The Short Answer, Issue #5

I have to admit, this one sort of snuck up on me. Earlier this week I realized that today, and not next Friday, is the last Friday in July. How am I supposed to remember that there aren't 32 days in July? I know there's some knuckle trick but I can't be bothered. The good news is that this paper is hot off the presses, published online four days ago, and it's pretty interesting. Here's the pdf.

It's alive! It's ALIVE!

Here is another piece of candidate cover art, this time for Nature Neuroscience. The authors have discovered a new type of neuron whose electrical action potential can trigger stem cells in the adult brain to make new neurons. Hooray! 

Candidate Cover Art for PNAS

It's been too long since I've shared any real illustrations, so it's about time. Dong Wang's group at UCSD has used sophisticated computer simulations to track the movement of an RNA polymerase along a DNA template at atomic resolution and on the millisecond timescale. They were able to get information that you just can't get from X-ray crystal structures, and identified two intermediate states that no one had ever known of before.

Though I actually may have believed that I had invented the idea that NMR and computational dynamics are to X-ray crystallography what film reels are to polaroid snapshots (first way back here), I suspect that may not be the case, and now that it's been used by someone else on the cover of this month's Nature Chemical Biology, I know it's time to retire the analogy, at least for my purposes.  

The Short Answer, Issue #3

I started this little series when business was a bit slow, and shortly thereafter I happily became very busy for a couple of months with three cover art candidates, two TOC graphics, a figure for a review article and another for a biotech's slide deck, and one very touching gift from some graduating seniors for their beloved undergraduate research advisor. So sometimes, "The Short Answer" will very literally live up to its name, such as in this particular installment. Here, I really picked out what I found most compelling and glossed over many details (maybe that is the point of this thing anyway?). There's plenty more meat to the story so I recommend checking out the full paper if you're interested. 

As always, click here for a pdf version, in case you don't have your magnifying glass handy. To see older installments you can check out the "archive" (of two additional issues) here


My thumb is famous. I have arrived.

Yesterday a big story hit multiple news outlets - that of a living organism that grows and divides with an expanded set of nucleotides. In addition to the usual G, A, T, and C, a group at the Scripps Research Institute led by Floyd Romesberg has discovered a novel synthetic base pair comprised of two nucleotides that, interestingly, don't even hydrogen bond with one another. They introduced these new bases into the DNA of bacteria, and lo and behold, the bacteria grew and divided, passing this strange new code to their progeny. 

I had been hired to design candidate cover art for the issue of Nature that this paper came out in yesterday, but the project was halted when they realized that the paper was being fast-tracked and the cover had already been chosen. Nevertheless, the clients kept the drafts of the designs we had been working on, just in case they may come in handy for press coverage. The next thing I knew, my thumb was on BBC News, NPR's blog, and a handful (no pun intended) of other news sites as well. If you click on the image below, you'll see a gallery including the other two drafts. The printing blocks were a very rough draft, but got picked up by Live Science. Apparently no one wanted to use our favorite - an idea I had while hanging out with my two-year old. So while both he and I still remain relatively anonymous, my thumb is skyrocketing to superstardom. 

The inaugural Journal Club!

So I recently had this idea. Journals publish highlights as supplements to a few of their articles, and journals also display cover art. Highlights are wonderful, but still a time investment to read. Cover art is beautiful (and please keep giving me those projects because I love them) but their information content is somewhat limited. Maybe what's missing is something in between, not to replace either one, but as an additional tool for communication.  One aspect of working in a lab that I really miss is journal club, or getting together with lab mates to discuss recent papers. One person would present a paper and everyone would discuss its merits and pitfalls. The format I've adopted here is inspired by that idea, but because I've also challenged myself to keep it to an 8.5 x 11-in print size, the analysis necessarily takes a back seat to the summary.

Shown below is the inaugural journal club. To download a pdf for easier viewing, click here. I won't say much about the paper itself since the idea is for the image to stand alone, but the topic is near and dear to my heart since I worked on Siglecs during my postdoc, and glycobiology in general since graduate school. I won't always be so self-serving, but the topics will primarily come from chemical biology. 

My goal is to start out at once a month and then try to increase it to every other week if I can, because another one of the challenges is to choose brand new papers and get these illustrations out quickly. But let's say for starters I'll post them on the last Friday of each month. That sounds like a perfectly procrastinatory schedule that should suit me just fine. Let's just hope this doesn't end up like the time I tried to start doing pilates, or the time I tried to start learning Mandarin, or the time I tried to.....

