Of Mushrooms and Puff Pastry

I’ve almost completed reading Nose Dive, the compendium describing molecules that give rise to the diverse smells that we humans experience. Given Harold McGee’s expertise in the chemistry of food, I was not surprised to read plenty of examples in these areas. Today I will highlight just two little bits related to foods I enjoy. I love eating mushrooms (perhaps I have some Hobbit genes) and I love the smell of buttery puff pastry. In homage to chapter titles in Tolkien’s Lord of the Rings, today’s blog post is a play on “Of Herbs and Stewed Rabbit” where chef Samwise Gamgee plays a starring role; there’s also “A Shortcut to Mushrooms” so let’s get to it!

 

The smell of mushrooms is brought to you by the number eight. Fungi produce a range of eight-carbon volatiles with names such as octanol, octanal, octanol, octenal, octanone, octenone, (note the tiny name differences) and well, you get the idea. I’ll now quote McGee: “The most common and characteristically mushroomy molecule, sometimes called the mushroom alcohol is an octenol. It’s toxic to microbes and repels the slugs that commonly prowl the forest floor.” Since I’m a chemist, let’s get very specific. Technically this is (R)-1-octen-3-ol. This specific name tells you the location of the double bond, the alcohol, and which stereoisomer you’re dealing with.

 

While this octenol is present in a wide range of mushrooms, specific varieties have specific other smells. The typical white/brown mushroom includes octanone and several benzyl derivatives. The straw mushroom also has octanol, octadienol, and interestingly, limonene, which is often associated with citrusy smells. The shiitake mushroom has octanone, but when it is dried, several sulfurous compounds emerge including the very interesting lenthionine and several other di-, tri-, and tetra-sulfur containing compounds. I’ve been cooking with these varieties for a long time, but about five years ago, I discovered the joy of king oyster mushrooms (the big ones!) which when cooked release sotolon, a lactone associated with the smell of fenugreek or curry. I think of it as “meaty”, far too vague a term for a pro like McGee.

 

Oddly, I’m not a big fan of truffles. I will eat them when present in a meal, but I don’t think they taste spectacular, nor will I go out of my way to get them. Truffles stay below the surface. They don’t make stalks and caps like other “fruiting” mushrooms that sprout up so that their “seed” can be dispersed. Instead they release strong volatiles, plenty of stinky (to us) sulfides to attract other creatures to dig them up. I’ve heard someone describe the smell as “hog’s heaven” which may explain why pigs are good at digging up truffles.

 

But let’s get to a smell that I particularly enjoy – the wafting buttery aromas of puff pastry! Puff pastry is brought to you by the numbers ten and four. The standard puff pastry made with margarine releases some ten-carbon aldehydes such as epoxy decenal and decadienal. Other volatiles include nine-carbon nonenal, and two smaller ring structures: strawberry smelling furaneol, and 2-acetyl-1-pyrroline often associated with freshly baked bread and fragrant rices. Buttery puff pastry has all these but also includes four-carbon butyric acid (and its derivatives) and the key molecule diacetyl – which as a chemist I would call butanedione or dioxobutanone.

 

I also enjoy butter cookies. From Nose Dive, I learned that the Germanic word “cookie” means “little cake”. What do you add to the butter? Sugar, eggs, flour. Now you have something more complex allowing for “more extensive caramelization reactions and browning reactions… [and from egg yolk] long fragmental fat chains and related molecules.” I also enjoy eggs and eat them regularly. But that’s another story!

Nose Dive

Welcome to the wide world of smells – the ‘osmocosm’. That’s the word coined by Harold McGee (famed author of On Food and Cooking) as he explores the cosmos of scents in his new book, Nose Dive. And yes, molecules are the stars of this story! There’s more than enough information to make a chemist’s mouth water, or should it be, nose twitch?

 

Nose Dive is more of a compendium. Like McGee’s aforementioned famous book, you don’t have to read it linearly (although I’m doing so) and you’re welcome to dip in here and there, or take a deep dive! There are five parts to the six-hundred-page tome. Part 1 begins with the simplest smells, the backstory being the Big Bang beginning of our universe. Part 2 discusses animal and animalistic bodily odors. I’m smack in the middle of Part 3, which comprises slightly over a third of the tome, on plants. Part 4 covers other smells of the lithosphere and the hydrosphere. Part 5, titled “chosen smells” will discuss cooked and cured/fermented foods.

 

As an origin-of-life researcher, I am familiar with many of the molecules mentioned in Part 1. But I hadn’t thought about their smell until prompted by McGee. Four small molecules he highlights that humans can smell are H₂S (“eggy, sulfurous”), SO₂ (“irritating, sulfurous”), NH₃ (associated with “household cleaning products, overripe cheeses and salamis, underripe animal manures, and urine”), and O₃ (named ozone “by a German chemist from the Greek root for smell” and associated with “lightning strikes, power-line arcing or prolonged use of high-voltage laser printers”).

 

I find it hard to describe smells because I don’t quite have the vocabulary for it. As a computational chemist who spends little time in a ‘wet lab’, this is clearly not my forte. (I have an aroma wheel pasted to an office filing cabinet to help me improve.) And it turns out that how one describes smells can be very personal and subjective depending on one’s prior experience. McGee has a great story about tribespeople who enjoy the taste of Amazonian ants, as told to him by Brazilian chef Alex Atala. Upon tasting the ant samples, McGee thought they tasted like lemongrass and ginger, tastes associated with Asian food. Atala went back to the cook who had made the ant broth presenting both lemongrass and ginger (that she had never encountered before), and she thought they tasted like ants! McGee refers back to this story throughout his book because it illustrates how we experience smells.

