Degree of explanation

Partial explanations are everywhere. That is, explanations citing causes that explain some but not all of an effect are ubiquitous across science, and these in turn rely on the notion of degree of explanation. I argue that current accounts are seriously deficient. In particular, they do not incorporate adequately the way in which a cause’s explanatory importance varies with choice of explanandum. Using influential recent contrastive theories, I develop quantitative definitions that remedy this lacuna, and relate it to existing measures of degree of causation. Among other things, this reveals the precise role here of chance, as well as bearing on the relation between causal explanation and causation itself

Integrating omics to characterize eco‐physiological adaptations: How moose diet and metabolism differ across biogeographic zones

1. With accelerated land conversion and global heating at northern latitudes, it becomes crucial to understand, how life histories of animals in extreme environments adapt to these changes. Animals may either adapt by adjusting foraging behavior or through physiological responses, including adjusting their energy metabolism or both. Until now, it has been difficult to study such adaptations in free‐ranging animals due to methodological constraints that prevent extensive spatiotemporal coverage of ecological and physiological data. 2. Through a novel approach of combining DNA‐metabarcoding and nuclear magnetic resonance (NMR)‐based metabolomics, we aim to elucidate the links between diets and metabolism in Scandinavian moose Alces alces over three biogeographic zones using a unique dataset of 265 marked individuals. 3. Based on 17 diet items, we identified four different classes of diet types that match browse species availability in respective ecoregions in northern Sweden. Individuals in the boreal zone consumed predominantly pine and had the least diverse diets, while individuals with highest diet diversity occurred in the coastal areas. Males exhibited lower average diet diversity than females. 4. We identified several molecular markers indicating metabolic constraints linked to diet constraints in terms of food availability during winter. While animals consuming pine had higher lipid, phospocholine, and glycerophosphocholine concentrations in their serum than other diet types, birch‐ and willow/aspen‐rich diets exhibit elevated concentrations of several amino acids. The individuals with highest diet diversity had increased levels of ketone bodies, indicating extensive periods of starvation for these individuals. 5. Our results show how the adaptive capacity of moose at the eco‐physiological level varies over a large eco‐geographic scale and how it responds to land use pressures. In light of extensive ongoing climate and land use changes, these findings pave the way for future scenario building for animal adaptive capacity

Low frequency of somatic mutations in the FH/multiple cutaneous leiomyomatosis gene in sporadic leiomyosarcomas and uterine leiomyomas

Germline mutations in the fumarate hydratase gene at 1q43 predispose to dominantly inherited skin and uterine leiomyomata and leiomyosarcomas. The enzyme, which is a component of the tricarboxylic acid cycle, acts as a tumour suppressor. To evaluate fumarate hydratase in respective sporadic tumours, we analysed a series of 26 leiomyosarcomas and 129 uterine leiomyomas (from 21 patients) for somatic mutations in fumarate hydratase and allelic imbalance around 1q43. None of the 26 leiomyosarcomas harboured somatic mutations in fumarate hydratase. Fifty per cent of leiomysarcomas tested showed evidence of allelic imbalance at 1q, but this was not confined to the vicinity of fumarate hydratase. Only 5% (seven out of 129) of the leiomyomas showed allele imbalance at 1q42-q43 and no somatic mutations in fumarate hydratase were observed. Our findings indicate that mutations in fumarate hydratase do not play a major role in the development of sporadic leiomyosarcomas or uterine leiomyomas

Effects of growing conditions and source habitat on plant traits and functional group definition

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/72499/1/j.1365-2435.2001.00487.x.pd

Mutations of the BRAF gene in human cancer

Cancers arise owing to the accumulation of mutations in critical genes that alter normal programmes of cell proliferation, differentiation and death. As the first stage of a systematic genome-wide screen for these genes, we have prioritized for analysis signalling pathways in which at least one gene is mutated in human cancer. The RAS RAF MEK ERK MAP kinase pathway mediates cellular responses to growth signals. RAS is mutated to an oncogenic form in about 15% of human cancer. The three RAF genes code for cytoplasmic serine/threonine kinases that are regulated by binding RAS. Here we report BRAF somatic missense mutations in 66% of malignant melanomas and at lower frequency in a wide range of human cancers. All mutations are within the kinase domain, with a single substitution (V599E) accounting for 80%. Mutated BRAF proteins have elevated kinase activity and are transforming in NIH3T3 cells. Furthermore, RAS function is not required for the growth of cancer cell lines with the V599E mutation. As BRAF is a serine/threonine kinase that is commonly activated by somatic point mutation in human cancer, it may provide new therapeutic opportunities in malignant melanoma

Radiatively Cooled Magnetic Reconnection Experiments Driven by Pulsed Power

We present evidence for strong radiative cooling in a pulsed-power-driven magnetic reconnection experiment. Two aluminum exploding wire arrays, driven by a 20 MA peak current, 300 ns rise time pulse from the Z machine (Sandia National Laboratories), generate strongly-driven plasma flows ($M_A \approx 7$) with anti-parallel magnetic fields, which form a reconnection layer ($S_L \approx 120$) at the mid-plane. The net cooling rate far exceeds the Alfv\'enic transit rate ($\tau_{\text{cool}}^{-1}/\tau_{\text{A}}^{-1} > 100$), leading to strong cooling of the reconnection layer. We determine the advected magnetic field and flow velocity using inductive probes positioned in the inflow to the layer, and inflow ion density and temperature from analysis of visible emission spectroscopy. A sharp decrease in X-ray emission from the reconnection layer, measured using filtered diodes and time-gated X-ray imaging, provides evidence for strong cooling of the reconnection layer after its initial formation. X-ray images also show localized hotspots, regions of strong X-ray emission, with velocities comparable to the expected outflow velocity from the reconnection layer. These hotspots are consistent with plasmoids observed in 3D radiative resistive magnetohydrodynamic simulations of the experiment. X-ray spectroscopy further indicates that the hotspots have a temperature (170 eV) much higher than the bulk layer ($\leq$ 75 eV) and inflow temperatures (about 2 eV), and that these hotspots generate the majority of the high-energy (> 1 keV) emission

