(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)

According to many philosophers, the world should embrace open borders – that is, let people move around the globe and settle as they wish, with exceptions made only in very specific cases such as fugitives or terrorists. Defenders of open borders have adopted two major argumentative strategies. The first is to claim that immigration restrictions involve coercion, and then show that such coercion cannot be morally justified. The second is to argue that adopting worldwide open borders policies would make the (...) world a much better place, particularly by improving average well-being. This essay contends that both of these argumentative strategies fail. Some immigration restrictions are not only morally justified, but morally required. (shrink)

In philosophical work on the ethics of conversational exchange, much has been written regarding the speaker side—i.e., on the rights and duties we have as speakers. This paper explores the relatively neglected topic of the duties pertaining to listeners’ side of the exchange. Following W.K. Clifford, we argue that it’s fruitful to think of our epistemic resources as common property. Furthermore, listeners have a key role in maintaining and improving these resources, perhaps a more important role than speakers. We develop (...) this idea by drawing from Hugo Mercier and Dan Sperber’s “interactionist” picture of reason, which suggests that reasoning is essentially dialogical and relies on the epistemic vigilance of listeners. The paper defends an imperfect, prima facie duty to listen, one that is sufficiently strong to place substantial demands on individuals, but not so overly demanding as to be implausible. (shrink)

Political protests, debates on college campuses, and social media tirades make it seem like everyone is speaking their minds today. Surveys, however, reveal that many people increasingly feel like they're walking on eggshells when communicating in public. Speaking your mind can risk relationships and professional opportunities. It can alienate friends and anger colleagues. Isn't it smarter to just put your head down and keep quiet about controversial topics? In this book, Hrishikesh Joshi offers a novel defense of speaking your (...) mind. He explains that because we are social creatures, we never truly think alone. What we know depends on what our community knows. And by bringing our unique perspectives to bear upon public discourse, we enhance our collective ability to reach the truth on a variety of important matters. Speaking your mind is also important for your own sake. It is essential for developing your own thinking. And it's a core aspect of being intellectually courageous and independent. Joshi argues that such independence is a crucial part of a well-lived life. The book draws from Aristotle, John Stuart Mill, Friedrich Nietzsche, Bertrand Russell, and a range of contemporary thinkers to argue that it's OK to speak your mind. Key Features Shows that we have not just a right but a moral duty to publicly share what we know. Argues that discussing your unique ideas with others is essential for developing as a critical thinker. Explores the value of intellectual honesty and independence in the writings of John Stuart Mill and Friedrich Nietzsche and connects their thinking to contemporary problems. Argues that avoiding cultural blind spots today is important for the fate of future generations. (shrink)

This paper argues for the existence of a certain type of defeater for one’s belief that P—the presence of social incentives not to share evidence against P. Such pressure makes it relatively likely that there is unpossessed evidence that would provide defeaters for P because it makes it likely that the evidence we have is a lopsided subset. This offers, I suggest, a rational reconstruction of a core strand of argument in Mill’s On Liberty. A consequence of the argument is (...) that on morally and politically laden issues in particular, a high degree of doxastic openness might be appropriate. (shrink)

Censorship involves, inter alia, adopting a certain type of epistemic policy. While much has been written on the harms and benefits of free expression, and the associated rights thereof, the epistemic preconditions of justified censorship are relatively underexplored. In this paper, I argue that examining intrapersonal norms of how we ought to treat evidence that might come to us over time can shed light on interpersonal norms of evidence generation and sharing that are relevant in the context of censorship. The (...) upshot is that justified censorship requires the censor to meet a very high epistemic burden regarding the target proposition(s)—importantly, one that exceeds knowledge. (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.

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)

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).

