This article is a systematic critical survey of work done in the philosophy of biology within the logical empiricist tradition, beginning in the 1930s and until the end of the 1950s. It challenges a popular view that the logical empiricists either ignored biology altogether or produced analyses of little value. The earliest work on the philosophy of biology within the logical empiricist corpus was that of Philipp Frank, Ludwig von Bertalanffy, and Felix Mainx. Mainx, in particular, provided a detailed analysis (...) of biology in the 1930s and 1940s in his contribution to the logical empiricists’ Encyclopedia of Unified Science. However, the most important contributions to the philosophy of biology were those of Joseph Henry Woodger and Ernest Nagel. Woodger is primarily remembered for deploying the axiomatic method in biology but he also used semiformal methods for the analysis of many biological problems. While Woodger’s axiomatic work was often derided by some later philosophers of biology (e.g., David Hull and Michael Ruse), this article defends both the biological and the philosophical significance of some of that work, for instance, those aspects that led to the recognition of the conceptual complexity of mereology and temporal identity in biological systems. Woodger’s semiformal analyses were even more important, for instance, his explication of the concepts of the Bauplan and of innateness. Nagel’s importance lies in his analyses of reduction and emergence in the context of all empirical sciences and his use of these analyses in a careful exploration of biological problems. While Nagel’s model of reduction was generally rejected by philosophers of science in the 1970s and 1980s, particularly for biological contexts, it has recently been sympathetically reconstructed by many commentators; this article defends its continued relevance for the philosophy of biology. (shrink)

Throughout its history, the relationship between government and science in the United States has been mutually beneficial but also contentious. This article reviews the recent history of this relationship and attributes the conflict to different norms and values in each of the institutions. A policy culture is the result. It sets the limits of government action and shapes the policy agenda, the debates, and their outcomes. The evolving norms of policy culture are examined on the basis of two specific controversies: (...) pork-barrel support of science and university-industry relations. The article concludes with a discussion of why the study of a policy culture helps us understand the ways in which values shape science policy. (shrink)

It is now twenty years since James Watson published his personal account of the discovery of the structure of DNA and triggered the growing scholarly study of the roots of molecular biology. Watson himself was not concerned with the study of nucleic acids before he became directly involved but at least three detailed histories of the early development of molecular biology have subsequently appeared, together with books, papers and reviews from others who took part, or their partisan representatives. Of these (...) three histories, only one does justice to Avery's work. His surviving DNA collaborator, MacLyn McCarty, believes that only Olby inThe Path to the Double Helixdeals adequately with Avery's contribution. (shrink)

In this article I consider some central aspects of the naturalist philosophy of science and science and technology studies in dealing with the contested status of technoscience in medicine. Focusing on the concepts of realism and representation, I argue that theories of science-as-practice in naturalist philosophy of science should expand their scope so as to reflect more thoroughly on the social and political context of technoscience. I develop a hermeneutic of technomedical objects in order to highlight the internal connectedness between (...) social action, material agency, and the actions of scientific communities. The framework thus developed is used to re-consider the genomic turn in medicine. Pointing to the discrepancies between socially dominant representations of genomic technology and the actual interventions brought about through those technologies, I raise the question of how and where to address problems of theory and policy. (shrink)

A major theme in biological research is the quest for mechanism, embodied in explanatory reductionism: the interpretation of phenomena through links to the entities and laws of more fundamental sciences. For example, the form of Starling's Law of the Heart, relating contractile force to heart volume, follows from the sliding-filament hypothesis of muscle contraction, a molecular concept. Although alternative mechanisms for muscle contraction and cardiac regulation could be deduced from biochemical principles, the formulation provides clear correspondence with the phenomena and (...) a deeper understanding of cardiac function. Moreover, even if the reduction provides no better formulation of the phenomenon, of the macro-regularity, it is still prized as a nearer approach to physical reality, as a step toward realizing fundamental unities and codifying general principles, and as a door to new experimental opportunities. (shrink)

