Francesca Merlin | Centre National de la Recherche Scientifique / French National Centre for Scientific Research (original) (raw)

Papers by Francesca Merlin

Acta Biotheoretica, 2017

The current debate over extending inheritance and its evolutionary impact has focused on adding n... more The current debate over extending inheritance and its evolutionary impact has focused on adding new categories of non-genetic factors to the classical transmission of DNA, and on trying to redefine inheritance. Transmitted factors have been mainly characterized by their directions of transmission (vertical, horizontal, or both) and the way they store variations. In this paper, we leave aside the issue of defining inheritance. We rather try to build an evolutionary conceptual framework that allows for tracing most, if not all forms of transmission and makes sense of their different tempos and modes. We discuss three key distinctions that should in particular be the targets of theoretical and empirical investigation, and try to assess the interplay among them and evolutionary dynamics. We distinguish two channels of transmission (channel 1 and channel 2), two measurements of the temporal dynamics of transmission, respectively across and within generations (durability and residency), and two types of transmitted factors according to their evolutionary relevance (selectively relevant and neutral stable factors). By implementing these three distinctions we can then map different forms of transmission over a continuous space describing the combination of their varying dynamical features. While our aim is not to provide yet another model of inheritance, putting together these distinctions and crossing them, we manage to offer an inclusive conceptual framework of transmission, grounded in empirical observation, and coherent with evolutionary theory. This interestingly opens possibilities for qualitative and quantitative analyses, and is a necessary step, we argue, in order to question the interplay between the dynamics of evolution and the dynamics of multiple forms of transmission.

Acta Biotheoretica, 2020

In this paper, we adopt a physiological perspective in order to produce an intelligible overview ... more In this paper, we adopt a physiological perspective in order to produce an intelligible overview of biological transmission in all its diversity. This allows us to put forward the analysis of transmission mechanisms, with the aim of complementing the usual focus on transmitted factors. We underline the importance of the structural, dynamical, and functional features of transmission mechanisms throughout organisms’ life cycles in order to answer to the question of what is passed on across generations, how and why. On this basis, we propose a vision of biological transmission as networks of heterogeneous physiological mechanisms, not restricted to transmission mechanisms stricto sensu. They prove to be themselves suited candidates for evolutionary explanations. They are processes both necessary for evolution to happen and resulting themselves from evolution. This leads us to call for a strategy of endogenization to account for transmission, and more specifically inheritance, as evolved and evolving physiological mechanisms.

Phenotypic Switching, 1st edition, Elsevier, 2020

THEORIA, 2020

What is a natural kind? This old yet lasting philosophical question has recently received new com... more What is a natural kind? This old yet lasting philosophical question has recently received new competing answers (e.g., Chakravartty, 2007; Magnus, 2014; Khalidi, 2013; Slater, 2015; Ereshefsky & Reydon, 2015). We show that the main ingredients of an encompassing and coherent account of natural kinds are actually on the table, but in need of the right articulation. It is by adopting a non-reductionist, naturalistic and non-conceptualist approach that, in this paper, we elaborate a new synthesis of all these ingredients. Our resulting proposition is a multiple-compartment theory of natural kinds that defines them in purely ontological terms, clearly distinguishes and relates ontological and epistemological issues-more precisely, two grains of ontological descriptions and two grains of explanatory success of natural kinds-, and which sheds light on why natural kinds play an epistemic role both within science and in everyday life. Short summary: This paper proposes a new take on the philosophical debate on natural kinds by elaborating a multi-compartment theory that defines them in purely ontological terms, and clearly distinguishes and relates ontological and epistemological issues. Our theory succeeds in articulating various existing important insights on natural kinds that have been structuring the debate in the last fifteen years in philosophy of science. 2

In José Luis Cómbita & Carlos Eduardo Maldonado, Biología Teórica y Complejidad, Universidad El Bosque Edition, 2020

