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Ingo Brigandt

University of Alberta, Philosophy, Faculty Member

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My work combines the history and philosophy of biology with epistemology and the philosophy of mind and language by attempting to understand scientific practice and concept use (including its historical change) from an epistemological and semantic point of view.
I am particularly interested in the field of evolutionary developmental biology (evo-devo) and its 19th and 20th century antecedents.
My recent research includes theories of concepts, the rationality of semantic change, how the context-sensitive use of scientific terms supports successful practice, integrating different approaches and explanations in evolutionary and developmental biology, and non-reduction in biology.
Phone: +1 780-492-9030
Address: Ingo Brigandt
Department of Philosophy
2-40 Assiniboia Hall
University of Alberta
Edmonton, AB T6G 2E7
Canada

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Robert Lickliter

Florida International University

The University of Texas at Austin

The University of Texas at Austin

Kristen J Gremillion

Ohio State University

Richard Bellamy

University College London

Shaun Gallagher

University of Memphis

Louis de Saussure

University of Neuchâtel

Armando Marques-Guedes

UNL - New University of Lisbon

Massachusetts Institute of Technology (MIT)

Gwen Robbins Schug

University of North Carolina at Greensboro

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Papers by Ingo Brigandt

Conceptual Roles of Evolvability across Evolutionary Biology: Between Diversity and Unification

by Cristina Villegas, Alan C Love, and Ingo Brigandt

Evolvability. A Unifying Concept in Evolutionary Biology?, 2023

Biologists and philosophers have noted the diversity of interpretations of evolvability in contem... more Biologists and philosophers have noted the diversity of interpretations of evolvability in contemporary evolutionary research. Different clusters of research identified by co-citation patterns or shared methodological orientation sometimes concentrate on distinct conceptions of evolvability. We examine five different activities where the notion of evolvability plays conceptual roles in evolutionary biological investigation: setting a research agenda, characterization, explanation, prediction, and control. Our analysis of representative examples demonstrates how different conceptual roles of evolvability are quasi-independent and yet exhibit important relationships across scientific activities. It also provides resources to detail two distinct strategies for how evolvability can help synthesize disparate areas of research and thereby potentially serve as a unifying concept in evolutionary biology.

Evolvability as a Disposition: Philosophical Distinctions, Scientific Implications

by Ingo Brigandt, Cristina Villegas, and Alan C Love

Evolvability: A Unifying Concept in Evolutionary Biology?, 2023

A disposition or dispositional property is a capacity, ability, or potential to display or exhibi... more A disposition or dispositional property is a capacity, ability, or potential to display or exhibit some outcome. Evolvability refers to a disposition to evolve. This chapter discusses why the dispositional nature of evolvability matters—why philosophical distinctions about dispositions can have scientific implications. To that end, we build a conceptual toolkit with vocabulary from prior philosophical analyses using a different disposition: protein foldability. We then apply this toolkit to address several methodological questions related to evolvability. What entities are the bearers of evolvability? What features causally contribute to the disposition of evolvability? How does evolvability manifest? The various possible answers to these questions available from philosophical distinctions suggest key implications for why the concept of evolvability as a disposition is useful in evolutionary research. These include (1) securing scientific virtues (e.g., explanatory depth and generalization, prediction or retrodiction, and control or manipulation) and (2) fostering interdisciplinary collaboration through the coordination of definitional diversity and different types of inquiry. Together these facilitate concentration on a variety of research questions at different levels of organization and on distinct time scales, all of which should be expected for a complex dispositional property such as evolvability.

How Are Biology Concepts Used and Transformed?

Historical and Philosophical Perspectives on the Study of Developmental Bias

Evolution & Development, 2020

Throughout the recent history of research at the intersection of evolution and development, notio... more Throughout the recent history of research at the intersection of evolution and development, notions such as developmental constraint, evolutionary novelty, and evolvability have been prominent, but the term ‘developmental bias’ has scarcely been used. And one may even doubt whether a unique and principled definition of bias is possible. I argue that the concept of developmental bias can still play a vital scientific role by means of setting an explanatory agenda that motivates investigation and guides the formulation of integrative explanatory frameworks. Less crucial is a definition that would classify patterns of phenotypic variation and unify variational patterns involving different traits and taxa as all being ‘bias.’ Instead, what we should want is a concept that generates intellectual identity across various researchers, and that unites the diverse fields and approaches relevant to the study of developmental bias, from paleontology to behavioral biology. I point to some advantages of conducting research specifically under the label of ‘developmental bias,’ compared to employing other, more common terms such as ‘evolvability.’

Strategic Conceptual Engineering for Epistemic and Social Aims

by Ingo Brigandt and Esther Rosario

Conceptual Engineering and Conceptual Ethics, 2020

Examining previous discussions on how to construe the concepts of gender and race, we advocate wh... more Examining previous discussions on how to construe the concepts of gender and race, we advocate what we call strategic conceptual engineering. This is the employment of a (possibly novel) concept for specific epistemic or social aims, concomitant with the openness to use a different concept (e.g., of race) for other purposes. We illustrate this approach by sketching three distinct concepts of gender and arguing that all of them are needed, as they answer to different social aims. The first concept serves the aim of identifying and explaining gender-based discrimination. It is similar to Haslanger's well-known account, except that rather than offering a definition of 'woman' we focus on 'gender' as one among several axes of discrimination. The second concept of gender is to assign legal rights and social recognitions, and thus is to be trans-inclusive. We argue that this cannot be achieved by previously suggested concepts that include substantial gender-related psychological features, such as awareness of social expectations. Instead, our concept counts someone as being of a certain gender solely based on the person's self-identification with this gender. The third concept of gender serves the aim of personal empowerment by means of one's gender identity. In this context, substantial psychological features and awareness of one's social situation are involved. While previous accounts of concepts have focused on their role in determining extensions, we point to contexts where a concept's role in explanation and moral reasoning can be more important.

