Early last year, the GenEthics Consortium (GEC) of the Washington Metropolitan Area convened at George Washington University to consider a complex case about genetic testing for Alzheimer disease (AD). The GEC consists of scientists, bioethicists, lawyers, genetic counselors, and consumers from a variety of institutions and affiliations. Four of the 8 co-authors of this paper delivered presentations on the case. Supplemented by additional ethical and legal observations, these presentations form the basis for the following discussion.

In June 1993, conjoined twins Amy and Angela Lakeberg became the focus of national attention. They shared a complex six‐chambered heart and one liver; only one could survive separation surgery, and even her chances were slim. The medical challenge was great and the ethical challenges were even greater.

The 1981 book Genes, Mind and Culture by Edward O. Wilson and Charles J. Lumsden attempts to offer a comprehensive theory of the linkage between biological and cultural evolution. In the following 21 May 1982 radio broadcast, produced by Julian Brown under the auspices of the British Broadcasting Corporation, Wilson is joined by a philosopher, a geneticist, and a religion scholar in a discussion of “gene culture co‐evolution” and of other issues raised by sociobiology. The discussion is introduced and (...) chaired by the editor of Nature, John Maddox. (shrink)

Metaphors used to describe new technologies mediate public understanding of the innovations. Analyzing the linguistic, rhetorical, and affective aspects of these metaphors opens the range of issues available for bioethical scrutiny and increases public accountability. This article shows how such a multidisciplinary approach can be useful by looking at a set of texts about one issue, the use of a newly developed technique for genetic modification, CRISPRcas9.

The ArgumentStylistic analysis of an admittedly speculative scientific article can suggest what is involved in the social act of speculation. Walter Gilbert's influential paper “Why Genes in Pieces?” serves as an example of the conflicting demands of the need to display politeness and the need to display the urgency and excitement of the issues. Socially significant stylistic features emerge in comparison with another paper Gilbert co-authored, where the speculations occur in the discussion section of an experimental report, and in comparison (...) with another, more typical “News and Views” article by another author. The stylistic features include the use of impersonal subjects, the hedging of verbs, the unusual uses of the present tense, and the reliance on repetition, rather than conjunctions or pronouns, for textual cohesion. Later references to the article assimilate it to various lines of research without suggesting its speculative style. (shrink)

In this controversial new book O'Hear takes a stand against the fashion for explaining human behavior in terms of evolution. He contends that while the theory of evolution is successful in explaining the development of the natural world in general, it is of limited value when applied to the human world. Because of our reflectiveness and our rationality we take on goals and ideals which cannot be justified in terms of survival-promotion or reproductive advantage. O'Hear examines the nature of human (...) self-consciousness, and argues that evolutionary theory cannot give a satisfactory account of such distinctive facets of human life as the quest for knowledge, moral sense, and the appreciation of beauty; in these we transcend our biological origins. It is our rationality that allows each of us to go beyond not only our biological but also our cultural inheritance: as the author says in the Preface, "we are prisoners neither of our genes nor of the ideas we encounter as we each make our personal and individual way through life.". (shrink)

Cytokinins are plant hormones which have long been associated with cell division and plastid differentiation. Recently, they have been found to play a central role also in the growth of plant tumors. Certain phytopathogenic bacteria, notably Agrobacterium tumefaciens and Pseudomonas syringae pv. savastanoi, can incite tumors on dicotyledonous plants and such tumors exhibit growth which is characteristic of the presence of excess auxin and cytokinin. Genes specifying cytokinin biosynthesis have now been isolated from both sets of bacteria. The genes encode (...) prenyl transferase responsible for cytokinin biosynthesis which, upon expression in E. coli,cause the production of the active cytokinin, zeatin. Expression of these genes in association with the plant is responsible for at least part of the tumor phenotype, although the molecular mechanisms of infection by these bacteria are apparently quite dissimilar. There is extensive homology between the cytokinin biosynthetic genes from the two sets of bacteria. (shrink)

