In this paper we address the issue of how to think about immunity. Many immunological writings suggest a straightforward option: the view that the immune system is primarily a system of defense, which naturally invites the talk of strong immunity and strong immune response. Despite their undisputable positive role in immunology, such metaphors can also pose a risk of establishing a narrow perspective, omitting from consideration phenomena that do not neatly fit those powerful metaphors. Building on this analysis, we argue (...) two things. First, we argue that the immune system is involved not only in defense. Second, by disentangling various possible meanings of ‘strength’ and ‘weakness’ in immunology, we also argue that such a construal of immunity generally contributes to the distortion of the overall picture of what the immune system is, what it does, and why it sometimes fails. Instead, we propose to understand the nature of the immune system in terms of contextuality, regulation, and trade-offs. We suggest that our approach provides lessons for a general understanding of the organizing principles of the immune system in health and disease. For all this to work, we discuss a wide range of immunological phenomena. (shrink)

The emerging field of synthetic biology aims to engineer novel biological entities. The envisioned future bio-based economy builds largely on “cell factories”: organisms that have been metabolically engineered to sustainably produce substances for human ends. In this paper, we argue that synthetic biology’s goal of creating efficient production vessels for industrial applications implies a set of ontological assumptions according to which living organisms are machines. Traditionally, a machine is understood as a technological, isolated and controllable production unit consisting of parts. (...) But modified organisms, or hybrids, require us to think beyond the machine paradigm and its associated dichotomies between artificial and natural, organisms and artefacts. We ask: How may we conceptualise hybrids beyond limiting ontological categories? Our main claim is that the hybrids created by synthetic biology should be considered not as machines but as metabolic systems. We shall show how the philosophical account of metabolism can inform an ontology of hybrids that moves beyond what we call the “machine ontology”, considering that metabolism enables thinking beyond the dominant dichotomies and allows us to understand and design lifeforms in a bio-based economy. Thus, the aim of this paper is twofold: first, to develop the philosophical ontology of hybrids, and second, to move synthetic biology beyond the problematically limiting view of hybrids. (shrink)

The notion of a genetic program has been widely criticized by both biologists and philosophers. But the debate has revolved around a narrow conception of what programs are and how they work, and many criticisms are linked to this same conception. To remedy this, I outline a modern and more apt idea of a program that possesses many of the features critics thought missing from programs. Moving away from over-simplistic conceptions of programs opens the way to a more fruitful interplay (...) of ideas between the complexity of biology and our most complex engineering discipline. (shrink)

In 1926, Haldane published an essay titled 'On Being the Right Size' in which he argued that the structure, function, and behavior of an organism are strongly conditioned by the physical forces that exert the greatest impact at the scale at which it exists. This chapter puts Haldane’s insight to work in the context of contemporary cell and molecular biology. Owing to their minuscule size, cells and molecules are subject to very different forces than macroscopic organisms. In a sense, macroscopic (...) and microscopic entities inhabit different “worlds”: the former is ruled by gravity and inertia, whereas the latter is governed by Brownian motion. One implication is that we should be extremely skeptical of models and analogies that seek to explain properties of microscopic entities by appealing to properties of macroscopic ones. Unfortunately, this is precisely what the appeal to engineering metaphors in molecular biology attempts to do. Molecular biologists routinely resort to such metaphors because they are familiar and intuitively intelligible. But if our machines were the size of molecules it would be impossible for them to function the way they do. It follows that we should avoid distorting biological reality by construing it in engineering terms. In this chapter I examine four key metaphors in molecular biology – “genetic program,” “cellular circuitry,” “molecular machine,” and “molecular motor” – and I argue that their deficiencies derive from their neglect of scale. I also try to explain why many biologists today appear to have forgotten the importance of scale that Haldane drew attention to in his essay. I suggest that the reason has to do with the influence of Schrödinger’s argument in 'What is Life?' regarding the stability of the gene. (shrink)

