This paper argues that besides mechanistic explanations, there is a kind of explanation that relies upon “topological” properties of systems in order to derive the explanandum as a consequence, and which does not consider mechanisms or causal processes. I first investigate topological explanations in the case of ecological research on the stability of ecosystems. Then I contrast them with mechanistic explanations, thereby distinguishing the kind of realization they involve from the realization relations entailed by mechanistic explanations, and explain how both (...) kinds of explanations may be articulated in practice. The second section, expanding on the case of ecological stability, considers the phenomenon of robustness at all levels of the biological hierarchy in order to show that topological explanations are indeed pervasive there. Reasons are suggested for this, in which “neutral network” explanations are singled out as a form of topological explanation that spans across many levels. Finally, I appeal to the distinction of explanatory regimes to cast light on a controversy in philosophy of biology, the issue of contingence in evolution, which is shown to essentially involve issues about realization. (shrink)

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. -/- The contributors investigate individuality and its relationship to evolution and the specific concept of organism; the tension between group evolution and individual adaptation; and the structure of collective individuals and the extent to which they can be defined by the same concept of individuality. These new perspectives on evolved individuality should trigger important revisions to both philosophical and biological conceptions of the individual. -/- Contributors: Frédéric Bouchard, Ellen Clarke, Jennifer Fewell, Andrew Gardner, Peter Godfrey-Smith, Charles J. Goodnight, Matt Haber, Andrew Hamilton, Philippe Huneman, Samir Okasha, Thomas Pradeu, Scott Turner, Minus van Baalen. (shrink)

This paper argues that in some explanations mathematics are playing an explanatory rather than a representational role, and that this feature unifies many types of non-causal or non-mechanistic explanations that some philosophers of science have been recently exploring under various names. After showing how mathematics can play either a representational or an explanatory role by considering two alternative explanations of a same biological pattern—“Bergmann’s rule”—I offer an example of an explanation where the bulk of the explanatory job is done by (...) a mathematical theorem, and where mechanisms involved in the target systems are not explanatorily relevant. Then I account for the way mathematical properties may function in an explanatory way within an explanation by arguing that some mathematical propositions involving variables non directly referring to the target system features constitute constraints to which a whole class of systems should comply, provided they are describable by a mathematical object concerned by those propositions. According to such “constraint account”, those mathematical facts are directly entailing the explanandum, as a consequence of such constraints. I call those explanations “structural”, because here properties of mathematical structures are accounting for the explanandum; various kinds of mathematical structures thereby define various types of structural explanations. (shrink)

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, or they may condition each other. 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. (shrink)

We propose that measures of information integration can be more straightforwardly interpreted as measures of agency rather than of consciousness. This may be useful to the goals of consciousness research, given how agency and consciousness are “duals” in many (although not all) respects.

Biologists explain organisms’ behavior not only as having been programmed by genes and shaped by natural selection, but also as the result of an organism’s agency: the capacity to react to environmental changes in goal-driven ways. The use of such ‘agential explanations’ reopens old questions about how justified it is to ascribe agency to entities like bacteria or plants that obviously lack rationality and even a nervous system. Is organismic agency genuinely ‘real’ or is it just a useful fiction? In (...) this paper we focus on two questions: whether agential explanations are to be interpreted ontically, and whether they can be reduced to non-agential explanations (thereby dispensing with agency). The Kantian approach we identify interprets agential explanations non-ontically, yet holds agency to be indispensable. Attributing agency to organisms is not to be taken literally in the way we attribute physical properties such as mass or acceleration, but nor is it a mere heuristic or predictive tool. Rather, it is an inevitable consequence of our own rational capacity: as long as we are rational agents ourselves, we cannot avoid seeing agency in organisms. (shrink)

