Studies in History and Philosophy of Science Part C Studies in History and Philosophy of Biological and Biomedical Sciences (Stud Hist Philos Sci C Stud Hist Philos Biol Biomed Sci)

Publications in this journal

• Article: Complexity, adaptive complexity and the Creative View of natural selection.

  Pablo Razeto-Barry
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  ABSTRACT: In this paper, I respond to arguments proposed by Brunnander in this journal issue concerning my position regarding the Creative View of natural selection (Razeto-Barry & Frick, 2011). Brunnander argues that (i) the Creative View we defend does not serve to answer William Paley's question because (ii) Paley's question is "why there are complex things rather than simple ones" and (iii) natural selection cannot answer this question. Brunnander's arguments for (iii) defend a Non-creative View of natural selection (sensu Razeto-Barry & Frick, 2011). Here I claim that Brunnander's arguments for (iii) are mistaken and I also argue that even accepting (iii) we do not have to accept (i), given that statement (ii) is historically and conceptually flawed. Thus here I analyze Paley's question from a historical point of view and from a contemporary perspective in a quest for the potential conceptual relevance of Paley's question today. In this vein I argue that from a contemporary point of view statement (iii) may be correct but for different reasons than those adduced by Brunnander.
  Studies in History and Philosophy of Science Part C Studies in History and Philosophy of Biological and Biomedical Sciences 05/2013;
• Article: "My appointment received the sanction of the Admiralty": Why Charles Darwin really was the naturalist on HMS Beagle.

  John van Wyhe
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  ABSTRACT: For decades historians of science and science writers in general have maintained that Charles Darwin was not the 'naturalist' or 'official naturalist' during the 1831-1836 surveying voyage of HMS Beagle but instead Captain Robert FitzRoy's 'companion', 'gentleman companion' or 'dining companion'. That is, Darwin was primarily the captain's social companion and only secondarily and unofficially naturalist. Instead, it is usually maintained, the ship's surgeon Robert McCormick was the official naturalist because this was the default or official practice at the time. Although these views have been repeated in countless accounts of Darwin's life, this essay aims to show that they are incorrect.
  Studies in History and Philosophy of Science Part C Studies in History and Philosophy of Biological and Biomedical Sciences 05/2013;
• Article: Unformed Minds: Juveniles, Neuroscience, and the Law.

  Oren Harman
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  ABSTRACT: Recently, the question of adolescent culpability has been brought before the Supreme Court of the United States for reconsideration. Neuroscience, adolescent advocates claim, is teaching us that young people cannot be found fully responsible for their actions. The reason: their brains are not fully formed. Here I consider the history of the use of scientific evidence in the courtroom, a number of adolescent murder cases, and the data now emerging from neuroscience, and argue that when it comes to brains, judges, just like the rest of us, are unnecessarily impressed. Ultimately, how we determine culpability should rest on normative and ethical considerations rather than on scientific ones.
  Studies in History and Philosophy of Science Part C Studies in History and Philosophy of Biological and Biomedical Sciences 05/2013;
• Article: Synthetic biology and its alternatives. Descartes, Kant and the idea of engineering biological machines.

  Werner Kogge, Michael Richter
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  ABSTRACT: The engineering-based approach of synthetic biology is characterized by an assumption that 'engineering by design' enables the construction of 'living machines'. These 'machines', as biological machines, are expected to display certain properties of life, such as adapting to changing environments and acting in a situated way. This paper proposes that a tension exists between the expectations placed on biological artefacts and the notion of producing such systems by means of engineering; this tension makes it seem implausible that biological systems, especially those with properties characteristic of living beings, can in fact be produced using the specific methods of engineering. We do not claim that engineering techniques have nothing to contribute to the biotechnological construction of biological artefacts. However, drawing on Descartes's and Kant's thinking on the relationship between the organism and the machine, we show that it is considerably more plausible to assume that distinctively biological artefacts emerge within a paradigm different from the paradigm of the Cartesian machine that underlies the engineering approach. We close by calling for increased attention to be paid to approaches within molecular biology and chemistry that rest on conceptions different from those of synthetic biology's engineering paradigm.
  Studies in History and Philosophy of Science Part C Studies in History and Philosophy of Biological and Biomedical Sciences 04/2013;
• Article: Basic science through engineering? Synthetic modeling and the idea of biology-inspired engineering.

