Synthetic biology is an umbrella term that covers a range of aims, approaches, and techniques. They are all brought together by common practices of analogizing, synthesizing, mechanicizing, and kludging. With a focus on kludging as the connection point between biology, engineering, and evolution, I show how synthetic biology’s successes depend on custom-built kludges and a creative, “make-it-work” attitude to the construction of biological systems. Such practices do not fit neatly, however, into synthetic biology’s celebration of rational design. Nor (...) do they straightforwardly embody Richard Feynman’s “last blackboard” statement that without creating something it cannot be understood. Reflecting further on the relationship between synthetic construction and knowledge making gives philosophy of science new avenues of insight into scientific practice. (shrink)

In this paper, I argue against John Beatty’s position in his paper “The Evolutionary Contingency Thesis” by counterexample. Beatty argues that there are no distinctly biological laws because the outcomes of the evolutionary processes are contingent. I argue that the heart of the Caspar–Klug theory of virus structure—that spherical virus capsids consist of 60T subunits (where T = k 2 + hk + h 2 and h and k are integers)—is a distinctly biological law even if the existence (...) of spherical viruses is evolutionarily contingent. (shrink)

Here is one way that philosophers and biologists sometimes speak of Darwin’s explanatory innovation: ‘Eyes, organs of echolocation, camouflage and the like are all wonderful instances of contrivance, of complex adaptation, of good design. Paley and the other natural theologians sought to explain this good design by appeal to an intelligent designer. Darwin, on the other hand, offers us a superior explanation for the appearance of this same property: Darwin shows us that we can explain good design (...) through the action of selection. Indeed, selection is the only process that can explain good design in nature. And that is why evolutionary biologists can continue to use a version of the argument from design called the argument from biological design: when we see an instance of good design in nature, we should infer not the guiding hand of God, but the hand of selection at work.’ -/- . (shrink)

Pierre-Henri Castel provides a short but richly argued precis of his recently published two-volume 1,000-page masterwork on the history of obsessive-compulsive disorder. Having not read the as-yet-untranslated books, I write this commentary from Plato’s cave, trying to infer the reality of Castel’s analysis from expository shadows. I am unlikely to be more successful than Plato’s poor troglodytes, so I apologize ahead of time for any misunderstandings. Moreover, I cannot assess Castel’s detailed evidential case for his substantive theses.1 I thus focus (...) on some key philosophical issues that impinge on an area of my concern, the concept of mental disorder. Castel is a rare breed of French.. (shrink)

There seems to be a widespread conviction — evidenced, for example, in the work of Mackie, Dawkins and Sober — that it is Darwinian rather than Humean considerations which deal the fatal logical blow to arguments for intelligent design. I argue that this conviction cannot be well-founded. If there are current logically decisive objections to design arguments, they must be Humean — for Darwinian considerations count not at all against design arguments based upon apparent cosmological fine-tuning. I (...) argue, further, that there are good Humean reasons for atheists and agnostics to resist the suggestion that apparent design — apparent biological design and/or apparent cosmological fine-tuning — establishes (or even strongly supports) the hypothesis of intelligent design. (shrink)

This lively book explores how to: Formulate hypotheses and predictions; Design critical observations and experiments to test them; Choose appropriate statistical analyses; Present results and write reports.

Recently something close to a consensus about the best way to naturalize the notion of biological function appears to be emerging. Nonetheless, teleological notions in biology remain controversial. In this paper we provide a naturalistic analysis for the notion of natural design. Many authors assume that natural design should be assimilated directly to function. Others find the notion problematic because it suggests that evolution is a directed process. We argue that both of these views are mistaken. Our (...) naturalistic account does not simply equate design with function. We argue that the distinction between function and design is important for understanding the evolution of the physical and behavioral traits of organisms. (shrink)

