The genotype-phenotype distinction: from Mendelian genetics to 21st century biology.

The Genotype-Phenotype (G-P) distinction was proposed in the context of Mendelian genetics, in the wake of late nineteenth century studies about heredity. In this paper, we provide a conceptual analysis that highlights that the G-P distinction was grounded on three pillars: observability, transmissibility, and causality. Originally, the genotype is the non-observable and transmissible cause of its observable and non-transmissible effect, the phenotype. We argue that the current developments of biology have called the validity of such pillars into question. First, molecular biology has unveiled the putative material substrate of the genotype (qua DNA), making it an observable object. Second, numerous findings on non-genetic heredity suggest that some phenotypic traits can be directly transmitted. Third, recent organicist approaches to biological phenomena have emphasized the reciprocal causality between parts of a biological system, which notably applies to the relation between genotypes and phenotypes. As a consequence, we submit that the G-P distinction has lost its general validity, although it can still apply to specific situations. This calls for forging new frameworks and concepts to better describe heredity and development.

Evolution and ethics viewed from within two metaphors: machine and organism.

How is moral thinking, ethics, related to evolutionary theorizing? There are two approaches, epitomized by Charles Darwin who works under the metaphor of the world as a machine, and by Herbert Spencer who works under the metaphor of the world as an organism. Although the author prefers the first approach, the aim of this paper is to give a disinterested account of both approaches.

Moreau de Tours: organicism and subjectivity. Part 1: Life and work.

This is the first of two articles analysing the importance of J.J. Moreau de Tours' work and its influence on the development of descriptive psychopathology from the mid-nineteenth century to the present. Part 1 focuses on biographical aspects and presents Moreau's main works in their social and cultural context, with special emphasis on his book Du Hachisch et de l'Aliénation mentale, published in 1845. The second article will concentrate on Moreau as a psychopathologist.

Moreau de Tours: organicism and subjectivity. Part 2: Moreau as psychopathologist.

These two articles analyse the importance of J.J. Moreau de Tours' work and its influence on the development of descriptive psychopathology from the mid-nineteenth century to the present. The first article focused on biographical aspects and presented Moreau's main works in their social and cultural contexts. This second article critically analyses Moreau's contributions from different perspectives: epistemological, psychopathological, clinical, therapeutic, and it also discusses his role as a public figure.

Information, programme, signal: dead metaphors that negate the agency of organisms.

The metaphorical adoption of the concepts of information, program and signal introduced into biology the logic and implicit causal structure of the mathematical theories of information; this is inimical to biology. In turn, those metaphors have hindered the development of a theory of organisms by transferring the agency of organisms to natural selection and to DNA. Moreover, those metaphors introduced into biology the dualism software-hardware and a Laplacian causal structure. Instead, we propose to uphold the agency of the living by adopting three foundational principles for a theory of organisms: namely, 1) the principle of biological inertia (i.e., the default state of cells is proliferation and motility), 2) the principle of variation, and 3) the principle of organization.

Challenging the Adaptationist Paradigm: Morphogenesis, Constraints, and Constructions.

In this paper, I argue that the German morphological tradition made a major contribution to twentieth-century study of form. Several scientists paved the way for this research: paleontologist Adolf Seilacher (1925-2014), entomologist Hermann Weber (1899-1956), and biologist Johann-Gerhard Helmcke (1908-1993) together with architect Frei Otto (1925-2015). All of them sought to examine morphogenetic processes to illustrate their inherent structural properties, thus challenging the neo-Darwinian framework of evolutionary theory. I point out that the German theoretical challenge to adaptationist thinking was possible through an exchange and transfer of practices, data, technologies, and knowledge between biologically oriented students of form and architects, designers, and engineers. This exchange of practices and knowledge was facilitated by the establishment of two collaborative research centers at the beginning of the 1970s. Hence, by showing the richness of topics, methods, and technologies discussed in German-speaking morphology between 1950 and the 1970s, this paper paves the way to a much broader comprehension of the shifts that have shaped twentieth-century evolutionary biology.

Neither superorganisms nor mere species aggregates: Charles Elton's sociological analogies and his moderate holism about ecological communities.