This book addresses several key issues in the biological study of death with the intent of capturing their genealogy, the assumptions and presuppositions they make, and the way that they open specific new research avenues. The book is divided into two sections: the first considers physiology and the second evolutionary biology. Huneman explains that biologists in the late 1950s put forth a research framework that evolutionarily accounts for death in terms of either an effect of the weakness of natural selection (...) or a by-product of natural selection for early reproduction. He illustrates how the biology of death is a central field and that studying it provides insight into the way that the epistemic structure of this knowledge has been constituted, persists until now, and may conflict with some traditional philosophical ideas. (shrink)

Following a previous elaboration of the concept of weak individuality and some examples of its instances in ecology and biology, the article focuses on general features of the concept, arguing that in any ontological field individuals are understood on the basis of our knowledge of interactions, through the application of these general formulas for extracting individuals from interactions. Then, the specificities of the individuality in the sense of this weak concept are examined in ecology; I conclude by addressing the differences (...) between ecosystems and organisms as they appear in the viewpoint of such concept. (shrink)

Biological individuals are usually defined by evolutionists through a reference to natural selection. This article looks for a concept of individuality that would hold at the same time for organisms and for communities or ecosystems, the latter being unaffected by natural selection. In the wake of Simon’s notion of “quasi-independence,” I elaborate a concept of “weak individuality” defined by probabilistic connections between sub-entities, read off our knowledge of their interactions. This formal scheme of connections allows one to infer what are (...) the individuals in the domain addressed by the theory of the interactions. The article argues that if ecosystems do not have strong individuality, they still possess a weak individuality, ecological theories providing the values of the variables in the formula for individuality. (shrink)

This paper investigates the conception of causation required in order to make sense of natural selection as a causal explanation of changes in traits or allele frequencies. It claims that under a counterfactual account of causation, natural selection is constituted by the causal relevance of traits and alleles to the variation in traits and alleles frequencies. The “statisticalist” view of selection (Walsh, Matthen, Ariew, Lewens) has shown that natural selection is not a cause superadded to the causal interactions between individual (...) organisms. It also claimed that the only causation at work is those aggregated individual interactions, natural selection being only predictive and explanatory, but it is implicitly committed to a process-view of causation. I formulate a counterfactual construal of the causal statements underlying selectionist explanations, and show that they hold because of the reference they make to ecological reliable factors. Considering case studies, I argue that this counterfactual view of causal relevance proper to natural selection captures more salient features of evolutionary explanations than the statisticalist view, and especially makes sense of the difference between selection and drift. I eventually establish equivalence between causal relevance of traits and natural selection itself as a cause. (shrink)

A collection of essays investigating key historical and scientific questions relating to the concept of natural purpose in Kant's philosophy of biology.

