Old Babylon School

We’re constantly hearing about how our students have changed, even more so in the wake of COVID-19. Not to mention there’s the constant drumbeat of pivoting away from non-traditional teaching approaches, as if there’s something bad about tradition. There’s a good reason tradition endures, and I think that lecturing has its usefulness, although it’s certainly not the only approach I employ from my pedagogical bag-of-tricks. If I’m feeling curmudgeonly about all this, I might refer to myself being old-school even as that term takes on increasingly negative connotations.

 

But my old-school isn’t all that old. I picked up useful tips observing my teachers, both what to try and what to avoid. It was one sign I knew that teaching was in the cards for me, because I found it interesting analyzing the varied teaching approaches I observed as a student. So if my teachers were old-school, I’ve retained parts of their pedagogy but infused it with what I bring to the table. I firmly believe that teachers should take advantage of their individual strengths and abilities, and so even if I admire a colleague’s teaching approach that’s very different from mine, I won’t necessarily emulate it.

 

As we go back in time, we know less and less about how school was conducted. There are caricatures aplenty of how old-school is out-of-date with modern technology, and we need to adapt or be deemed obsolete. How far can we go back? How old-school is the oldest schooling we’ve heard about? Turns out we know a little bit about school in Babylon. Not the Babylon of the Bible that sacked Jerusalem in 587 BCE, but older – what scholars today might call Old Babylon (circa 1900 to 1600 BCE). Why am I pondering this? Because I enjoy reading ancient history and archaeology and I’m working my way through Babylon: Mesopotamia and the Birth of Civilization, by Paul Kriwaczek. 

 

Mesopotamia is fascinating. Thanks to the birth of cuneiform and a tradition of writing, we have a bunch of tablets from Old Babylon. But today’s post will just focus on what we know about schooling. Here are translated excerpts from a student who had just graduated:

 

“I had three days of vacation each month: and since each month has three holidays when one does not work, I therefore spent twenty-four days in school each month. And it did not seem like a very long time to me! From now on I will be able to devote myself to recopying and composing tablets, undertaking all useful mathematical operations. Indeed, I have a thorough knowledge of the art of writing: how to put the lines in place and to write… Since I have attended school the requisite amount of time [not stated how long] I am abreast of Sumerian, of spelling, of the contents of all tablets…”

 

The graduate goes on to claim the ability to draw up documents and contracts of various sorts: trade, marriage, sales, adoption. It’s like a resume on a tablet. Kriwaczek contrasts this with a translated satirical story titled ‘Schooldays’ where the writer bemoans the drudgery of school, the old-school teacher who beat him for constantly “breaking rules”, making errors, having poor handwriting, and more. Bribing the teacher for better treatment ensued.

 

There’s much we don’t know about school in Old Babylon, but the evidence accumulated at present suggests that temple officials (priests) ran private schools, but it wasn’t mainly a religious education but a secular one: reading, writing, and numeracy. Students were being trained to be scribes. And yes, math was challenging – additionally so because the Babylonians used base-sixty rather than base-ten, and they didn’t use the numeral zero nor decimal points. Apparently they used multiplication tables and the equivalent of the logarithm books that I used during my schooldays before hand calculators were allowed.

 

The science of Old Babylon school was also much more about going through many specific examples, and less about distilling abstract or general principles. This meant lots of memorization, and what are tablets of writing if not aids for memorizing and working your way through math problems that you can’t do in your head with limited working memory. Omens and portents were taken seriously, as was astrology. This shouldn’t surprise us – if you don’t know why something happens, you try to make connections (hypotheses) and see how they turn out. There was a lot of guesswork. Very similar to what many students do when they begin organic chemistry – memorization and guesswork. But once they see the underlying principles, then things might start to click.

 

Our human brains and capacity for learning haven’t changed very much evolutionarily in the last three thousand years. But our tools have! Perhaps that’s why there’s always a dance between old-school and new-tech, one that I expect to continue for generations to come.