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)

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)

The integration of biomedical terminologies is indispensable to the process of information integration. When terminologies are linked merely through the alignment of their leaf terms, however, differences in context and ontological structure are ignored. Making use of the SNAP and SPAN ontologies, we show how three reference domain ontologies can be integrated at a higher level, through what we shall call the OBR framework (for: Ontology of Biomedical Reality). OBR is designed to facilitate inference across the boundaries of domain ontologies (...) in anatomy, physiology and pathology. (shrink)

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)

This chapter argues that governments have a duty to take reasonably effective and humane steps to minimize the occurrence of unauthorized migration and stay. While the effects of unauthorized migration on a country’s citizens and institutions have been vigorously debated, the literature has largely ignored duties of fairness to would-be immigrants. It is argued here that failing to take reasonable steps to prevent unauthorized migration and stay is deeply unfair to would-be immigrants who are not in a position to bypass (...) visa regulations. Importantly, the argument here is orthogonal to the debate as to how much and what kinds of immigration ought to be allowed. (shrink)

Within the immigration debate, libertarians have typically come down in favor of open borders by defending two main ideas: i) individuals have a right to free movement; and ii) immigration restrictions are economically inefficient, so that lifting them can make everyone better off. This entry describes the rationale for open borders from a libertarian perspective (in part by analogy to the debate around minimum wage laws). Three main objections within the immigration literature are then discussed: i) the view that states (...) may restrict immigration to protect the interests (e.g. jobs) of their domestic needy; ii) the claim that restrictions are justified as a means of preserving culture; and iii) the influential argument that the right to freedom of association entails a right to exclude. These arguments are well-known, and I describe some of the compelling responses to be found in the recent literature. The essay then turns to more neglected critiques. The first concerns how liberal regimes should think about immigration from countries where the dominant norms are illiberal. The second examines the idea that political and economic institutions are sensitive to immigration policy, especially in the long run. Both of these critiques approach the topic from a non-ideal theory perspective, emphasizing the “public choice” dimensions of immigration policy. The entry closes by suggesting that this form of critique is especially important for open-borders libertarians to respond to given their general commitments to non-ideal, non-romantic theorizing in the context of government institutions and policy. (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.

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)

According to G.A. Cohen, the principles of justice are insensitive to facts about human moral limitations. This assumption allows him to mount a powerful defense of socialism. Here, I present a dilemma for Cohen. On the one hand, if such socialism is to be realized through collective property ownership, then the information problem renders the ideal incoherent, not merely infeasible. On the other hand, if socialism is to incorporate private ownership of productive assets, then Cohen loses the resources to distinguish (...) his view from capitalism. For, if agents were ideally motivated, there would be no need for coercive taxation schemes and limitations on trade. Moreover, incorporating coercion drastically undermines Cohen’s original argument for socialism, which relies on an analogy to a camping trip among friends. (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)

The American political landscape exhibits significant polarization. People’s political beliefs cluster around two main camps. However, many of the issues with respect to which these two camps disagree seem to be rationally orthogonal. This feature raises an epistemic challenge for the political partisan. If she is justified in consistently adopting the party line, it must be true that her side is reliable on the issues that are the subject of disagreements. It would then follow that the other side is anti-reliable (...) with respect to a host of orthogonal political issues. Yet, it is difficult to find a psychologically plausible explanation for why one side would get things reliably wrong with respect to a wide range of orthogonal issues. While this project’s empirical discussion focuses on the US context, the argument generalizes to any situation where political polarization exists on a sufficiently large number of orthogonal claims. (shrink)

Consider a binary afterlife, wherein some people go to Heaven, others to Hell, and nobody goes to both. Would such a system be just? Theodore Sider argues: no. For, any possible criterion of determining where people go will involve treating very similar individuals very differently. Here, I argue that this point has deep and underappreciated implications for moral philosophy. The argument proceeds by analogy: many ethical theories make a sharp and practically significant distinction between persons and non-persons. Yet, just like (...) in the binary afterlife, this involves treating very similar individuals very differently. I propose two ways out. The first is to deny that such theories are strictly speaking true, but to claim that it is practically best if people adopt them. The second is to modify such theories so as to allow for continuous variation in the scope and strength of the moral obligations arising from personhood. (shrink)