Explanation of Molecular Processes without Tracking Mechanism Operation

Philosophy of Science, 2018

Philosophical discussions of systems biology have enriched the notion of mechanistic explanation ... more Philosophical discussions of systems biology have enriched the notion of mechanistic explanation by pointing to the role of mathematical modeling. However, such accounts still focus on explanation in terms of tracking a mechanism's operation across time (by means of mental or computational simulation). My contention is that there are explanations of molecular systems where the explanatory understanding does not consist in tracking a mechanism's operation and productive continuity. I make this case by a discussion of bifurcation analysis in dynamical systems, articulating the distinctive way in which explanatory understanding is provided, especially about the reversibility or irreversibility of molecular processes.

Philosophy of Molecular Biology

eLS: Encyclopedia of Life Sciences, 2018

Ongoing empirical discoveries in molecular biology have generated novel conceptual challenges and... more Ongoing empirical discoveries in molecular biology have generated novel conceptual challenges and perspectives. Philosophers of biology have reacted to these trends when investigating the practice of molecular biology and contributed to scientific debates on methodological and conceptual matters. This article reviews some major philosophical issues in molecular biology. First, philosophical accounts of mechanistic explanation yield a notion of explanation in the context of molecular biology that does not have to rely on laws of nature and comports well with molecular discovery. Second, reductionism continues to be debated and increasingly be rejected by scientists. Philosophers have likewise moved away from reduction toward integration across fields or integrative explanations covering several levels of organization. Third, although the gene concept has undergone substantial transformation and even fragmentation, it still enjoys widespread use by molecular biologists, which has prompted philosophers to understand the empirical reasons for this. At the same time, it has been argued the notion of 'genetic information' is largely an empty metaphor, which generates the illusion of explanatory understanding without offering an adequate explanation of molecular and developmental mechanisms.

Network Analyses in Systems Biology: New Strategies for Dealing with Biological Complexity

by Sara Green, Nicholaos Jones, and Ingo Brigandt

The increasing application of network models to interpret biological systems raises a number of i... more The increasing application of network models to interpret biological systems raises a number of important methodological and epistemological questions. What novel insights can network analysis provide in biology? Are network approaches an extension of or in conflict with mechanistic research strategies? When and how can network and mechanistic approaches interact in productive ways? In this paper we address these questions by focusing on how biological networks are represented and analyzed in a diverse class of case studies. Our examples span from the investigation of organizational properties of biological networks using tools from graph theory to the application of dynamical systems theory to understand the behavior of complex biological systems. We show how network approaches support and extend traditional mechanistic strategies but also offer novel strategies for dealing with biological complexity.

Systems Biology and Mechanistic Explanation

by Ingo Brigandt and Sara Green

The Routledge Handbook of Mechanisms and Mechanical Philosophy, 2018

We address the question of whether and to what extent explanatory and modelling strategies in sys... more We address the question of whether and to what extent explanatory and modelling strategies in systems biology are mechanistic. After showing how dynamic mathematical models are actually required for mechanistic explanations of complex systems, we caution readers against expecting all systems biology to be about mechanistic explanations. Instead, the aim may be to generate topological explanations that are not standardly mechanistic, or to arrive at design principles that explain system organization and behaviour in general, but not specific mechanisms. These abstraction strategies serve various aims, including prediction and control, that are central to understanding the epistemic diversity of systems biology.

Bodily parts in the structure-function dialectic

Biological Individuality: Integrating Scientific, Philosophical, and Historical Perspectives, 2017

Understanding the organization of an organism by individuating meaningful parts and accounting fo... more Understanding the organization of an organism by individuating meaningful parts and accounting for organismal properties by studying the interaction of bodily parts is a central practice in many areas of biology. While structures are obvious bodily parts and structure and function have often be seen as antagonistic principles in the study of organismal organization, my tenet is that structures and functions are on a par. I articulate a notion of function (functions as activities), according to which functions are bodily parts just as structures are. Recognizing part-whole relations among an organism’s various structures and functions permits fruitful investigation and multilevel explanation of organismal properties and functioning, across both developmental and evolutionary time. I show how my perspective clarifies debates surrounding homology and evolutionary novelty that stem from an alleged structure-function dichotomy.

