In this paper we propose an Ontology of Commercial Exchange (OCE) based on Basic Formal Ontology. OCE is designed for re-use in the Industrial Ontologies Foundry (IOF) and in other ontologies addressing different aspects of human social behavior involving purchasing, selling, marketing, and so forth. We first evaluate some of the design patterns used in the Financial Industry Business Ontology (FIBO) and Product Types Ontology (PTO). We then propose terms and definitions that we believe will improve the representation of contractual (...) obligations, sales processes, and their associated documents. A commercial exchange, for instance, involves mutual agreement to reciprocate actions, such as transferring money, performing a service, or transferring goods. (shrink)

We propose capability as a universal or type intermediate between function and disposition. A capability is, broadly speaking, a disposition that is of a type whose instances can be evaluated on the basis of how well they are realized. A function, on the view we are proposing, is a capability the possession of which is the rationale for the existence of its bearer. To say for example that a water pump has the function to pump water is to say that (...) the pump exists because something was needed that would pump water. A water pump may have many capabilities, including: to be weatherproof, to run without lubricant, to be transportable, and so forth. But its function is to pump water. We focus here on capabilities possessed by humans – such as piano playing or language using – and we explore the relation between capabilities of these sorts and structures in the brain. (shrink)

We propose a domain-level ontology of plays for the facilitation of play-based collaborative autonomy among unmanned and manned-unmanned aircraft teams in the Army’s Unmanned Aircraft System (UAS) mission domain. We define a play as a type of plan that prescribes some pattern of intentional acts that are intended to reliably result in some goal in some competitive context, and which specifies one or more roles that are realized by those prescribed intentional acts. The ontology is well suited to be extended (...) to other types of military and nonmilitary unmanned vehicle operations. (shrink)

We propose a definition of capability as a class intermediate between function and disposition as the latter are defined in Basic Formal Ontology (BFO). A disposition inheres in a material entity and is realized in a certain kind of process. An example is the disposition of a glass to break when struck, which is realized when it shatters. A function is a disposition which is (simply put) the rationale for the existence of its bearer. To say for example that a (...) water pump has the function to pump water is to say that the pump exists because something was needed that would pump water. Capabilities are a special sort of disposition in that that, like functions, they can be evaluated on the basis of how well they are realized. They differ from functions in that their realizations are not the rationale – not the primary reason – for the existence of their bearers. Thus, a water pump may have many capabilities, including to be weatherproof, to run without lubricant, and so forth, but only one function. All functions are capabilities on the view we defend, but not all capabilities are functions. We develop a series of axioms to distinguish capabilities formally from both dispositions and functions and provide examples of the use of ‘capability’ in a variety of domains. (shrink)

Applied ontologies have been used more and more frequently to enhance systems engineering. In this paper, we argue that adopting principles of ontological realism can increase the benefits that ontologies have already been shown to provide to the systems engineering process. Moreover, adopting Basic Formal Ontology (BFO), an ISO standard for top-level ontologies from which more domain specific ontologies are constructed, can lead to benefits in four distinct areas of systems engineering: (1) interoperability, (2) standardization, (3) testing, and (4) data (...) exploitation. Reaping these benefits in a model-based systems engineering (MBSE) context requires utilizing an ontology’s vocabulary when modeling systems and entities within those systems. If the chosen ontology abides by the principles of ontological realism, a semantic standard capable of uniting distinct domains, using BFO as a hub, can be leveraged to promote greater interoperability among systems. As interoperability and standardization increase, so does the ability to collect data during the testing and implementation of systems. These data can then be reasoned over by computational reasoners using the logical axioms within the ontology. This, in turn, generates new data that would have been impossible or too inefficient to generate without the aid of computational reasoners. (shrink)

