The study of biodiversity spans many disciplines and includes data pertaining to species distributions and abundances, genetic sequences, trait measurements, and ecological niches, complemented by information on collection and measurement protocols. A review of the current landscape of metadata standards and ontologies in biodiversity science suggests that existing standards such as the Darwin Core terminology are inadequate for describing biodiversity data in a semantically meaningful and computationally useful way. Existing ontologies, such as the Gene Ontology and others in the Open (...) Biological and Biomedical Ontologies (OBO) Foundry library, provide a semantic structure but lack many of the necessary terms to describe biodiversity data in all its dimensions. In this paper, we describe the motivation for and ongoing development of a new Biological Collections Ontology, the Environment Ontology, and the Population and Community Ontology. These ontologies share the aim of improving data aggregation and integration across the biodiversity domain and can be used to describe physical samples and sampling processes (for example, collection, extraction, and preservation techniques), as well as biodiversity observations that involve no physical sampling. Together they encompass studies of: 1) individual organisms, including voucher specimens from ecological studies and museum specimens, 2) bulk or environmental samples (e.g., gut contents, soil, water) that include DNA, other molecules, and potentially many organisms, especially microbes, and 3) survey-based ecological observations. We discuss how these ontologies can be applied to biodiversity use cases that span genetic, organismal, and ecosystem levels of organization. We argue that if adopted as a standard and rigorously applied and enriched by the biodiversity community, these ontologies would significantly reduce barriers to data discovery, integration, and exchange among biodiversity resources and researchers. (shrink)

The critic Cyril Connolly once pointed out that diarists don’t make novelists. He went on to describe the problem for the would-be writer. “Writing for oneself: no public. Writing for others: no privacy” (Cyril Connolly, Journal). This paper addresses Connolly's worry about the public ad private: how can we reconcile the inner and conscious dimension of speech with its outer and public dimension? For if what people mean by their words involves, or consists in, what they have in (...) mind when they speak then how can what someone has in mind — the meaning she attaches to her words — be at the same time publicly accessible to others on the basis of her behaviour? The issue is whether there is a notion of the linguistic meaning of an expression that can do justice to both speakers’ inner experience of comprehension and to what is outwardly available in their public practice. (shrink)

In her recent paper ‘The Epistemology of Propaganda’ Rachel McKinnon discusses what she refers to as ‘TERF propaganda’. We take issue with three points in her paper. The first is her rejection of the claim that ‘TERF’ is a misogynistic slur. The second is the examples she presents as commitments of so-called ‘TERFs’, in order to establish that radical (and gender critical) feminists rely on a flawed ideology. The third is her claim that standpoint epistemology can be used to establish (...) that such feminists are wrong to worry about a threat of male violence in relation to trans women. In Section 1 we argue that ‘TERF’ is not a merely descriptive term; that to the extent that McKinnon offers considerations in support of the claim that ‘TERF’ is not a slur, these considerations fail; and that ‘TERF’ is a slur according to several prominent accounts in the contemporary literature. In Section 2, we argue that McKinnon misrepresents the position of gender critical feminists, and in doing so fails to establish the claim that the ideology behind these positions is flawed. In Section 3 we argue that McKinnon’s criticism of Stanley fails, and one implication of this is that those she characterizes as ‘positively privileged’ cannot rely on the standpoint-relative knowledge of those she characterizes as ‘negatively privileged’. We also emphasize in this section McKinnon’s failure to understand and account for multiple axes of oppression, of which the cis/trans axis is only one. (shrink)

Contemporary discussions about operational definition often hark back to Stanley Smith Stevens’ classic papers on psychological operationism (1935ab). Still, he was far from the only psychologist to call for conceptual hygiene. Some of Stevens’ direct colleagues at Harvard---most notably B. F. Skinner and E. G. Boring---were also actively applying Bridgman’s conceptual strictures to the study of mind and behavior. In this paper, I shed new light on the history of operationism by reconstructing the Harvard debates about operational definition (...) in the years before Stevens published his seminal articles. Building on a large set of archival evidence from the Harvard University Archives, I argue that we can get a more complete understanding of Stevens’ contributions if we better grasp the operationisms of his former teachers and direct colleagues at Harvard’s Department of Philosophy and Psychology. (shrink)

