The "Xhosa" In Town, Revisited Urban Social Anthropology: A Failure of Method and Theory

The weaknesses of urban anthropology in South Africa are discussed from a methodological, analytical, and political point of view. The article asserts that colonial policy demands on urban anthropology placed limits on the choice of subject matter and concepts. This is illustrated from a three volume work, The Xhosa in Town , done in South Africa under the direction of Philip Mayer, the senior author.     

Literature Mining for the Discovery of Hidden Connections between Drugs,Genes and Diseases

The scientific literature represents a rich source for retrieval of knowledge on associations between biomedical concepts such as genes, diseases and cellular processes. A commonly used method to establish relationships between biomedical concepts from literature is co-occurrence. Apart from its use in knowledge retrieval, the co-occurrence method is also well-suited to discover new, hidden relationships between biomedical concepts following a simple ABC-principle, in which A and C have no direct relationship, but are connected via shared B-intermediates. In this paper we describe CoPub Discovery, a tool that mines the literature for new relationships between biomedical concepts. Statistical analysis using ROC curves showed that CoPub Discovery performed well over a wide range of settings and keyword thesauri. We subsequently used CoPub Discovery to search for new relationships between genes, drugs, pathways and diseases. Several of the newly found relationships were validated using independent literature sources. In addition, new predicted relationships between compounds and cell proliferation were validated and confirmed experimentally in an in vitro cell proliferation assay. The results show that CoPub Discovery is able to identify novel associations between genes, drugs, pathways and diseases that have a high probability of being biologically valid. This makes CoPub Discovery a useful tool to unravel the mechanisms behind disease, to find novel drug targets, or to find novel applications for existing drugs.     

Examining the Process of de Novo Gene Birth: An Educational Primer on “Integration of New Genes into Cellular Networks,and Their Structural Maturation”

SUMMARY New genes that arise from modification of the noncoding portion of a genome rather than being duplicated from parent genes are called de novo genes. These genes, identified by their brief evolution and lack of parent genes, provide an opportunity to study the timeframe in which emerging genes integrate into cellular networks, and how the characteristics of these genes change as they mature into bona fide genes. An article by G. Abrusán provides an opportunity to introduce students to fundamental concepts in evolutionary and comparative genetics and to provide a technical background by which to discuss systems biology approaches when studying the evolutionary process of gene birth. Basic background needed to understand the Abrusán study and details on comparative genomic concepts tailored for a classroom discussion are provided, including discussion questions and a supplemental exercise on navigating a genome database.     

"It Was Fine, if You Wanted to Leave": Educational Ambivalence in a Nova Scotian Coastal Community 1963–1998

This article reports on a study of schooling in southwest Nova Scotia. Using Bourdieu's concepts of cultural capital and habitus, I analyze rural men's relationships involving identity, work, place, and schooling to explain continuing high male dropout rates and local traditions of ambivalence and resistance to schooling. I conclude that the tension between formal schooling and place is endemic in many rural communities and that qualitative migration analysis can reveal the complexity of relationships between learning and leaving.     

Chapter V: The Active and Passive, "Receptive" and "Productive" in Learning a Second Language

Although in contemporary methods and (insofar as we are justified in using the term at all) in the contemporary psychology of foreign-language learning, the concepts of "active" and "passive" are widely used with reference to aspects of learning, to methods, habits, and models, these concepts are actually quite vague. This raises the necessity of systematically examining the main problems associated with maintaining a distinction between "active" and "passive" in language acquisition.     

基因间的同源关系

同源是指从共同祖先的特性遗传下来的通常带有分歧的两个特征之间的关系。同源概念组成了进化基因组学的基础并对功能基因组学有巨大作用,但基于对同源概念的不准确理解,当前对其有诸多模糊表述,因此了解其确切含义具有重要意义。本文就同源、直系同源和旁系同源的概念和性质进行综述。     

基因间的同源关系

同源是指从共同祖先的特性遗传下来的通常带有分歧的两个特征之间的关系。同源概念组成了进化基因组学的基础并对功能基因组学有巨大作用,但基于对同源概念的不准确理解,当前对其有诸多模糊表述,因此了解其确切含义具有重要意义。本文就同源、直系同源和旁系同源的概念和性质进行综述。     

Genes after the human genome project

While the Human Genome Nomenclature Committee (HGNC) concept of the gene can accommodate a wide variety of genomic sequences contributing to phenotypic outcomes, it fails to specify how sequences should be grouped when dealing with complex loci consisting of adjacent/overlapping sequences contributing to the same phenotype, distant sequences shown to contribute to the same gene product, and partially overlapping sequences identified by different techniques. The purpose of this paper is to review recently proposed concepts of the gene and critically assess how well they succeed in addressing the above problems while preserving the degree of generality achieved by the HGNC concept. I conclude that a dynamic interplay between mapping and syntax-based concepts is required in order to satisfy these desiderata.     

