Study Guides Revisited

Early in my career as a professor, a student asked for a study guide before the final exam. This was in a chemistry for non-science majors course. I obliged by creating a three-page document with bullet points of what the students should know and be able to do. I used action verbs (e.g. explain, define, solve) to make each point clear and simple; this was before they became the standard practice for “learning outcomes”. As an aside, I think the use of action verbs is useful for small and specific chunks of information, but NOT so useful when it comes to complex concepts. To quote H. L. Mencken: “For every complex problem, there is a clear and simple solution that is wrong.” But that’s another story.

 

I devote the last day of class (before the Final) to answering questions about the final exam and any course content we’ve covered. The students, armed with the study guide, essentially wanted me to go over the guide point-by-point. There’s no way to cram a semester’s worth of material into a single class session. But I tried to oblige by briefly hitting each major point. Within 30 minutes, everyone was exhausted, and it was unclear if I helped the students or just made them more stressed out.

 

The following year (in the same course) I included the study guide at the beginning of the semester, and encouraged student to use it as a guide throughout the semester. The vast majority of them did not. Very close to finals, students finally started looking at the guide, and got stressed out at what they perceived as a mountain of material. My perspective had been “look at how much you’ve learned!” but theirs was “look at how much I don’t know, I’m going to fail.” Waiting until the last minute and attempting to cram does NOT work well in chemistry. Despite my exhortations, my study guide was a bust, at least for many of the students. (There are always a number of students who ace the class but they might have still done so without my provided study guide. Maybe they have good study practices?)

 

I scrapped having these “final exam study guides” and pivoted to a different approach that I’ve used for many years. For each class, I tell them what to read, what to pay attention to, the main points we’ll cover in class. There’s often a statement akin to “you should be able to…” followed by some action verbs relating to course material. (I also did this for my general chemistry for science majors course.) Occasionally, close to finals, a student would ask if there was a study guide for the final exam. I would respond by pointing back to the information I gave for each class session, and that it essentially functions as a study guide. The student was usually disappointed by this, clearly it was not the answer they were looking for. I should also say that since I started teaching, I always spend the first few minutes of every class highlighting “here’s what was important from last time” and write keywords on the board.

 

This semester I’m piloting something new in my G-Chem class. I’m retaining the same setup of telling students how to prepare for each class meeting and what the key points will be. In class, I still have my regular low-stakes short quizzes, and highlight what was important from last time. But I’ve now added a half-page “Study Guide” for each class that includes some bullet points with action verbs, and a “Test Yourself” practice question or two that weaves a numerical problem with conceptual material. Why am I doing this? A decade ago we transitioned to online homework problems (this is now standard in introductory college chemistry) that are bundled with the e-textbook. There are a number of advantages to the online homework system for both students and instructors. But I want to highlight two challenges: (1) these systems do not handle conceptual questions sufficiently well, and (2) the way questions are phrased do not match how I would ask questions on an exam.

 

What I’m hoping that my study guide will do (if the students take them seriously) is to remind them, if they pay attention to it, of the conceptual parts of the course. Being able to solve numerical problems is important, and the ability to solve such problems on an exam indicates some conceptual knowledge. But my experience of grading exams over the years and helping students in office hours is that a lack of conceptual understanding trips students up in solving the numerical problems. And the numerical problem isn’t the end-all. It should lead to a conceptual point of knowledge. One might say that concepts are the bookends of numerical problems, the introduction and the conclusion – both very important parts! Furthermore, there is also much about chemical knowledge and understanding that is conceptual that does not translate into numerical problems.

 

Students also need to be prepared for their knowledge to be assessed through my exams, and that means getting them used to the way I phrase my questions and what I’m looking to see that they can demonstrate knowledge-wise. The online-homework-textbook isn’t sufficient; I daresay it has glaring holes in some areas. So students need to see how I ask questions and work problems. This is much of what takes place in class. They see questions that I ask and how I answer them. They take many of those low-stakes quizzes at the beginning of class. I used to provide previous year exams for practice, and then I pivoted to required self-tests essentially to make sure every student gets practice, not just the conscientious ones. The new “study guides for each class” are my latest experiment. I just sent an e-mail to my class yesterday reminding them to go through them after each class, while it’s still early in the semester. I keep trying new things. But at the end of the day, you can lead a horse to water but you can’t force it to drink.