Dream Job

It was with mixed emotion that I saw the completion of Behind the Scenes at MIT, a multi-year project whose goal it was to show undergraduates how the concepts they are learning are actually being applied to real research problems, and also to show the human side of research. Cathy Drennan, an HHMI professor and investigator in the departments of chemistry and biology at MIT, sought to create 2-3 minute videos in which researchers from graduate students to full professors describe their research to an undergraduate audience. These were accompanied by short personal videos with each researcher describing his or her background and what inspired them to choose their path. 

This is what my dream job looks like. First I was given the research video to watch, and then I created animations that would illustrate the research that was being described in words. Sometimes the producers would have an idea for an animation, and sometimes I was given carte blanche to come up with something. There are twelve research videos, and all told I think I made around 15-20 animations. Some of them can be found here on my website in the Flash animations portion of my portfolio, but all of them can be found embedded in their respective videos at http://chemvideos.mit.edu/all-videos/. I don't think I fully realized until the project was over how fortunate I was to work with such great people and to have a project of this scale that was both rewarding and fun. 

Here is former postdoc Sarah Bowman's research video. My animation comes in around 01:17 or so. I have a strong recollection of being very pregnant and moodily fighting with the flagella to get them to twirl just so. 

Happy New Year!

This year I resolve to get better at, and do more, 3D animations like the one below, which just came out as a supplement to a paper published in the January issue of the Journal of General Physiology

What I love most about animation is when a question arises in the making of one that gives the researchers pause, requiring them to think about the data in a way they hadn't before, or to take a deeper look at some aspect of their model. When you have to know not only how, but also when and where and in what order things happen, this can open up new questions and perhaps even spur future experiments. This functionality of illustration and animation doesn't get talked about as much as their important role in the communication of science, but perhaps it should. Many animators of science before me have figured this out, and are doing amazing things to pursue such avenues, including Janet Iwasa, Gaël McGill, and Graham Johnson, just to name a few. 

 

Nerdy nuptials

I'm eager to share a 3D animation that I recently finished, but I have to wait for it to be published. In the meantime, I am happy to share a wedding invitation that I designed for a friend and her intended, both of whom are scientists (some details have been removed to maintain their anonymity). It includes an X-ray crystal structure and a condensation reaction.

Here is how marriage is like a condensation reaction:

1. It doesn't always work.

2. There is a loss of (degrees of) freedom.

3. It can involve dehydration (primarily among the wedding attendees if there is an open bar).

4. It requires energy.

but more importantly, 

5. It can form a nice strong bond, and

6. The product can be much, much greater than the sum of its parts. 

 

In my experience, thermodynamics notwithstanding, I've found it to be quite favorable. 

One ring to transcribe them all...

This just came out last week. It's a project I did with an old classmate of mine from MIT who showed how important the 5-membered ribose ring of the DNA sugar-phosphate backbone is for transcriptional fidelity. When they opened it, or unlocked it, as they describe, the polymerase no longer discriminated between different bases. It takes me back to the time as first year grad students when we built an enormous 3D model of DNA in JoAnne Stubbe's class. Good times. 

A Chemical Perspective on Transcriptional Fidelity: Dominant Contributions of Sugar Integrity Revealed by Unlocked Nucleic Acids

Liang Xu, Steven W. Plouffe, Jenny Chong, Jesper Wengel, Dong Wang. Angew. Chemie Int. Ed. Volume 52Issue 47pages 12341–12345November 18, 2013

Passing the boron

I'm working on a new project that is, again, super secret until publication, but I can show this "old" one now, the teaser for which I posted last. The bimetallic catalyst shown at the top is capable of efficiently borylating aryl groups as demonstrated in this relay. First the catalyst breaks the B-H bond and breaks apart itself. The yellow boron (attached to hidden "R" groups) then gets traded for a H with benzene. As the borylated benzene leaves the track, the two halves of the catalyst, both now toting H's, come together to reform their bond and make diatomic hydrogen in the process.  

As a footnote let me add that atoms do not have arms. They have electrons. Which means that you cannot know both the position and momentum of the arms in this illustration. Which is a lot like how I dance. 

A teaser...

I can't say much about this yet, but the complete image, from which this slice was taken, is yet another cover art candidate.  That makes three that I'm awaiting decisions from editors on. I'm running out of fingers to cross. 

Another project under wraps

I've just finished another cover art piece, and like the previous project, the client has asked me to keep it to myself for a bit, this time just until the paper comes out. So for now I'll share another of my free-time creative endeavors. 

