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The WISL Thesis Award

Back in my second year of graduate school, UW-Madison chemistry professor and director of the Wisconsin Initiative for Science Literacy Bassam Shakhashiri issued a challenge to all of the department’s graduate students. Write a chapter in your thesis explaining your research to the general public, he said, and I’ll give you $500.

Thus was born the WISL thesis award. At the time, graduating and writing a thesis were only nominally on my radar – I had a good three years left before I really needed to worry about it. By the time I finally sat down to write my thesis, I wasn’t even sure the awards were being offered any more.

But the idea was still kicking around in my head, and since I was in full-on science communication mode at the time (I wrote most of my thesis DURING my summer as a AAAS Mass Media Fellow – not something I’d necessarily recommend!), I figured what the heck, why not. If nothing else, Bassam would probably still enjoy reading it, and I could send a copy to my parents, too.

The resulting chapter landed in Appendix B of my thesis, but then sat around on my hard drive for seven months before I finally remembered to send it to Bassam. But send it I did, and since it turns out the WISL thesis awards are still going, my thesis chapter is now out there for anyone and everyone to read.

I hope you’ll head on over and check it out, and take a look at what some of the other recent UW-Madison grads wrote about their research, too. And if you’re writing (or getting ready to write) a thesis of your own, even if you’re not a UW-Madison chemist, consider writing one of these thesis chapters yourself. If nothing else, it will give you some practice writing – and might give you something you can send to your parents.

P.S. Yes, it’s 11 pages long.  It’s a thesis chapter.  If you just want the upshot, try this:

I spent my graduate career sticking molecules to surfaces, and then blasting them with lasers to make them “dance.”  The idea was that figuring out how the molecules dance tells us a lot about what’s going on at the surface… but really, blasting stuff with high-powered research lasers is just really cool.

Happy? :-P

Revelations on starting a postdoc

As some of you know, I finished my journalism fellowship and defended my thesis in August, and have now moved on to a postdoc. Between defending and trying to get my bearings in a new city and a new lab, I haven’t had much time to think about this blog, but my friend Kaisa and I have challenged each other to do a post a week in November, so we’ll see how it goes! Here’s my first.


I have a confession to make: for much of the past few years, I was convinced I was a bad chemist.

In large part, this had to do with with my research field. As a physical chemist, I spent most of my time shooting lasers at things and writing computer code, rather than mixing chemicals together to make reactions happen.

The few times I did “do chemistry” in the latter sense, my project was such that it rarely made sense for me to try a reaction more than once or twice. If it failed the first time around, it was better for me to move on to something else rather than try to troubleshoot it.

The upshot of all of this was that I didn’t “do” chemistry very often, and when I did, the failures were much more frequent than the successes.

So I was a bit terrified to start a postdoc in a lab where I would actually be expected to do some synthesis. What if I couldn’t do it? What if every reaction I tried resulted in failure?

But two months in, having had the opportunity to try and re-try reactions and troubleshoot them until they work, I’ve realized that I’m better at this stuff than I thought I was. And I know more of these techniques than I thought I did.

Need to do an air-sensitive reaction? Oh yeah, one of the few molecules I made during grad school required me to use a Schlenk line. I know how to do that.

Need to recrystallize a product to remove impurities? Well, I haven’t done recrystallizations since sophomore organic lab, but I know how, and it’s not that hard to pick it up again. Just like riding a bike, really. I can do that.

And need to characterize the polymer I’ve made? Gel-permeation chromatography is just like doing HPLC to purify proteins. I can do that, too.

I don’t claim that I’m ever going to be a purely synthetic chemist, nor do I really want to. My interests really lie in understanding and manipulating the physical behavior of molecules and materials, rather than in devising new synthetic methods.

But at the same time, it feels really good to know that I can do synthesis when I need to. It feels like it removes a lot of the roadblocks to delving into new research areas. If there’s something I want to study, I don’t necessarily have to wait for someone to make it for me; if I want to, I can make it myself.

And beyond that, there’s also something really empowering about knowing I can transform simple molecules into things that are much more complex. Knowing I can take a bunch of colorless liquids and make sparkling yellow crystals, or knowing that I can take simple small molecules and string them into chains in a controlled way is sort of like knowing I can do magic.

I know I’ve still got a long way to go as a postdoc. There’s a lot to learn, and I’m sure I’ll run into many roadblocks I have to overcome along the way.

But for the moment, I feel like I’m discovering something new about myself, and it’s helping build my confidence that I can actually DO this.

Apparently I’m a chemist after all.

Don’t blame the chlorine, folks!

