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

A framework for the integration of development and evolution: The forgotten legacy of James Meadows Rendel

The historical challenges to bridge the gaps between developmental biology and population or statistical genetics under the explanatory dominance of the Modern Evolutionary Synthesis during the 20th century have been thoroughly documented. However, although several attempts to integrate these fields have been made, most have been deemed unsuccessful. As an example of those efforts, in this paper I discuss the work of James Meadows Rendel, a student of J. B. S. Haldane and disciple of Conrad Hal Waddington. I present his largely forgotten or unrecognized, but innovative, ideas about canalization and the role of development in phylogeny as a valuable piece to connect these fields that could still have important ramifications for today's evolutionary biology. In fact, it is expected that the legacy of J. M. Rendel will be rediscovered, and more importantly, incorporated and extended by future researchers, in light of the growth of evolutionary developmental biology in the last decades. What is more, this case offers a chance to critically revisit standard historiographies about the dichotomy between developmental and population genetics research frameworks in 20th century biology.

Scrutinizing microbiome determinism: why deterministic hypotheses about the microbiome are conceptually ungrounded

This paper addresses the topic of determinism in contemporary microbiome research. I distinguish two types of deterministic claims about the microbiome, and I show evidence that both types of claims are present in the contemporary literature. First, the idea that the host genetics determines the composition of the microbiome which I call "host-microbiome determinism". Second, the idea that the genetics of the holobiont (the individual unit composed by a host plus its microbiome) determines the expression of certain phenotypic traits, which I call "microbiome-phenotype determinism". Drawing on the stability of traits conception of individuality (Suárez in Hist Philos Life Sci 42:11, 2020) I argue that none of these deterministic hypotheses is grounded on our current knowledge of how the holobiont is transgenerationally assembled, nor how it expresses its phenotypic traits.

Thomas S. Kuhn: key to a better understanding of the extended evolutionary synthesis

In recent years, some scholars have explicitly questioned the desirability or utility of applying the classical and "old-fashioned" theories of scientific change by the likes of Karl Popper and Thomas S. Kuhn to the question of the precise nature and significance of the extended evolutionary synthesis (EES). Supposedly, these twentieth-century philosophers are completely irrelevant for a better understanding of this new theoretical framework for the study of evolution. Here, it will be argued that the EES can be fruitfully interpreted in terms of, as yet, insufficiently considered or even overlooked elements from Kuhn's theory. First, in his original, historical philosophy of science, Kuhn not only distinguished between small and big scientific revolutions, he also pointed out that paradigms can be extended and reformulated. In contrast with what its name suggests, the mainstream EES can be interpreted as a Kuhnian reformulation of modern evolutionary theory. Second, it has, as yet, also been overlooked that the EES can be interpreted in terms of Kuhn's later, tentative evolutionary philosophy of science. With the EES, an old dichotomy in evolutionary biology is maybe being formalized and institutionalized.

Between the genotype and the phenotype lies the microbiome: symbiosis and the making of 'postgenomic' knowledge

Emphatic claims of a "microbiome revolution" aside, the study of the gut microbiota and its role in organismal development and evolution is a central feature of so-called postgenomics; namely, a conceptual and/or practical turn in contemporary life sciences, which departs from genetic determinism and reductionism to explore holism, emergentism and complexity in biological knowledge-production. This paper analyses the making of postgenomic knowledge about developmental symbiosis in Drosophila melanogaster by a specific group of microbiome scientists. Drawing from both practical philosophy of science and Science and Technology Studies, the paper documents epistemological questions of artefactuality and representativeness of model organisms as they emerge in the day-to-day labour producing and being produced by the "microbiome revolution." Specifically, the paper builds on all the written and editorial exchanges involved in the troubled publication of a research paper studying the symbiotic role of the microbiota in the flies' development. These written materials permit us to delimit the network of justifications, evidence, standards of knowledge-production, trust in the tools and research designs that make up the conditions of possibility of a postgenomic fact. More than reframing the organism as a radically novel multiplicity of reactive genomes, we conclude, doing postgenomic research on the microbiota and symbiosis means producing a story that deviates from the scripts embedded into the sociotechnical experimental systems of post-Human Genome Project life sciences.