Return to Conferencing

It had been a while since I went to a large conference. No thanks to the pandemic. But last week I was back at the American Chemical Society national conference. This one was in San Francisco; I’ve blogged about my usual conference activities at such a meeting. While there were a few individuals who wore masks, it mostly felt like a pre-COVID conference. There didn’t seem to be social-distancing anxiety and folks were happy to shake hands instead of just elbow-bump.

 

This was in contrast to a smaller regional conference (~100 people) I attended last October, which was my first in-person conference in almost three years. Almost everyone was masked, appropriately so since the small lecture theater barely accommodated us – the organizers were not expecting such a good turnout. I guess we were itching to get back in person. I did take off my mask when I was speaking at the podium, as did the other speakers.

 

One of the themes of the big San Francisco meeting was Artificial Intelligence applications and machine learning. I went to several high-quality talks presented by folks from both academia and industry. Some were well attended, others sparsely so. This is a field that is moving very quickly, hype notwithstanding. I’m not an expert in machine learning, although I am picking up the newest lingo, and I have some basic knowledge of how computational neural networks work.

 

Of all the talks I attended this time around, three stood out. One was a machine-learning talk on protein engineering that had underlying intriguing results to protein evolution. I don’t think the speaker had origin-of-life research in mind, but it gave me an idea of how that research could be extended. Another was a statement that a speaker made in a Q&A, essentially that living systems invert our standard thermodynamic model. In a standard G-Chem or P-Chem undergraduate course, the environment (thermal surroundings, modeled by a water bath) is considered to be a large reservoir that is relatively invariant while the chemical system is where all the “changes” are taking place. However, living systems maintain homeostasis and stay out of equilibrium while adapting to the environment changing. I liked the pithy contrast!

 

The third talk was unusual. I was in a session celebrating valence bond theory where almost all the speakers talked about research. However, one person chose to talk about how he was incorporating valence bond theory into P-Chem. This is not the (pathetically simplistic) valence bond theory of G-Chem, but the more sophisticated version that quantum chemists use. I had started incorporating bits of this into my quantum course, and I’ve been trying to slowly enlarge that share, since my expertise is in chemical bonding. This has meant cutting out some other parts (including math). Anyway, I very much enjoyed the talk and it sparked some ideas that I plan on trying.

 

Overall a good conference, and that takes my travel tally to four in-person meetings this calendar year so far (which included going to the ESCIP and LABSIP workshops, sort of like mini-conferences). It’s refreshing to return to in-person conferencing after a lapse of several years. I’ve missed the interactions between fellow human beings without an intervening screen or device!

Circle of Knowledge

The word encyclopedia comes from the Greek enkyklios paideia which refers to “learning within the circle” or “all-round education”. I’m learning these interesting facts from Simon Garfield’s new book All the Knowledge in the World, subtitled “The extraordinary history of the encyclopedia”. The famous Encyclopaedia Britannica features prominently in many of the chapters (there are 26, with titles from A to Z), and I learned that Wikipedia plundered much from the prominent and possibly the most popular 11^th edition (conveniently no longer in copyright) to use as a starting base. A Guardian article from a decade ago pays homage to its magic and appeal.

 

But Britannica had competitors. I learned that Samuel Taylor Coleridge thought it was a travesty to publish each volume in alphabetical order over a period of years. He called it a “huge unconnected miscellany… a worthless monster”. His vision, realized in the Encyclopaedia Metropolitana “emphasized the systematic relationships within knowledge bases, presenting the sciences, the arts and other subjects as a rational and unified progression rather than a scattered constellation.” This reminds me of the strange palette of college core curricula; in most schools students are offered a grab-bag (take a course in Group A, two in Group B, etc). There are regular attempts to update the core curriculum meant to make it more “coherent” but it’s hard to agree what exactly that means. And it’s a time-consuming process. I speak from experience having gone through it twice!

