Adventures (near) Lyon! 4: Paris and the Pasteur Institute

We hit the road to Paris and paid a visit to the Pasteur Institute. The Institute’s museum is located in Pasteur’s former house and includes several rooms preserved since the 1800’s! One of my favorite rooms contained glassware, instruments, and even chemicals that Pasteur used in chronological order, tracing his work from fermentation to pasteurization to vaccination. The rest of the Institute is a scientific research center, something like an amalgamation of the CDC and National Laboratories in the United States.

Everybody with any interest in science has heard of Pasteur, but to a practicing scientist the myth of Pasteur seems a little too perfect. Pasteur’s productivity was a cut above everyone else’s during his time. To an extent, this was because he had latched onto a deep idea that everyone else had missed. At the same time, the story of Pasteur has a dark side: he kept his notebooks secret for his entire career. Once they became public, it was clear that he had exercised some deception in reporting his discoveries. I suppose we can conclude that in launching the field of microbiology, he was as much a marketer as a scientist. The whole issue of Pasteur’s legacy is interesting because his discoveries directly saved thousands of lives. It’s hard to argue that his deceptions weren’t worth it in the long run.

In the afternoon, we checked out some of the research facilities. I toured the protein crystallography center, where automated machines are used to set up thousands of crystallizations in a matter of a few minutes. The entire process of forming and handling crystals is managed by machines—all the scientist does is examine images and use computer interfaces to “grab” microscopic crystals. Truly amazing, as I can still remember when the process of protein crystallization was extremely painstaking and long winded!

For the rest of our time in Paris, I tried to get off the beaten path as much as I could (can’t stand waiting in lines). There are all kinds of interesting hidden gems in the vicinity of the more popular tourist attractions in Paris. For example, the Crypte Archéologique museum is underneath the Île de la Cité—while people were waiting to see Notre Dame above me, I was exploring Roman ruins unearthed at the center of Paris in the nineteenth century!

Earlier this year, I happened on a neat little book about experiencing Paris and its environs by train. The first chapter mentions several cathedrals that are just a short train ride from the center of Paris. The cathedral of St. Denis, near the end of the no. 13 Métro line, contains the remains of most of the kings and queens of France. In contrast to Westminster Abbey in London, this church is far from the center of Paris, evoking the classic image of the French aristocracy as detached and elitist. Smiling down on the unassuming sarcophagi of Marie Antoinette and Louis XVI is exactly as satisfying as it sounds! The crypt beneath the church also includes an ancient Roman cemetery containing the remains of Saint Denis himself.


Adventures (near) Lyon! 3: Grenoble on a Whim

Last Saturday, on a whim (and a waitress’s recommendation) I took a train to Grenoble in southeastern France. The city is just a jump over the mountains from Turin, Italy. It actually reminded me a lot of Denver, in that the city itself is mostly flat but massive mountains are visible just a few miles from town. I was hopeful that without a car, I could still find my way to some hiking trails…thankfully, that was the case!

Upon arriving at the SNCF station in the morning, I hopped out and took a walk through town, aiming to fuel up before hitting the mountains. After grabbing a sandwich I discovered Grenoble’s wonderful cable car, which takes passengers from the city proper up to the Grenoble Bastille, an old military fortress now home to a museum, restaurant, and monument to the famous French geologists of the Alps. Placards point out the names of mountains in the distance and recount the geological history of the region. Can you believe the view of the city from the Bastille?!

The Bastille is also the trailhead for a number of hiking trails heading up Mount Jalla, a peak in the foothills of the Alps. Signs point the way to key landmarks with both distances and estimated times. Near the summit I encountered a monument to the mountain troops of France, which were obviously critical during the World Wars. Lookouts along the trail give even more gorgeous views of the city below!

In case the mountains weren’t enough for you, Grenoble is also sporting a couple of rivers, the Isére and its branch the Drac. Unlike Lyon, the branching occurs somewhat outside of the city. The photo below shows the Drac, the smaller of the two. Not far from that river I found an office of the Communist Party of France: “champagne for the 1%…paid for by the 99%!”

Adventures in Lyon! 2: Homesickness

I was hit by a pretty bad bout of homesickness during my first few days in Lyon (still recovering). It came out of nowhere, but the feeling reminded me a lot of graduate school. One thing I’ve figured out is that “depression and anxiety” is a bad name for a nameless feeling that involves short periods of intensity followed by long, crippling fatigue. The two seem to occur over and over in a cycle, as intense “anxiety” tires one out and the ensuing “depression” results in inaction until a breaking point is reached. The dependence of the two make one follow from the other: “anxiety-and-depression” is a package deal, not two separate feelings. This cycle deserves a better name.

Being in a foreign country exacerbates the problem, as something as little as a breakdown in communication at a shop signals the fact that you’re surrounded by people who cannot understand you. You run into barriers—human barriers—at every turn, and they seem somehow more real than the walls one puts up when facing depression at home. The anxiety of the misunderstanding people around you feeds your anxiety.