Asking and answering questions is the cornerstone of science yet formal training in understanding this key process is often overlooked. "Asking Questions in Biology" unpacks this crucial process of enquiry, from a biological perspective, at its various stages. It begins with an overview of scientific question-asking in general, before moving on to demonstrate how to derive hypotheses from unstructured observations. It then explains in the main sections of the book, how to use statistical tests as tools to analyse data (...) and answer those questions before, finally, showing the best practice in presenting scientific reports. As such, it is an indispensable companion to all students of biology, but particularly those enrolled in courses concerning experimental design; data analysis; hypothesis testing; research methods; or any practical project work. The late Chris Barnard was Professor of Animal Behaviour at Nottingham University. Francis Gilbert is Associate Professor of Ecology at Nottingham University. Peter McGregor isa Reader in Applied Zoologyat Cornwall College. ". (shrink)

The protection of species ranks highly among environmentalist priorities, and many environmentalists expect the public to respect and support efforts to protect and rehabilitate endangered species. There are a range of instrumental and anthropocentric justifications for these attitudes, yet some environmentalists want more. It is unclear that more is to be had. In particular, it is challenging to justify some environmentalist attitudes without appealing to some version of the claim that species are intrinsically valuable. However, this has been a notoriously (...) difficult thesis to defend, and it is clearly not available to those who doubt the existence of species. In this paper, I show how a number of environmentalist commitments that appear to be about the value of species can be interpreted and defended in a way that is compatible with antirealism about species. According to my proposal, the proper target of environmentalists’ evaluative concern is the irreplaceable design that is embodied by the individuals that make up a (putative) species. This approach can capture and justify many environmentalist attitudes about the value of biological variety without attributing intrinsic value to species, or even requiring a place for species in our ontology. This enables environmentalists to effectively sidestep a number of puzzling issues surrounding the nature and value of species. (shrink)

The prevalence of optimality models in the literature of evolutionary biology is testimony to their popularity and importance. Evolutionary biologist R. C. Lewontin, whose criticisms of optimality models are considered here, reflects that "optimality arguments have become extremely popular in the last fifteen years, and at present represent the dominant mode of thought." Although optimality models have received little attention in the philosophical literature, these models are very interesting from a philosophical point of view. As will be argued, optimality models (...) are central to evolutionary thought, yet they are not readily accomodated by the traditional view of scientific theories. According to the traditional view, we would expect optimality models to employ general, empirical laws of nature, but they do not. Fortunately, the semantic view of scientific theories, a recent alternative to the traditional view, more readily accomodates optimality models. As we would expect on the semantic view, optimality models can be construed as specifications of ideal systems. These specifications may be used to describe empirical systems--that is, the specifications may have empirical instances. But the specifications are not empirical claims, much less general, empirical laws. Although philosophers have yet to discuss the general features and uses of optimality models, these topics have stimulated much recent discussion among evolutionary biologists. Their discussions raise a number of precautions concerning the proper use of optimality models. Moreover, many of their caveats can be interpreted as general reminders that 1) optimality models specify ideal systems whose empirical instantiations may be quite restricted, and that 2) optimality models should not be construed as general, empirical laws. As G. F. Oster and E. O. Wilson caution, "the prudent course is to regard optimality models as provisional guides to further empirical research and not necessarily as the key to deeper laws of nature." It seems, then, that the semantic view of theories is more sensitive to the nature and limitations of optimality models than is the more traditional view of theories. (shrink)

Design patterns are generalized solutions to frequently recurring problems. They were initially developed by architects and computer scientists to create a higher level of abstraction for their designs. Here, we extend these concepts to cell biology to lend a new perspective on the evolved designs of cells' underlying reaction networks. We present a catalog of 21 design patterns divided into three categories: creational patterns describe processes that build the cell, structural patterns describe the layouts of reaction networks, and (...) behavioral patterns describe reaction network function. Applying this pattern language to the E. coli central metabolic reaction network, the yeast pheromone response signaling network, and other examples lends new insights into these systems. (shrink)

