Ontological Issues in the Life Sciences

Participating institutions:

Egenis, the Centre for the Study of Life Sciences, Exeter
European School of Molecular Medicine (SEMM), Milan
Department of Health Sciences, University of Milan

Institut d’Histoire et de Philosophie des Sciences et des Techniques,
Paris-1 Panthéon - Sorbonne
KLI Institute, Klosterneuburg/Vienna
IUFE, Faculty of Science, University of Geneva
Department of Philosophy, Faculty of Humanities, University of Geneva
Department of Logic and Philosophy of Science, University of the Basque
Country, San Sebastian

Directors:
Giovanni Boniolo (Milan) & Werner Callebaut (Vienna)

Applications:

Young scholars (PhD students and post-doctoral researchers) in the history
and philosophy of the life sciences, including medicine, are invited to
apply. Candidates should send a letter of motivation along with their CV,
and a title and abstract of ca. 500 words in a single file labeled
‘Name-easpls2014.pdf’ to Isabella Sarto-Jackson: [email protected] .
Applicants will be notified of acceptance before the end of May.

Deadline for applications: March 31, 2014

The registration fee is 570 € (accommodation and lunches included; travel
and dinner expenses not included).

 EASPLS — General presentation:

The European Advanced School for the Philosophy of Life Sciences is
organized by top-level European institutions in the philosophy and history
of the life sciences. It aims at fostering research, advancement of
students, and collaborations in the field of the philosophy of the
biomedical sciences. Meetings are held every other year. After a
pre-liminary meeting in Gorino Sullam (Italy) in 2008, EASPLS met in
Geneva (Switzerland) in 2010 and 2012. This year’s meeting will be hosted
by the KLI Institute in its new setting in Klosterneuburg near Vienna
(Austria). Accommodation will be in a hotel situated close to the
institute.

The schedule mixes presentations of senior researchers, post-doctoral
researchers, and PhD students. The selected contributors will either be
asked to give a paper on the topic they propose, or to act as commentator,
according to decision by the program committee based on the examination of
the applications. Time allocated: senior’s presentation 35’; junior’s
presentation 25’; junior’s commentary 15’.

The best papers resulting from the meeting will be published in a thematic
issue of an international journal in the field. Submissions will be
subject to normal peer review.

Additional information about the seminar will progressively be made
available at: http://easpls.kli.ac.at .

Confirmed senior speakers:
John Dupré (philosophy of science, Exeter)
Eric Garnier (ecology, Montpellier)
Maria Kronfeldner (philosophy of biology, Bielefeld)

Francesca Merlin (philosophy of biology, Paris)
Matteo Mossio (philosophy of biology and cognition, Paris)
Gerd B. Müller (developmental and evolutionary biology, Vienna)
Marco J. Nathan (philosophy of science, Denver & Milan)
Daniel Nicholson (history and philosophy of biology, Exeter)
Kepa Ruiz-Mirazo (complex systems, San Sebastian)
Isabella Sarto-Jackson (neurobiology, Vienna)
Bruno Strasser (history of biology, Geneva)
Marcel Weber (philosophy of science, Geneva)

Ontological Issues in the Life Sciences:

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

Dictionaries such as Webster’s define ontology as the “branch of
metaphysics concerned 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 in Greek natural philosophy these entities were thought through the
lens of a strong and necessary ontological commitment, the modern sciences
that took shape after the Scientific 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 philosophical 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 investigation, his demolition of the
analytic/synthetic distinction, which the positivist edifice required for
its foundation, re-opened, maybe some­what paradoxically, the door for a
‘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 indirect, 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.

• 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 cor-respond” (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. Whereas
classical philosophical ontology was devoted to speculation on “what there
is”—the ‘fundamental’ entities in the world—nowadays, in particular in
what is called applied ontology, it deals increasingly with computerized
knowledge representation and data integration. From a computational
perspective, an ontology is a way of computationally modeling (i.e.,
representing) a particular 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, major advances in molecular biology and
genomic technologies have led to an information overload that cannot be
processed and analyzed by biological methods. Nowadays, most biological
subfields are computer-aided, resorting to powerful bioinformatics tools
that are required to store, organize, and index the continuously
increasing mass of data. But coupling these rapidly expanding fields
opened the door to the data deluge even wider: the amount of data produced
exceeds 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
basic ignorance of the history of science itself. First, even if many
computer scientists conceive of ontology in a simple way (without
considering its history), the philosophical tradition provides 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 methodological 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.


Werner Callebaut, PhD

Scientific Director, KLI
http://kli.ac.at
E-mail:         [email protected]
Phone:  +43 2243 30 27 40
Snail:  Martinstrasse 12, 3400 Klosterneuburg, Austria

President (2013-'15), International Society for the History, Philosophy
and Social Studies of Biology (ISHPSSB)
ishpssb.org/

Visiting Research Professor of Philosophy of Science
Department of Theoretical Biology
University of Vienna
http://theoretical.univie.ac.at/

Editor-in-Chief
Biological Theory: Integrating Development, Evolution, and Cognition
http://www.springer.com/philosophy/epistemology+and+philosophy+of+science/journal/13752