Considérations épistémologiques sur la modélisation mathématique en biologie

International audienceDans ce chapitre nous examinons quelques spécificités de la modélisation mathématiques en biologie, en ce qui concerne son élaboration et sa validation. La première section exposera plusieurs notions de “modèle” en science, en distinguant en particulier modèles de données, modèles phénoménologiques et modèles mécanistes, et en liant les deux derniers aux notions - omniprésentes en biologie - de « patterns » et de « process ». Concernant les modèles mécanistes on introduira alors l’argument de Levins (1966) sur l’impossibilité pour un tel modèle de satisfaire à la fois les valeurs épistémiques de précision, réalisme et généralité. La perspective adoptée sera donc celle d’un pluralisme des modèles mathématiques en biologie, et dans la suite nous nous interrogerons sur certaines complémentarités et incompatibilités entre types de modélisation mathématiques dans plusieurs domaines de la biologie. La première section s’achèvera par une distinction entre les opérations de vérification, validation, calibration et confirmation de modèles mathématiques, et en tirera les conséquences usuelles quant à la sous détermination des modèles par les données. La suite du chapitre se conformera à la distinction classique entre biologie des causes ultimes, ou évolutionnaire et biologie des causes prochaines, ou fonctionnelle, la section 2 concernant celle-là, et la section 3 traitant de celle-ci.La section 2 commencera par rappeler le rôle de la génétique des populations pour la science des processus de l’évolution. On considérera ensuite les diverses formulations de l’évolution par sélection naturelle en termes d’équation (équation de Price, équation des réplicateurs, règle de Hamilton, etc.) On contrastera cette vision avec les analyses de l’évolution en termes de modèles d’optimalité, en cours en écologie comportementale. On conclura par une tentative d’aborder de manière synoptique ces deux modélisations en rapport avec le modèle du paysage adaptatif ou paysage de fitness introduit par Sewall Wright (1932), afin de souligner le pluralisme des outils mathématiques requis en biologie de l’évolution, et les possibles correspondances qui les lient. La 3ème section abordera la modélisation mathématiques en biologie fonctionnelle. En rapport avec plusieurs exemples précis on s’y interrogera sur les rapports entre mécanismes biologiques et modélisations mathématiques. On se centrera en particulier sur trois modèles mathématiques du développement : le modèle de la morphogénèse de Turing, le modèle dit du French Flag de Wolpert, et la perspective récente des réseaux de gènes régulateurs, et plus généralement, l’usage d’outils de la théorie de graphes. Les deux dernières sections viseront à tirer des enseignements philosophiques de ces analyses. La section 4 abordera la question de la difference et des similitudes entre les modèles mathématiques traditionnels constitués d’équations, et les modèles plus récents du type simulation informatique: elle discutera en particulier la thèse selon laquelle les seconds remplacent les premiers lorsque les solutions des équations ne peuvent pas être calculées.La section 5 se demandera en quoi un modèle mathématiques peut être une explication, et, en particulier, examinera ce que la diversité des modèles mathématiques utilisés en biologie permet de conclure quant au caractère univoque ou pas de la nature de l’explication biologique

Emergence Made Ontological? Computational versus Combinatorial Approaches

International audienceI challenge the usual approach of defining emergence in terms of properties of wholes "emerging" upon properties of parts. This approach indeed fails to meet the requirement of nontriviality, since it renders a bunch of ordinary properties emergent; however, by defining emergence as the incompressibility of a simulation process, we have an objective meaning of emergence because the difference between the processes satisfying the incompressibility criterion and the other processes does not depend on our cognitive abilities. Finally, this definition fulfills the nontriviality and the scientific-adequacy requirements better than the combinatorial approach, emergence here being a predicate of processes rather than of properties

Neo-Aristotelian Naturalism and the Evolutionary Objection: Rethinking the Relevance of Empirical Science