Philosophical Dimensions of Individuality

by Ingo Brigandt and Alan C Love

Biological Individuality: Integrating Scientific, Philosophical, and Historical Perspectives, 2017

Although natural philosophers have long been interested in individuality, it has been of interest... more Although natural philosophers have long been interested in individuality, it has been of interest to contemporary philosophers of biology because of its role in different aspects of evolutionary biology. These debates include whether species are individuals or classes, what counts as a unit of selection, and how transitions in individuality occur evolutionarily. Philosophical analyses are often conducted in terms of metaphysics (“what is an individual?”), rather than epistemology (“how can and do researchers conceptualize individuals so as to address some of their scientific goals?”). We review several philosophical distinctions in order to shift attention from metaphysics to epistemology. Many controversies involve epistemological differences rather than metaphysical disagreement. This implies that a pluralist stance about individuality in biology is warranted and has metaphysical consequences because the pluralism emerges from the diversity of scientific interests that investigate the complexity of living phenomena.

Typology and Natural Kinds in Evo-Devo

Evolutionary Developmental Biology: A Reference Guide, 2017

The traditional practice of establishing morphological types and investigating morphological orga... more The traditional practice of establishing morphological types and investigating morphological organization has found new support from evolutionary developmental biology (evo-devo), especially with respect to the notion of body plans. Despite recurring claims that typology is at odds with evolutionary thinking, evo-devo offers mechanistic explanations of the evolutionary origin, transformation, and evolvability of morphological organization. In parallel, philosophers have developed non-essentialist conceptions of natural kinds that permit kinds to exhibit variation and undergo change. This not only facilitates a construal of species and higher taxa as natural kinds, but also broadens our perspective on the diversity of kinds found in biology. There are many different natural kinds relevant to the investigative and explanatory aims of evo-devo, including homologues and developmental modules.

Why the Difference between Explanation and Argument Matters to Science Education

Science & Education, 2016

Contributing to the recent debate on whether or not explanations ought to be differentiated from ... more Contributing to the recent debate on whether or not explanations ought to be differentiated from arguments, this article argues that the distinction matters to science education. I articulate the distinction in terms of explanations and arguments having to meet different standards of adequacy. Standards of explanatory adequacy are important because they correspond to what counts as a good explanation in a science classroom, whereas a focus on evidence-based argumentation can obscure such standards of what makes an explanation explanatory. I provide further reasons for the relevance of not conflating explanations with arguments (and having standards of explanatory adequacy in view). First, what guides the adoption of the particular standards of explanatory adequacy that are relevant in a scientific case is the explanatory aim pursued in this context. Apart from explanatory aims being an important aspect of the nature of science, including explanatory aims in classroom instruction also promotes students seeing explanations as more than facts, and engages them in developing explanations as responses to interesting explanatory problems. Second, it is of relevance to science curricula that science aims at intervening in natural processes, not only for technological applications, but also as part of experimental discovery. Not any argument enables intervention in nature, as successful intervention specifically presupposes causal explanations. Students can fruitfully explore in the classroom how an explanatory account suggests different options for intervention.

Do We Need a 'Theory' of Development?

Biology & Philosophy, 2016

Edited by Alessandro Minelli and Thomas Pradeu, Towards a Theory of Development gathers essays by... more Edited by Alessandro Minelli and Thomas Pradeu, Towards a Theory of Development gathers essays by biologists and philosophers, which display a diversity of theoretical perspectives. The discussions not only cover the state of art, but broaden our vision of what development includes and provide pointers for future research. Interestingly, all contributors agree that explanations should not just be gene-centered, and virtually none use design and other engineering metaphors to articulate principles of cellular and organismal organization. I comment in particular on the issue of how to construe the notion of a ‘theory’ and whether developmental biology has or should aspire to have theories, which four of the contributions discuss in detail while taking opposing positions. Beyond construing a theory in terms of its empirical content (established knowledge about biological phenomena), my aim is to shift the focus toward the role that theories have for guiding future scientific theorizing and practice. Such a conception of ‘theory’ is particularly important in the context of development, because arriving at a theoretical framework providing guidance for the discipline of developmental biology as a whole is more plausible than a unified representation of development across all taxa.

Social Values Influence the Adequacy Conditions of Scientific Theories: Beyond Inductive Risk

Canadian Journal of Philosophy, 2015

The ‘death of evidence’ issue in Canada raises the specter of politicized science, and thus the q... more The ‘death of evidence’ issue in Canada raises the specter of politicized science, and thus the question of what role social values may have in science and how this meshes with objectivity and evidence. I first criticize philosophical accounts that have to separate different steps of research to restrict the influence of social and other non-epistemic values. A prominent account that social values may play a role even in the context of theory acceptance is the argument from inductive risk. It maintains that the more severe the social consequences of erroneously accepting a theory would be, the more evidence is needed before the theory may be accepted. However, an implication of this position is that increasing evidence makes the impact of social values converge to zero; and I argue for a stronger role for social values. On this position, social values (together with epistemic values and other empirical considerations) may determine a theory’s conditions of adequacy, which among other things can include considerations about what makes a scientific account unbiased and complete. I illustrate this based on recent theories of human evolution and the social behaviour of non-human primates, where some of the social values implicated are feminist values. While many philosophical accounts (both arguments from inductive risk and from underdetermination) conceptualize the relevance of social values in terms of making inferences from evidence, I argue for the need for a broader philosophical framework, which is also motivated by issues pertaining to scientific explanation.