Corcoran’s 27 entries in the 1999 second edition of Robert Audi’s Cambridge Dictionary of Philosophy [Cambridge: Cambridge UP]. -/- ancestral, axiomatic method, borderline case, categoricity, Church (Alonzo), conditional, convention T, converse (outer and inner), corresponding conditional, degenerate case, domain, De Morgan, ellipsis, laws of thought, limiting case, logical form, logical subject, material adequacy, mathematical analysis, omega, proof by recursion, recursive function theory, scheme, scope, Tarski (Alfred), tautology, universe of discourse. -/- The entire work is available online free at more than (...) one website. Paste the whole URL. http://archive.org/stream/RobertiAudi_The.Cambridge.Dictionary.of.Philosophy/Robert.Audi_The.Cambrid ge.Dictionary.of.Philosophy -/- The 2015 third edition will be available soon. Before you think of buying it read some reviews on Amazon and read reviews of its competition: For example, my review of the 2008 Oxford Companion to Philosophy, History and Philosophy of Logic,29:3,291-292. URL: http://dx.doi.org/10.1080/01445340701300429 -/- Some of the entries have already been found to be flawed. For example, Tarski’s expression ‘materially adequate’ was misinterpreted in at least one article and it was misused in another where ‘materially correct’ should have been used. The discussion provides an opportunity to bring more flaws to light. -/- Acknowledgements: Each of these entries was presented at meetings of The Buffalo Logic Dictionary Project sponsored by The Buffalo Logic Colloquium. The members of the colloquium read drafts before the meetings and were generous with corrections, objections, and suggestions. Usually one 90-minute meeting was devoted to one entry although in some cases, for example, “axiomatic method”, took more than one meeting. Moreover, about half of the entries are rewrites of similarly named entries in the 1995 first edition. Besides the help received from people in Buffalo, help from elsewhere was received by email. We gratefully acknowledge the following: José Miguel Sagüillo, John Zeis, Stewart Shapiro, Davis Plache, Joseph Ernst, Richard Hull, Concha Martinez, Laura Arcila, James Gasser, Barry Smith, Randall Dipert, Stanley Ziewacz, Gerald Rising, Leonard Jacuzzo, George Boger, William Demopolous, David Hitchcock, John Dawson, Daniel Halpern, William Lawvere, John Kearns, Ky Herreid, Nicolas Goodman, William Parry, Charles Lambros, Harvey Friedman, George Weaver, Hughes Leblanc, James Munz, Herbert Bohnert, Robert Tragesser, David Levin, Sriram Nambiar, and others. -/- . (shrink)

When Adam Smith published his celebrated writings on economics and moral philosophy he famously referred to the operation of an invisible hand. Adam Smith's Political Philosophy makes visible the invisible hand by examining its significance in Smith's political philosophy and relating it to similar concepts used by other philosophers, revealing a distinctive approach to social theory that stresses the significance of the unintended consequences of human action. This book introduces greater conceptual clarity to the discussion of the (...) invisible hand and the related concept of unintended order in the work of Smith and in political theory more generally. By examining the application of spontaneous order ideas in the work of Smith, Hume, Hayek and Popper, Adam Smith's Political Philosophy traces similarities in approach and from these builds a conceptual, composite model of an invisible hand argument. While setting out a clear model of the idea of spontaneous order the book also builds the case for using the idea of spontaneous order as an explanatory social theory, with chapters on its application in the fields of science, moral philosophy, law and government. (shrink)

The Protein Ontology (PRO) provides a formal, logically-based classification of specific protein classes including structured representations of protein isoforms, variants and modified forms. Initially focused on proteins found in human, mouse and Escherichia coli, PRO now includes representations of protein complexes. The PRO Consortium works in concert with the developers of other biomedical ontologies and protein knowledge bases to provide the ability to formally organize and integrate representations of precise protein forms so as to enhance accessibility to results of protein (...) research. PRO (http://pir.georgetown.edu/pro) is part of the Open Biomedical Ontologies (OBO) Foundry. (shrink)

This paper is a companion piece to my earlier paper “Fallibilism and Concessive Knowledge Attributions”. There are two intuitive charges against fallibilism. One is that it countenances the truth (and presumably acceptability) of utterances of sentences such as “I know that Bush is a Republican, though it might be that he is not a Republican”. The second is that it countenances the truth (and presumably acceptability) of utterances of sentences such as “I know that Bush is a Republican, even though (...) I’m not certain that he is”, or “I know that Bush it a Republican, even though it isn’t certain that he is.” In “Fallibilism and Concessive Knowledge Attributions”, I argue that fallibilism in epistemology does not countenance the truth of utterances of sentences such as “I know that Bush is a Republican, though it might be that he is not a Republican”. In this paper, I argue that there are independent reasons for thinking that utterances of sentences such as “I know that Bush is a Republican, though I’m not certain that he is” and “I know that Bush is a Republican, though it’s not certain that he is” are unassertible. More specifically, I argue that these are simply instances of Moore’s Paradox, such as “Dogs bark, but I don’t know that they do.” The right account of Moore’s Paradox does not involve the falsehood of the semantic content of the relevant utterances, but rather their pragmatic unacceptability. So the anti-fallibilist intuitions turn out to have pragmatic, rather than semantic import, and therefore do not tell against the truth of fallibilism. Fallibilism in epistemology is often thought to be theoretically desirable, but intuitively problematic. My purpose with these two papers is to show that fallibilism is not intuitively problematic. (shrink)