Synthetic biology is described as a new field of biotechnology that models itself on engineering sciences. However, this view of synthetic biology as an engineering field has received criticism, and both biologists and philosophers have argued for a more nuanced and heterogeneous understanding of the field. This paper elaborates the heterogeneity of synthetic biology by clarifying the role of design and the variability of design methodologies in synthetic biology. I focus on two prominent design methodologies: rational (...) class='Hi'>design and directed evolution. Rational design resembles the design methodology of traditional engineering sciences. However, it is often replaced and complemented by the more biologically-inspired method of directed evolution, which models itself on natural evolution. These two approaches take philosophically different stances to the design of biological systems. Rational design aims to make biological systems more machine-like, whereas directed evolution utilizes variation and emergent features of living systems. I provide an analysis of the methodological basis of these design approaches, and highlight important methodological differences between them. By analyzing the respective benefits and limitations of these approaches, I argue against the engineering-dominated conception of synthetic biology and its “methodological monism”, where the rational design approach is taken as the default design methodology. Alternative design methodologies, like directed evolution, should be considered as complementary, not competitive, to rational design. (shrink)

The living world is an exciting and inexhaustible source of high performance solutions to the multitude of biological problems, which were attained as a result of a natural selection, during the millions and millions years evolution of life on Earth. This work presents and comments some examples of high performances of living beings, in the light of the universal principle governing the realm of living matter: Optimal Design Principle. At the same time, the transfer of these optimal solutions, (...) from living matter to the technologies, is also discussed. This transfer is offering new and fertile perspectives to future technologies, which must be more efficient, cheaper and in perfect harmony with the biosphere. (shrink)

Synthetic biology offers a powerful method to design and construct biological devices for human purposes. Two prominent design methodologies are currently used. Rational design adapts the design methodology of traditional engineering sciences, such as mechanical engineering. Directed evolution, in contrast, models its design principles after natural evolution, as it attempts to design and improve systems by guiding them to evolve in a certain direction. Previous work has argued that the primary difference between these (...) two is the way they treat variation: rational design attempts to suppress it, whilst direct evolution utilizes variation. I argue that this contrast is too simplistic, as it fails to distinguish different types of variation and different phases of design in synthetic biology. I outline three types of variation and show how they influence the construction of synthetic biological systems during the design process. Viewing the two design approaches with these more fine-grained distinctions provides a better understanding of the methodological differences and respective benefits of rational design and directed evolution, and clarifies the constraints and choices that the different design approaches must deal with. (shrink)

Charles Darwin's Origin of Species, published in 1859, was a revolutionary attempt “to overthrow the dogma of separate creations,” a declaration that provoked different reactions among the religious, ranging from mild enthusiasm to anger. Christians sympathetic to Darwin's effort sought to make Darwinism appear compatible with their religious beliefs. Two of Darwin's most prominent defenders in the United States were the Calvinists Asa Gray, a Harvard botanist, and George Frederick Wright, a cleric-geologist. Gray, who long favored a “special origination” in (...) connection with the evolution of humans and questioned whether natural selection can account for the formation of organs, the making of eyes, etc., embraced natural selection as the primary mechanism underlying the production of most species. He also went so far as to invoke divine providence, rather than randomness, to explain the variations on which natural selection acted. This chapter discusses creationism, intelligent design, and modern biology. (shrink)

Due to the variation, contingency and complexity of living systems, biology is often taken to be a science without fundamental theories, laws or general principles. I revisit this question in light of the quest for design principles in systems biology and show that different views can be reconciled if we distinguish between different types of generality. The philosophical literature has primarily focused on generality of specific models or explanations, or on the heuristic role of abstraction. This paper takes a (...) different approach in emphasizing a theory-constituting role of general principles. Design principles signify general dependency-relations between structures and functions, given a set of formally defined constraints. I contend that design principles increase our understanding of living systems by relating specific models to general types. The categorization of types is based on a delineation of the scope of biological possibilities, which serves to identify and define the generic features of classes of systems. To characterize the basis for general principles through generic abstraction and reasoning about possibility spaces, I coin the term constraint-based generality. I show that constraint-based generality is distinct from other types of generality in biology, and argue that general principles play a unifying role that does not entail theory reduction. (shrink)

Designer Biology: The Ethics of Intensively Engineering Biological and Ecological Systems consists of thirteen chapters that address the ethical issues raised by technological intervention and design across a broad range of biological and ecological systems. Among the technologies addressed are geoengineering, human enhancement, sex selection, genetic modification, and synthetic biology.

