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)
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)
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.
Philosophers of biology, along with everyone else, generally perceive life to fall into two broad categories, the microbes and macrobes, and then pay most of their attention to the latter. ‘Macrobe’ is the word we propose for larger life forms, and we use it as part of an argument for microbial equality. We suggest that taking more notice of microbes – the dominant life form on the planet, both now and throughout evolutionary history – will transform some of the philosophy (...) of biology’s standard ideas on ontology, evolution, taxonomy and biodiversity. We set out a number of recent developments in microbiology – including biofilm formation, chemotaxis, quorum sensing and gene transfer – that highlight microbial capacities for cooperation and communication and break down conventional thinking that microbes are solely or primarily single-celled organisms. These insights also bring new perspectives to the levels of selection debate, as well as to discussions of the evolution and nature of multicellularity, and to neo-Darwinian understandings of evolutionary mechanisms. We show how these revisions lead to further complications for microbial classification and the philosophies of systematics and biodiversity. Incorporating microbial insights into the philosophy of biology will challenge many of its assumptions, but also give greater scope and depth to its investigations. (shrink)
In 1890, Sergei Nikolaevich Vinogradskii (Winogradsky) proposed a novel life process called chemosynthesis. His discovery that some microbes could live solely on inorganic matter emerged during his physiological research in 1880s in Strassburg and Zurich on sulfur, iron, and nitrogen bacteria. In his nitrification research, Vinogradskii first embraced the idea that microbiology could have great bearing on agricultural problems. His critique of agricultural chemists and Kochian-style bacteriologists brought this message to the broader agricultural community, resulting in an heightened interest (...) in biological, rather than chemical methods to investigate soil processes. From 1891 to 1910, he directed the microbiological laboratory at the Imperial Institute of Experimental Medicine in St. Petersburg, Russia, where he expanded his chemosynthesis research to a broad investigation of the manifold significance of autotrophic organisms in soil processes. This work and that of his students attracted the serious attention of agricultural chemists and soil scientists in Russia and abroad, changing essentially the way they understood and investigated the role of microbes in the soil. His student, Vasilii Omelianskii, effectively integrated Vinogradskii’s approach into Russian and Soviet, and international agricultural microbiology. Vinogradskii’s activities in the late 19th century reflect the changes occurring more broadly in science. At that time, microbiologists such as Louis Pasteur, Eugenius Warming, and Martianus Beijerinck were contributing new laboratory methods and theoretical perspectives to incipient disciplines closely related to agriculture: ecology, soil science, and soil microbiology. (shrink)
Our understanding of what microbes are and how they evolve has undergone many radical shifts since the late nineteenth century, when many still believed that bacteria could be spontaneously generated and most thought microbial “species” (if any) to be unstable and interchangeable in form and function (pleomorphic). By the late twentieth century, an ontology based on single cells and definable species with predictable properties, evolving like species of animals or plants, was widely accepted. Now, however, genomic and metagenomic data show (...) that lateral gene transfer compromises this picture of stability and predictability, and refocuses our attention on multilineage communities. Treating such communities as unstable but identifiable evolving “individuals” makes us again pleomorphists, of a sort. (shrink)
The gelsolin gene family encodes a number of higher eukaryotic actin-binding proteins that are thought to function in the cytoplasm by severing, capping, nucleating or bundling actin filaments. Recent evidence, however, suggests that several members of the gelsolin family may have adopted unexpected nuclear functions including a role in regulating transcription. In particular, flightless I, supervillin and gelsolin itself have roles as coactivators for nuclear receptors, despite the fact that their divergence appears to predate the evolutionary appearance of nuclear receptors. (...) Flightless I has been shown to bind both actin and the actin-related BAF53a protein, which are subunits of SWI/SNF-like chromatin remodelling complexes. The primary sequences of some actin-related proteins such as BAF53a exhibit conservation of residues that, in actin itself, are known to interact with gelsolin-related proteins. In summary, there is a growing body of evidence supporting a biological role in the nucleus for actin, Arps and actin-binding proteins and, in particular, the gelsolin family of actin-binding proteins. (c) 2005 Wiley Periodicals, Inc. (shrink)
Wolbachia is an intracellular bacterium that is almost exclusively maternally transmitted, and its reproductive effects favor transmission of the intracellular bacterial agent at the expense of the arthropod population that is not infected. Wolbachia can cause cytoplasmic incompatibility, parthenogenesis and feminization in many arthropods.
I do not see why all philosophers should be interested in communicating their thoughts to the world. Philosophy is no different in this regard from pure mathematics or microbiology. The idea that every scientist should be a part-time public speaker is absurd.
