This paper attempts to elucidate three characteristics of causal relationships that are important in biological contexts. Stability has to do with whether a causal relationship continues to hold under changes in background conditions. Proportionality has to do with whether changes in the state of the cause “line up” in the right way with changes in the state of the effect and with whether the cause and effect are characterized in a way that contains irrelevant detail. Specificity is connected both to (...) David Lewis’ notion of “influence” and also with the extent to which a causal relation approximates to the ideal of one cause–one effect. Interrelations among these notions and their possible biological significance are also discussed. (shrink)

Ernst Mayr has argued that Darwinian theory discredited essentialist modes of thought and replaced them with what he has called "population thinking". In this paper, I characterize essentialism as embodying a certain conception of how variation in nature is to be explained, and show how this conception was undermined by evolutionary theory. The Darwinian doctrine of evolutionary gradualism makes it impossible to say exactly where one species ends and another begins; such line-drawing problems are often taken to be the decisive (...) reason for thinking that essentialism is untenable. However, according to the view of essentialism I suggest, this familiar objection is not fatal to essentialism. It is rather the essentialist's use of what I call the natural state model for explaining variation which clashes with evolutionary theory. This model implemented the essentialist's requirement that properties of populations be defined in terms of properties of member organisms. Requiring such constituent definitions is reductionistic in spirit; additionally, evolutionary theory shows that such definitions are not available, and, moreover, that they are not needed to legitimize population-level concepts. Population thinking involves the thesis that population concepts may be legitimized by showing their connections with each other, even when they are not reducible to concepts applying at lower levels of organization. In the paper, I develop these points by describing Aristotle's ideas on the origins of biological variation; they are a classic formulation of the natural state model. I also describe how the development of statistical ideas in the 19th century involved an abandoning of the natural state model. (shrink)

This paper aims to identify the key characteristics of model organisms that make them a specific type of model within the contemporary life sciences: in particular, we argue that the term “model organism” does not apply to all organisms used for the purposes of experimental research. We explore the differences between experimental and model organisms in terms of their material and epistemic features, and argue that it is essential to distinguish between their representational scope and representational target. We also examine (...) the characteristics of the communities who use these two types of models, including their research goals, disciplinary affiliations, and preferred practices to show how these have contributed to the conceptualization of a model organism. We conclude that model organisms are a specific subgroup of organisms that have been standardized to fit an integrative and comparative mode of research, and that it must be clearly distinguished from the broader class of experimental organisms. In addition, we argue that model organisms are the key components of a unique and distinctively biological way of doing research using models.Keywords: Experimental organism; Genetics; Model organism; Modeling; Philosophy of biology; Representation. (shrink)

The practical criteria by which developmental biologists choose their model systems have evolutionary correlates. The result is a sample that is not merely small, but biased in particular ways, for example towards species with rapid, highly canalized development. These biases influence both data collection and interpretation, and our views of how development works and which aspects of it are important.

The biological sciences employ a concept of normality that must be distinguished from statistical or value concepts. The concept of normality is presupposed in the standard explications of biological functions, and it is crucial to the strategy of explanation by approximations in, for example, physiology. Nevertheless, this concept of normality does not seem to be captured in the language of physics. Thus attempts at explaining the methodological relationship between the biological sciences and the physical sciences by concentrating only on the (...) concept of biological function cannot go very far. An analysis of the concept of normality is also necessary. (shrink)

The biological sciences have become increasingly reliant on so-called 'model organisms'. I argue that in this domain, the concept of a descriptive model is essential for understanding scientific practice. Using a case study, I show how such a model was formulated in a preexplanatory context for subsequent use as a prototype from which explanations ultimately may be generated both within the immediate domain of the original model and in additional, related domains. To develop this concept of a descriptive model, I (...) focus on use of the nematode worm Caenorhabditis elegans and the wiring diagrams that were developed as models of its neural structure. In addition, implications of the concept of a descriptive model, particularly its relevance for the data-phenomena distinction as well as its relation to long-standing debates on realism, are briefly examined. (shrink)

