The quality of doctoral-level biochemistry (N=139), botany (N=83), cellular/molecular biology (N=89), microbiology (N=134), physiology (N=101), and zoology (N=70) programs at United States universities was assessed, using 16 measures. These measures focused on variables related to: (1) program size; (2) characteristics of graduates; (3) reputational factors (scholarly quality of faculty, effectiveness of programs in educating research scholars/scientists, improvement in program quality during the last 5 years); (4) university library size; (5) research support; and (6) publication records. Chapter I discusses (...) prior attempts to assess quality in graduate education, development of the study plans, and the selection of disciplines and programs to be evaluated. Chapter II discusses the methodology used, focusing on each of the assessment measures. Chapters III to VIII present, respectively, findings from the analyses of the biochemistry, botany, cellular/molecular biology, microbiology, physiology, and zoology programs. Chapter IX includes a summary of results, correlations among measures, several additional analyses, and suggestions for future studies. Among the findings reported are those indicating that cellular/molecular biology programs had, on the average, the largest number of faculty and that students in cellular/molecular biology, biology, biochemistry, microbiology, and physiology received a relatively high fraction of financial support. (Survey instruments and supporting documentation are included in appendices.) (JN). (shrink)

Doctoral programs at U.S. universities play a critical role in the development of human resources both in the United States and abroad. This volume reports the results of an extensive study of U.S. research-doctorate programs in five broad fields: physical sciences and mathematics, engineering, social and behavioral sciences, biological sciences, and the humanities. Research-Doctorate Programs in the United States documents changes that have taken place in the size, structure, and quality of doctoral education since the widely used (...) 1982 editions. This update provides selected information on nearly 4,000 doctoral programs in 41 subdisciplines at 274 doctorate-granting institutions. This volume also reports the results of the National Survey of Graduate Faculty, which polled a sample of faculty for their views on the scholarly quality of program faculty and the effectiveness of doctoral programs in preparing research scholars/scientists. This much-anticipated update of such an essential reference will be useful to education administrators, university faculty, and students seeking authoritative information on doctoral programs. (shrink)

This article investigates whether there is an underlying morality in the ways that human beings seek to obtain economic security within our imperfect economy, which can be illuminated through evolutionary biology research. Two research questions are the focus of the analysis: (1) What is the transaction cognitive machinery that is specialized for the entrepreneurial task of exchange-based security-seeking? and, (2) What are the moral implications of the acquisition and use of such transaction cognitions?Evolutionary biology research suggests within (...) concepts that are more Darwin- v. Huxley-based, an underlying morality supportive of algorithm-governed economizing arising from the behaviors that are most worthy of long-term reproduction. Evolutionarily stable algorithm-enhanced security-seeking is argued to be a new view of entrepreneurship, but one that, somewhat ironically, is grounded in a primordially-based entrepreneurial morality that is at the core of economic security. (shrink)

The significance of the behavior of biological entities cannot be fully explained in terms of the physical and chemical processes upon which contemporary biological and medical research depends. The characteristic proper of biological entities is that they are systems marked by ‘inwardness’, that is, a capacity to interpret meanings in order to reach goals. The significance of this characteristic is given in examples from the author's morphological research. Keywords: biological research, inwardness, organism CiteULike (...) Connotea Del.icio.us What's this? (shrink)

The majority of biomedical and biological research relies on a few molecular biology techniques. Here we show that eight key molecular biology techniques would not exist without basic biological research.We also find that the scientific reward system does not sufficiently value basic biological research into molecular mechanisms.

