In the era of “big data,” science is increasingly information driven, and the potential for computers to store, manage, and integrate massive amounts of data has given rise to such new disciplinary fields as biomedical informatics. Applied ontology offers a strategy for the organization of scientific information in computer-tractable form, drawing on concepts not only from computer and information science but also from linguistics, logic, and philosophy. This book provides an introduction to the field of applied ontology that is of (...) particular relevance to biomedicine, covering theoretical components of ontologies, best practices for ontology design, and examples of biomedical ontologies in use. After defining an ontology as a representation of the types of entities in a given domain, the book distinguishes between different kinds of ontologies and taxonomies, and shows how applied ontology draws on more traditional ideas from metaphysics. It presents the core features of the Basic Formal Ontology (BFO), now used by over one hundred ontology projects around the world, and offers examples of domain ontologies that utilize BFO. The book also describes Web Ontology Language (OWL), a common framework for Semantic Web technologies. Throughout, the book provides concrete recommendations for the design and construction of domain ontologies. (shrink)

In lieu of an abstract, here is a brief excerpt of the content: Hypatia 14.4 (1999) 186-191 -/- [Access article in PDF] Simone De Beauvoir: a Critical Reader. Edited by Elizabeth Fallaize. London and New York: Routledge, 1998. As this special volume attests, there has been a recent resurgence of interest in Simone de Beauvoir. A number of books on her have been published in the last several years. However, Elizabeth Fallaize's book, Simone de Beauvoir: A Critical Reader (1998), occupies (...) a special niche. Many of its essays are excerpts from studies done of Beauvoir's work before this latest renaissance. Some of these studies are not in print in the United States. Some are perhaps unfamiliar to present-day readers or those from different disciplines. In addition, the articles reprinted here are otherwise not easily accessible. Fallaize has performed an important service by gathering them all in one place and by carefully editing, presenting, and, in some cases, translating them. -/- The book is divided into three sections, the first entitled "Readings of The Second Sex." Aside from Judith Okely's piece that assesses Beauvoir's chapter on myths from an anthropological standpoint, the essays mainly address the philosophical aspects of this work. Beauvoir herself of course swore that she was not a philosopher and that Jean-Paul Sartre's Being and Nothingness (1953) was the sole philosophical foundation for all her work. Some recent analyses have attempted to turn this picture on its head by arguing that Beauvoir was a central influence on, or even the origin of, the philosophical doctrines put forward in Being and Nothingness. None of the writers in this book addresses this issue. But two emphasize Beauvoir's intellectual independence from Sartre. -/- The Swedish scholar Eva Lundgren-Gothlin argues that Beauvoir turned to G. W. F. Hegel to find a satisfactory theoretical model with which to explain the subjugation of women (Lundgren-Gothlin's essay is taken from her book [End Page 186] Sex and Existence [1996]) . In opposition to other scholars, she argues that the French Hegelian Alexandre Kojève, not Sartre, influenced Beauvoir's interpretation of Hegel. Following Hegel and Kojève, Beauvoir envisioned a possible resolution to the struggle for recognition—reciprocal recognition—whereas Sartre's view of self-other relations in Being and Nothingness rules such reciprocity out. However, Lundgren-Gothlin judges, Beauvoir was not critical enough of the sexist presuppositions of Hegel's thought, citing the same pronouncements Beauvoir makes that subsequent feminists have criticized. -/- Another piece that stresses Beauvoir's philosophical originality is "Beauvoir: The Weight of Situation," taken from Sonia Kruks's book Situation and Human Existence (1990). For some time, Kruks has been doing excellent work placing Beauvoir within the wider phenomenological tradition. In this piece, she argues that, starting with the early essay Pyrrhus et Cinéas (1944) and culminating in The Second Sex (1989), Beauvoir elaborated a more nuanced position on the nature and extent of human freedom than Sartre did in Being and Nothingness. According to Beauvoir, human freedom, which Sartre dramatically proclaims is absolute, can under some conditions, notably conditions of severe oppression, "be reduced to no more than a suppressed potentiality" (Fallaize 1998, 57). In The Second Sex, Beauvoir definitively breaks with the philosophical framework of Being and Nothingness by implying that a woman's situation is a general one, not individually self-constituted, and one that she cannot transcend by an act of free choice. The phenomenology of Maurice Merleau-Ponty provides a better foundation for Beauvoir's conception of subjectivity as socially mediated and embodied than does Sartre's philosophy, Kruks suggests. -/- Another piece in this section, Judith Butler's landmark essay "Sex and Gender in Simone de Beauvoir's Second Sex" (1986), highlights Beauvoir's philosophical originality in a different way. In her introduction, Fallaize points out how this essay served as a foundation for Butler's own subsequent work on a performative theory of gender. Butler argues that Beauvoir's claim that one is not born but becomes a woman implies that gender is socially constructed and not natural, as people have insisted for centuries. But to the extent that we become women, gender is not something... (shrink)

