Everyday Scientist

what kind of jerk…

September 6, 2007 at 1:30 pm | sam | everyday science, grad life, lab safety

…would spill some crazy fluorescent* solution on the hallway floor and leave it there?

Well, it’s not nearly as bad as an unreported spill could be (think of this!), but it’s still annoying. I have no idea what this stuff is, and it’s right outside my office door. I’m right next to the NMR facility, so I suspect some jerk dropped their NMR tube and was so distraught—having lost their newly synthesized whatever—to be responsible enough to wipe up their spill with their tear-soaked handkerchief. Jerk

Instead, the Environmental Health and Safety people will have to come out here and do it. In fact, a guy just got here and is trying to clean it off the floor. His orange-cleaner stuff didn’t work, so I gave him toluene, acetone, and methanol—that runs the gamot for polarity. Ah! the acetone worked well (it took off the floor wax, too!).

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* Of course, the first thing I did was grab my trusty UV flashlight (385-nm diodes) and see how fluorescent it was. Cool show!

Would have been cooler with the lights off.

Laser Safety Glasses

August 6, 2007 at 3:08 pm | kendall | everyday science, lab safety

Always the skeptic, I decided to put my new pair of laser safety glasses to the test.

I was actually a little surprised with the results. Since we have doubled YAG (532nm), YLF (527nm), and VO4 (535nm), l figured the glasses should work work for each since they are rated OD>5 for 190 – 534. But as you can see, at 535, the OD is already down to only 3.5. That’s should still be enough (esp. at only 5W), but I guess you really do have to yield to their manufacturer warnings not to exceed the specified wavelengths. I was too lazy to use the nice CARY, so I can’t comment on their performance in the NIR.

inadvertent secret messages in skin

August 1, 2007 at 4:27 pm | sam | cool results, everyday science, nerd

Several days ago, I wrote a note on my hand to remind me to do something (fix the house N₂ system, although you wouldn’t be able to tell from my scribbles). I wrote the note in red pen (a Sanford Uni-Ball micro¹) and it disappeared in a few days.

Figure 1. My hand in room lighting.

Or so I thought! Today—days after the mark faded completely—I was looking at some dye solutions under a UV lamp and (voila!) there were the marks again.

Figure 2. My hand under UV illumination. (click to zoom)

Pretty cool. Unless you’re worried about degraded ink remaining under your skin for weeks.

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¹ By the way, don’t use these pens, even on paper. I’ve been using them for about a year, and just yesterday I discovered that the ink is very much not waterproof. I spilled water across my desk. Now none of my to-do lists make any sense.

From “publish to perish” to “patent and prosper”

July 25, 2007 at 12:35 pm | ilya | everyday science, grad life, literature, news, science community

Hey folks,

I recently came across a very interesting retrospective in the Journal of Biological Chemistry written by Howard Schachman, who’s been engaged in biochemistry research in Berkeley for over 50 years.

Schachman lays out the changing nature of research and academic life as he’s observed them over the past 50+ years. I, for one, am always interested to read about how things have changed and where they’re heading. Here’s a particularly interesting quote:

In 1953, while McCarthyism was rampant, the Federal Bureau of Investigation (FBI) began screening grantees. Based on FBI reports, Oveta Culp Hobby, as Secretary of Health, Education and Welfare (HEW) in the Eisenhower administration, interceded and ordered the cancellation of grants to Linus Pauling and other prominent scientists.

Read on to find out what happened! I guess that president Rove’s clumsy meddling isn’t as bad as it can get.

Rube Goldberg Science

July 13, 2007 at 8:27 am | david | everyday science, grad life, stupid technology

Most people have probably heard of or seen pictures of so called Rube Goldberg Machines. These are extremely complicated apparatuses which do extremely simple tasks. Here is an example from the Rube Goldberg website.

This one could actually be useful for those grad students who have bosses that keep track of time in lab.

There are even Rube Goldberg Machine contests, in which teams try to design a machine that can use the greatest number of steps to complete a simple task.

Now, science is often complicated and it doesn’t need any extra help from us grad students to make it more complicated but I fell into the trap myself and let this be a warning to all those who think they have a really good idea… think again.