Evolutionary developmental biology and the limits of philosophical accounts of mechanistic explanation

Explanation in Biology: An Enquiry into the Diversity of Explanatory Patterns in the Life Sciences, 2015

Evolutionary developmental biology (evo-devo) is considered a ‘mechanistic science,’ in that it c... more Evolutionary developmental biology (evo-devo) is considered a ‘mechanistic science,’ in that it causally explains morphological evolution in terms of changes in developmental mechanisms. Evo-devo is also an interdisciplinary and integrative approach, as its explanations use contributions from many fields and pertain to different levels of organismal organization. Philosophical accounts of mechanistic explanation are currently highly prominent, and have been particularly able to capture the integrative nature of multifield and multilevel explanations. However, I argue that evo-devo demonstrates the need for a broadened philosophical conception of mechanisms and mechanistic explanation.
Mechanistic explanation (in terms of the qualitative interactions of the structural parts of a whole) has been developed as an alternative to the traditional idea of explanation as derivation from laws or quantitative principles. Against the picture promoted by Carl Craver, that mathematical models describe but usually do not explain, my discussion of cases from the strand of evo-devo which is concerned with developmental processes points to qualitative phenomena where quantitative mathematical models are an indispensable part of the explanation. While philosophical accounts have focused on the actual organization and operation of mechanisms, properties of developmental mechanisms that are about how a mechanism reacts to modifications are of major evolutionary significance, including robustness, phenotypic plasticity, and modularity. A philosophical conception of mechanisms is needed that takes into account quantitative changes, transient entities and the generation of novel types of entities, feedback loops and complex interaction networks, emergent properties, and, in particular, functional-dynamical aspects of mechanisms, including functional (as opposed to structural) organization and distributed, system-wide phenomena. I conclude with general remarks on philosophical accounts of explanation.

From developmental constraint to evolvability: how concepts figure in explanation and disciplinary identity

Conceptual Change in Biology: Scientific and Philosophical Perspectives on Evolution and Development, 2015

The concept of developmental constraint was at the heart of developmental approaches to evolution... more The concept of developmental constraint was at the heart of developmental approaches to evolution of the 1980s. While this idea was widely used to criticize neo-Darwinian evolutionary theory, critique does not yield an alternative framework that offers evolutionary explanations. In current Evo-devo the concept of constraint is of minor importance, whereas notions as evolvability are at the center of attention. The latter clearly defines an explanatory agenda for evolutionary research, so that one could view the historical shift from ‘developmental constraint’ towards ‘evolvability’ as the move from a concept that is a mere tool of criticism to a concept that establishes a positive explanatory project. However, by taking a look at how the concept of constraint was employed in the 1980s, I argue that developmental constraint was not just seen as restricting possibilities (‘constraining’), but also as facilitating morphological change in several ways. Accounting for macroevolutionary transformation and the origin of novel form was an aim of these developmental approaches to evolution. Thus, the concept of developmental constraint was part of a positive explanatory agenda long before the advent of Evo-devo as a genuine scientific discipline. In the 1980s, despite the lack of a clear disciplinary identity, this concept coordinated research among paleontologists, morphologists, and developmentally inclined evolutionary biologists. I discuss the different functions that scientific concepts can have, highlighting that instead of classifying or explaining natural phenomena, concepts such as ‘developmental constraint’ and ‘evolvability’ are more important in setting explanatory agendas so as to provide intellectual coherence to scientific approaches. The essay concludes with a puzzle about how to conceptually distinguish evolvability and selection.

Multilevel research strategies and biological systems

by Ingo Brigandt and Alan C Love

Philosophy of Science, 2014

Multilevel research strategies characterize contemporary molecular inquiry into biological system... more Multilevel research strategies characterize contemporary molecular inquiry into biological systems. We outline conceptual, methodological and explanatory dimensions of these multilevel strategies in microbial ecology, systems biology, protein research, and developmental biology. This review of emerging lines of inquiry in these fields suggests that multilevel research in molecular life sciences has significant implications for philosophical understandings of explanation, modelling, and representation.

A critique of David Chalmers' and Frank Jackson's account of concepts

David Chalmers and Frank Jackson have promoted a strong program of conceptual analysis, which acc... more David Chalmers and Frank Jackson have promoted a strong program of conceptual analysis, which accords a significant philosophical role to the a priori analysis of (empirical) concepts. They found this methodological program on an account of concepts using two-dimensional semantics. This paper argues that Chalmers and Jackson’s account of concepts, and the related approach by David Braddon-Mitchell, is inadequate for natural kind concepts as found in biology. Two-dimensional semantics is metaphysically faulty as an account of the nature of concepts and concept possession. It is also methodologically flawed as a guideline for how to study scientific concepts. Proponents of two-dimensional semantics are criticized for not taking seriously semantic variation between persons and for failing to adequately account for the rationality of semantic change. I suggest a more pragmatic approach to natural kind term meaning, arguing that the epistemic goal pursued by a term’s use is an additional semantic property.

