Concepts of an organism’s biological environment and of niche construction as how organisms alter their environment and that of other organisms now play prominent roles in multiple sub-fields of biology, including ecology, evolution, and development. Some philosophers now use these concepts to understand the dynamics of scientific research. Others note divergences among the concepts of niche and niche construction employed in these biological fields, with implications for their possible conceptual integration. My (Rouse, 2015) account of scientific research as niche constructive (...) and of laws and lawful invariance in scientific practice illuminates these conceptual differences and their implications for integrating those domains of biological research in two ways. First, it accounts for the partial autonomy of these domains and their concepts as characteristic of scientific conceptual development. Second, it provides a more complex understanding of how research domains can be integrated, which shows how those different conceptions of niches and niche construction do not block their appropriate integration. The conclusion situates my account and its application to niche concepts both amid other philosophical uses of niche concepts to understand research environments and as exemplifying my revisionist conception of philosophical naturalism. (shrink)

Model organisms are a living form of scientific models. Despite the widespread use of model organisms in scientific research, the actual representational relationship between model organisms and their target species is often poorly characterized in the context of cross-species research. Many model organisms do not represent the target species adequately, let alone accurately. This is partly due to the complex and emergent life phenomena in the organism, and partly due to the fact that a model organism is always taken to (...) represent a broad range of diverse organisms. More often than not, model organisms are taken as a reference point for an extrapolation to be made to the unknown characteristics of other species. I propose to view model organisms as analogue simulators which represent the emergent phenomenon in the context of cross-species research. A model organism represents a wide range of species by simulating their molecular microstates which underlie various emergent phenomena. I show that although model organisms represent the target species inadequately at many levels of complexity, they have epistemic values as a simulator in virtue of which the emergent phenomenon can be modeled dynamically, a virtue that is hardly attainable by non-dynamic models. (shrink)

The traditional practice of establishing morphological types and investigating morphological organization has found new support from evolutionary developmental biology (evo-devo), especially with respect to the notion of body plans. Despite recurring claims that typology is at odds with evolutionary thinking, evo-devo offers mechanistic explanations of the evolutionary origin, transformation, and evolvability of morphological organization. In parallel, philosophers have developed non-essentialist conceptions of natural kinds that permit kinds to exhibit variation and undergo change. This not only facilitates a construal of species (...) and higher taxa as natural kinds, but also broadens our perspective on the diversity of kinds found in biology. There are many different natural kinds relevant to the investigative and explanatory aims of evo-devo, including homologues and developmental modules. (shrink)

The 1981 Dahlem conference was a catalyst for contemporary evolutionary developmental biology (Evo-devo). This introductory chapter rehearses some of the details of the history surrounding the original conference and its associated edited volume, explicates the philosophical problem of conceptual change that provided the rationale for a workshop devoted to evaluating the epistemic revisions and transformations that occurred in the interim, explores conceptual change with respect to the concept of evolutionary novelty, and highlights some of the themes and patterns in the (...) different contributions to the present volume, Conceptual Change in Biology: Scientific and Philosophical Perspectives on Evolution and Development. (shrink)

Many biological investigations are organized around a small group of species, often referred to as ‘model organisms’, such as the fruit fly Drosophila melanogaster. The terms ‘model’ and ‘modelling’ also occur in biology in association with mathematical and mechanistic theorizing, as in the Lotka–Volterra model of predator-prey dynamics. What is the relation between theoretical models and model organisms? Are these models in the same sense? We offer an account on which the two practices are shown to have different epistemic characters. (...) Theoretical modelling is grounded in explicit and known analogies between model and target. By contrast, inferences from model organisms are empirical extrapolations. Often such extrapolation is based on shared ancestry, sometimes in conjunction with other empirical information. One implication is that such inferences are unique to biology, whereas theoretical models are common across many disciplines. We close by discussing the diversity of uses to which model organisms are put, suggesting how these relate to our overall account. 1 Introduction2 Volterra and Theoretical Modelling3 Drosophila as a Model Organism4 Generalizing from Work on Model Organisms5 Phylogenetic Inference and Model Organisms6 Further Roles of Model Organisms6.1 Preparative experimentation6.2 Model organisms as paradigms6.3 Model organisms as theoretical models6.4 Inspiration for engineers6.5 Anchoring a research community7 Conclusion. (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)

