Nature Dis-Graced and Grace De-Natured: The Problematic of the Augustinian Doctrine of Grace for Contemporary Theology

Contemporary theologians, as one of their number has commented, have turned from a theology of the Word to a theology of the world. After a period during the first half of the twentieth century in which theologians concerned themselves primarily with questions of their discipline\u27s identity and character, they have in recent years turned to address as a matter of first principle the physical, the social, and the political issues in the world about them. In the course of this effort to shift theological direction, a number of fundamental issues have been raised which have yet to be fully examined. Perhaps the most urgent of these is the problematic of the western doctrine of grace. If contemporary theologians wish to develop a theology of the world, it is imperative that they come to grips with the fact that the soteriological categories of our western traditions offer precious little help in doing so. For the western doctrine of grace has concerned itself almost exclusively with the \u27innerness\u27 or the \u27soul\u27 of the individual, and has but rarely addressed itself to human being or human society or the material world as a whole. In point of fact, basic to the western doctrine has been the distinction between the world as a whole and salvation, i.e., between nature and grace a distinction which has had disastrous results , in that it has led to God and world\u27 and creation and redemption being torn asunder. If a theology of the world is ever to be developed, therefore, this disjunction, indeed, this virtual contradiction between \u27God and world\u27 and between creation and redemption in our thinking and doing must be addressed anew. This article seeks to begin to do so, first, by examining the theology of Augustine, the source of this western doctrine with its axiomatic separation of grace from nature, secondly, by exploring how that separation has characterized the western theological tradition, and third, by suggesting that Augustine himself points to a possible way beyond that separation through a theology of the Holy Spirit

A New Approach to Intensity-Dependent Normalization of Two-Channel Microarrays

A two-channel microarray measures the relative expression levels of thousands of genes from a pair of biological samples. In order to reliably compare gene expression levels between and within arrays, it is necessary to remove systematic errors that distort the biological signal of interest. The standard for accomplishing this is smoothing MA-plots to remove intensity-dependent dye bias and array-specific effects. However, MA methods require strong assumptions. We review these assumptions and derive several practical scenarios in which they fail. The dye-swap normalization method has been much less frequently used because it requires two arrays per pair of samples. We show that a dye-swap is accurate under general assumptions, even under intensity-dependent dye bias, and that a dye-swap provides the minimal information required for removing dye bias from a pair of samples in general. Based on a flexible model of the relationship between mRNA amount and single channel fluorescence intensity, we demonstrate the general applicability of a dye-swap approach. We then propose a common array dye-swap (CADS) method for the normalization of two-channel microarrays. We show that CADS removes both dye-bias and array-specific effects, and preserves the true differential expression signal for every gene. Finally, we discuss some possible extensions of CADS that circumvent the need to use two arrays per pair of samples

Optimal Feature Selection for Nearest Centroid Classifiers, With Applications to Gene Expression Microarrays

Nearest centroid classifiers have recently been successfully employed in high-dimensional applications. A necessary step when building a classifier for high-dimensional data is feature selection. Feature selection is typically carried out by computing univariate statistics for each feature individually, without consideration for how a subset of features performs as a whole. For subsets of a given size, we characterize the optimal choice of features, corresponding to those yielding the smallest misclassification rate. Furthermore, we propose an algorithm for estimating this optimal subset in practice. Finally, we investigate the applicability of shrinkage ideas to nearest centroid classifiers. We use gene-expression microarrays for our illustrative examples, demonstrating that our proposed algorithms can improve the performance of a nearest centroid classifier

Normalization of two-channel microarrays accounting for experimental design and intensity-dependent relationships

eCADS is a new method for multiple array normalization of two-channel microarrays that takes into account general experimental designs and intensity-dependent relationships and allows for a more efficient dye-swap design that requires only one array per sample pair

Detection of Microcystin Aerosol Particles

Harmful Algal Blooms (HABs) are a growing global concern due to their increased prevalence and magnitude, frequency, and duration in affecting both aquatic ecosystems and human health (Brooks et al. 2015). In a series of experiments, lab-generated aerosol particles containing Microcystis and Microseira were captured using filters to analyze for concentrations of Microcystin, Saxitoxin, and Lyngbya toxins. The solutions were found to contain aerosols but did not contain detectable levels of Microcystin, Saxitoxin, and Lyngbya toxins following analysis by HPLC-MS. While the techniques for generating aerosols were shown to be effective, the generation and analysis of toxins did not produce the expected results. The lack of toxin detection likely resulted from the lower level of toxin in the algae and/or the length of time air samples were extracted. Future research is proposed to consist of experiments in the lab with increased exposure times and in the field with naturally generated aerosols during periods of major bloom events

Settling the Reward Hypothesis

The reward hypothesis posits that, "all of what we mean by goals and purposes can be well thought of as maximization of the expected value of the cumulative sum of a received scalar signal (reward)." We aim to fully settle this hypothesis. This will not conclude with a simple affirmation or refutation, but rather specify completely the implicit requirements on goals and purposes under which the hypothesis holds