This volume handles in various perspectives the concept of function and the nature of functional explanations, topics much discussed since two major and conflicting accounts have been raised by Larry Wright and Robert Cummins’s papers in the 1970s. Here, both Wright’s ”etiological theory of functions’ and Cummins’s ”systemic’ conception of functions are refined and elaborated in the light of current scientific practice, with papers showing how the ”etiological’ theory faces several objections and may in reply be revisited, while its counterpart (...) became ever more sophisticated, as researchers discovered fresh applications for it. Relying on a firm knowledge of the original positions and debates, this volume presents cutting-edge research evincing the complexities that today pertain in function theory in various sciences. Alongside original papers from authors central to the controversy, work by emerging researchers taking novel perspectives will add to the potential avenues to be followed in the future. Not only does the book adopt no a priori assumptions about the scope of functional explanations, it also incorporates material from several very different scientific domains, e.g. neurosciences, ecology, or technology. In general, functions are implemented in mechanisms; and functional explanations in biology have often an essential relation with natural selection. These two basic claims set the stage for this book’s coverage of investigations concerning both ”functional’ explanations, and the ”metaphysics’ of functions. It casts new light on these claims, by testing them through their confrontation with scientific developments in biology, psychology, and recent developments concerning the metaphysics of realization. Rather than debating a single theory of functions, this book presents the richness of philosophical issues raised by functional discourse throughout the various sciences.​ Content Level » Research Keywords » Causal role theory of functions - Determination of content - Ecosystem selection - Etiological theory of function - Evolutionary biology - Functional explanations - Historical concepts in biology - Larry Wright - Neurosciences - New mechanism - Selected effects functions - Systemic theory of functions - William Wimsatt Related subjects » Anthropology & Archaeology - Epistemology & Philosophy of Science - Evolutionary & Developmental Biology - Neuroscience - Philosophy TABLE OF CONTENTS Introduction.- Section I. Biological functions and functional explanations: genes, cells, organisms and ecosystems.- Part 1.A. Functions, organization and development in life sciences.- Chapter 1. William C. Wimsatt. Evolution and the Stability of Functional Architectures.- Chapter 2. Denis M. Walsh. Teleological Emergence: The Autonomy of Evo-Devo.- Chapter 3. Jean Gayon. Does oxygen have a function, or: where should the regress of biological functions stop?.- Part 1.B. Functional pluralism for biologists? Chapter 4. Frédéric Bouchard. How ecosystem evolution strengthens the case for functional pluralism.- Chapter 5. Robert N. Brandon. A general case for functional pluralism.- Chapter 6. Philippe Huneman. Weak realism in the etiological theory of functions.- Section 2. Section II. Psychology, philosophy of mind and technology: Functions in a man’s world.- Part 2.A. 2A. Metaphysics, function and philosophy of mind.- Chapter 7. Carl Craver. Functions and Mechanisms in Contemporary Neuroscience.- Chapter 8. Carl Gillett. Understanding the sciences through the fog of ”functionalism.’.- 2.B. Philosophy of technology, design and functions.- Chapter 9. Fran¸ coise Longy. Artifacts and Organisms: A Case for a New Etiological Theory of Functions.- Chapter 10. Pieter Vermaas and Wybo Houkes. Functions as Epistemic Highlighters: An Engineering Account of Technical, Biological and Other Functions.- Epilogue.- Larry Wright. Revising teleological explanations: reflections three decades on. (shrink)

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. (shrink)

Kant’s analysis of the concept of natural purpose in the Critique of judgment captured several features of organisms that he argued warranted making them the objects of a special field of study, in need of a special regulative teleological principle. By showing that organisms have to be conceived as self-organizing wholes, epigenetically built according to the idea of a whole that we must presuppose, Kant accounted for three features of organisms conflated in the biological sciences of the period: adaptation, functionality (...) and conservation of forms..Kant’s unitary concept of natural purpose was subsequently split in two directions: first by Cuvier’s comparative anatomy, that would draw on the idea of adaptative functions as a regulative principle for understanding in reconstituting and classifying organisms; and then by Goethe’s and Geoffroy’s morphology, a science of the general transformations of living forms. However, such general transformations in nature, objects of an alleged ‘archaeology of nature’, were thought impossible by Kant in the §80 of the Critique of judgment. Goethe made this ‘adventure of reason’ possible by changing the sense of ‘explanation’: scientific explanation was shifted from the investigation of the mechanical processes of generation of individual organisms to the unveiling of some ideal transformations of types instantiated by those organisms. (shrink)

Kant’s analysis of the concept of natural purpose in the Critique of judgment captured several features of organisms that he argued warranted making them the objects of a special field of study, in need of a special regulative teleological principle. By showing that organisms have to be conceived as self-organizing wholes, epigenetically built according to the idea of a whole that we must presuppose, Kant accounted for three features of organisms conflated in the biological sciences of the period: adaptation, functionality (...) and conservation of forms..Kant’s unitary concept of natural purpose was subsequently split in two directions: first by Cuvier’s comparative anatomy, that would draw on the idea of adaptative functions as a regulative principle for understanding in reconstituting and classifying organisms; and then by Goethe’s and Geoffroy’s morphology, a science of the general transformations of living forms. However, such general transformations in nature, objects of an alleged ‘archaeology of nature’, were thought impossible by Kant in the §80 of the Critique of judgment. Goethe made this ‘adventure of reason’ possible by changing the sense of ‘explanation’: scientific explanation was shifted from the investigation of the mechanical processes of generation of individual organisms to the unveiling of some ideal transformations of types instantiated by those organisms. (shrink)

