Research

Pain perception 

(traditional medical systems; pain assessment; pain expression; philosophical anthropology)

My next project will investigate pain perception as part of an interdisciplinary collaboration. This ambitious project, aiming to demonstrate the practical value of philosophical investigations, combines phenomenology, philosophical anthropology and philosophy of religion, philosophy of science and mind, psychology, neuroscience and pharmacology in order to provide a better understanding of how cultural differences influence the perception and expression of pain.

As part of this project, I am currently investigating the concept of evidence in clinical research, the possibility of devising techniques and treatments in the absence of a thorough theoretical understanding of how a technique/treatment works (‘theory-free experimental investigation’), and the role knowledge of mechanisms plays in deciding whether a treatment is beneficial; these issues are highly pertinent to current debates in bioethics, public policy, and the new standards established by evidence-based medicine [‘The Hierarchy of Evidence and the Problem of External Validity in Clinical Research’ (in preparation-b); ‘Extrapolation in Biomedical Research: A Multi-Model Perspective’ (Germain and Baetu in preparation)].

 

Explanatory pluralism (project funded by a Konrad Lorentz Institute Fellowship 2012-2014, Konrad Lorentz Institute and University of Vienna)

(explanation; mechanism; mathematical model; systems biology; molecular biology)

I am currently investigating the plurality of explanations in science. There is little appreciation of the fact that science offers many kinds of explanations, most probably because philosophers are traditionally interested in providing a universal account of scientific explanation. I think, however, that there is a lot to be gained by adopting a pluralist perspective. By allowing, even provisionally, for pluralism, we can begin to ask a different set of questions that we wouldn’t think to ask if we assume a monistic perspective. We can begin to wonder about what is the relationship between different kinds of explanation. For instance, can there be a conflict between two distinct kinds of explanation of the same phenomenon? If so, how are these conflicts solved? Can there be an integration of different kinds of explanation into some kind of mosaic big picture? Or is one kind of explanation better than others, such that ultimately science thrives to upgrade its explanations to this best kind of explanation?

The project focuses on the explanatory role of mathematical models and computer simulations in science. Using systems biology as a case study, I show that mathematical models can reveal anomalies and unsuspected explanatory holes in previously accepted mechanistic models, and that this may result in a revision of mechanistic explanations [‘‘From Mechanisms to Mathematical Models and Back to Mechanisms: Quantitative Mechanistic Explanations’ (2015)]. I conclude that mathematical models play a distinct explanatory role, thus supporting a pluralist approach according to which the most comprehensive explanation of a given phenomenon is in fact a composite picture combining mechanisms and mathematical modeling, and that they may also provide the means to assess the completeness of mechanistic explanations [‘The Completeness of Mechanistic Explanations’ (forthcoming-b); ‘When is a Mechanistic Explanation Satisfactory? Reductionism and Antireductionism in the Context of Mechanistic Explanations’ (forhcoming)].

 

Models in biology 

(integration; extrapolation; confirmation holism; experiment)

Models are ubiquitous in contemporary life sciences, yet it is not clear what epistemic role they play.  I argue that contextualization is a particularly stringent requirement in biological sciences stemming from the fact that biological knowledge is not easily generalizable. Since what is true about one phenomenon, as it occurs in a given biological system, is not necessarily true of a similar phenomenon occurring in a different biological system, indiscriminately summing up data and results does not result in a coherent universal ‘big picture.’ In order to overcome this absence of a universal framework for integrating knowledge, data and results are systematically contextualized to well characterized models in order to allow for a meaningful comparison, evaluation and synthesis of knowledge about biological phenomena/systems [‘Models and the Mosaic of Scientific Knowledge. The Case of Immunology’ (2014)].

I discuss some of the most striking epistemic consequences and challenges raised by the extensive use of models in biology, namely the mosaic nature of ‘big picture’ accounts presented in review papers and biology textbooks; the more or less ambitious, but always potentially problematic extrapolations used to reconstruct these ‘big picture’ accounts; and some of the confirmation strategies used to justify these extrapolations [‘The ‘Big Picture’: The Problem of Extrapolation in Basic Research’ (forthcoming-a)]. I argue that, instead of adopting a disjunctive elimination strategy, whereby conflicting theoretical frameworks are pitted against each other by testing particular predictions about a given aspect of empirical reality, experimental biology advances primarily in a constructive conjunction manner, whereby individual pieces of experimental data about correlated and causally relevant factors are put together in an attempt to elucidate the causes and mechanisms responsible for producing a particular phenomenon and that, under this approach, holistic confirmation strategies play a crucial role [‘Duhem’s Problems and the Experimental Practice of Molecular Biology’ (in preparation-a)].

