This paper argues against the view that the standard explanation of phase transitions in statistical mechanics may be considered a causal explanation, a distortion that can nevertheless successfully represent causal relations.

A recurrent theme in the characterization of synthetic biology is the role of engineering. This theme is widespread in the accounts of scholars studying this field and the biologists working in it, in those of the biologists themselves, as well as in policy documents. The aim of this article is to open this black-box of engineering that is supposed to influence and change contemporary life sciences. Too often, both synthetic biologists and their critics assume a very narrow understanding of what (...) engineering is about, resulting in an unfruitful debate about whether synthetic biology possesses genuine engineering methodologies or not. By looking in more detail to the diversity of engineering conceptions in debates concerning synthetic biology, a richer perspective can be developed. In this article, I will examine five influential ways in which engineering is understood in these debates, namely engineering as applied science, as rational methodology, context-sensitive practice, cunning activity or design. The claim is first of all thus to argue that engineering must not be seen as something stable or characterized by a fixed essence. It rather has multiple meanings and interpretations. Secondly, the claim is that most of the debates on synthetic biology cannot be indifferent towards the question which conception of engineering is at play, since the specific questions and concerns that pop up depend to a great extent on the precise conception of engineering one has in account. Many of the existing debates around synthetic biology can thus be reinterpreted and readdressed once one is aware of which conception of engineering is at play. (shrink)

This article examines how minimal genome research mobilizes philosophical concepts such as minimality and essentiality. Following a historical approach the article aims to uncover what function this terminology plays and which problems are raised by them. Specifically, four historical moments are examined, linked to the work of Harold J. Morowitz, Mitsuhiro Itaya, Eugene Koonin and Arcady Mushegian, and J. Craig Venter. What this survey shows is a historical shift away from historical questions about life or descriptive questions about specific organisms (...) towards questions that explore biological possibilities: what are possible forms of minimal genomes, regardless of whether they exist in nature? Moreover, it highlights a fundamental ambiguity at work in minimal genome research between a universality claim and a standardization claim: does a minimal genome refer to the minimal gene set for any organism whatsoever? Or does it refer rather to a gene set that will provide stable, robust and predictable behaviour, suited for biotechnological applications? Two diagnoses are proposed for this ambiguity: a philosophical diagnosis of how minimal genome research either misunderstands the ontology of biological entities or philosophically misarticulates scientific practice. Secondly, a historical diagnosis that suggests that this ambiguity is part of a broader shift towards technoscience. (shrink)

Many scientific models in biology are how-possibly models. These models depict things as they could be, but do not necessarily capture actual states of affairs in the biological world. In contemporary philosophy of science, it is customary to treat how-possibly models as second-rate theoretical tools. Although possibly important in the early stages of theorizing, they do not constitute the main aim of modelling, namely, to discover the actual mechanism responsible for the phenomenon under study. In the paper it is argued (...) that this prevailing picture does not do justice to the synthetic strategy that is commonly used in biological engineering. In synthetic biology, how-possibly models are not simply speculations or eliminable scaffolds towards a single how-actually model, but indispensable design hypotheses for a field whose ultimate goal is to build novel biological systems. The paper explicates this by providing an example from the study of alternative genetic systems by synthetic biologist Steven Benner and his group. The case will also highlight how the method of synthesis, even when it fails, provides an effective way to limit the space of possible models for biological systems. (shrink)

The modern synthesis has been considered to be wrongly called a “synthesis”, since it had completely excluded embryology, and many other disciplines. The recent developments of Evo-Devo have been seen as a step in the right direction, as complementing the modern synthesis, and probably leading to a “new synthesis”.My argument is that the absence of embryology from the modern synthesis was the visible sign of a more profound lack: the absence of functional biology in the evolutionary synthesis. I will consider (...) the reasons for this absence, as well as the recent transformations which favoured a closer interaction between these two branches of biology. Then I will describe two examples of recent work in which functional and evolutionary questioning were tightly linked. The most significant part of the paper will be devoted to the transformation of evolutionary theory that can be expected from this encounter: a deep transformation, or simply an experimental confirmation of this theory? I will not choose between these two different possibilities, but will discuss some of the difficulties which make the choice problematic. (shrink)

