In Progress by Arnaud Pocheville
La théorie actuelle de l'évolution par sélection naturelle est basée sur un postulat : la tranmis... more 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 aménagements théoriques à faire pour accommoder ces nouveaux mécanismes ?
The idea that biological information is created by evolution, passed on in heredity, and expresse... more 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 biology have suggested that `biological information' is no more than a collection of loose metaphors. Others have offered their own theories of biological information, but most of these have been oddly unrelated to actual biological practice. Here we argue that the conception of information used by Francis Crick in his `sequence hypothesis' and `central dogma', a conception closely related to the older idea of `biological specificity', is adequate to state a substantial, general theory of biological information. There are two aspects to this account, corresponding to a fundamental duality in information theory between Shannon and Kolmogorov measures.
The interventionist account has gained momentum within philosophy of
causation. However, its abil... more 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, is an issue.
Here, we develop a solution to this issue. We leverage on differential cal-
culus to formalize interventions that are as precise as desired. Functions
and their time-derivatives can then be manipulated in a modular way at
any arbitrary degree of precision. This leads us to propose an interven-
tionist, causal interpretation of differential equations, similar to the causal
interpretation of structural equations. We emphasize that continuous time
dynamical systems can be approximated at an arbitrary degree of precision
by a causal graph approach. We conclude that causal graphs and continuous
time dynamical systems constitute two compatible, complementary causal
formalisms for interventionism.
Causal specificity has been recently proposed to be measurable by the mutual information between ... more Causal specificity has been recently proposed to be measurable by the mutual information between interventions on a causal variable and observations of an effect variable. We show that this amounts to considering interventions as variables to be included in a modified causal graph. We compare this account with a related measure of causal effect stemming from computer sciences, that of information flow, which does not rely on reifying interventions. We argue that causal specificity measures potential control, while information flow measures actual explanatory power. We show how causal interactions can lead to situations where causation stricto sensu does not entail that the causal variable enable either control or explanation. This final point has significant implications for the popular 'manipulationist' account of causation.
Philosophy by Arnaud Pocheville
A causal approach to biological information is outlined. There are two aspects to this approach: ... more A causal approach to biological information is outlined. There are two aspects to this approach: information as determining a choice between a set of 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 be used to analyse biological networks. This paper explores the prospects for a measure based on the second aspect, and suggests some applications for such a measure. These two aspects are not suggested to exhaust all the facets of biological information.
The British Journal for the Philosophy of Science, 2017
Recent work by Brian Skyrms offers a very general way to think about how information flows and ev... more 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 networks. In this paper, we argue there is a tension between how Skyrms talks of signalling networks and his formal measure of information. Although Skyrms refers to both how information flows through networks and that signals carry information, we show that his formal measure only captures the latter. We then suggest that to capture the notion of flow in signalling networks, we need to treat them as causal networks. This provides the formal tools to define a measure that does capture flow, and we do so by drawing on recent work defining causal specificity. Finally, we suggest that this new measure is crucial if we wish to explain how evolution creates information. For signals to play a role in explaining their own origins and stability, they cannot just carry information about acts: they must be difference-makers for acts.
The interventionist account of causation offers a criterion to distinguish causes
from non-cause... more 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 causation is formally equivalent to non-zero specificity,
and that there are natural, information-theoretic ways to explicate the distinction between potential and actual causal influence. We explicate the idea that
the description of causes should be proportional to that of their effects. Then
we draw a distinction between two ideas in the existing literature, the range of
invariance of a causal relationship and its stability. The range of invariance is
related to specificity and range of causal values. Stability concerns the effect of
additional variables on the relationship between some focal pair of cause and
effect variables. We show how to distinguish and measure the direct influence
of background variables on the effect variable, and their influence on the relationship between the focal cause and the effect variable. Finally, we discuss
the limitations of the information-theoretic approach, and offer prospects for
complementary approaches.
Philosophy of Science
Several authors have argued that causes differ in the degree to which they are ‘specific’ to thei... more 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 not well-defined without a probability distribution over the states of that variable. We demonstrate the tractability and interest of our proposed measure by measuring the specificity of coding DNA and other factors in a simple model of the production of mRNA.
