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.”. (shrink)

In his analysis of “the essential tension between tradition and innovation” Thomas S. Kuhn focused on the apparent paradox that, on the one hand, normal research is a highly convergent activity based upon a settled consensus, but, on the other hand, the ultimate effect of this tradition-bound work has invariably been to change the tradition. Kuhn argued that, on the one hand, without the possibility of divergent thought, fundamental innovation would be precluded. On the other hand, without a strong emphasis (...) on convergent thought, science would become a mess created by continuous theory changes and scientific progress would again be precluded. On Kuhn’s view, both convergent and divergent thought are therefore equally necessary for the progress of science. In this paper, I shall argue that a similar fundamental tension exists between the demands we see for novel insights of an interdisciplinary nature and the need for established intellectual doctrines founded in the classical disciplines. First, I shall revisit Kuhn’s analysis of the essential tension between tradition and innovation. Next, I shall argue that the tension inherent in interdisciplinary research between, on the one hand, intellectual independence and critical scrutiny and, on the other hand, epistemic dependence and trust is a complement to Kuhn’s essential tension within mono-disciplinary science between convergent and divergent thought. (shrink)

The author's concept of incommensurability is explicated by elaborating the claim that some terms essential to the formulation of older theories defy translation into the language of more recent ones. Defense of this claim rests on the distinction between interpreting a theory in a later language and translating the theory into it. The former is both possible and essential, the latter neither. The interpretation/translation distinction is then applied to Kitcher's critique of incommensurability and Quine's conception of a translation manual, both (...) of which take reference-preservation as the sole semantic criterion of translational adequacy. The paper concludes by enquiring about the additional criteria a successful translation must satisfy. (shrink)

A scientific community cannot practice its trade without some set of received beliefs. These beliefs form the foundation of the "educational initiation that prepares and licenses the student for professional practice". The nature of the "rigorous and rigid" preparation helps ensure that the received beliefs are firmly fixed in the student's mind. Scientists take great pains to defend the assumption that scientists know what the world is like...To this end, "normal science" will often suppress novelties which undermine its foundations. Research (...) is therefore not about discovering the unknown, but rather "a strenuous and devoted attempt to force nature into the conceptual boxes supplied by professional education". (shrink)

A highly condensed account of the author's present view of some philosophical problems unresolved in The Structure of Scientific Revolutions. The concept of incommensurability, now considerably developed, remains at center stage, but the evolutionary metaphor, introduced in the final pages of the book, now also plays a principal role.

Few philosophers of science have influenced as many readers as Thomas S. Kuhn. Yet no comprehensive study of his ideas has existed--until now. In this volume, Paul Hoyningen-Huene examines Kuhn's work over four decades, from the days before The Structure of Scientific Revolutions to the present, and puts Kuhn's philosophical development in a historical framework. Scholars from disciplines as diverse as political science and art history have offered widely differing interpretations of Kuhn's ideas, appropriating his notions of paradigm shifts and (...) revolutions to fit their own theories, however imperfectly. Hoyningen-Huene does not merely offer another interpretation--he brings Kuhn's work into focus with rigorous philosophical analysis. Through extended discussions with Kuhn and an encyclopedic reading of his work, Hoyningen-Huene looks at the problems and justifications of his claims and determines how his theories might be expanded. Most significantly, he discovers that The Structure of Scientific Revolutions can be understood only with reference to the historiographic foundation of Kuhn's philosophy. Discussing the concepts of paradigms, paradigm shifts, normal science, and scientific revolutions, Hoyningen-Huene traces their evolution to Kuhn's experience as a historian of contemporary science. From here, Hoyningen-Huene examines Kuhn's well-known thesis that scientists on opposite sides of a revolutionary divide "work in different worlds," explaining Kuhn's notion of a world-change during a scientific revolution. He even considers Kuhn's most controversial claims--his attack on the distinction between the contexts of discovery and justification and his notion of incommensurability--addressing both criticisms and defenses of these ideas. Destined to become the authoritative philosophical study of Kuhn's work, Reconstructing Scientific Revolutions both enriches our understanding of Kuhn and provides powerful interpretive tools for bridging Continental and Anglo-American philosophical traditions. (shrink)

Thomas S. Kuhn's classic book is now available with a new index.

