 addressed before contributions can stem from this approach. The expansion of the zoo of instrumentally formulated genetic entities in the last three decades has resulted in a rather loose and sometimes confusing usage of terminology in molecular genetics. For instance, what is the difference between regulatory element, cis--acting element, cis-acting sequence, regulatory sequence, and 5 regulator? It is quite clear that these terms substantially overlap in meaning, and most of them should be either eliminated or defined in more precise terms. Obviously, this problem cannot be solved merely by interpreting genes as sets of domains, but this interpretation can help by demanding that domains be clearly specified by structure and/or activity/function. Therefore, a first task would be to build a formal system to designate and describe domains in DNA, through efforts similar to the Gene Ontology Consortium (Ashburner et al., 2000).
The second development from Fogles ideas would be to establish formal procedures for the combinations of domains in DSATs or genes, taking in due account, as far as possible, the practices currently used by communities of geneticists and molecular biologists, since they would be the ones ultimately making use of the libraries of domains and formal rules of combination resulting from this effort.
The Brazilian researchers Pardini and Guimarães (1992) brought an interesting contribution to the discussions about the gene concept. They proposed a systemic concept of the gene, according to which "the gene is a combination of (one or more) nucleic acid (DNA or RNA) sequences, defined by the system (the whole cell, interacting with the environment, or the environment alone, in subcellular or pre-cellular systems), that corresponds to a product (RNA or polypeptide)" (ibid., p. 717; see also p. 713). This definition treats the genome as part of the cellular system, which "builds, defines and uses the genome as part of its memory mechanisms, as an interactive database" (Guimarães and Moreira, 2000, p. 249).
The systemic concept of the gene shows some similarities to Fogles conception of genes as sets of domains in DNA, even though Fogles proposal seems to be restricted to DNA genomes (Guimarães, pers. comm.). Pardini and Guimarães (1992, p. 716) stress the dynamics of the relationship between encoded information and the product of its decoding, which is quite complex, varying with the spatial and temporal conditions of occurrence. Guimarães and Moreira (2000) argue that the meaning of a DNA segment is relative, depending on the expression system in which it is embedded. Consequently, its meaning can be plural: the multivocal nature of genes, particularly in eukaryotes, stems from the context-dependence of gene expression. Even though it seems tempting to conclude that this approach is similar to Neumann-Helds process molecular gene concept, it is important to emphasize that this would be a mistake (Guimarães, pers. comm.). The systemic gene concept indeed alludes to the process which specifies or demarcates the gene, as an adequate combination of (one or more) genomic sequences corresponding to a product, but it takes this demarcation as the result of a process which is not included itself in the gene.
The gene seems to be now between the sword, as it is clearly under the risk of being deleted from the genetic vocabulary, and the cross, given current efforts to save it from this fate. In this review, I described how the gene concept arrived at these difficult circumstances, but I opted for the path of the cross, addressing alternatives to the usual understanding of this concept, which suggest interesting manners of rescuing it from its current crisis. The problem has its roots in the treatment of genes in Mendelian genetics as units in the genetic material. This treatment was updated in the classical molecular gene concept, which characterized a gene as a stretch of DNA encoding a functional product, a single polypeptide chain or RNA molecule. Our current knowledge about the physical organization and dynamics of genomes clearly shows that this juxtaposition of the molecular and the Mendelian gene is untenable. In this scenario, it is worth considering the possibility of treating the gene concept in such a manner that the unit concept is dispensed with. We find in Fogle (1990, 2000) an interesting proposal to this effect, in which genes are treated as sets of embedded, tandem, and overlapping domains in DNA. In a somewhat related vein, Pardini and Guimarães (1992) put forward a systemic concept of the gene, which treats the gene as a combination of nucleic acid sequences corresponding to a product (RNA or polypeptide), specified or demarcated by the cellular system.
Another proposal goes even further and moves from a substance- to a process-oriented view of genes, the process molecular gene concept (Griffiths and Neumann-Held, 1999; Neumann-Held, 2001). In these terms, genes are not conceptualized as sequences of nucleotides in DNA, but rather as the whole molecular process leading to the temporally and spatially regulated expression of a particular polypeptide or RNA product.
Finally, one important lesson we can draw from the above discussions concerns the demand for generality in biological definitions. As it is the case with other biological concepts (e.g., the concept of organism. See Sterelny and Griffiths, 1999), a gene concept need not be entirely general in order to be useful. A variety of gene concepts, each with a well-delimited domain of application, can have more explanatory and heuristic power than an allegedly universal definition of a gene. In a discussion about the nature of laws in biology, Weber (1999) argues for biological laws which generalize over a restricted domain of application. I am advocating that the same approach should be applied to the issue of the generality of biological concepts, including gene.
The ideas discussed in this review arguably offer interesting grounds to put into question standard ideas about genes, both in teaching and research, and, consequently, can pave the way to a replacement of the classical molecular gene concept by a new (and possibly plural) understanding of what is a gene, which seems to be under construction right under our noses.
I am indebted to Diogo Meyer and Romeu Guimarães for several comments on the original manuscript that led to improvements in the paper. I thank the Brazilian National Research Council (CNPq) for research grant n. 302495/ 02-9, post-doctoral studies grant n. 200402/03-0, and funding of the project n. 402708/2003-2.
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