Back to the future: education for systems-level biologists

We describe a graduate course in quantitative biology that is based on original path-breaking papers in diverse areas of biology; each of these papers depends on quantitative reasoning and theory as well as experiment. Close reading and discussion of these papers allows students with backgrounds in physics, computational sciences or biology to learn essential ideas and to communicate in the languages of disciplines other than their own.     

The Oligopoly of Academic Publishers in the Digital Era

The consolidation of the scientific publishing industry has been the topic of much debate within and outside the scientific community, especially in relation to major publishers’ high profit margins. However, the share of scientific output published in the journals of these major publishers, as well as its evolution over time and across various disciplines, has not yet been analyzed. This paper provides such analysis, based on 45 million documents indexed in the Web of Science over the period 1973-2013. It shows that in both natural and medical sciences (NMS) and social sciences and humanities (SSH), Reed-Elsevier, Wiley-Blackwell, Springer, and Taylor & Francis increased their share of the published output, especially since the advent of the digital era (mid-1990s). Combined, the top five most prolific publishers account for more than 50% of all papers published in 2013. Disciplines of the social sciences have the highest level of concentration (70% of papers from the top five publishers), while the humanities have remained relatively independent (20% from top five publishers). NMS disciplines are in between, mainly because of the strength of their scientific societies, such as the ACS in chemistry or APS in physics. The paper also examines the migration of journals between small and big publishing houses and explores the effect of publisher change on citation impact. It concludes with a discussion on the economics of scholarly publishing.     

The influence of German idealistic morphology on the development of C.J. van der Klaauw's epistemology

Notwithstanding the general rise of experimental disciplines in biology in the first decades of our century, in Germany and in the Netherlands the interest in the idealistic morphological tradition flourished, and compensated for a reductionistic causal approach to natural phenomena. This article analyses the influence of the German idealistic morphologists W. Lubosch and A. Meyer on the development of C.J. van der Klaauw's epistemology. It discusses the gradual incorporation of non-causal principles into van der Klaauw's concept of biology. Van der Klaauw's epistemological concept of holistic biology was shaped in a critical confrontation with German idealistic morphology, and his early considerations can be interpreted as a direct impulse towards the development of his theory of functional components. Van der Klaauw's theories, being an alternative to the reductionistic experimental sciences, were among the causes of the fact that in the first half of our century biology in the Netherlands took a course deviating from the development of biology in the Anglo-American countries.     

The “capacity to reason” in conservation biology and policy: the southern elephant seal branding controversy

Modern environmental research is typically governed by a number of protocols designed to embrace the epistemological and ethical values of society. These protocols evolve in response to changing values, and few disciplines in environmental science have received as much attention as biological conservation. This paper describes the events leading to a controversy regarding a particular research technique used to investigate the cause of a long-term population decline of southern elephant seals (Mirounga leonina) at Macquarie Island, south of Australia – hot-iron branding of individuals. We discuss procedures and protocols that were in place at the time the controversy erupted, the subsequent reflection of the researchers and authorities involved, and the steps taken to avoid future occurrences. Our treatment of the issue is framed within a discussion of modern ethical philosophy, and our aim is to identify the true source of the controversy. We offer several suggestions as to how such events can be avoided in the future, and provide a model framework for incorporating changing ethical values into important biological conservation objectives.     

“Positive” Results Increase Down the Hierarchy of the Sciences

The hypothesis of a Hierarchy of the Sciences with physical sciences at the top, social sciences at the bottom, and biological sciences in-between is nearly 200 years old. This order is intuitive and reflected in many features of academic life, but whether it reflects the “hardness” of scientific research—i.e., the extent to which research questions and results are determined by data and theories as opposed to non-cognitive factors—is controversial. This study analysed 2434 papers published in all disciplines and that declared to have tested a hypothesis. It was determined how many papers reported a “positive” (full or partial) or “negative” support for the tested hypothesis. If the hierarchy hypothesis is correct, then researchers in “softer” sciences should have fewer constraints to their conscious and unconscious biases, and therefore report more positive outcomes. Results confirmed the predictions at all levels considered: discipline, domain and methodology broadly defined. Controlling for observed differences between pure and applied disciplines, and between papers testing one or several hypotheses, the odds of reporting a positive result were around 5 times higher among papers in the disciplines of Psychology and Psychiatry and Economics and Business compared to Space Science, 2.3 times higher in the domain of social sciences compared to the physical sciences, and 3.4 times higher in studies applying behavioural and social methodologies on people compared to physical and chemical studies on non-biological material. In all comparisons, biological studies had intermediate values. These results suggest that the nature of hypotheses tested and the logical and methodological rigour employed to test them vary systematically across disciplines and fields, depending on the complexity of the subject matter and possibly other factors (e.g., a field''s level of historical and/or intellectual development). On the other hand, these results support the scientific status of the social sciences against claims that they are completely subjective, by showing that, when they adopt a scientific approach to discovery, they differ from the natural sciences only by a matter of degree.     

