view. (shrink)

In this article we survey Ásta’s (2008, 2013) conferralist account of essence, which provides a broadly anti-realist picture of essence. We first offer some thoughts on the difference between realist and anti-realist accounts of essence in general. Then we present Ásta’s notion of a conferred property and sketch her conferralist account of essence. Finally, we examine some critical questions conferralism faces.

The Unified Medical Language System and the Gene Ontology are among the most widely used terminology resources in the biomedical domain. However, when we evaluate them in the light of simple principles for wellconstructed ontologies we find a number of characteristic inadequacies. Employing the theory of granular partitions, a new approach to the understanding of ontologies and of the relationships ontologies bear to instances in reality, we provide an application of this theory in relation to an example drawn from the (...) context of the pathophysiology of hypertension. This exercise is designed to demonstrate how, by taking ontological principles into account we can create more realistic biomedical ontologies which will also bring advantages in terms of efficiency and robustness of associated software applications. (shrink)

The National Cancer Institute’s Thesaurus (NCIT) has been created with the goal of providing a controlled vocabulary which can be used by specialists in the various sub-domains of oncology. It is intended to be used for purposes of annotation in ways designed to ensure the integration of data and information deriving from these various sub-domains, and thus to support more powerful cross-domain inferences. In order to evaluate its suitability for this purpose, we examined the NCIT’s treatment of the kinds of (...) entities which are fundamental to an ontology of colon carcinoma. We here describe the problems we uncovered concerning classification, synonymy, relations and definitions, and we draw conclusions for the work needed to establish the NCIT as a reference ontology for the cancer domain in the future. (shrink)

An explicit formal-ontological representation of entities existing at multiple levels of granularity is an urgent requirement for biomedical information processing. We discuss some fundamental principles which can form a basis for such a representation. We also comment on some of the implicit treatments of granularity in currently available ontologies and terminologies (GO, FMA, SNOMED CT).

I discuss here the definition of computer simulations, and more specifically the views of Humphreys, who considers that an object is simulated when a computer provides a solution to a computational model, which in turn represents the object of interest. I argue that Humphreys's concepts are not able to analyse fully successfully a case of contemporary simulation in physics, which is more complex than the examples considered so far in the philosophical literature. I therefore modify Humphreys's definition of simulation. I (...) allow for several successive layers of computational models, and I discuss the relations that exist between these models, the computer, and the object under study. An aim of my proposal is to clarify the distinction between computational models and numerical methods, and to better understand the representational and the computational functions of models in simulations. (shrink)

All accepted proofs of the Four Colour Theorem (4CT) are computer-dependent; and appeal to the existence, and manual identification, of an ‘unavoidable’ set containing a sufficient number of explicitly defined configurations—each evidenced only by a computer as ‘reducible’—such that at least one of the configurations must occur in any chromatically distinguished, minimal, planar map. For instance, Appel and Haken ‘identified’ 1,482 such configurations in their 1977, computer-dependent, proof of 4CT; whilst Neil Robertson et al ‘identified’ 633 configurations as sufficient in (...) their 1997, also computer-dependent, proof of 4CT. However, treating any specific number of ‘reducible’ configurations in an ‘unavoidable’ set as sufficient entails a minimum number as necessary and sufficient. We now show that the minimum number of such configurations can only be the one corresponding to the ‘unavoidable’ set of a ‘reducible’, 4-sided configuration identified by Alfred Kempe in his, seemingly fatally flawed, 1879 ‘proof’ of 4CT. Although Kempe appealed to putative properties of ‘Kempe’ chains in a graphical representation to fallaciously argue that a 5-sided configuration was also in the ‘unavoidable’ set, and ‘reducible’, we shall show why the flaw in his ‘proof’ is not fatal when the argument is expressed geometrically; and that, essentially, Kempe correctly argued that any planar map which admits a chromatic differentiation with a five-sided area C that shares non-zero boundaries with four, all differently coloured, neighbours can be 4-coloured. (shrink)

that can serve as a foundation for more refined ontologies in the field of proteomics. Standard data sources classify proteins in terms of just one or two specific aspects. Thus SCOP (Structural Classification of Proteins) is described as classifying proteins on the basis of structural features; SWISSPROT annotates proteins on the basis of their structure and of parameters like post-translational modifications. Such data sources are connected to each other by pairwise term-to-term mappings. However, there are obstacles which stand in the (...) way of combining them together to form a robust meta-classification of the needed sort. We discuss some formal ontological principles which should be taken into account within the existing datasources in order to make such a metaclassification possible, taking into account also the Gene Ontology (GO) and its application to the annotation of proteins. (shrink)

