Ten Years

It’s hard to believe I made it to ten years. But my interest has waned, no thanks to data-scrapers vacuuming up writing to train their large language models. My number of blog posts has dropped by twenty percent the last two years and I expect it to dip further. Today is the day I will give myself permission to no longer feel obligated to keep up. I will probably write occasionally when the fancy strikes me, but I have other interests to take up my time.

 

Looking back at my mid-decade post, I would agree with past self. My writing in this format has gotten a little stagnant; that’s the diminishing returns part. I do still write primarily for myself, and to some extent my students. I have a few links as optional reading for students who are interested to get a slightly different perspective on some of the topics they see in class. My sense is that students who’ve read these optional posts found them helpful or at least amusing.

 

Have the things I write about changed?

·      Book reviews are now at 49%, up from 43%. I don’t think I’m reading more. I’m just blogging less about other things.

·      Teaching is at 33%, a slight drop, but not by much. I love thinking about teaching and learning. That won’t change – even when I retire from my full-time job as a professor.

·      Research dipped a little from 8 to 6%, although origin-of-life posts maintained steady at 11%.

·      Magic also dipped from 12 to 10%. I certainly think less about magic these days. And it’s been a while since I re-read Harry Potter or any other magic-related fiction. I’ve been reading sci-fi a little more; I suppose technology is a sort of magic but I haven’t labeled the posts as such.

 

Halloween does make me think of magic. Today, I read an article about the history of how Halloween is celebrated in the United States and how that has changed over time. It was both thoughtful and interesting. I have gotten into retro-gaming (computer games from the ‘80s) and some of the fantasy-themed role-playing-ish games feature magical systems. I haven’t written about them much, and the latest one I played hardly used it. [LINK] But I’ve started thinking about whether I could create a game and what a suitable magic system might look like. Maybe some of those thoughts will make it to future blog posts.

 

In any case, Happy Halloween, and to my readers, I hope at least some of the past blog posts have delighted or amused you, or even better – you learned something from them!

Astrobiology Frontiers

Mars gets a lot of press as the frontier in the search for extraterrestrial life on another orb. We Earthers have landed a bunch of probes, taken lots of pictures, and performed some in situ chemical analysis. We don’t know whether life existed once on Mars, although the working hypothesis is that early Mars was quite hospitable to life. The present red and rocky desert isn’t; but maybe life clings to existence in the subsurface. We have some very interesting and largely unexplored subsurface life right here on planet Earth.

 

In her recent book The Secret Life of the Universe, Nathalie Cabrol, director of the Carl Sagan Center at the SETI institute helped me broaden my frontier as to what’s interesting and potentially investigable in addition to Mars. She addresses the “veil of secrecy” of Venus and discusses possible habitable scenarios. I learned about new missions on the slate from NASA and ESA. She covers Mars, of course. But then she spends some time discussing Titan, Europa, Enceladus, Callisto and Ganymede. They’re all different, and each is uniquely interesting. I had previously heard or read about the first three as being interesting sites for finding life, but not the latter two.

 

But her book goes further afield. Ceres turns out to be quite interesting; it has geological seismic activity and possibly a liquid briny ocean beneath the ice. Pluto has “mountainous and glacial” terrain, and its partner Charon may have had a subsurface liquid ocean, I’m guessing made up of nitrogen and possibly ammonia (based on Pluto’s glaciers). I was previously under the impression that only planets in the “Goldilocks zone” of habitability where you were about the right distance from your sun to support liquid water were possible candidates for life. But Cabrol opened my gaze further afield. There could be very interesting and unique activity on a planet on a moon due to many factors, some of which might be conducive to complex chemistry arising.

 

One chapter is titled “Visions of Tatooine and Mordor”. Cabrol classifies the different exoplanets (over 5,500 and counting) into five categories, and then picks out specific examples of interest to astrobiologists. Kepler-16b is Tatooine – it has two suns. The gas giant Bespin could be Cloud City. And the ocean-world Kepler-22b could be Kamino. The interesting TRAPPIST system is also discussed. Cabrol discusses these many interesting orbs in the context of the Drake equation. Our ever-growing knowledge and discovery of so many planets, coupled with the possibility of the habitable zone being widened beyond the traditional Goldilocks parameters, suggests that E.T.’s existence is that much more likely.

 

I was particularly struck by her suggestion that “explaining the origin of life might not be enough to define it”. We’re blinkered by life-as-we-know-it, and it’s very difficult to imagine how else life might manifest. As to what it means to demonstrate the tasks of living, it may also be that “what life does is not what life is”. More questions, few answers. But it made me excited about potentially offering a course in astrochemistry. I’m certainly no expert, but it would be a great way to motivate myself to learn the material!