There is a trend within philosophy of biology to concentrate on questions that are strongly related to particular biological research programs rather than on the general scope of the field and its relation to other sciences. Projects of the latter kind, of course, are followed as well but will not be the topic of this review. Shifting the focus to particular research programs reflects philosophers’ increased interest in knowledge of, and contribution to, actual biological research, (...) which is organized in such programs. It is accompanied by the increasing enthusiasm of biologists to involve philosophers in the conceptual work of theoretical biology. I concentrate on the philosophies of four biological research programs, three of which are devoted to evolutionary biology, which is still the main field of interest among philosophers of biology: adaptationism, EvoDevo, and the developmental systems approach. In addition, a short sketch of the newly emerging philosophy of systems biology is given. Several lines of philosophical inquiry can be found in all of the fields considered here: philosophy contributes to the conceptual development of biological research programs, it analyzes structures and delineations of particular research programs, and sometimes it is involved in a comparative assessment of biological programs as well. Philosophical projects that start from the level of a particular research program may give rise to a bottom-up perspective on biology and allow for an integrative view of biological research. This may open up the opportunity to tackle “larger” questions again in an altered and fruitful manner. (shrink)

The historiography of the ‘dark age’ of biochemistry between 1910–1930 is examined. The biochemistry of the period is located within a larger contemporary debate on the interrelationship between structure and function on a submicroscopic level. It is suggested that biocolloid science was an understandable part of the historical development of biochemistry, representing a conceptual bridge between the cell biology of the late nineteenth century, and the era of structural macromolecular studies of proteins that began after 1930.

Virtually no one outside Germany, however, thought that Schramm's story was right. This was because of the war. It was inconceivable to most people that the German beasts would have permitted the extensive experiments underlying his claims to be routinely carried out during the last years of a war they were so badly losing. It was all too easy to image that the work had direct Nazi support and that his experiments were incorrectly analyzed. Wasting time to disprove Schramm was (...) not to most biochemists' liking. (shrink)

Biological research with legitimate scientific purpose that may be misused to pose a biological threat to public health and/or national security is termed dual use. In Poland there are adequate conditions for conducting experiments that could be qualified as dual use research, and therefore, a risk of attack on Poland or other countries exists. Optimal solutions for limiting such threats are required, and the national system of biosecurity should enable early, reliable, and complete identification of this (...) type of research. Scientists should have a fundamental role in this process, their duty being to immediately, upon identification, report research with dual use potential. An important entity in the identification system of dual use research should also be the Central Register of Biological and Biomedical Research, which gathers information about all biological and biomedical research being conducted in a given country. Publishers, editors, and review committees of journals and other scientific publications should be involved in evaluating results of clinical trials. The National Council of Biosecurity should be the governmental institution responsible for developing a system of dual use research threat prevention. Its role would be to develop codes of conduct, form counsel of expertise, and monitor the problem at national level, while the Dual Use Research Committee would be responsible for individual cases. In Poland, current actions aiming to provide biological safety were based on developing and passing an act about genetically modified organisms (GMO’s) and creating a GMO Committee. Considering experiences of other nations, one should view these actions as fragmentary, and thus insufficient protection against dual use research threats. (shrink)

Open Science policies encourage researchers to disclose a wide range of outputs from their work, thus codifying openness as a specific set of research practices and guidelines that can be interpreted and applied consistently across disciplines and geographical settings. In this paper, we argue that this “one-size-fits-all” view of openness sidesteps key questions about the forms, implications, and goals of openness for research practice. We propose instead to interpret openness as a dynamic and highly situated mode of valuing (...) the research process and its outputs, which encompasses economic as well as scientific, cultural, political, ethical, and social considerations. This interpretation creates a critical space for moving beyond the economic definitions of value embedded in the contemporary biosciences landscape and Open Science policies, and examining the diversity of interests and commitments that affect research practices in the life sciences. To illustrate these claims, we use three case studies that highlight the challenges surrounding decisions about how––and how best––to make things open. These cases, drawn from ethnographic engagement with Open Science debates and semistructured interviews carried out with UK-based biologists and bioinformaticians between 2013 and 2014, show how the enactment of openness reveals judgments about what constitutes a legitimate intellectual contribution, for whom, and with what implications. (shrink)

