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7/29/2019

What’s in a name?

Well, I decided to post a bit of a rant. I’m 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.

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 protein. 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.

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.

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 always wondering around carrying a giant pointy stick.

8/29/2018

Welcome new grads!

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We welcomed new grad students to Pitt last week, including our own Umbrella program. Guys – if you want to learn how to make spectacular images like this one – or dissect the intricacies of cell signaling pathways in living cells, in real time – reach out to Gerry. We do lots of state-of-the-art gene editing, chemo- and opto-genetics – we can give give you a crash course during a rotation!

We are recruiting…

 

3/2/2017

Celebration day…

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The lab celebrated our first lead-author paper with a swanky dinner and the kind of drinks that come with one giant ice cube. Well done guys! Many more to come.

 

2/20/2018

Publish or perish…

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We just got our first lead-author paper published in eLife! Check out the synopsis of the work on our website here, or else read the full article for free at 10.7554/elife.35588.

 

 

 

 

12/6/2017 – ASCB

Philly!

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Jonathan, Gerry, Rachel, Brady and James drove down to Philly for the 2017 ASCB/EMBO meeting. We had some pretty decent crowds at our posters and met loads of our colleagues from around the world. We also met up with Gerry’s old lab – which was great until Rachel asked them to share stories… and they were eager to comply!

 

7/5/2017 – Freezer defrosting

A (sadly departed) lab mascot

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Defrosting the lab freezer today, and we found a new addition living amongst the accumulated frost:

Meet Mr. Frosphoinositide!

 

 

 

1/5/2017

Happy New Year!

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“Lab meeting”

We managed to squeeze in one last group meeting before the holidays. Pressing topics included the merits of Rogue One over The Force Awakens and the nuanced rules and origins of fencing as a sport. We decided that regular discussion meetings would continue to be the forum for discussing experimental results and their various interpretations in 2017, as opposed to the alternative of trial by sword (sorry you got out-voted, James). We will re-appraise next year. Happy New Year, everyone!