The biophilosophic justification for the idea that “brain death” is death needs to support two claims: that what dies in human death is a human organism, not merely a psychological entity distinct from it; that total brain failure signifies the end of the human organism as a whole. Defenders of brain death typically assume without argument that the first claim is true and argue for the second by defending the “integrative unity” rationale. Yet the integrative unity rationale has fallen on (...) hard times. In this article, I give reasons for why we should think of ourselves as organisms, and why the “fundamental work” rationale put forward by the 2008 President’s Council is better than the integrative unity rationale, despite persistent objections to it. (shrink)

It has become customary to conceptualize the living cell as an intricate piece of machinery, different to a man-made machine only in terms of its superior complexity. This familiar understanding grounds the conviction that a cell's organization can be explained reductionistically, as well as the idea that its molecular pathways can be construed as deterministic circuits. The machine conception of the cell owes a great deal of its success to the methods traditionally used in molecular biology. However, the recent introduction (...) of novel experimental techniques capable of tracking individual molecules within cells in real time is leading to the rapid accumulation of data that are inconsistent with an engineering view of the cell. This paper examines four major domains of current research in which the challenges to the machine conception of the cell are particularly pronounced: cellular architecture, protein complexes, intracellular transport, and cellular behaviour. It argues that a new theoretical understanding of the cell is emerging from the study of these phenomena which emphasizes the dynamic, self-organizing nature of its constitution, the fluidity and plasticity of its components, and the stochasticity and non-linearity of its underlying processes. (shrink)

This chapter argues that scientific and philosophical progress in our understanding of the living world requires that we abandon a metaphysics of things in favour of one centred on processes. We identify three main empirical motivations for adopting a process ontology in biology: metabolic turnover, life cycles, and ecological interdependence. We show how taking a processual stance in the philosophy of biology enables us to ground existing critiques of essentialism, reductionism, and mechanicism, all of which have traditionally been associated with (...) substance ontology. We illustrate the consequences of embracing an ontology of processes in biology by considering some of its implications for physiology, genetics, evolution, and medicine. And we attempt to locate the subsequent chapters of the book in relation to the position we defend. (shrink)

This chapter draws on insights from non-equilibrium thermodynamics to demonstrate the ontological inadequacy of the machine conception of the organism. The thermodynamic character of living systems underlies the importance of metabolism and calls for the adoption of a processual view, exemplified by the Heraclitean metaphor of the stream of life. This alternative conception is explored in its various historical formulations and the extent to which it captures the nature of living systems is examined. Following this, the chapter considers the metaphysical (...) implications of reconceptualizing the organism from complex machine to flowing stream. What do we learn when we reject the mechanical and embrace the processual? Three key lessons for biological ontology are identified. The first is that activity is a necessary condition for existence. The second is that persistence is grounded in the continuous self-maintenance of form. And the third is that order does not entail design. (shrink)

The metaphor is used in the construction process of scientific knowledge. There are, however, metaphors that do not suit the objects they should represent, which thus impacts the accuracy of the knowledge which derives from these objects. It is the case of the machine metaphor, when resorted to in the study of living organisms. Canguilhem has tackled problems it created in twentieth-century life sciences head on. In his criticism, he links the analysis of Descartes’ work to his own philosophical thesis (...) on “biological normativity”. By doing so, he so sheds a light on the pitfalls, both historical and biological, over which the machine metaphor stumbles. He thereby orders sciences to periodically make sure of the relevance of their metaphors and explanatory models to their objects. (shrink)

