Potions and Poisons

In my non-majors class this semester, students will design a magical potion of their choice using chemical principles. This is a “theoretical” design because my class does not have a lab component, and I’m not sure I want them extracting and mixing a bunch of chemicals that vary in their hazard-ness. The students will write this up as part of a textbook chapter and work in small groups. The assignment makes up 20% of the course grade. For quality control purposes, and also to ease student anxiety about “out-of-the-box” assignments, my goal is to provide an example of what I’m looking for.

Over winter break, I mulled over the idea of choosing something whimsical that the students would not have thought of, and therefore unlikely to choose as their “potion of interest”. (I was planning to poll the students sometime in week 4 or 5 to gather a list of their potions of interest.) The first idea was a joke potion that would make your voice change at parties if someone slipped it into your drink. The active ingredient would be nitrous oxide (N₂O) but it would have to be appropriately “packaged” so that the chemical delivery happens at the right time – when the intended “victim” takes a beverage sip. A tiny capsule would be too obvious in a clear drink. But if you had a solid package or powder that dissolved too quickly, the N₂O would just bubble out of the beverage before the drink was consumed. I had a few ideas of some fancy liquid-soluble cavitands, but I would be making some complicated chemical leaps that may be rather challenging for the students.

So this weekend I started reading The Poisoner’s Handbook by Deborah Blum. Each chapter discusses a particular chemical substance used as a poison during the Jazz Age in New York. While there is some chemistry in the book, it is more interesting as a history and sign of the times. I learned many interesting factoids about how one sets up a toxicology lab and the types of analyses one could do a century ago, when we did not know as much chemistry as we do today. (There’s lots of trial and error. Not to mention court trials and errors in judgment!) A couple of days ago I read the chapter on wood alcohol, CH₃OH, sometimes called methyl alcohol (from the Greek words meaning wine and wood) or methanol (following IUPAC convention). With the backdrop of prohibition, wood alcohol was a popular cheap moonshine – even though it caused blindness, nausea, dizziness and death.

Grain alcohol, C₂H₅OH (ethanol), or ethyl alcohol is safer to consume because the biochemical pathways result in different chemical substances produced. In the case of methanol however, two of the problem-causing products in particular are formaldehyde (featured in my previous post!) and formic acid. I also read the chapter just in time for my General Chemistry class yesterday when we talked about fuels. After calculating the energy efficiency of hydrocarbons, we looked at compounds containing oxygen and nitrogen; methanol was one of the main examples used to illustrate the challenges in thinking about alternative fuels. (I worked on direct methanol fuel cells and partial methane oxidation many moons ago.) And I was able to appropriately warn my students not to consume methanol! (There was nervous laughter in class.)

Yesterday night I read the chapter on cyanides. Upon reading the symptoms of cyanide poisoning, I was immediately reminded of Harry Potter and the Half-Blood Prince where Ron gets temporarily poisoned when consuming a fine alcoholic beverage, ironically just after he has been given an antidote for a love potion gone awry. (I admit to having immediately cracking open Book 6 and reading the appropriate section to confirm the similarity in Ron’s symptoms.) Unlike a love potion that targets a specific individual, presumably through an ingredient that is pheromone-related, no “magic” ingredient was needed for the poison. One wonders if the poisoner knew something about chemistry to extract the appropriate cyanide compounds (there are many sources) and spike the drink. Professor Slughorn is too shocked to mix up an antidote, but quick-thinking Harry manages to save Ron with a bezoar. Given how fast cyanide acts, mixing up an antidote might have taken too long anyway.

Could one design a potion as an antidote for cyanide poisoning? Cyanide essentially acts by replacing oxygen in hemoglobin (the carrier of oxygen). So essentially you can’t “breathe”, your cells get deprived of oxygen, and then all sorts of nasty things happen metabolically. Hence, there are two general approaches to an antidote: (1) One could flush someone with a high dose of oxygen in an attempt to swamp out the cyanide. (2) One could add a substance that scavenges the cyanide away from hemoglobin, i.e., trapping the cyanide. Anything that you add must not cause more problems than it solves. A high dosage of oxygen can be potentially dangerous if not administered carefully. There are many other substances that can trap cyanide, but not many that you should consume. One possibility is hydroxocobalamin found in Vitamin B12. This molecule has some structural similarities to hemoglobin, notably the presence of a porphyrin ring surrounding a metal center. In hemoglobin, the metal is iron; in hydroxocobalamin it is cobalt. Cyanide binds to the metal ion.

I haven’t done the research to look at other possible substances, but it may be that a cocktail of substances mixed together could provide several ways to either displace cyanide from hogging the hemoglobin. Extracting these chemicals from natural sources (since that’s what Potions is about) both magical and non-magical and mixing them together in the right amounts could produce a suitable antidote potion. Vitamin B12 is found mainly in meat, eggs and dairy. Maybe there is a magical creature that has a related vitamin and therefore a slightly modified version of hydroxocobalamin that is particularly good at removing cyanide. (I also want my students to exercise some creativity and imagination.) The concoction might also contain some iron compounds that would form complexes with cyanide. For example, the “Prussian Blue” test to detect cyanide involves adding iron sulphate to a cyanide solution. Hopefully students would use chemical principles to think about how substances could be “modified” (creatively, of course) for the desired outcome.

Or maybe I could investigate the chemistry of a bezoar. Hmmm… so many interesting things to think about!

