Programs for invasive research in North American zoos and aquariums

Zoo-based research in North America is an emerging field, which has progressed from an ad hoc approach in a small number of zoos to a coordinated, integrated network of scientists with recognized research programs in approximately one half of the accredited institutions in North America. The disciplines most active in these programs--veterinary medicine and pathology, nutrition, reproductive biology, contraception, and behavior--are now becoming coordinated in zoos through Scientific Advisory Groups. Zoos with research programs generally establish either an institutional animal care and use committee or another committee to evaluate research proposals. In addition to scientific merit and experimental design, zoos evaluate proposals based on factors such as priority by conservation program/identified need; direct effect on species conservation, species type, and appropriateness; availability and location of animals; operational requirements/logistics; communication between institutions; and available funding. Euthanasia is considered only in rare circumstances. Zoo-based research has evolved into an integral component in animal management and conservation programs by providing practical information that is used to improve animal care, well-being, health, and reproduction. However, the degree to which zoos participate in invasive research varies considerably among institutions, due not only to resource limitations but also to how the term "invasive" is defined and accepted at each institution. A more standardized approach among zoological institutions for examining and approving research projects that are supported by zoo-based conservation programs would greatly facilitate the wildlife research efforts of North American zoos.     

Cultural Specificity and Comparison in Psychiatric Epidemiology: Walking the Tightrope in American Indian Research

Increasingly, the mental health needs of populations are measured using large-sample surveys with standardized measures and methods. Such efforts, however, rarely include sufficient number of smaller, culturally defined populations to draw defensible conclusions about their needs. Furthermore, without some adaptation, the standardized methods and measures may yield invalid results in such populations. Using a recently completed psychiatric epidemiology and services study with American Indian populations as a case example, this paper outlines issues facing epidemiologists working in such culturally diverse contexts. The issues discussed include the following: (1) persuading the scientific community and potential sponsors that work with distinct or culturally defined populations is important; (2) framing research questions and activities to meet the needs of communities; (3) defining a population of inference; (4) balancing the needs for comparability and cultural specificity; (5) maximizing scientific validity in light of the challenges in sample acquisition; and (6) developing and implementing data collection methods that uphold scientific standards but are also realistic given the context. The authors draw on their experiences—most recently in the American Indian Service Utilization, Psychiatric Epidemiology, Risk and Protective Factors Project (AI-SUPERPFP)—to illustrate these issues and suggest ways to address each. A goal of this paper is to challenge those invested in conducting culturally valid epidemiologic work in such populations to better articulate the nature of these efforts.     

What is the subject of science "bioinformatics"?

The paper is concerned with some problems of terminology, in particular the term "bioinformatics". In the last few years, the term "bioinformatics" has been intensively used among molecular biologists to indicate a subject that is only a constituent of genomics and is considered to involve a computer-assisted analysis of all data on nucleotide sequences of DNA. However, a wide circle of scientists, including biologists, physicists, mathematicians, and specialists in the field of cybernetics, informatics, and other disciplines have accepted and accept, as a rule, the "bioinformatics" as a synonym of science cybernetics and as a successor of this science. In this case, the subject of science "bioinformatics" should embrace not only genomics but practically all sections of the biological science. It should involve a study of information processes (storage, transfer, and processing of information, etc.) participating in the regulation and control at all levels of living systems, from macromolecules to the brain of higher animals and human.     

The replicability crisis in science and protected area research: Poor practices and potential solutions

The reliability of some published research from well-funded disciplines of medicine and psychology has been brought into question. This is because some researchers failed to achieve consistent results after replicating published studies using the same methodology. Researchers have referred to this as the ‘replicability in science crisis’ and have identified several practices contributing to unreliable science. Protected area and other conservation researchers are unlikely to be immune from these poor practices given they use the same scientific approaches as other disciplines. Fortunately, there are solutions to the poor practices contributing to unreliable science. In this paper I identify those poor practices and describe solutions as identified by researchers from a range of disciplines. These solutions are transferable to protected area science and related conservation disciplines. Most solutions are not costly or demanding to implement. Adopting these solutions can improve the reliability of both published and unpublished research.     

