Online research in philosophy

A far-reaching and influential view in evolutionary biology claims that species are cohesive units held together by gene flow. Biologists have recognized empirical problems facing this view; after sharpening the expression of the view, we present novel conceptual problems for it. At the heart of these problems is a distinction between two importantly different concepts of cohesion, what we call integrative and response cohesion. Acknowledging the distinction problematizes both the explanandum of species cohesion and the explanans of gene (...) flow that are central to the view we discuss. We conclude by tracing four broader implications for the study and conceptualization of species. (shrink)

Personalized genomics companies (PG; also called ‘direct-to-consumer genetics’) are businesses marketing genetic testing to consumers over the Internet. While much has been written about these new businesses, little attention has been given to their roles in science communication. This paper provides an analysis of the gene concept presented to customers and the relation between the information given and the science behind PG. Two quite different gene concepts are present in company rhetoric, but only one features in the science. (...) To explain this, we must appreciate the delicate tension between PG, academic science, public expectation, and market forces. (shrink)

The ‘gene of’ is a teleosemantic expression that conveys a simplistic and linear relationship between a gene and a phenotype. Throughout the 20th century, geneticists studied these genes of traits. The studies were often polemical when they concerned human traits: the ‘crime gene’, ‘poverty gene’, ‘IQ gene’, ‘gay gene’ or ‘gene of alcoholism’. Quite recently, a controversy occurred in 2006 in New Zealand that started with the claim that a ‘warrior gene’ exists (...) in the Mãori community. This claim came from a geneticist working on the MAOA gene. This article is interested in the responsibility of that researcher regarding the origin of the controversy. Several errors were made: overestimation of results, abusive use of the ‘gene of’ kind of expression, poor communication with the media and a lack of scientific culture. The issues of the debate were not taken into account sufficiently, either from the political, social, ethical or even the genetic points of view. After more than 100 years of debates around ‘genes of’ all kinds (here, the ‘warrior gene’), geneticists may not hide themselves behind the media when a controversy occurs. Responsibilities have to be assumed. (shrink)

The computational genomics community has come increasingly to rely on the methodology of creating annotations of scientific literature using terms from controlled structured vocabularies such as the Gene Ontology (GO). We here address the question of what such annotations signify and of how they are created by working biologists. Our goal is to promote a better understanding of how the results of experiments are captured in annotations in the hope that this will lead to better representations of biological reality (...) through both the annotation process and ontology development, and in more informed use of the GO resources by experimental scientists. (shrink)

Quantitative genetics (QG) analyses variation in traits of humans, other animals, or plants in ways that take account of the genealogical relatedness of the individuals whose traits are observed. “Classical” QG, where the analysis of variation does not involve data on measurable genetic or environmental entities or factors, is reformulated in this article using models that are free of hypothetical, idealized versions of such factors, while still allowing for defined degrees of relatedness among kinds of individuals or “varieties.” The (...) class='Hi'>gene - free formulation encompasses situations encountered in human QG as well as in agricultural QG. This formulation is used to describe three standard assumptions involved in classical QG and provide plausible alternatives. Several concerns about the partitioning of trait variation into components and its interpretation, most of which have a long history of debate, are discussed in light of the gene-free formulation and alternative assumptions. That discussion is at a theoretical level, not dependent on empirical data in any particular situation. Additional lines of work to put the gene-free formulation and alternative assumptions into practice and to assess their empirical consequences are noted, but lie beyond the scope of this article. The three standard QG assumptions examined are: (1) partitioning of trait variation into components requires models of hypothetical, idealized genes with simple Mendelian inheritance and direct contributions to the trait; (2) all other things being equal, similarity in traits for relatives is proportional to the fraction shared by the relatives of all the genes that vary in the population (e.g., fraternal or dizygotic twins share half of the variable genes that identical or monozygotic twins share); (3) in analyses of human data, genotype-environment interaction variance (in the classical QG sense) can be discounted. The concerns about the partitioning of trait variation discussed include: the distinction between traits and underlying measurable factors; the possible heterogeneity in factors underlying the development of a trait; the kinds of data needed to estimate key empirical parameters; and interpretations based on contributions of hypothetical genes; as well as, in human studies, the labeling of residual variance as a non-shared environmental effect; and the importance of estimating interaction variance. (shrink)

The chemical characterization of the substance responsible for the phenomenon of “transformation” of pneumococci was presented in the now famous 1944 paper by Avery, MacLeod, and McCarty. Reception of this work was mixed. Although interpreting their results as evidence that deoxyribonucleic acid (DNA) is the molecule responsible for genetic changes was, at the time, controversial, this paper has been retrospectively celebrated as providing such evidence. The mixed and changing assessment of the evidence presented in the paper was due to the (...) work’s interpretive flexibility – the evidence was interpreted in various ways, and such interpretations were justified given the neophytic state of molecular biology and methodological limitations of Avery’s transformation studies. I argue that the changing context in which the evidence presented by Avery’s group was interpreted partly explains the vicissitudes of the assessments of the evidence. Two less compelling explanations of the reception are a myth-making account and an appeal to the wartime historical context of its publication. (shrink)

Advances in molecular biological research in the last forty years have made the story of the gene vastly complicated: the more we learn about genes, the less sure we are of what a gene really is. Knowledge about the structure and functioning of genes abounds, but the gene has also become curiously intangible. This collection of essays renews the question: what are genes? Philosophers, historians, and working scientists re-evaluate the question in this volume, treating the gene (...) as a focal point of interdisciplinary and international research. This book is unique in that it is the first interdisciplinary volume solely devoted to the quest for the gene. It will be of interest to professionals and students in the philosophy and history of science, genetics, and molecular biology. (shrink)

One critic complained that my argument was ‘philosophical’, as though that was sufficient condemnation. Philosophical or not, the fact is that neither he nor anybody else has found any flaw in what I said. And ‘in principle’ arguments such as mine, far from being irrelevant to the real world, can be more powerful than arguments based on particular factual research. My reasoning, if it is correct, tells us something important about life everywhere in the universe. Laboratory and field research can (...) tell us only about life as we have sampled it here. (The Selfish Gene (second edn, p322 in endnotes). (shrink)

The discursive explosion that was provoked by the new genetics could support the impression that the ethical and social problems posed by the new genetics are somehow exceptional in their very nature. According to this view we are faced with special ethical and social problems that create a challenge so fundamental that the special label of genethics is needless to justify. The historical account regarding the evolution of the gene concepts could serve us to highlight the limits of what (...) we know about genes and what we can do with genes. The widespread notion about the exceptionality of genetic knowledge and its applicative possibilities is hardly justifiable and leads to misunderstandings regarding the conceptualization of the ethical and social problems we might face. Following a more realistic interpretation of the role of genes in human life we might avoid a whole set of fictive dilemmas and counterproductive regulatory efforts in bioethics. Bioethical discourse should move from the gene-centered scientific discourse toward the more sophisticated and complex discourses where human development represented as a matter of complex interactions between genomes and environments, between genes, educational factors, nutritional regimes, and other different developmental resources. If a gene is seen as one among the different developmental resources that are shaping a given human trait then both genethics and genetic exceptionalism could hardly be represented as a justified approach in discussing the ethical and social problems of genetics. (shrink)

This paper attempts to debunk the slippery-slope argument against human germ-line gene therapy by showing that the downside of the slope – genetic enhancement – need not be as unethical or unjust as some people have supposed. It argues that if genetic enhancement is governed by proper regulations and is accompanied by adequate education, then it need not violate recognized principles of morality or social justice. Keywords: germ-line therapy, slippery slope argument, future generations, social justice CiteULike Connotea Del.icio.us What's (...) this? (shrink)

This paper brings needed clarity to the influential view that species are cohesive entities held together by gene flow, and then develops an empirical argument against that view: Neglected data suggest gene flow is neither necessary nor sufficient for species cohesion. Implications are discussed. ‡I'm grateful to Rob Wilson, Alex Rueger and Lindley Darden for important comments on earlier drafts, and to Joseph Nagel, Heather Proctor, Ken Bond, members of the DC History and Philosophy of Biology reading group, (...) and audience members at the November 2006 meeting of the PSA, for helpful comments or discussion. Social Sciences and Humanities Research Council of Canada fellowship 752-2005-1208 supported research. †To contact the author, please write to: Philosophy Department, University of Wisconsin–Madison, 5185 Helen C. White Hall, 600 North Park Street, Madison, WI 53706; e-mail: mjbarker2@wisc.edu. (shrink)

