403: Spiral of black and white stones, on a go board. (Spiral)
( Jan. 27th, 2010 08:35 pm)
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.)
Neural correlates of interspecies perspective taking in the post-mortem Atlantic Salmon: An argument for multiple comparisons correction. Dead fish in an MRI, with a real point to the experiment? Someone's going after an IgNobel prize.

Dispatchwork seeks to whimsically repair the world's public spaces.

Now I need to write a 3min talk on the chemistry of the BZ reaction, and make some slides for it. Should get started.
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..you find yourself using the freshly-made bottle of NaOH solution as a handwarmer.
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403: A rack of test tubes with the caption "If you're not part of the solution, you're part of the precipitate". (Solution or precipitate)
( Nov. 16th, 2009 10:50 pm)
This afternoon, I picked up half of my order of chemicals for a class project. Half, because the other half had been returned to sender by someone in Lab Recieving. Still waiting on an explanation of how that happened. UPS either can't or won't divert packages in transit. The supplier tells me that they'll ship it back out promptly when it arrives, this time c/o'd to the purchasing manager so that it will hopefully stay here. It will most likely get back to me in two weeks.

This evening, I attended a discussion panel about "Faith and Science". The panelists were a Lutheran minister, a Catholic priest, an imam, and one Hillel staffer + a student who also teaches Jewish Sunday school (filling in for the rabbi, who's in the hospital after an accident involving a barbecue grill; he'll be fine but needs time to heal). Not one scientist. All of the religious leaders in attendance emphasized that their faiths are pro-science, within the bounds of what they consider ethical. (They all knew where they stood on issues like stem cell research and abortion. But animal testing threw them for a loop. Go figure.) I tried to add as much of a scientific perspective as I could from my position in the audience, and was only needed to make a religious point near the end, when the Jewish panelists couldn't give a solid answer to the animal testing question. (I've looked into the matter already because it might become relevant in my career.) On the whole the panel discussion turned out okay. There was the potential to be more than okay, but I'll take what I can get.
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.
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This morning, my employer discovered that her deep freezer had died, and the alarm didn't go off. The device is in the freezer room, where we don't often happen to walk past it, so we have no idea how long it's been nonfunctional - except that some of the samples had started growing mold.

So what I'm doing today? Disposing of spoiled samples, and cleaning dozens of test tubes and litle vials. And keeping my inhaler handy, since I'm allergic to mold spores.
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403: Igor (Igor)
( Oct. 22nd, 2009 11:42 pm)
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...
Today I...

...had a long day. )

I've had my feet elevated and on ice for more than 2h now. They still hurt - not just while walking around, but lying here in bed. That's not at all typical behavior for my body, so I can probably conclude that I pushed it too far today.

This is also not an isolated incident in the semester. I've long known that I can walk for extended periods without pain, but not stand still for them. The increased frequency of standing-only lab time this semester could easily be making things worse. My shoes seem unlikely to be a factor; they'd have to have deteriorated suddenly between the summer and fall semesters.

Which leaves the question of what to do about it. Aside from trying to take more breaks or to sit during certain labwork, no answer immediately presents itself.

Dear internets, do you have any suggestions?
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!
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A colleague of my summer research professor asked him to recommend an undergrad to her, since her previous assistant had graduated last spring. He sent me, and I was hired on the spot, which I was not at all expecting. There's some administrative hoops to jump through, but I start next Thursday.

The new subject area is astrochemistry. One of the things I'll be working on is extracting miniscule amounts of amino acids from the interior of meteorites. The chemistry isn't very complicated (prof. described it as "kitchen chemistry"), but since the masses involved are so small I expect it to need exacting precision. Good thing I'll be working in the afternoon, when I'm awake.

To sum up: YAY!
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403: Igor (Igor)
( Aug. 11th, 2009 01:30 pm)
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.
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403: Igor (Igor)
( Jul. 16th, 2009 03:28 am)
My problem reaction. It did something different!

Ordinarily it makes some combination of brown solid and red-brown sludge. Whatever the red chemical is, it's an unwanted side product.

This reaction has had a persistant issue with one of the starting materials being insufficiently soluble, so I decided to increase the amount of solvent until it would all remain in solution when the thing was in an ice bath (which is the recommended state for part of the reaction). When I ran the reaction this time, there was no solid, and no red by-product. It made an amber-to-brown oil that I have yet to identify. The intended product is amber-to-orange in solution, and makes brown or orange crystals.

I hope I've stumbled on something that works better!
403: Igor (Igor)
( Jun. 25th, 2009 11:50 pm)
...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.
I need access to this article, but my university doesn't subscribe to the archives. Could someone send it to me? (Even if I was willing to pay 27 quid for the paper, they don't take paypal, so I can't.)

ETA: The wonderful [livejournal.com profile] zeightyfiv hunted down the article for me.
Yesterday, I found a stoppered test tube of mercury in the back of a drawer. Since it was visibly dirty, the professor decided to dispose of it. I asked why we had it, and one of the graduate students replied, "The real question is, why do we have this?" - and pulled a liter jar of the stuff out of a bucket under a table. Apparently nobody knows. But it's still perfectly good mercury and would be very expensive to safely get rid of. So they keep it.

Other findings of note included approximately 1lb of sodium metal in the cabinet under my fume hood, distributed among at least three jars (that I noticed). Two are topped off with mineral oil, and one with kerosene, which strikes me as an odd choice. The fist-size chunk in the clear jar appears badly corroded, and all of the jars look to be old.
403: Igor (Igor)
( Jun. 9th, 2009 02:11 am)
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.
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