In a chapter of a book Mark White is currently writing, he addresses his thoughts on the principles of his work in trying to shake up longstanding practices in teaching the genetic code.

Atonement is an old word, but it carries a simple meaning. It
means becoming one again.

The word itself is a contraction of at and one. It describes the restoration of alignment where alignment has been broken. In that sense, atonement is not
punishment. It is not humiliation. It is not revenge. It is
correction. It is the repair of a relationship that has drifted
away from truth. That is the right word for what science now
needs with respect to the codon table.

Science has made a metaphysical choice to represent the code
of all life using a flat codon table. In doing so, it has chosen
to ignore the round codon table. That choice is not aligned
with reality, and it is no longer aligned with science itself.
Science does not need to become perfectly one with reality.
No human system can promise that. Every scientific model is
partial. Every representation preserves some properties and
omits others. Every theory remains open to revision. That is
not a failure of science. That is the nature of science. But
science does need to remain aligned with itself.

Science says hypotheses must be tested. Science says failed
hypotheses must be revised or rejected. Science says
correlation is not causation. Science says the map is not the
terrain. Science says predictions matter. Science says better
representations should replace weaker ones when the stronger
representation preserves more of the thing being represented.

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Those are not decorative slogans. They are the operating code
of science. The flat codon table violates that code when it is
treated as the code of life itself.
A flat codon table is useful. It links codons to amino acids. It
works as a lookup tool. It preserves real information. None
of that is in dispute. The problem begins when this useful
index becomes confused with the thing it claims to represent.
A lookup table is not a code. A map is not terrain. A partial
representation is not the structure itself.

The code of life requires more than lookup. It requires linked
properties. It requires adjacency, grouping, symmetry,
compression, constraint, and recursive structure. A flat table
does not preserve those properties. A round table preserves
more of them. That does not require science to accept every
conclusion immediately. But it does require science to
recognize that the representational question is real.

Atonement begins there.

The first step is simple. Science must admit that the flat
codon table is a representation, not the code itself.
The second step is equally simple. Science must ask what
properties the code actually requires.
The third step follows naturally. Science must compare
representations by the properties they preserve.
The fourth step is unavoidable. If a round representation
preserves relevant properties that a flat representation omits,
then the round representation deserves serious examination.
The fifth step is the hard one. Science must stop protecting
inherited representations merely because they are inherited.

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That is atonement. Not surrender. Not conversion. Not
obedience. Just science becoming one with science again.
This matters because the flat codon table did more than
simplify biology. It shaped the story biology told about itself.
It encouraged sequence-first thinking. It made history look
linear. It made structure look secondary. It made the code
appear flatter than it is. Once that representation became
familiar, it became invisible. Once invisible, it became
protected. That is how paradigms harden.
Atonement requires making the hidden choice visible again.
Flat or round. Index or recursive index. Lookup or code.
Sequence first or structure first. Once the choice becomes
visible, science can return to its own method. It can test. It
can compare. It can predict. It can correct. It can become
one with itself again. That is all atonement asks.
And that is enough. ~ Mark White