This paper aims to persuade its reader that libertarianism, at least in several of its varieties, is a species of the genus Michael Oakeshott referred to as ‘rationalism in politics’. I hope to demonstrate, employing the work of Oakeshott, as well as Aristotle and Onora O’Neill, how many libertarian theorists, who generally have a sincere and admirable commitment to personal liberty, have been led astray by the rationalist promise that we might be able to approach deductive certainty concerning the 'correctness' (...) of some political programme. Of course libertarians, in common with the adherents of almost any other political ‘stance’, are not a monolithic body, but exhibit a variety of more or less rationalist arguments for their views. For example, a thinker like Hayek, who is often placed in the libertarian camp, came to adopt much of Oakeshott’s critique of rationalism in his later work. And, of course, Oakeshott himself expressed an affinity for libertarian ideas in his essay, ‘The Political Economy of Freedom’ (1991 [1962]). But a general predilection to enhance individual freedom as far as is deemed practicable is quite a different matter from taking a stance in which liberty, and liberty conceived in a rather narrow fashion, is the only value deemed admissible into ‘reasonable’ political discourse. (We will see in a subsequent section that Oakeshott recognized this urge to sanctify one value above all others as a logical requirement of striving for deductive political truths.) I believe that a critique of such libertarian rationalism is particularly relevant given the present situation in the United States vis-à-vis civil rights and the ongoing ‘war on terror’, in that many non- libertarian supporters of peace and strong civil rights find themselves allied with libertarians on these issues—if libertarians have gotten these issues ‘correct’, then how might they have gone wrong elsewhere? Furthermore, the critique may aid libertarians themselves, because, if the title of this paper is accurate, such a single-minded exaltation of one value above all others is an enemy of true liberty, so that libertarians might want to rethink adopting such a position. As Philip Pettit demonstrates (1997), freedom as non-domination is more robust and inclusive of all that we value about freedom than is the libertarian concept of freedom as non-interference; by allowing, say, immense economic power to be concentrated in a single corporation, as intervention to break the company up would violate the principle of non-interference, libertarian ideas may greatly diminish the liberty of the people subject to that corporate power. (shrink)

Despite its importance, the linkage between genetic and cultural evolution has until now been little explored. An understanding of this linkage is needed to extend evolutionary theory so that it can deal for the first time with the phenomena of mind and human social history. We characterize the process of gene-culture coevolution, in which culture is shaped by biological imperatives while biological traits are simultaneously altered by genetic evolution in response to cultural history. A case is made from both (...) theory and evidence that genetic and cultural evolution are inseverable, and that the human mind has tended to evolve so as to bias individuals toward certain patterns of cognition and choice rather than others. With the aid of mathematical models we trace the coevolutionary circuit: The genes prescribe structure in developmental pathways that lay down endocrine and neural systems, imposing regularities in the development of cognition and behavior; these regularities translate upward into holistic patterns of culture, which can be predicted in the form of probability density distributions ; natural selection acts within human history to favor certain epigenetic rules over others; and the selection alters the frequencies of the underlying genes. The effects of genetic and cultural changes reverberate throughout the circuit and are consequently tested with the passage of each life cycle. In addition to modeling gene-culture coevolution, we apply methods from island biogeography and information theory to examine the cultural capacity of the genes, the factors determining the magnitude of cultural diversity, and the possible reasons for the uniqueness of the human achievement. (shrink)

Ernst Mayr’s influence on philosophy of biology has given the field a particular perspective on evolution, phylogeny and life in general. Using debates about the tree of life as a guide, I show how Mayrian evolutionary biology excludes numerous forms of life and many important evolutionary processes. Hybridization and lateral gene transfer are two of these processes, and they occur frequently, with important outcomes in all domains of life. Eukaryotes appear to have a more tree-like history because successful lateral (...) events tend to occur among more closely related species, or at a lower frequency, than in prokaryotes, but this is a difference of degree rather than kind. Although the tree of life is especially problematic as a representation of the evolutionary history of prokaryotes, it can function more generally as an illustration of the limitations of a standard evolutionary perspective. Moreover, for philosophers, questions about the tree of life can be applied to the Mayrian inheritance in philosophy of biology. These questions make clear that the dichotomy of life Mayr suggested is based on too narrow a perspective. An alternative to this dichotomy is a multidimensional continuum in which different strategies of genetic exchange bestow greater adaptiveness and evolvability on prokaryotes and eukaryotes. (shrink)

