Two decades ago, Rolf Landauer (1991) argued that “information is physical” and ought to have a role in the scientific analysis of reality comparable to that of matter, energy, space and time. This would also help to bridge the gap between biology and mathematics and physics. Although it can be argued that we are living in the ‘golden age’ of biology, both because of the great challenges posed by medicine and the environment and the significant advances that have been made—especially (...) in genetics and molecular and cell biology—we feel that information as an essential aspect of life has been neglected, or at least misunderstood. We therefore summon Maxwell’s Demon and its distant relative the ratchet, and apply these to biology. (shrink)

The notion of antifragility, an attribute of systems that makes them thrive under variable conditions, has recently been proposed by Nassim Taleb in a business context. This idea requires the ability of such systems to ‘tinker’, i.e., to creatively respond to changes in their environment. A fairly obvious example of this is natural selection-driven evolution. In this ubiquitous process, an original entity, challenged by an ever-changing environment, creates variants that evolve into novel entities. Analyzing functions that are essential during stationary-state (...) life yield examples of entities that may be antifragile. One such example is proteins with flexible regions that can undergo functional alteration of their side residues or backbone and thus implement the tinkering that leads to antifragility. This in-built property of the cell chassis must be taken into account when considering construction of cell factories driven by engineering principles. (shrink)

This collection of papers in epistemic logic is oriented towards applications to game theory and individual decision theory. Most of these papers were presented at the inaugural conference of the LOFT (Logic for the Theory and Games and Decisions) conference series, which took place in 1994 in Marseille. Among the notions dealt with are those of common knowledge and common belief, infinite hierarchies of beliefs and belief spaces, logical omniscience, positive and negative introspection, backward induction and rationalizable equilibria in game (...) theory. (shrink)

Since its origin in the early 20th century, the modern synthesis theory of evolution has grown to represent the orthodox view on the process of organic evolution. It is a powerful and successful theory. Its defining features include the prominence it accords to genes in the explanation of development and inheritance, and the role of natural selection as the cause of adaptation. Since the advent of the 21st century, however, the modern synthesis has been subject to repeated and sustained challenges. (...) In the last two decades, evolutionary biology has witnessed unprecedented growth in the understanding of those processes that underwrite the development of organisms and the inheritance of characters. The empirical advances usher in challenges to the conceptual foundations of evolutionary theory. Many current commentators charge that the new biology of the 21st century calls for a revision, extension, or wholesale rejection of the modern synthesis theory of evolution. Defenders of the modern synthesis maintain that the theory can accommodate the exciting new advances in biology, without forfeiting its central precepts. The original essays collected in this volume—by evolutionary biologists, philosophers of science, and historians of biology—survey and assess the various challenges to the modern synthesis arising from the new biology of the 21st century. Taken together, the essays cover a spectrum of views, from those that contend that the modern synthesis can rise to the challenges of the new biology, with little or no revision required, to those that call for the abandonment of the modern synthesis. (shrink)

Formal spaces have become commonplace conceptual and computational tools in a large array of scientific disciplines, including both the natural and the social sciences. Morphological spaces are spaces describing and relating organismal phenotypes. They play a central role in morphometrics, the statistical description of biological forms, but also underlie the notion of adaptive landscapes that drives many theoretical considerations in evolutionary biology. We briefly review the topological and geometrical properties of the most common morphospaces in the biological literature. In contemporary (...) geometric morphometrics, the notion of a morphospace is based on the Euclidean tangent space to Kendall’s shape space, which is a Riemannian manifold. Many more classical morphospaces, such as Raup’s space of coiled shells, lack these metric properties, e.g., due to incommensurably scaled variables, so that these morphospaces typically are affine vector spaces. Other notions of a morphospace, like Thomas and Reif’s skeleton space, may not give rise to a quantitative measure of similarity at all. Such spaces can often be characterized in terms of topological or pretopological spaces. (shrink)