Being Lost

It’s good to regularly put myself in the shoes of a student, so I remember what it feels like to struggle with learning something new that doesn’t necessarily come easily. Last weekend, at the ESCIP workshop, I learned how to use some python tools that I could potentially incorporate into my chemistry courses. Although I can code, I do so sparsely and poorly. It’s enough to accomplish my research goals. Pre-internet, I learned haphazardly through reading other people’s code (end users like myself) and reading books. These days, a quick search on the syntax for what I want to do is usually sufficient.

 

I don’t remember how I learned to break down a problem into code. I can do it in an old-school inefficient way. Some things in python are familiar, but many things are new to me – including the thinking process of formulating one’s script. So I’d consider myself a novice learner with some ancillary background, and I’m comfortable using the command line and the old-school vi text editor. Jupyter notebooks are new to me, but I’m trying to get more comfortable with them because I think they will work well in a classroom setting.

 

The main live-coding sessions were superbly taught, and I had no problem following along and even had time to consider the pedagogy being used by someone who is experienced in conducting live-coding workshops. However, I later attended an optional session on how to incorporate some special features into python code aimed at making interactive simulations (similar to PhET). This was facilitated by another faculty member (who may not have as much experience in teaching live-coding), but the pace was a little too quick in some places, at least for python-novice me. I got stuck at a particular point, and as I was trying to wrap my head around the problem to fix it, the instructor kept moving along. When I looked up a minute or two later, I was lost. I was lost for the next ten minutes and stopped typing anything and just looked up to try and absorb as much as I could, although it felt like I was in a daze.

 

That’s when I had my epiphany of being lost in class. I’m sure my students sometimes have this experience because the pace of my class can be intense. Missing a couple of minutes can sometimes mean feeling lost for the next fifteen. I didn’t want to interrupt the instructor because my quick scan of the room gave me the impression that most of the group were following along just fine. And I didn’t want to whisper to my neighbor for help. That must be how some of my students feel when they get lost. It is like being in a daze, and I was reminded of what that felt like.

 

Classes started this week and I’m trying to be extra careful about not going too quickly and being more cognizant about whether the students (especially those sitting further away) are following along. I’ve always incorporated strategic pauses into my classroom, but I’m trying to be more conscious about whether I’m leaving some students behind. This experience of being lost also opened my eyes to noticing the pedagogical differences between the experienced live-coding instructor and the (perhaps) less experienced one. Facilitating live-coding does require some different approaches in a classroom.

 

In the previous sessions where I was breezing along, I did notice others occasionally being lost (because I had the time to look around) but I didn’t feel it myself. Not feeling lost boosted my confidence that I could be successful learning python. My latter experience of being lost did the opposite and my confidence levels dropped. That feeling of efficacy as a student is important. I was challenged to consider the times when I had inadvertently made students feel that chemistry was too hard for them because they felt lost in class. Yes, there are students who are lost because they come to class unprepared and didn’t do the reading. But there are also those who feel lost because they had less background and confidence. And there are also those who did the reading, but are still puzzling over something I’ve said (or a problem I worked on the board), and then become lost when I move on. I need to do better. Being lost myself was a good experience and reminder.

 

P.S. As to my getting un-lost, I did catch up during a lull in the class while there was some Q&A discussion. I missed some technical parts, but I got the gist and recovered the confidence that I could figure some of these things out on my own.

Python for P-Chem

I just got back from an ESCIP Workshop. ESCIP stands for Enhancing Science Courses by Integrating Python. ESCIP partnered with MolSSI (the Molecular Sciences Institute) and hence this workshop was aimed at faculty members mainly in the physical sciences. The examples used were therefore well-geared towards someone like me who teaches both general chemistry and physical chemistry. The majority of us were chemists, but there were some physicists, and even one mathematician. There were around forty people, a nice size for a workshop.

 

Recently, one of my colleagues took the plunge and started incorporating python into our analytical chemistry lab course. Python is useful for data analysis and manipulation. I mean manipulation in a good way. Not faking data, but arranging and rearranging it to learn what is going on in our scientific experiments (or computations). My colleague had posed the possibility of scaffolding python across our curriculum. The next logical place for our chemistry majors to see python is P-Chem. While I considered taking the plunge last academic year, we were just getting back to in-person courses and I thought that students had enough to deal with so I held off. I’m not teaching P-Chem this academic year, but I’m slated for next academic year.