The history of what we call molecular biology today is not just the story of DNA. Molecular biology emerged from and was supported by a multiplicity of widely scattered, differently embedded, and loosely, if at all connected experimental systems for characterizing living beings to the level of biologically relevant macromolecules. By implementing different modes of technical analysis, these systems created a new space of representation in which the central concepts of molecular biology gradually became articulated. The paper describes the establishment (...) of the rat liverin vitro protein synthesis system of Paul Zamecnik and his group a the Collis P. Huntington Memorial Hospital of Harvard University between 1947 and 1952. Insofar as such systems orient the research activity, they may also prove helpful for the orientation of the historian. Experimental systems „have a life of their own. (shrink)

Although molecular biology has meant different things at different times, the term is often associated with a tendency to view cellular causation as conforming to simple linear schemas in which macro-scale effects are specified by micro-scale structures. The early achievements of molecular biologists were important for the formation of such an outlook, one to which the discovery of recombinant DNA techniques, and a number of other findings, gave new life even after the complexity of genotype–phenotype
relations had become apparent. Against this (...) background we outline how a range of scientific developments and conceptual considerations can be regarded as enabling and perhaps necessitating contemporary systems approaches. We suggest that philosophical ideas have a valuable part to play in making sense of complex scientific and disciplinary issues. (shrink)

One observes regulation at every biological level. Organisms, cells, and biochemical processes operate efficiently, normally wasting neither material nor energy, and adjusting their functions to external influences. Nature evidently has evolved mechanisms specifically dedicated to regulation at many levels. What is the molecular basis of this control?In the 1950s these molecular control mechanisms began to be explored seriously. The discoveries of feedback inhibition of enzyme activity were important because they gave an initial example of how regulation is achieved at the (...) molecular level. We showed that certain enzymes are composed of two parts, one for catalysis and another distinct part present only to regulate this catalysis. Catalytic activity can be either stimulated or inhibited when a small molecule in the environment combines with the enzyme's regulatory site. In particular, a final product of a metabolic pathway generates a feedback loop which automatically limits its own excessive production, by combining with the regulatory site of an early enzyme in that pathway. Later studies showed that catalytic and regulatory structures of some enzymes could be separated physically.The discovery of regulatory sites and their interaction with molecules unrelated to their substrates was the basis for the generalized allosteric concept. This concept extends the regulatory site idea to a wide variety of processes such as control of gene expression, hormone action, and cellular growth. (shrink)

The Pajama (Pardee, Jacob, Monod) experiment provided a breakthrough in our understanding of the molecular mechanisms by which gene expression is regulated. Today, twenty‐five years later it provides a paradigm for thinking about problems of gene expression, such as growth regulation and differentiation. From this experiment emerged entities such as repressors, regulatory genes, the operon as a group of jointly controlled genes, and messenger RNA.

Steve Fuller has argued that a scientific discovery will not be recognized unless it can be justified within the history of the relevant science. He cites Mendel's work on genetics, which was not recognized until thirty-five years after its publication, as an example. This essay argues that Mendel's work comes out of the tradition of work by both agricultural breeders and academics in nineteenth century Austria. Thus, Fuller is mistaken, and one must look elsewhere for the neglect of Mendel's work. (...) This essay also places Mendel's work within the philosophy of Jan Comenius, whose work was very likely known to Mendel.--------------------------------------------------------------------------------------------- ---------------------------------------------------------------------------------------------------- ---------------------------------------------------------------------------------------------------- ---------------------------------------------------------------------------------------------------- ---------------------------------------------------------------------------------------------------- ---------------------------------------------------------------------------------------------------- -----------------------------------------------. (shrink)