Genes cannot be selfish or unselfish, any more than atoms can be jealous, elephants abstract or biscuits teleological. This should not need mentioning, but Richard DawkinsÂ’s book The Selfish Gene has succeeded in confusing a number of people about it, including Mr J. L. Mackie.[1] What Mackie welcomes in Dawkins is a new, biological-looking kind of support for philosophic egoism. If this support came from DawkinsÂ’s producing important new facts, or good new interpretations of old facts, about animal life, (...) this could be very interesting. Dawkins, however, simply has a weakness for the old game of Brocken-spectre moralizing - the one where the player strikes attitudes on a peak at sunrise, gazes awe-struck at his gigantic shadow on the clouds, and reports his observations as cosmic truths. He is an uncritical philosophic egoist in the first place, and merely feeds the egoist assumption into his a priori biological speculations, only rarely glancing at the relevant facts of animal behaviour and genetics, and ignoring their failure to support him. There is nothing empirical about Dawkins. Critics have repeatedly pointed out that his notions of genetics are unworkable.[2] I shall come to this point later, but I shall not begin with it, because, damning though it is, it may seem to some people irrelevant to his main contention. It is natural for a reader to suppose that his over-simplified drama about genes is just a convenient stylistic device, because it seems obvious that the personification of them must be just a metaphor. Indeed he himself sometimes says that it is so. But in fact this personification, in its literal sense, is essential for his whole contention; without it he is bankrupt. His central point is that the emotional nature of man is exclusively selfinterested, and he argues this by claiming that all emotional nature is so. Since the emotional nature of animals clearly is not exclusively self-interested, nor based on any long-term calculation at all, he resorts to arguing from speculations about the emotional nature of genes, which he treats as the source and archetype of all emotional nature.. (shrink)

The present paper discusses Kitcher’s framework for studying conceptual change and progress. Kitcher’s core notion of reference potential is hard to apply to concrete cases. In addition, an account of conceptual change as change in reference potential misses some important aspects of conceptual change and conceptual progress. I propose an alternative framework that focuses on the inferences and explanations supported by scientific concepts. The application of my approach to the history of the gene concept offers a better account of (...) the conceptual progress that occurred in the transition from the Mendelian to the molecular gene than Kitcher’s theory. (shrink)

types of application of genetic engineering for the insertion of genes into humans. The scientific requirements and the ethical issues associated with each type are discussed. Somatic cell gene therapy is technically the simplest and ethically the least controversial. The first clinical trials will probably be undertaken within the next year. Germ line gene therapy will require major advances in our present knowledge and it raises ethical issues that are now being debated. In order to provide guidelines for (...) determining when germ line gene therapy would be ethical, the author presents three criteria which should be satisfied prior to the time that a clinical protocol is attempted in humans. Enhancement genetic engineering presents significant, and troubling, ethical concerns. Except where this type of therapy can be justified on the grounds of preventive medicine, enhancement engineering should not be performed. The fourth type, eugenic genetic engineering, is impossible at present and will probably remain so for the foreseeable future, despite the widespread media attention it has received. Keywords: genetic engineering, somatic cells, germ cells, enhancement, eugenics, humanhood CiteULike Connotea Del.icio.us What's this? (shrink)

The historian Raphael Falk has described the gene as a ‘concept in tension’ (Falk 2000) – an idea pulled this way and that by the differing demands of different kinds of biological work. Several authors have suggested that in the light of contemporary molecular biology ‘gene’ is no more than a handy term which acquires a specific meaning only in a specific scientific context in which it occurs. Hence the best way to answer the question ‘what is a (...) gene’, and the only way to provide a truly philosophical answer to that question is to outline the diversity of conceptions of the gene and the reasons for this diversity. In this essay we draw on the extensive literature in the history of biology to explain how the concept has changed over time in response to the changing demands of the biosciences . Finally, we outline some of the conceptions of the gene current today. The seeds of change are implicit in many of those current conceptions and the future of the gene concept looks set to be at as turbulent as the past. (shrink)

Although much has been learned about hereditary mechanisms since Gregor Mendel’s famous experiments, gene concepts have always remained vague, notwithstanding their central role in biology. During over hundred years of genetic research, gene concepts have often and dynamically changed to accommodate novel experimental findings, without ever providing a generally accepted definition of the ‘gene.’ Yet, the distinction between ‘regulatory genes’ and ‘structural genes’ has remained a common theme in modern gene concepts since the definition of the (...) operon-model. This distinction is now challenged by recent findings which suggest that, at least in eukaryotes, structural genes may in many situations have a regulatory function that is independent of the function of the gene product (protein or non-coding RNA molecule). This brief paper discusses these new findings and some possible implications for the notion of the ‘regulatory gene.’. (shrink)

We attempt to improve the understanding of the notion of agene being `for a phenotypic trait or traits. Considering theimplicit functional ascription of one thing being `for another,we submit a more restrictive version of `gene for talk.Accordingly, genes are only to be thought of as being forphenotypic traits when good evidence is available that thepresence or prevalence of the gene in a population is the resultof natural selection on that particular trait, and that theassociation between that trait and (...) the gene in question isdemonstrably causal. It is therefore necessary to gatherstatistical, biochemical, historical, as well as ecologicalinformation before properly claiming that a gene is for aphenotypic trait. Instead of hampering practical use of the `genefor talk, our approach aims at stimulating much needed researchinto the functional ecology and comparative evolutionary biologyof gene action. (shrink)

We outline three very different concepts of the gene - 'instrumental', 'nominal', and 'postgenomic'. The instrumental gene has a critical role in the construction and interpretation of experiments in which the relationship between genotype and phenotype is explored via hybridization between organisms or directly between nucleic acid molecules. It also plays an important theoretical role in the foundations of disciplines such as quantitative genetics and population genetics. The nominal gene is a critical practical tool, allowing stable communication (...) between bioscientists in a wide range of fields grounded in well-defined sequences of nucleotides, but this concept does not embody major theoretical insights into genome structure or function. The post-genomic gene embodies the continuing project of understanding how genome structure supports genome function, but with a deflationary picture of the gene as a structural unit. This final concept of the gene poses a significant challenge to conventional assumptions about the relationship between genome structure and function, and between genotype and phenotype. (shrink)

Despite widespread agreement that it would be ethical to use somatic cell gene therapy to correct serious diseases, there is still uneasiness on the part of the public about this procedure. The basis for this concern lies less with the procedure's clinical risks than with fear that genetic engineering could lead to changes in human nature. Legitimate concerns about the potential for misuse of gene transfer technology justify drawing a moral line that includes corrective germline therapy but excludes (...) enhancement interventions in both somatic and germline contexts. Keywords: somatic cell, germ line, genetic diseases, genetic engineering, humanness, enhancement, eugenics CiteULike Connotea Del.icio.us What's this? (shrink)

Although the ability to perform gene therapy in human germ-line cells is still hypothetical, the rate of progress in molecular and cell biology suggests that it will only be a matter of time before reliable clinical techniques will be within reach. Three sets of arguments are commonly advanced against developing those techniques, respectively pointing to the clinical risks, social dangers and better alternatives. In this paper we analyze those arguments from the perspective of the client-centered ethos that traditionally governs (...) practice in medical genetics. This perspective clarifies the merits of these arguments for geneticists, and suggests useful new directions for the professional discussion of germ-line gene therapy. It suggests, for example, that the much discussed prospect of germ-line therapy in human pre-embryos may always be more problematic for medical genetics than adult germ-line interventions, even though the latter faces greater technical difficulties. (shrink)