Neo-Aristotelian metaethical naturalism is a modern attempt at naturalizing ethics using ideas from Aristotle’s teleological metaphysics. Proponents of this view argue that moral virtue in human beings is an instance of natural goodness, a kind of goodness supposedly also found in the realm of non-human living things. Many critics question whether neo-Aristotelian naturalism is tenable in light of modern evolutionary biology. Two influential lines of objection have appealed to an evolutionary understanding of human nature and natural teleology to argue against this view. In this paper, I offer a reconstruction of these two seemingly different lines of objection as raising instances of the same dilemma, giving neo-Aristotelians a choice between contradicting our considered moral judgment and abandoning metaethical naturalism. I argue that resolving the dilemma requires showing a particular kind of continuity between the norms of moral virtue and norms that are necessary for understanding non-human living things. I also argue that in order to show such a continuity, neo-Aristotelians need to revise the relationship they adopt with empirical science and acknowledge that the latter is relevant to assessing their central commitments regarding living things. Finally, I argue that to move this debate forward, both neo-Aristotelians and their critics should pay attention to recent work on the concept of organism in evolutionary and developmental biology

The concept of organism: historical philosophical, scientific perspectives

Contents 0. Philippe Huneman and Charles T. Wolfe: Introduction 1. Tobias Cheung, “What is an ‘organism’? On the occurrence of a new term and its conceptual transformations 1680-1850” 2. Charles T. Wolfe, “Do organisms have an ontological status?” 3. John Symons, “The individuality of artifacts and organisms” 4. Thomas Pradeu, “What is an organism? An immunological answer” 5. Matteo Mossio & Alvaro Moreno, “Organisational closure in biological organisms” 6. Laura Nuño de la Rosa, “Becoming organisms. The organisation of development and the development of organisation” 7. Denis Walsh, “Two Neo-Darwinisms” 8. Philippe Huneman, “Assessing the prospects for a return of organisms in evolutionary biology” 9. Johannes Martens, “Organisms in evolution” 10. Susan Oyama, “Biologists behaving badly: Vitalism and the language of language

Man-machines and embodiment: From cartesian physiology to Claude Bernard’s “living machine”

A common and enduring early modern intuition is that materialists reduce organisms in general and human beings in particular to automata. Wasn’t a famous book of the time (1748) entitled L’Homme-Machine? In fact, the machine is employed as an analogy, and there was a specifically materialist form of embodiment, in which the body is not reduced to an inanimate machine, but is conceived as an affective, flesh-and-blood entity. This paper discusses how mechanist and vitalist models of organism exist in a more complementary relation than hitherto imagined, with conceptions of embodiment resulting from experimental physiology. From La Mettrie to Bernard, mechanism, body and embodiment are constantly overlapping, modifying and overdetermining one another; embodiment came to be scientifically addressed under the successive figures of vie organique and then milieu intérieur, thereby overcoming the often lamented divide between scientific image and living experience.A common and enduring early modern intuition is that materialists reduce organisms in general and human beings in particular to automata. Wasn't a famous book of the time (1748) entitled L'Homme-Machine? In fact, the machine is employed as an analogy, and there was a specifically materialist form of embodiment, in which the body is not reduced to an inanimate machine, but is conceived as an affective, flesh-and-blood entity. This paper discusses how mechanist and vitalist models of organism exist in a more complementary relation than hitherto imagined, with conceptions of embodiment resulting from experimental physiology. From La Mettrie to Bernard, mechanism, body and embodiment are constantly overlapping, modifying and overdetermining one another; embodiment came to be scientifically addressed under the successive figures of vie organique and then milieu intérieur, thereby overcoming the often lamented divide between scientific image and living experience

Robot life: simulation and participation in the study of evolution and social behavior.

This paper explores the case of using robots to simulate evolution, in particular the case of Hamilton's Law. The uses of robots raises several questions that this paper seeks to address. The first concerns the role of the robots in biological research: do they simulate something (life, evolution, sociality) or do they participate in something? The second question concerns the physicality of the robots: what difference does embodiment make to the role of the robot in these experiments. Thirdly, how do life, embodiment and social behavior relate in contemporary biology and why is it possible for robots to illuminate this relation? These questions are provoked by a strange similarity that has not been noted before: between the problem of simulation in philosophy of science, and Deleuze's reading of Plato on the relationship of ideas, copies and simulacra

Man-machines and embodiment: From cartesian physiology to Claude Bernard’s “living machine”