Edited and introduced by Robert Arp, _Revisiting Aquinas’ Proofs for the Existence of God_ is a collection of new papers written by scholars focusing on the famous Five Proofs or Ways for the existence of God put forward by St. Thomas Aquinas near the beginning of his unfinished tome, _Summa Theologica_.

This collection of specially commissioned essays puts top scholars head to head to debate the central issues in the lively and fast growing field of philosophy ...

What's Good on TV? Understanding Ethics Through Television presents an introduction to the basic theories and concepts of moral philosophy using concrete examples from classic and contemporary television shows. Utilizes clear examples from popular contemporary and classic television shows, such as The Office, Law and Order, Star Trek and Family Guy, to illustrate complex philosophical concepts Designed to be used as a stand-alone or supplementary introductory ethics text Features case studies, study questions, and suggested readings Episodes mentioned are from a (...) wide variety of television shows, and are easily accessible Offers a balanced treatment of a number of controversial ethical issues including environmental ethics, animal welfare, abortion, homosexuality, capital punishment, assisted suicide, censorship and the erosion of values Includes a companion website at http://whatsgoodontv.webs.com. (shrink)

Numerous research groups are now utilizing Basic Formal Ontology as an upper-level framework to assist in the organization and integration of biomedical information. This paper provides elucidation of the three existing BFO subcategories of realizable entity, namely function, role, and disposition. It proposes one further sub-category of tendency, and considers the merits of recognizing two sub-categories of function for domain ontologies, namely, artifactual and biological function. The motivation is to help advance the coherent ontological treatment of functions, roles, and dispositions, (...) to help provide the potential for more detailed classification, and to shed light on BFO’s general make-up and use. (shrink)

For researchers who study technology designs, the application and execution of so-called design-oriented research projects are a common way of funding their research. Against this background, we propose a new methodical approach with which VSD can easily be implemented in such projects and which we call “value declaration”. We share our experience with this method which we gained in two design-oriented research projects.

The informational nature of biological organization, at levels from the genetic and epigenetic to the cognitive and linguistic.

Was treibt seine Gegenspieler an? Ist Batman in seiner Menschlichkeit besser als Superman? Die Philosophie bei Batman bietet unterhaltsame Antworten und Einblicke in Batmans Welt.

Ontologies describe reality in specific domains in ways that can bridge various disciplines and languages. They allow easier access and integration of information that is collected by different groups. Ontologies are currently used in the biomedical sciences, geography, and law. A Biomedical Ethics Ontology would benefit members of ethics committees who deal with protocols and consent forms spanning numerous fields of inquiry. There already exists the Ontology for Biomedical Investigations (OBI); the proposed BMEO would interoperate with OBI, creating a powerful (...) information tool. We define a domain ontology and begin to construct a BMEO, focused on the process of evaluating human research protocols. Finally, we show how our BMEO can have practical applications for ethics committees. This paper describes ongoing research and a strategy for its broader continuation and cooperation. (shrink)