John Dupré explores recent revolutionary developments in biology and considers their relevance for our understanding of human nature and human society. Epigenetics and related areas of molecular biology have eroded the exceptional status of the gene and presented the genome as fully interactive with the rest of the cell. Developmental systems theory provides a space for a vision of evolution that takes full account of the fundamental importance of developmental processes. Dupré shows the importance of microbiology for a proper (...) understanding of the living world, and reveals how it subverts such basic biological assumptions as the organisation of biological kinds on a branching tree of life, and the simple traditional conception of the biological organism. -/- These topics are considered in the context of a view of science as realistically grounded in the natural order, but at the same time as pluralistic and inextricably integrated within a social and normative context. The volume includes a section that recapitulates and expands some of the author's general views on science; a section addressing a range of topics in biology, including the significance of genomics, the nature of the organism and the current status of evolutionary theory; and a section exploring some implications of contemporary biology for humans, for example on the reality or unreality of human races, and the plasticity of human nature. (shrink)
The pheneticist philosophy holds that biological taxa are clusters of entities united by a form of all-things-considered resemblance. This view of taxonomy has come in for almost universal criticism from philosophers, and has received little praise from biologists, over the past 30 years or so. This article defends a modest pheneticism, understood as part of a pluralist view of taxonomy. First, phenetic approaches to taxonomy are alive and well in biological practice, especially in the areas of microbiology and botany. (...) Second, the pheneticist notion of overall similarity is defensible, and is implicitly endorsed even by those (such as Quine) usually implicated in attacks on similarity. Third, there are limited biological domains within which pheneticism’s conception of species as kinds (rather than heterogeneous individuals) remains applicable. (shrink)
In this paper, I enquire whether there are Kuhnian paradigms in medicine, by way of analysing a case study from the history of medicine—the discovery of the germ theory of disease in the nineteenth century. I investigate the Kuhnian aspects of this event by comparing the work of the famous school of microbiology founded by Robert Koch with a rival school, powerful in the nineteenth century, but now almost forgotten, founded by Carl Nageli. Through my case study, I show (...) that medical science possesses some Kuhnian features. Within each school, scientists used similar exemplars and shared the same assumptions. Moreover, their research was resistant to novelty, and the results of one party were disregarded by the other. In other words, in a moderate sense, the Koch and Nageli groups worked within distinct paradigms. However, I reject the stronger Kuhnian claim that the terms used within the two paradigms were mutually unintelligible. Focusing on the semantic aspects, I argue that no account of incommensurability of reference can be given in this case, although, for sociological reasons, the two parties talked past each other. I suggest in addition that the rival scientists could have understood each other more easily if their theoretical commitments had not been so deeply ingrained, and I use the example of Pasteur to indicate that the causal account of meaning might have avoided the communication breakdown. (shrink)
Standard microbial evolutionary ontology is organized according to a nested hierarchy of entities at various levels of biological organization. It typically detects and defines these entities in relation to the most stable aspects of evolutionary processes, by identifying lineages evolving by a process of vertical inheritance from an ancestral entity. However, recent advances in microbiology indicate that such an ontology has important limitations. The various dynamics detected within microbiological systems reveal that a focus on the most stable entities (or (...) features of entities) over time inevitably underestimates the extent and nature of microbial diversity. These dynamics are not the outcome of the process of vertical descent alone. Other processes, often involving causal interactions between entities from distinct levels of biological organisation, or operating at different time scales, are responsible not only for the destabilisation of pre-existing entities, but also for the emergence and stabilisation of novel entities in the microbial world. In this article we consider microbial entities as more or less stabilised functional wholes, and sketch a network-based ontology that can represent a diverse set of processes including, for example, as well as phylogenetic relations, interactions that stabilise or destabilise the interacting entities, spatial relations, ecological connections, and genetic exchanges. We use this pluralistic framework for evaluating (i) the existing ontological assumptions in evolution (e.g. whether currently recognized entities are adequate for understanding the causes of change and stabilisation in the microbial world), and (ii) for identifying hidden ontological kinds, essentially invisible from within a more limited perspective. We propose to recognize additional classes of entities that provide new insights into the structure of the microbial world, namely “processually equivalent” entities, “processually versatile” entities, and “stabilized” entities. (shrink)