 

Collecting knowledge into some authoritative volume has been going on for a long time. Information explosion is not a new thing. But with the industrial revolution and the rapid advances in scientific knowledge, staying up-to-date became more challenging. There was a proliferation of encyclopedias that were geared to specific topics, for example there’s an Encyclopaedia of the Arctic. I can’t imagine an encyclopedia of chemistry today – the explosion of knowledge is exponential. I can hardly keep up with my own field; I suppose that’s why going to a focused conference is helpful because organizers usually invite good speakers that have breadth and depth. As an attendee, I can just soak in the material without having to go looking for it.

 

Who were the knowledgeable people writing entries for the encyclopedia? In the early years of Britannica, many of these were experts in their field. That, unfortunately, doesn’t necessarily make them readable. Experts often wrote for other experts, going deep into the weeds of their cherished subject matter. Entries were uneven in length, detail, readability, and more. Some writers were polemical, one-sided, and took the opportunity to demean their opponents. Some were tardy. I learned that Lord Rayleigh was supposed to “contribute the entry on the physical properties of Light for [the] ninth edition” but he missed the deadline. He then missed the deadlines on Optics and Undulating Light, but made up for it in the Wave Theory of Light (Volume 24).

 

Reading about the challenge of selling encyclopedias was interesting to me, not having grown up in what was then known as a “third-world” country where encyclopedias weren’t present. The showrunners and editors needed to constantly adapt to customer interests. This meant more standardization among entries, and ensuring that it was more readable to the lay public. Garfield includes a list of guidelines; #2 reads: “Be interesting, be lively, be picturesque. Do not antagonize, do not repel the reader by a dull, forbidding style.” There were appeals to write to a broader international English-speaking audience. And of course the sales pitch was that you were buying a high quality education by investing in Britannica, especially for your children to get ahead and be citizens of the world.

 

Today, bound volumes of such encyclopedias go for pennies. All sellers want is for you to come pick it up. Garfield was probably one of the few buyers. Why would anyone want these huge paperweights when you have Wikipedia and more in The Cloud? For researchers and historians, reading these old entries and comparing them from one edition to another illuminates the state of knowledge in the past and how it evolved. Garfield scatters such examples throughout his book. I also learned that the largest ever knowledge collection, much of which has been lost (fire, theft, rodents), was commissioned by the third emperor of China’s Ming Dynasty, Zhu Di, in the early fifteenth century. He tried to be comprehensive and encircle knowledge, but to no avail.

 

Every year, I take my students through a circuit of knowledge in my chemistry courses. Each cohort enters the circle and exits, hopefully gaining some knowledge in the process. In the two courses that I teach most years, General Chemistry and Physical Chemistry, there isn’t much new fundamental knowledge to add. I try to provide contemporary examples, and I regularly update my courses. But I keep going round and around. And as the fall semester approaches, I approach the beginning of the circle once again.

Time for Prep

In my first several years as a faculty member, much of my time went to class prep. The first time you teach a new class, the prep is substantial. This was certainly true of the standard lecture classes I taught: both semesters of General Chemistry, both semesters of Physical Chemistry, and one semester of Inorganic Chemistry. Coming up with all your course materials from scratch is a lot of work. Back then my lecture notes were handwritten, and updated regularly. I used an overhead projector when absolutely needed for visuals.

 

Teaching G-Chem lab was a little easier because we had materials prepped for the instructors thanks to a fantastic coordinator and lab-prep staff. My first Computational Chemistry elective course was also a ton of work because of the additional computer-lab exercises, but subsequent elective courses (e.g. Chemical Origins of Life) were essentially reading and discussing the primary literature. While I had to come up with the readings and discussion questions, I didn’t have to prepare lecture notes, make slides, assign homework, or write and grade exams. I haven’t taught Inorganic in a while (since we hired two inorganic chemists), and while I do update my G-Chem and P-Chem lectures every year, it’s not too time-consuming.

