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But let us now consider something that is even more interesting. Notice the two R groups, R1 and R2. These represent the side chains of each respective amino acid that we briefly discussed in the previous essay. What you should notice is that side chains do not participate in the linking of amino acids. On the contrary, they simply stick out as appendages on the backbone chain of amino and carboxyl groups. And because they do not participate in this linkage, it means that the sequence of side chains is not chemically determined by the process of polymerization. In essence, it is programmable.
But notice also the way the nitrogenous bases mimic the R groups of amino acids: they do not participate in the formation of the sugar-phosphate bond. On the contrary, they simply stick out as appendages on the sugar-phosphate backbone. And because they do not participate in this linkage, it means that the sequence of nitrogenous bases is not chemically determined by the process of polymerization. In essence, it is programmable.
Thus, what we have is a profound conceptual similarity between two unrelated molecules. It is this similarity in basic format that will allow the nucleic acids to encode the amino acid sequence of a protein.
Very interesting, Mike. This helps me understand why a designer would choose amino acids and nucleotides. If I were investigating this the way Eschenmoser does, I would want to try different amino acids and different nucleotides, to see if they would be better or worse design materials. And I would also wonder if there were other materials that would work better than amino acids or nucleotides.
Yes, I think you are on to something. The side chains and nitrogenous bases both function as appendages (I will begin exploring their role in the play in the next installment). So why these sets? There are two teleological frameworks that come to mind: 1.) The hypothesis you are thinking about "“ optimal function; 2) They act as channels toward to particular future (this is what I lean toward).