Species concepts and species reality: salvaging a Linnaean rank

The validity of the species category (rank) as a distinct level of biological organization has been questioned. Phenetic, cohesion and monophyletic species concepts do not delimit species-level taxa that are qualitatively distinct from lower or higher taxa: all organisms throughout the tree of life exhibit varying degrees of similarity, cohesion, and monophyly. In contrast, interbreeding concepts delimit species-level taxa characterized by a phenomenon (regular gene flow) not found in higher taxa, making the species category a distinct level of biological organization. Only interbreeding concepts delimit species-level taxa that are all comparable according to a biologically meaningful criterion and qualitatively distinct from entities assigned to other taxonomic categories. Consistent application of interbreeding concepts can result in counterintuitive taxonomies--e.g. many wide polytypic species in plants and narrow cryptic species in animals. However, far from being problematic, such differences are biologically illuminating--reflecting differing barriers to gene flow in different clades. Empirical problems with interbreeding concepts exist, but many of these also apply to other species concepts, whereas others are not as severe as some have argued. A monistic view of species using interbreeding concepts will encounter strong historical inertia, but can save the species category from redundancy with other categories, and thus justify continued recognition of the species category.     

Xerophytes, xeromorphs and sclerophylls: the history of some concepts in ecology

Research on xeromorphic and sclerophyllous (the literal meanings of which are "dry-form" and "hard-leaved") plants offers a case-history illustrating the nature of "progress" in one branch of science. The story runs from about 1890–1970, beginning with the birth of ecological concepts, including Warming's 1895 classification of plants into hydrophytes, xerophytes and meso-phytes, Schimper's pioneer work on the sclerophylls, and with the conceptions that lay behind this work; and so on through the main lines of research, concluding with an account of work on the "anomalous" distribution of the sclerophylls in Australia. This case-history shows how the problems of classification and categorization may be linked to conceptual and empirical problems of substance, and hence are not "merely" classificatory. Indeed, the hypotheses under test are not formulated explicitly, but are encapsulated in the terminology, as is so often the case in the biological sciences.     

Osmosis; ATP; Process-based approach

The teaching of r and K population strategies involves integrating biological, graphical, and mathematical concepts so that a complex ‘concept image’ is formed. This investigation identified the main problems encountered by students in studying this topic as being interpreting graphs, making links with biological processes, and drawing general conclusions from data. The use of a formal lecture and three approaches to using a spreadsheet are evaluated, and suggestions are made for effective teaching of these concepts.     

How to be a chaste species pluralist-realist: the origins of species modes and the synapomorphic species concept

The biological species (biospecies) concept applies only to sexually reproducing species, which means that until sexual reproduction evolved, there were no biospecies. On the universal tree of life, biospecies concepts therefore apply only to a relatively small number of clades, notably plants andanimals. I argue that it is useful to treat the various ways of being a species (species modes) as traits of clades. By extension from biospecies to the other concepts intended to capture the natural realities of what keeps taxa distinct, we can treat other modes as traits also, and so come to understand that theplurality of species concepts reflects the biological realities of monophyletic groups.We should expect that specialists in different organisms will tend to favour those concepts that best represent the intrinsic mechanisms that keep taxa distinct in their clades. I will address the question whether modes ofreproduction such as asexual and sexual reproduction are natural classes, given that they are paraphyletic in most clades.     

The use of evolutionary biology concepts for genome annotation

The past decade has seen the completion of numerous whole-genome sequencing projects, began with bacterial genomes and continued with eukaryotic species from different phyla: fungi, plants and animals. Besides, more biological information are produced and are shared thanks to information exchange systems, and more biological concepts, as well as more bioinformatics tools, are available. In this article, we will describe how the evolutionary biology concepts, as well as computer science, are useful for a better understanding of biology in general and genome annotation in particular. The genome annotation process consists of taking the raw DNA produced, for example, by the genome sequencing projects, adding the layers of analysis and interpretation necessary to extract its biological significance and placing it in the context of our understanding of biological processes. Genome annotation is a multistep process falling into two broad categories: structural and functional annotation.     

A decade of differential display

It has been 10 years since the invention of differential display (DD), a conceptually simple methodology that allows the detection and identification of differentially expressed genes. In the past decade, the number of publications describing successful applications of DD has outnumbered those using any other competing methodologies, including subtractive hybridization, representational difference analysis, serial analysis of gene expression, and DNA microarrays. This review will provide a glimpse of the current progress made in DD technological development, refinement, and automation. Excellent examples of DD applications in studying a variety of biological problems, in such diverse biological systems as bacteria, yeast, flies, plants, and higher mammals, are presented to provide a roadmap for those who would like to pursue a fruitful gene "fishing" expedition. Some of the fundamental differences between DD and DNA microarrays are also discussed.     