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. (shrink)

Among many properties distinguishing emergence, such as novelty, irreducibility and unpredictability, computational accounts of emergence in terms of computational incompressibility aim first at making sense of such unpredictability. Those accounts prove to be more objective than usual accounts in terms of levels of mereology, which often face objections of being too epistemic. The present paper defends computational accounts against some objections, and develops what such notions bring to the usual idea of unpredictability. I distinguish the objective unpredictability, compatible with determinism (...) and entailed by emergence, and various possibilities of predictability at emergent levels. This makes sense of practices common in complex systems studies that forge qualitative predictions on the basis of comparisons of simulations with multiple values of parameters. I consider robustness analysis as a way to ensure the ontological character of computational emergence. Finally, I focus on the property of novelty, as it is displayed by biological evolution, and ask whether computer simulations of evolution can produce the same kind of emergence as the open-ended evolution attested in Phanerozoic records. (shrink)

‘Statisticalists’ argue that the individual interactions of organisms taken together constitute natural selection. On this view, natural selection is an aggregated effect of interactions rather than some added cause acting on populations. The statisticalists’ view entails that natural selection and drift are indistinguishable aggregated effects of interactions, so that it becomes impossible to make a difference between them. The present paper attempts to make sense of the difference between selection and drift, given the main insights of statisticalism; basically, it will (...) disentangle the various kinds of indistinguishability between selection and drift that happen within biology, by examining the epistemological and metaphysical nature of the distinction between selection and drift. It will be based on a ‘difference-making account’ of selection. The first section will explicate the inscrutability of selection and drift, its various types in the statisticalist writings, and its implications. The second section specifies concepts of natural selection and drift in the difference making account of selection I am using, and shows that one can derive from this the statistical signatures of selection and drift. On this basis I focus on one sort of indistinguishability issue about selection and drift, which I call epistemic opacity, and explain why it mostly affects small populations. The last section explains why epistemic opacity does not raise an genuine epistemic problem for evolutionary biology. (shrink)

This paper proposes an interpretative framework for some developments of the philosophy of nature after Kant. I emphasize the critique of the economy of nature in the Critique of judgement. I argue that it resulted in a split of a previous structure of knowledge; such a structure articulated natural theology and natural philosophy on the basis of the consideration of the order displayed by living beings, both in their internal organisation and their ecological distribution. The possibility of a philosophical discourse (...) on nature that is neither mathematical nor theological stemmed from this shift. I call “hermeneutics of nature” such a program, since it aims at unpacking an immanent meaning in nature that is not explicated by the sciences of nature, which are dealing with the laws of nature. The Naturphilosophie, undertaken by Schelling, as well as the philosophies of nature of Hegel and Schopenhauer, are several realizations of this program. I highlight the structural traits that they share, such as a pregnant sense of conflicts in nature, an emphasis on the riddles of gender, and above all a prominent status given to organisms as a clue to the meaning of nature. Finally, I try to sketch the ramifications of this hermeneutics of nature in contemporary philosophy, especially phenomenology, and argue that the coming philosophy of nature, as shown by the attempts of syntheses between phenomenology and ecology, seems to depart from this hermeneutical program. (shrink)

I 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. †To contact the author, please write to: Institut d'Histoire et de Philosophie des Sciences et des Techniques (CNRS/Université Paris I Sorbonne), 13 rue du Four 75006, Paris; e‐mail: [email protected]. (shrink)

