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)

Performative accounts of personhood argue that group agents are persons, fit to be held responsible within the social sphere. Nonetheless, these accounts want to retain a moral distinction between group and individual persons. That: Group-persons can be responsible for their actions qua persons, but that group-persons might nonetheless not have rights equivalent to those of human persons. I present an argument which makes sense of this disanalogy, without recourse to normative claims or additional ontological commitments. I instead ground rights in (...) the different relations in which performative persons stand in relation to one another. (shrink)

We discuss recent progress in the development of cognitive ontologies and summarize three challenges in the coordinated development and application of these resources. Challenge 1 is to adopt a standardized definition for cognitive processes. We describe three possibilities and recommend one that is consistent with the standard view in cognitive and biomedical sciences. Challenge 2 is harmonization. Gaps and conflicts in representation must be resolved so that these resources can be combined for mark-up and interpretation of multi-modal data. Finally, Challenge (...) 3 is to test the utility of these resources for large-scale annotation of data, search and query, and knowledge discovery and integration. As term definitions are tested and revised, harmonization should enable coordinated updates across ontologies. However, the true test of these definitions will be in their community-wide adoption which will test whether they support valid inferences about psychological and neuroscientific data. (shrink)

Report on Dagstuhl Seminar 07132, Schloss Dagstuhl, March 27-30 , 2007.

Research has indicated that microRNAs (miRNAs), a special class of non-coding RNAs (ncRNAs), can perform important roles in different biological and pathological processes. miRNAs’ functions are realized by regulating their respective target genes (targets). It is thus critical to identify and analyze miRNA-target interactions for a better understanding and delineation of miRNAs’ functions. However, conventional knowledge discovery and acquisition methods have many limitations. Fortunately, semantic technologies that are based on domain ontologies can render great assistance in this regard. In our (...) previous investigations, we developed a miRNA domain-specific application ontology, Ontology for MIcroRNA Target (OMIT), to provide the community with common data elements and data exchange standards in the miRNA research. This paper describes (1) our continuing efforts in the OMIT ontology development and (2) the application of the OMIT to enable a semantic approach for knowledge capture of miRNA-target interactions. (shrink)

In recent years, sequencing technologies have enabled the identification of a wide range of non-coding RNAs (ncRNAs). Unfortunately, annotation and integration of ncRNA data has lagged behind their identification. Given the large quantity of information being obtained in this area, there emerges an urgent need to integrate what is being discovered by a broad range of relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a systematically structured and precisely defined controlled vocabulary for the (...) domain of ncRNAs, thereby facilitating the discovery, curation, analysis, exchange, and reasoning of data about structures of ncRNAs, their molecular and cellular functions, and their impacts upon phenotypes. The goal of NCRO is to serve as a common resource for annotations of diverse research in a way that will significantly enhance integrative and comparative analysis of the myriad resources currently housed in disparate sources. It is our belief that the NCRO ontology can perform an important role in the comprehensive unification of ncRNA biology and, indeed, fill a critical gap in both the Open Biological and Biomedical Ontologies (OBO) Library and the National Center for Biomedical Ontology (NCBO) BioPortal. Our initial focus is on the ontological representation of small regulatory ncRNAs, which we see as the first step in providing a resource for the annotation of data about all forms of ncRNAs. (shrink)

The Planteome project provides a suite of reference and species-specific ontologies for plants and annotations to genes and phenotypes. Ontologies serve as common standards for semantic integration of a large and growing corpus of plant genomics, phenomics and genetics data. The reference ontologies include the Plant Ontology, Plant Trait Ontology, and the Plant Experimental Conditions Ontology developed by the Planteome project, along with the Gene Ontology, Chemical Entities of Biological Interest, Phenotype and Attribute Ontology, and others. The project also provides (...) access to species-specific Crop Ontologies developed by various plant breeding and research communities from around the world. We provide integrated data on plant traits, phenotypes, and gene function and expression from 95 plant taxa, annotated with reference ontology terms. (shrink)