Cognitive Load in Learning Chemistry

Several things swirled in my mind the last couple of days culminating in the question. Does learning chemistry impose an additional cognitive load on students, perhaps even more so than the other sciences? Is there something unique about introductory level chemistry that requires special attention from us teachers in designing our learning activities?

I meet new people on occasion, and this past week, finding out that I teach chemistry led to a personal disclosure from my new acquaintance about how chemistry was hard and didn’t make sense in school. I don’t hear this as much about biology or physics, but that might just be a sampling effect due to my being a chemist. I’ve also been reading Reactions by Peter Atkins. It is beautifully illustrated with chemical substances at the molecular level on virtually every page. I did not find the prose as engaging, and I don’t personally recommend it if I wanted to get you excited about chemistry; Periodic Tales is much better. But one thing that Reactions does well is showing you lots of molecular level pictures. This “molecular view” is something my colleagues and I stress heavily in our introductory chemistry classes.

Why is the molecular view so important for chemists? That’s where all the action is! Chemistry is about making and breaking chemical bonds, a chaotic dance where atomic partners are swapped. But the problem is that we cannot see this frenetic molecular level activity with our own eyes. We see macroscopic changes such as bubbles, a color change, perhaps a spark of light, or glimpse the appearance or disappearance of a solid. As I’ve been thinking about cognitive load and the differences between how experts and novices learn and process new information, it’s perhaps worth taking a step back to see how one might view a chemical reaction.

Consider the hydration of formaldehyde to form methylene glycol. This is a reaction of interest to chemical engineers, atmospheric chemists, and those who study the chemistry of the origin-of-life such as myself. If I asked a student to write a chemical equation for this reaction, I might get CH₂O + H₂O --> CH₄O₂ from a student in an introductory chemistry class who knew the “chemical formulae” of each of these substances. A student in organic chemistry might write the product methylene glycol as CH₂(OH)₂ to represent something about how the atoms are connected in the molecule.

Thinking molecularly, one might imagine the reaction to look like:

A student in organic chemistry might “draw” the reaction as:

The carbonyl (C=O) bond of formaldehyde is emphasized since a key chemical reaction of carbonyls is to undergo “nucleophilic addition”. Methylene glycol is drawn as a “line structure” where carbons are not explicitly labeled and hydrogens attached to carbons are not shown.

A student thinking about how the reaction proceeds would consider what chemical bonds are broken in the reactants, and what bonds are being made when the product is formed. A simple representational drawing of the “transition state” as the midpoint within the chemical reaction is shown below. Dashed lines represent the bonds being “made and broken”. Also notice the C–H bonds that do not participate in the chemical reaction are drawn with wedges that show how the CH₂O and H₂O molecules approach each other in three-dimensional space for a productive reaction.

How does this reaction happen in practice? If you were an atmospheric chemist, volatile formaldehyde could dissolve in cloud droplets. You might therefore write the reaction as: CH₂O(g) + H₂O(l) --> CH₂(OH)₂(aq) with the phases of matter of each substance specified (g = gas, l = liquid, aq = aqueous, a solution of a substance dissolved in water). If you were measuring this reaction in a lab, it would never involve just two molecules colliding to form a new molecule. The formaldehyde molecule as it dissolves into water would encounter many water molecules. In fact there is likely to exist a different transition state where the presence of other water molecules assists (or catalyzes) the chemical reaction. Below is a different transition state that is much more likely to occur than the one previously shown because it is energetically more feasible. (Energy is the currency in chemical reactions!)

In fact, there are other transition states more complex than the one above that may be even more probable. (I know this because all my new research students from the last five years do a series of computations on this very reaction as their first test case.) Formaldehyde dissolving in water, viewed at the molecular level, is likely to look like just a lot of water! The water molecules are closely spaced as shown in the water “box” below. (Such boxes are a standard part of the simulator’s toolkit.) You’d be hard-pressed to find a formaldehyde molecule even in a relatively concentrated solution, such as a 1 M (or one molar) solution. In a 1 M solution, one mole of formaldehyde is dissolved in 1 L of water. That’s approximately 2 molecules of formaldehyde per 111 molecules of water.

When we teach students to write “balanced” chemical equations, and then calculate the amount of product formed given some amount of starting reactants, the chemical reactions are written in terms of the mole (6.022 x 10²³ molecules). So while on the one hand we want students to think of “balanced” chemical reactions at the molecular level (with molecular pictures in mind), we also want them to be able to think of these same reaction at the level of moles, or the macroscopic level. One mole of water, at18 mL in volume (or just over a tablespoon) is an amount you can physically observe.

As a chemistry professor (or the “expert”), shifting back and forth between the molecular level and the macroscopic level, not to mention thinking about all the different representations shown above, poses practically no cognitive load. All these ways of thinking about the reaction have become second nature, and my mind effortlessly moves to the representation I need for the problem at hand. But this is not true of the student (or the “novice”). The cognitive load can be substantial. One reason why the introductory college chemistry course is particularly challenging is that students enter college with highly varied backgrounds. The student who has taken Advanced Placement Chemistry is much more comfortable “shifting gears” than the students who has taken no chemistry, or barely understood any of it.

When I first conceived of a Potions for Muggles textbook, I thought it should be heavily illustrated with molecular pictures (like most popular chemistry textbooks today) because that’s how I think about chemistry as the expert. But I’m starting to see that an over-emphasis of the simple (and pretty) molecular pictures sometimes obscures understanding instead of illuminating it simply by imposing an additional cognitive load that a reader may not be ready for. The transition from novice to expert requires quickly identifying the key elements of a problem. Novices are awash in a sea of information and it’s hard to prioritize which representational view is going to help them tackle the issue at hand. I still think pictures are important but they should be chosen with care.