The hard problem of consciousness arises in most incarnations of present day physicalism. Why should certain physical processes necessarily be accompanied by experience? One possible response is that physicalism itself should be modified in order to accommodate experience: But, modified how? In the present work, we investigate whether an ontology derived from quantum field theory can help resolve the hard problem. We begin with the assumption that experience cannot exist without being accompanied by a subject of experience (SoE). While people (...) well versed in Indian philosophy will not find that statement problematic, it is still controversial in the analytic tradition. Luckily for us, Strawson has elaborately defended the notion of a thin subject—an SoE which exhibits a phenomenal unity with different types of content (sensations, thoughts etc.) occurring during its temporal existence. Next, following Stoljar, we invoke our ignorance of the true physical as the reason for the explanatory gap between present day physical processes (events, properties) and experience. We are therefore permitted to conceive of thin subjects as related to the physical via a new, yet to be elaborated relation. While this is difficult to conceive under most varieties of classical physics, we argue that this may not be the case under certain quantum field theory ontologies. We suggest that the relation binding an SoE to the physical is akin to the relation between a particle and (quantum) field. In quantum field theory, a particle is conceived as a coherent excitation of a field. Under the right set of circumstances, a particle coalesces out of a field and dissipates. We suggest that an SoE can be conceived as akin to a particle—a SelfOn—which coalesces out of physical fields, persists for a brief period of time and then dissipates in a manner similar to the phenomenology of a thin subject. Experiences are physical properties of selfons with the constraint (specified by a similarity metric) that selfons belonging to the same natural kind will have similar experiences. While it is odd at first glance to conceive of subjects of experience as akin to particles, the spatial and temporal unity exhibited by particles as opposed to fields and the expectation that selfons are new kinds of particles, paves the way for cementing this notion. Next, we detail the various no-go theorems in most versions of quantum field theory and discuss their impact on the existence of selfons. Finally, we argue that the time is ripe for a rejuvenated Indian philosophy to begin tackling the three-way relationship between SoEs (which may become equivalent to jivas in certain Indian frameworks), phenomenal content and the physical world. With analytic philosophy still struggling to come to terms with the complex worlds of quantum field theory and with the relative inexperience of the western world in arguing the jiva-world relation, there is a clear and present opportunity for Indian philosophy to make a worldcentric contribution to the hard problem of experience. (shrink)

Evidence-based medicine relies on the execution of clinical practice guidelines and protocols. A great deal of of effort has been invested in the development of various tools which automate the representation and execution of the recommendations contained within such guidelines and protocols by creating Computer Interpretable Guideline Models (CIGMs). Context-based task ontologies (CTOs), based on standard terminology systems like UMLS, form one of the core components of such a model. We have created DAML+OIL-based CTOs for the tasks mentioned in the (...) WHO guideline for hypertension management, drawing comparisons also with other related guidelines. The advantages of CTOs include: contextualization of ontologies, providing ontologies tailored to specific aspects of the phenomena of interest, dividing the complexity involved in creating ontologies into different levels, providing a methodology by means of which the task recommendations contained within guidelines can be integrated into the clinical practices of a health care set-up. (shrink)

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

The International Classification of Functioning, Disability and Health provides a classification of human bodily functions, which, while exhibiting non-conformance to many formal ontological principles, provides an insight into which basic functions such a classification should include. Its evaluation is an important first step towards such an adequate ontology of this domain. Presented at the 13th Annual North American WHO Collaborating Center Conference on the ICF, 2007.