Moral particularism, on some interpretations, is committed to a shapeless thesis: the moral is shapeless with respect to the natural. (Call this version of moral particularism ‘shapeless moral particularism’). In more detail, the shapeless thesis is that the actions a moral concept or predicate can be correctly applied to have no natural commonality (or shape) amongst them. Jackson et al. (Ethical particularism and patterns, Oxford University Press, Oxford, 2000) argue, however, that the shapeless thesis violates the platitude ‘predication supervenes on (...) nature’—predicates or concepts apply because of how things are, and therefore ought to be rejected. I defend shapeless moral particularism by arguing that Jackson et al’s contention is less compelling than it firstly appears. My defense is limited in the sense that it does not prove shapeless moral particularism to be right and it leaves open the possibility that shapeless moral particularism might attract criticisms different from the ones advanced by Jackson et al. But at the very least, I hope to say enough to undermine Jackson et al’s powerful attack against it. The plan of this paper is as follows. Section 1 glosses the view of moral particularism and why it is taken to be essentially committed to the shapeless thesis. Section 2 examines a Wittgensteinian argument for the shapeless thesis. I shall argue that the Canberrans’ counter-arguments against it on grounds of disjunctive commonality and conceptual competence do not succeed. Section 3 explicates Canberrans’ predication supervenience argument against the shapeless thesis. Section 4 offers my criticisms of the Canberrans’ predication supervenience argument. In view of the above discussions, in Sect. 5, I conclude that there is no compelling argument (from the Canberrans) to believe that the shapeless thesis fails (as I have argued in Sect. 4). In fact, there is some good reason for us to believe it (as I have argued in Sect. 2). If so, I contend that moral particularism, when construed as essentially committed to the shapeless thesis, still remains as a live option. (shrink)

Is the societal-level of analysis sufficient today to understand the values of those in the global workforce? Or are individual-level analyses more appropriate for assessing the influence of values on ethical behaviors across country workforces? Using multi-level analyses for a 48-society sample, we test the utility of both the societal-level and individual-level dimensions of collectivism and individualism values for predicting ethical behaviors of business professionals. Our values-based behavioral analysis indicates that values at the individual-level make a more significant contribution to (...) explaining variance in ethical behaviors than do values at the societal-level. Implicitly, our findings question the soundness of using societal-level values measures. Implications for international business research are discussed. (shrink)

REMARKS ON EVOLUTION AND TIME-SCALES, Graham Cairns-Smith; HODGSON'S BLACK BOX, Thomas Clark; DO HODGSON'S PROPOSITIONS UNIQUELY CHARACTERIZE FREE WILL?, Ravi Gomatam; WHAT SHOULD WE RETAIN FROM A PLAIN PERSON'S CONCEPT OF FREE WILL?, Gilberto Gomes; ISOLATING DISPARATE CHALLENGES TO HODGSON'S ACCOUNT OF FREE WILL, Liberty Jaswal; FREE AGENCY AND LAWS OF NATURE, Robert Kane; SCIENCE VERSUS REALIZATION OF VALUE, NOT DETERMINISM VERSUS CHOICE, Nicholas Maxwell; COMMENTS ON HODGSON, J.J.C. Smart; THE VIEW FROM WITHIN, Sean Spence; COMMENTARY ON HODGSON, Henry (...) Stapp. (shrink)

This review essay assesses Michael Jackson’s ongoing project of staging an encounter between anthropology and philosophy in two books: Lifeworlds (2013) and As Wide as the World Is Wise (2016). Considering his philosophical enrichment of ethnographic theory and method, this essay addresses foundational questions about the prospects and practices of interdisciplinary engagement. It also suggests future avenues for continued dialogue between philosophy and anthropology.

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)

Frankfurt cases are supposed to provide us with counterexamples to the principle of alternative possibilities. Among the most well known responses to these cases is what John Fischer has dubbed the flicker of freedom strategy. Here we revisit a version of this strategy, which we refer to as the fine-grained response. Although a number of philosophers, including some who are otherwise unsympathetic to Frankfurt’s argument, have dismissed the fine grained response, we believe there is a good deal to be said (...) on its behalf. We argue, in particular, that reflection on certain cases involving omissions undermines the main objections to the response and also provides the groundwork for an argument in support of it. (shrink)

A person presented with adequate but not conclusive evidence for a proposition is in a position voluntarily to acquire a belief in that proposition, or to suspend judgment about it. The availability of doxastic options in such cases grounds a moderate form of doxastic voluntarism not based on practical motives, and therefore distinct from pragmatism. In such cases, belief-acquisition or suspension of judgment meets standard conditions on willing: it can express stable character traits of the agent, it can be responsive (...) to reasons, and it is compatible with a subjective awareness of the available options. (shrink)

Introductory Chapter to the _Cambridge Handbook of Situated Cognition_ (CUP, 2009).

