EASPLS: General presentation

The European Advanced School for the Philosophy of the Life Sciences is organized by top level institutions in the philosophy and history of life sciences: the ESRC Centre for Genomics in Society (EGENIS, Exeter, UK); the European School of Molecular Medi-cine (SEMM), Milan, and the Department of Health Sciences, University of Milan; the Institut d’Histoire de la Médecine et de la Santé, Université de Genève; the Institut d’His-toire et de Philosophie des Sciences et des Techniques (IHPST, Paris-1 Sorbonne), the Konrad Lorenz Institute for Evolution and Cognition Research (KLI, Klosterneuburg); the Department of Philosophy, University of Bielefeld, and the Department of Logic and Philosophy of Science, University of the Basque Country. EASPLS aims at fostering research, the advancement of students, and collaborations in the field of the philosophy of the biomedical sciences, broadly conceived.

The EASPLS Advanced School is a biennial event. A preliminary meeting was held in Gorino Sullam, Italy, in 2008. The first seminar, on "Causation and Disease in the Post-genomic Era," and the second, on “In vivo, ex vivo, in vitro, in silico: Models in the Life Sciences” were held at the Fondation Brocher, Hermance, Switzerland, in 2010 and 2012, respectively.

The KLI is located in Klosterneuburg near Vienna, Austria. Accommodation will be in a hotel within walking distance of the institute.

The schedule mixes presentations of senior researchers and presentations by PhD stud-ents and post-doctoral researchers. The selected contributors will be asked to either give a paper on the topic they propose or to comment on a senior researcher’s presentation (time allocated: senior’s presentation 35’; junior’s commentary 15’; junior’s presentation 25’).

The best papers resulting from the meeting will be published in a thematic issue of an international journal in the field.

The Topic - Ontologies Issues In The Life Sciences

L’ontologie fait corps avec la science elle-même et ne peut en être séparée. 
Émile Meyerson

Dictionaries such as Webster’s define ontology as the “branch of metaphysics con-cerned with the nature and relations of being.” Western philosophy began as a quest for “the furniture of the world.” Think of Empedocles’ four ‘roots,’ which have become better known as the ‘elements’: Fire, Air, Water, and Earth. Aristotle related each of these four elements to two of the four ‘sensible qualities’: hot/cold, wet/dry. If these ontological entities in Greek natural philosophy were thought through the lens of a strong and necessary ontological commitment, the modern sciences that took shape after the Sci-entific Revolution, including biology, may be seen as transforming the ancient ontological quest in terms of specialization and the use of increasingly sophisticated experimental and other empirical tools (and later also modeling), in addition to the theorizing that was—and remains—so dear to philosophers.

On this “replacement of philosophy by science” picture, it might seem that the age of phi-losophical ontology has gone for good—a conclusion that the logical empiricists were eager to draw about a century ago. For them, philosophy’s only proper concern is the “logical analysis of the body of accepted scientific theories” (Carnap). Representatives of the Vienna Circle’s “scientific world-conception” such as Neurath no longer wanted to use the term ’philosophy’ for their work at all, “so as to emphasize the contrast with the philosophy of (metaphysical) systems even more strongly.”

However, whereas Quine’s ontological relativism killed whatever remained of the old dream of an aprioristic philosophical ontology that somehow ‘precedes’ scientific investi-gation, his demolition of the ‘analytic/synthetic’ distinction, which the positivist edifice required for its foundation, re-opened, maybe some­what paradoxically, the door for a (now ‘scientific’) metaphysics. As Alex Rosenberg (1985) has argued in a discussion of entelechy:

The justification for eliminating or embracing such notions as Driesch’s entelechy is no different in kind from that employed to assess claims about the existence of electrons, magnets, or virons. It differs from them by degree, and very great degree at that. But ridding biology of such notions is ... all a matter of applying some rule against useless metaphysics. For deciding on the existence or nonexistence of entelechies is nothing less than questioning the legitimacy of competing embryological theories altogether.

The ‘new’ philosophy of biology that took shape in the mid-1970s was informed by the post-positivist developments in philosophy of science (Quine’s influence being mostly in-direct, through the major impact of Kuhn). Among its subjects, ontological issues are legion; to mention but a few examples:

• If biological species evolve, they cannot be logical classes but must be ‘individuals’ of some sort (Ghiselin, Hull).
• In a discipline such as systematics, confusion as to the significance of definitions often leads to mistakes. “Definitions apply only to words, not to the things to which they correspond” (Ghiselin).
• The ‘gene’s eye view’ vs. multi-level accounts of living systems, ‘causal democracy’ of developmental resources, etc.
• The individuality of organisms—microbiological, immunological, and other issues.
• Ecosystems as organisms, organisms as ecosystems…

Whereas philosophy has traditionally shown but disdain for the ‘application’ of scientific knowledge, many theoretical changes in the life sciences today are initiated by practical and technological applications, and many theoretical advances are pursued to answer to technical problems.

This turn has been particularly evident concerning ontology. While classical philosophi-cal ontology was devoted to speculation on “what there is”—the ‘fundamental’ entities in the world—now, in particular in what is called applied ontology, it deals increasingly with computerized knowledge representation and data integration. From a computational per-spective, an ontology is a way of computationally modeling (i.e., representing) a parti-cular area of knowledge, or computationally integrating (i.e., representing) different areas of knowledge.

The rapidly growing field of applied ontology has recently acquired more and more relevance in the context of the sciences dealing with living beings. Bio-ontologies are proliferating in the management of many databases concerning living beings or parts of them (molecules, cells, tissues, etc.). This success is explained by the changing nature of biological research. While until some decades ago research in the life sciences was mainly observational, nowadays, due to the development of powerful computational tools, studies in the life sciences are computer-aided. The rapid development of computational instruments allowed the analysis of larger and larger data sets. This opened the door to the data deluge: the amount of data produced transcends the possibility of their analysis. Bio-ontologies are a candidate to manage this information explosion by modeling and integration, since they can also bridge different levels of research on living beings connecting data, for example, from molecular biology to clinical medicine, by aligning molecular details to pathology and anatomy.

However, this picture reveals a dangerous epistemological naiveté and a basic igno-rance of the history of science itself. First, even if many computer scientists conceive of ontology in a simple way (without considering the history of ontology itself), the philoso-phical tradition can provide many different approaches to ontological problems that can inspire new technical applications.

Second, a genuine epistemological analysis can provide theoretical support for another type of integration, knowledge integration, which is not separated from data integration, but rather constitutes its counterpart. Epistemological expertise, supported by up-to-date knowledge of the science, plays a crucial role in understanding the practice of actual research. Moreover, a scientific enterprise aware of its historical and epistemological dimensions can take advantage of this level of analysis to refine and shape its method-ological approach and the interpretation of those aspects of produced results that are normally neglected by scientists (the issue of theory-ladenness).

Applicants are welcome to submit abstracts related to any issues pertaining to the developments sketched above.