Skeletal myoblasts have their origin early in embryogenesis within specific somites. Determined myoblasts are committed to a myogenic fate; however, they only differentiate and express a muscle‐specific phenotype after they have received the appropriate environmental signals. Once proliferating myoblasts enter the differentiation programme they withdraw from the cell cycle and form post‐mitotic multinucleated myofibres (myogenesis); this transformation is accompanied by muscle‐specific gene expression. Muscle development is associated with complex and diverse protein isoform transitions, generated by differential gene expression (...) and mRNA splicing. The myofibres are in a state of dynamic adaptation in response to hormones, mechanical activity and motor innervation, which modulate differential gene expression and splicing during this functional acclimatisation. This review will focus on the profound effects of thyroid hormone on skeletal muscle, which produce alterations in gene and isoform expression, biochemical properties and morphological features that precipitate in modified contractile/mechanical characteristics. Insight into the molecular events that control these events was provided by the recent characterisation of the MyoD gene family, which encodes helix‐loop‐helix proteins; these activate muscle‐specific transcription and serve as targets for a variety of physiological stimuli. The current hypothesis on hormonal regulation of myogenesis is that thyroid hormones (1) directly regulate the myoD and contractile protein gene families, and (2) induce thyroid hormone receptor‐transcription factor interactions critical to gene expression. (shrink)

Despite its importance, the linkage between genetic and cultural evolution has until now been little explored. An understanding of this linkage is needed to extend evolutionary theory so that it can deal for the first time with the phenomena of mind and human social history. We characterize the process of gene-culture coevolution, in which culture is shaped by biological imperatives while biological traits are simultaneously altered by genetic evolution in response to cultural history. A case is made from both (...) theory and evidence that genetic and cultural evolution are inseverable, and that the human mind has tended to evolve so as to bias individuals toward certain patterns of cognition and choice rather than others. With the aid of mathematical models we trace the coevolutionary circuit: The genes prescribe structure in developmental pathways that lay down endocrine and neural systems, imposing regularities in the development of cognition and behavior; these regularities translate upward into holistic patterns of culture, which can be predicted in the form of probability density distributions ; natural selection acts within human history to favor certain epigenetic rules over others; and the selection alters the frequencies of the underlying genes. The effects of genetic and cultural changes reverberate throughout the circuit and are consequently tested with the passage of each life cycle. In addition to modeling gene-culture coevolution, we apply methods from island biogeography and information theory to examine the cultural capacity of the genes, the factors determining the magnitude of cultural diversity, and the possible reasons for the uniqueness of the human achievement. (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)

Philosophers of biology, along with everyone else, generally perceive life to fall into two broad categories, the microbes and macrobes, and then pay most of their attention to the latter. ‘Macrobe’ is the word we propose for larger life forms, and we use it as part of an argument for microbial equality. We suggest that taking more notice of microbes – the dominant life form on the planet, both now and throughout evolutionary history – will transform some of the philosophy (...) of biology’s standard ideas on ontology, evolution, taxonomy and biodiversity. We set out a number of recent developments in microbiology – including biofilm formation, chemotaxis, quorum sensing and gene transfer – that highlight microbial capacities for cooperation and communication and break down conventional thinking that microbes are solely or primarily single-celled organisms. These insights also bring new perspectives to the levels of selection debate, as well as to discussions of the evolution and nature of multicellularity, and to neo-Darwinian understandings of evolutionary mechanisms. We show how these revisions lead to further complications for microbial classification and the philosophies of systematics and biodiversity. Incorporating microbial insights into the philosophy of biology will challenge many of its assumptions, but also give greater scope and depth to its investigations. (shrink)

The ‘Tree of Life’ is intended to represent the pattern of evolutionary processes that result in bifurcating species lineages. Often justified in reference to Darwin’s discussions of trees, the Tree of Life has run up against numerous challenges especially in regard to prokaryote evolution. This special issue examines scientific, historical and philosophical aspects of debates about the Tree of Life, with the aim of turning these criticisms towards a reconstruction of prokaryote phylogeny and even some aspects of the standard evolutionary (...) understanding of eukaryotes. These discussions have arisen out of a multidisciplinary collaboration of people with an interest in the Tree of Life, and we suggest that this sort of focused engagement enables a practical understanding of the relationships between biology, philosophy and history. (shrink)

This paper considers Mary Midgley's views on evolution, especially as developed in her book Evolution as a Religion. In this she continues the critical campaign she waged against Dawkins’ notion of the selfish gene, but broadens her attack out to encompass many other thinkers, who are predicting dramatic and revolutionary futures for humanity, based supposedly on what evolutionary science tells us. Midgley argues that no such conclusions are scientifically warranted – hence evolution as a religion. Her own attempts to (...) absolve Darwin himself from this sort of scientism, and to remove from him any taint of social Darwinism are criticised, particularly by reference to The Descent of Man. Something is then said about Midgley's own alternative view of nature and humanity, a more holistic view, which itself has religious overtones. (shrink)