Metaphors are not just decorative rhetorical devices that make speech pretty. They are fundamental tools for thinking about the world and acting on the world. The language we use to make a better world matters; words matter; metaphors matter. Words have consequences - ethical, social and legal ones, as well as political and economic ones. They need to be used ‘responsibly’. They also need to be studied carefully – this is what we want to do through this editorial and the (...) related thematic collection. In the context of synthetic biology, natural and social scientists have become increasingly interested in metaphors, a wave of interest that we want to exploit and amplify. We want to build on emerging articles and books on synthetic biology, metaphors of life and the ethical and moral implications of such metaphors. This editorial provides a brief introduction to synthetic biology and responsible innovation, as well as a comprehensive review of literature on the social, cultural and ethical impacts of metaphor use in genomics and synthetic biology. Our aim is to stimulate an interdisciplinary and international discussion on the impact that metaphors can have on science, policy and publics in the context of synthetic biology. (shrink)

Synthetic biology is often described as a project that applies rational design methods to the organic world. Although humans have influenced organic lineages in many ways, it is nonetheless reasonable to place synthetic biology towards one end of a continuum between purely ‘blind’ processes of organic modification at one extreme, and wholly rational, design-led processes at the other. An example from evolutionary electronics illustrates some of the constraints imposed by the rational design methodology itself. These constraints reinforce the limitations of (...) the synthetic biology ideal, limitations that are often freely acknowledged by synthetic biology’s own practitioners. The synthetic biology methodology reflects a series of constraints imposed on finite human designers who wish, as far as is practicable, to communicate with each other and to intervene in nature in reasonably targeted and well-understood ways. This is better understood as indicative of an underlying awareness of human limitations, rather than as expressive of an objectionable impulse to mastery over nature. (shrink)

Recently, several critics of the multiple realizability thesis have argued that philosophers have tended to accept the thesis on too weak grounds. On the one hand, the analytic challenge has problematized how philosophers have treated the multiple realization relation itself, claiming that assessment of the sameness of function and the relevant difference of realizers has been uncritical. On the other hand, it is argued that the purported evidence of the thesis is often left empirically unverified. This paper provides a novel (...) strategy to answer these worries by introducing a role for multiple realizability in the context of biological engineering. In the field of synthetic biology, bioengineers redesign the evolutionary realizations of biological functions, even constructing artificial chemical surrogates in the laboratory. I show how in the rational design approach to biological engineering, multiple realizability can function as a design heuristic in which the sameness of function and difference of realizers can be controlled. Although practically motivated, this engineering approach has also a theoretical, exploratory component that can be used to study the empirical limitations of multiple realizability. Successful realization of the engineering designs would amount to a concrete demonstration of multiple realizability, taking evidence for MRT beyond what is readily found in nature. (shrink)

Critics of multiple realizability have recently argued that we should concentrate solely on actual here-and-now realizations that are found in nature. The possibility of alternative, but unactualized, realizations is regarded as uninteresting because it is taken to be a question of pure logic or an unverifiable scenario of science fiction. However, in the biological context only a contingent set of realizations is actualized. Drawing on recent work on the theory of neutral biological spaces, the paper shows that we can have (...) ways of assessing the modal dimension of multiple realizability that do not have to rely on mere conceivability. (shrink)

“Proof of concept” is a phrase frequently used in descriptions of research sought in program announcements, in experimental studies, and in the marketing of new technologies. It is often coupled with either a short definition or none at all, its meaning assumed to be fully understood. This is problematic. As a phrase with potential implications for research and technology, its assumed meaning requires some analysis to avoid it becoming a descriptive category that refers to all things scientifically exciting. I provide (...) a short analysis of proof of concept research and offer an example of it within synthetic biology. I suggest that not only are there activities that circumscribe new epistemological categories but there are also associated normative ethical categories or principles linked to the research. I examine these and provide an outline for an alternative ethical account to describe these activities that I refer to as “extended agency ethics”. This view is used to explain how the type of research described as proof of concept also provides an attendant proof of principle that is the result of decision-making that extends across practitioners, their tools, techniques, and the problem solving activities of other research groups. (shrink)

