The rapidly changing field of genetics affects society through advances in health-care and through implications of genetic research. This study addresses the impacts of new genetic discoveries and technologies on different segments of today's society. The book begins with a chapter on genetic complexity, and subsequent chapters discuss moral and ethical questions arising from today's genetics from the perspectives of health care professionals, the media, the general public, special interest groups and commercial interests.

This paper examines the species problem in microbiology and its implications for the species problem more generally. Given the different meanings of ‘species’ in microbiology, the use of ‘species’ in biology is more multifarious and problematic than commonly recognized. So much so, that recent work in microbial systematics casts doubt on the existence of a prokaryote species category in nature. It also casts doubt on the existence of a general species category for all of life (one that includes (...) both prokaryotes and eukaryotes). Prokaryote biology also undermines recent attempts to save the species category, such as the suggestion that species are metapopulation lineages and the idea that ‘species’ is a family resemblance concept. (shrink)

Microbes and microbiology are seldom encountered in philosophical accounts of the life sciences. Although microbiology is a well-established science and microbes the basis of life on this planet, neither the organisms nor the science have been seen as philosophically significant. This book will change that. It fills a major gap in the philosophy of biology by examining central philosophical issues in microbiology. Topics are drawn from evolutionary microbiology, microbial ecology, and microbial classification. These discussions are aimed (...) at philosophers and scientists who wish to gain insight into the basic philosophical issues of microbiology. (shrink)

Book Review Philosophy of Microbiology MAUREEN A. O’MALLEY.

The overblown, somewhat dramatic media interpretation of microbiota-gut-brain literature is highly misleading. This phenomenon is not new to neuroscience, wherein rapidly evolving research fields struggle to translate findings into clinical practice. Advances in microbiology might integrate our understanding of complex biological pathways that should be interpreted within neuropsychiatric symptom dimensions rather than specific disorders.

Thomas Kuhn had little to say about scientific change in biological science, and biologists are ambivalent about how applicable his framework is for their disciplines. We apply Kuhn’s account of paradigm change to evolutionary microbiology, where key Darwinian tenets are being challenged by two decades of findings from molecular phylogenetics. The chief culprit is lateral gene transfer, which undermines the role of vertical descent and the representation of evolutionary history as a tree of life. To assess Kuhn’s relevance to (...) this controversy, we add a social analysis of the scientists involved to the historical and philosophical debates. We conclude that while Kuhn’s account may capture aspects of the pattern of an episode of scientific change, he has little to say about how the process of generating new understandings is occurring in evolutionary microbiology. Once Kuhn’s application is limited to that of an initial investigative probe into how scientific problem-solving occurs, his disciplinary scope becomes broader. (shrink)

On the basis of findings from developmental biology, some researchers have argued that evolutionary theory needs to be significantly updated. Advocates of such a “developmental update” have, among other things, suggested that we need to re-conceptualize units of selection, that we should expand our view of inheritance to include environmental as well as genetic and epigenetic factors, that we should think of organisms and their environment as involved in reciprocal causation, and that we should reevaluate the rates of evolutionary change. (...) However, many of these same conclusions could be reached on the basis of other evidence, namely from microbiology. In this paper, I ask why microbiological evidence has not had a similarly large influence on calls to update biological theory, and argue that there is no principled reason to focus on developmental as opposed to microbiological evidence in support of these revisions to evolutionary theory. I suggest that the focus on developmental biology is more likely attributable to historical accident. I will also discuss some possible room for overlap between developmental and microbiology, despite the historical separation of these two subdisciplines. (shrink)

The American Society for Microbiology addresses issues of research integrity in several ways. There is a Code of Ethics for Society members and an Ethics Committee, a Publications Board has editorial oversight of ethical issues involved in Society journals and other publications, and the Public and Scientific Affairs Board is involved in ethical issues and scientific policies at the national level. In addition, the Society uses meetings and publications to inform and educate members about research integrity.

Experimental manipulations are a key means to establish causal relationships in microbiology. However, challenges remain to establish the applicability of such experiments beyond the precise conditions in which they were conducted. Ecological information can help address these challenges by describing the extent to which an experimentally-determined mechanism can explain the natural phenomenon that it is purported to cause.

Experimental manipulations are a key means to establish causal relationships in microbiology. However, challenges remain to establish the applicability of such experiments beyond the precise conditions in which they were conducted. Ecological information can help address these challenges by describing the extent to which an experimentally-determined mechanism can explain the natural phenomenon that it is purported to cause.