This book consists of thirteen chapters that address the ethical issues raised by technological intervention and design across a broad range of biological and ecological systems. Among the technologies addressed are geoengineering, human enhancement, sex selection, genetic modification, and synthetic biology.

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)

The history of British cybernetics offers us a different form of science and engineering, one that does not seek to dominate nature through knowledge. I want to say that one can distinguish two different paradigms in the history of science and technology: the one that Heidegger despised, which we could call the Modern paradigm, and another, cybernetic, nonModern, paradigm that he might have approved of. This essay focusses on work in the 1950s and early 1960s by two of Britain’s leading (...) cyberneticians, Stafford Beer and Gordon Pask, in the field of what one can call biological computing. My object is to get as clear as I can on what Beer and Pask were up to. At the end, I will discuss Beer’s hylozoist ontology of matter, mind and spirit. This material is not easy to get the hang of—but that is what one should expect from an unfamiliar paradigm. (shrink)

Rope Kojonen has presented a novel argument for design in biology by drawing on insights from evolutionary science. Without objecting to the explanatory role of evolution, he argues that there is further explanatory work to be done and that this is best achieved by an appeal to design. Here, I interpret his argument, and attempt to evaluate it, as a conjunctive explanation since he appeals to two explanations to account for the purposeful order and complexity of living organisms. (...) Understood in this way, I argue that he makes a very plausible case that two explanations (evolution and design) are better than one (evolution). I also explore the role that direct guidance by God might play in such an argument. (shrink)

This chapter contains sections titled: Introduction A Brief Historical Note Failed Shortcuts Looking Deeper The Richness of Biology The Persistence of Design Real Design? Conclusion Postscript: Counterpoint Notes References.

Autoinhibition is a design principle realized in many molecular mechanisms in biology. After explicating the notion of a design principle and showing that autoinhibition is such a principle, we focus on how researchers discovered instances of autoinhibition, using research establishing the autoinhibition of the molecular motors kinesin and dynein as our case study. Research on kinesin and dynein began in the fashion described in accounts of mechanistic explanation but, once the mechanisms had been discovered, researchers discovered that they (...) exhibited a second phenomenon, autoinhibition. The discovery of autoinhibition not only reverses the pattern in terms of which philosophers have understood mechanism discovery but runs counter to the one phenomenon-one mechanism principle assumed to relate mechanisms and the phenomena they explain. The ubiquity of autoinhibition as a design principle, therefore, necessitates a philosophical understanding of mechanisms that recognizes how they can participate in more than one phenomenon. Since mechanisms with this design are released from autoinhibition only when they are acted on by control mechanisms, we advance a revised account of mechanisms that accommodates attribution of multiple phenomena to the same mechanism and distinguishes them from other processes that control them. (shrink)

‘Biochromatology’ can be defined as the study of the relationships between colours, and between colours and design in nature. Certain laws concerning biochromatics can be formulated in the terminology of the Colour Circle. One of them is that planes in warm colours and planes in cold colours never adjoin. Another law is that design is never polychromatic. It seems that the observed biochromatical facts can be explained with the help of the principle “optimal manifestation of colour”, which in (...) turn is based on the formative principles of matter itself. (shrink)

In this paper, I treat the question of whether and in what regard Kant's theory of biology contains a version of the argument from design, which is the question of whether Kant considers the purposive order of organized nature as a physicotheological proof for the existence of God, and in turn, the existence of God as the supersensible ground for the teleological order of organized nature. As an introduction to the topic, I name traditional examples of the argument from (...) design (section 1). I then outline Kant's changing attitude towards the argument in his Theory of Heavens, his Argument essay and the three Critiques, highlighting Kant's return to the argument from design in the CPJ after examining and rejecting it in his earlier writings. I elaborate in detail Kant's different uses of the argument in the "Critique of the Teleological Power of Judgment" (section 2). In section 3, I develop a consistent reading of Kant's references to the physicotheological proof in the "Critique of the Teleological Power of Judgment": in the "Analytic" he develops a teleological account of nature that makes no use of the argument from design but is consistent with it. In the "Dialectic" and the "Methodology", however, Kant discusses more ambitious systematic questions: the unity of the theoretical laws of nature and the unity of the natural and the supernatural moral laws. These are questions that require an explicit reference to the argument from design (section 3). (shrink)

Phillip Johnson introduces the debate over intelligent design.

