Thermodynamic Warfare

Sometimes you just need an equation. Even if you’re writing a “popular” book where equations are discouraged. No, I’m not talking about E = mc² that shows up just to be associated with someone famous.

 

Karen Lloyd, the author of Intraterrestials is a superbly engaging writer. Her book is littered with well-chosen metaphors and analogies to explain how scientists study organisms hiding away deep in the subsurface of our planet. But I appreciate that the professor in her wants to teach her readers something useful and profound. She chose the Gibbs Free Energy equation:

 

I explain this equation every year to my G-Chem 2 students when we discuss thermodynamics. Lloyd does so with much more flair. In chapter 6 (“Breathing Rocks”) she opens with her life-harrowing yet exhilarating experience of sampling for microbes at a volcano caldera in Chile. After the scenario of physical heat and motion (get your samples quick so you don’t die!), she launches into the heat and motion associated with thermodynamics. She explains the Gibbs equation with colorful examples such as roller coasters and hand warmers. I could quote her for several paragraphs, but instead, I recommend you read her book in full. It’s a page-turner!

 

The crux is that subsurface organisms, unable to get their energy from the sun (like photosynthetic organisms) or eat food they can metabolize with oxygen (like most of us do) respire by breathing rocks. They eke out a low-energy lifestyle turning carbon dioxide (from carbonate rocks) into biomass with the help of nitrogen and sulfur compounds, also found in minerals. Such chemical reactions typically have a small negative delta-G, so you can’t get much energy from them, but they are still energetically “downhill” and thus favorable.

 

But things get even weirder when there’s competition for resources. In chapter 7 (“Life on the Edge”), Lloyd sets up the discussion with another vignette in the cold of Svalbard, Norway, where she is cutting sediment cores dug up for her research. While doing so, she ponders life in the cold Arctic with tremendously varying sunlight. And now I have to quote her: “But intraterrestials don’t care about sunlight or cold. They care about delta-G.” And unlike our familiar surface microbes that “secrete deadly antibotics, hoard nutrients, and grow ultrafast to get ahead” and beat out the competition, subsurface microbes have an additional weapon: “If one microbe’s delta-G is better than another one’s then the first microbe can asphyxiate the second.”

 

I was delighted that Lloyd chose sulfate-breathing microbes to illustrate her point since I’m studying the role of sulfur at the origin of life in competing autocatalytic cycles. She delves into the equation, now focusing on how delta-G can be modulated by Q, the reaction quotient. It’s counterproductive for them to grow big fast because that decreases sulfate diffusion in their cellular bodies. Releasing antibotics is also bad because it would kill symbiotic species in addition to its direct competitors. Molecular hydrogen is a required “food”; you can’t stop your competitors from getting it, but you can hoard enough so that you still have a borderline negative delta-G, while forcing the delta-G of your competitors to turn positive (“uphill”, energetically unfavorable) so their metabolism no longer yields energy and they die.

 

Lloyd writes: “Like a shipwrecked sailor dying of dehydration while surrounded by water, these microbes expire with their food right in front of them. Sulfate reducers win because they take the whole system to the bitter edge of their own thermodynamic capabilities, which pushes everyone else off the cliff.” Ugh. That’s war. But then as the amount of sulfate reduces, the sulfate reducers now face extinction. As they die off, their competitors (often methanogens) can access more hydrogen once again and a revolution takes place.

 

Life gets weirder still. Some microbes (methanogens!) can reverse their food and waste as delta-G switches, so they can keep eking energy. Others ferment; in Lloyd’s words: “takes one slice out of the pie and puts the rest back into the fridge for others to eat later. It’s very polite. Because of this restrained eating, fermentation ends up being one of the lowest-energy processes known to support life.” The low-energy living of intraterrestials suggests that they might live a long, long time without reproducing. It’s immortality of a sort, though not the one we might desire.

 

Reading Lloyd’s book rejuvenated my excitement about my research projects. It also reminded me that I want to be a better teacher and communicator. While this was a library book, I will be purchasing my own copy because it deserves re-reading, and I still need to delve into the scientific papers listed in the references!

 

Optimizing Learning and Attention

“Learning is the slow, ponderous and beautiful Galapagos tortoise, and online content is the invasive predator which will inevitably drive it to extinction.”

 

This quote from Daisy Christodolou’s article (“Why education can never be fun”) really struck me. Addictive online games and videos, she argues, only need to optimize in one dimension (fun!) while apps which might actually increase learning need to optimize in two dimensions (fun and learning). Sometimes the two parameters oppose each other. For many learners, this will be the case when learning material involving math. Your most engaging learning app will never beat the app that only needs to optimize for holding one’s attention. She writes: “However much fun you make learning, someone else will use the same techniques minus the constraint of learning. You are in an arms race where you have one arm tied behind your back.”