This paper sets out an account of trust in AI as a relationship between clinicians, AI applications, and AI practitioners in which AI is given discretionary authority over medical questions by clinicians. Compared to other accounts in recent literature, this account more adequately explains the normative commitments created by practitioners when inviting clinicians’ trust in AI. To avoid committing to an account of trust in AI applications themselves, I sketch a reductive view on which discretionary authority is exercised by AI (...) practitioners through the vehicle of an AI application. I conclude with four critical questions based on the discretionary account to determine if trust in particular AI applications is sound, and a brief discussion of the possibility that the main roles of the physician could be replaced by AI. (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)

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)

The adoption of web-based telecare services has raised multifarious ethical concerns, but a traditional principle-based approach provides limited insight into how these concerns might be addressed and what, if anything, makes them problematic. We take an alternative approach, diagnosing some of the main concerns as arising from a core phenomenon of shifting trust relations that come about when the physician plays a less central role in the delivery of care, and new actors and entities are introduced. Correspondingly, we propose an (...) applied ethics of trust based on the idea that patients should be provided with good reasons to trust telecare services, which we call sound trust. On the basis of this approach, we propose several concrete strategies for safeguarding sound trust in telecare. (shrink)

In recent years, sequencing technologies have enabled the identification of a wide range of non-coding RNAs (ncRNAs). Unfortunately, annotation and integration of ncRNA data has lagged behind their identification. Given the large quantity of information being obtained in this area, there emerges an urgent need to integrate what is being discovered by a broad range of relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a systematically structured and precisely defined controlled vocabulary for the (...) domain of ncRNAs, thereby facilitating the discovery, curation, analysis, exchange, and reasoning of data about structures of ncRNAs, their molecular and cellular functions, and their impacts upon phenotypes. The goal of NCRO is to serve as a common resource for annotations of diverse research in a way that will significantly enhance integrative and comparative analysis of the myriad resources currently housed in disparate sources. It is our belief that the NCRO ontology can perform an important role in the comprehensive unification of ncRNA biology and, indeed, fill a critical gap in both the Open Biological and Biomedical Ontologies (OBO) Library and the National Center for Biomedical Ontology (NCBO) BioPortal. Our initial focus is on the ontological representation of small regulatory ncRNAs, which we see as the first step in providing a resource for the annotation of data about all forms of ncRNAs. The NCRO ontology is free and open to all users. (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)

This article constructively retrieves St. Anselm of Canterbury’s theory of retributive justice and provides a defense of what can be called the retributive model of hell. In the first part of this article, we develop the place of retributive punishment in Anselm’s thinking and discuss how and when retributive punishment is a good thing. In the second part, we apply Anselm’s thinking on retributive justice to the problem of hell and provide a defense of how hell, defined as a state (...) of receiving retributive, damnatory, and irreversible punishment, is good. We then address a series of objections. Despite some criticism that both Anselm and the retributive model of hell receive in the contemporary literature, Anselm’s account of retributive justice can make unique and constructive contributions to the contemporary discussion of hell; by retrieving and applying Anselm’s thought to the problem of hell, we intend to kill two birds with one stone. (shrink)

The principle of alternative possibilities tells us that an agent is morally responsible for an action only if he could have done otherwise. Frankfurt-style cases provide an extremely influential challenge to the PAP . And Frankfurt-style compatibilists are motivated to accept compatibilism about responsibility and determinism in part due to FSCs. But there is a significant tension between our judgments about responsibility in FSCs and our judgments about responsibility in certain omissions cases. This tension has thus far largely been treated (...) as an internal puzzle for defenders of FSCs to solve. My goal here is to regiment this tension into a clear argument which undermines the FSC based critique of PAP. I will also argue that there is an in principle reason to doubt that Frankfurt-Style Compatibilists will be able to successfully respond to my argument. (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)

Recent work by Peijnenburg, Atkinson, and Herzberg suggests that infinitists who accept a probabilistic construal of justification can overcome significant challenges to their position by attending to mathematical treatments of infinite probabilistic regresses. In this essay, it is argued that care must be taken when assessing the significance of these formal results. Though valuable lessons can be drawn from these mathematical exercises (many of which are not disputed here), the essay argues that it is entirely unclear that the form of (...) infinitism that results meets a basic requirement: namely, providing an account of infinite chains of propositions qua reasons made available to agents. (shrink)

ABSTRACT Many of our common-sense moral judgments seemingly imply the existence of moral luck. I attempt to avoid moral luck while retaining most of these judgments. I defend a view on which agents have moral equality of opportunity. This allows us to account for our anti-moral-luck intuitions at less cost than has been previously recognized.