 

The really smelly stuff are the thiols, molecules that contain carbon-sulfur bonds. CH₃SH is associated with rotting cabbage, and humans are very sensitive to its scent. One of my organic chemistry colleagues works with thiols in his lab. I make it a point never to go into his lab. Some smells can stick with you. I think it’s both funny and marvelous that H₂S, COS, and organosulfur compounds likely played an important role in the chemistry of the origin of life. (For more info, look up Christian De Duve’s ‘thioester world’ hypotheses.) The beginning of life was a big stink!

 

My current interest in the organic molecules that may have contributed to the evolution of a proto-metabolism involve alcohols, aldehydes, ketones, and carboxylic acids. These all contain carbon, hydrogen, and oxygen; and in particular tend to be of the more ‘oxidized’ variety (although not in the very highest oxidation states). These small molecules often range from sharp vinegarish scents to cheesy and rancid notes, and pungent or ethereal wafts. Interestingly, formic acid comes from formica meaning ant! The larger versions of these molecules begin to introduce descriptors such as “fresh, green-apple, citrusy, waxy, soapy” and the smell of goat. Trivia I learned: the six-, eight- and ten-carbon simple carboxylic acids were originally known as caproic, caprylic, and capric acid respectively. The root word is capermeaning goat!

 

In Part 2, one chapter is devoted to the smells of the human body. What we call ‘bad breath’ comes from volatiles emitted from “microbial metabolism of mouth proteins”. This includes the stinky CH₃SH but also a number of nitrogen-containing compounds that have their characteristic stenches. These are described as fishy, spermous, and putrid. When I teach chemistry for non-science majors I often use putrescine and cadaverine as examples of ‘rotting’ smells. (No, I don’t bring them into the classroom, but I do draw their chemical structures.) But I hadn’t used spermine and spermidine as examples to show their close relation to their putrid cousins because I hadn’t looked up the structure until McGee mentioned it. The smells of life and death are intertwined.

 

Part 3 has been eye-opening. I’m amazed by the range and diversity of volatile compounds emitted by plants. There are many reasons of course. Plants, being relatively immobile compared to their animal counterparts, utilize chemical signals to attract pollinators and ward off pests that try to eat them, among other things. Having spent most of my time studying the more ‘oxidized’ compounds in metabolism, it was eye-opening to see mostly low-oxidation state ‘reduced’ compounds being emitted by plants. There are fruity esters (and lactones) that I discuss in my class; I also talk about isoprene and its relationship to rubber (both natural and synthetic) but I hadn’t considered the range of terpenoids and benzoins. Wow, there are a lot of them, they have very interesting structures, and such a diverse range of scents! It’s amazing what we food-cooking humans have done by utilizing many of these.

 

I had not thought of smells as having a visible component or affecting climate, and McGee illustrates this with some nice factoids. I’ll quote him here. “Both isoprene and terpenoids have another property that makes their initially invisible tides visible, as the haze that gives the world’s various Blue and Smoky mountains their names. As they react with other chemicals in the atmosphere, their by-products form clusters, some of which attract water molecules and develop into water droplets or ice crystals. These suspended particles, or aerosols, both absorb and scatter light – which is why they’re visible as haze – and thus deflect some of the sun’s energy from reaching the leaves… these isoprene and terpenoid aerosols encourage the formation of clouds… and so have significant effects on local climate and possibly global climate as well.”

 

In reading about flowers, I didn’t know that humans have been breeding the scent out of commercial flowers. Here’s McGee again: “Our love for flowers and our ability to produce them at will have conspired to drain them of both significance and smell. The modern global flower industry is the product of growing wealth and city markets for cut flowers, the professionalization of gardening and plant breeding, commercial flower shows, and plant-collecting expeditions. Its business is driven by the competitive breeding of visually striking new varieties that have a long vase life. This program has often meant a steep decline in floral scents: in part because volatile and pigment molecules share biochemical resources, so more color means less scent, in part because some scent volatiles are also plant hormones that shorten vase life. And in today’s largely deodorized world, buyers often prefer scentless flowers for their unobtrusiveness.”

 

There’s so much more that can be said about Nose Dive, and I’m not quite halfway through the tome. Yet I already have enough ideas if I ever teach a ‘Chemistry of Smell’ course. My department has recently discussed expanding the options and themes of our non-majors chemistry courses. In the past I’ve injected different themes when I teach the generically-named ‘Chemistry and Society’ course but these are often in dabs and smears and sprinkles. When I had an Infographic project several years ago, a significant number of the students chose to do things related to the cosmetics and perfumery industry. Certainly there’s interest in this sort of chemistry! I think many of them would enjoy a Nose Dive chemistry course.

Frantic Start

Ten minutes to the start of my 8am class. Zoom server site not found. Check my internet. It’s working fine. Maybe the LMS access link is broken. Use direct Zoom link for my institution. No luck. Try parent Zoom login site. Nothing. Dash a quick e-mail to I.T. services.

 

Four minutes to the start of class. Dash a quick e-mail to students telling them to take the quiz on the LMS. Start preparing for how to teach the day’s material asynchronously.

