In search of ontological emergence: diachronic, but non-supervenient

Most philosophical accounts of emergence are based on supervenience, with supervenience being an ontologically synchronic relation of determination. This conception of emergence as a relation of supervenience, I will argue, is unable to make sense of the kinds of emergence that are widespread in self-organizing and nonlinear dynamical systems, including distributed cognitive systems. In these dynamical systems, an emergent property is ontological (i.e., the causal capacities of P, where P is an emergent feature, are not reducible to causal capacities of the parts, and may exert a top-down causal influence on the parts of the system) and diachronic (i.e., the relata of emergence are temporally extended, and P emerges as a result of some dynamical lower-level processes that unfold in real time)

Loss of Nef-mediated CD3 down-regulation in the HIV-1 lineage increases viral infectivity and spread

Nef is an accessory protein of primate lentiviruses that is essential for efficient replication and pathogenesis of HIV-1. A conserved feature of Nef proteins from different lentiviral lineages is the ability to modulate host protein trafficking and down-regulate a number of cell surface receptors to enhance replication and promote immune evasion. Notably, the inability of Nef to down-regulate CD3 from infected T cells distinguishes HIV-1 Nef and its direct simian precursors from other primate lentiviruses. Why HIV-1 does not employ this potential immune evasion strategy is not fully understood. Using chimeric HIV-1 constructs expressing lentiviral Nef proteins that differ in their ability to down-modulate CD3, we show that retaining CD3 on the surface of infected primary T cells results in increased viral replication and cell-to-cell spread. We identified increased expression of envelope (Env) trimers at the cell surface and increased Env incorporation into virions as the determinants for the Nef- and CD3-dependent enhancement of viral infectivity. Importantly, this was independent of Nef-mediated antagonism of the host restriction factor SERINC5. CD3 retention on the surface of infected primary T cells also correlated with increased T cell signaling, activation, and cell death during cell-to-cell spread. Taken together, our results show that loss of an otherwise conserved function of Nef has a positive effect on HIV-1 replication, allowing for more efficient replication while potentially contributing to HIV-1 pathogenesis by triggering T cell activation and cell death during viral spread

Infanticide in Chimpanzees: Taphonomic Case Studies from Gombe

Objectives We present a study of skeletal damage to four chimpanzee (Pan troglodytes) infanticide victims from Gombe National Park, Tanzania. Skeletal analysis may provide insight into the adaptive significance of infanticide by examining whether nutritional benefits sufficiently explain infanticidal behavior. The nutritional hypothesis would be supported if bone survivorship rates and skeletal damage patterns are comparable to those of monkey prey. If not, other explanations, such as the resource competition hypothesis, should be considered. Methods Taphonomic assessment of two chimpanzee infants included description of breakage and surface modification, data on MNE, %MNE, and bone survivorship. Two additional infants were assessed qualitatively. The data were compared to published information on monkey prey. We also undertook a review of published infanticide cases. Results The cases were intercommunity infanticides (one male and three female infants) committed by males. Attackers partially consumed two of the victims. Damage to all four infants included puncture marks and compression fractures to the cranium, crenulated breaks to long bones, and incipient fractures on ribs. Compared to monkey prey, the chimpanzee infants had an abundance of vertebrae and hand/foot bones. Conclusions The cases described here suggest that chimpanzees may not always completely consume infanticide victims, while reports on chimpanzee predation indicated that complete consumption of monkey prey usually occurred. Infanticidal chimpanzees undoubtedly gain nutritional benefits when they consume dead infants, but this benefit may not sufficiently explain infanticide in this species. Continued study of infanticidal and hunting behavior, including skeletal analysis, is likely to be of interest

A tale of two densities: Active inference is enactive inference

The aim of this paper is to clarify how best to interpret some of the central constructs that underwrite the free-energy principle (FEP) – and its corollary, active inference – in theoretical neuroscience and biology: namely, the role that generative models and variational densities play in this theory. We argue that these constructs have been systematically misrepresented in the literature; because of the conflation between the FEP and active inference, on the one hand, and distinct (albeit closely related) Bayesian formulations, centred on the brain – variously known as predictive processing, predictive coding, or the prediction error minimisation framework. More specifically, we examine two contrasting interpretations of these models: a structural representationalist interpretation and an enactive interpretation. We argue that the structural representationalist interpretation of generative and recognition models does not do justice to the role that these constructs play in active inference under the FEP. We propose an enactive interpretation of active inference – what might be called enactive inference. In active inference under the FEP, the generative and recognition models are best cast as realising inference and control – the self-organising, belief-guided selection of action policies – and do not have the properties ascribed by structural representationalists