This paper analyzes the generation and function of hitherto ignored or misrepresented interfield theories , theories which bridge two fields of science. Interfield theories are likely to be generated when two fields share an interest in explaining different aspects of the same phenomenon and when background knowledge already exists relating the two fields. The interfield theory functions to provide a solution to a characteristic type of theoretical problem: how are the relations between fields to be explained? In solving this problem (...) the interfield theory may provide answers to questions which arise in one field but cannot be answered within it alone, may focus attention on domain items not previously considered important, and may predict new domain items for one or both fields. Implications of this analysis for the problems of reduction and the unity and progress of science are mentioned. (shrink)

: This essay explores some themes in use of a relativized Kantian a priori in the work of Thomas Kuhn and Michael Friedman. It teases out some shared and some divergent beliefs and attitudes in these two philosophers by comparing their characteristic questions and problems to the questions and problems that seem most appropriately to attend to an adequate understanding of games and their histories. It argues for a way forward within a relativized Kantian framework that is suggested but not (...) argued for in Friedman (2001): philosophers of science should move from a concern with unreason as meaninglessness to a concern with unreason as argumentative coercion. It ends with a few suggestions regarding a place for philosophy in the history of reason. (shrink)

This book is an attempt to get to the bottom of an acute and perennial tension between our best scientific pictures of the fundamental physical structure of the world and our everyday empirical experience of it. The trouble is about the direction of time. The situation (very briefly) is that it is a consequence of almost every one of those fundamental scientific pictures--and that it is at the same time radically at odds with our common sense--that whatever can happen can (...) just as naturally happen backwards. Albert provides an unprecedentedly clear, lively, and systematic new account--in the context of a Newtonian-Mechanical picture of the world--of the ultimate origins of the statistical regularities we see around us, of the temporal irreversibility of the Second Law of Thermodynamics, of the asymmetries in our epistemic access to the past and the future, and of our conviction that by acting now we can affect the future but not the past. Then, in the final section of the book, he generalizes the Newtonian picture to the quantum-mechanical case and (most interestingly) suggests a very deep potential connection between the problem of the direction of time and the quantum-mechanical measurement problem. The book aims to be both an original contribution to the present scientific and philosophical understanding of these matters at the most advanced level, and something in the nature of an elementary textbook on the subject accessible to interested high-school students. Table of Contents: Preface 1. Time-Reversal Invariance 2. Thermodynamics 3. Statistical Mechanics 4. The Reversibility Objections and the Past-Hypothesis 5. The Scope of Thermodynamics 6. The Asymmetries of Knowledge and Intervention 7. Quantum Mechanics Appendix: Gedankenexperiments with Heat Engines Index Reviews of this book: The foundations of statistical mechanisms are often presented in physics textbooks in a rather obscure and confused way. By challenging common ways of thinking about this subject, Time and Chance can do quite a lot to improve this situation. --Jean Bricmont, Science Albert is perfecting a style of foundational analysis that is uniquely his own...It has a surgical precision...and it is ruthless with pretensions. The foundations of thermodynamics is a topic that has accumulated a good deal of dead wood; this is a fire that will burn and burn. --Simon W. Saunders, Oxford University As usual with Albert's work, the exposition is brisk and to the point, and exceptionally clear...The book will be an extremely valuable contribution to the literature on the subject of philosophical issues in thermodynamics and statistical mechanics, a literature which has been thin on the ground but is now growing as it deserves to. --Lawrence Sklar, University of Michigan. (shrink)

Incommensurability may be regarded as driving specialisation, on the one hand, and as posing some problems to interdisciplinarity, on the other hand. It may be argued, however, that incommensurability plays no role in either specialisation or interdisciplinarity. Scientific specialties could be defined as simply 'different' (that is, about different things), rather than 'incommensurable' (that is, competing for the explanation of the same phenomena). Interdisciplinarity could be viewed as the co- ordinated effort of scientists possessing complemetary and interlocking skills, and not (...) as the overcoming of some sort of incommensurable divide. This article provides a comprehensive evaluative examination of the relations between specialisation, interdisciplinarity, and incommensurability. Its aim is to defend the relevance of incommensurability to both specialisation and interdisciplinarity. At the same time, it aims at correcting the tendency, common among many philosophers, to regard incommensurability in a restrictive manner - such as, for example, as an almost purely semantic issue. (shrink)