The fitness of human sociobiology: the future utility of four concepts in four subdisciplines.

Reported here are the results of a survey inquiring into the rate of acceptance of four sociobiological concepts in regard to their usefulness for future research. Included in the survey were members of four subdisciplines: animal behavior (biology), biological anthropology, cultural anthropology, and developmental psychology. Three types of institutions were included: universities, four- and five-year colleges, and community colleges. A total of 1,631 responses are reported with the degree of acceptance varying from highest to lowest as follows: biology, biological anthropology, developmental psychology, and cultural anthropology. These variations are related to the central concepts of each subdiscipline.     

森林植被中优势种的形成和分布规律及其应用

一森林多是天然植被(人工林除外),它经历了千百年的演化,在改造环境和适应环境过程中,形成了物种与外界环境的高度吻合,最后形成了多种稳定的森林植被类型,因而研究森林植被中优势种的形成和分布规律,较之农田生态系统等人工植被具有更多的便利条件。森林树种的分布遵循着一定的规律,搞清     

Botanical literacy: What and how should students learn about plants?

Botanists benefit from a scientifically literate society and an interested and botanically literate student population, and we have opportunities to promote literacy in our classes. Unfortunately, scientific illiteracy exists, in part, because students are technologically advanced but lack intellectual curiosity and rigor. Botanical illiteracy results from several interacting factors, including a lack of interest in plants and infrequent exposure to plant science before students reach college. If scientific or botanical literacy is a goal, we must understand what literacy means and how we can help students reach that goal. A model of biological literacy recognizes four levels; students enter courses at the lowest level possessing misconceptions about concepts; however, misconceptions can be used to our advantage, especially by using concept inventories. Inquiry-based instruction is advocated for all science courses, and learning theory supports inquiry. Seven principles of learning inform recommendations about how botanists should teach, including using themes and "thinking botanically" to illustrate all biological concepts. Overall, consideration of the botanical content taught is less critical than the methods used to teach that content. If botanists emphasize thinking and process skills with an understanding of concepts, we will prepare scientifically literate students and citizens and benefit from our efforts.     

Programmed cell death in plants

The modern concepts of programmed cell death (PCD) in plants are reviewed as compared to PCD (apoptosis) in animals. Special attention is focused on considering the potential mechanisms of implementation of this fundamental biological process and its participants. In particular, the proteolytic enzymes involved in PCD in animals (caspases) and plants (phytaspases) are compared. Emphasis is put on elucidation of both common features and substantial differences of PCD implementation in plants and animals.     

植物地上部与地下部的诱导防御反应研究综述

地球上大多数植物对病虫害的侵袭具有诱导防御反应。植物地上部与地下部之间存在着密切的生理生态关系,因此,地上部处理是否影响地下部的防御反应以及地下部处理是否影响地上部的防御反应,进而分别影响到地下部和地上部生物的行为成为当前研究的热点。本文系统地综述了地上部机械损伤、害虫取食、信号物质处理对植物地下部防御反应及生物行为影响以及地下部机械损伤、害虫取食、信号物质处理对植物地上部防御反应及生物行为影响的研究进展,并在此基础上提出了未来该领域值得进一步研究的方向,以期为深入研究植物地上部与地下部诱导防御间的相互关系提供科学依据。     

Highway or byway: the metabolic role of the GABA shunt in plants

Much of the recent work on the gamma-aminobutyrate (GABA) shunt in plants has concentrated on stress/pest-associated and signalling roles. However, fifty years after the structural elucidation of the pathway, aspects of its regulation and even of its biological significance remain largely obscure. Here, we assess the importance of GABA metabolism in plants, reviewing relevant biological circumstances and taking advantage of high-throughput data accessibility and computational approaches. We discuss the premise that GABA metabolism plays a major role in carbon and nitrogen primary metabolism. We further evaluate technological developments that will likely allow us to address the quantitative importance of this shunt within the biological processes to which it contributes.     

Conrad Hal Waddington: the last Renaissance biologist?

Conrad Hal Waddington was a leading embryologist and geneticist from the 1930s to the 1950s. He is remembered mainly for his concepts of the 'epigenetic landscape' and 'genetic assimilation'. This article reviews his life and work, and enquires to what extent his ideas are relevant tools for understanding the biological problems of today.     

The coordination of protein motors and the kinetic behavior of microtubule--a computational study

Utilizing the mechanical energy converted from chemical energy through hydrolysis of ATP, motor proteins drive cytoskeleton filaments to move in various biological systems. Recent technological advance has shown the potential of the motor proteins for powering future nano-bio-mechanical systems. In order to effectively use motor proteins as a biological motor, the interaction between the protein motors and bio-filaments needs to be well clarified, since such interaction is largely influenced by many factors, such as the coordination among the motors, their dynamic behavior, physical properties of microtubules, and the viscosity of solution involved, etc. In this study, a two-dimensional model was proposed to simulate the motion of a microtubule driven by protein motors based on a dissipative particle dynamics (DPD) method with attempt to correlate the microtubule's kinetic behavior to the coordination among protein motors.     

