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Emanuele Ratti

Emanuele Ratti
Academic Year: 
2016
Year of Study: 
Archive
Curricula: 
Medical Humanities
Research Center Affiliation: 
European Institute of Oncology (IEO)
THESIS TITLE: 
The context of discovery of data driven biology
Thesis Abstract: 

My PhD dissertation aims (1) at reconstructing the structure of the context of discovery of

‘data-driven’ (big data, data intensive) biology and (2) at comparing it to traditional

molecular approaches. Within the current debate in philosophy of science, ‘traditional

approaches’ in molecular biology should be understood as the discovery and heuristics

strategies identified by mechanistic philosophers such as Carl Craver and Lindley Darden.

Therefore, key questions of my thesis are: what is the structure of discovery of datadriven

biology? Is data-driven biology methodology different from traditional molecular

approaches?

 The reason for doing such an analysis comes from a recent controversy among

biologists. In particular, sides disagree on whether high throughput sequencing

technologies are stimulating the development of a new scientific method somehow

irreducible to traditional approaches. I will try to disentangle the debate by reconstructing

and comparing data-driven and traditional methodologies. The dissertation is composed

of five chapters.

The first chapter deals with methodological issues. How do I compare data-driven

and traditional molecular biology structures of discovery? Mechanistic philosophers have

extensively characterized the discovery structure of traditional molecular biology.

However, there is not such an analysis for data-driven biology. In order to do this, I will

critically revise the discovery/justification distinction. The debate on

discovery/justification has provided valuable tools on how discovery strategies might be

conceived, and it is clearly one of the main forefathers of recent philosophical discussions

on scientific methodologies in biology and physics.

In Chapter 2 I shall to try to infer a full-fledged account of discovery for datadriven

biology by means of the philosophical tools developed in Chapter 1. This analysis

will be done in parallel to the investigation of key examples of data-driven biology,

namely genome-wide association studies and cancer genomics. In Chapter 3 I analyze the

epistemic strategies enabled by biological databases in data-driven biology. In Chapter 4,

I will show how the discovery structure of ‘traditional molecular biology’ can be more

efficiently rephrased through the same theoretical framework that I use to characterize

data-driven biology.

Since data-driven and traditional molecular biology seem to adopt the same

discovery structure, one might consider the controversy motivating my research ill posed.

However, in Chapter 5 I shall argue that there is still a valuable reason of disagreement

between the sides. Actually, data-driven and traditional molecular biology endorse

different cognitive values, which provide the criteria for evaluating models and findings as

adequate or not. Here one might say that, although the structures of discovery (i.e. how  reasoning and experimental strategies are structured and depend on each other) of the

two sides are the same, the contexts of discovery  (i.e. the set of both

reasoning/experimental strategies and  epistemic values/background assumptions that

motivate discovery) are different. Therefore, in this last chapter I shall pinpoint the

cognitive values behind traditional and data-driven biology, and how these commitments

stimulate the heated disagreement motivating my research.

 

Areas of specialization: Philosophy of biology, philosophy of science

Research interests: Sociology of science, philosophy of information, bioinformatics

Education

 2011 MA in    Research University of Hertfordshire, UK
Supervisor: professor Luciano Floridi

Present position

PhD Student (2012-2016) in the program Foundations of the Life Sciences and Their Ethical Consequences, European School of Molecular Medicine, Ifom-Ieo Campus, Milan (Italy). This program is affiliated with the European Institute of Oncology (IEO) and the faculty of Health Sciences of the University of Milan.

Thesis Committee: dr Marco Nathan (Denver University), professor Giovanni Boniolo (University of Milan), professor Michael Weisberg (University of Pennsylvania), dr Francesca Ciccarelli (King's College)

Lab experience

  • January-May 2012. Diego Pasini's Lab: Epigenetic Mechanisms and Stem Cell Differentiation and Oncogenesis. Training in basic lab procedures: DNA extraction, PCR, transfection.
  • May 2012 - October 2012. Marina Mapelli's Lab: Molecular Basis of Asymmetric Cell Division. Training in basic procedures: DNA extraction, PCR, transfection, protein expression test
  • October 2012 - September 2013. Francesca Ciccarelli's Lab: Bioinformatics and Evolutionary Genomics of Cancer. Analysis of data from whole-genome and whole-exome screenings for the project Network of Cancer Genes 4.0

Other experiences

Visiting Student (09-2013/06-2014) at the department of philosophy of the University of Pennsylvania under the supervision of professor Michael Weisberg

Selected publications

  1. "Diverse Perspectives on Ontology" (with Emilio Sanfilippo, Francesca Quattri, Aleksandra Sojic, Federico Boem, Gaoussou Camara and Erik Chuck). Applied Ontology 2013, 8(8), 59-71, doi:10.3233/AO-13012
  2. "NCG4.0: the Network of Cancer Genes in the Era of Massive Mutational Screenings of Cancer Genomes" (with Omer An, Vera Pendino, Matteo D'Antonio, Marco Gentilini and Francesca Ciccarelli). Database: The Journal of Biological Databases and Curation. 2014, Vol. 2014, doi:10.1093/database/bau015
  3. "Junk or Functional DNA? ENCODE and the Function Controversy" (with Pierre-Luc Germain and Federico Boem). Biology & Philosophy. Forthcoming
  4. "Levels of Abstraction, Emergentism and Artificial Life". Journal of Theoretical and Experimental Artificial Intelligence (special issue "Inforgs and Infosphere: Themes from Luciano Floridi's Philosophy of Artificial Intelligence). Forthcoming

Selected presentations, conferences, seminars

Conferences:

  1. (with Federico Boem) "The Gene after ENCODE: a Wittgensteinian Approach", 9th July 2013, ISHPSSB 2013 Meeting, Montpellier
  2. "What is Integration in Bioinformatics Modeling of Big Data? A Proposal Based on Idealization", August 28-31 2013, Fourth conference of the European Philosophy of Science Association (EPSA), Helsinki

Organized Symposia:

  1.  "Ontology for and from Science: the Ontological Analysis of Biology", 11th March 2013, first international conference of the German Society for Philosophy of Science/Gesellschaft für Wissenschaftsphilosophie (GWP), University of Hannover
  2. "Models in Bioinformatics", August 28-31 2013, fourth conference of the European Philosophy of Science Association (EPSA), Helsink

Seminars:

  1. Seminar on Next-generation Digital Information Storage in DNA (Church et al.), Francesca Ciccarelli's Lab (25th February 2013), IFOM-IEO Campus, Milan
  2. (invited seminar) "The ENCODE Controversy", 28th May 2013, lgBIG-meeting, University of Geneva

References

Professor Giovanni Boniolo, University of Milan, giovanni.boniolo@ieo.eu

Dr Marco Nathan, University of Denver, marco.nathan@du.edu

Professor Michael Weisberg, University of Pennsylvania, weisberg@phil.upenn.edu