 

8:02am. One student makes it into Zoom class and sends me an e-mail. I try to get in but this doesn’t work the first time. Try a couple of other options. Eventually I make it in. A second student has arrived. It’s now 8:05am. I dash a quick e-mail to the class telling them that Zoom class is back on track. I start seeing a few others pop in, and I ask them to contact any of their other classmates (by text) to let them know.

 

8:10am. We’re finally ready to begin. I’m somewhat flustered, but manage my way through class in what’s clearly not the smoothest session. We’re learning the calculations for how to make buffer solutions. Thankfully, much of the groundwork was done in the previous class, and we’re mainly doing applications. My students bear with me, and I think we get through okay. I suppress the desire to rush but instead cut out a few non-essential parts and write a little less on the board. Phew!

 

Not a great way to start the day, and it reminded me that the limits of technology can strike at any moment. It could be an internet connection that stops working. It could be a particular server that goes down. Or a bandwidth problem. It could even be a loss of electricity. Or a device that has decided to croak or hang or misbehave. My students, with all their classes on Zoom, have experienced this several times over. I, on the other hand, have not for the most part. That’s because I teach my classes from my office with a stable ethernet (and I can use wifi as a backup), our campus has backup generators (should power fail, and the science building is high priority!), and my office desktop almost always behaves well. This reminded me how fortunate I am.

 

But I’m looking forward to when I no longer have to use Zoom. My campus is one among a growing number that will be requiring students to get vaccinations for the fall semester. We the faculty have been told that we’re expected to teach in-person. I hope there isn’t a summer Covid spike in my area. I’m not sure how I feel about teaching while masked and looking at the faces of my masked students, maybe feeling a little inhibited about in-person interactions. But I think it will be better than Zoom. As we’ve heard aplenty, we’re in the new normal.

 

So many parts have to run smoothly behind-the-scenes for an operation such as Zoom classes to run smoothly. It’s only when something doesn’t work that we perceive a glimpse of the complexity and how many things can go wrong. It’s amazing that it all works most of the time. Like the human body. It’s amazing how many things could go wrong, but most days I take it for granted that things will work well, and chug along happily. But as I age and take notice of the wear and tear, I’m thankful for how this living mass of cells keeps going. For now. Sometimes the wake-up call of a frantic start is a good reminder to be thankful.

Rethinking

Organizational psychologist Adam Grant’s new book Think Again starts off sounding like the stereotypical hit self-help book you see these days. There are engaging anecdotes, easy-to-remember stories, good common-sense advice, and the brisk narrative is designed to generate “aha!” moments. Much like the books of the brothers Heath, for example. There’s also a core idea that is dissected every which way, in this case: Rethinking. And it has a catchy subtitle: “The Power of Knowing What You Don’t Know” with a front-cover endorsement by Melinda and Bill Gates.

 

I read the first half briskly, being familiar with many of the anecdotal examples (re)used in Grant’s book, including the opener about the Mann Gulch fire, often discussed in disaster-related books. There are also humorous self-deprecating diagrams, bar-graphs, pie-charts, cartoons, which are eye-catching and get you to laugh at yourself – always a good sign of a popular pleasing book. Grant is an engaging writer, no doubt about that. So is Jamie Holmes. His book, Nonsense, has the opposite subtitle: “The Power of Not Knowing”. You’d think these books should go head-to-head, but alas, no such luck.

 

You’d think that the world would be a better place if only we could all apply the wisdom of these self-help books that seem to preach a lot of common sense. Doesn’t seem like that will happen in the near future. If anything, common sense seems to be getting less common thanks to media bubbles, fake news, and nasty polarization of political views. Grant does his part in trying to improve the situation, and multiple chapters are devoted to things like learning to embrace being wrong, focusing on the argument and not the arguer, how to debate or even persuade people you disagree with, and how to be more “open-minded”. My goal is not to be curmudgeonly about Grant’s book, or sound like a hater, I quite liked his book actually.

 

First, it reminded me of something that I’ve missed in the researcher part of my vocation once I became a faculty member. It sounds oxymoronic. Isn’t becoming a faculty member and running your own independent research (group, at least in the sciences) what you’re working towards? Yes, except that I’m at an undergraduate-focused liberal arts college where I’m the only computational chemist. (In a smaller department, there’s no reason to hire two computational chemists.) Unlike in graduate school and my postdoctoral research lab, where I was in large research groups and had plenty of people to argue with on a day-to-day basis, that was no longer the case once I started my faculty position.

 

I miss the arguing. That’s probably because I was fortunate to be in situations where I found people to argue with who cared very much about the “meat” of the argument, were very thoughtful, and avoided ad hominem attacks. I confess that I’m not an arguer by nature. My PhD adviser enjoyed getting into a robust argument (focused on the science), and I learned by watching. There was also a senior “pessimist” who people said I should talk to because he would dissect everything and help you think about the problem you were working on regardless of whether it was in his area. (He was very helpful but I had to be careful not to let his gloomy disposition infect me.) My postdoctoral adviser was the opposite: easy-going and argument-avoiding in general. But my office-mate, a fellow postdoc, enjoyed getting into robust arguments, and that’s when I learned to really argue (productively) as an equal with a fellow scientist. I’m honored to call him a good friend! As a result of reading Grant’s book, I approached a senior colleague with complementary expertise but related interests to be my arguing buddy. I plan to start regularly robust discussions where we disagree and try to do better science as a result. (He helped pick apart my draft of a grant proposal last month!)

