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)

A collection of texts by representative French materialist philosophers, including the Baron d'Holbach, Denis Diderot, Sylvain Maréchal, the Marquis de Sade, Jean-Baptiste Robinet, Pierre Jean Georges Cabanis, Claude Adrien Helvétius, and various others.

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)

This paper argues that Book 3 of Porphyry’s De abstinentia contains an overlooked argument in favor of vegetarianism for the sake of non-human animals themselves. The argument runs as follows: animals are essentially sentient creatures. Sentience (αἴσθησις) allows them to discern what is good for their survival and what is destructive to them, so that they can pursue the former and avoid the latter. As a result, animals (human and non-human) have preferences, desires, and hopes. Having purposeful strivings that can (...) be promoted or frustrated makes them recipients of justice and injustice. This means, for Porphyry, that animals, unlike plants, can be wronged since they are creatures that discern, and purposefully pursue, what is good or bad for them. This reading stands against interpretations that argue that Porphyry advocates vegetarianism only for our benefit, and not for the animals’ own sake. (shrink)

Les recherches sur le travail comme valeur au Moyen Âge se sont principalement attardées sur la malédiction prononcée lors de l'expulsion du jardin d'Eden, négligeant l'activité à laquelle se livrait Adam avant la chute (Gn 2,15). A la suite de Philon d'Alexandrie, Augustin a proposé une lecture littérale de ce premier travail, qui a eu un fort impact dans la culture médiévale, certains auteurs (franciscains) comprenant ce verset au sens d'une mission d'améliorer encore la création.

In Nicomachean Ethics 7.7 (= Eudemian Ethics 6.7), Aristotle distinguishes softness (malakia) from lack of self-control (akrasia) and endurance (karteria) from self-control (enkrateia). This paper argues that unqualified softness consists of a disposition to give up acting to avoid the painful toil (ponos) required to execute practical resolutions, and (coincidentally) to enjoy the pleasures of rest and relaxation. The enduring person, in contrast, persists in her commitments despite the painful effort required to enact them. Along the way, I argue that (...) this interpretation qualifies our understanding of the pleasures and pains with which temperance and intemperance are concerned. (shrink)

Neuroconstructivism: How the Brain Constructs Cognition proposes a unifying framework for the study of cognitive development that brings together (1) constructivism (which views development as the progressive elaboration of increasingly complex structures), (2) cognitive neuroscience (which aims to understand the neural mechanisms underlying behavior), and (3) computational modeling (which proposes formal and explicit specifications of information processing). The guiding principle of our approach is context dependence, within and (in contrast to Marr [1982]) between levels of organization. We propose that three (...) mechanisms guide the emergence of representations: competition, cooperation, and chronotopy; which themselves allow for two central processes: proactivity and progressive specialization. We suggest that the main outcome of development is partial representations, distributed across distinct functional circuits. This framework is derived by examining development at the level of single neurons, brain systems, and whole organisms. We use the terms encellment, embrainment, and embodiment to describe the higher-level contextual influences that act at each of these levels of organization. To illustrate these mechanisms in operation we provide case studies in early visual perception, infant habituation, phonological development, and object representations in infancy. Three further case studies are concerned with interactions between levels of explanation: social development, atypical development and within that, developmental dyslexia. We conclude that cognitive development arises from a dynamic, contextual change in embodied neural structures leading to partial representations across multiple brain regions and timescales, in response to proactively specified physical and social environment. (shrink)

In this paper, I provide an interpretation of Plato’s repeated claims in Republic V that women are “weaker” (asthenestera) than men. Specifically, I argue that Plato thinks women have a psychological propensity to get easily dispirited, which makes them less effective in implementing and executing their rational decisions. This interpretation achieves several things. It qualifies Plato’s position regarding women and their position in the polis. It provides the background against which we can interpret Aristotle’s claim in Politics I that women (...) possess a deliberative capacity that is not authoritative (akuron). It expands our understanding of the nature and role of spirit (thumos) in these authors. And, finally, it gives us insight into a kind of moral-psychological success that Plato and Aristotle consider central to both personal and political agency. (shrink)

In this collection of essays, Bromberger explores the centrality of questions and predicaments they create in scientific research. He discusses the nature of explanation, theory, and the foundations of linguistics.

