Mutations

I came across the following argument today.

1. Harmful mutations are usually eliminated.
2. Beneficial mutations are preserved.
3. Beneficial mutations quickly accumulate.

It is a fairly common one with many variations in wording. Mutations fatal to an organism tend to be eliminated for obvious reasons. Those that are slightly deleterious can accumulate. A beneficial mutation might be preserved but the larger question is would it become predominant throughout a population. The third point is poorly defined. How quick is quickly?

I wish to focus more on #2. The issue being not so much whether a beneficial mutation would be preserved but rather what would an actual pathway to an accumulation of such mutations look like?

Let's look at a specific system. Histone acetylation and deacetylation is associated with nucleosomes and gene regulation. A specific example of transcription inhibition occurs when histones are deacetylated by a complex of proteins known as N-CoR, Sin3 and RPD3.

What value does the above argument have in explaining how the proteins, involved in the above mentioned deacetylation function, came about? How did it occur sequentially? What value do the distinct proteins have when considered apart from the deacetylation protein complex? Anyone with sufficient imagination and a knowledge of homologous proteins can construct an explanatory story. Would it be testable though?

Proteins interact with other proteins. Protein complexes associated with specific functions are common. Changes occasioned by beneficial mutations rarely refer to such complexes when used in an educational context or a debating context for that matter.