In the first part of this investigation we highlight two, seemingly irreconcilable, beliefs that suggest an impending crisis in the teaching, research, and practice of—primarily state-supported—mathematics: (a) the belief, with increasing, essentially faith-based, conviction and authority amongst academics that first-order Set Theory can be treated as the lingua franca of mathematics, since its theorems—even if unfalsifiable—can be treated as ‘knowledge’ because they are finite proof sequences which are entailed finitarily by self-evidently Justified True Beliefs; and (b) the slowly emerging, but (...) powerfully rooted in economic imperatives, belief that only those Justified True Beliefs can be treated as ‘knowledge’ which are, further, categorically communicable as Factually Grounded Beliefs—hence as comprehensible pre-formal ‘mathematical truths’—by any intelligence that lays claims to a mathematical lingua franca. We argue that this seeming irreconcilability merely reflects a widening chasm between an increasing under-estimation of the value to society of ‘semantic arithmetical truth’, and an increasing over-estimation of the value to society of ‘syntactic set-theoretical provability’; a chasm which must be narrowed and bridged explicitly. We thus proffer a Complementarity Thesis which seeks to recognize that mathematical ‘provability’ and mathematical ‘truth’ need to be interdependent and complementary, ‘evidence-based’, assignments-by-convention to the formulas of a formal mathematical language; where (a) the goal of mathematical ‘proofs’ may be viewed as seeking to ensure that any mathematical language intended to formally represent our pre-formal conceptual metaphors and their inter-relatedness is unambiguous, and free from contradiction; whilst (b) the goal of mathematical ‘truths’ must be viewed as seeking to ensure that any such representation does, indeed, uniquely identify and adequately represent such metaphors and their inter-relatedness. Our thesis is that, by universally ignoring the need to introduce goal (b) in our curriculum, the teaching of, and research in, mathematics at the post-graduate level cannnot justify its value to society beyond the mere intellectual stimulation of individual minds. In the second part we appeal to some recent—and hitherto unsuspected—unarguably constructive Tarskian interpretations, of the first-order Peano Arithmetic PA, which establish PA as both finitarily consistent, and categorical. Since we also show that the second order subsystem ACA0 of Peano Arithmetic and PA cannot both be assumed provably consistent, we conclude that there can be no mathematical, or meta-mathematical, proof of consistency for Set Theory. Hence the theorems of any Set Theory are not sufficient for distinguishing between (i) what we can believe to be a ‘mathematical truth’; (ii) what we can evidence as a ‘mathematical truth’; and (iii) what we ought not to believe is a ‘mathematical truth’; whilst the theorems of the first-order Peano Arithmetic PA are sufficient for distinguishing between (i), (ii) and (iii). We conclude from this that the holy grail of mathematics ought to be ‘arithmetical truth’, not ‘set-theoretical proof’. (shrink)

Voting Advice Applications (VAAs) are interactive online tools designed to assist voters by improving the basis on which they decide how to vote. In recent years, they have been widely adopted, but their design is the subject of ongoing and often heated criticism. Most of these debates focus on whether VAAs accurately measure the standpoints of political parties and the preferences of users and on whether they report valid results while avoiding political bias. It is generally assumed that if their (...) methodology is sound, then VAAs can be seen as strengthening the democratic process. But as we argue in this chapter, the setup of VAAs raises basic questions of normative democratic theory as well. Insofar as VAAs are supposed to improve the functioning of the democratic process, it must be clarified in what sense they aim to make a contribution, before it even makes sense to discuss their effectiveness at doing so. -/- VAAs are often intended to enhance the democratic process by one or all of the following: (I) informing voters about the policy standpoints of political parties (or individual candidates), (2) increasing voter turnout, and (3) ensuring that the composition of parliaments more accurately reflects the political attitudes of the electorate. In the next three sections, we discuss three central bones of contention in current democratic theory that are crucial to these ways in which VAAs typically take themselves to contribute to strengthening the democratic process: -/- 1. Questions about citizen competence: What forms of competence do citizens need to have, and to what extent, for a democracy to function properly? -/- 2. Questions about political participation: What forms and extent of participation are vital to democracy? -/- 3. Questions about democratic representation: How should the relation between the elected and the electorate be understood? -/- For each issue we aim to show, first, how the design and setup of mainstream VAAs are tacitly structured by a specific conception of the democratic aim at issue and, second, what some alternative positions on these questions are within contemporary political theory. In the final section, we will discuss some of the implications of this analysis for the responsibilities of VAA developers, and particularly for the procedural neutrality to which they are typically committed. Our conclusion will be that once these issues are identified, developers of VAAs should either argue in favour of their views on democratic competence, participation and representation, or they should rethink the design of VA As in ways that move beyond their current assumptions, or both. (shrink)