Michael Moore’s recent book Mechanical Choices: The Responsibility of the Human Machine is full of rich, insightful discussion of many important issues related to free will and moral responsibility. I will focus on one particular issue raised by Moore: the question of whether we can have control over the past. Moore defends a compatibilist account of moral responsibility on which there are some possible cases in which agents do have such control. But Moore seeks to avoid positing too much control (...) over the past. I will argue that Moore’s attempt is not successful. Furthermore, I will try to show that compatibilists in general face a serious challenge regarding control over the past. In sections 1 and 2 I will explore Moore’s views. In section 3 and 4 I will offer a general argument against compatibilism about moral responsibility and determinism. (shrink)

The COVID-19 pandemic revealed numerous weaknesses in pandemic preparedness and response, including underfunding, inadequate surveillance, and inequitable distribution of countermeasures. To overcome these weaknesses for future pandemics, WHO released a zero draft of a pandemic treaty in February, 2023, and subsequently a revised bureau's text in May, 2023. COVID-19 made clear that pandemic prevention, preparedness, and response reflect choices and value judgements. These decisions are therefore not a purely scientific or technical exercise, but are fundamentally grounded in ethics. The latest (...) treaty draft reflects these ethical considerations by including a section entitled Guiding Principles and Approaches. Most of these principles are ethical—they establish core values that undergird the treaty. Unfortunately, the treaty draft's set of principles are numerous, overlapping, and show inadequate coherence and consistency. We propose two improvements to this section of the draft pandemic treaty. First, key guiding ethical principles should be clearer and more precise than they currently are. Second, the link between ethical principles and policy implementation should be clearly established and define boundaries on acceptable interpretation, ensuring that signatories abide by these principles. (shrink)

Does ?ought? imply ?can? for collectives' obligations? In this paper I want to establish two things. The first, what a collective obligation means for members of the collective. The second, how collective ability can be ascertained. I argue that there are four general kinds of obligation, which devolve from collectives to members in different ways, and I give an account of the distribution of obligation from collectives to members for each of these kinds. One implication of understanding collective obligation and (...) ability in the proposed way is that a group can be blameworthy for failing to realize its obligation even when no member of the group is blameworthy for failing to realize her obligation. (shrink)

Experiments in particle physics have hitherto failed to produce any significant evidence for the many explicit models of physics beyond the Standard Model (BSM) that had been proposed over the past decades. As a result, physicists have increasingly turned to model-independent strategies as tools in searching for a wide range of possible BSM effects. In this paper, we describe the Standard Model Effective Field Theory (SM-EFT) and analyse it in the context of the philosophical discussions about models, theories, and (bottom-up) (...) effective field theories. We find that while the SM-EFT is a quantum field theory, assisting experimentalists in searching for deviations from the SM, in its general form it lacks some of the characteristic features of models. Those features only come into play if put in by hand or prompted by empirical evidence for deviations. Employing different philosophical approaches to models, we argue that the case study suggests not to take a view on models that is overly permissive because it blurs the lines between the different stages of the SM-EFT research strategies and glosses over particle physicists' motivations for undertaking this bottom-up approach in the first place. Looking at EFTs from the perspective of modelling does not require taking a stance on some specific brand of realism or taking sides in the debate between reduction and emergence into which EFTs have recently been embedded. (shrink)

A retelling of Plato's famous cave allegory. Inspired by Dōgen, Nietzsche, and Wittgenstein.

Klein’s account of epistemic justification, infinitism, supplies a novel solution to the regress problem. We argue that concentrating on the normative aspect of justification exposes a number of unpalatable consequences for infinitism, all of which warrant rejecting the position. As an intermediary step, we develop a stronger version of the ‘finite minds’ objection.

The essay constructs an ontological theory designed to capture the categories instantiated in those portions or levels of reality which are captured in our common sense conceptual scheme. It takes as its starting point an Aristotelian ontology of “substances” and “accidents”, which are treated via the instruments of mereology and topology. The theory recognizes not only individual parts of substances and accidents, including the internal and external boundaries of these, but also universal parts, such as the “humanity” which is an (...) essential part of both Tom and Dick, and also “individual relations”, such as Tom’s promise to Dick, or their current handshake. (shrink)

Both Philip and Andrew are philosophy students whose interests converge around the philosophy of technology broadly understood. Philip's interest is specifically aimed toward the ethics of Transhumanism and depictions of Transhumanism in works of fiction. On the other hand, Andrew finds himself more focused on religious behavior in the technological world. While the two perspectives might not seem that close, there is certain to be an overlap in Andrew and Philip's shared understanding of how technological phenomena play (...) a crucial role concerning religion and society. (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)

Some properties are causally relevant for a certain effect, others are not. In this paper we describe a problem for our understanding of this notion and then offer a solution in terms of the notion of a program explanation.