  Tarja Knuuttila, Andrea Loettgers
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  ABSTRACT: Synthetic biology is often understood in terms of the pursuit for well-characterized biological parts to create synthetic wholes. Accordingly, it has typically been conceived of as an engineering dominated and application oriented field. We argue that the relationship of synthetic biology to engineering is far more nuanced than that and involves a sophisticated epistemic dimension, as shown by the recent practice of synthetic modeling. Synthetic models are engineered genetic networks that are implanted in a natural cell environment. Their construction is typically combined with experiments on model organisms as well as mathematical modeling and simulation. What is especially interesting about this combinational modeling practice is that, apart from greater integration between these different epistemic activities, it has also led to the questioning of some central assumptions and notions on which synthetic biology is based. As a result synthetic biology is in the process of becoming more "biology inspired."
  Studies in History and Philosophy of Science Part C Studies in History and Philosophy of Biological and Biomedical Sciences 04/2013;
• Article: Racial discrimination: How not to do it.

  Adam Hochman
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  ABSTRACT: The UNESCO Statements on Race of the early 1950s are understood to have marked a consensus amongst natural scientists and social scientists that 'race' is a social construct. Human biological diversity was shown to be predominantly clinal, or gradual, not discreet, and clustered, as racial naturalism implied. From the seventies social constructionists added that the vast majority of human genetic diversity resides within any given racialised group. While social constructionism about race became the majority consensus view on the topic, social constructionism has always had its critics. Sesardic (2010) has compiled these criticisms into one of the strongest defences of racial naturalism in recent times. In this paper I argue that Sesardic equivocates between two versions of racial naturalism: a weak version and a strong version. As I shall argue, the strong version is not supported by the relevant science. The weak version, on the other hand, does not contrast properly with what social constructionists think about 'race'. By leaning on this weak view Sesardic's racial naturalism intermittently gains an appearance of plausibility, but this view is too weak to revive racial naturalism. As Sesardic demonstrates, there are new arguments for racial naturalism post-Human Genome Diversity Project. The positive message behind my critique is how to be a social constructionist about race in the post-genomic era.
  Studies in History and Philosophy of Science Part C Studies in History and Philosophy of Biological and Biomedical Sciences 04/2013;
• Article: Trait fitness is not a propensity, but fitness variation is.

  Elliott Sober
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  ABSTRACT: The propensity interpretation of fitness draws on the propensity interpretation of probability, but advocates of the former have not attended sufficiently to problems with the latter. The causal power of C to bring about E is not well-represented by the conditional probability Pr(E|C). Since the viability fitness of trait T is the conditional probability Pr(organism O survives to adulthood|O has T), the viability fitness of the trait does not represent the degree to which having the trait causally promotes surviving. The same point holds for fertility fitness. This failure of trait fitness to capture causal role can also be seen in the fact that coextensive traits must have the same fitness values even if one of them promotes survival and the other is neutral or deleterious. Although the fitness of a trait does not represent the trait's causal power to promote survival and reproduction, variation in fitness in a population causally promotes change in trait frequencies; in this sense, fitness variation is a population-level propensity.
  Studies in History and Philosophy of Science Part C Studies in History and Philosophy of Biological and Biomedical Sciences 04/2013;
• Article: Did Darwin really answer Paley's question?

  Björn Brunnander
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  ABSTRACT: It is commonly thought that natural selection explains the rise of adaptive complexity. Razeto-Barry and Frick (2011) have recently argued in favour of this view, dubbing it the Creative View. I argue that the Creative View is mistaken if it claims that natural selection serves to answer Paley's question. This is shown by a case that brings out the contrastive structure inherent in this demand for explanation. There is, however, a rather trivial sense in which specific environmental conditions are crucial for the rise of specific adaptations, but this is hardly what opponents of the Creative View are denying.
  Studies in History and Philosophy of Science Part C Studies in History and Philosophy of Biological and Biomedical Sciences 04/2013;
• Article: Images as tools. On visual epistemic practices in the biological sciences.

