During the course of evolution, variations of a protein sequence is an ongoing phenomenon however limited by the need to maintain its structural and functional integrity. Deciphering the evolutionary path of a protein is thus of fundamental interest. With the development of new methods to visualize high dimension spaces and the improvement of phylogenetic analysis tools, it is possible to study the evolutionary trajectories of proteins in the sequence space. Using the data-driven high-dimensional scaling method, we show that it is (...) possible to predict and represent potential evolutionary trajectories by representing phylogenetic trees into a 3D projection of the sequence space. With the case of the aminodeoxychorismate synthase, an enzyme involved in folate synthesis, we show that this representation raises interesting questions about the complexity of the evolution of a given biological function, in particular concerning its capacity to explore the sequence space. (shrink)

Misunderstanding of the dynamical behavior of the ventilatory system, especially under assisted ventilation, may explain the problems encountered in ventilatory support monitoring. Proportional assist ventilation (PAV) that theoretically gives a breath by breath assistance presents instability with high levels of assistance. We have constructed a mathematical model of interactions between three objects: the central respiratory pattern generator modelled by a modified Van der Pol oscillator, the mechanical respiratory system which is the passive part of the system and a controlled ventilator (...) that follows its own law. The dynamical study of our model shows the existence of two crucial behaviors, i.e. oscillations and damping, depending on only two parameters, namely the time constant of the mechanical respiratory system and a cumulative interaction index. The same result is observed in simulations of spontaneous breathing as well as of PAV. In this last case, increasing assistance leads first to an increase of the tidal volume (VT), a further increase in assistance inducing a decrease in VT, ending in damping of the whole system to an attractive fixed point. We conclude that instabilities observed in PAV may be explained by the different possible dynamical behaviors of the system rather than changes in mechanical characteristics of the respiratory system. (shrink)

Fluorescence microscopy has provided a route to qualitatively analyze features of nuclear structures and chromatin domains with increasing resolution. However, it is becoming increasingly important to develop tools for quantitative analysis. Here, we present an automated method to quantitatively determine the enrichment of several endogenous factors, immunostained in pericentric heterochromatin domains in mouse cells. We show that this method permits an unbiased characterization of changes in the enrichment of several factors with statistical significance from a large number of nuclei. Furthermore, (...) the nuclei can be sorted according to the enrichment value of these factors. This method should prove useful to monitor events related to changes in the amount, rather than the presence or absence, of any factor. By adapting a few parameters, it could be extended to other nuclear structures and the benefit of using available software will permit its use in many biological labs. (shrink)

An extensive analysis of all social psychology textbooks included a history chapter published in French between 1947 and 2001, provides a rich corpus for the study of the history of social psychology. Drawing upon this corpus, in this article we study the historical spaces of social psychology in order to show how the discipline was located in geographical, urban, institutional and collective spaces. We argue that spaces are essentially related to some solitary and consensual scholars' names without any informative reference (...) to their institutions, nor to any trace of collective work. Moreover, we try to highlight several styles, ways and norms of collective writing the history of this discipline. (shrink)

Passive Brain-Computer interfaces (pBCIs) are a human-computer communication tool where the computer can detect from neurophysiological signals the current mental or emotional state of the user. The system can then adjust itself to guide the user towards a desired state. One challenge facing developers of pBCIs is that the system's parameters are generally set at the onset of the interaction and remain stable throughout, not adapting to potential changes over time such as fatigue. The goal of this paper is to (...) investigate the improvement of pBCIs with settings adjusted according to the information provided by a second neurophysiological signal. With the use of a second signal, making the system a hybrid pBCI, those parameters can be continuously adjusted with dynamic thresholding to respond to variations such as fatigue or learning. In this experiment, we hypothesize that the adaptive system with dynamic thresholding will improve perceived game experience and objective game performance compared to two other conditions: an adaptive system with single primary signal biocybernetic loop and a control non-adaptive game. A within-subject experiment was conducted with 16 participants using three versions of the game Tetris. Each participant plays 15 minutes of Tetris under three experimental conditions. The control condition is the traditional game of Tetris with a progressive increase in speed. The second condition is a cognitive load only biocybernetic loop with the parameters presented in Ewing et al. (2016). The third condition is our proposed biocybernetic loop using dynamic threshold selection. Electroencephalography was used as the primary signal and automatic facial expression analysis as the secondary signal. Our results show that, contrary to our expectations, the adaptive systems did not improve the participants' experience as participants had more negative affect from the BCI conditions than in the control condition. We endeavored to develop a system that improved upon the authentic version of the Tetris game, however, our proposed adaptive system neither improved players’ perceived experience, nor their objective performance. Nevertheless, this experience can inform developers of hybrid passive BCIs on a novel way to employ various neurophysiological features simultaneously. (shrink)