In this paper I examine the moral psychology of the Phaedo and argue that the philosophical life in this dialogue is a temperate life, and that temperance consists in exercising epistemic discernment by actively withdrawing assent from incorrect evaluations the body inclines us to make. Philosophers deal with bodily affections by taking a correct epistemic stance. Exercising temperance thus understood is a necessary condition both for developing and strengthening rational capacities, and for fixing accurate beliefs about value. The purification philosophers (...) strive for, and the purifying role of philosophy, should then be understood as a clarificatory act consisting in making one’s thoughts clear and withdrawing assent from erroneous evaluative content in our desires and pleasures. Along the way, I argue that philosophers must neither avoid situations and activities that cause bodily affections as much as possible, nor ignore or care little about them. (shrink)

This paper argues that Aristotelian practical wisdom (phronêsis) is a state of conviction (pistis) in the goodness of our goals based on proper grounds. This state of conviction can only be achieved if rational arguments and principles agree with how things appear to us. Since, for Aristotle, passions influence appearances, they can support or undermine our conviction in the goodness of ends that are worth pursuing. For this reason, we cannot be practically wise without virtuous dispositions to experience appropriate passions. (...) Along the way, I argue that this reading allows us to explain the shortcomings of self-controlled and akratic agents. -/- . (shrink)

This article focuses on the methodological issues involved in combining data collected by questionnaire and interview to study the barriers to educational and professional participation of young people (aged 15-26) living with cystic fibrosis. In addition to an exploratory survey of thirteen professionals, it is based on the cross-referencing of data produced from a short and adapted version of the Measure of the Quality of the Environment-MQE (n=100) and interviews of the “story of life and practices” type with high school (...) students, students, young people looking for work or in employment (n=29). The results show the discrepancy between the responses to the MQE and the narratives produced in the interviews. On the one hand, the responses to the MQE shed light on the impact of the physical environments and the spatial and temporal organisation of the school and work environments on the experience of disability. On the other hand, they seem to underestimate the weight of human environments in producing or reducing barriers to participation. The testimonies gathered in interviews allow us to reassess the importance of these environments. The use of mixed research methods therefore seems essential to understand the respective roles of the material and human components of environments in the production of educational and occupational disability. (shrink)

Intuitive predictions and judgements under uncertainty are often mediated by judgemental heuristics that sometimes lead to biases. Our micro-developmental study suggests that a presumption of rationality is justified for adult subjects, in so far as their systematic judgemental biases appear to be due to a specific executive-inhibition failure in working memory, and not necessarily to a lack of understanding of the fundamental principles of probability. This hypothesis was tested using an experimental procedure in which 60 adult subjects were trained to (...) inhibit the classical conjunction bias on a frequency judgement task derived from Tversky and Kahneman's work. Pre- and post-test performance was assessed via a probability judgement task. The data indicated a training effect, suggesting that subjects traditionally labelled as "irrational" with respect to the classical rules of inductive reasoning are in fact "inefficient inhibitors". These findings are discussed in terms of a polymorphous view of rationality. (shrink)

L'une des tâches séculaires de la philosophie est de surmonter ce que Locke nommait l'abus des mots; le dictionnaire des ntions s'efforce de l'accomplir en présentant une technologie des réseaux sémantiques.

Lien fondamental entre Platon et Epicure, ce trublion-penseur possède son propre génie qu'il prétend divin, notamment une très solide métaphysique et des positions scandaleuses pour bien des époques, tel son "féminisme", jusqu'à ...