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

We provide a methodology for the creation of ontological partitions in biomedicine and we test the methodology via an application to the phenomenon of blood pressure. An ontology of blood pressure must do justice to the complex networks of intersecting pathways in the organism by which blood pressure is regulated. To this end it must deal not only with the anatomical structures and physiological processes involved in such regulation but also with the relations between these at different levels of granularity. (...) For this purpose our ontology offers a variety of distinct partitions � of substances, processes and functions � and integrates these together within a single framework via transitive networks of part-whole and dependence relations among the entities in each of these categories. The paper concludes with a comparison of this methodology with the approaches of GOTM, KEGG, DIP and BIND and provides an outline of how the methodology is currently being applied in the field of biomedical database integration. (shrink)

Clinical guidelines are special types of plans realized by collective agents. We provide an ontological theory of such plans that is designed to support the construction of a framework in which guideline-based information systems can be employed in the management of workflow in health care organizations. The framework we propose allows us to represent in formal terms how clinical guidelines are realized through the actions of are realized through the actions of individuals organized into teams. We provide various levels of (...) implementation representing different levels of conformity on the part of health care organizations. Implementations built in conformity with our framework are marked by two dimensions of flexibility that are designed to make them more likely to be accepted by health care professionals than standard guideline-based management systems. They do justice to the fact 1) that responsibilities within a health care organization are widely shared, and 2) that health care professionals may on different occasions be non-compliant with guidelines for a variety of well justified reasons. The advantage of the framework lies in its built-in flexibility, its sensitivity to clinical context, and its ability to use inference tools based on a robust ontology. One disadvantage lies in its complicated implementation. (shrink)

The theory of granular partitions (TGP) is a new approach to the understanding of ontologies and other classificatory systems. The paper explores the use of this new theory in the treatment of task-based clinical guidelines as a means for better understanding the relations between different clinical tasks, both within the framework of a single guideline and between related guidelines. We used as our starting point a DAML+OIL-based ontology for the WHO guideline for hypertension management, comparing this with related guidelines and (...) attempting to show that TGP provides a flexible and highly expressive basis for the manipulation of ontologies of a sort which might be useful in providing more adequate Computer Interpretable Guideline Models (CIGMs) in the future. (shrink)

The paper presents the outlines of an ontology of plans and guidelines, which is then used as the basis for a framework for implementing guideline-based systems for the management of workflow in health care organizations. The framework has a number of special features, above all in that it enables us to represent in formal terms assignments of work-items both to individuals and to teams and to tailor guideline to specific contexts of application in health care organizations. It is designed also (...) to enable implementations to do justice to the fact that the processes carried out in health care organizations may deviate in different ways from the norms set forth in corresponding guideline definitions. This means that implementations built in conformity with the framework will be marked by a type of flexibility that might make them more likely to be accepted by healthcare professionals than are standard guideline-based management systems. (shrink)

Human Aspiration is the first chapter of the magnum opus book "Life Divine". Here in in this chapter Sri Aurobindo one of the most modern prolific philosophers of Renaissance India has highlighted his focal points as to what Man's eternal aspiration has been, that is, God, Light , Freedom & Eternity. Despite technological and scientific advancements, Mans is still thirsty, it is because he aspires for a Divine Life. The article talks about the "Human aspiration" of eternity in details.

