In a military-sponsored research project begun during the Second World War, inmates of the Stateville Penitentiary in Illinois were infected with malaria and treated with experimental drugs that sometimes had vicious side effects. They were made into reservoirs for the disease and they provided a food supply for the mosquito cultures. They acted as secretaries and technicians, recording data on one another, administering malarious mosquito bites and experimental drugs to one another, and helping decide who was admitted to the project (...) and who became eligible for early parole as a result of his participation. Thus, the prisoners were not simply research subjects; they were deeply constitutive of the research project. Because a prisoners time on the project was counted as part of his sentence, and because serving on the project could shorten ones sentence, the project must be seen as simultaneously serving the functions of research and punishment. Michel Foucault wrote about such mixed mechanisms in his Discipline and punish. His shining example of such a transparent and subtle style of punishment was the panopticon, Jeremy Benthams architectural invention of prison cellblocks arrayed around a central guard tower. Stateville prison was designed on Benthams model; Foucault featured it in his own discussion. This paper, then, explores the power relations in this highly idiosyncratic experimental system, in which the various roles of model organism, reagent, and technician are all occupied by sentient beings who move among them fluidly. This, I argue, created an environment in the Stateville hospital wing more panoptic than that in the cellblocks. Research and punishment were completely interpenetrating, and mutually reinforcing. (shrink)

Graphical AbstractThe sea anemone Nematostella vectensis has developed into a model organism for studying genome evolution and animal development.

In a military-sponsored research project begun during the Second World War, inmates of the Stateville Penitentiary in Illinois were infected with malaria and treated with experimental drugs that sometimes had vicious side effects. They were made into reservoirs for the disease and they provided a food supply for the mosquito cultures. They acted as secretaries and technicians, recording data on one another, administering malarious mosquito bites and experimental drugs to one another, and helping decide who was admitted to the project (...) and who became eligible for early parole as a result of his participation. Thus, the prisoners were not simply research subjects; they were deeply constitutive of the research project. Because a prisoner’s time on the project was counted as part of his sentence, and because serving on the project could shorten one’s sentence, the project must be seen as simultaneously serving the functions of research and punishment. Michel Foucault wrote about such ‘mixed mechanisms’ in his Discipline and punish. His shining example of such a ‘transparent’ and subtle style of punishment was the panopticon, Jeremy Bentham’s architectural invention of prison cellblocks arrayed around a central guard tower. Stateville prison was designed on Bentham’s model; Foucault featured it in his own discussion. This paper, then, explores the power relations in this highly idiosyncratic experimental system, in which the various roles of model organism, reagent, and technician are all occupied by sentient beings who move among them fluidly. This, I argue, created an environment in the Stateville hospital wing more panoptic than that in the cellblocks. Research and punishment were completely interpenetrating, and mutually reinforcing. (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)

This study focuses on the concept of a 'model organism' in the biomedical sciences through an historical and philosophical examination of research with the nematode Caenorhabditis elegans. I explore the choice of C. elegans in the mid-1960s, showing a rich context existed within which the organism was selected as the focus for a molecular biological research program, including an experimental life prior to Sydney Brenner's work. I argue that this choice can be seen as an obvious outcome (...) of what was a complex search procedure, and that the success of the 'worm project' depended not only on organismal choice but also on the conceptual and institutional framework at the Laboratory of Molecular Biology in Cambridge within which it was pursued. Examination of C. elegans work in the late 1960s through the early 1980s illuminates several additional theses. Although development and behavior were the general areas of interest for the project, the original goals and proposed methodology were extremely vague. As the project evolved, which investigations proved to be tractable using the worm depended not only on which methodologies were fruitful but also on the interests and skills of early workers. Much of the power of C. elegans as a model organism can be traced historically to the investment of resources which resulted in an unprecedented, complete description of the organism, and represented a return to a more naturalistic biological tradition. In light of the historical study, I develop a philosophical analysis of C. elegans as a model organism through exploration of the three kinds of modeling with the worm: modeling of structures, processes, and information. I expand the notion of a descriptive model, arguing that C. elegans is best understood as a prototype of the metazoa, and that C. elegans as a model organism has been not only heuristically valuable, but also essential to this research project particularly in its pre-explanatory stages. I conclude by suggesting that more investigation of descriptive prototypes such as those in the worm project must be done to capture important aspects of the biomedical sciences that will be neglected if explanatory models are the sole focus in the philosophy of science. (shrink)

