Some Assembly Required

Some Assembly Required is the title of Neil Shubin’s latest book. Its scope is ambitious; the book is subtitled “Decoding Four Billion Years of Life, from Ancient Fossils to DNA”. I find the cover art simple yet mesmerizing. As a chemist who studies the origin-of-life, the book’s title aptly describes my field – some (molecular) assembly is required indeed. Shubin is not a chemist, rather he combines paleontology and molecular biology in his research. He is famous for his work on Tiktaalik, well-chronicled in his delightful book Your Inner Fish. 

 

Some Assembly Required is about the seemingly large-scale adaptations in biological and organismal evolution that look like miraculous jumps. But the miracle lies on the molecular and cellular level. When you look both deeper and smaller, the story becomes very interesting. Our cells are molecular chop shops: using, adapting, and repurposing molecular structures to achieve all manner of tasks. Some of the instructions are baked into the DNA, but a host of molecular regulation controls what shows up when.

 

Today’s blog post highlights Chapter 5: Copycats. First, I’ll quote a paragraph from Shubin, so you have a taste of his marvelous prose.

 

The genome at every level resembles a musical score in which the same musical phrases are repeated in different ways to make vastly different songs. In fact, if nature were a composer, she would be one of the greatest copyright violators in history – everything, from parts of DNA to entire genes and proteins, is a modified copy of something else. Observing duplications in the genome is like wearing a new pair of glasses: the world looks different. Once you see duplications in the genome, you see them everywhere. New genetic material looks like copies of old stuff that was repurposed for new uses. The creative power of evolution is more like a copycat who duplicates and modifies ancient DNA, proteins, and even the blueprints that build organs, for billions of years.

 

Three protagonists grace the chapter. The first is Susumu Ohno, who apparently has “made a hobby of translating the structure of proteins into concert pieces for violin and piano” although he was a maestro of studying chromosomes in the 1960s. Looking closely at the staining patterns of light and dark bands, Ohno realized that the genome was full of duplicated genes. Over and over and over again. I was also impressed reading about Ohno’s low-tech proxy of figuring out how much genetic material different organisms had. He carefully and painstakingly made paper cutouts of his chromosome pictures… and weighed them! While I did not know about Ohno until reading Shubin’s book, I had heard of Roy Britten and Barbara McClintock, and their contributions to understanding the strange tale of genes duplicating themselves and jumping around the genome.

 

Reading the chapter made me think of the similarities of duplicating jumping stretches of DNA and the chemistry of autocatalysis. An autocatalytic cycle is set up when an intermediate or product in a chemical reaction enhances an increase in one of its precursors. A frenzy of duplication takes place leading to autocatalytic growth. At some point, this comes to a halt when all the starting material is used up. But what if you had two catalytic cycles? One produces the reactants the other needs and vice-versa. Cross-catalysis could lead not only to the sustenance of such cycles, but to growing new appendages – new sub-cycles that eventually lead to a vast complicated system. Life is like that. No man is an island. I am constantly exchanging molecules with the environment to stay alive, taking in oxygen and breathing out carbon dioxide being two prime examples. Photosynthetic organisms do the opposite exchange.

 

One seemingly odd feature of life is that it uses only a very small subset of molecules in biology. As a chemist, this is intriguing. Why doesn’t life utilize the brothers, sisters, cousins, nephews, nieces, that are structurally closely related? When the chemist tries to make a biomolecule from simpler molecules in a plausibly prebiotic way (i.e. no fancy reagents or catalysts that might not have existed at the dawn of life), we get an “embarrassment of riches” – the whole extended family. Why does life pick out just a few characters to star in its drama?

 

I think the copycat idea applies deep down at the chemical level when paired with autocatalysis. Chemical evolution is, perhaps at a fundamental level, not so different from biological evolution. The chop-shop is at a different level, but it functions in the same way: use, re-use, adapt, re-purpose. What is the fundamental driving force for this behavior? As I tell my students in G-Chem 1, chemistry is all about energy. When we get to G-Chem 2, entropy and energy dissipation will come into play. But we don’t get to its heart: non-equilibrium thermodynamics. I don’t even go there in P-Chem. Perhaps I should. Some assembly will be required. But maybe I should first go out and see what I can copy, use and re-purpose. That’s what life does.