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.     

Focus: Vaccines: Distorted Human Decision-Making as a Critical Aspect of Pandemic Planning and Preparedness

The United States continues to experience lower than expected vaccination rates against COVID-19 due to a variety of barriers such as lack of trust, lack of planning, cultural perspectives and issues, suboptimal communication, and political/economic conflicts of interest. In this paper issues of human behavior and decision-making are highlighted as integral to understanding the generally poor US response to the SARS-CoV-2 pandemic. In particular, the US pandemic response was significantly distorted through a combination of cultural and human behavior issues related to conflicting leadership, cultural individualism, the prevalent idea of the democratization of expertise, and a false epistemological lens for decision-making. Including experts from multiple disciplines reveals how to address the human behavioral side of pandemic planning and operations to increase vaccine coverage rates. Including content experts from psychology and the social sciences allows the explicit recognition and preparation for distorted human behavior in planning for future pandemic response.     

Caveats and pitfalls of ROC analysis in clinical microarray research (and how to avoid them)

The receiver operating characteristic (ROC) has emerged as the gold standard for assessing and comparing the performance of classifiers in a wide range of disciplines including the life sciences. ROC curves are frequently summarized in a single scalar, the area under the curve (AUC). This article discusses the caveats and pitfalls of ROC analysis in clinical microarray research, particularly in relation to (i) the interpretation of AUC (especially a value close to 0.5); (ii) model comparisons based on AUC; (iii) the differences between ranking and classification; (iv) effects due to multiple hypotheses testing; (v) the importance of confidence intervals for AUC; and (vi) the choice of the appropriate performance metric. With a discussion of illustrative examples and concrete real-world studies, this article highlights critical misconceptions that can profoundly impact the conclusions about the observed performance.     

Charles Darwin goes to school: the role of cartoons and narrative in setting science in an historical context

Science education is under revision. Recent changes in society require changes in education to respond to new demands. Scientific literacy can be considered a new goal of science education and the epistemological gap between natural sciences and literacy disciplines must be overcome. The history of science is a possible bridge to link these ‘two cultures’ and to foster an interdisciplinary approach in the classroom. This paper acknowledges Darwin's legacy and proposes the use of cartoons and narrative expositions to put this interesting chapter of science into its historical context. A five-lesson didactic sequence was developed to tell part of the story of Darwin's expedition through South America for students from 10 to 12 years of age. Beyond geological and biological perspectives, the inclusion of historical, social and geographical facts demonstrated the beauty and complexity of the findings that Darwin employed to propose the theory of evolution.     

Macroecology and consilience

Consilience means that all fields of human knowledge should be internally consistent. Within the broad span of the ecological and evolutionary sciences, there are many fields that seem only remotely related conceptually. Macroecology has emerged as a research programme that focuses on statistical patterns of ecological and biogeographically relevant traits among different species within a taxon. The concepts needed to understand these patterns require the interface of disciplines as different as systematics, ecosystem ecology, palaeontology and community ecology. By building conceptual links among a wide range of disciplines, macroecology is contributing, and will continue to contribute, to the growing realization that all of biology is indeed consilient.     

Typology Reconfigured: From the Metaphysics of Essentialism to the Epistemology of Representation

The goal of this paper is to encourage a reconfiguration of the discussion about typology in biology away from the metaphysics of essentialism and toward the epistemology of classifying natural phenomena for the purposes of empirical inquiry. First, I briefly review arguments concerning 'typological thinking', essentialism, species, and natural kinds, highlighting their predominantly metaphysical nature. Second, I use a distinction between the aims, strategies, and tactics of science to suggest how a shift from metaphysics to epistemology might be accomplished. Typological thinking can be understood as a scientific tactic that involves representing natural phenomena using idealizations and approximations, which facilitates explanation, investigation, and theorizing via abstraction and generalization. Third, a variety of typologies from different areas of biology are introduced to emphasize the diversity of this representational reasoning. One particular example is used to examine how there can be epistemological conflict between typology and evolutionary analysis. This demonstrates that alternative strategies of typological thinking arise due to the divergent explanatory goals of researchers working in different disciplines with disparate methodologies. I conclude with several research questions that emerge from an epistemological reconfiguration of typology.     

