Analysis of adaptive evolution at the amino acid level!

EDIT: Fixed multiple errors about 10 minutes after posting -- I misplaced my espresso....

Okay -- I admit it -- this sounds really boring. And, yes, it's on Drosophila... and it's full of maths and Greek letters and things that it assumes the reader knows what they are and what they mean... 

...what was I doing before I fell asleep...? oh yeah! This new bioRXiV thing! 

Maybe I'm tired of reading pure mass spec papers cause of this grant thing we've got to do this week that I worked on all weekend -- or maybe it always seems like all the evolutionary stuff is done at the nucleotide level, which seems lazy and somewhat naive. 

Natural selection acts on phenotypes. And phenotypes are controlled at the protein level. Sure, genetic info is where everything is passed along, but if the genetic changes don't change an amino acid, then unless there is a stop codon or something like a silencing event -- there is no change in phenotype and therefore no selective advantage is acquired. Seems like you could get a much more accurate measurement of evolutionary pressure by focusing on the protein sequences. These authors point out that people have been doing amino acid evolution stuff since the 70s and point out a big study from last year, so people do realize it. I bet it's 1 out of 100, though, and it's always good to see another contribution!  

What size steps, though?