WWWTP: Lipid edition


This photo from the New York Times caught my eye not because of the headline* but because of the lipid behind the gentleman in the photo.

It appears to be gamma linoleic acid drawn up, and note the numbering! Here’s the punch line: it’s actually correct!

So at first glance, it’s not obvious why that molecule is there, and it was probably drawn by an intern with a love for Wikipedia, but given how often these things are screwed up, I’m really proud to see it done right for once!

*I still haven’t read the article, believe it or not

Mental Health in Graduate School

If you’ve been following the chemistry blogosphere, you know that Chemjobber and Vinylogous have been having a conversation of sorts regarding mental health in graduate school, and I figured I would give my input.

To give some background, I am a second year graduate student at a top five program in organic chemistry, and up until ~ 6 months ago, I was miserable. However, I think it honestly had little to do with graduate school itself, and more my working relationship with my advisor; I found out the hard way, like many on the participating blogs have pointed out, that a horrible advisor can account for the greatest source of stress in graduate school. I changed advisors, and I was tempted to write about it at the time, but decided not to for a variety of reasons.

Given that I don’t have the benefit of anonymity, I won’t discuss the terms of why I left my previous lab. However, I will say that I was under a lot of pressure to produce results, and the manner in which the lab was run isolated students in terms of how obvious it was around the lab that someone was taking a beating. As a result, the weeks where I would work all seven days, only sleeping at my desk for a few hours, it was very easy to feel cut off from the world, even within the chemistry department. The person I shared a bay with was a seventh year graduate student fighting to get out in one piece, and with student-advisor conflicts arising constantly, I very nearly dropped out of graduate school altogether. I remember going home to visit family one holiday and nearly having a nervous breakdown describing my work schedule, and that feeling just built over time. By the time I had spent a year in the lab, I was reclusive, paranoid, quiet, and downright depressed.

However, my story has a happy ending. As I was thinking very seriously about calling my boss from a company I used to work for and beg for my old job back, I happened to meet a new assistant professor in the department, who told me about her research. I was interested enough that I made the decision to stay and switch advisors; once you drop out, you’re done, but if I could make it work in another lab, maybe I could at least get a degree out of this mess.

The biggest barrier to actually changing labs was somehow convincing myself that I wasn’t a bad person for doing so. For some reason, I had it in my head that I would be seen as a failure or a weakling if I changed groups. “He couldn’t cut it in Prof. X’s group,” they would surely say. “He’s so pathetic,” they might add. I can’t say for sure whether that was or wasn’t said, but I swallowed my fears and realized that if I was going to be sane and healthy, I couldn’t give a crap about what other people said. I remember discussing the possibility of working with my current advisor on a Tuesday (at that point I hadn’t realized that she had only started at the University two weeks before, and so I can’t imagine in retrospect how crazy it must have been from her perspective), and by Friday night I was in her lab, setting up reactions.

I make it seem somewhat straightforward, and I admit that making a change sooner than later likely helped the situation along, but it was terrifying. For weeks I was worried if I had made a mistake, if, had I stayed in my previous lab, I would have persevered and seen a happier me on the other side. It was a surprisingly stressful time, largely because no one really tells you how changing groups will go. You hear stories of people who have done it, and you know that it’s possible, but it’s not something that many people encourage. However, if you’re having problems with your advisor, know that history repeats itself. Be proactive about yourself and your career. Regardless of the outcome, at least you will have exerted some control over your situation. For me, it was like night and day. My advisor and I work together phenomenally well; we share many fundamental ideas of how research should be done, she respects the skills that I have, and she’s also not afraid to teach me to do things better. More than anything, though, being on the same page has made it much easier to understand what’s expected of me, and know where I stand. I still work just as hard, but now it’s because I want to, not because I’m being pressured by an advisor. To wit, we’re already putting the pieces of our first manuscript together, six months in, something I was worried I would never get to in my previous lab.

More importantly, though, the above changes in perception to how I operated in the lab made me feel more relaxed and outgoing than I ever was previously, despite still working “crazy” hours. Shortly after changing labs I began seeing my current girlfriend, I started some hobbies (as you may or may not know, I am a budding amateur aquarist now!), and overall I respond to “how are you doing” with “pretty well” instead of “I’m not dead yet.”