Epigenetic determinism in science and society

The epigenetic “revolution” in science cuts across many disciplines, and it is now one of the fastest-growing research areas in biology. Increasingly, claims are made that epigenetics research represents a move away from the genetic determinism that has been prominent both in biological research and in understandings of the impact of biology on society. We discuss to what extent an epigenetic framework actually supports these claims. We show that, in contrast to the received view, epigenetics research is often couched in language as deterministic as genetics research in both science and the popular press. We engage the rapidly emerging conversation about the impact of epigenetics on public discourse and scientific practice, and we contend that the notion of epigenetic determinism – or the belief that epigenetic mechanisms determine the expression of human traits and behaviors – matters for understandings of the influence of biology and society on population health.     

Protein-protein interactions: making sense of networks via graph-theoretic modeling

The emerging area of network biology is seeking to provide insights into organizational principles of life. However, despite significant collaborative efforts, there is still typically a weak link between biological and computational scientists and a lack of understanding of the research issues across the disciplines. This results in the use of simple computational techniques of limited potential that are incapable of explaining these complex data. Hence, the danger is that the community might begin to view the topological properties of network data as mere statistics, rather than rich sources of biological information. A further danger is that such views might result in the imposition of scientific doctrines, such as scale-free-centric (on the modeling side) and genome-centric (on the biological side) opinions onto this area. Here, we take a graph-theoretic perspective on protein-protein interaction networks and present a high-level overview of the area, commenting on possible challenges ahead.     

医院科研管理与创新对转化医学实施的推动作用

转化医学是近年来国际医学界推崇的一个重要医学理念,正日益成为生命科学和医学研究关注的热点。转化医学已不仅强 调临床医学与基础医学的结合,而且涉及多个学科之间的融会贯通。因此,医院科研管理的支持和重视程度转化医学实施的主要 动力,而科研项目的创新性、可行性是决定转化医学研究立项的关键。我院自2010 年成立转化医学研究中心以来,已将多项成果 成功转化并应用于临床实践,为生命科学研究领域中人类健康计划的发展提供了借鉴。本文结合我院实际,分析科研管理对转化 医学成果实施的促进作用,为医疗机构的科研管理人员提供参考。     

The roles of integration in molecular systems biology

A common way to think about scientific practice involves classifying it as hypothesis- or data-driven. We argue that although such distinctions might illuminate scientific practice very generally, they are not sufficient to understand the day-to-day dynamics of scientific activity and the development of programmes of research. One aspect of everyday scientific practice that is beginning to gain more attention is integration. This paper outlines what is meant by this term and how it has been discussed from scientific and philosophical points of view. We focus on methodological, data and explanatory integration, and show how they are connected. Then, using some examples from molecular systems biology, we will show how integration works in a range of inquiries to generate surprising insights and even new fields of research. From these examples we try to gain a broader perspective on integration in relation to the contexts of inquiry in which it is implemented. In today's environment of data-intensive large-scale science, integration has become both a practical and normative requirement with corresponding implications for meta-methodological accounts of scientific practice. We conclude with a discussion of why an understanding of integration and its dynamics is useful for philosophy of science and scientific practice in general.     

Non-Immunologic Factors in Allergic Diseases

Many different explanations of the mechanism of asthma and other allergic diseases have been offered. Of these, the immunologic concept has gained the greatest acceptance. During the past 25 years, a renewed attempt to place the diagnosis and treatment of allergic diseases on a firm scientific basis has yielded many fundamental facts and principles in such varied fields as immunology and psychiatry, but no one of these disciplines affords a satisfactory approach to the practical management of the individual patient. There is a vast gap between scientific fact and medical practice. The need at present is less for basic principles than for their rational application to diagnosis and treatment. This requires a broad knowledge of the basic sciences, and utilization of that which is applicable.     

