What is ontic structural realism?

In recent years a doctrine known as ontic structural realism (OSR) has achieved a degree of notoriety, but many people remain confused as to what exactly the doctrine amounts. In this paper three main variants of OSR are defined and discussed: (i) OSR1, which is the view that relations are ontologically primitive but objects and properties are not; (ii) OSR2, which is the view that objects and relations are ontologically primitive but properties are not; (iii) OSR3, which is the view that properties and relations are ontologically primitive but objects are not. Proponents of OSR claim that it is a “naturalistic” metaphysics, arguing that metaphysical views that take objects and/or properties as ontologically primitive are undermined by contemporary physics. In this paper it is argued that OSR1 and OSR2 are themselves undermined by contemporary physics. On the other hand, it is also argued that considerations about the objects of quantum mechanics and general relativity do seem to suggest that we should abandon some of our “common-sense” metaphysical intuitions, and that OSR3 is one of the metaphysical views that is compatible with what these theories seem to tell us about fundamental ontology.     

The role of dietary fiber in dung size of bushy-tailed woodrats, Neotoma cinerea : its potential application to paleoclimatic interpretation

A laboratory study was conducted to examine causes underlying variation in woodrat dung size. Eight bushy-tailed woodrats, Neotoma cinerea , were captured and sequentially fed 2 diets of 46% and 63% neutral detergent fiber (NDF). Dung pellets were collected for 2 days following 7 days of acclimation to each diet. Length and width of oven-dried pellets ranged, respectively, from 8.3 to 10.2 mm and 3.2 to 4.9 mm for diet 1, and 8.9 to 12.4 mm and 3.6 to 4.7 mm for diet 2. Body weight ranged from 232.0 to 504.5 g and did not significantly affect dung size. A series of 2-factor analyses of variance with repeated measures and sequential Bonferroni tests was used to assess the effect of dietary fiber consumption on dung size. An increase in fiber intake led to a significant increase in dung length and dry dung weight but not dung width or body weight. Results suggest a relationship between dung length in prehistoric woodrat middens and changing climate, although the relationship is not clearly understood and needs further evaluation.     

Comparison of desert valvata snail growth at three densities of the invasive New Zealand mudsnail

Invasive species are of concern to natural resource managers and conservation biologists. The New Zealand mudsnail ( Potamopyrgus antipodarum ) has invaded many freshwaters of the western United States with unknown consequences on the native benthic invertebrate fauna. We conducted a laboratory investigation to determine if mudsnails affected the growth of the desert valvata snail ( Valvata utahensis ), a species native to the Snake River in southern Idaho. Results indicated that increasing densities of mudsnails limited the growth rate and absolute growth of the desert valvata. We suggest that absolute growth is a better metric than growth rate for comparing snail species and assessing interactions between them.     

Natural history and invasion of Russian olive along eastern Montana rivers

Russian olive and tamarisk are introduced woody plants invading western North American riparian communities. Beavers can play an important role in structuring these communities by removing the dominant cottonwood trees. Our study explored the way in which beavers interact with cottonwood, Russian olive, and tamarisk along 4 rivers on the Great Plains of eastern Montana. We sampled cottonwood stands that supported populations of 1 or both exotic species, recording beaver damage and density in addition to size and age of cottonwood, Russian olive, and tamarisk. In stands where beaver had been present, they felled an average of 80% of cottonwood trees while rarely using Russian olive or tamarisk. Beaver foraging was apparent in nearly 90% of stands within 50 m of the river channel but only 21% of stands farther away, creating a sunny corridor along the river channel that may increase the invasive potential of Russian olive and tamarisk. Growth rates of both Russian olive and tamarisk were substantially higher where beavers had reduced the cottonwood canopy cover. Managers wishing to reintroduce beavers should consider the potential effect on invasive exotic plants.     

Beavers indirectly enhance the growth of Russian olive and tamarisk along eastern Montana rivers

Russian olive and tamarisk are introduced woody plants invading western North American riparian communities. Beavers can play an important role in structuring these communities by removing the dominant cottonwood trees. Our study explored the way in which beavers interact with cottonwood, Russian olive, and tamarisk along 4 rivers on the Great Plains of eastern Montana. We sampled cottonwood stands that supported populations of 1 or both exotic species, recording beaver damage and density in addition to size and age of cottonwood, Russian olive, and tamarisk. In stands where beaver had been present, they felled an average of 80% of cottonwood trees while rarely using Russian olive or tamarisk. Beaver foraging was apparent in nearly 90% of stands within 50 m of the river channel but only 21% of stands farther away, creating a sunny corridor along the river channel that may increase the invasive potential of Russian olive and tamarisk. Growth rates of both Russian olive and tamarisk were substantially higher where beavers had reduced the cottonwood canopy cover. Managers wishing to reintroduce beavers should consider the potential effect on invasive exotic plants.     

