A contestatory theory of political obligations

There is an orthodox approach towards questions of political obligation. This neatly divides all the philosophical terrain into two opposing views. On one side, the standard theory of political obligation to the state, on the other a sceptical view which is often described as philosophical anarchism. In this thesis I argue that this is a false distinction. I examine three important features of the major political principles thought to ground such obligations: their lack of specificity, the multiplicity of relevant political entities, and the intersecting claims of different political principles. Combining these with the defeasibility claimed by all models of political obligation, reveals that all the standard theories are in fact a form of plural multiple-principle theory. Further, sceptical approaches are also the same kind of multiple-principle theory of obligation. This false distinction has led us away from the radical potential of a theory of political obligation to illuminate the lived political experience of citizens. This dissertation develops a unified and contestatory theory of political obligations. This is a theory which is maximally plural, and also simultaneously a theory of political obedience and civil disobedience. It addresses the complexity of real world (i.e., non-ideal) duties and dilemmas of people confronted with the demands of the state. It maps out the political moral landscape for citizens. It engages with a range of partial political duties which are often in conflict. I consider the three most plausible kinds of political principles: natural duty, association and fair play. By taking a synoptic view of their normative impact, I show that while each may fail under the orthodox approach, they all still succeed, in interesting ways, to ground a range of partial and potentially contestatory duties for citizens. These obligations may support each other, and they may conflict. As circumstances change, the same set of political principles may recommend obedience to the law and other demands of the state, or actions orthogonal to such, or constitute a permission to disobey, or even make disobedience one’s political obligation. I explore two important implications of this theory. The first concerns philosophical anarchism. Here I demonstrate that models of philosophical anarchism and other sceptical models do not in fact constitute a substantively distinct alternative view but instead depict a theory of political obligation. Their position is not theoretically distinct and, in many respects advocates of either position have been talking past each other. The second concerns civil disobedience. The contestatory theory incorporates different political principles which may conflict with each other. In many circumstances, civil disobedience may represent the best way of responding to the normative demands of political life. To better accommodate this, I develop a new model of civil disobedience which is expansive and free of many of the fractures and constraints which characterise much of the post-Rawlsian philosophical theorising on civil disobedience. Although theoretically freestanding, it is designed to be complementary with the normative implications of the contestatory theory. The conception of civil disobedience I develop here is specifically designed to function as a moral and political shield for citizens against the overwhelming power of the state

The Protein Naming Utility: a rules database for protein nomenclature

Generation of syntactically correct and unambiguous names for proteins is a challenging, yet vital task for functional annotation processes. Proteins are often named based on homology to known proteins, many of which have problematic names. To address the need to generate high-quality protein names, and capture our significant experience correcting protein names manually, we have developed the Protein Naming Utility (PNU, http://www.jcvi.org/pn-utility). The PNU is a web-based database for storing and applying naming rules to identify and correct syntactically incorrect protein names, or to replace synonyms with their preferred name. The PNU allows users to generate and manage collections of naming rules, optionally building upon the growing body of rules generated at the J. Craig Venter Institute (JCVI). Since communities often enforce disparate conventions for naming proteins, the PNU supports grouping rules into user-managed collections. Users can check their protein names against a selected PNU rule collection, generating both statistics and corrected names. The PNU can also be used to correct GenBank table files prior to submission to GenBank. Currently, the database features 3080 manual rules that have been entered by JCVI Bioinformatics Analysts as well as 7458 automatically imported names

Photoproduction of K+K− meson pairs on the proton

The exclusive reaction γp→pK+K− was studied in the photon energy range 3.0–3.8  GeV and momentum transfer range 0.6<−t<1.3  GeV2. Data were collected with the CLAS detector at the Thomas Jefferson National Accelerator Facility. In this kinematic range the integrated luminosity was approximately 20  pb−1. The reaction was isolated by detecting the K+ and the proton in CLAS, and reconstructing the K− via the missing-mass technique. Moments of the dikaon decay angular distributions were extracted from the experimental data. Besides the dominant contribution of the ϕ meson in the P wave, evidence for S−P interference was found. The differential production cross sections dσ/dt for individual waves in the mass range of the ϕ resonance were extracted and compared to predictions of a Regge-inspired model. This is the first time the t-dependent cross section of the S-wave contribution to the elastic K+K− photoproduction has been measured