Attention to scientific practice offers a novel response to philosophical queries about how conceptual understanding is empirically accountable. The locus of the issue is thereby shifted, from perceptual experience to experimental and fieldwork interactions. More important, conceptual articulation is shown to be not merely ?spontaneous? and intralinguistic, but instead involves a establishing a systematic domain of experimental operations. The importance of experimental practice for conceptual understanding is especially clearly illustrated by cases in which entire domains of scientific investigation were first (...) made accessible to articulated conceptual understanding. We thereby see more clearly how experimental systems themselves, and not merely the theories and models they make possible, have an intentional directedness and ?representational? import. (shrink)

In 2015 scientists called for a partial ban on genome editing in human germline cells. This call was a response to the rapid development of the CRISPR–Cas9 system, a molecular tool that allows researchers to modify genomic DNA in living organisms with high precision and ease of use. Importantly, the ban was meant to be a trust-building exercise that promises a ‘prudent’ way forward. The goal of this paper is to analyse whether the ban can deliver on this promise. To (...) do so the focus will be put on the precedent on which the current ban is modelled, namely the Asilomar ban on recombinant DNA technology. The analysis of this case will show (a) that the Asilomar ban was successful because of a specific two-step containment strategy it employed and (b) that this two-step approach is also key to making the current ban work. It will be argued, however, that the Asilomar strategy cannot be transferred to human genome editing and that the current ban therefore fails to deliver on its promise. The paper will close with a reflection on the reasons for this failure and on what can be learned from it about the regulation of novel molecular tools. (shrink)

Advances in research on human cerebral organoids (HCOs) call for a critical review of current research policies. A challenge for the evaluation of necessary research regulations lies in the severe uncertainty about future trajectories the currently very rudimentary stages of neural cell cultures might take as the technology progresses. To gain insights into organotypic cultures, ethicists, legal scholars, and neuroscientists rely on resemblances to the human brain. They refer to similarities in structural or functional terms that have been established in (...) scientific practice to validate organotypic cultures as models for brain research. In ethical discourse, however, such similarities are also used to justify assumptions about the potential risk to cause harm to HCOs. Ethicists assume that as the technology advances, organotypic cultures will increasingly resemble the human brain, raising more complex ethical issues. I argue that such reasoning is not justified given the heterogeneity of HCOs that have been modified to enable scientists to pursue their research goals. I then discuss the implications this line of thought has for advocates of the precautionary principle, focussing on those suggestions which propose adopting research regulations to the presence of bodily warning signs deemed worthy of protection. In doing so, I illustrate that the prevalent assumptions on similarity in ethical discourse ultimately risk disproportionately restricting research. I conclude that given the severe uncertainty about the technology’s future development, ethical discourse might benefit from narrowing the time frame for anticipation. (shrink)

Si bien en la filosofía de las ciencias ya se han explorado algunos ejemplos provenientes de la bioquímica como casos de estudio, la filosofía de la bioquímica es una subdisciplina naciente. En este artículo estudiaremos dos problemas filosóficos de relevancia contemporánea en esta ciencia. Por un lado, examinaremos las bases epistemológicas del problema del plegamiento de proteínas. En particular lo relacionado con la predicción de la estructura tridimensional de las proteínas a partir de su secuencia, asunto que ha dado mucho (...) que hablar debido a los nuevos avances utilizando deep learning. Por otro lado, exploraremos el problema in-vitro/in-vivo y, más generalmente, el problema de la extrapolación en las ciencias biológicas. Finalmente, a partir de las consecuencias de ambos temas consideraremos algunas reflexiones filosóficas generales acerca del reduccionismo, el pluralismo y el lugar de la bioquímica en las ciencias biológicas. Palabras clave: Bioquímica, Plegamiento de proteínas, In-vitro/in-vivo, Pluralismo, Reduccionismo. (shrink)