If the question ``What is a gene?'' proves to be worth asking it must be able to elicit an answer which both recognizes and address the reasons why the concept of the gene ever seemed to be something worth getting excited about in the first place as well analyzing and evaluating the latest develops in the molecular biology of DNA. Each of the preceding papers fails to do one of these and sufferrs the consequences. Where Rolston responds to (...) the apparent failure of molecular biology to make good on the desideratum of the classical gene by veering off into fanciful talk about ``cybernetic genes,'' Griffiths and Stotz lose themselves in the molecular fine print and forget to ask themselves why ``genes'' should be of any special interst anyway. (shrink)

A phylogeny that allows for lateral gene transfer (LGT) can be thought of as a strictly branching tree (all of whose branches are vertical) to which lateral branches have been added. Given that the goal of phylogenetics is to depict evolutionary history, we should look for the best supported phylogenetic network and not restrict ourselves to considering trees. However, the obvious extensions of popular tree-based methods such as maximum parsimony and maximum likelihood face a serious problem—if we judge networks (...) by fit to data alone, networks that have lateral branches will always fit the data at least as well as any network that restricts itself to vertical branches. This is analogous to the well-studied problem of overfitting data in the curve-fitting problem. Analogous problems often have analogous solutions and we propose to treat network inference as a case of model selection and use the Akaike Information Criterion (AIC). Strictly tree-like networks are more parsimonious than those that postulate lateral as well as vertical branches. This leads to the conclusion that we should not always infer LGT events whenever it would improve our fit-to-data, but should do so only when the improved fit is larger than the penalty for adding extra lateral branches. (shrink)

A discussion of plasticity genes and the genetic architecture of gene-environment interactions.

In this paper we will argue: (1) that scholars, regardless of their normative stand against or for genetic enhancement indeed have a moral/professional obligation to hold on to a realistic and up-to-date conception of genetic enhancement; (2) that there is an unwarranted hype surrounding the issue of genetic enhancement in general, and gene doping in particular; and (3) that this hype is, at least partly, created due to a simplistic and reductionist conception of genetics often adopted by bioethicists.

A number of debates in philosophy of biology and psychology, as well as in their respective sciences, hinge on particular views about the relationship between genotypes and phenotypes. One such view is that the genotype-phenotype relationship is relatively straightforward, in the sense that a genome contains the ?genes for? the various traits that an organism exhibits. This leads to the assumption that if a particular set of traits is posited to be present in an organism, there must be a corresponding (...) number of genes in that organism's genome to account for those traits. This assumption underlies what can be called the ?counting argument,? in which empirical estimates of the number of genes in a genome are used to support or refute particular hypotheses in philosophical debates about biology and psychology. In this paper, we assess the counting argument as it is used in discussions of the alleged massive modularity of the brain, and conclude that this argument cannot be upheld in light of recent philosophical work on gene concepts and empirical work on genome complexity. In doing so, we illustrate that there are those on both sides of the debate about massive modularity who rely on an incorrect view of gene concepts and the nature of the genotype-phenotype relationship. (shrink)

Abstract Gene-selectionists define fundamental terms in non-standard ways. Genes are determinants of difference. Phenotypes are defined as a gene’s effects relative to some alternative whereas the environment is defined as all parts of the world that are shared by the alternatives being compared. Environments choose among phenotypes and thereby choose among genes. By this process, successful gene sequences become stores of information about what works in the environment. The strategic gene is defined as a set of (...) gene tokens that combines ‘actor’ tokens responsible for an effect with ‘recipient’ tokens whose replication is thereby enhanced. This set of tokens can extend across the boundaries of individual organisms, or other levels of selection, as these are traditionally defined. Content Type Journal Article Pages 1-19 DOI 10.1007/s10539-012-9315-5 Authors David Haig, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA Journal Biology and Philosophy Online ISSN 1572-8404 Print ISSN 0169-3867. (shrink)

Review of a book on going beyond the gene in the study of developmental and evolutionary biology.

Biologists and philosophers differ on whether selection should be analyzed at the level of the gene or of the individual. In Peter Godfrey-Smith’s book, Darwinian Populations and Natural Selection, he argues that individuals can be good members of Darwinian populations, whereas genes rarely can. I take issue with parts of this view, and suggest that Godfrey-Smith’s scheme for thinking about Darwinian populations is also applicable to populations of genes.

We defend a realistic attitude towards biological species. We argue that two species are not different species because they differ in intrinsic features, be they phenotypic or genomic, but because they are separated with regard to gene flow. There are no intrinsic species essences. However, there are relational ones. We argue that bearing a gene flow relation to conspecifics may serve as the essence of a species. Our view of the species as a Gene-Flow Community differs from (...) Mayr’s definition of the species as a reproductive community. In a reproductive community, each organism is able to successfully reproduce with each other. However, there are species in which geographically distant organisms lost their ability to successfully reproduce, due to strong genetic adaptations to the respective local environmental conditions. Despite this loss of the ability to mutually reproduce, they are still bound by gene flow via continuous intermediate populations. This replacement of Mayr’s notion of an interbreeding potential as a criterion for species membership has important implications for the treatment of populations in allopatry and sympatry. (shrink)

In this paper I address the question of whether the probabilities that appear in models of stochastic gene expression are objective or subjective. I argue that while our best models of the phenomena in question are stochastic models, this fact should not lead us to automatically assume that the processes are inherently stochastic. After distinguishing between models and reality, I give a brief introduction to the philosophical problem of the interpretation of probability statements. I argue that the objective vs. (...) subjective distinction is a false dichotomy and is an unhelpful distinction in this case. Instead, the probabilities in our models of gene expression exhibit standard features of both objectivity and subjectivity. (shrink)

The classical view of the gene prevailing during the 1910s and 1930s comprehended the gene as the indivisible unit of genetic transmission, genetic recombination, gene mutation and gene function. The discovery of intragenic recombination in the early 1940s led to the neoclassical concept of the gene, which prevailed until the 1970s. In this view the gene or cistron, as it was now called, was divided into its constituent parts, the mutons and recons, materially identified (...) as nucleotides. Each cistron was believed to be responsible for the synthesis of one single mRNA and concurrently for one single polypeptide. The discoveries of DNA technology, beginning in the early 1970s, have led to the second revolution in the concept of the gene in which none of the classical or neoclassical criteria for the definition of the gene hold strictly true. These are the discoveries concerning gene repetition and overlapping, movable genes, complex promoters, multiple polyadenylation sites, polyprotein genes, editing of the primary transcript, pseudogenes and gene nesting. Thus, despite the fact that our comprehension of the structure and organization of the genetic material has greatly increased, we are left with a rather , open and general concept of the gene. This article discusses past and present contemplations of genes, genomes, genotypes and phenotypes as well as the most recent advances of the study of the organization of genomes. (shrink)

According to a recent suggestion, the names of gene taxa should be conceived of as referring to individuals with concrete genes as their parts, just as the names of biological species are often understood as denoting individuals with organisms as their parts. Although prima facie this suggestion might advance the debate on gene concepts in a similar way as the species-are-individuals thesis advanced the debate on species concepts, I argue that the principal arguments in support of the (...) class='Hi'>gene-individuality thesis are much less compelling than the parallel arguments in the species case. In addition, I argue that the notion of biological function invoked in the gene-individuality thesis (selected effect) is not the one that biologists actually use when individuating genes. Contra the gene-individuality thesis, I argue that gene names refer to kinds, defined primarily (though not exclusively) by causal-role functions. (shrink)

This article presents the results of a study that investigates the way in which carriers of a mutation on the BRCA1 or the BRCA2 gene, associated with a high risk of breast and ovarian cancer, make their reproductive decisions. Using semi-structured interviews, the study explored the way in which these persons reflected on the acceptability of taking the risk of transmitting this mutation to the next generation, the arguments they used in favor or against taking that risk, and in (...) the light of these arguments, their opinion on the acceptability of preimplantation genetic diagnosis (PGD) as a reproductive option. The findings suggest that when carriers are planning to have a(nother) child, they are mainly concerned by the risk of transmitting ‘much more than a gene’: essentially painful experiences not only with respect to health, such as undergoing cancer surveillance or combatting one’s own illness, but also with regards to family life, such as witnessing the illness and death of a close relative, encountering difficulties in finding a partner or reconsidering one’s plans to have a family. As for opinions concerning the acceptability of PGD as a reproductive option, opinions about personal recourse were varied but all expressed the understanding that PGD should be made available to those persons who consider it their best option. (shrink)