We confront the core neoDarwinian tenet of blind variation, or random mutation, with classical a... more We confront the core neoDarwinian 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 fueling natural selection. Then, we examine a new hypothetical mechanism of genetic assimilation, relying on nonblind genetic variation. Yet, we show that such a model still relies on blind variation of some sort to explain adaptation. Last, we discuss the very meaning of the tenet of blind variation. We propose a formal characterization of the tenet and argue that it should not be understood solely as an empirical claim, but also as a core explanatory principle.
This chapter compares standard evolutionary theory to niche construction theory, in which an orga... more 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 proper to niche construction theory, and to suggest the existence of evolutionary phenomena that are not describable by standard evolutionary theory.
Handbook for Evolutionary Thinking - Springer, 2015
In this chapter, we first trace the history of the concept of ecological niche and see how its me... more 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, that would preexist the assembly of the ecosystem. The concept then slipped towards a sense in which the niche, no longer a pre-existing ecosystem structure, eventually became a variable that would in turn have to be explained by the competitive exclusion principle and the coevolution of species. The niche concept used at that time, while more operational from an empirical point of view than the previous one, suffered however from an ill-founded definition. A recent refoundation by Chase & Leibold enabled to overcome some of the definitional difficulties.
We then present how, in contemporary ecology, the niche concept is recruited to explain biodiversity and species coexistence patterns. We show how, in parallel, neutralist models, by succeedingly explaining some ecological patterns without resorting to explanations in terms of niche, have questioned the explanatory virtues of the niche concept.
In conclusion, it seems that the forunes and misfortunes of the niche concept can be seen as a reflection of the difficulties of ecology to give birth to a theory that would be both predictive and explanatory.
This thesis is an investigation on the niche concept and related theoretical frameworks: niche th... more This thesis is an investigation on the niche concept and related theoretical frameworks: niche theory and neutral theory in ecology, niche construction theory in evolutionary biology, and the stem cell niche in intraorganism ecology. The first chapter traces the history of the niche concept and compares niche theory to a competing theory, the neutral theory of biodiversity. The niche concept appears to be an explanans of species diversity and ecosystem structure. The second chapter compares standard evolutionary theory to the theory of niche construction, in which an organism can affect its environment and thus influence the selection to come. I show how to characterize this confrontation in terms of the time scales of the processes involved, which allows us to identify the range of validity truly unique to niche construction theory more explicitly than it has been in the past. The third chapter develops the research of the previous two chapters in the modeling of a gene therapy as a process of competition and ecological niche construction by cells. I present a family of models applied to different time scales of cellular dynamics , among which the careful modeler cannot choose without specific experimental results. I conclude on the conceptions of the relationship between an organism and its environment attached to the various facets of the concept.
Autour de la Simplexité, 2014
En parcourant un fil conducteur de l’évolution darwinienne, on trouve çà et là la formation du si... more 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 l’activité qu’ils rendent possible. Tout en prolongeant l’évolution des espèces, l’évolution de l’homme, jusqu’à son histoire, paraît aussi fournir, çà et là, des éléments de cette simplification qui choisit, transforme, organise l’action dans le monde, dont nous parlerons. On pourrait alors donner un sens historique à la notion de simplexité dans (Berthoz, 2009) :
– c’est le simple qui résulte d’une histoire complexe,
– du simple qui n’est jamais élémentaire (atomique, irréductible).
En physique, cette histoire peut être remplacée par une dynamique de modèles mathématiques qui aide à passer d’un système d’interactions locales, très complexe, à une situation globale, relativement plus simple, limite de la dynamique considérée. Ces dynamiques permettent de traiter les transitions critiques. Dans ce cas aussi, mais de façon fortement mathématisée, l’intégration globale de réseaux localement intelligibles, mais trop riches pour être saisis comme un tout, peut proposer un autre exemple de simplexité, plus technique, un exemple qui trouve son sens à la limite asymptotique. Les méthodes de renormalisation, auxquelles nous ferons informellement référence, en donnent un aperçu de grande puissance physico-mathématique. Nous considérons le passage de l’analyse mathématique de la criticité physique à l’analyse du biologique, en tant que situation critique étendue, une transition conceptuelle possible de la théorisation physique à celle de l’état vivant de la matière.
