Arnaud Pocheville

• PhD
• Fellow at French National Centre for Scientific Research

A causal approach to biological information is outlined. There are two aspects to this approach: information as determining a choice between alternative objects, and information as determining the construction of a single object. The first aspect has been developed in earlier work to yield a quantitative measure of biological information that can b...

In this chapter, we first trace the history of the concept of ecological niche and see how its meanings varied with the search for a theory of ecology. The niche concept has its roots in the Darwinian view of ecosystems that are structured by struggle for survival and, originally, the niche was perceived as an invariant place within the ecosystem,...

Le concept de niche imprègne l’écologie. Comme le concept de fitness en biologie évolutive, c’est un concept central, au sens parfois peu explicité, apte à subir des glissements, jusqu’à finalement pouvoir être qualifié de tautologique (Griesemer 1992). Comme définition préliminaire, disons, sans préciser davantage, que la niche est ce qui décrit l...

This chapter compares standard evolutionary theory to niche construction theory, in which an organism can affect its environment and can thus influence the selective process to come. We show how to characterize this confrontation in terms of the time-scales of the processes involved, which allows us to identify the range of applicability truly prop...

La génétique et sa petite soeur mystérieuse, l’épigénétique, plongent leurs racines profondes dans l’histoire de la biologie. Aujourd’hui, l’épigénétique revêt une importance capitale, tant dans les sciences que dans les techniques du vivant depuis la biologie moléculaire, le diagnostic et le traitement des maladies, en passant par l’agriculture.Ép...

We suggest that biogeomorphology should challenge the traditional dichotomy between living and non‐living components of Earth surface systems. To achieve this, biogeomorphologists should gain a better understanding of eco‐evolutionary models and empirical findings developing at the interface between ecology and evolutionary biology. Eco‐evolutionar...

Although conformity as a major driver for human cultural evolution is a well‐accepted and intensely studied phenomenon, its importance for non‐human animal culture has been largely overlooked until recently. This limited for decades the possibility of studying the roots of human culture. Here, we provide a historical review of the study of conformi...

The Genotype-Phenotype (G-P) distinction was proposed in the context of Mendelian genetics, in the wake of late nineteenth century studies about heredity. In this paper, we provide a conceptual analysis that highlights that the G-P distinction was grounded on three pillars: observability, transmissibility, and causality. Originally, the genotype is...

It is essential to examine all plausible hypotheses regarding the origin of COVID-19, in order to understand how this pandemic started and prevent future pandemics. The unfortunate reality is that this process has been stalled. The European Commission could play a decisive role in addressing this critical issue of European and global concern with t...

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

The use of functional information in the form of species traits plays an important role in explaining biodiversity patterns and responses to environmental changes. Although relationships between species composition, their traits, and the environment have been extensively studied on a case-by-case basis, results are variable, and it remains unclear...

Thornquist and Crickmore claim that systematic experimental error may explain the results of Danchin and colleagues. Their claim rests on mistakes in their analyses, for which we provide corrections. We reassert that conformity in fruitflies predicts long-lasting mate-preference traditions.

A comprehensive treatment of the concept of causation in evolutionary biology that makes clear its central role in both historical and contemporary debates. Most scientific explanations are causal. This is certainly the case in evolutionary biology, which seeks to explain the diversity of life and the adaptive fit between organisms and their surrou...

Recent discoveries show that early in life effects often have long-lasting influences, sometimes even spanning several generations. Such intergenerational effects of early life events appear not easily reconcilable with strict genetic inheritance. However, an integrative evolutionary medicine of early life effects needs a sound view of inheritance...

Table S1. A description of published models of non‐genetic inheritance and genetic assimilation. Table S2. Description of the model parameters.

Trendsetting flies Though once believed to be confined to humans, culture has now been demonstrated in many different animal species, from whales to parrots. Most such animals have high levels of cognition, but the basics of transmission and copying could easily occur in less cognitively advanced species. Danchin et al. show that mating culture can...