Systems biology and the integration of mechanistic explanation and mathematical explanation

The paper discusses how systems biology is working toward complex accounts that integrate explana... more The paper discusses how systems biology is working toward complex accounts that integrate explanation in terms of mechanisms and explanation by mathematical models—which some philosophers have viewed as rival models of explanation. Systems biology is an integrative approach, and it strongly relies on mathematical modeling. Philosophical accounts of mechanisms capture integrative in the sense of multilevel and multifield explanations, yet accounts of mechanistic explanation (as the analysis of a whole in terms of its structural parts and their qualitative interactions) have failed to address how a mathematical model could contribute to such explanations. I discuss how mathematical equations can be explanatorily relevant. Several cases from systems biology are discussed to illustrate the interplay between mechanistic research and mathematical modeling, and I point to questions about qualitative phenomena (rather than the explanation of quantitative details), where quantitative models are still indispensable to the explanation. Systems biology shows that a broader philosophical conception of mechanisms is needed, which takes into account functional-dynamical aspects, interaction in complex networks with feedback loops, system-wide functional properties such as distributed functionality and robustness, and a mechanism’s ability to respond to perturbations (beyond its actual operation). I offer general conclusions for philosophical accounts of explanation.

Conceptual Roles of Evolvability across Evolutionary Biology: Between Diversity and Unification

by Cristina Villegas, Alan C Love, and Ingo Brigandt

Evolvability. A Unifying Concept in Evolutionary Biology?, 2023

Biologists and philosophers have noted the diversity of interpretations of evolvability in contem... more Biologists and philosophers have noted the diversity of interpretations of evolvability in contemporary evolutionary research. Different clusters of research identified by co-citation patterns or shared methodological orientation sometimes concentrate on distinct conceptions of evolvability. We examine five different activities where the notion of evolvability plays conceptual roles in evolutionary biological investigation: setting a research agenda, characterization, explanation, prediction, and control. Our analysis of representative examples demonstrates how different conceptual roles of evolvability are quasi-independent and yet exhibit important relationships across scientific activities. It also provides resources to detail two distinct strategies for how evolvability can help synthesize disparate areas of research and thereby potentially serve as a unifying concept in evolutionary biology.

Evolvability as a Disposition: Philosophical Distinctions, Scientific Implications

by Ingo Brigandt, Cristina Villegas, and Alan C Love

Evolvability: A Unifying Concept in Evolutionary Biology?, 2023

A disposition or dispositional property is a capacity, ability, or potential to display or exhibi... more A disposition or dispositional property is a capacity, ability, or potential to display or exhibit some outcome. Evolvability refers to a disposition to evolve. This chapter discusses why the dispositional nature of evolvability matters—why philosophical distinctions about dispositions can have scientific implications. To that end, we build a conceptual toolkit with vocabulary from prior philosophical analyses using a different disposition: protein foldability. We then apply this toolkit to address several methodological questions related to evolvability. What entities are the bearers of evolvability? What features causally contribute to the disposition of evolvability? How does evolvability manifest? The various possible answers to these questions available from philosophical distinctions suggest key implications for why the concept of evolvability as a disposition is useful in evolutionary research. These include (1) securing scientific virtues (e.g., explanatory depth and generalization, prediction or retrodiction, and control or manipulation) and (2) fostering interdisciplinary collaboration through the coordination of definitional diversity and different types of inquiry. Together these facilitate concentration on a variety of research questions at different levels of organization and on distinct time scales, all of which should be expected for a complex dispositional property such as evolvability.

How Are Biology Concepts Used and Transformed?

Historical and Philosophical Perspectives on the Study of Developmental Bias

Evolution & Development, 2020

Throughout the recent history of research at the intersection of evolution and development, notio... more Throughout the recent history of research at the intersection of evolution and development, notions such as developmental constraint, evolutionary novelty, and evolvability have been prominent, but the term ‘developmental bias’ has scarcely been used. And one may even doubt whether a unique and principled definition of bias is possible. I argue that the concept of developmental bias can still play a vital scientific role by means of setting an explanatory agenda that motivates investigation and guides the formulation of integrative explanatory frameworks. Less crucial is a definition that would classify patterns of phenotypic variation and unify variational patterns involving different traits and taxa as all being ‘bias.’ Instead, what we should want is a concept that generates intellectual identity across various researchers, and that unites the diverse fields and approaches relevant to the study of developmental bias, from paleontology to behavioral biology. I point to some advantages of conducting research specifically under the label of ‘developmental bias,’ compared to employing other, more common terms such as ‘evolvability.’

Strategic Conceptual Engineering for Epistemic and Social Aims

by Ingo Brigandt and Esther Rosario

Conceptual Engineering and Conceptual Ethics, 2020

Examining previous discussions on how to construe the concepts of gender and race, we advocate wh... more Examining previous discussions on how to construe the concepts of gender and race, we advocate what we call strategic conceptual engineering. This is the employment of a (possibly novel) concept for specific epistemic or social aims, concomitant with the openness to use a different concept (e.g., of race) for other purposes. We illustrate this approach by sketching three distinct concepts of gender and arguing that all of them are needed, as they answer to different social aims. The first concept serves the aim of identifying and explaining gender-based discrimination. It is similar to Haslanger's well-known account, except that rather than offering a definition of 'woman' we focus on 'gender' as one among several axes of discrimination. The second concept of gender is to assign legal rights and social recognitions, and thus is to be trans-inclusive. We argue that this cannot be achieved by previously suggested concepts that include substantial gender-related psychological features, such as awareness of social expectations. Instead, our concept counts someone as being of a certain gender solely based on the person's self-identification with this gender. The third concept of gender serves the aim of personal empowerment by means of one's gender identity. In this context, substantial psychological features and awareness of one's social situation are involved. While previous accounts of concepts have focused on their role in determining extensions, we point to contexts where a concept's role in explanation and moral reasoning can be more important.

