Actually the 2nd law of thermodynamics could apply quite readily here because this is a system going to cosmos instead of chaos. It was a simple comparison and a thought experiment.
To explain your second part, you have to rememeber they come in pairs for replication purposes. 3 and 5 alphabet would not pair. Furthermore, 4^2 is only 16 amino acids, so it had to be 4^3. A base-6 system would also have duplicates.
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