The premise of biological modularity is an ontological claim that appears to come out of practice. We understand that the biological world is modular because we can manipulate different parts of organisms in ways that would only work if there were discrete parts that were interchangeable. This is the foundation of the BioBrick assembly method widely used in synthetic biology. It is one of a number of methods that allows practitioners to construct and reconstruct biological pathways and devices using DNA (...) libraries of standardized parts with known functions. In this paper, we investigate how the practice of synthetic biology reconfigures biological understanding of the key concepts of modularity and evolvability. We illustrate how this practice approach takes engineering knowledge and uses it to try to understand biological organization by showing how the construction of functional parts and processes can be used in synthetic experimental evolution. We introduce a new approach within synthetic biology that uses the premise of a parts-based ontology together with that of organismal self-organization to optimize orthogonal metabolic pathways in E. coli. We then use this and other examples to help characterize semisynthetic categories of modularity, parthood, and evolvability within the discipline. (shrink)

Philosophical investigation in synthetic biology has focused on the knowledge-seeking questions pursued, the kind of engineering techniques used, and on the ethical impact of the products produced. However, little work has been done to investigate the processes by which these epistemological, metaphysical, and ethical forms of inquiry arise in the course of synthetic biology research. An attempt at this work relying on a particular area of synthetic biology will be the aim of this chapter. I focus on the reengineering of (...) metabolic pathways through the manipulation and construction of small DNA-based devices and systems synthetic biology. Rather than focusing on the engineered products or ethical principles that result, I will investigate the processes by which these arise. As such, the attention will be directed to the activities of practitioners, their manipulation of tools, and the use they make of techniques to construct new metabolic devices. Using a science-in-practice approach, I investigate problems at the intersection of science, philosophy of science, and sociology of science. I consider how practitioners within this area of synthetic biology reconfigure biological understanding and ethical categories through active modelling and manipulation of known functional parts, biological pathways for use in the design of microbial machines to solve problems in medicine, technology, and the environment. We might describe this kind of problem-solving as relying on what Helen Longino referred to as “social cognition” or the type of scientific work done within what Hasok Chang calls “systems of practice”. My aim in this chapter will be to investigate the relationship that holds between systems of practice within metabolic engineering research and social cognition. I will attempt to show how knowledge and normative valuation are generated from this particular network of practitioners. In doing so, I suggest that the social nature of scientific inquiry is ineliminable to both knowledge acquisition and ethical evaluations. (shrink)

This paper analyzes the notion of possibility in biology and demonstrates how synthetic biology can provide understanding on the modal dimension of biological systems. Among modal concepts, biological possibility has received surprisingly little explicit treatment in the philosophy of science. The aim of this paper is to argue for the importance of the notion of biological possibility by showing how it provides both a philosophically and biologically fruitful category as well as introducing a new practically grounded way for its assessment. (...) More precisely, we argue that synthetic biology can provide tools to scientifically anchor reasoning about biological possibilities. Two prominent strategies for this are identified and analyzed: the design of functionally new-to-nature systems and the redesign of naturally occurring systems and their parts. These approaches allow synthetic biologists to explore systems that are not normally evolutionarily accessible and draw modal inferences that extend in scope beyond their token realizations. Subsequently, these results in synthetic biology can also be relevant for discussions on evolutionary contingency, providing new methods and insight to the study of various sources of unactualized possibilities in biology. (shrink)