 

Secondly, Grant’s book made me rethink the teaching of my quantum class offered in the upcoming Fall semester where I’ve finally decided to do away with the textbook. While Grant has a chapter titled “rewriting the textbook” about rethinking teaching in higher education, he repeats mostly popular punditry although he is a little more careful and thoughtful than others, at least in my opinion. That chapter wasn’t the spark, but for some reason after reading his book, I got really excited about what I could be doing differently and now I need to pick out some winners from my flood of ideas. I’ll blog about some of them this summer when I start formally re-working the course, but right now I’m enjoying the swirl of ideas. I suppose I’m Rethinking!

Thermoeconomics

Energy is like money. Or perhaps, moving energy around efficiently requires suitable energy carriers that function like money. (Think ATP!) Or perhaps the ability to capture larger proportions of energy is like money – wealth grows when one can funnel resources into objects (material or experiential) that can be subsequently utilized. Bartering is inefficient. The right people have to meet at the right time with the right objects and agree on the right price of exchange. But with money – ah, you can do so much more and so much more quickly!

 

Salt, grain, and gold, have been used as money in times past. Then we started using paper as proxy IOUs. And now we move 1’s and 0’s around in a seemingly ephemeral digital cloud. Does money really exist? For a quick, humorous, engaging, educational romp through this story, I recommend Jacob Goldstein’s book Money: The True Story of a Made-up Thing.

 

Energy seems to be ephemeral and nebulous, as my students are learning this semester. Is there a connection between energy and money? Between the second law of thermodynamics and economics? Maybe there used to be, and maybe we should move away from it. So says Peter Corning in his article “Thermoeconomics: Time to move beyond the Second Law” (Prog. Biophys. Mol. Biol. 2020, 158, 57-65).

 

The story starts out with Schrodinger’s Paradox, and moves through dissipative structures (à la Prigogine) and views that life is inevitable because of, and not despite, the second law of thermodynamics (à la Schneider & Kay). The confounding link between Boltzmann and Shannon entropy is described as a confusion in communication (pun intended). And Maxwell’s Demon makes its appearance for being taken too seriously by physicists. To quote Corning’s acerbic wit: “As an increasing degree of realism was introduced into the debate, along with various doomed attempts to add technological improvements to the demon, the physics community ultimately converted the experiment into a problem in information theory and, lately, into a pedagogical tool in introductory physics courses.”

 

Corning’s thesis sounds more like my first paragraph. He wants to excise the notions of order and disorder associated with the second law of thermodynamics. He argues for an economic view of how life evolves and utilizes energy: “Living systems must capture, or harvest the energy required to build biomass and do work; they must invest energy in their own development, maintenance, reproduction, and evolution over time. Life is a labor-intensive activity, and the energetic benefits must outweigh the costs (inclusive of entropy) if the system is to survive.” This is Corning’s First Law of Thermoeconomics.

 

You can’t get ‘order’ for free in your system from the second law even if you posit larger entropy increases in the universe. There are economic constraints. Free energy is not so free. Corning argues that thinking about energy in economic terms, and using its terminology (capital costs, amortization, operating cost, economic surplus) is more useful when it comes to explain Schrodinger’s Paradox: What is life? And why does it seem ordered and even purposeful? Corning thinks “the notion that there is some inherent economizing influence embedded in the laws of physics” is very limited to special cases in specific physical systems. (“Tornado in a Bottle” might be a good example, although Corning doesn’t specifically refer to it.)

 

Having read a chunk of the literature cited by Corning, I don’t think his view is diametrically opposed to those he criticizes, although I appreciate his witty polemic. I do think his reminder that we should be careful not to extend the notion of entropy too far, and perhaps just stick to its “energy dissipation” definition. Corning thinks that theorists caused the confusion by assuming “an equivalence between statistical order, energetic order, and physical order.” I think they are connected, but I agree with Corning that they are not equivalent and we should be careful when we throw around these terms. It’s a wonder our students are confused, possibly because so are we as scientists and teachers.

 

So what’s this business of energy dissipation? I end with a money analogy that popped into my head this morning. Imagine you received $20,000 in cash. You spread it around to a thousand friends passing them twenty bucks each. Later you want to buy a $20,000 car. To get your money back (let’s assume no easy internet banking or pay apps, and physical banknotes must be used), you’ll need all your friends to pass you back their twenty bucks. Not so easy. But not impossible. Possibly low probability if some of your friends are hard to track down. Now if only you had a mechanism to corral more money into your account… ah, now you’re talking evolution and economics!

Pure Science

A colleague recommended that I read Arrowsmith. Written in 1925 by Sinclair Lewis, the novel was awarded the Pulitzer Prize the following year, and Lewis apparently refused to accept the honor. It traces the life of a fictional scientist-doctor-bacteriologist, torn between different worlds, and only feeling most comfortable when he is immersed in the rush of pure scientific research. The protagonist’s name is Martin Arrowsmith.

 

I have little experience reading older novels. They seem slow and ponderous now that I’ve acclimated to action-packed movies and brisk narratives. I do still enjoy the slow descriptive pace of Tolkien’s Lord of the Rings, the only “old” fiction I read in my younger years. Reading Arrowsmith was like watching an old and slow-moving movie – something I rarely do. I almost gave up partway through Arrowsmith. But my colleague has astute observations, and I’m glad I persevered through the novel. I enjoyed the second half much more!

