Despite the ubiquity of “levels of organization” in the scientific literature, a nascent “levels skepticism” now claims that the concept of levels is an inherently flawed, misleading, or otherwise inadequate notion for understanding how life scientists produce knowledge about the natural world. However, levels skeptics rely on the maligned “layer-cake” account of levels stemming from Oppenheim and Putnam’s defense of the unity of science for their critical commentary. Recourse to layer-cake levels is understandable, as it is arguably the default conception (...) of levels in philosophy. However, relying on this conception of levels undermines the initial plausibility of general dismissals of the concept, because the problems skeptics identify within the “basic idea” of the concept “levels” are merely ones already widely acknowledged in this conception. I illustrate this “guilt by association” by looking at the embedded role of “levels” in articulating intertheoretical reductionism during the latter part of the 20th century. I conclude by suggesting a methodological framework focusing on local usage patterns as a promising means for future analysis of the levels concept. (shrink)

The definition of biological individuality is one of the most discussed topics in philosophy of biology, but current debate has focused almost exclusively on evolution-based accounts. Moreover, several participants in this debate consider the notions of a biological individual and an organism as equivalent. In this paper, I show that the debates would be considerably enriched and clarified if philosophers took into account two elements. First, physiological fields are crucial for the understanding of biological individuality. Second, the category of biological (...) individuals should be divided into two subcategories: physiological individuals and evolutionary individuals, which suggests that the notions of organism and biological individual should not be used interchangeably. I suggest that the combination of an evolutionary and a physiological perspective will enable biologists and philosophers to supply an account of biological individuality that will be both more comprehensive and more in accordance with scientific practices. (shrink)

The concept of levels of organization, despite its widespread scientific currency, has recently been criticized by a number of philosophers of science. This paper diagnoses the main source of problems facing theories of levels. On this basis, the problems with the usual criteria for distinguishing levels are evaluated: compositional relations, organizational types, and spatial scales. Drawing on some work on hierarchies in ecology, I argue in favor of an alternative conception of levels defined by the criterion of rates or time (...) scales of processes. (shrink)

This paper focuses on the consolidation of Molecular Evolution, a field originating in the 1960s at the interface of molecular biology, biochemistry, evolutionary biology, biophysics and studies on the origin of life and exobiology. The claim is made that Molecular Evolution became a discipline by integrating different sorts of scientific traditions: experimental, theoretical and comparative. The author critically incorporates Timothy Lenoir’s treatment of disciplines , as well as ideas developed by Stephen Toulmin on the same subject. On their account disciplines (...) are spaces where the social and epistemic dimensions of science are deeply and complexly interwoven. However, a more detailed account of discipline formation and the dynamics of an emerging disciplinary field is lacking in their analysis. The present essay suggests focusing on the role of scientific concepts in the double configuration of disciplines: the social/political and the epistemic order. In the case of Molecular Evolution the concepts of molecular clock and informational molecules played a central role, both in differentiating molecular from classical evolutionists, and in promoting communication between the different sorts of traditions integrated in Molecular Evolution. The paper finishes with a reflection on the historicity of disciplines, and the historicity of our concepts of disciplines. (shrink)

This article introduces a collection of studies of biological concepts crossing over to other disciplines and nonscholarly discourses. The introduction discusses the notion of nomadic concepts as introduced by Isabelle Stengers and explores its usability for conceptual history. Compared to traveling and interdisciplinary concepts, the idea of nomadism shifts the attention from concepts themselves toward the mobility of a concept and its effects. The metaphor of nomadism, as outlined in the introduction, helps also to question the relation between concepts' movement (...) and the production of boundaries. In this way conceptual history can profit from interaction with translation studies, where similar processes were recently discussed under the notion of cultural translation. (shrink)

