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.

Hydrothermal Conditions

I’ve been conflating hydrothermal vents and fields. I realized this after reading Chapter 3 of David Deamer’s Assembling Life. Most of us who study the origins of life are familiar with the hypothesis that life on Earth may have begun in submarine hydrothermal vents. The initial discovery in 1977, that life was teeming deep in the ocean bed where the water was locally hot around magma-driven minerals was a surprise! The heat and the minerals both act as energy sources (thermal and redox-chemical respectively). Since living organisms crave energy, they congregated to form a local ecosystem.

 

There are two types of hydrothermal vents. The first to be discovered were dubbed “black smokers” because that’s what the sulfide minerals look like under the very harsh conditions where temperatures could reach 400 Celcius. Water remains as a liquid because 2km deep in the ocean the pressure is approximately 300 atmospheres. The vent fluid is also quite acidic (pH 2-4) which can drive certain types of chemical reactions. Black smokers are transient, lasting up to a few hundred years before they collapse and reappear elsewhere along the mid-ocean ridge where the crust is thinner and underlying magma can break through.

 

Origin-of-life researchers have been more enthusiastic about “white smokers” because that’s what the carbonate minerals look like under the not-as-harsh conditions. Water temperatures might be 50-90 Celcius, and the vent fluid is alkaline (pH 9-11) which also drives chemical reactions. These vents can last thousands of years, perhaps longer, and are not associated with volcanic activity. Their existence was predicted before they were discovered in 2000, and the most famous of these, Lost City, is sometimes referred to as a hydrothermal field, which confuses things and likely contributed to my conflating vent and field. Abiotic chemical reactions at these minerals under these conditions can generate methane and molecular hydrogen, important precursors for prebiotic chemistry experiments. Scientists have set up experiments mimicking these alkaline vents and produced some key molecules that may be the building blocks of organic life.

 

Deamer distinguishes hydrothermal fields from vents in the following way. In the submarine vents, there is only one interface: mineral-seawater. Fields on the other hand have exposure to the atmosphere. Instead of being deep in the ocean, they are terrestrial in origin. In the aftermath of a volcanic eruption, the minerals slowly transform such that eventually rainwater collects to form pools. Hot springs and geysers at Yellowstone National Park are an example of such fields. There are three interfaces: mineral-water, mineral-atmosphere, and atmosphere-water. Crucially, the water initially derives from freshwater and although this will dissolve some of the minerals, the ionic strength of the solution is much lower than in seawater. This is critical if you want to form cellular structures from lipid molecules. The high Ca²⁺ and Mg²⁺ content in seawater inhibits the self-assembly of micelles and vesicles.

 

Another important feature of such pools is that the acidic water (pH 4-5) of hydrothermal fields also dissolves apatite (calcium phosphate), the same mineral that makes up your tooth enamel. Phosphate is a key constituent of living systems: it’s in your DNA backbone, it’s crucial in the energy transducing molecule ATP, and it’s also use as a biochemical tag in proteins. In neutral or alkaline pH, phosphate precipitates into a solid and is not available for chemistry in an aqueous solution; this is known as the “phosphate problem” in the origin of life. Sulfur compounds likely contribute to the acidity in hydrothermal field solutions, which is why I’m studying them.

 

Terrestrial pools of water have two other attractive features. Since they are not as deep, photosynthesis can play a role. By this I mean that an appropriate mix of molecules that can absorb solar photons that penetrate through the atmosphere provides an additional energy source of driving chemistry. There’s even a pigment-world hypothesis of the origin of life that makes this center-stage. Secondly, a shallow pool potentially allows for wet-dry cycling. This is important because as water evaporates, it concentrates the potential reactants in solution. In particular, evaporating conditions drive the assembly of polymers. If you’re deep in an ocean with lots of water, hydrolysis reigns and water chops up any short polymers back into smaller fragments. The wet-dry cycling of a shallower pool, on the other hand, allows polymers to form and re-form polymers, and a complex mixture could begin to “select” for the most robust ones.

 

Did life on Earth begin in hydrothermal fields (as opposed to vents)? I don’t know. Deamer makes an attractive case for the fields. But it’s a messy complex system and designing good experiments that allow you to extract good data is not easy. I’m thankful to Deamer for making the distinction between vents and fields explicit and I expect to use his definition in the future.