The formaldehyde hydration reaction is actually a bit more complicated because (1) it can go in reverse, and (2) formaldehyde can react with methylene glycol to form the C₂H₆O₃ molecule (HO-CH₂-O-CH₂-OH), depending on the relative amounts of formaldehyde and water. If one simply considered one molecule of formaldehyde and one molecule of water in a highly artificial system, then (1) is easy to deal with, and (2) is irrelevant. But in a real system involving moles of molecules, things could get much more complicated. For example, a third molecule of formaldehyde could add to the C₂H₆O₃  molecule, eliminate a water molecule in the process, and form the trioxane shown below.

Phew! Maybe that’s why people keep telling me chemistry is difficult. I spent my first two years of chemistry class without understanding some of the basics I just described above. Hopefully, I can help my students overcome the barrier and present the material systematically and with the right level of cognitive load.

First Week: Spring 2017 Edition

Looking back at my blog, I see that I have regularly posted about my first week of classes; at least I have done so the past three semesters. So without further ado, here is the Spring 2017 edition!

Having recently read Dylan Wiliam’s book, and giving my self two things to work in my teaching, I was very excited to make modifications to some of my class activities. I am teaching two classes this semester: (1) the honors section of second-semester general chemistry, and (2) a chemistry for non-science majors course themed around potions!

The honors general chemistry section is small, limited to 20 students this semester, partly because we are in a very tight classroom that just barely fits all of us. There’s a little room to spill out in an adjacent lab space; I expect to do so for some group activities that will require more space. The class has 17 women (85%), which tells you something of the trends we are seeing. (For reference, the baseline average is 60% female across the college, but my classes are typically two-thirds to three-quarters women.) The students seem eager to learn and I’ve had no trouble getting students to participate in class discussions and group work.

On the first day I gave a 15-minute quiz based on Energy concepts they should have known from last semester. (I had warned the students a week ahead via e-mail.) After the quiz I had the students work in groups to come up with a working definition of energy, list types of energies, and then generate a mind-map to relate their different ideas about energy. (Class went really well in my opinion.) After class I read through the responses, chose one question (a definition of the Ionization Energy of an atom) and picked out six student responses. The next class, we started with the students critiquing the anonymous responses to illustrate how one writes out a clear answer without vague or extraneously incorrect information. After discussing this as a class, I gave them back their ungraded quizzes and for homework, they would make any corrections they chose and resubmit the work the next class. (I’ve now graded it, and it was much improved.) Hopefully that set up the quality of work I will receive from the students as the semester progresses. We’re now knee-deep in the First Law of the Thermodynamics and how to calculate and make use of Enthalpies.

In my nonmajors class, we started by discussing “What is matter and why does it matter?” It is a story that starts with the students declaring that matter is made up of atoms, my challenging this assumption, and then a whirlwind tour through Greek philosophy, alchemy and attempts to synthesis the philosopher’s stone. (I’ve done this sequence many times!) Then we discussed the scientific method, and the importance of measurements in science, ending up with Archimedes’ eureka moment, different density of metals, the density of water and human beings, and body-mass index. Class #2 began with a slide on the making of Polyjuice Potion and alchemical thinking, and I’ve connected this to a quiz to calculate density of a liquid, and a “formative-assessment” question about what happens when two liquids are mixed. It required the students to take a scientific approach and reason possibly about what is happening with the molecules they cannot see. (The class material then continued into molecules, compounds, mixtures, and phases of matter. There were too many definitions so some parts of the class were rather tedious; I need to restructure this section a bit differently.)

Fun things I did include embedding a secret word (“snake”) in my syllabus to check if students read the syllabus before the first day of class. The majority did so, but some didn’t. The best guess from someone who hadn’t read it was “waffle crisps”! For my formative-assessment question and quiz, I have pictures of green liquids to match the Polyjuice Potion theme. For some reason, when you search the web and get hits on “making polyjuice potion for your party”, they all seem to be green liquids. Slytherin? Snake shedding its skin? I don’t know because I chose not to go down that web-surfing rabbit-hole.

Overall, my first week classes went quite well (in my, perhaps limited, opinion); a similar thing happened last semester. This counterbalances the research-related hardware problems I’ve been having. Besides the lab server going down, we’re fighting problems with the new blade cluster showing some odd behavior resulting in load spikes on some nodes – which then slow down all the other jobs possibly related to I/O. Perhaps it’s a good thing that Hogwarts and the magical world is forced to avoid electricity and computers. Sometimes the latter are a real headache. But for many of us Muggles, computers are the magical black boxes that keep things chugging along. Until they don’t.

Words Versus Numbers

This weekend I read a children’s classic, The Phantom Tollbooth by Norton Juster It’s not really a children’s book. Yes, a child would enjoy the fantastical adventures of Milo the protagonist and his companions, but I think adults would greatly appreciate the meaning behind the stories. Milo enters the Kingdom of Wisdom through the Phantom Tollbooth, and discovers that the lands are not in the best of states. The king’s two sons have quarreled and heach built up their realms centered upon the cities of Dictionopolis and Digitopolis.

Azaz the Unabridged, the prince of Dictionopolis, loves words. His court is staffed by the (worthy?) wordy. Everything runs on words, and the Word trade market bustles with business. Azaz disagrees on practically everything where his brother Mathemagician, the ruler of Dictionopolis, is concerned. Numbers are everything in that realm, and the big business there is to mine numbers like ore. I don’t know if the author had the big business of ‘data mining’ in mind when he wrote The Phantom Tollbooth back in 1961, but it’s oddly prescient.