Moti Mizrahi has argued that Thomas Kuhn does not have a good argument for the incommensurability of successive scientific paradigms. With Rouse, Andersen, and others, I defend a view on which Kuhn primarily was trying to explain scientific practice in Structure. Kuhn, like Hilary Putnam, incorporated sociological and psychological methods into his history of science. On Kuhn’s account, the education and initiation of scientists into a research tradition is a key element in scientific training and in his explanation of incommensurability (...) between research paradigms. The first part of this paper will explain and defend my reading of Kuhn. The second part will probe the extent to which Kuhn’s account can be supported, and the extent to which it rests on shaky premises. That investigation will center on Moti Mizrahi’s project, which aims to transform the Kuhnian account of science and of its history. While I do defend a modified kind of incommensurability, I agree that the strongest version of Kuhn’s account is steadfastly local and focused on the practice of science. (shrink)

The rosy dawn of my title refers to that optimistic time when the logical concept of a natural kind originated in Victorian England. The scholastic twilight refers to the present state of affairs. I devote more space to dawn than twilight, because one basic problem was there from the start, and by now those origins have been forgotten. Philosophers have learned many things about classification from the tradition of natural kinds. But now it is in disarray and is unlikely to (...) be put back together again. My argument is less founded on objections to the numerous theories now in circulation, than on the sheer proliferation of incompatible views. There no longer exists what Bertrand Russell called ‘the doctrine of natural kinds’—one doctrine. Instead we have a slew of distinct analyses directed at unrelated projects. (shrink)

Why, despite his enormous influence in the latter part of the twentieth century, has Kuhn left no distinctively Kuhnian legacy? I argue that this is because the development of Kuhn’s own thought was in a direction opposite to that of the mainstream of the philosophy of science. In the 1970s and 1980s the philosophy of science took on board the lessons of externalism as regards reference and knowledge, and became more sympathetic to a naturalistic approach to philosophical problems. Kuhn, on (...) the other hand, started out with a strong naturalistic streak, employing non-philosophical disciplines, primarily psychology, in order to build his accounts of scientific change and the nature of observation and scientific thought. But by the 1970s Kuhn’s work had taken on a much more purely philosophical, a priori, tone. His explanation of incommensurability moved from a psychological explanation to one embedded in the philosophy of language. Increasingly he gave his outlook a Kantian gloss. I suggest, nonetheless, that Kuhn’s most valuable contribution is to be found in The Structure of Scientific Revolutions and not in his later work, and that the naturalistic direction of the former has important links with connectionist research in cognitive science that deserve further study.Author Keywords: Kuhn; Scientific revolutions; Empiricism; Naturalism; Incommensurability; Reference. (shrink)

In his late years, Thomas Kuhn became interested in the process of scientific specialization, which does not seem to possess the destructive element that is characteristic of scientific revolutions. It therefore makes sense to investigate whether and how Kuhn’s insights about specialization are consistent with, and actually fit, his model of scientific progress through revolutions. In this paper, I argue that the transition toward a new specialty corresponds to a revolutionary change for the group of scientists involved in such a (...) transition. I will clarify the role of the scientific community in revolutionary changes and characterize the incommensurability across specialties as possessing both semantic and methodological aspects. The discussion of the discovery of the structure of DNA will serve both as an illustration of my main argument and as reply to one criticism raised against Kuhn—namely, that his model cannot capture cases of revolutionary yet non-disruptive episodes of scientific progress. Revisiting Kuhn’s ideas on specialization will shed new light on some often overlooked features of scientific change. (shrink)

Thomas Kuhn transformed the philosophy of science. His seminal 1962 work "The Structure of Scientific Revolutions" introduced the term 'paradigm shift' into the vernacular and remains a fundamental text in the study of the history and philosophy of science. This introduction to Kuhn's ideas covers the breadth of his philosophical work, situating "The Structure of Scientific Revolutions" within Kuhn's wider thought and drawing attention to the development of his ideas over time. Kuhn's work is assessed within the context of other (...) philosophies of science notably logical empiricism and recent developments in naturalized epistemology. The author argues that Kuhn's thinking betrays a residual commitment to many theses characteristic of the empiricists he set out to challenge. Kuhn's influence on the history and philosophy of science is assessed and where the field may be heading in the wake of Kuhn's ideas is explored. (shrink)

Statistical mechanics is one of the crucial fundamental theories of physics, and in his new book Lawrence Sklar, one of the pre-eminent philosophers of physics, offers a comprehensive, non-technical introduction to that theory and to attempts to understand its foundational elements. Among the topics treated in detail are: probability and statistical explanation, the basic issues in both equilibrium and non-equilibrium statistical mechanics, the role of cosmology, the reduction of thermodynamics to statistical mechanics, and the alleged foundation of the very notion (...) of time asymmetry in the entropic asymmetry of systems in time. The book emphasises the interaction of scientific and philosophical modes of reasoning, and in this way will interest all philosophers of science as well as those in physics and chemistry concerned with philosophical questions. The book could also be read by an informed general reader interested in the foundations of modern science. (shrink)