 

But for the first time this semester I will be teaching the first semester of Biochemistry lecture. Why? Because I really want to learn the material given my origin-of-life interests, and the best way to do so is to force myself to teach it. The biochemists finally agreed to let me take one section this coming fall semester. And the prep work is very substantial. I knew it would be ahead of time, but I’m still struggling with how much time it takes to put together one class session (the textbook reading guide, my lecture notes, my slides, the study guide, the homework assignments). I’m much more detailed now, because the students seem to need the extra support – but that means a lot more work on my part. I don’t begrudge it, in fact I’m enjoying thinking about how best to help the students learn the material, but it’s eating up gobs of my time. What’s being sacrificed? Research progress. That’s okay. It’s the choice I made. Also, my blogging has reduced by half.

 

I don’t like the feeling of being last-minute so I front-load my work. I have my overall course schedule laid out, I know what my goals are and what I want to achieve (having consulted with by biochemistry colleagues). Last semester, I sat in every class meeting in a colleague’s class. I took notes. I have copies of slides. But my teaching style is quite different from my biochemistry colleagues, and I need to play to my strengths. Thus, it’s almost as if I’m starting from scratch – certainly in creating and organizing all my materials. As a non-biochemist by training, and with a slant towards the origin of life, I have a unique way I’d like to teach the class that will still cover all the learning goals and outcomes. My physical chemistry background also influences the way I think about and teach chemistry.

 

At the moment, it’s taking me about 15 hours to complete a thorough and detailed production of one week’s worth of material. I hope to cut that time down a bit, or I might have to reduce my thoroughness somewhat. Essentially, I prepare to the point that I can walk into class and get through everything confidently. But my summer is coming to an end, and I still have to prep my other classes and get ready for a new class of academic advisees. I’m going to a national chemistry conference next week. (I had my talk prepped two weeks ago!) And once the semester starts, there’ll be more meetings, office hours, and besides Biochem I’m also teaching P-Chem and G-Chem. I’ve substantially prepped the first four weeks of P-Chem (with much of weeks 5-8 also done), updating my worksheets and problem sets, thanks to motivation from LABSIP. I’ve done a little reordering in G-Chem and don’t expect to make too many changes other than adding Study Guides that were quite successful last semester.

 

Wish me luck!

Too Much Oxygen

 

Once upon a time, oxygen levels on Planet Earth hit 35%. This purportedly took place circa 300 billion years ago as the Carboniferous period was giving way to the Permian. At the same time carbon dioxide levels were falling. One explanation is that carbon burial (coal formation) was especially rapid, and thus there was less carbon to combine with atmospheric oxygen to form carbon dioxide. Today, humans are reversing the process by extracting the coal and combusting it for energy.

 

What was special 300 billion years ago to cause this? It so happens to coincide with the formation of the supercontinent Pangaea with its wet climate and vast flood plains that favor the formation of coal swamps. The rise of trees with woody lignin-containing stems meant slow breakdown to release carbon because decomposing bacteria have a particularly hard time digesting lignin. I’m reading all this in Nick Lane’s Oxygen, a fascinating treatise that connects oxygen to energy, life, death, sex, and aging. I first read Lane’s book almost two decades ago, but I’m re-reading it again to refresh myself on interesting oxygen factoids to use as a theme in my upcoming Quantum chemistry class – which culminates in the unusual chemical bonding situation of molecular oxygen.

 

But back to our story on oxygen levels. Can we measure them from so long ago? We can certainly measure the carbon content in rocks from that era. And it is high, even after accounting for erosion and metamorphic processes. We can also measure the contents of air trapped in microscopic bubbles of ancient amber. (In Jurassic Park, dinosaur DNA was extracted from insects trapped in amber.) As a third measure, the relative proportion of carbon-12 and carbon-13 isotopes in limestone tells us how enriched the atmosphere was with oxygen. The evolution of plants and their selectivity for carbon-12 corroborates the story. While all these measures are indirect, taken together they strengthen the hypothesis of such high oxygen levels in the past.

