Knowledge-making practices in biology are being strongly affected by the availability of data on an unprecedented scale, the insistence on systemic approaches and growing reliance on bioinformatics and digital infrastructures. What role does theory play within data-intensive science, and what does that tell us about scientific theories in general? To answer these questions, I focus on Open Biomedical Ontologies, digital classification tools that have become crucial to sharing results across research contexts in the biological and biomedical sciences, and argue that (...) they constitute an example of classificatory theory. This form of theorizing emerges from classification practices in conjunction with experimental know-how and expresses the knowledge underpinning the analysis and interpretation of data disseminated online. (shrink)

The traditional mode of explanation in physics via deduction from partial differential equations is contrasted here with explanation via simulations. I argue that the different technologies employed constitute different languages, which support different sorts of narratives. The narratives that accompany simulations and articulate their meaning are typically historical or natural historical in kind. They explain complex phenomena by growing them rather than by referring them to general laws. Examples of such growth simulations and growth narratives come from the evolution of (...) wave functions in quantum chaos, snowflake formation, and Etruscan genetics. The examples suggest a few concluding remarks on historical explanation. (shrink)

The existing literature on the development of recombinant DNA technology and genetic engineering tends to focus on Stanley Cohen and Herbert Boyer's recombinant DNA cloning technology and its commercialization starting in the mid-1970s. Historians of science, however, have pointedly noted that experimental procedures for making recombinant DNA molecules were initially developed by Stanford biochemist Paul Berg and his colleagues, Peter Lobban and A. Dale Kaiser in the early 1970s. This paper, recognizing the uneasy disjuncture between scientific authorship and legal invention (...) in the history of recombinant DNA technology, investigates the development of recombinant DNA technology in its full scientific context. I do so by focusing on Stanford biochemist Berg's research on the genetic regulation of higher organisms. As I hope to demonstrate, Berg's new venture reflected a mass migration of biomedical researchers as they shifted from studying prokaryotic organisms like bacteria to studying eukaryotic organisms like mammalian and human cells. It was out of this boundary crossing from prokaryotic to eukaryotic systems through virus model systems that recombinant DNA technology and other significant new research techniques and agendas emerged. Indeed, in their attempt to reconstitute 'life' as a research technology, Stanford biochemists' recombinant DNA research recast genes as a sequence that could be rewritten thorough biochemical operations. The last part of this paper shifts focus from recombinant DNA technology's academic origins to its transformation into a genetic engineering technology by examining the wide range of experimental hybridizations which occurred as techniques and knowledge circulated between Stanford biochemists and the Bay Area's experimentalists. Situating their interchange in a dense research network based at Stanford's biochemistry department, this paper helps to revise the canonized history of genetic engineering's origins that emerged during the patenting of Cohen-Boyer's recombinant DNA cloning procedures. (shrink)

Historians and philosophers of twentieth-century life sciences have demonstrated that the choice of experimental organism can profoundly influence research fields, in ways that sometimes undermined the scientists’ original intentions. The present paper aims to enrich and broaden the scope of this literature by analysing the career of unicellular green algae of the genus Chlorella. They were introduced for the study of photosynthesis in 1919 by the German cell physiologist Otto H. Warburg, and they became the favourite research objects in this (...) field up to the 1960s. The paper argues that dealing with Chlorella’s high metabolic flexibility was crucial for the emergence of a new conception of photosynthesis, as a plastic, integrated system of pathways. At the same time, it led to new collaborations between physiologists and phycologists, both of whom started to re-orient their studies in ecologically informed directions. Following Chlorella’s trail, hence, not only elucidates how experimental organisms forced scientists to change their conceptual approaches and techniques, but also provides insight into the interaction of different lines of research of mid-twentieth century plant sciences. (shrink)

I propose we abandon the unit concept of "the evolutionary synthesis". There was much more to evolutionary studies in the 1920s and 1930s than is suggested in our commonplace narratives of this object in history. Instead, four organising threads capture much of evolutionary studies at this time. First, the nature of species and the process of speciation were dominating, unifying subjects. Second, research into these subjects developed along four main lines, or problem complexes: variation, divergence, isolation, and selection. Some calls (...) for 'synthesis' focused on these problem complexes (sometimes on one of these; other times, all). In these calls, comprehensive and pluralist compendia of plausibly relevant elements were preferred over reaching consensus about the value of particular formulae. Third, increasing confidence in the study of common problems coincided with methodological and epistemic changes associated with experimental taxonomy. Finally, the surge of interest in species problems and speciation in the 1930s is intimately tied to larger trends, especially a shifting balance in the life sciences towards process-based biologies and away from object-based naturalist disciplines. Advocates of synthesis in evolution supported, and were adapting to, these larger trends. (shrink)

