Philippe Huneman

Considering challenges to the modern synthesis (MS), this chapter reconstructs an explanatory scheme proper to the MS. It contrasts it with the explanatory scheme proper to some alternatives to the MS. It considers which empirical facts should compel us to adopt the alternative scheme, or stand with the MS, or consider a weakly attenuated form of its explanatory scheme. Hence the last section focuses on the form of variation: Given that many findings are accumulating concerning the not purely random nature of variation, it asks which specific patterns of variation would be likely to support an alternative explanatory scheme. It argues that neither biased variation nor random genotypic variation is likely to vindicate a specific explanatory scheme.

Network models are pervading ecology, genomics, epidemiology, as well as social science and neurosciences. In this paper, I survey the uses of network analysis in biological and social sciences, distinguishing between various jobs they can fulfill. I explore the various methods based on network analysis. I argue that in many cases they are indeed explanations, such explanations being “topological explanations”, which in turn is a subkind of structural explanations. I defend this view against the idea that network analysis is rather a description than an explanation, and against the claim that it is a kind of mechanistic explanation based on a focus on organization and hence very abstract. In the reasoning, I emphasize the difference between interaction and correlation networks, argue that both of them play roles in explanations, highlight their equivalence as graphs, and acknowledge that many of the debates raised by network analysis stem from the use of both families of networks, notwithstanding their differences. While ‘network analysis’ is not a natural kind, the explanatory potential it holds should be recognized, together with its potential for discovery in the study of complex systems.

Insofar as in etiological theory, “the function of X is Z” means that X has been selected for Z, while evolutionary biology often defines adaptation as what results from natural selection, the concepts of adaptation and function overlap. Should we then finally eliminate the selection-related notion of function, replace it with that of adaptation and use “function” only when it is a question of functions sensu the causal-role theory? I examine two limit cases for the etiological theory, in which emerges a tension between the notions of function and adaptation. First, there are cases of superiority of heterozygotes, such as sickle cell anemia. Here, from an etiological point of view, the recessive allele seems to have a function (equal to its adaptive character), whereas it is at the same time dysfunctional. The other problem is the selfish genetic elements (e.g. “selfish DNA”,), which also raise the question of levels of functionality in reference to adaptations. The selfish genetic elements make visible a presupposition of the etiological theory of function, namely a homogeneity or alignment in the levels of selection. In this sense, the acknowledgment of levels of selection motivates a rethinking of the etiological notion of function.

The ideas Darwin published in On the Origin of Species and The Descent of Man in the nineteenth century continue to have a major impact on our current understanding of the world in which we live and the place that humans occupy in it. Darwin’s theories constitute the core of the contemporary life sciences, and elicit enduring fascination as a potentially unifying basis for various branches of biology and the biomedical sciences. They can be used to understand the biological ground of human cognition, common behavioral patterns and disorders, and psychopathology more generally in psychology, psychiatry, and neuroscience. Perhaps the best known expression of this fact is Dobzhansky’s famous dictum that “nothing in biology makes sense except in the light of evolution” (Dobzhansky T. Am Zool 4:443–452, 1964: 449; Am Biol Teach 35:125–129, 1973: 125), and given that all human behavior supervenes on some biological basis, evolutionary thinking has a vast scope even just in this regard.