Culp (1994) provides a defense for a form of experimental reasoning entitled 'robustness'. Her strategy is to examine a recent episode in experimental microbiology--the case of the mistaken discovery of a bacterial organelle called a 'mesosome'--with an eye to showing how experimenters effectively used robust experimental reasoning (or could have used robust reasoning) to refute the existence of the mesosome. My plan is to criticize Culp's assessment of the mesosome episode and to cast doubt on the epistemic significance of (...) robustness. In turn, I present a different account of the experimental reasoning microbiologists used in arriving at the conclusion that mesosomes are artifacts. I call this form of reasoning 'reliable process reasoning', and close the paper with a brief discussion of how experimental microbiologists justify the claim that an experimental process is reliable. (shrink)
New concepts may prove necessary to profit from the avalanche of sequence data on the genome, transcriptome, proteome and interactome and to relate this information to cell physiology. Here, we focus on the concept of large activity-based structures, or hyperstructures, in which a variety of types of molecules are brought together to perform a function. We review the evidence for the existence of hyperstructures responsible for the initiation of DNA replication, the sequestration of newly replicated origins of replication, cell division (...) and for metabolism. The processes responsible for hyperstructure formation include changes in enzyme affinities due to metabolite-induction, lipid-protein affinities, elevated local concentrations of proteins and their binding sites on DNA and RNA, and transertion. Experimental techniques exist that can be used to study hyperstructures and we review some of the ones less familiar to biologists. Finally, we speculate on how a variety of in silico approaches involving cellular automata and multi-agent systems could be combined to develop new concepts in the form of an Integrated cell (I-cell) which would undergo selection for growth and survival in a world of artificial microbiology. (shrink)
In his recent article, Nicolas Rasmussen (2001) is harshly critical of what he terms 'empirical philosophy of science', a philosophy that takes seriously the history of science in advancing philosophical pronouncements about science. He motivates his criticism by reflecting on recent history in microbiology involving the 'discovery' of a new bacterial organelle, the mesosome, during the 1950's and 1960's, and the subsequent retraction of this discovery by experimental microbiologists during the late 1970's and early 1980's. In particular, he argues (...) that there was a lack of constancy in the methods microbiologists used in approaching the issue of the existence of mesosomes, and that in fact a similar sort of 'methodological flux' pervades all experimental work. My goal here is to refute Rasmussen's doctrine of flux, and in turn to re-establish order in our understanding of the methods and strategies of experimenters. My strategy in achieving this goal is to re-visit the same crucial research articles in the history of the mesosome episode that Rasmussen (2001) visits; and what I find upon returning to this literature is not flux, as Rasmussen seems to find, but a constancy of method in experimental reasoning, a constancy codified by what I call 'reliable process reasoning'. (shrink)
The definition of life has been one of the greatest philosophical questions of mankind. In recent years, this debate had intensified due to the discovery of naturally occurring biological entities, such as viruses and prions, which lie at the boundary of what we consider as living. “Are viruses alive?” has turned out to be the largest vote swinging debate in an introductory course to microbiology , with 79% of the students changing their opinions before and after the debate compared (...) to genetic engineering (56% opinion swing) and childhood immunization (25% opinion swing). Using boundary cases as classification criteria, also known as the decision boundary or decision surface, had been well established . (shrink)
Data from two national surveys of 4,000 faculty and doctoral students in chemistry, civil engineering, microbiology and sociology indicate that both faculty and students subscribe strongly to traditional norms but are more likely to see alternative counternorms enacted in their departments. They also show significant effects of departmental climate on normative orientations and suggest that many researchers express some degree of ambivalence about traditional norms.
: This article analyzes German debates on the microbiology of infectious diseases from 1865 to 1875 and asks how and when organic pollution in tissues became noteworthy for aetiology and pathogenesis. It was with Ernst Hallier's pleomorphistic microbiology that the organic character of alien material in tissues came to be regarded as important for pathology. The process that followed saw both vigorous biological critique and a number of medical applications of Hallier's work. Around 1874 contemporaries reached the conclusion (...) that pleomorphous vegetation was most likely of little importance if not accidental in relation to the aetiology of infectious diseases whereas the idea of monomorphous micro-organisms facilitated a causal explanation. It was only then that notions such a pure cultures, bacterial specificity, etc. favored by Ferdinand Julius Cohn and his school became popular in medical circles. (shrink)
As in other countries, medical ethics in Mexico has rescued the world of philosophical ethics from oblivion. The needs of clinical medicine gave birth to Mexican bioethics. After the growth of scientific and technologic subjects in medical schools, the humanities, such as medical history, deontology, and medical philosophy, were replaced by such core subjects as radiology, pharmacology, and microbiology. Since the 1950s, graduates from Mexican medical schools have not been exposed to any courses in the medical humanities.