Texting while walking is a dangerous behavior that can lead to injury and even death. While several studies have examined the relationship between smartphone use and stress, to our knowledge no studies have yet investigated the relationship between stress and TWW. The objective of the present study was to investigate this relationship by examining the effects of stress on TWW, the effects of TWW on subsequent stress, and the effect of stress on multitasking performance. A total of 80 participants completed (...) two sequential tasks in a laboratory while they walked on a treadmill and responded to a biological motion stimulus imitating the movement of another pedestrian. In the unrestricted task, participants were given the choice to use their personal phones. In the controlled task, they carried a text conversation with a research assistant while they walked and responded to the stimulus. Stress was measured via questionnaire and saliva collection for measure of cortisol before and after each task. Results show that greater psychological stress and cortisol variations were associated with a greater number of phone uses during the unrestricted task. Greater phone use during the unrestricted task was associated with lower subsequent psychological stress in women and total time of phone use was correlated with subsequent cortisol levels. Stress measured before the controlled task had no effect on multitasking performance, but participants with moderate performance were those with the highest cortisol levels. Our results suggest that stress could be a precursor to TWW and that it could affect a pedestrian’s ability to stay safe when using their smartphone. (shrink)

Descartes’s very brief explanations of human responsibility for sin and divine innocence of sin include references to the idea that evil is a privation rather than a real thing. It is not obvious, though, that privation fits naturally in Descartes’s reductionistic metaphysics, nor is it clear precisely what role his privation doctrine plays in his theodicy. These issues are made clear by contrasting Descartes’s use of privations with that of Suarez, particularly in light of reoccurring objections to privation theory. These (...) objections have no weight against Suarez’s use of privations, but Descartes’s mentions of privation are so few that it is not clear how his account avoids their consequences. Descartes’s brevity seems to have motivated some of his followers to develop creative accounts of the way in which privation fits in a Cartesian system. Pierre-Sylvain Régis accomplishes this task by reintroducing material causation. Régis holds that moral evil has no efficient cause since an efficient cause can only produce something real. Because he holds that moral evil can have a material cause, he is able to affirm that the soul is morally responsible for sin. In Régis’s case, accommodating this theological issue meant reincorporating Aristotelian resources into his Cartesian system. (shrink)

Le traité De radiis, ou Theorica artium magicarum, est quasi unanimement tenu pour une traduction latine faite au xii e siècle d’un traité arabe perdu d’al-Kindi. En se fondant sur le fait qu’il dépend de la tradition grammaticale relevant de Donat et Priscien, on démontre ici qu’en réalité il n’a pas été traduit de l’arabe mais qu’il a été rédigé par un auteur latin, très probablement dans les décennies 1250/1260.

Dans des écrits datant des années 1277-79, le théologien franciscain Pierre de Jean Olivi emploie à cinq reprise le mot averroista, pour critiquer, non pas tant la doctrine de l'unicité de l'intellect possible que ses implications anthropologiques ou angélologiques. Cette critique bien informée, convergente avec d'autres attaques franciscaines, notamment les dénonciations de Roger Bacon, démontre la réalité et l'ampleur d'une entreprise philosophique menée par des maîtres ès arts, s'inspirant d'Averroès, dans les années 1260-70 ; elle indique aussi la diversité (...) de leurs points de vue. Dès son apparition, il n'y a donc pas un, mais plusieurs 'averroïsmes' latin. (shrink)