A medical intervention is a medical procedure or application intended to relieve or prevent illness or injury. Examples of medical interventions include vaccination and drug administration. After a medical intervention, adverse events (AEs) may occur which lie outside the intended consequences of the intervention. The representation and analysis of AEs are critical to the improvement of public health. Description: The Ontology of Adverse Events (OAE), previously named Adverse Event Ontology (AEO), is a community-driven ontology developed to standardize and integrate data (...) relating to AEs arising subsequent to medical interventions, as well as to support computer-assisted reasoning. OAE has over 3,000 terms with unique identifiers, including terms imported from existing ontologies and more than 1,800 OAE-specific terms. In OAE, the term ‘adverse event’ denotes a pathological bodily process in a patient that occurs after a medical intervention. Causal adverse events are defined by OAE as those events that are causal consequences of a medical intervention. OAE represents various adverse events based on patient anatomic regions and clinical outcomes, including symptoms, signs, and abnormal processes. OAE has been used in the analysis of several different sorts of vaccine and drug adverse event data. (shrink)

The argument from ignorance mounted by John Schellenberg argues from the existence of non-faulty unbelief to the non-existence of God, from the fact of atheism or agnosticism to the truth of atheism. It relies on two putative conceptual relations: between the idea of love and that of personal relationship, and between personal relationship and existential belief on each side of the relation concerning the other relatum. I argue that each is debatable, and so the argument cannot proceed.

Fictionalist approaches to ontology have been an accepted part of philosophical methodology for some time now. On a fictionalist view, engaging in discourse that involves apparent reference to a realm of problematic entities is best viewed as engaging in a pretense. Although in reality, the problematic entities do not exist, according to the pretense we engage in when using the discourse, they do exist. In the vocabulary of Burgess and Rosen (1997, p. 6), a nominalist construal of a given discourse (...) is revolutionary just in case it involves a “reconstruction or revision” of the original discourse. Revolutionary approaches are therefore prescriptive. In contrast, a nominalist construal of a given discourse is hermeneutic just in case it is a nominalist construal of a discourse that is put forth as a hypothesis about how the discourse is in fact used; that is, hermeneutic approaches are descriptive. I will adopt Burgess and Rosen’s terminology to describe the two different spirits in which a fictionalist hypothesis in ontology might be advanced. Revolutionary fictionalism would involve admitting that while the problematic discourse does in fact involve literal reference to nonexistent entities, we ought to use the discourse in such a way that the reference is simply within the pretense. The hermeneutic fictionalist, in contrast, reads fictionalism into our actual use of the problematic discourse. According to her, normal use of the problematic discourse involves a pretense. According to the pretense, and only according to the pretense, there exist the objects to which the discourse would commit its users, were no pretense involved. My purpose in this paper is to argue that hermeneutic fictionalism is not a viable strategy in ontology. My argument proceeds in two steps. First, I discuss in detail several problematic consequences of any interesting application of hermeneutic fictionalism. Of course, if there is good evidence that hermeneutic fictionalism is correct in some cases, then some of these drastic consequences would have to be accepted.. (shrink)

We are concerned in this paper to establish the rationality of American legal realism by adopting a theory of reconstruction. American realism is plagued with dichotomies in relating theory and practice; and the need to broach these dichotomies involves transcendence of experience and transference of consciousness. In doing this, we have both to excavate and to justify its philosophy, logic and science. American legal realism has its root in the philosophy of pragmatism and a logic that sets out the essential (...) elements associated with the making and determination of the law through instrumentality of the court. The validity of this category of legal theory tends to lie on the extent of immediate use to which law can be put or the benefits it can afford the American society. Believing in the possibility of a realistic theory of law that is purely American precludes belief in universal understanding of human legal experience distinct from the understanding gained through the cultural lenses of the American people. Although American realists differ remarkably even within a single paradigm, nevertheless three areas of logical unity among them are that: They bear a cross relevance, a complementing and interlocking of results, and a similar faith in attacking legal problems. A completely empirical understanding of American legal realism seems nebulous, because causality presupposes the interaction of American liberal and legalistic political attitudes. Legalism is the life wire of American culture and this makes distribution of rights and legal predictability possible: incidentally language is an important instrument for making this happens. Countries seeking to adopt the American model of legal order or something similar to it should be capable of an equivalent orientation in terms of formulating their philosophy, logic and science of adjudication. (shrink)