The Gene Ontology is an important tool for the representation and processing of information about gene products and functions. It provides controlled vocabularies for the designations of cellular components, molecular functions, and biological processes used in the annotation of genes and gene products. These constitute three separate ontologies, of cellular components), molecular functions and biological processes, respectively. The question we address here is: how are the terms in these three separate ontologies related to each other? We use statistical methods and (...) formal ontological principles as a first step towards finding answers to this question. (shrink)

Recent work on the quality assurance of the Gene Ontology (GO, Gene Ontology Consortium 2004) from the perspective of both linguistic and ontological organization has made it clear that GO lacks the kind of formalism needed to support logic-based reasoning. At the same time it is no less clear that GO has proven itself to be an excellent terminological resource that can serve to combine together a variety of biomedical database and information systems. Given the strengths of GO, it is (...) worth investigating whether, by overcoming some of its weaknesses from the point of view of formal-ontological principles, we might not be able to enhance a version of GO which can come even closer to serving the needs of the various communities of biomedical researchers and practitioners. It is accepted that clinical and bioinformatics need to find common ground if the results of data-intensive biomedical research are to be harvested to the full. It is also widely accepted that no single method will be sufficient to create the needed common framework. We believe that the principles-based approach to life-science data integration and knowledge representation must be one of the methods applied. Indeed in dealing with the ontological representation of carcinomas, and specifically of colon carcinomas, we have established that, had GO (and related biomedical ontologies) followed some of the basic formal-ontological principles we have identified (Smith et al. 2004, Ceusters et al. 2004), then the effort required to navigate successfully between clinical and bioinformatics systems would have been reduced. We point here to the sources of ontologically-related errors in GO, and also provide arguments as to why and how such errors need to be resolved. (shrink)

It is widely understood that protein functions can be exhaustively described in terms of no single parameter, whether this be amino acid sequence or the three-dimensional structure of the underlying protein molecule. This means that a number of different attributes must be used to create an ontology of protein functions. Certainly much of the required information is already stored in databases such as Swiss-Prot, Protein Data Bank, SCOP and MIPS. But the latter have been developed for different purposes and the (...) separate data-structures which they employ are not conducive to the needed data integration. When we attempt to classify the entities in the domain of proteins, we find ourselves faced with a number of cross-cutting principles of classification. Our question here is: how can we bring together these separate taxonomies in order to describe protein functions? Our proposed answer is: via a careful top-level ontological analysis of the relevant principles of classification, combined with a new framework for the simultaneous manipulation of classifications constructed for different purposes. (shrink)

(Report assembled for the Workshop of the AMIA Working Group on Formal Biomedical Knowledge Representation in connection with AMIA Symposium, Washington DC, 2005.) Best practices in ontology building for biomedicine have been frequently discussed in recent years. However there is a range of seemingly disparate views represented by experts in the field. These views not only reflect the different uses to which ontologies are put, but also the experiences and disciplinary background of these experts themselves. We asked six questions related (...) to biomedical ontologies to what we believe is a representative sample of ontologists in the biomedical field and came to a number conclusions which we believe can help provide an insight into the practical problems which ontology builders face today. (shrink)

Recently, Kit Fine's (1994) view that modal truths aretrue in virtue of,grounded in, orexplained byessentialist truths has been under attack. In what follows we offer two responses to the wave of criticism against his view. While the first response is pretty straightforward, the second is based on the distinction between, what we call,Reductive Finean EssentialismandNon-Reductive Finean Essentialism. Engaging the work of Bob Hale onNon-Reductive Finean Essentialism, we aim to show that the arguments against Fine's view are unconvincing, while we acknowledge (...) the presence of a deep standoff between the two views. (shrink)

An important part of the Unified Medical Language System (UMLS) is its Semantic Network, consisting of 134 Semantic Types connected to each other by edges formed by one or more of 54 distinct Relation Types. This Network is however for many purposes overcomplex, and various groups have thus made attempts at simplification. Here we take this work further by simplifying the relations which involve the three Semantic Types – Diagnostic Procedure, Laboratory Procedure and Therapeutic or Preventive Procedure. We define operators (...) which can be used to generate terms instantiating types from this selected set when applied to terms designating certain other Semantic Types, including almost all the terms specifying clinical tasks. Usage of such operators thus provides a useful and economical way of specifying clinical tasks. The operators allow us to define a mapping between those types within the UMLS which do not represent clinical tasks and those which do. This mapping then provides a basis for an ontology of clinical tasks that can be used in the formulation of computer-interpretable clinical guideline models. (shrink)

