How to describe genes: enlightenment from the quaternary number system

As an open problem, computational gene identification has been widely studied, and many gene finders (software) become available today. However, little attention has been given to the problem of describing the common features of known genes in databanks to transform raw data into human understandable knowledge. In this paper, we draw attention to the task of describing genes and propose a trial implementation by treating DNA sequences as quaternary numbers. Under such a treatment, the common features of genes can be represented by a "position weight function", the core concept for a number system. In principle, the "position weight function" can be any real-valued function. In this paper, by approximating the function using trigonometric functions, some characteristic parameters indicating single nucleotide periodicities were obtained for the bacteria Escherichia coli K12's genome and the eukaryote yeast's genome. As a byproduct of this approach, a single-nucleotide-level measure is derived that complements codon-based indexes in describing the coding quality and expression level of an open reading frame (ORF). The ideas presented here have the potential to become a general methodology for biological sequence analysis.     

An experimental demonstration of the effect of group size on cultural accumulation

Cumulative culture is thought to have played a major role in hominin evolution, and so an understanding of the factors that affect cultural accumulation is important for understanding human evolution. Population size may be one such factor, with larger populations thought to be able to support more complex cultural traits. This hypothesis has been suggested by mathematical models and empirical studies of small-scale societies. However, to date there have been few experimental demonstrations of an effect of population size on cultural accumulation. Here we provide such a demonstration using a novel task, solving jigsaw puzzles. 80 participants divided into ten transmission chains solved puzzles in one of two conditions: one in which participants had access to one semi-completed puzzle from the previous generation, and the other in which participants simultaneously saw three semi-completed puzzles from the previous generation. As predicted, the mean number of pieces solved increased over time in the three-puzzle-per-generation condition, but not in the one-puzzle-per-generation condition. Thus, our experiment provides support for a hypothesized relationship between population size and cultural accumulation. In particular, our results suggest that the ability to simultaneously learn from multiple cultural models, and combine the knowledge of those multiple models, is most likely to allow larger groups to support more complex culture.     

Dialogue and causality: Global description from local observations and vague communications

We propose a dialogue-based society model which explains how the transitive law of the causality is originated. Causality is, in general, formalized by using axiomatic approaches. Instead of using axiomatic methods, we, however, compose a model consisting of agents who have knowledge about causal relations among objects. The model society can reveal the transitive law through interactional dialogues among themselves. The agents are reciprocally influenced, if they have either completely same opinions, or a particular pattern of opinions, that are regarded as the extension of such exact accordance. In addition, we add some vagueness to the dialogue, which is closer to a real communication than the former model. A set of knowledge of each agent is expressed as a directed graph, hence the every model can be construed as mere transformations of directed graphs through the interactions among directed graphs themselves. Following this perspective, the models are the systems that connect local logic with global one, while the union of the directed graphs is regarded as the global.     

Dialogue and causality: global description from local observations and vague communications

We propose a dialogue-based society model which explains how the transitive law of the causality is originated. Causality is, in general, formalized by using axiomatic approaches. Instead of using axiomatic methods, we, however, compose a model consisting of agents who have knowledge about causal relations among objects. The model society can reveal the transitive law through interactional dialogues among themselves. The agents are reciprocally influenced, if they have either completely same opinions, or a particular pattern of opinions, that are regarded as the extension of such exact accordance. In addition, we add some vagueness to the dialogue, which is closer to a real communication than the former model. A set of knowledge of each agent is expressed as a directed graph, hence the every model can be construed as mere transformations of directed graphs through the interactions among directed graphs themselves. Following this perspective, the models are the systems that connect local logic with global one, while the union of the directed graphs is regarded as the global.     

The growth of growth

Over a 40-year period, 1940 through the present, human growth research has increased from a minimal to a major part of physical anthropology. Such research, originally conducted at the major American growth centers, has become more diverse and more specialized, extending to National Probability Samplings, nutritional surveys, studies of twins, investigations restricted to the craniofacial complex, and studies of the growth and development of various primate species. Besides extending knowledge of growth and development in general and control mechanisms in particular, there has been major feedback into physical anthropology affording far greater understanding of human variability, of taxonomic differences, and of changes previously believed to be phylogenetic in nature. To the larger extent, all physical anthropologists have some degree of growth awareness.     