Remote First Day

I got into work bright and early at half past seven; that’s when the on-campus check-in kiosk opens to get a temperature check and receive a wristband thus allowing entry into buildings. (I filled out a self-declaration form before leaving home.) I felt relatively ready for my first ever remote teaching day. In my office, I opened the Zoom classroom session at 7:52am, and we started on time at 8am. There were just a couple of stragglers a couple of minutes late, but everyone showed up for General Chemistry 1. I have the Honors section which is nice because its a smaller class.

 

I have a First Day plan in my introductory chemistry courses, but I also take time to answer any questions on the syllabus that day. I’d like to think my syllabus is clear and organized (and for the most part I think the students found it so), however instead of the usual 10 minutes (in a face-to-face class), half the class time went by in Q&A. Perhaps this is not surprising when one has new college students in a new environment. I was forewarned by my colleagues (having missed last semester’s pivot) that “everything takes longer than usual”. It certainly did.

 

I had to trim the rest of my planned activities (i.e., group work and discussion) and resort to “mostly lecture” with a number of interactive question and answer segments. I had students pose answers and thoughts through the Chat, which was faster than individuals speaking up. Overall, we covered the necessary important content, and I think I didn’t rush things. I had practiced switching back and forth between sharing my screen and the “gallery” view of the class and things worked fine. After class, I stayed back to answer several other questions, and that went very smoothly. Overall, it was not a stellar class session, but not terrible, in my opinion. (Don’t know what the students thought.)

 

Office hours started at 9:30am, and I had one conscientious student who had read ahead (virtually) stop by to ask me a host of chemistry questions. They were excellent questions, the type you’d want your students to ask: the why questions! Close to 10am as I was answering the last few questions, the internet started to cut in and out. I assumed it was the student’s connection, but we managed to get through our discussion. Then disaster struck. There was a campus-wide internet outage, both wifi and hard-wired ethernet. While thankfully, I had finished class (and had no other students in office hours), some of my colleagues were not so lucky. If anyone else tried to get into office hours (unlikely), it wouldn’t have worked. What a bad omen for the first day! I’m sure many complaints were forwarded to the powers-that-be. I refrained.

 

I had already decided to have lunch at home and teach my afternoon origins-of-life class from there. It’s a discussion-based class and I don’t need to draw lots of structures or write a bunch of equations. I’m very pleased to say (in my opinion) that class went very smoothly. Everyone logged in by the start time of 2:30pm. Discussion was robust. Timing worked well. My planned activity discussing definitions of life went smoothly, including assigning students to breakout rooms and my hobnobbing from one group to another. Everyone seemed engaged and stayed on task, and I had fun in class. Hopefully the students did too! Not only did I survive, I might have thrived. Hurrah! (I recognize that because this is an elective class, only students who are really interested in the topic sign up, which usually makes the special topics class a joy to teach.)

 

Finally, I perused the recorded videos of my class sessions. My main editing task was to snip off the beginning and the end. There’s some meet and greet early on, and I try to interact with the students in the five minutes before class. At the end of my classes today, I was chatting with my advisees about class schedules, registration, and some catching up, since I was away on sabbatical all of last year. I did watch a few samples of myself explaining something or engaged in a discussion with students, and it was both instructional and entertaining. I’m more animated than I thought I would be even though I was sitting rather than standing, and I still gestured a lot. However, my gaze was all over the place because sometimes I’m looking at the chat, or the person speaking, or my slides, or some notes I have beside my computer. I also made many “ah” and “um” noisy pauses. Clearly, I need more practice to smooth out my remote teaching including timing issues, but I’m looking forward to the end of the semester when I look back and see how I have (hopefully) improved.

 

All in all, a decently good first day for me. A bad first day for I.T.

Deciphering the Unknown

I enjoy puzzles for fun. Jigsaw, Logic, Crossword, Rebus – they’re fun mind-teasers. As long as they’re not too difficult. Otherwise it feels too much like work rather than fun. Then again, working your way by increasing expertise can also be enjoyable. As a researcher, that’s true for me. As a teacher, I hope it’s true for my students too.

 

More than a decade ago, my spouse suggested working together on the New York Times crossword puzzle as a fun couple activity. Every evening, we’d block off a little time to fill in the squares. While we could usually successfully complete the Monday through Wednesday puzzles, Thursday through Saturday often went unfinished and we’d look up the answers the next day. The larger strongly themed Sunday puzzles were always fun too! Over time, we were able to complete the harder puzzles together. When she got an iPad, we started solving the puzzles individually, at least the easier ones – me on paper and she electronically. You know what happens next. We got so good at it that we can solve them individually in a single sitting. We even note how long it takes us. A couple’s collaborative activity turned into a light (but fun) competition.