Angela Mendelovici’s book The Phenomenal Basis of Intentionality is a paradigm-establishing monograph within the phenomenal intentionality research program. Mendelovici argues that extant theories of intentionality that do not appeal to consciousness are both empirically and metaphysically inadequate, and a coherent, consciousness-based alternative can adequately explain (or explain away) all alleged cases of intentionality. While I count myself a fellow traveler, I discuss four choice-points where Mendelovici has taken, I believe, the wrong fork. (1) The explanatory relation that holds between intentional (...) and phenomenal properties is not identity but realization. (2) The mechanism that generates derivatively representational states is not content self-ascription but neural re-wiring. (3) The source of semantic structure within phenomenal-intentional states is not external structure and/or second-order co-instantiation but primitive phenomenal ascription. (4) The mode of presence of contents within phenomenal-intentional states is not being part of a superficial characterization, but being monadically present as an intentional object. (shrink)

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)

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

This paper has two goals: (1) to defend a particular response to the problem of resultant moral luck and (2) to defend the claim that we are only responsible for what we could have avoided. Cases of overdetermination threaten to undermine the claim that we are only responsible for what we could have avoided. To deal with this issue, I will motivate a particular way of responding to the problem of resultant moral luck. I defend the view that one's degree (...) of responsibility is immune to moral luck but the scope of events for which one is responsible is subject to moral luck. I will then argue that this view allows us to explain away certain intuitions about responsibility and overdetermination (as well as similar intuitions regarding Frankfurt Cases). As a result, the claim that we are only responsible for what we could have avoided becomes significantly more plausible. (shrink)

According to a traditional view, humans are superior to their non‐human terrestrial companions because they alone are “rational animals.” Although the traditional view is presupposed by our social and legal institutions, it has been called into question by modern science: Darwin himself claimed that humans differ in degree rather than in kind from animals, and recent discoveries in comparative animal cognition have seemed to confirm Darwin's assertion. Sustaining the traditional view in light of these discoveries calls out for a careful (...) comparison of the human mind with its precursors, the vertebrate mind and the mammalian mind. Psychological capacities shared across the animal kingdom are repurposed in humans, rendering humans uniquely capable of rationality. To be rational is to respond appropriately to value. Humans as such are not rational animals, but have the potential to become rational animals. This potential marks a morally relevant difference in kind between humans and non‐human animals. (shrink)

We have a variety of different ways of dividing up, classifying, mapping, sorting and listing the objects in reality. The theory of granular partitions presented here seeks to provide a general and unified basis for understanding such phenomena in formal terms that is more realistic than existing alternatives. Our theory has two orthogonal parts: the first is a theory of classification; it provides an account of partitions as cells and subcells; the second is a theory of reference or intentionality; it (...) provides an account of how cells and subcells relate to objects in reality. We define a notion of well-formedness for partitions, and we give an account of what it means for a partition to project onto objects in reality. We continue by classifying partitions along three axes: (a) in terms of the degree of correspondence between partition cells and objects in reality; (b) in terms of the degree to which a partition represents the mereological structure of the domain it is projected onto; and (c) in terms of the degree of completeness with which a partition represents this domain. (shrink)

A theory of the first-person plural occupies a unique place in philosophical investigations into intersubjectivity and social cognition. In order for the referent of the first-person plural—“the We”—to come into existence, it seems there must be a shared ground of communicative possibility, but this requires a non-circular explanation of how this ground could be shared in the absence of a pre-existing context of communicative conventions. Margaret Gilbert’s and John Searle’s theories of collective intentionality capture important aspects of the We, but (...) fail to fully account for this shared ground of communicative possibility. This paper argues that Merleau-Ponty’s concept of intercorporeity helps reconcile the positive aspects of these accounts while also explaining how the genesis of the social world is continuous with perceptual life in general. This enables an account of the first-person plural as dependent on reciprocal communicative interaction without the need to posit a primitive or primordial “we-mode” of consciousness. “Intercorporeity” designates a bodily openness to others that is not fundamentally different in kind from the general style of bodily comportment found in Merleau-Ponty’s rich analyses of perceptual life. (shrink)