The chromodomain is a highly conserved sequence motif that has been identified in a variety of animal and plant species. In mammals, chromodomain proteins appear to be either structural components of large macromolecular chromatin complexes or proteins involved in remodelling chromatin structure. Recent work has suggested that apart from a role in regulating gene activity, chromodomain proteins may also play roles in genome organisation. This article reviews progress made in characterising mammalian chromodomain proteins and emphasises their emerging role in (...) the regulation of gene expression and genome organisation. BioEssays 22:124–137, 2000. ©2000 John Wiley & Sons, Inc. (shrink)

The detection and spread of pandemic 2009 H1N1 influenza in the United States led to a complex and multi-faceted response by the public health system that lasted more than a year. When the first domestic case of the virus was detected in California on April 15, 2009, and a second, unrelated case was identified more than 130 miles away in the same state on April 17, 2009, the unique combination of influenza virus genes in addition to its emergence and rapid (...) spread at the end of the typical Northern Hemisphere influenza season suggested the potential for a high morbidity, high mortality event. In response, federal, state, and local public health officials conducted epidemiologic investigations with federal and state laboratory support to help to determine the scope of the H1N1 pandemic. On April 26, the Secretary of the U.S. Department of Health and Human Services declared a public health emergency that was renewed through June 23, 2010. The pandemic that ensued tested virtually every aspect of U.S. public health preparedness and response systems, from laboratory capabilities and capacities to social distancing plans. (shrink)

Although the cell is commonly addressed as the unit of life, historians and philosophers have devoted relatively little attention to this concept in comparison to other fundamental concepts of biology such as the gene or species. As a partial remedy to this neglect, we introduce the cell as a major point of connection between various disciplinary approaches, epistemic strategies, technological vectors and overarching biological processes such as metabolism, growth, reproduction and evolution. We suggest that the role of the cell (...) as a nexus forms the basis for a new philosophical and historical appreciation of cell biology. This perspective focuses less on the cell as a well-defined, stable object and places more emphasis on its role as a mediator of fundamental biological processes. (shrink)

Exposure of man to chemical agents can occur intentionally, as in the treatment of disease, or inadvertently because the environment contains a wide range of synthetic or naturally occurring chemicals. The alkylating agents are a diverse group of compounds (Fig. 1) and comprise a good example of such xenobiotics, since much is known about their occurrence, and their biological effects include carcinogenicity, mutagenicity, toxicity and teratogenicity.Exposure to potentially carcinogenic alkylating agents such as nitrosamines may occur occupationally, from cigarette smoke, from (...) certain foodstuffs and even endogenously through the ingestion of the appropriate precursor chemicals.1 At the other extreme, the cytotoxic effects of agents such as the chloroethylating nitrosamides or mustards have been exploited in the design of certain antitumour drugs.2 The effectiveness of antitumour agents and the other, mostly adverse, biological effects of alkylating agents have been ascribed to their ability to damage cellular macromolecules, in particular DNA. This review concentrates on investigations carried out over the past two years on the role of DNA damage in carcinogenesis, but we shall see how recent advances in this area of research have also led to a better understanding of the mechanisms of the cytotoxic effects of alkylating antitumour agents. (shrink)

Research consent processes must provide potential participants with the necessary information to help them decide if they wish to join a study. On the Oxford ‘A’ Research Ethics Committee we’ve found that current research proposals mostly provide adequate detail (even if not in an easily comprehensible format), but often fail to support decision making, a view supported by published evidence. In a previous paper, we described how consent might be structured, and here we develop the concept of an Information and (...) Decision Aid (IDA) that can support decision making and be used to guide the dialogue between researcher and potential participant. Our proposal requires limited changes to current processes or paperwork and would provide an easily accessible document for others that the potential participant might approach for advice. It could later be integrated with the Informed Consent Form to ensure all matters of concern to the individual participant have been addressed before consent is formally signed off. (shrink)

One of the central issue of developmental biology concerns the molecular mechanisms whereby a multipotent cell gives rise to distinct differentiated progeny. Differences between specialised cell types reflect variations in their patterns of gene expression. The regulation of transcription initiation is an important control point for gene expression and it is, therefore, not surprising that transcription factors play a pivotal role in mammalian development and differentiation.Haemopoiesis offers a uniquely tractable system for the study of lineage commitment and differentiation. (...) The importance of transcription factor in the normal regulation of haemopoiesis is underlined by the frequency with which transcription factors are targeted by leukaemogenic mutations. Studies of the function and regulation of haemopoietic transcription factors, especially those expressed in lineage‐restricted patterns, should greatly increase our understanding of the molecular control of haemopoiesis. In this review we have focused on insights provided by recent studies of the GATA and SCL proteins. (shrink)