This is a slightly belated entry for the #chemsummer blog carnival. Between thesis-ing and writing for the Journal Sentinel, I’m a little behind on a lot of these things! Hope you’ll enjoy it anyway.

When I think summer, I think backyard barbecues, running through sprinklers, and jumping into swimming pools. Or diving into swimming pools, actually – one of the most terrifying moments of my elementary-school life was when my friend Katie (a competitive diver) convinced me to jump off the 3-meter board at a local pool.

Katie had blonde hair. And she spent so much time in the water that by mid-summer, her hair took on a semi-permanent green tinge.

Me, I have brown hair, so I never suffered this terrible fate. But now, 20 years later, my chemist brain asks — why green?

Growing up, we always thought it was the chlorine. And it was one of those things that we just *knew* and didn’t need to question.

But the answer, it turns out, isn’t chlorine. It’s copper.

Copper gets into swimming pools in a couple of ways. Copper salts, like copper sulfate, are used as algicides. But copper can also get into the water as copper plumbing in the pool corrodes.

And while copper metal is a pretty reddish-brown color, copper compounds can be red or bright green or blue or even black. This color change happens because the energy levels of the copper atoms shift as the copper oxidizes (loses electrons) and binds to other chemical apendages (ligands).

Taking images of cross-sections of single strands of hair shows that the copper is mostly confined to the hair’s outer layer and doesn’t penetrate too far inside.

From what I could find, however, scientists aren’t exactly sure how copper binds to hair, though it sounds like it might be because carboxylic acid sidechains in the keratin in hair grab onto the copper ions.

And this provides a clue to why some of the oft-recommended home remedies might work for getting rid of that greenish tinge: two of the classic recommendations, lemon juice and tomato juice, both contain large amounts of citric acid, which can also grab onto, or chelate, metal ions.

If these acidic juices don’t work, other chelating agents can do the trick as well. EDTA is supposedely a common ingredient in swimmers’ shampoo, and case-reports suggest penicillamine shampoos also work. But normal shampoo probably won’t — detergents don’t do much to grab that metal and get it out of there.

But perhaps the best solution is simply to not get the copper into your hair in the first place. Swim cap, anyone?

Further reading:

Here’s a research paper on how different hair pre-treatments affect the amount of copper hair picks up, and includes scanning electron microscope images of where the copper sits in the hair fiber

Here’s a nice description of crystal field theory, which explains what controls the color of transition metal compounds

Shining Light on the Toxic Effects of Nanoparticles

This post is long overdue, both because I haven’t posted in  more than a month, and because I’ve actually had this research highlight written since January – it was one of the writing samples I submitted for my application to the AAAS Mass Media Fellowship this spring.

I’m pleased to say that I’ve received the fellowship this year, and will be spending the summer writing for the Milwaukee Journal Sentinel before heading off to do a postdoc in the fall.  This will make my graduation & moving plans a little complicated, but I’m really excited about this opportunity.

At any rate, I’ll keep you updated as I go, but for the moment – zebrafish!


Shining Light on the Toxic Effects of Nanoparticles

Exposure to light and tiny titanium dioxide nanoparticles can be a lethal combination – at least, if you’re a zebrafish.

According to researchers at the University of Wisconsin-Madison, raising zebrafish in water containing titanium dioxide nanoparticles and exposing them to light caused the fish to be badly deformed and die much more quickly than fish raised in normal environments.

Understanding the toxicity of these materials is critical because titanium dioxide nanoparticles are finding their way into a growing range of consumer products.

Titanium dioxide nanoparticles are especially useful in sunscreens, because they effectively absorb harmful UV rays without making the sunscreen pasty and opaque. However, similar nanoparticles also form the foundation of some next-generation solar cells and are used to treat wastewater in sewage plants.

Yet according to the researchers at UW-Madison, nobody really knows what effects these nanoparticles have when they get out into the environment.

The UW team explored this question by raising zebrafish embryos in water containing titanium dioxide nanoparticles. They kept some fish in the dark and exposed others to light to see whether or not light exposure changed the nanoparticles’ effects.

Other researchers have studied nanoparticle toxicity using isolated cells grown in the lab. However, the toxic effects on cells in a dish can sometimes be different than the effects on a whole organism.

By using zebrafish, the researchers at UW-Madison were able to look at the toxicity on a larger scale. Zebrafish are ideal for these sorts of experiments because they grow quickly. They are also clear, so the researchers can easily see any growth defects that appear.

Researcher Ofek Bar-Ilan and coworkers found that fish exposed to the nanoparticles but kept in the dark looked normal. Fish exposed to the nanoparticles and kept under bright light, however, had deformed heads and tails, and their growth was stunted. The fish exposed to both nanoparticles and light also died much more quickly than fish kept in the dark.