L’épigénétique, à savoir l’ensemble des modifications héritables étroitement liées au génome mais sans être basées sur des modifications de séquences de l’ADN, a émergé ces dernières années comme une discipline incontournable pour la compréhension des processus biologiques. Les avancées considérables des techniques de séquençage permettent aujourd’...

After decades of debate about the existence of non‐genetic inheritance, the focus is now slowly shifting towards dissecting its underlying mechanisms. Here, we propose a new mechanism that, by integrating non‐genetic and genetic inheritance, may help build the long‐sought inclusive vision of evolution. After briefly reviewing the wealth of evidence...

La théorie actuelle de l'évolution par sélection naturelle est basée sur un postulat : la tranmission de caractères acquis est impossible. Il est maintenant clair que l'hérédité épigénétique invite à réviser ce postulat. Ce constat pose une double question: quelles sont les modalités précises de l'hérédité des caractères acquis, et quels sont les a...

Two main theories aim at understanding carcinogenesis: the reductionist SMT locates cancer in cancer cells, while the organi-cist TOFT locates cancer at the tissue level. For TOFT, the 'cancer cell' is a phlogiston, SMT is an old paradigm which ought to be replaced. Recently two critics have argued that TOFT and SMT, despite their apparent strong i...

The idea that biological information is created by evolution, passed on in heredity, and expressed during development is an attractive gloss on what has been revealed by the last century of advances in biology. But on closer examination it is hard to see what scientific substance corresponds to this vision. Several biologists and philosophers of bi...

The interventionist account has gained momentum within philosophy of causation. However, its ability to account for explanations derived from dynamical systems has been put into question. In particular, it has been argued that the fact that one cannot intervene on a function and its time-derivative in a modular way, i.e. without affecting the other...

The lack of a rigorous account of biological information as a proximal causal factor in biological systems is a striking gap in the scientific worldview. In this talk, we will present a way to give substance to the idea of biological information, based on the original account by Francis Crick in 1958. Presented at AAP 2016, Melbourne; PSA 2016, Atl...

A brief introduction to information theory and causal information theory.

Recent work by Brian Skyrms offers a very general way to think about how information flows and evolves in biological networks – from the way monkeys in a troop communicate, to the way cells in a body coordinate their actions. A central feature of his account is a way to formally measure the quantity of information contained in the signals in these...

Three qualitative notions play an important role in current debates about causal explanation: Specificity: ``the notion we are trying to capture is that the state of C exerts a fine-grained kind of control over which state of E is realized’’ (Woodward 2010, 305) Proportionality: ``proportional in the sense that they should be just `enough’ for thei...

Mate choice can strongly affect fitness in sexually reproducing organisms. A form of mate choice is mate copying, in which individuals use information about potential mates by copying the mate choice of other individuals. While many studies have documented mate copying, little is known about the effect of environmental conditions on this behaviour....

Darwin introduced the concept that random variation generates new living forms. In this paper, we elaborate on Darwin's notion of random variation to propose that biological variation should be given the status of a fundamental theoretical principle in biology. We state that biological objects such as organisms are specific objects. Specific object...

Organisms, be they uni- or multi-cellular, are agents capable of creating their own norms; they are continuously harmonizing their ability to create novelty and stability, that is, they combine plasticity with robustness. Here we articulate the three principles for a theory of organisms proposed in this issue, namely: the default state of prolifera...

We confront the neo-Darwinian core tenet of blind variation, or random mutation, with classical and recent models of genetic assimilation. We first argue that all the mechanisms proposed so far rely on blind genetic variation fuelling natural selection. Then, we examine a new hypothetical mechanism of genetic assimilation, relying on non-blind gene...

Several authors have argued that causes differ in the degree to which they are ‘specific’ to their effects. Woodward has used this idea to enrich his influential interventionist theory of causal explanation. Here we propose a way to measure causal specificity using tools from information theory. We show that the specificity of a causal variable is...

