University of Alberta

Funded Research Projects

Standards, Aims, and Values: Biological Explanation and Beyond   (2016–2022)

Philosophy of science has traditionally construed and studied science in terms of representations of the natural world, such as data and theories. Yet as an additional dimension, my approach will emphasize values held by scientists, including explanatory and other investigative aims as well as methodological and explanatory standards. Particular aims and standards need to be philosophically made explicit to critically evaluate scientific frameworks and to understand the process of science and practice of scientists. For the specific aims and standards that come to be accepted by a group of researchers account for (changes in) their practice. Indeed, even though some of my project is framed in terms of ‘scientific explanation,’ I will show that this philosophical issue needs to be approached from the larger practice in which explanations are developed, with an eye on how the role of values in scientific inquiry is a matter of public concern.

My project will develop and illustrate this philosophical framework based on case studies from three biological domains. (1) In the context of systems biology, which mathematically models the operation of molecular and cellular systems, I will investigate how different models are used in a coordinated fashion. Attention will be paid to the modelling strategies used and the representational or explanatory aims that necessitate the joint use of several models. (2) In the case of the evolution of complexity, I will investigate some scientific disagreements about explanatory frameworks and standards. Models of the evolution of multicellular animals as well as multispecies microbial communities attempt to capture this complexity while still making various idealizations, and I will study what representational aims can justify such simplifications. (3) Apart from epistemic values (e.g., explanatory scope), there are social and environmental values. Philosophers have argued that also the latter matter in science, but I set out to articulate a stronger role for social values, exploring the implications for scientific objectivity. Focusing on feminist values, I will develop this position in the domains of human evolution and the social behaviour of non-human primates.

Integrating Different Biological Approaches: A Philosophical Contribution   (2008–2012)

The traditional account about the relation of scientific fields was ‘theory reduction’, the idea that the knowledge of one field (e.g. developmental biology) can be logically deduced from a more fundamental theory (e.g. molecular biology). This account has been abandoned because it fails to capture actual biology and its diversity of methods and explanations. As a result, many philosophers of biology have come to embrace ‘pluralism’ about methods, theories, and explanations. However, philosophical accounts emphasizing pluralism often have not pursued the question of how different fields and concepts are related or can be integrated. This is unsatisfactory because the proliferation of biological subdisciplines not only promotes effective research, but creates potential communication problems across disciplines due to them using language differently and preferring different methods and kinds of explanations.

The goal of the project was to develop philosophical accounts of the relation and integration of various epistemic units (approaches, concepts, explanations, methods) in biology in order to: (1) provide a philosophical understanding of the nature of the partially existing integration in biology (e.g. which epistemic conditions make it possible or limit it), so as to put forward a more general philosophical theory that amounts neither to reduction nor mere pluralism; (2) use this framework to facilitate future integration in biology by interacting with scientists.

The focal area of study was evolutionary developmental biology, as it is a recent and ongoing attempt to synthesize knowledge from various disciplines bearing on evolution, such as evolutionary genetics, developmental biology, phylogeny, paleontology, theoretical biology, morphology, and ecology. In aspiring to solve problems that have been beyond the scope of traditional neo-Darwinian evolutionary biology, evolutionary developmental biology faces the significant challenge of integrating quite different methods and explanations, such as experimental and theoretical approaches, microevolutionary and macroevolutionary models, developmental and population genetic explanations. The project studied ongoing biological research addressing the complex problem of explaining the evolutionary origin of novelties in the vertebrate skeleton, e.g. fins and limbs.

This 4-year project was funded by the Social Sciences and Humanities Research Council of Canada (Standard Research Grant, $66,652 incl. teaching release stipend). I was the principal investigator, and my official collaborators were Alan Love and Todd Grantham, in addition to several biologists and other philosophers attending the project meetings. In 2009 and 2010 we held two workshops bringing together biologists, philosophers, and historians of biology. The purpose of this was (i) to gather researchers that (as a group) possess knowledge covering the various biological approaches and fields relevant for explanations of the evolutionary origin of novelties, and (ii) to conduct in-depth discussion on the biological case so as to generate and criticize philosophical notions about the possibility and limits of integration in biology. A third workshop was held in September 2011 at the Minneosota Center for Philosophy of Science, which broadened the scope by addressing interdisciplinary research across different parts of biology. In addition to conference symposia organized, the project results were disseminated by the below journal special issues and individual publications.

