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)

The major transcript variants of human protein‐coding genes are annotated to a certain degree of accuracy combining manual curation, transcript data, and proteomics evidence. However, there is considerable disagreement on the annotation of about 2000 genes—they can be protein‐coding, noncoding, or pseudogenes—and on the annotation of most of the predicted alternative transcripts. Pure transcriptome mapping approaches seem to be limited in discriminating functional expression from noise. These limitations have partially been overcome by dedicated algorithms to detect alternative spliced micro‐exons and (...) wobble splice variants. Recently, knowledge about splice mechanism and protein structure are incorporated into an algorithm to predict neighboring homologous exons, often spliced in a mutually exclusive manner. Predicted exons are evaluated by transcript data, structural compatibility, and evolutionary conservation, revealing hundreds of novel coding exons and splice mechanism re‐assignments. The emerging human pan‐genome is necessitating distinctive annotations incorporating differences between individuals and between populations. (shrink)

We review and discuss A. H. Louie’s book “More than Life Itself: A Reflexion on Formal Systems and Biology” from an interdisciplinary viewpoint, involving both biology and mathematics, taking into account new developments and related theories.

Genetic determinism can be described as the attribution of the formation of traits to genes, where genes are ascribed more causal power than what scientific consensus suggests. Belief in genetic determinism is an educational problem because it contradicts scientific knowledge, and is a societal problem because it has the potential to foster intolerant attitudes such as racism and prejudice against sexual orientation. In this article, we begin by investigating the very nature of belief in genetic determinism. Then, we investigate whether (...) knowledge of genetics and genomics is associated with beliefs in genetic determinism. Finally, we explore the extent to which social factors such as gender, education, and religiosity are associated with genetic determinism. Methodologically, we gathered and analyzed data on beliefs in genetic determinism, knowledge of genetics and genomics, and social variables using the “Public Understanding and Attitudes towards Genetics and Genomics” instrument. Our analyses of PUGGS responses from a sample of Brazilian university freshmen undergraduates indicated that belief in genetic determinism was best characterized as a construct built up by two dimensions or belief systems: beliefs concerning social traits and beliefs concerning biological traits; levels of belief in genetic determination of social traits were low, which contradicts prior work; associations between knowledge of genetics and genomics and levels of belief in genetic determinism were low; and social factors such as age and religiosity had stronger associations with beliefs in genetic determinism than knowledge. Although our study design precludes causal inferences, our results raise questions about whether enhancing genetic literacy will decrease or prevent beliefs in genetic determinism. (shrink)

The dialectic discourse of the ‘gene’ as the unit of heredity deduced from the phenotype, whether an intervening variable or a hypothetical construct, appeared to be settled with the presentation of the molecular model of DNA: the gene was reduced to a sequence of DNA that is transcribed into RNA that is translated into a polypeptide; the polypeptides may fold into proteins that are involved in cellular metabolism and structure, and hence function. This path turned out to be more bewildering (...) the more the regulation of products and functions were uncovered in the contexts of integrated cellular systems. Philosophers struggling to define a unified concept of the gene as the basic entity of genetics confronted those who suggested several different ‘genes’ according to the conceptual frameworks of the experimentalists. Researchers increasingly regarded genes de facto as generic terms for describing their empiric data, and with improved DNA-sequencing capacities these entities were as a rule bottom-up nucleotide sequences that determine functions. Only recently did empiricists return to discuss conceptual considerations, including top-down definitions of units of function that through cellular mechanisms select the DNA sequences which comprise ‘genomic-footprints’ of functional entities. (shrink)

In the last few years, the lack of a unitary notion of gene across biological sciences has troubled the philosophy of biology community. However, the debate on this concept has remained largely historical or focused on particular cases presented by the scientific empirical advancements. Moreover, in the literature there are no explicit and reasonable arguments about why a philosophical clarification of the concept of gene is needed. In our paper, we claim that a philosophical clarification of the concept of gene (...) does not contribute to biology. Unlike the question, for example, “What is a biological function?”, we argue that the question “What is a gene?” could be answered by means of empirical research, in the sense that biologists' labour is enough to shed light on it. (shrink)

This inaugural handbook documents the distinctive research field that utilizes history and philosophy in investigation of theoretical, curricular and pedagogical issues in the teaching of science and mathematics. It is contributed to by 130 researchers from 30 countries; it provides a logically structured, fully referenced guide to the ways in which science and mathematics education is, informed by the history and philosophy of these disciplines, as well as by the philosophy of education more generally. The first handbook to cover the (...) field, it lays down a much-needed marker of progress to date and provides a platform for informed and coherent future analysis and research of the subject. -/- The publication comes at a time of heightened worldwide concern over the standard of science and mathematics education, attended by fierce debate over how best to reform curricula and enliven student engagement in the subjects There is a growing recognition among educators and policy makers that the learning of science must dovetail with learning about science; this handbook is uniquely positioned as a locus for the discussion. -/- The handbook features sections on pedagogical, theoretical, national, and biographical research, setting the literature of each tradition in its historical context. Each chapter engages in an assessment of the strengths and weakness of the research addressed, and suggests potentially fruitful avenues of future research. A key element of the handbook’s broader analytical framework is its identification and examination of unnoticed philosophical assumptions in science and mathematics research. It reminds readers at a crucial juncture that there has been a long and rich tradition of historical and philosophical engagements with science and mathematics teaching, and that lessons can be learnt from these engagements for the resolution of current theoretical, curricular and pedagogical questions that face teachers and administrators. (shrink)