The brothers’ feud mirrors themes in The Two Cultures by C.P. Snow (1959), concerning the divide between the humanities and the sciences. The Two Cultures is constantly mentioned in discussions about a liberal arts education. Outside of academics and other ‘elites’, I’m not sure how many other people have read The Two Cultures or know of its existence. On the other hand, I’m pretty sure The Phantom Tollbooth has a much higher readership, and it’s message echoes many similarities to Snow’s thesis. The humanities are caricatured by Dictionopolis while STEM folks are the denizens of Digitopolis. The two princes represent extreme cases of taking words or numbers to the point of ridiculousness. The feud between the brothers has resulted in the banishment of Rhyme and Reason, their sisters, and Milo’s task-adventure is to bring Rhyme and Reason back to the Kingdom of Wisdom and restore the friendship of the brothers.

There is plenty of punditry in higher education circles about the ‘crisis’ in the humanities and the liberal arts in general. In recent years I have noticed more of an emphasis on the phrase ‘liberal arts and sciences’ from folks trying to remind other folks that the sciences are not in opposition to the humanities – an attempt to bridge the Two Culture gap. It’s an attempt to differentiate the sciences (and math) from being equated to professional training, the latter being seen in its narrow definition of worker-training being ‘opposed’ to the goals of a liberal arts education. It’s like the redrawing of lines to bring in more supporters into one’s camp. We would all do well to revisit Juster’s tongue-in-cheek book.

The version I have is a newer edition that includes an appreciation by Maurice Sendak (of Where The Wild Things Are fame) written in 1996. Part of the appreciation is worth quoting. Re-reading the book 35 years later, Sendak has this to say: “It provides the same shock of recognition as it did then – the same excitement and sheer delight in glorious lunatic linguistic acrobatics. It is also prophetic and scarily pertinent to late-nineties urban living. The book treats in fantastical terms, the dread problems of excessive specialization, lack of communication, conformity, cupidity, and all the alarming ills of our time.”

That was the mid ‘90s. With the current state of the U.S. and the antics of its current president, Sendak’s appreciation is prescient over 20 years later. He goes on: “Things have gone from bad to worse. The dumbing down of America is proceeding apace. Juster’s allegorical monsters have become all too real. The Demons of Ignorance, the Gross Exaggeration (whose wicked teeth were made ‘only to mangle the truth’), and the shabby Threadbare Excuse are inside the walls of the Kingdom…” With what we’ve seen in the past ten days post-inauguration of the new president, Juster’s book is sobering indeed. How Rhyme and Reason can be brought back in the present situation is a good question.

Politics aside, one demon that caught my eye was the “Terrible Trivium, demon of petty tasks and worthless jobs, ogre of wasted effort, and monster of habit.” Milo and his companions are tricked into doing worthless tasks that seem so important while they are under the demon’s spell, but the spell is eventually broken by a magic staff that makes Milo start to think and wonder. He asks the demon why one should do only unimportant things. The demon responds: “Think of all the trouble it saves… If you only do the easy and useless jobs, you’ll never have to worry about the important ones which are so difficult. You just won’t have the time. For there’s always something to do to keep you from what you really should be doing, and if not for [the staff], you’d never know how much time you were wasting.”

This made me stop to think about my Procrastination strategy, wherein I formulate a larger somewhat-nebulous grand-sounding blue-skies task, and never work on it – and instead, I am able to get all my smaller tasks done. Perhaps I need to pause to think about the grand task, make it less nebulous and more worthwhile, and then actually pursue it. In my research, I’m very good at getting the low-hanging fruit and perhaps I’m avoiding directly tackling the big questions I’m actually interested in. I have all sorts of excuses: keeping the grant money & publication virtuous cycle going (why mess with an approach that has worked well for many years?), or using the primary involvement of undergraduates (we have no graduate program) as an excuse not to dig deep because I need to keep having ‘bite-sized’ and ‘digestible’ projects for them. I’m sure I have a litany of excuses; some may be threadbare.

I’m not quite ready to overhaul everything right this minute, but The Phantom Tollbooth made me stop and think. The one who stops thinking or paying attention gets stuck in the Doldrums (as Milo does for a short stint) where essentially nothing worthwhile happens even though there’s a fair bit of ‘activity’. Now that I’m paying attention, let’s see where this thinking leads me.

Archive Copies

There was a massive computer server failure in my research lab this week. What started out as a routine hard drive swap a couple of weeks ago, which went smoothly, somehow went awry. The server was set up with a RAID 5 array. It had been stable for years, but we discovered one hard drive had failed during the move last summer when the lab was renovated. Since this was just before the Fall semester started, and everything was operational, I decided not to replace it yet. That’s the beauty of RAID. (Side note: the server is named “beauty”, replacing an old server named “beast” although beauty is more of a beast in terms of size and power). Everything still runs fine even if you lose a hard drive. So while still in winter break, a couple of weeks ago, we swapped hard drives and allowed the RAID to rebuild itself incorporating the new hard drive. Everything looked good.

This past Monday morning, I found the server completely down with orange blinking lights everywhere. It would not come back up even with the help of several systems administrators. The timing was particularly bad because it was the first week of classes, and I was also starting to train my new research students that same morning. Thankfully, I could get the workstations off NIS, create local accounts, and the students were able to proceed with learning Linux and the computational chemistry software. Most of the computations are done on clusters separate from my local lab server, so the students were able to proceed with their projects. I had moved most of my important data off the local server some time ago, so I won’t lose too much if we are not able to revive the server. The problem with RAID is that when it fails, it fails badly. This got me thinking about how one goes about making copies and archiving data, both in our world and in the magical world.

