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)

If the problem of the origin of life is conceptualized as a process of emergence of biochemistry from proto-biochemistry, which in turn emerged from the organic chemistry and geochemistry of primitive earth, then the resources of the new sciences of complex systems dynamics can provide a more robust conceptual framework within which to explore the possible pathways of chemical complexification leading to living systems and biosemiosis. In such a view the emergence of life, and concomitantly of natural selection and biosemiosis, (...) is the result of deep natural laws (the outlines of which we are only beginning to perceive) and reflects a degree of holism in those systems that led to life. Further, such an approach may lead to the development of a more general theory of biology and of natural organization, one informed by semiotic concepts. (shrink)

Histories of ocean science have emphasized the ways that state-sponsored deep-sea expeditions ushered in a new age of oceanic understanding during the late eighteenth and early nineteenth centuries. This essay, on the other hand, examines the ways that shallow waters played host to less formal but nevertheless important efforts to create oceanic natural knowledge, often centuries earlier. By documenting the legends and experiences of people who worked on and lived by the ocean—divers, sailors, and fishermen, among others—and corroborating their stories (...) with firsthand observation, seventeenth- and early eighteenth-century natural historians built a nascent science of the sea. In its close focus on “sea beans” and “barnacle geese,” subjects of wide conjecture and earnest curiosity, the essay shows how shallow waters welcomed new actors onto the scientific stage and decentered the geographies of knowledge production, thereby advancing contemporary knowledge of oceanic circulation as well as the taxonomies and ecologies of coastal creatures. (shrink)

ABSTRACT: How can we think about a universal ethics that could be adopted by any intelligent being, including the rising population of cyborgs, intelligent machines, intelligent algorithms or even potential extraterrestrial life? We generally give value to complex structures, to objects resulting from a long work, to systems with many elements and with many links finely adjusted. These include living beings, books, works of art or scientific theories. Intuitively, we want to keep, multiply, and share such structures, as well as (...) prevent their destruction. Such objects have value not because more information would simply mean more value. Instead, they have value because they require a long computational history, numerous interactions for their construction that we can assimilate to a computation, and they display what we call organized complexity. To propose the foundations of a universal ethics based on the intrinsic value of organized complexity, we first discuss conceptions of complexity, and argue that Charles Bennett’s logical depth is certainly a first approximation of what we are looking for. We then put forward three fundamental imperatives: to preserve, augment and recursively promote organized complexity. We show a broad range of applications with human, non-human and non-living examples. Finally, we discuss some specific issues of our framework such as the distribution of complexity, of managing copies and erasures, and how our universal ethics tackles classical ethical issues. In sum, we propose a clear, homogenous and consistent ethical foundation that can integrate many universal ethics desiderata. (shrink)

In this review, we describe some of the central philosophical issues facing origins-of-life research and provide a targeted history of the developments that have led to the multidisciplinary field of origins-of-life studies. We outline these issues and developments to guide researchers and students from all fields. With respect to philosophy, we provide brief summaries of debates with respect to (1) definitions (or theories) of life, what life is and how research should be conducted in the absence of an accepted theory (...) of life, (2) the distinctions between synthetic, historical, and universal projects in origins-of-life studies, issues with strategies for inferring the origins of life, such as (3) the nature of the first living entities (the “bottom up” approach) and (4) how to infer the nature of the last universal common ancestor (the “top down” approach), and (5) the status of origins of life as a science. Each of these debates influences the others. Although there are clusters of researchers that agree on some answers to these issues, each of these debates is still open. With respect to history, we outline several independent paths that have led to some of the approaches now prevalent in origins-of-life studies. These include one path from early views of life through the scientific revolutions brought about by Linnaeus (von Linn.), Wöhler, Miller, and others. In this approach, new theories, tools, and evidence guide new thoughts about the nature of life and its origin.We also describe another family of paths motivated by a” circularity” approach to life, which is guided by such thinkers as Maturana & Varela, Gánti, Rosen, and others. These views echo ideas developed by Kant and Aristotle, though they do so using modern science in ways that produce exciting avenues of investigation. By exploring the history of these ideas, we can see how many of the issues that currently interest us have been guided by the contexts in which the ideas were developed. The disciplinary backgrounds of each of these scholars has influenced the questions they sought to answer, the experiments they envisioned, and the kinds of data they collected. We conclude by encouraging scientists and scholars in the humanities and social sciences to explore ways in which they can interact to provide a deeper understanding of the conceptual assumptions, structure, and history of origins-of-life research. This may be useful to help frame future research agendas and bring awareness to the multifaceted issues facing this challenging scientific question. (shrink)