Agential autonomy and biological individuality

What is a biological individual? How are biological individuals individuated? How can we tell how many individuals there are in a given assemblage of biological entities? The individuation and differentiation of biological individuals are central to the scientific understanding of living beings. I propose a novel criterion of biological individuality according to which biological individuals are autonomous agents. First, I articulate an ecological-dynamical account of natural agency according to which, agency is the gross dynamical capacity of a goal-directed system to bias its repertoire to respond to its conditions as affordances. Then, I argue that agents or agential dynamical systems can be agentially dependent on, or agentially autonomous from, other agents and that this agential dependence/autonomy can be symmetrical or asymmetrical, strong or weak. Biological individuals, I propose, are all and only those agential dynamical systems that are strongly agentially autonomous. So, to determine how many individuals there are in a given multiagent aggregate, such as multicellular organism, a colony, symbiosis, or a swarm, we first have to identify how many agential dynamical systems there are, and then what their relations of agential dependence/autonomy are. I argue that this criterion is adequate to the extent that it vindicates the paradigmatic cases, and explains why the paradigmatic cases are paradigmatic, and why the problematic cases are problematic. Finally, I argue for the importance of distinguishing between agential and causal dependence and show the relevance of agential autonomy for understanding the explanatory structure of evolutionary developmental biology.

The elephant in the room: The biomimetic principle in bio-robotics and embodied AI

In recent years, bio-inspired robots have shaped numerous domains of technical and scientific production. Bio-inspired robots can now be found in all areas of industry, medicine, architecture, and even culture. Despite the wealth of historiographic and philosophical studies published on this topic, a philosophical investigation of the mimetic principle used in bio-robotics is still missing. In this paper, I will ask a simple question: what is the role of biomimetic and bio-inspired processes in the different practices of bio-robotics? In the following pages, I will first make some conceptual order. I discuss the differences between several bio-inspired disciplines to clearly identify the biomimetic principle. Second, I introduce the discussion on the necessity of imitating nature in early twentieth-century bio-robotics. Third, I state the broader philosophical issue at stake in the debate on the biomimetic principle: the model-world relation, as discussed in the philosophical literature on models and idealization. In section 4, I address several emblematic case studies in which the imitation of nature, variously declined, is fundamental for producing knowledge, thus providing cursory taxonomy of the biomimetic principle. In the conclusion, I will come back to the elephant in the room and suggest how to tackle it further in a fruitful manner. As a broader result, my proposed taxonomy might be used by historians of science and technology as a starting point for historicizing the different practices of current bio-robotics as well as by philosophers to further problematize the various philosophical frameworks that have been accepted and developed in bio-robotics.

Homeorhesis: envisaging the logic of life trajectories in molecular research on trauma and its effects

What sets someone on a life trajectory? This question is at the heart of studies of 21st-century neurosciences that build on scientific models developed over the last 150 years that attempt to link psychopathology risk and human development. Historically, this research has documented persistent effects of singular, negative life experiences on people's subsequent development. More recently, studies have documented neuromolecular effects of early life adversity on life trajectories, resulting in models that frame lives as disproportionately affected by early negative experiences. This view is dominant, despite little evidence of the stability of the presumably early-developed molecular traits and their potential effects on phenotypes. We argue that in the context of gaps in knowledge and the need for scientists to reason across molecular and phenotypic scales, as well as time spans that can extend beyond an individual's life, specific interpretative frameworks shape the ways in which individual scientific findings are assessed. In the process, scientific reasoning oscillates between understandings of cellular homeostasis and organisms' homeorhesis, or life trajectory. Biologist and historian François Jacob described this framework as the "attitude" that researchers bring to bear on their "objects" of study. Through an analysis of, first, historical and contemporary scientific literature and then ethnographic research with neuroscientists, we consider how early life trauma came to be associated with specific psychological and neurobiological effects grounded in understandings of life trajectories. We conclude with a consideration of the conceptual, ontological, and ethical implications of interpreting life trajectories as the result of the persistence of long-embodied biological traits, persistent life environments, or both.

