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)

François Jacob is known as one of the key figures in the history of molecular biology. His elaboration, together with Jacques Monod, of the operon model and the basic features of the regulation of gene expression in bacteria, as well as the concept of genetic messenger, won him the Nobel Prize in 1965. Both notions were decisive for the novel imagery of molecular genetics in which the notion of information came to stand central. From a close reading, this article tries (...) to reconstruct how the new language of molecular genetics took shape in the scientific writings of Jacob. In particular, it analyzes how the notions of regulation, information, and language came to be articulated, and how this articulation changed and underwent modulations over time. It shows that a scientific language consists of several layers and thus, as a rule, forms a hybrid structure. The time span covered reaches from the early experiments done together with Monod and Arthur Pardee between 1958 and 1960, also known as the “PaJaMo” experiment, to Jacob’s book on the history of heredity, The Logic of Life, which appeared in 1970. (shrink)

The role played by the concept of genetic coding in biology is discussed. I argue that this concept makes a real contribution to solving a specific problem in cell biology. But attempts to make the idea of genetic coding do theoretical work elsewhere in biology, and in philosophy of biology, are probably mistaken. In particular, the concept of genetic coding should not be used (as it often is) to express a distinction between the traits of whole organisms that are coded (...) for in the genes, and the traits that are not. (shrink)

Philosophers have traditionally conceived of discovery in terms of internal cognitive acts. Close consideration of Rosalind Franklin's role in the discovery of the DNA double helix, however, reveals some problems with this traditional conception. This article argues that defining discovery in terms of mental operations entails problematic conclusions and excludes acts that should fall within the domain of discovery. It proposes that discovery be expanded to include external acts of making visible. Doing so allows for a reevaluation of Franklin's role (...) in the discovery of the structure of DNA. (shrink)

The first part of this paper has shown that the development of regulatory genetics and the lactose operon model stemmed from laboratory cultures rooted in local traditions. A "physiological" culture may be recognized in the Pasteurian context. The institutional continuity provided the basis for a tenuous link between Pasteur, Lwoff, and Monod. My claim is that the "national" value of regulatory and physiological genetics is an artifact produced in the course of the legitimization process accompanying the institutionalisation of the discipline. (...) In the 1960s, the lactose operon model was turned into a "flag-object," a symbol of the new culture. The work done by the Pasteurian group became therefore the most important, if not the only, exemplar of molecular biology in France.The second part o f the paper described the origins of general patterns that dominated the building of molecular biology in France. The study of the relationships between molecular biologists and biochemists or immunologists revealed the existence of alternatives to the development of operon research, or to the convergence with molecular biology. Both examples uncover specific paths leading to achievements that might be viewed as international trends: the expansion of RNA and translation studies, and the development of cellular immunology. They illustrate two possible patterns of linking local settings and disciplinary traditions: an oligopolistic situation where a few groups or one institution dominate an entire field, and the emergence of "collective" trends through collaboration networks or schools. (shrink)

This paper investigated the part played by collaborative practices in chaneling the work of prominent biochemists into the development of molecular biology. The RNA collaborative network that emerged in the 1960s in France encompassed a continuum of activities that linked laboratories to policy-making centers. New institutional frameworks such as the DGRST committees were instrumental in establishing new patterns of funding, and in offering arenas for multidisciplinary debates and boundary assessment. It should be stressed however, that although this collaborative network was (...) based on centralized initiatives aimed at developing molecular biology as a new biological specialty, it operated above all as a nexus of practices. The main argument of this paper is that the central allocation of funds and resources, exemplified by the DGRST operation, actually enhanced the creation of a self-conscious community of biochemists turned molecular biologists by virtue of an increased circulation of tools, skills, and results that took place within the RNA network and a few analogous systems of exchange.Having hands on “things” viewed as identical for all practical purposes was a potent factor in changing the experimental systems and their meanings. Limited but shared means of doing helped to reduce uncertainties, change representations, and turn contingent decisions into meaningful choices. The collaborative enterprises then resulted in personal contacts and the transfer of skills and materials, which gradually incorporated the biochemical tools into systems producing facts relevant to molecular biology as defined by its early practitioners. In that sense, networking was a regulatory process that stabilized new research objects and acculturated French biochemists.The mere existence of such a collaborative network also changed the scale of the disciplining process. Collaborations may have been started for contingent motives, but multiple exchanges resulted in the emergence of a new collective, and amplified small displacements. Collaborations, however, worked both ways, and the RNA network may be viewed as an efficient “trading-post.” An unexpected outcome of the development of a conversion zone is the fact that, by the late 1960s, the former biochemists dominated the “new” world of molecular biology — both in terms of research habits, since interests in structural studies dominated the field, and in terms of institutional initiatives such as the creation of laboratories and institutes for molecular biology.As an example of the cognitive displacements achieved by the network, I have focused here on the stabilization of “messenger RNA” as a new biological entity. This process illustrates the role of “boundary objects” and other mediating innovations in the development of disciplinary structures. Students of science trained in the symbolic interactionism tradition have proposed that “boundary objects” enhance the multiple interactions between heterogeneous social worlds: they are robust enough to enhance unity, but plastic enough to be manipulated in different social and cultural contexts.81 Within the emerging network, messenger RNA was a weakly structured “genetic information carrier” in common use, but it could, at the same time, be a strongly structured “macromolecular structure” adapted to practical and local uses. Consequently, messenger RNA favored the association of groups of heterogeneous scientists with backgrounds and interests in medical biochemistry, genetics, physical chemistry, organic chemistry, and so forth. This contrast between general and local uses was also instrumental in integrating the manipulation of things and the negotiation of aims. In contrast to transfer RNAs, which in the French context remained objects for chemical (and mainly structural) studies, messenger RNA became a key component of the new culture of “genetic information”. Messenger RNA was a loose theoretical entity described as a “genetic information carrier” in the policy-making documents, while operational but tacit and more conflicting definitions prevailed at the bench. In other words, messenger RNA was not only a classical “boundary object” but also a “flag object,” which tightened the collaborative network by mediating between the DGRST offices and the laboratories. (shrink)