In “Toward an Ontology of Commercial Exchange” [11], we proposed human readable definitions for terms that are central to an ontology of commercial exchange. This paper furthers that project in two ways. First, the definitions have been modified to be compatible with the Common Core Ontologies (CCO). CCO is used in a wide variety of domains including the industrial and military domains. Having a commerce ontology compatible with CCO allows data about the exchange of goods relevant to those domains to (...) be tagged with compatible ontologies. Second, we propose preliminary formalizations of these definitions, with the aim of informing the creation of an ontology which can be used to assist in reasoning over businessrelated data. (shrink)

The COVID-19 pandemic prompted immense work on the investigation of the SARS-CoV-2 virus. Rapid, accurate, and consistent interpretation of generated data is thereby of fundamental concern. Ontologies––structured, controlled, vocabularies––are designed to support consistency of interpretation, and thereby to prevent the development of data silos. This paper describes how ontologies are serving this purpose in the COVID-19 research domain, by following principles of the Open Biological and Biomedical Ontology (OBO) Foundry and by reusing existing ontologies such as the Infectious Disease Ontology (...) (IDO) Core, which provides terminological content common to investigations of all infectious diseases. We report here on the development of an IDO extension, the Virus Infectious Disease Ontology (VIDO), a reference ontology covering viral infectious diseases. We motivate term and definition choices, showcase reuse of terms from existing OBO ontologies, illustrate how ontological decisions were motivated by relevant life science research, and connect VIDO to the Coronavirus Infectious Disease Ontology (CIDO). We next use terms from these ontologies to annotate selections from life science research on SARS-CoV-2, highlighting how ontologies employing a common upper-level vocabulary may be seamlessly interwoven. Finally, we outline future work, including bacteria and fungus infectious disease reference ontologies currently under development, then cite uses of VIDO and CIDO in host-pathogen data analytics, electronic health record annotation, and ontology conflict-resolution projects. (shrink)

COVID-19 often manifests with different outcomes in different patients, highlighting the complexity of the host-pathogen interactions involved in manifestations of the disease at the molecular and cellular levels. In this paper, we propose a set of postulates and a framework for systematically understanding complex molecular host-pathogen interaction networks. Specifically, we first propose four host-pathogen interaction (HPI) postulates as the basis for understanding molecular and cellular host-pathogen interactions and their relations to disease outcomes. These four postulates cover the evolutionary dispositions involved (...) in HPIs, the dynamic nature of HPI outcomes, roles that HPI components may occupy leading to such outcomes, and HPI checkpoints that are critical for specific disease outcomes. Based on these postulates, an HPI Postulate and Ontology (HPIPO) framework is proposed to apply interoperable ontologies to systematically model and represent various granular details and knowledge within the scope of the HPI postulates, in a way that will support AI-ready data standardization, sharing, integration, and analysis. As a demonstration, the HPI postulates and the HPIPO framework were applied to study COVID-19 with the Coronavirus Infectious Disease Ontology (CIDO), leading to a novel approach to rational design of drug/vaccine cocktails aimed at interrupting processes occurring at critical host-coronavirus interaction checkpoints. Furthermore, the host-coronavirus protein-protein interactions (PPIs) relevant to COVID-19 were predicted and evaluated based on prior knowledge of curated PPIs and domain-domain interactions, and how such studies can be further explored with the HPI postulates and the HPIPO framework is discussed. (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)

Volume 20, Issue 8, August 2020, Page 96-98.

The COVID-19 pandemic prompted immense work on the investigation of the SARS-CoV-2 virus. Ontologies – structured, controlled, vocabularies – are designed to support consistency of interpretation, and thereby to prevent the development of data silos. This paper describes how ontologies are serving this purpose in the virus research domain, following the principles of the Open Biological and Biomedical Ontology (OBO) Foundry and drawing on the resources of the Infectious Disease Ontology (IDO) Core. We report the development of the Virus Infectious (...) Disease Ontology (VIDO), a reference ontology extending IDO Core covering viral infectious diseases. We examine newly minted terms, showcase ontology term reuse, and illustrate the use of VIDO by annotating selections from recent life science research on SAR-CoV-2, in the interest of supporting machine learning projects. (shrink)

Pavarini et al. argue for the potential benefits of using games and other technologies to collect empirical data to enhance bioethics research. They propose a methodology called “design bioe...