 

I’ve never learned python properly. When I taught myself to code and write scripts, python didn’t exist. There’s an inertia to learning something new, especially since I can do what I want (for my research) in a more archaic programming language. But for our students today, and especially for the science majors, it would be a disservice if they did not learn some fundamentals of utilizing an open-source scripting language. It’s super useful in so many contexts, and I think python is the right choice today. But if I want my students to do something, I should be able to do it myself.

 

The workshop was fantastic! And very well organized. I prepared for the workshop by doing some python tutorials through MolSSI. There were live-coding sessions, and the primary instructor was very experienced in moving us through the process. I learned some good pedagogical practices just by observing the instructor(s) in action. Even more valuable was the opening of my eyes to resources I didn’t know existed. The workshop brought folks who had built and maintained excellent resources, and as participants we were able to tap directly into their expertise. I also appreciate learning about the many caveats and tricky points from those who had gone before.

 

While I’m normally introverted and quiet at conferences, I made an extra effort to meet new people and get to know them. I made a number of connections that will help me as I incorporate python into P-Chem starting in the fall semester. I’m glad I waited because after seeing the resources and making the connections with experts at this workshop, I feel better prepared and more motivated! It was also a wonderful experience to be with so many other physical chemists in the same room. At most small schools and liberal arts college (and many of us were from these types of institutions), there aren’t many physical chemists. Only students majoring in chemistry (and in some cases biochemistry) need to take P-Chem. That’s a much smaller proportion than students who take G-Chem or O-Chem, so one doesn’t need to hire many P-Chemists. I loved exchanging ideas with these colleagues, many of whom were younger early career folks who were enthusiastic and got me excited about what can be done in our P-Chem courses. This was one of the highlights of the workshop.

 

But now I’m back to focusing on the start of my spring semester this week. Once things get underway, I’ll be able to devote some time to strategizing for python in P-Chem in the fall. In any case, I feel energized by this workshop and hope to bring that energy into the classroom as I meet my students for the first time in class this week!

Ecosystem Evolution

What is the big picture of the evolution life on Earth? A global view that takes into account chemistry and thermodynamics is provided by R. J. P. Williams and J. J. R. Frausto da Silva in their book The Chemistry of Evolution, subtitled The Development of our Ecosystem. It’s not an easy book to read; sometimes dense, sometimes opaque, sometimes repetitive, and difficult to wrap your mind around. Systems thinking is difficult, and those seemingly circular parts are a grasp at something potentially profound. Or it could be rubbish masquerading as erudition.

 

Why did I read this book? Origin-of-life research has mainly focused on organic compounds composed of the elements C, H, O, N, S, P. When inorganic elements are mentioned (~15 of the metals utilized in extant life), these are usually in very specific contexts without considering their co-evolution with the organic compounds. I’m also about to teach a special topics class titled “Metals in Biochemistry” and I want my students to appreciate the big picture view before they get into the weeds of specific enzymes, co-enzymes or signal/transport factors. I estimate it took me ~24 hours to read through the eleven chapters, one chapter per day.

 

Here’s the big picture, partly in my own words, and partly quoted from the concluding chapter of the book.

 

Thermodynamics rules. You can try to ignore it, but you won’t get very far. Most scientists have some familiarity with equilibrium thermodynamics, the type that applies to isolated systems. The second law of thermodynamics states that the system inevitably moves towards equilibrium by maximizing entropy production. But living organisms are open systems; energy (and materials) flow through the system building biomass, excreting waste, and engaging in the properties of staying alive. On Earth, the main source of energy comes from the sun, and in particular its high-energy (or high-frequency) photons. Living organisms degrade this into low-energy (high-entropy) “heat”. The analog of the second law in non-equilibrium thermodynamics, according to Williams and Frausto da Silva, is this:

 

“… in an open system the absorption of effective energy of high frequency sets in motion flow and that this flow adjusts materials aiming as far as possible to generate thermal low-frequency energy as it moves towards an optimal cyclic material steady state. This final cyclic steady state is one which retains a fixed amount of energy in the flow of material while generating optimum energy output and degradation. It thereby generates a randomisation more rapidly than would otherwise have been the case… The rule is in accord with the second law… but relates to kinetic, not equilibrium thermodynamic, factors.”

