Background If trials of therapeutic interventions are to serve society's interests, they must be of high methodological quality and must satisfy moral commitments to human subjects. The authors set out to develop a clinical - trials compendium in which standards for the ethical treatment of human subjects are integrated with standards for research methods. Methods The authors rank-ordered the world's nations and chose the 31 with >700 active trials as of 24 July 2008. Governmental and other authoritative entities of the (...) 31 countries were searched, and 1004 English-language documents containing ethical and/or methodological standards for clinical trials were identified. The authors extracted standards from 144 of those: 50 designated as ‘core’, 39 addressing trials of invasive procedures and a 5% sample of the remainder. As the integrating framework for the standards we developed a coherent taxonomy encompassing all elements of a trial's stages. Findings Review of the 144 documents yielded nearly 15 000 discrete standards. After duplicates were removed, 5903 substantive standards remained, distributed in the taxonomy as follows: initiation, 1401 standards, 8 divisions; design, 1869 standards, 16 divisions; conduct, 1473 standards, 8 divisions; analysing and reporting results, 997 standards, four divisions; and post-trial standards, 168 standards, 5 divisions. Conclusions The overwhelming number of source documents and standards uncovered in this study was not anticipated beforehand and confirms the extraordinary complexity of the clinical trials enterprise. This taxonomy of multinational ethical and methodological standards may help trialists and overseers improve the quality of clinical trials, particularly given the globalisation of clinical research. (shrink)

There has been a growing concern over establishing norms that ensure the ethically acceptable and scientifically sound conduct of clinical trials. Among the leading norms internationally are the World Medical Association's Declaration of Helsinki, guidelines by the Council for International Organizations of Medical Sciences, the International Conference on Harmonization's standards for industry, and the CONSORT group's reporting norms, in addition to the influential U.S. Federal Common Rule, Food and Drug Administration's body of regulations, and information sheets by the Department of (...) Health and Human Services. There are also many norms published at more local levels by official agencies and professional groups.Any account of international standards should cover both scientific and ethical norms at once – the two are conceptually intertwined. Recent sources recognize that “[s]cientifically unsound research on human subjects is unethical in that it exposes research subjects to risks without possible benefit.”. (shrink)

This paper focuses on invasive therapeutic procedures, defined as procedures requiring the introduction of hands, instruments, or devices into the body via incisions or punctures of the skin or mucous membranes performed with the intent of changing the natural history of a human disease or condition for the better. Ethical and methodological concerns have been expressed about studies designed to evaluate the effects of invasive therapeutic procedures. Can such studies meet the same standards demanded of those, for example, evaluating pharmaceutical (...) agents? This paper describes a research project aimed at examining the interplay and sometimes apparent conflict between ethical standards for human research and standards for methodological rigor in trials of invasive procedures. The paper discusses how the authors plan to develop a set of consensus standards that, if met, would result in substantial and much-needed improvements in the methodological and ethical quality of such trials. (shrink)

Though many agree that we need to account for the role that social factors play in inquiry, developing a viable social epistemology has proved to be difficult. According to Longino, it is the processes that make inquiry possible that are aptly described as "social," for they require a number of people to sustain them. These processes, she claims, not only facilitate inquiry, but also ensure that the results of inquiry are more than mere subjective opinions, and thus deserve to be (...) called "knowledge." In this paper, I (a) explain Longino's epistemology, and (b) defend it against charges that have recently been raised by Kitcher, Schmitt, and Solomon. Longino rightly recognizes that not all social factors have the same (adverse) affect on inquiry. She also recommends that we distinguish knowledge from mere opinion by reference to a social standard. (shrink)

I examine the epistemic import of collaborative research in science. I develop and defend a functional explanation for its growing importance. Collaborative research is becoming more popular in the natural sciences, and to a lesser degree in the social sciences, because contemporary research in these fields frequently requires access to abundant resources, for which there is great competition. Scientists involved in collaborative research have been very successful in accessing these resources, which has in turn enabled them to realize the epistemic (...) goals of science more effectively than other scientists, thus creating a research environment in which collaboration is now the norm. (shrink)