This paper analyzes community ecologist Charles Elton's ideas on animal communities, and situates them with respect to the classical opposition between organicist-holistic and individualistic-reductionist ecological views drawn by many historians of ecology. It is argued that Elton espoused a moderate ecological holism, which drew a middle way between the stricter ecological holism advocated by organicist ecologists and the merely aggregationist views advocated by some of their opponents. It is also argued that Elton's moderate ecological holism resonated with his preference for analogies between ecological communities and human societies over more common ones between communities and individual organisms. I discuss, on the one hand, how the functionalist-interactionist approach to community ecology introduced by Elton entailed a view of ecological communities as more or less self-maintaining functionally organized wholes, and how his ideas on this matter were incorporated into their views by organicist ecologists Frederic Clements, Victor Shelford, and Warder C. Allee et al. On the other hand, I identify some important divergences between Elton's ecological ideas and those of organicist ecologists. Specifically, I show (1) how Elton's ideas on species distribution, animal migrations, and ecological succession entailed a view of animal communities as exhibiting a weaker degree of part-whole integration than that attributed to them by Clements and Shelford; and (2) how Elton's mixed stance on the balance of nature idea and his associated views on community stability attributed to communities a weaker form of self-regulation than that attributed to them by Allee et al.

The myth of Frederic Clements's mutualistic organicism, or: on the necessity to distinguish different concepts of organicism.

In the theory and history of ecology, Frederic Clements's theory of plant communities is usually presented as the historical prototype and a paradigmatic example of synecological organicism, characterised by the assumption that ecological communities are functionally integrated units of mutually dependent species. In this paper, I will object to this standard interpretation of Clements's theory. Undoubtedly, Clements compares plant communities with organisms and calls them "complex organisms" and "superorganisms". Further, he can indeed be regarded as a proponent of ecological organicism-provided that one defines ecological organicism as the interpretation of synecological units according to the model of the individual organism. However, Clements's theory does not include the assumption that mutual dependence is a principle of the organisation of plant communities. Rather, he interprets plant communities as top-down control-hierarchical entities, in which subordinate species depend on dominant species-but not the other way around. Therefore, his theory represents what may be called 'control-hierarchical organicism' as against 'mutualistic organicism'. The erroneous attribution to Clements of 'mutualistic organicism' might be due to an unawareness of the existence of different concepts of the organism. This unawareness results in the projection on Clements's theory of a seemingly self-evident mutualistic concept of organism that Clements himself did not use as a basis for his theory of plant communities.

O Organism, Where Art Thou? Old and New Challenges for Organism-Centered Biology.

This paper addresses theoretical challenges, still relevant today, that arose in the first decades of the twentieth century related to the concept of the organism. During this period, new insights into the plasticity and robustness of organisms as well as their complex interactions fueled calls, especially in the UK and in the German-speaking world, for grounding biological theory on the concept of the organism. This new organism-centered biology (OCB) understood organisms as the most important explanatory and methodological unit in biological investigations. At least three theoretical strands can be distinguished in this movement: Organicism, dialectical materialism, and (German) holistic biology. This paper shows that a major challenge of OCB was to describe the individual organism as a causally autonomous and discrete unit with consistent boundaries and, at the same time, as inextricably interwoven with its environment. In other words, OCB had to conciliate individualistic with anti-individualistic perspectives. This challenge was addressed by developing a concept of life that included functionalist and metabolic elements, as well as biochemical and physical ones. It allowed for specifying organisms as life forms that actively delimit themselves from the environment. Finally, this paper shows that the recent return to the concept of the organism, especially in the so-called "Extended Evolutionary Synthesis," is challenged by similar anti-individualistic tendencies. However, in contrast to its early-twentieth-century forerunner, today's organism-centered approaches have not yet offered a solution to this problem.

A historiographic study of psychiatric treatments in Brazil: mentalism and organicism from 1830 to 1859.

Our aim is to investigate two major tendencies in nineteenth-century Brazilian alienism: mentalism and organicism, by conducting a descriptive study of original Brazilian documents on medical health treatments in the 1830s, 1840s and 1850s. Primary sources of Brazilian alienism were theses, memoirs, official reports, and documents written by clinicians and asylum directors. We analysed early mental treatment in Brazilian lunatic asylums, exploring the relative contributions of two main theoretical orientations: moral treatment (based on Pinel and Esquirol) and 'medical-organicist therapeutic orientation'. Intertextuality was used to assess reports of medical organicist treatment in Brazil. We concluded that contemporaneous textual sources indicate that mid-nineteenth-century alienism in Brazil was predominantly influenced by organicism exported from European countries. Pinel's mentalist view, nevertheless, remained the reference point for clinical issues associated with the doctor-patient relationship.