Happy Mole Day

It’s the middle week of the semester. We don’t have a mid-semester Fall Break. And this year mole day is smack in the middle of the week. Our department student affiliate chapter has organized several fun activities. Liquid nitrogen ice-cream is quite popular. (I was in a meeting so I missed it.) There’s also lab-coat tie-dyeing. Personally, I prefer my pristinely white lab coat. As a computational chemist I don’t spend any time in lab running chemical reactions, although I have taught general chemistry lab and I have on occasion subbed in an advanced lab class for several hours.

 

I don’t have any mole-specific thoughts today. In G-Chem 1, we’re smack in the middle of chemical bond. I’ve been thinking about what we might omit if we moved thermochemistry from G-Chem 2 to G-Chem 1. Do we need to discuss the exceptions in electronic configurations? Do we need to discuss the kinks in the trend of first ionization energy across the row in the periodic table? Do we need to discuss hybridization of orbitals? Can we omit the photoelectric effect? In addition to discussing wave-particle duality, I use it as a springboard to introduce energy diagrams. I’ve been trying to include energy diagrams as much as possible: hydrogen atom (and Bohr model), photoelectron spectroscopy, electron configurations, and bond energy curves.

 

In P-Chem 1 we have just finished the hydrogen atom. I promised the students we’d be there by mid-semester so that we can get to molecules! With more electrons! Many of the students will also be happy to see the math load decrease. The next problem set will still be math-ugly (or math-elegant, depending on your point of view) because we’ll be covering the variational principle and perturbation theory. Once we get past the Born-Oppenheimer approximation, the problem sets will get much less math-intensive. We’ll draw pictures of models and try to extract conceptual information from them. But first students will need to get pass the dreaded Exam 2 coming up on Friday.

 

September was for getting settled in (and ahead) in my classes. October was when I wanted to start working on a research article. I have gotten started but it’s slow-going. I think I have most of the data tables done and I’ve outlined the key figure for the paper with lots of chemical structures and a bunch of arrows. But there’s still quite a-ways to go and it’s been hard for me to get motivated to write. I’d much rather spend time thinking about my classes, or two side-projects that I’ve been exploring that may turn into collaborations with experimentalists. So I am getting some research done, but it’s slow. I did spend a chunk of September training two new research students; the first month is full of “how do I do that again?” but I think they’re getting the hang of it now and are starting to produce their first tranche of results.

 

As we head towards cooler temperatures, and with thermochemistry still on my mind, I’ve been musing about the nature of hot and cold. What is cold? The absence of heat, I suppose; although heat is not a noun. Let’s just say that when heat flows out of the system, if that leads to a loss in thermal energy, then the system gets colder. The zeroth law is constantly trying to make the temperature uniform everywhere. That makes refridgeration a neat trick when you don’t want to be using blocks of ice to cool stuff down. I grew up with a refridgerator in the house so I don’t know what it felt like to be without one. You’d have to eat up your fresh produce quickly enough so it wouldn’t spoil. Higher temperatures mean chemical reactions are occurring more quickly on average! And what is temperature? It’s a statistical average of the thermal energy of gazillions of molecules – six gazillion if it’s a mole of molecules. Aha, I was able to tie this back to the mole. Happy Mole Day!

Antepenult

Antepenult is an obscure Ultima clone, created for the Amiga in the 1980s by Paul Falstad, and distributed as shareware. This summer, I learned about it by stumbling onto the CRPG Addict blog; the writer Chester Bolingbroke is playing his way through old computer games in the role-playing-game genre. He’s an excellent and engaging writer, and my quick skim of his first two articles convinced me that I should give it a try. I did not read these closely so I would avoid detailed spoilers. After all, the fun part is solving the puzzles for yourself!

 

Unlike Nox Archaist, which pays homage to the Ultima series, but is much more streamlined with modern design sensibilities, Antepenult is indeed a child of the 1980s. And it really is an Ultima clone – down to most of the graphics and much of the gameplay. I’d classify it as a mishmash of Ultima II, III, and IV. You’re a single player; there is no party. You consume food. There are basic weapons, armor, and supplies (torches, keys, gems). You can obtain other special items, some of which provide the equivalent of magic. You get gold by fighting the same denizens you’d see in Ultima. It feels very familiar. You begin near a castle and a town; and the ruler of the castle sets you on your quest. Basically, you need to conquer evil and save the world. Nothing new there.