This is the second of two articles in which I reflect on “generalized Darwinism” as currently discussed in evolutionary economics. In the companion article (Callebaut, Biol Theory 6. doi: 10.1007/s13752-013-0086-2, 2011, this issue) I approached evolutionary economics from the naturalistic perspectives of evolutionary epistemology and the philosophy of biology, contrasted evolutionary economists’ cautious generalizations of Darwinism with “imperialistic” proposals to unify the behavioral sciences, and discussed the continued resistance to biological ideas in the social sciences. Here I assess Generalized Darwinism (...) as propounded by Geoffrey Hodgson, Thorbjørn Knudsen, and others, concentrating on the roles of theory and model building in science (and the roles of analogy and metaphor therein), generative replication, and the relation between selection and self-organization. I then point to advances in current biology that promise to be more fruitful as sources of inspiration for evolutionary economics than the project to generalize Darwinism in its current, “hardened Modern Synthesis” form; and I draw some conclusions. (shrink)

Synthetic biology is a new biotechnology that is developing at an impressive pace and attracting a considerable amount of attention from outside the scientific community as well. In this article, two main philosophically and ethically relevant characteristics of this field of research will be laid bare, namely its reliance on mechanistic metaphors to denominate simple forms of life and its appeal to the semantic field of creativity. It is argued that given these characteristics synthetic biology can be understood as a (...) prime example of a kind of human interference with reality that German philosopher Hannah Arendt called “fabrication.” This kind of self-world-relation contrasts to “action,” a relation that introduces, among other things, the idea of an inherent value of the object acted upon. Taking up this latter perspective, one scientific and two ethical challenges to synthetic biology’s take on the realm of life are identified. (shrink)

The paper discusses methodological guidelines for evaluating mechanistic explanations. According to current accounts, a satisfactory mechanistic explanation should include all of the relevant features of the mechanism, its component entities and activities, and their properties and organization, as well as exhibit productive continuity. It is not specified, however, how this kind of mechanistic completeness can be demonstrated. I argue that parameter sufficiency inferences based on mathematical model simulations provide a way of determining whether a mechanism capable of producing the phenomenon (...) of interest can be constructed from mechanistic components organized, acting, and having the properties described in the mechanistic explanation. (shrink)

Multidisciplinary models aggregating ‘lower-level’ biological and ‘higher-level’ psychological and social determinants of a phenomenon raise a puzzle. How is the interaction between the physical, the psychological and the social conceptualized and explained? Using biopsychosocial models of pain as an illustration, I argue that these models are in fact level-neutral compilations of empirical findings about correlated and causally relevant factors, and as such they neither assume, nor entail a conceptual or ontological stratification into levels of description, explanation or reality. If inter-level (...) causation is deemed problematic or if debates about the superiority of a particular level of description or explanation arise, these issues are fueled by considerations other than empirical findings. (shrink)

Multidisciplinary models aggregating ‘lower-level’ biological and ‘higher-level’ psychological and social determinants of a phenomenon raise a puzzle. How is the interaction between the physical, the psychological and the social conceptualized and explained? Using biopsychosocial models of pain as an illustration, I argue that these models are in fact level-neutral compilations of empirical findings about correlated and causally relevant factors, and as such they neither assume, nor entail a conceptual or ontological stratification into levels of description, explanation or reality. If inter-level (...) causation is deemed problematic or if debates about the superiority of a particular level of description or explanation arise, these issues are fueled by considerations other than empirical findings. (shrink)

A survey of models in immunology is conducted and distinct kinds of models are characterized based on whether models are material or conceptual, the distinctiveness of their epistemic purpose, and the criteria for evaluating the goodness of a model relative to its intended purpose. I argue that the diversity of models in interdisciplinary fields such as immunology reflects the fact that information about the phenomena of interest is gathered from different sources using multiple methods of investigation. To each model is (...) attached a description specifying how information about a phenomenon of interest has been acquired, highlighting points of commonality and difference between the methodological and epistemic histories of the information encapsulated in different models. These points of commonality and difference allow investigators to integrate findings from different models into more comprehensive explanatory accounts, as well as to troubleshoot anomalies and faulty accounts by going back to the original building blocks. (shrink)