This article introduces some soft computing methods generally used for data analysis and flow pattern detection in fluid dynamics. These techniques decompose the original flow field as an expansion of modes, which can be either orthogonal in time, or in space or in time and space, or they can simply be selected using some sophisticated statistical techniques. The performance of these methods is tested in the turbulent wake of a wall-mounted square cylinder. This highly complex flow is suitable to show (...) the ability of the aforementioned methods to reduce the degrees of freedom of the original data by only retaining the large scales in the flow. The main result is a reduced-order model of the original flow case, based on a low number of modes. A deep discussion is carried out about how to choose the most computationally efficient method to obtain suitable reduced-order models of the flow. The techniques introduced in this article are data-driven methods that could be applied to model any type of non-linear dynamical system, including numerical and experimental databases. (shrink)

Plasmodium falciparum is the most deadly human malarial parasite, responsible for an estimated 207 million cases of disease and 627,000 deaths in 2012. Recent studies reveal that the parasite actively regulates a large fraction of its genes throughout its replicative cycle inside human red blood cells and that epigenetics plays an important role in this precise gene regulation. Here, we discuss recent advances in our understanding of three aspects of epigenetic regulation in P. falciparum: changes in histone modifications, nucleosome occupancy (...) and the three‐dimensional genome structure. We compare these three aspects of the P. falciparum epigenome to those of other eukaryotes, and show that large‐scale compartmentalization is particularly important in determining histone decomposition and gene regulation in P. falciparum. We conclude by presenting a gene regulation model for P. falciparum that combines the described epigenetic factors, and by discussing the implications of this model for the future of malaria research. (shrink)

Edited by Hans-Christoph Schmidt am Busch & Christopher Zurn. This volume collects original, cutting-edge essays on the philosophy of recognition by international scholars eminent in the field. By considering the topic of recognition as addressed by both classical and contemporary authors, the volume explores the connections between historical and contemporary recognition research and makes substantive contributions to the further development of contemporary theories of recognition.

In Philosophy of Psychedelics, Letheby provides a convincing basis for the idea that psychedelics primarily derive their therapeutic potential through mediating favourable changes to self-related belief systems. In this commentary, we take a closer look at the role that contextual factors play in Letheby’s two-factor account of psychedelic therapy. While Letheby acknowledges that psychedelic effects are highly context-dependent, the exact role that context plays in self-modelling during the acute experience is not entirely clear. We argue that context plays an essential (...) role in shaping the ‘discovery’ of alternate self-conceptions during the acute experience. Specifically, users are more likely to experience alterations in self-conception that are consistent with context-dependent features, such as one’s prior mindset and aspects of the external environment. This is consistent with a REBUS model of psychedelic effects, where a corollary effect of relaxing high-level prior beliefs is that the system becomes increasingly sensitised to bottom-up information from lower-level intrinsic sources and the sensory periphery. Furthermore, it may explain why a positive well-intentioned state of mind and a supportive therapeutic environment are more likely to result in positive acute experiences and long-term improvements in mental wellbeing. We see this position as being largely compatible with Letheby’s proposal, but may shift some aspects of its emphasis and framing. In particular, it may conflict with Letheby’s notion that psychedelics lead to a ‘level cognitive playing field’, where self-related hypotheses are thought to be assigned more or less equal probability. (shrink)

Explanations of cognitive processes provided by traditional artificial intelligence were based on the notion of the knowledge level. This perspective has been challenged by new AI that proposes an approach based on embodied systems that interact with the real‐world. We demonstrate that these two views can be unified. Our argument is based on the assumption that knowledge level explanations can be defined in the context of Bayesian theory while the goals of new AI are captured by using a well established (...) robot based model of learning and problem solving, called Distributed Adaptive Control (DAC). In our analysis we consider random foraging and we prove that minor modifications of the DAC architecture renders a model that is equivalent to a Bayesian analysis of this task. Subsequently, we compare this enhanced, “rational,” model to its “non‐rational” predecessor and a further control condition using both simulated and real robots, in a variety of environments. Our results show that the changes made to the DAC architecture, in order to unify the perspectives of old and new AI, also lead to a significant improvement in random foraging. (shrink)