The emergence of ecological engineering as a discipline

Pioneering efforts in ecological engineering (a precedent setting engineering and applied science discipline in which the self-engineering capabilities of ecosystems are managed for the benefit of the environment and humankind) research and practice have proven to be tremendous strides toward establishing a new engineering discipline with a science base in ecology. Case studies, demonstrations and applications pertaining to restoration, rehabilitation, conservation, sustainability, reconstruction, remediation and reclamation of ecosystems using ecological engineering techniques are numerous. This has brought the field to the current level where many scientists and engineers adequately support the concept of, and need for, ecological engineering, and generally agree that ecological engineering has been sufficiently defined. There is also general agreement that full emergence as an engineering discipline remains a difficult task. Certain general characteristics of existing engineering disciplines can guide the emergence of ecological engineering and thus are a vital context covered in this paper. From the context of engineering practice, three concepts are evident including: (1) establishment of formal foundations for ecological engineering research and development; (2) development of core ecological engineering sciences and curricula; and (3) certification in ecological design. These elements are important components of a formal approach to develop ecological engineering as a principled, quantitative, recognized, practical, novel, and formal engineering discipline that coalesces past and future research and practice into cohesive underpinnings.     

A conceptual framework for understanding the perspectives on the causes of the science–practice gap in ecology and conservation

Applying scientific knowledge to confront societal challenges is a difficult task, an issue known as the science–practice gap. In Ecology and Conservation, scientific evidence has been seldom used directly to support decision‐making, despite calls for an increasing role of ecological science in developing solutions for a sustainable future. To date, multiple causes of the science–practice gap and diverse approaches to link science and practice in Ecology and Conservation have been proposed. To foster a transparent debate and broaden our understanding of the difficulties of using scientific knowledge, we reviewed the perceived causes of the science–practice gap, aiming to: (i) identify the perspectives of ecologists and conservation scientists on this problem, (ii) evaluate the predominance of these perspectives over time and across journals, and (iii) assess them in light of disciplines studying the role of science in decision‐making. We based our review on 1563 sentences describing causes of the science–practice gap extracted from 122 articles and on discussions with eight scientists on how to classify these sentences. The resulting process‐based framework describes three distinct perspectives on the relevant processes, knowledge and actors in the science–practice interface. The most common perspective assumes only scientific knowledge should support practice, perceiving a one‐way knowledge flow from science to practice and recognizing flaws in knowledge generation, communication, and/or use. The second assumes that both scientists and decision‐makers should contribute to support practice, perceiving a two‐way knowledge flow between science and practice through joint knowledge‐production/integration processes, which, for several reasons, are perceived to occur infrequently. The last perspective was very rare, and assumes scientists should put their results into practice, but they rarely do. Some causes (e.g. cultural differences between scientists and decision‐makers) are shared with other disciplines, while others seem specific to Ecology and Conservation (e.g. inadequate research scales). All identified causes require one of three general types of solutions, depending on whether the causal factor can (e.g. inadequate research questions) or cannot (e.g. scientific uncertainty) be changed, or if misconceptions (e.g. undervaluing abstract knowledge) should be solved. The unchanged predominance of the one‐way perspective over time may be associated with the prestige of evidence‐based conservation and suggests that debates in Ecology and Conservation lag behind trends in other disciplines towards bidirectional views ascribing larger roles to decision‐makers. In turn, the two‐way perspective seems primarily restricted to research traditions historically isolated from mainstream conservation biology. All perspectives represented superficial views of decision‐making by not accounting for limits to human rationality, complexity of decision‐making contexts, fuzzy science–practice boundaries, ambiguity brought about by science, and different types of knowledge use. However, joint knowledge‐production processes from the two‐way perspective can potentially allow for democratic decision‐making processes, explicit discussions of values and multiple types of science use. To broaden our understanding of the interface and foster productive science–practice linkages, we argue for dialogue among different research traditions within Ecology and Conservation, joint knowledge‐production processes between scientists and decision‐makers and interdisciplinarity across Ecology, Conservation and Political Science in both research and education.     