Explanation of Molecular Processes without Tracking Mechanism Operation

Philosophy of Science, 2018

Philosophical discussions of systems biology have enriched the notion of mechanistic explanation ... more Philosophical discussions of systems biology have enriched the notion of mechanistic explanation by pointing to the role of mathematical modeling. However, such accounts still focus on explanation in terms of tracking a mechanism's operation across time (by means of mental or computational simulation). My contention is that there are explanations of molecular systems where the explanatory understanding does not consist in tracking a mechanism's operation and productive continuity. I make this case by a discussion of bifurcation analysis in dynamical systems, articulating the distinctive way in which explanatory understanding is provided, especially about the reversibility or irreversibility of molecular processes.

Philosophy of Molecular Biology

eLS: Encyclopedia of Life Sciences, 2018

Ongoing empirical discoveries in molecular biology have generated novel conceptual challenges and... more Ongoing empirical discoveries in molecular biology have generated novel conceptual challenges and perspectives. Philosophers of biology have reacted to these trends when investigating the practice of molecular biology and contributed to scientific debates on methodological and conceptual matters. This article reviews some major philosophical issues in molecular biology. First, philosophical accounts of mechanistic explanation yield a notion of explanation in the context of molecular biology that does not have to rely on laws of nature and comports well with molecular discovery. Second, reductionism continues to be debated and increasingly be rejected by scientists. Philosophers have likewise moved away from reduction toward integration across fields or integrative explanations covering several levels of organization. Third, although the gene concept has undergone substantial transformation and even fragmentation, it still enjoys widespread use by molecular biologists, which has prompted philosophers to understand the empirical reasons for this. At the same time, it has been argued the notion of 'genetic information' is largely an empty metaphor, which generates the illusion of explanatory understanding without offering an adequate explanation of molecular and developmental mechanisms.

Network Analyses in Systems Biology: New Strategies for Dealing with Biological Complexity

by Sara Green, Nicholaos Jones, and Ingo Brigandt

The increasing application of network models to interpret biological systems raises a number of i... more The increasing application of network models to interpret biological systems raises a number of important methodological and epistemological questions. What novel insights can network analysis provide in biology? Are network approaches an extension of or in conflict with mechanistic research strategies? When and how can network and mechanistic approaches interact in productive ways? In this paper we address these questions by focusing on how biological networks are represented and analyzed in a diverse class of case studies. Our examples span from the investigation of organizational properties of biological networks using tools from graph theory to the application of dynamical systems theory to understand the behavior of complex biological systems. We show how network approaches support and extend traditional mechanistic strategies but also offer novel strategies for dealing with biological complexity.

Systems Biology and Mechanistic Explanation

by Ingo Brigandt and Sara Green

The Routledge Handbook of Mechanisms and Mechanical Philosophy, 2018

We address the question of whether and to what extent explanatory and modelling strategies in sys... more We address the question of whether and to what extent explanatory and modelling strategies in systems biology are mechanistic. After showing how dynamic mathematical models are actually required for mechanistic explanations of complex systems, we caution readers against expecting all systems biology to be about mechanistic explanations. Instead, the aim may be to generate topological explanations that are not standardly mechanistic, or to arrive at design principles that explain system organization and behaviour in general, but not specific mechanisms. These abstraction strategies serve various aims, including prediction and control, that are central to understanding the epistemic diversity of systems biology.

Bodily parts in the structure-function dialectic

Biological Individuality: Integrating Scientific, Philosophical, and Historical Perspectives, 2017

Understanding the organization of an organism by individuating meaningful parts and accounting fo... more Understanding the organization of an organism by individuating meaningful parts and accounting for organismal properties by studying the interaction of bodily parts is a central practice in many areas of biology. While structures are obvious bodily parts and structure and function have often be seen as antagonistic principles in the study of organismal organization, my tenet is that structures and functions are on a par. I articulate a notion of function (functions as activities), according to which functions are bodily parts just as structures are. Recognizing part-whole relations among an organism’s various structures and functions permits fruitful investigation and multilevel explanation of organismal properties and functioning, across both developmental and evolutionary time. I show how my perspective clarifies debates surrounding homology and evolutionary novelty that stem from an alleged structure-function dichotomy.

Philosophical Dimensions of Individuality

by Ingo Brigandt and Alan C Love

Biological Individuality: Integrating Scientific, Philosophical, and Historical Perspectives, 2017

Although natural philosophers have long been interested in individuality, it has been of interest... more Although natural philosophers have long been interested in individuality, it has been of interest to contemporary philosophers of biology because of its role in different aspects of evolutionary biology. These debates include whether species are individuals or classes, what counts as a unit of selection, and how transitions in individuality occur evolutionarily. Philosophical analyses are often conducted in terms of metaphysics (“what is an individual?”), rather than epistemology (“how can and do researchers conceptualize individuals so as to address some of their scientific goals?”). We review several philosophical distinctions in order to shift attention from metaphysics to epistemology. Many controversies involve epistemological differences rather than metaphysical disagreement. This implies that a pluralist stance about individuality in biology is warranted and has metaphysical consequences because the pluralism emerges from the diversity of scientific interests that investigate the complexity of living phenomena.