What is the best way to analyse abstraction in scientific modelling? I propose to focus on abstracting as an epistemic activity, which is achieved in different ways and for different purposes depending on the actual circumstances of modelling and the features of the models in question. This is in contrast to a more conventional use of the term ‘abstract’ as an attribute of models, which I characterise as black-boxing the ways in which abstraction is performed and to which epistemological advantage. (...) I exemplify my claims through a detailed reconstruction of the practices involved in creating two types of models of the flowering plant Arabidopsisthaliana, currently the best-known model organism in plant biology. This leads me to distinguish between two types of abstraction processes: the ‘material abstracting’ required in the production of Arabidopsis specimens and the ‘intellectual abstracting’ characterising the elaboration of visual models of Arabidopsis genomics. Reflecting on the differences between these types of abstracting helps to pin down the epistemic skills and research commitments used by researchers to produce each model, thus clarifying how models are handled by researchers and with which epistemological implications. (shrink)

The ArgumentThis paper argues that different epistemic styles exist in science, and that these make up an important unit of analysis for studying science. On occasion these different sets of commitments to ways of doing and knowing about the world may fall along national boundaries. The case presented here examines German and American embryology around 1900 and shows that differences in goals and approaches make up different epistemic styles.In particular, the Germans sought causal mechanical explanations of as many phenomena as (...) possible, guided by strong theories which achieved confirmation when they fit with as much of the available data as possible. The Americans, in contrast, sought definitive facts, as many as possible, which might be quite specific or narrowly based. These facts could lead to empirical generalizations which, in turn, could guide the generation of new knowledge in the form of new facts. Thus, the two epistemic styles emphasized different goals, processes of investigation, and standards of evidence. (shrink)

Idealization is a reasoning strategy that biologists use to describe, model and explain that purposefully departs from features known to be present in nature. Similar to other strategies of scientific reasoning, idealization combines distinctive strengths alongside of latent weaknesses. The study of ontogeny in model organisms is usually executed by establishing a set of normal stages for embryonic development, which enables researchers in different laboratory contexts to have standardized comparisons of experimental results. Normal stages are a form of idealization because (...) they intentionally ignore known variation in development, including variation associated with phenotypic plasticity (e.g. via strict control of environmental variables). This is a tension between the phenomenon of plasticity and the practice of staging that has consequences for evolutionary developmental investigation because variation is conceptually removed as a part of rendering model organisms experimentally tractable. Two compensatory tactics for mitigating these consequences are discussed: employing a diversity of model organisms and adopting alternative periodizations. (shrink)

ZusammenfassungTrotz seiner großen Verbreitung in den Lebenswissenschaften wurde dem Aquarium bisher wenig wissenschafts- und technikhistorische Aufmerksamkeit zuteil. Dies ist nicht zuletzt durch den Umstand begründet, dass das Aquarium und seine Geschichte bisher größtenteils als außerwissenschaftlich aufgefasst wurden. Dabei spielen so unterschiedliche Kontexte wie Akklimatisierung, Amateurnaturkunde und bürgerliche Populärkultur eine wichtige Rolle. Gleichzeitig ist die Entwicklung des Aquariums aber auch eng mit der Geschichte der Lebenswissenschaften verbunden. Mit Blick auf die zweite Hälfte des 19. Jahrhunderts verstehe ich das Aquarium als techno-natural (...) assemblage, in der Technologie, Kultur und Natur zu einem künstlichen Naturraum verbunden sind. Seine Geschichte beginnt in der britischen Amateurnaturkunde und der französischen Akklimatisierungsbewegung. Im Deutschland des späten 19. Jahrhunderts entwickelte sich das Aquarium zu einem Massenphänomen. Gleichzeitig hielt es Einzug in die Lebenswissenschaften, wo es als Einfallstor, Instrument und Umwelt Verwendung fand. Wie sich zeigt, ist das Aquarium eine hochgradig konstruierte Technologie, die sich aus einer Verbindung unterschiedlicher Traditionen herausgebildet und das Leben in die Lebenswissenschaften gebracht hat. (shrink)

Diagrams make it possible to present scientific facts in more abstract and generalized form. While some detail is lost, simplified and accessible knowledge is gained. E. B. Wilson's work in cytology provides a case study of changing uses of diagrams and accompanying abstraction. In his early work, Wilson presented his data in photographs, which he saw as coming closest to “fact.” As he gained confidence in his interpretations, and as he sought to provide a generalized textbook account of cell development, (...) he relied on increasingly abstract diagrams. In addition, he came to see that highly abstract and even schematic drawings could provide more than pictures directly from life. (shrink)