Biodiversity is arguably a major topic in ecology. Some of the key questions of the discipline are: why are species distributed the way they are, in a given area, or across areas? Or: why are there so many animals (as G. Evelyn Hutchinson asked in a famous paper)? It appears as what is supposed to be explained, namely an explanandum of ecology. Various families of theories have been proposed, which are nowadays mostly distinguished according to the role they confer to competition and the competitive exclusion principle. Niche theories, where the difference between “fundamental” and “realised” niches (Hutchinson GE, Am Nat 93:145–159, 1959) through competitive exclusion explains species distributions, contrast with neutral theories, where an assumption of fitness equivalence, species abundance distributions are explained by stochastic models, inspired by (Hubbell SP, The unified neutral theory of biodiversity and biogeography. Princeton University Press, Princeton, 2001).Yet, while an important part of community ecology and biogeography understands biodiversity as an explanandum, in other areas of ecology the concept of biodiversity rather plays the role of the explanans. This is manifest in the long lasting stability-diversity debate, where the key question has been: how does diversity beget stability? Thus explanatory reversibility of the biodiversity concept in ecology may prevent biodiversity from being a unifying object for ecology.In this chapter, I will describe such reversible explanatory status of biodiversity in various ecological fields (biogeography, functional ecology, community ecology). After having considered diversity as an explanandum, and then as an explanans, I will show that the concepts of biodiversity that are used in each of these symmetrical explanatory projects are not identical nor even equivalent. Using an approach to the concept of biodiversity in terms of “conceptual space”, I will finally argue that the lack of unity of a biodiversity concept able to function identically as explanans and explanandum underlies the structural disunity of ecology that has been pointed out by some historians and philosophers.

Besides mechanistic explanations of phenomena, which have been seriously investigated in the last decade, biology and ecology also include explanations that pinpoint specific mathematical properties as explanatory of the explanandum under focus. Among these structural explanations, one finds topological explanations, and recent science pervasively relies on them. This reliance is especially due to the necessity to model large sets of data with no practical possibility to track the proper activities of all the numerous entities. The paper first defines topological explanations and then explains why topological explanations and mechanisms are different in principle. Then it shows that they are pervasive both in the study of networks—whose importance has been increasingly acknowledged at each level of the biological hierarchy—and in contexts where the notion of selective neutrality is crucial; this allows me to capture the difference between mechanisms and topological explanations in terms of practical modelling practices. The rest of the paper investigates how in practice mechanisms and topologies are combined. They may be articulated in theoretical structures and explanatory strategies, first through a relation of constraint, second in interlevel theories (Sect. 3), or they may condition each other (Sect. 4). Finally, I explore how a particular model can integrate mechanistic informations, by focusing on the recent practice of merging networks in ecology and its consequences upon multiscale modelling (Sect. 5).

Emergence is a word that plays a central role in the natural or manifest image of the world, within which we organize our ordinary knowledge. Even though some interpretations of the “scientific image” leave no place for emergence, sciences increasingly made use of this word. But many philosophical arguments have been made against the consistence or validity of this concept. This chapter presents a computational view of emergence, alternative to the usual combinatorial view common among philosophers, that is formulated in terms of parts and wholes. It shows that computational emergence can be characterized in terms of causation, and that a subclass of computationally emergent processes displays many of the connotations of the scientific use of the term. After having so captured a concept of emergence, I turn to the question of applying the concept and testing whether some instantiations exist.

“Organicism” often refers to the idea that ecosystems or communities are, or are like, organisms. Often implicit in early twentieth century, it has been theorized by Clements, relying on physiological and developmental concepts. I investigate the fate of this idea in major attempts of a theoretical synthesis of ecology in the first part of the twentieth century. I first consider Bioecology (1939), by Clements and Shelford, which elaborates clementsian organicism as a general framework for plant and animal ecology. Then I investigate the major animal ecology treatise of the Chicago school ecologists C. Allee, T. Park, O. Park, K. Schmidt and A. Emerson, Principles of animal ecology (1949). I show how they shifted organicism from physiology to evolution, synthesizing inspiration from both Clements and Sewall Wright, got their inspiration in evolutionary biology, and built a systematic correspondence between cells, organisms and communities. I claim that the focus on populations allowed them to apply Darwinian insights at the level of communities. Finally I argue that this theoretical synthesis fell apart in the next decade because of the rise of density-dependent accounts of population regulation.

Our intuitive assumption that only organisms are the real individuals in the natural world is at odds with developments in cell biology, ecology, genetics, evolutionary biology, and other fields. Although organisms have served for centuries as nature's paradigmatic individuals, science suggests that organisms are only one of the many ways in which the natural world could be organized. When living beings work together--as in ant colonies, beehives, and bacteria-metazoan symbiosis--new collective individuals can emerge. In this book, leading scholars consider the biological and philosophical implications of the emergence of these new collective individuals from associations of living beings. The topics they consider range from metaphysical issues to biological research on natural selection, sociobiology, and symbiosis.