Evolutionary developmental biology is a rapidly growing discipline whose ambition is to address questions that are of relevance to both evolutionary biology and developmental biology. This field has been increasingly progressing as a new and independent comparative science. However, we argue that evo-devo’s comparative approach is challenged by several metaphysical, methodological and socio-disciplinary issues related to the foundation of heuristic functions of model organisms and the possible criteria to be adopted for their selection. In addition, new tools have to be (...) developed to deal with newly chosen model organisms. Therefore, we present a modelling framework suitable to integrate data on individual variation into evo-devo studies on new model organisms and thus to compensate for current idealization practices deliberately suppressing variation. (shrink)

Evolutionary developmental biology (Evo-devo) is a vibrant area of contemporary life science that should be (and is) increasingly incorporated into teaching curricula. Although the inclusion of this content is important for biological pedagogy at multiple levels of instruction, there are also philosophical lessons that can be drawn from the scientific practices found in Evo-devo. One feature of particular significance is the interdisciplinary nature of Evo-devo investigations and their resulting explanations. Instead of a single disciplinary approach being the most explanatory or (...) fundamental, different methodologies from biological disciplines must be synthesized to generate empirically adequate explanations. Thus, Evo-devo points toward a non-reductionist epistemology in biology. I review three areas where these synthetic efforts become manifest as a result of Evo-devo’s practices (form versus function reasoning styles; problem-structured investigations; idealizations related to studying model organisms), and then sketch some possible applications to teaching biology. These philosophical considerations provide resources for life science educators to address (and challenge) key aspects of the National Science Education Standards and Benchmarks for Scientific Literacy. (shrink)

Diatoms are a species‐rich group of photosynthetic eukaryotes, with enormous ecological significance and great potential for biotechnology. During the last decade, diatoms have begun to be studied intensively using modern molecular techniques and the genomes of four diatoms have been wholly or partially sequenced. Although new insights into the biology and evolution of diatoms are accumulating rapidly due to the availability of reverse genetic tools, the full potential of these molecular biological approaches can only be fully realized if experimental control (...) of sexual crosses becomes firmly established and widely accessible to experimental biologists. Here we discuss the issue of choosing new models for diatom research, by taking into account the broader context of diatom mating systems and the place of sex in relation to the intricate cycle of cell size reduction and restitution that is characteristic of most diatoms. We illustrate the results of our efforts to select and develop experimental systems in diatoms, using species with typical life cycle attributes, which could be used as future model organisms to complement existing ones. BioEssays 30:692–702, 2008. © 2008 Wiley Periodicals, Inc. (shrink)

The spiders Cupiennius salei and Achaearanea tepidariorum are firmly established laboratory models that have already contributed greatly to answering evolutionary developmental questions. Here we appraise why these animals are such useful models from phylogeny, natural history and embryogenesis to the tools available for their manipulation. We then review recent studies of axis formation, segmentation, appendage development and neurogenesis in these spiders and how this has contributed to understanding the evolution of these processes. Furthermore, we discuss the potential of comparisons of (...) silk production between Cupiennius and Achaearanea to investigate the origins and diversification of this evolutionary innovation. We suggest that further comparisons between these two spiders and other chelicerates will prove useful for understanding the evolution of development in metazoans. BioEssays 30:487–498, 2008. © 2008 Wiley Periodicals, Inc. (shrink)