A recent Supreme Court decision, Kumho Tire Co., Ltd. v. Carmichael, may have substantial impact on psychological expert testimony. Previous criteria for admissibility of scientific expert testimony now apply broadly to expert testimony, not just testimony narrowly grounded in scientific evidence. Judges will determine the relevance and reliability of all expert testimony, including that based on clinical experience or training. Admissible testimony will either satisfy the criteria established in Daubert v. Merrell Dow Pharmaceuticals, Inc. or meet similarly rigorous standards (...) judged appropriate to the particular field involved. Because psychological testimony has varied in its evidentiary basis, sometimes relying on science and otherwise on clinical training or experience, court decisions will gradually determine the precedent for its admissibility. We also discuss long-term consequences for the credibility of psychological expert testimony and the relation between psychology and law. (shrink)

This book provides a philosophical overview of Umberto Eco's historical and cultural development as a unique, internationally recognized public intellectual who communicates his ideas to both an academic and a popular audience. It describes Eco's intellectual development from his childhood during World War II and student involvement as a Catholic youth activist and scholar of the Middle Ages, to his early writings on the "openness" of modern works such as Joyce's Finnegans Wake. Merrell also explores Eco's pioneering role in (...) semiotics and his later career as a novelist. (shrink)

From the time of Locke, discussions of personal identity have often ignored the question of our basic metaphysical nature: whether we human people are biological organisms, spatial or temporal parts of organisms, bundles of perceptions, or what have you. The result of this neglect has been centuries of wild proposals and clashing intuitions. What Are We? is the first general study of this important question. It beings by explaining what the question means and how it differs from others, such as (...) questions of personal identity and the mind-body problem. It then examines in some depth the main possible accounts of our metaphysical nature, detailing both their theoretical virtues and the often grave difficulties they face. The book does not endorse any particular account of what we are, but argues that the matter turns on more general issues in the ontology of material things. If composition is universal--if any material things whatever make up something bigger--then we are temporal parts of organisms. If things never compose anything bigger, so that there are only mereological simples, then we too are simples--perhaps the immaterial substances of Descartes--or else we do not exist at all (a view Olson takes very seriously). The intermediate view that some things compose bigger things and others do not leads almost inevitably to the conclusion that we are organisms. So we can discover what we are by working out when composition occurs. (shrink)

Consider the following three claims. (i) There are no truths of the form ‘p and ~p’. (ii) No one holds a belief of the form ‘p and ~p’. (iii) No one holds any pairs of beliefs of the form {p, ~p}. Irad Kimhi has recently argued, in effect, that each of these claims holds and holds with metaphysical necessity. Furthermore, he maintains that they are ultimately not distinct claims at all, but the same claim formulated in different ways. I find (...) his argument suggestive, if not entirely transparent. I do think there is at least an important kernel of truth even in (iii), and that (i) ultimately explains what’s right about the other two. Consciousness of an impossibility makes belief in the obtaining of the corresponding state of affairs an impossibility. Interestingly, an appreciation of this fact brings into view a novel conception of inference, according to which it consists in the consciousness of necessity. This essay outlines and defends this position. A central element of the defense is that it reveals how reasoners satisfy what Paul Boghossian calls the Taking Condition and do so without engendering regress. (shrink)

Concepts: Core Readings traces the develoment of one of the most active areas of investigation in cognitive science. This comprehensive volume brings together the essential background readings on concepts from philosophy, psychology, and linguistics, while providing a broad sampling of contemporary research. The first part of the book centers around the fall of the Classical Theory of Concepts in the face of attacks by W.V.O. Quine, Ludwig Wittgenstein, Eleanor Rosch, and others, emphasizing the emergence and development of the Prototype Theory (...) and the controversies it spurred. The second part surveys a broad range of contemporary theories—Neoclassical Theories, the Prototype Theory, the Theory-Theory, and Conceptual Atomism. (shrink)