LSST: from Science Drivers to Reference Design and Anticipated Data Products

(Abridged) We describe here the most ambitious survey currently planned in the optical, the Large Synoptic Survey Telescope (LSST). A vast array of science will be enabled by a single wide-deep-fast sky survey, and LSST will have unique survey capability in the faint time domain. The LSST design is driven by four main science themes: probing dark energy and dark matter, taking an inventory of the Solar System, exploring the transient optical sky, and mapping the Milky Way. LSST will be a wide-field ground-based system sited at Cerro Pach\'{o}n in northern Chile. The telescope will have an 8.4 m (6.5 m effective) primary mirror, a 9.6 deg$^2$ field of view, and a 3.2 Gigapixel camera. The standard observing sequence will consist of pairs of 15-second exposures in a given field, with two such visits in each pointing in a given night. With these repeats, the LSST system is capable of imaging about 10,000 square degrees of sky in a single filter in three nights. The typical 5$\sigma$ point-source depth in a single visit in $r$ will be $\sim 24.5$ (AB). The project is in the construction phase and will begin regular survey operations by 2022. The survey area will be contained within 30,000 deg$^2$ with $\delta<+34.5^\circ$, and will be imaged multiple times in six bands, $ugrizy$, covering the wavelength range 320--1050 nm. About 90\% of the observing time will be devoted to a deep-wide-fast survey mode which will uniformly observe a 18,000 deg$^2$ region about 800 times (summed over all six bands) during the anticipated 10 years of operations, and yield a coadded map to $r\sim27.5$. The remaining 10\% of the observing time will be allocated to projects such as a Very Deep and Fast time domain survey. The goal is to make LSST data products, including a relational database of about 32 trillion observations of 40 billion objects, available to the public and scientists around the world.Comment: 57 pages, 32 color figures, version with high-resolution figures available from https://www.lsst.org/overvie

A Computational Framework Discovers New Copy Number Variants with Functional Importance

Structural variants which cause changes in copy numbers constitute an important component of genomic variability. They account for 0.7% of genomic differences in two individual genomes, of which copy number variants (CNVs) are the largest component. A recent population-based CNV study revealed the need of better characterization of CNVs, especially the small ones (<500 bp).We propose a three step computational framework (Identification of germline Changes in Copy Number or IgC2N) to discover and genotype germline CNVs. First, we detect candidate CNV loci by combining information across multiple samples without imposing restrictions to the number of coverage markers or to the variant size. Secondly, we fine tune the detection of rare variants and infer the putative copy number classes for each locus. Last, for each variant we combine the relative distance between consecutive copy number classes with genetic information in a novel attempt to estimate the reference model bias. This computational approach is applied to genome-wide data from 1250 HapMap individuals. Novel variants were discovered and characterized in terms of size, minor allele frequency, type of polymorphism (gains, losses or both), and mechanism of formation. Using data generated for a subset of individuals by a 42 million marker platform, we validated the majority of the variants with the highest validation rate (66.7%) was for variants of size larger than 1 kb. Finally, we queried transcriptomic data from 129 individuals determined by RNA-sequencing as further validation and to assess the functional role of the new variants. We investigated the possible enrichment for variant's regulatory effect and found that smaller variants (<1 Kb) are more likely to regulate gene transcript than larger variants (p-value = 2.04e-08). Our results support the validity of the computational framework to detect novel variants relevant to disease susceptibility studies and provide evidence of the importance of genetic variants in regulatory network studies

Women and ARVâ based prevention: opportunities and challenges

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/138349/1/jia29419.pd

Pathema: a clade-specific bioinformatics resource center for pathogen research

Pathema (http://pathema.jcvi.org) is one of the eight Bioinformatics Resource Centers (BRCs) funded by the National Institute of Allergy and Infectious Disease (NIAID) designed to serve as a core resource for the bio-defense and infectious disease research community. Pathema strives to support basic research and accelerate scientific progress for understanding, detecting, diagnosing and treating an established set of six target NIAID Category A–C pathogens: Category A priority pathogens; Bacillus anthracis and Clostridium botulinum, and Category B priority pathogens; Burkholderia mallei, Burkholderia pseudomallei, Clostridium perfringens and Entamoeba histolytica. Each target pathogen is represented in one of four distinct clade-specific Pathema web resources and underlying databases developed to target the specific data and analysis needs of each scientific community. All publicly available complete genome projects of phylogenetically related organisms are also represented, providing a comprehensive collection of organisms for comparative analyses. Pathema facilitates the scientific exploration of genomic and related data through its integration with web-based analysis tools, customized to obtain, display, and compute results relevant to ongoing pathogen research. Pathema serves the bio-defense and infectious disease research community by disseminating data resulting from pathogen genome sequencing projects and providing access to the results of inter-genomic comparisons for these organisms

The E-ELT first light spectrograph HARMONI: capabilities and modes

Trabajo presentado en SPIE Astronomical Telescopes, celebrado en San Diego (California), del 26 de junio al 1 de julio de 2016HARMONI is the E-ELT's first light visible and near-infrared integral field spectrograph. It will provide four different spatial scales, ranging from coarse spaxels of 60 × 30 mas best suited for seeing limited observations, to 4 mas spaxels that Nyquist sample the diffraction limited point spread function of the E-ELT at near-infrared wavelengths. Each spaxel scale may be combined with eleven spectral settings, that provide a range of spectral resolving powers (R 3500, 7500 and 20000) and instantaneous wavelength coverage spanning the 0.5 - 2.4 ¿m wavelength range of the instrument. In autumn 2015, the HARMONI project started the Preliminary Design Phase, following signature of the contract to design, build, test and commission the instrument, signed between the European Southern Observatory and the UK Science and Technology Facilities Council. Crucially, the contract also includes the preliminary design of the HARMONI Laser Tomographic Adaptive Optics system. The instrument's technical specifications were finalized in the period leading up to contract signature. In this paper, we report on the first activity carried out during preliminary design, defining the baseline architecture for the system, and the trade-off studies leading up to the choice of baseline