Industrial ecology,climate adaptation,and financial risk

Climate adaptation has become an important topic for risk management in companies. This article investigates the usefulness of Industrial Ecology tools and concepts in this context. The conclusion is that the established tools and concepts were not designed with the purpose of assisting managers in the climate adaptation and related financial risk context. Nevertheless, the tools and concepts offer plenty of aspects and features that are helpful for the assessment and management of climate risks. The tools primarily provide guidance for the managerial decision‐making process, notably in terms of data handling. The concepts can be used as a starting point for developing new climate risk management frameworks.     

从泛甲壳动物新假说评述节肢动物系统进化的研究进展

Giribet et al(2001)构建的节肢动物系统树中,将六足动物（昆虫）完全合并到甲壳动物之中,共同构成一个新的类群：泛甲壳动物（Pancrustacea）。这与近百年来经典的节肢动物系统发生概念有很大的不同。现拟重温上个世纪以来最主要的4个假说,简要评述节肢动物系统发生研究的近况,并给予展望。     

Citric acid cycle as a "one-step" reaction

One of the most familiar metabolic pathways is the citric acid cycle. This reaction sequence is characterized by intermediates which can be detected in aqueous solution. The recent success in isolating an enzyme cluster with five cycle activities suggests that the cyclic sequence should find a counterpart in a highly organized enzyme system for effective catalysis. In the present article, a new way of looking at this complex reaction sequence is proposed utilizing the hydrophobicity of active sites to define the entrance or exit of substrates as a first or last reaction step. With this view, highly reactive intermediates can be formulated which are able to react in a quasi "one step" mechanism to stable end-products. It is possible to derive the known intermediates of the citric acid cycle by a transition from a proposed hydrophobic catalytic site into the aqueous phase. A variety of biochemical concepts in use ("energy-rich"-bonds, group transfer, substrate-channelling, transporters, etc.) can be understood to be derived from methodology commonly in use. The proposed reaction mechanism demands a specific organization of the proteins forming the enzymatic activity(ies). Isolated and purified enzymes should, in consequence, be seen as isolation products, differing from their functionally organized form in a living cell. In this paper, a new concept is proposed by which a variety of observations and concepts can be unified.     

Identifying Correlations between Chromosomal Proximity of Genes and Distance of Their Products in Protein-Protein Interaction Networks of Yeast

In this article we present evidence for a relationship between chromosome gene loci and the topological properties of the protein-protein interaction network corresponding to the set of genes under consideration. Specifically, for each chromosome of the Saccharomyces cerevisiae genome, the distribution of the intra-chromosome inter-gene distances was analyzed and a positive correlation with the distance among the corresponding proteins of the protein-protein interaction network was found. In order to study this relationship we used concepts based on non-parametric statistics and information theory.We provide statistical evidence that if two genes are closely located, then it is likely that their protein products are closely located in the protein-protein interaction network, or in other words, that they are involved in the same biological process.     

On the origins of morphological variation, canalization, robustness, and evolvability

Canalization is a concept, introduced by Waddington that describesthe reduced sensitivity of a phenotype to genetic and environmentalperturbations. Some research in canalization assumes that lackof variation in a trait in one genotype with respect to anothergenotype in a population, is due to the existence of bufferingmechanisms against environmental and/or genetic variation. Thisarticle criticizes this assumption and out points out otherpossible problems with the concepts of canalization, robustness,and evolvability. These involve: the neglect of alternativeexplanations for the lack of variation in a trait, the incompatibilitywith current understanding of development, the way the mutivariatenature of morphological variation is considered. In addition,this article tries to explain that these concepts implicitlyassume, although not generally acknowledged, that without bufferingany genetic or environmental variation should give rise to adistinct phenotypic outcome. This can be avoided by restrictingthe use of canalization to cases in which, as in hsp90, thereis direct evidence of buffering. For the other cases it wouldbe clearer to talk about variational properties or simply typeof variation. The concept of evolvability is also biased towardsunivariate comparisons and is dependent on selective pressures.It is suggested that this can be replaced by "type of phenotypicvariation" from a genotype or variational properties. Overall,this article proposes that the concepts of canalization andevolvability involve some assumptions that, in most situations,unnecessarily complicate the study of evolution and development.     