Le Liber ostensor quod adesse festinant tempora, rédigé en 1356 dans la prison du Soudan à Avignon, est le plus important des écrits conservés du visionnaire et prophète et franciscain Jean de Roquetaillade. Son édition, par une équipe dirigée par A. Vauchez, offre des matériaux très riches pour l'histoire religieuse et culturelle du XIVe siècle. On note toutefois quelques lacunes dans la bibliographie et l'identification des sources, et notamment dans la notice consacrée aux emprunts faits à Pierre de Jean (...) Olivi. Au-delà des citations explicites, on peut mettre en évidence une dépendance bien plus grande, que masque pour partie une stratégie d'écriture carcérale. (shrink)

Autour de 1100, pour les jeunes femmes de l’aristocratie éduquées dans des monastères, l’écriture de lettres d’amour fictives à leur maître de rhétorique constituait un apprentissage aussi bien littéraire qu’émotionnel. Comme le rappelle Barbara Newman, les Epistolae duorum amantium, correspondance échangée par Héloïse et Pierre Abélard durant leur liaison, doivent se comprendre dans cette lumière. Leur singularité tient largement au fait qu’Héloïse a choisi de donner corps à une figure poétique, en s’identifiant aux héroïnes tragiques d’Ovide.

Au mois de mai 1940 deux chefs de guerre s’affrontent. L’un a été le colonel du premier régiment où l’autre est arrivé en sortant de Saint Cyr et lui a, par la suite, servi de mentor. Mais des conceptions de ce qu’est la France, les mythes fondateurs de la nation auxquels ils se référent, de même que leur position les sépare. L’un est maréchal, le seul général en chef survivant de la guerre précédente alors que l’autre vient d’être nommé (...) général. Cependant, ce dernier sera rejoint par d’ardents jeunes gens, entrés récemment dans une carrière ou ne l’ayant pas encore abordée, et saura coordonner les mouvements dispersés de résistance. Aidé par les circonstances, qu’il a su exploiter, il vaincra.Les temporalités permettant de mettre en perspective ce récit sont diverses : elles vont du temps figé de la métaphore et du mythe, en passant par la chronologie linéaire. Mais la temporalité qui se révèle cruciale est celle du moment opportun et de la capacité à le saisir, qui, dans un premier temps est utilisée par les deux protagonistes, pour les différencier définitivement par la suite. (shrink)

Peu d’ouvrages publiés par des universitaires sur un sujet apparemment universitaire auront fait autant de bruit que celui de Sylvain Gouguenheim, intitulé Aristote au Mont Saint-Michel. Les racines grecques de l’Europe. Si le point de départ de cet intérêt extraordinaire a peut-être été la recension parue dans le journal Le Monde,..

One of the most mature achievements of the Cartesian philosophy is the aim to diffuse Descartes’ thought among a wider audience by presenting his philosophy in an encyclopedic way. A relevant contribution in this field is Pierre Sylvain Régis’s Système. Régis’s contribution consists both in reconciling the new scientific discoveries with les principes de Monsieur Descartes by combining them into a scholarly manual whose aim is to stimulate the ars inveniendi and in recognizing the relevance of Arnauld’s and (...) Nicole’s L’art de penser as manual of Cartesian logic. In an article published on the «Annali della Scuola Normale Superiore di Pisa», pp. 517-55: L’«Art de penser» nella logica del «Système» di Régis) I analysed Régis’s logic in order to point out that, even if L’art de penser represents its only source, La logique of the Système has not to be considered as a mere compendium of the Port-Royal Logique, but as a revision of the latter according to a specific philosophical system, characterized by the empirical interpretation of Descartes’s philosophy. In this paper I provide a synopsis of the comparison between the logic of the Système and the Logique of Port-Royal, in order to resume in a schematic way the results of my research. (shrink)

The Système de philosophie by Pierre Sylvain Régis can be considered as the achievement both of the scientific liveliness of the Académie des Sciences in the 17th century and of its fruitful relationship with the Royal Society. Since it aims to shape the new conception of the universe in terms of a system, the Système represents one of the most mature achievements of Cartesian philosophy and it is characterized by an empirical interpretation of Descartes’ thought. The Système therefore (...) reflects two important phenomena occurring in the Europe of the 17th century: the scientific revolution and the proliferation of Academies. In fact, this ambitious work could be undertaken with the support of the Académie des Sciences and the Journal des Sçavants. My paper will analyse the French context by focusing to outline the role which the Académie de France had both in France, as the medium of dissemination of the new philosophy despite censorship, and abroad, in particular through the relationship with the Royal Society in England. I aim to analyse the role of the Journal des Sçavants as a means to share ideas other than by correspondence and as a trait d’union between “rationalist France” and “empiricist England”. I intend to question whether it is possible to establish a connection between the empirical interpretation of French Cartesianism, the consolidation of the Académie de France and the employment of new means of academic communication. The paper will show that the second half of 17th century France represents a remarkable exception to the conventional picture, which states that in 17th century Europe, following the success of a mechanistic interpretation of reality, two philosophical school clashed: rationalism, predominating on the continent, and empiricism, in England. (shrink)

