Papers by philippe huneman
Biology, 2021
Many separate fields and practices nowadays consider microbes as part of their legitimate focus. ... more Many separate fields and practices nowadays consider microbes as part of their legitimate focus. Therefore, microbiome studies may act as unexpected unifying forces across very different disciplines. Here, we summarize how microbiomes appear as novel major biological players, offer new artistic frontiers, new uses from medicine to laws, and inspire novel ontologies. We identify several convergent emerging themes across ecosystem studies, microbial and evolutionary ecology, arts, medicine, forensic analyses, law and philosophy of science, as well as some outstanding issues raised by microbiome studies across these disciplines and practices. An ‘epistemic revolution induced by microbiome studies’ seems to be ongoing, characterized by four features: (i) an ecologization of pre-existing concepts within disciplines, (ii) a growing interest in systemic analyses of the investigated or represented phenomena and a greater focus on interactions as their root causes, (iii) the intent to use op...
BMC biology, Jan 29, 2018
The classic Darwinian theory and the Synthetic evolutionary theory and their linear models, while... more The classic Darwinian theory and the Synthetic evolutionary theory and their linear models, while invaluable to study the origins and evolution of species, are not primarily designed to model the evolution of organisations, typically that of ecosystems, nor that of processes. How could evolutionary theory better explain the evolution of biological complexity and diversity? Inclusive network-based analyses of dynamic systems could retrace interactions between (related or unrelated) components. This theoretical shift from a Tree of Life to a Dynamic Interaction Network of Life, which is supported by diverse molecular, cellular, microbiological, organismal, ecological and evolutionary studies, would further unify evolutionary biology.
Oxford Scholarship Online, 2017
A common and enduring early modern intuition is that materialists reduce organisms in general and... more 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.
The Quarterly Review of Biology, 2016
The neutral theory of biodiversity assumes that coexisting organisms are equally able to survive,... more The neutral theory of biodiversity assumes that coexisting organisms are equally able to survive, reproduce and disperse (ecological equivalence), 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.
Chapitre 7. Biologie évolutionniste, vie artificielle et algorithmes : sur l’épistémologie des modèles computationnels
Les modèles, possibilités et limites, 2014
From groups to individuals. New issues in biological individuality
Our intuitive assumption that only organisms are the real individuals in the natural world is at ... more 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.
Erkenntnis, 2015
Your article is protected by copyright and all rights are held exclusively by Springer Science +B... more Your article is protected by copyright and all rights are held exclusively by Springer Science +Business Media Dordrecht. This e-offprint is for personal use only and shall not be selfarchived in electronic repositories. If you wish to self-archive your article, please use the accepted manuscript version for posting on your own website. You may further deposit the accepted manuscript version in any repository, provided it is only made publicly available 12 months after official publication or later and provided acknowledgement is given to the original source of publication and a link is inserted to the published article on Springer's website. The link must be accompanied by the following text: "The final publication is available at link.springer.com".
This paper discusses the claim that alternative views to evolutionary biology based on the novel ... more This paper discusses the claim that alternative views to evolutionary biology based on the novel advances in understanding molecular and developmental bases of variation and inheritance should be captured as a shift from 'statistical' to 'mechanistic' explanatory schemes (Müller and Pi-gliucci 2011). Granted, statistical approaches characterized population genetics and hence the Modern Synthesis, but by examining epistemic features of postgenomic science I will claim that this is not a proper characterization of the current epistemic shift, if such a shift has to occur. I will first characterize the dual nature of gene in development and inheritance, accounting for it in terms of difference between two sorts of causal ascriptions. After the shift that happened regarding the concepts of genes, variation and inheritance in the postgenomic science, I will first argue that, rather than with mechanis-tic explanations, they provide us with novel topological explanatory frameworks to approach genomic networks of many sorts. Then, considering successively the ENCODE program and the GWAS studies of genetic bases of diseases I will show that the role of genes in inheritance is now addressed through novel and nucleotide-focused statistical tools, that are actually incommensurable to the statistics used by gene-focused Modern Synthesis models, but are even less likely to translate directly into mechanis-tic modeling of causal roles. The paper claims that instead of addressing epistemic changes on the basis of the classical statistics vs. mechanisms difference one should rather acknowledge the diversification of explanatory modes proper to postgenomic science, and to its consequences for evolutionary biology.
Biodiversity is arguably a major concept in ecology. Some of the key questions of the discipline ... more Biodiversity is arguably a major concept in ecology. Some of the key questions of the discipline are: why are the species distributed the way they are, in a given area, or across areas? or: why are there so many animals (as 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 nowadays are 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 1959) through competitive exclusion explain species distributions, contrast with neutral theories, where an assumption of fitness equivalence, species abundance distributions are explained by stochastic models, inspired by Hubbell (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 longlasting stability-diversity debate, where the key question was: how does diversity beget stability? Thus explanatory reversibility of the biodiversity concept in ecology may prevent biodiversity to be a unifying object for ecology.
In this chapter, I’ll 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’ll 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’ll 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.
