Homology in comparative, molecular, and evolutionary developmental biology: the radiation of a concept

The present paper analyzes the use and understanding of the homology concept across different biological disciplines. It is argued that in its history, the homology concept underwent a sort of adaptive radiation. Once it migrated from comparative anatomy into new biological fields, the homology concept changed in accordance with the theoretical aims and interests of these disciplines. The paper gives a case study of the theoretical role that homology plays in comparative and evolutionary biology, in molecular biology, and in evolutionary developmental biology. It is shown that the concept or variant of homology preferred by a particular biological field is used to bring about items of biological knowledge that are characteristic for this field. A particular branch of biology uses its homology concept to pursue its specific theoretical goals.     

Practising Conservation Biology in a Virtual Rainforest World

The interdisciplinary science of conservation biology provides undergraduate biology students with the opportunity to connect the biological sciences with disciplines including economics, social science and philosophy to address challenging conservation issues. Because of its complexity, students do not often have the opportunity to practise conservation biology. To increase exposure to this science, this paper describes a virtual rainforest island on which students collect data related to forest carbon storage, while also confronting ethical issues. Students are asked to independently make decisions, collect data and explore the island before writing a research report with recommendations for the future management of the island’s forests. The ethics of decision-making are addressed in the students’ research reports and are reinforced through guided class discussion. Students will complete this activity with increased ethical awareness, as well as a better understanding of the challenges associated with the practise of conservation biology.     

Using Tinbergen��s Four Questions (Plus One) to Facilitate Evolution Education for Human-Oriented Disciplines

Nikolaas Tinbergen provided an elegantly comprehensive guide to behavioral research with his Four Questions. Unsurprisingly, these questions summarize the different aspects that are vital to an evolutionary perspective. In this article, the authors describe how they use these Four Questions (plus one they have added regarding the role of culture) to facilitate evolution education in the human-oriented disciplines. The use of evolutionary theory in these fields is young, and educating new members of these fields in evolutionary theory is an even newer idea. Tinbergen’s Four Questions (Plus One) make the goals of an evolutionary perspective clear and the application of the mechanisms of evolution apparent. It can effectively dispel myths that surround evolutionary theory, like genetic determinism and hyperadaptationism, and can help ameliorate other ideological concerns. Finally, it is suggested that it is a heuristic that encourages students to make the transition from understanding the mechanisms of evolution in biology to applying this knowledge in cross-disciplinary research.     

Conceptual assessment in the biological sciences: a National Science Foundation-sponsored workshop

Twenty-one biology teachers from a variety of disciplines (genetics, ecology, physiology, biochemistry, etc.) met at the University of Colorado to begin discussions about approaches to assessing students' conceptual understanding of biology. We considered what is meant by a "concept" in biology, what the important biological concepts might be, and how to go about developing assessment items about these concepts. We also began the task of creating a community of biologists interested in facilitating meaningful learning in biology. Input from the physiology education community is essential in the process of developing conceptual assessments for physiology.     

Advantages and clinical applications of natural killer cells in cancer immunotherapy

The past decade has witnessed a burgeoning of research and further insight into the biology and clinical applications of natural killer (NK) cells. Once thought to be simple innate cells important only as cytotoxic effector cells, our understanding of NK cells has grown to include memory-like responses, the guidance of adaptive responses, tissue repair, and a delicate paradigm for how NK cells become activated now termed “licensing” or “arming.” Although these cells were initially discovered and named for their spontaneous ability to kill tumor cells, manipulating NK cells in therapeutic settings has proved difficult and complex in part due to our emerging understanding of their biology. Therapies involving NK cells may either activate endogenous NK cells or involve transfers of exogenous cells by hematopoietic stem cell transplantation or adoptive cell therapy. Here, we review the basic biology of NK cells, highlighting characteristics which make NK cells particularly useful in cancer therapies. We also explore current treatment strategies that have been used for cancer as well as discuss potential future directions for the field.     

