Genes in the postgenomic era (original) (raw)
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BioScience, 1999
The many faces of the gene espite the centrality of the term "gene" to modern biology, its definition remains a matter of controversy. A univocal definition may not be necessary or even desirable; different "gene concepts" may be useful in different areas of biology. However, it is necessary to clearly distinguish these different concepts and to use each in its proper domain.
The concept of gene in the twenty-first century: What are the open avenues?
Contrastes. Revista Internacional de Filosofía, 2013
ABSTRACTThe view of the gene as a structural and functional unit has been increasingly challenged by findings mostly resulting from eukaryote research. We can classify these challenges in three kinds: (i) one-to-many correspondences between DNA segments and RNAs/polypeptides (as, for instance, in alternative splicing); (ii) many-to-one correspondences between DNA segments and RNAs/polypeptides (as in genomic rearrangements, say, those involved in the generation of diversity in lymphocyte antigen receptors); (iii) lack of correspondence between DNA segments and RNAs/polypeptides (as, for example, in mRNA editing). However, even if a single definition of a gene may not be a realistic (or even helpful) goal, being able to have different definitions connected to each other –operationally and theoretically– is of central importance.KEYWORDSGENE CONCEPT, DEFINITION, DNARESUMENLa idea según la cual el gen es una unidad estructural y funcional se ha visto cada vez más cuestionada a causa de...
The Evolving Definition of the Term “Gene”
Genetics, 2017
This paper presents a history of the changing meanings of the term "gene," over more than a century, and a discussion of why this word, so crucial to genetics, needs redefinition today. In this account, the first two phases of 20th century genetics are designated the "classical" and the "neoclassical" periods, and the current molecular-genetic era the "modern period." While the first two stages generated increasing clarity about the nature of the gene, the present period features complexity and confusion. Initially, the term "gene" was coined to denote an abstract "unit of inheritance," to which no specific material attributes were assigned. As the classical and neoclassical periods unfolded, the term became more concrete, first as a dimensionless point on a chromosome, then as a linear segment within a chromosome, and finally as a linear segment in the DNA molecule that encodes a polypeptide chain. This last definition, from the early 1960s, remains the one employed today, but developments since the 1970s have undermined its generality. Indeed, they raise questions about both the utility of the concept of a basic "unit of inheritance" and the long implicit belief that genes are autonomous agents. Here, we review findings that have made the classic molecular definition obsolete and propose a new one based on contemporary knowledge.
Faculty of 1000 evaluation for The evolving definition of the term "gene
F1000 - Post-publication peer review of the biomedical literature
This paper presents a history of the changing meanings of the term "gene," over more than a century, and a discussion of why this word, so crucial to genetics, needs redefinition today. In this account, the first two phases of 20th century genetics are designated the "classical" and the "neoclassical" periods, and the current molecular-genetic era the "modern period." While the first two stages generated increasing clarity about the nature of the gene, the present period features complexity and confusion. Initially, the term "gene" was coined to denote an abstract "unit of inheritance," to which no specific material attributes were assigned. As the classical and neoclassical periods unfolded, the term became more concrete, first as a dimensionless point on a chromosome, then as a linear segment within a chromosome, and finally as a linear segment in the DNA molecule that encodes a polypeptide chain. This last definition, from the early 1960s, remains the one employed today, but developments since the 1970s have undermined its generality. Indeed, they raise questions about both the utility of the concept of a basic "unit of inheritance" and the long implicit belief that genes are autonomous agents. Here, we review findings that have made the classic molecular definition obsolete and propose a new one based on contemporary knowledge.
Between the cross and the sword: the crisis of the gene concept
Genetics and Molecular Biology, 2007
Challenges to the gene concept have shown the difficulty of preserving the classical molecular concept, according to which a gene is a stretch of DNA encoding a functional product (polypeptide or RNA). The main difficulties are related to the overlaying of the Mendelian idea of the gene as a ‘unit’: the interpretation of genes as structural and/or functional units in the genome is challenged by evidences showing the complexity and diversity of genomic organization. This paper discusses the difficulties faced by the classical molecular concept and addresses alternatives to it. Among the alternatives, it considers distinctions between different gene concepts, such as that between the ‘molecular’ and the ‘evolutionary’ gene, or between ‘gene-P’ (the gene as determinant of phenotypic differences) and ‘gene-D’ (the gene as developmental resource). It also addresses the process molecular gene concept, according to which genes are understood as the whole molecular process underlying the capacity to express a particular product, rather than as entities in ‘bare’ DNA; a treatment of genes as sets of domains (exons, introns, promoters, enhancers, etc.) in DNA; and a systemic understanding of genes as combinations of nucleic acid sequences corresponding to a product specified or demarcated by the cellular system. In all these cases, possible contributions to the advancement of our understanding of the architecture and dynamics of the genetic material are emphasized.
What is a gene, post-ENCODE? History and updated definition
2008
What is a gene, post-ENCODE? History and updated definition data Supplementary http://www.genome.org/cgi/content/full/17/6/669/DC1 "Fig._1_Timeline_Poster.pdf" References http://www.genome.org/cgi/content/full/17/6/669#otherarticles Article cited in: http://www.genome.org/cgi/content/full/17/6/669#References
How to Understand the Gene in the 21st Century?
Science & Education, vol. 22, n. 2, pp. 345-374, 2013
It is widely acknowledged in the literature on philosophy of biology and, more recently, among biologists themselves that the gene concept is currently in crisis. This crisis concerns the so-called “classical molecular concept”, according to which a gene is a DNA segment encoding one functional product, which can be either a RNA molecule or a polypeptide. In this paper, we first describe three categories of anomalies that challenge this way of understanding genes. Then, we discuss proposals for revising the gene concept so as to accommodate the increasingly known complexity of genomic architecture and dynamics. Our intention is to provide an informative overview of recent proposals concerning how we should conceive of genes, which are probably not very familiar to many science educators and teachers, but can bring relevant contributions to genetics teaching, in particular, to a more critical treatment of genes and their role in living systems.
Genes after the human genome project
While the Human Genome Nomenclature Committee (HGNC) concept of the gene can accommodate a wide variety of genomic sequences contributing to phenotypic outcomes, it fails to specify how sequences should be grouped when dealing with complex loci consisting of adjacent/overlapping sequences contributing to the same phenotype, distant sequences shown to contribute to the same gene product, and partially overlapping sequences identified by different techniques. The purpose of this paper is to review recently proposed concepts of the gene and critically assess how well they succeed in addressing the above problems while preserving the degree of generality achieved by the HGNC concept. I conclude that a dynamic interplay between mapping and syntax-based concepts is required in order to satisfy these desiderata.
2010
The purpose of this article is to update and defend syntax-based (conserved DNA-sequence motifs) 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.