Ludger Jansen

Currently, there is not yet a full-fledged philosophical sub-discipline devoted to artifacts. In order to establish such a general philosophical discourse on artifacts, two topics are of special importance: artifact functionality and artifact categorization. Both are central to the question of what artifacts are in general and in particular. This introduction first presents the current state of the art in the debates on functions, both in general and in the domain of artifacts in particular. It then unfolds the three debates relevant for artifact kinds, namely the ontological, epistemological and semantic debates on artifact categorization, and presents the most important theory options currently under scrutiny in these fields. It proceeds by introducing the contributions in this special issue on the functions and kinds of art works and other artifacts, and discusses possible perspectives for a general philosophy of artifacts.

This broad and insightful book presents current scholarship in important subfields of philosophy of science and addresses an interdisciplinary and multidisciplinary readership. It groups carefully selected contributions into the four fields of I) philosophy of physics, II) philosophy of life sciences, III) philosophy of social sciences and values in science, and IV) philosophy of mathematics and formal modeling. Readers will discover research papers by Paul Hoyningen-Huene, Keizo Matsubara, Kian Salimkhani, Andrea Reichenberger, Anne Sophie Meincke, Javier Suárez, Roger Deulofeu, Ludger Jansen, Peter Hucklenbroich, Martin Carrier, Elizaveta Kostrova, Lara Huber, Jens Harbecke, Antonio Piccolomini d'Aragona and Axel Gelfert. This collection fosters dialogue between philosophers of science working in different subfields, and brings readers the finest and latest work across the breadth of the field,illustrating that contemporary philosophy of science has successfully broadened its scope of reflection. It will interest and inspire a wide audience of philosophers as well as scholars of the natural sciences, social sciences and the humanities. The volume shares selected contributions from the prestigious second triennial conference of the German Society for Philosophy of Science/ Gesellschaft für Wissenschaftsphilosophie (GWP.2016, March 8, 2016 - March 11, 2016).

Die Zeiten, in denen der Leib-Seele-Dualismus als Ansatz der Philosophie des Geistes durch ein herrschendes Dogma als diskussionsunwürdig galt, sind vorbei. Der Dualismus darf wieder diskutiert werden. Er muß diskutiert werden, wenn in diskussionswürdiger Strenge für ihn argumentiert wird – auch wenn das, wie sich zeigen wird, manchmal ein ziemlich technisches Geschäft ist. In diesem Sinne soll im folgenden Richard Swinburnes Versuch behandelt werden, die Existenz einer Seele und damit die Wahrheit des Substanzdualismus aus einigen zunächst recht unspektakulär aussehenden Prämissen mit Hilfe der modernen Modallogik formal zu beweisen. Zugleich sei damit auf eine kleine Debatte aufmerksam gemacht, die sich inzwischen um Swinburnes Argument entwickelt hat. Die Untersuchung führt zu einem doppelten negativen Ergebnis: Zum einen sind Swinburnes Prämissen nicht plausibel, zum anderen ist ein wichtiger Teil seines Beweisversuches formal nicht in Ordnung. Swinburnes Argument ist also weder überzeugend noch gültig . Allerdings ist das nicht auf den ersten Blick ersichtlich, denn Swinburnes Argument ist alles andere als trivial. Eine eingehende Kritik dieses Arguments soll zeigen, daß, selbst wenn der Dualismus wahr sein sollte, er nicht ganz so einleuchtend ist, wie Swinburne meint

In "On Social Facts" (1989) and subsequent works, Margaret Gilbert has suggested a plural subject account of the semantics of ‘we’ that claims that a central or standard use of ‘we’ is to refer to an existing or anticipated plural subject. This contrasts with the more general approach to treat plural pronouns as expressions referring to certain pluralities. I argue that (i) the plural subject approach cannot account for certain syntactic phenomena and that (ii) the sense of intimacy, which Gilbert cites as evidence for her plural subject account, has a different source than the existence of joint commitments constituting a respective plural subject. Moreover, (iii) there is a wide varie-ty of phenomena in the linguistic record, which, while not constituting conclusive evidence against the plural subject account, nevertheless, are dealt with better by the plurality account. ‘We’ thus refers to pluralities, which may or may not be plural subjects. The precise analysis of ‘we’ thus reveals a multi-layered ontology of groups.

The 2013 Rostock Symposium on Systems Biology and Bioinformatics in Aging Research was again dedicated to dissecting the aging process using in silico means. A particular focus was on ontologies, as these are a key technology to systematically integrate heterogeneous information about the aging process. Related topics were databases and data integration. Other talks tackled modeling issues and applications, the latter including talks focussed on marker development and cellular stress as well as on diseases, in particular on diseases of kidney and skin.