Microbial diversity has become a leitmotiv of contemporary microbiology, as epitomized in the concept of the microbiome, with significant consequences for the classification of microbes. In this paper, I contrast microbiology’s current diversity ideal with its influential predecessor in the twentieth century, that of purity, as epitomized in Robert Koch’s bacteriological culture methods. Purity and diversity, the two polar opposites with regard to making sense of the microbial world, have been operationalized in microbiological practice by tools such as (...) the “clean” Petri dish versus the “dirty” Winogradsky column, the latter a container that mimics, in the laboratory, the natural environment that teems with diverse microbial life. By tracing the impact of the practices and concepts of purity and diversity on microbial classification through a history of techniques, tools, and manuals, I show the shifts in these concepts over the last century. Juxtaposing the dominant purity ideal with the more restricted, but continuously articulated, diversity ideal in microbial ecology not only provides a fresh perspective on microbial classification that goes beyond its intellectual history, but also contextualizes the present focus on diversity. By covering the period of a century, this paper outlines a revised longue durée historiography that takes its inspiration from artifacts, such as Petri dish and the Winogradsky column, and thereby simple, but influential technologies that often remain invisible. This enables the problem of historical continuity in modern science to be addressed and the accelerationist narratives of its development to be countered. (shrink)

Microbial diversity has become a leitmotiv of contemporary microbiology, as epitomized in the concept of the microbiome, with significant consequences for the classification of microbes. In this paper, I contrast microbiology’s current diversity ideal with its influential predecessor in the twentieth century, that of purity, as epitomized in Robert Koch’s bacteriological culture methods. Purity and diversity, the two polar opposites with regard to making sense of the microbial world, have been operationalized in microbiological practice by tools such as (...) the “clean” Petri dish versus the “dirty” Winogradsky column, the latter a container that mimics, in the laboratory, the natural environment that teems with diverse microbial life. By tracing the impact of the practices and concepts of purity and diversity on microbial classification through a history of techniques, tools, and manuals, I show the shifts in these concepts over the last century. Juxtaposing the dominant purity ideal with the more restricted, but continuously articulated, diversity ideal in microbial ecology not only provides a fresh perspective on microbial classification that goes beyond its intellectual history, but also contextualizes the present focus on diversity. By covering the period of a century, this paper outlines a revised longue durée historiography that takes its inspiration from artifacts, such as Petri dish and the Winogradsky column, and thereby simple, but influential technologies that often remain invisible. This enables the problem of historical continuity in modern science to be addressed and the accelerationist narratives of its development to be countered. (shrink)

Microbiological scientists around the world often have only a vague notion about the nature of the international organization with which their national microbiological societies are affiliated. This article provides answers to questions that are usually raised about IUMS; it is reproduced with permission from Microbiological Sciences.

Microbiological scientists around the world often have only a vague notion about the nature of the international organization with which their national microbiological societies are affiliated. This article provides answers to questions that are usually raised about IUMS; it is reproduced with permission from Microbiological Sciences.

Historians of science have attributed the emergence of ecology as a discipline in the late nineteenth century to the synthesis of Humboldtian botanical geography and Darwinian evolution. In this essay, I begin to explore another, largely neglected but very important dimension of this history. Using Sergei Vinogradskii’s career and scientific research trajectory as a point of entry, I illustrate the manner in which microbiologists, chemists, botanists, and plant physiologists inscribed the concept of a “cycle of life” into their investigations. Their (...) research transformed a longstanding notion into the fundamental approaches and concepts that underlay the new ecological disciplines that emerged in the 1920s. Pasteur thus joins Humboldt as a foundational figure in ecological thinking, and the broader picture that emerges of the history of ecology explains some otherwise puzzling features of that discipline – such as its fusion of experimental and natural historical methodologies. Vinogradskii’s personal “cycle of life” is also interesting as an example of the interplay between Russian and Western European scientific networks and intellectual traditions. Trained in Russia to investigate nature as a super-organism comprised of circulating energy, matter, and life; over the course of five decades – in contact with scientists and scientific discourses in France, Germany, and Switzerland – he developed a series of research methods that translated the concept of a “cycle of life” into an ecologically conceived soil science and microbiology in the 1920s and 1930s. These methods, bolstered by his authority as a founding father of microbiology, captured the attention of an international network of scientists. Vinogradskii’s conceptualization of the “cycle of life” as chemosynthesis, autotrophy, and global nutrient cycles attracted the attention of ecosystem ecologists; and his methods appealed to practitioners at agricultural experiment stations and microbiological institutes in the United States, Western Europe, and the Soviet Union. (shrink)

Philosophers have usually highlighted how the weakness and paucity of historical evidence underdetermine the choice between rival historical explanations. Focusing underdetermination on the link between theory and evidence comes, I argue, with three assumptions: competing hypotheses are easy to generate, investigators agree on the constitution and interpretation of the evidence and a plurality of hypotheses is a useful evil to reach consensus. The last assumption implies that the sustained coexistence of incompatible hypotheses is considered as a scientific failure. I argue (...) that this negative vision of sustained disagreement has monistic undertones. By drawing from a case study in evolutionary biology, this paper defends a form of scientific pluralism. Firstly, I show that underdetermination is not only found at the inferential level but also at the level of the constitution and interpretation of the evidence, on the choice of investigative scaffolds and when interpreting background theories. Because of that, competing hypotheses exhibit a degree of methodological incommensurability. While catastrophic from a monistic standpoint, I defend that scientific pluralism gives a different, and I think richer, account of such situations. On the plus side, competing approaches benefit from their sustained coexistence and interaction. I argue that this generates direct and indirect epistemic goods independently of whether the controversy is solved. Scientific pluralism also shifts our attention from achieving consensus to managing disagreement. The challenge becomes to maintain the conditions for fruitful interactions in a community with incommensurable approaches and heterogeneous expertise. (shrink)