I investigate the relationship between adaptation, as defined in evolutionary theory through natural selection, and the concept of emergence. I argue that there is an essential correlation between the former, and “emergence” defined in the field of algorithmic simulations. I first show that the computational concept of emergence (in terms of incompressible simulation) can be correlated with a causal criterion of emergence (in terms of the specificity of the explanation of global patterns). On this ground, I argue that emergence in (...) general involves some sort of selective processes. Finally, I show that a second criterion, concerning novel explanatory regularities following the emergence of a pattern, captures the robustness of emergence displayed by some cases of emergence (according to the first criterion). Emergent processes fulfilling both criteria are therefore exemplified in evolutionary biology by some so-called “innovations”, and mostly by the new units of fitness or new kinds of adaptations (like sexual reproduction, multicellular organisms, cells, societies) sometimes called “major transitions in evolution”, that recent research programs (Maynard-Smith and Szathmary 1995 ; Michod 1999 ) aims at explaining. (shrink)

The Darwinian theory of evolution is itself evolving and this book presents the details of the core of modern Darwinism and its latest developmental directions. The authors present current scientific work addressing theoretical problems and challenges in four sections, beginning with the concepts of evolution theory, its processes of variation, heredity, selection, adaptation and function, and its patterns of character, species, descent and life. The second part of this book scrutinizes Darwinism in the philosophy of science and its usefulness in (...) understanding ecosystems, whilst the third section deals with its application in disciplines beyond the biological sciences, including evolutionary psychology and evolutionary economics, Darwinian morality and phylolinguistics. The final section addresses anti-Darwinism, the creationist view and issues around teaching evolution in secondary schools. The reader learns how current experimental biology is opening important perspectives on the sources of variation, and thus of the very power of natural selection. This work examines numerous examples of the extension of the principle of natural selection and provides the opportunity to critically reflect on a rich theory, on the methodological rigour that presides in its extensions and exportations, and on the necessity to measure its advantages and also its limits. Scholars interested in modern Darwinism and scientific research, its concepts, research programs and controversies will find this book an excellent read, and those considering how Darwinism might evolve, how it can apply to the human sciences and other disciplines beyond its origins will find it particularly valuable. Originally produced in French (Les Mondes Darwiniens), the scope and usefulness of the book have led to the production of this English text, to reach a wider audience. This book is a milestone in the impressive penetration by Francophone scholars into the world of Darwinian science, its historiography and philosophy over the last two decades. Alex Rosenberg, R. Taylor Cole Professor of Philosophy, Duke University Until now this useful and comprehensive handbook has only been available to francophones. Thanks to this invaluable new translation, this collection of insightful and original essays can reach the global audience it deserves. Tim Lewens, University of Cambridge. (shrink)

The problem of generation has been, for Kant scholars, a kind of test of Kant's successive concepts of finality. Although he deplores the absence of a naturalistic account of purposiveness (and hence of reproduction) in his pre-critical writings, in the First Critique he nevertheless presents a "reductionist" view of finality in the Transcendental Dialectic's Appendices. This finality can be used only as a language, extended to the whole of nature, but which must be filled with mechanistic explanations. Therefore, in 1781, (...) mechanism and teleology are synonymous languages. Despite the differences between its two authors, the Wolffian embryology, exposed in the Theorie der Generation (1764), and debated by Blumenbach's dissertation on Bildungstrieb, enabled Kant to resolve the philosophical problem of natural generation, and subsequently to determine what is proper to the explanation of living processes. Thus, in the Third Critique he could give another account of purposiveness, restricted to the organism, and more realistic than his former one; this philosophical reappraisal of purposiveness in embryology required the new concept of "simply reflexive judgement", and the correlated notion of "regulative principle". Thus framed, this naturalized teleology provided some answers to the Kantian problem of order and contingency after the end of classical (Leibnizian) metaphysics. (shrink)