People maintain a positive identity in at least two ways: They evaluate themselves more favorably than other people, and they judge themselves to be better now than they were in the past. Both strategies rely on autobiographical memories. The authors investigate the role of autobiographical memories of lying and emotional harm in maintaining a positive identity. For memories of lying to or emotionally harming others, participants judge their own actions as less morally wrong and less negative than those in which (...) other people lied to or emotionally harmed them. Furthermore, people judge those actions that happened further in the past to be more morally wrong than those that happened more recently. Finally, for periods of the past when they believed that they were very different people than they are now, participants judge their actions to be more morally wrong and more negative than those actions from periods of their pasts when they believed that they were very similar to who they are now. The authors discuss these findings in relation to theories about the function of autobiographical memory and moral cognition in constructing and perceiving the self over time. (shrink)

We describe a strategy for integration of data that is based on the idea of semantic enhancement. The strategy promises a number of benefits: it can be applied incrementally; it creates minimal barriers to the incorporation of new data into the semantically enhanced system; it preserves the existing data (including any existing data-semantics) in their original form (thus all provenance information is retained, and no heavy preprocessing is required); and it embraces the full spectrum of data sources, types, models, and (...) modalities (including text, images, audio, and signals). The result of applying this strategy to a given body of data is an evolving Dataspace that allows the application of a variety of integration and analytic processes to diverse data contents. We conceive semantic enhancement (SE) as a lightweight and flexible process that leverages the richness of the structured contents of the Dataspace without adding storage and processing burdens to what, in the intelligence domain, will be an already storage- and processing-heavy starting point. SE works not by changing the data to which it is applied, but rather by adding an extra semantic layer to this data. We sketch how the semantic enhancement approach can be applied consistently and in cumulative fashion to new data and data-models that enter the Dataspace. (shrink)

The Neo-Fregean view individuates concepts at the level of Fregean senses. It is an internalist view according to which concepts can be described as ways of thinking that imply classifications and epistemic/normative inferences. In this paper, I argue that the Neo-Fregean view of concepts adequately characterises the targets of conceptual engineering (CE), which I depict as the activity of purposefully changing our concepts in order to change classifications and/or concept-implicit inferences. I discuss and reject rival views that either reduce the (...) targets of CE to linguistic meanings or classification procedures or characterise concepts in a psychological or concept-externalist manner. I argue that the Neo-Fregean view is a more encompassing and adequate characterisation of the targets of CE. (shrink)

Mental and behavioral disorders represent a significant portion of the public health burden in all countries. The human cost of these disorders is immense, yet treatment options for sufferers are currently limited, with many patients failing to respond sufficiently to available interventions and drugs. High quality ontologies facilitate data aggregation and comparison across different disciplines, and may therefore speed up the translation of primary research into novel therapeutics. Realism-based ontologies describe entities in reality and the relationships between them in such (...) a way that – once formulated in a suitable formal language – the ontologies can be used for sophisticated automated reasoning applications. Reference ontologies can be applied across different contexts in which different, and often mutually incompatible, domain-specific vocabularies have traditionally been used. In this contribution we describe the Mental Functioning Ontology (MF) and Mental Disease Ontology (MD), two realism-based ontologies currently under development for the description of humanmental functioning and disease. We describe the structure and upper levels of the ontologies and preliminary application scenarios, and identify some open questions. (shrink)

The study aimed to investigate the language learning strategies and their contribution to the language competence of English major students in the teacher education program at Kapalong College of Agriculture Sciences and Technology. The researcher utilized a mixed-method design using the convergent parallel approach. Participants were English major students across all year levels at the college institution, with 204 students randomly selected for the quantitative phase and approximately 10 students purposively selected for the qualitative phase: 5 for in-depth interviews and (...) 5 for focused group discussions. The results indicated that both the level of language learning strategies and language competence were high; the findings were rejected, which reveals that there is significant relationship between them. Further, the findings from both the quantitative and qualitative phases largely converged however, there was one divergent indicator. The study confirmed that language learning strategies significantly impact the enhancement of language competencies among English major students, facilitating effective and efficient language use in realistic contexts. It is recommended that language learners must also prioritize memory strategies despite from the indicators’ lowest mean based from the results, such as mnemonic devices and spaced repetition techniques, to enhance vocabulary and grammar retention. Additionally, to improve speaking competency, students should engage in practical applications of the language within their specific contexts, allowing them to practice and develop fluency, essential for effective communication in professional, social, and academic environments. (shrink)

If, relative to a context, what a sentence says is necessarily true, then what it says must be so. If, relative to a context, what a sentence says is possible, then what it says could be true. Following natural philosophical usage, it would thus seem clear that in assessing an occurrence of a sentence for possibility or necessity, one is assessing what is said by that occurrence. In this paper, I argue that natural philosophical usage misleads here. In assessing an (...) occurrence of a sentence for possibility or necessity, one is not assessing the modal status of the proposition expressed by that occurrence of the sentence. (shrink)