 

Here’s my visual aid comparing the two. In an isolated system, the high-energy (and therefore less stable) compound A converts into the lower energy (and more stable) compound B, which can continue this process turning into C and finally into D (the most stable of the lot). As this conversion takes place, (chemical) energy is dissipated from the compounds into “heat” which cannot be recovered. In the beginning, the reaction proceeds from left to right, but over time the reverse reactions also take place until at some point equilibrium is reached. The rates of the forward reactions equal the rates of their reverse reactions. All the arrows are the same size as shown in the upper representation. There is no longer net dissipated heat. You’ve reached thermodynamic death.

 

Contrast this with a system that receives energy from an external source. As long as that energy is provided, the long-term fate of the system is to organize itself in a cycle so that no material is wasted. The reaction rates of the clockwise cycle continue to be larger than those of the anti-clockwise cycle, as indicated by the different sized arrows in the lower representation of a tiny cycle. The energy flowing into the system continues to be dissipated as heat in accordance with the second law. In reality, each of the reaction steps is likely to generate some “waste” molecules and therefore the entirety of the chemical materials is not truly cyclic. However, that waste could be incorporated into another cycle, and so on, until everything is recycled (no waste!). Cycles coupled to other cycles, cycles within cycles. This is the ideal climax of an ecosystem, assuming no change to the energy source.

 

What sorts of chemical reactions are driven by the external energy source? In life, redox reactions. Essentially “there is reductive synthesis in life and oxidised chemical waste… and there was the possibility that the waste would have just accumulated and would have diminished the capacity or even poisoned the living system. For example, all carbon could have finished as trapped wasted coal, while oxygen could have built up as a poisonous gas.” Anaerobic organisms today essentially try to avoid oxidative environments. Without the evolution of aerobes, the “system is unstable and doomed to die”. This is also true “if individual organisms lived forever [with] no return of elements to starting material, no cycle, and any evolution would be frustrated.” Life on Earth is evolving to reach the ideal climax, following the thermodynamic imperative. It hasn’t reached that point. Nor will it do so anytime soon, and our sun will die out some day.

 

The authors use the example of light as an example of chemical and biological adaptation. (Ultraviolet light is still damaging to surface organisms today.) The overall sequence is that a new environmental factor that initially acts as a poison leads to protective adaptation and subsequently to adaptive use. Here are their six steps.

·      new environment (light) -> damage to proteins

·      protein damage requires new protein production

·      new protein production involves local loss of DNA protection [as it necessarily becomes exposed to be transcribed]

·      loss of local DNA production -> localised random mutation

·      localised random mutations -> proteins protective against light

·      further mutation of local region -> proteins making use of light

 

Thus, seemingly random variation at the smaller time-scale local level is, in the big picture, driven by a longer time-scale process that is governed by chemical thermodynamics. But humans might be upsetting the natural process on Earth that has occurred for 4.5 billion years. We are making use of much more than the twenty elements in the periodic table utilised by extant life. We have created wondrous new materials from concrete to computers. We have generated new waste rapidly that cannot be recycled in a short period of time. We are driving changes in the environment much faster than ever before. (And yes, the environment is always changing.) We’ve created tools to modify entire ecosystems exponentially more rapid than nature without humans could ever do. Ecosystem evolution has taken a different turn in the Age of Man.

 

A final word about the book. If you’re curious about why extant life uses just 15-20 elements, you’ll get a reasonable explanation by the authors. It has to do with availability both physically and chemically. Other questions which you might have pondered: Why are Na, K, Cl ions involved in nerve cells? Why is Mg²⁺ involved in ATP activity while Ca²⁺ is a widespread signaling ion? Why were Zn²⁺ and Cu²⁺ incorporated later in proteins? Why do they do play such different roles in biochemistry? Why are they found in superoxide dismutase of eukaryotes while prokaryotes use iron and manganese? What is the effect of different metals used in porphyrins? Why are there iron-recovery subsystems? Why is selenium used in life, but not arsenic? All these and more are discussed, if you’re willing to plow through the book. It was a slog, but I’m glad I did, and I now have a broader picture of the interplay between metals and organic compounds in biochemistry. Gotta go write up my syllabus!

Arm-Waving Quantum Mechanics

Nobody really understands quantum mechanics. As an instructor who views this subject through a chemistry lens, I purposefully arm-wave my way through some of the mathematics (where I deem it not crucial for the students). I occasionally arm-wave my way through a physical analogy of what’s going on – in my experience students find this helpful despite the limitations of any (and every) analogy. But I’ve never asked students to arm-wave their way through learning quantum mechanics. It sounds like asking the students to recite rubbish.