In the last part of the Timaeus, where Plato presents his ideas about human physiology but also about biology in general, we find the combined activity of Intellect and Necessity. In this essay I investigate whether Plato, apart from his general statement about the combined activity of Reason and Necessity, proposes a more specific method of biological research. For this purpose I am going to examine some methodological passages as well as the way in which he exposes and (...) develops his views about the human body and its organs. (shrink)

A major theme in biological research is the quest for mechanism, embodied in explanatory reductionism: the interpretation of phenomena through links to the entities and laws of more fundamental sciences. For example, the form of Starling's Law of the Heart, relating contractile force to heart volume, follows from the sliding-filament hypothesis of muscle contraction, a molecular concept. Although alternative mechanisms for muscle contraction and cardiac regulation could be deduced from biochemical principles, the formulation provides clear correspondence with the (...) phenomena and a deeper understanding of cardiac function. Moreover, even if the reduction provides no better formulation of the phenomenon, of the macro-regularity, it is still prized as a nearer approach to physical reality, as a step toward realizing fundamental unities and codifying general principles, and as a door to new experimental opportunities. (shrink)

Should medical researchers not participate in military biological research? The argument for “no participation” falsely assumes there is no practical and moral distinction between offensive and defensive military biological research.

In many fields of biology, researchers explain a phenomenon by characterizing the responsible mechanism. This requires identifying the candidate mechanism, decomposing it into its parts and operations, recomposing it so as to understand how it is organized and its operations orchestrated to generate the phenomenon, and situating it in its environment. Mechanistic researchers have developed sophisticated tools for decomposing mechanisms but new approaches, including modeling, are increasingly being invoked to recompose mechanisms when they involve nonsequential organization of nonlinear operations. The (...) results often are dynamical mechanistic explanations. The steps in mechanistic research are illustrated using research on circadian rhythms. (shrink)

This paper presents, from the perspectives of both social scientists and microbiologists, a case study of the implementation and practice of Responsible Innovation (RI) in a UK-based synthetic biology project. We highlight the impact of interdisciplinary working and examine the benefits that arise from creating the time and space for shared reflection on research. Our discussions over the course of the project included concerns about the potential escape to the environment of laboratory-constructed genetic material and alternatives to the role (...) that antibiotic resistance genes play in synthetic biology. As a result, the design of a key product of the project was altered in ways that go beyond normal institutional requirements. We highlight our view of the importance of continued interdisciplinary collaboration and the utility of the framework of Responsible Innovation in achieving this. We conclude with observations on the difficulties of sustaining such collaborations. (shrink)

How does a complex organism develop from a relatively simple, homogeneous mass? The usual answer is: through the (context‐dependent) execution of species‐specific genetic instructions specifying the development of that organism. Commentators are sometimes skeptical of this usual answer, but of course not all commentators, and not always for the same reasons. Here I attempt to lay bare the logical structure of the usual answer through an extended analysis of the heuristics and methodological principles at play in the exploration and explanation (...) of development—and also to show a critical ambiguity that renders the usual answer suspect. (shrink)

Science is about conceptualizing the natural world in a way that can be understood by human beings while at the same time reflecting as much as possible what we can empirically infer about how the world actually is. Among the crucial tools that allow scientists to formulate hypotheses and to contribute to a progressive understanding of nature are the use of imagery and metaphors, on the one hand, and the ability to assume certain starting points on which to build new (...) avenues of inquiry on the other hand. The premise of this work is that, in the words of philosopher of science Daniel Dennett, "There is no such thing as philosophy-free science; there is only science whose philosophical baggage is taken on board without examination." The purpose here is precisely to examine some of this philosophical baggage, and to see where such analysis may lead us. Obviously, it is not possible for a single project to take on science as a whole, or even an entire discipline such as physics, or ecology. Therefore, the core of this work is constituted by a series of eight case studies drawn from the field of evolutionary biology, with which I am particularly familiar as a practicing biologist. The hope is that combining expertise in both philosophy and science in one person, the resulting insights might be useful for the practicing scientist as well as because of their value as philosophical inquires. The dissertation is a combination of conceptual analysis and science criticism applied to specific questions in organismal biology, largely of an evolutionary nature, with the eight case studies grouped into three broad categories: Unexamined Baggage, Bad Habits, and Good and bad metaphors. (shrink)

This paper aims to illustrate the advantages of critical realism for biological scientists and to offer an example, for others in philosophy and the social sciences, of applied natural science in p...