Enzyme directed genetic mechanisms causing random DNA sequence alterations are ubiquitous in both eukaryotes and prokaryotes. A number of molecular geneticist have invoked adaptation through natural selection to account for this fact, however, alternative explanations have also flourished. The population geneticist G.C. Williams has dismissed the possibility of selection for mutator activity on a priori grounds. In this paper, I attempt a refutation of Williams' argument. In addition, I discuss some conceptual problems related to recent claims made by microbiologists on (...) the adaptiveness of molecular variety generators in the evolution of prokaryotes. A distinction is proposed between selection for mutations caused by a mutator activity and selection for the mutator activity proper. The latter requires a concept of fitness different from the one commonly used in microbiology. (shrink)
Scientists and historians have often presumed that the divide between biochemistry and molecular biology is fundamentally epistemological.100 The historiography of molecular biology as promulgated by Max Delbrück's phage disciples similarly emphasizes inherent differences between the archaic tradition of biochemistry and the approach of phage geneticists, the ur molecular biologists. A historical analysis of the development of both disciplines at Berkeley mitigates against accepting predestined differences, and underscores the similarities between the postwar development of biochemistry and the emergence of molecular biology (...) as a university discipline. Stanley's image of postwar biochemistry, with its focus on viruses as key experimental systems, and its preference for following macromolecular structure over metabolism pathways, traced the outline of molecular biology in 1950.Changes in the postwar political economy of research universities enabled the proliferation of disciplines such as microbiology, biochemistry, biophysics, immunology, and molecular biology in universities rather than in medical schools and agricultural colleges. These disciplines were predominantly concerned with investigating life at the subcellular level-research that during the 1930s had often entailed collaboration with physicists and chemists. The interdisciplinary efforts of the 1930s (many fostered by the Rockefeller Foundation) yielded a host of new tools and reagents that were standardized and mass-produced for laboratories after World War II. This commercial infrastructure enabled “basic” researchers in biochemistry and molecular biology in the 1950s and 1960s to become more independent from physics and chemistry (although they were practicing a physicochemical biology), as well as from the agricultural and medical schools that had previously housed or sponsored such research. In turn, the disciplines increasingly required their practitioners to have specialized graduate training, rather than admitting interlopers from the physical sciences.These general transitions toward greater autonomy for biochemistry and allied disciplines should not mask the important particularities of these developments on each campus. At the University of Caliornia at Berkeley, agriculture had provided, with medicine, significant sponsorship for biochemistry. The proximity of Lawrence and his cyclotrons supported the early development of Berkeley as a center for the biological uses of radioisotopes, particularly in studies of metabolism and photosynthesis. Stanley arrived to establish his department and virus institute before large-scale federal funding of biomedical research was in place, and he courted the state of California for substantial backing by promising both national prominence in the life sciences and virus research pertinent to agriculture and public health. Stanley's venture benefited significantly from the expansion of California's economy after World War II, and his mobilization against viral diseases resonated with the concerns of the Cold War, which fueled the state's rapid growth. The scientific prominence of contemporary developments at Caltech and Stanford invites the historical examination of the significance of postwar biochemistry and molecular biology within the political and cultural economy of the Golden State.In 1950, Stanley presented a persuasive picture of the power of biochemistry to refurbish life science at Berkeley while answering fundamental questions about life and infection. In the words of one Rockefeller Foundation officer,There seems little doubt in [my] mind that as a personality Stanley will be well able to dominate the other personalities on the Berkeley campus and will be able to drive his dream through to completion, which, incidentally, leaves Dr. Hubert [sic] Evans and the whole ineffective Life Sciences building in the somewhat peculiar position of being by-passed by much of the truly modern biochemistry and biophysics research that will be carried out at Berkeley. Furthermore, it seems likely that Dr. S's show will throw Dr. John Lawrence's Biophysics Department strongly in the shade both figuratively and literally, but should make the University of California pre-eminent not only in physics but in biochemistry as well.101Stanley, Sproul, Weaver, and this officer (William Loomis) all testified to a perceptible postwar opportunity to capitalize on public support for biological research that relied on the technologies from physics and chemistry without being captive to them, and that addressed issues of medicine and agriculture without being institutionally subservient. What is striking, given the expectation by many that Stanley would ‘be able to drive his dream through to completion,” was that in fact he did not. Biochemists who had succeeded in making their expertise valued in specialized niches were resistant to giving up their affiliations to joint Stanley's “liberated” organization. Stanley's failure was not simply due to institutional factors: researchers as well as Rockefeller Foundation officers faulted him for his lack of scientific imagination, which made it difficult for him to gain credibility in leading the field. Moreover, many biochemists did not share Stanley's commitment to viruses as the key material for the “new biochemistry.”In the end, Stanley's free-standing department did become a first-rate department of biochemistry, but only after freeing itself from Stanley's leadership and his single-minded devotion to viruses. Nonetheless, the falling-out with the Berkeley biochemists was rapidly followed by the establishment of a Department of Molecular Biology, attesting to the unabating economic and institutional possibilities for an authoritative “general biology” (or two, for that matter) to take hold. In each case, following Stanley's dream sheds light on how the possible and the real shaped the (re)formation of biochemistry and molecular biology as postwar life sciences. (shrink)