A common and enduring early modern intuition is that materialists reduce organisms in general and human beings in particular to automata. Wasn’t a famous book of the time (1748) entitled L’Homme-Machine? In fact, the machine is employed as an analogy, and there was a specifically materialist form of embodiment, in which the body is not reduced to an inanimate machine, but is conceived as an affective, flesh-and-blood entity. This paper discusses how mechanist and vitalist models of organism exist in a more complementary relation than hitherto imagined, with conceptions of embodiment resulting from experimental physiology. From La Mettrie to Bernard, mechanism, body and embodiment are constantly overlapping, modifying and overdetermining one another; embodiment came to be scientifically addressed under the successive figures of vie organique and then milieu intérieur, thereby overcoming the often lamented divide between scientific image and living experience

“Man-Machines and Embodiment: From Cartesian Physiology to Claude Bernard’s ‘Living Machine’”

A common and enduring early modern intuition is that materialists reduce organisms in general and human beings in particular to automata. Wasn’t a famous book of the time entitled L’Homme-Machine? In fact, the machine is employed as an analogy, and there was a specifically materialist form of embodiment, in which the body is not reduced to an inanimate machine, but is conceived as an affective, flesh-and-blood entity. We discuss how mechanist and vitalist models of organism exist in a more complementary relation than hitherto imagined, with conceptions of embodiment resulting from experimental physiology. From La Mettrie to Bernard, mechanism, body and embodiment are constantly overlapping, modifying and overdetermining one another; embodiment came to be scientifically addressed under the successive figures of vie organique and then milieu intérieur, thereby overcoming the often lamented divide between scientific image and living experience

Kant, race, and natural history

This article presents a new argument concerning the relation between Kant’s theory of race and aspects of the critical philosophy. It argues that Kant’s treatment of the problem of the systematic unity of nature and knowledge in the Critique of Pure Reason and the Critique of the Power of Judgment can be traced back a methodological problem in the natural history of the period – that of the possibility of a natural system of nature. Kant’s transformation of the methodological problem from natural history into a set of philosophical (and specifically epistemological) problems proceeds by way of the working out of his own problem in natural history – the problem of the natural history of the human races – and specifically the problem of the unity in diversity of the human species, in response to which he develops a theory of race. This theory of race is, further, the first developed model of the use of teleological judgment in Kant’s work. The article thus argues that Kant’s philosophical position on the systematic unity of nature and of knowledge in the first and third Critiques, and his account and defense of teleological judgment, are developed out of problems first articulated in his solution to the problem of the unity in diversity of the human species – that is, in his theory of race. The article does not seek to establish that these aspects of the critical philosophy are therefore racialised. But it does demonstrate, against those who deny its salience to his philosophy, how the problem of the unity in diversity of the human species and Kant’s theory of race is significant for the development of aspects of the critical philosophy and thus contributes to their philosophical problematics

Pemahaman Etika dan Komitmen Mahasiswa untuk tidak Korupsi, pendekatan Utilitarianism Theory

Penelitian ini melihat fenomena korupsi yang menunjukkan indeks persepsi korupsi negara Indonesia buruk dibandingkan dengan negara lain. Pemerintah sudah bekerja keras untuk memerangi korupsi melalui KPK, tetapi hal tersebut belum cukup. Dibutuhkan peran serta perguruan tinggi untuk menanamkan nilai nilai kejujuran kepada mahasiswa, khususnya mahasiswa yang telah menempuh mata kuliah Agama, Pancasila dan Kewarganegaraan. Penelitian ini dilakukan untuk melihat dampak yang diberikan oleh pemahaman etika terhadap komitmen untuk tidak korupsi. Demikian juga dengan dampak dari pemahaman etika bisnis terhadap komitmen untuk tidak korupsi. Penelitian menggunakan data primer dengan penyebaran kuisioner penelitian. Reponden penelitian ini adalah mahasiswa di Indonesia. Data yang direkap dari jawaban responden akan disajikan dalam bentuk statistik deskriptif, khususnya untuk mengetahui rata-rata dari setiap variabel penelitian. Selanjutkan akan dilakukan uji outer loadings, composite reliability, dan cross loadings untuk mengetahui bahwa data jawaban responden layak. Selanjutnya dilakukan uji hipotesis dengan menggunakan bantuan software Smart PLS. Hasil penelitian membuktikan bahwa kedua variabel independen tersebut memiliki pengaruh terhadap komitmen untuk tidak korupsi