I outline and defend a limited realism in socio-political conceptual amelioration (RSCA). RSCA claims that, in some cases, socio-political concepts are ameliorated to represent parts of a concept-independent reality more accurately. My main aim is to dissolve a seeming dilemma for RSCA: Whereas social kinds are mind-dependent (i.e. depending on human thought and action), realism implies that the kinds represented are ontologically independent of the concepts representing them. To dissolve this dilemma, I suggest considering two different roles concepts play concerning (...) social kinds. Concepts can both generate social kinds and represent social kinds. Once a concept has generated a social kind, this social kind is part of a concept-independent reality that can be represented by different concepts. Thereby, RSCA allows amelio-rated concepts to represent social kinds (e.g., rape, marriage) more accurately while acknowledging that human actions or concepts have generated these social kinds. (shrink)

People seem more divided than ever before over social and political issues, entrenched in their existing beliefs and unwilling to change them. Empirical research on mechanisms driving this resistance to belief change has focused on a limited set of well-known, charged, contentious issues and has not accounted for deliberation over reasons and arguments in belief formation prior to experimental sessions. With a large, heterogeneous sample (N = 3,001), we attempt to overcome these existing problems, and we investigate the causes and (...) consequences of resistance to belief change for five diverse and less contentious socio-political issues. After participants chose initially to support or oppose a given socio-political position, they were provided with reasons favoring their chosen position (affirming reasons), reasons favoring the other, unchosen position (conflicting reasons), or all reasons for both positions (reasons for both sides). Our results indicate that participants are more likely to stick with their initial decisions than to change them no matter which reasons are considered, and that this resistance to belief change is likely due to a motivated, biased evaluation of the reasons to support their initial beliefs (prior-belief bias). More specifically, they rated affirming reasons more favorably than conflicting reasons—even after accounting for reported prior knowledge about the issue, the novelty of the reasons presented, and the reported strategy used to make the initial decision. In many cases, participants who did not change their positions tended to become more confident in the superiority of their positions after considering many reasons for both sides. (shrink)

Bio-ontologies are essential tools for accessing and analyzing the rapidly growing pool of plant genomic and phenomic data. Ontologies provide structured vocabularies to support consistent aggregation of data and a semantic framework for automated analyses and reasoning. They are a key component of the Semantic Web. This paper provides background on what bio-ontologies are, why they are relevant to botany, and the principles of ontology development. It includes an overview of ontologies and related resources that are relevant to plant science, (...) with a detailed description of the Plant Ontology (PO). We discuss the challenges of building an ontology that covers all green plants (Viridiplantae). Key results: Ontologies can advance plant science in four keys areas: 1. comparative genetics, genomics, phenomics, and development, 2. taxonomy and systematics, 3. semantic applications and 4. education. Conclusions: Bio-ontologies offer a flexible framework for comparative plant biology, based on common botanical understanding. As genomic and phenomic data become available for more species, we anticipate that the annotation of data with ontology terms will become less centralized, while at the same time, the need for cross-species queries will become more common, causing more researchers in plant science to turn to ontologies. (shrink)

From the early reception of Thomas Aquinas up to the present, many have interpreted his theory of liberum arbitrium to imply intellectual determinism: we do not control our choices, because we do not control the practical judgments that cause our choices. In this paper we argue instead that he rejects determinism in general and intellectual determinism in particular, which would effectively destroy liberum arbitrium as he conceives of it. We clarify that for Aquinas moral responsibility presupposes liberum arbitrium and thus (...) the ability to do otherwise, although the ability to do otherwise applies differently to praise and blame. His argument against intellectual determinism is not straightforward, but we construct it by analogy to his arguments against other deterministic threats. The non-determinism of the intellect’s causality with respect to the will results from his claims that practical reasoning is defeasible and that the reasons for actions are not contrastive reasons. (shrink)

Maintaining systems of military plans is critical for military effectiveness, but is also challenging. Plans will become obsolete as the world diverges from the assumptions on which they rest. If too many ad hoc changes are made to intermeshed plans, the ensemble may no longer lead to well-synchronized and coordinated operations, resulting in the system of plans becoming itself incoherent. We describe in what follows an Adaptive Planning process that we are developing on behalf of the Air Force Research Laboratory (...) (Rome) with the goal of addressing problems of these sorts through cyclical collaborative plan review and maintenance. The interactions of world state, blue force status and associated plans are too complex for manual adaptive processes, and computer-aided plan review and maintenance is thus indispensable. We argue that appropriate semantic technology can 1) provide richer representation of plan-related data and semantics, 2) allow for flexible, non-disruptive, agile, scalable, and coordinated changes in plans, and 3) support more intelligent analytical querying of plan-related data. (shrink)