 

Chapter 5 of Lane’s book, from which I’ve taken this information, is titled “The Bolsover Dragonfly: Oxygen and the Rise of the Giants”. There were huge insects in the Carboniferous period! Dragonflies and mayflies had wingspans approaching 20 inches; there were meter-long millipedes, and scarily large spiders (though not quite the size of Aragog). Megafauna! Or perhaps I should say Mesofauna. Was this all because of elevated oxygen levels? More oxygen, more energy, faster growth? Speculations abound, but the one I found most interesting is that the large size lengthened the diffusion of oxygen through the organism so that by the time it reached the mitochondria, the concentrations were much lower. Otherwise, oxygen poisoning would result.

 

There was practically no free oxygen at the origin of life on Earth. We are descended from single-celled prokaryotic hydrogen-breathers. Living systems can’t get as much metabolic energy from hydrogen as they can from oxygen. Aerobes thrive energy-wise while anaerobes live on subsistence. Molecular oxygen is unique with its oddly weak double bond making it thermodynamically stable; yet it is oddly kinetically stable despite being a diradical (with two unpaired electrons). It’s much stranger than it looks at first glance, and I’m hoping to take my P-Chem students through that story this coming semester.

 

Oxygen might be good for life, at least we aerobes think so. But we’ve also evolved a bag of tricks not to be poisoned by it. That’s the topic of Chapter 10 in Lane’s book: “The Antioxidant Machine: A Hundred and One Ways of Living with Oxygen”. Oxygen loves to accept electrons. It does so one electron at a time, forming superoxide and then hydrogen peroxide (by also stealing protons). When oxygen steals an electron from another molecule, the latter now has an unpaired electron and becomes reactive (kinetically unstable). It then tries to steal an electron from some other neighbor, and so on, potentially resulting in a cascading chain reaction. Anti-oxidant molecules halt this process, often by donating an electron to stabilize the radical.

 

To counter the effect of peroxidation reactions that are ultimately due to too much oxygen, there are multiple antioxidant strategies. Heme proteins (similar to hemoglobin) detect oxygen levels, “binding to excess oxygen and releasing it only slowly, maintaining a constant and low concentration of oxygen in the immediate environment.” Mucus secretion is a very effective strategy. In bacteria, the negatively charged polymers in the mucus capture positive metal ions, and these react with the marauding radicals. Biochemistry utilizes sulfur-containing compounds to react directly with peroxides or indirectly by regenerating antioxidant molecules such as vitamin C. Recently my research has focused attention on the role of sulfur-compounds in proto-metabolism so I’m learning a lot about this area. Lane’s discussion of the enzyme superoxide dismutase is now much more fascinating, compared to two decades ago when I lacked appreciation in my first reading of his book.

 

One thing you might be wondering: If oxygen levels were so high, shouldn’t there have been massive forest fires? And wouldn’t these have consumed the oxygen thereby maintaining balance? Lane tackles this head-on by estimating what would be needed to maintain the balance – the unrealistic total vaporization of all the forests. It turns out that forest fires tend to promote the burial of carbon and coal formation. Also, the previous estimates that oxygen levels above 25% would cause conflagration were dependent on setting moistened paper on fire. Paper has little lignin, and furthermore real plants accumulate silica which acts as a fire retardant. Turns out that more shiny coal indicates it was formed at higher temperatures likely with more oxygen in the atmosphere. The coal from the Carboniferous is particularly shiny, further evidence of high oxygen levels.