The organism is neither a discovery like the circulation of the blood or the glycogenic function of the liver, nor a particular biological theory like epigenesis or preformationism. It is rather a concept which plays a series of roles – sometimes overt, sometimes masked – throughout the history of biology, and frequently in very normative ways, also shifting between the biological and the social. Indeed, it has often been presented as a key-concept in life science and the ‘theorization’ of Life, (...) but conversely has also been the target of influential rejections: as just an instrument of transmission for the selfish gene, but also, historiographically, as part of an outdated ‘vitalism’. Indeed, the organism, perhaps because it is experientially closer to the ‘body’ than to the ‘molecule’, is often the object of quasi-affective theoretical investments presenting it as essential, sometimes even as the pivot of a science or a particular approach to nature, while other approaches reject or attack it with equal force, assimilating it to a mysterious ‘vitalist’ ontology of extra-causal forces, or other pseudo-scientific doctrines. This paper does not seek to adjudicate between these debates, either in terms of scientific validity or historical coherence; nor does it return to the well-studied issue of the organism-mechanism tension in biology. Recent scholarship has begun to focus on the emergence and transformation of the concept of organism, but has not emphasized so much the way in which organism is a shifting, ‘go-between’ concept – invoked as ‘natural’ by some thinkers to justify their metaphysics, but then presented as value-laden by others, over and against the natural world. The organism as go-between concept is also a hybrid, a boundary concept or an epistemic limit case, all of which partly overlap with the idea of ‘nomadic concepts’. Thereby the concept of organism continues to function in different contexts – as a heuristic, an explanatory challenge, a model of order, of regulation, etc. – despite having frequently been pronounced irrelevant and reduced to molecules or genes. Yet this perpetuation is far removed from any ‘metaphysics of organism’, or organismic biology. (shrink)

The idea of levels of organization plays a central role in the philosophy of the life sciences. In this article, I first examine the explanatory goals that have motivated accounts of levels of organization. I then show that the most state-of-the-art and scientifically plausible account of levels of organization, the account of levels of mechanism proposed by Bechtel and Craver, is fundamentally problematic. Finally, I argue that the explanatory goals can be reached by adopting a deflationary approach, where levels of (...) organization give way to more well-defined and fundamental notions, such as scale and composition. (shrink)

I show that the recent account of levels in neuroscience proposed by Craver and Bechtel is unsatisfactory since it fails to provide a plausible criterion for being at the same level and is incompatible with Craver and Bechtel’s account of downward causation. Furthermore, I argue that no distinct notion of levels is needed for analyzing explanations and causal issues in neuroscience: it is better to rely on more well-defined notions such as composition and scale. One outcome of this is that (...) apparent cases of downward causation can be analyzed away. (shrink)

The concept of hierarchical organization is commonplace in science. Subatomic particles compose atoms, which compose molecules; cells compose tissues, which compose organs, which compose organisms; etc. Hierarchical organization is particularly prominent in ecology, a field of research explicitly arranged around levels of ecological organization. The concept of levels of organization is also central to a variety of debates in philosophy of science. Yet many difficulties plague the concept of discrete hierarchical levels. In this paper, we show how these difficulties undermine (...) various implications ascribed to hierarchical organization, and we suggest the concept of scale as a promising alternative to levels. Investigating causal processes at different scales offers a way to retain a notion of quasi-levels that avoids the difficulties inherent in the classic concept of hierarchical levels of organization. Throughout, our focus is on ecology, but the results generalize to other invocations of hierarchy in science and philosophy of science. (shrink)

I defend a view of the species category, pluralistic realism, which is designed to do justice to the insights of many different groups of systematists. After arguing that species are sets and not individuals, I proceed to outline briefly some defects of the biological species concept. I draw the general moral that similar shortcomings arise for other popular views of the nature of species. These shortcomings arise because the legitimate interests of biology are diverse, and these diverse interests are reflected (...) in different legitimate approaches to the classification of organisms. In the final section, I show briefly how the pluralistic approach can help to illuminate some areas of biological and philosophical dispute. (shrink)

We outline three very different concepts of the gene—instrumental, nominal, and postgenomic. The instrumental gene has a critical role in the construction and interpretation of experiments in which the relationship between genotype and phenotype is explored via hybridization between organisms or directly between nucleic acid molecules. It also plays an important theoretical role in the foundations of disciplines such as quantitative genetics and population genetics. The nominal gene is a critical practical tool, allowing stable communication between bioscientists in a wide (...) range of fields grounded in well-defined sequences of nucleotides, but this concept does not embody major theoretical insights into genome structure or function. The post-genomic gene embodies the continuing project of understanding how genome structure supports genome function, but with a deflationary picture of the gene as a structural unit. This final concept of the gene poses a significant challenge to conventional assumptions about the relationship between genome structure and function, and between genotype and phenotype. (shrink)

