Cognitive Metaphor Theory (CMT) provides at least two methods that can enable us to systematize what is literal, what is metonymic and what is metaphorical (and how) in biosemiotics in general, and especially in connection with the genetic code. These rigorous and systematic methods can help us avoid the distortions and misunderstandings that ensue from taking metaphors literally or literal statements metaphorically.
The first method is the MIPVU (Metaphor Identification Procedure VU University Amsterdam), "based on extensive methodological and empirical corpus-linguistic research" with good inter-coder reliability (Steen et al. 2010). The second approach involves Dunn's (2015) methods of 'measuring' degrees of abstractness and metaphoricity; these could help in determining the basic meaning of "code", "information", "language", "alphabet", "letters" etc. from abstract and metaphorical contextual meanings with the fact-status and function-status decision trees.
The CMT (as the theoretical basis) would inter alia provide a clearer distinction between metaphor and metonymy. The argument is as follows: 1. if we accept Barbieri's definition of "code", viz. "A code is a set of rules that create a correspondence between two independent worlds." (Barbieri et al. 2012), and 2.
If we accept that "The genetic code is a correspondence between triplets of nucleotides, called codons, and amino acids. What is essential in all codes is that the coding rules are not dictated by the laws of physics.
They are arbitrary in the sense that they are independent from physical necessity and this implies that they can be established only by natural or by cultural conventions." (Barbieri et al. 2012; cf. Barbieri 2008, Markoš 2014); then it follows that the genetic code really is a literal code (or s-code, Eco 1976), "more than a metaphor" (Abel and Trevors 2006).