This paper examines the ethics of the Australian business community’s responses to the phenomenon of modern slavery. Engaging a critical discourse approach, we draw upon a data set of submissions by businesses and business representatives to the Australian government’s Joint Standing Committee on Foreign Affairs, Defence and Trade ‘Parliamentary Inquiry into Establishing a Modern Slavery Act in Australia’—which preceded the signing into law of Australia’s Modern Slavery Act 2018—to examine the business community’s discursive construction in their submissions of the ethical–political (...) concept of freedom. The paper shows how the concept of freedom was employed by Australian business in a manner that privileged their own subject status and advocated for legislation with minimal burden. Relating this contemporary case to a longer historical context, we show how Australian business responses towards modern slavery map onto liberal and neoliberal ethics in which the freedom of the propertied takes precedent over that of the property-less. Further, we show discursive similarities in the arguments presented by modern Australian businesses and certain historical efforts by members of the business community to privilege commercial freedoms in responses to 18th and 19th Century abolitionist movements. Overall, our research makes two important contributions: first, it highlights the value of a critical discourse lens in business ethics research to show how business and other stakeholders in the field construct and shape their own and other’s ethically-laden understanding of reality; and second, it presents a case for considerable scepticism about the motivation of business to employ the freedoms made available to it under neo/liberal discourse to confront a key human rights challenge. (shrink)

Biomedical ontologies are emerging as critical tools in genomic and proteomic research where complex data in disparate resources need to be integrated. A number of ontologies exist that describe the properties that can be attributed to proteins; for example, protein functions are described by Gene Ontology, while human diseases are described by Disease Ontology. There is, however, a gap in the current set of ontologies—one that describes the protein entities themselves and their relationships. We have designed a PRotein Ontology (PRO) (...) to facilitate protein annotation and to guide new experiments. The components of PRO extend from the classification of proteins on the basis of evolutionary relationships to the representation of the multiple protein forms of a gene (products generated by genetic variation, alternative splicing, proteolytic cleavage, and other post-translational modification). PRO will allow the specification of relationships between PRO, GO and other OBO Foundry ontologies. Here we describe the initial development of PRO, illustrated using human proteins from the TGF-beta signaling pathway. (shrink)

David Hull accounts for the success of science in terms of an invisible hand mechanism, arguing that it is difficult to reconcile scientists' self-interestedness or their desire for recognition with traditional philosophical explanations for the success of science. I argue that we have less reason to invoke an invisible hand mechanism to explain the success of science than Hull implies, and that many of the practices and institutions constitutive of science are intentionally designed by scientists with an eye to realizing (...) the very goals that Hull believes need to be explained by reference to an invisible hand mechanism. Thus, I reduce the scope of Hull's invisible hand explanation and supplement it by appealing to a hidden hand explanation. (shrink)

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

ABSTRACT We have previously argued that there are forms of greenhouse gas offsetting for which, when one emits and offsets, one imposes no risk. Orri Stefansson objects that our argument fails to distinguish properly between the people who stand to be harmed by one’s emissions and the people who stand to be benefited by one’s offsetting. We reply by emphasizing the difference between acting with a probability of making a difference to the distribution of harm and acting in a way (...) that worsen’s someone’s prospect. (shrink)

Searle’s tool for understanding culture, law and society is the opposition between brute reality and institutional reality, or in other words between: observer-independent features of the world, such as force, mass and gravitational attraction, and observer-relative features of the world, such as money, property, marriage and government. The question posed here is: under which of these two headings do moral concepts fall? This is an important question because there are moral facts – for example pertaining to guilt and responsibility – (...) which hover uncomfortably close to the boundary between the observer-relative and the observer-independent. By means of a thought experiment involving an imagined Chinese society in which guilt is determined by the random throwing of sticks, I seek to show that moral concepts threaten the foundations of Searle’s philosophy of social reality. (shrink)