Several authors have argued that causes differ in the degree to which they are ‘specific’ to their effects. Woodward has used this idea to enrich his influential interventionist theory of causal explanation. Here we propose a way to measure causal specificity using tools from information theory. We show that the specificity of a causal variable is...

Background: Information talk is pervasive in biology, yet it remains highly controversial among theoretical biologists and philosophers of biology. Here, we propose to ground information talk in measures of causal influence in biological networks. Roughly, how informative a cause will be with respect to an effect in a given system will depend on th...

The interventionist account of causation offers a criterion to distinguish causes from non-causes. It also aims at defining various desirable properties of causal relationships, such as specificity, proportionality and stability. Here we apply an information-theoretic approach to these properties. We show that the interventionist criterion of causa...

Cet article s'intéresse à la manière dont sont considérées les interactions entre les organismes et leur environnement dans deux champs scientifiques contemporains : l'hypothèse Gaïa et la théorie de la construction de niche, car ce sont eux qui ont ces dernières décennies le plus oeuvré à proposer des approches théoriques nouvelles mettant en avan...

In Danchin & Pocheville (2014), we urged that physiology and evolution be better integrated, as it is more and more apparent that they represent two facets of a single biological process. The first reason for this integration is somehow classical but still essential. Physiology is central in determining the selective value of organisms, and thus th...

In this article, we apply the perspective of intraorganismal ecology by investigating a family of ecological models suitable to describe a gene therapy for a particular metabolic disorder, the adenosine deaminase deficiency. The gene therapy is modeled as the prospective ecological invasion of an organ (here, bone marrow) by genetically modified st...

In this article, we discuss the perspective of intraorganismal ecology by investigating a family of ecological models. We consider two types of models. First-order models describe the population dynamics as being directly affected by ecological factors (here understood as nutrients, space, etc). They might be thought of as analogous to Aristotelian...

Physiology and evolutionary biology have developed as two separated disciplines, a separation that mirrored the hypothesis that the physiological and evolutionary processes could be decoupled. We argue that non-genetic inheritance shatters the frontier between physiology and evolution, and leads to the coupling of physiological and evolutionary pro...

En parcourant un fil conducteur de l’évolution darwinienne, on trouve çà et là la formation du simple, comme résultat de la complexité des trajectoires évolutives : par exemple, la variété, la richesse, la … complexité des bauplan de la faune de Burgess et Ediacara (Gould, 1989) s’est transformée en la « simplicité » des bauplan qui suivront et de...

Cellular behavior is sustained by genetic programs that are progressively disrupted in pathological conditions-notably, cancer. High-throughput gene expression profiling has been used to infer statistical models describing these cellular programs, and development is now needed to guide orientated modulation of these systems. Here we develop a regre...

Biological thinking is structured by the notion of level of organization. We will show that this notion acquires a precise meaning in critical phenomena: they disrupt, by the appearance of infinite quantities, the mathematical (possibly equational) determination at a given level, when moving at an “higher” one. As a result, their analysis cannot be...

This thesis is an investigation of the niche concept and of some related major theoretical frameworks: the niche theory and neutral theory in ecology, the niche construction theory in evolutionary biology, and stem cell niche in intra-organism ecology. The first chapter traces the history of the niche concept and compares the niche theory to a comp...

This thesis is an investigation of the niche concept and of some related major theoretical frameworks: the niche theory and neutral theory in ecology, the niche construction theory in evolutionary biology, and stem cell niche in intra-organism ecology. The first chapter traces the history of the niche concept and compares the niche theory to a comp...

In eusocial Hymenoptera, the ability of workers to reproduce is a cause of conflict, both between the queen and workers and among workers. Reproductive decisions by workers depend on parameters such as colony size (which reduces the cost of selfish reproduction for the colony) or queen fertility. Indeed, queen signals inhibit reproduction from work...