In the late nineteenth century, French naturalists were global leaders in microbial research. Louis Pasteur advanced sterilization techniques and demonstrated that dust particles in the air could contaminate a putrefiable liquid. Pasteur’s discoveries prompted a new research program for the naturalists of the Talisman and Travailleur expeditions: to recover uncontaminated water and mud samples from the deep sea. French naturalists Adrien Certes and Paul Regnard both independently conducted experiments to address the question of whether microorganisms inhabited the oceans and whether (...) organic material in the deep sea was subject to decomposition. The experiments of Certes and Regnard have largely been omitted from histories of microbiology and marine science. However, an examination of their work is crucial for understanding the context in which marine microbiology first developed. At the end of the nineteenth century, marine microbiology emerged from the disciplinary melding of terrestrial microbial ecology, experimental physiology, and the then-nascent field of deep-sea biology. (shrink)

El microscopio constituye un instrumento de vital importancia para la Microbiología y para muchas otras ramas de la Medicina. Se realizó una revisión bibliográfica con el objetivo de profundizar los conocimientos sobre el microscopio, sobre la historia de este en el período comprendido desde su creación hasta la actualidad a nivel mundial y más brevemente en Cuba. El trabajo aborda también, con una corta descripción, los diferentes tipos existentes, así como algunas de las aplicaciones más importantes en la Microbiología. This (...) bibliographic review was carried out with the objective to deepen the existing knowledge about the history of the microscope since its origin up to date worldwide which and in Cuba, taking into account that it constitutes an instrument of vital importance for microbiology and for many other branches of medicine. This work also deals with a brief description of the different types of microscopes as well as some of the most important applications in microbiology. (shrink)

Continuous culture techniques were developed in the early twentieth century to replace cumbersome studies of cell growth in batch cultures. In contrast to batch cultures, they constituted an open concept, as cells are forced to proliferate by adding new medium while cell suspension is constantly removed. During the 1940s and 1950s new devices have been designed—called “automatic syringe mechanism,” “turbidostat,” “chemostat,” “bactogen,” and “microbial auxanometer”—which allowed increasingly accurate quantitative measurements of bacterial growth. With these devices cell growth came under the (...) external control of the experimenters and thus accessible for developing a mathematical theory of growth kinetics—developed mainly by Jacques Monod, Aron Novick and Leo Szilard in the early 1950s and still in use today. The paper explores the development of continuous culture devices and claims that these devices are simulators for standard cells following specific requirements, in particular involving mathematical constraints in the design and setting of the devices as well as experiments. These requirements have led to contemporary designs of continuous culture techniques realizing a specific event-based flow algorithm able to simulate directed evolution and produce artificial cells and microorganisms. This current development is seen as an alternative approach to today’s synthetic biology. (shrink)

In a pioneering book, Philosophy of Microbiology, Maureen O’Malley argues for the philosophical importance of microbes through an examination of their impact on ecosystems, evolution, biological classification, collaborative behavior, and multicellular organisms. She identifies many understudied conceptual issues in the study of microbes. If philosophers follow her lead, the philosophy of biology will be expanded and enriched.

Species are considered the basic unit of biological classification and evolution. Hence, they are used as a benchmark in several fields, although the ontological status of such a category has always been a matter of debate. This paper aims to discuss the problem of the definition of species within the new mechanistic approach. Nevertheless, the boundary between entities, activities, and mechanisms remains difficult to establish and always requires an analysis of what is meant by explanation. As a case study, the (...) paper describes the debate concerning the species category by considering different kingdoms: Animals, Bacteria, and Fungi. The inherently biological differences between those groups prevent the use of a single, universally applicable concept of species that could fit the mechanisms responsible for the variability present in these kingdoms. The same issue is encountered within each group, as highlighted through a focus on mammals and microbes. This controversy has given rise to opposite approaches, namely: monism, which looks for a single definition that might account for all species, and pluralism, which admits that different groups of organisms require somewhat different definitions. In order to develop an adequate definition of species, we propose to apply a new mechanistic framework, which considers the ontic-epistemic dimensions of scientific explanation in close parallel. The apt correlation between epistemic and the ontic aspects highlights the way in which the concept of species and the reference to data are strictly co-determined. This suggests that the concept of species is better understandable within a dual ontic-epistemic approach. (shrink)

Se realizó una revisión bibliográfica con el objetivo de conocer acerca de personalidades científicas cubanas y sus obras en el ámbito de la microbiología, para ampliar y profundizar los conocimientos de médicos generales y microbiólogos. En síntesis, se describe la vida de quienes efectuaron contribuciones trascendentales a la medicina cubana y universal. A literature review was made aiming at learning about Cuban scientific personalities and their works in the field of Microbiologyin order to broaden and deepen the knowledge of general (...) practitioners and microbiologists. In short, it describes the life of those who made momentous contributions to Cuban and universal medicine. (shrink)