Needlestack

Needing a break from making lecture slides now and then, I'm excited to have this project to work on. I first posted a rough(er) version of it here on December 14th. My very good friend has just embarked on her independent academic career in a top-ranked chemistry department, and of course needs some graphics for her website. In her lab they use fancy mass spectrometry techniques to identify enzymes in their active state within complex biological systems - the proverbial needle in the haystack. A needle in a haystack could be found with a strong enough magnet though. Their problem is much much harder.  It's more like finding a needle in a needlestack. Wait, no, that would be easy. How about finding a specific needle in a needlestack? There we go. Let's say they want to find the needle in the needlestack that only sews up toe holes on pink sweatsocks, for example, and of those, only the ones that are currently in business. So they throw in a holey pink sweatsock. They wait for the needle to start sewing, and then pull out the sock. In the illustration above, an enzyme's reactive cysteine (needle) has been trapped upon reacting with (sewing) an iodoacetimide (pink sock). In the interest of full disclosure, I personally have as much experience with activity-based protein profiling as I do with sewing (that being none), so I may not be the most qualified to make this analogy.

Mapping out Chemistry Lectures

Well, it's not chemistry poetry, but if I do my job well enough I should be increasing the market for it. I'm using Apple's Keynote to make these, but was inspired by the Prezi software, which allows you to navigate around a map like this and pan in and out to different locations. I haven't decided exactly how I'll present it, but the non-linearity of it helps me organize my thoughts. Deciding where to draw connections gets me to ask myself questions that I otherwise probably wouldn't. Now I think that "Periodic Table Organization" is taking up way too much real estate, and I should just toss it and put the "properties" node in the middle. Yeesh, that's going to get messy. Okay, back to it. Classes start in a week and a half.

The futility of advertising in my comments section

You may have noticed that people or computers have been using the comments sections of this sketch blog as spots for advertisement. I do appreciate the additional traffic that this could lead to. I imagine that shoppers searching for fur-lined moon boots or the fashions favored by Jon Gosselin of Jon & Kate Plus Eight fame might fortuitously stumble across my website. I imagine them exclaiming, "What's this now? You mean I can get high-quality scientific graphics from an illustrator with a dozen years of research experience? Well for goodness sake, get me to the contact page at once!" However, to be fair, I feel obligated to admit that my readership is actually quite small. To illustrate this, I made the following 3D infographic. This should make it clear that it isn't really worth the time it takes to place these ads here.

Chemistry Poetry Book is Finished!

In the past four days, I've left the apartment for a total of exactly one hour. After lunch yesterday, having hit the rather low point of eating the only thing I could find - Quaker Oats - out of the saucepan I made it in, I decided a trip to the store and a bit of fresh air would be good. The reason for my apparent seclusion is that Mala and I have been putting the finishing touches on the chemistry poetry book so we can send it off for publication soon. It is just amazing how long that can take. But now it's in good shape, and here is one more illustration. Please refrain from telling me if you see a mistake. The following is an excerpt from the poem (by Mala Radhakrishnan) that it illustrates. (Note: The poem never explicitly states which base she is, so I decided to make her lithium hydroxide, thus giving her a somewhat proportional head. Never mind that the indicator strip is nowhere near to scale...)

She looked in the mirror and stared at her face.
It just wasn’t easy being a base.
All that she wanted: a shoulder to cry on
And ways to remove her hydroxide ion.

...

Her molecular orbitals so unattractive,
Her hydroxide ion was not yet reactive.
All of her neighbors, they managed to hate her,
Except for her one friend, an indicator.

This friend would say, “It’s tough knowing you.
Wherever we go, you keep me so blue.

...

'Zyme 'Zine

Years ago while I was living in Cambridge, MA, a philosophy graduate student at Tufts told me that I should start a magazine about enzymes. “You could call it The ‘Zyme ‘Zine.” he said. He had an enormous handlebar moustache and his name was Gabriel Love, which made me think I should hear him out. I was reminded of the ‘zyme ‘zine idea while reading “Art of McSweeney’s”, a wonderful Christmas gift from my brother-in-law and sister-in-law.  But I was too busy to start a magazine then, and I’m too busy now.  I wish someone would do it though. It could be dedicated to the wonder of those amazing proteinaceous catalysts. I’ll volunteer to do the cover designs (see mock-up above), and I could submit a story about the enzyme that got me a Ph.D. – a glycosyltransferase with the unlikely habit of transferring two mannose residues with distinct linkage specificity.  McEnzyme's is not just a play on McSweeney's. McEnzyme is actually the name of a dog that belongs to a brilliant and famous enzymologist who recently asked me, “So this is what you’re doing with your life?”



Kylanders

Here's something I put together as a bonus Christmas present for husband Kyle. It's a mish-mash of logos from his three favorite professional sports teams and proof that he is no fair-weather fan. None of these teams have been particularly inspiring of late, so I made this as a celebration of the loyal fan.

(Just to be clear, this is not for sale or distribution. It was made from images owned by the NY Islanders, NY Mets, and Dallas Cowboys)

 

O'Reilly Law Firm - Help when you are hurt

This is a placeholder graphic I threw together today for my Dad's website, which I've been putting together for him while I'm home for a visit. Eventually we'll get some photos but I didn't want to leave it so sparse in the meantime. He is a workers compensation lawyer in Indiana, and recently decided it was time to expand his advertising beyond the yellow pages. Not much of an early adopter, he at one point on Christmas Eve looked around at a house full of people on iPhones, Droids, and laptops, and said, with a sigh, "If you'll all excuse me I'm going outside to club a dinosaur."