Recombinant DNA technology will soon allow physicians an opportunity to carry out both somatic cell- and Germ-Line gene therapy. While somatic cell gene therapy raises no new ethical problems, gene therapy of gametes, fertilized eggs or early embryos does raise several novel concerns. The first issue discussed here relates to making a distinction between negative and positive eugenics; the second issue deals with the evolutionary consequences of lost genetic diversity. In distinguishing between positive and negative eugenics, the (...) concept of malady is applied as a definitional criterion for identifying genetic disorders that could qualify for Germ-Line therapy. Because gene replacement techniques are currently unavailable for humans, and because even if they were possible the number of people involved would be quite small, the loss of diversity concern seems moot. Finally, we dissuss the issue of iatrogenic disorders associated with gene therapy and discuss several ‘real world considerations.’ Keywords: Germ-Line therapy, malady, slippery slope CiteULike Connotea Del.icio.us What's this? (shrink)

The article investigates the validity of two different versions of the slippery slope argument construed in relation to human gene therapy: the empirical and the conceptual argument. The empirical version holds that our accepting somatic cell therapy will eventually cause our accepting eugenic medical goals. The conceptual version holds that we are logically committed to accepting such goals once we have accepted somatic cell therapy. It is argued that neither the empirical nor the conceptual version of the argument can (...) provide a conclusive moral reason for banning somatic cell therapy. According to a third interpretation, referred to as the arbitrary result argument, the many apparent similarities between somatic cell therapy and eugenic-based human genetic engineering drive us to make principled choices concerning what differences and similarities between the two practices should be regarded as morally (ir)relevant. Decisions of this kind are likely to have unpredictable moral consequences. Thus formulated, the slippery slope argument has much plausibility. One objects to somatic cell therapy not so much because of what is at the bottom of the slope on which it lies, but because it is on a slope of which one does not know what is at the bottom. While the arbitrary result argument does not provide a conclusive reason for prohibiting human gene therapy, it reminds of a very important thing: when making bioethical decisions, we should be as specific and as consistent as possible about our basic moral and medical concepts. (shrink)

Natural selection is an important force that shapes the evolution of all living things by determining which individuals contribute the most descendents to future generations. The biological unit upon which selection acts has been the subject of serious debate, with reasonable arguments made on behalf of populations, individuals, individual phenotypic characters and, finally, individual genes themselves. In this essay, I argue that the usual unit of selection is the gene. There are powerful logical arguments in favor of this conclusion, (...) as well as many real-world examples. I also explore the possibility that epigenetic differences between individuals may be heritable between generations. Although few such examples exist, epigenetic differences provide an exciting source of potentially heritable variation that may allow rapid evolutionary change to occur, perhaps in response to environmental influences. (shrink)

We discuss the impact of horizontal gene transfer (HGT) on phylogenetic reconstruction and taxonomy. We review the power of HGT as a creative force in assembling new metabolic pathways, and we discuss the impact that HGT has on phylogenetic reconstruction. On one hand, shared derived characters are created through transferred genes that persist in the recipient lineage, either because they were adaptive in the recipient lineage or because they resulted in a functional replacement. On the other hand, taxonomic patterns (...) in microbial phylogenies might also be created through biased gene transfer. The agreement between different molecular phylogenies has encouraged interpretation of the consensus signal as reflecting organismal history or as the tree of cell divisions; however, to date the extent to which the consensus reflects shared organismal ancestry and to which it reflects highways of gene sharing and biased gene transfer remains an open question. Preferential patterns of gene exchange act as a homogenizing force in creating and maintaining microbial groups, generating taxonomic patterns that are indistinguishable to those created by shared ancestry. To understand the evolution of higher bacterial taxonomic units, concepts usually applied in population genetics need to be applied. (shrink)

In this paper, I examine an experimental technique, gene targeting, used for establishing genotype/phenotype relationships. Through analyzing a case study, I identify many pitfalls that may lead to false conclusions about these relationships. I argue that some of these pitfalls may seriously affect gene targeting's usefulness for associating phenotypes with genes cataloged by the Human Genome Project. This case also shows the use of gene targeted mice as model systems for studying genotype/phenotype relationships in humans. Moreover, I (...) argue that it reveals the weakness of one attempt to draw conclusions about the biological determination of sexual and aggressive behaviors in humans. (shrink)

The Unified Medical Language System and the Gene Ontology are among the most widely used terminology resources in the biomedical domain. However, when we evaluate them in the light of simple principles for wellconstructed ontologies we find a number of characteristic inadequacies. Employing the theory of granular partitions, a new approach to the understanding of ontologies and of the relationships ontologies bear to instances in reality, we provide an application of this theory in relation to an example drawn from (...) the context of the pathophysiology of hypertension. This exercise is designed to demonstrate how, by taking ontological principles into account we can create more realistic biomedical ontologies which will also bring advantages in terms of efficiency and robustness of associated software applications. (shrink)

The aim of this paper is to offer a new biological interpretation of Fisher’s ‘Fundamental Theorem of Natural Selection’ and from this to consider optimality properties of gene frequency changes. These matters are of continuing interest to biologists and philosophers alike. In particular, the extent to which biological evolution can be calculated from the ‘gene’s-eye’ point of view is also discussed. In this sense, the paper bears indirectly on the concepts of the unit of selection and of the (...) ‘selfish gene’. A new biological significance for the Fundamental Theorem, not previously found in the literature, is offered, together with an optimality principle connected with this theorem. (shrink)

At this point in time, it is hard to say which consequences for the concept of mental illness result from modern genetics. Current research projects are trying to find significant statistical correlations between the diagnosis of a disease and a gene locus or an endophenotype. Up until now, there has not been any identification of alleles or mutations causing mental illness. In the meantime, the relations between the genetic basis and the disease are given the term genetic vulnerability as (...) a placeholder; this concept simplifies the complex relations between the DNA and even the simplest cell functions observed in modern genetics. According to complex gene models like the systemic theory of DNA, it will not be possible to identify the genetic factors without a precise knowledge of the factors which modulate the gene expression. The significance of genetics as part of the concept of mental illness will not be able to be defined without further progress in developmental biology and psychology. Currently, psychological theory fails to acknowledge the complexity of the relationship between the DNA and the environment. Some starting points from which to develop such an understanding can be received from developmental studies and studies of the psychophylogenesis . An interdisciplinary concept of the biological basis of the psyche is needed. (shrink)

In a widely acclaimed study from 2002, researchers found a case of gene-environment interaction for a gene controlling neuroenzymatic activity (low vs. high), exposure to childhood maltreatment, and antisocial personality disorder (ASPD). Cases of gene-environment interaction are generally characterized as evincing a genetic predisposition; for example, individuals with low neuroenzymatic activity are generally characterized as having a genetic predisposition to ASPD. I first argue that the concept of a genetic predisposition fundamentally misconstrues these cases of gene-environment (...) interaction. This misconstrual will be diagnosed, and then a new concept—interactive predisposition—will be introduced. I then show how this conceptual shift reconfigures old questions and raises new questions for genetic screening. Attempts to screen embryos or fetuses for the gene associated with low neuroenzymatic activity with an eye towards selecting against the low-activity variant fall prey to the myth of pre-environmental prediction; attempts to screen newborns for the gene associated with low neuroenzymatic activity with an eye towards early intervention will have to face the interventionist’s dilemma. (shrink)

Abstract The presence of gene–environment statistical interaction ( G x E ) and correlation ( rGE ) in biological development has led both practitioners and philosophers of science to question the legitimacy of heritability estimates. The paper offers a novel approach to assess the impact of G x E and rGE on the way genetic and environmental causation can be partitioned. A probabilistic framework is developed, based on a quantitative genetic model that incorporates G x E and rGE , (...) offering a rigorous way of interpreting heritability estimates. Specifically, given an estimate of heritability and the variance components associated with estimates of G x E and rGE , I arrive at a probabilistic account of the relative effect of genes and environment. Content Type Journal Article Category Regular Article Pages 1-13 DOI 10.1007/s10441-011-9139-8 Authors Omri Tal, School of Philosophy and The Cohn Institute for the History and Philosophy of Science and Ideas, Tel Aviv University, Tel Aviv, 69978 Israel Journal Acta Biotheoretica Online ISSN 1572-8358 Print ISSN 0001-5342. (shrink)