 

Oxygen is an enigmatic molecule. We aerobes can’t live without it, but it’s killing us at the same time it’s fueling our way of life. Lane spotlights this tension in his engaging and very readable book, peppered with fascinating anecdotes. Did you know that silica was used in paints as a fire retardant during the Second World War? Or that the males of many ants and bees are haploid possibly for similar reasons as human sperm? And if not for skin pigments such as melanin, you’d change from red to a blue hue when you engaged in vigorous bodily exertion? Lane provides memorable and colorful analogies. My favorite is his description of the Fenton reaction: “Hydrogen peroxide is a gangland thug. Normally quiet, posing little danger to casual passers-by, it turns violent on meeting a rival gang member. Damage to proteins containing embedded iron can be as swift and specific…” More importantly, I was reminded of how biochemistry tunes itself to avoid redox catastrophe. Living with oxygen is a fine balance indeed.

Sleep Anxiety

I used to have insomnia. For two decades. Then sometime after turning forty, my sleeping problems diminished. I’m not sure why. Probably a combination of factors, foremost of which might simply have been the slow shift of my circadian rhythms over time. I was a late night-owl as a teenager, but made an abrupt shift to an earlier schedule when I arrived in the U.S. as a college student in my early twenties. In my tropical home country, we ate dinner later and there was a tradition of a late-night supper when the weather was cooler.

 

Because of my insomnia, I have read many books and articles on sleep over the years. I continue to do so as a matter of habit, and simply because sleep still remains mysterious even though scientists have amassed a lot of interesting data and we now know much more than we used to. I didn’t experience significant sleep anxiety during my two decades of insomnia; I just got used to it and it didn’t significantly impair my work performance. Napping helped. And I have significant chunks of time to myself, which is a great boon as an introvert.

 

The Sleep Prescription is a mini-book by Aric Prather, a sleep scientist at UCSF. Published last year, its tagline is “7 Days to Unlocking Your Best Rest”. The author provides a good mix of the scientific underpinnings of sleep along with engaging anecdotal stories of anxious insomniacs trying everything they can to improve their sleep. I was familiar with much of the science, but I still appreciated Prather’s approach in this book – very practical with easy-to-remember tips. Here’s my summary of his seven points for seven days.

 

#1. Set your wake-up time and stick to it! Yes, even on the weekends. I used to sleep in on weekends to catch up on my deficit. I stopped doing so a long time ago. It helped. I no longer confuse my circadian rhythm. At least until I travel internationally and my body clock gets messed up. But that’s okay because I give myself time to readjust.

 

#2. Sleep problems are often tied to waking life problems. Particularly stress. Prather discusses the role of cortisol in the sympathetic nervous system and its role in waking you up from sleep. I am blessed to have led a relatively stress-free life. I didn’t feel the pressure to “get all A’s” as a college student. Early on in my career as an academic, I decided I didn’t need to be a star, and I instituted strong work-life boundaries. I’d say work stress wasn’t much a factor in my insomnia. Although sometimes I would lie awake thinking about work-related ideas in my teaching and research. (These were positive thoughts but still kept me awake.) Prather’s advice is to “ease off the gas” and schedule micro-breaks from work stress. I already take regular breaks mostly so I’m not sitting for too long.

 

#3. Energize when you need to during the day. Prather mentions sticking your head in the freezer for cold shock. I’d heard this before, but I don’t do it. He also discusses managing your caffeine. I avoid caffeine so that’s not an issue. Is it okay to nap? Yes, but not for too long. Prather explains the sleep cycle and how to relieve sleep pressure without getting into the phase where you wake up groggy. Turns out forty winks is a good measure. I lie down for forty minutes. I might not fall asleep but if I do so, it might be for twenty or thirty minutes. It works. But you must set an alarm and not hit the snooze button.

 

#4. Set aside time blocks to worry and not too late in the day. The strategy behind this is to reduce anxiety because you can tell yourself that you have time to worry. It sounds weird, but Prather assures the readers that it works. He provides several “levels” of doing this. I’m thankful I don’t feel the need to do this, but I can see its usefulness for folks who are in much more stressful situations.

