The emergence of theoretical biology: Two fundamental works of Ervin Bauer (1890-1938) in English translation.

Ervin Bauer (1890-1938) outlined the paradigm of theoretical biology from the perspective of biophysics and bioenergetics. His molecular-based biological theory is centered on the principle of sustainable non-equilibrium, which is continuously produced and maintained by all biological systems throughout their life. Ervin Bauer became the victim of Stalin's Great Terror. Here we present two of the fundamental works of Ervin Bauer in English translation: the paper "The definition of the living being on the basis of its thermodynamic properties and the fundamental biological principles that follow from it" published in Naturwissenschaften (1920)Naturwissenschaften (1920) and the excerpts from his magnum opus "Theoretical Biology" (1935). These works became a bibliographical rarity. A complete English translation of "Theoretical Biology" is an important task for the future.

Revisiting the 'nuclear species' concept: do we really know what we think we know?

The idea of 'nuclear species' has received a lot of attention in mixed-species flock research. Our impression of this literature is that referenced statements tend to cite the same papers in support of a small set of ideas, and often there is a mismatch between what papers contain and what they're cited for. Motivated by these impressions, we built and quantitatively examined a database of referenced statements about nuclearity in flocks. This confirmed our impression quantitatively, but more strikingly, a single paper stood out in its influence on ideas around nuclearity in flocks. Moynihan's 1962 monograph on mixed-species flocks in Panama, 'The organization and probable evolution of some mixed-species flocks of neotropical birds' published in Smithsonian Miscellaneous Collections, was cited twice as much as the next most-cited paper and was the most-cited paper for 10 out of 15 most-discussed ideas related to nuclearity. Further, a number of other highly cited papers are strongly influenced by Moynihan's ideas, i.e. its influence is much greater than what a count of citations conveys. We also found that Moynihan was mis-cited frequently. We juxtapose what we found from the citation analysis with what the paper actually contains to better understand the nature of support that Moynihan provides, and discuss the implications of our findings for what we know about and how we research nuclearity in flocks. This article is part of the theme issue 'Mixed-species groups and aggregations: shaping ecological and behavioural patterns and processes'.

Composite Animals: Then and Now.

Since the early twentieth century, the term "chimera" has been used to describe many experimental composite plants and animals. Composite animals and embryos, involving the transfer of cells from different species to make chimeras, continue to be a fundamental cornerstone of biomedical research. However, the twenty-first century appears to be offering a new role for composite animals. Over the last fifteen to twenty years, composite animals and embryos have taken on a different form of life-an institutional life. With this institutional life, I argue, comes an opportunity to recast differences between humans and other animals and to reconsider how research on human health is governed.

Alexander Dalrymple, the Utility of Coral Reefs, and Charles Darwin's Structure and Distribution of Coral Reefs.

This paper aims to establish the connection between the theoretical and practical aims of the Office of the Hydrographer of the British Admiralty and Charles Darwin's (1809-1882) work on coral reefs from 1835 to 1842. I also emphasize the consistent zoological as well as geological reasoning contained in these texts. The Office's influences have been previously overlooked, despite the Admiralty's interest in using coral reefs as natural instruments. I elaborate on this by introducing the work of Alexander Dalrymple (1737-1808), the first hydrographer of the Admiralty and a figure who has flown under the radar of the history of coral reef theories. I show that Dalrymple introduced a unified account of coral reefs in which multiple features of the coral reefs, such as their shape, slope of the sides, ridges, channels, and elevation relative to the water, were all explained by the action of the winds and waves-and proposed that one could use these features to predict seafaring conditions around the islands. Then, I show that Darwin's "Coral Islands" (1835) and his Coral Reefs monograph (1842) spoke to these hydrographical issues and did so, at times, by way of zoological reasoning. It was, for instance, the coral behavior and the related notion of a zoological or botanical station that ultimately proved the biggest blow to the Admiralty's aim to use the coral reefs as instruments because it eroded many uniform predictions regarding the past or future of a coral reef. Connecting these themes leads us to a surprising conclusion: that Darwin's theory of coral reefs, long a model instance of Darwin making uniform predictable inferences, was, in actuality, also his first formal encounter with something at times the entire opposite.

The third-way third wave and the enduring appeal of bioexceptionalism.