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)

This chapter contains sections titled: Introduction: The Design Argument The Design Argument in Antiquity Christian Authors Hume's Onslaught William Paley's Natural Theology The Bridgewater Treatises Intelligent Design: A Political Movement Eyes to See No “There” There Blood and Tears Gambling to Non‐existence Natural Selection Natural Selection and Design Postscript: Counterpoint Notes References.

This book tells the history of the many analogies that have been made between the evolution of organisms and the human production of artefacts, especially buildings. It examines the effects of these analogies on architectural and design theory and considers how recent biological thinking has relevance for design. Architects and designers have looked to biology for inspiration since the early 19th century. They have sought not just to imitate the forms of plants and animals, but to find (...) methods in design analogous to the processes of growth and evolution in nature. This new revised edition of this classic work adds an extended Afterword covering recent developments such as the introduction of computer methods in design in the 1980s and ‘90s, which have made possible a new kind of ‘biomorphic’ architecture through ‘genetic algorithms’ and other programming techniques. (shrink)

In the recent literature on explanation in biology, increasing attention is being paid to the connection between design explanation and mechanistic explanation, viz. the role of design principles and heuristics for mechanism discovery and mechanistic explanation. In this paper we extend the connection between design explanation and mechanism discovery by prizing apart two different types of design explanation and by elaborating novel heuristics that one specific type offers for mechanism discovery across species. We illustrate our claims (...) in terms of two lines of biological research on the biological advantages of organismal traits, one on the eye-size of giant squid, the other on foraging habits of specific bat species. We argue that this research illustrates useful heuristics for mechanism discovery across species, viz. reasoning strategies to infer likely mechanisms for a certain biological role based on assessments of the environmental conditions in which the role is performed efficiently and less or in-efficiently. We bring out the novel features of our analysis in terms of a comparison with mechanistic approaches to mechanism discovery, amongst which graph-theoretical ones, and by comparing the different types of design explanation and the discovery heuristics they support. (shrink)

This volume provides a guide to the discussion among biologists and philosophersabout the role of concepts such as function and design in an evolutionary understanding oflife.

In the recent literature on explanation in biology, increasing attention is being paid to the connection between design explanation and mechanistic explanation, viz. the role of design principles and heuristics for mechanism discovery and mechanistic explanation. In this paper we extend the connection between design explanation and mechanism discovery by prizing apart two different types of design explanation and by elaborating novel heuristics that one specific type offers for mechanism discovery across species. We illustrate our claims (...) in terms of two lines of biological research on the biological advantages of organismal traits, one on the eye-size of giant squid, the other on foraging habits of specific bat species. We argue that this research illustrates useful heuristics for mechanism discovery across species, viz. reasoning strategies to infer likely mechanisms for a certain biological role based on assessments of the environmental conditions in which the role is performed efficiently and less or in-efficiently. We bring out the novel features of our analysis in terms of a comparison with mechanistic approaches to mechanism discovery, amongst which graph-theoretical ones, and by comparing the different types of design explanation and the discovery heuristics they support. (shrink)

The Hooks et al. review of microbiota-gut-brain literature provides a constructive criticism of the general approaches encompassing MGB research. This commentary extends their review by: highlighting capabilities of advanced systems-biology “-omics” techniques for microbiome research and recommending that combining these high-resolution techniques with intervention-based experimental design may be the path forward for future MGB research.