The required task is: Do a pump-probe anisotropy measurement using infrared light. Simple enough at face value, but all you visible spectroscopists out there must keep in mind that IR polarizers are ~1000 times worse than visible polarizers and there is no such thing as a broadband IR half wave plate. Tack onto that the fact that IR detectors are much less efficient that visible detectors and you’ve got a passel of stumbling blocks in front of you when you’re trying to do this experiment. I’ve tried a number of different techniques and because the IR polarizers and half wave plates are a little sketchy, transmission always seems to screw things up. So I thought to myself, what if we did everything using reflections! Then it would be achromatic and everything would be hunky dory. Here’s a schematic diagram of what the pump beam is subjected to in this scheme. The actual layout is much more complicated but I didn’t have a digital camera with me.

The periscope serves to change the polarization of the pump beam so that it will be parallel or perpendicular to the probe. The bottom mirror in this periscope is on a computer controlled rotation stage so that it can rotate to spit the beam out in two different directions depending on the polarization you want. In addition to that, since there are now two beam paths we added a computer controlled mirror that could flip in and out of the beam depending on which beam path you were using (which polarization). It was a thing of wonder to watch these things rotate and flip on the click of a mouse button, almost mesmerizing and utterly satisfying as well. Needless to say, it didn’t actually work for the purpose it was designed for. I wasn’t able to align the two beam paths well enough and/or the mechanical devices weren’t repeatable enough to consistently steer the beams in the same direction. Bummer. Like so many things that seem perfect on paper, real life imperfections rear their ugly head when you try to make it work in practice.

Now, this experiment isn’t a simple task by any stretch of the imagination, but making it more complicated is certainly not going to make it work better. It was only after I was humbled by the lack of repeatability of my fancy new system that I remembered Rube Goldberg and kicked myself for falling into his trap.

Aerogel Jewelry

July 2, 2007 at 5:55 pm | kendall | everyday science

Source

Aerogel Jewelery: +10 nerd, +4 chemistry cred, and -10 charisma*. Personally, I’m holding out for a pendant full of radium, Curie style.

*These statements have not been evaluated by the FDA. This product is not intended to diagnose, treat, cure, or prevent any disease.

sonicator rules

June 26, 2007 at 4:13 pm | sam | everyday science, hardware

I’ve got a question to all the chemists out there: Why can’t I put anything on the bottom of the sonicator bath? It says not to right here:

But we often put stuff directly on the bottom of the bath while the sonicator is on:

I mean, what’s the big deal? Does anyone have a good reason? Could it damage the sample or the sonicator?

The latter would explain why we’ve gone through a baker’s dozen of sonicators in the last six months.

deconvoluting deconvolving

June 6, 2007 at 10:13 pm | sam | everyday science, journal club, literature, nerd, open thread

We were discussing some grammar at Chemical Physics Journal Club this week: which is the (more) correct sentence?

1. It is important to deconvolute the fluorescence lifetime from the instrument-response function.

2. It is important to deconvolve the fluorescence lifetime from the instrument-response function.

I think sentence 2 is better. To me, “convolve” is to (usu. mathematically) roll together multiple things, while “convolute” means to make complex: you can convolve two mathematical functions or signals, and you can convolute a sentence. (Unfortunately, the noun form of each is “convolution.”)

I don’t think the official Webster or Wikipedia definitions agree with me, or clear up the mess (it’s so convoluted!), but my argument makes so much sense in my head that I can’t give it up. I get annoyed when scientific papers state they “deconvoluted” something, unless they mean that they made something less complicated.

I suppose convolving is a type of convoluting.

Other thoughts, here?

watching over the lab

June 5, 2007 at 1:18 pm | sam | everyday science, grad life, great finds, lab safety, nerd

There has been a wave of thefts in the physics buildings on campus—losers stealing lab equipment—so we decided to have someone watch over our labs all night and day:

He startles us often. But he’s the hardest working grad student!

impeccable flawlessness

May 25, 2007 at 8:12 am | Charles | everyday science, nerd, wild web

As a sophomore in Honors Physics, we had to do “special projects” and have websites associated with them. A friend just sent me a link to my team’s old website…. it’s pretty funny looking back.

The Impeccable Mechanics of the Flawless Trebuchet

Caution…there’s music, and it’s loud.

open SIF

May 21, 2007 at 8:40 am | sam | everyday science, software

My lab has a few Andor CCD cameras for imaging, and I was happy to find an plugin for opening Andor .sif files directly into ImageJ.* I was happier to see that my friend Stirling Churchman wrote the plugin originally. Thanks Stirling!