We may induce from a longue durée examination of Anglo-American History of Biology that the impulse to reject reduc - tionism persists and will continue to percolate cyclically. This impulse I deem "bioexceptionalism": an intuition, stance, attitude, or activating metaphor that the study of living beings requires explanations in addition to exclusively bottom-up causal explanations and the research programs constructed upon that bottom-up philosophical foundation by non-organismal biologists, biochemists, and biophysicists - the explanations, in other words, that Wadding - ton (1977) humorously termed the "Conventional Wisdom of the Dominant Group, or cowdung." Bioexceptionalism might indicate an ontological assertion, like vitalism. Yet most often in the last century, it has been defined by a variety of methodological or even sociological positions. On three occasions in the interval from the late nineteenth century to the present, a small but significant group of practicing biologists and allies in other research disciplines in the UK and US adopted a species of bioexceptionalism, rejecting the dominant explanatory philosophy of reductionistic mechanism. Yet they also rejected the vitalist alternative. We can refer to their subset of bioexceptionalism as a "Third-Way" approach, though participants at the time called it by a variety of names, including "organicism." Today's appeals to a Third-Way are but the latest eruption of this older dissensus and retain at least heuristic value apart from any explanatory success.

From Organismic Biology as History and Philosophy to the History and Philosophy of Biology-the Work of Hans-Jörg Rheinberger in the German Context.

In this paper, I ask about the broader context of the history and philosophy of biology in the German-speaking world as the place in which Hans-Jörg Rheinberger began his work. Three German philosophical traditions-neo-Kantianism, phenomenology, and Lebensphilosophie-were interested in the developments and conceptual challenges of the life sciences in the late nineteenth and early twentieth centuries. Their reflections were taken up by life scientists under the terms theoretische Biologie (theoretical biology) and allgemeine Biologie (general biology), i. e., for theoretical and methodological reflections. They used historical and philosophical perspectives to develop vitalistic, organicist, or holistic approaches to life. In my paper, I argue that the resulting discourse did not come to an end in 1945. Increasingly detached from biological research, it formed an important context for the formation of the field of history and philosophy of biology. In Rheinberger's work, we can see the "Spalten" and "Fugen"-the continuities and discontinuities-that this tradition left there.

An Epistemology of Scientific Practice: Positioning Hans-Jörg Rheinberger in Twentieth-Century History and Philosophy of Biology.

In this article, I first outline the professionalization of the history and philosophy of biology from the 1960s onward. Then, I attempt to situate the work of Hans-Jörg Rheinberger with respect to this field. On the one hand, Rheinberger was marginal with respect to Anglo-American philosophical tradition; on the other, he was very influential in building up an integrated history and philosophy of the life sciences community at the Max Planck Institute for the History of Science in Berlin and beyond. This marginality results, I suggest, from three main sources: his use of concepts coming from continental traditions in the study of the life sciences, which are foreign to Anglo-American philosophers of science; his focus on practices instead of theories; and his research trajectory as a molecular biologist, which led him to be critical of disciplinary boundaries. As a first step in situating and historicizing Rheinberger's trajectory, this article invites comparative studies and calls for a history of "continental philosophy of biology" in the twentieth century.

Ciência e gênero, feminismo e história das ciências: entrevista com Evelyn Fox Keller / Science and gender, feminism and history of science: interview with Evelyn Fox Keller

Resumo A entrevista aborda a trajetória de Evelyn Fox Keller, professora emérita de história e filosofia das ciências do Massachusetts Institute of Technology. Keller reflete sobre seu percurso e sobre os desafios que precisou enfrentar para expandir as fronteiras dos estudos de ciências com seu trabalho pioneiro relacionando linguagem, gênero e ciências, que tem sido muito influente em mudar a visão da história das ciências.

Abstract This interview covers the trajectory of Evelyn Fox Keller, emeritus professor of history and philosophy of science at the Massachusetts Institute of Technology. Keller reflects on her career and the challenges she had to overcome to push back the frontiers of science with her pioneering work on language, gender, and science, which has been very influential in changing views in the history of science.

Vitalism, Holism, and Metaphorical Dynamics of Hans Spemann's "Organizer" in the Interwar Period.