Même s’il existe des inégalités environnementales, la crise écologique concerne l’espèce humaine dans son ensemble. Elle suppose de ce fait l’élaboration d’un concept d’espèce à ce jour absent du répertoire théorique des sciences sociales. Cet article a pour objectif de contribuer à cette élaboration. Pour cela, il s’interrogera sur les liens entre deux concepts : l’un issu des sciences sociales, et en particulier du marxisme, le concept de besoin ; l’autre issu de la biologie, le concept de niche écologique. Se situant chacun à l’articulation de la nature et de la culture, ces concepts obligent à problématiser la distinction entre les deux. Ils permettent aussi de rendre concrète la manière dont on pourrait enquêter sur la dynamique de la crise environnementale. Le besoin et la niche écologique constituent les fondements potentiels d’un concept d’espèce opératoire pour les sciences sociales. Comme on le montrera, ce concept est indissociable du contexte de crise environnementale, d’où il émerge.

This anthology of essays presents a sample of studies from recent philosophy of medicine addressing issues which attempt to answer very general (interdependent) questions: (a) what is a disease and what is health? (b) How do we (causally) explain diseases? (c) And how do we distinguish diseases, id est define classes of diseases and recognize that an instance X of disease belongs to a given class B? (d) How do we assess and choose cure/ therapy? The book is divided into three sections: classification, disease, and evidence. In general, attention is focused on statistics in medicine and epidemiology, issues in psychiatry, and connecting medicine with evolutionary biology and genetics. Many authors position the theories that they address within their historical contexts. The nature of health and disease will be addressed in several essays that also touch upon very general questions about the definition of medicine and its status. Several chapters scrutinize classification because of its centrality within philosophical problems raised by medicine and its core position in the philosophical questioning of psychiatry. Specificities of medical explanation have recently come under a new light, particularly because of the rise of statistical methods, and several chapters investigate these methods in specific contexts such as epidemiology or meta-analysis of random testing. Taken together this collection addresses the question of how we gather, use and assess evidence for various medical theories. The rich assortment of disciplines featured also includes epidemiology, parasitology, and public health, while technical aspects such as the application of game theory to medical research and the misuse of the DSM in forensic psychiatry are also given an airing. The book addresses more than the construction of medical knowledge, however, adding cogent appraisal of the processes of decision making in medicine and the protocols used to justify therapeutic choices.

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.

The concept of “organism” has been central to modern biology, with its definition and philosophical implications evolving since the nineteenth century. In contemporary biology, the divide between developmental and physiological approaches and evolutionary approaches has influenced the definition of organism. The convergence between molecular biology and evolutionary biology has led to the term “suborganismal biology,” while the return to the organism has been characterized by animal behavior studies and Evo-devo. The philosophical approach to the concept of individual is divided between a Kantian understanding of organism, which defines necessary and sufficient conditions for any X to be a “natural purpose,” and an evolutionary approach, which considers what a biological individual is and confers natural selection a key role in this definition. While the former aims to find necessary and sufficient conditions for an organism, the latter thinks in terms of conceptual spaces, being much more liberal in pointing out organisms in the world. The paper examines possible connections between these two approaches and assesses the prospects of a reconciliation between them.

La question qu’on nomme aujourd’hui des « genres naturels » en métaphysique porte sur les « jointures » du monde : quelles classes de choses constituent le monde et existent réellement? Si nominalistes et réalistes s’opposent depuis longtemps sur la possibilité même de répondre à cette question, les sciences modernes proposent des découpages en genres naturels qui contrastent souvent avec l’image naturelle du monde. Cet article se concentre sur les genres naturels en biologie. Après avoir présenté le principe de réponse offert par la biologie évolutive, à savoir la systématique cladistique, j’expose le paradoxe du poisson, puisque « poisson » n’y est pas un nom de classe objectif, et semble donc aussi peu réel que « légume ». Je montre ensuite comment ce paradoxe est abordé différemment par des conceptions réalistes ou pragmatistes des genres naturels, et, en distinguant plusieurs sortes de pragmatismes en fonction des pratiques sociales auxquelles ils réfèrent la vérité des énoncés, je défendrai un pragmatisme modéré quant aux genres naturels en biologie.