This paper takes up the cause of species pluralism. An argument for species pluralism is provided and standard monist objections to pluralism are answered. A new form of species pluralism is developed and shown to be an improvement over previous forms. This paper also offers a general foundation on which to base a pluralistic approach to biological classification.

By what mechanisms of organizational and institutional change do different specialties succeed in accommodating and working with one another? How do these mechanisms function over time to support and retard the emergence and stability of new knowledge? This paper considers two such mechanisms, metawork and common knowledge. These mechanisms integrate specialties by making the activities of multiple specialties dependent upon one another, and by segmenting the common effort from the parent specialties. Integration of specialties can lead to the development of (...) new specialties.Integration is facilitated and impeded by the anchoring of specialties in the system of institutions that participate in research. Host organizations, degree programs, sponsors, associations, regulators, and other organizations provide resources and impose demands that shape research. Some of these impacts are obvious and direct; others are indirect and more subtle.The research specialties form a network in which connections constantly form and reform, and in which the influence of different anchoring institutions are constantly waxing and waning. The complexity of connections and their pattern of change are especially obvious in the life sciences, which are an especially good place to study problems of integration. (shrink)

The concept of 'levels of organization' has come under fire recently as being useless for scientific and philosophical purposes. In this paper, we show that 'levels' is actually a remarkably resilient and constructive conceptual tool that can be, and in fact is, used for a variety of purposes. To this effect, we articulate an account of the importance of the levels concept seen in light of its status as a major organizing concept of biology. We argue that the usefulness of (...) ‘levels’ is best seen in the heuristic contributions the concept makes to treating and structuring scientific problems. We illustrate this with two examples from biological research. (shrink)

No comprehensive theory of development is available yet. Traditionally, we regard the development of animals as a sequence of changes through which an adult multicellular animal is produced, starting from a single cell which is usually a fertilized egg, through increasingly complex stages. However, many phenomena that would not qualify as developmental according to these criteria would nevertheless qualify as developmental in that they imply nontrivial (e.g., non degenerative) changes of form, and/or substantial changes in gene expression. A broad, comparative (...) approach is badly needed. In the Cnidaria, for example, even the boundary between generations is problematic. Describing their life cycle in terms of metagenesis (alternation between polyp generation and medusa generation) or in terms of metamorphosis (polyp as larva or juvenile) are matters of semantics more than biology. The life cycle of other metazoans, described in textbooks in terms of larva-to-adult metamorphosis, is hardly different from a typical metagenetic life cycle of cnidarians. This applies to holometabolous insects and to marine invertebrates like sea urchins, where most of the larval cells are discarded at metamorphosis. The uncertain temporal and spatial boundaries of individual development are also shown by the widespread lack of a strict correspondence between adult and mature. A comprehensive theory of development should start with a zero principle of “developmental inertia,” corresponding to an indeterminate local self-perpetuation of cell-level dynamics. Indeterminate growth, scale-invariance, segmentation, and regeneration provide examples of developmental dynamics close to that. (shrink)

The paper works towards an account of explanatory integration in biology, using as a case study explanations of the evolutionary origin of novelties-a problem requiring the integration of several biological fields and approaches. In contrast to the idea that fields studying lower level phenomena are always more fundamental in explanations, I argue that the particular combination of disciplines and theoretical approaches needed to address a complex biological problem and which among them is explanatorily more fundamental varies with the problem pursued. (...) Solving a complex problem need not require theoretical unification or the stable synthesis of different biological fields, as items of knowledge from traditional disciplines can be related solely for the purposes of a specific problem. Apart from the development of genuine interfield theories, successful integration can be effected by smaller epistemic units (concepts, methods, explanations) being linked. Unification or integration is not an aim in itself, but needed for the aim of solving a particular scientific problem, where the problem's nature determines the kind of intellectual integration required. (shrink)