Model organisms became an indispensable part of experimental systems in molecular developmental and cell biology, constructed to investigate physiological and pathological processes. They are thought to play a crucial role for the elucidation of gene function, complementing the sequencing of the genomes of humans and other organisms. Accordingly, historians and philosophers paid considerable attention to various issues concerning this aspect of experimental biology. With respect to the representational features of model organisms, that is, their status as models, the main focus (...) was on generalization of phenomena investigated in such experimental systems. Model organisms have been said to be models for other organisms or a higher taxon. This, however, presupposes a representation of the phenomenon in question. I will argue that prior to generalization, model organisms allow researchers to built generative material models of phenomena – structures, processes or the mechanisms that explain them – through their integration in experimental set-ups that carve out the phenomena from the whole organism and thus represent them. I will use the history of zebrafish biology to show how model organism systems, from around 1970 on, were developed to construct material models of molecular mechanisms explaining developmental or physiological processes. (shrink)

Anton Dohrn rejected the popular Amphioxus-ascidian theory of vertebrate origin, which saw Amphioxus as the most primitive vertebrate and ascidians as vertebrate ancestors. Instead he argued for the segmented annelids as the more likely candidate. Attacked for being 'unscientific' by such popular morphologists as Carl Gegenbaur and Ernst Haeckel, Dohrn countered with similar accusations. Since the debate peaked as Dohrn was establishing his Stazione Zoologica in Naples at the end of the nineteenth century, it gained him valuable attention and may (...) have encouraged him to retain his view even in the face of new and problematic evidence. This paper explores Dohrn's contributions and the underlying commitments revealing what he regarded as important in science. (shrink)

This article unpacks a particular use of ‘cases’ within developmental biology, namely as a means of describing the typical or canonical patterns of phenomena. The article explores how certain cases have come to be established within the field and argues that although they were initially selected for reasons of convenience or ease of experimental manipulation, these cases come to serve as key reference points within the field because of the epistemological structures imposed on them by the scientists using them and, (...) hence, become usable in a wider variety of circumstances including future theory development. (shrink)

This paper aims to clarify the consequences of new scientific and philosophical approaches for the practical-theoretical framework of modern developmental biology. I highlight normal development, and the instructive-permissive distinction, as key parts of this framework which shape how variation is conceptualised and managed. Furthermore, I establish the different dimensions of biological variation: the units, temporality and mode of variation. Using the analytical frame established by this, I interpret a selection of examples as challenges to the instructive-permissive distinction. These examples include (...) the phenomena of developmental plasticity and transdifferentiation, the role of the microbiome in development, and new methodological approaches to standardisation and the assessment of causes. Furthermore, I argue that investigations into organismal development should investigate the effects of a wider range of kinds of variation including variation in the units, modes and temporalities of development. I close by examining various possible opportunities for producing and using normal development free of the assumptions of the instructive-permissive distinction. These opportunities are afforded by recent developments, which include new ways of producing standards incorporating more natural variation and being based on function rather than structure, and the ability to produce, store, and process large quantities of data. (shrink)

By 1900 most biologists accepted experimentation as appropriate for at least parts of biology. Some claimed experimentation as the best or only proper approach to biology, while others regarded it as an acceptable addition to existing methodologies. Different researchers defined experimentation in different ways, and they held different aspirations for their experimental programs. This paper explores three sets of ideas, represented respectively by the French in the 1870s, the Germans in the 1880s, and the Americans in the 1890s. It examines (...) what an experiment was thought to be, what experimentation was, and what the goals of experimentation were for each group, revealing suggestive differences. (shrink)

Edmund Beecher Wilson is generally celebrated for his contribution to chromosome theory and genetics, whereas opinion concerning his cytological thinking is often restricted to the idea that he provided evidence for the dominant role of the nucleus. But Wilson's cell theory was much more. It was a child of the German Zellforschung, and its attempt to provide a comprehensive cellular answer to a wide range of biological and physiological questions. Wilson developed a corpuscular, micromeristic and preformistic concept, and treated the (...) cell as an organism subject to ontogenetic and phylogenetic processes. He defended his comprehensive theory even in the 1920's, when cytological research had become specialised and directed at more practical goals. For many of his younger readers this concept might have seemed antiquated, but today many of its features sound surprisingly modern. (shrink)