The discovery and ongoing investigation of microRNAs suggest important conceptual and methodological lessons for philosophers and historians of biology. This paper provides an account of miRNA research and the shift from viewing these tiny regulatory entities as minor curiosities to seeing them as major players in the post-transcriptional regulation of genes. Conceptually, the study of miRNAs is part of a broader change in understandings of genetic regulation, in which simple switch-like mechanisms were reinterpreted as aspects of complex cellular and genome-wide (...) processes. Among them are the activities of small RNAs, previously regarded as non-functional. Methodologically, the miRNA story suggests new ways of characterizing biological research that should prove helpful to philosophers of science who seek to develop more pluralistic, pragmatic models of scientific inquiry. miRNA research displays iterative movements between multiple modes of investigation that include not only the proposal and testing of hypotheses but also exploratory, technology-oriented and question-driven modes of research. As an exemplary story of scientific discovery and development, the miRNA case illustrates transitions from genetics to genomics and systems biology, and it shows how diverse configurations of research practice are related to major scientific advances. (shrink)

Over the course of the last three decades, computer simulations have become a major tool of doing science and engaging with the world, not least in an effort to predict and intervene in a future to come. Born in the context of the Second World War and the discipline of physics, simulations have long spread into most diverse fields of enquiry and technological application. This paper introduces a topical collection focussing on simulations in the life sciences. Echoing the current state (...) of tinkering, fast developments, segmentation of knowledge and interdisciplinary collaboration, and in an effort to bridge the science-humanities divide, the contributors to this collection come from multiple disciplinary backgrounds, including information studies, cognitive sciences, philosophy and biology. The ambiguous character of simulations, their cutting across scientific disciplines, analysis and prediction, understanding and doing, gave rise to their success in contemporary life sciences and has been the object of much scientific debate. One of the main aims of this topical collection, by contrast, is to call into question the assumption of an obvious use and easy transfer of methods between fields of knowledge as diverse as, e.g. physics and biology. The collection presents historical case studies from various biological sub-fields. The articles study how simulations are used and the ways they contribute specifically to our understanding of life. Taking up Sergio Sismondo’s description of simulations as “compromises” and “glue”, they also critically engage with the question of what exactly the life sciences have been gluing together over the last two decades. (shrink)

This paper argues that we can acknowledge the existence of moral truths and moral progress without being committed to moral realism. Rather than defending this claim through the more familiar route of the attempted analysis of the ontological commitments of moral claims, I show how moral belief change for the better shares certain features with theoretical progress in the natural sciences. Proponents of the better theory are able to convince their peers that it is formally and empirically superior to its (...) rivals, and the better theory may be promoted to the status of the truth. Yet there is no 'decision-procedure' for ethics any more than there is for molecular biology. The betterness of true theories can be grasped through what I term 'undirectional narratives' of progress. And while there are true moral claims and perhaps numerous moral truths yet to be discovered, we should reject currently popular forms of moral realism with bivalence. Some moral claims lend themselves to the construction of fully reversible, bi-directional narratives and are likely neither true nor false. (shrink)

The existing literature on the development of recombinant DNA technology and genetic engineering tends to focus on Stanley Cohen and Herbert Boyer's recombinant DNA cloning technology and its commercialization starting in the mid-1970s. Historians of science, however, have pointedly noted that experimental procedures for making recombinant DNA molecules were initially developed by Stanford biochemist Paul Berg and his colleagues, Peter Lobban and A. Dale Kaiser in the early 1970s. This paper, recognizing the uneasy disjuncture between scientific authorship and legal invention (...) in the history of recombinant DNA technology, investigates the development of recombinant DNA technology in its full scientific context. I do so by focusing on Stanford biochemist Berg's research on the genetic regulation of higher organisms. As I hope to demonstrate, Berg's new venture reflected a mass migration of biomedical researchers as they shifted from studying prokaryotic organisms like bacteria to studying eukaryotic organisms like mammalian and human cells. It was out of this boundary crossing from prokaryotic to eukaryotic systems through virus model systems that recombinant DNA technology and other significant new research techniques and agendas emerged. Indeed, in their attempt to reconstitute 'life' as a research technology, Stanford biochemists' recombinant DNA research recast genes as a sequence that could be rewritten thorough biochemical operations. The last part of this paper shifts focus from recombinant DNA technology's academic origins to its transformation into a genetic engineering technology by examining the wide range of experimental hybridizations which occurred as techniques and knowledge circulated between Stanford biochemists and the Bay Area's experimentalists. Situating their interchange in a dense research network based at Stanford's biochemistry department, this paper helps to revise the canonized history of genetic engineering's origins that emerged during the patenting of Cohen-Boyer's recombinant DNA cloning procedures. (shrink)