 

#5. You are not a computer, you can’t just shut down. That’s the title of chapter five. When I had insomnia, I learned the importance of having a wind-down routine. I do many of the things you’ve likely heard about. I have relaxing activities. I take a warm shower. I have a tiny cup of cereal with milk. And I’m adamant about not doing any work in the evenings, which also means I hardly use my computer then. When I was younger and my insomnia was worse, having the routine helped. I also kept a sleep diary (as Prather recommends) to help me discover what worked and what did not. I stopped doing so in my early forties; I no longer needed the diary. But the routines have stayed.

 

#6. You can retrain your brain. Prather has a number of good tips, including “do not get into your bed until you’re sleepy.” This is a tough one for me because I like lazing in bed. It’s physically soothing and I feel happy when I’m in bed with my pillows. It doesn’t help my sleep though. Prather also says that if you don’t fall asleep after 20-30 minutes, get up and do something else that’s still relaxing. And don’t bring your book or laptop into bed. If you have to, do it differently – in a different position, at a different corner of the bed, etc. I like to read in bed and it is part of my wind-down routine. Prather understands these things and discusses compromises. While I don’t necessarily follow his advice here, I’m reminded of his suggestions and I found myself readjusting to them.

 

#7. Stay up late to build up sleep pressure if needed. Prather has a scheme for doing so and provides appropriate guidelines. While I would use this strategy when shifting time zones, I wasn’t always consistent. I like Prather’s approach and I will try it the next time I need to get over jet lag. I was also reminded, not just in this chapter but throughout the book, that the goal is not perfect sleep, but good-enough sleep. What is good enough? Prather has a straightforward scheme for you to calculate this from a 7-day log of your sleep. I like his guidelines and his approach of keeping all these strategies low-stress.

 

If you are anxious about your sleep issues, I highly recommend Prather’s book. I find it practical and research-informed. Sleep anxiety should not rule your life. Your body is built for sleep and wakefulness. Prather recognizes that individuals have different sleep needs and his book might help you find a happy medium.

Skinny Core

I just returned from a LABSIP workshop. What is LABSIP? Lowering Activation Barriers to Success In P-Chem. While the acronym doesn’t roll off the tongue, I find the name amusing. Then again, I once gave a talk at a chemistry conference titled “Getting Over the Curve”, a subtle reference to the same “energy diagrams” that those of us who teach P-Chem agonize over, because our students are frequently confused by the graph axes among other things.

 

The workshop was a blast. There was plenty of nerdy P-Chem humor. I met old friends and acquaintances, and made new ones. It was a targeted small in-person workshop with just 25 invited participants with a packed schedule. I was not involved in organizing it, and was able to fully enjoy the time without worrying about administrative details. In today’s blog post, I will discuss one of the activities we attempted: Can we agree on and distill a “skinny core” list of topics that should be in physical chemistry courses?

 

Before this in-person group meeting, there had been a Zoom meeting with a few hundred participants. From the AllOurIdeas online polling system (here are the Quantum results), the group found that there was actually a good consensus on what the community of physical chemists thought was important in a potential two course outlay dubbed Quantum and Thermo. One of our jobs in the small workshop was to hash out a “skinny core” that provided a guideline for instructors who teach a wide variety of P-Chem courses. Some of us teach the standard two-semester sequence for chemistry majors. Others teach it in three-quarters. Others squeeze it into two. Yet others teach a one-semester grab bag that includes both broad areas. Some teach P-Chem for engineers, or biochemists, or some other subgroup.

 

What should the core ideas be? We came up with an initial set which still needs more discussion, refinement and editing. Eventually it will be published by LABSIP and hopefully this provides a service to the community of P-Chem instructors regardless of the flavor of our classes. A little later in the post, I will reveal my personal version for the Quantum half based on the discussions I participated in. It does not reflect the group consensus although there is significant overlap. I’m teaching Quantum in the upcoming fall semester so this exercise felt timely for me.