This article offers a historical analysis of the relationship between the practice of participant-observation among American sociologists and Erving Goffman’s dramaturgical model of the self. He was a social scientist who privileged ethnography in the field over the laboratory experiment, the survey questionnaire, or the mental test. His goal was a natural history of communication among humans. Rather than rely upon standardizing technologies for measurement, Goffman tried to obtain accurate recordings of human behavior through secretive observations. During the 1950s, (...) he conducted three major studies as a participant-observer, disguised from those studied through insincere performances. As originally presented, his dramaturgical theory did not draw upon the theater as the governing metaphor, but rather the confidence game. It is suggested that Goffman’s writings exemplify what Gerd Gigerenzer calls the tools-to-theories heuristic. Goffman’s depiction of the confidence man’s behavior closely mirrored how he and his fellow sociologists described the practice of participant-observation. Both were represented as embedded and attentive yet coolly detached observers skilled at playing different roles as the situation necessitated. The similarities between his own professional behavior and the activities of the confidence man may have suggested to Goffman the latter as a model for human nature. (shrink)

Community databases have become crucial to the collection, ordering and retrieval of data gathered on model organisms, as well as to the ways in which these data are interpreted and used across a range of research contexts. This paper analyses the impact of community databases on research practices in model organism biology by focusing on the history and current use of four community databases: FlyBase, Mouse Genome Informatics, WormBase and The Arabidopsis Information Resource. We discuss the standards (...) used by the curators of these databases for what counts as reliable evidence, acceptable terminology, appropriate experimental set-ups and adequate materials (e.g., specimens). On the one hand, these choices are informed by the collaborative research ethos characterising most model organism communities. On the other hand, the deployment of these standards in databases reinforces this ethos and gives it concrete and precise instantiations by shaping the skills, practices, values and background knowledge required of the database users. We conclude that the increasing reliance on community databases as vehicles to circulate data is having a major impact on how researchers conduct and communicate their research, which affects how they understand the biology of model organisms and its relation to the biology of other species. (shrink)

One might be inclined to assume, given the mouse donning its cover, that the behavior of interest in Nicole Nelson's book Model Behavior (2018) is that of organisms like mice that are widely used as “stand-ins” for investigating the causes of human behavior. Instead, Nelson's ethnographic study focuses on the strategies adopted by a community of rodent behavioral researchers to identify and respond to epistemic challenges they face in using mice as models to understand the causes of disordered human (...) behaviors associated with mental illness. Although Nelson never explicitly describes the knowledge production activities in which her behavioral geneticist research subjects engage as “exemplary”, the question of whether or not these activities constitute “model behavior(s)”—generalizable norms for engaging in scientific research—is one of the many thought-provoking questions raised by her book. As a philosopher of science interested in this question, I take it up here. (shrink)

How to use a model organism to study phenotypic integration and constraints on evolution.

Chelicerates (scorpions, horseshoe crabs, spiders, mites and ticks) are the second largest group of arthropods and are of immense importance for fundamental and applied science. They occupy a basal phylogenetic position within the phylum Arthropoda, and are of crucial significance for understanding the evolution of various arthropod lineages. Chelicerates are vectors of human diseases, such as ticks, and major agricultural pests, such as spider mites, thus this group is also of importance for both medicine and agriculture. The developmental genetics of (...) chelicerates is poorly understood and a challenge for the future progress for many aspects of chelicerate biology is the development of a model organism for this group. Toward this end, we are developing a chelicerate genetic model: the two‐spotted spider mite Tetranychus urticae. T. urticae has the smallest genome of any arthropod determined so far (75 Mbp, 60% of the size of the Drosophila genome), undergoes rapid development and is easy to maintain in the laboratory. These features make T. urticae a promising reference organism for the economically important, poorly studied and species‐rich chelicerate lineage. BioEssays 29:489–496, 2007. © 2007 Wiley Periodicals, Inc. (shrink)

Modern science’s ability to produce, store, and analyze big datasets is changing the way that scientific research is practiced. Philosophers have only begun to comprehend the changed nature of scientific reasoning in this age of “big data.” We analyze data-focused practices in biology and climate modeling, identifying distinct species of data-centric science: phenomena-laden in biology and phenomena-agnostic in climate modeling, each better suited for its own domain of application, though each entail trade-offs. We argue that data-centric practices in science are (...) not monolithic because the opportunities and challenges presented by big data vary across scientific domains. (shrink)

Men think in terms of models. Their sense organs abstract the events which touch them; their memories store traces of these events as coded symbols; and they may recall them according to patterns which they learned earlier, or recombine them in patterns that are new. In all this, we may think of our thought as consisting of symbols which are put in relations or sequences according to operating rules. Both symbols and operating rules are acquired, in part directly from interaction (...) with the outside world, and in part from elaboration of this material through internal recombination. Together, a set of symbols and a set of rules may constitute what we may call a calculus, a logic, a game or a model. Whatever we call it, it will have some structure, i.e., some pattern of distribution of relative discontinuities, and some “laws” of operation. (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 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)