 

You begin in the land of Havilah. If you’ve read the bible, some of the non-player characters (NPCs) have biblical names, some are the early church fathers, and then there’s a whole bunch of Greek mythology thrown in. I met Homer and Asaph in the same hallway of a city. They were composing songs and poems about the evil that had come and my eventual victorious quest. To complete said quest, I needed to explore different towns and worlds and talk to NPCs. I was given a list of items to collect, and many of the NPCs strung me along by telling me the next person to talk to. The four elements of Earth, Water, Air, Fire, feature prominently. I had to discover how to access these different worlds. And if you guessed it, the waterworld is called Atlantis and its king is Neptune. Two towns in that world were Tyre and Sidon. Yes, it’s a mishmash. And the special items you collect are Ultima-cloney. I won’t say much in case you ever want to try the game yourself.

 

I’d never used an Amiga before but I was able to eventually get FS-UAE working several moons ago. So as not to interfere with my workweek, I only played Antepenult for some number of hours each weekend. I took copious notes and I started to make maps. When I really got stuck, I would skim the CRPG Addict’s articles and get a clue as to how to proceed. This didn’t happen very often and it has been interesting to compare Bolingbroke’s play-through with my own. We used similar strategies overall, and occasionally got stuck in the same spaces. But any seasoned old-school Ultima player would probably do the same things. Some patience is needed. A teenager today would probably find it b-o-r-i-n-g. But someone who played Ultima as a teenager will feel the nostalgia when discovering some clever and amusing parts in the game.

 

Here I am at the final castle of the big bad boss.

 

After defeating him, instead of getting a “Congratulations! You won!” message, I got confused as fire and black spots suddenly started appearing and I wasn’t sure what to do and whether I needed to run out of the castle. Everything goes black.

 

I wake up in a restored castle Pergamum and as I walked through the hallways I am thanked by its many inhabitants for saving the world. Asaph was one of them. As were a number of the church father namesakes who gave me clues for my quest. One character who I saved from a high school in hell sets up a possible sequel. (I thought I killed the hag, but apparently she got away. I must have just killed the daemon inhabiting a body that claimed her name.)

 

The king of Havilah, Lord Hypnos, tells me how to return to my own world. Very Ultima. When I enter the portal to do so, there’s an amusing sequence at the very end. Another hint of a possible sequel. No sequel ever came. According to Bolingbroke, this was Falstad’s only game and he programmed it when he was young, and before adulting became a fulltime job.

 

I’ve now read in detail all Bolingbroke’s Antepenult articles. If you’d like to just get a sense of the nostalgia by living vicariously through his playthrough, you won’t be disappointed by his articles. If you want the full experience, get an Amiga emulator and give it a go. My copy was unregistered which makes the game harder when you’re in Tartarus, but not insurmountable. In his articles, Bolingbroke provides enough information whenever you’re stuck. My overall rating of Antepenult? It’s not as good as Nox Archaist, but it has some very clever bits. When I finish my adulting phase-of-life, maybe I will take up writing a retro-game themed on the four elements. I have imagined some of my own clever bits. Maybe my game will be the Antepenult sequel.

Exam Readiness

Augustine of Hippo (circa 400 A.D.), in a remarkable chapter on the nature of time in Confessions, confesses the following:  If no one asks me, I know: if I wish to explain it to one that asketh, I know not”.

 

This is why I tell students that it’s very important to try and explain aloud their answers to conceptual questions. You think you know it in your head, but you actually don’t know what you don’t know until you try to verbalize it or write it out in full. Several years ago, I revamped my daily study guides to phrase what students needed to know in question form, and I also added “test yourself” questions to each of the study guides. Whether or not students use them effectively is an open question, but this semester I have assignments requiring students to turn in a subset of their answers. (The students get full credit for the attempt regardless if they got the answers right, wrong, or something in between.)

 

In my course materials, I have a section on “how to be successful in this class” that informs students what they should be doing from the get-go. I also provide detailed information on what students should read before class, and the main things we will cover in class. It’s short and pithy. Students follow it to varying degrees, or at least they claim to do so. But if they really wanted to be successful in any class, they should read Daniel Willingham’s new book, Outsmart Your Brain. It doesn’t just provide strategies; it explains the why behind them. It also explains why your brain’s instinct is to resort to less optimal strategies that require less effort but give you a false sense of thinking you’ve learned when you haven’t. I’ve read many of Willingham’s research articles over the years but these were not aimed primarily at students. Now there’s a good book I can recommend to students!