La investigación ecológica a largo plazo (Long Term Ecological Research, LTER) maneja problemas que abarcan décadas o plazos más largos. El programa y su nombre formal comenzaron en Estados Unidos en 1980. Si bien los estudios y observaciones a largo plazo comenzaron tempranamente en 1400 y 1800 en Asia y Europa, respectivamente, el enfoque a largo plazo no se formalizó sino hasta el establecimiento de los programas de investigación ecológica de largo plazo en Estados Unidos. Estos programas han permitido experimentos (...) a nivel de ecosistemas y comparaciones entre sitios que condujeron a una mejor comprensión de la estructura y funcionamiento de la biosfera. El enfoque ecosistémico holístico de esta iniciativa permite también la incorporación de la dimensión humana en la ecología, y recientemente ha dado lugar al nuevo concepto de investigación socio-ecológica de largo plazo (LTSER). Hoy los programas de investigación socio-ecológica a largo plazo existen en por lo menos 32 países (esto es, los miembros de la Red Internacional de Investigación Ecológica a Largo Plazo o ILTER (International Long Term Ecological Research). Sin embargo, la consolidación de la red internacional dentro del paradigma de investigación socio-ecológica a largo plazo todavía requiere: (1) inclusión de algunas regiones remotas del mundo que aún están poco representadas, como el suroeste de América del Sur; (2) modificaciones en el tipo de investigación realizado, tales como la integración de las ciencias sociales y naturales con las humanidades y la ética, y (3) la incorporación de las conclusiones y resultados dentro de los procesos sociales y políticos. En este contexto, la naciente red de investigación socio-ecológica a largo plazo en Chile, que se extiende en el rango latitudinal más largo de bosque templado en el Hemisferio Sur, agrega una nueva región remota a las investigaciones ecológicas de largo plazo que había sido pasada por alto anteriormente. Además, la colaboración con la Universidad de North Texas y otros asociados internacionales ayuda a desarrollar un enfoque interdisciplinario para integrar las ciencias ecológicas y la filosofía ambiental, junto con los conocimientos ecológicos tradicionales, la educación informal y formal, la política, las humanidades, los procesos socio-políticos y la conservación biocultural. (shrink)

In previous work, I have looked in detail at the capacity and the limits of the linguistics model as applied to gene expression. The recent use of a primitive applied linguistic model in Apple's SIRI system allows further analysis. In particular, the failings of this system resemble those of the HGP; the model used also helps point out the shortcomings of the concept of the "gene". This is particularly urgent as we are entering an era of applied biology (...) in the absence of theory, and indeed an era with a near-epidemic of retracted papers. There are a few workarounds proposed. One is to add to the nascent field of biosemiotics a more explicit concern with syntax. At the time of writing, Apple is being sued for false advertising of its iphone 4s, with the associated claim that apple had solved many of the problems of natural language processing by computer . The system was bought by Apple from a company called SIRI, and in turn was based on the notion, trumpeted by the prior art in a company called Dejima, that nlpbc could be done by keywords alone. Yet the hype resembles nothing so much as the misrepresentation of the Human Genome Project fed to the media in the glory days at the beginning of this millennium, and it says a lot for the status of scientists in society that they have avoided Apple's fate. In this paper, a short review of several current themes in theoretical and applied biology is first proposed. Then the tensions implicit in the notion that the "gene" is simultaneously to be identified as a unit of inheritance and spatially located over spatially well-defined nucleotides is explored and the notion is found to be incoherent. An expanded notion of inheritance is proposed in the context of a focus on inheritance as necessarily involving species, population and organism over time. While it is premature to talk about a paradigm shift, it is certainly arguable that biology urgently needs a sophisticated theory of how symbols work substantially more sophisticated than that implicit in the HGP; Biosemiotics affords a framework in which this might be tried. Indeed, as this paper concludes, there may yet be room for a "Bionoetics", a perspective in which biological explanation can be extended to include cognition in all its forms. Finally, a working sketch of a modeling environment written in LISP, one that shows promise in reflecting the complexities discussed in the paper, is included. Normal 0 false false false EN-US X-NONE X-NONE /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Table Normal"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-priority:99; mso-style-qformat:yes; mso-style-parent:""; mso-padding-alt:0in 5.4pt 0in 5.4pt; mso-para-margin:0in; mso-para-margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:11.0pt; font-family:"Calibri","sans-serif"; mso-ascii-font-family:Calibri; mso-ascii-theme-font:minor-latin; mso-fareast-font-family:"Times New Roman"; mso-fareast-theme-font:minor-fareast; mso-hansi-font-family:Calibri; mso-hansi-theme-font:minor-latin; mso-bidi-font-family:"Times New Roman"; mso-bidi-theme-font:minor-bidi;} Normal 0 false false false EN-US X-NONE X-NONE /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Table Normal"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-priority:99; mso-style-qformat:yes; mso-style-parent:""; mso-padding-alt:0in 5.4pt 0in 5.4pt; mso-para-margin:0in; mso-para-margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:11.0pt; font-family:"Calibri","sans-serif"; mso-ascii-font-family:Calibri; mso-ascii-theme-font:minor-latin; mso-fareast-font-family:"Times New Roman"; mso-fareast-theme-font:minor-fareast; mso-hansi-font-family:Calibri; mso-hansi-theme-font:minor-latin; mso-bidi-font-family:"Times New Roman"; mso-bidi-theme-font:minor-bidi;}. (shrink)