 

Causation and mechanisms (project funded by a Fonds de la recherche sur la société et la culture post-doctoral scholarship 2008-2010, University of Maryland)

(law; mechanistic constraint; discovery; experiment; chance; regularity; reproducibility)

Mechanistic accounts provide novel solutions to fundamental dilemmas in philosophy of science [‘Mechanisms in Molecular Biology’ (in preparation-d)]. For example, many authors agree that there are no such things as universal/necessary laws in biology. However, if the notion of law is completely abandoned, then anything will turn out to be possible in evolution, and this does not seem to be the case. I argue that generalizations in biology can be accounted for as ‘mechanistic constraints’ generating probabilistic biases towards preferred outcomes [‘Mechanistic Constraints on Evolutionary Outcomes’ (2012f)]. Thus, mechanistic constraints bridge the gap between the more fundamental law-like generalizations in the physical sciences and contingent generalizations in the life sciences.

I am interested in finding out how chance correlations are distinguished from potential phenomena produced by mechanisms [‘Chance, Experimental Reproducibility, and Mechanistic Regularity’ (2013)]; how mechanisms are inferred from bits and pieces of knowledge of causally-relevant factors [‘Filling In the Mechanistic Details: Two-Variable Experiments as Tests for Constitutive Relevance’ (2012c)]; and how mechanisms are different from modular assemblages of causal factors [‘How Mechanisms Relate to Causes: Disentangling the Relationship between Causal Dependence and Productive Mechanisms’ (in preparation-c)].

 

Integration and transfer of knowledge across the life sciences 

(relationships between theories; integration; reduction; species concepts; mechanism)

As a philosopher of science, I published extensively on issues concerning the integration, growth, and transfer of scientific knowledge across different fields of investigation and different periods of time. Throughout my published papers, I defend an integrative alternative to a traditional reductionist-antireductionist dichotomy. While it is true that reductionism fails to adequately capture the relationship between theories, I defend the view that it is not enough to assert the pragmatic value of a pluralistic antireductionism. Many disagreements between reductionists and antireductionists stem from a failure to acknowledge that biological phenomena are analyzed at a variety of levels of composition, thus creating a false dichotomy between reductionism and antireductionism [‘Emergence, Therefore Antireductionism? A Critique of Emergent Antireductionism’(2012b)].

My goal is to provide a framework capable of accounting for the high level of integration of different scientific practices, theories, and fields. Using genetics and speciation as case studies, I elaborate a mechanistic framework for understanding the complex relationships between scientific theories [‘Mechanism Schemas and the Relationship between Biological Theories’ (2011b)] and concepts [‘Defining Species: A Multi-Level Approach’ (2012a)].

 

Genes and genomes (project funded by a Fonds de la recherche sur la société et la culture scholarship 2005-2008, Université of Montréal)

(concept of the gene; genomics; post-genomics)

An important part of my research targeted the evolution of the concept of the gene from classical genetics, to molecular biology, to present-day genomics. I show how partial co-reference of concepts associated with different fields of investigation plays a crucial role in bridging the transfer of knowledge from one field to another, thus promoting their integration [‘The Referential Convergence of Gene Concepts Based on Classical and Molecular Analyses’ (2010)].

I discuss and analyze novel, bioinformatics (‘syntax-based’) concepts of the gene [‘A Defense of Syntax-Based Gene Concepts in Postgenomics: ‘Genes as Modular Subroutines in the Master Genomic Program’’ (2011a)]. I show how concepts of the gene are revised in light of new discoveries, and I argue that contemporary experimental practice relies on a dynamic interplay between two distinct families of gene concepts, thus resisting attempts to collapse different concepts into a unified, over-arching concept [‘Genes After the Human Genome Project’ (2012d)].

Finally, I argue that ‘genomic programs’ are in fact abstract representations of mechanisms highlight ing the genomic determinants of inheritance and their organizational features at work in the wider context of the mechanisms of genome expression [‘Genomic Programs as Mechanism Schemas: A Non-Reductionist Interpretation’ (2012e)]. Most notably, these abstract representations play an important role in mediating the transfer of information between experimental branches of biology, such as molecular and developmental biology, and more fields of investigation adopting more theoretical approaches, such as bioinformatics and systems biology.