In days of yore, there were etchings on clay, stone, bone and whatever else worked. Parchment and Paper made their debut a few thousand years ago. How was information preserved for future generations? You could etch it into your city walls or on a large imposing obelisk. The ancient equivalent of a photograph might be a carved statue. You could store scrolls in jars of clay and hide them in dry caves. Making copies was tedious. You needed human copyists. What better way to keep monks occupied or to educate the young by having them write out copies. Learning by rote was an important part of your education – you wrote out your own “textbooks” as the teacher recited the lesson.

Let’s fast forward to my lifetime. My first job as a copyist was in first grade. My teacher had a son in second-grade who came down with what I think was mumps, and therefore had to miss something like two weeks of class. (My memory is rather hazy.) Apparently I had a faster-than-average writing speed because my teacher would send me to her son’s class to copy down what was on the blackboard there halfway through the lesson. My teacher was a fierce woman, so as a seven-year old I simply did as instructed. I vaguely remember being paid ten or twenty cents per day. (I didn’t ask to be paid nor did I negotiate the salary.) I didn’t understand what I was writing, but I was good at copying. My writing must have been quite legible then, because several years later I had a teacher toss my written exercises out the window as a punishment for terrible handwriting. I attribute it to learning cursive and writing at increased speeds to finish my work as fast possible so I could go play.

My mother was also a school-teacher (at a different school) and I was drafted to help make copies. By that I mean using a typewriter to prepare a stencil. I’d like to attribute it to my relatively fast two-finger typing that was for the most part error-free. But it could have simply been one of the ways of keeping me out of trouble. I learned that the stencil would then go into a cyclostyle machine, and out would come the copies! I vaguely remember what the cyclostyle looked like – it is probably what one would call a mimeograph here in the U.S. Thankfully, when I became a teacher, we had Xerox machines. And now? I can just submit a print-and-copy job directly to the multi-function printer down the hall. At my leisure I can walk over and pick up the copies. Unless of course there’s a printer jam. Then I get irritated, especially if it was caused by the previous person’s job. (I’m sure this has happened to you too!)

Before the Wonderful World of the Wide Web, information to be learned was safely archived in physical textbooks. Since I am technically a Physical Chemist, I have a bunch of physical Physical Chemistry textbooks! Above is a snapshot of the appropriate shelf in my office. There were no e-textbooks when I started teaching, and students despaired of lugging their heavy textbooks around. When the publisher sent me a second (gratis) copy of the textbook, I put it in the student lounge with the promise from my students that it would not leave the lounge. Everyone followed this rule, and no one stole the textbook, but fat heavy P-Chem textbooks aren’t theft-worthy. More trouble than they are worth, perhaps? I’m sure some of my students thought so.

The principle of the Xerox machine for photocopying information isn’t too different from the mimeograph. You need ink, paper, and an apparatus that puts the ink in the right places on the paper per the master copy. In fact for most any physical object manufactured in bulk, you have the appropriate industrial machine that can produce these with the appropriate starting materials and molds. Robots easily do the task on an assembly line today. In biological replication (which is all biochemistry!) exquisite molecular machines work in harmony to assemble new genetic information, new proteins, new cellular materials, leading to new organisms, with an intricacy far exceeding any of our macroscopic machinery.

Today, information is increasingly stored as 1’s and 0’s on microchips. They are easy to move and easy to copy – perhaps too easy, thanks to the lightning speed of electrons. And while microchips and hard drives are physical objects that will slowly degrade over time, the digitally stored information can be cheaply, easily and quickly moved. Backup, Backup, Backup! (I almost lost most of my undergraduate thesis shortly before printing when my floppy became “corrupted”, but thankfully I had a backup on a lab computer that no one had erased yet.)

Do we even need physical books anymore? The Kindle and other modern tablets running on silicon rather than etchings on silica are starting to displace the physical book. Just think how many books you can carry on your sleek device? A library’s worth! At least for textbooks, we are starting to see increasingly better open-source materials. In one of my classes, I am only using Open Education Resources as part of a library initiative. We’ll see how the students take to my curated list. In scientific research, digital publishing of journal articles has clearly won out over print. The fight for e-advertising space and bandwidth drives billions of dollars of commerce today.

Thanks to computers, microchips and the channeling of electricity, we’ve migrated to a large extent to digital electronic storage and duplication. But in the magical world of Harry Potter, where home electronics (among other devices) interfere with magic, it seems to be old-school: paper, quills, ink and books. How are books duplicated? Is there a magical duplication spell? This is unclear. In Book 7, at the home of Xenophilius Lovegood, Harry spots a printing press described as a “wooden object covered in magically turning cogs and wheels”. The machine still seems to be required, although it is run magically. (We could replace magic with a robot in our world.) When Harry breaks into the Ministry of Magic, he sees hard-at-work employees. “They were all waving and twiddling their wands in unison, and squares of colored paper were flying in every direction… what he was watching was the creation on pamphlets – that the paper squares were pages, which, when assembled, folded, and magicked into place, fell into neat stacks…” It isn’t clear if the ministry employees use magic directly to “ink” the pamphlets, or if they were just assembling inked pages.