I suppose this was an ad hoc story that summarizes to the point that grad school is incredibly difficult, but it doesn’t need to be demoralizing. I think too many people (especially organic chemists) assume that being beaten down by their advisor is “part of the process,” but I think I’ve proved that this is hardly true. By taking control of the situation and identifying what was bothering me (my choice of advisor) and changing the heart of the problem, I’m happier and more productive than I ever would have imagined I could be in graduate school. That said, I’m still poor and tired, but at least I’m still living the #phdlife.

How to draw catalytic cycles in ChemDraw

So it’s NSF proposal and seminar season at UIUC and all of the ugliest catalytic cycles are on display around the department. No, I’m not talking about the reactions themselves, but those circular arrows. Ugh! Gross!

If your cycles look like the one on the right, FOR SHAME.

I realized that this is not something they teach in class, so as a public service, I created this video on how one can make gorgeous catalytic cycles using ChemDraw’s Pen Tool.

You’re welcome.

The Perception of Scientists

So, I realize this post is long overdue, but I feel it’s still important that I write about what I consider to be the most important challenge to overcoming chemophobia: America believes that scientists are antisocial wimps who are on a leash held by some evil corporate overlord.

Honestly, the thought occurred to me when I was reading the webcomic Questionable Content a few months back. There was a tangential story arc in which the characters visited a space station (out of context, this sounds quite strange), one of which featured this comic:

QC comic

More importantly, the caption read:

Scienceweight is one division up from Mistakeweight and one division below Kittenweight.

Now don’t get me wrong, if he wants to write characters that are total dorks, that is A-OK with me. His comic is his creation, but the caption exists outside of the “QC Universe” as he calls it. I didn’t appreciate the implication that a kitten could generally beat up a scientist. It’s not even the case that I can name some scientists who are buff: the large majority of scientists that I know and interact with are perfectly well-socialized and I’d like to think that the bulk of us are no less physically fit than any other trade. Sure, I’m no prizefighter, but I’m not a kitten either.

Pictured above: Just a few chemists who could all totally kick a kitten’s ass.

“But Marshall, surely you must know that stereotypes exist for a reason! There must be more examples of dorky, sunlight-fearing chemists than those who can be classified as ‘normal!'” Bull. There was once a day when chemistry, dare I say science as a whole, was the cool thing to do. Back when NASA was the ideal workplace for any kid, there wasn’t this weird bias against scientists. Let’s face it, things have changed: back in BASF’s glory days, being a chemist was a well-respected position. Now I get accused of not having a personality when I tell the barista at Starbucks that I’m a scientist.

There are not words to express how awesome this picture is. V8, really?

So is this really damaging to our field? Certainly. Kids who grow up thinking that scientists are nerds (alright, many of us are, but when was that a bad thing?!) grow up thinking that math and science are either too hard or something that they are “too cool” to do. Those kids then grow up to be students of other disciplines, which is great, except when they then get to be congressmen who don’t understand the things that they have to decide whether to fund or not. Hell, in Europe the funding of synthetic organic chemistry was all but outlawed, and I can’t see a reason for that other than pure ignorance.

Dearest readers, what do you think? Am I full of it? Or have you ever been on a date, revealed your trade and suddenly been treated like some sort of madman? I’m not sure what we can do to combat this image, I would be delighted to hear suggestions.

Continuous Liquid-Liquid Extractor in Action!

While I have three different posts in various states of drafts, I bring you a video of a seldom-used piece of laboratory equipment in action! The Continuous Extractor is for those stubborn molecules that don’t want to come out of the water layer. Why use liters of ether when you can simply run the extraction infinitely with a fixed volume?!

The extractor works with a pot of organic phase (right) that is heated to reflux. This solvent goes up the arm into the main part of the extractor, where it hits the condenser (similar to a Dean-Starke) and drips into a funnel. This funnel brings it to the bottom of the aqueous phase, where it then bubbles up to the top layer. As more organic layer refluxes over, the level of the organic phase increases, and eventually spills back over to the refluxing pot, where it starts all over again, but deposits your desired material before becoming vapor again! Tl;dr the liquid refluxes over to the aqueous phase before spilling back over to the first pot with your product in hand.

Stay tuned for more posts, too!

Click below!

Poll: Staples vs Paper Clips (vs other lesser things)

Courtesy of Prof. Lancaster (UEA), we have a poll for all of you chemicacademics: Which do you prefer for work turned in to you: Staples or Paper clips?

Click here to chime in!

I have some strong opinions on the matter, so expect a post detailing my choice later on today, but for now, let us see where the dice clips fall!