Recently some philosophers have emphasized a potentially irreconcilable conceptual antagonism between the statistical characterization of natural selection and the standard scientific discussion of natural selection in terms of forces and causes. Other philosophers have developed an account of the causal character of selectionist statements represented in terms of counterfactuals. I examine the compatibility between such statisticalism and counterfactually based causal accounts of natural selection by distinguishing two distinct statisticalist claims: firstly the suggested impossibility for natural selection to be a cause (...) acting upon populations and secondly the conceptualization that all evolutionary causes occur at the level of interactions between individual organisms. I argue that deriving the latter from the former involves supplementary assumptions concerning precisely what causation is. I critically examine two of these assumptions purportedly preventing natural selection being regarded as a cause: the locality claim and the modularity claim. I conclude that justifying the strongest version of statisticalism—i.e. evolutionary causation only occurs at the level of individual interactions between organisms—would require further metaphysical arguments that are likely to be deemed highly problematic. Additionally, I argue that such a metaphysical position would be considered incongruous with both our scientific and ordinary use of the concepts of causality and explanation as employed within our everyday epistemological framework. (shrink)

This paper interprets the two pages devoted in the Critique of Pure Reason to a critique of Leibniz’s view of organisms as infinitely organized machines. It argues that this issue of organisms represents a crucial test-case for Kant in regard to the conflicting notions of space, continuity and divisibility held by classical metaphysics and by criticism. I first present Leibniz’s doctrine and its justification. In a second step, I explain the general reasoning by which Kant defines the problem of the (...) Antinomies, and then I specify the case of the Second Antinomy. Then, I ask why the organism raises specific issues for Kant’s solution of the Second Antinomy, and why it sheds light on the nature of Leibniz’s metaphysical assumptions about organisms. The last section considers this critique of Leibniz from the perspective of Kant’s future theory of organisms in the third Critique, specifying its role in the development of a Kantian view of organisms with regard to the changes occurring at the same time in the life sciences. (shrink)

Ecology in principle is tied to evolution, since communities and ecosystems result from evolution and ecological conditions determine fitness values. Yet the two disciplines of evolution and ecology were not unified in the twentieth-century. The architects of the Modern Synthesis, and especially Julian Huxley, constantly pushed for such integration, but the major ideas of the Synthesis—namely, the privileged role of selection and the key role of gene frequencies in evolution—did not directly or immediately translate into ecological science. In this paper (...) I consider five stages through which the Synthesis was integrated into ecology and distinguish between various ways in which a possible integration was gained. I start with Elton’s animal ecology, then consider successively Ford’s ecological genetics in the 1940s, the major textbook Principles of animal ecology edited by Allee et al., and the debates over the role of competition in population regulation in the 1950s, ending with Hutchinson’s niche concept and McArthur and Wilson’s Principles of Island Biogeography viewed as a formal transposition of Modern Synthesis explanatory schemes. I will emphasize the key role of founders of the Synthesis at each stage of this very nonlinear history. (shrink)

The neutral theory of biodiversity assumes that coexisting organisms are equally able to survive, reproduce and disperse, but predicts that stochastic fluctuations of these abilities drive diversity dynamics. It predicts remarkably well many biodiversity patterns, although substantial evidence for the role of niche variation across organisms seems contradictory. Here, we discuss this apparent paradox by exploring the meaning and implications of ecological equivalence. We address the question whether neutral theory provides an explanation for biodiversity patterns and acknowledges causal processes. We (...) underline that ecological equivalence, although central to neutral theory, can emerge at local and regional scales from niche-based processes through equalizing and stabilizing mechanisms. Such emerging equivalence corresponds to a weak conception of neutral theory, as opposed to the assumption of strict equivalence at individual level in the strong conception. We show that this duality is related to diverging views on hypothesis-testing and modeling in ecology. In addition, the stochastic dynamics exposed in neutral theory are pervasive in ecological systems and, rather than a null hypothesis, ecological equivalence is best understood as a parsimonious baseline to address biodiversity dynamics at multiple scales. (shrink)

