TBH I think some of the language we use in publications is absurd; but, I have been guilty of it.
I disagree, sometimes gene names can be a little over the top, but protein names tend to be pretty accurate (Kinase target, structure isomerase, etc) and in general a lot of the language makes sense in the context of the history of the research. Given the precedent already set by past research, I'd say that returning to a flat numbering scheme would be counter-productive and just complicate discussion over them. It's at least easier to add a note when talking about a protein if it's function differs from its name.
Oftentimes researchers come up with pretty new methods / patterns that require new / descriptive names. Yeah, it means you have to spend time learning the language if you want to be able to understand, but wuzzy language hurts communication, and domain-specific vocabulary are pretty common among most research fields (Try reading a math publication with only a bio background).
There is something to say about language duplicated from more general fields (Re-inventing math terms in biology / chem / etc), but that's easy to criticize, but hard to fix, given that scientists will often hide their newest projects from others, preventing them from gaining the comments from more knowledgeable peers on what to call it. Then you just have peer-reviewers as the safety net, and things fall past them all the time.
I work with miRNA a lot, and one thing I love about miRNA, is that they each are just given a number. It's so liberating and much more honest IMO.
How common is it to have defined functions (Catalysis, binding certain chemistries, etc) when it comes to miRNA?
Thanks for the post, BTW.
Oh, no, thank you all for the discussion, I love getting to talk with others about hardcore science :D