 

I’ve tried other types of crosswords. In my opinion, the British ones seem harder than the American ones, and not as interestingly themed. There are also some very challenging puzzles where you just have an empty grid and part of the challenge is figuring out where the black squares should be. I don’t enjoy those, and I don’t have the tenacity to put in the time and effort to figure them out. We each have our limits, I suppose. As an educator, part of my job is to figure out where my students are at, and design materials slightly outside their comfort zone, pushing them to learn new things without being overwhelming, and hoping they derive the same type of enjoyment I do in figuring things out!

 

A decade ago, I dipped my toes into a new area of research, the chemical origins of life – a topic I occasionally blog about here in Potions for Muggles. It’s a very complex, challenging problem, and one that I don’t think will be figured out in my lifetime. My nuts-and-bolts research is aimed at tackling a tiny narrow slice of the problem, but I do enjoy reading widely in the field and allows me to dabble in learning some biology, geoscience, history, philosophy, physics, and religion. I don’t consider myself a hardcore researcher in the area. I’m more of a dilettante working at the edges. Perhaps, once again, I lack the tenacity.

 

Because of my lived experience thus far, I thoroughly enjoyed reading The Riddle of the Labyrinth by Margalit Fox. The narrative threads through the lives of three key characters, two well-known, and one that should have received more recognition. The puzzle in this case was how to decipher Linear B, a tantalizing script first unearthed on the island of Crete in the year 1900 by Arthur Evans. The archaeologist Evans is the first of the three protagonists, and his story is well known. He tried, but failed, to crack the riddle even though he had exclusive access to all the primary materials.

 

Working on what was published, a mere tenth of the carefully guarded Evans horde, was the classical scholar Alice Kober. Her story is the most remarkable part of Fox’s book, which does a great service in bringing Kober’s contributions to light. Very methodical and very restrained in publicizing her work, Kober doggedly and almost single-handedly laid the key groundwork that would eventually lead to deciphering Linear B. I would definitely categorize her as a hardcore researcher. Spending years of her evenings working on the script (she had a full-time day job as a college instructor), she painstakingly devised data-management systems presaging computer punch-cards. Even her preparation for the task was staggering – the mastering of many ancient and modern languages, which were crucial in supporting her meticulous and methodical approach. She scorned the way of the dilettante.

 

If Kober hadn’t passed away suddenly, she might have gone down in her-story as the woman who deciphered Linear B. But this was not to be. The honor goes to architect wunderkind Michael Ventris, an outsider and seeming dilettante to the field, who also died young, just a few years after his crowning achievement. His story is also well known. But Fox shows how Kober paved the way for Ventris, who hardly mentioned her name when explaining his discovery in the many invited talks he would be festooned with upon achieving fame.

 

The unveiling of Ventris’ work took place via BBC radio in July 1952. I will quote Fox quoting Ventris on the nature of the problem:

 

“It is often alleged to be impossible to decipher a set of inscriptions where both the writing and the language are unknown quantities, and where there is no bilingual to help us. But provided there is enough material to work on, the situation is not hopeless at all. It simply means that, instead of a mechanical piece of decoding, a rather more subtle process of deduction has to be undertaken. It is rather like doing a crossword puzzle on which the positions of the black squares have not been printed for you.”

 

I can’t resist quoting Fox’s marvelous prose in highlighting Kober’s key contributions paving the way.

 

But it had been Kober, after all, who supplied those first black squares – enough of them to let the puzzle be solved. It was she who, after poring for years over the snarl of symbols and cutting out tens of thousands of cards, identified the language of Linear B as inflected. That was the decipherment’s essential first step. It was she who put her finger on the singular interaction between an inflected language and a syllabic script, pinpointing the “bridging” character. That was the second step. And in the third step – her masterstroke – it was she who realized that it was possible to plot the relationships among characters in the abstract, drawing up the very grid on which Ventris later built.

 

It was also she who had determined at the start that the only hope of cracking the code lay in hunting down and analyzing internal patterns in the script, without speculating on either the underlying language or the sound-value of any character. And that was as essential to the decipherment as anything.