Molecular biology and gene transfer in atherosclerosis in the stenting era

Atherosclerosis is the major cause of death in the developed world. Understanding the pathogenesis of atherosclerosis has been a major challenge to cardiovascular research over the past several decades. During this period a number of advances in various scientific disciplines has increased our understanding of this disease. These include improved understanding of the structural and functional components of normal vessel wall and more recently the use of cell biology and molecular biology techniques to elucidate the pathogenesis of atherosclerosis. None of these advances has been more dramatic nor has potentially more far reaching consequences as the application of molecular biology and gene technology to the practice of cardiovascular medicine. These developments have already opened new and exciting areas of vascular research and may in the future provide for earlier identification of genetic predisposition to atherosclerosis, strategic planning of preventive therapy and more tailored pharmacologic approaches for established disease.     

Complex systems in pulmonary medicine: a systems biology approach to lung disease

The lung is a highly complex organ that can only be understood by integrating the many aspects of its structure and function into a comprehensive view. Such a view is provided by a systems biology approach, whereby the many layers of complexity, from the molecular genetic, to the cellular, to the tissue, to the whole organ, and finally to the whole body, are synthesized into a working model of understanding. The systems biology approach therefore relies on the expertise of many disciplines, including genomics, proteomics, metabolomics, physiomics, and, ultimately, clinical medicine. The overall structure and functioning of the lung cannot be predicted from studying any one of these systems in isolation, and so this approach highlights the importance of emergence as the fundamental feature of systems biology. In this paper, we will provide an overview of a systems biology approach to lung disease by briefly reviewing the advances made at many of these levels, with special emphasis on recent work done in the realm of pulmonary physiology and the analysis of clinical phenotypes.     

Systems biology in animal sciences

Systems biology is a rapidly expanding field of research and is applied in a number of biological disciplines. In animal sciences, omics approaches are increasingly used, yielding vast amounts of data, but systems biology approaches to extract understanding from these data of biological processes and animal traits are not yet frequently used. This paper aims to explain what systems biology is and which areas of animal sciences could benefit from systems biology approaches. Systems biology aims to understand whole biological systems working as a unit, rather than investigating their individual components. Therefore, systems biology can be considered a holistic approach, as opposed to reductionism. The recently developed 'omics' technologies enable biological sciences to characterize the molecular components of life with ever increasing speed, yielding vast amounts of data. However, biological functions do not follow from the simple addition of the properties of system components, but rather arise from the dynamic interactions of these components. Systems biology combines statistics, bioinformatics and mathematical modeling to integrate and analyze large amounts of data in order to extract a better understanding of the biology from these huge data sets and to predict the behavior of biological systems. A 'system' approach and mathematical modeling in biological sciences are not new in itself, as they were used in biochemistry, physiology and genetics long before the name systems biology was coined. However, the present combination of mass biological data and of computational and modeling tools is unprecedented and truly represents a major paradigm shift in biology. Significant advances have been made using systems biology approaches, especially in the field of bacterial and eukaryotic cells and in human medicine. Similarly, progress is being made with 'system approaches' in animal sciences, providing exciting opportunities to predict and modulate animal traits.     

Prebiotic world, macroevolution, and Darwin’s theory: a new insight

Darwin’s main contribution to modern biology was to make clear that all history of life on earth is dominated by a simple principle, which is usually summarised as 'descent with modification'. However, interpretations about how this modification is produced have been controversial. In light of the data provided by recent studies on molecular biology, developmental biology, genomics, and other biological disciplines we discuss, in this paper, how Darwin's theory may apply to two main 'types' of evolution: that occurring in the prebiotic world and that regarding the acquisition of major key-innovations differentiating higher-taxa, which makes up part of the so-called macroevolution. We argue that these studies show that evolution is a fascinating, complex and multifaceted process, with different mechanisms drivin it on different occasions and in different places.     

Zooming in on the cell biology of disease

Today’s cell biology could be considered a fusion of disciplines that blends advanced genetics, molecular biology, biochemistry, and engineering to answer fundamental as well as medically relevant scientific questions. Accordingly, our understanding of diseases is greatly aided by an existing vast knowledge base of fundamental cell biology. Gunter Blobel captured this concept when he said, “the tremendous acquisition of basic knowledge will allow a much more rational treatment of cancer, viral infection, degenerative disease and mental disease.” In other words, without cell biology can we truly understand, prevent, or effectively treat a disease?

