SEPRAN:A Versatile Finite-Element Package for a Wide Variety of Problems in Geosciences

Numerical modelling of geological processes, such as mantle convection, flow in porous media, and geothermal heat transfer, has become quite common with the increase in computing and the availability o...     

Kant and the scope of analogy in the life sciences

In the present paper I investigate the role that analogy plays in eighteenth-century biology and in Kant's philosophy of biology. I will argue that according to Kant, biology, as it was practiced in the eighteenth century, is fundamentally based on analogical reflection. However, precisely because biology is based on analogical reflection, biology cannot be a proper science. I provide two arguments for this interpretation. First, I argue that although analogical reflection is, according to Kant, necessary to comprehend the nature of organisms, it is also necessarily insufficient to fully comprehend the nature of organisms. The upshot of this argument is that for Kant our understanding of organisms is necessarily limited. Second, I argue that Kant did not take biology to be a proper science because biology was based on analogical arguments. I show that Kant stemmed from a philosophical tradition that did not assign analogical arguments an important justificatory role in natural science. Analogy, according to this conception, does not provide us with apodictically certain cognition. Hence, sciences based on analogical arguments cannot constitute proper sciences.     

Rich Pictures: Collaborative Communication Through Icons

A visual language of pictures, such as the rich picture used in the Soft System Methodology, offers a way of global communication that far exceeds the limitations of text and speech. Simple graphics can be rapidly communicated, processed and transmitted within a large and culturally diverse constituency. This paper looks at the benefits and interpretative risks when using rich pictures for system understanding. The aim of this paper is twofold: firstly to report upon an observation of a large scale collaborative diagramming workshop and compare the resulting pictures with a previous workshop study. Secondly, to develop further ongoing research which suggests rich picture construction can be aided by providing an icon legend. This paper compares 2 rich picture workshops: the diagramming workshop at the Open University eSTEeM Diagramming Colloquium in March 2012 and a workshop held in Heriot Watt University in February 2012. The comparative results are set against the ongoing empirically grounded rich picture research within Heriot-Watt University in Scotland. Preliminary results suggest there are a set of distinguishable icons and shapes that are generic across all rich pictures regardless of domain. Further analysis of the early results suggests a natural intrinsic grammar is manifested within rich pictures in terms of relationships, icons, context and connectors.     

Integrative taxonomy of the gymnophthalmid lizard Neusticurus rudis Boulenger, 1900 identifies a new species in the eastern Pantepui region,north-eastern South America

ABSTRACT

The gymnophthalmid lizard genus Neusticurus Duméril and Bibron, 1839 currently contains six described species. One of them, Neusticurus rudis Boulenger, 1900 has a long history of taxonomic confusion, and uncertainty remains about the number of species involved under that name, especially in the Pantepui region. Our molecular phylogenetic (concatenation and species tree) and morphological (morphometrics, external and hemipenial morphology) analyses confirm Neusticurus rudis as a species complex with several candidate species in the eastern Pantepui region. Neusticurus rudis is here redescribed based on the re-examination of the holotype and 10 specimens from the vicinity of the type locality (ca. 15 km airline) in Guyana. The geographic distribution of N. rudis sensu stricto is restricted to east of the Venezuelan Gran Sabana, extending from the slopes of Mount Roraima in Venezuela through the slopes of Maringma-tepui and Wayalayeng to Mount Ayanganna in Guyana, between 678 and 1500 m elevation. Populations tentatively assigned to N. rudis also occur from Mount Wokomung in the Pakaraima Mountains of Guyana to the Iwokrama Forest Reserve in Guyana, between 159 and 1234 m elevation. A new Neusticurus species is described from the uplands and highlands of the eastern Pantepui region, west of the Venezuelan Gran Sabana in Brazil and Venezuela, between 900 and 2200 m elevation. Populations provisionally assigned to the new species were also found from the La Escalera region to Chivatón, the summit of Abakapá-tepui and the slopes and summit of Auyán-tepui, Venezuela, between 1100 and 2203 m elevation. Our results suggest the Gran Sabana as a possible recent biogeographical barrier for the genus in the region and indicate that tepui-summit Neusticurus populations derive from uplands populations that shifted their habitat preference.

www.zoobank.org/lsid:zoobank.org:pub:33DCF862-11CF-4FD0-B4D6-706E2C6A339E     

Chymotrypsin C (CTRC) variants that diminish activity or secretion are associated with chronic pancreatitis

Chronic pancreatitis is a persistent inflammatory disease of the pancreas, in which the digestive protease trypsin has a fundamental pathogenetic role. Here we have analyzed the gene encoding the trypsin-degrading enzyme chymotrypsin C (CTRC) in German subjects with idiopathic or hereditary chronic pancreatitis. Two alterations in this gene, p.R254W and p.K247_R254del, were significantly overrepresented in the pancreatitis group, being present in 30 of 901 (3.3%) affected individuals but only 21 of 2,804 (0.7%) controls (odds ratio (OR) = 4.6; confidence interval (CI) = 2.6-8.0; P = 1.3 x 10(-7)). A replication study identified these two variants in 10 of 348 (2.9%) individuals with alcoholic chronic pancreatitis but only 3 of 432 (0.7%) subjects with alcoholic liver disease (OR = 4.2; CI = 1.2-15.5; P = 0.02). CTRC variants were also found in 10 of 71 (14.1%) Indian subjects with tropical pancreatitis but only 1 of 84 (1.2%) healthy controls (OR = 13.6; CI = 1.7-109.2; P = 0.0028). Functional analysis of the CTRC variants showed impaired activity and/or reduced secretion. The results indicate that loss-of-function alterations in CTRC predispose to pancreatitis by diminishing its protective trypsin-degrading activity.     

Genomic buffering mitigates the effects of deleterious mutations in bacteria

The relationship between the number of randomly accumulated mutations in a genome and fitness is a key parameter in evolutionary biology. Mutations may interact such that their combined effect on fitness is additive (no epistasis), reinforced (synergistic epistasis) or mitigated (antagonistic epistasis). We measured the decrease in fitness caused by increasing mutation number in the bacterium Salmonella typhimurium using a regulated, error-prone DNA polymerase (polymerase IV, DinB). As mutations accumulated, fitness costs increased at a diminishing rate. This suggests that random mutations interact such that their combined effect on fitness is mitigated and that the genome is buffered against the fitness reduction caused by accumulated mutations. Levels of the heat shock chaperones DnaK and GroEL increased in lineages that had accumulated many mutations, and experimental overproduction of GroEL further increased the fitness of lineages containing deleterious mutations. These findings suggest that overexpression of chaperones contributes to antagonistic epistasis.     

Torque-generating units of the flagellar motor of Escherichia coli have a high duty ratio

Rotation of the bacterial flagellar motor is driven by an ensemble of torque-generating units containing the proteins MotA and MotB. Here, by inducing expression of MotA in motA- cells under conditions of low viscous load, we show that the limiting speed of the motor is independent of the number of units: at vanishing load, one unit turns the motor as rapidly as many. This result indicates that each unit may remain attached to the rotor for most of its mechanochemical cycle, that is, that it has a high duty ratio. Thus, torque generators behave more like kinesin, the protein that moves vesicles along microtubules, than myosin, the protein that powers muscle. However, their translation rates, stepping frequencies and power outputs are much higher, being greater than 30 microm s(-1), 12 kHz and 1.5 x 10(5) pN nm s(-1), respectively.