Where does normativity come from? Or alternatively, in virtue of what do facts about what an agent has reason to do obtain? On one class of views, reason facts obtain in virtue of agents’ motivations. It might seem like a truism that at least some of our reasons depend on what we desire or care about. However, some philosophers, notably Derek Parfit, have convincingly argued that no reasons are grounded in this way. Typically, this latter, externalist view of reasons has (...) been thought to enjoy the advantage of extensional adequacy—that is, the ability to account for all the reasons we intuitively think people have. This paper provides a novel argument against this assumption by considering a type of case wherein the relative strengths of the agent’s reasons can only be adequately explained by reference to what she cares about. Adding some further assumptions yields that there are at least some internally sourced reasons. (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)

A pervasive feature of democracy is disagreement. And in general, when we encounter disagreement from someone who is at least more reliable than chance, this puts some pressure on us to moderate our beliefs. But this raises the specter of asymmetric compliance—it’s not obvious what to do when we moderate our beliefs but the other party refuses to do so. Whereas an elegant solution is available when it comes to how we can to respond to our higher-order evidence while still (...) preserving democratic fairness, I argue that no such solution is forthcoming when we consider zetetic intransigence—that is, asymmetric compliance with regards to how we inquire, or gather evidence. The upshot is that democratic participation can involve messy tradeoffs with no entirely satisfactory resolution. (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)

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)

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)

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)

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)

Following Anthony Downs’s classic economic analysis of democracy, it has been widely noted that most voters lack the incentive to be well-informed. Recent empirical work, however, suggests further that political partisans can display selectively lazy or biased reasoning. Unfortunately, political knowledge seems to exacerbate, rather than mitigate, these tendencies. In this paper, I build on these observations to construct a more general skeptical challenge which affects what I call creedal beliefs. Such beliefs share three features: (i) the costs to the (...) individual of being wrong are negligible, (ii) the beliefs are subject to social scrutiny, and (iii) the evidential landscape relevant to the beliefs is sufficiently complex so as to make easy verification difficult. Some philosophers and social scientists have recently argued that under such conditions, beliefs are likely to play a signaling, as opposed to a navigational role, and that our ability to hold beliefs in this way is adaptive. However, if this is right, I argue there is at least a partial debunker for such beliefs. Moreover, this offers, I suggest, one way to develop the skeptical challenge based on etiological explanation that John Stuart Mill presents in On Liberty when he claims that the same causes which lead someone to be a devout Christian in London would have made them a Confucian in Peking. Finally, I contend that this skeptical challenge is appropriately circumscribed so that it does not over-extend in an implausible way. (shrink)

Formal principles governing best practices in classification and definition have for too long been neglected in the construction of biomedical ontologies, in ways which have important negative consequences for data integration and ontology alignment. We argue that the use of such principles in ontology construction can serve as a valuable tool in error-detection and also in supporting reliable manual curation. We argue also that such principles are a prerequisite for the successful application of advanced data integration techniques such as ontology-based (...) multi-database querying, automated ontology alignment and ontology-based text-mining. These theses are illustrated by means of a case study of the Gene Ontology, a project of increasing importance within the field of biomedical data integration. (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)

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)

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)

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)

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)

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)

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)

The automatic integration of information resources in the life sciences is one of the most challenging goals facing biomedical informatics today. Controlled vocabularies have played an important role in realizing this goal, by making it possible to draw together information from heterogeneous sources secure in the knowledge that the same terms will also represent the same entities on all occasions of use. One of the most impressive achievements in this regard is the Gene Ontology (GO), which is rapidly acquiring the (...) status of a de facto standard in the field of gene and gene product annotations, and whose methodology has been much intimated in attempts to develop controlled vocabularies for shared use in different domains of biology. The GO Consortium has recognized, however, that its controlled vocabulary as currently constituted is marked by several problematic features - features which are characteristic of much recent work in bioinformatics and which are destined to raise increasingly serious obstacles to the automatic integration of biomedical information in the future. Here, we survey some of these problematic features, focusing especially on issues of compositionality and syntactic regimentation. (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.