The concept of epigenetics has evolved since Waddington defined it from the late 1930s as the stu... more The concept of epigenetics has evolved since Waddington defined it from the late 1930s as the study of the causal mechanisms at work in development. It has become a multi-faceted notion with different meanings, depending on the disciplinary context it is used. In this article, we first analyse the transformations of the concept of epigenetics, from Waddington to contemporary accounts, in order to identify its different meanings and traditions, and to come up with a typology of epigenetics throughout its history. Second, we show on this basis that epigenetics has progressively turned its main focus from biological problems regarding development, toward issues concerning evolution. Yet, both these different epistemological aspects of epigenetics still coexist. Third, we claim that the classical opposition between epigenesis and preformationism as ways of thinking about the developmental process is part of the history of epigenetics and has contributed to its current various meanings. With these objectives in mind, we first show how Waddington introduced the term “epigenetics” in a biological context in order to solve a developmental problem, and we then build on this by presenting Nanney's, Riggs' and Holliday's definitions, which form the basis for the current conception of “molecular epigenetics”. Then, we show that the evo-devo research field is where some particular uses of epigenetics have started shifting from developmental issues to evolutionary problems. We also show that epigenetics has progressively focused on the issue of epigenetic inheritance within the Extended Evolutionary Synthesis' framework. Finally, we conclude by presenting a typology of the different conceptions of epigenetics throughout time, and analyse the connections between them. We argue that, since Waddington, epigenetics, as an integrative research area, has been used to bridge the gap between different biological fields.

Review of Johnson, Curtis (2015) Darwin’s Dice: The Idea of Chance in the Thought of Charles Darw... more Review of Johnson, Curtis (2015) Darwin’s Dice: The Idea of Chance in the Thought of Charles Darwin. New York: Oxford University Press, ISBN: 978-0-19-936141-0, 253 pp, U.S. $29.95 (hardcover)

The current debate over extending inheritance and its evolutionary impact has been focused on lis... more The current debate over extending inheritance and its evolutionary impact has been focused on listing new categories of non-genetic factors to be added to the classical transmission of DNA, and on trying to redefine inheritance. Transmitted factors have been mainly characterized by their directions of transmission (vertical, horizontal or both) and the way they store variations. In this paper, we leave aside the issue of defining inheritance. We rather try to build an evolutionary conceptual framework that allows tracing most, if not all, forms of transmission and makes sense of their different tempos and modes. We discuss three key distinctions that should be particularly the targets of theoretical and empirical investigation, and try to assess the interplay among them and with evolutionary dynamics. We distinguish two channels of transmission (channel 1 and channel 2), two measures of the temporal dynamics of transmission, respectively across and within generations (durability and residency), and two types of transmitted factors according to their evolutionary relevance (selectively relevant and neutral stable factors). By implementing these three distinctions we can then map different forms of transmission over a continuous space describing the combination of their varying dynamical features. While our aim is not to provide yet another model of inheritance, putting together these distinctions and crossing them, we manage to offer an inclusive conceptual framework of transmission, grounded in empirical observation, and coherent with evolutionary theory. This interestingly opens possibilities for qualitative and quantitative analyses, and is a necessary step, we argue, in order to question the interplay between the dynamics of evolution and the dynamics of multiple forms of transmission.
Link: http://rdcu.be/pfCP

In his famous book Le hasard et la nécessité, essai sur la philosophie naturelle de la biologie m... more In his famous book Le hasard et la nécessité, essai sur la philosophie naturelle de la biologie moderne (1970) 1 , Jacques Monod claims that the evolution of living systems is based on chance and necessity, which are both required for the interplay of perturbations and invariance to result in evolutionary adaptive change. More precisely, on the one hand, if there was no chance, there would be no new variation because of the intrinsic rigorous invariance of living beings, and so no evolution. On the other hand, with no necessity (i.e., the intrinsic conservative character of living beings), life on Earth would die out driven by the negative effects of chance; anyway, the novelty produced by chance could not be integrated into living systems (the reign of necessity) and would fail to be conserved over evolutionary time.

This essay addresses the question of the extension of biological inheritance in the light of the ... more This essay addresses the question of the extension of biological inheritance in the light of the fact that organisms inherit much more than DNA. Starting from recent proposals to reconceive the concept of biological inheritance, I show that one of the main assumptions in the literature is simply taken for granted without providing any evidence or argument to support it. The analysis of four distinctions⎯and of the lessons drawn from them⎯allows me to propose a redefinition of inheritance, which brings to the fore its privileged link with reproduction and the specific theoretical role of this concept in biology.