Scientific risk evaluations are constructed by specific evidence, value judgements and biological background assumptions. The latter are the framework-setting suppositions we apply in order to understand some new phenomenon. That background assumptions co-determine choice of methodology, data interpretation, and choice of relevant evidence is an uncontroversial claim in modern basic science. Furthermore, it is commonly accepted that, unless explicated, disagreements in background assumptions can lead to misunderstanding as well as miscommunication. Here, we extend the discussion on background assumptions from (...) basic science to the debate over genetically modified (GM) plants risk assessment. In this realm, while the different political, social and economic values are often mentioned, the identity and role of background assumptions at play are rarely examined. We use an example from the debate over risk assessment of stacked genetically modified plants (GM stacks), obtained by applying conventional breeding techniques to GM plants. There are two main regulatory practices of GM stacks: (i) regulate as conventional hybrids and (ii) regulate as new GM plants. We analyzed eight papers representative of these positions and found that, in all cases, additional premises are needed to reach the stated conclusions. We suggest that these premises play the role of biological background assumptions and argue that the most effective way toward a unified framework for risk analysis and regulation of GM stacks is by explicating and examining the biological background assumptions of each position. Once explicated, it is possible to either evaluate which background assumptions best reflect contemporary biological knowledge, or to apply Douglas' 'inductive risk' argument. (shrink)

In recent years, the publication of the studies on the transmissibility in mammals of the H5N1 influenza virus and synthetic genomes has triggered heated and concerned debate within the community of scientists on biological dual-use research; these papers have raised the awareness that, in some cases, fundamental research could be directed to harmful experiments, with the purpose of developing a weapon that could be used by a bioterrorist. Here is presented an overview regarding the dual-use concept and (...) its related international agreements which underlines the work of the Australia Group Export Control Regime. It is hoped that the principles and activities of the AG, that focuses on export control of chemical and biological dual-use materials, will spread and become well known to academic researchers in different countries, as they exchange biological materials and scientific papers. To this extent, and with the aim of drawing the attention of the scientific community that works with yeast to the so called Dual-Use Research of Concern, this article reports case studies on biological dual-use research and discusses a synthetic biology applied to the yeast Saccharomyces cerevisiae, namely the construction of the first eukaryotic synthetic chromosome of yeast and the use of yeast cells as a factory to produce opiates. Since this organism is considered harmless and is not included in any list of biological agents, yeast researchers should take simple actions in the future to avoid the sharing of strains and advanced technology with suspicious individuals. (shrink)

Multilevel research strategies characterize contemporary molecular inquiry into biological systems. We outline conceptual, methodological, and explanatory dimensions of these multilevel strategies in microbial ecology, systems biology, protein research, and developmental biology. This review of emerging lines of inquiry in these fields suggests that multilevel research in molecular life sciences has significant implications for philosophical understandings of explanation, modeling, and representation.

This paper proposes an extended version of the interventionist account for causal inference in the practical context of biological mechanism research. This paper studies the details of biological mechanism researchers’ practices of assessing the evidential legitimacy of experimental data, arguing why quantity and variety are two important criteria for this assessment. Because of the nature of biological mechanism research, the epistemic values of these two criteria result from the independence both between the causation of data (...) generation and the causation in question and between different interventions, not techniques. The former independence ensures that the interventions in the causation in question are not affected by the causation that is responsible for data generation. The latter independence ensures the reliability of the final mechanisms not only in the empirical but also the formal aspects. This paper first explores how the researchers use quantity to check the effectiveness of interventions, where they at the same time determine the validity of the difference-making revealed by the results of interventions. Then, this paper draws a distinction between experimental interventions and experimental techniques, so that the reliability of mechanisms, as supported by the variety of evidence, can be safely ensured in the probabilistic sense. The latter process is where the researchers establish evidence of the mechanisms connecting the events of interest. By using case studies, this paper proposes to use ‘intervention’ as the fruitful connecting point of literature between evidence and mechanisms. (shrink)