Explanations of cognitive processes provided by traditional artificial intelligence were based on the notion of the knowledge level. This perspective has been challenged by new AI that proposes an approach based on embodied systems that interact with the real‐world. We demonstrate that these two views can be unified. Our argument is based on the assumption that knowledge level explanations can be defined in the context of Bayesian theory while the goals of new AI are captured by using a well established (...) robot based model of learning and problem solving, called Distributed Adaptive Control (DAC). In our analysis we consider random foraging and we prove that minor modifications of the DAC architecture renders a model that is equivalent to a Bayesian analysis of this task. Subsequently, we compare this enhanced, “rational,” model to its “non‐rational” predecessor and a further control condition using both simulated and real robots, in a variety of environments. Our results show that the changes made to the DAC architecture, in order to unify the perspectives of old and new AI, also lead to a significant improvement in random foraging. (shrink)

Advancements in novel neurotechnologies, such as brain computer interfaces and neuromodulatory devices such as deep brain stimulators, will have profound implications for society and human rights. While these technologies are improving the diagnosis and treatment of mental and neurological diseases, they can also alter individual agency and estrange those using neurotechnologies from their sense of self, challenging basic notions of what it means to be human. As an international coalition of interdisciplinary scholars and practitioners, we examine these challenges and make (...) recommendations to mitigate negative consequences that could arise from the unregulated development or application of novel neurotechnologies. We explore potential ethical challenges in four key areas: identity and agency, privacy, bias, and enhancement. To address them, we propose democratic and inclusive summits to establish globally-coordinated ethical and societal guidelines for neurotechnology development and application, new measures, including “Neurorights,” for data privacy, security, and consent to empower neurotechnology users’ control over their data, new methods of identifying and preventing bias, and the adoption of public guidelines for safe and equitable distribution of neurotechnological devices. (shrink)

Throughout the biological and biomedical sciences there is a growing need for, prescriptive ‘minimum information’ (MI) checklists specifying the key information to include when reporting experimental results are beginning to find favor with experimentalists, analysts, publishers and funders alike. Such checklists aim to ensure that methods, data, analyses and results are described to a level sufficient to support the unambiguous interpretation, sophisticated search, reanalysis and experimental corroboration and reuse of data sets, facilitating the extraction of maximum value from data sets (...) them. However, such ‘minimum information’ MI checklists are usually developed independently by groups working within representatives of particular biologically- or technologically-delineated domains. Consequently, an overview of the full range of checklists can be difficult to establish without intensive searching, and even tracking thetheir individual evolution of single checklists may be a non-trivial exercise. Checklists are also inevitably partially redundant when measured one against another, and where they overlap is far from straightforward. Furthermore, conflicts in scope and arbitrary decisions on wording and sub-structuring make integration difficult. This presents inhibit their use in combination. Overall, these issues present significant difficulties for the users of checklists, especially those in areas such as systems biology, who routinely combine information from multiple biological domains and technology platforms. To address all of the above, we present MIBBI (Minimum Information for Biological and Biomedical Investigations); a web-based communal resource for such checklists, designed to act as a ‘one-stop shop’ for those exploring the range of extant checklist projects, and to foster collaborative, integrative development and ultimately promote gradual integration of checklists. (shrink)

This is the outline: Introduction — La question de la cybernétique et de l'information — Une « pensée du milieu » — Cybernétique et homologie — Une théorie de l'apprentissage — L'information vue de l'autre côté — Champ et domaine unitaire — La thèse des « autres-je » — Le passage par l'axiologie — La rétroaction vraie — L'ontologie de Ruyer — Le bruissement de l'être même.