This paper aims to provide a fresh historical perspective on the debates on vitalism and holism in Germany by analyzing the work of the zoologist Hans Spemann (1869-1941) in the interwar period. Following up previous historical studies, it takes the controversial question about Spemann's affinity to vitalistic approaches as a starting point. The focus is on Spemann's holistic research style, and on the shifting meanings of Spemann's concept of an organizer. It is argued that the organizer concept unfolded multiple layers of meanings (biological, philosophical, and popular) during the 1920s and early 1930s. A detailed analysis of the metaphorical dynamics in Spemann's writings sheds light on the subtle vitalistic connotations of his experimental work. How Spemann's work was received by contemporary scientists and philosophers is analyzed briefly, and Spemann's holism is explored in the broader historical context of the various issues about reductionism and holism and related methodological questions that were so prominently discussed not only in Germany in the 1920s.

A hapless mathematical contribution to biology : Chromosome inversions in Drosophila, 1937-1941.

This is the story, told in the light of a new analysis of historical data, of a mathematical biology problem that was explored in the 1930s in Thomas Morgan's laboratory at the California Institute of Technology. It is one of the early developments of evolutionary genetics and quantitative phylogeny, and deals with the identification and counting of chromosomal inversions in Drosophila species from comparisons of genetic maps. A re-analysis of the data produced in the 1930s using current mathematics and computational technologies reveals how a team of biologists, with the help of a renowned mathematician and against their first intuition, came to an erroneous conclusion regarding the presence of phylogenetic signals in gene arrangements. This example illustrates two different aspects of a same piece: (1) the appearance of a mathematical in biology problem solved with the development of a combinatorial algorithm, which was unusual at the time, and (2) the role of errors in scientific activity. Also underlying is the possible influence of computational complexity in understanding the directions of research in biology.

Cut and Paste: The Mexican Axolotl, Experimental Practices and the Long History of Regeneration Research in Amphibians, 1864-Present.

The Mexican axolotl (Ambystoma mexicanum) is one of the most important models in contemporary regeneration research and regenerative medicine. This is the result of the long history of the species as an experimental and laboratory bred animal. One of many research questions investigated in the axolotl is regeneration. The species' astonishing ability to regenerate tissues and entire body parts already became apparent shortly after the first 34 living axolotls had been brought from Mexico to Europe in 1864. In the context of their unclear status as larvae or adults and the mysterious transformation of some animals into an adult form, the Paris zoologist Auguste Duméril cut off the gills of several individuals in an attempt to artificially induce the metamorphosis. This produced the first reports on the animals' regenerative powers and led to sporadic but continuous investigations. But it remained just one of the many phenomena studied in axolotls. Only at the beginning of the 20th century, regeneration became a more prominent aspect in the experimental investigations of axolotls. In experimental embryology, regeneration in axolotls was used in three different ways: it was studied as a phenomenon in its own right: more importantly, it served as a macroscopic model for normal development and, together with other techniques like grafting, became a technical object in the experimental systems of embryologists. In my paper, I will look into how the axolotl became an experimental animal in regeneration research, the role of practices and infrastructures in this process and the ways in which regeneration in the axolotl oscillated between epistemic thing and technical object.

Pluralismo evolutivo e o ideal de unificação da biologia / Evolutionary pluralism and the ideal of a unified biology

Resumo A evolução biológica é frequentemente considerada um eixo central e unificador da biologia. O artigo discute aspectos históricos desse ideal de unificação, bem como os seus sinais de desintegração entre os anos 1960 e 1980. Argumentamos que apesar das novas propostas de síntese do conhecimento biológico, a biologia evolutiva contemporânea é caracterizada por um pluralismo. Os principais pontos a favor do pluralismo evolutivo são discutidos, e algumas consequências dessa perspectiva são apresentadas, particularmente em relação ao ideal de unificação da biologia. Por fim, defendemos um pluralismo evolutivo crítico do ideal de unificação como um objetivo da ciência, mas ainda favorável a integrações locais.

Abstract Biological evolution is often regarded as a central and unifying axis of biology. This article discusses historical aspects of this ideal of unification, as well as signs of its disintegration from the 1960s to 1980s. We argue that despite new proposals for the synthesis of biological knowledge, contemporary evolutionary biology is characterized by pluralism. The main points in favor of evolutionary pluralism are discussed and some consequences of this perspective are presented, particularly in terms of the ideal of a unified biology. Finally, we defend an evolutionary pluralism that critiques the ideal of unification as a scientific objective, but still favors local integrations.