 

Arthur Evans fell into the trap of speculation what the Rebus puzzle reads. So did Michael Ventris and many others. Fox describes the lure of such speculation that had confounded the many who had tried and failed. Ventris was able to give up long-cherished speculation before the great breakthrough. But after the puzzle of decipherment was solved, Ventris lost interest in all the now-readable content of the clay tablets. They would turn out to be mostly about mundane issues: recording taxes, and keeping accounts of crops, animals, goods, weapons, and gifts. Not flashy perhaps, but still a gift to our history about the everyday life of people three-and-a-half millenia ago. And Evans was lucky to find them. If not for the fire at Knossos that baked the clay tablets, the information would have been erased annually, allowing fresh recording on recycled tablets. We get to read the last bits of historical information before disaster struck.

 

Are there lessons to be learned about cracking the code of why life abounds here on planet Earth? Not DNA or even RNA, but what came before. What does it mean to carry out the functions of the living? Perhaps we can read the writing by observing the molecules that come and go, destroyed and remade. But how do we understand the language? Without our cherished speculative preconceptions about what living means? Is measuring energy transduction the key? Or looking for dynamic kinetic stability? Or quantifying entropy and dissipation? I don’t know, and I’m tempted to speculate. I’ve certainly read a lot of the speculation out there, both sober and wild, both from experts and dilettantes. It’s a bigger labyrinth. A more difficult riddle.

Feeling like a Gryffindor

Last Chance. Relive the Magic.

 

Since AT&T is my internet provider, I have access to HBO Max. Other than re-watching some Studio Ghibli classics, I have hardly taken advantage of what else is available. This is my first streaming service, so pardon my ignorance – I was surprised that opportunities come and go. All eight Harry Potter movies, probably contracted to build subscription when the service launched, are in the Last Chance category. HBO Max is telling me that I have a limited time to Relive the Magic.

 

I watched all eight movies when they were released on the big screen, but that was a while ago. And since I had been feeling like a dinosaur, and I wanted instead to be feeling like a Gryffindor, I thought this a good opportunity to revisit the movies before the new semester begins. Having re-read the books this January, I was reminded of how excellent they are!

 

Almost two decades ago, shortly after the first movie was released, I talked to one of my friends who had seen the movie, but had not read the books. I remember his remarks to this day: He thought the visuals were good, but had trouble following the story – he felt there were bits and pieces stitched together, but not necessarily well connected, and that the story seemed to jump from one event to another. It made me realize what a different experience watching the movies might be if you haven’t read the books. For me, it was cool to “see” Hogwarts. You get some sense of the school and its grounds, but there is some movie magic seeing it on the big screen. It was also interesting to see and hear the different characters, and be immersed in Harry’s world through a different medium.

 

This time around, I decided to skip the first two movies, partly because I remembered my friend’s remarks, partly due to my finding Lockhart in Book 2 annoying, and partly to avoid the dissonance when the actor playing Dumbledore switches from Richard Harris to Michael Gambon. Also, my favorite book is Book 3, and I had a vague memory that while the movie deviated considerably from the book, the depiction of the parallel key events that form the climax was cleverly done. I enjoyed the movie, although I found it “darker” than I remember (i.e., less suitable for kids), and I had forgotten how much the movie differed from the book. Having recently re-read the books, I was regularly surprised in many scenes, and thinking to myself “wait… that’s not how it happened”.

 

Now I do understand that when you adapt a book to a movie, you have multiple considerations: leveraging the different (visual) medium, the reduced time to tell the story, making hard choices to streamline the plot, and accounting for an audience that might not necessarily have read the books. I had given this issue a lot of thought when Peter Jackson’s Lord of the Rings movies were released. I’m somewhat of a Tolkien geek, having read the trilogy close to twenty times. Of the five DVDs I own, three of them are part of the boxed set extended-version. I’ve watched the movies maybe three to five times total, and I have many a bone to pick with Jackson’s choices, but I think I understand some of the choices made when deviating from the books.

 

But back to the Harry Potter movies. I contemplated skipping #4 and #5 on the list, because they are in the lower half of my book rankings. But then I talked myself into watching them to see the kids grow up. Also, Book 4 is a pivotal turn in the series; we get to see students from other schools, the behind-the-scenes “faithful servant” storyline is clever, and there are the spectacles of the Quidditch World Cup and the Triwizard tournament. The only vague memory I had of the movie was that the First Task was theatrically over-done and the Third Task was disappointing with moving hedges and wind blowing. My fresh viewing experience was disappointing indeed. My vague memory not only proved correct, I was unimpressed by the simplifying shortcuts that turned a rich story into a drab one. The simplified or modified portrayal of key characters was, I thought, poorly done.

