Genes

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.

My aim in this paper is to quickly sketch a teleological approach to the problem of isolating the impact of genes on phenotypic characters. I begin by arguing that it is a mistake to think that there will be only one analysis of genetic input suitable for all theoretical interests. My principle focus is Richard Dawkins' argument for genic selectionism. I argue that a teleological analysis of genetic input is what Dawkins requires to establish the right kind of mapping of (...) gene onto phenotype. This comes at a certain cost, however. Accepting the analysis will threaten Dawkins' claims about the teleogogical priority of gene over phenotype. (shrink)

Children's competence to refuse or consent to medical treatment or surgery tends to be discussed in terms of the child's ability or maturity. This paper argues that the social context also powerfully influences the child's capacity to consent. Inner attributes and external influences are discussed using an analogy of the genes and the stars.

Burns proposes an intriguing hypothesis by suggesting that the “schizophrenia genes” might not be regulatory genes themselves, but rather closely associated with regulatory genes directly involved in the proper growth of the social brain. We point out that this account would benefit from incorporating the effects of localized lesions and aberrant hemispheric asymmetry on cortical connectivity underlying the social brain. In addition, we argue that the evolutionary framework is superfluous.

In this commentary, we critique the appropriate behavioural features for evolutionary genetic analysis, the role of the environment, and the viability of a general evolutionary genetic model for all common mental disorders. In light of these issues, we suggest that the authors may have prematurely discounted the role of some of the mechanisms they review, particularly balancing selection. (Published Online November 9 2006).

New concepts may prove necessary to profit from the avalanche of sequence data on the genome, transcriptome, proteome and interactome and to relate this information to cell physiology. Here, we focus on the concept of large activity-based structures, or hyperstructures, in which a variety of types of molecules are brought together to perform a function. We review the evidence for the existence of hyperstructures responsible for the initiation of DNA replication, the sequestration of newly replicated origins of replication, cell division (...) and for metabolism. The processes responsible for hyperstructure formation include changes in enzyme affinities due to metabolite-induction, lipid-protein affinities, elevated local concentrations of proteins and their binding sites on DNA and RNA, and transertion. Experimental techniques exist that can be used to study hyperstructures and we review some of the ones less familiar to biologists. Finally, we speculate on how a variety of in silico approaches involving cellular automata and multi-agent systems could be combined to develop new concepts in the form of an Integrated cell (I-cell) which would undergo selection for growth and survival in a world of artificial microbiology. (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)

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)

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 gelsolin gene family encodes a number of higher eukaryotic actin-binding proteins that are thought to function in the cytoplasm by severing, capping, nucleating or bundling actin filaments. Recent evidence, however, suggests that several members of the gelsolin family may have adopted unexpected nuclear functions including a role in regulating transcription. In particular, flightless I, supervillin and gelsolin itself have roles as coactivators for nuclear receptors, despite the fact that their divergence appears to predate the evolutionary appearance of nuclear receptors. (...) Flightless I has been shown to bind both actin and the actin-related BAF53a protein, which are subunits of SWI/SNF-like chromatin remodelling complexes. The primary sequences of some actin-related proteins such as BAF53a exhibit conservation of residues that, in actin itself, are known to interact with gelsolin-related proteins. In summary, there is a growing body of evidence supporting a biological role in the nucleus for actin, Arps and actin-binding proteins and, in particular, the gelsolin family of actin-binding proteins. (c) 2005 Wiley Periodicals, Inc. (shrink)

Patents have been issued in the United States for genes and gene sequences since 1980. Patent protection has provided incentives to aggressively probe the genome of humans and non-humans alike in search of profitable applications. Yet it is not clear that patent protection should have been afforded to genes and gene sequences and it is increasingly clear that patent protection, as currently formulated, is not an appropriate means to realize the full benefits of genetic research. As we stand on the (...) threshold on a genetically enhanced future, in which we shall have the power to consciously steer our evolution as a species, we need to carefully consider how to shape the benefits of genetic research and how to recognize and contain its detriments. (shrink)

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.