Some moral theorists argue that being an innocent beneficiary of significant harms inflicted by others may be sufficient to ground special duties to address the hardships suffered by the victims, at least when it is impossible to extract compensation from those who perpetrated the harm. This idea has been applied to climate change in the form of the beneficiary-pays principle. Other philosophers, however, are quite sceptical about beneficiary pays. Our aim in this article is to examine their critiques. We conclude (...) that, while they have made important points, the principle remains worthy of further development and exploration. Our purpose in engaging with these critiques is constructive — we aim to formulate beneficiary pays in ways that would give it a plausible role in allocating the cost of addressing human-induced climate change, while acknowledging that some understandings of the principle would make it unsuitable for this purpose. (shrink)

The Protein Ontology (PRO; http://proconsortium.org) formally defines protein entities and explicitly represents their major forms and interrelations. Protein entities represented in PRO corresponding to single amino acid chains are categorized by level of specificity into family, gene, sequence and modification metaclasses, and there is a separate metaclass for protein complexes. All metaclasses also have organism-specific derivatives. PRO complements established sequence databases such as UniProtKB, and interoperates with other biomedical and biological ontologies such as the Gene Ontology (GO). PRO relates to (...) UniProtKB in that PRO’s organism-specific classes of proteins encoded by a specific gene correspond to entities documented in UniProtKB entries. PRO relates to the GO in that PRO’s representations of organism-specific protein complexes are subclasses of the organism-agnostic protein complex terms in the GO Cellular Component Ontology. The past few years have seen growth and changes to the PRO, as well as new points of access to the data and new applications of PRO in immunology and proteomics. Here we describe some of these developments. (shrink)

We take as our starting point a thesis to the effect that, at least for true judgments of many varieties, there are parts of reality which make such judgments are true. We argue that two distinct components are involved in this truthmaker relation. On the one hand is the relation of necessitation, which holds between an object x and a judgment p when the existence of x entails the truth of p. On the other hand is the dual notion of (...) projection, which holds between a judgment p and an object x when the truth of p entails the existence of x. A truthmaker for a judgment p is then a necessitator for p which satisfies the further constraint that it is part of p’s projection. We offer a formal theory of the truthmaker relation thus defined, exploiting ontological tools of basic mereology and the theory of dependence. We then apply the theory to a range of problems connected with generic expressions, ellipsis, vagueness, and indexical and perceptual judgments. (shrink)

The current COVID-19 pandemic and the previous SARS/MERS outbreaks of 2003 and 2012 have resulted in a series of major global public health crises. We argue that in the interest of developing effective and safe vaccines and drugs and to better understand coronaviruses and associated disease mechenisms it is necessary to integrate the large and exponentially growing body of heterogeneous coronavirus data. Ontologies play an important role in standard-based knowledge and data representation, integration, sharing, and analysis. Accordingly, we initiated the (...) development of the community-based Coronavirus Infectious Disease Ontology in early 2020. -/- As an Open Biomedical Ontology (OBO) library ontology, CIDO is open source and interoperable with other existing OBO ontologies. CIDO is aligned with the Basic Formal Ontology and Viral Infectious Disease Ontology. CIDO has imported terms from over 30 OBO ontologies. For example, CIDO imports all SARS-CoV-2 protein terms from the Protein Ontology, COVID-19-related phenotype terms from the Human Phenotype Ontology, and over 100 COVID-19 terms for vaccines (both authorized and in clinical trial) from the Vaccine Ontology. CIDO systematically represents variants of SARS-CoV-2 viruses and over 300 amino acid substitutions therein, along with over 300 diagnostic kits and methods. CIDO also describes hundreds of host-coronavirus protein-protein interactions (PPIs) and the drugs that target proteins in these PPIs. CIDO has been used to model COVID-19 related phenomena in areas such as epidemiology. The scope of CIDO was evaluated by visual analysis supported by a summarization network method. CIDO has been used in various applications such as term standardization, inference, natural language processing (NLP) and clinical data integration. We have applied the amino acid variant knowledge present in CIDO to analyze differences between SARS-CoV-2 Delta and Omicron variants. CIDO's integrative host-coronavirus PPIs and drug-target knowledge has also been used to support drug repurposing for COVID-19 treatment. -/- CIDO represents entities and relations in the domain of coronavirus diseases with a special focus on COVID-19. It supports shared knowledge representation, data and metadata standardization and integration, and has been used in a range of applications. (shrink)