Photon Conserving Radiative Transfer around Point Sources in multi-dimensional Numerical Cosmology

Many questions in physical cosmology regarding the thermal and ionization history of the intergalactic medium are now successfully studied with the help of cosmological hydrodynamical simulations. Here we present a numerical method that solves the radiative transfer around point sources within a three dimensional cartesian grid. The method is energy conserving independently of resolution: this ensures the correct propagation speeds of ionization fronts. We describe the details of the algorithm, and compute as first numerical application the ionized region surrounding a mini-quasar in a cosmological density field at z=7.Comment: 5 pages, 4 figures, submitted to ApJ

Ferromagnetic phase transition for the spanning-forest model (q \to 0 limit of the Potts model) in three or more dimensions

We present Monte Carlo simulations of the spanning-forest model (q \to 0 limit of the ferromagnetic Potts model) in spatial dimensions d=3,4,5. We show that, in contrast to the two-dimensional case, the model has a "ferromagnetic" second-order phase transition at a finite positive value w_c. We present numerical estimates of w_c and of the thermal and magnetic critical exponents. We conjecture that the upper critical dimension is 6.Comment: LaTex2e, 4 pages; includes 6 Postscript figures; Version 2 has expanded title as published in PR

Multiscale Integration: Beyond Internalism and Externalism

We present a multiscale integrationist interpretation on the boundaries of cognitive systems, using the Markov blanket formalism of the variational free energy principle (FEP). This interpretation is intended as a corrective for the philosophical debate over internalist and externalist interpretations of cognitive boundaries; we stake out a compromise position. We first survey key principles of new radical (extended, enactive, embodied) views of cognition. We then describe an internalist interpretation premised on the Markov blanket formalism. Having reviewed these accounts, we develop our positive multiscale account. We argue that the statistical seclusion of internal from external states of the system – entailed by the existence of a Markov boundary – can coexist happily with the multiscale integration of the system through its dynamics. Our approach does not privilege any given boundary (whether it be that of the brain, body, or world), nor does it argue that all boundaries are equally prescient. We argue that the relevant boundaries of cognition depend on the level being characterised and the explanatory interests that guide investigation. We approach the issue of how and where to draw the boundaries of cognitive systems through a multiscale ontology of cognitive systems, which offers a multidisciplinary research heuristic for cognitive science

A promising new device for the prevention of parastomal hernia.

Parastomal hernia (PSH) is the most frequent long-term stoma complication with serious negative effects on quality of life. Surgical revision is often required and has a substantial morbidity and recurrence rate. The development of PSH requires revisional surgery with a substantial perioperative morbidity and high failure rate in the long-term follow-up. Prophylactic parastomal mesh insertion during stoma creation has the potential to reduce the rate of PSH, but carries the risk of early and late mesh-related complications such as infection, fibrosis, mesh shrinkage, and/or bowel erosion. We developed a new stomaplasty ring (KORING), which is easy to implant, avoids potential mesh-related complications, and has a high potential of long-term prevention of PSH. Here we describe the technique and the first use

Photoconductivity Parameters In Lithium Niobate

Measurements on a variety of doped (magnesium and/or iron) and undoped lithium niobate crystals in the oxidized state demonstrate an Arrhenius dependence of dark conductivity on reciprocal temperature between 460 and 590 K. All of the crystals had roughly the same conductivity and activation energy (1.21 eV) over the temperature range, implying that all have about the same free-carrier concentration and mobility. The enhanced photoconductivity of magnesium-doped lithium niobate is attributed to a greatly reduced trapping cross section of Fe3+ for electrons, the smaller cross section being due to a changed substitutional site for Fe3+. The Fe3+ trapping cross section is calculated from photoconductivity data to be of order 10-18 m2 in undoped lithium niobate. This implies a photoelectron lifetime of order 6x10-11 s in a relatively pure (2-ppm Fe) oxidized crystal