WHAT IS A GENE? THE MOLECULAR GENE CONCEPT IN SCIENTIFIC PRACTICE
How should contemporary scientific metaphysicians answer the question, “What is a gene ?” Most philosophers weighing in on this question have concluded that trying to answer it is hopeless. For example, consider the prevalent idea that genes are units in DNA that “code for” polypeptides. (Some background: DNA is a macromolecule consisting of two complementary linear sequences of nucleotides; RNA is a macromolecule consisting of one linear sequence of nucleotides; a polypeptide is a molecule made up of a linear sequence of amino acids.) According to this prevalent idea, genes are subsequences of nucleotides in a strand of DNA. The basic story behind this conception goes as follows. A linear sequence of nucleotides in DNA comprises a gene, and this sequence is “transcribed” into a corresponding sequence of nucleotides making up an individual RNA molecule during RNA synthesis. Subsequently, the linear sequence of nucleotides in this RNA molecule is “translated” into a linear sequence of amino acids making up a polypeptide molecule during polypeptide synthesis. But it turns out that the syntheses of RNA and polypeptide molecules are far more complicated than this story suggests. These complications render this simplistic conception of genes ambiguous, vague, and exception-ridden.
On this basis, Evelyn Fox Keller (2000) argues that the term “gene” has outlived its usefulness, and many philosophers of biology agree with Keller. Much of the philosophical literature on this topic implies that the fundamental units of genetics exist at smaller scales and are more varied than suggested above. Some philosophers have argued that the real “molecular-level” units of genetics are not genes, but what were once thought to be parts of genes: promoters, enhancers, exons, and introns. Some philosophers have also argued that genes exist, but only at the “higher level” of classical genetics. Other philosophers have proposed novel gene concepts that seem to depart significantly from conceptual practice. For example, one idea is that genes are processes rather than entities (Griffiths and Neumann-Held 1999). But for the most part, philosophers have decided that today’s science tells us that there is no such thing as a gene at the “molecular level.”
I have argued that an analysis of how contemporary geneticists reason when they use the term “gene” reveals that they use a multiplicity of concepts (Waters 1994). Sometimes it is useful to be vague, and in such contexts biologists invoke a blunt concept akin to the gene concept of classical genetics (described in section 3). In other contexts it is important to be precise. When precision is important, biologists employ what I have called the molecular gene concept (Waters 1994, 2000).
The molecular gene concept has placeholders. When the placeholders are filled, the concept can be used to pick out precise segments of DNA. So this concept is precise. But it is also flexible because the placeholders of the concept can be filled out in a multiplicity of ways, and the different instantiations that result can be used to pick out different segments of nucleotides in DNA. Some instantiations pick continuous segments; others pick out discontinuous segments. Some instantiations pick out segments that overlap segments picked out by other instantiations. The overall situation is very messy. But the flexibility of this concept enables biologists to pick out different precise segments of DNA that are relevant to different explanatory, investigative, and manipulative interests.
The molecular gene concept can be specified as follows:
A gene g for linear sequence l in productp synthesized in cellular context c is a potentially replicating nucleotide sequence, n, usually contained in DNA, that determines the linear sequence l in product p at some stage of DNA expression.
The referent of any gene,g, is a specific sequence of nucleotides. The exact sequence to which a g refers depends on how the placeholders l, p, and c are filled out.11 As figure i illustrates, this provides biologists with the conceptual means to pick out precisely what DNA segments determine different linear sequences in different stages and contexts of DNA expression.
The molecular gene concept is a remarkable conceptual tool. It gives biologists the flexibility they need to pick out DNA segments that line up with different causal chains (or processes) within the incredible complexities of DNA expression and development. It does so by providing the basis for partitioning the DNA molecule in a multiplicity of different ways.
In answer to the question, “What is a gene ?,’’ a contemporary scientific metaphysician adopting the traditional approach might answer that a gene is any segment of nucleotides that satisfies the analysis presented in this section. After all (trusting this analysis), this is what the best scientific theorizing of today employs as its gene concept.
-  Paul Teller comments that chemistry employs different concepts of the atom in a similar way. Some conceptsare useful in certain contexts because they are blunt. Other concepts are useful in other contexts because theyare precise. Although what I say here is directly about genetics and allied sciences, I believe it applies to sciencesmore generally.