Despite the burgeoning interest in new and more complex accounts of the organism-environment dyad by biologists and philosophers, little attention has been paid in the resulting discussions to the history of these ideas and to their deployment in disciplines outside biology—especially in the social sciences. Even in biology and philosophy, there is a lack of detailed conceptual models of the organism-environment relationship. This volume is designed to fill these lacunae by providing the first multidisciplinary discussion of the topic (...) of organism-environment interaction. It brings together scholars from history, philosophy, psychology, anthropology, medicine, and biology to discuss the common focus of their work: entangled life, or the complex interaction of organisms and environments. (shrink)

Complexity is pleased to announce the installment of Prof Hiroki Sayama as its new Chief Editor. In this Editorial, Prof Sayama describes his feelings about his recent appointment, discusses some of the journal’s journey and relevance to current issues, and shares his vision and aspirations for its future.

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)

This Element presents a philosophical exploration of the concept of the 'model organism' in contemporary biology. Thinking about model organisms enables us to examine how living organisms have been brought into the laboratory and used to gain a better understanding of biology, and to explore the research practices, commitments, and norms underlying this understanding. We contend that model organisms are key components of a distinctive way of doing research. We focus on what makes model organisms (...) an important type of model, and how the use of these models has shaped biological knowledge, including how model organisms represent, how they are used as tools for intervention, and how the representational commitments linked to their use as models affect the research practices associated with them. This title is available as Open Access on Cambridge Core. (shrink)

In this paper we argue that an operational organism concept can help to overcome the structural deficiency of mathematical models in biology. In our opinion, the structural deficiency of mathematical models lies mainly in our inability to identify functionally relevant biological characters in biological systems, and not so much in a lack of adequate mathematical representations of biological processes. We argue that the problem of character identification in biological systems is linked to the question of a properly formulated (...) class='Hi'>organism concept. Lastly, we demonstrate how a decomposition of an organism into independent characters in the context of a specific biological process--such as adaptation by means of natural selection--depends on the dynamical properties and invariance conditions of the equations that describe this process. (shrink)

Holistic accounts of the natural environment in environmental ethics fail to stress the distinction between the concepts of comnlunity and organism. Aldo Leopold’s “Land Ethic” adds to this confusion, for it can be interpreted as promoting either a community or an organic model of nature. The difference between the two concepts lies in the degree of autonomy possessed by constituent entities within the holistic system. Members within a community are autonomous, while the parts of an organism are (...) not. Different moral conclusions and environmental policies may result from this theoretical distinction. Treating natural entities as parts of an organism downgrades their intrinsic value as individual natural beings, since the only relevant moral criterion in an organic environmental ethic is the instrumental value that each natural entity has for the system. This ethic allows instances of the “substitution problem”-the replacement of one entity in an ecosystem by another provided that the overall functioning of the system is notharmed. However, since substitution violates environmentalist principles, for example, calling for respect for the integrity of the entities in a natural system, an organic environmental ethic must be rejected. A community model focuses on both the functional value and the autonomous intrinsie value of natural entities in a system. A community environmental ethic thus avoids the substitution problem. (shrink)

In recent years, biologists and philosophers of science have argued that evolutionary theory should incorporate more seriously the idea of ‘reciprocal causation.’ This notion refers to feedback loops whereby organisms change their experiences of the environment or alter the physical properties of their surroundings. In these loops, in particular niche constructing activities are central, since they may alter selection pressures acting on organisms, and thus affect their evolutionary trajectories. This paper discusses long-standing problems that emerge when studying such reciprocal causal (...) processes between organisms and environments. By comparing past approaches to reciprocal causation from the early twentieth century with contemporary ones in niche construction theory, we identify two central reoccurring problems: All of these approaches have not been able to provide a conceptual framework that allows maintaining meaningful boundaries between organisms and environments, instead of merging the two, and integrating experiential and physical kinds of reciprocal causation. By building on case studies of niche construction research, we provide a model that is able to solve these two problems. It allows distinguishing between mutually interacting organisms and environments in complex scenarios, as well as integrating various forms of experiential and physical niche construction. (shrink)

Through an examination of the actual research strategies and assumptions underlying the Human Genome Project (HGP), it is argued that the epistemic basis of the initial model organism programs is not best understood as reasoning via causal analog models (CAMs). 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)

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)

While there is often good reason to study our world by abstracting properties from its parts to the point where the result can be modelled as mechanisms, there is no need to do so when humans are ….

