Beware of the Butane

Courtesy of my colleague, I came across this article on Yahoo about the perils of eating chicken nuggets.

Broadly speaking, the article speaks good sense. Chicken nuggets are quite vile concoctions (and showing your kids a video of how they are made is pretty good at stopping them wanting to eat them, or at least it worked for us). However, there is one line in there that stopped the chemists here dead in their tracks:

Another additive is tertiary butylhydroquinone (TBHQ), a form of butane.

Really? A form of butane?

Even the briefest visit to Wikipedia tell us that tert-butylhydroquinone is not very closely related to butane at all. It is a flavorless preservative, used in a wide range of foods at carefully controlled levels (well below any level that might be considered dangerous). It is not a volatile hydrocarbon and I doubt it is very flammable. Plus that rather overlooks most of the molecule.

Close Encounter With Toxicodendron radicans

My week so far has been rather occupied by the fall-out of a close encounter my wife had with Toxicodendron radicans, also known as poison ivy.

My wife is very sensitive to this plant. Despite great care, wearing gloves and long shirt, with a thorough wash afterwards, even the tiniest contact causes the familiar rash. The cause is urushiol, which is in fact a series of catechol derivatives (with the R group referring to a series of different long chain alkyl groups).

In this particular case, she was pruning our grape vine and apparently there were other vines in among the grape one. The familiar 3 leaf warning sign was of course absent (this being January); really, all you have to go on is that the hairy vines are bad and the general assumption that anywhere there are vines, some of them could well be poison ivy (and here in North Carolina, it is a very good bet).

She’s suffered at the hands of the vine before, but this time was by far the worst. It started with the itching on the hands and arms but a day or two later, it was affecting her face and we ended up going to Urgent Care, her eyes had swollen up so much she could not see any more. This is a fact of life with allergies – with each repeated exposure, the body’s response becomes more vigorous and forceful, in extreme cases leading to anaphylaxis. We have found out the hard way that the urushiol-induced allergic reaction can occur due to exposure from other sources – did you know urushio is in cashew nuts? Especially the outer coating – we had some nuts once like that and my wife was itching the next day, especially on the fingers where she brushed away the brown outer coating.

In our case, Benadryl had been ineffective, so the doctor didn’t take much time in giving her a shot of prednisone, followed by a course of the same drug in pill form. This is a steroid drug (actually a pro-drug of the active form, prednisolone. It is a glucocorticoid that acts to tune down the immune response. It doesn’t actually cure the problem, but makes the symptoms more bearable until the body has dealt with the problem. It also is not a drug you can take once and then be done, with a phased withdrawal of the drug over 2 weeks. Abrupt cessation can cause problems in two ways. One, it has only covered the initial problem and that could lead to a re-energizing of the immune response. But also, taking a steroid of this type for over a week suppresses the production of the body’s natural corticosteroids (such as cortisol) and there is a danger of dependency if the drug is not gradually removed.

It has been quite effective though, my wife is able to see again, actually was able to go to work yesterday, even if she looks like she’s been on a crazy weekend bender.

All this biochemistry leads to a simple conclusion: looks like I am getting more yard work to do.

Sad News From Scynexis

Sad and bad news for the RTP scientific community this week, as Scynexis laid off 12 people this week.

Now in the grand scheme of things maybe 12 people is not so many but here it was quite a hit. Scynexis along with GSK are the main employers of organic chemists in the Triangle. Although with cuts at both places now, I am no longer sure who employs the most any more. So that is an indicator of the local job market. More personally, I know many of those laid off and I know it had to have been really hard to let them go. Sad day.

I’m keeping all the folks down there in my thoughts, both inside and outside the company. Good luck to all of them.

Stupid Things to do with Liquid Nitrogen

I like explosions. I think a lot of chemists get into chemistry because of the excitement of sodium in water or the Thermite reaction. But it is all fun and games until someone loses an eye. Or a hand.