Predicting how pollinator behavior causes reproductive isolation

Pollinator behavior is an important contributor to plants speciation, yet how variation in pollinator behavior causes variation in reproductive isolation (RI) is largely uncharacterized. Here I present a model that predicts how two aspects of pollinator behavior, constancy and preference, contribute to a barrier to reproduction in plants. This model is motivated by two observations: most co‐occurring plants vary in frequency over space and time, and most plants have multiple pollinators that differ in behavior. Thus, my goal was to understand how relative frequencies of plants and pollinators in a community influence ethological RI between co‐occurring plants. I find that RI for a focal plant generally increases with increasing relative plant frequency, but the shape of this relationship is highly dependent on the strength of pollinator behavior (constancy and preference). Additionally, when multiple pollinators express different behavior, I find that pollinators with stronger preference disproportionately influence RI. But, I show that RI caused by constancy is the average RI predicted from constancy of each pollinator weighted by pollinator frequency. I apply this model to examples of pollinator‐mediated RI in Phlox and in Ipomopsis to predict the relationships between plant frequency and ethological RI in natural systems. This model provides new insights into how and why pollinator specialization causes RI, and how RI could change with changing biological communities.     

植食性昆虫寄主植物嗅觉搜寻述介

植食性昆虫与寄主植物关系的本质是化学。植食性昆虫搜寻寄主的嗅觉媒介是植物气味即化学信息物质。在介绍植物气味构成及其扩散模型基础上,阐述了植物气味在地上植食性昆虫成虫、幼虫和地下植食性昆虫搜寻寄主过程中的嗅觉导向作用,并指出了今后相关研究需要注意的问题。从植物与环境因子的关系来看,植物气味包括构成性气味和诱发性气味两类,这两类气味的概念既相联系而又不同。构成性气味组分及构成因植物分类地位等而不同。诱发性气味组分因植食性昆虫取食、植物病原微生物、机械致伤等因子的胁迫而变化,这种变化性状随植物属和/或种、植株生长发育阶段、胁迫因子性质及其作用方式而不同。无论是哪种植物气味,其释放均具有节律性。气味扩散过程比较复杂,扩散状态可用数学模型表征。对于地上植食性昆虫成虫,植物气味对其寄主搜寻行为具有导向特异性,重点分析了这种特异性形成的两个假说;鳞翅目昆虫幼虫,能够利用植物化学信息物质趋向寄主植物或回避非寄主植物;地下植食性昆虫搜寻寄主,既与寄主植物地下组织释放或分泌的次级代谢物有关,又与一些初级代谢物有关。初级代谢物中的CO₂,起着“搜寻触发器”作用。有助于增强人们对昆虫与植...     

Verification, validation and sensitivity studies in computational biomechanics

Computational techniques and software for the analysis of problems in mechanics have naturally moved from their origins in the traditional engineering disciplines to the study of cell, tissue and organ biomechanics. Increasingly complex models have been developed to describe and predict the mechanical behavior of such biological systems. While the availability of advanced computational tools has led to exciting research advances in the field, the utility of these models is often the subject of criticism due to inadequate model verification and validation (V&V). The objective of this review is to present the concepts of verification, validation and sensitivity studies with regard to the construction, analysis and interpretation of models in computational biomechanics. Specific examples from the field are discussed. It is hoped that this review will serve as a guide to the use of V&V principles in the field of computational biomechanics, thereby improving the peer acceptance of studies that use computational modeling techniques.     

基于植物重组蛋白产量提高的研究进展

重组蛋白为疾病治疗提供了新手段,同时创造了可观的经济效益。利用经济作物(主要是烟草)、谷类作物、豆科作物和蔬菜作物生产具有药用价值的重组蛋白是“分子农业”最热门的研究内容。尽管许多重组蛋白已在植物中表达,但只有一小部分已成功投入使用。为了极大地克服限制植物生产重组蛋白发展的问题,研究人员改进表达系统以增加重组蛋白的产量。本文从分析植物产生重组蛋白产量低和/或生物活性低等问题入手,综述了近些年来解决这些问题的优化策略,同时提出了提高植物生产重组蛋白产量的研究方向。     

Applications of fractal geometry to biology

The applications of concepts derived from fractal geometry tobiological problems are described. Three major applicationsare identified: modelling of structures; investigation of theoreticalproblems; and the measurment of complexity. The review concentrateson methods and algorithms, including potential problems, whichcan be used with biological problems. These algorithms are drawnfrom a wide range of literature, including some non–biologicalsources.