I argue that to have an attitude is, primarily, (1.) to have a dispositional profile that matches, to an appropriate degree and in appropriate respects, a stereotype for that attitude, typically grounded in folk psychology, and secondarily, (2.) in some cases also to meet further stereotypical attitude-specific conditions. To have an attitude, on the account I will recommend here, is mainly a matter of being apt to interact with the world in patterns that ordinary people would regard as characteristic of (...) having that attitude. I contrast this view with alternative views that treat having an attitude as a matter of possessing some particular internally stored representational content or some other "deep" structural feature. (shrink)

Rationalization, in our intended sense of the term, occurs when a person favors a particular conclusion as a result of some factor (such as self-interest) that is of little justificatory epistemic relevance, if that factor then biases the person’s subsequent search for, and assessment of, potential justifications for the conclusion. Empirical evidence suggests that rationalization is common in people’s moral and philosophical thought. We argue that it is likely that the moral and philosophical thought of philosophers and moral psychologists is (...) also pervaded by rationalization. Moreover, although rationalization has some benefits, overall it would be epistemically better if the moral and philosophical reasoning of people, including professional academics, were not as heavily influenced by rationalization as it likely is. We discuss the significance of our arguments for cognitive management and epistemic responsibility. (shrink)

We present evidence that mainstream Anglophone philosophy is insular in the sense that participants in this academic tradition tend mostly to cite or interact with other participants in this academic tradition, while having little academic interaction with philosophers writing in other languages. Among our evidence: In a sample of articles from elite Anglophone philosophy journals, 97% of citations are citations of work originally written in English; 96% of members of editorial boards of elite Anglophone philosophy journals are housed in majority-Anglophone (...) countries; and only one of the 100 most-cited recent authors in the Stanford Encyclopedia of Philosophy spent most of his career in non-Anglophone countries writing primarily in a language other than English. In contrast, philosophy articles published in elite Chinese-language and Spanish-language journals cite from a range of linguistic traditions, as do non-English-language articles in a convenience sample of established European-language journals. We also find evidence that work in English has more influence on work in other languages than vice versa and that when non-Anglophone philosophers cite recent work outside of their own linguistic tradition it tends to be work in English. (shrink)

Unconscious logical inference seems to rely on the syntactic structures of mental representations (Quilty-Dunn & Mandelbaum 2018). Other transitions, such as transitions using iconic representations and associative transitions, are harder to assimilate to syntax-based theories. Here we tackle these difficulties head on in the interest of a fuller taxonomy of mental transitions. Along the way we discuss how icons can be compositional without having constituent structure, and expand and defend the “symmetry condition” on Associationism (the idea that associative links and (...) transitions are perfectly symmetric). In the end, we show how a BIT (“bare inferential transition”) theory can cohabitate with these other non-inferential mental transitions. (shrink)

Philosophers tend to be pretty impressed by human self-knowledge. Descartes (1641/1984) thought our knowledge of our own stream of experience was the secure and indubitable foundation upon which to build our knowledge of the rest of the world. Hume – who was capable of being skeptical about almost anything – said that the only existences we can be certain of are our own sensory and imagistic experiences (1739/1978, p. 212). Perhaps the most prominent writer on self-knowledge in contemporary philosophy is (...) Sydney Shoemaker. The central aim of much of his work has been to show that certain sorts of error are impossible (1963, 1988, 1994). David Chalmers has likewise attempted to show that, for a suitably constrained class of beliefs about one’s own consciousness, error is impossible (2003, sec. 4.1). Even philosophers most of the community thinks of as pessimistic about self-knowledge of consciousness seem to me, really, to be fairly optimistic. Paul Churchland, famous for his disdain of ordinary people’s knowledge about the mind, compares the accuracy of introspection to the accuracy of sense perception – pretty good, presumably, about medium-sized, nearby matters (1985, 1988). Dan Dennett, often cited as a pessimist about introspective report, actually says that we can come close to infallibility when charitably interpreted (2002). The above references concern knowledge of the stream of conscious experience, but philosophers have also tended to be impressed with our self-knowledge of our attitudes, such as our beliefs and desires. Consider this: Although I can be wrong about its being sunny outside, I can’t in the same way be wrong, it seems, about the fact that I think it’s sunny outside. Some.. (shrink)