This book discusses the philosophy of influential contemporary philosopher Peter van Inwagen. Looking at perennial philosophical problems from a modern point of view, Peter van Inwagen’s philosophy masterfully combines positions that have been considered irreconcilable: incompatibilism concerning free will, materialism, organicism, theism and realism concerning fictional entities. As readers will discover, his arguments are witty, surprising and deep. The book includes Peter van Inwagen’s Münster Lecture of 2015 on free will, as well as eleven papers from the Münster colloquium discussing central themes of his philosophy, and a reply to each paper by Peter van Inwagen himself. Introducing his philosophy and relating his work to other contemporary views, this book is of interest to graduate students and professionals in philosophy alike.

Given the assertion of a relation between two types, like: “Epidermis has part some Keratinocyte”, we define silent change as any kind of change of the instance-relata of the relation in question that does not change the truth-value of the respective type-level assertion. Such assertions are notoriously difficult to model in OWL 2. To address this problem, we distinguish different modes of type-level relatedness giving rise to this problem and describe a conservative extension to the BFO top-level ontology that allows expressing these modes.

A popular argument goes thus: This is a construction, hence it is not real. Adding an appropriate adjective (social, mental, human, …) in front of “construction” or cognate terms like “(legal) fiction” yields a whole family of related arguments, all of which, or so I will argue, are fallacious. Contrary to popular opinion, these arguments fail both on the epistemic and the ontic sense of construction. Ontic constructions exist at least at one point in time, while epistemic constructions may well correspond to reality. The motivation behind these fallacious arguments can often be found in a misconceived conception of ontology and reality. A full theory of reality must take constructed entities into account because important domains of reality (mental life, social reality, technical artefacts, art and fiction) essentially depend on mental or social constructions.

Margaret Gilbert has defended the claim that her plural subject theory can give a reasonable account of retrospective (or backward-looking) collective responsibility. On one occasion, publishing in this periodical, she writes that she deliberately left out the discussion of prospective (or forward-looking) collective responsibility, or the “responsibilities” of a collective. In the present paper, I want to show that plural subject theory, in fact, also allows accounting for prospective responsibilities of groups and institutions. In order to do so, I will first sketch the social ontological background of my discussion which is, in fact, an amended version of Gilbert’s theory of plural subjects (§ 2). Based on the assumption that a prospective responsibility accrues from some kind of commissioning, I will then discuss a variety of possible sources of prospective collective responsibilities: self-commissioning, third-party commissioning and what I will call commissioning by unique capability (§ 3). Having done so, I will discuss some consequences of this account and defend it against objections (§ 4).

Tun und Können erläutert und diskutiert den Gründungstext der Modalontologie: das neunte Buch der Metaphysik des Aristoteles. Aristoteles' Thesen und Argumente werden zum ersten Mal in Gänze mit formalen analytischen Mitteln rekonstruiert und auf ihre Kohärenz und Gültigkeit geprüft. Erstmals verwendet der Autor dazu eine adverbiale Analyse von Ausdrücken des Könnens und des Vermögens als Prädikatmodifikatoren. Das Buch zeigt, dass Aristoteles' Theorie der Vermögen nicht nur eine konsistente, sondern auch eine leistungsfähige Analyse von Dispositionen und Dispositionsprädikaten bietet. Die Neuausgabe wurde vollständig durchgesehen und um weiterführende Anhänge ergänzt. Der Inhalt: Können, Tun und Möglichkeit. Eine Einführung • Die kausale Dimension von Vermögen • Die ontologische Dimension von Vermögen• Eine notwendige Bedingung für Vermögen • Hindernisse und Verwirklichung • Prioritätsfragen • Aristotle’s Theory of Dispositions • Das Problem des Neuen • Planners, Deciders, Performers

BACKGROUND In biomedical ontologies, mereological relations have always been subject to special interest due to their high relevance in structural descriptions of anatomical entities, cells, and biomolecules. This paper investigates two important subrelations of has_proper_part, viz. the relation has_grain, which relates a collective entity to its multiply occurring uniform parts (e.g., water molecules in a portion of water), and the relation has_component, which relates a compound to its constituents (e.g., molecules to the atoms they consist of). METHOD We distinguish between four kinds of complex entities and characterize them in first order logic. We then discuss whether similar characterizations could be given in description logics, and finally apply the results to mixtures. RESULTS At first sight, collectives and compounds seem to be disjoint categories. Their disjointness, however, relies on agreement about what are uniform entities, and thus on the granularity of description. For instance, the distinction between isomeric subtypes of a molecule can be important in one use case but might be neglected in another one. We demonstrate that, as implemented in the BioTop domain upper level ontology, equivalence or subsumption between different descriptions of same or similar entities cannot be achieved. Using OWL-DL, we propose a new design pattern that avoids primitive subrelations at the expense of more complex descriptions and thus supports the needed inferences.