 

Turns out asking students to arm-wave can be helpful. I stand corrected by a delightful article titled “Waving arms around to teach quantum mechanics” by Kelby Hahn and Elizabeth Gire, published in the American Journal of Physics (Oct 22 issue, DOI:10.1119/5.0073946). Here’s the abstract.

 

The authors discuss using a “spins-first” approach to teach quantum mechanics, something I could see a physicist doing but not a chemist. We have different goals in teaching quantum mechanics to students, which is why these classes are offered separately for physics and chemistry majors. I have had the experience of explaining why to an administrator who once asked me why they can’t be combined into a single class (that would have higher enrollment), but I won’t bore you with those details. Let’s talk about arm-waving instead!

 

The article outlines five activities they use which are hierarchically scaffolded, each new one building on the earlier ones. The authors also clearly discuss what the students should know ahead of each activity, what to emphasize, where students get confused, and they share “noteworthy anecdotes” on each activity. The orientation step gets each student to stretch out their left arm to represent an Argand diagram so they can bodily (or kinesthetically) learn three ways to represent complex numbers. I do wave my arm when first introducing polar coordinates, but I should get students to stand up and do it too! Here’s the first picture.

 

In subsequent exercises, students pair up to get a sense of how spin operators in Cartesian space can be represented as linear combinations. Then they learn about relative phase. At some point, they get to representing time evolution of quantum states, which now requires rotating their arms. A culminating activity is to transition from spins to a wavefunction. This last activity is particularly clever because they have to form larger groups to handle higher spin states and eventually when they start thinking about “position” of a quantum “particle”, they start to visualize what it might mean to be a “continuous” wavefunction.

 

I’m unlikely to implement this approach in my quantum chemistry course – because my goals are quite different. Even though I can read bra-ket notation, I don’t introduce it to my chemistry students. And I don’t spend too much time on spin states in my course; we use it for spectroscopic notation, for selection rules, and when discussing Hund’s rule; it also gets embedded in our mathematical representation of the Pauli Exclusion Principle via the Slater determinant. That being said, I really liked the approach used by the authors, and it motivated me to rethink how I introduce spin in my course. I’m reminded that students do get confused by the spin operators, and it takes them some problem-set practice to figure out how they work and why they are useful. There’s likely some gist that I can borrow from the waving arms approach to help my students, and I will ponder this a bit more for when I teach quantum again next fall. I’ve also been thinking on spending an entire class period on the O₂ molecule – its triplet ground state and its surprising kinetic stability. Arm-waving may not be good after all.

Taking Notes

Some students take very good lecture notes in class. A few even take the time to reorganize and rewrite those notes shortly after class. Other students don’t take good notes in class, often incomplete and occasionally riddled with errors. You can probably guess which students get higher grades and which ones don’t do well (on average, because there are always outliers). I suspect, but I can’t prove, that the students who read ahead take better notes than those who don’t. (In G-Chem, I explicitly tell students what to read in the textbook and what to pay attention to, be they definitions, figures, or sample worked problems.) However, I think the percentage of students who actually read ahead is small. If more students read ahead, they would likely understand more during class and perform better on quizzes and exams.

 

I do not give out my lecture notes to G-Chem students. Students who miss class have to find a friend to get those notes. (These days that’s easy with smartphones with good cameras.) My feeling is that if I provided my lecture notes, more students would skip class and their learning would be diminished. I also think that the act of taking your own notes is part of learning; you allow the material to percolate through your mind and sift through it. Preparing your mind (by reading ahead) will aid this process of note-taking and engaged learning in class. But the reality is that students who are unprepared, come to class expecting to be spoonfed the material, and take notes like zombies. Their minds are disengaged and they’re just writing down what I write on the board in the hope that it will make sense to them later – usually during last-minute studying right before an exam.

 

Part of the problem is that the pace of my class is brisk. That’s my fault, I suppose. I expect students to read beforehand (and remind them regularly to do so). The semester is peppered with five-minute quizzes at the beginning of class – and those who are prepared ace the questions, while those who don’t… well, don’t. Part of the problem is that I often teach the 8am MWF section, and it’s tough for many 18-20 year-old students who are simply less alert because of their biological clock. That being said, the grade averages aren’t worse for the 8am class, so the starting time itself isn’t necessarily problematic.