Basic Formal Ontology (BFO) is a top-level ontology used in hundreds of active projects in scientific and other domains. BFO has been selected to serve as top-level ontology in the Industrial Ontologies Foundry (IOF), an initiative to create a suite of ontologies to support digital manufacturing on the part of representatives from a number of branches of the advanced manufacturing industries. We here present a first draft set of axioms and definitions of an IOF upper ontology descending from BFO. The (...) axiomatization is designed to capture the meanings of terms commonly used in manufacturing and is designed to serve as starting point for the construction of the IOF ontology suite. (shrink)

This paper presents a puzzle for Act Consequentialists who do not want to shoot Pelé. The puzzle arises from cases involving the promotion of virtue, and motivates a systematic restriction on the separability of reasons.

The paper is a contribution to formal ontology. It seeks to use topological means in order to derive ontological laws pertaining to the boundaries and interiors of wholes, to relations of contact and connectedness, to the concepts of surface, point, neighbourhood, and so on. The basis of the theory is mereology, the formal theory of part and whole, a theory which is shown to have a number of advantages, for ontological purposes, over standard treatments of topology in set-theoretic terms. One (...) central goal of the paper is to provide a rigorous formulation of Brentano's thesis to the effect that a boundary can exist as a matter of necessity only as part of a whole of higher dimension which it is the boundary of. It concludes with a brief survey of current applications of mereotopology in areas such as natural-language analysis, geographic information systems, machine vision, naive physics, and database and knowledge engineering. (shrink)

In this paper, I draw jointly upon a Foucauldian ethical discourse and the example of the so-called ‘Manchester school’ of Foucauldian labour process theory (LPT) to question the political/ethical aspirations and effects of critical management studies. Specifically, I question the ethics and effects of LPT researchers’ relationships with those they/we research. I organize the discussion around four Foucauldian ethical themes or feelings. I thread these ethical themes throughout the paper to argue that, though Foucauldian LPT may be understood to abstractly (...) resonate with these themes, its contribution is seriously undermined through the authors’ lack of attention to ways of embodying this ethics in relations with the researched. By not embodying these commitments, the marriage between Foucault and LPT risks being read more as a marriage of convenience than commitment. And, further, a marriage that reproduces a politically problematic ‘modernist/positivist’ self–other separation or divorce between researcher and researched. (shrink)

Our aim in this brief essay is not to defend a particular policy or attitude toward lockdown measures in the United States or elsewhere, but to consider the scope and limits of different types of arguments that can be offered for them. Understanding the complexity of these issues will, we hope, go some way to helping us understand each other and our attitudes toward state responses to the pandemic.

In his book The Sensory Order, Hayek anticipates many of the central ideas behind what we now call the connectionist paradigm, and develops on this basis a theory of the workings of the human mind that extends the thinking of Hume and Mach. He shows that the idea of neural networks is can be applied not only in psychology and neurology but also in the sphere of economics. For the mind, from the perspective of The Sensory Order, is a dynamic, (...) relational affair that is in many respects analogous to a market process. The mind, as Hayek puts it, is a 'continuous stream of impulses, the significance of each and every contribution of which is determined by the place in the pattern of channels through which they flow' , so that the flow of representative neural impulses can be compared 'to a stock of capital being nourished by inputs and giving a continuous stream of outputs'. (shrink)

Ontology, since Aristotle, has been conceived as a sort of highly general physics, a science of the types of entities in reality, of the objects, properties, categories and relations which make up the world. At the same time ontology has been for some two thousand years a speculative enterprise. It has rested methodologically on introspection and on the construction and analysis of elaborate world-models and of abstract formal-ontological theories. In the work of Quine and others this ontological theorizing in abstract (...) fashion about the world was supplemented by the study, based on the use of logical methods, of the ontological commitments or presuppositions embodied in scientific theories. In recent years both types of ontological study have found application in the world of information systems, for example in the construction of frameworks for knowledge representation and in database design and translation. As ontology is in this way drawn closer to the domain of real-world applications, the question arises as to whether it is possible to use empirical methods in studying ontological theories. More specifically: can we use empirical methods to test the ontological theories embodied in human cognition? We set forth the outlines of a framework for the formulation and testing of such theories as they relate to the specific domain of geographic objects and categories. (shrink)

