In my previous essay about proteins-as-design-material, I noted:

This all raises some interesting questions. For example, without proteins, and their manufacturing process, what becomes of the blind watchmaker? Without proteins, and the latent functions contained within, might not the blind watchmaker exist as the impotent, crippled, blind watchmaker with no one to notice its existence? If so, how much credit does the blind watchmaker really deserve?

The vast and immense Tree of Life is a protein-dependent output. Point to
some evidence of evolution and I’ll point to the proteins that underlie it.
Without proteins, would there be a Tree of Life 3.5 billion years after the
RNA world took root? How do we know? If we believe so, would the Tree be
as immense and vast as it is today? A life form composed of nucleic acids,
carbohydrates, and lipids would suffice for the purposes of the blind
watchmaker. But could the blind watchmaker turn this material into
something that is analogous to an Ash tree filled with squirrels, beetles,
and birds?

Look at it this way. What do we need for the blind watchmaker to exist? A
finite, changing world, something that replicates, and imperfect
replication. The first and the third are givens due to the nature of
creation. The second is more iffy. In living cells, proteins play the key
role in replicating things (they replicate the DNA, they divide the cell,
and coordinate both). But if we entertain the notion of an RNA world, the
proteins are not needed for replication (then again, proteins are not needed
for chemical reactions to take place). But what the proteins do is amplify
and enhance this replication property, and thus enhance the blind
watchmakers’ abilities. What’s more, the same molecule that enhances
replication also opens up a whole vast world of phenotypes not available to
the blind watchmaker earlier. You can almost think of proteins are a form
of tech material designed to exploit and prop up the blind watchmaker. And
maybe even give the blind watchmaker a little guidance.