Typology and Natural Kinds in Evo-Devo

Evolutionary Developmental Biology: A Reference Guide, 2017

The traditional practice of establishing morphological types and investigating morphological orga... more The traditional practice of establishing morphological types and investigating morphological organization has found new support from evolutionary developmental biology (evo-devo), especially with respect to the notion of body plans. Despite recurring claims that typology is at odds with evolutionary thinking, evo-devo offers mechanistic explanations of the evolutionary origin, transformation, and evolvability of morphological organization. In parallel, philosophers have developed non-essentialist conceptions of natural kinds that permit kinds to exhibit variation and undergo change. This not only facilitates a construal of species and higher taxa as natural kinds, but also broadens our perspective on the diversity of kinds found in biology. There are many different natural kinds relevant to the investigative and explanatory aims of evo-devo, including homologues and developmental modules.

Why the Difference between Explanation and Argument Matters to Science Education

Science & Education, 2016

Contributing to the recent debate on whether or not explanations ought to be differentiated from ... more Contributing to the recent debate on whether or not explanations ought to be differentiated from arguments, this article argues that the distinction matters to science education. I articulate the distinction in terms of explanations and arguments having to meet different standards of adequacy. Standards of explanatory adequacy are important because they correspond to what counts as a good explanation in a science classroom, whereas a focus on evidence-based argumentation can obscure such standards of what makes an explanation explanatory. I provide further reasons for the relevance of not conflating explanations with arguments (and having standards of explanatory adequacy in view). First, what guides the adoption of the particular standards of explanatory adequacy that are relevant in a scientific case is the explanatory aim pursued in this context. Apart from explanatory aims being an important aspect of the nature of science, including explanatory aims in classroom instruction also promotes students seeing explanations as more than facts, and engages them in developing explanations as responses to interesting explanatory problems. Second, it is of relevance to science curricula that science aims at intervening in natural processes, not only for technological applications, but also as part of experimental discovery. Not any argument enables intervention in nature, as successful intervention specifically presupposes causal explanations. Students can fruitfully explore in the classroom how an explanatory account suggests different options for intervention.

Do We Need a 'Theory' of Development?

Biology & Philosophy, 2016

Edited by Alessandro Minelli and Thomas Pradeu, Towards a Theory of Development gathers essays by... more Edited by Alessandro Minelli and Thomas Pradeu, Towards a Theory of Development gathers essays by biologists and philosophers, which display a diversity of theoretical perspectives. The discussions not only cover the state of art, but broaden our vision of what development includes and provide pointers for future research. Interestingly, all contributors agree that explanations should not just be gene-centered, and virtually none use design and other engineering metaphors to articulate principles of cellular and organismal organization. I comment in particular on the issue of how to construe the notion of a ‘theory’ and whether developmental biology has or should aspire to have theories, which four of the contributions discuss in detail while taking opposing positions. Beyond construing a theory in terms of its empirical content (established knowledge about biological phenomena), my aim is to shift the focus toward the role that theories have for guiding future scientific theorizing and practice. Such a conception of ‘theory’ is particularly important in the context of development, because arriving at a theoretical framework providing guidance for the discipline of developmental biology as a whole is more plausible than a unified representation of development across all taxa.

Social Values Influence the Adequacy Conditions of Scientific Theories: Beyond Inductive Risk

Canadian Journal of Philosophy, 2015

The ‘death of evidence’ issue in Canada raises the specter of politicized science, and thus the q... more The ‘death of evidence’ issue in Canada raises the specter of politicized science, and thus the question of what role social values may have in science and how this meshes with objectivity and evidence. I first criticize philosophical accounts that have to separate different steps of research to restrict the influence of social and other non-epistemic values. A prominent account that social values may play a role even in the context of theory acceptance is the argument from inductive risk. It maintains that the more severe the social consequences of erroneously accepting a theory would be, the more evidence is needed before the theory may be accepted. However, an implication of this position is that increasing evidence makes the impact of social values converge to zero; and I argue for a stronger role for social values. On this position, social values (together with epistemic values and other empirical considerations) may determine a theory’s conditions of adequacy, which among other things can include considerations about what makes a scientific account unbiased and complete. I illustrate this based on recent theories of human evolution and the social behaviour of non-human primates, where some of the social values implicated are feminist values. While many philosophical accounts (both arguments from inductive risk and from underdetermination) conceptualize the relevance of social values in terms of making inferences from evidence, I argue for the need for a broader philosophical framework, which is also motivated by issues pertaining to scientific explanation.

Evolutionary developmental biology and the limits of philosophical accounts of mechanistic explanation

Explanation in Biology: An Enquiry into the Diversity of Explanatory Patterns in the Life Sciences, 2015

