Gene skeptics claim that there is no coherence to the way gene is used at the molecular level and that this term does not designate a natural kind; rather, gene is allegedly used to pick out many different kinds of units in DNA. DNA consists of “coding” regions that are transcribed into RNA, different kinds of regulatory regions, and in higher organisms, a number of regions whose functions are less clear and perhaps in cases non-existent. Skepticism about genes is based in part on the idea that the term is sometimes applied to only parts of a coding region, sometimes to an entire coding region, sometimes to parts of a coding region and to regions that regulate that coding region, and sometimes to an entire coding region and regulatory regions affecting or potentially affecting the transcription of the coding region. Skeptics (e.g., Burian 1986, Portin 1993, and Kitcher 1992) have concluded, as Kitcher succinctly puts it: “a gene is whatever a competent biologist chooses to call a gene” (Kitcher 1992, p. 131).
Biological textbooks contain definitions of gene and it is instructive to consider one in order to show that the conceptual situation is indeed unsettling. The most prevalent contemporary definition is that a gene is the fundamental unit that codes for a polypeptide. One problem with this definition is that it excludes many segments that are typically referred to as genes. Some DNA segments code for functional RNA molecules that are never translated into polypeptides. Such RNA molecules include transfer RNA, ribosomal RNA, and RNA molecules that play regulatory and catalytic roles. Hence, this definition is too narrow.
Another problem with this common definition is that it is based on an overly simplistic account of DNA expression. According to this simple account, a gene is a sequence of nucleotides in DNA that is transcribed into a sequence of nucleotides making up a messenger RNA molecule that is in turn translated into sequence of amino acids that forms a polypeptide. (Biologists talk as if genes “produce the polypeptide molecules” or “provide the information for the polypeptide”.) The real situation of DNA expression, however, is often far more complex. For example, in plants and animals, many mRNA molecules are processed before they are translated into polypeptides. In these cases, portions of the RNA molecule, called introns, are snipped out and the remaining segments, called exons, are spliced together before the RNA molecule leaves the cellular nucleus. Sometimes biologists call the entire DNA region, that is the region that corresponds to both introns and exons, the gene. Other times, they call only the portions of the DNA segment corresponding to the exons the gene. (This means that some DNA segments that geneticists call genes are not continuous segments of DNA; they are collections of discontinuous exons. Geneticists call these split genes.) Further complications arise because the splicing of exons in some cases is executed differentially in different tissue types and at different developmental stages. (This means that there are overlapping genes.) The problem with the common definition that genes are DNA segments that “code for polypeptides” is that the notion of “coding for a polypeptide” is ambiguous when it comes to actual complications of DNA expression. Gene skeptics argue that it is hopelessly ambiguous (Burian 1986, Fogle 1990 and 2000, Kitcher 1992, and Portin 1993).
Clearly, this definition, which is the most common and prominent textbook definition, is too narrow to be applied to the range of segments that geneticists commonly call genes and too ambiguous to provide a single, precise partition of DNA into separate genes. Textbooks include many definitions of the gene. In fact, philosophers have often been frustrated by the tendency of biologists to define and use the term gene in a number of contradictory ways in one and the same textbook. After subjecting the alternative definitions to philosophical scrutiny, gene skeptics have concluded that the problem isn't simply a lack of analytical rigor. The problem is that there simply is no such thing as a gene at the molecular level. That is, there is no single, uniform, and unambiguous way to divide a DNA molecule into different genes. Gene skeptics have often argued that biologists should couch their science in terms of DNA segments such exon, intron, promotor region, and so on, and dispense with the term gene altogether (most forcefully argued by Fogle 2000).
https://plato.stanford.edu/entries/molecular-genetics/#WhaGen