The Spemann-Mangold organizer discovery and society.

This paper analyzes the influence of Hans Spemann and Hilde Mangold's discovery of the embryonic organizer on society outside the narrower confines of embryology. It begins by overviewing how in the 1920s-1930s, the organizer discovery fit well into the agenda of both right-wing and left-wing political camps, as it supported holistic theories of biological development that aligned with their ideological views. The paper then explores the organizer's influence on the formation and interdisciplinary discussions of the 1930s Cambridge Theoretical Biology Club. Club member C.H. Waddington's concept of the epigenetic landscape, inspired in part by Spemann and Mangold's work, went on to impact diverse fields including mathematics, psychology, anthropology, architecture, and art. Examples include mathematician René Thom's catastrophe landscapes and the field of ekistics (the science of human settlements). Spemann and Mangold's creation of an embryo chimera by combining tissues from different newt species also helped shape philosophers' and artists' understanding of the relationship between nature and technology as an integrated whole rather than separate entities. Additionally, Spemann's embryonic field concept helped influence field theories in other areas of science, and thinkers have pointed out metaphorical similarities between the organizer experiment and philosophical dialectics, film editing, or historical events. However, several factors likely limited the long-term societal impact of Spemann's holistic perspective, notably the rise of molecular biology and DNA-centric reductionist views of biology in the mid-late 20th century. While such reductionism still dominates public perceptions of biology, there seems to be a renewed openness to holistic perspectives reminiscent of Spemann's views.

Rethinking some roots of ecosystem approach in aquatic ecology: between the food cycle and lake metabolism.

The present study provides new insight into the key aspects of the early formative period of the ecosystem concept in aquatic ecology. Raymond Lindeman's trophodynamics is known to be a starting point for the development of the modern concept of ecosystem. The trophodynamic approach in ecology was proposed by Lindeman in his widely cited paper of 1942. Lindeman's views are analyzed in comparison with the contemporary production studies in aquatic ecology. It is shown that a similar theoretical system has been proposed in the USSR at the end of the 1930s by Georgiy G. Vinberg. He introduced the concept of biotic balance based on the wide appraisal of the dark and light bottles method. The study shows that both Lindeman's trophodynamics and Vinberg's concept of biotic balance relied on an energy-based approach in considering the wholeness of a water body. The two scientists, however, differed in several important aspects concerning the interpretation of the role of living organisms. The holistic interpretation of ecosystem by Lindeman and Vinberg can be seen as part of the dilemma between physicalism and organicism. At the same time, the main emphasis in the concepts of both Vinberg and Lindemann was on the primary production component, a feature that was common to the first holistic systems in production hydrobiology (e.g., E. Naumann's regional limnology). It is clear that modern problems of aquatic ecology should be addressed from the perspective of the organismocentric understanding of the ecosystem, but undoubtedly at the new level of development of this view.

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.

The cancer puzzle: Welcome to organicism.

During the fifty years since President Nixon declared the "War on Cancer", those inside and outside the cancer community have witnessed the systematic moving of the goalposts attitude to accommodate evidence into an inadequate theory, that is, the Somatic Mutation Theory (SMT). This sorry state promoted a renewable yearly promise that at the end of the next 10-year period the promises uttered in 1971 would become reality. Each failure triggered calls to do more of the same research under the same theory, routinely using more and more sophisticated technology. Meanwhile, in the last few years, an unambiguous general consensus has emerged acknowledging that this overall long, intensive effort has failed, and that it is likely that the solution to the cancer problem resides elsewhere, namely, in alternative theoretical principles of biology. In this essay we concentrate, first, on the big picture, from the philosophical stance (reductionism versus organicism) to the need to adopt rigorous theories. From this novel perspective we conceptualize cancer as a disease of tissue organization akin to development gone awry. Finally, having identified both a promising stance and a useful theory, i.e., the tissue organization field theory (TOFT), we call for abandoning the SMT and for adopting the more promising TOFT.