  Nina Samuel
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  ABSTRACT: Contemporary visual epistemic practices in the biological sciences raise new questions of how to transform an iconic data measurements into images, and how the process of an imaging technique may change the material it is 'depicting'. This case-oriented study investigates microscopic imagery, which is used by system and synthetic biologists alike. The core argument is developed around the analysis of two recent methods, developed between 2003 and 2006: localization microscopy and photo-induced cell death. Far from functioning merely as illustrations of work done by other means, images can be determined as tools for discovery in their own right and as objects of investigation. Both methods deploy different constellations of intended and unintended interactions between visual appearance and underlying biological materiality. To characterize these new ways of interaction, the article introduces the notions of 'operational images' and 'operational agency'. Despite all their novelty, operational images are still subject to conventions of seeing and depicting: Phenomena emerging with the new method of localization microscopy have to be designed according to image traditions of older, conventional fluorescence microscopy to function properly as devices for communication between physicists and biologists. The article emerged from a laboratory study based on interviews conducted with researchers from the Kirchhoff-Institute for Physics and German Cancer Research Center (DKFZ) at Bioquant, Heidelberg, in 2011.
  Studies in History and Philosophy of Science Part C Studies in History and Philosophy of Biological and Biomedical Sciences 04/2013;
• Article: Synthetic biology and the technicity of biofuels.

  Adrian Mackenzie
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  ABSTRACT: The principal existing real-world application of synthetic biology is biofuels. Several 'next generation biofuel' companies-Synthetic Genomics, Amyris and Joule Unlimited Technologies-claim to be using synthetic biology to make biofuels. The irony of this is that highly advanced science and engineering serves the very mundane and familiar realm of transport. Despite their rather prosaic nature, biofuels could offer an interesting way to highlight the novelty of synthetic biology from several angles at once. Drawing on the French philosopher of technology and biology Gilbert Simondon, we can understand biofuels as technical objects whose genesis involves processes of concretisation that negotiate between heterogeneous geographical, biological, technical, scientific and commercial realities. Simondon's notion of technicity, the degree of concretisation of a technical object, usefully conceptualises this relationality. Viewed in terms of technicity, we might understand better how technical entities, elements, and ensembles are coming into being in the name of synthetic biology. The broader argument here is that when we seek to identify the newness of disciplines, their newness might be less epistemic and more logistic.
  Studies in History and Philosophy of Science Part C Studies in History and Philosophy of Biological and Biomedical Sciences 04/2013;
• Article: Synthetic biology and genetic causation.

  Gry Oftedal, Veli-Pekka Parkkinen
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  ABSTRACT: Synthetic biology research is often described in terms of programming cells through the introduction of synthetic genes. Genetic material is seemingly attributed with a high level of causal responsibility. We discuss genetic causation in synthetic biology and distinguish three gene concepts differing in their assumptions of genetic control. We argue that synthetic biology generally employs a difference-making approach to establishing genetic causes, and that this approach does not commit to a specific notion of genetic program or genetic control. Still, we suggest that a strong program concept of genetic material can be used as a successful heuristic in certain areas of synthetic biology. Its application requires control of causal context, and may stand in need of a modular decomposition of the target system. We relate different modularity concepts to the discussion of genetic causation and point to possible advantages of and important limitations to seeking modularity in synthetic biology systems.
  Studies in History and Philosophy of Science Part C Studies in History and Philosophy of Biological and Biomedical Sciences 04/2013;
• Article: Integration of approaches in David Wake's model-taxon research platform for evolutionary morphology.