Palaeontology developed as a field dependent upon comparison. Not only did reconstructing the fragmentary records of fossil organisms and placing them within taxonomic systems and evolutionary lineages require detailed anatomical comparisons with living and fossil animals, but the field also required thinking in terms of behavioural, biological and ecological analogies with modern organisms to understand how prehistoric animals lived and behaved. Yet palaeontological material often worked against making easy linkages, bringing a sense of mystery and doubt. This paper will look (...) at an animal whose study exemplified these problems: the Chalicothere. Increasingly recognized as a specific type from finds across North America and Eurasia from the early nineteenth century onwards, these prehistoric mammals showed short back legs terminating in pawed feet, long front limbs ending in sharp claws, a long flexible neck, and herbivorous grinding teeth. The Chalicothere became a significant organism within palaeontological studies, as the unexpected mix of characters made it a textbook example against the Cuvierian notion of “correlation of parts,” while explaining how the animal moved, fed and behaved became puzzling. However, rather than prevent comparisons, these actually led to comparative analogies becoming flexible and varied, with different forms of comparison being made with varying methods and degrees of confidence, and with the anatomy, movement and behaviour of giraffes, bears, horses, anteaters, primates and other organisms all serving at various points as potential models for different aspects of the animal. This paper will examine some of the attempts to reconstruct and define the Chalicotheres across a long timescale, using this to show how multiple comparisons and analogies could be deployed in a reconstructive and evolutionary science like palaeontology, and illustrate some of the limits and tensions in comparative methods, as they were used to reconstruct organisms which were thought to be incomparable to any modern animal. (shrink)

This article critically examines one of the most prevalent metaphors in modern biology, namely the machine conception of the organism (MCO). Although the fundamental differences between organisms and machines make the MCO an inadequate metaphor for conceptualizing living systems, many biologists and philosophers continue to draw upon the MCO or tacitly accept it as the standard model of the organism. This paper analyses the specific difficulties that arise when the MCO is invoked in the study of development (...) and evolution. In developmental biology the MCO underlies a logically incoherent model of ontogeny, the genetic program, which serves to legitimate three problematic theses about development: genetic animism, neo-preformationism, and developmental computability. In evolutionary biology the MCO is responsible for grounding unwarranted theoretical appeals to the concept of design as well as to the interpretation of natural selection as an engineer, which promote a distorted understanding of the process and products of evolutionary change. Overall, it is argued that, despite its heuristic value, the MCO today is impeding rather than enabling further progress in our comprehension of living systems. (shrink)

In lieu of an abstract, here is a brief excerpt of the content:Journal of the History of Philosophy 40.1 (2002) 122-123 [Access article in PDF] Book Review Spirits and Clocks: Machine & Organism in Descartes Dennis Des Chene. Spirits and Clocks: Machine & Organism in Descartes. Ithaca, NY and London: Cornell University Press, 2001. Pp. xiii + 181. Cloth, $39.95. Confronted with the thousandth "entirely new" interpretation of the Cartesian mind-body union, one sometimes wonders whether anything new can (...) in fact be said about the great Descartes. Once again, after his invaluable and prize-winning Physiologia (Cornell University Press, 1996), Des Chene proves that a serious historian, with a keen awareness of historical context, actually can. Unlike the usual accounts of Descartes's animal-machine, Des Chene does not concentrate on the all too familiar set of questions whether or not machines can think, sense, etc. Instead, Des Chene interprets the machine-metaphor the way Descartes meant it to be, viz. as a model for explaining animal and human physiology instead of (cognitive) psychology. Des Chene's central claim is that the Traité de l'Homme and Descartes's later (unpublished) physiological tracts are an attempt to replace scholastic commentaries on Aristotle's De Anima, itself discussed in this book's companion volume Life's Forms (Cornell University Press, 2000). Spirits and Clocks investigates how Descartes's general mechanistic program (outlined in Physiologia) is applied to the field of animal and human life. This project in itself had a far more lasting influence than Descartes's specific and often bizarre physiological explanations. Therefore, Des Chene rightly concentrates on the philosophical aspects of Descartes's general project of "mechanizing" physiology. His short but illuminating book studies a wide range of ontological, epistemological, and even aesthetic aspects of the machine metaphor and, although this is not the express goal [End Page 122] of the book, it also sheds new light on the epistemology and metaphysics of the Meditations. In this sense Spirits and Clocks is not only a significant contribution to the history of biology but first and foremost a must for historians of philosophy.Des Chene explains that the use of a machine model in physiology was neither new nor entirely unacceptable to the Aristotelians. What is new is Descartes's use of it. His mechanistic understanding of the body as a machine is incompatible with accepting the soul as the source of life and the principle of all our physiological and psychological capacities, while Aristotelians had no problem in accepting both the soul and certain machine models of the body. (Aristotle himself uses the lever to explain animal motion.) Des Chene sketches Descartes's attempt to explain all physiological processes by means of the physical properties of material parts that obey the general laws of motion, excluding all talk of ends. In this context, the use of illustrations is of considerable importance: though they cannot per se convey a denial of a "soul-model" of physiology, they strongly suggest that the (mechanistically understood) machine is all there is to say about the functions of human and animal bodies. Des Chene offers an interesting, albeit sometimes somewhat speculative and ahistoric, discussion of the aesthetic aspects of the machine model.As Des Chene showed in his Physiologia, the rejection of teleology is one of the main goals of Descartes's physics. However, although Descartes may be successful in rejecting the view that stones fall down from some kind of desire to reach their final destiny, he is less successful in denying that the eye is meant for seeing (and hence for our self-preservation). Des Chene gives a truly fascinating account of the limits of Descartes's denial of teleology in physiology. This includes questions about the physical unity of the human body: how can I explain why I have this body and how can I even identify this body as a unit without invoking ends? Similarly, Descartes takes the healthy, "normally" functioning body as the norm of his investigations. But, again, can he do so without acknowledging some form of teleology? Descartes's answer in most of these cases is that the final goals... (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)

