0 comment Tuesday, June 24, 2014 | admin
Just got the galleys back on my review paper...very few real edits because I am a kick-ass proof-reader. But strangely, tons of gene/protein nomenclature changes. Some of them were WTF?!? There is a standard accepted nomenclature for my model organism (OK, who am I kidding? For the mouse). It is published online and updated regularly, and specifically referred to by the publishers in the submission guideline. Some of the protein abbreviations that the editorial assistant is suggesting make no sense. They are not even accepted synonyms for the protein in question.Weirder still is that they wanted all the protein symbols (even the mouse ones) in ALL CAPS. Conventionally, human genes and proteins are denoted like this: GENE and PROT...all caps all the time. Italics indicate a gene or transcript, non-italics are the protein product. Mouse genes and proteins are denoted Gene and Prot...the first letter only is capitalized (with rare exception), otherwise the same italicizing rules as humans. Or so I was taught, very explicitly, in my first year of grad school - I even have the table from my notes summarizing all these rules photocopied and hanging by my desk so I can refer to it as I write. Apparently, someone decided that mouse and human nomenclature should be identical in recent years. When I yelped about this as I looked through the galleys for the text of my article, the two other grad students at neighboring desks said that they found the same to be true when they submitted their first papers...and they also had a hard time accepting this.It makes so much more sense to have distinct notation for mice and humans. Primarily because mouse and human genes and their products tend to be remarkably similar (in general)...but there are enough that are divergent in sequence or in function, that it is worth not introducing a mechanism for confusing the two of them. With the previous (better, in case my position on the matter isn't clear by now) nomenclature system, it is easy to distinguish in any given paper which species the authors are deriving their loci and molecules from...without having to add extra letter to an already alphabet soup. Instead of hGENE and mPROT you could just say GENE and Prot and everyone would know that you were talking about a human gene sequence and a mouse protein product. You wouldn't have to write into sentences reviewing previous work that "this study was conducted in mice" or "the gene sequence from human tumor X". The notation speaks for itself. Or at least it used to.I think it's strange that it changed sometime in the last 4 years (since my class in the 1st year of grad school when it all made sense) and I had no idea. Since not all journals are particularly fussy about this you will see various publications that follow the rules and others that don't. I think it's strange that the official nomenclature website for the mouse makes no note of this change --presumably there are many more senior scientists who are much more entrenched in the previous system than I and they probably still need reminders about this. Was I taught to do it wrong 4 years ago? It's conceivable that the professor who taught us this wasn't up to date on the mouse nomenclature (she worked in C. elegans). Why didn't GrAdvisor catch all this in his proofreading? He's really anal about getting the italics right to accurately reflect whether you're talking about a gene or transcript rather than a protein, so I'm surprised that he didn't get fussy about capitalization if he knew that mouse and human nomenclature is now noted in precisely the same way.I've now been in grad school long enough to witness (er...be ignorant of) a fairly major systematic change in a standing convention of my field. I can now say things like "I remember back in the day when... mouse genes were noted differently than human genes."This makes me feel...old. Particularly since I am still a student.Blergh.Oh well, off to look over my manuscript (again!) with a magnifying glass and a fine-tooth typographic comb. Joy.
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