After 1900, the selective breeding of a few standard animals for research in the life sciences changed the way science was done. Among the pervasive changes was a transformation in scientists' assumptions about relationship between diversity and generality. Examination of the contents of two prominent physiology journals between 1885 and 1900, reveals that scientists used a diverse array of organisms in empirical research. Experimental physiologists gave many reasons for the choice of test animals, some practical and others truly comparative. But, (...) despite strong philosophical differences in the approaches they represented, the view that it was best to incorporate as many species as possible into research on physiological processes was widespread in both periodicals. Authors aimed for generality, but they treated it as a conclusion that would or would not follow from the examination of many species. After 1900, an increasing emphasis on standardization, the growth of the experimental method and the growing industrialization of the life sciences led to a decline in the number of species used in research. In this context, the selective breeding of animals for science facilitated a change in assumptions about the relationship between generality and diversity. As animals were increasingly viewed as things that were assumed to be fundamentally similar, scientific generality became an a priori assumption rather than an empirical conclusion. (shrink)

In America by the 1930s, albino rats had become a kind of generic standard in research on physiology and behavior that de-emphasized diversity across species. However, prior to about 1915, the early work of many of the pioneer rat researchers in America and in central Europe reflected a strong interest in species differences and a deep regard for diversity. These scientists sought broad, often medical, generality, but their quest for generality using a standard animal did not entail a de-emphasis of (...) organic diversity. They chose white rats as test animals for two primary reasons. First, rats develop very slowly. They therefore made features of physiological, neural and psychological development accessible to the experimental method at a time when its application to the phenomena of development remained controversial. Secondly, rats were thought to have unusually strong sex drives. For this reason they became central to the experimental study of sexuality and, in the work of the reproductive physiologist Eugen Steinach, sexual development. Connections among three research institutes that stressed experimental approaches to the study of brain and development demonstrate the importance of the rat's institutional role. As the emphasis on experimentation in the study of development grew, two of these institutes bred rats to provide uniform materials. Eventually, however, their reasons for selecting rats were lost; and the ready availability of a uniform test animal led to a shift in scientists' presumptions about diversity, as the standard rat became a tool for assuring generality. (shrink)

Biologists having rediscovered amphioxus, also known as the lancelet or Branchiostoma, it is time to reassess its place in early Darwinist debates over vertebrate origins. While the advent of the ascidian–amphioxus theory and challenges from various competitors have been documented, this article offers a richer account of the public appeal of amphioxus as a primitive ancestor. The focus is on how the ‘German Darwin’ Ernst Haeckel persuaded general magazine and newspaper readers to revere this “flesh of our flesh and blood (...) of our blood”, and especially on Das neue Laienbrevier des Haeckelismus (The new lay breviary of Haeckelism) by Moritz Reymond with cartoons by Fritz Steub. From the late 1870s these successful little books of verse introduced the Neapolitan discoveries that made the animal’s name and satirized Haeckel’s rise as high priest of its cult. One song is reproduced and translated here, with a contemporary “imitation” by the Canadian palaeontologist Edward John Chapman, and extracts from others. Predating the American “It’s a long way from amphioxus” by decades, these rhymes dramatize neglected ‘species politics’ of Darwinism and highlight the roles of humour in negotiating evolution. (shrink)

American biologists in the late nineteenth century pioneered the descriptive-comparative study of all cell divisions from zygote to gastrulation -- the cell lineage. Data from cell lineages were crucial to evolutionary and developmental questions of the day. One of the main questions was the ultimate causation of developmental patterns -- historical or mechanical. E. B. Wilson's groundbreaking lineage work on the polychaete worm Nereis in 1892 set the stage for (1) an attack on Haeckel's phylogenetic-historical notion of recapitulation and (2) (...) support for mechanistic explanations of cleavage patterns. As more lineage work -- especially Lillie's work on "Unio" and Conklin's on "Crepidula" -- became available in the mid-late 1890s, mechanism was tempered with more evolutionary, homology-based views. However, as I show by focusing on three major issues -- homology, body plans and life history -- these views were primarily based on the precocious segregation and prospective significance -- what the cell became not what it was. Even on issues like adaptation, most lineagists argued teleologically from the adult backward. Most cell lineage workers, by 1900, were to varying degrees mechanist/experimentalist and recapitulationist simultaneously. The exception was E. G. Conklin, whose views were more akin to a Darwinian evolutionist than either mechanist or recapitulationist. Lineage work eventually declined and by 1907 published accounts of new lineages had basically stopped. I argue that established workers and younger researchers stopped wanting to take on cell lineage projects because the general patterns were the same for all the spiralians while the specifics showed too much variation. It was hard to theoretically encompass or analyze the minutiae of variation in a recapitulationist or mechanist framework. The only established worker who continued to do comparative lineage studies was E. G. Conklin, perhaps because the variation could best be accommodated by Darwinian evolution. (shrink)