Developmental biology is a theory of interpretation. Developmental signals are interpreted differently depending on the previous history of the responding cell. Thus, there is a context for the reception of a signal. While this conclusion is obvious during metamorphosis, when a single hormone instructs some cells to proliferate, some cells to differentiate, and other cells to die, it is commonplace during normal development. Paracrine factors such as BMP4 can induce apoptosis, proliferation, or differentiation depending upon the history of the responding (...) cells. In addition, organisms have evolved to alter their development in response to differences in temperature, diet, the presence of predators, or the presence of competitors. This allows them to develop the phenotype, within the limits imposed by the genotype, best suited for the immediate habitat of the organism. Most developing organisms have also evolved to expect developmental signals from symbionts, and these organisms develop abnormally if the symbiont signals are not present. Thus Hoffmeyer’s “vertical semiotic system” of genetic communication and “horizontal semiotic system” of ecological communication are integrated during development. (shrink)

Historically, philosophers of biology have tended to sidestep the problem of development by focusing primarily on evolutionary biology and, more recently, on molecular biology and genetics. Quite often too, development has been misunderstood as simply, or even primarily, a matter of gene activation and regulation. Nowadays a growing number of philosophers of science are focusing their analyses on the complexities of development, and in Embryology, Epigenesis and Evolution Jason Scott Robert explores the nature of development against current trends in biological (...) theory and practice and looks at the interrelations between development and evolution, an area of resurgent biological interest. Clearly written, this book should be of interest to students and professionals in the philosophy of science and the philosophy of biology. (shrink)

This 1983 book is a lively and clearly written introduction to the philosophy of natural science, organized around the central theme of scientific realism. It has two parts. 'Representing' deals with the different philosophical accounts of scientific objectivity and the reality of scientific entities. The views of Kuhn, Feyerabend, Lakatos, Putnam, van Fraassen, and others, are all considered. 'Intervening' presents the first sustained treatment of experimental science for many years and uses it to give a new direction to debates about (...) realism. Hacking illustrates how experimentation often has a life independent of theory. He argues that although the philosophical problems of scientific realism can not be resolved when put in terms of theory alone, a sound philosophy of experiment provides compelling grounds for a realistic attitude. A great many scientific examples are described in both parts of the book, which also includes lucid expositions of recent high energy physics and a remarkable chapter on the microscope in cell biology. (shrink)

Throughout the history of genetics, the concept of the gene has been a hot topic. Theories of the gene as a coherent structured particle, a large molecule, or part of such molecule, were prominent from the 1920s until well after the discovery of DNA structure and its function in the production of proteins in the 1950s and 1960s. As knowledge of the material basis of heredity advanced, new and more sophisticated definitions were proposed (see, for example, Gerstein et al. 2007; (...) Müller-Wille and Rheinberger 2012). But rapid growth of knowledge about the molecular basis of biological heredity and individual development during the last half-century has made the idea of a particulate “gene” more and more elusive. Or .. (shrink)

The incredible achievements of modern scientific theories lead most of us to embrace scientific realism: the view that our best theories offer us at least roughly accurate descriptions of otherwise inaccessible parts of the world like genes, atoms, and the big bang. In Exceeding Our Grasp, Stanford argues that careful attention to the history of scientific investigation invites a challenge to this view that is not well represented in contemporary debates about the nature of the scientific enterprise. The historical record (...) of scientific inquiry, Stanford suggests, is characterized by what he calls the problem of unconceived alternatives. Past scientists have routinely failed even to conceive of alternatives to their own theories and lines of theoretical investigation, alternatives that were both well-confirmed by the evidence available at the time and sufficiently serious as to be ultimately accepted by later scientific communities. Stanford supports this claim with a detailed investigation of the mid-to-late 19th century theories of inheritance and generation proposed in turn by Charles Darwin, Francis Galton, and August Weismann. He goes on to argue that this historical pattern strongly suggests that there are equally well-confirmed and scientifically serious alternatives to our own best theories that remain currently unconceived. Moreover, this challenge is more serious than those rooted in either the so-called pessimistic induction or the underdetermination of theories by evidence, in part because existing realist responses to these latter challenges offer no relief from the problem of unconceived alternatives itself. Stanford concludes by investigating what positive account of the spectacularly successful edifice of modern theoretical science remains open to us if we accept that our best scientific theories are powerful conceptual tools for accomplishing our practical goals, but abandon the view that the descriptions of the world around us that they offer are therefore even probably or approximately true. (shrink)

In this book Bruno Latour brings together these different approaches to provide a lively and challenging analysis of science, demonstrating how social context..

