We present two case studies from contemporary biology in which we observe conflicts between established and emerging approaches. The first case study discusses the relation between molecular biology and systems biology regarding the explanation of cellular processes, while the second deals with phylogenetic systematics and the challenge posed by recent network approaches to established ideas of evolutionary processes. We show that the emergence of new fields is in both cases driven by the development of high-throughput data generation technologies and the (...) transfer of modeling techniques from other fields. New and emerging views are characterized by different philosophies of nature, i.e. by different ontological and methodological assumptions and epistemic values and virtues. This results in a kind of conflict we call “epistemic competition” that manifests in two ways: On the one hand, opponents engage in mutual critique and defense of their fundamental assumptions. On the other hand, they compete for the acceptance and integration of the knowledge they provide by a broader scientific community. Despite an initial rhetoric of replacement, the views as well as the respective audiences come to be seen as more clearly distinct during the course of the debate. Hence, we observe—contrary to many other accounts of scientific change—that conflict results in the formation of new niches of research, leading to co-existence and perceived complementarity of approaches. Our model thus contributes to the understanding of the pluralization of the scientific landscape. (shrink)

The Tree of Life has traditionally been understood to represent the history of species lineages. However, recently researchers have suggested that it might be better interpreted as representing the history of cellular lineages, sometimes called the Tree of Cells. This paper examines and evaluates reasons offered against this cellular interpretation of the Tree of Life. It argues that some such reasons are bad reasons, based either on a false attribution of essentialism, on a misunderstanding of the problem of lineage identity, (...) or on a limited view of scientific representation. I suggest that debate about the Tree of Cells and other successors to the traditional Tree of Life should be formulated in terms of the purposes these representations may serve. In pursuing this strategy, we see that the Tree of Cells cannot serve one purpose suggested for it: as an explanation for the hierarchical nature of taxonomy. We then explore whether, instead, the tree may play an important role in the dynamic modeling of evolution. As highly-integrated complex systems, cells may influence which lineage components can successfully transfer into them and how they change once integrated. Only if they do in fact have a substantial role to play in this process might the Tree of Cells have some claim to be the Tree of Life. (shrink)

Ernst Mayr’s influence on philosophy of biology has given the field a particular perspective on evolution, phylogeny and life in general. Using debates about the tree of life as a guide, I show how Mayrian evolutionary biology excludes numerous forms of life and many important evolutionary processes. Hybridization and lateral gene transfer are two of these processes, and they occur frequently, with important outcomes in all domains of life. Eukaryotes appear to have a more tree-like history because successful lateral events (...) tend to occur among more closely related species, or at a lower frequency, than in prokaryotes, but this is a difference of degree rather than kind. Although the tree of life is especially problematic as a representation of the evolutionary history of prokaryotes, it can function more generally as an illustration of the limitations of a standard evolutionary perspective. Moreover, for philosophers, questions about the tree of life can be applied to the Mayrian inheritance in philosophy of biology. These questions make clear that the dichotomy of life Mayr suggested is based on too narrow a perspective. An alternative to this dichotomy is a multidimensional continuum in which different strategies of genetic exchange bestow greater adaptiveness and evolvability on prokaryotes and eukaryotes. (shrink)

The taxa that appear in biological classifications are commonly seen as representing information about the traits of their member organisms. This paper examines in what way taxa feature in the storage and retrieval of such information. I will argue that taxa do not actually store much information about the traits of their member organisms. Rather, I want to suggest, taxa should be understood as functioning to localize organisms in the genealogical network of life on Earth. Taxa store information about where (...) organisms are localized in the network, which is important background information when it comes to establishing knowledge about organismal traits, but it is not itself information about these traits. The view of species and higher taxa that is proposed here follows from examining three problems that occur in contemporary biological systematics and are discussed here: the problem of generalization over taxa, the problem of phylogenetic inference, and the problematic nature of the Tree of Life. (shrink)

Stem cells did not become a proper research object until the 1960 s. Yet the term and the basic mind-set—namely the conception of single undifferentiated cells, be they embryonic or adult, as the basic units responsible for a directed process of development, differentiation and increasing specialisation—were already in place at the end of the nineteenth century and then transmitted on a non-linear path in the form of tropes and diagrams. Ernst Haeckel and August Weismann played a special role in this (...) story. The first coined the term Stammzelle (stem cell), the second was the author of the first cellular stem-tree diagram. Even today, I shall argue, the understanding of stem cells, especially the popular perception, is to a large extent a Haeckelian–Weismannian one. After having demonstrated this, by analysing the terminology, in this essay I will focus on the use of cytogenetic tree diagrams between 1892 and 1925 and on the tacit understanding of stem cells that they transmit. (shrink)