Natural selection is often envisaged as the ultimate cause of the apparent rationality exhibited by organisms in their specific habitat. Given the equivalence between selection and rationality as maximizing processes, one would indeed expect organisms to implement rational decision-makers. Yet, many violations of the clauses of rationality have been witnessed in various species such as starlings, hummingbirds, amoebas and honeybees. This paper attempts to interpret such discrepancies between economic rationality and biological rationality. After having distinguished two kinds of rationality we (...) introduce irrationality as a negation of economic rationality by biologically rational decision-makers. Focusing mainly on those instances of irrationalities that can be understood as exhibiting inconsistency in making choices, i.e. as non-conformity of a given behaviour to axioms such as transitivity or independence of irrelevant alternatives, we propose two possible families of Darwinian explanations that may account for these apparent irrationalities. First, we consider cases where natural selection may have been an indirect cause of irrationality. Second, we consider putative cases where violations of rationality axioms may have been directly favored by natural selection. Though the latter cases seem to clearly contradict our intuitive representation of natural selection as a process that maximizes fitness, we argue that they are actually unproblematic; for often, they can be redescribed as cases where no rationality axiom is violated, or as situations where no adaptive solution exists in the first place. (shrink)

This paper uses formal Darwinism as elaborated by Alan Grafen to articulate an explanatory pluralism that casts light upon two strands of controversies running across evolutionary biology, viz., the place of organisms versus genes, and the role of adaptation. Formal Darwinism shows that natural selection can be viewed either physics-style, as a dynamics of alleles, or in the style of economics as an optimizing process. After presenting such pluralism, I argue first that whereas population genetics does not support optimization, optimality (...) can still be taken as a default hypothesis when modeling evolutionary processes; and second, that organisms have an explanatory role in evolutionary theory, since they are involved in the economic perspective of optimization. Finally, in order to ask whether the Modern Synthesis can indeed provide a theory of organisms, I apply a Kantian-inspired theoretical view of organisms (underlying much developmental modeling), according to which they are both designed entities and subjects of intrinsic circular processes involving the whole organism and its parts. I first show that the design aspect is accountable for in terms of the Modern Synthesis understood in the formal Darwinism framework. I then question whether the latter aspect of organisms can also be ultimately captured in the same framework, and to this purpose devise an empirical test relying on an assessment of the relative weight of genetic elements in developmental and functional gene regulatory networks. (shrink)

This paper questions the form and prospects of “extended theories” which have been simultaneously and independently advocated both in the philosophy of mind and in the philosophy of biology. It focuses on Extend Mind Theory (EMT) and Developmental Systems Theory (DST). It shows first that the two theories vindicate a parallel extension of received views, the former concerning extending cognition beyond the brain, the latter concerned with extending evolution and development beyond the genes. It also shows that both arguments rely (...) on the demonstration of causal parities, which have been undermined by the classical received view. Then I question whether the argument that there is an illegitimate inference from parities or coupling to constitution claims, which has been objected by Adams and Aizawa in The bounds of cognition, (2008) to EMT, also holds against DST. To this aim, I consider two defenses against DST that are parallel to two defenses against EMT, one about intrinsic content, the other about the difference between what’s in principle possible and what happens in practice. I conclude by claiming that the weaknesses and strengths of both theories are different regarding these two kinds of objections. (shrink)

The pervasive use of computer simulations in the sciences brings novel epistemological issues discussed in the philosophy of science literature since about a decade. Evolutionary biology strongly relies on such simulations, and in relation to it there exists a research program (Artificial Life) that mainly studies simulations themselves. This paper addresses the specificity of computer simulations in evolutionary biology, in the context (described in Sect. 1) of a set of questions about their scope as explanations, the nature of validation processes (...) and the relation between simulations and true experiments or mathematical models. After making distinctions, especially between a weak use where simulations test hypotheses about the world, and a strong use where they allow one to explore sets of evolutionary dynamics not necessarily extant in our world, I argue in Sect. 2 that (weak) simulations are likely to represent in virtue of the fact that they instantiate specific features of causal processes that may be isomorphic to features of some causal processes in the world, though the latter are always intertwined with a myriad of different processes and hence unlikely to be directly manipulated and studied. I therefore argue that these simulations are merely able to provide candidate explanations for real patterns. Section 3 ends up by placing strong and weak simulations in Levins’ triangle, that conceives of simulations as devices trying to fulfil one or two among three incompatible epistemic values (precision, realism, genericity). (shrink)