Dignity is traditionally thought to apply to almost all and almost only humans. However, I argue that an account of a distinctly human dignity cannot achieve a coherent and non-arbitrary justification; either it must exclude some humans or include some nonhumans. This conclusion is not as worrying as might be first thought. Rather than attempting to vindicate human dignity, dignity should extend beyond the human, to include a range of nonhuman animals. Not only can we develop a widely inclusive account (...) of dignity by pursuing this route, but we can still defend the three core principles that lie at the heart of contemporary thinking about dignity: that bearers of dignity possess dignity to an equal degree, in virtue of possessing the same intrinsic worth, and that this generates direct and claimable rights. I thus develop an account of dignity that includes nonhuman animals. I argue that the capacity to value most plausibly grounds dignity. This capacity arises from valenced sentience: a being values insofar as they have experiences that matter to them. I then characterise what follows from this. First, I contend that it is only the capacity to value grounds dignity because this produces the most plausible, simplest, and most explanatorily powerful account of dignity. We ought to reject pluralist accounts which assert a sharp distinction between bearers and non-bearers of rational agency, and biocentric accounts which include non-sentient organic entities. Second, I argue this property grounds an account of dignity that is non-hierarchical. There are no degrees of dignity. Instead, all possessors of the capacity to value have the same kind of intrinsic value, and the same equal fundamental right: to consideration of their interest in leading a life of value. Finally, I argue that since the fundamental right is to consideration, moral agents have claimable duties to engage in a deliberative procedure with actionable requirements. Specific rights are instantiations of this general procedure. Certain revisionist conclusions follow on my view, for instance, that nonhumans should be given greater weight and inclusion in a far wider range of cases, but my account is sensitive to the range of different things different beings value, so it does not generate counterintuitive implications. I conclude that dignity extends beyond the human. (shrink)

The truthmaker theory rests on the thesis that the link between a true judgment and that in the world to which it corresponds is not a one-to-one but rather a one-to-many relation. An analogous thesis in relation to the link between a singular term and that in the world to which it refers is already widely accepted. This is the thesis to the effect that singular reference is marked by vagueness of a sort that is best understood in supervaluationist terms. (...) In what follows we show that the supervaluationist approach to singular reference, when wedded to the truthmaker idea, yields a framework of surprising power, which offers a uniform set of solutions to a range of problems regarding identity, reference and knowledge, problems which have hitherto been dealt with on an ad hoc basis. (shrink)

The paper is an exercise in descriptive ontology, with specific applications to problems in the geographical sphere. It presents a general typology of spatial boundaries, based in particular on an opposition between bona fide or physical boundaries on the one hand, and fiat or human-demarcation-induced boundaries on the other. Cross-cutting this opposition are further oppositions in the realm of boundaries, for example between: crisp and indeterminate, complete and incomplete, enduring and transient, symmetrical and asymmetrical. The resulting typology generates a corresponding (...) categorization of the different sorts of objects which (complete) boundaries determine or demarcate. The theory is applied first of all in the areas of geography and of administrative and property law. Indications are then given as to how the typology may be applied also in other fields where physical and fiat boundaries are at work, including the field of cognitive linguistics and the related field of the ontology of truth. (shrink)

The computational genomics community has come increasingly to rely on the methodology of creating annotations of scientific literature using terms from controlled structured vocabularies such as the Gene Ontology (GO). We here address the question of what such annotations signify and of how they are created by working biologists. Our goal is to promote a better understanding of how the results of experiments are captured in annotations in the hope that this will lead to better representations of biological reality through (...) both the annotation process and ontology development, and in more informed use of the GO resources by experimental scientists. (shrink)