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)

This chapter offers a critique of intelligent design arguments against evolution and a philosophical discussion of the nature of science, drawing several lessons for the teaching of evolution and for science education in general. I discuss why Behe’s irreducible complexity argument fails, and why his portrayal of organismal systems as machines is detrimental to biology education and any under-standing of how organismal evolution is possible. The idea that the evolution of complex organismal features is too unlikely to have occurred (...) by random mutation and selection (as recently promoted by Dembski) is very widespread, but it is easy to show students why such small probability arguments are fallacious. While intelligent design proponents have claimed that the exclusion of supernatural causes mandated by scientific methods is dogmatically presupposed by science, scientists have an empirical justification for using such methods. This justification is instructive for my discussion of how to demarcate science from pseudoscience. I argue that there is no universal account of the nature of science, but that the criteria used to judge an intellectual approach vary across historical periods and have to be specific to the scientific domain. Moreover, intellectual approaches have to be construed as practices based on institutional factors and values, and to be evaluated in terms of the activities of their practitioners. Science educators should not just teach scientific facts, but present science as a practice and make students reflect on the nature of science, as this gives them a better appreciation of the ways in which intelligent design falls short of actual science. (shrink)

The Safe-by-Design approach in synthetic biology holds the promise of designing the building blocks of life in an organism guided by the value of safety. This paves a new way for using biotechnologies safely. However, the Safe-by-Design approach moves the bulk of the responsibility for safety to the actors in the research and development phase. Also, it assumes that safety can be defined and understood by all stakeholders in the same way. These assumptions are problematic and might actually (...) undermine safety. This research explores these assumptions through the use of a Group Decision Room. In this set up, anonymous and non-anonymous deliberation methods are used for different stakeholders to exchange views. During the session, a potential synthetic biology application is used as a case for investigation: the Food Warden, a biosensor contained in meat packaging for indicating the freshness of meat. Participants discuss what potential issues might arise, how responsibilities should be distributed in a forward-looking way, who is to blame if something would go wrong. They are also asked what safety and responsibility mean at different phases, and for different stakeholders. The results of the session are not generalizable, but provide valuable insights. Issues of safety cannot all be taken care of in the R&D phase. Also, when things go wrong, there are proximal and distal causes to consider. In addition, capacities of actors play an important role in defining their responsibilities. Last but not least, this research provides a new perspective on the role of instruction manuals in achieving safety. (shrink)

Book Information Nature's Purposes: Analyses of Function and Design in Biology. Edited by Allen Colin, Bekoff Mark and Lauder George. MIT Press. Cambridge. 1998. Pp. vi + 597. Paperback, US$31.50.

Synthetic biology is an emerging technology that aims to design and engineer DNA and molecular structures of single cell organisms. Existing organisms can be altered, novel organisms can be created. In doing so, synthetic biology makes use of specific technoscientific understandings of living beings. This volume sets out to explore and assess synthetic biology and its notions of life from philosophical, ethical, social, and legal perspectives. Contents Concepts, Metaphors, Worldviews.- Public Good and Private Ownership.Social and Legal Ramifications.- Opportunities, Risks, (...) Governance. Target Groups Scholars of sociology, philosophy, theory of science, history of science, biology, engineering Politicians and policymakers The Editor Dr. Joachim Boldt is Deputy Director at the Institut für Ethik und Geschichte der Medizin in Freiburg, Germany. (shrink)

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. (shrink)

Sober has reconstructed the biological design argument in the framework of likelihoodism, purporting to demonstrate that it is defective for intrinsic reasons. We argue that Sober’s restriction on the introduction of auxiliary hypotheses is too restrictive, as it commits him to rejecting types of everyday reasoning that are clearly valid. Our account shows that the design argument fails, not because it is intrinsically untestable but because it clashes with the empirical evidence and fails to satisfy certain theoretical (...) desiderata (in particular, unification). Likewise, Sober’s critique of the arguments from imperfections and from evil against design is off the mark. (shrink)

The Safe-by-Design approach in synthetic biology holds the promise of designing the building blocks of life in an organism guided by the value of safety. This paves a new way for using biotechnologies safely. However, the Safe-by-Design approach moves the bulk of the responsibility for safety to the actors in the research and development phase. Also, it assumes that safety can be defined and understood by all stakeholders in the same way. These assumptions are problematic and might actually (...) undermine safety. This research explores these assumptions through the use of a Group Decision Room. In this set up, anonymous and non-anonymous deliberation methods are used for different stakeholders to exchange views. During the session, a potential synthetic biology application is used as a case for investigation: the Food Warden, a biosensor contained in meat packaging for indicating the freshness of meat. Participants discuss what potential issues might arise, how responsibilities should be distributed in a forward-looking way, who is to blame if something would go wrong. They are also asked what safety and responsibility mean at different phases, and for different stakeholders. The results of the session are not generalizable, but provide valuable insights. Issues of safety cannot all be taken care of in the R&D phase. Also, when things go wrong, there are proximal and distal causes to consider. In addition, capacities of actors play an important role in defining their responsibilities. Last but not least, this research provides a new perspective on the role of instruction manuals in achieving safety. (shrink)