Using learning networks to understand complex systems: a case study of biological,geophysical and social research in the Amazon

Developing high‐quality scientific research will be most effective if research communities with diverse skills and interests are able to share information and knowledge, are aware of the major challenges across disciplines, and can exploit economies of scale to provide robust answers and better inform policy. We evaluate opportunities and challenges facing the development of a more interactive research environment by developing an interdisciplinary synthesis of research on a single geographic region. We focus on the Amazon as it is of enormous regional and global environmental importance and faces a highly uncertain future. To take stock of existing knowledge and provide a framework for analysis we present a set of mini‐reviews from fourteen different areas of research, encompassing taxonomy, biodiversity, biogeography, vegetation dynamics, landscape ecology, earth‐atmosphere interactions, ecosystem processes, fire, deforestation dynamics, hydrology, hunting, conservation planning, livelihoods, and payments for ecosystem services. Each review highlights the current state of knowledge and identifies research priorities, including major challenges and opportunities. We show that while substantial progress is being made across many areas of scientific research, our understanding of specific issues is often dependent on knowledge from other disciplines. Accelerating the acquisition of reliable and contextualized knowledge about the fate of complex pristine and modified ecosystems is partly dependent on our ability to exploit economies of scale in shared resources and technical expertise, recognise and make explicit interconnections and feedbacks among sub‐disciplines, increase the temporal and spatial scale of existing studies, and improve the dissemination of scientific findings to policy makers and society at large. Enhancing interaction among research efforts is vital if we are to make the most of limited funds and overcome the challenges posed by addressing large‐scale interdisciplinary questions. Bringing together a diverse scientific community with a single geographic focus can help increase awareness of research questions both within and among disciplines, and reveal the opportunities that may exist for advancing acquisition of reliable knowledge. This approach could be useful for a variety of globally important scientific questions.     

Societal views and animal welfare science: understanding why the modified cage may fail and other stories

The innovations developed by scientists working on animal welfare are often not adopted in practice. In this paper, we argue that one important reason for this failure is that the solutions proposed do not adequately address the societal concerns that motivated the original research. Some solutions also fail because they do not adequately address perceived constraints within the industry. Using examples from our own recent work, we show how research methods from the social sciences can address both of these limitations. For example, those who persist in tail-docking cattle (despite an abundance of evidence showing that the practice has no benefits) often justify their position by citing concern for cow cleanliness. This result informs the nature of new extension efforts directed at farmers that continue to tail dock, suggesting that these efforts will be more effective if they focus on providing producers with methods (of proven efficacy) for keeping cows clean. Work on pain mitigation for dehorning shows that some participants reluctant to provide pain relief believe that the pain from this procedure is short lasting and has little impact on the calf. This result informs the direction of new biological research efforts to understand both the magnitude and duration of any suffering that result from this type of procedure. These, and other examples, illustrate how social science methodologies can document the shared and divergent values of different stakeholders (to ensure that proposed solutions align with mainstream values), beliefs regarding the available evidence (to help target new scientific research that meets the perceived gaps), and barriers in implementing changes (to ease adoption of ideas by addressing these barriers).     

Evolving research trends in bioinformatics

The cross-disciplinary nature of bioinformatics entails co-evolution with other biomedical disciplines, whereby some bioinformatics applications become popular in certain disciplines and, in turn, these disciplines influence the focus of future bioinformatics development efforts. We observe here that the growth of computational approaches within various biomedical disciplines is not merely a reflection of a general extended usage of computers and the Internet, but due to the production of useful bioinformatics databases and methods for the rest of the biomedical scientific community. We have used the abstracts stored both in the MEDLINE database of biomedical literature and in NIH-funded project grants, to quantify two effects. First, we examine the biomedical literature as a whole and find that the use of computational methods has become increasingly prevalent across biomedical disciplines over the past three decades, while use of databases and the Internet have been rapidly increasing over the past decade. Second, we study the recent trends in the use of bioinformatics topics. We observe that molecular sequence databases are a widely adopted contribution in biomedicine from the field of bioinformatics, and that microarray analysis is one of the major new topics engaged by the bioinformatics community. Via this analysis, we were able to identify areas of rapid growth in the use of informatics to aid in curriculum planning, development of computational infrastructure and strategies for workforce education and funding.     