For something so small, the nanoparticles seemed to do a lot of damage.

Read more…

The Cookie Experiment, Part II

So, on Wednesday, I told you about an experiment that my friend Tracey and I did to look at the effects of different flour-weighing methods on cookie consistency (and taste!).  I left you hanging right after telling you about our baking procedure, but never fear: the rest is coming today. So, without further ado:

Results and Discussion

1. Visual appearance & spread

Batch 1 (sifted flour) appeared thin and nicely browned. Batch 2 (scooped flour) did not spread as thin as Batch 1 and browned nicely on the edges but remained poofy in the center. Batch 3 (packed flour) only browned on the very bottom and was very poofy (almost appearing uncooked) on the top. Photographs of the 3 different batches are given below.

We also quantified the spread of the different batches by measuring their diameter with a ruler. The diameters as a function of flour content are reported below:

Cookie diameter as a function of mass of flour used.  Probably should have reported the x axis as percent weight rather than absolute weight, but didn't weigh the entire batch!

Cookie diameter as a function of mass of flour used. Probably should have reported the x axis as percent weight rather than absolute weight, but didn’t weigh the entire batch!

We found that cookies made with less flour spread more during the baking process – we suspect this is because the flour soaked up a lot of the liquid (fat & water) in the dough and dramatically decreased its viscosity, but we didn’t have a good way to check this in our experiment.

2. Taste-test obsevations

Read more…

Weigh it out: the cookie experiment, part I

A few months ago, I got a new cookbook and was delighted to find that the author included weights for all of her dry ingredients. While measuring dry ingredients by weight is de rigeur in Europe, it’s somewhat uncommon in the US.

But as a chemist, weighing my dry ingredients rather than measuring them by volume is almost second nature. In the lab, we always measure powdered chemicals by weight, because their volume can vary a lot depending on how tightly they’re packed!

This isn’t something that we usually worry about too much in the kitchen, but it can make a big difference. So, my lab-mate Tracey and I recently did a little kitchen experiment to demonstrate how much different measuring techniques can affect the final properties of a dish.

We chose to study chocolate chip cookies, because really, who doesn’t like cookies? (Also, we were sort of inspired by this experiment). The idea behind the experiment was simple: make three batches of cookies, and measure the same volume of flour by different methods in each batch.

In one batch, we would sift the flour; in another, we’d scoop it like normal, and in the third we’d pack it tightly in the measuring cups. We hypothesized that sifting the flour would give us much less flour (by weight) while packing it would give us much more. We also hypothesized that the amount of flour in the cookies would affect their texture, with more flour leading to dryer, denser cookies.

Clearly, this is important research, necessary to baking enthusiasts everywhere, right? Good – glad you agree! Without further ado, I’ll walk you through our procedure and our results… it’s like a lab report, but way tastier :-D

Tracey is ready to make some cookies - are you?

Tracey is ready to make some cookies – are you?

Read more…

Notes on why nanowires might make better batteries

As I mentioned in my last post, I wrote a “news story” for a fellowship application about new materials for lithium ion batteries that I really wasn’t happy with. However, I realized after canning the story that the notes I wrote for myself – in the format of a series of questions followed by answers culled from the paper – were actually kind of a neat research highlight on their own.

So, I’ve rewritten them in a readable format, and in reasonably general terms. Take a look – I’d love some feedback on whether this version “works” or not.

1) So what’s the big picture? Who did this experiment, and what did they study?

This paper was on an experiment done by Linsen Li and Fei Meng in Song Jin’s research group at the University of Wisconsin-Madison. Jin’s group investigated whether a new material (nanowires made of a compound called ferric fluoride) could be used to make better cathodes for lithium ion batteries.

2) Don’t we already have good lithium ion batteries? Why do we need to make them better?

Lithium ion batteries have a pretty high energy density. This makes them really useful for portable devices where we want to be able to carry around lots of stored energy without much weight.

However, current lithium ion battery technologies have limited storage capacity. Their capacity is fine for relatively low-power devices like cell phones and laptops, but they generally can’t supply enough energy for large-scale applications like electric vehicles and storage on the power grid.

New materials (like the ferric fluoride nanowires in this paper) have the potential to solve these problems. Using these types of new materials, we might be able to make lithium ion batteries that can store more energy and are more useful for large-scale energy needs.

3) Why is ferric fluoride useful?

Read more…

Reflections on a failed (?) writing sample

As some of you know, I recently applied for the AAAS Mass Media Fellowship (okay, technically called the “AAAS Mass Media Science & Engineering Fellows Program”, but that’s a mouthful). The application required two writing samples. The first was allowed to be on any topic and in any style appropriate for the general public; I submitted a revised version of this post.

