403: forbidden

In order to let go of the chaos of the past couple days, this evening I decided to prune my houseplants. By the time I was halfway done with the wormwood proto-bonsai, I realized that it smelled different than it did when I started. Not just the usual crushed leaves and fresh sap. Sharper, perhaps. A sticky kind of scent. My sinuses were finally clear today, after a week or more of hardly being able to breath through them. Maybe that was the difference.

So I opened a window to let the apartment air out. Washed the sap and chemicals off my hands - wormwood is poisonous, keep away from eyes, food, etc. The next plant was the desert ironwood, and it takes a more cautious approach, if only to avoid dulling the pruning shears. (Fun fact: the wood is dense enough that it sinks in water.) After 15-ish minutes of pruning, I noticed the odd smell again. The wormwood was on the other side of the room, but the scent was distinctly right nearby. I was beginning to suspect what it might be.

Another cleanup and a trip to the grocery store confirmed it. I could get the same smell from leeks and cabbage, with their roots still on. Even from the loose salad mix, although fainter. A smell not just of agriculture, but of animal life. A silent, vegetative scream - "I'm being eaten!"

I had a salad for dinner. It was delicious.



(Happy Rabbit Hole Day. I can't stand salad.)

..you find yourself using the freshly-made bottle of NaOH solution as a handwarmer.

The "dead sample" (really, uncomfortably alive sample) tally is up to 112, plus 8 vials of meteorite residue.

The project that made them was only three or four years old, but had generated three papers so far. It was on the synthesis of sugars in conditions approximating those in the early solar system, which explains why so many of them were vulnerable to the mold.

I noticed an interesting aside while paging through my Intro to Chaos textbook, just now:

Incidentally, there was a violent controversy about this subject [catastrophe theory] in the late 1970s. If you like watching fights, have a look at Zahler and Sussman (1977) and Kolata (1977).

Since the textbook is interested in analyzing the math, not the social context in which the math evolved, it says nothing further about the conflict. And it's less than half an hour before I should be going to bed, and I have class in the morning, so I really shouldn't be trying to find those original papers right now. No matter how curious I am about what they were arguing over...

Atomic force microscopy permits us to view individual atoms and chemical bonds.

If you're mystified by why I think this is so great, consider that chemists work every day with tools whose functional units we can't actually see. We know they must be there. We can infer a great deal about their properties and functions. But at times we also have heated debates about the shape of those tools, because we can't see them. Benzene was isolated in 1825, but it took another 40 years for someone to reason their way to the correct structure, and more than a century to confirm the theory by direct measurement (1929, with x-ray crystallography, which maps electron density among the atoms in a crystal).

And now... we can turn on a computer and look at pictures of molecules which are every bit as valid as ones taken by a digital camera. This, my friends, is Science!

Since just about this time last week, I've been trying to write up the results of my summer internship. So far, I've reframed them to the point where it doesn't sound like I wasted the time I spent there. I do still have four, or perhaps five, different ways not to perform the reaction I was studying. But I'm milking all the data out of them that I possibly can, and that's got to be good for something.

All of the product-extraction end of the process will be generalizable to Doing It Right, whatever that turns out to be. And I've been exicted about this for several days, because I think I can modify it in such a way as to get rid of the benzene. The greatest benefit here is that I wouldn't need to expose myself to a highly toxic substance. The fact that the new version uses ordinary lab hazards like chloroform and toluene is just circumstantial icing - I should be able to use one of the rotavaps that reliably works, rather than the not-quite-broken hazmat one.

Yesterday, though, I spent in the frustrating search for figures that I'm not sure anyone has reported. The reaction liberates kind've a lot of energy, and it'd be nice to be able to calculate how much. But that requires knowing the standard enthalpies of all reactants and all products, in the same phase. (Ideally liquid, 'cause that's what I'm actually using.) So far, that number for my product only appears to be available for the substance as a gas.. And without the corresponding data point for enthalpy of vaporization. Now that I've thrown so much time at it, though, I'm reluctant to not say anything on the subject.

...in a really long week.

I forgot to mention that yesterday's interview went quite well. I don't want to do computer stuff as a career (that makes it less fun), but can do so well when I have to. They say they're planning to have a decision on that one by Friday, so I should know by Monday or Tuesday whether I got the job.

Today, though. Started with a lit search in the attempt to show that the reaction I'm tinkering with can be done in a fraction of the time that my predecessor used for his writeup. The end of this search was in the science library - where it turned out that the most promising article was on a reel of microfilm that had disappeared years ago, and the paper copy of the journal was MIA. I suspect it's been mislaid somewhere; it can't be checked out, and there's not generally much call for Nature articles from 1946.

So I went, empty-handed, to talk with the professor. Fortunately it turned out that there was a notebook from the first student to do the reaction, which indeed shows it working just fine at half the time, and at warmer temperatures. It also happened that I got a nice set of NMRs back, proving that I'd made the correct thing all these past weeks, despite the orange fluffy crystals looking nothing like the brown-to-beige chunky ones made by my predecessors. And that was nice.

I set up another run of the reaction, this time following the original procedure. Initial results are promising. There's a solid where before I'd gotten a red-brown sludge (which I'm still trying to squeeze all the product from, argh). It's chilling in the 'fridge until tomorrow.

Then, research group meeting. We were informed that the health and safety inspection would be tomorrow (Friday), at 10:00. This meant substantial cleaning for everyone. ASAP.

I got home at about 23:00, ate dinner, and will probably be going to sleep Real Soon Now.

Learn to smell underwater with the star-nosed mole.

This is why I love the natural sciences.

Internship is going well, aside from some bureaucracy that means I have to wait even longer for keys to the lab. (I picked up a set with my name on them Friday... and they turned out to be the wrong keys.) Borrowed a set from the professor in order to work late today.

I set up a reaction around 16:00, then left it alone. Came back at 20:00 to do the workup on that and increment purification of the previous batch of products. Left just before 02:00. It was quiet and peaceful, and really feels like I got a lot done. (Some deceptively okay-looking busted equipment notwithstanding.)

I'm also finding that it's not just me who thinks the professor's idea of safety is a bit skewed. He learned chemistry in a time where chloroform was a standard component in cough syrup, benzene came from the hardware store, and Coca-cola had real coca and kola extracts in it*. It seems to have left him with a rather cavalier attitude towards useful but potentially harmful substances. That aspect of his practice isn't normative, fortunately.


* Edit: It has been pointed out to me that Coke still contains natural coca and kola flavorings. Since the early 1900s, the coca leaves have been processed to remove cocaine (before being shipped to Coca-Cola Co.), while the kola component remains unchanged.