How to Understand the Gene in the Twenty-First Century?

Abstract

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.

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Notes

  1. 1.

    By “molecular pleiotropy”, Burian refers to the production of distinct molecules out of a single putative gene, with a major role being played by the cellular and external environments in determining which protein is produced.

  2. 2.

    “Molecular epigenesis” concerns the revision of sequence-based information through alteration of molecular conformations or action of noninformational molecules, which plays a major role in development.

  3. 3.

    In alternative splicing, a pre-mRNA molecule is processed—in particular, spliced—in a diversity of manners, so that different combinations of exons emerge in the mature mRNA. In this manner, several distinct mRNAs and, thus, polypeptides can be obtained from the same DNA sequence. In the case of DSCAM in Drosophila melanogaster, for instance, alternative splicing can lead to ca. 38,016 protein products (Celotto and Graveley 2001).

  4. 4.

    A gene is said to be nested when it is entirely located inside another gene.

  5. 5.

    Genes are said to be overlapping when they share DNA sequences.

  6. 6.

    In transplicing, mature RNA is formed during processing from RNA transcripts of DNA regions from different chromosomes.

  7. 7.

    mRNA editing is an alteration of mRNA nucleotides during processing, so that there can be a lack of correspondence between nucleotide sequences in mature mRNA and nucleotide sequences in DNA.

  8. 8.

    The generation of the diverse antigen receptors found in lymphocytes, and, consequently, of antibody specificity depends on a combinatorial set of genomic rearrangements between different DNA segments called variable segments, constant segments, and diversity and joining segments.

  9. 9.

    Pseudogenes are genomic DNA sequences which are derived from, and similar to protein-coding genes, but show signs diagnostic of protein-coding deficiency, such as frameshifts and premature stop codons, and are usually non-functional. Transcribed pseudogenes are copies of protein-coding genes that have accumulated such indicators of coding sequence decay, but are still transcribed, and could be potentially functional in the regulation of gene transcription (Khachane and Harrison 2009).

  10. 10.

    An open reading frame is the DNA or RNA sequence located between the initiation codon, where the codons that will be translated into amino acids in protein synthesis begin to be read, and the termination codon, where protein synthesis comes to an end.

  11. 11.

    It is important to avoid losing from sight that the distinction between gene-P and gene-D is not identical to the distinction between classical and molecular genes. Molecular entities can be treated as genes-P, as when we speak of the gene for cystic fibrosis (see Moss 2001, 2003a).

  12. 12.

    Moss appeals to a central notion in Susan Oyama’s “developmental systems theory” or “perspective”, namely, causal parity between genes and other developmental resources (See Oyama [1985]2000; Oyama et al. 2001). This perspective highlights the missing element in deterministic accounts of the genotype-phenotype relationship, namely, development, in which genes, organisms, and environments interact with each other in such a way that each is both cause and effect in a complex way (Lewontin 1983, 2000).

  13. 13.

    In order to put Fogle’s proposal to work, one has to deal with the rather loose and sometimes confusing usage of terminology in molecular genetics, resulting from the expansion of the zoo of instrumentally formulated genetic entities in the last three decades (Falk 1986). Fogle demands that domains should be clearly specified by structure and/or activity. Therefore, a first task is to build a formal system to designate and describe domains in DNA. This can be done through gene ontology efforts, as developed, for instance, by the Gene Ontology Consortium (Ashburner et al. 2000) and the ENCODE Project (The ENCODE Project Consortium 2007). A second development is suggested, however, by Fogle’s ideas, namely, the establishment of formal procedures for the combinations of domains in genes, taking in due account, as far as possible, the practices currently used by the communities of geneticists and molecular biologists. After all, they would ultimately have to make use of the libraries of domains and formal rules of combination resulting from such an effort.

  14. 14.

    http://www.ornl.gov/sci/techresources/Human_Genome/glossary/glossary_g.shtml. Accessed at August 8th 2011.

  15. 15.

    The ENCODE database can be reached at http://www.genome.gov/10005107#4. The participants of the ENCODE can be found at http://www.genome.gov/26525220. See also (The ENCODE Project Consortium 2007).

  16. 16.

    A polycistronic pre-mRNA is a single long transcript coding for the syntheses of more than one protein.

  17. 17.

    The regulome is the complete set of components involved with regulation in a cell.

  18. 18.