衰老及相关基因群

综述20世纪与基因相关的衰老原理的探索及其进展,整体动物水平的衰老研究归纳了衰老了诸多表象但疏于对衰老本质的探讨。线粒体－自由基衰老学说阐述了线粒体DNA的损伤与衰老有很大的相关性,由Hayflic k分裂限制衍生的端粒衰老学说给衰老机制提供了重要信息,目前狭隘的基因程序化衰老学说已和损伤衰老概念有机的联系在了一起。总之,自由基衰老学说得到了氧化衰老学说和糖基化衰老学说的补充逐渐形成了生化副反应与基因衰老学说的大统一衰老机制板块理论。     

From illness narratives to social commentary: a Pirandellian approach to "nerves"

The concept of "nerves" is an integral component of the language of distress found in a number of societies. Individuals, however, often extend its meaning well beyond the realm of suffering. In this article, I examine some Sicilian-Canadian uses of "nerves" from a Pirandellian perspective. This, I believe, gives us an insight into how people (1) make use of illness narratives to give meaning to their life experiences, and (2) attempt to influence the thought and behavior of significant others. In the process, I address the question how do we move away from anthropological definitions and explanations that tend to simplify or mask some of the rich complexities surrounding the meaning(s) of "folk" concepts?     

Teaching "Species"

A clear understanding of the term "species" is fundamental to the subject of evolution. However, introductory textbooks often fail to address this topic until one of the later chapters, after having used the term species in all preceding chapters. Furthermore, definitions of terms critical to a clear understanding of this subject are often vague or absent in chapters on species concepts. We feel the popular notion of a "species problem" has been unnecessarily inflated by this less-than-effective educational approach. Clearly addressing this essential subject at the beginning of a course on evolution will prepare students to learn the details and complexities of evolution. Here we provide the background for an alternative approach to this foundational topic, followed by an outlined lesson plan. We emphasize early introduction of this subject in texts and courses using unambiguous terminology and including the historical development of species concepts.     

Compelling classroom demonstrations that link visual system anatomy,physiology, and behaviour

One of our approaches to teaching a course in anatomy and physiology is to stress the fundamental, systems-level concepts. One successful strategy we use is to continually highlight the relationships among anatomy, physiology, and behavior. In this article, we describe a set of classroom demonstrations that stress these links while fostering critical thinking. These demonstrations, on the topic of sensory system structure and function, rely on two perceptual consequences of neural adaptation in the visual system: afterimages and aftereffects. Viewing specific visual stimuli under binocular or monocular conditions with interocular transfer permits several concepts to be observed and discussed, including neural adaptation, anatomical and functional segregation of visual system pathways, and the relationship among visual system structure, function, and perception. This article discusses how to produce and present the required visual stimuli, suggests a set of questions to stimulate critical thinking, and presents student evaluation of this activity.     

The Multiple Meanings of Jewish Genes

This article addresses contemporary social challenges created by new genetic research on Jews and by Jews, and its implications for the meanings of Jewish identity, on both the individual and the collective levels. The article begins with a brief overview of selective genetic studies of Jewish populations and the controversies they have generated. It continues with an examination of the emerging field of Jewish genetic demography, which employs genetic tests to identify lineages, claim kin, and support Jewish historical and political claims. Here the article explores how Jewish genetic demographers interpret genetic studies to reinforce oral tradition and Biblical prophecy about the origins of the Jews and their experience in the Diaspora. This research is then juxtaposed with debates that emerge from contemporary rabbinic deliberations over the appropriate uses of new reproductive technologies, debates that, contrary to the assertions of Jewish genetic demographers, suggest genes are believed to possess limited ability to confer or create Jewishness in the traditional rabbinic imagination. In the final section of this article, a debate is staged about contemporary biomedical practices that allow for the exchange and transfer of body parts and bodily substances, as a strategy for challenging genetic notions of Jewish identity.