Jeffery Aubin ,Marie Chantal ,Dianne Cole ,Julio Chaves ,Cathelyne Duchesne ,Christel Freu ,Steve Johnston ,Brice Jones ,Amaury Levillayer ,Stéphanie Machabée ,Paul-Hubert Poirier ,Philippe Therrien ,Jonathan von Kodar ,Martin Voyer ,Jennifer Wees ,Eric Crégheur.

1. Bd. Moralia Horatiana; das ist, Die horazische Sittenlehre, von P. von Zesen.--2. Bd. La doctrine des moeurs, tiree de la philosophie des stoiques, par M. Le R. de Gomberville.

The present work is aimed at investigating the effects of myocardial infarction and ischemia on induction of ventricular fibrillation. Electrophysiologic effects of global and local ischemia (variation of the dispersion of refractory periods as well as conduction velocity) on initiation of reentry mechanisms was studied by means of computer simulations based on a cellular automata model of propagation of activation wave through a ventricular surface element. A local area of ischemia where effects of the dispersion of refractory periods are investigated (...) is then simulated. This is made using a Gaussian distribution characterized by its mean and standard deviation. These simulations show that ischemia is capable of initiating reentry phenomena which propagate through the whole ventricle; they are responsible for ventricular fibrillation which causes sudden cardiac death, even when ischemia only involves limited parts of the myocardium. Statistical study of the probability of reentries as a function of both of the size of ischemic zones and the rate of dispersion of refractory periods shows that the latter parameter is of primary importance in triggering cardiac reentries. (shrink)

Physical activity and sedentary behaviour have been linked to the mental health of children and adolescents, yet the timing of behaviours may play a role in this relationship and clarifying this could inform interventions. We explored cross-sectional associations of PA and SED in varying time segments throughout the school day with the mental health of school-aged children and adolescents from rural Northeastern Ontario, Canada. A total of 161 students wore accelerometers for 8 days and completed a self-report survey. Mental health (...) was measured using the Strengths and Difficulties Questionnaire. Accelerometer-measured SED, light PA, and moderate and vigorous PA were estimated in the time-segments before school, school time, after school, and evenings. Associations were tested with multilevel linear regressions while adjusting for confounding factors. Students spent 72.6 min in MVPA, 209.0 min in LPA, and 621.0 min in SED per day. Daily SED was associated with less conduct problems. Evening LPA was inversely associated with hyperactivity, while SED was associated with hyperactivity and with peer problems before school, and during school. No associations were observed for MVPA, emotional symptoms, or prosocial behaviour. In conclusion, displacing SED with LPA in some specific periods of the day may benefit the mental health of students; taking this into account could strengthen interventions. (shrink)

The Declaration of Helsinki and the Council of the International Organization of Medical Sciences provide guidance on standards of care and prevention in clinical trials. In the current and increasingly challenging research environment, the ethical status of a trial design depends not only on protection of participants, but also on social value, feasibility, and scientific validity. Using the example of a study assessing efficacy of a vaccine to prevent human papilloma virus in HIV-1 infected adolescent girls in low resource countries (...) without access to the vaccine, we compare several trial designs which rank lower on some criteria and higher on others, giving rise to difficult trade-offs. This case demonstrates the need for developing more nuanced guidance documents to help researchers balance these often conflicting criteria. (shrink)

Louise Chardon écrit à l'automne 1901 son autobiographie ; elle a 25 ans mais Louise n'est pas une demoiselle : elle a quitté l'école à onze ans pour entrer comme apprentie chez une échantillonneuse ; abusée sexuellement par un parent de son employeuse, placée dans diverses maison de refuge prostestantes, Louise a sombré dans la marginalité ; arrêtée plusieurs fois pour vagabondage, elle est recueillie par son oncle et sa femme, M. et Mme Joly, à Saint-Etienne ; mais devenue l'amante (...) de son o... (shrink)