Christian Sachse’s Philosophie de la biologie offers a well-written and timely introduction to co... more Christian Sachse’s Philosophie de la biologie offers a well-written and timely introduction to contemporary issues in philosophy of biology, which is easily accessible to both undergraduate and graduate students with no training in life sciences. This book fills a major gap in philosophy of biology textbooks in French: since François Duchesneau’s Philosophie de la biologie, published in 1997, no volume providing an introductory and systematic analysis of philosophical debates about biology had been published in French-speaking countries.As stated at the beginning of the introduction, Sachse’s book is focused on the philosophical problems raised by evolutionary theory. This is unfortunate since, until fairly recently, philosophy of biology had been dominated by reflections on evolutionary biology to the expense of other biological disciplines dealing with the construction and functioning of individual organisms, such as molecular and developmental biology, physiology and related discipl

Biological Theory, Apr 25, 2014

Blue Whales (2006), Bonner goes here a step further in stating that size -is a supreme regulator ... more Blue Whales (2006), Bonner goes here a step further in stating that size -is a supreme regulator of all matters biological‖ (2006, ch.1). Not only size is a major player in evolution because it can only come with changes in structure and in function, and brings about evolutionary innovations; size also has an impact on the role that randomness plays in evolution. More explicitly, Bonner introduces what he calls the -size-complexity rule‖ stating that the increase in size is fundamentally tied to an increase in complexity, the latter being required for size increase. Then, he argues for a corresponding decrease in the role of randomness in evolution. He concludes that the effect of randomness is higher for microorganisms, whose morphology is less affected by natural selection than that of higher and more complex ones, like larger mammals.

In C Malaterre & P-A Braillard (eds), How does Biology Explain? An Enquiry into the Diversity of Explanatory Patterns in the Life Sciences, History, Philosophy and Theory of the Life Sciences Series, Springer, 2014

Recent research in molecular developmental biology has shown that the stochastic character of dev... more Recent research in molecular developmental biology has shown that the stochastic character of development (i.e., developmental noise) can produce phenotypic heterogeneity even in the absence of any other source of change (genetic and environmental). More precisely, developmental noise triggers phenotypic heterogeneity amongst the members of a clonal population (synchronic heterogeneity) and even within an individual organism over time (diachronic heterogeneity), in a stable and homogeneous environment. This paper deals with such stochasticity in order to explore its epistemological relevance and role, both as explanans and as explanandum. First, I investigate whether developmental noise is part of the explanation of the physical characteristics of individual organisms (i.e., the phenotypic outcome of development).

In T Heams et al (eds.), Darwinian Worlds, Springer, 2014

Does biological evolution play dice? To what extent is it (in)deterministic? Biologists readily a... more Does biological evolution play dice? To what extent is it (in)deterministic? Biologists readily acknowledge that the theory of evolution is stochastic insofar as it only enables to make probabilistic predictions as regards the way genic and genotypic frequencies change in populations over generations. The issue at stake in a recent and lively debate in philosophy of biology concerns the very origin and nature of such a stochasticity. This debate seems to have been ignited, among others, by a section of Elliott Sober's The Nature of Selection (1984): in this book, Sober examines the possibility that some macroscopic evolutionary phenomena might by influenced by some underlying microscopic indeterminism, and in particular through the "percolation" of quantum indeterminism. The debate truly began in the Philosophy of Science in 1996 when Robert Brandon and Scott Carson published an article in which they argue for an indeterministic point of view against Alex and Barbara Horan's (1994) deterministic theses. In 1999, Rosenberg and Horan refined their arguments and elaborated a response to Brandon and Carson's attacks in collaboration with Leslie Graves. Other contributions to the indeterministic thesis came from David Stamos and Bruce Glymour (2001). Roberta assessed that the debate was going to a dead end and defended rather an agnostic attitude towards this issue of the origin and nature of the stochastic character of evolutionary theory. 3 In this chapter, we first examine the main arguments exchanged in this debate, which happens to be rather polarized around two extreme theses. We then argue that the answer to the question at stake (i.e., the origin of the stochastic character of evolutionary theory) requires first that one answers the question of the relative contribution of the different factors of evolution. This leads us to defend a more nuanced vision of the origin of the stochastic character of evolutionary theory.