 

Still I shouldered on. I couldn’t remember anything about the fifth movie, which should have been a Grim omen. Book #5 is lowest in my ranking. (It’s still good.) Yet it does have scenes of St Mungo’s and the Ministry of Magic, and if anything, the movie could take advantage of its visual medium to immerse the viewer in these settings. However I was even less impressed re-watching the fifth movie. No St Mungo’s. And I had the strong feeling of a story being chopped into tiny bits and strung along. I think it would be incomprehensible, or misleading, to someone who hadn’t read the book. Ugh. There’s much I could rant about, but I won’t. After watching it, I remarked to my spouse (who was also disappointed with the movie) that I can’t believe I paid money to watch this the first time around. She had a good reply: When you’re watching it for the first time on the big screen, perhaps you ignore some of the flaws. But on the small screen, there was no worthwhile magic to relive in this movie.

 

The sixth movie was a breath of fresh air. I had almost no recollection from my previous viewing, and I found the present viewing rather enjoyable! The story arc was well-maintained, and deviations from the book to streamline the key plots were, in my opinion, well done and effective. The new musical score, and judicious use of humorous scenes, kept the movie lighthearted and brisk, while taking seriously the darker parts of the plotline. There was only one significantly extraneous scene that I thought highly unnecessary, but as a whole, the movie held its own very well. I would even rate the sixth movie above the third movie (although I rank Book 3 higher than Book 6). I plan to watch the two movies covering Book 7 during the coming weekend. Back when they were released, I remember holding the minority view that the less action-packed Part 1 was as a movie, better than Part 2. We’ll see if I change my mind.

 

Overall, throughout the movies there were some cool Gryffindor scenes including being in classrooms and common rooms, the Quidditch pitch, and other areas in Hogwarts and Hogsmeade. For brief moments, it was feeling like a Gryffindor. As I apprehensively approach the online semester, I’d like to be a Gryffindor. Some of my students will probably think I’m a Ravenclaw. Others will think I’m an evil Slytherin. But I’m happy to be Hufflepuff. Just gotta keep putting in the hard work!

 

*Images from Google Web Search for Hogwarts House Banners. Not sure who first designed them.

Feeling Like a Dinosaur

My department had a tip-trading session on best practices as we prepare to go all-remote this Fall. Since I didn’t experience the Spring pivot, I found the meeting very useful, benefiting from the experiences of those who had gone before. Straight talk from folks teaching in a similar subject area and context gets to the heart of the matter in a way that videos and articles from people in other institutions do not (even if they are slickly produced or well-written). I still don’t feel ready but I am preparing to do my best when classes start a week from Monday.

 

I was impressed by my colleagues. What a great bunch of folks! Different individuals tried different things, and I was amazed at how quickly some of them were able to adapt to the technology. I also heard about their frustrations as to what didn’t work so well, but overall the session was full of positive “here’s what worked for me” examples. After the session, however, I felt somewhat deflated. Reflecting on this during my Zoom break, I realized that I was feeling like a dinosaur. Here’s Emily the Brontosaurus (from the excellent time-traveling card game Chrononauts) to illustrate. 

I’m not a Luddite by any stretch of the imagination, given that I’m a computational chemist, however I’m certainly not an early adopter, and much of my teaching looks “old school”. I do use some slides in class (showing Figures from the textbook) but by and large my classes resemble an interactive session of problem-solving with students using the white board. I rarely use the Learning Management System and have found it more efficient, quick, and compact, to use my simple old-school HTML-hacked (institutional) home-page to deliver my course materials. I’m not sure anyone else in the university uses these pages, and few outside of ITS these days even know of their existence.

 

Perhaps I’m only good at using the technology I was socialized into in my younger days, when I was more adaptable. I found it more efficient to stick with the old ways even as technology progressed. In that sense, I might be like a dinosaur. A very old-school teacher with old-school tricks that have served me (and I’d argue my students) well over the years. But it might no longer do so in a remote environment. The environmental change has forced me to adapt. Or die. Evolution in action. Perhaps I’ll do okay after all. I have shown some capacity to adapt, although often because I was forced to do so – like when ITS told me they would no longer support my use of Unix e-mail clients and that I must switch over to the newer clients. (Apparently, I was one of the last five or ten people to switch over, although this was well over a decade ago.)