We argue that the physics of complex materials and self-organizing processes should be made central to the biology of form. Rather than being encoded in genes, form emerges when cells and certain of their molecules mobilize physical forces, effects, and processes in a multicellular context. What is inherited from one generation to the next are not genetic programs for constructing organisms, but generative mechanisms of morphogenesis and pattern formation and the initial and boundary conditions for reproducing the specific traits of (...) a taxon. There is no inherent antagonism between this “physicalist” perspective and genetics, since physics acts on matter, and gene products are essential material components of living systems whose variability affects the systems’ parameters. We make this notion concrete by summarizing the concept of “dynamical patterning modules” (DPMs; Newman and Bhat, Phys Biol 5:1–14, 2008; Int J Dev Biol 53:693–705, 2009), an explicit physico-genetic framework for the origin and evolution of multicellular form in animals, as well as (when differences in interaction toolkit genes and applicable physical processes are taken into account) in multicellular plants (Hernández-Hernández et al., Int J Dev Biol 56:661–674, 2012). DPMs provide the missing link between development and evolution by revealing how genes acting in concert with physics can generate and transform morphology in a heritable fashion. (shrink)

François Jacob’s The Logic of Life: A History of Heredity has shown an enduring relevance for the history and philosophy of biology. In this article, resisting the received view that regards this book merely as an application of Foucault’s archaeological method, I reconstruct a silent debate between François Jacob and Jacques Monod. More precisely, I argue that Jacob’s history of biology offers a riposte to Monod’s claims in Chance and Necessity. First, I show that the distinction between a “history of (...) ideas” and a “history of objects” captures two ways of looking at the history of science that characterize Monod’s and Jacob’s own approaches. Next, I present Monod’s search for a “theory of the natural selection of ideas.” Then I argue that the concept of “integron,” introduced by Jacob in his conclusion, covertly undermines Monod’s argument for the use of evolutionary models of cultural and scientific change. These contrasting perspectives shed new light on why the Nobel colaureates and former colleagues expressed little interest in each other’s books. More generally, the Monod-Jacob divide illustrates the use and rejection of biological models in writing the history of science and the importance of situating Jacob within his own milieu. (shrink)

In this paper the scientific trajectory of Spanish influential biochemist Alberto Sols (1917–1989) is presented in comparative perspective. His social and academic environment, his research training under the Cori's in the US in the early 1950s and his works when coming back to Spain to develop his own scientific career are described in order to present the central argument of this paper on his path from physiological research to research on enzymatic regulation. Sols' main contributions were both scientific and academic. (...) He and his collaborators not only contributed to biological knowledge on the biochemistry of metabolic regulation but to the active reception of biochemistry in the Spanish academia and to update of Spanish medical education. -/- . (shrink)

The central dogma of biology holds that genetic information normally flows from DNA to RNA to protein. As a consequence it has been generally assumed that genes generally code for proteins, and that proteins fulfil not only most structural and catalytic but also most regulatory functions, in all cells, from microbes to mammals. However, the latter may not be the case in complex organisms. A number of startling observations about the extent of non-protein-coding RNA (ncRNA) transcription in the higher eukaryotes (...) and the range of genetic and epigenetic phenomena that are RNA-directed suggests that the traditional view of the structure of genetic regulatory systems in animals and plants may be incorrect. ncRNA dominates the genomic output of the higher organisms and has been shown to control chromosome architecture, mRNA turnover and the developmental timing of protein expression, and may also regulate transcription and alternative splicing. This paper re-examines the available evidence and suggests a new framework for considering and understanding the genomic programming of biological complexity, autopoletic development and phenotypic variation. BioEssays 25:930-939,2003. (C) 2003 Wiley Periodicals, Inc. (shrink)

The concept of mechanism is analyzed in terms of entities and activities, organized such that they are productive of regular changes. Examples show how mechanisms work in neurobiology and molecular biology. Thinking in terms of mechanisms provides a new framework for addressing many traditional philosophical issues: causality, laws, explanation, reduction, and scientific change.