This article compares the epistemic roles of theoretical models and model organisms in science, and specifically the role of non-human animal models in biomedicine. Much of the previous literature on this topic shares an assumption that animal models and theoretical models have a broadly similar epistemic role—that of indirect representation of a target through the study of a surrogate system. Recently, Levy and Currie have argued that model organism research and theoretical modelling differ in the justification of (...) model-to-target inferences, such that a unified account based on the widely accepted idea of modelling as indirect representation does not similarly apply to both. I defend a similar conclusion, but argue that the distinction between animal models and theoretical models does not always track a difference in the justification of model-to-target inferences. Case studies of the use of animal models in biomedicine are presented to illustrate this. However, Levy and Currie’s point can be argued for in a different way. I argue for the following distinction. Model organisms function as surrogate sources of evidence, from which results are transferred to their targets by empirical extrapolation. By contrast, theoretical modelling does not involve such an inductive step. Rather, theoretical models are used for drawing conclusions from what is already known or assumed about the target system. Codifying assumptions about the causal structure of the target in external representational media allows one to apply explicit inferential rules to reach conclusions that could not be reached with unaided cognition alone. (shrink)

Historically embryogenesis has been among the most philosophically intriguing phenomena. In this paper I focus on one aspect of biological development that was particularly perplexing to the ancients: self-organisation. For many ancients, the fact that an organism determines the important features of its own development required a special model for understanding how this was possible. This was especially true for Aristotle, Alexander, and Simplicius, who all looked to contemporary technology to supply that model. However, they did not (...) all agree on what kind of device should be used. In this paper I explore the way these ancients made use of technology as a model for the developing embryo. I argue that their different choices of device reveal fundamental differences in the way each thinker understood the nature of biological development itself. In the final section of the paper I challenge the traditional view (dating back to Alexander's interpretation of Aristotle) that the use of automata in GA can simply be read off from their use in the de motu. (shrink)

The evolutionary implications of environmental change due to organismic action remain a controversial issue, after a decades—long debate on the subject. Much of this debate has been conducted in qualitative fashion, despite the availability of mathematical models for organism–environment interactions, and for gene frequencies when allele fitness can be related to exploitation of a particular environmental resource. In this article we focus on representative models dealing with niche construction, ecosystem engineering, the Gaia Hypothesis and community interactions of Lotka–Volterra type, (...) and show that their quantitative character helps bring into sharper focus the similarities and differences among their respective theoretical contexts. (shrink)

Based on Kolchinsky and Wolpert’s work on the semantics of autonomous agents, I propose an application of Mathematical Logic and Probability to model cognitive processes. In this work, I will follow Bateson’s insights on the hierarchy of learning in complex organisms and formalize his idea of applying Russell’s Type Theory. Following Weaver’s three levels for the communication problem, I link the Kolchinsky–Wolpert model to Bateson’s insights, and I reach a semantic and conceptual hierarchy in living systems as an (...) explicative model of some adaptive constraints. Due to the generality of Kolchinsky and Wolpert’s hypotheses, I highlight some fundamental gaps between the results in current Artificial Intelligence and the semantic structures in human beings. In light of the consequences of my model, I conclude the paper by proposing a general definition of knowledge in probabilistic terms, overturning de Finetti’s Subjectivist Definition of Probability. (shrink)