Fred Sanger, the inventor of the first protein, RNA and DNA sequencing methods, has traditionally been seen as a technical scientist, engaged in laboratory bench work and not interested at all in intellectual debates in biology. In his autobiography and commentaries by fellow researchers, he is portrayed as having a trajectory exclusively dependent on technological progress. The scarce historical scholarship on Sanger partially challenges these accounts by highlighting the importance of professional contacts, institutional and disciplinary moves in his career, spanning (...) from 1940 to 1983. This paper will complement such literature by focusing, for the first time, on the transition of Sanger's sequencing strategies from degrading to copying the target molecule, which occurred in the late 1960s as he was shifting from protein and RNA to DNA sequencing, shortly after his move from the Department of Biochemistry to the Laboratory of Molecular Biology, both based in Cambridge (UK). Through a reinterpretation of Sanger's papers and retrospective accounts and a pioneering investigation of his laboratory notebooks, I will claim that sequencing shifted from the working procedures of organic chemistry to those of the emergent molecular biology. I will also argue that sequencing deserves a history in its own right as a practice and not as a technique subordinated to the development of molecular biology or genomics. My proposed history of sequencing leads to a reappraisal of current STS debates on bioinformatics, biotechnology and biomedicine. (shrink)

Fred Sanger, the inventor of the first protein, RNA and DNA sequencing methods, has traditionally been seen as a technical scientist, engaged in laboratory bench work and not interested at all in intellectual debates in biology. In his autobiography and commentaries by fellow researchers, he is portrayed as having a trajectory exclusively dependent on technological progress. The scarce historical scholarship on Sanger partially challenges these accounts by highlighting the importance of professional contacts, institutional and disciplinary moves in his career, spanning (...) from 1940 to 1983. This paper will complement such literature by focusing, for the first time, on the transition of Sanger’s sequencing strategies from degrading to copying the target molecule, which occurred in the late 1960s as he was shifting from protein and RNA to DNA sequencing, shortly after his move from the Department of Biochemistry to the Laboratory of Molecular Biology, both based in Cambridge (UK). Through a reinterpretation of Sanger’s papers and retrospective accounts and a pioneering investigation of his laboratory notebooks, I will claim that sequencing shifted from the working procedures of organic chemistry to those of the emergent molecular biology. I will also argue that sequencing deserves a history in its own right as a practice and not as a technique subordinated to the development of molecular biology or genomics. My proposed history of sequencing leads to a reappraisal of current STS debates on bioinformatics, biotechnology and biomedicine. (shrink)

Shannon's theory lays the foundation for understanding the flow of information from world into brain: There must be a set of possible messages. Brain structure determines what they are. Many messages convey quantitative facts. It is impossible to consider how neural tissue processes these numbers without first considering how it encodes them.