A central reason that undergirds the significance of evo-devo is the claim that development was left out of the Modern synthesis. This claim turns out to be quite complicated, both in terms of whether development was genuinely excluded and how to understand the different kinds of embryological research that might have contributed. The present paper reevaluates this central claim by focusing on the practice of model organism choice. Through a survey of examples utilized in the literature of the Modern synthesis, (...) I identify a previously overlooked feature: exclusion of research on marine invertebrates. Understanding the import of this pattern requires interpreting it in terms of two epistemic values operating in biological research: theoretical generality and explanatory completeness. In tandem, these values clarify and enhance the significance of this exclusion. The absence of marine invertebrates implied both a lack of generality in the resulting theory and a lack of completeness with respect to particular evolutionary problems, such as evolvability and the origin of novelty. These problems were salient to embryological researchers aware of the variation and diversity of larval forms in marine invertebrates. In closing, I apply this analysis to model organism choice in evo-devo and discuss its relevance for an extended evolutionary synthesis. (shrink)

The concept of plasticity has always been present in the history of developmental biology, both within the theory of epigenesis and within morphogenesis studies. However this tradition relies also upon a genetic conception of plasticity. Founded upon the concepts of ‘‘phenotypic plasticity’’ and ‘‘reaction norm,’’ this genetic conception focuses on the array of possible phenotypic change in relation to diversified environments. Another concept of plasticity can be found in recent publications by some developmental biologists (Gilbert, West-Eberhard). I argue that these (...) authors adopt a ‘‘broad conception of plasticity’’ that is closely related to a notion of development as something that is ongoing throughout an organism’s lifecycle, and has no clear-cut boundaries. However, I suggest that given a narrow conception of plasticity, one can define temporal boundaries for development that are linked to specific features of the morphological process, which are different from behavioral and physiological processes. (shrink)

This special issue of Biological Theory is focused on development; it raises the problem of the temporal and spatial boundaries of development. From a temporal point of view, when does development start and stop? From a spatial point of view, what is it exactly that "develops", and is it possible to delineate clearly the developing entity? This issue explores the possible answers to these questions, and thus sheds light on the definition of development itself.

Leading philosophical accounts presume that Thomas H. Morgan’s transmission theory can be understood independently of experimental practices. Experimentation is taken to be relevant to confirming, rather than interpreting, the transmission theory. But the construction of Morgan’s theory went hand in hand with the reconstruction of the chief experimental object, the model organism Drosophila melanogaster . This raises an important question: when a theory is constructed to account for phenomena in carefully controlled laboratory settings, what knowledge, if any, indicates the theory’s (...) relevance to phenomena outside highly controlled settings? The answer, I argue, is found within the procedural knowledge embedded within laboratory practice. †To contact the author, please write to: Minnesota Center for Philosophy of Science, University of Minnesota, Department of Philosophy, 831 Heller Hall, 271 19th Ave., University of Minnesota, Minneapolis, MN 55455‐0310; e‐mail: [email protected]. (shrink)

The Darwinian theory of evolution is itself evolving and this book presents the details of the core of modern Darwinism and its latest developmental directions. The authors present current scientific work addressing theoretical problems and challenges in four sections, beginning with the concepts of evolution theory, its processes of variation, heredity, selection, adaptation and function, and its patterns of character, species, descent and life. The second part of this book scrutinizes Darwinism in the philosophy of science and its usefulness in (...) understanding ecosystems, whilst the third section deals with its application in disciplines beyond the biological sciences, including evolutionary psychology and evolutionary economics, Darwinian morality and phylolinguistics. The final section addresses anti-Darwinism, the creationist view and issues around teaching evolution in secondary schools. The reader learns how current experimental biology is opening important perspectives on the sources of variation, and thus of the very power of natural selection. This work examines numerous examples of the extension of the principle of natural selection and provides the opportunity to critically reflect on a rich theory, on the methodological rigour that presides in its extensions and exportations, and on the necessity to measure its advantages and also its limits. Scholars interested in modern Darwinism and scientific research, its concepts, research programs and controversies will find this book an excellent read, and those considering how Darwinism might evolve, how it can apply to the human sciences and other disciplines beyond its origins will find it particularly valuable. Originally produced in French (Les Mondes Darwiniens), the scope and usefulness of the book have led to the production of this English text, to reach a wider audience. This book is a milestone in the impressive penetration by Francophone scholars into the world of Darwinian science, its historiography and philosophy over the last two decades. Alex Rosenberg, R. Taylor Cole Professor of Philosophy, Duke University Until now this useful and comprehensive handbook has only been available to francophones. Thanks to this invaluable new translation, this collection of insightful and original essays can reach the global audience it deserves. Tim Lewens, University of Cambridge. (shrink)