 

The subject that I teach, chemistry, is hard. While there is some math involved in the introductory levels, what is more challenging is the abstraction of having to juggle three aspects simultaneously – known as Johnstone’s Triangle. Chemistry is abstract by nature. We’re trying to explain everything in terms of tiny things that we can’t see. Hence, we have to think about chemistry using models. None are complete-in-itself; expertise in chemistry involves fluidly moving amongst a panoply of such models. This is not easy for the novice learner.

 

As more tasks become facile with the aid of technology, we humans who outsource our thinking to such machines will become less adept at the basics. In many instances, that might be okay. I have no interest in going back to the stone age, and I’m glad I was not born a century ago. I like my technology-aided creature comforts. I even blog to offload some of my cognitive effort. But something is lost in the process. It’s okay if what I’m losing isn’t crucial, but if it’s something important such as basic numeracy, facility with language, concentration skills, or thinking deeply and actively, then this is a problem. It’s possible that humankind is heading towards a general idiocracy with a small number of elites controlling the levers. Or it could be worse – the oligarchs might be just richer and power-wielding members of the idiocracy.

 

Learning science and math is not easy, but I think it is important to understanding the world we live in. It will sometimes be a slog. No pain, no gain. As educators, we should try to make our subject matter interesting and relevant, but there is only so much you can do to gamify your course before running into the hard reality of actually learning difficult material. Passively consuming short-form videos from creators who are optimizing eyeballs may give you a false sense that you know something. But that knowledge might be superficial at best, or possible misleading, or simply wrong. And if you don’t have the basic knowledge, you won’t be able to tell when you’re consuming crap.

 

After thinking about this, I took a moment to think more carefully about some seemingly basic concepts in chemical bonding that are much more than meets the eye. I needed to remind myself of things that I had read a year or two or more, but have since forgotten because I haven’t practiced the effortful cognition needed to retain some of these ideas. But if I don’t keep making the hard effort, I will slowly but surely be joining the idiocracy and not even realize it.

Hermione's Handbag

The Nobel Prize in Chemistry was announced this morning! The winners were pioneers in constructing metal-organic frameworks (MOFs). These are three-dimensional porous materials made up of metal centers and organic molecule linkers that have a surprising amount of empty space. This empty space could be used for storage, gas uptake, and separating mixtures.

 

When I got to work this morning I made a slide, then gave a five-minute presentation to each of my three classes about these materials and why they were considered Nobel-prize worthy. I was also happy to tell them that an alum of our program (who was a student in a couple of classes) went on to a graduate program to work with one of the Nobelists, and then recently started a company based on these materials. I also mentioned one of my colleagues who was working on MOFs.

 

Then I told them about my brief MOF fling. My graduate program had a “proposal exam” where I had to write three proposals (two out-of-field) and defend them in a grilling oral exam. It was the late ‘90s and MOFs were a nascent field. I figured no one knew much about them so I wouldn’t get grilled too badly, so I wrote about MOF research as one of my out-of-field proposals. I passed! I then parlayed that proposal into my research statement when applying for faculty positions. But after I started my position, I got distracted by other interesting projects and never ended up working on MOFs. Oh, well. I’m still happy working on self-assembly problems, even if they are not MOF related.

 

The mass media quickly followed suit with their announcement of the Nobel Prize awarded today. The moniker that has caught on to describe the work is “Hermione’s Handbag”. I also told students about this, which garnered a lot of smiles. For those who don’ t know what this magical object is, Hermione (of Harry Potter fame), the cleverest witch of her age, had a handbag where the inside could hold much more than you might expect if you saw the small bag from the outside. An “extension” charm is supposedly used to do this, although how it works in practice is less than clear. Does it shrink all the materials when you put it into the bag? I’ve previously discussed the tricky chemical considerations of shrinking the size of atoms. Or does it give you access to some other adjacent space not part of the standard three-dimensions we experience? Folded space maybe, as string theorists might postulate. Or maybe a wormhole to some other space… all speculation at this point. Space-filling might be an odd duck; or an Occamy.

 

MOFs are not like Hermione’s Handbag; they have no magical extension to occupy more volume than the size of their pores. What was surprising was how many more molecules they could uptake compared to zeolites, another porous material that had been known for decades. There was both early excitement and skepticism about MOFs in those early years. I kept up with the literature through the decade of the aughts, but not so much after that. I’m pleased that I actually know something about the content for this year’s prize, and I’m pleased that a Harry Potter magical object analogy was used, even if it’s wrong. It gives the sense of the surprise you might have in your first encounter with Hermione’s Handbag.