Organic form and evolution: the morphological problem in twentieth-century italian biology

This paper examines the efforts in evolution research to understand form's structure that developed in Italy during the first half of the twentieth century. In particular, it analyzes how the organic approach in biology and the study of organic form merged in the morphological research agendas of Giuseppe Colosi (1892-1975) and Giuseppe Levi (1872-1965). These biologists sought to understand form's inner composition and structure. First, I will briefly outline the morphological practices and frameworks used to study form changes and structures in the early twentieth century. Second, I will discuss what the Italian biologist Antonio Pensa (1874-1970) called the morphological problem. Third, I will examine Colosi's response to the morphological problem. Fourth, I will analyze Levi's morphological research program. As a result, this paper paves the way for a more nuanced and varied picture of the so-called "organicism movement" in the first half of the twentieth century by calling attention to morphology as practiced in Italian-speaking biology. In fact, alongside dialectical materialism and holistic biology, two of the main strands within organicism, the architectural approach to evolution as practiced in Italy and elsewhere had a profound impact on twentieth- and twenty-first-century organicism specifically and on evolutionary biology generally.

Organisms as subjects: Jakob von Uexküll and Adolf Portmann on the autonomy of living beings and anthropological difference

This paper focuses on the links between Jakob von Uexküll's theoretical biology and Adolf Portmann's conception of organic life. Its main purpose is to show that Uexküll and Portmann not only share a view of the living being as an autonomous and holistically organized entity, but also base this view on the seminal idea of the subjectivity of the organism. In other words, the respective holistic principles securing the autonomy of the living being-the Bauplan, for Uexküll; the Innerlichkeit, for Portmann-share an essentially subjective character. Such principles, indeed, express themselves in a centrally directed and formative way; moreover, in organisms endowed with a central nervous system, they also extend their influence on the overt behavioral sphere and on the organism's capacity to give meaning to the surrounding reality. The conclusion of the article will show how, though starting from this common background, the two authors develop divergent positions on the issue of the anthropological difference. If Portmann emphasizes the special status of the relationship between the human animal and the world, Uexküll tends to see a substantial continuity in the biosemiotic processes through which human and non-human animals constitute their species-specific worlds of experience (Umwelten).

Turing's cascade instability supports the coordination of the mind, brain, and behavior

Turing inspired a computer metaphor of the mind and brain that has been handy and has spawned decades of empirical investigation, but he did much more and offered behavioral and cognitive sciences another metaphor-that of the cascade. The time has come to confront Turing's cascading instability, which suggests a geometrical framework driven by power laws and can be studied using multifractal formalism and multiscale probability density function analysis. Here, we review a rapidly growing body of scientific investigations revealing signatures of cascade instability and their consequences for a perceiving, acting, and thinking organism. We review work related to executive functioning (planning to act), postural control (bodily poise for turning plans into action), and effortful perception (action to gather information in a single modality and action to blend multimodal information). We also review findings on neuronal avalanches in the brain, specifically about neural participation in body-wide cascades. Turing's cascade instability blends the mind, brain, and behavior across space and time scales and provides an alternative to the dominant computer metaphor.

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.

Analysis and/or Interpretation in Neurophysiology? A Transatlantic Discussion Between F. J. J. Buytendijk and K. S. Lashley, 1929-1932

In the interwar period, biologists employed a diverse set of holistic approaches that were connected to different research methodologies. Against this background, this article explores attempts in the 1920s and 1930s to negotiate quantitative and qualitative methods in the field of neurophysiology. It focuses on the work of two scientists on different sides of the Atlantic: the Dutch animal psychologist and physiologist Frederik J.J. Buytendijk and the American neuropsychologist Karl S. Lashley, specifically analyzing their critical correspondence, 1929-1932, on the problems surrounding the term intelligence. It discusses the inexplicable anomalies in neurophysiology as well as the reliability of quantitative and qualitative methods. While in his laboratory work Lashley adhered to a strictly analytic approach, Buytendijk tried to combine quantitative methods with phenomenological and hermeneutical approaches. The starting point of their discussion is Lashley's monograph on Brain Mechanisms and Intelligence (1929) and the rat experiments discussed therein. Buytendijk questioned the viability of the maze-learning method and the use of statistics to test intelligence in animals; he reproduced Lashley's experiments and then confronted Lashley with his critical findings. In addition to elucidating this exchange, this paper will, more generally, shed light on the nature of the disagreements and shared assumptions prevalent among interwar neurophysiologists. In turn, it contributes to historiographical debates on localization and functionalism and the discrepancy between analytic (quantitative) and interpretative (qualitative) approaches.