Glycemia Regulation: From Feedback Loops to Organizational Closure.

Endocrinologists apply the idea of feedback loops to explain how hormones regulate certain bodily functions such as glucose metabolism. In particular, feedback loops focus on the maintenance of the plasma concentrations of glucose within a narrow range. Here, we put forward a different, organicist perspective on the endocrine regulation of glycaemia, by relying on the pivotal concept of closure of constraints. From this perspective, biological systems are understood as organized ones, which means that they are constituted of a set of mutually dependent functional structures acting as constraints, whose maintenance depends on their reciprocal interactions. Closure refers specifically to the mutual dependence among functional constraints in an organism. We show that, when compared to feedback loops, organizational closure can generate much richer descriptions of the processes and constraints at play in the metabolism and regulation of glycaemia, by making explicit the different hierarchical orders involved. We expect that the proposed theoretical framework will open the way to the construction of original mathematical models, which would provide a better understanding of endocrine regulation from an organicist perspective.

Social Solidarity and Herbert Spencer: Not the Oxymoron That Might Be Assumed.

This article attempts to retrieve important aspects of Spencer's sociology from the general neglect and misrepresentation which threatens to overwhelm it all. It does touch in passing on many such highly dubious contentions as that he was a "social Darwinist," but the prime focus is to deal with three linked themes. First, the article examines the significance of his attribution to individuals of "social self-consciousness" as part of sociality, thus distancing it from Durkheim's influential but suspect reading of Spencer's individuals as egoistic. Second, it rescues his concept of "the social organism" from misinterpretation. His own writings show it to be a more rigorous and suggestive attempt to configure the morphology of "the social" than commonly assumed. Third, it reconstructs the status of his contrast between "militant" and "industrial" social forms as a contrast between different but more general forms of social life that those descriptions in fact register. With the focus on these three linked themes the article improves the historical accuracy of our understanding of Spencer's sociology. It also repositions key aspects of it as not alien, quaint and a spent force, but ontologically challenging and possibly prescient for debates about the meaning of "the social" today.

The schism in chiropractic through the eyes of a 1st year chiropractic student.

Since its inception, the chiropractic profession has been divided along ideological fault lines. These divisions have led to a profession wide schism, which has limited mainstream acceptance, utilisation, social authority and integration. The authors explore the historical origins of this schism, taking time to consider historical context, religiosity, perpetuating factors, logical fallacies and siege mentality. Evidence is then provided for a way forward, based on the positioning of chiropractors as mainstream partners in health care.

Epigenesis by experience: Romantic empiricism and non-Kantian biology.

Reconstructions of Romantic-era life science in general, and epigenesis in particular, frequently take the Kantian logic of autotelic "self-organization" as their primary reference point. I argue in this essay that the Kantian conceptual rubric hinders our historical and theoretical understanding of epigenesis, Romantic and otherwise. Neither a neutral gloss on epigenesis, nor separable from the epistemological deflation of biological knowledge that has received intensive scrutiny in the history and philosophy of science, Kant's heuristics of autonomous "self-organization" in the third Critique amount to the strategic capture of epigenesis from nature, for thought, in thought's critical transcendence of nature. This essay looks to Jean-Baptiste Lamarck and his English contemporary Erasmus Darwin to begin to reconstruct the rigorously materialist, naturalist, and empiricist theories of epigenesis (still) marginalized by Kantian argumentation. As theorists of environmental and social collaboration in the ontogeny of viable forms, Lamarck and Darwin illuminate features of our own epigenetic turn obscured by the rhetoric of "self-organization," allowing us to glimpse an alternative Romantic genealogy of the biological present.

Theoretical principles for biology: Organization.

In the search of a theory of biological organisms, we propose to adopt organization as a theoretical principle. Organization constitutes an overarching hypothesis that frames the intelligibility of biological objects, by characterizing their relevant aspects. After a succinct historical survey on the understanding of organization in the organicist tradition, we offer a specific characterization in terms of closure of constraints. We then discuss some implications of the adoption of organization as a principle and, in particular, we focus on how it fosters an original approach to biological stability, as well as and its interplay with variation.