We are developing the Neurological Disease Ontology (ND) to provide a framework to enable representation of aspects of neurological diseases that are relevant to their treatment and study. ND is a representational tool that addresses the need for unambiguous annotation, storage, and retrieval of data associated with the treatment and study of neurological diseases. ND is being developed in compliance with the Open Biomedical Ontology Foundry principles and builds upon the paradigm established by the Ontology for General Medical Science (OGMS) (...) for the representation of entities in the domain of disease and medical practice. Initial applications of ND will include the annotation and analysis of large data sets and patient records for Alzheimer’s disease, multiple sclerosis, and stroke. (shrink)

Autobiography of Barry Smith; emphasizes the role of Dummett and Husserl, Austrian philosophy and economics, and the Munich-Göttingen-Kraków school of realist phenomenology.

The National Center for Biomedical Ontology is now in its seventh year. The goals of this National Center for Biomedical Computing are to: create and maintain a repository of biomedical ontologies and terminologies; build tools and web services to enable the use of ontologies and terminologies in clinical and translational research; educate their trainees and the scientific community broadly about biomedical ontology and ontology-based technology and best practices; and collaborate with a variety of groups who develop and use ontologies and (...) terminologies in biomedicine. The centerpiece of the National Center for Biomedical Ontology is a web-based resource known as BioPortal. BioPortal makes available for research in computationally useful forms more than 270 of the world's biomedical ontologies and terminologies, and supports a wide range of web services that enable investigators to use the ontologies to annotate and retrieve data, to generate value sets and special-purpose lexicons, and to perform advanced analytics on a wide range of biomedical data. (shrink)

Religion’s persistent and new visibility in political life has prompted a significant global debate. One of its key features concerns the nature and impact of secularization. This book intervenes in two ways. Firstly, it provides summative accounts of the history, culture and legal interactions that have informed Australia’s unique example. Secondly, it critically analyzes secular political theory concerning the public sphere, deliberative politics and democratic practices. The compendium aims to propel the debate in new directions and promote urgently needed public (...) understanding. My own contribution focused on hermeneutics in deliberative democracies. (shrink)

As biological and biomedical research increasingly reference the environmental context of the biological entities under study, the need for formalisation and standardisation of environment descriptors is growing. The Environment Ontology (ENVO) is a community-led, open project which seeks to provide an ontology for specifying a wide range of environments relevant to multiple life science disciplines and, through an open participation model, to accommodate the terminological requirements of all those needing to annotate data using ontology classes. This paper summarises ENVO’s motivation, (...) content, structure, adoption, and governance approach. (shrink)

According to the principle of Conjunction Closure, if one has justification for believing each of a set of propositions, one has justification for believing their conjunction. The lottery and preface paradoxes can both be seen as posing challenges for Closure, but leave open familiar strategies for preserving the principle. While this is all relatively well-trodden ground, a new Closure-challenging paradox has recently emerged, in two somewhat different forms, due to Backes :3773–3787, 2019a) and Praolini :715–726, 2019). This paradox synthesises elements (...) of the lottery and the preface and is designed to close off the familiar Closure-preserving strategies. By appealing to a normic theory of justification, I will defend Closure in the face of this new paradox. Along the way I will draw more general conclusions about justification, normalcy and defeat, which bear upon what Backes :2877–2895, 2019b) has dubbed the ‘easy defeat’ problem for the normic theory. (shrink)

Introduction and translation of “The Four Phases of Philosophy” by Franz Brentano.

A belief one has is safe if either (i) it could not easily be false or (ii) in any nearby world in which it is false, it is not formed using the method one uses to form one’s actual belief. It seems our mathematical beliefs are safe if mathematical pluralism is true: if, loosely put, almost any consistent mathematical theory is true. It seems, after all, that in any nearby world where one’s mathematical beliefs differ from one’s actual beliefs, one (...) would believe some other true, consistent theory. Focusing on Justin Clarke-Doane’s recent discussion, I argue the thesis that mathematical beliefs are safe given pluralism faces some obstacles. I argue (i) is true of mathematical belief given pluralism only if we deny plausible claims about the interpretation of non-pluralists who many of us could easily be. Unless strong metasemantic theses are true, it is plausible many of us could easily deny or refuse to believe a consistent and true mathematical theory we actually believe. Since philosophical arguments and controversies permeate the methodology of foundational mathematics, I argue we cannot confidently distinguish the methods we use in mathematics between worlds, thus raising doubts about (ii). (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)