Physicochemical Biology and Knowledge Transfer: The Study of the Mechanism of Photosynthesis Between the Two World Wars

In the first decades of the twentieth century, the process of photosynthesis was still a mystery: Plant scientists were able to measure what entered and left a plant, but little was known about the intermediate biochemical and biophysical processes that took place. This state of affairs started to change between the two world wars, when a number of young scientists in Europe and the United States, all of whom identified with the methods and goals of physicochemical biology, selected photosynthesis as a topic of research. The protagonists had much in common: They had studied physics and chemistry (although not necessarily plant physiology) to a high level; they used physicochemical methods to study the basic processes of life; they believed these processes were the same, or very similar, in all life forms; and they were affiliated with institutions that fostered this kind of study. This set of cognitive, methodological, and material resources enabled these protagonists to transfer their knowledge of the concepts and techniques from microbiology and human biochemistry, for example, to the study of plant metabolism. These transfers of knowledge had a great influence on the way in which the biochemistry and biophysics of photosynthesis would be studied over the following decades. Through the use of four historical cases, this paper analyzes these knowledge transfers, as well as the investigative pathways that made them possible.

What's Wrong with Evolutionary Causation?

This review essay reflects on recent discussions in evolutionary biology and philosophy of science on the central causes of evolution and the structure of causal explanations in evolutionary theory. In this debate, it has been argued that our view of evolutionary causation should be rethought by including more seriously developmental causes and causes of the individual acting organism. I use Tobias Uller's and Kevin Laland's volume Evolutionary Causation as well as recent reviews of it as a starting point to reflect on the causal role of agency, individuality, and the environment in evolution. In addition, I critically discuss classical philosophical frameworks of theory change (i.e. Popper's, Kuhn's and Lakatos') used in this debate to understand changing views of evolutionary causation.

Kant, Linnaeus, and the economy of nature

Ecology arguably has roots in eighteenth-century natural histories, such as Linnaeus's economy of nature, which pressed a case for holistic and final-causal explanations of organisms in terms of what we'd now call their environment. After sketching Kant's arguments for the indispensability of final-causal explanation merely in the case of individual organisms, and considering the Linnaean alternative, this paper examines Kant's critical response to Linnaean ideas. I argue that Kant does not explicitly reject Linnaeus's holism. But he maintains that the indispensability of final-causal explanation depends on robust modal connections between types of organism and their functional parts; relationships in Linnaeus's economy of nature, by contrast, are relatively contingent. Kant's framework avoids strong metaphysical assumptions, is responsive to empirical evidence, and can be fruitfully compared with some contemporary approaches to biological organization.

Population and organismal perspectives on trait origins

Some biologists and philosophers of biology claim selection can "create" novel traits. Others claim creativity is to be found only in development. I here endorse the former claim, but take seriously and address the concerns that underlie the latter. My discussion of these issues is informed by recent work that champions the "return of the organism" to mainstream evolutionary biology, and I suggest how population and organismal perspectives on trait origins can be reconciled.

Developmental bias in the fossil record

The role of developmental bias and plasticity in evolution is a central research interest in evolutionary biology. Studies of these concepts and related processes are usually conducted on extant systems and have seen limited investigation in the fossil record. Here, I identify plasticity-led evolution (PLE) as a form of developmental bias accessible through scrutiny of paleontological material. I summarize the process of PLE and describe it in terms of the environmentally mediated accumulation and release of cryptic genetic variation. Given this structure, I then predict its manifestation in the fossil record, discuss its similarity to quantum evolution and punctuated equilibrium, and argue that these describe macroevolutionary patterns concordant with PLE. Finally, I suggest methods and directions towards providing evidence of PLE in the fossil record and conclude that such endeavors are likely to be highly rewarding.

The Extended Evolutionary Synthesis: what is the debate about, and what might success for the extenders look like?

Debate over the Extended Evolutionary Synthesis (EES) ranges over three quite different domains of enquiry. Protagonists are committed to substantive positions regarding (1) empirical questions concerning (for example) the properties and prevalence of systems of epigenetic inheritance; (2) historical characterizations of the modern synthesis; and (3) conceptual/philosophical matters concerning (among other things) the nature of evolutionary processes, and the relationship between selection and adaptation. With these different aspects of the debate in view, it is possible to demonstrate the range of cross-cutting positions on offer when well-informed evolutionists consider their stance on the EES. This overview of the multiple dimensions of debate also enables clarification of two philosophical elements of the EES debate, regarding the status of niche-construction and the role of selection in explaining adaptation. Finally, it points the way to a possible resolution of the EES debate, via a pragmatic approach to evolutionary enquiry.