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)

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.

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)

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)

Deep Brain Stimulation is an invasive device-based neuromodulation technique that allows the therapeutic direct stimulation of subcortical and deep cortical structures following the surgical placement of stimulating electrodes. DBS is approved by the U.S. Federal Drug Administration for the treatment of movement disorders and obsessive-compulsive disorder, while new indications, including Major Depressive Disorder, are in experimental development. We report the case of a patient with MDD who received DBS to the ventral internal capsule and ventral striatum bilaterally and presented with (...) 2 weeks of voltage-dependent Tourette-like symptoms including brief transient episodes of abrupt-onset and progressively louder coprolalia and stuttered speech; tic-like motor behavior in his right arm and leg; rushes of anxiety, angry prosody, angry affect; and moderate amnesia without confusion. We describe the results of the inpatient neuropsychiatric workup leading to the diagnosis of iatrogenic voltage-dependent activation of cortico-subcortical circuits and discuss insights into the pathophysiology of Tourette as well as safety considerations raised by the case. (shrink)