This work takes into account three Cartesian manuals diffused in 17th century France ; Jacques Rohault, Traité de physique ; Pierre-Sylvain Régis, Cours entier de philosophie, ou système general selon les principes de M. Descartes contenant la logique, la metaphysique, la physique et la morale ) in order to question if the development of an empirical attitude in the scientific research influenced their approaches to the study of motion. The article intends to deepen the role that these authors (...) give to God in the physical structure of the universe with the purpose of investigating whether their analysis of motion is untainted by the metaphysical component or on what terms it remains linked to it. (shrink)

Pierre-Sylvain Regis, once a well-known defender of Cartesianism, offers an unusually rich and innovative refutation of Spinoza. While many of his early modern contemporaries raised narrower objections to particular claims in Spinoza's _Ethics_, Regis develops a broader anti-Spinozistic position, one that threatens the very core of Spinoza's metaphysical ambitions and offers a philosophically robust alternative. However, as with any far-reaching philosophical commitment, Regis's gambit comes with substantive costs of its own, including creating instabilities within the core of his (...) own philosophical system. Far from diminishing the significance of Regis's anti-Spinozism, this critical appraisal helps us better appreciate both the conceptual pull of Spinozism within early modern metaphysics and one sweeping, albeit costly way of escaping its orbit. (shrink)

In lieu of an abstract, here is a brief excerpt of the content:The Breakdown of C i M phy " artes an eta sacs RICHARD A. WATSON WITHIN CARTESIANISMthere arose many problems deriving from conflicts between Cartesian principles. Inadequate attempts to solve these problems were crucial reasons for the breakdown of Cartesian metaphysics in the late seventeenth and early eighteenth centuries. The major difficulties derived from the acceptance of a dualism of substances seated in a system which included epistemological and (...) causal likeness principles plus an ontological framework in which the categories of substance and modification were exhaustive. The major solutions involved either denying the likeness principles or altering the ontological framework. The first led to unintelligibility ; the second, culminating in Hume, opened the way to non-Cartesian metaphysics. The first section of this study contains a characterization of late seventeenth -century Cartesian metaphysics. The second is an exposition of Foucher 's four major criticisms of this system. In the third section, monistic solutions suggested in Descartes and by Spinoza, Foucher, Leibniz, and Locke are considered; in the fourth, the dualistic solutions of the orthodox Cartesians Rohault, R~gis, Desgabets, La Forge, Le Grand, and Arnauld; and in the fifth, the occasionalist solution of Malebranche. The sixth section is an analysis of these orthodox and occasionalist solutions, showing how each ultimately fails because of dependence upon the ontology of substance and modification. The seventh section is a consideration of Berkeley and Hume in the Cartesian context. A consideration of their systems as offering solutions to Cartesian problems illuminates in new light both the systems and the problems. In broad terms, this study moves from a consideration of problems arising from an ontology of two substances, to a consideration of problems arising from the ontological pattern of substance and modification. The Cartesians were concerned with relationships between two substances, but they saw no difficulties connected with the relationship between a substance and its modifications (or properties). Berkeley's treatment (deriving from Male- [177] 178 HISTORY OF PHILOSOPHY branche) of the relationships between mind and idea, and between mind and notion, is illuminated by a consideration of the extent to which he took these relationships for granted in the Cartesian way, and of the extent to which he saw difficulties in the relationship between substance and modification. The Berkeleian solution to Cartesian problems, like that of Malebranche before him, was not successful; Malebranche belittled, and Berkeley denied the dualism of substances, but neither philosopher could break entirely with the ontological pattern of substance and modification. The final breakdown of Cartesian metaphysics came with Hume, who, in providing the culmination of a most important trend in modern philosophy, opened the way to new metaphysics and became the father of contemporary philosophy. I A model late seventeenth-century Cartesian metaphysical system. The last grand expositor of the Cartesian philosophy was Antoine Le Grand who in 1694 published An Entire Body of Philosophy. The characterization of the late seventeenth-century Cartesian system given below follows Le Grand's exposition more closely than others, but it also incorporates elements from those of Rohault, R6gis, Desgabets, La Forge, Malebranche, and Arnauld.1 None of these philosophers professed a system of exactly the sort this characterization pictures, nor is it implied here that they do. The guide and rationale for drawing from them such a model Cartesianism is the polemical writing of Simon Foucher. Foucher's series of attacks upon Cartesianism (of which the second is his criticism of Malebranche of 1675, Critique de la Rdcherche de la veritd) give clearly the most important objections against Cartesian metaphysics.2The system outlined below, while more com1Le Grand, Antoine, An Entire Body of Philosophy According to the Principles of the Famous Renate des Cartes (London, 1694); Rohault, Jacques, Traitd de physique (Paris, 1671); R6gis, Pierre-Sylvain, Syst~me de philosophie, contenant la logique, la mdtaphysique, la physique et la morale (Lyon, 1690); Desgabets, Robert, Critique de la Critique de la Recherche de la veritd, oCt l'on decouvre le chemin qui conduit aux connoissances solides. Pour servir de rdsponse gtla Lettre d'un academicien (Paris, 1675); La Forge, Louis de, Traitd de l'dme humaine, de ses facultds et fonctions et de son union avec le corps, d'apr~s les principes de... (shrink)