 

While part of me is annoyed at having to adapt, another part of me sees this as a good thing – a chance to learn some new tricks, and maybe even improve my own teaching as a result. It has certainly made me read a lot about pedagogy in the new age of remote, and allowed me to ponder the many pros and cons, both practically and philosophically. Perhaps I won’t feel so dinosaur-ish after several weeks of online teaching under my belt. I’d like to shake that old, tired, feeling. A change would be nice!

Generalized Domain Knowledge

In technical subjects such as chemistry, students quickly get lost in the details. Those details are important, but they support a larger edifice, which in turn supports those details. Students need the whole shebang to grasp what’s going on. But how should we sequence the approach so that students aren’t drinking from a firehose and overwhelming their precious cognitive resources?

 

Here’s one study with a tantalizing, but jargon, title.

 

I’ve only shown half the abstract, because the rest is technical jargon that won’t make sense unless you’re in the field or you’ve read and understood the paper. But in the last line shown you can see that it’s a very small-scale study so the result should be taken cautiously.

 

First, we need to clear up some jargon.

 

Domain-specific knowledge is what helps those with expertise in a domain to efficiently solve problems in that field. It typically requires explicit instruction in the early stages, and requires conscious use of working memory to help consolidate the new knowledge. It consciously feels like your brain is working hard and thinking. Schools focus on teaching domain-specific knowledge because acquiring it without being explicitly taught is difficult and highly inefficient. Once you have some background expertise, it becomes easier to teach yourself more in that area, but you’ll still have to work hard at it.

 

Domain-general knowledge is what we seem able to acquire unconsciously simply through repeated exposure; it likely has an evolutionary component. It is not tied to a specific area of expertise or domain. You don’t need to be explicitly taught the material. You probably don’t remember how you learned it; and you’d be hard-pressed to articulate the process of learning without resorting to (weak) post-hoc rationalization. It seems automated and doesn’t feel like you’re having to think hard when you acquire and use such knowledge. However it isn’t useful for solving complex domain-related problems – any technical problem or any problem requiring some depth being prime examples.

 

Educators focus on the former rather than the latter for good reason. The first needs to be taught. The second does not. Given the increasing technical complexity of the world we live in, this explicitly taught domain-specific knowledge becomes even more important. Not that you can’t acquire such knowledge on your own – it’s just highly inefficient to do so on your own through seemingly passive observation without conscious engagement of what feels like hard thinking.

 

Kalyuga, the author of the article, splits domain-specific knowledge into two categories: specific domain knowledge and generalized domain knowledge. Note that both focus on the domain area. Here are the definitions. “Specific domain knowledge is applicable to a narrow range of tasks in the domain. Generalized domain knowledge is applicable to a wider class of different tasks in this domain; however it remains a part of domain-specific knowledge… [it] may provide a compromise in the trade-off between the generality and power of knowledge.”

 

The study aims to test whether constructing and providing a generalized domain knowledge schema is better at helping learners acquire and retain domain-specific knowledge. There is some evidence from their small study that providing a general-to-specific schema is slightly superior to a specific-to-general schema. So perhaps sequence matters. Both these outperform not providing a schema (which you can think of as scaffolding statements related to learning the material). Interestingly, the participants do not self-report significant differences in cognitive load in any of these. The technical task was to learn how an air-conditioner works, and participants were pre-screened to assess prior domain-specific knowledge.

 

I’m less interested in the result itself, but rather I’d like to consider what providing schemas for generalized domain knowledge looks like in areas that I teach.

 

First-year college chemistry textbooks (at least in the U.S.) have moved to what is called an atoms-first approach. Instead of stoichiometry, balancing chemical reactions, and doing lots of calculations involving moles and masses, early on in the first semester, these topics are now shifted later in the semester. Taking their place early are the interaction of light and matter, electronic configurations, and chemical bonding. It’s hard to say whether these broad moves constitute general-to-specific or specific-to-general schemes. If one argues that the macroscopic is central, then the move feels specific-to-general. If one argues the microscopic (or nanoscopic) is central, then it feels general-to-specific. The tricky part is that in the grand scheme of things (pun intended), both are equally important in my opinion. (See Johnstone’s Triangle.)