What are the passions? And what, if anything, do they have to do with our intellectual lives? I argue that, according to Aristotle, the passions are complex states that carry information about the value things have. More specifically, Aristotelian passions are constituted by fine-grained evaluative appearances—a kind of truth-apt, cognitive, yet non-rational representation that non-human animals also entertain. Given that the passions are representations of value, they can be the basis for coming to know and understand the peculiar value of (...) things. So, the passions can serve as grounds for intellectual achievements that are essential to a good life. In particular, I argue that, for Aristotle, the passions contribute substantively to three intellectual achievements that are required for a flourishing life: practical wisdom, certain instances of contemplation, and the appreciation of art. Since Aristotelian passions carry rich information and discriminate value, they are cognitive states that can shape and enrich not only our lives as agents, but also our lives as knowers. The passions can play an epistemic role by serving as warrant for intellectually discerning the normative features of the situations we inhabit, the kinds of characters that surround us, and what is good and fine in them and us. Furthermore, in virtue of their epistemic role, the passions can be the basis for the intellectual aspects of a moral education. (shrink)

In De usu partium, Galen argues that the parts of the human body are designed to fulfill functions that contribute to the continued existence and well-being of the organism as a whole. Synthesizing Plato’s and Aristotle’s views on teleology, Galen highlights the importance of a functional framework for anatomical research. For Galen, teleology is as much a method for anatomical inquiry as it is a metaphysical commitment. In particular, teleology guides the main tool of anatomical investigation: dissection. According to Galen, (...) the success of medical research and practice requires classifying, individuating, and explaining anatomical parts in light of their functional contributions. (shrink)

This research investigates the potential for a “fair” co-branding operation. A major corporate brand is fictitiously allied with a Fair Trade labelling organization brand. The sample for the study is composed of 540 respondents, representative of the French population. By considering commercial brands and Fair Trade labels as dissimilar in terms of customers’ perceived Fair Trade orientations, this article studies how this lack of similarity impacts perceived congruence between both entities and how prior brand attitudes and congruence influence customers’ evaluation (...) of the co-branded product. The results of this research demonstrate that: Consumer prior brand attitudes toward the partner brands influence very little customers’ evaluation. Perceived similarity of the partner brands has a strong influence toward congruence of the co-branding operation. Results also indicate that congruence has a strong influence upon customers’ evaluation. An inverted U-shaped relationship exists between perceived similarity and relevancy of the alliance, and between expectancy and customers’ evaluation. The results obtained through the test of a partial least square model, and inverted U-shaped hypothesis, represent a new insight into co-branding theory. The high discursive power of fair co-branding is a key issue: the corporate brand provides the alliance with its leading position, while the Fair Trade brand provides the ethical attribute. (shrink)

Using the matching bias example, the aim of the present studies was to show that adults' reasoning biases are due to faulty executive inhibition programming. In the first study, the subjects were trained on Wason's classical card selection task; half were given training in how to inhibit the perceptual matching bias (experimental group) and half in logic without the inhibition component (control group). On the pre- and post-tests, their performance was assessed on the Evans conditional rule falsification task (with a (...) negation in the antecedent of the rule), a task that also involves matching bias. In addition, subjects were tested for perceptual field dependence/independence using the Embedded Figures Test. The results brought out a specific inhibition training effect, as well as a clear-cut relationship in the experimental group between receptiveness to training and perceptual field independence. In the second study, the training paradigm was the same except that on the pre- and post-tests, the negation was in the consequent of the conditional rule (in this case, the perceptual matching response corresponds to the logical response). The subjects succeeded on the pre-test, and the matching-bias inhibition training had a negative effect on post-test performance. This specific negative priming effect confirms the inhibitory impact of our experimental training and outlines the dissociation of inhibition and logical components. (shrink)

This paper argues that Aristotelian thumos is a non-reducible mental phenomenon that plays a central role in Aristotle’s theory of the mind, motivation, and action. For Aristotle, thumos is not primarily, as others have argued, a desire for the noble, social appraisal, or retaliation; rather, it is an inner drive or impulse to act. More precisely, it is an executory urge to implement or enact one’s ends or goals, whatever they are. Thumos accounts for someone’s proneness to spring into action (...) and can contribute to bringing about rational or non-rational, first-order desires. It is a second-order motivation, which both human and non-human animals have and that comes in degrees: we can be more or less thumotic, which amounts to being more or less disposed to making first-order desires effective so that they issue in actions. Aristotelian thumos, then, anticipates features of the modern notion of the will. Along the way, I argue that thumos is key to Aristotle’s efforts to differentiate and hierarchically organize species, characters, genders, and peoples. (shrink)