Ontologies of living things are increasingly grounded on the concepts and practices of current life science. Biological development is a process, undergone by living things, which begins with a single cell and (in an important class of cases) ends with formation of a multicellular organism. The process of development is thus prima facie central for ideas about biological individuality and organismality. However, recent accounts of these concepts do not engage developmental biology. This paper aims to fill the gap, proposing (...) the lineage view of stem cells as an ontological framework for conceptualizing organismal development. This account is grounded on experimental practices of stem cell research, with emphasis on new techniques for generating biological organization in vitro. On the lineage view, a stem cell is the starting point of a cell lineage with a specific organismal source, time-interval of existence, and ‘tree topology’ of branch-points linking the stem to developmental termini. The concept of ‘enkapsis’ accommodates the cell-organism relation within the lineage view; this hierarchical notion is further explicated by considering the methods and results of stem cell experiments. Results of this examination include a (partial) characterization of stem cells’ developmental versatility, and the context-dependence of developmental processes involving stem cells. (shrink)

Developmental models that account for the metabolic effect of temperature variability on poikilotherms, such as degree-day models, have been widely used to study organism emergence, range and development, particularly in agricultural and vector-borne disease contexts. Though simple and easy to use, structural and parametric issues can influence the outputs of such models, often substantially. Because the underlying assumptions and limitations of these models have rarely been considered, this paper reviews the structural, parametric, and experimental issues that arise when using (...) degree-day models, including the implications of particular structural or parametric choices, as well as assumptions that underlie commonly used models. Linear and non-linear developmental functions are compared, as are common methods used to incorporate temperature thresholds and calculate daily degree-days. Substantial differences in predicted emergence time arose when using linear versus non-linear developmental functions to model the emergence time in a model organism. The optimal method for calculating degree-days depends upon where key temperature threshold parameters fall relative to the daily minimum and maximum temperatures, as well as the shape of the daily temperature curve. No method is shown to be universally superior, though one commonly used method, the daily average method, consistently provides accurate results. The sensitivity of model projections to these methodological issues highlights the need to make structural and parametric selections based on a careful consideration of the specific biological response of the organism under study, and the specific temperature conditions of the geographic regions of interest. When degree-day model limitations are considered and model assumptions met, the models can be a powerful tool for studying temperature-dependent development. (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)

Traditional frameworks for evaluating scientific models have tended to downplay their exploratory function; instead they emphasize how models are inherently intended for specific phenomena and are to be judged by their ability to predict, reproduce, or explain empirical observations. By contrast, this paper argues that exploration should stand alongside explanation, prediction, and representation as a core function of scientific models. Thus, models often serve as starting points for future inquiry, as proofs of principle, as sources of potential explanations, and as (...) a tool for reassessing the suitability of the target system. This is illustrated by a case study of the varied career of reaction-diffusion models in the study of biological pattern formation, which was initiated by Alan Turing in a classic 1952 paper. Initially regarded as mathematically elegant, but biologically irrelevant, demonstrations of how, in principle, spontaneous pattern formation could occur in an organism, such Turing models have only recently rebounded, thanks to advances in experimental techniques and computational methods. The long-delayed vindication of Turing’s initial model, it is argued, is best explained by recognizing it as an exploratory tool. (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 (...) class='Hi'>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)

Although the interdisciplinary nature of contemporary biological sciences has been addressed by philosophers, historians, and sociologists of science, the different ways in which engineering concepts and methods have been applied in biology have been somewhat neglected. We examine - using the mechanistic philosophy of science as an analytic springboard - the transfer of network methods from engineering to biology through the cases of two biology laboratories operating at the California Institute of Technology. The two laboratories study gene regulatory networks, but (...) in remarkably different ways. The research strategy of the Davidson lab fits squarely into the traditional mechanist philosophy in its aim to decompose and reconstruct, in detail, gene regulatory networks of a chosen model organism. In contrast, the Elowitz lab constructs minimal models that do not attempt to represent any particular naturally evolved genetic circuits. Instead, it studies the principles of gene regulation through a template-based approach that is applicable to any kinds of networks, whether biological or not. We call for the mechanists to consider whether the latter approach can be accommodated by the mechanistic approach, and what kinds of modifications it would imply for the mechanistic paradigm of explanation, if it were to address modelling more generally. (shrink)

SynopsisThe response to physics and chemistry which characterized mid-nineteenth century physiology took two major directions. One, found most prominently among the German physiologists, developed explanatory models which had as their fundamental assumption the ultimate reducibility of all biological phenomena to the laws of physics and chemistry. The other, characteristic of the French school of physiology, recognized that physics and chemistry provided potent analytical tools for the exploration of physiological activities, but assumed in the construction of explanatory models that the (...) class='Hi'>organism involved special levels of organization and that there must, in consequence, be special biological laws.The roots of this argument about concept formation in physiology are explored in the works of Theodor Schwann, Johannes Müller, François Magendie and Claude Bernard among others. (shrink)

