Despite 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. In this article, we argue for a strict differentiation between two gene concepts: the “molecular gene” and the “evolutionary gene.” The definition of both is highly problematic. The molecular gene is, roughly speaking, a DNA sequence that codes for a polypeptide. But, as we will discuss, this general conception raises several problems: Does a “gene” include its introns? Does it include its regulator and promoter sequences? In cases in which the spliced mRNA transcript undergoes further editing, does the gene include the machinery that dictates the sequence of the final transcript? We believe that these questions point to a tension between two theoretical goals. The first goal is to identify genes with particular DNA segments on chromosomes, thus maintaining one of the theoretical commitments of classical genetics; the second is to make genes a core part of the developmental explanation of phenotypic traits—especially, although not exclusively, the heritable trait differences studied by classical genetics. As we will discuss, the first goal is simply not achievable in light of current knowledge about how final gene products are constructed. Abandoning the first goal in favor of the second leads to what we call the “molecular process” concept of the gene.
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