In 'Metaphysics IX.6' (1048b 18-35) Aristotle presents a test to distinguish between "kinesis" and "energeia," based on relations between the perfective and the imperfective aspect of the verb. This passage has been interpreted as drawing a linguistic distinction between classes of verbs (e.g., stative verbs) by means of a linguistic criterion (Ackrill, Graham). But such an interpretation is in conflict with the text. Aristotle's test must, therefore, be understood as a metaphysical criterion between items in the world (rather than lingual items) by means of a metaphysical criterion, exploiting properties of these items. These items are events, and 'Metaphysics IX.6' exhibits Aristotle's awareness to certain topics discussed in modern event ontology.

BACKGROUND Understanding, modelling and influencing the transition between different states of cells, be it reprogramming of somatic cells to pluripotency or trans-differentiation between cells, is a hot topic in current biomedical and cell-biological research. Nevertheless, the large body of published knowledge in this area is underused, as most results are only represented in natural language, impeding their finding, comparison, aggregation, and usage. Scientific understanding of the complex molecular mechanisms underlying cell transitions could be improved by making essential pieces of knowledge available in a formal (and thus computable) manner. RESULTS We describe the outline of two ontologies for cell phenotypes and for cellular mechanisms which together enable the representation of data curated from the literature or obtained by bioinformatics analyses and thus for building a knowledge base on mechanisms involved in cellular reprogramming. In particular, we discuss how comprehensive ontologies of cell phenotypes and of changes in mechanisms can be designed using the entity-quality (EQ) model. CONCLUSIONS We show that the principles for building cellular ontologies published in this work allow deeper insights into the relations between the continuants (cell phenotypes) and the occurrents (cell mechanism changes) involved in cellular reprogramming, although implementation remains for future work. Further, our design principles lead to ontologies that allow the meaningful application of similarity searches in the spaces of cell phenotypes and of mechanisms, and, especially, of changes of mechanisms during cellular transitions.

Wether the chicken or the egg came first, is not only a mind-boggling but a substantial question. Its answer depends on the biological background theory one assumes. I review recent work on the topic (by Teichmann, Sorensen, Waller and Raatzsch) and resolve some of the disputes between these authors by borrowing from Aristotle the distinction between chicken-producing eggs. I then introduce the concept of a quasi-species to make explicit the vagueness involved in species-terms and prove 13 different priority-claims within a Darwinian framework.

Background: In order to improve ontology quality, tool- and language-related tutorials are not sufficient. Care must be taken to provide optimized curricula for teaching the representational language in the context of a semantically rich upper level ontology. The constraints provided by rigid top and upper level models assure that the ontologies built are not only logically consistent but also adequately represent the domain of discourse and align to explicitly outlined ontological principles. Finally such a curriculum must take into account the pre-existing skills and knowledge of the target audience. Objective: To develop a well-structured curriculum aligned to the particular requirements of life science professionals, in order to enable them to create logically sound, domain adequate and predicable ontologies using the Web Ontology Language (OWL) in Protégè. Methods: Content selection for the curriculum was based on the literature, pre-existing tutorials, and a guideline for good ontology development (i.e ontology design enhancing domain adequacy, sustainability and interoperability) that drew on the authors previous experiences with large ontology development projects. Learning objectives were formulated according to a needs assessment of the targeted learners, who were students trained in life sciences with basic knowledge and practical skills in computer science. As instructional format we choose an approach with a high amount of practical exercises. The curriculum was first implemented with 24 Students and 7 lecturers/ tutors over 5 full days. The curriculum was evaluated by gathering the participants feedback via a questionnaire. Results: Curricular development produced 16 modules of approximately 2 hours each, which covered basic principles of Applied Ontology, description logic syntax and semantics, as well as best design practices outlined in ontology design patterns and variants of the BioTop upper ontology. An opinion survey based on questionnaires indicated that the participants took advantage from the teaching strategies applied, as they indicated good knowledge gain and acknowledged the relevance of the modules. The difficulty was rated slightly lower. Conclusion: The development of teaching material for principled ontology design and best practices is of crucial importance in order to enhance the quality of biomedical ontologies. Here, we present a curriculum for a week long workshop, leveraging on current educational principles, focusing on interactive hands-on exercises, group interactions, and problem-oriented learning. Whereas evaluation clearly showed the success of this approach, in particular regarding student’s satisfaction, the objective measurement of traceable effects on the quality of the generated ontology, although of much higher interest, has just started.