D'Arcy W. Thompson's On Growth and Form: A landmark for the mathematical foundations of epigenetics.

The celebrated 1917 work "On Growth and Form" of D'Arcy W. Thompson has established a landmark for mathematical biology, introducing new perspectives of study and research in biology, providing mathematical methods to morphology of biological systems. In this brief historical essay, we recall the novelties and relevance of the work from a retrospective stance, above all pointing out the crucial role played by it in the dawning of epigenetic standpoint. The role of underlying epigenetic processes in generation of biological forms via similarity transformations is analyzed within the framework of D'Arcy Thompson. The significance of D'Arcy Thompson as a predecessor of the relational biology and of the epigenetic concepts of evolution is discussed.

"Microbiota, symbiosis and individuality summer school" meeting report.

How does microbiota research impact our understanding of biological individuality? We summarize the interdisciplinary summer school on "Microbiota, symbiosis and individuality: conceptual and philosophical issues" (July 2019), which was supported by a European Research Council starting grant project "Immunity, DEvelopment, and the Microbiota" (IDEM). The summer school centered around interdisciplinary group work on four facets of microbiota research: holobionts, individuality, causation, and human health. The conceptual discussion of cutting-edge empirical research provided new insights into microbiota and highlights the value of incorporating into meetings experts from other disciplines, such as philosophy and history of science. Video Abstract.

Ernst Haeckel, Nikolai Miklucho-Maclay and the racial controversy over the Papuans.

BACKGROUND: The "German Darwin" Ernst Haeckel (1834-1919) was a key figure during the first "Darwinian revolution", a time when the foundations of the modern evolutionary theory were laid. It was Haeckel, who crucially contributed to the visualization of the Darwinian theory by designing "genealogical-trees" illustrating the evolution of various species, including humans. Although the idea of explaining human evolution by natural selection belongs to Darwin, Haeckel was the first who attempted to create a new exact anthropology based on the Darwinian method. DISCUSSION: Trying to immediately reconstruct human evolution proceeding from the description of modern populations led Haeckel to the views which, from the contemporary perspective, are definitely racist. Haeckel created racial anthropology intending to prove human origins from a lower organism, but without the intention of establishing a discriminatory racial praxis. Although hierarchical in its outcome, the Haeckelian method did not presuppose the necessity of a racial hierarchy of currently living humans. It is crucial to grasp in what sense Haeckel's theoretical explorations in human evolution were racist, and in what sense they were not. Our argument flows as follows. One of Haeckel's pupils was the Russian ethnographer, anthropologist and zoologist Nikolai Nikolajewitsch Miklucho-Maclay (1846-1888). Maclay and Haeckel worked closely together for several years; they traveled jointly and Maclay had enough time to learn the major methodological principles of Haeckel's research. Yet in contrast to Haeckel, Maclay is regarded as one of the first scientific anti-racists, who came to anti-racist views using empirical field studies in Papua-New Guinea. CONCLUSIONS: We claim that while conducting these studies Maclay applied scientific principles to a significant extent acquired from Haeckel. The paper contributes to the view that Haeckel's theoretical racism did not follow the Darwinian method he used.

Friedrich Miescher's Discovery in the Historiography of Genetics: From Contamination to Confusion, from Nuclein to DNA.

In 1869, Johann Friedrich Miescher discovered a new substance in the nucleus of living cells. The substance, which he called nuclein, is now known as DNA, yet both Miescher's name and his theoretical ideas about nuclein are all but forgotten. This paper traces the trajectory of Miescher's reception in the historiography of genetics. To his critics, Miescher was a "contaminator," whose preparations were impure. Modern historians portrayed him as a "confuser," whose misunderstandings delayed the development of molecular biology. Each of these portrayals reflects the disciplinary context in which Miescher's work was evaluated. Using archival sources to unearth Miescher's unpublished speculations-including an analogy between the hereditary material and language, and a speculation that a series of asymmetric carbon atoms could account for hereditary variation-this paper clarifies the ways in which the past was judged through the lens of contemporary concerns. It also shows how organization, structure, function, and information were already being considered when nuclein was first discovered nearly 150 years ago.

Scientific encounters between Colombia and the United States analyzed through publishing practices in Caldasia journal: The birds of the Republic of Colombia as a publishing event.