All complex systems are complex, but some are more complex than others are. Biological systems are generally more complex than physical systems. How do biologists tackle complex systems? In this talk, we will consider two biological systems, the genome and the brain. Scientists know much about them, but much more remains unknown. Ignorance breeds philosophical speculation. Reductionism makes a strong showing here, as it does in other frontier sciences where large gaps remain in our understanding. I will show that reductionism (...) and its claims have no bases in actual scientific research and results. The Human Genome Project will serve as a case in point.. (shrink)

This paper deals with the interrelationship between causal explanation and methodology in a relatively young discipline in biology: epigenetics. Based on cases from molecular and ecological epigenetics, I show that James Woodward’s interventionist account of causation captures essential features about how epigeneticists using highly diverse methods, i.e. laboratory experiments and purely observational studies, think about causal explanation. I argue that interventionism thus qualifies as a useful unifying explanatory approach when it comes to cross-methodological research efforts. It can act as a (...) guiding rationale (i) to link causal models in molecular biology with statistical models derived from observational data analysis and (ii) to identify test-criteria for reciprocal transparent studies in different fields of research, which is a shared issue across the sciences.Este artículo trata de la relación entre explicaciones causales y metodología en una disciplina biológica relativamente joven, la epigenética. Basándome en casos de la epigenética molecular y ecológica, muestro que la concepción intervencionista de la causalidad desarrollada por James Woodward capta algunos rasgos esenciales del modo en que los epigenetistas conciben la explicación causal usando métodos sumamente diversos: e.g., experimentos de laboratorio o estudios observacionales. Defiendo que el intervencionismo es útil como aproximación unificadora a la explicación cuando se trata de empresas investigadoras transdisciplinares. Puede servir como guía para (i) conectar los modelos causales en biología molecular con los modelos estadísticos derivados del análisis de datos observacionales y (ii) para identificar criterios de prueba para estudios recíprocos en diferentes ámbitos de investigación, un problema de interés común en diferentes ciencias. (shrink)

The purpose of this article is to update and defend syntax-based gene concepts. I show how syntax-based concepts can and have been extended to accommodate complex cases of processing and gene expression regulation. In response to difficult cases and causal parity objections, I argue that a syntax-based approach fleshes out a deflationary concept defining genes as genomic sequences and organizational features of the genome contributing to a phenotype. These organizational features are an important part of accepted molecular explanations, provide the (...) theoretical basis for a large number of experimental techniques and practical applications, and play a crucial role in in annotating the genome, deriving predictions and constructing bioinformatics models. (shrink)

Experiential factors such as long-term deliberate practice are powerful and necessary conditions for outstanding achievement. Nevertheless, to be able to reject the role of biology based individual differences (including genetic ones) in the manifestation of talent requires designs that expose heterogeneous samples to so-called testing-the-limits conditions, allowing asymptotic levels of performance to be analyzed comparatively. When such research has been conducted, as in the field of lifespan cognition, individual differences, including biology based ones, come to the fore and demonstrate that (...) the orchestration of excellence requires joint attention to genetic–biological and experiential factors. (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)

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)

Peer reporting is a specific form of whistelblowing in which an individual discloses the wrongdoing of a peer. Previous studies have examined situational variables thought to influence a person's decision to report the wrongdoing of a peer. The present study looked at peer reporting from the individual level. Five hypotheses were developed concerning the relationships between (1) religiosity and ethical ideology, (2) ethical ideology and ethical judgments about peer reporting, and (3) ethical judgments and intentions to report peer wrongdoing.Subjects read (...) a vignette concerning academic cheating, and were asked to respond to a question-naire concerning the vignette. Data were analyzed using structural equation methodology. (shrink)

Differences in ethical ideology are thought to influence individuals'' reasoning about moral issues (Forsyth and Nye, 1990; Forsyth, 1992). To date, relatively little research has addressed this proposition in terms of business-related ethical issues. In the present study, four groups, representing four distinct ethical ideologies, were created based on the two dimensions of the Ethical Position Questionnaire (idealism and relativism), as posited by Forsyth (1980). The ethical judgments of individuals regarding several business-related issues varied, depending upon their ethical ideology.

The present study extends the study of individuals' ethical ideology withinthe context of marketing ethics issues. A national sample of marketing professionals participated. Respondents' ethical ideologies were classified as absolutists, situationists, exceptionists, or subjectivists using the Ethical Position Questionnaire (Forsyth, 1980). Respondents then answered questions about three ethically ambiguous situations common to marketing and sales. The results indicated that marketers' ethical judgments about the situations differed based on their ethical ideology, with absolutists rating the actions as most unethical. The findings (...) are consistent with those of two earlier studies that utilized samples of business students (Barnett et al., 1994, 1995). The results suggest that personal moral philosophy is an important influence on ethical decision making that should be considered in empirical studies of business ethics. The results also support the utility of the Ethical Position Questionnaire (Forsyth, 1980) as a means for researchers and practitioners to assess individuals' ethical ideology. (shrink)

We agree that much of language evolution is likely to be adaptation of languages to properties of the brain. However, the attempt to rule out the existence of language-specific adaptations a priori is misguided. In particular, the claim that adaptation to cannot occur is false. Instead, the details of gene-culture coevolution in language are an empirical matter.