 

But I wonder if my policy of not giving my own lecture notes simply hurts the academically weaker students who don’t know how to take good notes, and exacerbates the gulf between the high-scoring and low-scoring students. These last few post-pandemic years I’ve noticed that widening gulf. I suspect that students did not learn as much of the background content knowledge (especially in math and science) and did not learn how to take good notes as proficiently, compared to in-person class. Maybe I should be giving out my own lecture notes to level the playing field. But would that cause students to skip class or perhaps not give them practice in learning how to take good notes? I suppose I won’t know for sure unless I try the experiment.

 

One thing I have done the last three years is beef up the preparatory information I provide students. Here’s what you should read. Here are some pre-class questions to think about ahead of time so you’re prepared when we talk about them in class. Here are the most important points we’ll be covering in class. After today’s class, these are things you should be able to do. Please be sure to work these problems right after class, and certainly before the next class. Since this is college, I treat the students as adults and let them make their own choices. Maybe that’s part of the problem. In any case, I’ve been thinking about whether to expand this information into pre-class worksheets that students need to turn in. Or maybe I need to have more worksheets in class. It feels like college is becoming more like grade school. Maybe that’s part of the problem.

 

I still have a couple of weeks before the start of the new semester to decide whether or not to provide my G-Chem students with lecture notes so they aren’t zombie-copying notes that I write on the board. Or whether I will instead work on pre-class or post-class worksheets that don’t need to be turned in. (Honestly, I don’t want to have to grade these for each class meeting.) Do I keep treating the students like adults or do I shift a little towards grade-school practices? I don’t know. Or perhaps I need to teach students how to take good notes. I’m not sure I know how to do that, nor do I understand how I evolved my own note-taking abilities. Lots of questions. Not many answers. Teaching still keeps me on my toes.

Click-Clack Chemical Bonds

What would you like non-science majors to know about the essence of chemistry? For chemist Sason Shaik at the Hebrew University, it would be the beauty of molecules and then anyone can learn how to construct them by imagining molecular LEGO. After teaching and refining his short-course in chemistry, he even wrote a book. Published in 2016, it is titled Chemistry as a Game of Molecular Construction: The Bond-Click Way. 

 

As a computational chemist with some expertise in chemical bonding, I’ve read a lot of Shaik’s work. I particularly appreciate his versatility with making connections between valence bond theory and molecular orbital theory, showing that both are useful and complement each other. Some of these ideas have permeated my classes, in particular quantum chemistry and inorganic chemistry. But I’ve never met Shaik, and I didn’t realize his enthusiasm for teaching until reading his Bond-Click book.

 

Okay, I admit I skimmed many parts of the book – mostly because this was material I was familiar with. But I slowed down when reading his mock interviews that begin each chapter and pondered certain conceptual bits that related to my own teaching. It’s been a while since I’ve taught the non-science major chemistry course in my department (after the core curriculum was revised and the science requirement reduced). But I still teach general chemistry (for science majors) every year, so there’s much that is relevant. Here are some of my observations, in no particular order.

 

Shaik dives quickly into chemical bonding by starting with Lewis dot structures of atoms. A single unpaired electron on an atom can pair up with another single unpaired electron on a different atom – you “click” them together to make a bond, similar to clicking together two LEGO blocks. This is, in fact, the way I teach Lewis Structures in G-Chem 1, which is somewhat different from traditional textbooks. Maybe theoretical chemists think alike. He begins with two hydrogen atoms forming a H–H bond (see below) and then immediately introduces the bond energy curve. I actually introduce the bond energy curve first, so I agree with his approach that students should see this early!

 

But when do you stop clicking? Shaik introduces the Law of Nirvana, essentially the octet rule. I also talk about the octet rule, but emphasize that it is a rule-of-thumb for identifying stable molecular structures. Nirvana sounds like happy bliss, but one has to be careful not to go overboard with the (un)Happy Atoms story. In any case, he starts illustrating the construction of small simple molecules from their constituent atoms. Because he wants to get quickly to structures of organic molecules, he quickly moves on to molecular fragments. I agree with this approach in a non-majors chemistry course. One doesn’t need to introduce the “harder” parts of drawing complex Lewis structures at that level although he will touch on these aspects later. The point is to get students to see how interesting (biologically relevant) molecules are constructed from their parts. Shaik also peppers his lecture with interesting stories about these molecules!