 

Martin is a provincial kid restless to find his way in the world. When he gets to medical school, he is attracted to the “pure science” research of bacteriology, the realm of a seemingly cranky irascible old professor. His request to work in that lab is initially denied, but Martin perseveres and thence begins a love-hate relationship with his mentor and with himself. His mentor, catches a glimpse in Martin as one who may have the heart of a true scientist, if not yet the mind. But youthful Martin gets caught up in other things, and it is some time before he finds his way back to his mentor. Part of a long admonishment, here is an excerpt of his mentor’s speech describing Pure Science:

 

“To be a scientist – it is not just a different job, so that a man should choose between being a scientist and being an explorer or a bond-salesman or a physician or a king or a farmer. It is a tangle of very obscure emotions, like mysticism, or wanting to write poetry; it makes its victim all different from the good normal man… the scientist is intensely religious… he will not accept quarter-truths, because they are an insult to his faith. He wants that everything should be subject to inexorable laws… He must be heartless. He lives in a cold, clear light. The world has always been ruled by the Philantropists: by the doctors that want to use therapeutic methods they do not understand… by the preachers that yearn to make everybody listen to them… by the eloquent statesmen and soft-hearted authors – and what a fine mess of hell they have made of the world! Maybe now it is time for the scientist, who works and searches and never goes around howling how he loves everybody!”

 

The true scientist is a rare bird, seldom found. There’s a purity of heart and mind, yet complex in nature. It’s interesting how Lewis, the novel’s author, compares it to mysticism, poetry, religion, and how pure science “grabs” you rather than you grasping it. There is an aspect of seeming dehumanization – to be heartless – yet for the greater good of mankind. Martin will later face the hard choice of being a philanthropic physician or a cold-hearted scientist in the midst of a plague pandemic; and this part of the novel brought to mind how science and its protocols have changed in the last hundred years, especially this past year in the scramble to develop a Covid-19 vaccine.

 

Martin is a bacteriologist, but both his old mentor and a contemporary chemist colleague shame him into learning more math and physical chemistry. Ha! I was not expecting that in the second half of the novel. Remember we’re in the early twentieth century, before the dawn of quantum theory. While some classical thermodynamics has been established, the law of mass action is recent, as is the work on kinetics by Svante Arrhenius, recent Nobel prize winner. Today, these basic concepts are what I teach in first-year college chemistry, along with much that has yet to be discovered. Martin’s mentor admonishes: “You can do nothing till you know a little mathematics… All living things are physicochemical machines… how can you make progress if you do not know physical chemistry, and how can you know physical chemistry without such mathematics?”

 

And what does poor Martin do? With the help of his chemistry colleague as a tutor, he starts to learn algebra, quadratic functions, logarithms, trigonometry. These are all things I take for granted that my students know when they get to G-Chem. Isn’t that amazing? Viewed in this light, 18-year old students know so much compared to scientists of yester-century, and yet perhaps still so little. Just this past week, I was jarred when grading a quiz in realizing that some of my students don’t quite understand logarithms. Several wrote that the equilibrium constant can be a negative number (rather than a number with a negative exponent). And we’ve been using them for weeks! Eeeks! I hastily wrote a short e-mail to my class to remind them of some basics.

 

As a physical chemist, I rate my mathematical abilities as mediocre, and possibly below average. (My chemistry students mistakenly think I’m a whiz at math.) I found it very amusing to read about Martin’s diving into math and P-Chem so he can be an outstanding bacteriologist, since I have been partially doing the opposite – teaching myself biology and biochemistry, as part of my study into the chemical origins of life. But as I delve into modelling the complex world of biology, I’m reminded of my mathematical inadequacies. Ironically, or perhaps fittingly so, I’m starting to bone up on more math; I recently ordered two books to help me do so as one of my summer projects. To keep myself motivated, I’ve also been reading some fun articles. A recent one that I recommend is “A mathematician’s view of the unreasonable effectiveness of mathematics in biology” by Andre Borovik (Biosystems 2021, 104110).

 

But before I get too enamored with math, Martin’s chemistry colleague/tutor reminds him not to put too much trust in math, and “confused him with references to the thermodynamical derivation of the mass action law, and to the oxidation reduction potential, that he stumbled again into raging humility, again saw himself as an impostor…” Well, I’m certainly confused by the math as I’m teaching myself non-equilibrium thermodynamics. My students are confused by math in equilibrium thermodynamics, that looks clear to me. And I suspect they will be confused by oxidation-reduction potentials when we get to them in the last week of G-Chem 2. In my calculus-heavy P-Chem classes, I constantly remind students that math is their friend. I’m not sure they believe me.

 

I’m also reminded not to be cocky about increasing my own knowledge, although this is unlikely to be a problem as I’m generally not impressed with myself. But I’m aware of the danger. I don’t have low self-confidence either, which our protagonist Martin suffers bouts from when not in the ecstasy of pure research. In any case, here’s what happens when Martin learns more P-Chem (perhaps contemporarily G-Chem 2): “He learned the involved mysteries of freezing point determinations, osmotic pressure determinations… he became absorbed in mathematical laws which strangely predicted natural phenomena: his world was cold, exact, austerely materialistic, bitter to those who founded their logic on impressions. He was daily more scornful toward the counters of paving stones, the renamers of species, the compiler of irrelevant data.”