These are potential logos for my son's babysitter's photography business. She will pay in babysitting hours, thus enabling a nice long afternoon birthday brewery tasting tour for the hubs. Here in San Diego you can't throw your surfwax without hitting a craft brewery, so it was easy to find a rash of excellent tasting rooms to sample that are not too far from us. As much as I miss the east, it is hard to complain about living here (and rightfully so, no one would listen if I did). 

Back to basics

Over the past week I created two images for a new client who is applying for academic jobs this fall. 'Tis the season! The illustrations are for his original research proposals, and though I didn't have to sign a CDA, he doesn't really want the ideas getting out there. It of course flattered me that he thought that my readership is such that this might be a concern, but you just never know. So I'll hold off on posting them anywhere until he deems it safe and I'll share a couple of drawings I did over the past week instead. 

No matter where I am in my career I will always periodically go back and tune up my drawing skills. Over the past few years my nights have been consumed with preparing chemistry lectures and grading never ending piles of exams and quizzes. Now that I have my nights back again I've been stepping away from the computer more and more. I just learned this method of sharpening charcoal pencils with a razor blade from Jeffrey Watts of Watts Atelier in San Diego. It is an art form unto itself and if you look closely you'll see my technique still leaves a lot to be desired. But I was inspired to give it a try and so I grabbed a few nice geometrical objects from around the house to draw. I stole some toys from my son and dug up this old mannequin, then settled into the garage (which ironically has the best lighting) with a podcast and a couple of albums from The Walkmen. Now that football is back I don't think that I was too terribly missed. And it's nice to be getting my hands dirty again.

If it's good enough for Norman

This is an early draft of an illustration I'm working on for a Systems Biology textbook. It is meant to very simply get the point across that transcription is way more complicated in eukaryotes than in prokaryotes (the distinction is made from the previous figure in the book). One of the challenges of doing these illustrations is that the book will be printed in duotone, which means grayscale plus one color - that color being a particular shade of red that was specified by the publisher. The lighter pink that you see is just a partially transparent version of the red, a trick to get more colors out by taking advantage of the value range.  

If I thought at first that this seemed restrictive, I quickly remembered that from the time of Norman Rockwell's inaugural Saturday Evening Post cover in 1916 until 1926, when the Post printed their first color cover, he had to do all of his covers in duotone, also relying on a specific shade of red. Sure, he didn't have to distinguish different classes of biomolecules from one another or try to make sense of hulking multi-protein complexes, but how frustrating it must have been for him as a painter. I used to live in Massachusetts and I visited his well-preserved studio in Stockbridge. I stood in the spot where many a model stood for him, a perfectly northern-lit space that ensured that the colors changed as little as possible as the sun moved through the sky. A fat lot of good that did him while every tube of paint but red, white and black must have sat gathering dust in the back. Obviously I can't compare my work to Normal Rockwell's, but I can draw a lot of inspiration from his gorgeous use of duotone and his uncanny talent to tell an entire story with a single image. 

Up and running with Maya!

So I finally got around to purchasing and learning how to use Maya, the 3D modeling and animation software that is also used in gaming and many animated and CG-laden Hollywood movies. It's been widely adopted by science illustrators and animators, which made it an easy choice because there are some fantastic tutorials available for importing X-ray crystal structures from the PDB, not to mention many other tutorials that are specific to cellular and molecular processes. 

Not long after, I was commissioned to create cover art for a journal that always has exquisitely beautiful covers. No metaphorical cartoons cutting it here. I knew I had to do something really striking, so I was relieved that I had added Maya to my skill set just in time. The paper is about the discovery of a link between a specific gene and the invasiveness of certain cancer cells, so I decided on a close-up of a metastasizing cancer cell invading neighboring tissue. Now, with this kind of ridiculously complicated (for a newbie) modeling project under my belt, I feel pretty comfortable with the software, even though I know I've only just scratched the surface.  Animation, I'm coming for you next. 

We are still waiting for a decision on the journal cover, but in the meantime it is being used by a couple of university news outlets.  I'll post the original reference once the issue is out.

Pretty excited about my new business cards

By a complete coincidence I stumbled upon this husband-wife duo (Byvik Ink, even love the name) who runs a 19th century letterpress out of their garage. Then I realized that they are in the San Diego area. Done. And as it turns out, really lovely people. So here is one of the cards, which were printed on 100# Speckletone Starch White paper from French Paper (which, despite the name, is in Michigan). They feel amazing and the embossment makes them seem like they are from another time. Love them. I don't know if I can give them away. It's a good thing I got 250.

Not my first rodeo

Okay, this isn't a rodeo, and furthermore, if it was, it would most certainly be my first. But this is the title that got stuck in my head for the draft below which follows from the last post.  

torerodraft.jpg