Infrared Spectroscopy begs to be animated

I put together this little animation this morning for my general chemistry students, who collected spectra on the IR this afternoon.

Happy Halloween!

I am drunk on toasted pumpkin seeds.

Work-in-Progress

Here's another work-in-progress. It's sort of terrible right now but I have plans for much improvement. It has to do with a mechanism to thwart a common cancer-associated upregulation of survival/proliferation pathways in epithelial cells. Right now it looks like the treatment is Pepto-Bismol. I assure you it is not. The colors need some work.

Update on Monday, November 8, 2010 at 11:08AM by Mary

Here's what I've done with it so far. Normally I would avoid such a heavy-handed use of red, a color normally chosen to highlight, but there are two other banner images in the series with which I am trying to keep things consistent. The first one, which I posted on Oct. 19th, involves a colorimetric assay in which the starting solution is red. Turns out for this one, I couldn't have planned it better if I tried. To make the proteins pop against a red background, I colored them green, apropos indeed as these are mucins, or the proteoglycans that make mucous slimy. Voila!

Anniversary trip to Portland

To celebrate our first anniversary, which was yesterday, the husband and I took a weekend trip up to Portland, OR. Neither of us had been, so we decided to just go explore. With a B&B gift card burning a hole in our pockets, we built a whole trip around it.  Like good little tourists, we hit the rose garden in Washington Park, the Saturday Market, VooDoo doughnuts (bacon-topped maple bars... pure, unbridled genius), Powell's bookstore (want to take up permanent residence inside of it), and the waterfalls of Columbia River Gorge. We also hit four different breweries and tasted a lot of craft beer (while meanwhile, back in San Diego, a black IPA bubbled away in our closet). Our favorite was Rogue Brewery, although the photo above is from Lucky Labrador Brewery. Another highlight for me was the gorgeous fall foliage. Compared to San Diego it was like being back east again, with rain and all. I loved it. Great city, great trip.

Update to three ring circus movie

Now it's got some concerted action, that's more like it. Again, much better viewed on Safari. Also, sorry iPhone/iPad users...

His tag to NTA - more than just a pretty purification strategy

This is a work-in-progress, and part of a new project I have to help re-design the website of a biotech company in Massachuesetts. The image is based on a gold nanoparticle-based assay. More soon!

Nurse Flower ponders her coffee

Nurse Flower is bored but curious as she stirs. This is the result of a sort of mad-libs for art exercise, done with pen and ink with an ink wash finish. Hope you enjoy it.

Three ring circus

This reaction scheme taken from a step in diterpene biosynthesis shows no fewer than three cyclizations occuring in a single enzyme active site, with a net gain of two new rings. (Animations here are best viewed with Safari, not so much with Firefox) This is a project that just came to me last week, and I was excited to get to it, though it's still a work-in-progress. I don't like having five bonds to carbon, even for less than a second, and the geometry of the final product looks a little uncomfortable, but I was eager to post this. There is something so inexplicably satisfying to me about making animations. I completely understand how, before we used computers to do this, animators could bring themselves to painstakingly draw the same illustration over and over and over again with only the slightest modification from one to the next. Because Flash does the heavy lifting for me, I can only imagine the feeling they had when they finally put them all together and flipped through the pages.

Use your words

I now have three consecutive days worth of evidence to suggest that working part-time from home may be seriously damaging my verbal and cognitive skills. I suspected that this might happen, I just didn't expect it to so soon.

Exhibit A. This happened yesterday:

Exhibit B: On Monday, a completely inappropriate response to a statement, like when a TSA agent tells you to have a nice flight and you say, "You too!"

Often times when this happens I like to think that maybe these sorts of gaffes go unnoticed. It wasn't such a big deal, right? Until I have one in front of the husband. Exhibit C (Sunday):

This was followed by a brief pause, and then, maniacal laughter and, ultimately, ridicule. "Tome? haha. Did you say tome instead of time?! hahaha!", etc.  In all fairness, I would have done exactly the same.  It's nice to have the reality check sometimes.

IgA-gobbling cell

When I was a postdoc, I found this phenomenon in which a self-assembled multivalent complex designed in our lab was selectively taken up by acute lymphoblastic leukemia B cells over normal B cells in a mixture of white blood cells. I wasn't able to explain why this was, and my main hypothesis was wrong, so I didn't ever try to publish it. Instead, I'll just make an animation of it. This is sort of a flash sketch, just to get me thinking about how I might be able to depict endocytosis with 2D animation.When I was a postdoc, I found this phenomenon in which a self-assembled multivalent complex designed in our lab was selectively taken up by acute lymphoblastic leukemia B cells over normal B cells in a mixture of white blood cells. I wasn't able to explain why this was, and my main hypothesis was wrong, so I didn't ever try to publish it. Instead, I'll just make an animation of it. This is sort of a flash sketch, just to get me thinking about how I might be able to depict endocytosis with 2D animation.