Multicellular organisms contain numerous symbiotic microorganisms, collectively called microbiomes. Recently, microbiomic research has shown that these microorganisms are responsible for the proper functioning of many of the systems of multicellular organisms. This has inclined some scholars to argue that it is about time to reconceptualise the organism and to develop a concept that would place the greatest emphasis on the vital role of microorganisms in the life of plants and animals. We believe that, unfortunately, there is a problem with (...) this suggestion, since there is no such thing as a universal concept of the organism which could constitute a basis for all biological sciences. Rather, the opposite is true: numerous alternative definitions exist. Therefore, comprehending how microbiomics is changing our understanding of organisms may be a very complex matter. In this paper we will demonstrate that this pluralism proves that claims about a change in our understanding of organisms can be treated as both true and untrue. Mainly, we assert that the existing concepts differ substantially, and that only some of them have to be reconsidered in order to incorporate the discoveries of microbiomics, while others are already flexible enough to do so. Taking into account the plurality of conceptualisations within different branches of modern biology, we will conduct our discussion using the developmental and the cooperation–conflict concepts of the organism. Then we will explain our results by referring to the recent philosophical debate on the nature of the concept of the organism within biology. (shrink)

New health technologies are rapidly emerging from various areas of bioscience research, such as gene editing, regenerative medicine and synthetic biology. These technologies raise promising medical possibilities but also a range of ethical considerations. Apart from the issues involved in considering whether novel health technologies can or should become part of mainstream medical treatment once established, the process of research translation to develop such therapies itself entails particular ethical concerns. In this paper I use synthetic biology as an (...) example of a new and largely unexplored area of health technology to consider the ways in which novel health technologies are likely to emerge and the ethical challenges these will present. I argue that such developments require us to rethink conventional attitudes towards clinical research, the roles of doctors/researchers and patients/participants with respect to research, and the relationship between science and society; and that a broader framework is required to address the plurality of stakeholder roles and interests involved in the development of treatments based on novel technologies. (shrink)

Two overriding considerations shaped the development of early research on the biological effects of microwave radiation—possible medical application and uncertainty about the hazards of exposure to radar. Reports in the late 1940s and early 1950s of hazards resulting from microwave exposure led to the near abandonment of medical research related to microwave diathermy at the same time that military and industrial concern over hazards grew, culminating in the massive research effort known as ‘the Tri-Service program’ . (...) Both the early focus on medical application and the later search for hazards played important roles in dictating how this field of research developed as a science. (shrink)

Synthetic genomics is a new field of research in which small DNA pieces are assembled in a series of steps into whole genomes. The highly reduced genomes of host‐associated bacteria are now being used as models for de novo synthesis of small genomes in the laboratory. Bacteria with the smallest genomes identified in nature provide nutrients to their hosts, such as amino acids, co‐factors and vitamins. Comparative genomics of these bacteria enables predictions to be made about the gene sets (...) required for core cellular functions and the associated metabolic network for the biosynthesis of host‐selected compounds. Synthetic biology may ultimately enable researchers to make customized cell‐specific organelles for the production and delivery of drugs to humans and domestic animals. Synthetic genomics may also become the method of choice for functional analyses of genes and genomes from bacteria that cannot be cultivated in the laboratory. (shrink)