Les Mondes Darwiniens. L'évolution de l'évolution, 2011
Le concept de niche imprègne l’écologie. Comme le concept de fitness en biologie évolutive, c’est... more 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’écologie d’une espèce, ce qui peut signifier son rôle dans l’écosystème, son habitat, etc. Le concept, inspiré par la biologie darwinienne, a connu une fortune croissante au cours du XXe siècle, à la croisée des disciplines écologiques en développement, avant de tomber en disgrâce dans les années 1980 (Chase & Leibold 2003). Dans une première partie, nous retraçons l’histoire du concept et de ses sens, de ses diverses fortunes et infortunes. Dans une deuxième partie, nous examinons plus précisément les rapports que le concept entretient avec les explications de la coexistence et de la diversité. Dans une troisième partie, nous exposons la récente controverse entre la théorie basée sur le concept de niche et la théorie neutre, et discutons son bien-fondé. En conclusion, nous revenons sur les vertus et difficultés des différents sens du concept.
Ecole Normale Supérieure, Dec 15, 2010
This thesis is an investigation of the niche concept and of some related major theoretical framew... more 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 competing theory, the neutral theory. The niche concept appears to be an explanans of species diversity and ecosystem structure.
The second chapter compares the standard evolutionary theory to the theory of niche construction, in which an organism can affect its environment and thus influence the selection to come. We show how to characterize this confrontation in terms of time scales of processes involved, which allows us to identify the range of validity truly unique to the theory of niche construction more explicitly than it has been in the past.
The third chapter develops the research of the previous two chapters in the modeling of a gene therapy as a process of competition and ecological niche construction by cells. We present a family of models applied to different time scales of cellular dynamics, among which the careful modeler can not choose without specific experimental results.
We conclude on the conceptions of the relationship between an organism and its environment attached to the various facets of the concept.
Biology by Arnaud Pocheville
Science, 2018
Despite theoretical justification for the evolution of animal culture, empirical evidence for it ... more Despite theoretical justification for the evolution of animal culture, empirical evidence for it beyond mammals and birds remains scant, and we still know little about the process of cultural inheritance. In this study, we propose a mechanism-driven definition of animal culture and test it in the fruitfly. We found that fruitflies have five cognitive capacities that enable them to transmit mating preferences culturally across generations, potentially fostering persistent traditions (the main marker of culture) in mating preference. A transmission chain experiment validates a model of the emergence of local traditions, indicating that such social transmission may lead initially neutral traits to become adaptive, hence strongly selecting for copying and conformity. Although this situation was suggested decades ago, it previously had little empirical support.
Biological reviews, 2018
We review evidence suggesting that mechanisms of information transfers may exist between differen... more We review evidence suggesting that mechanisms of information transfers may exist between different channels of inheritance (genetic, epigenetic, behavioural, etc), which is still almost universally regarded as impossible. This has the potential to change our vision of evolution, especially of the role of genes in evolution.
Evolutionary Causation. Biological and philosophical reflections., 2018
The core, new idea of Darwinism is that natural selection over heritable blind variation provides... more The core, new idea of Darwinism is that natural selection over heritable blind variation provides a naturalistic explanation for adaptation. Challengers to current evolutionary theory target this core idea. In this contribution, I recast pro and con arguments. I argue that Darwinian explanations of adaptation require decoupling times and levels of development and selection, and that modern challengers call this decoupling into question. This provides a sharp, salient articulation between current evolutionary theory and challenging developments. I argue that decoupling should not be abandoned lightly, but speculate that non-decoupling (entanglement) may lead to a new vision of evolution.
Organisms. Journal of Biological Sciences, 2017
Two main theories aim at understanding carcinogenesis: the reductionist SMT locates cancer in can... more Two main theories aim at understanding carcinogenesis: the reductionist SMT locates cancer in cancer cells, while the organicist 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 incompatibilities, are actually compatible. Here we review their arguments. We show that these arguments are based on interpretation mistakes that become understandable once one grants that criticizing a paradigm from the point of view of another, in which words do not have the same signification, bears the risk of strong misunderstandings. These misunderstandings, in our experience, are common. We hope that this discussion will help clarifying the differences between TOFT and SMT.