This book explores a question central to philosophy--namely, what does it take for a belief to be justified or rational? According to a widespread view, whether one has justification for believing a proposition is determined by how probable that proposition is, given one's evidence. In this book this view is rejected and replaced with another: in order for one to have justification for believing a proposition, one's evidence must normically support it--roughly, one's evidence must make the falsity of that proposition (...) abnormal in the sense of calling for special, independent explanation. This conception of justification bears upon a range of topics in epistemology and beyond. Ultimately, this way of looking at justification guides us to a new, unfamiliar picture of how we should respond to our evidence and manage our own fallibility. This picture is developed here. (shrink)

Although Gilles Deleuze never explicitly developed what might be considered a ‘philosophy of technology’, this article nonetheless attempts to outline the rudiments of a Deleuzian approach to technology by proposing a series of interrelated concepts: (1) prosthesis (technological artefacts are externalised organs); (2) proto-technicity, or originary technicity (but this technicity already exists in Nature, all the way down, and precedes any ‘theory’); (3) exodarwinism (the fact that evolutionary time has bifurcated, and technology evolves in a faster and accelerating time scale); (...) (4) de-specialisation or de-differentiation (what conditions the externalisation of organs is their deterritorialisation); (5) motricity (the link between the brain and the hand/mouth is primarily one of movement); (6) inscription, or graphism (the link between mouth and hand takes place through phonetic writing, when the hand reproduces speech in graphic inscriptions); (7) maker's knowledge (we know the organisations of matter found in nature through the organisations of matter that we ourselves have created); and finally, (8) totipotence (like a stem cell, the body is capable of externalising an almost unlimited number of forms and functions; it is itself an abstract and the source of abstractions). (shrink)

The Plant Ontology (PO; http://www.plantontology.org/) is a publicly-available, collaborative effort to develop and maintain a controlled, structured vocabulary (“ontology”) of terms to describe plant anatomy, morphology and the stages of plant development. The goals of the PO are to link (annotate) gene expression and phenotype data to plant structures and stages of plant development, using the data model adopted by the Gene Ontology. From its original design covering only rice, maize and Arabidopsis, the scope of the PO has been expanded (...) to include all green plants. The PO was the first multi-species anatomy ontology developed for the annotation of genes and phenotypes. Also, to our knowledge, it was one of the first biological ontologies that provides translations (via synonyms) in non-English languages such as Japanese and Spanish. There are about 2.2 million annotations linking PO terms to over 110,000 unique data objects representing genes or gene models, proteins, RNAs, germplasm and Quantitative Traits Loci (QTLs) from 22 plant species. In this paper, we focus on the plant anatomical entity branch of the PO, describing the organizing principles, resources available to users, and examples of how the PO is integrated into other plant genomics databases and web portals. We also provide two examples of comparative analyses, demonstrating how the ontology structure and PO-annotated data can be used to discover the patterns of expression of the LEAFY (LFY) and terpene synthase (TPS) gene homologs. (shrink)

Recently two distinct forms of rule-utilitarianism have been introduced that differ on how to measure the consequences of rules. Brad Hooker advocates fixed-rate rule-utilitarianism, while Michael Ridge advocates variable-rate rule-utilitarianism. I argue that both of these are inferior to a new proposal, optimum-rate rule-utilitarianism. According to optimum-rate rule-utilitarianism, an ideal code is the code whose optimum acceptance level is no lower than that of any alternative code. I then argue that all three forms of rule-utilitarianism fall prey to two fatal (...) problems that leave us without any viable form of rule-utilitarianism. (shrink)

Every domain-specific ontology must use as a framework some upper-level ontology which describes the most general, domain-independent categories of reality. In the present paper we sketch a new type of upper-level ontology, which is intended to be the basis of a knowledge modelling language GOL (for: 'General Ontological Language'). It turns out that the upper- level ontology underlying standard modelling languages such as KIF, F-Logic and CycL is restricted to the ontology of sets. Set theory has considerable mathematical power and (...) great flexibility as a framework for modelling different sorts of structures. At the same time it has the disadvantage that sets are abstract entities (entities existing outside the realm of time, space and causality), and thus a set-theoretical framework should be supplemented by some other machinery if it is to support applications in the ripe, messy world of concrete objects. In the present paper we partition the entities of the real world into sets and urelements, and then we introduce several new ontological relations between these urelements. In contrast to standard modelling and representation formalisms, the concepts of GOL provide a machinery for representing and analysing such ontologically basic relations. (shrink)