Human Biological Materials are an invaluable resource in biomedical research. Objective To determine if researchers and a Research Ethics Committee at a South African institution addressed ethical issues pertaining to HBMs in collaborative research with developed countries. Study Design Ethically approved retrospective cross-sectional descriptive audit. Results Of the 1305 protocols audited, 151 fulfilled the study's inclusion criteria. Compared to other developed countries, a majority of sponsors were from the USA . The principle investigators in all 151 (...) protocols informed the REC of their intent to store HBMs. Only 132 protocols informed research participants . In 148 protocols informed consent was obtained from research participants, 116 protocols solicited broad consent compared to specific consent [p < 0.0001]. In 105 cases a code was used to maintain confidentiality. HBMs were anonymised in 14 protocols [p < 0.0001]. More protocols informed the REC than the research participants that HBMs would be exported . Export permits and Material Transfer Agreements were not available in 109 and 143 protocols, respectively. Conclusions Researchers and the REC did not adequately address the inter-related ethical and regulatory issues pertaining to HBMs. There was a lack of congruence between the ethical guidelines of developed countries and their actions which are central to the access to HBMs in collaborative research. HBMs may be leaving South Africa without EPs and MTAs during the process of international collaborative research. (shrink)

It is estimated that typhoid fever (TF) annually affects more than 12 million persons, worldwide. TF is the result of a generalized infection by the enterobacterium Salmonella typhi. Patients with TF, most of whom live in developing countries have impaired activity for several weeks resulting in an important loss in productivity and welfare. Death may occur, with the single most frequent cause being intestinal perforation. While the first priority must be to develop better methods of disease prevention, there is also (...) an urgent need to devise easy, accurate, and inexpensive diagnostic assays that will allow early routine distinction of TF from other febrile illnesses. Research on TF offers the opportunity to explore many aspects of pathogenesis and the host immune response, as well as to contribute toward the development of new vaccines and diagnostic laboratory tests. (shrink)

Human Biological Materials (HBMs) are an invaluable resource in biomedical research.ObjectiveTo determine if researchers and a Research Ethics Committee (REC) at a South African institution addressed ethical issues pertaining to HBMs in collaborative research with developed countries.Study DesignEthically approved retrospective cross‐sectional descriptive audit.ResultsOf the 1305 protocols audited, 151 (11.57%) fulfilled the study's inclusion criteria. Compared to other developed countries, a majority of sponsors (90) were from the USA (p = 0.0001). The principle investigators (PIs) in all (...) 151 protocols informed the REC of their intent to store HBMs. Only 132 protocols informed research participants (P < 0.0001). In 148 protocols informed consent (IC) was obtained from research participants, 116 protocols (76.8%) solicited broad consent compared to specific consent (32; 21.2%) [p < 0.0001]. In 105 cases a code was used to maintain confidentiality. HBMs were anonymised in 14 protocols [p < 0.0001]. More protocols informed the REC (90) than the research participants (67) that HBMs would be exported (p = 0.011). Export permits (EPs) and Material Transfer Agreements (MTAs) were not available in 109 and 143 protocols, respectively.ConclusionsResearchers and the REC did not adequately address the inter‐related ethical and regulatory issues pertaining to HBMs. There was a lack of congruence between the ethical guidelines of developed countries and their actions which are central to the access to HBMs in collaborative research. HBMs may be leaving South Africa without EPs and MTAs during the process of international collaborative research. (shrink)

Asking and answering questions is the cornerstone of science yet formal training in understanding this key process is often overlooked. "Asking Questions in Biology" unpacks this crucial process of enquiry, from a biological perspective, at its various stages. It begins with an overview of scientific question-asking in general, before moving on to demonstrate how to derive hypotheses from unstructured observations. It then explains in the main sections of the book, how to use statistical tests as tools to analyse data (...) and answer those questions before, finally, showing the best practice in presenting scientific reports. As such, it is an indispensable companion to all students of biology, but particularly those enrolled in courses concerning experimental design; data analysis; hypothesis testing; research methods; or any practical project work. The late Chris Barnard was Professor of Animal Behaviour at Nottingham University. Francis Gilbert is Associate Professor of Ecology at Nottingham University. Peter McGregor isa Reader in Applied Zoologyat Cornwall College. ". (shrink)