    In the post-genomic era, researchers have been pushed into adopting a “systemic” perspective, which has given rise to a wave of “systems biology” in the fields of molecular biology, genomics, and proteomics. Systems biology is often presented as a non-reductionistic approach (Chong and Ray 2002; Barabási and Oltvai 2004; Nature 2005). Many genomic researchers seem quite eager, indeed, to declare that they have overcome “fallacies” such as determinism and reductionism (see, e.g., Venter et al. 2001, p. 1348), even though a sort of embarrassed determinism (cf. Leite 2007) lives on in their writings. But it is not clear, at present, what “systems biology” really means in these fields (Keller 2005), and, furthermore, it can be put into question if it is really such a non-reductionistic approach as many of its advocates claim (Bruni 2003; Morange 2006; El-Hani et al. 2009), much in the same sense as systems ecology was previously charged of being nothing but a large-scale reductionistic approach (e.g., Levins and Lewontin 1985; Bergandi 1995).

  19. 19.

    We added this remark by inspiration of a comment made by a reviewer of the original manuscript, who called attention to this sentence as such a take-home message, stimulating us to highlight it in the paper.

  20. 20.

    For a semiotic interpretation of signaling pathways, also based on C. S. Peirce’s theory of signs, see El-Hani et al. (2007).

  21. 21.

    Here we can clearly see how Keller and Harel’s dene concept is different from Gerstein and colleagues’ treatment of the gene as a union of genomic sequences encoding a coherent set of potentially overlapping functional products. In this latter concept, the gene is taken to be the union of all sequences encoding functional products synthesized by means of the differentially spliced mRNA molecules. The dene, in turn, is a statement about each of the differentially spliced mRNAs.

  22. 22.

    Small interfering RNA: a class of small double-stranded RNA molecules, which play several roles in the cell, including a key involvement in RNA interference, an important phenomenon of genetic regulation discovered in the 1990s. RNA interference silences gene expression in a highly specific manner.

  23. 23.

    Micro-RNAs: short RNA molecules that act as post-transcriptional regulators by binding to complementary sequences on target mRNAs, usually resulting in repression of protein synthesis and, thus, gene silencing. Although the first miRNAs were characterized in the early 1990s, their recognition as a distinct class of biologic regulators only took place in the early 2000s. Nowadays, they were shown to play several functions in gene repression and activation.

  24. 24.

    Small nucleolar RNAs: a class of small RNA molecules that guide chemical modifications of other RNAs, such as rRNAs and tRNAs.

  25. 25.

    A “genomic domain” is defined by Scherrer and Jost (2007b, p. 106) as a “DNA domain containing fragments of one or several genes coordinated by cis controls, […] often unit of transcription and, in some cases, of replication”.

  26. 26.

    The notion of ‘program’, particularly when conceived in terms of “genetic programs”, is highly controversial (e.g., Oyama [1985]2000; Nijhout 1990; Moss 1992; Griffiths and Neumann-Held 1999; Keller 2000), but we will not pursue this discussion here, since it would take us away from our major goals in this paper. Scherrer and Jost do not elaborate on the concept of “programme”. They remark, however, that the genon and transgenon constitute a flexible, not rigidly defined program, to the extent that epigenetic mechanisms of gene expression and transmission modify both the genon and its precursors at the DNA level. In these modifications, the genon and transgenon may be modified with no changes being made at the DNA level. The genon, for instance, can be changed by epigenetic modifications such as DNA methylation, while the transgenon can be modified by the addition or elimination of factors originated either in the genome or in the environment, according to cell compartment, physiological context, cell age, etc.

  27. 27.

    Evidently, this is highly reminiscent of Fogle’s and Pardini and Guimarães’ accounts about the gene.

  28. 28.

    The prefix ‘cis’ is used to denote a sequence that is in the same DNA molecule, in the same chromosome, in relation to another sequence of interest.

  29. 29.

    The prefix ‘trans’ is used to denote a sequence (or its product) at a different DNA molecule or chromosome, in relation to a sequence of interest.

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Acknowledgments

We would like to thank the Coordination for the Improvement of Higher Education Personnel (CAPES) and the State of Bahia Foundation for the Support of Research (FAPESB) for graduate studies grants, and the National Council for Scientific and Technological Development (CNPq) and FAPESB for financial support. We also thank CNPq for a grant for productivity in research. We are also indebted to Vanessa Carvalho dos Santos and Leyla Mariane Joaquim for suggestions about the manuscript.

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Correspondence to Charbel Niño El-Hani.

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Meyer, L.M.N., Bomfim, G.C. & El-Hani, C.N. How to Understand the Gene in the Twenty-First Century?. Sci & Educ 22, 345–374 (2013). https://doi.org/10.1007/s11191-011-9390-z

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Keywords

  • Gene
  • DNA
  • Unit
  • Crisis
  • Genetic teaching