Local knowledge of biotic diversity and its conservation in Rural Hausaland, Northern Nigeria

Because biodiversity is debated primarily from western perspectives, the significance of threatened taxa has not been properly assessed in the cultural and ecological contexts of their use. Instead, conservable species tend to be identified by outsiders who are culturally and politically detached from the threatened environments. However, over the last decade or so a growing number of studies document why and how indigenous knowledge and people can become part of development and sustainable conservation. Presented here is a Nigerian example that illustrates how formal conservation efforts are handicapped by their failure to take into account local environmental knowledge. I argue that the potential erosion of biodiversity in Hausaland has been checked by the varied management of cultivated and other lands, and by the use of plants in overlapping contexts—as medicines, foods, and the like.     

Genetic defects or generative prototypes? Competing models for livestock improvement in southern Bolivia

Following neo-liberal 'structural adjustments' in Bolivia, peasant llama-herders are expected to become entrepreneurs and their animal products to compete in global markets. To facilitate the entry of llama produce into global trade, scientifically trained experts working for NGOs give herders 'capacity-building' courses in livestock management and organize livestock shows to teach them about animal conformation. This article examines negotiations and accommodations between indigenous knowledge and science, and in particular focuses upon competing claims to knowledge about herd management and animal improvement. While experts look to improve animals from without – through hybridization with animals from other areas, which also constitutes exchanges in genetic capital – herders expect improvement to come from within – placing emphasis on the unity of their herds as reproductive groups and regarding animals condemned as 'defective' by experts as generative prototypes that indicate the herds' fertility.     

miR-21: a small multi-faceted RNA

More than 1000 microRNAs (miRNAs) are expressed in human cells, some tissue or cell type specific, others considered as house-keeping molecules. Functions and direct mRNA targets for some miRNAs have been relatively well studied over the last years. Every miRNA potentially regulates the expression of numerous protein-coding genes (tens to hundreds), but it has become increasingly clear that not all miRNAs are equally important; diverse high-throughput screenings of various systems have identified a limited number of key functional miRNAs over and over again. Particular miRNAs emerge as principal regulators that control major cell functions in various physiological and pathophysiological settings. Since its identification 3 years ago as the miRNA most commonly and strongly up-regulated in human brain tumour glioblastoma [ 1 ], miR-21 has attracted the attention of researchers in various fields, such as development, oncology, stem cell biology and aging, becoming one of the most studied miRNAs, along with let-7, miR-17–92 cluster ('oncomir-1'), miR-155 and a few others. However, an miR-21 knockout mouse has not yet been generated, and the data about miR-21 functions in normal cells are still very limited. In this review, we summarise the current knowledge of miR-21 functions in human disease, with an emphasis on its regulation, oncogenic role, targets in human cancers, potential as a disease biomarker and novel therapeutic target in oncology.     

Randomization Analyses: Mimicry, Geographic Variation and Cultural Evolution of Song in Brood-Parasitic Straw-Tailed Whydahs, Vidua fischeri

Although bird song has been an important model for investigating questions of behavior development, cultural evolution and population differentiation, the quantitative methods of analysis have been problematic. Here we develop and apply quantitative randomization methods to test hypotheses about these processes in a natural population of birds. Songs of the African brood-parasitic straw-tailed whydahs ( Vidua fischeri ) and songs of their host species, the purple grenadier ( Granatina ianthinogaster ), were compared in audiospectrograms for similarity to test the following hypotheses: Whydahs mimic the songs of their host species, they have local song dialects, neighboring males match their song themes, local males match the songs of local hosts, remote populations have different songs according to their geographic distance, and songs undergo cultural evolution over time across generations. Randomization analyses were completed using (1) Mantel matrix statistics and (2) tree-based measures employing Sankoff optimization of Manhattan matrices and approximate randomizations. Our results provide evidence for song mimicry, local song dialects, matching song themes between neighboring males, song matching of local whydah mimics and grenadier song models, correspondence of song differences and geographic distance, and cultural continuity with change in song traditions within a local population. These randomization methods may be useful in other studies of animal communication, and they are sufficiently general for use both with distance matrices derived either from naturalistic impressions of song similarity as in our example or from acoustic measurements.     