Do textbooks have to be printed the “old”-fashioned way? In Book 6, when Harry and Ron are without their Advanced Potions textbooks, they have to order new copies. No one attempts to magically duplicate an existing textbook. Is there a Wizarding Law that prevents duplication? To protect certain commercial interests? Or is there something inherently difficult in magicking a permanent duplication? (One could temporarily Transfigure an object to look like another, I suppose.) Can you easily copy an essay of a fellow Hogwarts student using magic? You can magically change words around as Roonil Wazlib proves. Rita Skeeter uses a Quick-Quotes Quill. Could one attach such a quill to a polygraph (magical, of course) and produce a duplicate piece of writing?

If copying information is challenging in the magical world, how about storing information? Certainly there are books and magical diaries. One could enchant ink to be permanent or make a book impervious to most types of decay and destruction. There are magical ways of extracting and storing a memory, and then viewing it in a pensieve. These memories are archive copies. Some that are deemed important (such as a significant prophecy) are stored in the ministry. What about a Horcrux? By splitting his soul, isn’t Voldemort making archive copies of himself? Or is it more than just an archive? Perhaps like a RAID array. You might destroy one Horcrux but nothing of significance is lost. Do the other Horcruxes redistribute the bits and bytes of his soul?

One problem with Voldy’s approach is that his Horcruxes are localized, thus leading to his destruction in a massive failure of Horcruxes. What if you could upload your essence into the “cloud”? A distributed array of supercomputers houses Will Caster in the movie Transendence; it is much, much more difficult to kill such a being. It just keeps coming back to life, like Skynet in Terminator sequels. Somehow though, the heroes are always able to find the link causing the system to fail and fail badly; perhaps never to recover. We’ll see if that happens to my system. I’d like to be able to bring it up temporarily just to get some data off. Thinking that this was just a simple hard drive swap, I forgot my own rule of Backup, Backup, Backup! I admit feeling a moment of dread that parts of my life are at the mercy of metal boxes with wires and chips, and a desire to “get off the grid”. Then reality struck back, and I decided to write this blog post. Hmmm… I wonder where my blog is archived.

Ursuppe: Amoebae in the Primordial Soup

This past winter break I have been revisiting older boardgames in my collection. Maybe it’s the scientist in me, but I have amassed a decent set of evolution-themed boardgames. I’ve always been interested in puzzles and games, but I only started growing my collection in the late 1990s when introduced to games coming out of Germany. These combine strategy, luck, shorter rule-books, and shorter playing times compared to the “wargame” beasts of yesteryear.  One of the early games I acquired, back when you could still find really good deals on eBay (now crowded by commercial sellers), harks back to the beginning of life on Earth. That game is Ursuppe by Doris & Frank.

Ursuppe was published in 1997, twenty years ago. It was re-released for the English-speaking market as Primordial Soup in 2004. I have the older German version, with English rules included. Since this was a used copy, the owner had already assembled the amoebae, requiring the hammering of a stick into a wooden base. One amoeba was cracked by this process but the owner had glued it back together and even provided a new replacement in case I did not like the glue job (which was fine). I’m glad I didn’t have to assemble the amoebae myself. Those were the days when games had some assembly required!

I looked back at my games log and was shocked to see that between 2003 and 2006, I had only played five games of Ursuppe, and that it hadn’t been played in the last ten years! I did play it more often prior to 2003 (before logging plays) when I had a smaller collection of games. But as the collection grew, god but older games got less love – a rather sad situation. My goal is to try and remedy that situation by bringing out some old favourites. So without further ado, here’s what Ursuppe is about accompanied by a couple of pictures from my one game (so far) in January 2017.

In Ursuppe, each player manages a family of amoebae*. The goal is to grow the family both in numbers and in evolutionary traits. Each turn, players score points for the number of amoebae they have on the board and how many evolutionary traits their family possesses. Players start the game with two amoebae in the soup. Each “sector” of soup also contains two food cubes of each colour (red, blue, yellow, green). A game turn has six phases; the first is “Movement and Feeding”. An amoeba may drift in the soup or attempt to move against the drift. The direction of drift changes each turn according to the environment card in the middle of the board. To move an amoeba against the drift, a player must pay one biological point (BP), rolls a die, and moves in the direction indicated. (Rolling a six allows the player to choose the direction.)

A key part of the game is keeping your amoebae alive. They must eat to survive. After movement or drift, each of your amoebae eats one food cube of every other colour, and then “poops” two food cubes of its own colour. So if you are the blue family, your amoebae eat red, yellow and green cubes, while pooping blue cubes. (One amoeba’s poop is another’s food!) Thus, the distribution of food cubes changes as the game progresses leading to all sorts of different strategies to stay alive and possibly even thrive! Amoebae unable to feed suffer damage. (A grey sphere is threaded through the stick.) After two damage points, an amoeba dies. Unless it has the evolutionary trait Life Expectancy, in which case it only dies after accumulating three damage points. The picture above shows the game board after several turns. You can see the different distributions of food in each sector, and several of the amoebae have taken one grey damage sphere. When amoebae die, they are converted to food cubes of each colour thus replenishing the food supply.

Biological Points (BPs) are the currency of the game. Among other things, they can be used to attempt active moments in the soup, to acquire new evolutionary traits, and to increase your family size by binary fission! The picture below shows the blue player with three evolutionary traits: Spores, Struggle for Survival, and Intelligence. The cost of each card is indicated under Price. The number in the square (Mutation Points) indicates how susceptible these traits are to mutation due to ultraviolet damage from the environment. In this example, the Environment card indicates the number 8. The blue player has 4+4+3 = 11. During the Environment phase, the player can choose to either lose one of these traits (so that the mutation point total is 8 or below) or pay 3 BPs to make up the difference between 8 and 11. Thus, it becomes costly to accumulate too many evolutionary traits, and these are gained and lost as players try to adapt to the changing situation. Their amoebae evolve!