Evolutionary developmental biology (evo-devo) is considered a ‘mechanistic science,’ in that it c... more Evolutionary developmental biology (evo-devo) is considered a ‘mechanistic science,’ in that it causally explains morphological evolution in terms of changes in developmental mechanisms. Evo-devo is also an interdisciplinary and integrative approach, as its explanations use contributions from many fields and pertain to different levels of organismal organization. Philosophical accounts of mechanistic explanation are currently highly prominent, and have been particularly able to capture the integrative nature of multifield and multilevel explanations. However, I argue that evo-devo demonstrates the need for a broadened philosophical conception of mechanisms and mechanistic explanation.
Mechanistic explanation (in terms of the qualitative interactions of the structural parts of a whole) has been developed as an alternative to the traditional idea of explanation as derivation from laws or quantitative principles. Against the picture promoted by Carl Craver, that mathematical models describe but usually do not explain, my discussion of cases from the strand of evo-devo which is concerned with developmental processes points to qualitative phenomena where quantitative mathematical models are an indispensable part of the explanation. While philosophical accounts have focused on the actual organization and operation of mechanisms, properties of developmental mechanisms that are about how a mechanism reacts to modifications are of major evolutionary significance, including robustness, phenotypic plasticity, and modularity. A philosophical conception of mechanisms is needed that takes into account quantitative changes, transient entities and the generation of novel types of entities, feedback loops and complex interaction networks, emergent properties, and, in particular, functional-dynamical aspects of mechanisms, including functional (as opposed to structural) organization and distributed, system-wide phenomena. I conclude with general remarks on philosophical accounts of explanation.

From developmental constraint to evolvability: how concepts figure in explanation and disciplinary identity

Conceptual Change in Biology: Scientific and Philosophical Perspectives on Evolution and Development, 2015

The concept of developmental constraint was at the heart of developmental approaches to evolution... more The concept of developmental constraint was at the heart of developmental approaches to evolution of the 1980s. While this idea was widely used to criticize neo-Darwinian evolutionary theory, critique does not yield an alternative framework that offers evolutionary explanations. In current Evo-devo the concept of constraint is of minor importance, whereas notions as evolvability are at the center of attention. The latter clearly defines an explanatory agenda for evolutionary research, so that one could view the historical shift from ‘developmental constraint’ towards ‘evolvability’ as the move from a concept that is a mere tool of criticism to a concept that establishes a positive explanatory project. However, by taking a look at how the concept of constraint was employed in the 1980s, I argue that developmental constraint was not just seen as restricting possibilities (‘constraining’), but also as facilitating morphological change in several ways. Accounting for macroevolutionary transformation and the origin of novel form was an aim of these developmental approaches to evolution. Thus, the concept of developmental constraint was part of a positive explanatory agenda long before the advent of Evo-devo as a genuine scientific discipline. In the 1980s, despite the lack of a clear disciplinary identity, this concept coordinated research among paleontologists, morphologists, and developmentally inclined evolutionary biologists. I discuss the different functions that scientific concepts can have, highlighting that instead of classifying or explaining natural phenomena, concepts such as ‘developmental constraint’ and ‘evolvability’ are more important in setting explanatory agendas so as to provide intellectual coherence to scientific approaches. The essay concludes with a puzzle about how to conceptually distinguish evolvability and selection.

Multilevel research strategies and biological systems

by Ingo Brigandt and Alan C Love

Philosophy of Science, 2014

Multilevel research strategies characterize contemporary molecular inquiry into biological system... more Multilevel research strategies characterize contemporary molecular inquiry into biological systems. We outline conceptual, methodological and explanatory dimensions of these multilevel strategies in microbial ecology, systems biology, protein research, and developmental biology. This review of emerging lines of inquiry in these fields suggests that multilevel research in molecular life sciences has significant implications for philosophical understandings of explanation, modelling, and representation.

A critique of David Chalmers' and Frank Jackson's account of concepts

David Chalmers and Frank Jackson have promoted a strong program of conceptual analysis, which acc... more David Chalmers and Frank Jackson have promoted a strong program of conceptual analysis, which accords a significant philosophical role to the a priori analysis of (empirical) concepts. They found this methodological program on an account of concepts using two-dimensional semantics. This paper argues that Chalmers and Jackson’s account of concepts, and the related approach by David Braddon-Mitchell, is inadequate for natural kind concepts as found in biology. Two-dimensional semantics is metaphysically faulty as an account of the nature of concepts and concept possession. It is also methodologically flawed as a guideline for how to study scientific concepts. Proponents of two-dimensional semantics are criticized for not taking seriously semantic variation between persons and for failing to adequately account for the rationality of semantic change. I suggest a more pragmatic approach to natural kind term meaning, arguing that the epistemic goal pursued by a term’s use is an additional semantic property.

Systems biology and the integration of mechanistic explanation and mathematical explanation

The paper discusses how systems biology is working toward complex accounts that integrate explana... more The paper discusses how systems biology is working toward complex accounts that integrate explanation in terms of mechanisms and explanation by mathematical models—which some philosophers have viewed as rival models of explanation. Systems biology is an integrative approach, and it strongly relies on mathematical modeling. Philosophical accounts of mechanisms capture integrative in the sense of multilevel and multifield explanations, yet accounts of mechanistic explanation (as the analysis of a whole in terms of its structural parts and their qualitative interactions) have failed to address how a mathematical model could contribute to such explanations. I discuss how mathematical equations can be explanatorily relevant. Several cases from systems biology are discussed to illustrate the interplay between mechanistic research and mathematical modeling, and I point to questions about qualitative phenomena (rather than the explanation of quantitative details), where quantitative models are still indispensable to the explanation. Systems biology shows that a broader philosophical conception of mechanisms is needed, which takes into account functional-dynamical aspects, interaction in complex networks with feedback loops, system-wide functional properties such as distributed functionality and robustness, and a mechanism’s ability to respond to perturbations (beyond its actual operation). I offer general conclusions for philosophical accounts of explanation.