 

That last sentence I quoted is an ongoing theme throughout Arrowsmith. While there are many caricatured characters in the novel, there is much scorn aimed at the culture of Assessment and Administration. It is the realm of the “Men of Measured Merriment” – members of “high” society, not true scientists even if they hold the purse strings for funding science. Some think of themselves as scientists, but seem more interested in money, comfort, glory, fame, or the bourgeois lifestyle. They might even be well-meaning Philantropists, but true pure scientists they are not. They never will be. And perhaps they never were to begin with. I’m certainly not pure of heart and mind, and I don’t worship the god Science. I’m more the philanthropist – the teaching kind! I enjoy my research, but I also love teaching, and much else outside the singular pursuit of scientific truth.

 

Ultimately the novel is not so much about science but about humans, with their desires, greivances, and foibles, as they muddle through life. On the one hand, certain aspects of life do seem quite different a century ago (and I found parts of the novel, well… novel). On the other hand, human nature has not changed much. The human aspects of today’s scientist are not so different than those portrayed in Arrowsmith, even when caricatured. In that sense, Pure Science is a caricature, a mirage, an idealized image that we sometimes portray as professors to our students.

Curricular Complexity

Happy Friday! I’ve been catching up on my blog reading. One of the blogs I regularly read is Bryan Alexander’s (author of Academia Next), and a couple of weeks ago he posted a video and summary on the topic of curricular analytics with guest presenter Gregory Heileman, who is both an administrator and an engineering professor. The video and Q&A bring up many interesting points that could fill multiple blog posts. Today I’ll just focus on one of those: Curricular Complexity.

 

What is curricular complexity? (Watch the video!) In a nutshell, it’s an ad hoc way of quantifying who complicated it is for a student to go through the pathway of a major given prerequisites, corequisites, and timing of the classes offered. Science and engineering majors, which tend to be more hierarchical than humanities majors score high in curricular complexity – and this has potential downsides. For one, there is a negative correlation between the four-year graduation rate and curricular complexity. And once you dig into the data you find all sorts of other interesting correlations, for example, curricular complexity is inversely correlated with university reputation (at least in electrical engineering). Hmmm… I’m sure you’re starting to wonder why this might be.

 

Well, it’s complicated. Or I should say multi-factorial. We could discuss elitism, student preparedness, selection methods, accrediting bodies, history, narrow-minded professors, differences in disciplines, education costs, laboratories, bottlenecks, weed-out courses, and so much more. Many of these do not have easy answers and the relationships are a tangled web. I’m not going to do that here. Instead I turn my eye to how the curriculum in my department has changed over the years and consider some of the factors underpinning its logic.

 

First, some background: I’ve been at my institution for about twenty years and we’ve made a number of curricular changes over that time period. I’m ensconced in a liberal arts college (with no graduate programs in chemistry and biochemistry) focused on undergraduates. When I started we averaged slightly less than twenty majors per year. These days we typically have forty or so majors per year. When I started we just had a chemistry major that included a biochemistry pathway. There were only minor differences between the “straight” chem major and the biochem path. Three major factors have driven our curricular changes: rising numbers of students in our classes, the design of a new separate biochemistry major, and the addition of a research requirement for our majors. Our chemistry majors are ACS-accredited, and our biochemistry majors are ASBMB-accredited, i.e., our curriculum meets the requirements of the professional bodies in chemistry and biochemistry respectively.

 

In Heileman’s presentation (watch the video!), curricula are analyzed as graph-networks. Turns out I’ve recently taught myself the basics of network and graph theory for a grant proposal I just submitted, so I’m reasonably versed. But you don’t need those details to get the presentation (you won’t even notice the few non-crucial bits of jargon). I decided to draw out our present curricula using the framework. I haven’t included the numerical “complexity factor” because it’s not important unless you’re trying to compare across a bunch of different curricula at a bunch of different schools.

 

Here’s our current chemistry major. I’ve slotted things into semesters over a four-year plan (the large majority of our majors graduate in four years) based both on the recommended pathway and what students tend to do. Not being a large university, we do not have the bandwidth or resources to offer every class every semester. While G-Chem 1, Biochem 1 lecture, Analytical chem, Research Methods, are offered every semester; the other courses in our major are not. Both semesters of calculus and physics (taught by other departments) are offered every semester; but Physics 1 is offered mostly in the Spring and Physics 2 is offered mostly in the Fall, and I’ve placed them when many of our students take them.

 

The two key things to think about in the graph are: (1) What are the longest sequential paths through the network? (2) Where are the bottlenecks? The longest pathway is five arrows tracing from G-Chem through O-Chem to Inorganic to Advanced Synthesis. This means that technically a student can finish the major in three years, although most do it in four. There are two “hubs”: The key hub is G-Chem 2 which must be completed before getting to any of the other classes. The secondary hub is O-Chem 2 which is a prerequisite for Biochem 1 lecture, Inorganic and Advanced Synthesis. The majority of our electives require O-Chem as a prerequisite, but not all.

 

We previously had prerequisites linking up P-Chem 1 with P-Chem 2 and Inorganic, but we removed these when we redesigned our new biochemistry major. Along with this we streamlined our “senior” labs from four rotating offerings (with different prerequisites) to just two that all our chemistry majors must take. The overall effect of breaking these links is a reduction in Heileman’s definition of complexity. One could say this change makes the pathways easier for students to get through, in a sense. Has it actually been easier? I don’t know because most of our students graduate in four years both before and after the change.

 

Here’s our biochemistry major. Technically the required biology classes are independent of our chem/biochem offerings although we’ve been advising the students to take Mol Bio Techniques before they take Biochem Lab (usually in either semester senior year). Many of our biochem majors delay P-Chem until their very last semester, and find it a miserable experience. There are a variety of reasons for this including being behind in the math/physics pre-requisites, trying to shelter one’s GPA when applying for medical school, thinking that P-Chem 2 (stat them) is easier than P-Chem 1 (quantum), and others that I shall not mention as someone who teaches in the P-Chem sequence.