Cooption and modularity are informative concepts in evolutionary developmental biology. Genes function within complex networks that act as modules in development. These modules can then be coopted in various functional and evolutionary contexts. Hormonal signaling, the main focus of this review, has a modular character. By regulating the activities of genes, proteins and other cellular molecules, a hormonal signal can have major effects on physiological and ontogenetic processes within and across tissues over a wide spatial and temporal scale. Because of (...) this property, we argue that hormones are frequently involved in the coordination of life history transitions (LHTs) and their evolution (LHE). Finally, we promote the usefulness of a comparative, non-model system approach towards understanding how hormones function and guide development and evolution, highlighting thyroid hormone function in echinoids as an example. BioEssays 27:64–75, 2005. © 2004 Wiley Periodicals, Inc. (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)

Extrapolation from a well-understood base population to a less-understood target population can fail if the base and target populations are not sufficiently similar. Differences between laboratory mice and humans, for example, can hinder extrapolation in medical research. Mice that carry a partial or complete human physiological system, known as humanized mice, are supposed to make extrapolation more reliable by simulating a variety of human diseases. But what justifies our belief that these mice are similar enough to their human counterparts to (...) simulate human disease? I argue that, unless three requirements are met in the process of humanizing mice, very little does. My requirements are not meant to provide necessary and sufficient conditions that guarantee a particular outcome. Instead, they serve as a heuristic for guiding scientific judgments involving extrapolation. In developing each requirement, I engage with philosophical issues concerning the nature of model-based science and the mechanistic approach (and its limits) to making generalizations in the life sciences. (shrink)

This paper discusses what it means and what it takes to integrate data in order to acquire new knowledge about biological entities and processes. Maureen O’Malley and Orkun Soyer have pointed to the scientific work involved in data integration as important and distinct from the work required by other forms of integration, such as methodological and explanatory integration, which have been more successful in captivating the attention of philosophers of science. Here I explore what data integration involves in more detail (...) and with a focus on the role of data-sharing tools, like online databases, in facilitating this process; and I point to the philosophical implications of focusing on data as a unit of analysis. I then analyse three cases of data integration in the field of plant science, each of which highlights a different mode of integration: inter-level integration, which involves data documenting different features of the same species, aims to acquire an interdisciplinary understanding of organisms as complex wholes and is exemplified by research on Arabidopsis thaliana; cross-species integration, which involves data acquired on different species, aims to understand plant biology in all its different manifestations and is exemplified by research on Miscanthus giganteus; and translational integration, which involves data acquired from sources within as well as outside academia, aims at the provision of interventions to improve human health and is exemplified by research on Phytophtora ramorum. Recognising the differences between these efforts sheds light on the dynamics and diverse outcomes of data dissemination and integrative research; and the relations between the social and institutional roles of science, the development of data-sharing infrastructures and the production of scientific knowledge. (shrink)

Through an examination of the actual research strategies and assumptions underlying the Human Genome Project, it is argued that the epistemic basis of the initial model organism programs is not best understood as reasoning via causal analog models. In order to answer a series of questions about what is being modeled and what claims about the models are warranted, a descriptive epistemological method is employed that uses historical techniques to develop detailed accounts which, in turn, help to reveal forms of (...) reasoning that are explicit, or more often implicit, in the practice of a particular field of scientific study. It is suggested that a more valid characterization of the reasoning structure at work here is a form of case-based reasoning. This conceptualization of the role of model organisms can guide our understanding and assessment of these research programs, their knowledge claims and progress, and their limitations, as well as how we educate the public about this type of biomedical research. (shrink)