Paul at ChemBark posted a video of someone messing with liquid nitrogen. Go watch it if you haven’t already. Myself, I sat there literally stunned afterwards, possibly for as long as the video itself was – a historic ratio. I could not believe how dumb the people shooting the video were being.

The lack of any kind of appropriate protective equipment is the first sign (the single latex glove when the fool picks up the bottle again doesn’t quite count). The lack of any consideration about what might go wrong is another. They at least were not idiotic enough to use a glass bottle for their little experiment.

The point here is that most accidents happen when the person involved does not consider the consequence or simply does not understand what is going on in the flask and what that means. In this case, liquid nitrogen becoming gaseous nitrogen. The transition from liquid to gas creates pressure. The extremely low temperature of the liquid nitrogen certainly caused the plastic of the bottle to become brittle. The touch of the warm hand more than likely caused a weak point to form, setting off the destruction that followed.

Controlled explosions – fireworks for example – are definitely fun. I’ll even go for a dry ice in a bottle explosion for some silly entertainment, but I’ll make sure it is WAY over there and I am safely over here.

I Wouldn’t Do That New Reaction Today If I Were You

One for Friday the 13th.

A subject that comes up from time to time is that of scientists with superstitions. Is it surprising that supposedly rational scientific people would subject themselves to irrational superstitions? Clearly they do: ChemJobber had a post on this very thing (with some great comments) and before that Nature Chemistry covered it.

I’ve known some reactions that really did seem like you should check the phase of the moon before you ran them. I’ve known people with a lucky separatory funnel (one guy took it with him when he left!). I can’t say that I’ve noticed my reactions working less well on Friday 13th and I do try to dissuade myself from having such foibles, though I share ChemJobber’s preference to not assume a reaction has worked until the NMR is in hand. And it does seem that saying a reaction will be easy is asking for trouble.

It looks like not wanting to tempt fate is a natural instinct though. A TierneyLab column in the New York Times covered it quite well: the reaction to a negative outcome is much greater than the alternative. So if you don’t take your umbrella and it doesn’t rain, you forget about it, but it you get soaked, you remember it vividly. So that becomes an instinct to take the umbrella or else it will rain. Or in other words, it is best to be prepared for the worst.

But good luck with that tricky palladium cross-coupling today anyway.

An Important Message About Sharpies

A colleague walks into the lab and says, very casually, “Your sharpies are upside down.”

The Sharpie is very common in the laboratory for the obvious reason that we use it to label things (on the glass directly mostly) and then it can be removed with a little acetone once we are done. So imagine my surprise when I found out yesterday that I had been storing them wrong. If you want maximum performance from your writing implement then you need the ink at the business end and that means keeping them point down. I didn’t want to just take my colleague’s word for it, so I asked the smart word box and the font of all some wisdom, Yahoo Answers, confirmed the story.

Cleverly, the company sells them with a clip on the cap so you can hook them in a top pocket. This is convenient and also brilliant, as the ink runs away from the tip and makes the pen run out quicker, thus making you get a new Sharpie sooner. Fiendish.

They might claim it is so they don’t leak all over your shirt, but we are onto them now.

Medicine TEDTalk Takedown on Chemistry Blog

I read the blog post by Azamanam about a proposed way to reinvent the pharmaceutical industry, given as a TEDTalk by Thomas Pogge, with increasing incredulity. If you have not, go read Azamanam’s piece.

The fellow appears to have absolutely no idea how the real pharmaceutical companies work. Importantly, he doesn’t seem to realize what it takes to discover and, importantly, develop new drugs. It is a hugely costly endeavor, fraught with unexpected difficulties and can fail at the last hurdle. In fact, it can fail after the last hurdle when further exposure to the population at large reveals new side effects. Given the enormous expenses and the number of projects that just never make it to market, I find it entirely unsurprising that pharmaceutical companies charge so much more for a drug than the cost for making it. Because you are not paying for the costs of the goods inside the pill, but also for the research, effort and time that made that particular combination of chemicals possible.