Anton de Bary is best known for his elucidation of the life cycle of Phytopthora infestans, the causal organism of late blight of potato and the crop losses that caused famine in nineteenth-century Europe. But while practitioner histories often claim this accomplishment as a founding moment of modern plant pathology, closer examination of de Bary’s experiments and his published work suggest that his primary motiviation for pursing this research was based in developmental biology, not agriculture. De Bary shied away from (...) making any recommendations for agricultural practice, and instead focused nearly exclusively on spontaneous generation and fungal development – both concepts promoted through prize questions posted by the Académie des Sciences in the 1850s and 1860s. De Bary’s submission to the Académie’s 1859 Alhumbert prize question illustrates his own contributions to debates about spontaneous generation and demonstrates the practical applications of seemingly philosophical questions – such as the origin of life. (shrink)

Historians tend to speak of the problem of the origin of species or the species question, as if it were a monolithic problem. In reality, the phrase refers to a, historically, surprisingly fluid and pluriform scientific issue. It has, in the course of the past five centuries, been used in no less than ten different ways or contexts. A clear taxonomy of these separate problems is useful or relevant in two ways. It certainly helps to disentangle confusions that have inevitably (...) emerged in the literature in its absence. It may, secondly, also help us to gain a more thorough understanding, or sharper view, of the history of evolutionary thought. A consequent problem-centric look at that history through the lens of various origin of species problems certainly yields intriguing results, including and particularly for our understanding of the genesis of the Wallace–Darwin theory of evolution through natural selection. (shrink)

Louis Pasteur’s defeat of belief in spontaneous generation has been a classical rationalist example of how the experimental approach of modern science can reveal superstition. Farley and Geison told a counter-story of how Pasteur’s success was due to political and ideological support rather than superior experimental science. They claimed that Pasteur violated proper norms of scientific method, and that the French Academy of Science did not see this, or did not want to. Farley and Geison argued that Pouchet’s experiments were (...) as valid as those of Pasteur. In this paper I argue that the core of the scientific debate was not general theories for or against spontaneous generation but the outcome of specific experiments. It was on the conduct of these experiments that the Academy made judgements favorable to Pasteur. Claude Bernard was a colleague of Pasteur, supportive and sometimes critical. I argue that Bernard’s fact-oriented methodology of “experimental medicine” is a better guide to explaining the controversy than the hypothetic-deductive view of scientific method typical of logical empiricism. (shrink)

In the nineteenth century protozoology and early cell biology intersected through the nexus of Darwin's theory of evolution. As single-celled organisms, amoebae offered an attractive focus of study for researchers seeking evolutionary relationships between the cells of humans and other animals, and their primitive appearance made them a favourite model for the ancient ancestor of all living things. Their resemblance to human and other metazoan cells made them popular objects of study among morphologists, physiologists, and even those investigating animal behaviour. (...) The amoeba became the exemplar of the new protoplasmic cell concept of mid-century and because its apparent simplicity made it widely generalizable it became a popular subject in a breadth of experimental investigations and theoretical speculations. It was able to do this because "the amoeba" denotes not a particular organism, but a general type of behaviour common to the cells of a range of protozoa, simple plants and higher animals. Its status as an exemplary cell also rested upon auxiliary philosophical assumptions about what constitutes a primitive characteristic and the thesis that evolution is a progressive development of order from chaos. (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)

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)