 

The longest path is once again five arrows starting from G-Chem 1 and ending at Biochem 2 lecture. G-Chem 2 is still a hub, but not O-Chem 2. Overall, our biochemistry major would have a lower complexity score (per Heileman) compared to our chemistry major, but not by much. On average 80% of our majors are in biochemistry with 20% in chemistry. Once again, there are a variety of reasons for this: Many students are interested in health careers and the biochemistry major fulfils the biology pre-requisites. Also, only one semester of P-Chem is required rather than two. (Most of our students don’t enjoy physics, and P-Chem is almost always rated as the hardest class, whichever semester our biochem majors take.)

 

Before the redesign of both our majors, they were more hierarchical. That is to say, they previously resembled similar majors at large public universities (that also offer graduate programs). Interestingly, small selective liberal arts colleges (SLACs) tend to have less hierarchical majors – and therefore lower “complexity” – and they offer the option of taking some additional electives if a student wants to be ACS-certified. Several SLACs now only require one semester of P-Chem (so a student who wants an ACS-certified degree opts to take a second semester). This allows a wider range of electives and for students to create different pathways through the major based on their interests. We offer a small range of electives because of other constraints at our institution. However, if we’re willing to forego the professional body certification, we could reduce the complexity of our majors. Several SLACs also have an “O-Chem first” track and/or a single semester of “accelerated” G-Chem. You can do this if you know the vast majority of your students have a solid high school chemistry background (at an “honors” or AP-level, or even just excelled at a single year of chemistry).

 

Math skills are also important for success in G-Chem, and at many SLACs, students come in “calculus-ready”, i.e., they can either comfortably slot into first-semester college calculus (and it’s a breeze) or they go directly into a more advanced math course. That’s not the case at my institution on average (although it is true for the better-prepared students). It was interesting to see this as a key factor in Heileman’s presentation of engineering pathways which have multiple math and physics prerequisites. Pondering all this has made me wonder if we should consider scrapping our Calc II and Physics II requirements and instead teach a “physics for chemistry” class that then serves as a pre-requisite for P-Chem. Students would be less shocked when they encounter P-Chem and they’d be happy to replace two courses for one (including one less lab). I need to think about this a bit more carefully before I consider proposing it to my department (and I might not).

 

One thing I have proposed is to re-envision the O-Chem sequence so that O-Chem 1 leads to Biochem 1 lecture, so that only our majors take both semesters of O-Chem. The majority of our students in O-Chem 2 (+ lab) and Biochem 1 are majoring in other departments but trying to complete requirements for pre-health majors (e.g. medical school, dental school, vet school). No, we haven’t made the change for a variety of reasons I won’t discuss here, but we typically have 150 students in O-Chem 2, most of whom hate being there. (And I know what it’s like to teach a class that students greatly dislike being “forced” to take.) Over the years, we’ve seen the elite medical schools no longer require O-Chem 2, but would like to see Biochem in a student’s transcript. Not surprisingly, other medical schools are following suit. (Roughly a third still required O-Chem 2 + lab, at least a couple of years ago when I last checked.)

 

Our department has been entertaining the idea of more flexibility and different pathways in our majors, and perhaps not being wedded to our degrees all being certified by ACS or ASBMB. This might allow more combinations and for students to choose things they are interested in. We might be able to offer a greater spread of electives more often. And we might attract more students to our majors, who are otherwise opting for other perceived “easier” options that have recently been offered in other departments that “complete the pre-health requirements”. This last point used to be something I was not concerned about (because we were seeing year-on-year increases in our major which brought its own challenges especially with our research requirement); but as I see administrative moves towards thinking of budgets more atomistically. I now see potential danger ahead that if we lose majors, we lose budgetary dollars, and one gets into a downward vicious cycle – you can see this play out across the U.S. in the humanities.

 

So how important is curricular complexity? I see moves towards decreasing complexity, for a variety of reasons – complex, multifactorial ones – and this blog post is already getting too long. One can make many arguments for and against. There might be an optimal or sweet spot, but it is likely to change over time as other factors vary. Perhaps the subject of another blog post!

Origins: How we became human

Motivated by recently reading Against the Grain, which provides a sweeping yet non-mainstream view of human civilization and the rise of population centers, I decided to revisit the boardgame Origins: How We Became Human. Games designed by Phil Eklund have a learning curve, but they’re immersive, interesting, and chock-full of science – you might say they’re very nerdy. They also introduce me to non-mainstream views in an intriguing way, even if I don’t always agree with them. That’s certainly true of Origins.

 

I wrote an early review at the BoardGameGeek, after I finally finished a game (without the expansion) which took me four tries. In today’s review, I will be self-plagiarizing from that old review over ten years ago, now that I’ve played over thirty games, and have much more experience with it. The “living rules” (last updated 2012) are an improvement over the original, and my recent games use all their optional suggestions. This game should not be confused with its descendant Bios Origins (see my review here) which borrows many of the themes and mechanisms, but in my opinion is quite a different playing experience.

