DNA to represent proteins

Recently I have read Bas C van Fraassen Scientific Representation: Paradoxes of Perspective where a representation is defined as

 p. 21 “Z uses X to depict Y as F

Does it make sense to say “Z uses” when Z is not a human being? For example, what is a meaning of a sentence “a robot uses X to depict Y as F“?

Below I will present some sense for the statement that a DNA is a representation of proteins. I will go along arguments of Marcello Barbieri expressed in

Barbieri, M. (2007). Is the cell a semiotic system? In: Introduction to Biosemiotics: The New Biological Synthesis. Eds.: M. Barbieri, Springer: 179-208.

Well, if a cell could be considered as a semiotic system then it should be also possible to find a representation of a protein in the DNA. First it is worthy to be mentioned that according to Barbieri

“Genes and proteins, in short, are assembled by molecular robots on the basis of outside instructions. They are manufactured molecules, as different from ordinary molecules as artificial objects are from natural ones. Indeed, if we accept the commonsense view that molecules are natural when their structure is determined from within, and artificial when it is determined from without, then genes and proteins can truly be referred to as artificial molecules, as artifacts made by molecular machines. This in turn implies that all biological objects are artifacts, and we arrive at the general conclusion that life is artifact-making.”

This means that in principle the result should concern robots as well. In our case, it is easy to identify X, Y, and F in the definition of a representation:

Z uses a gene in DNA to depict a protein as a primary sequence“.

What is left is to find out a meaning of “Z uses” in respect to a biological cell. This could be, according to Barbieri, a codemaker:

“Protein synthesis arose therefore from the integration of two different processes, and the final machine was a code-and-template-dependent-peptide-maker, or, more simply, a codemaker. The second Major Transition of the history of life (Maynard Smith and Szathmáry, 1995) is generally described as the origin of proteins, but it would be more accurate to say that it was the origin of codemaking, or the origin of codemakers, the first molecular machines that discovered molecular coding and started populating the Earth with codified proteins.”

“It is an experimental fact, at any rate, that every cell contains a system of RNAs and ribonucleoproteins that makes proteins according to the rules of a code, and that can be described therefore as a “code-and-template-dependent-protein-maker”, i.e. as a “codemaker”. That is the third party that makes of every living cell a trinity of genotype, phenotype and ribotype. The genotype is the seat of heredity, the phenotype is the seat of metabolism and the ribotype is the seat of the genetic code, the codemaker of the cell.”

In my understanding, a codemaker then is a collection of molecules (a molecular machine) that produces a protein from a DNA. Now similar to the logic in Barbieri’s paper one can write

“A codemaker uses a gene in DNA to depict a protein as a primary sequence”.

The sentence is complete now. For me however the question remains if such a sentence has a meaning. Let me quote Barbieri again:

‘The sequence of a gene and the sequence of a protein, in conclusion, may look like “objective” properties of these molecules, but they are not. They are “codemaker-dependent” entities because they do not exist without a codemaking process, and because they would be different if the codemaker had a different conformation. The sequences of genes and proteins, in short, have the essential characteristics that define signs and meanings, and we can say therefore that they “are” organic signs and organic meanings.

More precisely, we can say that “an organic sign is the sequence used by a codemaker in a coding process”, and that “an organic meaning is the sequence produced by a codemaker in a coding process”. All we need to keep in mind is that signs and meanings are mental entities when the codemaker is the mind, but they are organic entities when the codemaker is made of organic molecules.’

It well might be that we can employ “depict” in such a sense but in my view not without remaining strain.