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Models, Mechanisms and Algorithms: University of Helsinki Tentative programme Monday 2.5.2011:
Tuesday 3.5.2011 Closed workshop day. More informal presentations on work in progress
Science may define itself by standard procedures on a methodological level. With modern biology however standardization is no longer a question of methods only, it takes place on a material level as well: model organisms, standard materials. What Tom Knight called »biobricks« looks like the latest step in this direction. Images play a crucial role in this process of standardization on a material level.
Jane Calvert (University of Edinburgh) Synthetic Biology aims to construct novel living systems, and redesign existing ones for useful purposes. What makes it particularly interesting is that diverse groups including social scientists, ethicists, lawyers, policy makers, artists, designers and publics are becoming involved in the field from the outset. This paper explores a subset of these new forms of collaboration, by drawing on data from the ‘Synthetic Aesthetics’ project, which brings six artists and designers together with six synthetic biologists in reciprocal embedded residences. A feature of synthetic biology that lends itself to these kinds of collaborations is the desire to make biology into a product of design choices, rather than evolutionary pressures. These design choices could include industrial, political and aesthetic concerns. Importantly, if something is designed then this gives rise to questions such as: For what purpose is it designed? And, who is it designed for? These questions bring in values and politics, and open up the field to broader discussion. This ‘opening up’ is also an aspiration of many social scientists working in synthetic biology. Social scientists, artists and designers have much in common in this sense: they are actively engaged in forging new collaborations with synthetic biology, they aim to critically interrogate the science, and they are concerned with exploring implicit assumptions and possible alternatives to these. The paper ends by evaluating the project's on-going attempts to develop new forms of collaboration, to provide new spaces for cooperation and debate, and to promote critical reflection on all sides. Ursula Dam (Weimar) Questions are asked in Twitter or put to Google; “world knowledge” is updated on the Internet where the horizon of knowledge is determined by the precision and scope of algorithms. Programme updates of search engines and web portals are the tides of the "Cloud". Not only is the mind experiencing a technology driven update of reality, but engineers of synthetic biology have drafted new types of symbiosis, better pets and livestock or enable the breaking down of physical boundaries."Self" awareness is cultivated on a framework of technology. These developments are barely visible in contemporary art, for technical tools rarely find their way into this discipline. Although digital technologies have become a matter of course in production processes, it is only in the fields of Science & Art and Media Art that the discourse on technology informs the work’s message. The domain of art is in museums, galleries, art fairs, studios, collections and living rooms. For most people it is a leisure pursuit and is categorically separated from the daily work routine.So who is designing the lifestyles of tomorrow? Hasn’t it long been the engineers, whose work so greatly impacts on our daily way of life? Are engineers aware that they are not only drafting technical artefacts, but also shaping culture? Based on these questions we artists and researchers (based at Ruprecht-Karls University Heidelberg and the Bauhaus-University Weimar) have allowed our thoughts to wander to the near future and created a web shop full of speculative, synthetic biological products: super-cell.org. The scientists have charmed us with their curiosity for images of the future that illustrate the promises of their discoveries. Together we have brought these perspectives to life and taken them one step further. We found a scenario between reckless fantasy and timid fear of the uncertain consequences. In both, we have attempted to develop strategies for action, dedicated to meaningfulness but also the necessity to interpret the diverse emotions that arose in the course of our research. Kathrin Friedrich (Academy of Media Arts Cologne) Recent attempts to design, model and produce synthetic biological entities significantly rely on computer-aided design tools and the integration as well as standardization of graphical notation systems. But projects to establish a community wide consistent visual language in biology are not new and could also be linked to developments in information visualisation and graphic semiology. The presentation traces back exemplarily efforts and shows the ‘promises and perils’ of some of the latest developments in visual programming within the fields of systems and synthetic biology.