 

Each chapter of the book also ends with notes to instructors on how to facilitate student learning. A number of those are things I already do in my classes, but there were others I had forgotten or not thought as deeply about. This week I’ve been making a better effort to not assume students know how and why I have organized the material for each class in a particular way; I’ve been making more statements about what we’re doing, why we’re doing it, and how we will proceed. I have not been putting these up on a slide, because as Willingham says, students just copy things from a slide regardless of whether it’s useful to them or not instead of paying attention to what I am saying.

 

So how should students prepare for exams? They should prepare a study guide, according to Willingham. Turns out I already help them with this by posing questions in my guides. But Willingham has helpful tips of how to pose questions bidirectionally and at multiple levels. And he tells students you need to memorize some of your answers, not necessarily word-for-word but meaningfully. Forcing oneself to recall in different places and at different times works best in solidifying the material. And saying it aloud, of course! While I encourage students to study together, Willingham explains why this is useful, and how to do it effectively. When students discuss with each other their fragmented knowledge, it introduces variation to how questions and answers are posed. Different individuals help notice things others have missed. And students can test each other! Being tested is one of the best ways to prepare for exams.

 

Chapter 7 (“How to Judge Whether You’re Ready for an Exam”) had some particularly good reminders. It’s not enough to ‘understand’ something when someone else explains it, you have to try and explain it yourself – and not just in your head. Rereading can mislead you into thinking you know something you don’t really know it; rather you just have a passing familiarity and unless you’re forced to recall (without looking) you won’t know if you actually know. (Willingham recommends letting at least thirty minutes pass between reading and testing yourself.) I’ve stopped giving previous year’s exams to students because they fail to utilize it effectively, either giving themselves a false sense of readiness or going into a panic. (Read Willingham’s book for the explanation!) In distinguishing learning from performance, Willingham recommends overlearning – essentially “study until you know it, and then keep studying… It protects against forgetting [even though] it feels as though it’s not working.” He has a great quote from a friend when he was in college who said: “When leaves blowing around on the quad look like organic compounds to me, I know I’m ready.”

 

There’s also a chapter on how to take exams including what’s effective and what’s not. This mirrors some of what I highlighted from Barbara Oakley’s book. But I liked the early chapters on the importance of active listening in lectures, how to prepare for a lecture class, how to take notes, and how to reorganize one’s notes. Willingham thinks students should take their own notes in class, regardless of whether the instructor provides notes or slides or recordings. He also explains why being in class and engaging your mind right there and then is more effective than missing class and getting notes later from a friend. There’s an interesting section on whether one should do the reading before or after the lecture – that’s dependent on how the instructor organizes the class. And he gives good advice on how to ask good questions – ones that don’t annoy your instructors or your classmates.

 

Willingham reminded me that most students don’t take good lecture notes. It’s for a variety of reasons and he provides tips to students on how to improve, but I particularly appreciated his reminders to instructors. These are things I need to pay more attention to:

·      Talk more slowly. (I talk too fast sometimes, okay, maybe most of the time in class.)

·      Signal when something should be written and pause to allow time to write it down. (I’m getting better at this.)

·      Distribute copies of figures/visuals; let students know which ones they don’t need to copy. (I think I’m good at this. Maybe, maybe not.)

·      Students copy what’s on slides, whether doing so makes sense or not. (I’ve become much more judicious in the way I use slides.)

I liked Willingham’s suggestion of how students should work together and share lecture notes. Very importantly, it is not by dividing the effort among group members, but rather that everyone should take as complete notes as they can, and then once-a-week get together so each person can fill in any missing gaps and compare how different people organized their notes to see if any improvements can be made.

 

One thing that is emphasized in Outsmart Your Brain is how effortful learning actually is. Our brain would prefer to conserve energy and get away with quick-and-easy pattern recognition, maybe. I can’t speak to other fields, but the natural sciences are full of phenomena that are counter-intuitive, conceptually challenging, and theoretically abstract. Yet, they are crucial to understanding the field. Chemistry is hard to learn. I know it from my own experience as a learner, and I certainly see the same for my students. I hope to convey some of the tips and explanations from this book to my students.

Curator and Guide

Pondering what I do as a chemistry instructor made me think of the role of a curator. I’ve never met a curator in person, but I have seen their invisible hand when I visit a museum or a gallery. Someone decided what will be displayed, how it will be displayed, and what information will accompany each of the displays. There is likely a theme that collects various objects together. Sometimes this is made explicit in the information given; other times it is not.