  James Griesemer
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  ABSTRACT: What gets integrated in integrative scientific practices has been a topic of much discussion. Traditional views focus on theories and explanations, with ideas of reduction and unification dominating the conversation. More recent ideas focus on disciplines, fields, or specialties; models, mechanisms, or methods; phenomena, problems. How integration works looks different on each of these views since the objects of integration are ontologically and epistemically various: statements, boundary conditions, practices, protocols, methods, variables, parameters, domains, laboratories, and questions all have their own structures, functions and logics. I focus on one particular kind of scientific practice, integration of "approaches" in the context of a research system operating on a special kind of "platform." Rather than trace a network of interactions among people, practices, and theoretical entities to be integrated, in this essay I focus on the work of a single investigator, David Wake. I describe Wake's practice of integrative evolutionary biology and how his integration of approaches among biological specialties worked in tandem with his development of the salamanders as a model taxon, which he used as a platform to solve, re-work and update problems that would not have been solved so well by non-integrative approaches. The larger goal of the project to which this paper contributes is a counter-narrative to the story of 20th century life sciences as the rise and march of the model organisms and decline of natural history.
  Studies in History and Philosophy of Science Part C Studies in History and Philosophy of Biological and Biomedical Sciences 04/2013;
• Article: Confusions about race: A new installment.

  Neven Sesardic
  Studies in History and Philosophy of Science Part C Studies in History and Philosophy of Biological and Biomedical Sciences 04/2013;
• Article: The simulation approach in synthetic biology.

  Gabriele Gramelsberger
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  ABSTRACT: Synthetic biology and systems biology are often highlighted as antagonistic strategies for dealing with the overwhelming complexity of biology (engineering versus understanding; tinkering in the lab versus modelling in the computer). However, a closer view of contemporary engineering methods (inextricably interwoven with mathematical modelling and simulation) and of the situation in biology (inextricably confronted with the intrinsic complexity of biomolecular environments) demonstrates that tinkering in the lab is increasingly supported by rational design methods. In other words: Synthetic biology and systems biology are merged by the use of computational techniques. These computational techniques are needed because the intrinsic complexity of biomolecular environments (stochasticity, non-linearities, system-level organization, evolution, independence, etc.) require advanced concepts of bio bricks and devices. A philosophical investigation of the history and nature of bio parts and devices reveals that these objects are imitating generic objects of engineering (switches, gates, oscillators, sensors, etc.), but the well-known design principles of generic objects are not sufficient for complex environments like cells. Therefore, the rational design methods have to be used to create more advanced generic objects, which are not only generic in their use, but also adaptive in their behavior. Case studies will show how simulation-based rational design methods are used to identify adequate parameters for synthesized designs (stability analyses), to improve lab experiments by 'looking through noise' (estimation of hidden variables and parameters), and to replace laborious and time-consuming post hoc tweaking in the lab by in-silico guidance (in-silico variation of bio brick properties). The overall aim of these developments, as will be argued in the discussion, is to achieve adaptive-generic instrumentality for bio parts and devices and thus increasingly merging systems and synthetic biology.
  Studies in History and Philosophy of Science Part C Studies in History and Philosophy of Biological and Biomedical Sciences 04/2013;
• Article: Cancer and the goals of integration.

  Anya Plutynski
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  ABSTRACT: Cancer is not one, but many diseases, and each is a product of a variety of causes acting (and interacting) at distinct temporal and spatial scales, or "levels" in the biological hierarchy. In part because of this diversity of cancer types and causes, there has been a diversity of models, hypotheses, and explanations of carcinogenesis. However, there is one model of carcinogenesis that seems to have survived the diversification of cancer types: the multi-stage model of carcinogenesis. This paper examines the history of the multistage theory, and uses the theory as a case study in the limits and goals of unification as a theoretical virtue, comparing and contrasting it with "integrative" research.
  Studies in History and Philosophy of Science Part C Studies in History and Philosophy of Biological and Biomedical Sciences 04/2013;
• Article: Two sides of the same coin? The (techno)epistemic cultures of systems and synthetic biology.

