Posted on behalf of Sugar Daddy

Sorry for my extended absence. I was reading some old posts in the Skeptical Chymist for inspiration for today’s post, and I found one by Catherine that encourages us to name more chemical reactions after people. In the post, she further asks whether we would prefer to have a reaction or a football stadium bear our name. I’d like to take that one step further.

If I discovered a new reaction, I would like to sell the naming rights to a corporation. There are many benefits – good press for the company for supporting basic scientific research, excellent promotion for the inventors of the reaction, and of course, most importantly, a much-needed income supplement for the graduate student inventor so he/she can put food on his/her table. There are some good candidate reaction/company partners already available:

The Henry reaction (“O’Hungry?”)

The Suzuki coupling (“Driving aryl-aryl bond formation since 1979”)

The McMurry coupling (“Would you like a side of TiCl4 with that?”),

The Huisgen [3+2] cycloaddition (“Buy the LEGO “click” kit today!”),

And, of course, the Corey-Bakshi-Shibata reduction (“America’s most-watched enantioselective reduction of ketones to secondary alcohols” – I think that slogan might have to be improved, but it can’t hurt too much – they are already trailing NBC and ABC quite badly in the 6 o’clock news ratings anyway.)

Any further suggestions?

Posted by Catherine Goodman at 09:12 AM | Permalink | Comments (2) | TrackBacks (0)

Posted on behalf of Sugar Daddy

Sometimes there are those days in grad school when I feel like I have a zillion different things to do. I’ll have multiple experiments going, timers on my belt beeping, and I’m running around lab (uh, I mean walking, of course) like one of those lottery balls inside the big spinning containers that used to come on the TV right after Mad About You and before the news, at like 5:58 pm. At the end of those days, my brain and legs are both so thoroughly exhausted from overuse that it’s hard to stay awake until 10 pm, let alone muster up enough energy to cook dinner.

Today, however, is not one of those days.

I’m sitting at the HPLC, waiting for my peak to come off. I’m aware that I could use a fraction collector, but I just don’t trust them enough given how precious this compound is. And plus, it’s kind of a nice excuse to be “doing work” but also be surfing the web at the same time. So I sit, staring at a growing trace. It’s baseline for a long time, and then a spike. Is it what I want? Is it real? Who knows, I guess I’ll figure out later. And then it’s back to baseline. It kind of looks like an EKG, but of quite an arrhythmic patient. Boy, I wouldn’t want to have that guy’s heart. Or maybe, it is a metaphor for grad school. Baseline, baseline, and then, eventually, usually when you’re not looking, a peak comes. Is it desirable? Often, but not always. And then back to baseline.

I guess the metaphor only goes so far, because the HPLC run will definitely be finished by a certain, pre-determined time, whereas, well, grad school? Who knows… Ah, another peak. Why does this reaction have so many peaks? My advisor likes to joke that a reaction that gives you 15 different spots isn’t so much a failure as it is combinatorial chemistry. But more on that later...

Posted by Catherine Goodman at 12:00 PM | Permalink | Comments (0) | TrackBacks (0)

Posted on behalf of Sugar Daddy

The qualifying exam.

If there is ever a moment in graduate school that usually receives about 100 times more preparation and 100,000 times more anxiety than necessary, it is the qualifying exam. For those of you who are not in grad school (or those that have been through it and somehow, shockingly, blocked the thing from your memory), here’s a primer. Of course, it depends on the school, but the basic scenario is that as a second- or third-year student, you have to stand up in front of three or four professors and defend your research. Or so you think. It actually, I think, usually goes something more like this:

Student: “I’ve been interested in studying the mechanistic details of how [some enzyme that is inexplicably fascinating to you, your advisor, and maybe four other people on the face of the earth] is involved in the biosynthesis of [some natural product that sounds like a really nasty infection and always looks misspelled]. The locus for the gene was identified in--”

Professor 1: “Draw the structure of cytosine.”

Student: [Starts to draw structure of cytosine correctly]

Professor 2: [Interrupting] “Which is higher, the intracellular or extracellular concentrations of potassium in the central nervous system?”

Student: [Begins to answer, but stumbles]

Professor 2: “Why don’t you draw a neuron. What is the action potential? How do ion channels function in its propagation? What different types of ion channels exist? Which ions are the principal players, and what are their functions? What structural information exists on ion channels and what is the functional significance of the structural studies? What are the major classes of ion channel-blocking compounds? What are their relative affinities for different classes of ion channels?”

Student: “The action potential is--”

Professor 3: “Draw the mechanism for the Horner-Wadsworth-Emmons reaction.”

And so it goes… I guess what I can say is that you don’t really know what the professors will ask, and they will probably form an opinion of your ability in the first five minutes (if they hadn’t already by reading or hearing what your advisor had to say about you prior to your exam). So much for a blind audition…

Today, we will conclude with a haiku, in the poetic style that seems to be all the rage on the Sceptical Chymist:

Study as you wish
but predict the questions you
won’t. Good luck, sucker!

Posted by Catherine Goodman at 01:59 PM | Permalink | Comments (2) | TrackBacks (0)

[Editor's note: another guest blogger has joined our team...]

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Posted on behalf of Sugar Daddy:

I guess Sugar Daddy is a somewhat ironic nickname, as I am a graduate student, and my friends make anywhere from 2- to 5-fold more money than I do in the so-called “real world,” which I hope (for their sake) is nothing like the MTV reality TV show of the same name. But I do work with carbohydrates, so maybe we should just roll with it.

Anyway, I am in my fourth year of a PhD program working in a chemical biology lab. My research involves the proverbial “little bit of synthesis, little bit of biology,” and things have been going well. I guess you could say I’m living the chemical biology dream: synthesize a molecule, show that it has biological activity in cells, and then take it all the way to a living organism.

This week, I’ve been simultaneously thinking about the past and the future. It is recruiting season in our department, and therefore many wide-eyed first-year students are showing up asking to be told about the research projects in my lab. As I describe my work, which I can more or less do on autopilot, I start to reminisce about what it was like to be a first-year student - how random all the decisions I made then seem in hindsight. Did I choose my school because I “had a better gut feeling” about it? No, I tell myself, it was because I liked the students and professors I had met, and of course the research interested me the most as compared to other schools. And why did I pick this lab? Did I pick my project or was I gently nudged toward it? No complaints, but how much did I really know about what I was getting myself into at any stage of the game? Was I delusional, thinking that I had complete control over my scientific destiny, at least on the five-year timescale? As the saying goes, a little knowledge is a dangerous thing.

And speaking of “as sayings go,” the whole autopilot experience (of describing my project without really having to think too hard about what to say) reminds me of a moment in high school (where we really were naïve, that’s for sure), and specifically in English class. My teacher had us read “Politics and the English Language,” a 1946 essay by George Orwell about how the English language had deteriorated to the point that people merely strung together short familiar fragments rather than construct novel phrases and ideas. I think this essay should be required reading for every scientist, or at least those that will ever have to write a paper, book, or grant proposal. Okay, for the next first-year that shows up, I’m going to describe my project in a completely novel, illuminating way. Ugh, that certainly feels like it’ll be an endothermic process.

So, that was the thinking about the past. How about the future? A post-doc is on the horizon. (There, by the way, is Orwell’s thesis in action.) More on that next time. With all this thought about the past and the future, I suppose that doesn’t leave much time for the present. Guess I’ll wait until tomorrow to HPLC that compound…

Posted by Catherine Goodman at 03:40 PM | Permalink | Comments (0) | TrackBacks (0)