This is a book-length study of two of Descartes's most innovative successors, Robert Desgabets and Pierre-Sylvain Regis, and of their highly original contributions to Cartesianism. The focus of the book is an analysis of radical doctrines in the work of these thinkers that derive from arguments in Descartes: on the creation of eternal truths, on the intentionality of ideas, and on the soul-body union. As well as relating their work to that of fellow Cartesians such as Malebranche and (...) Arnauld, the book also establishes the important though neglected role played by Desgabets and Regis in the theologically and politically charged reception of Descartes in early modern France. This is a major contribution to the history of Cartesianism that will be of special interest to historians of early modern philosophy and historians of ideas. (shrink)

Arguing for controversial readings of many of the canonical figures, the book also focuses on lesser-known writers such as Pierre-Sylvain Regis, Nicolas ...

This chapter analyses Malebranche’s theory that the human, finite mind participates in two separate and, at least prima facie, incompatible unions: one with the body to which it is joined and one with God. By looking at the way that Malebranche borrows from both the mechanical philosophy as articulated by Descartes and Augustine’s dictum that we are not “lights unto” ourselves, the unique, difficult, and at times problematic Malebranchean philosophy of mind is revealed. This discussion is divided into two main (...) parts. First, it situates Malebranche’s view of the nature of mind in relation to Descartes’ and Augustine’s views by way of discussion of the roles of intellect and will, the intelligibility of mind, and the manner in which the mind is involved in sensation, imagining, and passionate responses. These are the operations that depend on the mind’s relationship to its body. Second, the chapter moves to explore Malebranche’s view of the operations of the mind as united to God: ideation, which involves a discussion of Malebranche’s famous doctrine of the Vision of All Things in God, and pure understanding. In this second part, attention is paid to Malebranche’s disputes with Antoine Arnauld, Pierre-Sylvain Régis, and Dortous de Mairan over the central philosophical principle that underwrites the Malebranchean view of ideas: intelligible extension. While intelligible extension is the legitimate object of critique, it is suggested here that Malebranche, by relying on faith, can answer his critics. The chapter concludes by articulating the manner in which that Malebranche sees the relationship between the two unions of the mind, with body and with God, in his science of man. -/- . (shrink)