In On Empirically Equivalent Systems of the World from 1975, Quine formulated a thesis of underdetermination roughly to the effect that every scientific theory has an empirically equivalent but logically incompatible rival, one that cannot be discarded merely as a terminological variant of the former. For Quine, the truth of this thesis was an open question. If true, some would argue that it undermines any belief in scientific theories that is based purely on their empirical success. But despite its potential (...) significance, surprisingly little has been done by way of establishing or refuting it. My aim is to establish the thesis for as large a class of theories as possible. Under various precisifications of the concepts involved, I show that it holds for all consistent and recursively axiomatizable theories that postulate infinitely many theoretical entities. (shrink)

On an intellectualist approach to belief, the intellectual endorsement of a proposition (such as “The working poor deserve as much respect as the handsomely paid”) is sufficient or nearly sufficient for believing it. On a pragmatic approach to belief, intellectual endorsement is not enough. Belief is behaviorally demanding. To really, fully believe, you must also “walk the walk.” This chapter argues that the pragmatic approach is preferable on pragmatic grounds: It rightly directs our attention to what matters most in thinking (...) about belief. (shrink)

Eric Martin and Daniel N. Osherson present a theory of inductive logic built on model theory. Their aim is to extend the mathematics of Formal Learning Theory to a more general setting and to provide a more accurate image of empirical inquiry. The formal results of their study illuminate aspects of scientific inquiry that are not covered by the commonly applied Bayesian approach.

Can large language models produce expert‐quality philosophical texts? To investigate this, we fine‐tuned GPT‐3 with the works of philosopher Daniel Dennett. To evaluate the model, we asked the real Dennett 10 philosophical questions and then posed the same questions to the language model, collecting four responses for each question without cherry‐picking. Experts on Dennett's work succeeded at distinguishing the Dennett‐generated and machine‐generated answers above chance but substantially short of our expectations. Philosophy blog readers performed similarly to the experts, while ordinary (...) research participants were near chance distinguishing GPT‐3's responses from those of an “actual human philosopher”. (shrink)

Once again available in paperback, Plato is the first half of Eric Voegelin's Plato and Aristotle, the third volume of his five-volume Order and History, which ...

In this book, Eric Havelock presents a challenging account of the development of the idea of justice in early Greece, and particularly of the way justice changed as Greek oral tradition gradually gave way to the written word in a literate society. He begins by examining the educational functions of poets in preliterate Greece, showing how they conserved and transmitted the traditions of society, a thesis adumbrated in his earlier book Preface to Plato. Homer, he demonstrates, has much to (...) say about justice, but since that idea is nowhere in the epics directly stated or expressed, it must be deduced from the speech and actions of the characters. Havelock's careful reading of the Iliad and the Odyssey is original and revealing; it sheds light both on Homeric notions of justice and on the Archaic Greek society depicted in the poems. As Havelock continues his inquiry from Hesiod to Aeschylus, his findings become more complex. The oral Greek world shades into a literate one. Words lose some kinds of meanings, gain others, and steadily become more suited to the conceptualization that Plato strove for and achieved. This evolution of language itself, Havelock shows, was one of the principal accomplishments of the Greek world. Lucidly written and forcefully argued, this book is a major contribution to our knowledge of ancient Greece--its politics, philosophy, and literature, from Homer to Plato. (shrink)

One big question in biology is what life is, but another is how life divides into living things. This is the problem of biological individuality. Proposed statements of the problem have been vague and incomplete. And proposed theories of biological individuality are not detailed enough to solve the problem even if they are correct. The root of these troubles is that their authors have not recognized the metaphysical claims presupposed in their statement of the problem. Making these claims explicit will (...) enable us to see better what the problem is and what form a solution to it would need to have. (shrink)

Trust me: my chair isn't big enough for two. You may doubt that every rational, conscious being is a person; perhaps there are beings that mistakenly believe themselves to be people. If so, read ‘rational, conscious being’ or the like for 'person'.