Despite its pervasiveness, the concept of ‘levels of organization’ has received relatively little attention in its own right. I propose here an emerging approach that posits ‘levels’ as a fragmentary concept situated within an interest-relative matrix of operational usage within scientific practice. To this end I propose one important component of meaning, namely the epistemic goal motivating the term’s usage, which recovers a remarkably conserved and sufficiently unifying significance attributable to ‘levels’ across different instances of usage. This epistemic goal, to (...) provide structure to scientific problems, delegates tasks whose execution generates the term’s expressed content in a given instance. This treatment of levels does not diminish the concept’s general importance to science, but rather allows for its use in, and usefulness for, scientific practice to be better contextualized to particular tasks encompassing varying breadths of activity. (shrink)

The organism is neither a discovery like the circulation of the blood or the glycogenic function of the liver, nor a particular biological theory like epigenesis or preformationism. It is rather a concept which plays a series of roles, sometimes masked, often normative, throughout the history of biology. Indeed, it has often been presented as a key-concept in life science and its ‘theorization’, but conversely has also been the target of influential rejections: as just an instrument of transmission for the (...) selfish gene, but also, historiographically, as part of an outdated ‘vitalism’. Indeed, the organism, perhaps because it is experientially closer to the ‘body’ than to the ‘molecule’, is often the object of quasi-affective theoretical investments presenting it as essential, as the pivot of a science or a particular approach to nature, while other approaches reject or attack it with equal force, assimilating it to a mysterious ‘vitalist’ ontology of extra-causal forces, or other pseudo-scientific doctrines. I do not seek to adjudicate between these debates, either regarding scientific validity or historical coherence; nor do I return to the well-studied issue of the organism-mechanism tension in biology. Recent scholarship has begun to discuss the emergence and transformation of the organism concept, but has not emphasized the way the latter is a shifting, ‘go-between’ concept – invoked as ‘natural’ by some thinkers to justify their metaphysics, but then presented as value-laden by others, over and against the natural world. The organism as go-between concept is also a hybrid, a boundary concept or a limit case, which continues to function in different contexts – as a heuristic, an explanatory challenge, a model of order, of regulation, etc. – despite having frequently been pronounced irrelevant and reduced to molecules or genes. Yet this perpetuation is far removed from any ‘metaphysics of organism’, or organismic biology. (shrink)

Many aspects of biology, such as population genetics and senescence, are predicated on identifying individuals and generations. Conventional demarcations of individuals and generations, such as physiological autonomy, unicellular bottlenecks, and alternation of generation, are rife with problems. Do physically separated cuttings or plant ramets constitute separate individuals or generations? Are chimaeras one or more individuals? To resolve these problems, Clarke : 321–361, 2012) proposed that individuals are circumscribed by mechanisms that constrain heritable variance in fitness. Simultaneously, Gorelick and Heng : (...) 1088–1098 2011) showed that sex constrains heritable variance Therefore, for eukaryotes, meiosis and karyogamy provide a consistent way to demarcate individuals and generations. Epigenetic reset associated with meiosis and karyogamy rejuvenates the next generation, but not the parent that engaged in the sex act. Wholesale epigenetic resets that probably only occur with meiosis and karyogamy imply that monozygotic twins are two different individuals, but apomictic progeny are diffuse parts of one disaggregated individual. Mitotic heritability circumscribes an individual, whereas meiotic heritability demarcates new individuals and generations. (shrink)