A master of molecular disguises

Here is a rough sketch for a chemistry poem illustration. I love this poetry book illustration project. This 007-inspired poem has Bond bonding all over the place to turn himself into TNT, nitric acid (to neutralize his basic enemy), nitrous oxide (laughing gas), cyanide, NO, and more. I should check my Lewis structures but this was just to get down some ideas. Recently I was working on a similar sketch in this series on a cross-country flight, and a flight attendant said, "Aren't YOU a good artist!", as though I were 5. Was she making fun of me? I'll never know. I just looked down and blushed, burrowed my toe into the floor and hid behind the nearest skirt I could find. Okay, I didn't do any of those things, but that was how it felt.

Dreams and Nightmares

Here's a project I did for my Photoshop class, which is part of the Digital Design Certificate program I'm enrolled in. Out of a few options, I chose the dreams and nightmares theme, and incorporated a few of my recurring nightmares using most of the Photoshop tools I've learned to date in the class. The pattern-making tool is one of my newest favorites. My feet are supposed to be huge and heavy, making it impossible to run away from whatever is chasing me. It may just look like I'm sporting bell bottom pajamas though.

And no more shall we part

This is an oil painting of my grandmother that I did during the summer between my freshman and sophomore years of college, from a black and white photo taken when she had been about the same age. I painted it two years after she passed away, following a struggle with Parkinson's disease, and gave it to my grandfather hesitantly, not knowing whether he would want a painful reminder of a much happier time of his life.

My grandfather had retired from his career as an engineer to care for her, and found himself, at 72, wondering what he would do with himself now that she was gone. His biggest fear was to be idle, so he followed a calling, the seed of which had been planted decades earlier, and became a Catholic priest. Since then, he has served his community tirelessy and grieved for his wife daily. This painting hung above his fireplace. Every time I saw him, he told me that he talked to her every day, while assuring me, lest I be concerned, that she had not started talking back yet. 

Yesterday, on what would have been his 88th birthday, we gathered the family together for his funeral, a service attended by two bishops and enough priests to keep everyone on their very best behavior. I borrowed the title of this post from a Nick Cave song, because I think what comforts the family most right now is the thought that he is finally reunited with his beloved wife.

Thin Layer Chromatography

This week my part-time teaching job has felt a bit like a full-time teaching job. No complaints about that at all, it just means that the only thing I've really sketched this week is ideas for ways to explain the concept of thin layer chromatography to my organic chemistry students. No perspective, no shading, just trying to use simple images to make a complicated subject easier to wrap their minds around. Good thing my students are bright.

Fossil find in Soho

Just came back from a weekend in New York, celebrating a handful of family milestones with my truly delightful in-laws and getting to see some great friends. While walking through Soho with husband, we came across The Evolution Store, which I hadn't heard of but was drawn to by the sign outside advertising the meeting of science and art within.  It's a tiny space bursting at the seams with ancient fossils, human (and other) skulls, rare minerals, and taxodermied animals. In a puzzling juxtaposition, a taxodermied raccoon sits atop the glass counter holding a basket full of male raccoon genitalia bones. Anyway, we found this ammonite, a now extinct marine animal, particularly beautiful. I also chose it because I was facing a birthday, and it is hard to feel old in the presence of a 120 million year old fossil.

Everything is connected

These icons represent just a portion of what's going on in Mycoplasma genitalium, even though it's the smallest known free-living bacterium, and has one of the smallest genomes ever found. Understanding how all of these processes communicate between one another to keep the organism thriving is a huge feat, and I am excited to be peripherally involved (if only artistically) in the effort.

Now wait just a dipole moment.

Just getting psyched for the first day of organic chemistry lab, when the students will use a molecular modeling software program to learn about polarity of molecules in preparation for week 2 - thin layer chromatography!

Safety first (or, my new pencil holder)

This week I am gearing up to teach a couple of undergraduate chemistry labs, and have been hearing a lot about safety. This pencil holder, which I recently repurposed from a broken cassette tape deck adaptor, is a good reminder of what can happen to monsters who attack pencil-wielding prey if they do not first put on a pair of safety goggles. PPE is no joke people!

Creepy disembodied extremeties

I've had the very good fortune to get to know a talented and well known medical illustrator around here. I've talked to him about my plans and gotten some very good advice. From our first conversation he's been curious about my past and ongoing fine art training, reminding me that no matter how many cool tricks I can pull off in Illustrator, it is important to stay strong in the fundamentals. When I told him we had to draw our hand in class, he told me we should have been drawing our hands and feet about 20 times, using different types of pencils, methods of shading, and lengths of time. So, here are some of my attempts. The sketches took anywhere from 5 minutes to an hour. They were done with charcoal or pencils at 6 or softer. Some are blended, some are not. 8 down, 12 to go. Or is it 32 to go? The topmost sketch is the one I did today. The foot in the last panel is not bleeding, it's just a smudge.

Adolescent angst for B cells

In order for pre-B cells to fully mature, they need a functional B cell receptor. Now here's a discovery proving yet again that carbohydrates are worth paying attention to. Turns out, the pre-B cell receptor has a crucial asparagine-linked glycosylation site, and taking it away leaves these inexperienced cells trapped in limbo and unable to progress to maturity. Hmm... like grad school?

For the full story see Ubelhart et al. Nature Immunology 2010, 11(8), 759.