Life, and therefore evolution, is a creative process; creativity is not an attribute of a few gifted people. The way we think obscures this truth. Three ways of dealing with a problem are creativity, calculation, and choice. Creativity can occur when a single idea is held in two contradictory frames of reference. Thus to be creative we have to put aside our usual ways of thinking, which are based on either/or. When we put aside this way of thinking we will (...) see that things do not change: they are change. (shrink)

In 1948, a dynamic junior member of the Johns Hopkins Biology Department, William McElroy, became the first director of the McCollum—Pratt Institute for the Investigation of Micronutrient Elements. The Institute was founded at the university to further studies into the practicalities of animal nutrition. Ultimately, however, the Institute reflected McElroy's vision that all biological problems, including nutrition, could be best investigated through basic biochemical and enzymes studies. The Institute quickly became a hub of biochemical research over the following decade, producing (...) foundational work on metabolism and a respected series of symposia. In this paper, I argue that McElroy's biochemical vantage on biology also permeated the traditionally morphological and embryological Biology Department at Hopkins. Largely due to the activity of McElroy and the Institute, the faculty, course offerings, and research underwent a radical reorientation toward biochemistry and molecular biology in the 1950s, even while maintaining a commitment to developmental biology. While the history of postwar biology is often told as the ascendancy of the "new" biology over "traditional" biology, the case of McElroy and the McCollum—Pratt Institute affords an opportunity for historical examination of biochemical and molecular science as a lens through which all branches of biology at an institution were reconceived and unified. (shrink)

In 1948, a dynamic junior member of the Johns Hopkins Biology Department, William McElroy, became the first director of the McCollum—Pratt Institute for the Investigation of Micronutrient Elements. The Institute was founded at the university to further studies into the practicalities of animal nutrition. Ultimately, however, the Institute reflected McElroy's vision that all biological problems, including nutrition, could be best investigated through basic biochemical and enzymes studies. The Institute quickly became a hub of biochemical research over the following decade, producing (...) foundational work on metabolism and a respected series of symposia. In this paper, I argue that McElroy's biochemical vantage on biology also permeated the traditionally morphological and embryological Biology Department at Hopkins. Largely due to the activity of McElroy and the Institute, the faculty, course offerings, and research underwent a radical reorientation toward biochemistry and molecular biology in the 1950s, even while maintaining a commitment to developmental biology. While the history of postwar biology is often told as the ascendancy of the "new" biology over "traditional" biology, the case of McElroy and the McCollum—Pratt Institute affords an opportunity for historical examination of biochemical and molecular science as a lens through which all branches of biology at an institution were reconceived and unified. (shrink)

In 1958, Francis Crick distinguished the flow of information from the flow of matter and the flow of energy in the mechanism of protein synthesis. Crick’s claims about information flow and coding in molecular biology are viewed from the perspective of a new characterization of mechanisms and from the perspective of information as holding a key to distinguishing work in molecular biology from that of biochemistry in the 1950s–1970s . Flow of matter from beginning to end does not occur in (...) the protein synthesis mechanism; flow of information does. The flow of information and coding in molecular biological mechanisms are distinguished, on the one hand, from formal information theory, and, on the other, from information as used in cognitive neuroscience, where information and representation are often coupled. (shrink)

This essay recognizes that the interactions that define medical care are problematic and that narrative is invoked to overcome these strains. Being grounded in science, medicine, too, might be influenced by a particular world-view that arose in the natural philosophy of the Scientific Revolution. If narrative responds to this sort of medicine, it may retain traces of this mindset. A feminist approach responds to this viewpoint and may used beneficially to analyze both the story of medicine and the stories within (...) medicine. Tensions discussed from this perspective are those between sickness and health and those between patient and provider; also questioned are suitable form(s) of narrative and whose narratives are valued. Suggestions for broadening narrative to address these issues include letting the body speak for itself, overcoming the power differential in the patient/provider interaction and using standpoints to foster a more equal and just medical system. (shrink)

Current philosophical and legal bioethical reflection on reprogenetics provides little more than a rationalization of the interests of science. There are two reasons for this. First, bioethicists attempt to address ethical issues in a “language of precision” that characterizes science, and this works against analogical and narratological modes of discourse that have traditionally provided guidance for understanding human nature and purpose. Second, the current ethical and legal debate is framed by a public/private distinction that banishes robust norms to the private (...) realm, and leaves a minimalist public discourse of harm avoidance that is insufficient for regulating the science. In this essay, I argue that Mark Hanson's account of anxiety provides a valuable starting point for addressing deficiencies in the current philosophical and legal debate, and it highlights the need for a theological discourse on genetic enhancements. Through an assessment of Joel Shumann's criticism of the public/private distinction, I show how the needed theological discourse should be situated in the context of robust communities, and how such a communitarian inter-ethic is compatible with a variant of liberalism. Finally, I critically assess James Keenan's account of virtue and perfection, in order to outline what a sufficient discourse on reproductive and genetic enhancements requires. (shrink)