 

One of my areas of expertise (as a quantum chemist) is chemical bonding, so perhaps I’m biased in putting chemical bonding center-stage. The atoms-first move works well for my pedagogy overall, although I still quibble with the arrangement and flow of topics in any textbook out there. (No, I haven’t had sufficient motivation to write my own textbook.) A few years ago, I made a significant change to how I approach chemical bonding by spending an entire hour-long class session on what I think would squarely fall under providing a schema for Kalyuga’s generalized domain knowledge. You can see the scope in this previous blog post. Too bad that’s the only clear example I can think of that I use in G-Chem.

 

Throughout the semester, I’d like to claim in every class session (although I’m not sure if that’s true), I make statements in reference to generalized domain knowledge – but these are scattered throughout mainly as context reminders rather than explicitly teaching a schema. I do use a mind-map-ish activity in second-semester G-Chem for students to connect concepts in energy and thermodynamics, and there was once when I devoted an entire class session to discussing the idea of energy in conjunction with a Feynman reading. But otherwise I haven’t worked on designing an explicitly taught general-to-specific schema of the type that Kalyuga refers to. I’m not worried about this. I think the approach I’ve refined over the years works well, although I will be sorely put to the test going all-remote this semester. My schemes may or may not work. I’m likely to blog an end-of-semester update reflecting on how things went.

Preparing for a Remote Fall

It was no surprise when my institution finally officially announced that the Fall semester will begin remotely. The language leaves open a pivot to in-person classes, but that will depend among other things on state and county guidelines. Earlier in the summer, as cases were dying down in late May and early June, I was very much looking forward to in-person meetings with my students. And although I have been expecting that we would be all-remote since early July as cases surged, I still felt oddly deflated by the official announcement. And I can no longer procrastinate over class prep.

 

Classes begin in two weeks. Most of my class prep time the past two weeks was for my special topics origin-of-life course. Since I expected we would go remote, I have returned to using our institution’s LMS. Regular readers will know I’m not a fan of Blackboard, but if I want to do my best this coming semester, I will need to utilize its features for online engagement and security. (I normally use my own bare-bones, but efficient, HTML course website.) Also, the look and feel is also different because we’ve upgraded to Blackboard Ultra, a minor annoyance. Being all-remote means I will need to make the online atmosphere welcoming and engaging, without being too burdensome. So I spent some time designing the look and feel of my course, and I’m pleased with the results. Here’s a snapshot of the landing page.

 

I need to do a bit more editing before releasing the page for student consumption later this week. However, to start engagement before class begins, I e-mailed a brief welcome to my students and shared with them links to my recent post on Silicon Life and our library’s link to the e-Book that we’ll be reading and discussing as part of the course. No one has dropped the class yet (since the all-remote announcement) so that’s a good sign, I suppose. We’ll be primarily discussing the primary literature in class (over Zoom). I’ve figured out the syllabus and collected all the readings. For online engagement, the students will blog and contribute to the discussion board.

 

This week I’m starting to work intensely on two fronts. I have twenty new first-year advisees, and I have been looking at their course schedules, transfer credit, and planning for the advising meetings we will be having starting a week from today. In parallel I am starting to put together my G-Chem course (that these twenty students are also enrolled in). We’ve switched textbooks again. I was on sabbatical last year and did not participate in the discussion. I have a slight preference for the textbook we were using previously (I think it is better written and arranges the topics more suitably to my approach) but the companion e-Homework system was more problematic. We’re back to a system I have some familiarity with, but also has differences because it has been upgraded (another minor annoyance).

 

I will also need to make arrangements to get new research students set up remotely. I don’t anticipate a problem setting up student accounts on our local high-performance computing cluster or getting them VPN access. I will have to figure out how to do the ‘training’ remotely. Usually, I spent two days carefully walking the students through the ins and outs of Linux, using a text editor, and using our specific computational chemistry software. This will not be as smooth in a remote setting, but it’s nowhere as problematic as running an experimental ‘wet’ lab. So I’m thankful for that fateful day when a professor in graduate school made his research group sound so interesting that I decided (with little experience) to join his group and try out computational chemistry. I taught myself Irix (SGI’s version of Unix) and a scripting language on the fly, and I haven’t looked back since.

 

I haven’t sorted through how I feel about a potential pivot back to in-person classes. While I personally would prefer it (and I’ve considered the potential risks), I don’t think it would be practical for a variety of reasons. Having never taught remotely/online and missing the harsh pivot last spring, I’m trying to look at the bright side: I’m acquiring some new skills, and these might enhance my teaching in the long run. We’ll see how long this run is.