Genetic information is becoming increasingly used in modern life, extending beyond medicine to familial history, forensics and more. Following this expansion of use, the effect of genetic information on people’s identity and ultimately people’s quality of life is being explored in a host of different disciplines. While a multidisciplinary approach is commendable and necessary, there is the potential for the multidisciplinarity to produce conceptual misconnection. That is, while experts in one field may understand their use of a term like ‘ (...) class='Hi'>gene’, ‘identity’ or ‘information’ for experts in another field, the same term may link to a distinctly different concept. These conceptual misconnections not only increase inefficiency in complex organisational practices, but can also have important ethical, legal and social consequences. This paper comes at the problem of conceptual misconnection by clarifying different uses of the terms ‘gene’, ‘identity’ and ‘information’. I start by looking at three different conceptions of the gene; the Instrumental, the Nominal and the Postgenomic Molecular. Secondly, a taxonomy of four different concepts of identity is presented; Numeric, Character, Group and Essentialised, and their use is clarified. A general concept of Information is introduced, and finally three distinct kinds of information are described. I then introduce Concept Creep as an ethical problem that arises from conceptual misconnections. The primary goal of this paper is to reduce the potential for conceptual misconnection when discussing genetic identity and genetic information. This is complimented by three secondary goals—1) to clarify what a conceptual misconnection is, 2) to explain why clarity of use is particularly important to discussions of genes, identity and information and 3) to show how concept creep between different uses of genetic identity and genetic information can have important ethical outcomes. (shrink)

The recent conception of biodiversity proposed by James Maclaurin and Sterelny was developed mostly with macrobiological life in mind. They suggest that we measure biodiversity by dividing life into natural units (typically species) and quantifying the differences among units using phenetic rather than phylogenetic measures of distance. They identify problems in implementing quantitative phylogenetic notions of difference for non-prokaryotic species. I suggest that if we focus on microbiological life forms that engage in frequent, promiscuous lateral gene transfer (LGT), and (...) their associated reticulated phylogenies, we need to rethink the notion of species as the natural unit, and we discover additional problems with phylogenetic notions of distance. These problems suggest that a phenetic approach based on morphospaces has just as much appeal, if not more, for microbes as they do for multi-cellular life. Facts about LGT, however, offer no new insight into the additional challenge of reconciling units and differences into a single measure of biodiversity. (shrink)

To discern the ethical issues involved incurrent gene therapy research, to explore theproblems inherent in possible future genetherapies, and to encourage debate within thescientific community about ethical questionsrelevant to both, we surveyed American Societyof Human Genetics scientists who engage inhuman genetics research. This study of theopinions of U.S. scientific experts about theethical issues discussed in the literature ongene therapy contributes systematic data on theattitudes of those working in the field as wellas elaborative comments. Our survey finds thatrespondents are highly (...) supportive of thepotential use of somatic cell gene therapy tocure serious diseases in adults and children aswell as prospective offspring. A clearmajority, however, believe that using suchgenetic techniques for enhancement purposes isunacceptable. Delineating the line betweendisease/disorder and improvement/enhancementposes a problem not easily resolved and oneconducive to the growth of slippery-slopeapprehensions. The majority of respondents alsoadvocate germ-line therapy, in theory at least,and under similar restrictions, but theyrecognize the roadblock that the existence ofunanticipated negative consequences currentlypresents. Another complex matter involvestrying to determine appropriate reasons forchoosing target diseases for research, forwhich the dichotomy between rare single-geneand common multifactorial diseases reveals anongoing dilemma. (shrink)

This note argues that the charge of reductionism levelled against Richard Dawkins is false. It does so by examining the development of his notion of the genes in his books The Selfish Gene (TSG), and The Extended Phenotype (TEP).

In this paper I begin by examining a particularly disturbing eliminativist argument from Evelyn Fox Keller against the continued use of the very concept of the gene. If Fox Keller’s argument were to work, then any attempt to continue with or attempt to revise behavioral genetics would be doomed. In the course of replying to Fox Keller’s argument a revised, functional concept of the gene is presented and defending. Using this revised conception of the gene I then (...) consider how appeal to a functional approach to the gene can itself lead to a more general functionalist revision of the basic behavioral genetics project. In the third part of the paper I then turn to examining the advantages with respect to scientific explanation that such a functionalist account can provide. And, I end by considering how such an account might provide some help in dealing with additional ethical worries, including additional ethical arguments from Fox Keller against the continued use of the concept of the gene as well as ethical concerns that have been raised regarding behaviorally designed babies. (shrink)

In this paper I deal with ethical factors surrounding germline gene therapy. Such implications include intergenerational responsibility, human dignity, moral status of embryos and so on. I will explore the relevance of the above mentioned issues to discuss the ethical implication of human germline gene therapy (HGLT). We will see that most of arguments claimed by bioethicists do not provide valid reason to oppose HGLT. I will propose an alternative view, based on personal identity issues, to discuss the (...) ethics of human inheritable gene modification. (shrink)

Though the target article is not without fertile suggestions, at least two problems limit its overall validity: (1) the extended gene-culture coevolutionary framework is not an alternative to standard evolutionary theory; (2) the proposed model does not explain how much time is necessary for selective pressure to determine the stabilization of a new aspect of the genotype.

As the potential for the first human trials of somatic cell gene therapy nears, two ethical issues are examined: (1) problems of moral choice for members of institutional review boards who consider the first protocols, for parents, and for the clinical researchers, and the special protections that may be required for the infants and children to be involved, and (2) ethical objections to somatic cell therapy made by those concerned about a putative inevitable progression of genetic knowledge from therapy (...) to mass genetic engineering in human reproduction. The author's viewpoint is that a consensus exists on the required moral approach to somatic cell therapy, but that no moral approach yet exists for experiments beyond this level, especially in the germline cells of human beings. Keywords: gene therapy, somatic cells, germ cells, institutional review boards, genetic engineering CiteULike Connotea Del.icio.us What's this? (shrink)

In Life Beyond the Gene, Steven Rose offers a theory of life which insists that we as humans -- and indeed all living creatures -- create our own futures, though in circumstances not of our own choosing. Placing the organism at the center of life, Rose confronts the ideology of reductionism and ultra-Darwinism, with its insistence that all aspects of human life from sexual preference to infanticide, political orientation to violence, male domination to alcoholism, are in our genes and (...) are the inevitable consequences of natural selection. These claims, Rose asserts, are not only socially naive, but fundamentally misunderstand the active and irreducible nature of living processes. Rose argues that life depends on the elaborate web of interactions that occur within cells, organisms, and ecosystems, in which DNA has one part to play. From early in their development, living organisms have to be capable of quasi-independent existence while growing to maturity. If we are to understand life, we must recapture an understanding of the entire living organism and its trajectory through time and space. Rose calls these trajectories lifelines. Provocative and incisive, Life Beyond the Gene provides a compelling response to those enthusiasts of the gene who would deny the complexity of life. (shrink)

Understanding the operation and evolution of gene regulation networks is critical to understanding ontogeny and evolution. According to Stuart Kauffman's view, (1) each cell type cycles through its own repeated pattern of gene expression, (2) the order of ontogeny is dependent on these cycles being short, and (3) evolution is possible because these cycles mutate gradually. This view of gene regulation reflects Kauffman's view that ontogeny is fundamentally the process of cells repeating cycles of activity. I criticize (...) Kauffman's view of gene regulation networks and offer the connectionist theory of gene regulation as an alternative. On this view, the generic order of gene regulation mechanisms is due to the qualitatively consistent way that one gene product influences the expression of another. This allows networks to be stable and evolve to regulate accurately, allowing cells to react appropriately to their microenvironments, due to design by natural selection. Introduction Kauffman's Model of Gene Regulation Explaining the Order of Kauffman's K = 2 Networks The Importance and Relevance of Kauffman's Explanations of the Order of Gene Regulation Additional Orderly Facts of Transcription The Order of Network Accuracy The Accuracy of Connectionist Networks The Evolvability of Gene Regulation Networks Laws of Structure CiteULike Connotea Del.icio.us What's this? (shrink)

I show that gene regulation networks are qualitatively consistent and therefore sufficiently similar to linearly seperable connectionist networks to warrant that the connectionist framework be applied to gene regulation. On this view, natural selection designs gene regulation networks to overcome the difficulty of development. I offer some general lessons about their evolvability that can be learned by examining the generic features of connectionist networks.