The paper presents the outlines of an ontology of plans and guidelines, which is then used as the basis for a framework for implementing guideline-based systems for the management of workflow in health care organizations. The framework has a number of special features, above all in that it enables us to represent in formal terms assignments of work-items both to individuals and to teams and to tailor guideline to specific contexts of application in health care organizations. It is designed also (...) to enable implementations to do justice to the fact that the processes carried out in health care organizations may deviate in different ways from the norms set forth in corresponding guideline definitions. This means that implementations built in conformity with the framework will be marked by a type of flexibility that might make them more likely to be accepted by healthcare professionals than are standard guideline-based management systems. (shrink)

Outcomes research in healthcare has been a topic much addressed in recent years. Efforts in this direction have been supplemented by work in the areas of guidelines for clinical practice and computer-interpretable workflow and careflow models.In what follows we present the outlines of a framework for understanding the relations between organizations, guidelines, individual patients and patient-related functions. The derived framework provides a means to extract the knowledge contained in the guideline text at different granularities, in ways that can help us (...) to assign tasks within the healthcare organization and to assess clinical performance in realizing the guideline. It does this in a way that preserves the flexibility of the organization in the adoption of the guidelines. (shrink)

All acknowledged proofs of the Four Colour Theorem (4CT) are computerdependent. They appeal to the existence, and manual identification, of an ‘unavoidable’ set containing a sufficient number of explicitly defined configurations—each evidenced only by a computer as ‘reducible’—such that at least one of the configurations must occur in any chromatically distinguished, putatively minimal, planar map. For instance, Appel and Haken ‘identified’ 1,482 such configurations in their 1977, computer-dependent, proof of 4CT; whilst Neil Robertson et al ‘identified’ 633 configurations as sufficient (...) in their 1997, also computer-dependent, proof of 4CT. However, treating any specific number of ‘reducible’ configurations in an ‘unavoidable’ set as sufficient entails a minimum number as necessary and sufficient. We now show that the minimum number of such configurations can only be the one corresponding to the ‘unavoidable’ set of the single, ‘reducible’, 4-sided configuration identified by Alfred Kempe in his, seemingly fatally flawed, 1879 ‘proof’ of 4CT. We shall further show that although Kempe fallaciously concluded that a 5-sided configuration was also in the ‘unavoidable’ set, and appealed to unproven properties of ‘Kempe’ chains in a graphical representation to then argue for its ‘reducibility’, neither flaw in his ‘proof’ is fatal when the argument is expressed geometrically; and that, essentially, Kempe correctly argued that any planar map which admits a chromatic differentiation with a five-sided area C that shares non-zero boundaries with four, all differently coloured, neighbours can be 4-coloured. (shrink)

This chapter has two main goals: to update philosophers on the state of the art in the scientific psychology of intelligence, and to explain and evaluate challenges to the measurement invariance of intelligence tests. First, we provide a brief history of the scientific psychology of intelligence. Next, we discuss the metaphysics of intelligence in light of scientific studies in psychology and neuroimaging. Finally, we turn to recent skeptical developments related to measurement invariance. These have largely focused on attributability: Where do (...) the mechanisms and dispositions that explain people’s performance on tests of intelligence inhere – in the agent, in the local testing environment, in the culture, or in the interactions among these? After explaining what measurement invariance is in the context of intelligence testing, we explore the phenomenon of stereotype threat as a challenge to measurement invariance, as well as more recent work on overcoming or buffering against stereotype threat. (shrink)

Author: Thomas Sören Hoffmann. Translated by Pedro Sepúlveda Zambrano.