Felony Charges for UCLA and Professor Harran

Few will forget the tragic circumstances around the death of young chemist Sheri Sangji, who died from injuries sustained while using t-butyl lithium in the laboratory of Professor Patrick Harran at UCLA. The amazing report of Jyllian Kemsley in C&E News is here. I wrote about it back then too.

This story took another turn when the Los Angeles district attorney’s office filed felony charges against both UCLA and Professor Harran. The LA Times report is here.

This obviously is a huge story in the chemistry blogosphere, with ChemBark, ChemJobber, the Chemistry Blog and of course In The Pipeline posting on the subject today. There are some very thoughtful opinions in that list.

I found myself nodding along with a lot of what has already been written. Criminal charges do seem extreme for a professor, but there is the pervading sense that academic safety is not taken very seriously. And this professor was the one who was unlucky enough to be the one that had the fatal accident in his lab. But let us not forgot that part, the most important: someone died in this incident, a young life taken away. If nothing else, it brings into sharp relief the importance of being safe in the lab and the culture of long hours and minimal oversight needs to end. Industry has much higher standards of safety because it will affect their business if they do not. And this in labs where there are often people there with 10 or more years of experience. The person in an academic lab with even 5 years is considered a grizzled veteran.

There is a danger of over-reaction. Of imposing such stringent safety measures that research becomes painfully slow. But there is certainly a balance that can be attained between getting work done and doing it safely and that is a balance that (if you’ll forgive the huge generalization) academic labs have yet to achieve.

Update: Some interesting thoughts from Curious Wavefunction on the culpability of the professor in this case and an excellent piece from Jyllian Kemsley, summarizing the situation, tackling some misperceptions and also including quite a blog roll of folks who have written about the subject this week.

Isco gold columns

The Isco is the work horse of our lab. So it was not unusual to find me running a purification on it the other day, though perhaps the size of the column (a 330 gram) was larger than usual. Now normally, it is such that you set it up and then can more or less walk away – periodic checks that everything is running smoothly are all that is needed. But this one was having a few pressure problems and that was requiring my attention.

When the Isco runs into a pressure issue, it tries to get around it by reducing the flow rate, first by half then by a quarter. This is sometimes enough to allow the purification to run its course, even if it does take longer and, being hands off, it does not matter much if it takes longer as long as you are not having to stand there collecting fractions. Being the guy waiting for the instrument to be available is not much fun, but still. It goes. This one was having enough problems that even at quarter flow rate it was occasionally maxing out and then it stops, asks you to correct the problem and waits for you to do so. One of the reasons periodic checks are needed on the thing even if it is otherwise going well.

A coworker came by to talk to me – the reaction was one he had done originally – and he pointed out that the gold columns that we have are capable of dealing with higher pressures than the older ones. But the instrument didn’t know I was on a gold column, so it was assuming that anything over 50 psi was a problem.

The trouble is that there is no default method on the menu for a gold column. If you just pick the default method for a 330 gram column, it still doesn’t know you have the better column installed. The only way I have found of getting it to realize is by getting it to ask you if you want it to detect the column installed (that sometimes comes up when you try to put a new column in) and then for a gold column it asks if you want Speed or Resolution. I did exactly this for another purification I ran and it was pumping away merrily with a 60 psi pressure.

It is mostly on the bigger columns this is a problem, as the small ones don’t run into pressure issues if running normally at the flow rates they run at. But 80 gram or larger can be pumping hard enough to cause pressure problems and though they do resolve by a halving of flow rate, that makes the already longer separation time needed for a big column twice as long or more.

I just did a quick search and haven’t found another way of pulling up the gold column methods, though I had not been using the ‘let it scan your column’ way of selecting a method because it was simply quicker to pull it up on the menu – plus it seems erratic about when it likes to do the column scan. However, especially for the bigger columns it seems like it is well worth the little extra time it takes to set it up for a problem free purification run.