Let’s take a look at what the cards do. As the blue player, Spores allows me to place a new amoeba anywhere on the board not already occupied by one of my own amoeba in the Cell Division phase. Otherwise, I would have to place it in a sector adjacent to one that has an existing blue amoeba. Chances are there isn’t much remaining food of the needed colours near my other amoeba; that’s why Spores is useful. Struggle for Survival allows my amoeba that is unable to eat the needed food the opportunity to chomp on another amoeba in the same sector. It costs one BP to make an attack. It is successful unless the other player’s amoeba has Escape, Defense or Armour evolutionary traits. Intelligence is “completely useless” as these are amoebae and it makes for a fun joke. However it is the cheapest card, and having evolutionary traits increases your victory points acquired each turn!

There are many other fun and interesting traits and the cards interact well with one another and with the changing environment. There is a UV protection trait that reduces the sum of mutation points on your cards so you can have more of them. A Tentacle trait allows you to pull food cubes as your amoeba moves or drifts. A Movement card allows you to roll two dice instead of one when moving against the drift (you choose one of the dice as your final movement). Frugality allows you to eat one colour less but one cube more at Feeding time. Defense allows you to fend off an attacker in a struggle for survival. In Ursuppe, the cards are double-sided. The side with English text is black and white, but if you read German, the other side is coloured! There are no other language-dependent components. (In the Environment card, east is the letter “O” for “Osten”, the German word for East. The other directions have the same first letter: N, W, S)

A full game of Ursuppe typically takes 1.5–2 hours. The game accommodates three or four players, but not two. There is an expansion allowing up to six players, and also features new gene cards, but I have no plans to acquire it. In this day and age, it is no longer as easy to find other folks willing to spend more than two hours to play a boardgame (and the expansion will almost surely extend the playing time). I personally enjoy playing Ursuppe, both for the theme and because the game is fluid (pun-intended) with the ever-changing environment and the evolution of traits. Twenty years ago, when the choice of games was more limited, this would have been played more often. But today there are many games streamlined to play in the sweet spot of 40-60 minutes, while still containing a good dose of strategy and luck, and able to accommodate 2-5 players. This limits Ursuppe to a niche crowd.

Ursuppe is easy to learn and fun to play, in my opinion, but it simply takes more time, and there can be a bit of analysis-paralysis for new players trying to choose what new evolutionary traits to acquire. The 2014 game Evolution allows for 2-6 players, plays in half the time, and does a great job simulating evolution and adaptation. If one were hosting a boardgame night, Evolution would probably be picked over Ursuppe the majority of the time. (I will feature Evolution in a future post.) At the other end of things, Bios Genesis is fantastic thematically but takes a good 3-4 hours and much more patience to learn a set of complex rules. Shorter and more streamlined games often have to sacrifice some thematic elements for streamlined game-play (and rules explanation). Evolution is essentially a card game. You don’t move creatures around to eat food and/or other creatures; unlike in Ursuppe where you have the tactile feel of moving wooden pieces on a game board. (Many of the games from that era coming out of Germany, Settlers of Catan being the most widely known example.)

I’m not sure when I will play Ursuppe again, but I’m glad I was able to revisit it and be reminded of why I like the game and why it will likely stay in my collection even with limited play. Primordial Soup!

*Technically, the first organisms that would demonstrate what we think of as “alive” would be prokaryotes, bacteria or archaea. The amoeba is a eukaryote, significantly more complex than a prokaryote. But since the game refers to “amoeba” that’s what I will call them in this post.

Designing Questions to Probe Learning

If you ask me today what is the best book to read about teaching, I will say Embedded Formative Assessment by Dylan Wiliam. After the many good books that I’ve read the past five years, I don’t know why I didn’t come across this gem earlier. No doubt I will encounter better books in the future, but this one really gave me that kick-in-the-pants encouragement to make larger inroads into improving my teaching, which would hopefully improve student learning. Why “hopefully”? That’s because Wiliam is very realistic about the centrality of assessment in the learning process. This is not Assessment of the generate-more-paperwork administrative mandate pervading our institutions. It is the assessment we should all be doing as teachers embedded in our lesson plans.

In chapter two, where the author makes the case for formative assessment, there is a section titled “Assessment: The Bridge Between Teaching and Learning”. I will quote several sentences. “Assessment occupies such a central position in good teaching because we cannot predict what students will learn, no matter how we design our teaching… Students do not [necessarily] learn what we teach. If they did, we would not need to keep gradebooks. We could, instead, simply record what we have taught. But anyone who has spent any time in a classroom knows that what students learn as a result of our instruction is unpredictable. We teach what we think are good lessons, but after we collect our students’ [work], we wonder how they could have misinterpreted what we said so completely.”

Before I elaborate on the author’s suggestions, let me first describe how I presently assess student learning. Outside of occasional project work and writing assignments, I generally grade four types of content-based assessments: worksheets, quizzes, homework (or problem sets) and exams. One might call these summative assessments, although they partly function as formative assessments – at least in the standard lingo. (It’s not the grading that makes something formative or summative in my opinion.) I don’t always collect worksheets or homework, i.e., sometimes the work is ungraded, so to speak. While a significant portion of my class time is spent systematically going through worked examples (one of the best ways to learn many chemical concepts), students also have opportunities to “work problems” and get feedback from me in class. In addition I get feedback from them as I observe what difficulties they run into.