Mate choice can strongly affect fitness in sexually reproducing organisms. A form of mate choice ... more 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. Here, we report the first evidence that Drosophila melanogaster females can acquire a sexual preference for one male characteristic after witnessing a single mate choice event (i.e. speed learning). We also found that mate copying was correlated with air pressure and air pressure changes, so that females copied far more when air pressure was high and increasing, i.e. in good and improving weather conditions. These results reveal a quick social observational learning and highlight the potential importance of meteorological conditions for mate copying, a trait potentially driving reproductive isolation.
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In Progress by Arnaud Pocheville
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, is an issue.
Here, we develop a solution to this issue. We leverage on differential cal-
culus to formalize interventions that are as precise as desired. Functions
and their time-derivatives can then be manipulated in a modular way at
any arbitrary degree of precision. This leads us to propose an interven-
tionist, causal interpretation of differential equations, similar to the causal
interpretation of structural equations. We emphasize that continuous time
dynamical systems can be approximated at an arbitrary degree of precision
by a causal graph approach. We conclude that causal graphs and continuous
time dynamical systems constitute two compatible, complementary causal
formalisms for interventionism.
Philosophy by Arnaud Pocheville
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 causation is formally equivalent to non-zero specificity,
and that there are natural, information-theoretic ways to explicate the distinction between potential and actual causal influence. We explicate the idea that
the description of causes should be proportional to that of their effects. Then
we draw a distinction between two ideas in the existing literature, the range of
invariance of a causal relationship and its stability. The range of invariance is
related to specificity and range of causal values. Stability concerns the effect of
additional variables on the relationship between some focal pair of cause and
effect variables. We show how to distinguish and measure the direct influence
of background variables on the effect variable, and their influence on the relationship between the focal cause and the effect variable. Finally, we discuss
the limitations of the information-theoretic approach, and offer prospects for
complementary approaches.
We then present how, in contemporary ecology, the niche concept is recruited to explain biodiversity and species coexistence patterns. We show how, in parallel, neutralist models, by succeedingly explaining some ecological patterns without resorting to explanations in terms of niche, have questioned the explanatory virtues of the niche concept.
In conclusion, it seems that the forunes and misfortunes of the niche concept can be seen as a reflection of the difficulties of ecology to give birth to a theory that would be both predictive and explanatory.
– c’est le simple qui résulte d’une histoire complexe,
– du simple qui n’est jamais élémentaire (atomique, irréductible).
En physique, cette histoire peut être remplacée par une dynamique de modèles mathématiques qui aide à passer d’un système d’interactions locales, très complexe, à une situation globale, relativement plus simple, limite de la dynamique considérée. Ces dynamiques permettent de traiter les transitions critiques. Dans ce cas aussi, mais de façon fortement mathématisée, l’intégration globale de réseaux localement intelligibles, mais trop riches pour être saisis comme un tout, peut proposer un autre exemple de simplexité, plus technique, un exemple qui trouve son sens à la limite asymptotique. Les méthodes de renormalisation, auxquelles nous ferons informellement référence, en donnent un aperçu de grande puissance physico-mathématique. Nous considérons le passage de l’analyse mathématique de la criticité physique à l’analyse du biologique, en tant que situation critique étendue, une transition conceptuelle possible de la théorisation physique à celle de l’état vivant de la matière.
The first chapter traces the history of the niche concept and compares the niche theory to a competing theory, the neutral theory. The niche concept appears to be an explanans of species diversity and ecosystem structure.
The second chapter compares the standard evolutionary theory to the theory of niche construction, in which an organism can affect its environment and thus influence the selection to come. We show how to characterize this confrontation in terms of time scales of processes involved, which allows us to identify the range of validity truly unique to the theory of niche construction more explicitly than it has been in the past.
The third chapter develops the research of the previous two chapters in the modeling of a gene therapy as a process of competition and ecological niche construction by cells. We present a family of models applied to different time scales of cellular dynamics, among which the careful modeler can not choose without specific experimental results.