Since 2002 we have been testing and refining a methodology for ontology development that is now being used by multiple groups of researchers in different life science domains. Gary Merrill, in a recent paper in this journal, describes some of the reasons why this methodology has been found attractive by researchers in the biological and biomedical sciences. At the same time he assails the methodology on philosophical grounds, focusing specifically on our recommendation that ontologies developed for scientific purposes should be (...) constructed in such a way that their terms are seen as referring to what we call universals or types in reality. As we show, Merrill’s critique is of little relevance to the success of our realist project, since it not only reveals no actual errors in our work but also criticizes views on universals that we do not in fact hold. However, it nonetheless provides us with a valuable opportunity to clarify the realist methodology, and to show how some of its principles are being applied, especially within the framework of the OBO (Open Biomedical Ontologies) Foundry initiative. (shrink)

The ontology of language is concerned with the relations between uses of language, both overt and covert, and other entities, whether in the world or in the mind of the thinking subject. We attempt a first survey of the sorts of relations which might come into question for such an ontology, including: relations between referring uses of expressions and their objects, relations between the use of a (true) sentence and that in the world which makes it true, relations between mental (...) acts on the one hand and underlying mental states (attitudes, beliefs), on the other, relations between my acts and states, associated uses of language and overt actions on my part and on the part of those other subjects with whom I communicate. (shrink)

This review focuses on the Ogdoas scholastica by Jacob Lorhard, published in 1606. The importance of this document turns on the fact that it contains what is almost certainly the first published occurrence of the term “ontology.” The body of the work consists in a series of diagrams called “diagraphs.” Relevant features of this compendium of diagraphs are: 1. that it does not in fact contain the word “ontology,” and 2. that Lorhard himself was not responsible for its content.

A survey of theories of part, whole and dependence from Aristotle to the Gestalt psychologists, with special attention to Husserl’s Third Logical Investigation “On the Theory of Parts and Wholes”.

Ontology is a burgeoning field, involving researchers from the computer science, philosophy, data and software engineering, logic, linguistics, and terminology domains. Many ontology-related terms with precise meanings in one of these domains have different meanings in others. Our purpose here is to initiate a path towards disambiguation of such terms. We draw primarily on the literature of biomedical informatics, not least because the problems caused by unclear or ambiguous use of terms have been there most thoroughly addressed. We advance a (...) proposal resting on a distinction of three levels too often run together in biomedical ontology research: 1. the level of reality; 2. the level of cognitive representations of this reality; 3. the level of textual and graphical artifacts. We propose a reference terminology for ontology research and development that is designed to serve as common hub into which the several competing disciplinary terminologies can be mapped. We then justify our terminological choices through a critical treatment of the ‘concept orientation’ in biomedical terminology research. (shrink)

If media studies are to become established as a genuine science, then it needs to be determined what the subject matter of this science is to be. I propose a specification of this subject matter as consisting in: 1. the new sorts of digital entities that have been added to social reality through the invention of the digital computer, and 2. the new sorts of interactions involving human beings which such entities make possible. I support this proposal by examining examples (...) of some of the ways in which the digital products of emerging media differ from entities of other sorts. I then draw consequences from this examination to demonstrate how these products mark out a new realm within the larger domain of social ontology. (shrink)

Credentials play an important role in all modern societies, but the analysis of their nature and function has thus far been neglected by social philosophers. We present a view according to which the function of credentials is certify the identity and the institutional status (including the rights) of individuals. More importantly, credentials enable rights-holders to exercise their rights, so that for a particular right to be exercisable the right-holder should possess, carry and sometimes show to an authority (or QR code (...) scanner) a document of a specific kind. Driving licenses, identity cards, passports, boarding passes, library passes, credit cards, ATM cards, health insurance cards are all examples of credentials in this sense. Credentials have in every case a bearer, and the bearer should be able to carry them easily on his or her person. Credentials should also be inspectable – not least because credentials can be forged. The authors analyse several historical and contemporary examples of credentials, focusing on the credentials carried by the pilgrims of the Way of Saint James. (shrink)

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)

A collection of material on Husserl's Logical Investigations, and specifically on Husserl's formal theory of parts, wholes and dependence and its influence in ontology, logic and psychology. Includes translations of classic works by Adolf Reinach and Eugenie Ginsberg, as well as original contributions by Wolfgang Künne, Kevin Mulligan, Gilbert Null, Barry Smith, Peter M. Simons, Roger A. Simons and Dallas Willard. Documents work on Husserl's ontology arising out of early meetings of the Seminar for Austro-German Philosophy.