A philosopher explores the many dimensions of a beguilingly simple question. Why did triceratops have horns? Why did World War I occur? Why does Romeo love Juliet? And, most importantly, why ask why? Through an analysis of these questions and others, philosopher Philippe Huneman describes the different meanings of "why," and how those meanings can, and should (or should not), be conflated. As Huneman outlines, there are three basic meanings of why: the cause of an event, the reason of a belief, and the reason why I do what I do (the purpose). Each of these meanings, in turn, impacts how we approach knowledge in a wide array of disciplines: science, history, psychology, and metaphysics. Exhibiting a rare combination of conversational ease and intellectual rigor, Huneman teases out the hidden dimensions of questions as seemingly simple as "Why did Mickey Mouse open the refrigerator?" or as seemingly unanswerable as "Why am I me?" In doing so, he provides an extraordinary tour of canonical and contemporary philosophical thought, from Plato and Aristotle, through Descartes and Spinoza, to Elizabeth Anscombe and Ruth Millikan, and beyond. Of course, no proper reckoning with the question "why?" can afford not to acknowledge its limits, which are the limits, and the ends, of reason itself. Huneman thus concludes with a provocative elaboration of what Kant called the "natural need for metaphysics," the unallayed instinct we have to ask the question even when we know there can be no unequivocal answer.

This volume aims to clarify the epistemic potential of applying evolutionary thinking outside biology, and provides a survey of the current state of the art in research on relevant topics in the life sciences, the philosophy of science, and the various areas of evolutionary research outside the life sciences. By bringing together chapters by evolutionary biologists, systematic biologists, philosophers of biology, philosophers of social science, complex systems modelers, psychologists, anthropologists, economists, linguists, historians, and educators, the volume examines evolutionary thinking within and outside the life sciences from a multidisciplinary perspective. While the chapters written by biologists and philosophers of science address theoretical aspects of the guiding questions and aims of the volume, the chapters written by researchers from the other areas approach them from the perspective of applying evolutionary thinking to non-biological phenomena. Taken together, the chapters in this volume do not only show how evolutionary thinking can be fruitfully applied in various areas of investigation, but also highlight numerous open problems, unanswered questions, and issues on which more clarity is needed. As such, the volume can serve as a starting point for future research on the application of evolutionary thinking across disciplines.

Throughout my university career, and since I began my Ph.D., Jean Gayon was there. Unlike many contributors to this volume, to the early or mid-career researchers who do French philosophy of biology today, I did not know Jean as a dissertation supervisor or a professor, but as a dissertation examiner, as expert witness to the beginning of my career and as indisputable scientific authority. For fifteen years I have been doing philosophy of evolutionary biology with Jean Gayon. In this chapter, I do not offer an analysis of “evolutionary biology according to Gayon” but I aim to pay tribute to a philosopher who was at once a “major contemporary”, a colleague, a friend, and an inspiration.

Ever since its inception, the theory of evolution has been reified into an “-ism”: Darwinism. While biologists today tend to shy away from the term in their research, the term is still actively used in the broader academic and societal contexts. What exactly is Darwinism, and how precisely are its various uses and abuses related to the scientific theory of evolution? Some call for limiting the meaning of the term “Darwinism” to its scientific context; others call for its abolition; yet others claim the term refers to a myth-like story. In this paper we propose a conceptually grounded overview of the term. We show how the scientific dimension of Darwinism feeds into, and is influenced by, guises of Darwinism as a methodology and as an ethically and politically charged “worldview”. The full meaning of Darwinism, as well as how this meaning has changed over time, can only be understood through the complex interaction between these three dimensions.