Scientific hypotheses may either predict particular unknown facts or accommodate previously-known data. Although affirmed predictions are intuitively more rewarding than accommodations of established facts, opinions divide whether predictive hypotheses are also epistemically superior to accommodation hypotheses. This paper examines the contribution of predictive hypotheses to discoveries of several bio-molecular systems. Having all the necessary elements of the system known beforehand, an abstract predictive hypothesis of semiconservative mode of DNA replication was successfully affirmed. However, in defining the genetic code whose biochemical (...) basis was unclear, hypotheses were only partially effective and supplementary experimentation was required for its conclusive definition. Markedly, hypotheses were entirely inept in predicting workings of complex systems that included unknown elements. Thus, hypotheses did not predict the existence and function of mRNA, the multiple unidentified components of the protein biosynthesis machinery, or the manifold unknown constituents of the ubiquitin–proteasome system of protein breakdown. Consequently, because of their inability to envision unknown entities, predictive hypotheses did not contribute to the elucidation of cation theories remained the sole instrument to explain complex bio-molecular systems, the philosophical question of alleged advantage of predictive over accommodative hypotheses became inconsequential. (shrink)

A longstanding philosophical premise perceives simplicity as a desirable attribute of scientific theories. One of several raised justifications for this notion is that simple theories are more likely to indicate the true makeup of natural systems. Qualitatively parsimonious hypotheses and theories keep to a minimum the number of different postulated entities within a system. Formulation of such ontologically simple working hypotheses proved to be useful in the experimental probing of narrowly defined bio systems. It is less certain, however, whether qualitatively (...) parsimonious theories are effective indicators of the true nature of complex biological systems. This paper assesses the success of ontologically simple theories in envisaging the makeup of three complex systems in bacteriology, immunology, and molecular biology. Evidence shows that parsimonious theories completely misconstrued the actual ontologically complex constitutions of the three examined systems. Since evolution and selective pressures typically produce ontologically intricate rather than simple bio systems, qualitatively parsimonious theories are mostly inapt indicators of the true nature of complex biological systems. (shrink)

During the 1960s, Howard M. Temin (1934-1994), dared to advocate a "heretical" hypothesis that appeared to be at variance with the central dogma of molecular biology, understood by many to imply that information transfer in nature occurred only from DNA to RNA. Temin's provirus hypothesis offered a simple explanation of both virus replication and viral-induced cancer and stated that Rous sarcoma virus, an RNA virus, is replicated via a DNA intermediate. Popular accounts of this scientific episode, written after the discovery (...) of an RNA-directed DNA polymerase in 1970, tend to describe the reaction to his proposition as ardent opposition. Typically these accounts use a 'molecular biology' standpoint emphasizing the central dogma's part in its rejection. In this article, however, this episode will be examined from a joint perspective of virology and experimental cancer research. From this perspective it is clear that Temin's work was well within the epistemological and methodological boundaries of virology and cancer research. Still, scientists did have reasons to doubt the provirus hypothesis, but these do not seem to be good enough to either justify an account that portrays Temin as a renegade or his ideas as heretical. (shrink)

Diagrams can serve as representational models in scientific research, yet important questions remain about how they do so. I address some of these questions with a historical case study, in which diagrams were modified extensively in order to elaborate an early hypothesis of protein synthesis. The diagrams’ modelling role relied mainly on two features: diagrams were modified according to syntactic rules, which temporarily replaced physico-chemical reasoning, and diagram-to-target inferences were based on semantic interpretations. I then explore the lessons for the (...) relative roles of syntax, semantics, external marks, and mental images, for justifying diagram-to-target inferences, and for the “artefactual approach” to scientific models. (shrink)

Research ethics education in the biosciences has not historically been a priority for research universities despite the fact that funding agencies, government regulators, and the parties involved in the research enterprise agree that it ought to be. The confluence of a number of factors, including scrutiny and regulation due to increased public awareness of the impact of basic research on society, increased public and private funding, increased diversity and collaboration among researchers, the impressive success and speed of research advances, and (...) high-profile cases of misconduct, have made it necessary to reexamine how the bioscience research community at all levels provides ethics education to its own. We discuss the need to and reasons for making ethics integral to the education of bioscientists, approaches to achieving this goal, challenges this goal presents, and responses to those challenges. (shrink)

The “top-down” and “bottom-up” approaches have been thought to exhaust the possibilities for doing cognitive neuroscience. We argue that neither approach is likely to succeed in providing a theory that enables us to understand how cognition is achieved in biological creatures like ourselves. We consider a promising third way of doing cognitive neuroscience, what might be called the “neural dynamic systems” approach, that construes cognitive neuroscience as an autonomous explanatory endeavor, aiming to characterize in its own terms the states and (...) processes responsible for brain-based cognition. We sketch the basic motivation for the approach, describe a particular version of the approach, so-called ‘Dynamic Causal Modeling’ (DCM), and consider a concrete example of DCM. This third way, we argue, has the potential to avoid the problems that afflict the other two approaches. (shrink)