In this multi-disciplinary investigation we show how an evidence-based perspective of quantification---in terms of algorithmic verifiability and algorithmic computability---admits evidence-based definitions of well-definedness and effective computability, which yield two unarguably constructive interpretations of the first-order Peano Arithmetic PA---over the structure N of the natural numbers---that are complementary, not contradictory. The first yields the weak, standard, interpretation of PA over N, which is well-defined with respect to assignments of algorithmically verifiable Tarskian truth values to the formulas of PA under the interpretation. (...) The second yields a strong, finitary, interpretation of PA over N, which is well-defined with respect to assignments of algorithmically computable Tarskian truth values to the formulas of PA under the interpretation. We situate our investigation within a broad analysis of quantification vis a vis: * Hilbert's epsilon-calculus * Goedel's omega-consistency * The Law of the Excluded Middle * Hilbert's omega-Rule * An Algorithmic omega-Rule * Gentzen's Rule of Infinite Induction * Rosser's Rule C * Markov's Principle * The Church-Turing Thesis * Aristotle's particularisation * Wittgenstein's perspective of constructive mathematics * An evidence-based perspective of quantification. By showing how these are formally inter-related, we highlight the fragility of both the persisting, theistic, classical/Platonic interpretation of quantification grounded in Hilbert's epsilon-calculus; and the persisting, atheistic, constructive/Intuitionistic interpretation of quantification rooted in Brouwer's belief that the Law of the Excluded Middle is non-finitary. We then consider some consequences for mathematics, mathematics education, philosophy, and the natural sciences, of an agnostic, evidence-based, finitary interpretation of quantification that challenges classical paradigms in all these disciplines. (shrink)

Conventional wisdom dictates that proofs of mathematical propositions should be treated as necessary, and sufficient, for entailing `significant' mathematical truths only if the proofs are expressed in a---minimally, deemed consistent---formal mathematical theory in terms of: * Axioms/Axiom schemas * Rules of Deduction * Definitions * Lemmas * Theorems * Corollaries. Whilst Andrew Wiles' proof of Fermat's Last Theorem FLT, which appeals essentially to geometrical properties of real and complex numbers, can be treated as meeting this criteria, it nevertheless leaves two (...) questions unanswered: (i) Why is x^n +y^n = z^n solvable only for n < 3 if x, y, z, n are natural numbers? (ii) What technique might Fermat have used that led him to, even if only briefly, believe he had `a truly marvellous demonstration' of FLT? Prevailing post-Wiles wisdom---leaving (i) essentially unaddressed---dismisses Fermat's claim as a conjecture without a plausible proof of FLT. -/- However, we posit that providing evidence-based answers to both queries is necessary not only for treating FLT as significant, but also for understanding why FLT can be treated as a true arithmetical proposition. We thus argue that proving a theorem formally from explicit, and implicit, premises/axioms using rules of deduction---as currently accepted---is a meaningless game, of little scientific value, in the absence of evidence that has already established---unambiguously---why the premises/axioms and rules of deduction can be treated, and categorically communicated, as pre-formal truths in Marcus Pantsar's sense. Consequently, only evidence-based, pre-formal, truth can entail formal provability; and the formal proof of any significant mathematical theorem cannot entail its pre-formal truth as evidence-based. It can only identify the explicit/implicit premises that have been used to evidence the, already established, pre-formal truth of a mathematical proposition. Hence visualising and understanding the evidence-based, pre-formal, truth of a mathematical proposition is the only raison d'etre for subsequently seeking a formal proof of the proposition within a formal mathematical language (whether first-order or second order set theory, arithmetic, geometry, etc.) By this yardstick Andrew Wiles' proof of FLT fails to meet the required, evidence-based, criteria for entailing a true arithmetical proposition. -/- Moreover, we offer two scenarios as to why/how Fermat could have laconically concluded in his recorded marginal noting that FLT is a true arithmetical proposition---even though he either did not (or could not to his own satisfaction) succeed in cogently evidencing, and recording, why FLT can be treated as an evidence-based, pre-formal, arithmetical truth (presumably without appeal to properties of real and complex numbers). It is primarily such a putative, unrecorded, evidence-based reasoning underlying Fermat's laconic assertion which this investigation seeks to reconstruct; and to justify by appeal to a plausible resolution of some philosophical ambiguities concerning the relation between evidence-based, pre-formal, truth and formal provability. (shrink)

