• John Tyler Bonner: Remembering a scientific pioneer
    with L. A. Katz, V. Nanjundiah, S. F. Gilbert, P. R. Grant, B. R. Grant, Alan Love, S. A. Newman, and M. J. West-Eberhard
    Journal of Experimental Evolution (Mol Dev Evol) 332 365-370. 2019.
    Throughout his life, John Tyler Bonner contributed to major transformations in the fields of developmental and evolutionary biology. He pondered the evolution of complexity and the significance of randomness in evolution, and was instrumental in the formation of evolutionary developmental biology. His contributions were vast, ranging from highly technical scientific articles to numerous books written for a broad audience. This historical vignette gathers reflections by several prominent research…Read more
  •  3
    Accounting for the evolutionary origins of morphological novelty is one of the core challenges of contemporary evolutionary biology. A successful explanatory framework requires the integration of different biological disciplines, but the relationships between developmental biology and standard evolutionary biology remain contested. There is also disagreement about how to define the concept of evolutionary novelty. These issues were the subjects of a workshop held in November 2009 at the Universi…Read more
  •  85
    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 d…Read more
  •  28
    Engaging with science, values, and society: introduction
    Canadian Journal of Philosophy 52 (3). 2022.
    Philosophical work on science and values has come to engage with the concerns of society and of stakeholders affected by science and policy, leading to socially relevant philosophy of science and socially engaged philosophy of science. This special issue showcases instances of socially relevant philosophy of science, featuring contributions on a diversity of topics by Janet Kourany, Andrew Schroeder, Alison Wylie, Kristen Intemann, Joyce Havstad, Justin Biddle, Kevin Elliott, and Ingo Brigandt.
  •  22
    Menschenbildkonflikte: Evolutionstheorie und Naturalismus
    In Michael Zichy (ed.), Handbuch Menschenbilder, Springer. Doi:10.1007/978-3-658-32138-3_40-1. 2022.
    Ein naturalistisches Menschenbild sieht berechtigterweise uns Menschen und unsere geistigen Fähigkeiten als materielle Phänomene und durch Evolution entstanden. Dies ist immer wieder der Anlass zu Menschenbildkonflikten, insbesondere mit religiös fundierten Menschenbildern. Aber auch innerhalb der Verhaltens- und Kognitionswissenschaft kann man suspekte Menschenbilder finden, die kulturell bedingte Verhaltensmuster und soziale Organisationsformen als biologisch-genetisch bestimmt sehen. Zum Beis…Read more
  •  42
    A number of biologists and philosophers have noted the diversity of interpretations of evolvability in contemporary evolutionary research. Different clusters of research defined 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, predi…Read more
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    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 addr…Read more
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    The theory of concepts advanced in the dissertation aims at accounting for a) how a concept makes successful practice possible, and b) how a scientific concept can be subject to rational change in the course of history. Traditional accounts in the philosophy of science have usually studied concepts in terms only of their reference; their concern is to establish a stability of reference in order to address the incommensurability problem. My discussion, in contrast, suggests that each scientific c…Read more
  •  117
    Recent rival attempts in the philosophy of science to put forward a general theory of the properties that all (and only) natural kinds across the sciences possess may have proven to be futile. Instead, I develop a general methodological framework for how to philosophically study kinds. Any kind has to be investigated and articulated together with the human aims that motivate referring to this kind, where different kinds in the same scientific domain can answer to different concrete aims. My core…Read more
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    Historical and Philosophical Perspectives on the Study of Developmental Bias
    Evolution & Development 22 (1-2): 7-19. 2020.
    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 …Read more
  •  154
    Multilevel Research Strategies and Biological Systems
    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 (5): 811-828. 2014.
    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, modeling, and represent…Read more
  •  105
    Homology in comparative, molecular, and evolutionary developmental biology: The radiation of a concept
    Journal of Experimental Zoology (Molecular and Developmental Evolution) 299 9-17. 2003.
    The present paper analyzes the use and understanding of the homology concept across different biological disciplines. It is argued that in its history, the homology concept underwent a sort of adaptive radiation. Once it migrated from comparative anatomy into new biological fields, the homology concept changed in accordance with the theoretical aims and interests of these disciplines. The paper gives a case study of the theoretical role that homology plays in comparative and evolutionary biology…Read more
  •  71
    Philosophy of Molecular Biology
    eLS: Encyclopedia of Life Sciences. 2018.
    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…Read more
  •  780
    Strategic Conceptual Engineering for Epistemic and Social Aims
    In Alexis Burgess, Herman Cappelen & David Plunkett (eds.), Conceptual Engineering and Conceptual Ethics, Oxford University Press. pp. 100-124. 2020.
    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 concep…Read more
  •  60
    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 ca…Read more
  •  103
    Typology and Natural Kinds in Evo-Devo
    In Laura Nuño De La Rosa & Gerd Müller (eds.), Evolutionary Developmental Biology: A Reference Guide, Springer. pp. 483-493. 2021.
    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-essentialis…Read more
  •  85
    Systems Biology and Mechanistic Explanation
    with Sara Green and Maureen O'Malley
    In Stuart Glennan & Phyllis McKay Illari (eds.), The Routledge Handbook of Mechanisms and Mechanical Philosophy, Routledge. 2018.
    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 organizat…Read more
  •  118
    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 on…Read more
  •  315
    This essay discusses Elliott Sober’s Evidence and Evolution: The Logic Behind the Science. Valuable to both philosophers and biologists, Sober analyzes the testing of different kinds of evolutionary hypotheses about natural selection or phylogenetic history, including a thorough critique of intelligent design. Not at least because of a discussion of different schools of hypothesis testing (Bayesianism, likelihoodism, and frequentism), with Sober favoring a pluralism where different inference met…Read more
  •  69
    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 …Read more
  •  180
    Homology: Homeostatic Property Cluster Kinds in Systematics and Evolution
    with Leandro Assis
    Evolutionary Biology 36 248-255. 2009.
    Taxa and homologues can in our view be construed both as kinds and as individuals. However, the conceptualization of taxa as natural kinds in the sense of homeostatic property cluster kinds has been criticized by some systematists, as it seems that even such kinds cannot evolve due to their being homeostatic. We reply by arguing that the treatment of transformational and taxic homologies, respectively, as dynamic and static aspects of the same homeostatic property cluster kind represents a good …Read more
  •  176
    The philosophy of science that grew out of logical positivism construed scientific knowledge in terms of set of interconnected beliefs about the world, such as theories and observation statements. Nowadays science is also conceived of as a dynamic process based on the various practices of individual scientists and the institutional settings of science. Two features particularly influence the dynamics of scientific knowledge: epistemic standards and aims (e.g., assumptions about what issues are c…Read more
  •  61
    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 been 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…Read more
  •  80
    Philosophy of Biology
    In Steven French & Juha Saatsi (eds.), The Bloomsbury Companion to the Philosophy of Science, Bloomsbury Academic. pp. 246-267. 2011.
    This overview of philosophy of biology lays out what implications biology and recent philosophy of biology have for general philosophy of science. The following topics are addressed in five sections: natural kinds, conceptual change, discovery and confirmation, explanation and reduction, and naturalism.
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    Integration in biology: Philosophical perspectives on the dynamics of interdisciplinarity
    Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 44 (4): 461-465. 2013.
    This introduction to the special section on integration in biology provides an overview of the different contributions. In addition to motivating the philosophical significance of analyzing integration and interdisciplinary research, I lay out common themes and novel insights found among the special section contributions, and indicate how they exhibit current trends in the philosophical study of integration. One upshot of the contributed papers is that there are different aspects to and kinds of…Read more