'You shouldn't drink too much. The Earth is round. Milk is good for your bones.' Are any of these claims true? How can you tell? Can you ever be certain you are right? For anyone tackling philosophical logic and critical thinking for the first time, Critical Thinking: An Introduction to Reasoning Well provides a practical guide to the skills required to think critically. From the basics of good reasoning to the difference between claims, evidence and arguments, Robert Arp and Jamie (...) Carlin Watson cover the topics found in an introductory course. Now revised and fully updated, this Second Edition features a glossary, chapter summaries, more student-friendly exercises, study questions, diagrams, and suggestions for further reading. Topics include: the structure, formation, analysis and recognition of arguments deductive validity and soundness inductive strength and cogency inference to the best explanation truth tables tools for argument assessment informal and formal fallacies With real life examples, advice on graduate school entrance exams and an expanded companion website packed with additional exercises, an answer key and help with real life examples, this easy-to-follow introduction is a complete beginner's tool set to good reasoning, analyzing and arguing. Ideal for students in basic reasoning courses and students preparing for graduate school. (shrink)

Simone de Beauvoir published a number of philosophical essays and novels before writing The Second Sex. The most important of these was The Ethics of Ambiguity, in which she argues that one’s freedom is always intertwined with that of others. The Bonds of Freedom examines de Beauvoir’s ideas on ethics, demonstrating her importance in contemporary philosophy.

Breaking Bad, hailed by Stephen King, Chuck Klosterman, and many others as the best of all TV dramas, tells the story of a man whose life changes because of the medical death sentence of an advanced cancer diagnosis. The show depicts his metamorphosis from inoffensive chemistry teacher to feared drug lord and remorseless killer. Driven at first by the desire to save his family from destitution, he risks losing his family altogether because of his new life of crime. In defiance (...) of the tradition that viewers demand a TV character who never changes, Breaking Bad is all about the process of change, with each scene carrying forward the morphing of Walter White into the terrible Heisenberg. Can a person be transformed as the result of a few key life choices? Does everyone have the potential to be a ruthless criminal? How will we respond to the knowledge that we will be dead in six months? Is human life subject to laws as remorseless as chemical equations? When does injustice validate brutal retaliation? Why are drug addicts unsuitable for operating the illegal drug business? How can TV viewers remain loyal to a series where the hero becomes the villain? Does Heisenberg's Principle of Uncertainty rule our destinies? In Breaking Bad and Philosophy, a hand-picked squad of professional thinkers investigate the crimes of Walter White, showing how this story relates to the major themes of philosophy and the major life decisions facing all of us. (shrink)

American auteur Jeffrey Jacob "J. J." Abrams's genius for creating densely plotted scripts has won him broad commercial and critical success in TV shows such as Felicity, Emmy-nominated Alias, Emmy and Golden Globe-winning Lost, and the critically acclaimed Fringe. In addition, his direction in films such as Cloverfield, Super 8, and the new Mission Impossible and Star Trek films has left fans eagerly awaiting his revival of the Star Wars franchise. As a writer, director, producer, and composer, Abrams seamlessly combines (...) geek appeal with blockbuster intuition, leaving a distinctive stamp on all of his work and establishing him as one of Tinsel Town's most influential visionaries. In The Philosophy of J.J. Abrams, editors Patricia L. Brace and Robert Arp assemble the first collection of essays to highlight the philosophical insights of the Hollywood giant's successful career. The filmmaker addresses a diverse range of themes in his onscreen pursuits, including such issues as personal identity in an increasingly impersonal digitized world, the morality of terrorism, bioethics, friendship, family obligation, and free will. Utilizing Abrams's scope of work as a touchstone, this comprehensive volume is a guide for fans as well as students of film, media, and culture. The Philosophy of J.J. Abrams is a significant contribution to popular culture scholarship, drawing attention to the mind behind some of the most provocative television and movie plots of our day. (shrink)

In contradistinction to the many monographs and edited volumes devoted to historical, cultural, or theological treatments of demonology, this collection features newly written papers by philosophers and other scholars engaged specifically in philosophical argument, debate, and dialogue involving ideas and topics in demonology. The contributors to the volume approach the subject from the perspective of the broadest areas of Western philosophy, namely metaphysics, epistemology, logic, and moral philosophy. The collection also features a plurality of religious, cultural, and theological views on (...) the nature of demons from both Eastern and Western thought, in addition to views that may diverge from these traditional roots. _Philosophical Approaches to Demonology_ will be of interest to philosophers of religion, theologians, and scholars working in philosophical theology and demonology, as well as historians, cultural anthropologists, and sociologists interested more broadly in the concept of demons. (shrink)

The Problem of Evil: New Philosophical Directions brings together a diversity of philosophical views, methods, and approaches to the much-discussed topic of evil and its bearing on religious belief. Through both general and specific examinations of the problem of evil, this book proposes new directions for philosophical thought.

