Well, I decided to post a bit of a rant. I was recently writing a literature review, and I just know that the editors are going to want me to define all of the acronyms that form the basis of most gene names I’m discussing. In particular, I’m struggling with ORPs – i.e. OSBP-Related Proteins.
OS-what now? Oxysterol Binding Protein-Related Proteins. Got it? Oxysterol-Binding Protein-Related Proteins (Is that right? I literally just had to look it up. Yes. Its right). Okey, say it three times really quickly. Is that how we say it? Well, not really. You could just call them by their letters: O. R. P. Flows off the tongue a little easier, doesn’t it? Or how about doing what all of us professional biologists do – pronounce it like a word. ORP is “orp” in my head. I know about orps. I’m writing a review about them.
I’ll give you another example from this field. A protein called STIM1. STIM1 is a protein that stimulates calcium entry into cells. Good name, right? Want to know what STIM1 stands for? Well I’m going to tell you anyway. Stromal interacting molecule 1. Why 1? Because they found a 2 as well, and named them in order (instead of Diplodocus and Tyrannosaurus, think dinosaur 1 and dinosaur 2). Why did the authors name them “stromal interacting molecules?” Because they cloned them from tumors (and stroma is the non-cancery bit of tumors). What does this have to do with calcium entry? Nothing. The name just comes from where the protein was found. Not what it does. Instead of Diplodocus, think Colorado dinosaur 1.
What bugs me is that as soon as we’re derive these acronyms in writing, we’re generating exceptionally long and hard to read sentences. And its not like our literature is exactly easy reading to begin with. “But,” says the copy editor, “it helps the reader understand what the proteins are.” Does it? I’m already introducing ORPs as lipid transfer proteins. Do you really need to know that they where discovered as proteins related to an oxysterol binding protein? That we now think transports sterols by the way – not simply binds oxysterols – though not everyone agrees so lets not get into that.
To the credit of the discovers of STIM1, they came up with a catchy name that fits our contemporary understanding; its not wrong or misleading. This is not always the case; some genes are discovered and named for functions that turn out to be plain wrong. And then we’re stuck with them. I could list several examples from our own field of inositol lipid signaling – but I won’t, since some folks who did that might read this, and those guys review my grants and papers. And they’re all fabulous, intelligent scientists 😉
Scientists name genes based on all sorts of basis; how a mutant fly looks (Hedgehog), the context of discovery (STIM1), the biochemical activity (PI 4-kinase). These might prove correct and reproducible over time, but often they don’t… yet the name endures. They can and usually do become completely arbitrary.
So, I’m meandering to a point here. Most of our acronyms have a wordy-look and sound that we use, and like any other word in any language, they make sense when you understand what they are, and you use them in context. So let’s just stick with those names, please. The provenance of the acronym is usually arcane at best, and darn right misleading more often than you might think.
Let me put it another way. If I meet you at a conference, I’ll stick my hand out and say “Hi, I’m Gerry”. That’s fine isn’t it? I doubt you’ll find it helpful if I introduce myself with “Hi, I’m Gerry. Short for Gerald, a germanic masculine name meaning ‘ruler of the spear’”. Plus you’ll be wondering why I’m not carrying a giant pointy stick. – GH.