* ImageJ is a great open-source image processing program developed by the NIH. I’ve been really happy with it (especially the plugins!).

Motivators

May 15, 2007 at 6:23 pm | Charles | everyday science, grad life, nerd

The folks over at despair.com have a new motivator generator – here are a few chemistry motivation posters that I came up with. Have fun. Click on any of them for the full-size image.

shitting your pants for science

May 9, 2007 at 5:29 pm | sam | everyday science, grad life

This is not my story. This is my friend’s story. Let’s call her X. X is dedicated to science. So dedicated that she shit her pants for science. Here’s the story (as best I can remember it)…

At some point in X’s grad-school career, she required some specific protein—some tubulin, I think. Now this tubulin was very expensive: for the amount she needed, her lab would have to pay upwards of $500k. Needless to say, they didn’t have the spare cash to buy a vial of this stuff. The other option for obtaining this tubulin was to purify it themselves … from calf brains.*

So X and two of her colleagues traveled the two hours to the nearest slaughterhouse … for calf brains. Once they got there, the workers discovered that they didn’t have any cow heads small enough to fit into their head-splitter (yes, apparently slaughterhouses have head-splitters on hand, but small ones). So the three scientists had to drive the two hours back to lab empty-handed.

After the third such trip, X and her labmates were successful (if you can call it that) in getting—still warm, mind you—calf brains. They threw the brains on ice and drove quickly back to lab. Unfortunately, all three had some digestion issues, and they had to stop several times on the trip back to use the restroom.</foreshadowing>

Now they had to do each step of the ~20-hour purification without stopping or the protein would be unusable. So X and her labmates were many many hours into this purification. She was doing one repetative pipetting step in the coldroom while her labmates were elsewhere in the lab. Suddenly, she felt a rumbling in her gut and a dreadful loosening of her sphincter. Continuing to pipet, she called out to her labmates. Her yelling was to no avail, because the insulated door to the coldroom blocked her cries for assistance.

A dilemma: to stop the purification and destroy many hours of collective effort and delay an essential experiment, or to shit one’s pants. For X, the decision was clear: she shat her pants between plunges of the pipetter.

When her labmates eventually returned, X excused herself and said she’d be back in an hour or so, went home and cleaned up, then returned to lab to help finish the purification.

You know, I never asked her whether the experiment with the tubulin actually worked…

[Update: X read this post and had this to say: “the only factual correction i would like to contribute is that i didn’t even go home after i shit my pants – we still had protein to harvest, sam, and i couldn’t abandon my colleagues. i just went to the bathroom, threw out the soiled underpants, cleaned up, and went back to the prep.” Now that is dedication! I would have just stolen the $500k at gunpoint from a local bank….

X also said: “i should also come clean and say that the tubulin was only worth $150k. the prep worked great—nice clean bands on a protein gel. finally, i should let you know that a former postdoc in [my old] lab told me that he once participated in a tubulin prep at an institution that didn’t have any cooperative slaughterhouses nearby. this meant that he had to SPLIT THE HEADS HIMSELF WITH A CHAINSAW. seriously. “]

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* Just a side note that X is vegetarian. So am I, so I can’t officially condone using animal parts. But, for science, some exceptions to ethical guidelines must be made. Like running stoplights. And using byproducts of the meat industry. Just the other day, I had to buy some gelatin in the name of science. ;)

aqueous gel sample prep

April 18, 2007 at 4:46 pm | sam | everyday science, science community

Does anyone have any experience making samples (preferably thin-film, ~100 nm) using agarose, gelatin, or some other transparent aqueous gel/biopolymer? For my poly(methyl methacrylate) samples, I spin-coat at 2500 RPM for 30 s and get a ~30-nm film. I can experiment with conditions, but I thought I’d ask first.

I’m trying to measure fluorescence from a relatively concentrated sample (~10^-6 M fluorophore in biogel) on a glass coverslip using epi-illumination.

If I get any answers, I’ll let you know here.

NoChromix Volcano

April 11, 2007 at 8:47 am | kendall | cool results, everyday science

A new twist on an old favourite. To make the NoChromix volcano, add one package of NoChromix® to your favourite H2SO4 and stir. Insert a cherished piece of glassware contaminated with whatever the hell pissed off the bath, slam the sash, and enjoy!

(I know what you’re thinking, but I scrubbed the hell out of those filters, rinsed them with nitric, then triple rinsed them with H2O before putting them in the bath).