Drawing from the stimulus-organism-response model, this study examines how and under what circumstances perceived environmental corporate social responsibility affects innovative behavior of employees in the context of environmental protection. Using a sample of 398 employees from different firms in the high energy-consuming industry of China, the results indicate that, at first, perceived ECSR provides a positive effect on organizational identification. Secondly, organizational identification has a positive influence on the innovative behavior of employees. Thirdly, organizational identification plays an important (...) mediating effect between perceived ECSR and the innovative behavior of employees. Fourthly, both the effect of perceived ECSR on organizational identification and the indirect effect of perceived ECSR on the innovative behavior of the employees via organizational identification will be stronger when the levels of organizational trust are high. These findings add new insights into the perceived ECSR-employees’ innovative behavior relationship and provide important managerial implications for enhancing ECSR perception to improve the innovative behavior of employees. (shrink)

The self/non-self model, first proposed by F.M. Burnet, has dominated immunology for 60 years now. According to this model, any foreign element will trigger an immune reaction in an organism, whereas endogenous elements will not, in normal circumstances, induce an immune reaction. In this paper we show that the self/non-self model is no longer an appropriate explanation of experimental data in immunology, and that this inadequacy may be rooted in an excessively strong metaphysical conception of biological (...) identity. We suggest that another hypothesis, one based on the notion of continuity, gives a better account of immune phenomena. Finally, we underscore the mapping between this metaphysical deflation from self to continuity in immunology and the philosophical debate between substantialism and empiricism about identity. (shrink)

Starting from a philosophical perspective, which states that the living structures are actually a combination between matter and information, this article presents the results on an analysis of the bipolar information-matter structure of the human organism, distinguishing three fundamental circuits for its survival, which demonstrates and supports this statement, as a base for further development of the informational model of consciousness to a general informational model of the human organism. For this, it was examined the Informational (...) System of the Human Body and its components from the perspective of the physics/information/neurosciences concepts, showing specific functions of each of them, highlighting the correspondence of these centers with brain support areas and with their projections in consciousness, which are: Center of Acquisition and Storing of Information (CASI) reflected in consciousness as memory, Center of Decision and Command (CDC) (decision), Info-Emotional Center (IES) (emotions), Maintenance Informational System (MIS) (personal status), Genetic Transmission System (GTS) (associativity/genetic transmission) and Info Genetic Generator (IGG) related by the body development and inherited behaviors. The Info Connection (IC), detected in consciousness as trust and confidence can explain the Near-Death Experiences (NDEs) and associated phenomena. This connection is antientropic and informational, because from the multitude of uncertain possibilities is selected a certain one, helping/supporting the survival and life. The human body appears therefore as a bipolar structure, connected to two poles: information and matter. It is argued that the survival, which is the main objective of the organism, is complied in three main ways, by means of: (i) the reactive operation for adaptation by attitude; (ii) the info-genetic integration of information by epigenetic processes and genetic transmission of information for species survival, both circuits (i) and (ii) being associated to the information pole; (iii) maintenance of the material body (defined as informed matter) and its functions, associated to the matter pole of the organism. It results therefore that the informational system of the human body is supported by seven informational circuits formed by the neuro-connections between the specific zones of the brain corresponding to the informational subsystems, the cognitive centers, the sensors, transducers and execution (motor/mobile) elements. The fundamental informational circuits assuring the survival are the reactive circuit, expressible by attitude, the epigenetic/genetic circuit, absorbing and codifying information to be transmitted to the next generations, and the metabolic circuit, connected to matter (matter pole). The presented analysis allows to extend the informational modeling of consciousness to an Informational Model of Consciousness and Organism, fully describing the composition/functions of the organism in terms of information/matter and neurosciences concept. (shrink)

This paper examines one of the central complaints regarding Locke’s Essay, namely, its supposed incoherence. The question is whether Locke can successfully maintain a materialistic conception of matter, while advancing a theory of knowledge that will constrain the possibilities for a cognitive accessto matter from the start. In approaching this question I concentrate on Locke’s account of unity. While material unity can be described in relation to Locke’s account of substance, real essence, and nominal essence, a separate discussion will be (...) called for altogether in the case of organic unity. In closing, I turn to Kant as a model for locating Locke’s purported incoherence, suggesting that his “skeptical idealism” yields the same epistemic advantages as those won by Kant’s “empirical realism.”. (shrink)

The word “organism” represents an original keyword of the early-modern philosophical world. As it was first developed by Leibniz, it seems to blend together two different conceptual paradigms: the Cartesian model of the “machines” and the Aristotelian legacy of the “individual natures”. According to the first, nature represents itself the prototype of any good mechanical functioning, but at the same time its inner development is explained by the occurrence of a normative dimension that rules the world of primitive (...) forces in the dynamics. For such reasons, the “organism” lexicon is affected by an internal stress that is extremely interesting to analyze for it seems to posit a normative turn acting from the within of a mechanically conceived notion of life. (shrink)