OSA holiday party

Knocked off a little early over here today for the first annual O'Reilly Science Art holiday party.  While it was undoubtedly a festive affair full of holiday cheer (thank you Bear Republic), it wasn't exactly like the holiday parties I'm used to. As it turns out, potlucks and white elephant gift exchanges really work better with more than one person (though uncannily I still somehow wound up with scented candles like I do every year). On the other hand, my jokes were unanimously funny and I did not have to wear shoes.

Scientists tackle graphic design

I spent the better part of the morning today poring over the proofs for an article on some of my postdoc work that was recently accepted into the Journal of Immunology. This is Figure 7. It may not look like much, but that is what I think makes it remarkable. Thanks to my former postdoc advisor, Jim Paulson, who sent me back to the drawing board over and over and over and over again, this simple little diagram describes three different complicated-to-explain assays that I did to ultimately demonstrate that a certain cell surface receptor is able to recycle back to the cell surface after being internalized by the cell. This was by far the best training in design that I have ever had, and I just wanted to post this as a little reminder to myself.

Doodling

Just having some fun brainstorming/doodling on a new project I have for a good friend of mine. She and I had too much fun celebrating with the newly minted Dr. Angelyn Larkin over the weekend to get much work done on it though. Congratulations Angelyn!

A new chapter in icons

The fourteen chapters of Mala Radhakrishnan's chemistry poetry book have titles like Gases, States of Matter and Intermolecular Forces, Solubility and Equilibrium, Periodic Trends, etc. I designed these simple icons to introduce new chapters along with the titles. Obviously we are in the late stages of getting it together, and it should be available  in early 2011!

Guess which previously posted sketch was a draft of this image

Well I'll tell you. I posted the first draft of this image on October 30th, and if not for the telltale bottle-brush shaped mucins, it would hardly be recognizable as the same project. I can't tell yet whether this is the final version, but if I may say, I'm pleased with the degree of improvement that came from just a couple rounds of editing. (After all I described my version 1 as "sort of terrible".) I let go of the red background to give a little more overall brightness, and went instead with red tones for the cells. This pushes the background back and brings the cells forward. Also, instead of using morphology, I used color saturation to help depict the cell changing from normal to cancerous (uncontrolled growth) to apoptotic (dying).

Unanimity is overrated

Right now I'm working on some late stage (hopefully) editing of a website banner image (above) for a biotech client. To get an idea of you how much editing was done, you can revisit the November 6th post, which is the first draft of the image. Apparently there was some disagreement among the clients about my original interpretation, which I am thrilled about. While effectively communicating science is always my main goal, a close second is getting people to look at their work in a new light, and maybe even question some assumptions that had been lying dormant. At the very least, just deciding what is important to convey in an image can be a powerful exercise. My former postdoc advisor is great at this. I have no idea if any of this occurred among my clients, but it's nice to think about as I agonize over hues, draw endless stretches of polymer, and skootch objects around nearly imperceptibly, pixel by pixel.

Getting by with a little help from my embossments

Last week, since I didn't have any classes to teach, I was very lucky to tag along with the husband on a work trip to Hong Kong. I still had to do some work there, but I was doing it with a view of Hong Kong Island from the Kowloon peninsula. Most of our activities revolved around eating a gluttonous amount of delicious food, but another highlight was the journey to Lantau Island to see the 26m-tall, 202-ton bronze Buddha statue. It was breathtaking, but there is a catch. You have to take an absolutely terrifying ride on a gondola high up above mountains and water (see above, photo courtesy of husband). It didn't actually occur to me at the time, but I later realized that I was carrying in my purse some symbols I had made using an embosser and some scratch paper the day before at the Hong Kong Museum of Art. From top to bottom they are clouds, which represent luck; a bat, for good fortune and well-being; a butterfly, for blessings, longevity, and happiness; and finally, the symbol for longevity. I wonder whether, as I clutched the bench, I would have felt any better knowing that these were with me. Probably not. Maybe I would think, "I wonder if anyone will find my embossments after they scrape me from the ground? They're definitely toast if we fall in the water. I wish I had a Ziploc baggie. They're quite nice." Well, I'm glad I survived to share them.

The Atoms' Family

More from Mala Radhakrishnan's book of chemistry poetry, "Atomic Romances, Molecular Dances", coming soon!

"There’s “Na,” my sister. She’s over there.
Like me, she ought to be sealed up with care.
She’ll react with water or even the air,
Giving her ’lectron up anywhere.

And here is potassium. He is my brother,
Ionically bonding with things like no other.
Quite social like I am, and much like my sister,
He just met a halogen, has already kissed her!

My parents, “Rb” and “Cs” are they,
They’re dying to give their electrons away.
To ours are their properties mostly the same,
But they’re so extreme they can put us to shame.

You cannot see francium, here in this snap.
He left in a radioactive mishap.
The legend reports that he was unstable.
To me, his existence is merely a fable.

And there is a rumor that’s having a run,
That hydrogen’s my illegitimate son.
I swear he was left, though, on our front stoop,
And we’re not really sure he belongs in our group!"

Which one of these is not like the others?

Not likely to be seen on Sesame Street, this illustration-in-progress describes a tortured enantiomer named Danny who thinks he's finally found his niche with the Asymmetric Dancing Team. As the poem "Enantiomer in the Mirror" by Mala Radhakrishnan explains:

"Danny was absolutely excited,

For never he’d similar molecules sighted.

So now he could not keep his eagerness in.

“I’m finally going to really fit in!”

 

But then, as the dancers composed a straight line,

The massive formation was no longer fine.

“Hey Danny, what’s wrong with your orientation?

This line must be perfect with no deviation!”

 

So Danny then flipped all around and turned,

But soon, he became extremely concerned.

Although he’d the very same groups attached,

The others’ appearance he just couldn’t match."