In recent years, a handful of model systems from the basal metazoan phylum Cnidaria have emerged to challenge long-held views on the evolution of animal complexity. The most-recent, and in many ways most-promising addition to this group is the starlet sea anemone, Nematostella vectensis. The remarkable amenability of this species to laboratory manipulation has already made it a productive system for exploring cnidarian development, and a proliferation of molecular and genomic tools, including the currently ongoing Nematostella genome project, further enhances (...) the promise of this species. In addition, the facility with which Nematostella populations can be investigated within their natural ecological context suggests that this model may be profitably expanded to address important questions in molecular and evolutionary ecology. In this review, we explore the traits that make Nematostella exceptionally attractive as a model organism, summarize recent research demonstrating the utility of Nematostella in several different contexts, and highlight a number of developments likely to further increase that utility in the near future. BioEssays 27:211–221, 2005. © 2005 Wiley Periodicals, Inc. (shrink)

Stem cell scientists and ethicists have focused intently on questions relevant to the developmental stage and developmental capacities of stem cells. Comparably less attention has been paid to an equally important set of questions about the nature of stem cells, their common characteristics, their non‐negligible differences and their possible developmental species specificity. Answers to these questions are essential to the project of justly inferring anything about human stem cell biology from studies in non‐human model systems—and so to the possibility of (...) eventually developing human therapies based on stem cell biology. After introducing and discussing these questions, I conclude with a brief discussion of the creation of novel model systems in stem cell biology: human‐to‐animal embryonic chimeras. Such novel model systems may help to overcome obstacles to extrapolation, but they are also scientifically and ethically contentious. BioEssays 26:1005‐1012, 2004. © 2004 Wiley Periodicals, Inc. (shrink)

The comprehension of living organisms in all their complexity poses a major challenge to the biological sciences. Recently, systems biology has been proposed as a new candidate in the development of such a comprehension. The main objective of this paper is to address what systems biology is and how it is practised. To this end, the basic tools of a systems biological approach are explored and illustrated. In addition, it is questioned whether systems biology ‘revolutionizes’ molecular biology and ‘transcends’ its (...) assumed reductionism. The strength of this claim appears to depend on how molecular and systems biology are characterised and on how reductionism is interpreted. Doing credit to molecular biology and to methodological reductionism, it is argued that the distinction between molecular and systems biology is gradual rather than sharp. As such, the classical challenge in biology to manage, interpret and integrate biological data into functional wholes is further intensified by systems biology’s use of modelling and bioinformatics, and by its scale enlargement. (shrink)

It is assumed that scientific models contain no superfluous model elements in scientific representation. A representational model is constructed with all the model elements serving the representational purpose. The received view has it that there are no redundant model elements which are non-representational. Contrary to this received view, I argue that there exist some non-representational model elements which are essential in scientific representation. I call them representation-supporting model elements in virtue of the fact that they play the role to support (...) the representational role of representational model elements. Representation-supporting model elements, which have a characteristic of dependability, are not to be eliminated in the process of modeling although they are playing second fiddle to representational model elements in scientific representation. (shrink)

This review surveys three central issues in philosophy of stem cell biology: the nature of stem cells, stem cell experiments, and explanations of stem cell capacities. First, I argue that the fundamental question ‘what is a stem cell?’ has no single substantive answer. Instead, the core idea is explicated via an abstract model, which accounts for many features of stem cell experiments. The second part of this essay examines several of these features: uncertainty, model organisms, and manipulability. The results shed (...) light on the form of our emerging knowledge of stem cells: mechanistic explanations. The third part of the essay sketches some key features of these explanations, which are constructed by a collaborative experimenting community. (shrink)