转型期城市生态学前沿研究进展

城市是一类以人类活动为中心听社会－经济－自然复合生态系统。城市人类活动对局地、区域和全球环境的胁迫效应,自然生态系统的响应机制,城市时、空、量、构、序的耦合规律、动力学机制和控制论方法是当前国际社会和学术界关注的热点。介绍了转型期城市人类生态影响研究的一些主要国际科学计划,如ＳＣＯＰＥ及ＩＨＤＰ等,综述了城市生态学研究三大前沿领域的国际研究动向和案例,即人居生态学、产业生态学和城镇生命支持系统生态     

Productivity in Physical and Chemical Science Predicts the Future Economic Growth of Developing Countries Better than Other Popular Indices

Scientific productivity of middle income countries correlates stronger with present and future wealth than indices reflecting its financial, social, economic or technological sophistication. We identify the contribution of the relative productivity of different scientific disciplines in predicting the future economic growth of a nation. Results show that rich and poor countries differ in the relative proportion of their scientific output in the different disciplines: countries with higher relative productivity in basic sciences such as physics and chemistry had the highest economic growth in the following five years compared to countries with a higher relative productivity in applied sciences such as medicine and pharmacy. Results suggest that the economies of middle income countries that focus their academic efforts in selected areas of applied knowledge grow slower than countries which invest in general basic sciences.     

Allerton III. Beyond livestock genomics

Throughout the Allerton III Conference, several consistent research needs were identified across scientific disciplines. First, additional basic research is needed to identify genomic mechanisms and novel genes/proteins in a variety of tissues under different conditions. Second, expansion of the infrastructure of the scientific community is needed. This can best be accomplished by additional competitive grants programs for training grants, program project grants, and multidisciplinary research projects. Third, the need for improved tools for animal bioinformatics was emphasized. Fourth, competitive grants programs for extension/outreach efforts and application of genomic technologies to production systems are needed. Finally, efforts to publicize and document the benefits of animal genomics for improved human health and animal production systems to members of Congress and the general public should be enhanced.     

Senescence, Growth, and Gerontology in the United States

This paper discusses how growth and aging became interrelated phenomena with the creation of gerontology in the United States. I first show that the relation of growth to senescence, which had hardly attracted scientific attention before the twentieth century, started to be investigated by several experimental scientists around the 1900s. Subsequently, research on the connection between the two phenomena entered a new domain through the birth of gerontology as a scientific field comprised of various disciplines, many of which addressed growth. Due to gerontologists’ efforts, the association between aging and growth became stronger and more multifaceted within the discursive and organizational matrix constituting the new science, leading to a broader definition of senescence with an ambiguous connection to chronological age. Furthermore, as gerontologists borrowed the cultural agendas as well as research methods from studies of growth, aging began to be defined as a phenomenon that could be actively controlled and managed in both social arenas and laboratory environments.     

Spatially Explicit Data: Stewardship and Ethical Challenges in Science

Scholarly communication is at an unprecedented turning point created in part by the increasing saliency of data stewardship and data sharing. Formal data management plans represent a new emphasis in research, enabling access to data at higher volumes and more quickly, and the potential for replication and augmentation of existing research. Data sharing has recently transformed the practice, scope, content, and applicability of research in several disciplines, in particular in relation to spatially specific data. This lends exciting potentiality, but the most effective ways in which to implement such changes, particularly for disciplines involving human subjects and other sensitive information, demand consideration. Data management plans, stewardship, and sharing, impart distinctive technical, sociological, and ethical challenges that remain to be adequately identified and remedied. Here, we consider these and propose potential solutions for their amelioration.