When governments collect data relating to economic activity they commonly employ a distinction between goods and services. Both goods and services have economic value. Goods (cars, houses, bottles of milk) are, very roughly, independent continuants which can be alienated (sold, gifted, rented, and so forth). Services (hairdressing, gardening, teaching) are, again very roughly, occurrents. They are occurrents which are further often said to be marked by the fact that production and consumption coincide. Social services under both headings typically involve combinations (...) of service provision. The patterns in question are primarily those of the family (where the patterns to be maintained or restored are, roughly, those characteristic of a healthy family life) and of the child (patterns characteristic of healthy development, provided by child protective services, who work to prevent child abuse). (shrink)

If we are to develop efficient, reliable and secure means for sharing information across healthcare systems and organizations, then a careful analysis of human actions will be needed. To address this need, the HL7 organization has proposed its Reference Information Model (RIM), which is designed to provide a comprehensive representation of the entire domain of healthcare centered around the phenomenon of human action. Taking the Basic Formal Ontology as our starting point, we examine the RIM from an ontological point of (...) view, describing how it fails to provide a representation of the healthcare domain which would enjoy the sort of clarity, coherence, rigor and completeness that is claimed on its behalf. (shrink)

This paper develops the Value-Based Theory of Reasons in some detail. The central part of the paper introduces a number of theoretically puzzling features of normative reasons. These include weight, transmission, overlap, and the promiscuity of reasons. It is argued that the Value-Based Theory of Reasons elegantly accounts for these features. This paper is programmatic. Its goal is to put the promising but surprisingly overlooked Value-Based Theory of Reasons on the table in discussions of normative reasons, and to draw attention (...) to a number of areas for fruitful further research. (shrink)

This paper applies the ontological framework developed by Roman Ingarden in his Controversy over the Existence of the World to the domain of mathematics, concluding with some remarks on parallels between the mode of existence of mathematical entities on the one hand and of values on the other.

Elon Musk famously predicted that an artificial intelligence superior to the smartest individual human would arrive by the year 2025. In response, Gary Marcus offered Musk a $1 million bet to the effect that he would be proved wrong. In specifying the conditions of this bet (which Musk did not take) Marcus lists the following ‘tasks that ordinary people can perform’ which, he claimed, AI will not be able to perform by the end of 2025. • Reliably drive a car (...) in a novel location that they haven’t previously encountered, even in the face of unusual circumstances like hand lettered signs, without the assistance of other humans. • Learn to ride a mountain bike off-road through forest trails. • Babysit children in an unfamiliar home and keep them safe. • Tend to the physical and psychological needs of an elderly or infirm person. Each of these tasks involves the application of practical or tacit knowledge, or what is also called ‘knowing how’, which is to say knowledge of a sort that is captured not by means of sentences or propositions or explicit rules, but rather through the expertise demonstrated in human actions. The talk addresses the puzzle that nowhere in the AI literature do we find a discussion of knowing how as a feature of human intelligence. (shrink)

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

This essay is a response to Luis M. Augusto’s intriguing paper on the rift between mainstream and formal ontology. I will show that there are in fact two questions at issue here: 1. concerning the links between mainstream and formal approaches within philosophy, and 2. concerning the application of philosophy (and especially philosophical ontology) in support of information-driven research for example in the life sciences.