Since the 1930s, scientists studying the neurological disease scrapie had assumed that the infectious agent was a virus. By the mid 1960s, however, several unconventional properties had arisen that were difficult to reconcile with the standard viral model. Evidence for nucleic acid within the pathogen was lacking, and some researchers considered the possibility that the infectious agent consisted solely of protein. In 1982, Stanley Prusiner coined the term `prion' to emphasize the agent's proteinaceous nature. This infectious protein hypothesis was denounced (...) by many scientists as `heretical'.This two-part essay asks why the concept of an infectious protein was considered controversial. Some biologists justified their evaluation of this hypothesis on the grounds that an infectious protein contradicted the `central dogma of molecular biology'. Others referred to vague theoretical constraints such as molecular biology's `theoretical structure' or `framework'. Examination of the objections raised by researchers reveals exactly what generalizations were being challenged by a protein model of infection.This two-part survey of scrapie and prion research reaches several conclusions: A theoretical framework is present in molecular biology, exerting its influence in hypothesis formation and evaluation; This framework consists of several related, yet separable, generalizations or `elements', including Francis Crick's Central Dogma and Sequence Hypothesis, plus notions concerning infection, replication, protein synthesis, and protein folding; The term `central dogma' has stretched beyond Crick's original 1958 definition to encompass at least two other `framework elements': replication and protein synthesis; and From the study of scrapie and related diseases, biological information has been delineated into at least two classes: sequential and what I call `conformational'.In Part I of this essay, a brief review of the central dogma was given, and the developments in scrapie research from 1965 to 1972 were traced. This section summarized many of the puzzling, non-virus-like properties of the scrapie agent. Alternative hypotheses to the viral explanation were presented, including early versions of a protein-only hypothesis. Part II of this essay will follow the developments in scrapie and prion research from the mid-1970s through 1991. The growing prominence of a protein-only model of infection will be countered by continued objections from many researchers to a pathogen devoid of nucleic acid. These objections will help illuminate those generalizations in molecular biology that were indeed challenged by a protein-only model of infection. (shrink)

Since the 1930s, scientists studying the neurological disease scrapie had assumed that the infectious agent was a virus. By the mid 1960s, however, several unconventional properties had arisen that were difficult to reconcile with the standard viral model. Evidence for nucleic acid within the pathogen was lacking, and some researchers considered the possibility that the infectious agent consisted solely of protein. In 1982, Stanley Prusiner coined the term `prion' to emphasize the agent's proteinaceous nature. This infectious protein hypothesis was denounced (...) by many scientists as `heretical'.This essay asks why the concept of an infectious protein was considered controversial. Some biologists justified their evaluation of this hypothesis on the grounds that an infectious protein contradicted the `central dogma of molecular biology'. Others referred to vague theoretical constraints such as molecular biology's `theoretical structure' or `framework'. Examination of the objections raised by researchers reveals exactly what generalizations were being challenged by a protein model of infection.This two-part survey of scrapie and prion research reaches several conclusions: A theoretical framework is present in molecular biology, exerting its influence in hypothesis formation and evaluation; This framework consists of several related, yet separable, generalizations or `elements', including Francis Crick's Central Dogma and Sequence Hypothesis, plus notions concerning infection, replication, protein synthesis, and protein folding; The term `central dogma' has stretched beyond Crick's original 1958 definition to encompass at least two other `framework elements': replication and protein synthesis; and From the study of scrapie and related diseases, biological information has been delineated into at least two classes: sequential and what I call `conformational'.In Part I of this essay, a brief review of the central dogma, as outlined by both Francis Crick and James Watson, will be given. The developments in scrapie research from 1965 to 1972 will then be traced. This section will summarize many of the puzzling, non-viral-like properties of the scrapie agent. Alternative hypotheses to the viral explanation will also be presented, including early versions of a protein-only hypothesis. Part II of this essay will follow the developments in scrapie and prion research from the mid 1970s through 1991. The growing prominence of a protein-only model of infection will be balanced by continued objections from many researchers to a pathogen devoid of nucleic acid. These objections will help illuminate those generalizations in molecular biology that were indeed challenged by a protein-only model of infection. (shrink)

