First name
Federico
Last name
Boem
Year of Study
Research Center
Thesis Title
A matter of style. How map thinking and bio-ontologies shape contemporary molecular research
Thesis Abstract
The aim of this thesis is to provide an epistemic analysis of the
transformations occurring in contemporary biological research by considering
the relation between molecular biology and computational biology. In particular,
I will focus on bio-ontologies, as the tool which incarnates at best the new face
of biomedical research. Such a choice is not arbitrary. By appealing to the
notion of style of reasoning and way of knowing, I will show that bio-ontologies
exemplify the rise and success of map thinking as the signature of a new way of
doing molecular biology, while the theoretical tenets, established more than 30
years ago, still maintain their epistemic prominence. This is neither to say that
experimentalism will disappear from science, nor that the experiments power
will be diminished but rather that experiments will have a new role in the
architecture of scientific efforts, precisely because of the increasing importance
of classificatory approaches. Therefore, such a transition within biomedical
research is indeed radical and profound but it does not involve paradigm shifts
but rather a change in the practice. In this sense, it is a matter of style.
transformations occurring in contemporary biological research by considering
the relation between molecular biology and computational biology. In particular,
I will focus on bio-ontologies, as the tool which incarnates at best the new face
of biomedical research. Such a choice is not arbitrary. By appealing to the
notion of style of reasoning and way of knowing, I will show that bio-ontologies
exemplify the rise and success of map thinking as the signature of a new way of
doing molecular biology, while the theoretical tenets, established more than 30
years ago, still maintain their epistemic prominence. This is neither to say that
experimentalism will disappear from science, nor that the experiments power
will be diminished but rather that experiments will have a new role in the
architecture of scientific efforts, precisely because of the increasing importance
of classificatory approaches. Therefore, such a transition within biomedical
research is indeed radical and profound but it does not involve paradigm shifts
but rather a change in the practice. In this sense, it is a matter of style.
Email
federico.boem@ieo.eu
Additional Info
Areas of specialisation: Philosophy of biomedical research, philosophy of bioinformatics
Research interest: Philosophy of Biology and Bioinformatics, Semantic Modeling, Sociology of Biomedicine, Science Policy
Education:
2015 - Phd in Foundations of the Life Sciences and their Ethical ConsequencesThesis: “A MATTER OF STYLE. HOW MAP THINKING AND BIO-ONTOLOGIES SHAPE CONTEMPORARY MOLECULAR RESEARCH”Internal supervisors: Giovanni Boniolo and Gioacchino Natoli (IEO), External supervisor: Paola Roncaglia (EBI, UK)
2011 - MA History and Philosophy of Biology, University of Exeter
2009 - Laurea in Filosofia (course: Logic and Philosophy of Science), University of Florence
Lab experience
Giuliana Pelicci’s group - Biology and signal transduction of normal and cancer neural stem cells.
- Theoretical work on the notion of stemness.
- Practical experience of Western blot tecnique (under the supervision of dr. Daniela Osti).