Publications stemming from this project:

“From developmental constraint to evolvability: how concepts figure in explanation and disciplinary identity.” In: Conceptual Change in Biology: Scientific and Philosophical Perspectives on Evolution and Development. A. C. Love (ed), Springer, Dordrecht, pp. 305–325 (2015).      [penultimate draft, published article, published volume]

Integration in Biology: Philosophical Perspectives on the Dynamics of Interdisciplinarity. Special section of Studies in History and Philosophy of Biological and Biomedical Sciences, Volume 44, Issue 4, Part A, pp. 461–571 (2013). Edited by Ingo Brigandt.      [published articles]

“Integration in biology: philosophical perspectives on the dynamics of interdisciplinarity” (introduction to the special section). Studies in History and Philosophy of Biological and Biomedical Sciences 44: 461–465 (2013).      [postprint, published article]

Perspectives on Evolutionary Novelty and Evo-Devo. Special issue of the Journal of Experimental Zoology Part B: Molecular and Developmental Evolution, Volume 318, Issue 6 (2012). Edited by Ingo Brigandt.      [published articles]

“Conceptualizing evolutionary novelty: moving beyond definitional debates” (with Alan C. Love). Journal of Experimental Zoology Part B: Molecular and Developmental Evolution 318: 417–427 (2012).      [postprint, published article]

“Beyond reduction and pluralism: toward an epistemology of explanatory integration in biology.” Erkenntnis 73: 295–311 (2010).      [penultimate draft, published article]

“Evolutionary novelty and the evo-devo synthesis: field notes” (with Alan C. Love). Evolutionary Biology 37: 93–99 (2010).      [postprint, published article]

Other Research Projects

Mechanistic explanation and systems biology:   Philosophical accounts of mechanistic explanation have been developed as an alternative to the traditional vision of explanation as the derivation from laws of quantitative principles, which proved to be problematic not only in the domain of molecular biology. However, by focusing on explanation in terms of a mechanism's spatial parts and their qualitative interactions, philosophical discussions of mechanistic explanation fail to address what a mathematical model adds to some explanations. This holds in particular for the domain of systems biology, which develops mathematical models of molecular, cellular, and other complex systems, using experimentally generated data about these systems. This project studies how systems biology integrates mathematical modelling and mechanistic explanation, arguing that there are even qualitative explananda whose mechanistic explanation necessitates the use of a quantitative account. Systems biology calls for a broader philosophical conception of both mechanistic explanation and what a mechanism is.

“Explanation of molecular processes without tracking mechanism operation.” Philosophy of Science (in press).

“Network analyses in systems biology: new strategies for dealing with biological complexity” (fifth author, with Sara Green, Maria Şerban, Raphael Scholl, Nicholaos Jones, and William Bechtel). Synthese, doi:10.1007/s11229-016-1307-6 (2017).      [preprint, published article]

“Systems biology and mechanistic explanation” (with Sara Green and Maureen A. O'Malley). In: The Routledge Handbook of Mechanisms and Mechanical Philosophy. S. Glennan and P. Illari (eds), Routledge, New York, pp. 362–374 (2017).      [postprint, published volume]

“Evolutionary developmental biology and the limits of philosophical accounts of mechanistic explanation.” In: Explanation in Biology: An Enquiry into the Diversity of Explanatory Patterns in the Life Sciences. P.-A. Braillard and C. Malaterre (eds), Springer, Dordrecht, pp. 135–173 (2015).      [postprint, published article, published volume]

“Multilevel research strategies and biological systems.” (second author, with Maureen A. O'Malley, Alan C. Love, John W. Crawford, Jack A. Gilbert, Rob Knight, Sandra D. Mitchell, and Forest Rohwer). Philosophy of Science 81: 811–828 (2014).      [postprint, published article]

“Systems biology and the integration of mechanistic explanation and mathematical explanation.” Studies in History and Philosophy of Biological and Biomedical Sciences 44: 477–492 (2013).      [postprint, published article]