 

Immunology (project funded by a Fonds pour la formation de chercheurs et l’aide à la recherche scholarship 1999-2001, McGill University)

(immune response; viral infection; transcriptional control; apoptosis; T-cell regulation)

I gained my first research experience while I completed my Masters’ degree in Microbiology and Immunology at McGill University (Montréal, Canada; 2001). I worked on a project investigating the regulation of immune responses in cancer and HIV patients. I gained valuable experience designing and performing experiments, writing papers and presenting my research at international conferences, as well as successfully collaborating with other researchers. I published two first author papers in highly quoted scientific journals (Journal of immunology, impact factor 5.745; Cytokine and Growth Factor Reviews, impact factor 9.832). These publications have been quoted numerous times, demonstrating the quality of my research project [Web of Knowledge citation indexes of 75 (Baetu et al. 2001) and 62 (Baetu and Hiscott 2002)].

 

List of papers

Baetu, T. M. 2010. “The Referential Convergence of Gene Concepts Based on Classical and Molecular Analyses”, International Studies in the Philosophy of Science 24 (4):411-27.

———. 2011a. “A Defense of Syntax-Based Gene Concepts in Postgenomics: ‘Genes as Modular Subroutines in the Master Genomic Program’”, Philosophy of Science 78 (5):712-23.

———. 2011b. “Mechanism Schemas and the Relationship between Biological Theories”, in P. McKay, J. Williamson and F. Russo (eds.), Causality in the Sciences, Oxford: Oxford University Press.

———. 2012a. “Defining Species: A Multi-Level Approach”, Acta Biotheoretica 60 (3):239-55.

———. 2012b. “Emergence, Therefore Antireductionism? A Critique of Emergent Antireductionism”, Biology and Philosophy 27 (3):433–48.

———. 2012c. “Filling In the Mechanistic Details: Two-Variable Experiments as Tests for Constitutive Relevance”, European Journal for Philosophy of Science 2 (3):337-53.

———. 2012d. “Genes After the Human Genome Project”, Studies in History and Philosophy of Biological and Biomedical Sciences 43 (1):191–201.

———. 2012e. “Genomic Programs as Mechanism Schemas: A Non-Reductionist Interpretation”, British Journal for the Philosophy of Science 63 (3):649-71.

———. 2012f. “Mechanistic Constraints on Evolutionary Outcomes”, Philosophy of Science 79 (2):276-94.

———. 2013. “Chance, Experimental Reproducibility, and Mechanistic Regularity”, International Studies in History and Philosophy of Science 27 (3):255-73.

———. 2014. “Models and the Mosaic of Scientific Knowledge. The Case of Immunology”, Studies in History and Philosophy of Biological and Biomedical Sciences 45:49–56.

———. 2015. “From Mechanisms to Mathematical Models and Back to Mechanisms: Quantitative Mechanistic Explanations”, in P.-A. Braillard and C. Malaterre (eds.), Explanation in Biology. An Enquiry into the Diversity of Explanatory Patterns in the Life Sciences, Dordrecht: Springer.

———. forhcoming. “When is a Mechanistic Explanation Satisfactory? Reductionism and Antireductionism in the Context of Mechanistic Explanations”, in G. Sandu, I. Parvu and I. Toader (eds.), Romanian Studies in the History and Philosophy of Science, Dordrecht: Springer.

———. forthcoming-a. “The ‘Big Picture’: The Problem of Extrapolation in Basic Research”, British Journal for the Philosophy of Science.

———. forthcoming-b. “The Completeness of Mechanistic Explanations”, Philosophy of Science.

———. in preparation-a. “Duhem’s Problems and the Experimental Practice of Molecular Biology”.

———. in preparation-b. “The Hierarchy of Evidence and the Problem of External Validity in Clinical Research”.

———. in preparation-c. “How Mechanisms Relate to Causes: Disentangling the Relationship between Causal Dependence and Productive Mechanisms”.

———. in preparation-d. “Mechanisms in Molecular Biology”, in Stuart Glennan and Phyllis Illari (eds.), Routledge Handbook of mechanisms, London: Routledge.

Baetu, T. M. , and J.  Hiscott. 2002. “On the TRAIL to Apoptosis”, Cytokine & Growth Factors Reviews 13:199-207.

Baetu, T. M. , H. Kwon, S. Sharma, N. Grandveaux, and J. Hiscott. 2001. “Disruption of NF-kB Signalling Reveals a Novel Role for NF-kB in the Regulation of TNF-Related Apoptosis-Inducing Ligand Expression”, Journal of Immunology 167:3164-73.

Germain, P.-L., and T. M. Baetu. in preparation. “Extrapolation in Biomedical Research: A Multi-Model Perspective”, in Marco Nathan and Giovanni Boniolo (eds.), Foundational Issues in Molecular Medicine, London: Routledge.