In order to solve problems, humans are able to synthesize apparently unrelated concepts, take advantage of serendipitous opportunities, hypothesize, invent, and engage in other similarly abstract and creative activities, primarily through the use of their visual systems. In _Scenario Visualization_, Robert Arp offers an evolutionary account of the unique human ability to solve nonroutine vision-related problems. He argues that by the close of the Pleistocene epoch, humans evolved a conscious creative problem-solving capacity, which he terms scenario visualization, that enabled them (...) to outlive other hominid species and populate the planet. Arp shows that the evidence for scenario visualization -- by which images are selected, integrated, and then transformed and projected into visual scenarios -- can be found in the kinds of complex tools our hominid ancestors invented in order to survive in the ever-changing environments of the Pleistocene world. Arp also argues that this conscious capacity shares an analogous affinity with neurobiological processes of selectivity and integration in the visual system, and that similar processes can be found in the activities of organisms in general. The evolution of these processes, he writes, helps account for the modern-day conscious ability of humans to use visual information to solve nonroutine problems creatively in their environments. Arp's account of scenario visualization and its emergence in evolutionary history suggests an answer to two basic questions asked by philosophers and biologists concerning human nature: why we are unique; and how we got that way. Robert Arp is Postdoctoral Research Fellow at the National Center for Biomedical Ontology. His areas of specialization include philosophy of biology and philosophy of mind. He is the author of numerous articles and the forthcoming An Integrated Approach to the Philosophy of Mind. (shrink)

The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies that provide a representation of biomedical knowledge from the Open Biological and Biomedical Ontologies (OBO) project and adds the ability to describe how this knowledge was derived. We here describe the state of OBI and several applications that are using it, such as adding semantic expressivity to (...) existing databases, building data entry forms, and enabling interoperability between knowledge resources. OBI covers all phases of the investigation process, such as planning, execution and reporting. It represents information and material entities that participate in these processes, as well as roles and functions. Prior to OBI, it was not possible to use a single internally consistent resource that could be applied to multiple types of experiments for these applications. OBI has made this possible by creating terms for entities involved in biological and medical investigations and by importing parts of other biomedical ontologies such as GO, Chemical Entities of Biological Interest (ChEBI) and Phenotype Attribute and Trait Ontology (PATO) without altering their meaning. OBI is being used in a wide range of projects covering genomics, multi-omics, immunology, and catalogs of services. OBI has also spawned other ontologies (Information Artifact Ontology) and methods for importing parts of ontologies (Minimum information to reference an external ontology term (MIREOT)). The OBI project is an open cross-disciplinary collaborative effort, encompassing multiple research communities from around the globe. To date, OBI has created 2366 classes and 40 relations along with textual and formal definitions. The OBI Consortium maintains a web resource providing details on the people, policies, and issues being addressed in association with OBI. (shrink)

Are there universal ethical principles that should govern the conduct of medicine and research worldwide? -- Is it morally acceptable to buy and sell organs for human transplantation? -- Were it physically safe, would human reproductive cloning be acceptable? -- Is the deliberately induced abortion of a human pregnancy ethically justifiable? -- Is it ethical to patent or copyright genes, embryos, or their parts? -- Should minors have the right to refuse treatment, even when against the will of their parents (...) or guardians? -- Is physician-assisted suicide ever ethical? -- Should stem cell research utilizing embryonic tissue be conducted? -- Should we prohibit the use of chimpanzees and other great apes in biomedical research? -- Should the United States of America adopt universal health care? -- Is there a legitimate place for human genetic enhancement? -- Can there be agreement as to what constitutes human death? -- Is there ever a circumstance in which a doctor may withhold information? -- Should in vitro fertilization be an option for a woman? -- Are international clinical trials exploitative? (shrink)