The second writing sample was required to be a “news article” on a recent paper from the scientific literature. Unfortunately, most of my articles for the Daily Cardinal weren’t recent enough, but while browsing through journal abstracts I found a neat paper recently published by a couple of research groups here at UW-Madison and decided to write on that instead.

But… it turns out that UW-Madison doesn’t actually have a subscription to the journal this paper was published in(*).

So, I ended up writing my story off a proof borrowed from one of the authors. But as I pulled all my application materials together a few days the deadline, I realized that I needed an official copy of the paper to submit with the application (the proof I was using didn’t have the publication date on it), and I panicked a bit because I wasn’t sure that interlibrary loan would come through in time.

Which meant that I ended up hurriedly sifting through my feed of recent UW-Madison research, found an interesting article, and wrote a backup story.

Read more…

New Year, New Resolutions (and research on chocolate chip cookies!)

I’ve been silent on this blog and on Twitter for over a month now, mostly because I’ve been preoccupied with other things. Applying for postdocs and a fellowship, writing papers, even performing in the Nutcracker(*) – you name it, I was probably doing it.

But, while I’ve still got some work to do on my postdoc applications, and there are always more papers to be written, I’m determined to get back to this blog in the new year. My goal last year was to average a post every two weeks, which I didn’t quite manage (I wrote 16 science-related posts and 5 articles for the Daily Cardinal over the 11 months since starting this blog), so I’m going to try for that again this year, and hopefully I’ll make it this time.

I have plenty of ideas – and several half-written posts – floating around on my Google Docs account, so it’s mostly just a matter of making myself sit down and write. Prod me if I start to fall behind, okay?

In the spirit of “catching up”, I spent half an hour yesterday reading through all of the items in my RSS feeds that I neglected over the holidays. In particular, I have a feed that sends me the titles of every single science- and medicine-related paper published by UW-Madison researchers each week. This feed averages 90 to 150 items a week(+), and when I logged in to Google Reader this week I found 345 unread items.

There are a couple of pretty cool topics in there, ranging from using nanowires to make high-capacity cathodes for lithium ion batteries to studying whether giving birth to twins affects cows’ future reproductive success.

But my favorite, by far, is a paper from food science in which the authors studied chocolate chip cookies. I couldn’t resist writing a short research highlight on this one just for fun… because really, how cool is it to bake chocolate chip cookies for research?!

Read more…

Growing up with Kitchen Chemistry (and my abiding love for Harold McGee)

When I picture my mother’s kitchen at home in California, I see sunlight streaming through the window above the sink. I see her red Kitchen Aide, the white stovetop, and the oven and fridge bookending the narrow galley kitchen. And on the bookshelf above her kitchen counter, I see a familiar red book.

This book is one of the few books I know is on my mother’s kitchen bookshelf, and surprisingly, it’s not a cookbook. Instead, it’s Harold McGee’s On Food and Cooking, which is easily one of my favorite chemistry books of all time.

(Yes, this is actually a photo of my mother’s kitchen bookshelf, delivered from California by the magic of an iPhone and the internet.)

Harold McGee has been a fixture in my mom’s kitchen for as long as I can remember. We frequently referenced him during our kitchen adventures when I was growing up. Want to know why whisking eggs and oil makes a nicely emulsified mayonnaise, while whisking water and oil just makes a quickly-separating mess? Look in Harold McGee. Want to know why melted chocolate siezes and gets really gross if you add too much liquid? Check Harold McGee.

Sometimes, it felt like we were on a first-name basis with him. It wasn’t just, “look it up in Harold McGee,” but instead, “ask Harold!” It was as if he was a trusted friend and teacher, standing by to answer even our most mundane kitchen chemistry questions.

The answers often straddled the border between simple and magical, and if you kept reading, you almost always learned something new. Mayonnaise forms a nice emulsion, for example, because egg yolks contain proteins and other molecules that coat oil droplets and help keep them suspended in water. But did you also know that when you beat a single tablespoon of oil into a mayonnaise, it gets broken up into something like 30 billion tiny droplets?

When I started thinking about topics for this week’s food chemistry carnival, I pulled out my copy of McGee and turned to the section on pastries, thinking it would be fun to write about what exactly it is that makes the perfect pie crust (which, it seems, is a popular topic this week – for the record, my favorite is the Cook’s Illustrated vodka pie crust!). But as I started flipping through the book, getting sidetracked by countless other tidbits of food-related information, I realized that I really just ought to write about On Food and Cooking itself.

Read more…


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