We present a novel methodology for calculating the improvements obtained in successive versions of biomedical ontologies. The theory takes into account changes both in reality itself and in our understanding of this reality. The successful application of the theory rests on the willingness of ontology authors to document changes they make by following a number of simple rules. The theory provides a pathway by which ontology authoring can become a science rather than an art, following principles analogous to those that (...) have fostered the growth of modern evidence-based medicine. Although in this paper we focus on ontologies, the methodology can be generalized to other sorts of terminology-based artifacts, including Electronic Patient Records. (shrink)

Relevance logic has become ontologically fertile. No longer is the idea of relevance restricted in its application to purely logical relations among propositions, for as Dunn has shown in his (1987), it is possible to extend the idea in such a way that we can distinguish also between relevant and irrelevant predications, as for example between “Reagan is tall” and “Reagan is such that Socrates is wise”. Dunn shows that we can exploit certain special properties of identity within the context (...) of standard relevance logic in a way which allows us to discriminate further between relevant and irrelevant properties, as also between relevant and irrelevant relations. The idea yields a family of ontologically interesting results concerning the different ways in which attributes and objects may hang together. Because of certain notorious peculiarities of relevance logic, however,1 Dunn’s idea breaks down where the attempt is made to have it bear fruit in application to relations among entities which are of homogeneous type. (shrink)

For as long as there have been markets, there have been complaints about market motives. For much of this history, the two sides have talked past one another. Optimists about markets have mostly addressed other optimists, and failed to take seriously the kinds of relational values that might be at stake and the range of possible alternatives to market-based production. Pessimists about markets have mostly addressed other pessimists, and failed to take seriously the full range of market-involving economic structures and (...) the different kinds of psychologies compatible with market interactions. Recently, there has been a break-through, on behalf of the optimists. According to the model of exchange as mutual assistance, an exchange can be perceived as a joint activity for mutual benefit - and needn't involve self-directed motives at all. This essay pushes back, on behalf of the market pessimists. The essay develops a contrast between exchange as mutual assistance and an ideal of production as caring solidarity, in which production is a joint activity of caring about one another. This alternative ideal draws on Marxist, socialist, feminist, and Christian traditions, and, in particular, on recent work on care, solidarity, and alienation. These two models – exchange as mutual assistance and production as caring solidarity – share key features, including an emphasis on reasoning from a ‘we-perspective’, on trusting one another, and on resisting a familiar self/other motivational dichotomy. Key differences are developed in detail. The essay concludes by discussing the implications for an economics of caring solidarity, with discussion of the limitations of various market socialist strategies. (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)

Many political theorists defend the view that egalitarian justice should extend from the domestic to the global arena. Despite its intuitive appeal, this ‘global egalitarianism’ has come under attack from different quarters. In this article, we focus on one particular set of challenges to this view: those advanced by domestic egalitarians. We consider seven types of challenges, each pointing to a specific disanalogy between domestic and global arenas which is said to justify the restriction of egalitarian justice to the former, (...) and argue that none of them – both individually and jointly – offers a conclusive refutation of global egalitarianism. (shrink)

This short paper seeks to throw light on the sense in which the prior knowledge used by AlphaFold is to be understood in ontological terms. The paper is a comment on the 2022 ICBO presentation by Jobst Landgrebe entitled “What AlphaFold teaches us about deep learning with prior knowledge”.

Can there be a theory-free experience? And what would be the object of such an experience. Drawing on ideas set out by Husserl in the “Crisis” and in the second book of his “Ideas”, the paper presents answers to these questions in such a way as to provide a systematic survey of the content and ontology of common sense. In the second part of the paper Husserl’s ideas on the relationship between the common-sense world (what he called the ‘life-world’) and (...) the world of physical theory are subjected to a critical evaluation. The relation of Husserl’s ideas to current work in folk psychology and naive physics and to the direct realism of J. J. Gibson are also treated. (shrink)

This paper is a fresh attempt to articulate the role of a theory of truthmakers. We argue that truthmaker theory constitutes a cornerstone of good methodology in metaphysics, but that a conflation of truthmaker theory with the theory of truth has been responsible for certain excesses associated with truthmaker-based approaches in the recent literature. If truthmaker theory is not a component of a theory of truth, then truthmaker maximalism – the view that every truth has a truthmaker – loses its (...) primary motivation. More generally, if the task of truthmaker theory is not to provide a definition or account of truth in truthmaker terms, there is no pressing need for hard, a priori principles stating which truths have truthmakers and which do not. (shrink)