In 1948, American ornithologist Rodolphe Meyer de Schauensee began publishing what would be the most complete list of birds from Colombia that had ever been printed up to that time. His work was called The Birds of the Republic of Colombia (TBRC), and at the invitation of Armando Dugand, the director of the Instituto de Ciencias Naturales at the Universidad Nacional de Colombia and of the Caldasia journal, this work was exclusively published in the journal in five installments spanning four years. This paper analyzes the publishing aspects that particularly influenced the process of carrying out this work, with the objective of showing that scientific practices and publishing practices are not two absolutely separate domains. The circuit of communication present in TBRC's development is analyzed, specifically the efforts of the editor, printer and author to bring this work to fruition. This analysis demonstrates the following: (i) how the scientific interests of Meyer and the Instituto de Ciencias Naturales converge, (ii) the contradictions between scientific interests that promoted the publication of TBRC and the publishing rationale of a journal and (iii) how unforeseen publishing issues of the time, such as the increase in printing costs due to inflation, influenced the final structure of the work.

E. E. Just's broad, yet hidden, influence on modern cell and developmental biology.

This year, 2019, marks the centennial of embryologist E. E. Just's discovery of what is known as the fast block to polyspermy. Just's observation of the subtle changes that occur at the egg's surface during fertilization (and in experimental parthenogenesis) led him to postulate that the egg, and indeed every cell, possesses a property he called independent irritability, which represents the cell's ability to respond in a physiologically-relevant way to a variety of signals or triggers. In this paper, I argue that Just's concept of independent irritability informed his contemporary Johannes Holtfreter as Holtfreter attempted to explain the phenomena of embryonic induction and competence and that Holtfreter, in turn, influenced Marc Kirschner and John Gerhart in their formulation of the theory of facilitated variation. Just's influence is especially evident in Gerhart and Kirschner's presentations of what they call weak linkage-a property of living systems that allows core processes and components to be mixed and matched in different ways to generate novel traits. Unfortunately, the connection between Holtfreter's work and Just's has remained hidden. This paper gives examples of phenomena that exhibit weak linkage, and it lays out the case that Just's concept of independent irritability, through Holtfreter, Gerhart, and Kirschner, has broadly infiltrated modern cell and developmental biology.

Statistical analysis of word usage in biological publications since 1965: Historical delineation highlighting an emergence of function-oriented discourses in contemporary molecular and cellular biology.

Typical studies on the history of science, or particularly of biology, have been focused on a particular scientist or book, but this selection has a risk of being arbitrary. To find a more objective way of studying history of biology, we applied a statistical method. First, we downloaded from the PubMed database all available titles and abstracts of 934,807 articles in 32 selected journals from 1965 to 2014, and extracted most frequently used 322 terms by text mining. Clustering of these terms according to the annual frequency of usage resulted in three main clusters: Cluster 1 represented terms that were no longer used frequently, Cluster 3 included terms that became abundantly used recently, and Cluster 2 contained terms constantly used. Three phases were delineated in the history of biology over the past 50 years, with transitions in 1987 and 1997. In contrast with our tacit understanding that "function" is a key notion in biological thinking, the results suggest that function-oriented discourses are a new habit of biologists in the genomic era after 1997, in which biological researches focus on identifying a link between a molecule or a structure with its function. We hypothesize that, in spite of repeated warnings, function-related discourses have a teleological connotation, which is easily misunderstood by general audience and, with emphatic expressions such as "important" and "essential", fit to the need for justification of researches as part of researcher's responsibility for public funding.

Creating life and the media: translations and echoes.

Synthetic biology is the engineering view on biotechnology that ultimately aims at fulfilling the quest of building an artificial cell. From the very first attempts of synthesizing life, this subject has made an impact on the media through, very often, misleading headlines and news. We review here the historical journalistic approach on synthetic biology and related disciplines, from the early twentieth century to the lastest achievements on designing protocells or genome reduction. However, it would be very naive to consider the research community and the media to be unidirectionally linked, with the latter being mere displayers (and disrupters) of the research "reality". On the contrary, the research community has also received a strong influence from the media, as evidenced by statements from researchers, common metaphors and, even, a trend to unconsciously develop shared techno-social paradigms. We conclude that, beyond overstatements from researchers and journalists' misunderstandings, both communities provide strong feedback to each other and, together, contribute to define the dream that synthetic biologists are aiming for.