This paper is devoted to computer modelling of the development and regeneration of multicellular biological structures. Some species are able to regenerate parts of their body after amputation damage, but the global rules governing cooperative cell behaviour during morphogenesis are not known. Here, we consider a simplified model organism, which consists of tissues formed around special cells that can be interpreted as stem cells. We assume that stem cells communicate with each other by a set of signals, and (...) that the values of these signals depend on the distance between cells. Thus the signal distribution characterizes location of stem cells. If the signal distribution is changed, then the difference between the initial and the current signal distribution affects the behaviour of stem cells—e.g. as a result of an amputation of a part of tissue the signal distribution changes which stimulates stem cells to migrate to new locations, appropriate for regeneration of the proper pattern. Moreover, as stem cells divide and form tissues around them, they control the form and the size of regenerating tissues. This two-level organization of the model organism, with global regulation of stem cells and local regulation of tissues, allows its reproducible development and regeneration. (shrink)

This paper is devoted to computer modelling of the development and regeneration of multicellular biological structures. Some species are able to regenerate parts of their body after amputation damage, but the global rules governing cooperative cell behaviour during morphogenesis are not known. Here, we consider a simplified model organism, which consists of tissues formed around special cells that can be interpreted as stem cells. We assume that stem cells communicate with each other by a set of signals, and (...) that the values of these signals depend on the distance between cells. Thus the signal distribution characterizes location of stem cells. If the signal distribution is changed, then the difference between the initial and the current signal distribution affects the behaviour of stem cells—e.g. as a result of an amputation of a part of tissue the signal distribution changes which stimulates stem cells to migrate to new locations, appropriate for regeneration of the proper pattern. Moreover, as stem cells divide and form tissues around them, they control the form and the size of regenerating tissues. This two-level organization of the model organism, with global regulation of stem cells and local regulation of tissues, allows its reproducible development and regeneration. (shrink)

Although the basis of modern biology is Cartesian, Descartes’s theories of biology have been more often ridiculed than studied. Yet, Dennis Des Chene demonstrates, the themes, arguments, and vocabulary of his mechanistic biology pervade the writings of many seventeenth-century authors. In his illuminating account of Cartesian physiology in its historical context, Des Chene focuses on the philosopher’s innovative reworking of that field, including the nature of life, the problem of generation, and the concepts of health and illness. Des Chene begins (...) by surveying works that Descartes would likely have encountered, from late Aristotelian theories of the soul to medical literature and treatises on machines. The Cartesian theory of vital operations is examined, with particular attention to the generation of animals. Des Chene also considers the role of the machine-model in furnishing a method in physiology, the ambiguities of the notion of machine, and of Descartes’s problem of simulation. Finally, he looks at,the various kinds of unity of the body, both in itself and in its union with the soul. Spirits and Clocks continues Des Chene’s highly regarded exploration -- begun in his previous book, Life’s Form -- of the scholastic and Cartesian sciences as well as the dialogue between these two worldviews. Introduction 1 Part One - Tales of the Bête-Machine [ 1 ] - Self-Movers 13 [ 2 ] - Where Do Machines Come From? 32 [ 3 ] - The Uses of Usus 53 Part Two - Machines, Mechanisms, Bodies, Organs [ 4 ] - Tools of Knowledge 71 [ 5 ] - Jeux D’Artifice 103 [ 6 ] - Unity of the Body 116 Conclusion 153 Bibliography 159 Index 177. (shrink)

Consumer well-being is a micromarketing concept that emphasizes on contributions of marketing activities in social welfare. The major objective of the current study is to analyze the impact of self-incongruence on brand dissatisfaction, brand hate, and consumer well-being. This study has utilized the Self-incongruity Theory and the Stimulus-Organism-Response model to test the impact of self-incongruity on anti-consumption and consumer voice behaviors, and subsequent effects on consumer well-being. Data were collected from young consumers of technology products from major cities (...) of Pakistan. A total of 592 consumers answered a paper-and-pencil questionnaire using purposive sampling technique. The data were analyzed by partial least square structural equation modeling. The findings of this study reveal that functional and symbolic incongruity predict brand hate and dissatisfaction, which is positively related with brand retaliation. Brand retaliation is negatively related with consumer well-being. This study offers implications for product designers, marketers, advertisers and other stakeholders to improve congruence between what young consumers of technology products expect and what brands are offering to mitigate negative attitudes and behaviors and increase consumer well-being. (shrink)