In G Ramsey & C Pence (eds), Chance in Evolution, Chicago: Chicago University Press, 2014

Chapter Abstract: The concept of chance, when used to characterize genetic mutation, has often be... more Chapter Abstract: The concept of chance, when used to characterize genetic mutation, has often been analyzed and defined from the evolutionary point of view, i.e., looking at the relationship between mutation, selection, and adaptation. More precisely, chance mutation in this sense means that the mutation is not specifically provoked with a view to the adaptation of the organism concerned. However, genetic mutations, as other sources of biological variation (e.g., recombination), are said to be "chancy" or "random" events from the molecular point of view as well, and no philosophical analysis of this discourse has been developed until now. Which notion of chance is invoked in this context? The present chapter provides an answer to this question by introducing and defining two notions of randomness: "strong randomness" and "weak randomness". On the basis of recent research advances on the mutational process and its biased character, I show that all genetic mutations are "weak random" molecular events. I conclude the chapter by replying to three possible objections that might be raised against my view.

Erkentnnis, 2014

The paper provides a new critical perspective on the propensity interpretation of fitness, by inv... more The paper provides a new critical perspective on the propensity interpretation of fitness, by investigating its relationship to the propensity interpretation of probability. Two main conclusions are drawn. First, the claim that fitness is a propensity cannot be understood properly:

Bulletin d’histoire et d’épistémologie des sciences du vivant, 18 (1) : 79-108, 2011

Philosophy & Theory in Biology, Volume 2(e103), 2010

Acta Biotheoretica, 2017

Acta Biotheoretica, 2020

Phenotypic Switching, 1st edition, Elsevier, 2020

THEORIA, 2020

In José Luis Cómbita & Carlos Eduardo Maldonado, Biología Teórica y Complejidad, Universidad El Bosque Edition, 2020

Biological Theory, Apr 25, 2014

In T Heams et al (eds.), Darwinian Worlds, Springer, 2014

In G Ramsey & C Pence (eds), Chance in Evolution, Chicago: Chicago University Press, 2014

Erkentnnis, 2014

Bulletin d’histoire et d’épistémologie des sciences du vivant, 18 (1) : 79-108, 2011

Philosophy & Theory in Biology, Volume 2(e103), 2010

Editions Matériologiques, 2018

Cet ouvrage, unique en son genre, présente un panorama des problématiques contemporaines en phi... more Cet ouvrage, unique en son genre, présente un panorama des problématiques contemporaines en philosophie de la biologie.
Réunissant les contributions de vingt-cinq spécialistes français et étrangers, l’ouvrage couvre l’ensemble des grandes questions qui animent, aujourd’hui, la recherche en biologie, depuis l’origine de la vie et le fonctionnement de la cellule jusqu’à la coopération au sein des populations naturelles et l’évolution des espèces.
Ce précis est utile aussi bien aux philosophes qu’aux biologistes. Il constitue pour les étudiants en Licence et Master de biologie et de philosophie des sciences un indispensable outil d’appro- fondissement des cours et de préparation aux concours de l’enseignement.

Les mutations génétiques sont-elles le fruit du hasard, ou ont-elles lieu en vue de l'adaptation ... more Les mutations génétiques sont-elles le fruit du hasard, ou ont-elles lieu en vue de l'adaptation des organismes à leur environnement ? Depuis la publication de L'Origine des espèces de Darwin en 1859, le rôle du hasard dans l'origine de la variation chez les organismes vivants est au cœur de nombreuses controverses tant scientifiques que philosophiques. Aujourd'hui, à la lumière des recherches des trente dernières années sur les mécanismes de mutation, doit-on considérer que le lien entre hasard et variation, au cœur de la théorie classique de l'évolution, est remis en question ? Sommes-nous en train d'assister à un véritable bouleversement de ce cadre théorique, qui devrait dès lors intégrer des idées à penchant lamarckien afin de rendre compte de certains types de mutation génétique ? Le but du présent ouvrage est d'interroger la légitimité de cette remise en cause, fondamentale pour la biologie. En analysant les différents usages que les biologistes font de la notion de hasard au sein de leurs modèles et théories, Francesca Merlin soutient que les développements récents en biologie ne mettent pas en question le pilier central de la conception traditionnelle, darwinienne, de l'évolution, à savoir le caractère "au hasard" des mutations génétiques.