Evo-Devo exhibits a plurality of scientific “cultures” of practice and theory. When are the cultures acting—individually or collectively—in ways that actually move research forward, empirically, theoretically, and ethically? When do they become imperialistic, in the sense of excluding and subordinating other cultures? This chapter identifies six cultures – three /styles/ (mathematical modeling, mechanism, and history) and three /paradigms/ (adaptationism, structuralism, and cladism). The key assumptions standing behind, under, or within each of these cultures are explored. Characterizing the internal structure of (...) the cultures is necessary for understanding how they collaborate or compete, and how they are fragmented or integrated, in the rich interdisciplinary /trading zone/ (Galison 1997) of Evo-Devo. Evo-Devo is an important example of how science can progress through a radical plurality of perspectives and cultures. (shrink)

Model organisms are central to contemporary biology and studies of embryogenesis in particular. Biologists utilize only a small number of species to experimentally elucidate the phenomena and mechanisms of development. Critics have questioned whether these experimental models are good representatives of their targets because of the inherent biases involved in their selection (e.g., rapid development and short generation time). A standard response is that the manipulative molecular techniques available for experimental analysis mitigate, if not counterbalance, this concern. But the most (...) powerful investigative techniques and molecular methods are applicable to single-celled organisms (‘microbes’). Why not use unicellular rather than multicellular model organisms, which are the standard for developmental biology? To claim that microbes are not good representatives takes us back to the original criticism leveled against model organisms. Using empirical case studies of microbes modeling ontogeny, we break out of this circle of reasoning by showing: (a) that the criterion of representation is more complex than earlier discussions have emphasized; and, (b) that different aspects of manipulability are comparable in importance to representation when deciding if a model organism is a good model. These aspects of manipulability harbor the prospect of enhancing representation. The result is a better understanding of how developmental biologists conceptualize research using experimental models and suggestions for underappreciated avenues of inquiry using microbes. More generally, it demonstrates how the practical aspects of experimental biology must be scrutinized in order to understand the associated scientific reasoning. (shrink)

Is it possible, and in the first place is it even desirable, to define what "development" means and to determine the scope of the field called "developmental biology"? Though these questions appeared crucial for the founders of "developmental biology" in the 1950s, there seems to be no consensus today about the need to address them. Here, in a combined biological, philosophical, and historical approach, we ask whether it is possible and useful to define biological development, and, if such a definition (...) is indeed possible and useful, which definition can be considered as the most satisfactory. (shrink)

The diploblastic Cnidaria form one of the most ancient metazoan phyla and thus provide a useful outgroup for comparative studies of the molecular control of development in the more complex, and more often studied, triploblasts. Among cnidarians, the reef building coral Acropora is a particularly appropriate choice for study. Acropora belongs to the Anthozoa, which several lines of evidence now indicate is the basal class within the phylum Cnidaria, and has the practical advantages that its reproduction is predictable, external and (...) accessible and that the base content of its genome is not strongly biased. The Acropora system has already provided insights into ancestral linkages of homeobox genes and the evolution of the Pax genes, and has the potential to provide further new perspectives on the age, role in development, and evolution of these and other gene families. BioEssays 22:291–296, 2000. © 2000 John Wiley & Sons, Inc. (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)

Contrary to concerns of some critics, we present evidence that biomedical research is not dominated by a small handful of model organisms. An exhaustive analysis of research literature suggests that the diversity of experimental organisms in biomedical research has increased substantially since 1975. There has been a longstanding worry that organism‐centric funding policies can lead to biases in experimental organism choice, and thus negatively impact the direction of research and the interpretation of results. Critics have argued that a focus on (...) model organisms has unduly constrained the diversity of experimental organisms. The availability of large electronic databases of scientific literature, combined with interest in quantitative methods among philosophers of science, presents new opportunities for data‐driven investigations into organism choice in biomedical research. The diversity of organisms used in NIH‐funded research may be considerably lower than in the broader biomedical sciences, and may be subject to greater constraints on organism choice. (shrink)