Recognition of the plasticity of development — from gene expression to neuroplasticity — is increasingly undermining the traditional distinction between structure and function, or anatomy and behavior. At the same time, dynamic systems theory — a set of tools and concepts drawn from the physical sciences — has emerged as a way of describing what Maurice Merleau-Ponty calls the “dynamic anatomy” of the living organism. This article surveys and synthesizes dynamic systems models of development from biology, neuroscience, and psychology in (...) order to propose an integrated account of growth, learning, and behavior. Key to this account is the concept of self-differentiation or symmetry-breaking. I argue that development can be understood as a cascade of symmetry-breaking events brought about by the ongoing interactions of multiple, nested, nonlinear dynamic systems whose self-organizing behaviors gradually alter their own anatomical conditions. I begin by introducing the concept of symmetry-breaking as a way of understanding anatomical development. I then extend this approach to motor development by arguing that the organism’s behavior grows along with its body, like a new organ. Finally, I argue that the organism’s behavior and its world grow together dialectically, each driving the other to become more complex and asymmetrical through its own increasing asymmetry. Thus development turns out to be a form of cognition or sense-making, and cognition a form of development. (shrink)

The notion of biological function is fraught with difficulties—intrinsically and irremediably so, we argue. The physiological practice of functional ascription originates from a time when organisms were thought to be designed and remained largely unchanged since. In a secularized worldview, this creates a paradox which accounts of functions as selected effect attempt to resolve. This attempt, we argue, misses its target in physiology and it brings problems of its own. Instead, we propose that a better solution to the conundrum of (...) biological functions is to abandon the notion altogether, a prospect not only less daunting than it appears, but arguably the natural continuation of the naturalisation of biology. (shrink)

This introduction to a special section of Phenomenology and the Cognitive Sciences reviews some historical and contemporary results concerning the role of development in cognition and experience, arguing that at this juncture development is an important topic for research in phenomenology and the cognitive sciences. It then suggests some ways in which the concept of development is in need of rethinking, in relation to the phenomena, and reviews the contributions that articles in the section make toward this purpose.

We develop here a semiotic model of evolution. We point out the role of confusion and choice as a condition for semiosis, which is a precondition for semiotic learning and semiotic adaptation. Semiosis itself as interpretation and decision-making between options requires phenomenal present. The body structure of the organism is largely a product of former semiosis. The organism’s body together with the structure of the ecosystem serves also as a scaffolding for the sign processes that carry on the ontogenetic cycle (...) and the organisms’ behaviour, providing the experience-based channels for decision making in the indeterminate situations of choice. The stability and persistence of ontogenesis and behaviour are based on the plasticity, or the multiviality of organic dynamics. The same plasticity or multivial dynamics is providing the material for further potential evolution. Evolution has occurred when some change becomes irreversible via its stabilization, and it usually means a modification of existing constraints, or scaffoldings. Some examples of these processes are described in the article. (shrink)

A crucial question for a process view of life is how to identify a process and how to follow it through time. The genidentity view can contribute decisively to this project. It says that the identity through time of an entity X is given by a well-identified series of continuous states of affairs. Genidentity helps address the problem of diachronic identity in the living world. This chapter describes the centrality of the concept of genidentity for David Hull and proposes an (...) extension of Hull’s view to the ubiquitous phenomenon of symbiosis. Finally, using immunology as a key example, it shows that the genidentity view suggests that the main interest of a process approach is epistemological rather than ontological and that its principal claim is one of priority, namely that processes precede and define things, and not vice versa. (shrink)

This article is concerned with two interrelated questions: what, if anything, distinguishes synthetic from natural organisms, and to what extent, if any, creating the former is of moral significance. These are ontological and ethical questions, respectively. As the title indicates, I address both from a broadly neo-Aristotelian perspective, i.e. a teleological philosophy of life and virtue ethics. For brevity’s sake, I shall not argue for either philosophical position at length, but instead hope to demonstrate their legitimacy through their explanatory power. (...) I firstly argue that synthetic organisms differ in kind from natural organisms and machines, and differ only by degree from genetically modified organisms. I then suggest that this is nevertheless sufficient to give us specific ethical reservations about synthetic biology: namely, that more than any other widely used biotechnology, it is characterised by a drive to mastery that stands opposed to due appreciation of the giftedness of life. (shrink)