Preface -- Introduction -- How to value democracy -- Paper stones, the ethics of participation -- Philosophers-citizens -- Superdeliberators -- What is it like to be a citizen? -- Democracy's ethics of belief -- The division of democratic labor -- Representing principles -- Democratic complicity -- Not in my name, macrodemocratic design.

In his work on Wu wei, Edward Slingerland argues that the classical Chinese ideal is an inherently paradoxical concept that is first and foremost spiritual and political only secondarily. Through a close reading of the Dao de Jing, the first major classical text to substantially deploy and develop the concept, I argue that Wu wei isn’t inherently paradoxical and that this is seen precisely when it is viewed in terms of its political primacy. On my reading, the emergence of Wu (...) wei in the Daoist canon is an equilibrating moment of political mediation between the highly intentionalized sphere of human pursuits and the purposeless fluidity and boundless flux of the natural world. Wu wei here takes on a different aspect—mystery rather than paradox—when considered within a form of political collectivity in which the intentional and the innate, purposive and natural are constantly juxtaposed and contending with one another. (shrink)

The advanced division of cognitive labor generates a set of challenges and opportunities for professional philosophers. In this paper, I re-characterize the nature of synthetic philosophy in light of these challenges and opportunities. In part 1, I’ll remind you of the centrality of the division of labor to Plato’s Republic, and why this is especially salient in his banishment of the poets from his Kallipolis. I’ll then focus on the significance of an easily overlooked albeit rather significant character, Damon, mentioned (...) in that dialogue. I’ll argue that if we take the relationship between Socrates and Damon seriously, we’ll notice that in modeling imperfect polities, Plato inscribes Socrates within the advanced division of cognitive labor who defers to Damon as an expert on a key feature of the art of government. In fact, I’ll argue that in Republic, Plato offers us at least two ways to conceptualize philosophy’s relationship to the sciences, and that he alerts us to the social significance of this. In part 2, I’ll re-introduce my conceptualization of synthetic philosophy and restate it. Back in 2019 I published a short paper on it that went viral and was immediately used by others. Reflection on their use instructed me about an ambiguity in my position. Building on the material in parts 1-2, in part 3, I’ll contrast my account with a number of ways that Philip Kitcher has conceptualized synthetic philosophy in order to make more precise the version promoted here. (shrink)

How diverse is philosophy? In this paper we explore recent data on the racial, ethnic, and gender diversity of philosophy students and faculty in the United States. We have found that women are underrepresented in philosophy at all levels from first-year intention to major through senior faculty. The past four years have seen an increase in the percentage of women philosophy majors at the undergraduate level, but it remains to be seen if this recent increase in the percentage of women (...) will eventually also show at more advanced stages. Temporal trends since 2000 also show substantial increases in the racial and ethnic diversity of philosophy majors at all levels of education from first-year undergraduate through PhD, with substantial declines in the percentage of non-Hispanic White philosophy majors and substantial increases in all other commonly measured racial/ethnic groups except for Native American / Alaska Native. Despite generally increasing diversity, people who identify as Hispanic (any race), or non-Hispanic Native American, Alaska Native, or Black remain substantially underrepresented in philosophy at all levels compared to their presence in the U.S. population, and in some cases also as compared to other majors. (shrink)

This chapter surveys the origins and development in Greek philosophy of the thought that living well requires living as a citizen of the world.