How to interpret the “molecular gene” concept is discussed in this paper. I argue that the architecture of biological systems is hierarchical and multi-layered, exhibiting striking similarities to that of modern computers. Multiple layers exist between the genotype and system level property, the phenotype. This architectural complexity gives rise to the intrinsic complexity of the genotype-phenotype relationships. The notion of a gene being for a phenotypic trait or traits lacks adequate consideration of this complexity and has limitations in (...) explaining the genotype-phenotype relationships. I explore ways toward an integrative interpretation of the gene in the context of multi-layered biological systems. A gene, I argue, should be interpreted as a functional unit that is responsible for the trans-generation passage of the capacity to dynamically produce a biochemical activity or biochemical activities. At the molecular level, a gene is a genetic unit, a stretch of DNA sequence, which dictates the behavior and the dynamic production of the encoded cellular component(s). Embedded in a gene’s quadruple DNA code are the regulatory signals, such as those for RNA splicing and/or editing, as well as for transcription factor binding. A regulatory signal can be recognized by the gene expression machinery in one state, but not in another. The confusion caused by RNA splicing, editing, and a gene’s selective tissue distribution pattern is addressed. Instead of a context-dependent definition of the gene, I argue for the view that it is the same gene displaying multiple meanings, subject to differential interpretation by the cellular machinery in different states. In other words, the same gene gives rise to different products and expression levels under different conditions. (shrink)

This paper concerns periodic solutions of a class of equations that model gene regulatory networks. Unlike the vast majority of previous studies, it is not assumed that all decay rates are identical. To handle this more general situation, we rely on monotonicity properties of these systems. Under an alternative assumption, it is shown that a classical fixed point theorem for monotone, concave operators can be applied to these systems. The required assumption is expressed in geometrical terms as an alignment (...) condition on so-called focal points . As an application, we show the existence and uniqueness of a stable periodic orbit for negative feedback loop systems in dimension 3 or more, and of a unique stable equilibrium point in dimension 2. This extends a theorem of Snoussi, which showed the existence of these orbits only. (shrink)

Various algorithms have been proposed for learning (partial) genetic regulatory networks through systematic measurements of differential expression in wild type versus strains in which expression of specific genes has been suppressed or enhanced, as well as for determining the most informative next experiment in a sequence. While the behavior of these algorithms has been investigated for toy examples, the full computational complexity of the problem has not received sufficient attention. We show that finding the true regulatory network requires (in the (...) worst-case) exponentially many experiments (in the number of genes). Perhaps more importantly, we provide an algorithm for determining the set of regulatory networks consistent with the observed data. We then show that this algorithm is infeasible for realistic data (specifically, nine genes and ten experiments). This infeasibility is not due to an algorithmic flaw, but rather to the fact that there are far too many networks consistent with the data (10 18 in the provided example). We conclude that gene perturbation experiments are useful in confirming regulatory network models discovered by other techniques, but not a feasible search strategy. (shrink)

Mike Gene and I used to be quite active on a private listserve some years back. I even arranged for him to give a keynote address at a private ID conference in the fall of 1997. When we were on that listserve together, I used to keep many of his posts because I thought that they were so insightful (unfortunately many were lost when a computer virus chewed up my email program). In all that time I do not recall (...) ever taking sharp exception to him. But this time it's happened. My beef centers on Mike's comments on my exchange with Scott and Branch. (shrink)

The use of socially learned information (culture) is central to human adaptations. We investigate the hypothesis that the process of cultural evolution has played an active, leading role in the evolution of genes. Culture normally evolves more rapidly than genes, creating novel environments that expose genes to new selective pressures. Many human genes that have been shown to be under recent or current selection are changing as a result of new environments created by cultural innovations. Some changed in response to (...) the development of agricultural subsistence systems in the Early and Middle Holocene. Alleles coding for adaptations to diets rich in plant starch (e.g., amylase copy number) and to epidemic diseases evolved as human populations expanded (e.g., sickle cell and G6PD defi- ciency alleles that provide protection against malaria). Large-scale scans using patterns of linkage disequilibrium to detect recent selection suggest that many more genes evolved in response to agriculture. Genetic change in response to the novel social environment of contemporary modern societies is also likely to be occurring. The functional effects of most of the alleles under selection during the last 10,000 years are currently unknown. Also unknown is the role of paleoenvironmental change in regulating the tempo of hominin evolution. Although the full extent of culture-driven gene-culture coevolution is thus far unknown for the deeper history of the human lineage, theory and some evidence suggest that such effects were profound. Genomic methods promise to have a major impact on our understanding of gene-culture coevolution over the span of hominin evolutionary history. (shrink)

Our primary interest is in determining how many gene perturbation experiments are required to determine the Various algorithms have been proposed for learning..

The concept of projection from one space to another, with a consequent loss of information, can be seen in the relationships of gene to protein and language description to real situation. Such a transformation can only be reversed if extra external information is re-supplied. The genetic algorithm embodying this idea is now used in applied mathematics for exploring a configuration space. Such a dialectic – transformation back and forth between two kinds of description – extends the traditional Hegelian concept (...) used by Engels and others of change as resulting from a resolution of the conflict of two opposing tendencies and provides for evolution of the joint system. (shrink)

The so-called genetics revolution rests on a history which at its least can be described as controversial. Modern genetics needs to bear this history in mind. In particular, as with the past, the area of reproductive choice seems particularly vulnerable to potential abuse. Courts in the UK and elsewhere have already shown themselves willing to interfere with the choices of women in the management of their pregnancies. Medical advance, perhaps particularly the capacity to visualise the developing foetus, has added complexity (...) to the question of whether the health care provider has one patient (the woman) or two patients (the woman and the foetus). Additionally, pregnancy is thoroughly monitored in modern medical practice and genetics may provide a further impetus or incentive to mandate increased policing of pregnancy. Gene therapy, once offered, will add further to the desire to ensure that women make the 'right' choice, especially when the invasion required is relatively minimal. Further, genetic information is at best predictive, but may, because of its scientific nature, appear to those receiving it to be certain. Thus, the provision of genetic information may reduce rather than enhance choice, unless carefully and sensitively provided. A mature and sophisticated debate about the role of genetics in reproduction is required-engaging rather than bypassing the public-if the real potential of genetics is to be vindicated. (shrink)

The interrelationships among recent theories on the regulation of gene activity and differentiation in higher organisms are reviewed. Interpretations within these theories of the various components of chromosomes are re-evaluated and a unified conceptual framework of hierarchical genetic control mechanisms in eukaryotes is presented.