 

As chemists, we want students to learn how the quantum world applies to chemical questions; this means we are interested in things at the scale of atoms and molecules. Solving the Schrodinger (wave) equation is at the heart of quantum chemistry. This requires learning about eigenvalue equations and using operators. It also means coming to grips with the strange nature of quantum measurement, the ideas of wave-particle duality, and the Heisenberg Uncertainty Principle. As instructors, many of us use both historical and more recent research to highlight what’s cool about the quantum, but we don’t all use the same examples.

 

In my opinion, what science does to elucidate how the natural world works, is to build models. Models, by their very nature, cannot capture all aspects of a complex system. But by constructing a model, we can test our understanding of nature, make predictions, and thus refine our theories. In P-Chem, these models are grounded in mathematics. There was very broad consensus that as chemists we should cover the particle-in-a-box, harmonic oscillator, and hydrogen atom models. Some of us discuss the rigid rotor as an additional model, others fold it into the hydrogen atom or cover particle-in-a-ring models. Everyone agreed that there should be some mention of electron spin. We also agreed that one should go beyond the hydrogen atom and discuss models relevant to chemistry where the Schrodinger equation cannot be solved exactly. Thus approximate methods and their accompanying theories and models should be included. I think all of us covered at least the helium atom and the Born Oppenheimer approximation, i.e., cases with multiple electrons and multiple nuclei respectively. For me, that’s a core that covers 7-10 weeks, suitable for a half-semester or quarter-long quantum course. Most of us include a bit of spectroscopy, but I think it could also be done in a separate course (e.g. P-Chem lab).

 

Here’s an outline of my semester-long quantum course. My version of the skinny core is in bold, what I think is common consensus but I left out of the core is in italics, and things where there is less agreement is in unaccented text. As a computational chemist who is also interested in chemical bonding, there are certain things I want the students to appreciate in my Quantum course that are unique to me, and these optional items are also in unaccented text. (In my early days, I taught computational chemistry as an elective, but I have pivoted to origin-of-life which is a topic of broader interest to students.) Our LABSIP group did not specify an order that topics should be covered; I think there are different ways to skin the quantum cat, so the following order is my own. It’s somewhat close to a “traditional” sequence, but there are good reasons for doing so to take advantage of topics building on each other.

 

·      Dawn of the Quantum (bits of history)

·      De Broglie Hypothesis and the Heisenberg Uncertainty Principle

·      The Bohr Atom

·      Classical wave equation (to teach some differential equations)

·      Schrodinger Equation and Particle-in-a-Box models

·      Operators, Expectation Values, Commutators

·      Postulates of Quantum Mechanics, wavefunction properties

·      Quantum Tunneling

·      Harmonic Oscillator model

·      Infrared Spectroscopy, Normal Modes, Anharmonicity

·      Rigid Rotor Model, Rotational Spectra, Rovibrational Coupling

·      Spherical Harmonics and the Hydrogen Atom model; Atomic Orbitals

·      Electron Spin, Term Symbols

·      Helium Atom and the Variational Principle

·      Alternative Orbital Wavefunctions, Basis Sets, Hartree-Fock Theory

·      Perturbation Theory

·      Pauli Exclusion Principle

·      Multi-Electron Atoms and Hund’s Rule

·      Born Oppenheimer Approximation, Molecular Hydrogen Cation Model

·      Molecular Orbital Theory (Diatomics)

·      Electronic Transitions, Franck-Condon Principle

·      Polyatomics and Hybridization Theory

·      Huckel Theory

·      Advances in Valence Bond Theory (beyond the 2c-2e Heitler-London bond)

 

Whew! We get through a lot, but I hope at the end of the course, the students have a newfound appreciation for the importance of the quantum to fundamental questions in chemistry, and that what we call the chemical “bond” is a strange beast that’s largely imaginative (although grounded in different theories). I’ve rearranged my course over the 20+ years I’ve taught P-Chem. Topics such as group theory, lasers, NMR spectroscopy, have rotated in and out. I expect my class will continue to evolve, and I think that’s a good thing. But I also expect to preserve the skinny core.