Thomas Kuhn had little to say about scientific change in biological science, and biologists are ambivalent about how applicable his framework is for their disciplines. We apply Kuhn’s account of paradigm change to evolutionary microbiology, where key Darwinian tenets are being challenged by two decades of findings from molecular phylogenetics. The chief culprit is lateral gene transfer, which undermines the role of vertical descent and the representation of evolutionary history as a tree of life. To assess Kuhn’s relevance to (...) this controversy, we add a social analysis of the scientists involved to the historical and philosophical debates. We conclude that while Kuhn’s account may capture aspects of the pattern of an episode of scientific change, he has little to say about how the process of generating new understandings is occurring in evolutionary microbiology. Once Kuhn’s application is limited to that of an initial investigative probe into how scientific problem-solving occurs, his disciplinary scope becomes broader. (shrink)

Exploratory experimentation and high-throughput molecular biology appear to have considerable affinity for each other. Included in the latter category is metagenomics, which is the DNA-based study of diverse microbial communities from a vast range of non-laboratory environments. Metagenomics has already made numerous discoveries and these have led to reinterpretations of fundamental concepts of microbial organization, evolution, and ecology. The most outstanding success story of metagenomics to date involves the discovery of a rhodopsin gene, named proteorhodopsin, in marine bacteria that (...) were never suspected to have any photobiological capacities. A discussion of this finding and its detailed investigation illuminates the relationship between exploratory experimentation and metagenomics. Specifically, the proteorhodopsin story indicates that a dichotomous interpretation of theory-driven and exploratory experimentation is insufficient and that an interactive understanding of these two types of experimentation can be usefully supplemented by another category, "natural history experimentation". Further reflection on the context of metagenomics suggests the necessity of thinking more historically about exploratory and other forms of experimentation. (shrink)

Stalking the elusive physicalist thesis Content Type Journal Article Pages 1-5 DOI 10.1007/s11016-011-9528-2 Authors D. Gene Witmer, Department of Philosophy, University of Florida, P. O. Box 118545, Gainesville, FL 32611-8545, USA Journal Metascience Online ISSN 1467-9981 Print ISSN 0815-0796.

Several groups of large DNA viruses successfully utilise the rich resource provided by insect hosts. Defining the mechanisms that enable these pathogens to optimise their relationships with their hosts is of considerable scientific and practical importance, but our understanding of the processes involved is, as yet, rudimentary. Here we describe an informatics-based approach that uses comparison of viral genomic sequences to identify candidate genes likely to be specifically involved in this process. We hypothesise that such genes should satisfy two essential (...) criteria, namely, that they should be (i) present in those members of a virus family that infect insects, but absent from those that infect other hosts, and (ii) found in at least two unrelated taxa of insect viruses. These criteria currently identify six groups of viral genes, including one that encodes the fusolin/gp37 proteins. Demonstration that the fusolin/gp37 proteins can enhance oral infectivity of insect viruses provides a primary validation of this approach to the examination of insectvirus relationships. BioEssays 23:184–193, 2001. © 2001 John Wiley & Sons, Inc. (shrink)

In this paper we discuss the scientific value of the human genome project. To what extent is the data obtained by sequencing the entire human genome useful in the gene dicovery process? Responding to Alex Rosenberg' skepticism about the value of such data, we maintain that brute sequence data is much more useful than he suggests.