We consider the argument that Tarski's classic definitions permit an intelligence---whether human or mechanistic---to admit finitary evidence-based definitions of the satisfaction and truth of the atomic formulas of the first-order Peano Arithmetic PA over the domain N of the natural numbers in two, hitherto unsuspected and essentially different, ways: (1) in terms of classical algorithmic verifiabilty; and (2) in terms of finitary algorithmic computability. We then show that the two definitions correspond to two distinctly different assignments of satisfaction and truth (...) to the compound formulas of PA over N---I_PA(N; SV ) and I_PA(N; SC). We further show that the PA axioms are true over N, and that the PA rules of inference preserve truth over N, under both I_PA(N; SV ) and I_PA(N; SC). We then show: (a) that if we assume the satisfaction and truth of the compound formulas of PA are always non-finitarily decidable under I_PA(N; SV ), then this assignment corresponds to the classical non-finitary putative standard interpretation I_PA(N; S) of PA over the domain N; and (b) that the satisfaction and truth of the compound formulas of PA are always finitarily decidable under the assignment I_PA(N; SC), from which we may finitarily conclude that PA is consistent. We further conclude that the appropriate inference to be drawn from Goedel's 1931 paper on undecidable arithmetical propositions is that we can define PA formulas which---under interpretation---are algorithmically verifiable as always true over N, but not algorithmically computable as always true over N. We conclude from this that Lucas' Goedelian argument is validated if the assignment I_PA(N; SV ) can be treated as circumscribing the ambit of human reasoning about `true' arithmetical propositions, and the assignment I_PA(N; SC) as circumscribing the ambit of mechanistic reasoning about `true' arithmetical propositions. (shrink)

Andrew Wiles' analytic proof of Fermat's Last Theorem FLT, which appeals to geometrical properties of real and complex numbers, leaves two questions unanswered: (i) What technique might Fermat have used that led him to, even if only briefly, believe he had `a truly marvellous demonstration' of FLT? (ii) Why is x^n+y^n=z^n solvable only for n<3? In this inter-disciplinary perspective, we offer insight into, and answers to, both queries; yielding a pre-formal proof of why FLT can be treated as a true (...) arithmetical proposition (one which, moreover, might not be provable formally in the first-order Peano Arithmetic PA), where we admit only elementary (i.e., number-theoretic) reasoning, without appeal to analytic properties of real and complex numbers. We cogently argue, further, that any formal proof of FLT needs---as is implicitly suggested by Wiles' proof---to appeal essentially to formal geometrical properties of formal arithmetical propositions. (shrink)

Good old-fashioned cognitive science characterizes human thinking as symbol manipulation qua computation and therefore emphasizes the processing of symbolic representations as a necessary if not sufficient condition for “general intelligent action.” Recent alternative conceptions of human thinking tend to deemphasize if not altogether eschew the notion of representation. The present paper shows how classical American pragmatist conceptions of human thinking can successfully avoid either of these extremes, replacing old-fashioned conceptions of representation with one that characterizes both representatum and representans in (...) externalist terms. (shrink)

Although the Four Colour Theorem is passe, we give an elementary pre-formal proof that transparently illustrates why four colours suffice to chromatically differentiate any set of contiguous, simply connected and bounded, planar spaces; by showing that there is no minimal 4-coloured planar map M. We note that such a pre-formal proof of the Four Colour Theorem highlights the significance of differentiating between: (a) Plato's knowledge as justified true belief, which seeks a formal proof in a first-order mathematical language in order (...) to justify a belief as true; and (b) Piccinini's knowledge as factually grounded belief, which seeks a pre-formal proof, in Pantsar's sense, in order to justify the axioms and rules of inference of a first-order mathematical language which can, then, formally prove the belief as justifiably true under a well-defined interpretation of the language. (shrink)