Abstract Terminology within the biological sciences gets its import not just from semantic meaning, but also from the way it functions within the rhetorics of the various disciplinary practices. The ?sociobiology? of human behavior inherits three distinct rhetorics from the genetic disciplines. Sociobiologists use population genetic, biometrical genetic, and molecular genetic rhetorics, without acknowledging the conceptual and experimental constraints that are assumed by geneticists. The eclectic blending of these three rhetorics obscures important differences of context and meaning. Sociobiologists use foundational (...) terms in genetics, such as ?gene?, ?fitness?, ?evolution?, ?heritability?, ?trait? and ?polygenic inheritance?, in starkly different ways from geneticists, while basing their analysis of human behavior on the implied authority of genetics. As a free?floating ?gene talk? moves across different disciplinary contexts, and before different audiences, it takes the form of an over?simplified and misleading arch?determinism. The result is widespread application of vague, incomplete, and distorted biological theory. If most sociobiologists, do not deliberately promote biological determinism, still less a political agenda, there is ample evidence that they misconstrue the implications of the genetic language that they borrow. (shrink)

Control of DNA supercoiling by the free-energy of hydrolysis of ATP that involves gene expression is analyzed in terms of three levels of unconnected metabolic pathways. These are synthesis and breakdown of topoisomerase mRNAs, synthesis and breakdown of topoisomerase proteins and supercoiling and relaxation of DNA. The so-called square-matrix method previously developed for the control of metabolic pathways, is extended to deal with this hierarchical control system. It turns out that also in this case, the matrix of control coefficients (...) is equal to the inverse of the so-called elasticity matrix, which contains all relevant elasticity coefficients as well as information about the structure and connectedness of the pathways involved. For a simpler case of a hierarchy of two systems, we demonstrate that the explicit matrix inversion method may be replaced by an implicit method in which the regulatory effects that run through the other level are described by an additional elasticy coefficient which may then be treated as if local. (shrink)

We support the ambitious goal of unification within the behavioral sciences. We suggest that Darwinian evolution by means of natural selection can provide the integrative glue for this purpose, and we review our own work on selective investment theory (SIT), which is an example of how other-regarding preferences can be accommodated by a gene-centered account of evolution. (Published Online April 27 2007).

Of the many proposals for inferring genetic regulatory structure from microarray measurements of mRNA transcript hybridization, several aim to estimate regulatory structure from the associations of gene expression levels measured in repeated samples. The repeated samples may be from a single experimental condition, or from several distinct experimental conditions; they may be “equilibrium” measurements or time series; the associations may be estimated by correlation coefficients or by conditional frequencies (for discretized measurements) or by some other statistic. This paper describes (...) two elementary statistical difficulties for all such procedures, no matter whether based on Bayesian updating, conditional independence testing, or other machine learning procedures such as simulated annealing or neural net pruning. One difficulty obtains if large numbers of cells are aggregated in a measurement of expression levels from a common population of cells; the other obtains if small numbers of cells are aggregated or if samples are separately aggregated over different populations of cells. (shrink)

Within academic circles, the “deficit” model of public understanding of science has been subject to increasing critical scrutiny by those who favor more constructivist approaches. These suggest that “the public” can articulate sophisticated ideas about the social and ethical implications of science regardless of their level of technical knowledge. The seminal studies following constructivist approaches have generally involved small-scale qualitative investigations, which have minimized the pre-framing of issues to a greater or lesser extent. This article describes the Gene Week (...) Project, sponsored by the Wellcome Trust, which attempted to extend this work to a large-scale consultation on genetics and health through the medium of a local daily newspaper. Readers were invited to respond to a set of open-ended questions that accompanied stimulus material published each day for five consecutive weekdays. The articles were written with the intention of extending the limited range of discourses around genetics and biotechnology that are usually presented by the popular media (hope, fear, tragedy and bravery). Responses raised overarching issues about the place of emerging health technologies in society reminiscent of previous open-ended consultations in this field. The paper ends with a critical discussion about the potential of this method to contribute to the further development of open-ended public consultations. (shrink)

Empirical research with young people in Finland, Germany, Spain and Britain was carried out as part of the BIOCULT project funded by the European Union. The project focused on their attitudes to biotechnology and, in particular, the formation of arguments about risk and safety. This paper looks at the responses of 14–18 year olds to a story about the so called anti-obesity gene, in the form of advice to a friend who is taking it. The majority advised against taking (...) it with some differences by gender and country. Most reservations were on grounds of safety and the feeling that ‘natural’ ways to lose weight are better: A minority questioned the idea of striving for a ‘perfect’ body. The types of arguments used by the young people reveal underlying perspectives on the place of human beings in the world and whether they have a right to manipulate nature and their own bodies. (shrink)

In response to adverse events in retroviral gene therapy clinical trials conducted in France to correct for X-linked severe combined immune deficiency disorder (X-SCID), an advisory committee of the Food and Drug Administration convened in October 2002, February 2003, and March 2005, to deliberate and provide recommendations for similarly sponsored research in the United States. A similar National Institutes of Health committee met in February 2003. In this article, I review the transcripts and/or minutes of these meetings to evaluate (...) the extent to which the ethical dimension of the research was engaged even as the molecular and clinical evidence was reviewed. I then provide representative ethical arguments to demonstrate the sort of ethical reasoning that should be included as part of the agenda of such committee meetings. (shrink)

An experimental consensus conference on the topic of gene therapy was held in order to discover whether the method, a means for participatory technology assessment born in Denmark in 1986, could be feasible in Japan. This article summarises the overall experience of this experiment and concludes that the method is indeed feasible in Japan. Enumerating some issues and problems we faced in this project, I will discuss their meaning and significance from the viewpoint of practitioner or initiator of participatory (...) technology assessment in Japan. (shrink)

Brussen, Kerri Anne A patent provides the exclusive legal right to a person or company to regulate the distribution, manufacture or use of their invention. This paper examines some of the issues surrounding Gene Patents. Although there is a drive to abolish Gene Patents, we argue that refined and clearly defined regulation would continue to support medical research, avoid exploitation, and be of benefit to public health.

Of the many proposals for inferring genetic regulatory structure from microarray measurements of mRNA transcript hybridization, several aim to estimate regulatory structure from the associations of gene expression levels measured in repeated samples. The repeated samples may be from a single experimental condition, or from several distinct experimental conditions; they may be “equilibrium” measurements or time series; the associations may be estimated by correlation coefficients or by conditional frequencies (for discretized measurements) or by some other statistic. This paper describes (...) two elementary statistical difficulties for all such procedures, no matter whether based on Bayesian updating, conditional independence testing, or other machine learning procedures such as simulated annealing or neural net pruning. One difficulty obtains if large numbers of cells are aggregated in a measurement of expression levels from a common population of cells; the other obtains if small numbers of cells are aggregated or if samples are separately aggregated over different populations of cells. (shrink)

This article seeks to explain the transformation of culture using the mechanism of evolutionary theory. Social biologists have been dealing with this issue for many years now. However, these scholars have not sufficiently allowed for the importance of factors independent of genes. They have primarily thought of culture as nothing more than the expansion of genes, as an increase in the rate of genetic adaptation. Namely, they have focused less on culture itself and more on its natural origins. Even while (...) accepting the dual inheritance model that the structure of biological genes and cultural transmission is different, this article seeksto take a step further. My aim is to show how culture that takes shape on the group level is explainable on the cultural genetic level. Seen from the point of view of culture genetics, the transformation of culture signifies the transformation in the frequency of a cultural gene. At this point, we are thus faced with the following questions: 1) Is it possible to concretize the units of culture genes? 2) What is the fundamental characteristic of a culture gene? and 3) What relationship is there between biological genes and cultural genes? This article will prove that it is indeed possible to concretize the units of culture genes, that the most substantialfundamental characteristic of a cultural gene is, as would be expected, to clone itself, and that cultural genes and biological genes exist within multiple relationships of cooperation, conflict, and reciprocity. Finally, this article will further concretize the dual inheritance model with a careful examination of its two patterns of evolutionary explanation, the reductionist on the one hand, and the non-reductionist on the other. This examination will conclude that, in terms of culture, the non-reductionist model is the most suitable. (shrink)

The finding of the same language deficit in half the members of the KE family is taken as suggesting that a specific allele (FOXP2) is normally involved in the development of language. Recent studies, however, question the exclusivity of FOXP2, and it is argued that the finding of a gene that disrupts language should not be taken as strong evidence for the existence of genes that underlie it.