Hermione's Helping Hand

I’m on vacation and was inspired to re-read the Harry Potter series. This seemed like an appropriate time given that today, July 31, is Harry Potter’s birthday. Also, in a recent family conversation about the re-telling of fairy tales, we mused about the different experiences you might have with an “updated” fairy tale, or one that takes a different perspective from an original source, depending on whether you had read the original version. I remember back in 2001 talking to a friend who had watched the first Harry Potter movie in the cinema, but who had not read the books beforehand. Being from a different country, he had also not been exposed to the Western canon of fairy tales. He enjoyed the movie, but found it a bit disjointed, and was confused what some scenes were about.

 

So, I wondered what it would feel like to re-read the books with some of these thoughts in mind. I have to admit that the first book is not as good as I remembered. That being said, every fresh re-reading rewires how one thinks about the text so perhaps all this is not surprising. I found the text clunky in some parts, possibly because I have not read any fiction catering to eleven-year olds in a while. Another thing I noticed this time around is how much guiding the author uses to set up a future scene. Is it a helping hand for younger readers? I don’t know.

 

My reading is also coloured by my profession as an educator. I’m constantly noticing what may be “teachable moments”. This time around, Hermione’s nagging, her drawing up study schedules for Harry and Ron, her checking of their work, made me wonder if students today need more Hermiones. It may not seem cool, but having a friend and peer want you to do well academically and makes the effort to help, even when it seems like being a nag, might be a good thing. That sort of helping hand might not be welcome, but in this case, Ron and Harry greatly benefit from it. Once Harry gets on the Quidditch team and his timetable gets tight, it’s Hermione’s strategies that gets him through the end of the year and final exams.

 

The title of today’s post comes from Book 6. In that instance, the beneficiary is Ron, but the help is particularly un-Hermione-esque. And throughout the books, the influence runs both ways. I’d like to think that Ron and Harry learn good study habits with Hermione’s help, but this aspect isn’t emphasized. If Hermione wasn’t there to nag them, would Ron and Harry be diligent in their classes? Rather when Hermione decides to stray from her straight-laced approach and become more “rebellious”, this is what’s celebrated. I’m not sure what the lesson is here. (For example, I previously blogged about Hermione organizing an illegal study group.)

 

Finally, an observation made by my sister after she had read the books has stuck with me. One of Hermione’s roles is to help provide information to the reader. In the first book, Hermione does so by quoting books she has read such as Hogwarts, A History. This keeps the story moving along without being bogged down. Need a factoid to keep things going? The Hermione character provides a way to insert knowledge. Other characters in the book also do this, but none as much as Hermione. Her helping hand is integral to the books!

On Not Reading

To read or not to read. That is the question. Even if you don’t read a book, in no way does it prevent you from talking about it. Or if you feel obligated to skim, ten minutes might be enough. It might even be preferable for you not to read if you are a book critic. This advice sounds positively blasphemous if you love reading and talking about books. But it does come packaged in a witty and humorous book by Pierre Bayard, aptly titled How to Talk About Books You Haven’t Read.

 

I’ve written about many books on this blog. I assure you I’ve read all of them. I even read most of Bayard’s but I did skip a few chapters and skimmed others. I think the author would be proud of me. On the one hand, the book made me think that literary criticism is an absolutely vacuous activity. On the other hand, Bayard emphasizes the non-static nature of a book. Read or not, it provides a jumping point to talk about opinions, ideas, musings, speculations, and engage in other human-like activities. It seems apt that books, read or unread, can promote the idealism of the humanities. Or it might just be a load of rubbish.

 

Ideas are two-faced. Janus-like. That was my biggest takeaway from Bayard’s musings. Two people can have completely different ideas when encountering some reading material, especially if they differ greatly in their backgrounds. There’s a most amusing chapter cherry-picking conversations that an anthropologist has with the Tiv tribe in Africa where she tries to tell them (or perhaps sell them) on the universal human tale of Hamlet. The Tiv may disagree with the typical literature interpretations you might encounter in a college classroom but they interact with the story nevertheless as they ridicule its tropes. I have never read Hamlet although I know enough of the story to quote from it.