Since the 1930s, scientists studying the neurological disease scrapie had assumed that the infectious agent was a virus. By the mid 1960s, however, several unconventional properties had arisen that were difficult to reconcile with the standard viral model. Evidence for nucleic acid within the pathogen was lacking, and some researchers considered the possibility that the infectious agent consisted solely of protein. In 1982, Stanley Prusiner coined the term `prion' to emphasize the agent's proteinaceous nature. This infectious protein hypothesis was denounced (...) by many scientists as `heretical'.This two-part essay asks why the concept of an infectious protein was considered controversial. Some biologists justified their evaluation of this hypothesis on the grounds that an infectious protein contradicted the `central dogma of molecular biology'. Others referred to vague theoretical constraints such as molecular biology's `theoretical structure' or `framework'. Examination of the objections raised by researchers reveals exactly what generalizations were being challenged by a protein model of infection.This two-part survey of scrapie and prion research reaches several conclusions: A theoretical framework is present in molecular biology, exerting its influence in hypothesis formation and evaluation; This framework consists of several related, yet separable, generalizations or `elements', including Francis Crick's Central Dogma and Sequence Hypothesis, plus notions concerning infection, replication, protein synthesis, and protein folding; The term `central dogma' has stretched beyond Crick's original 1958 definition to encompass at least two other `framework elements': replication and protein synthesis; and From the study of scrapie and related diseases, biological information has been delineated into at least two classes: sequential and what I call `conformational'.In Part I of this essay, a brief review of the central dogma was given, and the developments in scrapie research from 1965 to 1972 were traced. This section summarized many of the puzzling, non-virus-like properties of the scrapie agent. Alternative hypotheses to the viral explanation were presented, including early versions of a protein-only hypothesis. Part II of this essay will follow the developments in scrapie and prion research from the mid-1970s through 1991. The growing prominence of a protein-only model of infection will be countered by continued objections from many researchers to a pathogen devoid of nucleic acid. These objections will help illuminate those generalizations in molecular biology that were indeed challenged by a protein-only model of infection. (shrink)

Genes and messages have a long association in biology, dating back at least to Weismann. But, through most of this history, even with the dramatic concreteness that molecular biology lent to this association, the image dominating most thinking about messages was drawn from the nineteenth-century technology of the telegraph. In the mid-twentieth century, a new technology, the computer, arrived to displace the telegraph. With that displacement, the meanings of many terms—of “message,” “information,” “organization,” indeed, “organism” —have, over the past few (...) decades, all been transformed. In this article, I explore the computer’s impact on biological representation of the organism in two disciplines: molecular biology and developmental biology. (shrink)

The ArgumentThis paper focuses on the opening of a discursive space: the emergence of informational and scriptural representations of life and their self-negating consequences for the construction of biological meaning. It probes the notion of writing and the book of life and shows how molecular biology's claims to a status of language and texuality undermines its own objective of control. These textual significations were historically contingent. The informational representations of heredity and life were not an outcome of the internal cognitive (...) momentum of molecular biology; they were not a logical necessity of the unravelling of the base-pairing of the DNA double-helix. They were transported into molecular biology still within the protein paradigm of the gene in the 1940s and permeated nearly every discipline in the life and social sciences. These information-based models, metaphors, linguistic, and semiotic tools which were central to the formulation of the genetic code were transported into molecular biology from cybernetics, information theory, electronic computing, and control and communication systems — technosciences that were deeply embedded with the military experiences of world war II and the Cold War. The information discourse thus became fixed in molecular biology not because it worked in the narrow epistemic sense (it did not), but because it positioned molecular biology within postwar discourse and culture, perhaps within the transition to a post-modern information-based society. (shrink)

