Trans-Planckian philosophy of cosmology

I provide some philosophical groundwork for the recently proposed ‘trans-Planckian censorship’ conjecture in theoretical physics. In particular, I argue that structure formation in early universe cosmology is, at least as we typically understand it, autonomous with regards to quantum gravity, the high energy physics that governs the Planck regime in our universe. Trans-Planckian censorship is then seen as a means of rendering this autonomy an empirical constraint within ongoing quantum gravity research.     

Towards a proteome-scale map of the human protein-protein interaction network

Systematic mapping of protein-protein interactions, or 'interactome' mapping, was initiated in model organisms, starting with defined biological processes and then expanding to the scale of the proteome. Although far from complete, such maps have revealed global topological and dynamic features of interactome networks that relate to known biological properties, suggesting that a human interactome map will provide insight into development and disease mechanisms at a systems level. Here we describe an initial version of a proteome-scale map of human binary protein-protein interactions. Using a stringent, high-throughput yeast two-hybrid system, we tested pairwise interactions among the products of approximately 8,100 currently available Gateway-cloned open reading frames and detected approximately 2,800 interactions. This data set, called CCSB-HI1, has a verification rate of approximately 78% as revealed by an independent co-affinity purification assay, and correlates significantly with other biological attributes. The CCSB-HI1 data set increases by approximately 70% the set of available binary interactions within the tested space and reveals more than 300 new connections to over 100 disease-associated proteins. This work represents an important step towards a systematic and comprehensive human interactome project.     

Non-equilibration of hydrostatic pressure in blebbing cells

Current models for protrusive motility in animal cells focus on cytoskeleton-based mechanisms, where localized protrusion is driven by local regulation of actin biochemistry. In plants and fungi, protrusion is driven primarily by hydrostatic pressure. For hydrostatic pressure to drive localized protrusion in animal cells, it would have to be locally regulated, but current models treating cytoplasm as an incompressible viscoelastic continuum or viscous liquid require that hydrostatic pressure equilibrates essentially instantaneously over the whole cell. Here, we use cell blebs as reporters of local pressure in the cytoplasm. When we locally perfuse blebbing cells with cortex-relaxing drugs to dissipate pressure on one side, blebbing continues on the untreated side, implying non-equilibration of pressure on scales of approximately 10 microm and 10 s. We can account for localization of pressure by considering the cytoplasm as a contractile, elastic network infiltrated by cytosol. Motion of the fluid relative to the network generates spatially heterogeneous transients in the pressure field, and can be described in the framework of poroelasticity.     

Spectroscopic evidence for a lava fountain driven by previously accumulated magmatic gas

Lava fountains are spectacular continuous gas jets, propelling lava fragments to heights of several hundred metres, which occasionally occur during eruptions of low-viscosity magmas. Whether they are generated by the effervescent disruption of fast-rising bubbly melt or by the separate ascent of a bubble foam layer accumulated at depth still remains a matter of debate. No field measurement has yet allowed firm discrimination between these two models. A key insight into the origin of lava fountains may be gained by measuring the chemical composition of the driving gas phase. This composition should differ markedly depending on whether the magma degassing occurs before or during eruption. Here we report the analysis of magmatic gas during a powerful (250-600 m high) lava fountain, measured with Fourier transform infrared spectroscopy on Mount Etna, Sicily. The abundances of volcanic gas species, determined from absorption spectra of lava radiation, reveal a fountain gas having higher CO2/S and S/Cl ratios than other etnean emissions, and which cannot derive from syn-eruptive bulk degassing of Etna basalt. Instead, its composition suggests violent emptying of a gas bubble layer previously accumulated at about 1.5 km depth below the erupting crater.     

A single-nucleotide polymorphism tagging set for human drug metabolism and transport

Interindividual variability in drug response, ranging from no therapeutic benefit to life-threatening adverse reactions, is influenced by variation in genes that control the absorption, distribution, metabolism and excretion of drugs. We genotyped 904 single-nucleotide polymorphisms (SNPs) from 55 such genes in two population samples (European and Japanese) and identified a set of tagging SNPs that represents the common variation in these genes, both known and unknown. Extensive empirical evaluations, including a direct assessment of association with candidate functional SNPs in a new, larger population sample, validated the performance of these tagging SNPs and confirmed their utility for linkage-disequilibrium mapping in pharmacogenetics. The analyses also suggest that rare variation is not amenable to tagging strategies.     

Trading zones and interactional expertise

The phrase ‘trading zone’ is often used to denote any kind of interdisciplinary partnership in which two or more perspectives are combined and a new, shared language develops. In this paper we distinguish between different types of trading zone by asking whether the collaboration is co-operative or coerced and whether the end-state is a heterogeneous or homogeneous culture. In so doing, we find that the voluntary development of a new language community—what we call an inter-language trading zone—represents only one of four possible configurations. In developing this argument we show how different modes of collaboration result in different kinds of trading zone, how different kinds of trading zone may be ‘nested’ inside each other and discuss how a single collaboration might move between different kinds of trading zone over time. One implication of our analysis is that interactional expertise is a central component of at least one class of trading zone.     

Grass rhizosheaths: associated bacterial communities and potential for nitrogen fixation

Rhizosheaths are structures composed of mucilage secreted from plants and adherent soil particles that form a cylinder around the root. Using scanning electron microscopy (SEM), we observed bacteria associated with rhizosheaths of the grasses Achnatherum hymenoides, Calamovilfa longifolia, Hesperostipa comata, and Pascopyrum smithii from a sand dune area in Harding County in northwestern South Dakota. The greatest numbers of bacteria, observed with SEM (529 mm –2 ), and the greatest number of culturable bacteria (9.9 × 10 7 CFU ? g –1 or 5178 CFU ? mm –2 ) were on rhizosheaths of C. longifolia. Rhizosheaths of all the grasses examined contained a higher density of bacteria than the surrounding soil. Nitrogen fixation, as assayed by reduction of acetylene to ethylene, was present in some rhizosheaths. Bacterial nif H gene sequences amplified from bacteria associated with rhizosheaths were most similar to those from Alcaligenes latus and Mesorhizobium loti .     

研制中的新一代仿生人

目前,欧美科学家在仿生学方面进行着广泛地研究,他们即将推出以塑料肌肉和硅芯片有机结合制作的仿生人,令人难以分辨真人与机器人。仿生装置除了替代残疾人体部位外,在防御和治疗疾患上正日益显现出难能可贵的应用潜力。在美国新墨西哥州立大学一所杂乱喧嚣的实验室内,一架人体骨骼复制品轻盈悠然地踩着一辆练习用自行车。这绝非别出心裁的人体技艺展示,人称博尼（Bony）先生的仿生人正在用电池驱动的人工肌肉蹬踏自行车。40年前,瑞典工程师阿尼·拉尔森（ArneLarsson）在首都斯德哥尔摩的卡罗琳斯克研究所研制出第一台完全植入式…