Thankfully, I have a wife at home who understands all this and has been extremely supportive. That’s made the transition to living in Lyon a lot easier. The key, I’ve found, is to recognize and name the feeling as it’s happening. Being mindful of it doesn’t even necessarily make it go away, but does prime the mind to recognize it the next time it comes around, softening the blow. Slowly but surely, it happens less and less. I’m still in the adjustment process, but I have noticed improvement over time. Perhaps there’s room for me in Lyon yet…

I don’t want to imply that it’s been all bad, either! The history here is incredible. Roman, medieval, and modern European history coexist in a mishmash that is in some ways disordered, but in other ways reflects enduring norms in the city. I’ve been chugging my way through a 950-page book on the history of the Holy Roman Empire, of which Lyon was a part until the 14th century. The photos below are from a hill above Vieux Lyon, which includes Roman ruins, a Roman amphitheater still in use for shows today, and a gorgeous cathedral built in the 1800s (alongside a tower built by scientists as a competing monument). You can’t find architecture spanning this length of time anywhere in my neck of the woods!

Adventures in Lyon! 1: Arriving and Settling In

Greetings from Lyon, France! I’m here to teach organic chemistry to students from Georgia Tech while soaking up as much culture and language from France as I can. It’s taken a couple of days for me to get settled in, but now that the jet lag has worn off, blogging can commence.

All told, the journey to Lyon was fairly uneventful. If you’ve never been, ATL is not only the world’s largest airport; it is also in my experience the most pleasurable to get through—so much so that it has subconsciously softened my stance on the TSA in recent years. (This time, I found myself incredulous that I had actually made it through security without one internal rant about security theater. It seemed like I blinked and was on the other side of the metal detectors. That may have been because last time I went through, it was with a toddler.) I didn’t even have to take the plane train to reach my gate—a rare treat!

My wife claims that in-flight movies are the best part of international flights, and this one had a cornucopia of good stuff. I took in Star Wars: The Last Jedi, Avengers: Age of Ultron (a nice opportunity to figure out what was going on in Infinity War), and Black Panther. Things took a nasty turn when it was time to sleep, though…

I am such a Bob Ross nut that my wife got me a joke book of BR quotes for my birthday last year (best gift ever). With the first Bob Ross collection disappearing on May 31, I was not a happy camper upon discovering that The Joy of Painting isn’t even available outside of the US, not to mention the rest of Netflix on the plane. Mindfulness meditation had to do. As the plane lights dimmed and people one by one nodded off, I was reminded of an experience from my childhood…

Upon arriving in Paris, I hopped onto the cheap alternative to the SNCF train network, Ouigo. This is essentially the cutesy counterpart to the overpriced big guy, similar to Lyft (in the early days, at least) versus the taxi companies. Great ride. Although I feared that getting from the Lyon airport to the center of the city was going to be a pain, it turned out to be a breeze. I’d finally made it to Vieux Lyon!

Settling in has been interesting. I’m getting dead tired around 4:00 pm each day, but I can make it through the day without needing a nap. So far, I’ve visited the university quarter (INSA and CPE…there’s a whole post’s worth of interesting differences between American and French universities), the Musée des Confluences (where the Rhône and Saône rivers meet), and various cafés and markets around town.

I thought I could speak French…I totally cannot speak French. 😅 See below for a few photos from my first few days in Lyon.


Optical Structure Recognition: Where Patents and Homework Collide

At this very moment, there are hundreds of pages of unreturned Organic Chemistry I assignments sitting on the floor of my office. These papers collectively bear well over one thousand Lewis structures, some computer generated and others hand drawn. This is an amazing trove of information about students’ quirks, habits, and misconceptions. But those insights will most likely never be dug up, because it would take a human many days of work to find them and automated digitization of the structures into a format with chemical meaning is not yet possible.

Somewhere in Washington, DC, there is a patent office with a similar problem. I know this because in researching my solution to the problem, I discovered that it has also been explored by patent offices sitting on mounds of old patents containing structures on paper. Conversion of these structures into a computational format that can be indexed or searched would be an amazing step forward…but it’s not a job that any human wants to do (without adequate compensation, of course).

When I taught organic chemistry in a flipped format with online homework and fully computer-based problem solving, I would often find myself having an internal debate about hand-drawn versus computer-generated structures. I came up on hand-drawn structures and still appreciate the kinetic aspect of putting pencil to paper. The synergy between a mental representation of a molecule and its physical representation on a piece of paper helped reinforce my learning. And yet, most of those structures never received any sort of feedback. It was only through sheer force of will (and a growing love of organic chemistry) that I managed to diagnose and correct errors in drawing structures and mechanisms. Creating these representations on a computer enables continuous feedback in a way that no hand-drawn problem set ever could.