The seventeenth century witnesses the demise of two core doctrines in the theory of perception: naive realism about color, sound, and other sensible qualities and the empirical theory, drawn from Alhacen and Roger Bacon, which underwrote it. This created a problem for seventeenth century philosophers: how is that we use qualities such as color, feel, and sound to locate objects in the world, even though these qualities are not real? -/- Ejecting such sensible qualities from the mind-independent world at once (...) makes for a cleaner ontology, since bodies can now be understood in purely geometrical terms, and spawns a variety of fascinating complications for the philosophy of perception. If sensible qualities are not part of the mind-independent world, just what are they, and what role, if any, do they play in our cognitive economy? We seemingly have to use color to visually experience objects. Do we do so by inferring size, shape, and motion from color? Or is it a purely automatic operation, accomplished by divine decree? -/- This volume traces the debate over perceptual experience in early modern France, covering such figures as Antoine Arnauld, Robert Desgabets, and Pierre-Sylvain Regis alongside their better-known countrymen Rene Descartes and Nicolas Malebranche. (shrink)

This chapter compares rationalist theories of sense perception to previously held theories of perception (especially of vision) and examines rationalist accounts of sensory qualities and sensory representation, of the role of the sense-based passions in guiding behavior, of the epistemological benefits and dangers of sense perception, and of mind–body relations. Each section begins with Descartes, the first major rationalist of the seventeenth century. The other major rationalists, Malebranche, Spinoza, and Leibniz, and also lesser known figures such as Pierre Regis, (...) Jacques Rohault, and Antoine Le Grand, were well acquainted with Descartes' work. Indeed, the first three were each deeply influenced by Descartes in their early years before developing their own philosophical systems, and the latter three were all advocates of Descartes' philosophy (perhaps with slight revision). Each of the major rationalists, while sharing some positions in common, developed a distinctive metaphysics of perception and of the mind–body relation. Earlier sections chart these differences and a final section sums up common features and touches on the continuing significance of their views. (shrink)

Recent re-evaluation of the question of the exact role of experience in the Cartesian philosophy has emerged from many quarters. The metaphysical issue of innate ideas has been raised by such scholars as McRae and Miles, and a close examination of the role of empirical enquiry and methodology in Cartesian science have been undertaken by Clarke, Garber, Buchdahl and Laudan, to mention only a few. These recent reappraisals of the role of experience in Descartes's philosophy have been cast mostly in (...) twentieth-century terms with a specific view to concerns of the present. ;My research centres on an examination of the philosophical works of three Cartesians, Antoine Le Grand, Robert Desgabets, and Pierre-Sylvain Regis. Though they are relatively minor figures in the history of ideas, their defence of Descartes's thesis concerning the free creation of the eternal truths, and their emphasis on the importance of experience, provide a unique opportunity to reevaluate the role of experience in the Cartesian philosophy in terms that are common in the period. ;There was a strongly empirical component in the philosophical doctrines and practices of these seventeenth-century Cartesians. Le Grand's view of truth as created and dependent on the will of God led him to assign experiment and experience the role of "making manifest" the operation of laws in the physical universe. Desgabets rejected innate ideas, and argued that all ideas depend on the operation of the senses. Regis emphasized the immutability and total dependence of truths and essences on the free will of God, and thereby undermined the rationalist foundation for the Cartesian doctrine of essences. ;My goal in this approach to the question of the nature and role of experience in the Cartesian philosophy is to explore the philosophical basis of the empiricist tendencies found in Descartes as developed by three of his disciples. My hope is that my study of Le Grand, Regis, and Desgabets, who are relatively unknown today, will not only serve to place them appropriately within the history of ideas, but will dislodge the common misconception of Cartesianism as having been an inherently rationalist philosophy. (shrink)

In recent years there has been increasing interest in two relatively unknown French Cartesians, Robert Desgabets and his disciple Pierre-Sylvain Régis.1 The attention is well deserved because their...

Descartes's claim that the eternal truths were freely created by God is fraught with interpretive difficulties. The main arguments in the literature are classified as concerning the ontological status or the modalities of possibility and necessity of the eternal truths. The views of the principal defenders of the Creation Doctrine – Robert Desgabets, Pierre Sylvain Régis, and Antoine Le Grand are contrasted with those of Nicolas Malebranche. In clarifying the theological, ontological, and logical terms of the debate we (...) can see that what was at stake was the objectivity and certainty of the truths of mathematics and physics. I conclude by suggesting that this issue might fruitfully be used to clarify the disparate discussions in the contemporary literature. (shrink)