Binary black hole shadows, chaotic scattering and the Cantor set

We investigate the qualitative features of binary black hole shadows using the model of two extremally charged black holes in static equilibrium (a Majumdar–Papapetrou solution). Our perspective is that binary spacetimes are natural exemplars of chaotic scattering, because they admit more than one fundamental null orbit, and thus an uncountably infinite set of perpetual null orbits which generate scattering singularities in initial data. Inspired by the three-disc model, we develop an appropriate symbolic dynamics to describe planar null geodesics on the double black hole spacetime. We show that a one-dimensional (1D) black hole shadow may constructed through an iterative procedure akin to the construction of the Cantor set; thus the 1D shadow is self-similar. Next, we study non-planar rays, to understand how angular momentum affects the existence and properties of the fundamental null orbits. Taking slices through 2D shadows, we observe three types of 1D shadow: regular, Cantor-like, and highly chaotic. The switch from Cantor-like to regular occurs where outer fundamental orbits are forbidden by angular momentum. The highly chaotic part is associated with an unexpected feature: stable and bounded null orbits, which exist around two black holes of equal mass M separated by a1 < a < √ 2a1, where a1 = 4M/√ 27. To show how this possibility arises, we define a certain potential function and classify its stationary points. We conjecture that the highly chaotic parts of the 2D shadow possess the Wada property. Finally, we consider the possibility of following null geodesics through event horizons, and chaos in the maximally extended spacetime

The GOGREEN survey : Internal dynamics of clusters of galaxies at redshift 0.9-1.4

Context. The study of galaxy cluster mass profiles (M(r)) provides constraints on the nature of dark matter and on physical processes affecting the mass distribution. The study of galaxy cluster velocity anisotropy profiles (beta (r)) informs the orbits of galaxies in clusters, which are related to their evolution. The combination of mass profiles and velocity anisotropy profiles allows us to determine the pseudo phase-space density profiles (Q(r)); numerical simulations predict that these profiles follow a simple power law in cluster-centric distance.Aims. We determine the mass, velocity anisotropy, and pseudo phase-space density profiles of clusters of galaxies at the highest redshifts investigated in detail to date.Methods. We exploited the combination of the GOGREEN and GCLASS spectroscopic data-sets for 14 clusters with mass M-200 >= 10(14) M-circle dot at redshifts 0.9 = 10(9.5) M-circle dot. We used the MAMPOSSt method to constrain several M(r) and beta (r) models, and we then inverted the Jeans equation to determine the ensemble cluster beta (r) in a non-parametric way. Finally, we combined the results of the M(r) and beta (r) analysis to determine Q(r) for the ensemble cluster.Results. The concentration c(200) of the ensemble cluster mass profile is in excellent agreement with predictions from Lambda cold dark matter (Lambda CDM) cosmological numerical simulations, and with previous determinations for clusters of similar mass and at similar redshifts, obtained from gravitational lensing and X-ray data. We see no significant difference between the total mass density and either the galaxy number density distributions or the stellar mass distribution. Star-forming galaxies are spatially significantly less concentrated than quiescent galaxies. The orbits of cluster galaxies are isotropic near the center and more radial outside. Star-forming galaxies and galaxies of low stellar mass tend to move on more radially elongated orbits than quiescent galaxies and galaxies of high stellar mass. The profile Q(r), determined using either the total mass or the number density profile, is very close to the power-law behavior predicted by numerical simulations.Conclusions. The internal dynamics of clusters at the highest redshift probed in detail to date are very similar to those of lower-redshift clusters, and in excellent agreement with predictions of numerical simulations. The clusters in our sample have already reached a high degree of dynamical relaxation.Peer reviewe

Benefits and tradeoffs of reduced tillage and manure application methods in a Zea mays silage system

A critical question is whether there are agricultural management practices that can attain the multiple management goals of increasing yields, preventing nutrient losses, and suppressing greenhouse gas (GHG) emissions. No-till and manure application methods, such as manure injection, can enhance nutrient retention, but both may also enhance emissions of nitrous oxide (N2O), a powerful GHG. We assessed differences in soil N2O and carbon dioxide (CO2) emissions, nitrate and ammonium retention, and crop yield and protein content under combinations of vertical-till, no-till, manure injection, and manure broadcast without incorporation in a corn (Zea mays L.) silage system. During the growing seasons of 2015–2017, GHG emissions and soil mineral nitrogen (N) were measured every other week or more frequently after management events. Crop yield and protein content were measured annually at harvest. No-till reduced CO2 emissions but had no impact on N2O emissions relative to vertical-till. Manure injection increased N2O and CO2 emissions, with the magnitude of this effect being greatest for 1 mo post-application. Manure injection also increased soil ammonium and nitrate but did not increase yield or crop quality relative to broadcast application. Similarly, tillage did not affect crop yield or protein content. Despite the tradeoffs between mineral N retention and elevated GHG emissions, manure injection in no-till systems benefits farmers by reducing soil carbon losses as CO2, retaining mineral N, and maintaining crop yields and quality