Within biology and in society, living creatures have long been described using metaphors of machinery and computation: ‘bioengineering’, ‘genes as code’ or ‘biological chassis’. This paper builds on Lakoff and Johnson’s argument that such language mechanisms shape how we understand the world. I argue that the living machines metaphor builds upon a certain perception of life entailing an idea of radical human control of the living world, looking back at the historical preconditions for this metaphor. I discuss how design is (...) perceived to enable us to shape natural beings to our will, and consider ethical, epistemological and ontological implications of the prevalence of this metaphor, focusing on its use within synthetic biology. I argue that we urgently need counter-images to the dominant metaphor of living machines and its implied control and propose that artworks can provide such counter-images through upsetting the perception of life as controllable. This is argued through discussion of artworks by Oron Catts and Ionat Zurr, by Tarsh Bates and by Ai Hasegawa, which in different ways challenge mechanistic assumptions through open-ended engagement with the strangeness and messiness of life. (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)

La biología sintética encierra un enorme potencial transformador de los organismos vivos, incluyendo en un futuro quizás no muy lejano la transformación del propio genoma humano. Son claras las conexiones que pueden establecerse entre este enorme potencial transformador y las pretensiones de los partidarios del biomejoramiento humano. La construcción de genomas completamente sintéticos puede cambiar de forma definitiva e irreversible aspectos fundamentales de la vida humana, quizás hasta el punto de dar lugar a un organismo que difiera de nuestra especie (...) como ahora nosotros podemos diferir de los grandes simios. En este artículo se discuten los principales pros y contras que ha suscitado este debate, señalando algunos de los presupuestos más problemáticos de las propuestas recientes sobre el biomejoramiento humano. (shrink)

A widespread and influential characterization of synthetic biology emphasizes that synthetic biology is the application of engineering principles to living systems. Furthermore, there is a strong tendency to express the engineering approach to organisms in terms of what seems to be an ontological claim: organisms are machines. In the paper I investigate the ontological and heuristic significance of the machine analogy in synthetic biology. I argue that the use of the machine analogy and the aim of producing rationally designed organisms (...) does not necessarily imply a commitment to mechanical biology. The ideal of applying engineering principles to biology is best understood as expressing recognition of the machine-unlikeness of natural organisms and the limits of human cognition. The paper suggests an interpretation of the identification of organisms with machines in synthetic biology according to which it expresses a strategy for representing, understanding, and constructing living systems that are more machine-like than natural organisms. (shrink)

It is widely assumed that functional and dispositional properties are not identical to their physical base, but that there is some kind of asymmetrical ontological dependence between them. In this regard, a popular idea is that the former are realized by the latter, which, under the non-identity assumption, is generally understood to be a non-causal, constitutive relation. In this paper we examine two of the most widely accepted approaches to realization, the so-called ‘flat view’ and the ‘dimensioned view’, and we (...) analyze their explanatory relevance in the light of a number of examples from the life sciences, paying special attention to developmental phenomena. Our conclusion is that the emphasis placed by modern-day biology on such properties as variability, evolvability, and a whole collection of phenomena like modularity, robustness, and developmental constraint or developmental bias requires the adoption of a much more dynamic perspective than traditional realization frameworks are able to capture. (shrink)

There is a belief that exercise has a major role to play in the current health and wellbeing agendas. Consequently, health interventions are implemented based upon the recommendations of the ACSM and similar exercise research organizations. However this development has been challenged through both social and political perspectives. Specifically accusations of medicalization have been raised against the increasing relationship between the exercise and medical domains. The purpose of this article is to present a similar critique of the growing emergence of (...) a medical paradigm within the exercise domain. In this instance the focus will examine the relationship between exercise professional, exercise science and the proposed medical paradigm. Through the use of philosophical essay and systematic review of literature, it is argued that a continuing shift by exercise science to mirror the medical paradigm will cause a number of issues and potential hazards in the working practices of its professionals. (shrink)