R. M. Perera     

The histochemistry and cell biology vade mecum: a review of 2005–2006

The procurement of new knowledge and understanding in the ever expanding discipline of cell biology continues to advance at a breakneck pace. The progress in discerning the physiology of cells and tissues in health and disease has been driven to a large extent by the continued development of new probes and imaging techniques. The recent introduction of semi-conductor quantum dots as stable, specific markers for both fluorescence light microscopy and electron microscopy, as well as a virtual treasure-trove of new fluorescent proteins, has in conjunction with newly introduced spectral imaging systems, opened vistas into the seemingly unlimited possibilities for experimental design. Although it oftentimes proves difficult to predict what the future will hold with respect to advances in disciplines such as cell biology and histochemistry, it is facile to look back on what has already occurred. In this spirit, this review will highlight some advancements made in these areas in the past 2 years.     

Classic limb patterning models and the work of Dennis Summerbell

Dennis Summerbell was a leading contributor to our understanding of limb patterning prior to the advent of molecular biology. He published several groundbreaking papers, including one that developed a key model for patterning the limb from the shoulder to the fingertips and another that presented the co-discovery of the effect of retinoids on limb morphogenesis. He brought detailed quantitative analyses to bear on these studies, as highlighted in two of his insightful papers published in the Journal of Embryology and Experimental Morphology, in which he provided elegant models that, today, remain relevant to limb patterning, as well as to many disciplines of developmental biology.     

Disciplinary baptisms: a comparison of the naming stories of genetics, molecular biology, genomics, and systems biology

Understanding how scientific activities use naming stories to achieve disciplinary status is important not only for insight into the past, but for evaluating current claims that new disciplines are emerging. In order to gain a historical understanding of how new disciplines develop in relation to these baptismal narratives, we compare two recently formed disciplines, systems biology and genomics, with two earlier related life sciences, genetics and molecular biology. These four disciplines span the twentieth century, a period in which the processes of disciplinary demarcation fundamentally changed from those characteristic of the nineteenth century. We outline how the establishment of each discipline relies upon an interplay of factors that include paradigmatic achievements, technological innovation, and social formations. Our focus, however, is the baptism stories that give the new discipline a founding narrative and articulate core problems, general approaches and constitutive methods. The highly plastic process of achieving disciplinary identity is further marked by the openness of disciplinary definition, tension between technological possibilities and the ways in which scientific issues are conceived and approached, synthesis of reductive and integrative strategies, and complex social interactions. The importance--albeit highly variable--of naming stories in these four cases indicates the scope for future studies that focus on failed disciplines or competing names. Further attention to disciplinary histories could, we suggest, give us richer insight into scientific development.     

Understanding self and others: from origins to disorders

In order to interpret and engage with the social world, individuals must understand how they relate to others. Self–other understanding forms the backbone of social cognition and is a central concept explored by research into basic processes such as action perception and empathy, as well as research on more sophisticated social behaviours such as cooperation and intergroup interaction. This theme issue integrates the latest research into self–other understanding from evolutionary biology, anthropology, psychology, neuroscience and psychiatry. By gathering perspectives from a diverse range of disciplines, the contributions showcase ways in which research in these areas both informs and is informed by approaches spanning the biological and social sciences, thus deepening our understanding of how we relate to others in a social world.     

Watching the grin fade: Tracing the effects of polyploidy on different evolutionary time scales

Polyploidy, or whole-genome duplication (WGD), is a recurrent mutation both in cell lineages and over evolutionary time. By globally changing the relationship between gene copy number and other cellular entities, it can induce dramatic changes at the cellular and phenotypic level. Perhaps surprisingly, then, the insights that these events can bring to understanding other cellular features are not as well appreciated as they could be. In this review, we draw on examples of polyploidy from animals, plants and yeast to explore how investigations of polyploid cells have improved our understanding of the cell cycle, biological network complexity, metabolic phenotypes and tumor biology. We argue that the study of polyploidy across organisms, cell types, and time scales serves not only as a window into basic cell biology, but also as a basis for a predictive biology with applications ranging from crop improvement to treating cancer.     

What will result from the interaction between functional and evolutionary biology?