An interdisciplinary fusion between the philosophy of science and the teaching of science can help to eradicate the disciplinary rigidity entrenched in both. In this paper I approach the history of sciencethematically, identifying general themes which transcend the boundaries of individual disciplines. Such conceptual themes can be used as a basis for an interdisciplinary introduction to university science, encouraging certain important cognitive skills not exercised during the disciplinary training emphasised in traditional approaches. Courses which teach themes such as conservation, randomness, (...) and holism/reductionism have already proved successful, and these innovations should encourage philosophers and historians to explore the exciting new possibilities which arise from stepping outside the confines of a single discipline. (shrink)

The Bermuda Principles for DNA sequence data sharing are an enduring legacy of the Human Genome Project. They were adopted by the HGP at a strategy meeting in Bermuda in February of 1996 and implemented in formal policies by early 1998, mandating daily release of HGP-funded DNA sequences into the public domain. The idea of daily sharing, we argue, emanated directly from strategies for large, goal-directed molecular biology projects first tested within the “community” of C. elegans researchers, and were introduced (...) and defended for the HGP by the nematode biologists John Sulston and Robert Waterston. In the C. elegans community, and subsequently in the HGP, daily sharing served the pragmatic goals of quality control and project coordination. Yet in the HGP human genome, we also argue, the Bermuda Principles addressed concerns about gene patents impeding scientific advancement, and were aspirational and flexible in implementation and justification. They endured as an archetype for how rapid data sharing could be realized and rationalized, and permitted adaptation to the needs of various scientific communities. Yet in addition to the support of Sulston and Waterston, their adoption also depended on the clout of administrators at the US National Institutes of Health and the UK nonprofit charity the Wellcome Trust, which together funded 90% of the HGP human sequencing effort. The other nations wishing to remain in the HGP consortium had to accommodate to the Bermuda Principles, requiring exceptions from incompatible existing or pending data access policies for publicly funded research in Germany, Japan, and France. We begin this story in 1963, with the biologist Sydney Brenner’s proposal for a nematode research program at the Laboratory of Molecular Biology at the University of Cambridge. We continue through 2003, with the completion of the HGP human reference genome, and conclude with observations about policy and the historiography of molecular biology. (shrink)

Cells are cognitive entities possessing great computational power. DNA serves as a multivalent information storage medium for these computations at various time scales. Information is stored in sequences, epigenetic modifications, and rapidly changing nucleoprotein complexes. Because DNA must operate through complexes formed with other molecules in the cell, genome functions are inherently interactive and involve two-way communication with various cellular compartments. Both coding sequences and repetitive sequences contribute to the hierarchical systemic organization of the genome. By virtue of nucleoprotein complexes, (...) epigenetic modifications, and natural genetic engineering activities, the genome can serve as a read-write storage system. An interactive informatic conceptualization of the genome allows us to understand the functional importance of DNA that does not code for protein or RNA structure, clarifies the essential multidirectional and systemic nature of genomic information transfer, and emphasizes the need to investigate how cellular computation operates in reproduction and evolution. (shrink)

In this paper I shall defend the idea that there is an abstract and general core meaning of objectivity, and what is seen as a variety of concepts or conceptions of objectivity are in fact criteria of, or means to achieve, objectivity. I shall then discuss the ideal of value-free science and its relation to the objectivity of science; its status can be at best a criterion of, or means for, objectivity. Given this analysis, we can then turn to the (...) problem of inductive risk. Do the value judgements regarding inductive risk really pose a threat to the objectivity of science? I claim that this is not the case because they do not lower the thresholds scientifically postulated for objectivity. I shall conclude the paper with a discussion of under-appreciated influences of values on science, which indeed pose a serious threat to the objectivity of some scientific disciplines. (shrink)