This paper surveys questions about the nature of the Modern Synthesis as a historical event : was it rather theoretical than institutional? When and where did it actually happen? Who was involved? It argues that all answers to these questions are interrelated, and that systematic sets of answers define specific perspectives on the Modern Synthesis that are all complementary.

ArgumentThis paper considers how certain ideas elaborated by the Montpellier vitalists influenced the rise of French alienism, and how those ideas framed the changing view of passions during the eighteenth century. Various kinds of evidence attest that the passions progressively became the focus of medical attention, rather than a theme specific to moralists and philosophers. Vitalism conceived of organisms as animal economies understandable through the transformations of the various modes of their sensibility. This allowed some physicians to define a kind (...) of anthropological program, which viewed human beings as a whole, with no distinction betweenle physiqueandle moral. The passions in this context became a specific alteration of the animal economy. Such an anthropological program was the framework within which Pinel understood the various classes of madness as disease – those troubles being general disturbances of the animal economy, which presupposed a knowledge of the latter, to be addressed and cured. In this view, and departing from the vitalist writers with regard to the specificity of mental illness as such, Pinel proposed another conception of the relations between passions and madness, and elaborated a general view of their status in etiology and therapeutics; those views were taken up and systematized by Esquirol, who finally defined a new kind of continuity between passion and madness, demonstrated by the idea that some kinds of madness that he called “monomania” had as a principle a “ruling passion” that the alienist, this novel medical specialist, had to unveil and address. (shrink)

Dans cet article, j’entends analyser la spécificité du cas clinique tel qu’il apparaît dans l’aliénisme de Pinel, et la manière dont la structure de son récit éclaire certains aspects de l’institution de la psychiatrie médicale. Le cas clinique est si naturellement vu comme un objet de plein droit médical, qu’il nous semble que le médecin parle de cas comme le botaniste parle de plantes. Rien de plus...

I consider recent uses of the notion of neutrality in evolutionary biology and ecology, questioning their relevance to the kind of explanation recently labeled ‘topological explanation’. Focusing on fitness landscapes and genotype-phenotype maps, I explore the explanatory uses of neutral subspaces, as modeled in two perspectives: hyperdimensional fitness landscapes and RNA sequence-structure maps. I argue that topological properties of such spaces account for features of evolutionary systems: respectively, capacity for adaptive evolution toward global optima and mutational robustness of genotypes. Thus (...) many models appealing to “neutral” manifolds provide topological alternatives to hypothetical mechanisms. (shrink)

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. (shrink)

This chapter surveys the philosophical problems raised by the two Darwinian claims of the existence of a Tree of a life, and the explanatory power of natural selection. It explores the specificity of explanations by natural selection, emphasizing the high context-dependency of any process of selection. Some consequences are drawn about the difficulty of those explanations to fit a nomological model of explanation, and the irreducibility of their historic-narrative dimension. The paper introduces to the debates about units of selection, stating (...) the compelling force of genic selectionnism but highlighting some critiques. Then it addresses the limits of selectionist explanations : the compared status of selection, drift and phylogenetic inertia are investigated, and the debates over adaptationism are presented, with the aim of defining the varieties of adaptationisms as research programs. In order to assess the scope of natural selection, the chapter addresses weak and strong challenges to the Synthetic theory of evolution, both from paleontology (punctuated equilibria, Gould’s contingency thesis) and evolutionary theory of development. We finally sketch some consequences of evolutionary theory concerning philosophical questions about human nature, on the basis of the hypothesis of the universality of selectionist explanations: this part deals mostly with epistemology and psychology. (shrink)

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. (shrink)