Posted on behalf of Sugar Daddy

With the changing of the guard in Washington, late-night night television hasn't quite been the same. I guess the new guy in charge is a harder target for comics. Anyway, to a certain extent, the late-night hosts have been turning their attention elsewhere, and eventually chemistry was bound to make it. In this clip, Conan O'Brien draws attention to, among other things, the discovery of a fourth form of pure elemental boron.

The humor in the clip originates from a recent New York Times article that had mistakenly counted the number of pure forms of boron, and Conan was mocking them for not being able to correctly count to four. The surprise for me was that Conan whipped out a big poster board with crystal structures of the various forms of boron and then started to describe them in rather gory scientific detail. I don't think this will help the public understand chemistry any better, but it's better than nothing, I guess. Plus, he's funny.

Posted by Catherine Goodman at 02:35 PM | Permalink | Comments (1) | TrackBacks (0)

Posted on behalf of Sugar Daddy, with a nod to Andy's recent post

As a fifth-year chemical biology graduate student, I sometimes wonder if I'll know when I've been in grad school too long. Maybe I'll want to finish that last project, or start something anew to pass along to a new student. Maybe a personal life decision is playing a factor in my wanting to leave now or stay longer. Maybe I look around at group meeting and realize that free pizza once per week isn't as great as it used to be, partially because I know what everyone in the group is working on and am slightly less interested in it than I used to be. Maybe I read every paper in my field with such a critical eye that it all seems boring now when it was so exciting only a few years ago.

But sometimes you need something more direct, like a kick in the face, a surefire sign that it's time to pack up the pipets, file away the round bottom flasks, and start looking for greener pastures in some other field of science. Last week, I think I got that sign: VWR and Fisher simultaneously told me that the world is out of acetonitrile. Yup, that's right. If I ever need a sign to graduate, it's that the world has run out of one of the two solvents that I use on the HPLC. (Given that the other solvent is water, I guess if I had to pick which one I'd rather run dry... I guess the situation could be worse.)

The story there is somewhat interesting. I'll write what I've heard, and please write any comments if what I'm saying is rubbish or not. Basically, the most economically viable way -- and currently the only way -- that acetonitrile is produced is as by-product of acrylonitrile production. Acrylonitrile is a monomer that finds its way into nylon, acrylic, plastics, and all sorts of products; it is a much more important product in the global marketplace than pitiful little acetonitrile, the by-product of acrylonitrile production.

So, acetonitrile supplies are tied to the laws of supply and demand in the acrylonitrile market. Given the global economic situation, building construction projects and the general production of goods -- that is, things that rely on products made ultimately from acrylonitrile -- are all way down. Therefore, demand for acrylonitrile is down; the price of acrylonitrile has plummeted in the last few months, and production is drying up. Unfortunately for us chemists, the demand for acetonitrile, the bastard step-child of acrylonitrile production, has remained relatively constant, because HPLCs still need to run even if Lehman Brothers has closed up shop and GM isn't far behind.

Wikipedia claims that the situation was caused by a shutdown of acrylonitrile production in China last summer because of the Olympics and damage to a plant in Galveston, Texas due to Hurricane Ike, but as I understand it, these are medium-sized blips that are only exacerbating a larger market situation.

Acetonitrile shortages have happened before and will happen again. Like the famously flamboyant former Canadian prime minister, Pierre Trudeau, once said about Canada's proximity to and geopolitical entanglement with the United States, "Living next to you is in some ways like sleeping with an elephant. No matter how friendly and even-tempered is the beast, if I can call it that, one is affected by every twitch and grunt."

So, basically, we're not in a very good place until someone can figure out how to make acetonitrile independent of acrylonitrile production in a way that is economically viable. Then we can finally kick the elephant out of our bed, allow the acetonitrile market to be regulated by its very own market forces, and maybe keep me from interviewing for postdocs and writing up my thesis.

Hmm... perhaps a good puzzle for a lazy Thanksgiving afternoon? Thanks for the idea, SD! Catherine

Posted by Catherine Goodman at 03:43 PM | Permalink | Comments (0) | TrackBacks (0)

Posted on behalf of Sugar Daddy

There seems to be this mindset among scientists, particularly chemists, that what we do is noble and somehow above the fray. Perhaps it comes from our training as graduate students. We live lives often completely removed from the world around us. We have friends who go home at 5 pm, cook dinner every night, watch TV programs, write books, do crossword puzzles, or other "normal" things. These people don't "take" the whole weekend off; it is naturally given to them, an unalienable right of living in the "real world". We are in a research lab and when we leave for brief periods, we don't leave our work behind. Now that's not necessarily a bad thing, but every now and then -- going to get your driver's license renewed, or "taking" a day off to go to some tourist site because a family member or friend is in town -- we cross paths with the real world around us.

Bubble, meet daylight.

Long hours and an physico-emotional connection to our work are probably two of the most hackneyed topics amongst graduate students in science. But why is it that way? The obvious answer is ambition, a state of mind that isn't unique to aspiring young scientists but can be applied to aspiring people in any walk of life -- lawyers, politicians, chefs, artists, sports players, etc. But there is something unique about science. Many of us have a sense of elitism, that what we do really is that important, so noble, and there's this sense of urgency that we can never put it down for fear of being overtaken. And that feeling, I think, contributes to a sense that we really shouldn't be doing much else at all with our time. Do you think that? I know some graduate students do, and I'm curious as to where this feeling comes from: ourselves, our advisors, who are typically the ones who have risen to the top (one particularly cynical comment to a previous post comes to mind), our work environment, or other influences entirely?

Posted by Catherine Goodman at 03:30 PM | Permalink | Comments (2) | TrackBacks (0)

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)