Genetic determinism is the idea that many significant human characteristics are rendered inevitable by the presence of certain genes. The psychologist Susan Oyama has famously compared arguing against genetic determinism to battling the undead. Oyama suggests that genetic determinism is inherent in the way we currently represent genes and what genes do. As long as genes are represented as containing information about how the organism will develop, they will continue to be regarded as determining causes no matter how much evidence (...) exists to the contrary. Philip Kitcher has strongly disputed Oyama’s diagnosis, arguing that the conventional ‘interactionist’ perspective on development is the correct framework for understanding the role of the genes in development. While acknowledging the legitimacy of many of Kitcher’s observations, I believe that Oyama’s view is substantially correct. In this paper I provide several lines of support for support the Oyama diagnosis. (shrink)

‘Information’ and ‘code’ originated as technical terms within linguistics and information theory but are now widely used in genetics and developmental biology. Against this background, it is examined if coded information distinguishes genes from other information carriers, i.e., whether there are genetic words or sentences by virtue of the genetic code, and, if so, whether they have any semantic content. It is concluded that there is no genetic language with semantic content, but that the genetic code still enables unique language-like (...) modes of transmission and interpretation of causal information. (shrink)

: This paper discusses the morality of patenting human genes and genetic technologies. After examining arguments on different sides of the issue, the paper concludes that there are, at present, no compelling reasons to prohibit the extension of current patent laws to the realm of human genetics. However, since advances in genetics are likely to have profound social implications, the most prudent course of action demands a continual reexamination of genetics laws and policies in light of ongoing developments in science (...) and technology. (shrink)

Mendelian genes have become molecular genes, with increasing puzzlement about locating them, due to increasing complexity in genomic webworks. Genome science finds modular and conserved units of inheritance, identified as homologous genes. Such genes are cybernetic, transmitting information over generations; this too requires multi-leveled analysis, from DNA transcription to development and reproduction of the whole organism. Genes are conserved; genes are also dynamic and creative in evolutionary speciation—most remarkably producing humans capable of wondering about what genes are.

At the beginning of the 21st century, biology will try to address the function of a large number of new genes. From the perspective of technologies applied today to functional genomics, this task appears to be more complex than the effort invested in the sequencing of the human genome. Conceptually, a high-throughput approach permitting correlation between newly discovered genes and functional properties of their protein products has yet to be developed. To address relationships between tens of thousands of genes and (...) their cognate proteins, novel interdisciplinary technologies need to emerge. In this paper, a new idea of immunomics is presented and an experimental strategy is outlined to circumvent some of the restrictions associated with methodologies currently in use. It is proposed that cloned segments of genomic DNA are used for genetic immunization to obtain a large collection of antibodies, and to generate microarrays of these antibodies for tracing differentially expressed cellular proteins. (shrink)

The properties of DNA -- DNA as universal property -- DNA as intellectual property -- DNA as national property -- DNA as personal property -- DNA as academic property -- DNA as taxable propety.

In Italy, a judge reduced the sentence of a defendant by 1 year in response to evidence for a genetic predisposition to violence. The best characterized of these genetic differences, those in the monoamine oxidase A (MAOA), were cited as especially relevant. Several months previously in the USA, MAOA data contributed to a jury reducing charges from 1st degree murder (a capital offence) to voluntary manslaughter. Is there a rational basis for this type of use of MAOA evidence in criminal (...) court? This paper will review in context recent work on the MAOA gene–environment interaction in predisposing individuals to violence and address the relevance of such findings to murder trials. Interestingly, the MAOA genetic variants impact future violence and aggression only when combined with the adverse environmental stimuli of childhood maltreatment. Thus nature and nurture interact to determine the individual’s risk. Based on current evidence, I argue there is a weak case for mitigation. But should future experiments confirm the hypothesis that individual differences in impulse control and response to provocation found in MAOA-L men (without abuse) are significantly magnified when combined with childhood maltreatment, the case could turn into a stronger one. (shrink)

Advancing the reductionist conviction that biology must be in agreement with the assumptions of reductive physicalism (the upward hierarchy of causal powers, the upward fixing of facts concerning biological levels) A. Rosenberg argues that downward causation is ontologically incoherent and that it comes into play only when we are ignorant of the details of biological phenomena. Moreover, in his view, a careful look at relevant details of biological explanations will reveal the basic molecular level that characterizes biological systems, defined by (...) wholly physical properties, e.g., geometrical structures of molecular aggregates (cells). In response, we argue that contrary to his expectations one cannot infer reductionist assumptions even from detailed biological explanations that invoke the molecular level, as interlevel causal reciprocity is essential to these explanations. Recent very detailed explanations that concern the structure and function of chromatin—the intricacies of supposedly basic molecular level—demonstrate this. They show that what seem to be basic physical parameters extend into a more general biological context, thus rendering elusive the concepts of the basic level and causal hierarchy postulated by the reductionists. In fact, relevant phenomena are defined across levels by entangled, extended parameters. Nor can the biological context be explained away by basic physical parameters defining molecular level shaped by evolution as a physical process. Reductionists claim otherwise only because they overlook the evolutionary significance of initial conditions best defined in terms of extended biological parameters. Perhaps the reductionist assumptions (as well as assumptions that postulate any particular levels as causally fundamental) cannot be inferred from biological explanations because biology aims at manipulating organisms rather than producing explanations that meet the coherence requirements of general ontological models. Or possibly the assumptions of an ontology not based on the concept of causal powers stratified across levels can be inferred from biological explanations. The incoherence of downward causation is inevitable, given reductionist assumptions, but an ontological alternative might avoid this. We outline desiderata for the treatment of levels and properties that realize interlevel causation in such an ontology. (shrink)

Comparative genomicists seem to be convinced that the unit of measurement employed in their studies is a gene that drives the function of cells and ultimately organisms. As a result, they have come to some substantive conclusions about how similar humans are to other organisms based on the percentage of genetic makeup they share. I argue that the actual unit of measurement employed in the studies corresponds to a structural rather than a functional gene concept, thus rendering many (...) of the implications drawn from comparative genomic studies largely unwarranted, if not completely mistaken. †To contact the author, please write to: Department of Philosophy, University of Utah, 215 South Central Campus Drive, Carolyn Tanner Irish Humanities Building, 4th Floor, Salt Lake City, UT 84112; e‐mail: monika.piotrowska@utah.edu. (shrink)

I argue that four of the fundamental claims of those calling themselves `genic pluralists'Philip Kitcher, Kim Sterelny, and Ken Watersare defective. First, they claim that once genic selectionism is recognized, the units of selection problems will be dissolved. Second, Sterelny and Kitcher claim that there are no targets of selection (interactors). Third, Sterelny, Kitcher, and Waters claim that they have a concept of genic causation that allows them to give independent genic causal accounts of all selection processes. I argue (...) that each one of these claims is either false or misleading. Moreover, the challenge that arises from the availability of genic causal accounts, namely, the inability to choose on rational grounds among genic and higher-level accounts, is unsupported. (shrink)

The purpose of the patent system is to provide incentives for the development of new and useful products and processes. Such products and processes are generally referred to as ‘inventions’. Whilst patents have historically been sought and granted for mechanical and chemical inventions only, the biotechnology revolution of the last 30 years has radically changed this by precipitating a mass of patent applications in respect of living and biological matter. Applications of this nature have forced a re-examination by courts and (...) policy makers of traditional understandings of what can be patented. In particular, they have forced consideration of the extent (if any) to which life and nature can be viewed as ‘inventions’ so as to be capable of supporting a patent. In considering this question the central guiding principle has been the distinction, on which all of patent law is said to rest, between man-made inventions on the one hand and discoveries of nature on the other. (shrink)

Social institutions are the laws, informal rules, and conventions that give durable structure to social interactions within a population. Such institutions are typically not designed consciously, are heritable at the population level, are frequently but not always group benefi cial, and are often symbolically marked. Conceptualizing social institutions as one of multiple possible stable cultural equilibrium allows a straightforward explanation of their properties. The evolution of institutions is partly driven by both the deliberate and intuitive decisions of individuals and collectivities. (...) The innate components of human psychology coevolved in response to a culturally evolved, institutional environment and refl ect a prosocial tendency of choices we make about institutional forms. (shrink)

IT sounds like something out of the satirical journal Annals of Improbable Research: a team of Swedish neuroscientists scanned people's brains as they smelled a testosterone derivative found in men's sweat and an estrogen-like compound found in women's urine. In heterosexual men, a part of the hypothalamus (the seat of physical drives) responded to the female compound but not the male one; in heterosexual women and homosexual men, it was the other way around. But the discovery is more than just (...) a shoo-in for that journal's annual Ig Nobel Prize - it raises provocative questions about the science and ethics of human sexuality. (shrink)