论壮族传统文化对生物多样性的保护: 以广西靖西市为例

本文在文献研究和实地调查的基础之上, 结合目前开展的关于壮族生物多样性相关传统知识的调查、整理与编目工作, 分别从酸食文化、织染文化、地名文化和文学艺术的角度对壮族文化多样性和生物多样性之间的关系进行了初步探究, 并从自然崇拜、乡规民约和习惯法、传统生态观念以及传统医药文化等几个方面探讨了传统文化对当地生物多样性的保护作用。结果表明: (1)壮族文化多样性与生物多样性密切相关。丰富的生物多样性孕育了传统文化, 而传统文化的形成和发展又直接或间接地丰富了当地的生物多样性; (2)壮族人民在长期生产生活中创造的传统文化和传统知识促进了当地生物多样性的保护与可持续利用; 而对生物多样性的保护又进一步保障了当地传统文化的传承。本文还对传统知识和传统文化的发展现状及受威胁因素进行了讨论, 并以此为基础, 提出传承壮族传统文化、保护和可持续利用传统知识的相关建议, 即应通过加强宣传和立法, 建立传统知识数据库和发展乡村旅游等形式, 加强对传统知识与传统文化的保护。     

Cultural traits as units of analysis

Cultural traits have long been used in anthropology as units of transmission that ostensibly reflect behavioural characteristics of the individuals or groups exhibiting the traits. After they are transmitted, cultural traits serve as units of replication in that they can be modified as part of an individual's cultural repertoire through processes such as recombination, loss or partial alteration within an individual's mind. Cultural traits are analogous to genes in that organisms replicate them, but they are also replicators in their own right. No one has ever seen a unit of transmission, either behavioural or genetic, although we can observe the effects of transmission. Fortunately, such units are manifest in artefacts, features and other components of the archaeological record, and they serve as proxies for studying the transmission (and modification) of cultural traits, provided there is analytical clarity over how to define and measure the units that underlie this inheritance process.     

The role of infectious diseases in biological conservation

Recent increases in the magnitude and rate of environmental change, including habitat loss, climate change and overexploitation, have been directly linked to the global loss of biodiversity. Wildlife extinction rates are estimated to be 100–1000 times greater than the historical norm, and up to 50% of higher taxonomic groups are critically endangered. While many types of environmental changes threaten the survival of species all over the planet, infectious disease has rarely been cited as the primary cause of global species extinctions. There is substantial evidence, however, that diseases can greatly impact local species populations by causing temporary or permanent declines in abundance. More importantly, pathogens can interact with other driving factors, such as habitat loss, climate change, overexploitation, invasive species and environmental pollution to contribute to local and global extinctions. Regrettably, our current lack of knowledge about the diversity and abundance of pathogens in natural systems has made it difficult to establish the relative importance of disease as a significant driver of species extinction, and the context when this is most likely to occur. Here, we review the role of infectious diseases in biological conservation. We summarize existing knowledge of disease-induced extinction at global and local scales and review the ecological and evolutionary forces that may facilitate disease-mediated extinction risk. We suggest that while disease alone may currently threaten few species, pathogens may be a significant threat to already-endangered species, especially when disease interacts with other drivers. We identify control strategies that may help reduce the negative effects of disease on wildlife and discuss the most critical challenges and future directions for the study of infectious diseases in the conservation sciences.     

Class IIa bacteriocins: biosynthesis, structure and activity

In the last decade, a variety of ribosomally synthesized antimicrobial peptides or bacteriocins produced by lactic acid bacteria have been identified and characterized. As a result of these studies, insight has been gained into fundamental aspects of biology and biochemistry such as producer self protection, membrane-protein interactions, and protein modification and secretion. Moreover, it has become evident that these peptides may be developed into useful antimicrobial additives. Class IIa bacteriocins can be considered as the major subgroup of bacteriocins from lactic acid bacteria, not only because of their large number, but also because of their activities and potential applications. They have first attracted particular attention as listericidal compounds and are now believed to be the next in line if more bacteriocins are to be approved in the future. The present review attempts to provide an insight into general knowledge available for class IIa bacteriocins and discusses common features and recent findings concerning these substances.     