Over the last decades, science has grown increasingly collaborative and interdisciplinary and has come to depart in important ways from the classical analyses of the development of science that were developed by historically inclined philosophers of science half a century ago. In this paper, I shall provide a new account of the structure and development of contemporary science based on analyses of, first, cognitive resources and their relations to domains, and second of the distribution of cognitive resources among collaborators and (...) the epistemic dependence that this distribution implies. On this background I shall describe different ideal types of research activities and analyze how they differ. Finally, analyzing values that drive science towards different kinds of research activities, I shall sketch the main mechanisms underlying the perceived tension between disciplines and interdisciplinarity and argue for a redefinition of accountability and quality control for interdisciplinary and collaborative science. (shrink)

Divided into three parts, this work is a record of the direction Kuhn was taking during the last two decades of his life. It consists of essays in which he refines the basic concepts set forth in "Structure"--Paradigm shifts, incommensurability, and the nature of scientific progress.

The picture of synthetic biology as a kind of engineering science has largely created the public understanding of this novel field, covering both its promises and risks. In this paper, we will argue that the actual situation is more nuanced and complex. Synthetic biology is a highly interdisciplinary field of research located at the interface of physics, chemistry, biology, and computational science. All of these fields provide concepts, metaphors, mathematical tools, and models, which are typically utilized by synthetic biologists by (...) drawing analogies between the different fields of inquiry. We will study analogical reasoning in synthetic biology through the emergence of the functional meaning of noise, which marks an important shift in how engineering concepts are employed in this field. The notion of noise serves also to highlight the differences between the two branches of synthetic biology: the basic science-oriented branch and the engineering-oriented branch, which differ from each other in the way they draw analogies to various other fields of study. Moreover, we show that fixing the mapping between a source domain and the target domain seems not to be the goal of analogical reasoning in actual scientific practice. (shrink)

Incommensurability and Related Matters draws together some of the most distinguished contributors to the critical literature on the problem of the incommensurability of scientific theories. It addresses all the various problems raised by the problem of incommensurability, such as meaning change, reference of theoretical terms, scientific realism and anti-realism, rationality of theory choice, cognitive aspects of conceptual change, as well as exploring the broader implications of incommensurability for cultural difference. While it offers new work, and new directions of discussion, on (...) the topic of incommensurability, the book also recapitulates the history of the discussion of the topic that has taken place within the literature on incommensurability. (shrink)

This is an extensive review of recent work on the foundations of statistical mechanics.

Both in the bibliography and in the citation in the text, Michelle Gibbons’ article below has been mistakenly attributed to “Gibson.” The proper reference to the article should be: Gibbons, M.. Reassessing discovery: Rosalind Franklin, scientific visualization, and the structure of DNA. _Philosophy of Science, 79_, 63–80.

A highly condensed account of the author's present view of some philosophical problems unresolved in The Structure of Scientific Revolutions. The concept of incommensurability, now considerably developed, remains at center stage, but the evolutionary metaphor, introduced in the final pages of the book, now also plays a principal role.

Presenting a critical history of the philosophy of science in the twentieth century, focusing on the transition from logical positivism in its first half to the ...

Stars are conspicuously absent from reflections on natural kinds and scientific classifications, with gold, tiger, jade, and water getting all the philosophical attention. This is too bad for, as this paper will demonstrate, interesting philosophical lessons can be drawn from stellar taxonomy as regards two central, on-going debates about natural kinds, to wit, the monism/pluralism debate and the realism/antirealism debate. I’ll show in particular that stellar kinds will not please the essentialist monist, nor for that matter will it please the (...) pluralist embracing promiscuous realism à la Dupré. (shrink)

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. (shrink)

Thomas Kuhn's post-1980 writings have increasingly emphasized the role played by language in the characterization of scientific revolutions and incommensurability. We argue that Kuhn's `linguistic turn' can be understood best against the background of a Whorfian conception of language and certain neo-Kantian themes. While this enables Kuhn to refine and unify his earlier views, it also creates some difficulties.