Axel Gelfert (National University of Singapore): Synthetic biology presents a challenge for traditional accounts of biology: Whereas traditional biology emphasises the evolvability, variability, and heterogeneity of living organisms, synthetic biology envisions a future technoscience of homogeneous, artificially designed systems that may be combined in modular fashion. Nowhere is this contrast clearer than in attempts to develop ‘biobricks’ – that is, homogeneous building blocks that conform to clear manufacturing protocols and exhibit predictable behaviour in accordance with technical specifications. In the present paper, I argue that this development not only is revisionist of the character of (the dominant mode of) theoretical knowledge in biology, but that it also adds a new dimension to the role of models in biology, and especially our conception of ‘model organisms’. Traditionally, model organisms were derived from extant species through controlled breeding. Synthetic biology holds the promise of developing – from scratch, through the construction of artificial life forms – new material instantiations of biological processes, which in turn may then function as representations of more complex organisms. One might suspect this development to lead to an intrusion of ‘top-down’ modes of theorising into biology. By contrast, I wish to argue that synthetic biology represents a shift away from theoretical knowledge and explanation, towards ‘thing knowledge’, which derives its justification from instrumental success. With the increasingly likely creation of synthetic life forms (such as Mycoplasma laboratorium), the contrast between technical artifacts and living systems is likely to be eroded, thereby posing a challenge to the traditional focus on representation and explanation in our scientific accounts of how biological systems work. Gabriele Gramelsberger (Freie Universität Berlin) Cell biology is a scientific discipline, which is widely based on wet lab experiments and ‘thing knowledge’. But during the past years computer based simulations have extensively entered the scene. Most important, they have influenced the experimental style of cell biology by introducing a more process orientated knowledge into biology. For instance, experiments have turned from start/end experiments into time resolved experiments. The reason therefore is to gain increasing knowledge about time based processes and developments, which are required for running and evaluating computer based simulations. The paper will explore the ‘process knowledge’ in biology, which increasingly allows merging simulation and experimentation. Furthermore, it will argue that–introducing a process resp. simulation approach–introduces the ‘engineering paradigm’ into biology. As the term ‘engineering’ is often interlinked with practices and ‘thing knowledge’, the paper will instead discuss Gaston Bachelard’s theory-orientated concept of ‘technical realism’ in order to show that the process resp. simulation approach interfere even in the run-up of wet lab experiments, turning cell biology necessarily into synthetic biology.
Tarja Knuuttila (University of Helsinki): In philosophical discussion models have typically been located between theories and experiments. Although the relationship between models and theories may seem closer than the one between models and experiments, there is a growing body of literature that focuses on the similarities and differences between modeling and experimentation. The modeling practice of synthetic biology seems especially interesting from this mediating perspective on modeling as it combines experiments on model organisms, mathematical models (and their simulations), and synthetic models. Often the very same scientists perform all these three different types of epistemic activities. Presumably, there are good reasons for why synthetic biologists proceed in such a combinatorial manner. We will argue that this is due to the characteristic constraints of each of the aforementioned model types and the various materialities they embody. We will exemplify this claim by examining a specific synthetic model, the Repressilator, and its place in the modeling practice of synthetic biology. The Repressilator, like other synthetic models, is of the same materiality as model organisms since it is made of biological materials, such as genes and proteins. On the other hand, it differs from model organisms in that it is not a result of any evolutionary process, being instead an engineered entity designed on the basis of a specific mathematical model. In synthetic modeling, as exemplified by the case of the Repressilator, the biological system/mechanism under investigation is explored by a two-way strategy: First, by constructing the model from the “same stuff” (Morgan 2003) and second, by inquiring to which extent the structure and dynamics of the model agrees with what is known of biological systems (Parker 2009).
Synthetic biology implies the expectation that it will become possible to construct biological functional systems (machines) by means of engineering. Accordingly, “engineering” and “design” are crucial terms in the discourse around synthetic biology. My paper investigates the presuppositions upon which that expectation rests. To this end, I first clarify the relationship between the concept of engineering and the concept of design, and ask what “design” means in this context. I then draw on Descartes and Kant to outline the problems to be found in the project of engineering the properties of living beings within the paradigm of the Cartesian machine. In a third step, I address alternative conceptions of the machine, showing that the expectations placed in biological machines in fact more closely match the concept of the machine which, precisely, escapes “engineering by design”, key aspects here being situatedness, robustness and autonomy. In the paper’s conclusion, a paradigm of biotechnological action emerges that differs markedly – in the mode of its procedures, the nature of its capabilities and the manner in which it is learned – from synthetic biology’s current engineering paradigm.