Interface Biology of Implants

Implants are widely used in various clinical disciplines to replace or stabilize organs. The challenge for the future is to apply implant materials to specifically control the biology of the surrounding tissue for repair and regeneration. This field of research is highly interdisciplinary and combines scientists from technical and life sciences disciplines. To successfully apply materials for regenerative processes in the body, the understanding of the mechanisms at the interface between cells or tissues and the artificial material is of critical importance. The research focuses on stem cells, design of material surfaces, and mechanisms of cell adhesion. For the third time around 200 scientists met in Rostock, Germany for the international symposium “Interface Biology of Implants”. The aim of the symposium is to promote the interdisciplinary dialogue between the scientists from the different disciplines to develop smart implants for medical use. In addition, researchers from basic sciences, notably cell biology presented new findings concerning mechanisms of cell adhesion to stimulate research in the applied field of implant technology.     

Education and taxonomy: the role of the Field Studies Council and AIDGAP

The taxonomic disciplines, classification and identification, are fundamental to most biological sciences. Yet, taxonomic teaching and research have declined to a level where adequate support for the other sciences can no longer be sustained. New teaching initiatives are needed, combined with the provision of suitable resource materials and identification guides. Bodies such as the Field Studies Council and the Linnean Society have a tradition of publishing identification keys, but the experience of the AIDGAP project, first started in 1976, shows that considerable thought must be given to content and presentation. Testing prior to publication is vital.     

The application of atomic force microscopy to the study of living vertebrate cells in culture

Atomic force microscopy (AFM), a relatively new variant of scanning probe microscopy developed for the material sciences, is becoming an increasingly important tool in other disciplines. In this review I describe in nontechnical terms some of the basic aspects of using AFM to study living vertebrate cells. Although AFM has some unusual attributes such as an ability to be used with living cells, AFM also has attributes that make its use in cell biology a real challenge. This review was written to encourage researchers in the biological and biomedical sciences to consider AFM as a potential (and potent) tool for their cell biological research.     

Giving Voice to Children's Voices: Practices and Problems, Pitfalls and Potentials

In this article, I explore the lessons that the anthropological debates of the 1980s about writing culture might have for contemporary childhood research within anthropology and the social sciences more generally. I argue that the current rhetoric about "giving voice to children," commonplace both inside and outside the academy, poses a threat to the future of childhood research because it masks a number of important conceptual and epistemological problems. In particular, these relate to questions of representation, issues of authenticity, the diversity of children's experiences, and children's participation in research, all of which need to be addressed by anthropologists in their own research practices with children. Unless anthropologists do so, childhood research risks becoming marginalized once more and will fail to provide an arena within which children are seen as social actors who can provide a unique perspective on the social world about matters that concern them as children.     

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.     

谈中国植物科学基础研究与农业发展

该文讨论了加强植物科学基础研究的必要性及其对我国农业发展的重要影响。为了更好地为中国的农业发展服务,进一步加强植物科学基础研究非常重要。为了促进植物科学的发展,我国既要积极参与国际竞争,又要重视知识创新、技术发展以及技术平台建设等多个方面,还要重视传统学科如植物分类学等的发展。过去10年间,我们见证了中国科学家在植物科学领域取得的重要成就,随着越来越多的高水平人才回国,建议国家增加投入支持我国的植物科学基础研究。     

谈中国植物科学基础研究与农业发展

该文讨论了加强植物科学基础研究的必要性及其对我国农业发展的重要影响。为了更好地为中国的农业发展服务, 进一步加强植物科学基础研究非常重要。为了促进植物科学的发展, 我国既要积极参与国际竞争, 又要重视知识创新、技术发展以及技术平台建设等多个方面, 还要重视传统学科如植物分类学等的发展。过去10年间, 我们见证了中国科学家在植物科学领域取得的重要成就, 随着越来越多的高水平人才回国, 建议国家增加投入支持我国的植物科学基础研究。