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)

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)

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)

We argue the thesis that if (1) a physical process is mathematically representable by a Cauchy sequence; and (2) we accept that there can be no infinite processes, i.e., nothing corresponding to infinite sequences, in natural phenomena; then (a) in the absence of an extraneous, evidence-based, proof of `closure' which determines the behaviour of the physical process in the limit as corresponding to a `Cauchy' limit; (b) the physical process must tend to a discontinuity (singularity) which has not been reflected (...) in the Cauchy sequence that seeks to describe the behaviour of the physical process. We support our thesis by mathematical models of the putative behaviours of (i) a virus cluster; (ii) an elastic string; and (iii) a Universe that recycles from Big Bang to Ultimate Implosion, in which parity and local time reversal violation, and the existence of `dark energy' in a multiverse, need not violate Einstein's equations and quantum theory. We suggest that the barriers to modelling such processes in a mathematical language that seeks unambiguous communication are illusory; they merely reflect an attempt to ask of the language chosen for such representation more than it is designed to deliver. (shrink)

The aim of this dissertation is to comprehensively study various robustness arguments proposed in the literature from Levins to Lloyd as well as the opposition offered to them and pose enquiry into the degree of epistemic virtue that they provide to the model prediction results with respect to climate science and modeling. Another critical issue that this dissertation strives to examine is that of the actual epistemic notion that is operational when scientists and philosophers appeal to robustness. In attempting to (...) explicate this idea, the discussion turns to arguments provided by Schupbach who completely rejects probabilistic independence in favour of explanatory reasoning, Stegenga and Menon who still see some value in probabilistic independence, and Winsberg who takes applies Schupbach’s to climate science, going beyond models to involve multi-modal evidence. After an exhaustive discussion on these arguments, this dissertation attempts to provide a thorough and updated notion of robustness in climate modeling and climate science. (shrink)

With the growth of data, data-intensive approaches for sustainability are becoming widespread and have been endorsed by various stakeholders. To understand their implications, in this paper data-intensive approaches for sustainability will be explored by conducting an extensive review. The current data-intensive approaches are defined as an amalgamation of traditional data-collection methods, like surveys and data from monitoring networks, with new data-collection methods that involve new information communication technology. Based on a comprehensive review of the current dataintensive approaches for sustainability, key (...) challenges are identified: the lack of data availability, diverse indicators developed from a narrowly viewed base, diverse definitions and values, skewed global representation, and the lack of social and economic information collected, especially among the business indicators. To clarify the implications of these trends, four major research assumptions regarding dataintensive approaches are elaborated: the methodology, epistemology, normativity, and ontology. Caution is required when data-intensive approaches are masked as “objective”. Overcoming this issue requires interdisciplinary and community-based approaches that can offer ways to address the subjectivities of data-intensive approaches. The current challenges to interdisciplinarity and community-based approaches are also identified, and possible solutions are explored, so that researchers can employ them to make the best use of data-intensive approaches. (shrink)

Tumors, abscesses, cysts, scars, fractures are familiar types of what we shall call pathological continuant entities. The instances of such types exist always in or on anatomical structures, which thereby become transformed into pathological anatomical structures of corresponding types: a fractured tibia, a blistered thumb, a carcinomatous colon. In previous work on biomedical ontologies we showed how the provision of formal definitions for relations such as is_a, part_of and transformation_of can facilitate the integration of such ontologies in ways which have (...) the potential to support new kinds of automated reasoning. We here extend this approach to the treatment of pathologies, focusing especially on those pathological continuant entities which arise when organs become affected by carcinomas. (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)

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)