A un secolo e mezzo dalla pubblicazione dell'Origine delle specie, la nozione di omologia di Owen, che implica che due organi o due funzioni a confronto possono essere riconosciuti come “la stessa cosa” continua a dominare gli attuali approcci al problema dell’omologia. L'idea che i caratteri possano “rimanere se stessi” attraverso un numero indefinito (anche se finito) di stati alternativi che si susseguono nel corso dell'evoluzione è probabilmente basato su un'interpretazione idealistica di come gli organismi si evolvono. Se si dà (...) per scontata l'esistenza di caratteristiche del corpo che conservano la loro identità nel cambiamento, l'esistenza di omologhi può essere spiegata (i) in termini di leggi universali della forma, magari nella forma moderna dello strutturalismo di processo, o (ii) come il prodotto di discendenza comune, o (iii) in termini di cause prossime responsabili della comparsa di moduli di sviluppo conservati. Tuttavia, leggendo la storia della vita attraverso la lente dell’evoluzione, appare molto problematico descrivere un organismo come una somma di caratteri che, una volta apparsi come novità evolutive, rimangono poi come unità costruttive essenzialmente immutabili tra le quali possiamo predicare (o negare) omologia. Tutti i tratti sono meglio interpretati come incroci complessi e mutevoli di un numero indeterminato di elementi e dei processi che li modellano nel corso dell’ontogenesi e della filogenesi. Di conseguenza, appare raccomandabile un approccio fattoriale, o combinatorio, all’omologia. (shrink)

When the history of life on earth is viewed as a history of cell division, all of life becomes a single cell lineage. The growth and differentiation of this lineage in reciprocal interaction with its environment can be viewed as a developmental process; hence the evolution of life on earth can also be seen as the development of life on earth. Here, in reviewing this field, some potentially fruitful research directions suggested by this change in perspective are highlighted. Variation and (...) selection become, for example, bidirectional information flows between scales, while the notions of “cooperation” and “competition” become scale relative. The language of communication, inference, and information processing becomes more useful than the language of causation to describe the interactions of both homogeneous and heterogeneous living systems at any scale. Emerging scale‐free theoretical frameworks such as predictive coding and active inference provide conceptual tools for reconceptualizing biology as the study of a unified, multiscale dynamical system. (shrink)

Contrary to the traditional claim that needs for unambiguous communication about animal and plant species are best served by a single set of names ruled by international Codes, I suggest that a more diversified system is required, especially to cope with problems emerging from aggregation of biodiversity data in large databases. Departures from Linnaean nomenclature are sometimes intentional, but there are also other, less obvious but widespread forms of not Code-compliant grey nomenclature. A first problem is due to the circumstance (...) that the Codes are intended to rule over the way names are applied to species and other taxonomic units, whereas users of taxonomy need names to be applied to specimens. For different reasons, it is often impossible to refer a specimen with certainty to a named species, and in those cases an open nomenclature is employed. Second, molecular taxonomy leads to the discovery of clusters of gene sequence diversity not necessarily equivalent to the species recognized and named by taxonomists. Those clusters are mostly indicated with informal names or formulas that challenge comparison between different publications or databases. In several instances, it is not even clear if a formula refers to an individual voucher specimen, or is a provisional species name. The use of non-Linnaean names and formulas must be revised and strengthened by fixing standard formats for the different kinds of objects or hypotheses and providing permanent association of ‘grey names’ with standardized source information such as author and year. In the context of a broad-scope revisitation of aims and scope of scientific nomenclature, it may be worth rethinking if natural objects like plant galls and lichens, although other than the ‘single-entity’ objects traditionally covered by biological classifications, may nevertheless deserve taxonomic names. (shrink)

Moderate pluralism is a popular position in contemporary philosophy of biology. Despite its popularity, various authors have argued that it tends to slide off off into a radical form of pluralism that is both normatively and descriptively ueptable. This paper looks at at the case of biological species classification, and evaluates a popular way of avoiding radical pluralism by relying on the shared aims and norms of a discipline. The main contention is that while these aims and norms may play (...) an important role in the legitimacy of species classifications, they fail to fend off radical pluralism. It follows from this that the legitimacy of species classifications is also determined by local decisions about the aims of research and how to operationalize and balance these. This is important, I argue, because it means that any acceptable view on the legitimacy of classification should be able to account for these local decisions. (shrink)

This chapter contains sections titled: Introduction A Brief History of Developmental Explanations of Phenotypic Evolution Research Questions of Evo‐Devo Unifying Themes of the Conceptual Basis of Evo‐Devo Conclusion: A Mechanistic Theory of Evo‐Devo Challenges the Modern Synthesis Postscript: Counterpoint References.