We conclude on the conceptions of the relationship between an organism and its environment attached to the various facets of the concept.
Biology by Arnaud Pocheville
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, is an issue.
Here, we develop a solution to this issue. We leverage on differential cal-
culus to formalize interventions that are as precise as desired. Functions
and their time-derivatives can then be manipulated in a modular way at
any arbitrary degree of precision. This leads us to propose an interven-
tionist, causal interpretation of differential equations, similar to the causal
interpretation of structural equations. We emphasize that continuous time
dynamical systems can be approximated at an arbitrary degree of precision
by a causal graph approach. We conclude that causal graphs and continuous
time dynamical systems constitute two compatible, complementary causal
formalisms for interventionism.
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 causation is formally equivalent to non-zero specificity,
and that there are natural, information-theoretic ways to explicate the distinction between potential and actual causal influence. We explicate the idea that
the description of causes should be proportional to that of their effects. Then
we draw a distinction between two ideas in the existing literature, the range of
invariance of a causal relationship and its stability. The range of invariance is
related to specificity and range of causal values. Stability concerns the effect of
additional variables on the relationship between some focal pair of cause and
effect variables. We show how to distinguish and measure the direct influence
of background variables on the effect variable, and their influence on the relationship between the focal cause and the effect variable. Finally, we discuss
the limitations of the information-theoretic approach, and offer prospects for
complementary approaches.
We then present how, in contemporary ecology, the niche concept is recruited to explain biodiversity and species coexistence patterns. We show how, in parallel, neutralist models, by succeedingly explaining some ecological patterns without resorting to explanations in terms of niche, have questioned the explanatory virtues of the niche concept.
In conclusion, it seems that the forunes and misfortunes of the niche concept can be seen as a reflection of the difficulties of ecology to give birth to a theory that would be both predictive and explanatory.
– c’est le simple qui résulte d’une histoire complexe,
– du simple qui n’est jamais élémentaire (atomique, irréductible).
En physique, cette histoire peut être remplacée par une dynamique de modèles mathématiques qui aide à passer d’un système d’interactions locales, très complexe, à une situation globale, relativement plus simple, limite de la dynamique considérée. Ces dynamiques permettent de traiter les transitions critiques. Dans ce cas aussi, mais de façon fortement mathématisée, l’intégration globale de réseaux localement intelligibles, mais trop riches pour être saisis comme un tout, peut proposer un autre exemple de simplexité, plus technique, un exemple qui trouve son sens à la limite asymptotique. Les méthodes de renormalisation, auxquelles nous ferons informellement référence, en donnent un aperçu de grande puissance physico-mathématique. Nous considérons le passage de l’analyse mathématique de la criticité physique à l’analyse du biologique, en tant que situation critique étendue, une transition conceptuelle possible de la théorisation physique à celle de l’état vivant de la matière.
The first chapter traces the history of the niche concept and compares the niche theory to a competing theory, the neutral theory. The niche concept appears to be an explanans of species diversity and ecosystem structure.
The second chapter compares the standard evolutionary theory to the theory of niche construction, in which an organism can affect its environment and thus influence the selection to come. We show how to characterize this confrontation in terms of time scales of processes involved, which allows us to identify the range of validity truly unique to the theory of niche construction more explicitly than it has been in the past.
The third chapter develops the research of the previous two chapters in the modeling of a gene therapy as a process of competition and ecological niche construction by cells. We present a family of models applied to different time scales of cellular dynamics, among which the careful modeler can not choose without specific experimental results.
We conclude on the conceptions of the relationship between an organism and its environment attached to the various facets of the concept.
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 their effects, neither omitting too much relevant detail nor containing too much irrelevant detail'' (Woodward 2010, 297)
Stability: ``the stability of this relationship of counterfactual dependence has to do with whether it would continue to hold in a range of other background circumstances'' (Woodward 2010, 292)
Causal information theory applies Shannon information measures to the results of interventions on a causal graph. It allows us to clarify these three concepts and define measures of them.
Presented at AAP 2016, Melbourne; PSA 2016, Atlanta; MuST 10 2017, Sydney.