Gioacchino Natoli's group - Transcriptional control in inflammation and cancer
- PCR
- Transfection
- ChIP-seq
- Elements of R programming
- Gene Ontology enrichment analysis
Publications
Junk or Functional DNA? ENCODE and the Function Controversy’ (with Pierre-Luc Germain and Emanuele Ratti). Biology & Philosophy doi: 10.1007/s10539-014-9441-3
‘Diverse Perspectives on Ontology’ (with Emilio Sanfilippo, Francesca Quattri, Aleksandra Sojic, Emanuele Ratti, Gaoussou Camara and Erik Chuck). Applied Ontology 8(8), 59-71, doi:10.3233/AO-130121
‘Ontological Issues in the Life Sciences’ (with James DiFrisco, Gaëlle Pontarotti, Guillaume Schlaepfer, Ewelina Sokolowska, and Eva Fernández-Labandera). Biological Theory, doi:1007/s13752-015-0207-1
‘Stratification and Biomedicine: How Philosophy Stems from Medicine and Biotechnology’ (with Giovanni Boniolo and Zsuzsa Pavelka) in The Future of Scientific Practice (edited by Marta Bertolaso), Pickering & Chatto
‘Dalla filosofia della biologia alla filosofia dalla biologia’ in Vivi perché diversi (edited by Elena Gagliasso), ETS edizioni
Elementi per una genetica forense, (co-edited with Luca Marelli), Mondadori,
Posters and presentations:
"Defining life?" - presentation at the conference "Materia e materia vivente", 2012 University of Florence,
"What is stemness?" - at the international conference of the German Society for Philosophy of Science/Gesellschaft für Wissenschaftsphilosophie (GWP), 11-14 March 2013 - University of Hannover
"The gene after encode: a Wittgensteinian approach" - at the ISHPSSB, 7-12 July 2013 - University of Montpellier III
"Models in bioinformatics - GO a representation of what?" - at EPSA conference, 28-31 August 2013 - University of Helsinki
Other experiences:
2012 - Summer School in Ontological Analysis, IAOA, University of Trento
2010 - Natural History Museum of the University of Florence, working on collection
Research interest: Philosophy of Biology and Bioinformatics, Semantic Modeling, Sociology of Biomedicine, Science Policy
Education:
2015 - Phd in Foundations of the Life Sciences and their Ethical ConsequencesThesis: “A MATTER OF STYLE. HOW MAP THINKING AND BIO-ONTOLOGIES SHAPE CONTEMPORARY MOLECULAR RESEARCH”Internal supervisors: Giovanni Boniolo and Gioacchino Natoli (IEO), External supervisor: Paola Roncaglia (EBI, UK)
2011 - MA History and Philosophy of Biology, University of Exeter
2009 - Laurea in Filosofia (course: Logic and Philosophy of Science), University of Florence
Lab experience
Giuliana Pelicci’s group - Biology and signal transduction of normal and cancer neural stem cells.
- Theoretical work on the notion of stemness.
- Practical experience of Western blot tecnique (under the supervision of dr. Daniela Osti).
Gioacchino Natoli's group - Transcriptional control in inflammation and cancer
- PCR
- Transfection
- ChIP-seq
- Elements of R programming
- Gene Ontology enrichment analysis
Publications
Junk or Functional DNA? ENCODE and the Function Controversy’ (with Pierre-Luc Germain and Emanuele Ratti). Biology & Philosophy doi: 10.1007/s10539-014-9441-3
‘Diverse Perspectives on Ontology’ (with Emilio Sanfilippo, Francesca Quattri, Aleksandra Sojic, Emanuele Ratti, Gaoussou Camara and Erik Chuck). Applied Ontology 8(8), 59-71, doi:10.3233/AO-130121
‘Ontological Issues in the Life Sciences’ (with James DiFrisco, Gaëlle Pontarotti, Guillaume Schlaepfer, Ewelina Sokolowska, and Eva Fernández-Labandera). Biological Theory, doi:1007/s13752-015-0207-1
‘Stratification and Biomedicine: How Philosophy Stems from Medicine and Biotechnology’ (with Giovanni Boniolo and Zsuzsa Pavelka) in The Future of Scientific Practice (edited by Marta Bertolaso), Pickering & Chatto
‘Dalla filosofia della biologia alla filosofia dalla biologia’ in Vivi perché diversi (edited by Elena Gagliasso), ETS edizioni
Elementi per una genetica forense, (co-edited with Luca Marelli), Mondadori,
Posters and presentations:
"Defining life?" - presentation at the conference "Materia e materia vivente", 2012 University of Florence,
"What is stemness?" - at the international conference of the German Society for Philosophy of Science/Gesellschaft für Wissenschaftsphilosophie (GWP), 11-14 March 2013 - University of Hannover
"The gene after encode: a Wittgensteinian approach" - at the ISHPSSB, 7-12 July 2013 - University of Montpellier III
"Models in bioinformatics - GO a representation of what?" - at EPSA conference, 28-31 August 2013 - University of Helsinki
Other experiences:
2012 - Summer School in Ontological Analysis, IAOA, University of Trento
2010 - Natural History Museum of the University of Florence, working on collection
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