"The genetic code is a real code" is this debate over yet?

[Dan_Eastwood]

Hi Jon!
I might need to review that last discussion, but my position on this is that genetics are chemistry; nothing about it requires it to be a code. Humans need codes to assign meaning to message, so when we look at a strand of codons and call it a code we are assigning a meaning - and our usage makes it a code.
Shorter: It is not a code in itself, but our description of it is.

Earlier this year @sfmatheson posted an article about a new discovery regarding the order in which amino acids were recruited to the genetic code …

Order of amino acid recruitment into the genetic code resolved by LUCA's protein domains

Very interesting new paper from the Masel lab at the University of Arizona*. Below are some excerpts that I found important. From the Intro: Previous analyses focused on the age of orthologous gene families (20–22); ours infers which protein domains date back to LUCA. Protein domains are the basic units of proteins, that can fold, function, and evolve independently (23). Proteins often contain multiple protein domains, each of which might have a different age (Fig. 1). For the purpose of inferring ancient amino acid usage, what matters is the age of the protein domain, not that of the whole protein that it is part of. Beginning of the Discussion: The evolution of the current genetic code proceeded via stepwise incorporation of amino acids, driven in part by changes in early life’s environment and requirements. Contemporary proteins retain information about which amino acids were part of the code at the time of their birth, allowing us to infer the order of recruitment on the bas…

In short, this is evidence that genetic encoding has evolved. Information is being encoded in new ways that were not an original properties of the coding. That is not something that is allowed in any human defined coding scheme, where a sender and receiver must have prior agreement on the encoding to be used. It’s hard to clearly define the notion of what “sender and receiver” means in this context, much less to how they might “agree” to change the encoding.