Franz Huber’s (2008a) attempt to unify inductivist and hypothetico-deductivist intuitions on confirmation by means of a single measure are examined and compared with previous work on the theory of verisimilitude or truthlikeness. The idea of connecting ‘the logic of confirmation’ with ‘the logic of acceptability’ is also critically discussed, and it is argued that ‘acceptability’ takes necessarily into account some pragmatic criteria, and that at least two normative senses of ‘acceptability’ must be distinguished: ‘acceptable’ in the sense of ‘being allowed (...) to accept’, and ‘acceptable’ in the sense of ‘being obliged to accept’. Lastly, some connections of confirmation theory with naturalism, intertheoretic reduction, and explanation vs. understanding are explored. (shrink)

This paper investigates the complexity hypothesis in microbial evolutionary genetics from a philosophical vantage. This hypothesis, in its current version, states that genes with high connectivity are likely to be resistant to being horizontally transferred. We defend four claims. There is an important distinction between two different ways in which a gene family can persist: vertically and horizontally. There is a trade-off between these two modes of persistence, such that a gene better at achieving one will be worse at achieving (...) the other. At least some genes are likely to experience selection favoring increased transferability. One consequence of this can be encapsulated as the “simplicity hypothesis”: horizontally persisting genes will experience selection favoring reduced connectivity. In order to make sense of the simplicity hypothesis, we need to consider evolutionary populations that transcend species boundaries. Vertical and horizontal persistence are therefore not two competing ways of succeeding at the same game, but involve playing two different games altogether. The complexity hypothesis can be understood in terms of two related notions: entrenchment and Cuvierian functionalism. This framing reveals previously unrecognized and philosophically interesting connections between reasoning about deep conservation and horizontal transfer. (shrink)

En los últimos años, algunos autores han venido sosteniendo que la validez de la representación arborescente del patrón filético generado por la evolución está siendo menoscabada por el reconocimiento del impacto evolutivo que tendrían la transferencia genética horizontal, la simbiogénesis, la especiación por hibridación y la introgresión. Esa concepción o representación cladogenética de la evolución sólo nos dejaría ver un aspecto parcial de las relaciones de filiación que conectan a los diferentes linajes de seres vivos; ocultando otro aspecto cuya representación (...) más adecuada sería un reticulado de relaciones entre taxones. Con todo, aún sin poner en tela de juicio la frecuencia y la relevancia explicativa de dichos fenómenos, en este trabajo se intentará mostrar que su admisión y reconocimiento no tiene por qué ir en detrimento de esa concepción cladogenética de la evolución cuya relativización se está pregonando. Por el contrario, la comprensión y la representación de tales fenómenos supone dicha concepción. Palabras clave: Filogénesis, Especiación por hibridación, Introgresión, Simbiogénesis, TGH. (shrink)

This paper defends an ontology of weak entity realism for homeostatic property cluster (HPC) theories of natural kinds, adapted from Bird’s (Synthese 195(4):1397–1426, 2018) taxonomy of such theories. Weak entity realism about HPC kinds accepts the existence of natural kinds. Weak entity realism denies two theses: that (1) HPC kinds have mind-independent essences, and that (2) HPC kinds reduce to entities, such as complex universals, posited only by metaphysical theories. Strong entity realism accepts (1) and (2), whereas moderate entity realism (...) accepts only (1). Given its commitment to (2), strong entity realism is more theoretically complex than weak entity realism, with little explanatory payoff. Given their commitment to (1), moderate and strong entity realisms cannot explain how the identity conditions of HPC kinds are to be straightforwardly knowable. I argue that weak entity realism avoids such epistemic difficulties. I further rebut two plausible criticisms of weak entity realism, namely that weak entity realism cannot account for quantification over kinds, and that weak entity realism cannot provide identity conditions for HPC kinds which are both scientifically useful and objective. Given the theoretical costs of strong and moderate entity realism, and weak entity realism’s adequate response to its most plausible challenges, weak entity realism about HPCs is to be preferred, especially for biological and chemical kinds. (shrink)