Biological ontologies are used to organize, curate, and interpret the vast quantities of data arising from biological experiments. While this works well when using a single ontology, integrating multiple ontologies can be problematic, as they are developed independently, which can lead to incompatibilities. The Open Biological and Biomedical Ontologies Foundry was created to address this by facilitating the development, harmonization, application, and sharing of ontologies, guided by a set of overarching principles. One challenge in reaching these goals was that the (...) OBO principles were not originally encoded in a precise fashion, and interpretation was subjective. Here we show how we have addressed this by formally encoding the OBO principles as operational rules and implementing a suite of automated validation checks and a dashboard for objectively evaluating each ontology’s compliance with each principle. This entailed a substantial effort to curate metadata across all ontologies and to coordinate with individual stakeholders. We have applied these checks across the full OBO suite of ontologies, revealing areas where individual ontologies require changes to conform to our principles. Our work demonstrates how a sizable federated community can be organized and evaluated on objective criteria that help improve overall quality and interoperability, which is vital for the sustenance of the OBO project and towards the overall goals of making data FAIR. Competing Interest StatementThe authors have declared no competing interest. (shrink)

In this paper, I first present the ideas and arguments put forward by evolutionary psychologists that humans evolved certain capacities to creatively problem solve. Specifically, Steven Mithen thinks that creative problem solving is possible because the mind has evolved a conscious capacity he calls cognitive fluidity, the flexible exchange of information between and among mental modules. While I agree with Mithen that cognitive fluidity acts as a necessary condition for creative problem solving, I disagree that cognitive fluidity alone will suffice (...) for such an activity. I argue further that the flexible exchange of information between and among modules, as well as what I call scenario visualization - a conscious ability to segregate and integrate visual images in future scenarios - evolved in our species and accounts for certain kinds of creative problem solving. (shrink)

A dream team of philosophers relentlessly cross-examines the Perry Mason stories.

In the biological realm, a complete explanation of a trait seems to include an explanation in terms of function. It is natural to ask of some trait, "What is its function?" or "What purpose in the organism does the particular trait serve?" or "What is the goal of its activity?" There are several views concerning the appropriate definition of function for biological matters. Two popular views of function with respect to living things are Cummins' organizational account and the Griffiths/Godfrey-Smith modern (...) history account. Whereas Cummins argues that a trait functions so as to contribute to the general organization of some organism's present structure, Griffiths, and Godfrey-Smith argue that a trait functions because of its fitness with respect to the organism's recent evolutionary history. In this paper, I show how these accounts can be made compatible and compliment one another. Given that structure, organization, operational flexibility, function, and evolutionary history are all factors to be considered in an organism's makeup, we should expect that the traits of an organism function the way they do because such traits presently contribute to the overall organization of the organism (Cummins) as well as were selected for in the organism's species' recent ancestry (Griffiths/Godfrey-Smith). (shrink)

In this paper, I give an account of how our hominin ancestors evolved a conscious ability I call scenario visualization that enabled them to manufacture novel tools so as to survive and flourish in the ever-changing and complex environments in which they lived. I first present the ideas and arguments put forward by evolutionary psychologists that the mind evolved certain mental capacities as adaptive responses to environmental pressures. Specifically, Steven Mithen thinks that the mind has evolved cognitive fluidity, viz., an (...) ability to exchange information flexibly between and among mental modules. Showing the deficiency in Mithen’s view, I then argue that the flexible exchange of information between and among modules together with scenario visualization is what explains the ability to construct the novel tools needed to survive and flourish in the environments in which our hominin ancestors resided. Finally, I trace the development of the multi-purposed javelin, from its meager beginnings as a stick, in order to illustrate scenario visualization in novel tool manufacturing. (shrink)

Fifteen philosophers look at the deeper issues raised in the highly popular TV drama, including common morality, legal correctness and legal ethics, discussing the gray areas of legal battles and maneuvering. Original.

This book looks at the television saga Downton Abbey to explore a variety of interpersonal issues that are still relevant today. This includes the emotional importance of particular places; how war and epidemics tell us about life in peacetime and in good health; as well as manners, women's roles, class and more.

