# Alphabet Anchoring

A global one-to-one renaming of the amino-acid alphabet leaves alignment-level statistics, column entropies and pairwise edit distances unchanged, yet contact maps from ESM-2, MSA Transformer and AMPLIFY collapse, while an inverse-covariance Potts model stays bit-identical. Across nine proteins and three seeds, ESM-2 650M keeps an overlap of only 0.015 with its own original contact set after random relabeling of all twenty residues, versus 0.655 when relabeling stays inside BLOSUM62 similarity groups. The contact readout therefore depends on canonical residue identity and cannot be cited as proof that these models have internalized coevolutionary statistics.

A global one-to-one renaming of the amino-acid alphabet leaves alignment-level statistics, column entropies and pairwise edit distances unchanged, yet contact maps from ESM-2, MSA Transformer and AMPLIFY collapse, while an inverse-covariance Potts model stays bit-identical. Across nine proteins and three seeds, ESM-2 650M keeps an overlap of only 0.015 with its own original contact set after random relabeling of all twenty residues, versus 0.655 when relabeling stays inside BLOSUM62 similarity groups. The contact readout therefore depends on canonical residue identity and cannot be cited as proof that these models have internalized coevolutionary statistics.