Epistemic and Non-Epistemic Values in Science:   In addition to various scientific representations (theories, observation statements, laws, models, and explanations), whose relations have been the focus of philosophical discussions, there are aspects of scientific knowledge (or at least scientific practice) that are not representations of the natural world, such as epistemic values. This includes scientific aims (what currently is deemed to be an important scientific problem and what phenomena are deemed to be in need of explanation) and explanatory standards (what currently counts as a satisfactory explanation in a certain domain). Such epistemic values influence the way in which scientific representations are revised and developed in the first place, and thus are important for any philosophical perspective that attempts to understand the dynamic operation of scientific knowledge and/or normatively evaluate scientific practice. I have even tied the use of individual concepts to epistemic aims in my work on scientific concepts (mentioned below).

“Philosophical dimensions of individuality” (second author, with Alan C. Love). In: Biological Individuality: Integrating Scientific, Philosophical, and Historical Perspectives. S. Lidgard and L. K. Nyhart (eds), University of Chicago Press, Chicago, pp. 318–348 (2017).      [postprint, published volume]

“Why the difference between explanation and argument matters to science education.” Science & Education 25: 251–275 (2016).      [postprint, published article]

“Do we need a 'theory' of development?” Review essay of Towards a Theory of Development edited by Alessandro Minelli and Thomas Pradeu, Oxford University Press, 2014. Biology & Philosophy 31: 603–617 (2016).      [postprint, published article]

“Social values influence the adequacy conditions of scientific theories: beyond inductive risk.” Canadian Journal of Philosophy 45: 326–356 (2015).      [penultimate draft, published article]

“Intelligent design and the nature of science: philosophical and pedagogical points.” In: The Philosophy of Biology: A Companion for Educators. K. Kampourakis (ed), Springer, Dordrecht, pp. 205–238 (2013).      [penultimate draft, published article, published volume]

“Explanation in biology: reduction, pluralism, and explanatory aims.” Science & Education 22: 69–91 (2013).      [postprint, published article]

“The dynamics of scientific concepts: the relevance of epistemic aims and values.” In: Scientific Concepts and Investigative Practice. U. Feest and F. Steinle (eds), de Gruyter, Berlin, pp. 75–103 (2012).      [penultimate draft, published article, published volume]

Concepts and the Rationality of Semantic Change:   While accounts of concepts in the philosophy of science have typically focused on the reference of terms, the notion of reference does not explain what makes semantic change – including change in a term's reference – rational and progressive. I suggest that each scientific concept consists of three components of content: 1) the concept's reference, 2) its inferential role, and 3) the epistemic goal pursued with the concept's use. In the course of history a concept can change in any of these three components. I introduce the epistemic goal pursued by a term's use as a genuine semantic property of terms, as it accounts for the rationality of semantic change (change in any of a concept's components). The two main cases studied are the development of the homology concept in the 19th and 20th century, and the change of the gene concept in the 20th century.

“The dynamics of scientific concepts: the relevance of epistemic aims and values.” In: Scientific Concepts and Investigative Practice. U. Feest and F. Steinle (eds), de Gruyter, Berlin, pp. 75–103 (2012).      [penultimate draft, published article, published volume]

“Natural kinds and concepts: a pragmatist and methodologically naturalistic account.” In: Pragmatism, Science and Naturalism. J. Knowles and H. Rydenfelt (eds), Peter Lang Publishing, Frankfurt am Main, pp. 171–196 (2011).      [draft, published volume]

“The epistemic goal of a concept: accounting for the rationality of semantic change and variation.” Synthese 177: 19–40 (2010).      [postprint, published article]

Context-Sensitive and Communal Use of Scientific Terms:   Despite the idea that a concept should have a clear-cut definition and stable reference, the usage and reference of the contemporary gene concept varies from case to case. This project attempts to understand how the context-sensitive use of biological terms promotes successful scientific practice. The challenge is to find an adequate semantic framework capturing context-sensitivity, given that the context that determines a biological term's varying reference is essentially intentional and epistemic. Furthermore, in contrast to the idea that all individuals possessing a concept meet the same condition (e.g., having grasped the same definition), due to the division of scientific labour different biologists sharing a concept may have different beliefs and epistemic abilities. I study how the particular variation in a term's use within a scientific community underwrites successful practice and influences the direction of conceptual change. This communal nature of concepts is used to trace implications for theories of concepts and concept possession.