In each of the four “graded” items mentioned above, I get information on different scales. Worksheets tell me immediately which students understood the lesson material of the day, who didn’t understand it, and who helped whom. (My classes are small enough that I can circulate through all groups at least once, often more.) Quizzes tell me if students individually understood one key thing from the previous class period. (My quizzes are taken in the first five minutes of class.) Problem Sets tell me if students learned a chunk of material usually over the course of 3-4 class meetings, and in particular whether they were able to apply the concepts to different but related problems (not identical to ones worked in class). Sometimes solving the problems requires integrating multiple concepts. Exams assess individual student learning over a larger chunk, usually about a month; the final exam is cumulative Students can work together on problem sets and worksheets. Quizzes and exams are individual assessments.

What feedback do the students get? On worksheets and problem sets, the students get their graded work back along with a detailed answer key. If there is a particularly egregious common error, I discuss it briefly the next class meeting. For quizzes, I provide the answer immediately in class before I’ve seen the student responses. I grade a stack of 3x5 index cards after class. Rarely do I look through the responses in class. For graded exams, the students can see what they got right and wrong accompanied by a detailed answer key, but I don’t discuss it in class. In rare instances, when I observe a widely common error, I would mention this in class. I attribute the rarity of such an occurence to students having to work individually on exams. When they work in groups with other students, the same error tends to propagate widely – often traced to one of the more capable and confident students who first made the error.

While I think I am mostly asking the right questions on exams from a summative assessment perspective, I’m not sure I’m doing well in the earlier stages. My questions focus on what I think the students should know, but don’t necessarily reveal how they think or where a misconception may lie. Of course when I discover a common misconception when grading, I make it a point to relay this to the students. But my in-class questions might not being do the best or even the right job from a formative assessment point of view. Wiliam writes: “Questions that provide a window into students’ thinking are not easy to generate, but they are crucially important if we are to improve the quality of students’ learning.”

I think that’s the really hard part: constructing excellent questions at the formative stage. These should be questions that expose previous learning and probe for potential misconceptions. Given the brevity of his book (a good thing overall), Wiliam provides just a handful of examples of standard questions, and then builds on these with much better constructed questions. While his examples are mainly in middle school math (his training is as a math teacher), one gets the gist of the type of question that really gets at the nub of learning. I need to ask much better questions but haven’t taken the time to do so. Lest, I use this as an excuse, Wiliam addresses the matter head-on.

“One common objection […] is that teachers do not have time to develop such questions, not least because they are too busy grading, but this just shows how ineffective many of our standard classroom routines are. Every teacher has had the experience of writing the same thing on [multiple student] notebooks because the students were allowed to leave the classroom before the teacher discovered that the students had failed to understand some crucial point. So the important issue is this: does the teacher only discover this once he looks at the students’ notebooks? Viewed from tis perspective, grading can be seen as the punishment given to teachers for failing to find out that they did not achieve the intended learning when the students were in front of them.”

I consider myself appropriately schooled. What I really need to do is build up a stock of excellent questions for formative assessment, particularly at the introductory level. I have enough teaching experience to know where the tricky parts are in my courses. I should also work with others who are teaching the same sections to pool and share knowledge; we have many of these at the introductory levels. One thing I am going to do this semester is to devote some time to coming up with good in-class probing questions. And perhaps, I can do less grading which seems like a more-than-reasonable trade-off.

Although a short book, Embedded Formative Assessment is chock full of great practical examples. The author does a fantastic job getting straight to the point, providing the necessary theory and scaffolding, chooses good representative examples to make his point, and keeps moving things forward. All these are marks of an excellent teacher. His experience shows. On the other hand, as I went through the book I was partly self-berating myself for not reading this book sooner, and thinking about how I’d potentially let down hundreds of students in the course of my teaching while floundering around repeating the same mistakes. (On average I teach 100-150 students per year.) I could have built up a set of really good formative assessment questions by now. As it is, I have plenty of great summative assessment questions (that I do reuse) but a limited set of great formative assessment questions. The author anticipates my despair! Here’s what he says in the epilogue.

“The problem with being provided with so many techniques is that […] too much choice can be paralyzing and dangerous. When teachers try to change more than two or three things about their teaching at the same time, the typical result is that their teaching deteriorates and they go back to doing what they were doing before. My advice is that each teacher chooses one or two of the techniques, […] tries them out […] If they appear to be effective […] practice them until they become second nature. If they are [not] … try another technique or [modify a previous one].”

I’ve decided to pick two things to work on this semester. The first is to come up with some great formative assessment questions in class. For a start, I’ll set myself the goal of one insightful one each week that I will build into my classes. The second is one I had mentioned in a blog post last summer during an assessment exercise. I came up with a great suggestion: having students critique written answers from students in a previous year. Of course, these would be carefully curated for maximum learning to take place. (Wiliam recommends this in his book!) I got so busy this past Fall that I did not do this at all. Shame on me! This semester, I will remedy things. I dug up final exams from the equivalent class last year, and I plan to make appropriate selections when the corresponding topic is covered in class. I should also commit on blogging about my trials and errors – for accountability!

I end this post with a final quote from the author. He exhorts teachers to “accept the need to improve practice, not because [we] are not good enough, but because [we] can be even better, and focus on the things that make the biggest difference to [our] students”. What great advice! His book receives my highest recommendation.