A program that could reliably convert hand-drawn structures into computational structure files would allow us the best of both worlds, ending my internal debate on the spot. Now that is a future of organic chemical education that I would like to see! Continue reading “Optical Structure Recognition: Where Patents and Homework Collide”

WTF is “Systems Thinking”? A Book Recommendation

When I started as a general chemistry lab coordinator five years ago, I realized just how much I didn’t know about chemistry. Being steeped in organic and biochemistry for five years had left me with some blind spots, so I spent a good bit of time revisiting topics I hadn’t looked at in years. It was a bit like meeting old acquaintances I hadn’t seen in forever, now with the time and countenance to sit down and have long, slow conversations with them. An undergraduate chemistry degree is more like speed dating than a long-term relationship. Of course there are good reasons for that—the ability to get cozy with a field is a luxury that very few other than academics can afford.

In practicing and studying chemistry, one can’t help but appreciate the importance and usefulness of chemical thermodynamics. Connecting enthalpy, entropy, and free energy to molecular structure gives one a unique sense of empowerment. Even so, it is difficult to establish a firm foundation in the ideas that gave rise to it all—often we have to accept that thermodynamics “just works.” But what’s going on under the surface?

I’ve written before about Howard Reiss’s Methods of Thermodynamics, my favorite book on the subject. His deep insight, one that caused me to completely rearrange thermodynamics in my head, was that the subject is really about constraints and boundaries. How a system is defined via its boundaries and how it is constrained determine its equilibrium state. To get at the deep nature of a thermodynamic system, it is necessary to answer questions about its constraints and boundaries. Furthermore, in applying thermodynamics in practice, how the system is defined is even more important than the underlying laws governing the behavior of the system. The laws of thermodynamics merely represent the implementation and “revelation” of the practitioner’s choice of system. Different choices of system can sometimes lead to dramatically different results, especially at very large or very small scales!

I was reminded of these points recently while reading Donella Meadows’s excellent book Thinking in Systems. Chemical engineers will find the central idea of the book a comfortable generalization and simplification of the Principles of Chemical Processes course. She defines a system as a set of interconnected and interdependent stocks (“reservoirs” might be a better word) and flows. Through a series of examples spanning a variety of disciplines, she shows how the structure of the system gives rise to its behavior, and how subtle changes in system structure—or even how we think about it—can result in significant changes in system behavior.

Books like hers always seem to fill me with hope for the future, because they show that the ways in which we conceptualize the world still matter. The youth of today won’t think like me and this alone has the potential to alter the world radically for the better.

If, like me, you find the term “systems thinking” to be unacceptably vague, check this book out! It will change your perspective.

“So I Should Memorize…”

Coming from a student of organic chemistry, the title phrase used to incense me. It wasn’t just that I knew brute-force memorization to be an inferior strategy for learning (a fact I never hesitated to impart on self-proclaimed memorizers). I felt that these students displayed a profound disrespect for the content of the course by subjecting it to the intellectual equivalent of throwing a can against a wall until it busts open. All I’m asking you to do is pick up and study a can opener. So many students of organic chemistry are just shown open cans over and over again and expected to master how a can opener works, I would tell myself. They should consider themselves lucky that I show them the can opener at all.

The selfish bitterness in that attitude is painful in retrospect. I found myself taking a different tack when I was approached by a student after class recently. In this class I had presented the equivalent of the mechanistic can opener: ten elementary steps of polar organic reaction mechanisms shown in one fell swoop as the foundation of all two-electron organic reactivity.

So essentially I should memorize these ten elementary steps?

Breathe. I found myself avoiding my usual anti-memorization crusade: “no, you shouldn’t memorize anything in this course…” Instead, I informed her that the alternative was memorizing reaction mechanisms individually as the course progresses, which will be far more arduous than learning the ten elementary steps now. I told her that these were the key to reaching a higher plane of abstract mechanistic thinking. Against my own expectations of myself, I affirmed memorization.

I think, on some level, I accepted that this student had worked her butt off to even get to my classroom. If memorization (as she called it) was essential to that work, who am I to judge how she learns the essential concepts of the course? Memorize away, my friend. I’m guessing that if you memorize this foundational framework now, you’ll thank me later anyway. On the other hand, if success in the course doesn’t follow, that will be a much more powerful deterrent to memorization than my saying “no, don’t memorize” in an impromptu meeting after class.

Students who connect painful, challenging, or even deliberate learning with “memorization” used to grate on my nerves beyond belief. I couldn’t shake the question of how much my course structure versus those students’ intellectual backgrounds promoted memorization. What was I doing wrong that kept students from wanting to learn rather than memorize what I’m teaching? Now, I don’t worry so much. Students have diverse backgrounds. Not all of them will become chemists, or even want to, or even could want to after experiencing “perfect” teaching. My goal shouldn’t be pumping out a bunch of mini-chemists—that’s impossible! Instead, my goal should be to meet all students where they are intellectually, trying where I can to push the boundaries of their knowledge, skill, and especially curiosity.