 

What surprised me is that Shaik didn’t just build up linear and branched alkanes (which I would do), he also builds up cyclic alkanes using the same approach even starting with reactive molecules such as cyclopropane and cyclobutane. He then discusses tetrahedrane C₄H₄ (very unstable) and cubane C₈H₈, before building his way to dodecahedrane C₂₀H₂₀. I particularly enjoyed pondering this series of examples! After this he discusses diamond and graphite, something I also do in G-Chem 1, before talking about buckyball. I usually go further and discuss nanotubes – at which point the engineers in my class perk up and start to ask questions as I talk about constructing a “space elevator”.

 

Molecules can react with other molecules to form larger molecules. How so? According to Shaik, first you clack (by breaking a bond) and then you click (by forming new bonds). He illustrates this by discussing the formation of polyesters and polyamides in condensation reactions. He calls this the clack-click approach.

 

I liked how he approached hypervalent molecules by having students think about “electron-rich” molecules. He illustrates this with phosphoric acid (among other examples) which is then tied to ATP and DNA. Then eventually he gets to molecular shape by discussing the Pauli Exclusion Principle in a simple way without making use of quantum numbers. I found his approach effective. He even gets around discussing free rotation around single bonds versus cis-trans isomerism in C=C double bonds without resorting to hybridization or sigma versus pi bonds. Once again, I found his approach effective. It was a good reminder that a teacher can come up with simplifying yet effective explanations while skipping some of the background material. I’ve even considered jettisoning orbitals in G-Chem, although I’m unlikely to do so.

 

Ionic bonding is covered towards the end, after covalent bonds, and after introducing electronegativity and polar-covalent bonds. This is unlike many G-Chem textbooks that cover ionic bonding first. In a sense, ionic bonding is easier to “explain” since students don’t question why opposite charges attract (via Coulomb’s Law). It’s unclear why sharing a pair of electrons in a covalent bond provide an energy stabilization, at least at the G-Chem level, without going into quantum chemistry. Shaik only touches on metallic bonding briefly (as do I) but the way he emphasizes delocalized bonds is by fragment-building. He doesn’t push the model very far. I spent some time thinking about the effectiveness of the approach, but it might be tricky because crystal structure comes into play. One could just focus on the first column where the bulk metals have a body-centered-cubic structure. (I used to discuss band theory briefly in G-Chem but have axed it.)

 

Shaik sprinkles stoichiometry amidst discussing structures of molecules and chemical reactions. This is unlike a traditional G-Chem course where stoichiometry gets its own dedicated block of time. I tend to spend a little less time on calculational-problems in stoichiometry compared to some of my colleagues, mostly because I’m more focused on the conceptual parts. Maybe forty years ago stoichiometry-calculations were important to the chemist working in a lab, but in today’s working world for the chemist, I think this is much less important. Yes, I still cover it. Yes, there are exam questions on it. But it’s a smaller chunk of the topics I cover in G-Chem 1. In that sense, I liked Shaik’s approach, and it reminded me of how little emphasis I placed on calculational-stoichiometry when I regularly taught the non-majors course.

 

What I most got out of this book was Shaik’s enthusiasm! It made me feel excited about the next time I teach G-Chem 1 (next fall) and consider some new examples to use in my class. Seeing a different approach to teaching similar material is, in my opinion, something that we teachers need to do more regularly. I lament my not taking the time to discuss these sorts of teaching details with my colleagues in recent years. (I was much better at doing so in my earlier years as a teacher.) Shaik’s book was a reminder to me that I should get back to regular and substantive pedagogical discussions.

Carboniferous

I’m usually unimpressed by non-fiction historical re-enactments as seen on TV. It resembles a farce with bad acting, bad costumes, bad directing. The more ancient the history, the more I cringe. Reading it in small snippets doesn’t seem so bad – at least when I encounter it while reading science aimed at a broader audience. Hence, when I first read a review of Otherlands, I dismissed it as something that might make me cringe, especially when the review mentioned the author taking imaginative license in setting the scene. But as more gushing praise registered on my radar, I decided to give it a chance and borrowed the book from my local library. For a new book, it didn’t have a long list of people waiting on it. Not so popular, it seems. An ominous sign?

 

I need not have worried. Otherlands, written by Thomas Halliday, is mesmerizing. Halliday is a paleontologist and molecular biologist, and he has a gift for descriptive science writing. The book is subtitled “A Journey through Earth’s Extinct Worlds”. Each chapter describes a scene at a specific location during a specific period in geobiological history. It begins with the most recent Pleistocene and works its way back in time (in sixteen chapters) to the Ediacaran period. Otherlands proves that you don’t need fancy graphics and sound to imagine the past – Halliday does it engagingly with the power of written words. Creatures, plants, landscapes and even the local weather – seemingly strange and alien – come to life in each vignette.