Beauvoir's essay “Pyrrhus and Cineas” serves as an excellent introduction to existentialism for students. People today still try to bring meaning to their lives in the ways she examines: through religion, humanitarianism, the scientific worldview, or a focus on the present moment (inspired nowadays by the West's fascination with Eastern mysticism). She points out the numerous questions these points of view leave unanswered. Her existentialist conclusion is that we ourselves give meaning to our lives and cannot justify our life decisions (...) solely by appeal to external standards. (shrink)

An important insight derived from Kant about the workings of the mind is that conscious activity involves both the selection of relevant information, and the integration of that information, so as to form mental coherency. The conscious mind can then utilize this coherent information to solve problems, invent tools, synthesize concepts, produce works of art, and the like. In this paper, it will be suggested that just as biological processes, in general, exhibit selective and integrative functions, and just as visual (...) integration performs the function of selecting and integrating visual module areas, so too, consciousness emerged as a property of the brain to act as a kind of meta-cognitive process that selects and integrates relevant information from psychological modules. The upshot is to establish a psycho-neuro-biological continuum by suggesting that the conscious psychological properties of selectivity and integration are possible because of similar properties that other neurobiological and biological processes exhibit. (shrink)

A comparison of six alternative definitions of the term 'cellular pathway' against the background of ontological realism.

Covering philosophical issues ranging from tattooed religious symbols to a feminist aesthetics of tattoo, _Tattoos and Philosophy_ offers an enthusiastic analysis of inking that will lead readers to consider the nature of the tattooing arts in a new and profound way. Contains chapters written by philosophers, tattoo artists, and tattoo enthusiasts that touch upon many areas in Western and Eastern philosophy Enlightens people to the nature of tattoos and the tattooing arts, leading readers to think deeply about tattoos in new (...) ways Offers thoughtful and humorous insights that make philosophical ideas accessible to the non-philosopher. (shrink)

This paper is divided into two main sections. In the first, I attempt to show that the characterization of Frege as a redundancy theorist is not accurate. Using one of Wolfgang Carl's recent works as a foil, I argue that Frege countenances a realm of abstract objects including truth, and that Frege's Platonist commitments inform his epistemology and embolden his antipsychologistic project. In the second section, contrasting Frege's Platonism with pragmatism, I show that even though Frege's metaphysical position concerning truth (...) has been criticized as reproachable, I argue that it may be useful for people to think like Platonists while conducting their scientific and philosophical inquiries. (shrink)

There is a two-fold problem the phenomenologist must face: the first has to do with thinking like a phenomenologist given that one is always already steeped in the mundane sphere; the second has to do with the phenomenologist entering into dialogue with those scientists, psychologists, sociologists and other laypersons who still remain in the mundane sphere. I address the first problem by giving an Husserlian-inspired account of the movement from the mundane to the transcendental, and show that there are decent (...) prospects for getting life-world folks to start thinking like phenomenologists. I address the second problem by showing that Husserl has himself caught in a dilemma: either the reduction takes place and no communication is possible between phenomenologist and non-phenomenologist, or the reduction does not take place and the phenomenological method remains a psychological makeshift, supposedly accessible to Husserl and his esoteric followers. (shrink)

Edited and introduced by Robert Arp, _Revisiting Aquinas’ Proofs for the Existence of God_ is a collection of new papers written by scholars focusing on the famous Five Proofs or Ways for the existence of God put forward by St. Thomas Aquinas near the beginning of his unfinished tome, _Summa Theologica_.

The ancient Athenians believed that their forebears sprang directly from the earth rather than being created by gods or born of human parents. In some version of the myth, the ancestor was depicted as having a man's form above the waist and a snake's form below: "Having emerged from the earth, he still in part resembled the creature that slips to and fro between the upper and lower worlds."'1 At the beginning of her 1947 work, The Ethics of Ambiguity, Simone (...) de Beauvoir asserts that there is a fundamental ambiguity to human life. According to her, every human, like the chthonic ancestor of the Athenians, exists at the same time in two realms: "he is still part of the world of which he is conscious."2 Rooted as they are in the earth, humans can transcend their material origin in thought but they can never escape it. (shrink)