The modern synthesis has been considered to be wrongly called a "synthesis", since it had completely excluded embryology, and many other disciplines. The recent developments of Evo-Devo have been seen as a step in the right direction, as complementing the modern synthesis, and probably leading to a "new synthesis". My argument is that the absence of embryology from the modern synthesis was the visible sign of a more profound lack: the absence of functional biology in the evolutionary synthesis. I will consider the reasons for this absence, as well as the recent transformations which favoured a closer interaction between these two branches of biology. Then I will describe two examples of recent work in which functional and evolutionary questioning were tightly linked. The most significant part of the paper will be devoted to the transformation of evolutionary theory that can be expected from this encounter: a deep transformation, or simply an experimental confirmation of this theory? I will not choose between these two different possibilities, but will discuss some of the difficulties which make the choice problematic.     

Introduction to the symposium "New frontiers from marine snakes to marine ecosystems"

Interest in sea snakes and mythological "sea serpents" dates to ancient times and is represented in the writings of Aristotle, early voyagers, and explorers, and references in the Bible. Since then, awareness of the myriad species of snakes inhabiting the oceans has grown at a gradual pace. Scientific investigations into the biology of marine snakes-especially those in behavior, physiology, and other disciplines requiring living animals or tissues-have been comparatively challenging owing to difficulties in acquiring, transporting, handling, and husbanding these secondarily marine vertebrates. A broadening perspective with increasing interest in these animals peaked during the 1960s and 1970s, and literature from this period contributed to a growing knowledge that marine snakes comprise a very diverse fauna and are a significant part of marine ecosystems. Two persons figured prominently as influential drivers of research on sea snakes during this period, namely William Dunson and Harold Heatwole, and this symposium recognizes the contributions of these two individuals. Following a decline in scientific publications on sea snakes during the 1980s and 1990s, there has been a renaissance of scientific interest in recent years, and a wealth of new research findings has improved the understanding of phylogeny and diversity of marine snakes while simultaneously recognizing threats to marine ecosystems arising from climate change and other anthropogenic causes. The purposes of the symposium are to (1) illustrate the importance and relevance of sea snakes as contributors to better understanding a range of issues in marine biology, (2) establish and promote the use of marine systems as models for investigating conceptual issues related to environment, changing climate, and persistence of biological communities, with focus on marine snakes as novel or useful examples, (3) promote interest in sea snakes as useful organisms for study by scientists in a range of disciplines who might presently work with other organisms or systems, and (4) identify leading-edge topics for which studies of marine snakes might contribute uniquely to the advancement of research.     

Ecological modelling in an evolutionary context

I argue that one of the strong features in disciplines like molecular biology and cosmology is the extent ot which they use a powerful theoretical framework to generate and test quantitative predictions. Studies of biological evolution can exploit a similar advantage by integrating our current understanding of physiological and sociobiological processes to generate models of much greater sophistication than has commonly been the practice hitherto. I illustrate this with a number of examples drawn from the evolutionary biology of human and nonhuman primates.     

The use of passerine bird species in laboratory research: implications of basic biology for husbandry and welfare

Passerine birds are important models in fundamental biological research, with as many as 300,000 individuals used in laboratory experiments worldwide annually. However, because the use of passerines is rare compared with that of more conventional laboratory animals, there is often a lack of information about the basic biology and husbandry requirements of these species. We aim to address this deficit by providing an overview of the most salient aspects of passerine biology and their implications for laboratory husbandry and welfare. We start by describing the characteristics that make these birds useful and interesting research subjects. Specifically, we highlight features (e.g., birdsong) of passerine biology that differentiate these birds from more common laboratory animals. Next, we consider the implications of passerine biology for husbandry in the laboratory. Many of the aspects of passerine biology that make these species valuable to scientists are also likely to be affected by environmental variables; a good knowledge of these variables is necessary in order to choose appropriate laboratory conditions for passerines. We outline how the developmental history of the birds and choices of caging, feeding, and environmental regimes might influence their physiology and behavior and thus affect both the welfare of the birds and the quality of the resulting data. We stress the importance of a sound understanding of the biology of any species to ensure good welfare and good science.     

浅谈传粉生物学中几个术语的含义及其中文译名

准确理解外来的专业术语并给予合适的中文译名,不仅有助于推动学科的发展,而且有利于同行之间的交流。传粉生物学是近年来在我国迅速发展的一个生态学与进化生物学的分支领域。本文讨论了该学科中的几个重要术语的含义和它们的中文译名,建议将pollen discounting和seed discounting译为“花粉折损”和“种子折损”,herkogamy译为 “雌雄异位”,trade-off译为“权衡”。