Early in his career Thomas Hunt Morgan was interested in embryology and dedicated his research to studying organisms that could regenerate. Widely regarded as a regeneration expert, Morgan was invited to deliver a series of lectures on the topic that he developed into a book, Regeneration. In addition to presenting experimental work that he had conducted and supervised, Morgan also synthesized and critiqued a great deal of work by his peers and predecessors. This essay probes into the history of regeneration (...) studies by looking in depth at Regeneration and evaluating Morgan’s contribution. Although famous for his work with fruit fly genetics, studying Regeneration illuminates Morgan’s earlier scientific approach which emphasized the importance of studying a diversity of organisms. Surveying a broad range of regenerative phenomena allowed Morgan to institute a standard scientific terminology that continues to inform regeneration studies today. Most importantly, Morgan argued that regeneration was a fundamental aspect of the growth process and therefore should be accounted for within developmental theory. Establishing important similarities between regeneration and development allowed Morgan to make the case that regeneration could act as a model of development. The nature of the relationship between embryogenesis and regeneration remains an active area of research. (shrink)

The Cnidaria represent the most ancient eumetazoan phylum. Members of this group possess typical animal cells and tissues such as sensory cells, nerve cells, muscle cells and epithelia. Due to their unique phylogenetic position, cnidarians have traditionally been used as a reference group in various comparative studies. We propose the colonial marine hydroid, Hydractinia, as a convenient, versatile platform for basic and applied research in developmental biology, reproduction, immunology, environmental studies and more. In addition to being a typical cnidarian representative, (...) Hydractinia offers many practical and theoretical advantages: studies that are feasible in Hydra like regeneration, pattern regulation, and cell renewal from stem cells, can be supplemented by genetic analyses and classical embryology in Hydractinia. Metamorphosis of the planula larva of Hydractinia can be used as a model for cell activation and communication and the presence of a genetically controlled allorecognition system makes it a suitable model for comparative immunology. Most importantly, Hydractinia may be manipulated at most aspects of its (short) life cycle. It has already been the subject of many studies in various disciplines, some of which are discussed in this essay. BioEssays 23:963–971, 2001. © 2001 John Wiley & Sons, Inc. (shrink)

Evolutionary developmental biologists categorize many different kinds of things, from ontogenetic stages to modules of gene activity. The process of categorization—the establishment of “kinds”—is an implicit part of describing the natural world in consistent, useful ways, and has an essentially practical rather than philosophical basis. Kinds commonly serve one of three purposes: they may function (1) as practical tools for communication; (2) to support prediction and generalization; or (3) as a basis for theoretical discussions. Beyond the minimal requirement that classifications (...) reflect biological reality, what sorts of kinds or classification will be useful in advancing a research program depends on the epistemological context. Thus, the important meaning of “natural” in “natural kinds” is not “natural with respect to nature,” but “natural with respect to the question.” This conclusion arises from the recognition that the proper role of concepts (e.g. natural kind, module, homology, model) is not to answer biological questions, but rather to help frame them. From a scientist’s perspective, arguing about the wording (or existence) of a single definition of “natural” or “kind” is beside the point: we get more work done by letting the question at hand determine what kinds of kinds are natural, on the basis of their ability to help answer it. We should be content to let “natural kinds” remain vague, multivalent, and–therefore broadly useful. For a philosopher like Hacking, the diverse, disparate, and ultimately incommensurable uses of the term “natural kind” have diluted its value so far that it loses all meaning. For practicing scientists, however, defining useful kinds in the context of particular questions and systems remains a productive epistemological strategy. (shrink)

Model organismism—the over-reliance on model organisms without sufficient attention to the adequacy of the models—continues to hobble our understanding of human brains and behaviors. I outline the problem of model organismism in contemporary biology and biomedicine, and discuss the virtues of a genuinely comparative biology for understanding ourselves, our evolutionary history, and our place in nature.