Emerging concepts in acute mountain sickness and high-altitude cerebral edema: from the molecular to the morphological

Acute mountain sickness (AMS) is a neurological disorder that typically affects mountaineers who ascend to high altitude. The symptoms have traditionally been ascribed to intracranial hypertension caused by extracellular vasogenic edematous brain swelling subsequent to mechanical disruption of the blood–brain barrier in hypoxia. However, recent diffusion-weighted magnetic resonance imaging studies have identified mild astrocytic swelling caused by a net redistribution of fluid from the “hypoxia-primed” extracellular space to the intracellular space without any evidence for further barrier disruption or additional increment in brain edema, swelling or pressure. These findings and the observation of minor vasogenic edema present in individuals with and without AMS suggest that the symptoms are not explained by cerebral edema. This has led to a re-evaluation of the relevant pathogenic events with a specific focus on free radicals and their interaction with the trigeminovascular system. (Part of a multi-author review.)     

The tetracycline resistome

Resistance to tetracycline emerged soon after its discovery six decades ago. Extensive clinical and non-clinical uses of this class of antibiotic over the years have combined to select for a large number of resistant determinants, collectively termed the tetracycline resistome. In order to impart resistance, microbes use different molecular mechanisms including target protection, active efflux, and enzymatic degradation. A deeper understanding of the structure, mechanism, and regulation of the genes and proteins associated with tetracycline resistance will contribute to the development of tetracycline derivatives that overcome resistance. Newer generations of tetracyclines derived from engineering of biosynthetic genetic programs, semi-synthesis, and in particular recent developments in their chemical synthesis, together with a growing understanding of resistance, will serve to retain this class of antibiotic to combat pathogens.     

To be disordered or not to be disordered: is that still a question for proteins in the cell?

There is ample evidence that many proteins or regions of proteins lack a well-defined folded structure under native-like conditions. These are called intrinsically disordered proteins (IDPs) or intrinsically disordered regions (IDRs). Whether this intrinsic disorder is also their main structural characteristic in living cells has been a matter of intense debate. The structural analysis of IDPs became an important challenge also because of their involvement in a plethora of human diseases, which made IDPs attractive targets for therapeutic development. Therefore, biophysical approaches are increasingly being employed to probe the structural and dynamical state of proteins, not only in isolation in a test tube, but also in a complex biological environment and even within intact cells. Here, we survey direct and indirect evidence that structural disorder is in fact the physiological state of many proteins in the proteome. The paradigmatic case of α-synuclein is used to illustrate the controversial nature of this topic.     

Earthquakes triggered by silent slip events on Kīlauea volcano, Hawaii

Slow-slip events, or 'silent earthquakes', have recently been discovered in a number of subduction zones including the Nankai trough in Japan, Cascadia, and Guerrero in Mexico, but the depths of these events have been difficult to determine from surface deformation measurements. Although it is assumed that these silent earthquakes are located along the plate megathrust, this has not been proved. Slow slip in some subduction zones is associated with non-volcanic tremor, but tremor is difficult to locate and may be distributed over a broad depth range. Except for some events on the San Andreas fault, slow-slip events have not yet been associated with high-frequency earthquakes, which are easily located. Here we report on swarms of high-frequency earthquakes that accompany otherwise silent slips on Kīlauea volcano, Hawaii. For the most energetic event, in January 2005, the slow slip began before the increase in seismicity. The temporal evolution of earthquakes is well explained by increased stressing caused by slow slip, implying that the earthquakes are triggered. The earthquakes, located at depths of 7-8 km, constrain the slow slip to be at comparable depths, because they must fall in zones of positive Coulomb stress change. Triggered earthquakes accompanying slow-slip events elsewhere might go undetected if background seismicity rates are low. Detection of such events would help constrain the depth of slow slip, and could lead to a method for quantifying the increased hazard during slow-slip events, because triggered events have the potential to grow into destructive earthquakes.     

Bacterial RNA and small antiviral compounds activate caspase-1 through cryopyrin/Nalp3

Missense mutations in the CIAS1 gene cause three autoinflammatory disorders: familial cold autoinflammatory syndrome, Muckle-Wells syndrome and neonatal-onset multiple-system inflammatory disease. Cryopyrin (also called Nalp3), the product of CIAS1, is a member of the NOD-LRR protein family that has been linked to the activation of intracellular host defence signalling pathways. Cryopyrin forms a multi-protein complex termed 'the inflammasome', which contains the apoptosis-associated speck-like protein (ASC) and caspase-1, and promotes caspase-1 activation and processing of pro-interleukin (IL)-1beta (ref. 4). Here we show the effect of cryopyrin deficiency on inflammasome function and immune responses. Cryopyrin and ASC are essential for caspase-1 activation and IL-1beta and IL-18 production in response to bacterial RNA and the imidazoquinoline compounds R837 and R848. In contrast, secretion of tumour-necrosis factor-alpha and IL-6, as well as activation of NF-kappaB and mitogen-activated protein kinases (MAPKs) were unaffected by cryopyrin deficiency. Furthermore, we show that Toll-like receptors and cryopyrin control the secretion of IL-1beta and IL-18 through different intracellular pathways. These results reveal a critical role for cryopyrin in host defence through bacterial RNA-mediated activation of caspase-1, and provide insights regarding the pathogenesis of autoinflammatory syndromes.