The design argument for the existence of God took a probabilistic turn in the 17 th and 18 th centuries. Earlier versions, such as Thomas Aquinas' 5 th way, usually embraced the premise that goal-directed systems (things that "act for an end" or have a function) must have been created by an intelligent designer. This idea – which we might express by the slogan "no design without a designer" – survived into the 17 th and 18 th centuries, (...) 1 and it is with us still in the writings of many creationists. The new version of the argument, inspired by the emerging mathematical theory of probability, removed the premise of necessity. It begins with the thought that goal-directed systems might have arisen by intelligent design or by chance; the problem is to discern which hypothesis is more plausible. With the epistemic concept of plausibility characterized in terms of the mathematical concept of probability, the design argument was given a new direction. The new probabilistic perspective did not extinguish the older idea of "no design without a designer." The two conflicting approaches coexisted, often with less than perfect clarity about their fundamental difference. At the same time, the details of how the probabilistic perspective ought to be articulated were slow in emerging. These characteristics of uneven development are exemplified in a debate that took place in the 18 th century among three probabilists – John Arbuthnot, Nicholas Bernoulli, and Abraham DeMoivre – on the proper explanation of human sex ratio. Arbuthnot proposed a probabilistic version of the design argument, claiming that it is intelligent design, not chance, that provides the better explanation of why slightly more boys than girls are born each year. Bernoulli rejected Arbuthnot's argument. DeMoivre defended Arbuthnot against Bernoulli's criticisms. The problem of explaining sex ratio, both in human populations and in the rest of nature, experienced another transformation after 1859 --it became a problem for the theory of evolution by natural selection. Darwin (1871) addressed the question in the first edition of The Descent of Man but withdrew his suggestion in the second (Darwin 1874). Carl Düsing (1884) provided a mathematical model that moved beyond the explanation Darwin offered. Fisher (1930) added the new idea of parental expenditure. Williams (1966) argued that the sex ratios found in nature provide the opportunity to test hypotheses of group selection against hypotheses of individual selection. Hamilton (1967) constructed a model that generalizes Fisher's approach and represents the effects of both group and individual selection. The theory of natural selection gradually developed the ability to predict sex ratios, not just explain them post hoc. (shrink)

In his Natural Theology, the eighteenth-century Anglican theologian William Paley compares a watch with objects in nature, arguing that “every manifestation of design, which existed in the watch, exists in the works of nature…” Charles Darwin read Paley's Natural Theology as a young man and offered natural selection as an alternative, naturalistic explanation of Paley's explanandum: the appearance of design in nature. Many of Paley's successors diverged from him in their approach to the living world. This chapter examines (...) some of these alternative approaches and the extent to which the literature of natural theology had trodden the path between Paley's watchmaker and Darwin's natural selection prior to the publication of the latter's Origin of Species. In particular, it focuses on the Bridgewater Treatises, a series of eight highly popular works published in the 1830s, which illustrate the far-reaching development that took place in natural theology in Britain during the early nineteenth century. (shrink)

Design thinking in general, and optimality modeling in particular, have traditionally been associated with adaptationism—a research agenda that gives pride of place to natural selection in shaping biological characters. Our goal is to evaluate the role of design thinking in non-evolutionary analyses. Specifically, we focus on research into abstract design principles that underpin the functional organization of extant organisms. Drawing on case studies from engineering-inspired approaches in biology we show how optimality analysis, and other design-related (...) methods, play a specific methodological role that is tangential to the study of adaptation. To account for the role of these reasoning strategies in contemporary biology, we therefore suggest a reevaluation of the connection between design thinking and adaptationism. (shrink)