 

My favorite chapter is #11. Titled “Fuel”, it explores a scene in what is now Mazon Creek in Illinois, U.S.A, during the Carboniferous period. Each chapter begins with a map showing the location of the continents. At this point in Earth’s history, Gondwana and Laurentia have joined en route to Pangaea, but the Tethys Ocean is still wide, half-ringed by island landmasses that will eventually form China. Unlike most of the other chapters that focus on creatures that swim, crawl, or fly, this chapter mainly focuses on plants. Normally I’d find plants more boring than animals, but Halliday easily gets me immersed in his story. Here’s how he opens the chapter.

 

“Crushing humidity and invigorating heat. An almost impenetrable mire of vegetation, sinking into still, still black waters. Proud, straight horsetails and sprays of tree ferns stand tall, clambering over one another to reach the sunlight. The air is intoxicating – the massed plant material all over the planet has pumped the atmosphere full of oxygen, with levels 50 per cent higher than in the modern day…”

 

“Standing close-knit in the peaty mire is a large patch of trees, each no more than a couple of metres from its nearest neighbours and a relatively uniform 10 metres tall. Their trunks are crocodile-green, and textured with diamonds, overlapping like scales. Because each scale is slightly offset from those above and below, together they tessellate into a helix, giving the impression of coiling staircases, leading up into the dark fuzz above…”

 

There’s much more to this description, and I encourage you to read Otherlands for yourself. The protagonist in this story is the tree Lepidodendron. Those diamond scales? They’re photosynthetic! Why do they all grow to a uniform height? Why do the nearby waters smell of rotting trunks of this tree? How did they stand so tall given that no tree had yet evolved the strong, hardy, woody bark we see today? Were you to look underground, you’d see that the roots “grow round one another, tightly interweaving with the roots of their neighbours in the incipiently peaty soil… an extensive firm base to hold all the trees in the ground.” And with that, Halliday introduces his readers to the rhizosphere, the “root-world”. If one were to fall, it could well bring down many of its neighbours in a fatal cascade. Which turns out to be an evolutionary choice – grow as one, die as one.

 

There’s also a creature profiled in this story: Tullimonstrum, or the Tully Monster. It’s a strange beast indeed. Halliday writes: “They have a segmented torpedo of a body, and at the rear, two rippling tail fins that look a little like the wings of a squid. At the front, a long, thin feature, something like the hose of a vacuum cleaner, wiggles, with a tiny, tooth-filled grabbing claw at its end. Adding further confusion, there is a solid bar running from side to side across the top of the creature, horizontal stalks on which are set bulbous organs of some kind, which are generally assumed to be its eyes… The closest superficial similarity is with a five-eyed Cambrian oddity called Opabinia, a creature not otherwise known in 250 million years…”

 

What is it? We still don’t know, or at least paleontologists don’t, even with many fossil examples. What’s particularly impressive is that it is a soft-body creature. We normally think of fossils being just bones, but there are a number of geochemical processes that allow the remains to be encased in stone. Halliday’s description of this process is more lyrical than mine. The plants, on the other hand, turn into coal in the swamp peat. The Carboniferous is so-named because of the large quantities of organic material that became black gold – the foundation of modern industry and energy-hungry human beings and their marvellous machines. Why was there so much coal from that period and no others? We don’t know either. But locations where they were found wrote the history of the industrial revolution in nineteenth century Britain, Germany, and Illinois, U.S.A.

 

The humid Carboniferous will give rise to the dry Permian, and eventually a catastrophe that was likely the largest extinction event in the history of life on Earth. But then we enter the Mesozoic Era with the eventual rise of the dinosaurs. Reading Otherlands, I couldn’t help but be caught up in the drama of evolution writ large with changes in climate and continental shift forcing the adaptation to new niches, new ecologies. And how best to satisfy the itch than playing Bios Megafauna this past weekend! (It had been a while so I had to relearn the rules.) Interestingly, the dinosaur ancestors seem to do better than the mammalian ancestors in the few games I played, but only one of those made it into the Proterozoic Era. I should play more games and start keeping statistics. I should also get back to playing Bios Genesis and see if I can evolve into Opabinia. And if you found any of today’s blog post interesting, I highly recommend reading Otherlands. Your local library might even have a copy.