Gry Oftedal (University of Oslo): I will present the PSBio project, what it is and what it aims at, and possible connections from PSBio questions to philosophical questions in synthetic biology. PSBio is a NOS-HS project based at the University of Oslo with participants in Oslo, Helsinki and Copenhagen. It centres on philosophy of systems biology and the sub-themes “systems and parts”, “levels and causes” and “methods and epistemological issues”. So far the main focus has been on systems level causation, reduction, mechanistic explanations, and differing norms, concepts, and research approaches among systems biology researchers. Veli-Pekka Parkkinen (University of Oslo): This paper investigates the evidential and explanatory import of gene-knockout experiments in the light of counterfactual and mechanistic theories of explanation. The idea that knockouts provide causal information by revealing counterfactual dependencies between gene-activation and phenotype is analyzed in terms of Woodward’s (2003) counterfactual-interventionist theory of causal explanation. Given that the robustness features of biological systems often prevent the effects of knockouts from satisfying Woodward’s criteria for causal intervention, it is argued that such results alone are poor evidence for claims of genetic causation of phenotypes. The paper then employs the central ideas of Craver’s (2007) mechanistic theory of explanation to characterize the knockout as a method for discovering compositional relations. Taking to account the constitutive nature of mechanistic understanding of system behavior, the knockout can be seen as an investigation into how a targeted intervention on a composite part induces a system-level reaction – a bottom-up experiment in Craver's terminology. Implications of this type of explanatory strategy for interpreting knockout phenotypic outcomes are assessed. A hierarchy of explanatory relevance is then outlined, where genetic causes may be invoked in answering two types of explanation-seeking questions phenotypic properties. Genes as active parts in mechanisms that constitutively explain system properties answer questions about the causal capacities of the organism at a certain time. Genes as parts of mechanisms whose activities lead to developmental changes serve to answer questions about why the organism has a particular constitution at a certain point in time. Biological explanations describing developmental processes are mixtures of causal and constitutive explanations, as development is a series of changes in the organism’s constitution, and causes of these changes are partly inherent in the operation of the mechanisms that constitute the organism’s developmental capacities at a certain time. Nina Samuel (Freie Universität Berlin) Caught in between the materiality they represent and the abstract level they are meant to display, scientific images are intersections of form and meaning. They function properly both as epistemic tools and communication devices, while the 'invisibility' of their production in the laboratory is based on a tacit consent. In many cases they are considered to be the more objective and truthful, the more sophisticated they are in respect to the technologies used to make them. The presentationis to examine this asymmetrical relation of the visual form as an artifact that is determined by scientific contexts on the one hand and an agent of meaning on the other – or as Nietzsche has put it, Our writing tools are also working on our thoughts. By adopting this famous saying, the presentation intends to convey the argument that “imaging technologies co-operate our thoughts”. But in which way does the visible affect the material? Pursuing the attempt to launch an ‘art history of science’ as a method one has to carefully take into account both the capacities and the restrictions of an art historical methodology as well as to distinguish between various configurations (and causalities) of specific forms of materiality, visual surfaces and scientific practices to comprehend and process ‘epistemic things’ (Rheinberger). Looking closely at two case studies of contemporary biological image practices as recently observed at the Bioquant research center in Heidelberg, Germany, the presentation wants to discuss both a suggestion for a preliminary ‘archaeology of operational images’ as well as the question if there has emerged a new kind of visuality that takes up a double status as both objects of investigation and as tools.
Georg Trogemann (Academy of Media Arts Cologne): Traditionally, computer programming deals with the question of how to arrange a set of primitive operations so that through a series of elementary steps a certain type of final state will be reached. With the occurrence of unconventional computing models like Biocomputing and Hypercomputation as well as advances in other research fields like Nanotechnology or Self-assembly Systems, this paradigm changes drastically. Although the general programming strategy still sounds similar (e.g. for molecular computing we now ask: how to design a set of initial molecules so that a certain type of molecular complexes will be formed), our view on computing is fundamentally challenged.
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