  Karen Kastenhofer
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  ABSTRACT: Systems and synthetic biology both emerged around the turn of this century as labels for new research approaches. Although their disciplinary status as well as their relation to each other is rarely discussed in depth, now and again the idea is invoked that both approaches represent 'two sides of the same coin'. The following paper focuses on this general notion and compares it with empirical findings concerning the epistemic cultures prevalent in the two contexts. Drawing on interviews with researchers from both fields, on participatory observation in conferences and courses and on documentary analysis, this paper delineates differences and similarities, incompatibilities and blurred boundaries. By reconstructing systems and synthetic biology's epistemic cultures, this paper argues that they represent two 'communities of vision', encompassing heterogeneous practices. Understanding the relation of the respective visions of understanding nature and engineering life is seen as indispensible for the characterisation of (techno)science in more general terms. Depending on the conceptualisation of understanding and construction (or: science and engineering), related practices such as in silico modelling for enhancing understanding or enabling engineering can either be seen as incommensurable or 'two sides of one coin'.
  Studies in History and Philosophy of Science Part C Studies in History and Philosophy of Biological and Biomedical Sciences 04/2013;
• Article: Digital 'faces' of synthetic biology.

  Kathrin Friedrich
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  ABSTRACT: In silicio design plays a fundamental role in the endeavour to synthesise biological systems. In particular, computer-aided design software enables users to manage the complexity of biological entities that is connected to their construction and reconfiguration. The software's graphical user interface bridges the gap between the machine-readable data on the algorithmic subface of the computer and its human-amenable surface represented by standardised diagrammatic elements. Notations like the Systems Biology Graphical Notation (SBGN), together with interactive operations such as drag & drop, allow the user to visually design and simulate synthetic systems as 'bio-algorithmic signs'. Finally, the digital programming process should be extended to the wet lab to manufacture the designed synthetic biological systems. By exploring the different 'faces' of synthetic biology, I argue that in particular computer-aided design (CAD) is pushing the idea to automatically produce de novo objects. Multifaceted software processes serve mutually aesthetic, epistemic and performative purposes by simultaneously black-boxing and bridging different data sources, experimental operations and community-wide standards. So far, synthetic biology is mainly a product of digital media technologies that structurally mimic the epistemological challenge to take both qualitative as well as quantitative aspects of biological systems into account in order to understand and produce new and functional entities.
  Studies in History and Philosophy of Science Part C Studies in History and Philosophy of Biological and Biomedical Sciences 04/2013;
• Article: When one model is not enough: Combining epistemic tools in systems biology.

  Sara Green
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  ABSTRACT: In recent years, the philosophical focus of the modeling literature has shifted from descriptions of general properties of models to an interest in different model functions. It has been argued that the diversity of models and their correspondingly different epistemic goals are important for developing intelligible scientific theories (Leonelli, 2007; Levins, 2006). However, more knowledge is needed on how a combination of different epistemic means can generate and stabilize new entities in science. This paper will draw on Rheinberger's practice-oriented account of knowledge production. The conceptual repertoire of Rheinberger's historical epistemology offers important insights for an analysis of the modelling practice. I illustrate this with a case study on network modeling in systems biology where engineering approaches are applied to the study of biological systems. I shall argue that the use of multiple representational means is an essential part of the dynamic of knowledge generation. It is because of-rather than in spite of-the diversity of constraints of different models that the interlocking use of different epistemic means creates a potential for knowledge production.
  Studies in History and Philosophy of Science Part C Studies in History and Philosophy of Biological and Biomedical Sciences 04/2013;
• Article: Creating parts that allow for rational design: Synthetic biology and the problem of context-sensitivity.

  Stephan Güttinger
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  ABSTRACT: The parts-based engineering approach in synthetic biology aims to create pre-characterised biological parts that can be used for the rational design of novel functional systems. Given the context-sensitivity of biological entities, a key question synthetic biologists have to address is what properties these parts should have so that they give a predictable output even when they are used in different contexts. In the first part of this paper I will analyse some of the answers that synthetic biologists have given to this question and claim that the focus of these answers on parts and their properties does not allow us to tackle the problem of context-sensitivity. In the second part of the paper, I will argue that we might have to abandon the notions of parts and their properties in order to understand how independence in biology could be achieved. Using Robert Cummins' account of functional analysis, I will then develop the notion of a capacity and its condition space and show how these notions can help to tackle the problem of context-sensitivity in biology.
  Studies in History and Philosophy of Science Part C Studies in History and Philosophy of Biological and Biomedical Sciences 04/2013;