Tackling ‘ghost nets’: Local solutions to a global issue in northern Australia

Summary We describe the inception and development of the Carpentaria Ghost Nets Programme, located across the Gulf of Carpentaria, which spans north Queensland and the Northern Territory. The program has grown from a small grass‐roots idea addressing issues around marine debris to become an internationally acknowledged project headed by the Northern Gulf Resource Management Group. This program, involving more than 18 Indigenous communities and over 90 Indigenous rangers, has become a way of building bridges across cultures and communities for a shared, common interest in land and sea protection. By incorporating traditional values and approaches to managing an international issue at a local scale, we have worked with local communities to increase pride and ownership on country whilst providing transferrable job skills. Success of this program ultimately depends upon the continued active engagements of the Indigenous communities and ranger groups. The project aims to address the fundamental issue of tackling the ghost nets problem at its source through cross‐cultural interactions between rangers and fishermen, increasing public, political and economic awareness, and ultimately reducing the incidental and intentional loss of fishing nets that act as ghost nets and result in tremendous biological, cultural and economic impacts. By putting in place long term management measures to ensure monitoring efforts, we can track ghost net debris arrival and changes through time, providing information to policy and cultural changes at regional and international scales.     

Spatiotemporal dimensions of community assembly

Ecological communities are assembled through a series of multiple processes, including dispersal, abiotic and biotic filtering, and ecological drift. Although these assembly processes act in concert to structure local communities, their relative importance is considerably variable among study systems. While such contingency of community assembly has been widely appreciated, the empirical and theoretical evidence is scattered around in the literature, and few efforts have been made to synthesize it. In this mini-review, we summarize the accumulated evidence of the context-dependency of community assembly rules, to reach a rough generalization of the contingency. Specifically, we argue that spatial and temporal dimensions can serve as general axes that regulate the relative importance of assembly processes. To this end, we synthesize the current understanding of how the relative importance of multiple assembly processes changes with spatial scales and complexity, and with time in the long and short terms. This review concludes that spatial and temporal dimensions can be common currencies of community assembly rules that are shared across various systems.     

Conflicting values: ecosystem services and invasive tree management

Tree species have been planted widely beyond their native ranges to provide or enhance ecosystem services such as timber and fibre production, erosion control, and aesthetic or amenity benefits. At the same time, non-native tree species can have strongly negative impacts on ecosystem services when they naturalize and subsequently become invasive and disrupt or transform communities and ecosystems. The dichotomy between positive and negative effects on ecosystem services has led to significant conflicts over the removal of non-native invasive tree species worldwide. These conflicts are often viewed in only a local context but we suggest that a global synthesis sheds important light on the dimensions of the phenomenon. We collated examples of conflict surrounding the control or management of tree invasions where conflict has caused delay, increased cost, or cessation of projects aimed at invasive tree removal. We found that conflicts span a diverse range of taxa, systems and countries, and that most conflicts emerge around three areas: urban and near-urban trees; trees that provide direct economic benefits; and invasive trees that are used by native species for habitat or food. We suggest that such conflict should be seen as a normal occurrence in invasive tree removal. Assessing both positive and negative effects of invasive species on multiple ecosystem services may provide a useful framework for the resolution of conflicts.     

EMOTIONS IN THE FIELD: WHAT ARE WE TALKING ABOUT?

In the anthropology of emotion, rival approaches – cultural relativism and a universalism based on common humanity or shared experience – imply different forms of engagement in the field. This article, a sceptical appraisal, suggests that ethnographers commonly fail to build the diversity of emotional practice into their accounts and have therefore provided a flawed basis for theorizing and comparison. With reference to two Indonesian cases – Nias and Java – I suggest that the domain of emotion is diversely bounded cross-culturally and is inconsistently constructed in particular contexts. This has critical implications for fieldwork methodology, cross-cultural comparison, and theories of human development.     

Translation, Value, and Space: Theorizing an Ethnographic and Engaged Environmental Anthropology

In this article, I argue for placing the politics of translation and theories of value and spatial production at the center of environmental anthropology. For the past ten years, the Gimi-speaking peoples living in Maimafu village, Papua New Guinea, have taken part in an integrated conservation and development project attempting to foster a local system of valuing "nature" by tying biological diversity to economic markets through the creation of "eco-enterprises." However, the project fails to consider how Gimi produce, theorize, transmit, and express knowledge. Using ethnographic material concerned with hunting and song composition, I show that Gimi understand their forests to be part of a series of transactive dialectical relationships that work to produce identity and space. I also demonstrate that, as part of this project, Gimi social relations with their forests have been translated in ways that fit their beliefs into generic and easily understandable categories. This has been detrimental to the conservation project and it is politically problematic for an engaged environmental anthropology.