The desideratum of semantic interoperability has been intensively discussed in medical informatics circles in recent years. Originally, experts assumed that this issue could be sufficiently addressed by insisting simply on the application of shared clinical terminologies or clinical information models. However, the use of the term ‘ontology’ has been steadily increasing more recently. We discuss criteria for distinguishing clinical ontologies from clinical terminologies and information models. Then, we briefly present the role clinical ontologies play in two multicentric research projects. Finally, (...) we discuss the interactions between these different kinds of knowledge representation artifacts and the stakeholders involved in developing interoperational real-world clinical applications. We provide ontology engineering examples from two EU-funded projects. (shrink)

Ontologies are being developed throughout the biomedical sciences to address standardization, integration, classification and reasoning needs against the background of an increasingly data-driven research paradigm. In particular, ontologies facilitate the translation of basic research into benefits for the patient by making research results more discoverable and by facilitating knowledge transfer across disciplinary boundaries. Addressing and adequately treating mental illness is one of our most pressing public health challenges. Primary research across multiple disciplines such as psychology, psychiatry, biology, neuroscience and pharmacology (...) needs to be integrated in order to promote a more comprehensive understanding of underlying processes and mechanisms, and this need for integration only becomes more pressing with our increase in understanding of differences among individuals and populations at the molecular level concerning susceptibility to specific illnesses. Substance addiction is a particularly relevant public health challenge in the developed world, affecting a substantial percentage of the population, often co-morbid with other illnesses such as mood disorders. Currently, however, there is no straightforward automated method to combine data of relevance to the study of substance addiction across multiple disciplines and populations. In this contribution, we describe a framework of interlinked, interoperable bio-ontologies for the annotation of primary research data relating to substance addiction, and discuss how this framework enables easy integration of results across disciplinary boundaries. We describe entities and relationships relevant for the description of addiction within the Mental Functioning Ontology, Chemical Entities of Biological Interest Ontology, Protein Ontology, Gene Ontology and the Neuroscience Information Framework ontologies. (shrink)

According to a popular view in philosophy, intuition is a singular propositional attitude. In this paper, I outline an opposite account on “garden-variety intuition”, i.e. intuition that people experience in their daily lives. The account is based on a distinction between intuition on the processing level, ‘intuitive belief’ and ‘intuition that p’. Immediacy and certainty prove to be the phenomenal features of intuitive beliefs and intuitions that p. Regarding the processing level, I suggest to combine dual-process theory and the theory (...) of mental models, and I claim that this results in non-propositional intuitions. Finally, I argue that non-propositional intuitions are fundamental for garden-variety intuition: They constitute inclinations to believe, possibly resulting in intuitive beliefs or intuitions that p. (shrink)

Projects of conceptual engineering that aim to ameliorate concepts face the challenge of topic continuity. In some instances of conceptual amelioration, a particularly strong kind of continuity is needed: Sameness of subject matter. This paper examines how sameness of subject matter can be maintained in conceptual amelioration. It starts from a view that sees concepts as ways of thinking, implying that to change a concept is to replace it. At first sight, this view seems incompatible with maintaining sameness of subject (...) matter in conceptual amelioration. Accordingly, Sally Haslanger and Sarah Sawyer have suggested accounts of conceptual amelioration that do without replacing concepts. On their accounts, the persisting concept is supposed to guarantee sameness of subject matter. However, both accounts face problems. Therefore, I suggest a different account to maintain sameness of subject matter inspired by Bartels’s chains of meaning theory. On this account, sameness of subject matter is guaranteed through a common referent of the pre- and the post-amelioration concept, established from the post-amelioration perspective. The account allows for sameness of subject matter even though concepts are replaced in the ameliorative process. (shrink)

The central hypothesis of the collaboration between Language and Computing (L&C) and the Institute for Formal Ontology and Medical Information Science (IFOMIS) is that the methodology and conceptual rigor of a philosophically inspired formal ontology greatly benefits application ontologies. To this end r®, L&C’s ontology, which is designed to integrate and reason across various external databases simultaneously, has been submitted to the conceptual demands of IFOMIS’s Basic Formal Ontology (BFO). With this project we aim to move beyond the level of (...) controlled vocabularies to yield an ontology with the ability to support reasoning applications. Our general procedure has been the implementation of a meta-ontological definition space in which the definitions of all the concepts and relations in LinKBase® are standardized in a framework of first-order logic. In this paper we describe how this standardization has already led to an improvement in the LinKBase® structure that allows for a greater degree of internal coherence than ever before possible. We then show the use of this philosophical standardization for the purpose of mapping external databases to one another, using LinKBase® as translation hub, with a greater degree of success than possible hitherto. We demonstrate how this offers a genuine advance over other application ontologies that have not submitted themselves to the demands of philosophical scrutiny. LinKBase® is one of the world’s largest applications-oriented medical domain ontologies, and BFO is one of the world’s first philosophically driven reference ontologies. The collaboration of the two thus initiates a new phase in the quest to solve the so-called “Tower of Babel”. (shrink)