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)

This paper explores the case of using robots to simulate evolution, in particular the case of Hamilton’s Law. The uses of robots raises several questions that this paper seeks to address. The first concerns the role of the robots in biological research: do they simulate something or do they participate in something? The second question concerns the physicality of the robots: what difference does embodiment make to the role of the robot in these experiments. Thirdly, how do life, embodiment and (...) social behavior relate in contemporary biology and why is it possible for robots to illuminate this relation? These questions are provoked by a strange similarity that has not been noted before: between the problem of simulation in philosophy of science, and Deleuze’s reading of Plato on the relationship of ideas, copies and simulacra. (shrink)

This article unpacks a particular use of ‘cases’ within developmental biology, namely as a means of describing the typical or canonical patterns of phenomena. The article explores how certain cases have come to be established within the field and argues that although they were initially selected for reasons of convenience or ease of experimental manipulation, these cases come to serve as key reference points within the field because of the epistemological structures imposed on them by the scientists using them and, (...) hence, become usable in a wider variety of circumstances including future theory development. (shrink)

The massive expansion of US higher education after World War II is a sociological puzzle: a spectacular feat of state capacity-building in a highly federated polity. Prior scholarship names academic leaders as key drivers of this expansion, yet the conditions for the possibility and fate of their activity remain under-specified. We fill this gap by theorizing what Randall Collins first callededucational entrepreneurshipas a special kind of strategic action in the US polity. We argue that the cultural authority and organizational centrality (...) of universities in the US national context combine with historical contingency to episodically produce conditions under which academic credentials can be made viable solutions to social problems. We put our theorization to the test by revisiting and extending a paradigmatic case: the expansion of engineering education at Stanford University between 1945 and 1969. Invoking several contemporaneous and subsequent cases, we demonstrate the promise of theorizing educational expansion as an outcome of strategic action by specifically located actors over time. (shrink)

The provocative paper by John Forrester ‘If p, Then What? Thinking in Cases’ (1996) opened up the question of case thinking as a separate mode of reasoning in the sciences. Case-based reasoning is certainly endemic across a number of sciences, but it has looked different according to where it has been found. This article investigates this mode of science – namely thinking in cases – by questioning the different interpretations of ‘If p?’ and exploring the different interpretative responses of what (...) follows in ‘Then What?’. The aim is to characterize how ‘reasoning in, within, with, and from cases’ forms a mode of scientific investigation for single cases, for runs of cases, and for comparative cases, drawing on materials from a range of different fields in which case-based reasoning appears. (shrink)

This paper links two domains of recent interest in science and technology studies, complexity and ignorance, in the context of knowledge practices observed among synthetic biologists. Synthetic biologists are recruiting concepts and methods from computer science and electrical engineering in order to design and construct novel organisms in the lab. Their field has taken shape amidst revised assessments of life’s complexity in the aftermath of the Human Genome Project. While this complexity is commonly taken to be an immanent property of (...) biological systems, this article presents an epistemological view of complexity according to which complexity relates to a specific scientific theory or model and refers to that which exceeds the theory or model’s explanatory power. This epistemological view allows us to narrate a particular story about the changing relationship between biology and synthetic biology in the last decade and accounts for early knowledge practices in synthetic biology that “ignored” biology. This article further argues that while the failure of ignorance to produce clear-cut results for synthetic biologists has led practitioners back to biology, the entanglements between different pragmatic orientations and ways of knowing trouble the implications of this return for assessments of the complexity of biological systems. (shrink)