 

The other interesting idea comes in the very first chapter with quotes from a book that I hadn’t heard of, The Man Without Qualities by Robert Musil. In it, there is a most peculiar librarian who pointedly never reads any book in the library other the table of contents so that the book can be situated with other books it is related to. An exasperated patron wants to know why. The librarian says that were he to read the actual book, he might “lose perspective”. That sounds preposterous but it turns out the librarian in fact loves all books, so much so, that “incites him to remain prudently on their periphery, for fear that too pronounced an interest in one of them might cause him to neglect the others.” By taking a step back and having a more expansive view, it is the dynamic relationship between books that is more important than one book’s particular content. It’s holistic knowledge by taking preservation of the whole to the extreme.

 

Most books have not been read by most people. And if you do read a book, you begin to forget the moment you start reading. I find this to be more and more true as I’ve aged. I retain the gist of books, stories, TV shows, movies, but I’ve forgotten the details. If enough time has passed, I can’t even tell you the gist. I could consult my blog to reacquaint myself with what I thought of it back when I read it the first time, but a second reading might induce a different response. I’m a different person now than when I first read the book and may interact with it differently as my constellation of ideas has shifted over time. But I don’t think I will ever be like Musil’s librarian. I love the pleasure of reading a book even if it means I miss out on others. Or even re-reading. Since skimming Bayard’s book, I have a hankering to re-read the Harry Potter series. Fresh eyes might provide more fodder for my blog!

In Search of Nothing

Nature abhors a vacuum. At least on the surface of Planet Earth which supports a gaseous atmosphere at a pressure of 760 mm Hg. How did we know this number? One of Galileo’s students, Torricelli, turned a tube of mercury upside down into a bowl of mercury. As long as the tube is more than 760mm long, there will be a gap of nothing at the top. It’s not an air gap. It’s a gap of Nothing.

 

Toricelli was actually looking for the mystical aether, the sacred material breathed by the gods, the fifth element, the quintessence. Supposedly it “allowed light from the stars to propagate” and was “also holding planets in their orbits”. I’m learning about this history reading through Mark Miodownik’s It’s a Gas. Toricelli had finally isolated the aether, a quest of the alchemists, some of whom thought it associated with the philosopher’s stone that would balance the four humours and cure all illnesses. Perhaps it could even prevent death. No wonder that Voldemort coveted it.

 

The trick to creating vacuum is to pump out all the air molecules from a closed container. That container must be truly air-tight. No leaks! Miodownik writes: “We take the accuracy and intricacy of screws, gaskets and valves for granted today. In the seventeenth century such precision engineering was just beginning.” What shot vacuum to fame was the famous demonstration at Magdeburg by Otto von Guericke. He didn’t use the chemical techniques of the alchemists. He just used mechanics to make an airtight pump. Once the air was pumped out of two hemispheres cupped into a sphere not held together by any other means, two teams of eight horses each could not pull the hemispheres apart.

 

What are the properties of Nothing? Now that scientists could reliably make it. They could start running tests. No living thing survived. (Oxygen was yet to be discovered.) Sound does not travel through vacuum, although light does, and magnetism is unaffected. Turns out that metal wires will glow hot in an enclosed vacuum tube when a voltage is applied, and  Voila! Electric lighting is invented! Even if the wire breaks, you can sometimes get electricity to flow. (Electrons leap across but they didn’t know that yet!) This led to vacuum tubes. And now you have TV. Once you’ve mastered manufacturing silicon chips in vacuum conditions, you now have computers and all manner of smart devices. Who would have anticipated that Nothing would be so important!

 

Miodownik also relates the now-familiar story of the discovery of the noble or inert gases. They upended Mendeleev’s Periodic Table. It took painstaking evidence to show that they existed. They weren’t just Nothing even though they seemed to have no chemical reactivity. How were the noble gases discovered? Rayleigh was unhappy with the imperfections of the masses of the chemical elements. They almost followed a beautiful mathematical pattern, but not quite, and so he decided to measure their masses again with high precision. This is much harder than it sounds. You needed to create a vacuum in a flask and weigh it, then pipe the gas in and weigh it again. But the pressure, temperature, and humidity of the room can affect this measurement. You needed to more than triple-check everything. Most scientists didn’t believe Rayleigh, even after Ramsay provided an independent confirmation. Eventually argon was joined by helium, neon, krypton and radon. Chemistry’s 1904 Nobel Prize went to Ramsay for his discoveries. And eventually scientists and engineers found uses for all these gases that at first glance did Nothing!