 

Origins traces the development of humans from hunter-gatherer times (Turn 1 starts roughly 120,000 years ago) to the present. It’s an audacious and ambitious game. How do you gamify human evolution? Eklund breaks it down into four Eras. In Era I, the Age of Instinct, new brain developments proceed as instinct progressively turns into intention. Era II, the Bicameral Age, owes its controversial ideas to the Julian Jaynes about how humans functioned with sort of a “split” brain (I’m simplifying greatly). Era III is the Age of Faith, with the rise of religion and its many-sided effects. The base game ends here, but the expansion allows you entry into Era IV, the Age of Reason, into the Renaissance and the so-called Modern Age.

 

In line with what you might guess about evolution, Origins is a difficult and unforgiving game, with a fascinating theme and innovative game mechanics to match. Each player starts out as one of the five possible proto-species (Archaic Homo Sapiens, Cro-Magnon, Hobbit, Neanderthal, Peking Man) in their respective locations on a world map. In Era I, each player has a Brain Map card that has different areas associated with certain instincts (Social Skills, Natural History Knowledge, Technological Knowledge, Language). Each player starts with one or two of these instincts, and progresses by developing the other instincts. This is done mainly through playing cards that allow “removal of Brain Units” that initially block these instincts. Each of these instincts has several uses that permit the player to perform certain actions or acquire certain advancements. Once all the Brain Units are unblocked, one can progress into Era II, the Bicameral Age. Advancements in knowledge and infrastructure allow one to progress into subsequent eras, particularly via the ability to use Energy. (I particularly like this as I view biological evolution as finding ways to transduce more energy.)

Each Era has an associated card deck. Cards are needed for advances in infrastructure and also to satisfy the victory conditions of the game. Each player has a different set of victory conditions. Players try to maximize two out of four areas: Information, Culture, Administration or Specialists (called “Elders” in the game). The first three are acquired by bidding for appropriate Public Cards. The Specialists are important in this regard – the player with the most Specialists often is able to outbid the others for the best cards. However, specialists are only useful when they are Producers rather than Consumers. An important part of the game is managing when and how to use your Specialists and cycling them between the two states Producer and Consumer.

 

The picture above shows the player mat for Cro-Magnon Man (homo sapiens) in a late stage of the game. The top left shows five elders (two producers, three consumers). They have reached Era IV, has Innovation Level 3 and Population Level 2 which indicate an aging society with not too many young people. Public cards are shown at the bottom. They score  for Information cards (Accounting Tokens) and Culture cards (Megalith monument and Advertising). Below is the player mat for Peking Man (homo erectus) who eventually won this game. There are seven elders (all producers) with some who are foreign workers (non-red cubes). With an innovation of 3 and a population of 3, there are many young and old people and this is a very productive society. You can see many Public Cards here.

 

Besides advancing through cardplay, each player will expand their tribe and start to occupy larger tracts of inhabitable area across the globe. They build cities, cultivate crops, domesticate animals, and mine resources. Players soon encroach on each other’s areas as they expand sometimes resulting in armed conflict. Advances in metallurgy aid the war efforts. Advances in maritime infrastructure allows the crossing of seas and oceans. There can also global climate swings. An ice age allows the crossing of shallow straits but it can turn into a tropical age and flood continental shelves. Desert and jungle climates turn swaths of land into uninhabitable areas unless the necessary advancements are made in Energy and immunology. In line with its nerdiness, the rulebook Appendix has detailed descriptions of Dansgaard-Oeschger and Milankovitch Cycles, but a successful playing of the game does not require detailed knowledge about these things. They’re just icing on the cake for the player who really wants to be immersed in the theme. Here’s a pictures of a third of the mapboard. Descendants of the Hobbits (homo floresiensis) are in North and Central America, while Peking Man’s descendants are in the South.
 

The advancements I described above are divided into five categories: Footprint, Metallurgy, Maritime, Energy and Immunology. Players gain advantages with each advancement, and a fair chunk of the game involves players trying to move along each of the five tracks. Some of these steps are reasonably easy to achieve, but there are some huge bottlenecks where the order in which one tries to advance is crucial. Playing certain advancement cards allows you to move forward. So can domesticating or mining. You can also make infrastructure/specialist exchanges with other players. It took me a few games to figure out what are the best ways to do this, and if I’m teaching new players, it is very important to help point out what some of these optimum pathways are – it’s not clear at all to most newcomers. Below is a picture showing the Advancement tracks.

 

There’s a fair bit of luck in the game – die rolls are used to determine how the climate changes (which can affect areas of the map being inaccessible and units cut off from others) and if certain advancements can be successfully made. A string of bad rolls can really setback a player’s tribe. This part of the game feels very unforgiving, but I think realistically matches the theme. I feel the same way about Bios Genesis, a Phil Eklund game where I was a chemistry consultant – a great way to use my knowledge of origin-of-life chemistry! It is a long game and there is a learning curve, so unless you have some dedicated players willing to spend 3-5 hours, the game will not hit the table.

But is it fun? Yes. I think it’s excellent, now that I’ve gotten the hang of it over many games. Figuring out how best to advance your tribe, watching your brain encephalize as you “free your mind!”, domesticating plants and animals, mining for resources, watching how the climate isolates populations, balancing your population growth with your number of specialists while trying not to fall into Chaos (entering a Dark Age) when you don’t want to – all this makes for a very intriguing game. There’s lots of thinking and planning involved, but the best-laid plans (like life) sometimes don’t work out. Overall, I think the theme meshes well with the game mechanics. The pace of the game has a nice variation to it, starting slow and accelerating at the end as new discoveries catapult the human species into today!