The question on how the diverse forms of cooperative behavior in humans and nonhuman animals could have evolved under the pressure of natural selection has been a challenge for evolutionary biology ever since Darwin himself. In this chapter, we briefly review and summarize results from the last 50 years of research on human and nonhuman cooperativeness from a theoretical (biology) and an experimental perspective (experimental economics). The first section presents six concepts from theoretical biology able to explain a variety of (...) forms of cooperativeness which evolved in many different species. These are kin selection, mutualism, reciprocity, green-beard altruism, costly signaling, and cultural group selection. These considerations are complemented by two short examples of evolved cooperative behavior, one from microbiology and one from ethology. The second main section focuses on recent experimental research on human cooperativeness. We present a brief review of factors known to impact individual human decision-making in social dilemmas, most prominently communication, punishment, reputation, and assortment. Our conclusion then draws attention to tasks for further research in this area. (shrink)
The recent conception of biodiversity proposed by James Maclaurin and Sterelny was developed mostly with macrobiological life in mind. They suggest that we measure biodiversity by dividing life into natural units (typically species) and quantifying the differences among units using phenetic rather than phylogenetic measures of distance. They identify problems in implementing quantitative phylogenetic notions of difference for non-prokaryotic species. I suggest that if we focus on microbiological life forms that engage in frequent, promiscuous lateral gene transfer (LGT), and their (...) associated reticulated phylogenies, we need to rethink the notion of species as the natural unit, and we discover additional problems with phylogenetic notions of distance. These problems suggest that a phenetic approach based on morphospaces has just as much appeal, if not more, for microbes as they do for multi-cellular life. Facts about LGT, however, offer no new insight into the additional challenge of reconciling units and differences into a single measure of biodiversity. (shrink)
Since the microbiological revolution, most infectious diseases have been defined and classified according to an etiologic criterion, i.e. the identification of single, external necessary causes (for example, Mycobacterium for tuberculosis). This is not the case with cancer. Not only external necessary causes of cancer have not been identified, but also the morphological classification cannot be based on univocal criteria. Although neoplasia and anaplasia appear to be universal attributes of cancer, these events are only quantitative. Neoplastic growth can be fast or (...) slow (development may take weeks or years), and tissue pathologies are difficult to detect from normal tissue in some cancers but are obvious in others. Common special properties of anaplasia appear to be concealed in the wide range of morphologies. In the absence of a coherent morphological definition, and of external necessary causes (such as bacteria for infectious diseases), a mechanistic definition could be adopted. However, unless molecular biology discovers specific mechanistic steps in carcinogenesis, which indicate the existence of necessary events in carcinogenesis, we cannot adopt a univocal (monothetic) definition of cancer. The alternative is to use a polythetic definition, according to Wittgenstein's model of a long rope twisted together out of many shorter fibres. (shrink)
Microbial ecology is flourishing, and in the process, is making contributions to how the ecology and biology of large organisms is understood. Ongoing advances in sequencing technology and computational methods have enabled the collection and analysis of vast amounts of molecular data from diverse biological communities. While early studies focused on cataloguing microbial biodiversity in environments ranging from simple marine ecosystems to complex soil ecologies, more recent research is concerned with community functions and their dynamics over time. Models and concepts (...) from traditional ecology have been used to generate new insight into microbial communities, and novel system-level models developed to explain and predict microbial interactions. The process of moving from molecular inventories to functional understanding is complex and challenging, and never more so than when many thousands of dynamic interactions are the phenomena of interest. We outline the process of how epistemic transitions are made from producing catalogues of molecules to achieving functional and predictive insight, and show how those insights not only revolutionize what is known about biological systems but also about how to do biology itself. Examples will be drawn primarily from analyses of different human microbiota, which are the microbial consortia found in and on areas of the human body, and their associated microbiomes (the genes of those communities). Molecular knowledge of these microbiomes is transforming microbiological knowledge, as well as broader aspects of human biology, health and disease. (shrink)