system
Given the following post, respond as if you're commenting on Reddit:
human
Where are the codons defined?

DNA and RNA are typically "read" in groups of 3 that we call codons. Each of those combinations of bases codes for a specific (but not necessarily unique) protein or other "instruction", like start and stop. The entire collection of codons in a genome, in their particular order, "defines" an organism, so to speak. 

But where are the codons themselves defined? What determines which groups of 3 bases results in which amino acids? Is it included in the genome itself, like a compiler written in its own programming language? Or is it entirely reliant on the cellular machinery already existing from the parent with the codons pre-determined? I know there are some examples of different codons between different species but also that it's mostly the same among all life; has it really just been passed down through the unbroken chain of reproduction without ever being encoded?
gpt
Your description is a little confused. DNA is not read in triplets, rather pieces of DNA are transcribed into RNA (there are sites that promote the transcription). The RNA in eukaryotes is then spliced to form a messenger RNA. If a given mRNA encodes a protein, a ribosome will bind to it and find a start codon. It will recruit tRNAs that have an anti-codon matching the codon, and link amino acids (not proteins) carried by the tRNA to form an amino acid polymer (protein).

These are not instructions, but physical objects. Some proteins are predominantly structural, some are organic catalysts, some bind other things with various effects.

Much more than just the primary sequence of proteins (formed by translation of codons) “defines” an organism.

Which amino amino acid maps to which codon is defined by enzymes called tRNA synthetases and the tRNAs themselves, which are indeed encoded in the organism’s genome. There are 31 known variations on the mapping of codons and their amino acids, though plants and animals use a common translation (the variations are in fungi, archaebacteria, and mitochondria).