Philosophy of Science, 2018
This paper considers recent uses of the notion of neutrality in evolutionary biology and ecology,... more This paper considers recent uses of the notion of neutrality in evolutionary biology and ecology, questioning their relevance to the kind of explanation recently labeled 'topological explanation'. I focus on fitness landscapes and genotype-phenotype maps, and explore in each case the definition and explanatory use of neutral subspaces, as they are modeled in two recent modeling perspectives: the hyperdimensional fitness landscapes (Gavrilets 2005) and the RNA sequence-structure maps (Stadler et al. 2001). I will argue that in each case topological properties of such spaces account for specific features of evolutionary systems: capacity for adaptive evolution towards global fitness optima on one hand, mutational robustness and evolvability of genotypes on the other hand. Thus many models appealing to " neutral " manifolds provide alternatives to hypothetical mechanisms, and instantiate topological explanations. I conclude by showing the connection between this type of explanation and some instances of neutrality in evolutionary models.
History and Philosophy of Life Sciences, 2017
Natural selection is often envisaged as the ultimate cause of the apparent rationality exhibited ... more 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 (defined by the main axioms of rational choice theory) and biological rationality (defined by natural selection). 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 irrational-ities. 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 (prima facie) 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.
Monist, 2017
Contemporary biology is affected by a controversy between the adaptationist viewpoint , central t... more Contemporary biology is affected by a controversy between the adaptationist viewpoint , central to the neo-Darwinian Modern Synthesis (MS), and the developmentalist viewpoint, central in Evo-Devo. The possibility of a synthesis between those viewpoints , as granting unity between the laws of form and the laws of function in biology, is therefore currently hotly debated. Kant's concept of organism is often seen as the philosophical precursor of developmentalism. Yet this view is incomplete, and Kant's unique regulative notion of purposiveness relies on two criteria in order to capture organisms as natural purposes: a design criterion and an epigenesis criterion. While the former is fulfilled within MS, the latter is satisfied by organisms from the developmen-talist viewpoint. Under some conditions, Kant's notion of organism can thus allow for a synthesis of developmentalism and adaptationism.
Oikos, 2017
In the current context of global change and a biodiversity crisis, there are increasing demands f... more In the current context of global change and a biodiversity crisis, there are increasing demands for greater predictive power in ecology, in both the scientific literature and at the science–policy interface. The implicit assumption is that this will increase knowledge and, in turn lead to better decision-making. However, the justification for this assumption remains uncertain, not least because the definition of ‘prediction’ is unclear. We propose that two types of prediction should be distinguished: corroboratory- prediction is linked to the validation of theories; and anticipatory-prediction is linked to the description of possible futures. We then discuss four families of obstacles to prediction, linked to the specific features of ecosystems: 1) they are historical entities, 2) they are complex, 3) their dynamics are stochastic, and 4) they are influenced by socio-economic drivers. A naïve understanding of ecological science suggests that the two types of predictions are simply two phases in a sequence in which scientists first improve their knowledge of ecological systems via corroboratory-predictions, and then apply this knowledge in order to forecast future states of ecosystems via anticipatory-predictions in order to help policy makers taking decisions. This sequence is however not straightforward, partly because corroboration and anticipation are not affected by the obstacles to prediction in the same way. We thus invite to reconsider the role of ecological prediction as a tool in a deliberative model of decision-making rather than as external scientific information aimed at enlightening the political process. Doing so would be beneficial for both the policy- relevance of anticipatory-prediction and the theoretical-relevance of corroboratory-prediction.
Studies in History and Philosophy of Science A, 2017
What realization is has been convincingly presented in relation to the way we determine what coun... more What realization is has been convincingly presented in relation to the way we determine what counts as the realizers of realized properties. The way we explain a fact of realization includes a reference to what realization should be, therefore it informs in turn our understanding of the nature of realization. Conceptions of explanation are therefore included in the views of realization as a metaphysical property. Recently, several major views of realization such as Polger and Shapiro's or Gillett and Aizawa's, however competing, have relied on the neo-mechanicist theory of explanations (e.g. Darden and Caver 2013), currently popular among philosophers of science. However, it has also been increasingly argued that some explanations are not mechanistic (e.g. Batterman 2009). Using an account given in Huneman (2017), I argue that within those explanations the fact that some mathematical properties are instantiated is explanatory, and that this defines a specific explanatory type called " structural explanation " , whose subtypes could be: optimali-ty explanations (usually found in economics), topological explanations, etc. This paper thereby argues that all subtypes of structural explanation define several kinds of realizability, which are not equivalent to the usual notion of realization tied to mechanistic explanations, onto which many of the philosophical investigations are focused.
Argumenta, Jul 2017
This paper proposes a critical assessment of the concept of “conspiracy theory” as a coherent obj...
Uploads
Papers by philippe huneman
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 longlasting stability-diversity debate, where the key question was: how does diversity beget stability? Thus explanatory reversibility of the biodiversity concept in ecology may prevent biodiversity to be a unifying object for ecology.
In this chapter, I’ll 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’ll 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’ll 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.