Frequent lateral genetic transfer undermines the existence of a unique “tree of life” that relates all organisms. Vertical inheritance is nonetheless of vital interest in the study of microbial evolution, and knowing the “tree of cells” can yield insights into ecological continuity, the rates of change of different cellular characters, and the evolutionary plasticity of genomes. Notwithstanding within-species recombination, the relationships most frequently recovered from genomic data at shallow to moderate taxonomic depths are likely to reflect cellular inheritance. At the (...) same time, it is clear that several types of ‘average signals’ from whole genomes can be highly misleading, and the existence of a central tendency must not be taken as prima facie evidence of vertical descent. Phylogenetic networks offer an attractive solution, since they can be formulated in ways that mitigate the misleading aspects of hybrid evolutionary signals in genomes. But the connections in a network typically show genetic relatedness without distinguishing between vertical and lateral inheritance of genetic material. The solution may lie in a compromise between strict tree-thinking and network paradigms: build a phylogenetic network, but identify the set of connections in the network that are potentially due to vertical descent. Even if a single tree cannot be unambiguously identified, choosing a subnetwork of putative vertical connections can still lead to drastic reductions in the set of candidate vertical hypotheses. (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.’. (shrink)

Biologists rely heavily on the language of information, coding, and transmission that is commonplace in the field of information theory developed by Claude Shannon, but there is open debate about whether such language is anything more than facile metaphor. Philosophers of biology have argued that when biologists talk about information in genes and in evolution, they are not talking about the sort of information that Shannon’s theory addresses. First, philosophers have suggested that Shannon’s theory is only useful for developing a (...) shallow notion of correlation, the so-called causal sense of information. Second, they typically argue that in genetics and evolutionary biology, information language is used in a semantic sense, whereas semantics are deliberately omitted from Shannon’s theory. Neither critique is well-founded. Here we propose an alternative to the causal and semantic senses of information: a transmission sense of information, in which an object X conveys information if the function of X is to reduce, by virtue of its sequence properties, uncertainty on the part of an agent who observes X. The transmission sense not only captures much of what biologists intend when they talk about information in genes, but also brings Shannon’s theory back to the fore. By taking the viewpoint of a communications engineer and focusing on the decision problem of how information is to be packaged for transport, this approach resolves several problems that have plagued the information concept in biology, and highlights a number of important features of the way that information is encoded, stored, and transmitted as genetic sequence. (shrink)

Advances in molecular biological research in the latter half of the twentieth century 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. It will be of interest to professionals and students in the philosophy and history of science, genetics and molecular biology. (shrink)

: The following comments on Paul Root Wolpe's article "If I Am Only My Genes, What Am I? Genetic Essentialism and a Jewish Response" address (1) his presentation of the relationship between science and culture or religion as unimodal; (2) his misconception of the Jewish view of the physical corpus; and (3) his essential question of genetic determinism by examining the traditional Jewish view of the spiritual aspects of the human.

Is the gene ‘special’ for historians? What effects, if any, has the notion of the ‘gene’ had on our understanding of history? Certainly, there is a widespread public and professional perception that genetics and history are or should be in dialogue with each other in some way. But historians and geneticists view history and genetics very differently – and assume very different relationships between them. And public perceptions of genes, genetics, genomics, and indeed the nature and meanings of ‘history’ differ (...) yet again. Here, in looking at the meaning, and the implications – the significance – of the gene specifically to historians, I will focus on two aspects of the discourse. First, I will examine the ways in which historians have thus far approached genes and genetics, and the impact such studies have had on the field. There is considerable overlap between the subject matter of genetics/genomics and many of the most widely used analytic categories of contemporary historiography – race, gender, sexuality, ethnicity, ability, among others. Yet the impact of genetics and genomics on society has been studied principally by anthropologists, sociologists and ethicists.2 Only two historical sub-disciplines have engaged with the rise of genetics to any significant degree: the histories of science and of medicine. What does this indicate or suggest? Second, I will explore the impact of the ‘gene’ and genetic understandings on public conceptions of history itself. (shrink)