“The dynamics of scientific concepts: the relevance of epistemic aims and values.” In: Scientific Concepts and Investigative Practice. U. Feest and F. Steinle (eds), de Gruyter, Berlin, pp. 75–103 (2012).      [penultimate draft, published volume]

“The epistemic goal of a concept: accounting for the rationality of semantic change and variation.” Synthese 177: 19–40 (2010).      [postprint, published article]

Intuitions and Philosophical Method:   A common method of analyzing a philosophical concept (e.g., knowledge, reference, causation) or criticizing rival accounts consists in consulting one's intuitions as to how the concept applies to various hypothetical scenarios. However, all this method can achieve is to make explicit one's current concept, whereas the philosophical aim should be to develop an improved concept. (The nowadays popular use of experimental philosophy surveys in itself does not address this issue either.) In this metaphilosophy project, which is in its first stages, I attempt to use the way in which biologists revise their concepts as a model for philosophical practice, using my past work on conceptual change in biology. The aim is to get clearer about the philosophical aims that underlie accounts of knowledge, reference, and causation and the standards that determine what counts as an improved philosophical account in each case. I also criticize the way in which David Chalmers and Frank Jackson have used two-dimensional semantics to found their project of armchair conceptual analysis.

“A critique of David Chalmers and Frank Jackson's account of concepts.” ProtoSociology 30: 64–89 (2013).     [published article, published volume]

“Natural kinds and concepts: a pragmatist and methodologically naturalistic account.” In: Pragmatism, Science and Naturalism. J. Knowles and H. Rydenfelt (eds), Peter Lang Publishing, Frankfurt am Main, pp. 171–196 (2011).      [draft, published volume]

Natural Kinds in Scientific Practice:   Philosophical accounts of natural kinds have traditionally been based on kinds as found in physics and chemistry (e.g., by deeming a natural kinds to be defined by a microstructural essence), but such views of natural kinds often fail to address kinds as found in biology (most prominently species). A broader vision of natural kinds is needed capture kinds as they occur in the special sciences; in fact, quite different considerations can be part of a kind's identity in different empirical cases. Beyond a purely metaphysical construal of kinds, a major prong of the project is to pay attention to epistemological issues on the how kinds figure in actual scientific practice, in particular what epistmic aims scientists want to and can (or cannot) meet by grouping certain object into a kind.

“Natural kinds and concepts: a pragmatist and methodologically naturalistic account.” In: Pragmatism, Science and Naturalism. J. Knowles and H. Rydenfelt (eds), Peter Lang Publishing, Frankfurt am Main, pp. 171–196 (2011).      [draft, published volume]

“Natural kinds in evolution and systematics: metaphysical and epistemological considerations.” Acta Biotheoretica 57: 77–97 (2009).      [penultimate draft, published article]

“Homology: homeostatic property cluster kinds in systematics and evolution” (with Leandro C. S. Assis). Evolutionary Biology 36: 248–255 (2009).      [penultimate draft, published article]

“When traditional essentialism fails: biological natural kinds” (with Robert A. Wilson and Matthew J. Barker). Philosophical Topics 35: 189–215 (2007).      [postprint, published article]

Material Inference and Scientific Reasoning:   Inference is predominantly viewed as formal inference, i.e., as being good in virtue of its logical form. Many accounts of theory reduction, scientific explanation, and confirmation are based on the idea that inference is formal inference. This project is working toward a novel perspective by viewing inference as material inference. A material inference is good in virtue of the empirical content of the concepts contained in the premises and the conclusion. I suggest that viewing different forms of scientific reasoning – reasoning involved in justification, explanation, and discovery – as based on material inference yields a more adequate account of these matters than formal models of inference. The project pays attention to theories of concepts and reasoning from recent cognitive psychology, as they exhibit parallels to the idea that scientific reasoning is material inference.

“Scientific reasoning is material inference: combining confirmation, discovery, and explanation.” International Studies in the Philosophy of Science 24: 31–43 (2010).      [penultimate draft, published article]