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 , 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 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. (shrink)

The interpretive plasticity of Kuhn’s philosophical work has been reinforced by readings informed by other philosophical, historiographic or sociological projects. This paper highlights several aspects of Kuhn’s work that have been neglected by such readings. First, Kuhn’s early contribution to several subsequent philosophical developments has been unduly neglected. Kuhn’s postscript discussion of “exemplars” should be recognized as one of the earliest versions of a conception of theories as “mediating models.” Kuhn’s account of experimental practice has also been obscured by readings (...) that assimilate his views to Quinean holism. Second, three distinctive Kuhnian themes have been insufficiently recognized. Kuhn’s challenge to received philosophical views has been domesticated by reading him as offering an alternative conception of scientific knowledge. Kuhn is better understood as rejecting knowledge-centric accounts altogether, in favor of understanding the practice of research. Kuhn’s conception of that activity, as conceptual “articulation,” has accordingly also not been given its due. Finally, Kuhn’s career-long insistence on the mutual accountability of philosophy of science and the philosophy of mind and language calls attention to the extent to which these fields have now drifted apart. (shrink)

Many studies of the unification of science focus on the theories of different disciplines. The model for integration is the theory reduction model. This paper argues that the embodiment of theories in scientists, and the institutions in which scientists work and the instruments they employ, are critical to the sort of integration that actually occurs in science. This paper examines the integration of scientific endeavors that emerged in cell biology in the period after World War II when the development of (...) cell fractionation and electron microscopy made serious investigations of cell organelles possible. One surprising feature of such integration is that it generated further disintegration as the new institutions of cell biology separated the practitioners of the new discipline from other, closely related biological disciplines. (shrink)

Species pluralism gives us reason to doubt the existence of the species category. The problem is not that species concepts are chosen according to our interests or that pluralism and the desire for hierarchical classifications are incompatible. The problem is that the various taxa we call 'species' lack a common unifying feature.

Philosophers of physics are very familiar with foundational problems in quantum mechanics and in the theory of relativity. In both fields, the puzzles, if not solved, are at least reasonably well formulated and possess well-characterized solution strategies. Sklar’s book Physics and Chance focuses on a pair of theories, thermodynamics and statistical mechanics, for which puzzles and foundational paradoxes abound, but where there is very little agreement upon the means with which they may best be approached. As he notes in the (...) introduction. (shrink)

Kuhn's Structure of Scientific Revolutions has been enduringly influential in philosophy of science, challenging many common presuppositions about the nature of science and the growth of scientific knowledge. However, philosophers have misunderstood Kuhn's view, treating him as a relativist or social constructionist. In this book, Brad Wray argues that Kuhn provides a useful framework for developing an epistemology of science that takes account of the constructive role that social factors play in scientific inquiry. He examines the core concepts of Structure (...) and explains the main characteristics of both Kuhn's evolutionary epistemology and his social epistemology, relating Structure to Kuhn's developed view presented in his later writings. The discussion includes analyses of the Copernican revolution in astronomy and the plate tectonics revolution in geology. The book will be useful for scholars working in science studies, sociologists and historians of science as well as philosophers of science. (shrink)

Statistical mechanics is one of the crucial fundamental theories of physics, and in his new book Lawrence Sklar, one of the pre-eminent philosophers of physics, offers a comprehensive, non-technical introduction to that theory and to attempts to understand its foundational elements. Among the topics treated in detail are: probability and statistical explanation, the basic issues in both equilibrium and non-equilibrium statistical mechanics, the role of cosmology, the reduction of thermodynamics to statistical mechanics, and the alleged foundation of the very notion (...) of time asymmetry in the entropic asymmetry of systems in time. The book emphasises the interaction of scientific and philosophical modes of reasoning, and in this way will interest all philosophers of science as well as those in physics and chemistry concerned with philosophical questions. The book could also be read by an informed general reader interested in the foundations of modern science. (shrink)

Interdisciplinary integration has fundamental limitations. This is not sufficiently realized in science and in philosophy. Concerning scientific theories there are many examples of pseudo-integration which should be unmasked by elementary philosophical analysis. For example, allegedly over-arching theories of stress which are meant to unite biology and psychology, upon analysis, turn out to represent terminological rather than substantive unity. They should be replaced by more specific, local theories. Theories of animal orientation, likewise, have been formulated in unduly general terms. A natural (...) history approach is more suitable for the study of animal orientation. The tendency to formulate overgeneral theories is also present in evolutionary biology. Philosophy of biology can only deal with these matters if it takes a normative turn. Undue emphasis on interdisciplinary integration is a modern variant of the old unity of science ideal. The replacement of the ideal by a better one is an important challenge for the philosophy of science. (shrink)