This paper serves as an introduction to the special issue on “Reconciling Nature and Nurture in Behavior and Cognition Research” and sets its agenda to resolve the 'interactionist' dichotomy of nature as the genetic, and stable, factors of development, and nurture as the environmental, and plastic influences. In contrast to this received view it promotes the idea that all traits, no matter how developmentally fixed or universal they seem, contingently develop out of a single-cell state through the interaction of a (...) multitude of developmental resources that defies any easy, dichotomous separation. It goes on to analyze the necessary ingredients for such a radical, epigenetic account of development, heredity and evolution: 1. A detailed understanding of the epigenetic nature of the regulatory mechanisms of gene expression; 2. The systematical questioning of preconceptions of 'explanatory' categories of behavior, such as 'innate' or 'programmed'; 3. Especially in psychological research the integration of the concepts of 'development' and 'learning', and a richer classification of the concept of 'environment' in the production of behavior; 4. A fuller understanding of the nature of inheritance that transcends the restriction to the genetic material as the sole hereditary unit, and the study of the process of developmental niche construction; and last 5. Taking serious the role of ecology in development and evolution. I hope that an accomplishment of the above task will then lead to a 'postgenomic' synthesis of nature and nurture that conceptualizes 'nature' as the natural phenotypic outcome 'nurtured' by the natural developmental process leading to it. (shrink)

Reification is to abstraction as disease is to health. Whereas abstraction is singling out, symbolizing, and systematizing, reification is neglecting abstractive context, especially functional, historical, and analytical-level context. William James and John Dewey provide similar and nuanced arguments regarding the perils and promises of abstraction. They share an abstraction-reification account. The stages of abstraction and the concepts of “vicious abstractionism,” “/the/ psychologist’s fallacy,” and “the philosophic fallacy” in the works of these pragmatists are here analyzed in detail. For instance, in (...) 1896 Dewey exposes various fallacies associated with reifying dualistic reflex arc theory. The conclusion prescribes treatments (pluralism and assumption archaeology) for de-reifying ill models (i.e., universalized, narrowed, and ontologized models) in contemporary scientific fields such as cognitive science and biology. (shrink)

In the past century, nearly all of the biological sciences have been directly affected by discoveries and developments in genetics, a fast-evolving subject with important theoretical dimensions. In this rich and accessible book, Paul Griffiths and Karola Stotz show how the concept of the gene has evolved and diversified across the many fields that make up modern biology. By examining the molecular biology of the 'environment', they situate genetics in the developmental biology of whole organisms, and reveal how the molecular (...) biosciences have undermined the nature/nurture distinction. Their discussion gives full weight to the revolutionary impacts of molecular biology, while rejecting 'genocentrism' and 'reductionism', and brings the topic right up to date with the philosophical implications of the most recent developments in genetics. Their book will be invaluable for those studying the philosophy of biology, genetics and other life sciences. (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 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 paper argues against the central dogma and its interpretation by C. Kenneth Waters and Alex Rosenberg. I argue that certain phenomena in the regulation of gene expression provide a break with the central dogma, according to which sequence specificity for a gene product must be template derived. My thesis of 'molecular epigenesis' with its three classes of phenomena, sequence 'activation', 'selection', and 'creation', is exemplified by processes such as transcriptional activation, alternative cis- and trans-splicing, and RNA editing. It argues (...) that other molecular resources share the causal role of genes; the sequence specificity for the linear sequence of any gene product is distributed between the coding sequence, cis-acting sequences, trans-acting factors, environmental signals, and the contingent history of the cell (thesis of distributed causal specificity). I conclude that the central dogma has unnecessarily restricted genetic research to the sequencing of protein-coding genes, unilinear pathway analyses, and the focus on exclusive specificity. (shrink)

I present an account of classical genetics to challenge theory-biased approaches in the philosophy of science. Philosophers typically assume that scientific knowledge is ultimately structured by explanatory reasoning and that research programs in well-established sciences are organized around efforts to fill out a central theory and extend its explanatory range. In the case of classical genetics, philosophers assume that the knowledge was structured by T. H. Morgan’s theory of transmission and that research throughout the later 1920s, 30s, and 40s was (...) organized around efforts to further validate, develop, and extend this theory. I show that classical genetics was structured by an integration of explanatory reasoning and investigative strategies . The investigative strategies, which have been overlooked in historical and philosophical accounts, were as important as the so-called laws of Mendelian genetics. By the later 1920s, geneticists of the Morgan school were no longer organizing research around the goal of explaining inheritance patterns; rather, they were using genetics to investigate a range of biological phenomena that extended well beyond the explanatory domain of transmission theories. Theory-biased approaches in history and philosophy of science fail to reveal the overall structure of scientific knowledge and obscure the way it functions.Author Keywords: Investigation; Genetic approach; Structure of knowledge; Classical genetics. (shrink)

In this article we examine the “phenotype” concept in light of recent technological advances in Genome-Wide Association Studies . By observing the technology and its presuppositions, we put forward the thesis that at least in this case genotype and phenotype are effectively coidentifled one by means of the other. We suggest that the coidentiflcation of genotype-phenotype couples in expression-based GWAS also indicates a conceptual dependence, which we call “co-deñnition.” We note that viewing these terms as codeflned runs against possible expectations, (...) viz., that genotypes and phenotypes could ultimately be expressed independently from one another. In addition, the co-definition of genotypes and phenotypes in this context emphasizes the correlative character of both genotypes and phenotypes in GWAS. (shrink)

A recent cover of the German news magazine Der Spiegel announced: “Victory over Genes. Smarter, healthier, happier: How we can outwit our genome” (2010). The magazine’s article, instead, emphasizes the importance of epigenetics. According to Florian Maderspacher (2010), who reprinted the cover in his editorial in Current Biology, the relief or “schadenfreude” about the apparent victory over genes—which the cover, the article, and commentaries to it reveal—is, in part, a German phenomenon. It echoes “a latent anti-scientific attitude in parts of (...) the German public,” which for historic reasons is particularly strong with regard to genetics: “After all, the idea that people’s properties—good or bad—are determined by .. (shrink)