 

I have gone on a guided tour before. In some cases, it was a Walkman and headphones that talked me through where to walk and what to look at. In other cases, it was a live human being who could also answer questions and engage in back-and-forth conversation. The guide adds another layer of detail to whatever is being displayed, calling attention to some features while making no mention of others. Time also plays a constraining role as a live guide moves you through one display to another. A Walkman guide with a pause button, or no guide at all, allows me to decide how much or how little time I will spend with a particular exhibit.

 

The author of a textbook could be compared to a curator. Most students have never met the author, and in many classes, the textbook author never makes an explicit appearance. But the textbook arranges the material in a particular way following a particular logic. When I use a textbook as part of a class, I am akin to the guide. I add flourish to some areas while downplaying others according to what I think is important for my students. But since I have eschewed using the textbook in most of the classes I teach, I have become both curator and guide.

 

It's been freeing in some ways; I feel less constraint in rearranging the material the way I deem fit. But I’ve only reached this point of feeling that I can be a curator after I’ve taught a course multiple times and developed my own internal logic of how I personally think the material should be presented. There is no one right way. But some arrangements work better than others, certainly in chemistry where a significant chunk of the conceptual knowledge is hierarchical. Concepts build on each other and the complexity ratches up. It’s more work to be both curator and guide, instead of just focusing on the latter, but it’s work that I enjoy.

 

A museum guide has never given me a quiz to test my knowledge after the tour. In my job as an instructor, I can’t stop at being just a curator and guide. I also have to be an evaluator. Have you learned something from this tour of chemical knowledge? What have you actually learned? Can you demonstrate that you have learned what I wanted you to learn? This is not the most fun part of the job for instructor or student, but I admit that I am eager to know what and whether my students learned. I start grading exams almost immediately after the exam is over, so students can get their feedback by the next class period. But it also gives me feedback so I can improve what I do as a guide and as a curator. A museum might get feedback from a visitor based on their interactions. A curator almost never does, at least not directly. In any case, my students help me improve my role as curator and guide in the breathtaking tour of the chemical world!

Life in the Rocks: Cold Version

I vicariously followed the adventures of Tullis Onstott and his colleagues in Chapter Nine of Deep Life. Nunavut, Canada, is cold, cold, cold. Could there be life down in the rocks below the permafrost? If so, it might tell us how to hunt for life on Mars below its barren surface. While I mentioned the challenges of field work in my previous blog post, and how I am ill-suited to undertake such arduous, reading about it is exciting. I recommend Deep Life for the blow-by-blow accounts.

 

In this icy cold chapter, the scientific team successfully isolates a prokaryote that makes its living via chemolithoautotrophy. That’s chemistry in the rocks where you make your own food by using energy from the redox gradient from rock chemistry. The autotrophs we are most familiar with are green plants which are photoautotrophs. They make their own food with energy streaming down as photons from the sun. Trying to determine what this microorganism does or how it makes its living is challenging. You have to chop up its DNA, determine its sequence, then try and match it up to known sequences that code for proteins that do biochemistry you’ve seen before.

 

They got to name their organism: Desulforudis audaxviator. It lives through reduction of sulfur compounds (desulfo), it is rod-shaped (rudis), and it is a ‘bold traveler’ (audax viator) thanks to having genes that indicate flagella for motility. They even have a scanning electron microscope picture (read the book!). But what was shocking is that it also had the genes for a complete nitrogen-fixation pathway. That’s very expensive biochemically. Were these just a relic or does the microbe use them? I don’t know. It’s acetyl-CoA pathway also resembled that found in archaea. That’s of interest to me in relation to my origin-of-life research.

 

The author has a great cartoon picture (shown above) showing its potential biochemistry from the sequencing data. They have the audacious proposal that radiolysis provides energy that splits water producing H₂O₂ which oxidizes pyrite (FeS₂) providing sulfate for the microbe. H₂ is also a byproduct for more reducing power! Mineral transformations in the environment are included in the cartoon, which I thought was a very nice touch that you don’t see in a biochemistry textbook. This microorganism might have been able to make a wide range of co-factors including cobalamin (for vitamin B12). It has a typical wide range of transporter proteins providing info on what might go in and out, and it has the usual carbon fixation pathways that I’m interested in.

 

It’s amazing that micro-organisms are found in tiny cracks of rock in the tens of nanometers wide. Very little water can penetrate in, yet somehow enough does for it to make a living in thin films of water just nanometers thick. I’m dumbfounded. Life does find a way to adapt, even in the freezing cold below the surface where stones are turned into bread. Could something be found on Mars? I don’t know. But it will be very expensive to find out and you’ll need quick-thinking knowledgeable Swiss-army-knife folks who know how to adapt.