Thermodynamic Terminology

One of my biochemistry colleagues was telling me about students being confused in class about the meaning or significance of delta-G (the change in free energy) in thermodynamics. Part of the problem stems from using ‘spontaneity’ to describe reactions with negative values of delta-G. In thermodynamics, spontaneity has a narrow meaning. It tells us the direction that the chemical reaction is likely to proceed, all things being equal (i.e., no other external factors are present to putz with the system). Importantly, delta-G does not indicate how quickly the reaction might take place.

 

In present-day usage, ‘spontaneous’ is used to refer to something ‘suddenly’ happening, which seems to imply it happens quickly. But historically (from the Latin spontaneous), it meant “occurring without external stimulus, proceeding from an internal impulse” (according to this etymology website). The historical definition fits with the narrow meaning I mentioned above. I take great pains to emphasize to my G-Chem students that delta-G does not tell you about the rate or the kinetics of a chemical reaction. I do this multiple times throughout the semester like an old nag; this is from experience – students so quickly forget and mix up thermodynamics and kinetics.

 

When I discuss delta-G, I try to get the students to think about it from more than one perspective. Since it is an energy term, a reaction with a negative delta-G is lowering its energy, thus becoming more stable. This is energetically favorable. We also discuss why G is the (Gibbs) free energy, defined as the maximum energy available to extract (non-PV) work from the system, after paying the entropy debt. I also introduce students to the terms endergonic and exergonic to describe reactions with positive and negative delta-G values. Furthermore, delta-G under standard (or reference) conditions can be related to the equilibrium constant. That’s a lot of stuff. No wonder the students can sometimes get confused.

 

This made me wonder if I can just delete the use of the word ‘spontaneous’ from the vocabulary of thermodynamics. If we didn’t use it, students wouldn’t trip up. But words don’t exist in a vacuum. I may not use it. But a textbook might. Or the internet surely does (which is where students are looking up most of their information), and all sorts of errors and confusion proliferate from this. Hence, I surmise that my best bet is to keep doing what I’m doing: emphasize why the word ‘spontaneity’ is confusing (and that students should be careful), teach them terminology that is used for historical reasons, use multiple conceptual ways of getting students to think about what delta-G means, and repeat, repeat, repeat.

 

Delta-G is particularly important to chemists and biochemists. But it comes from constituent parts: delta-H, the change in enthalpy; and delta-S, the change in entropy. While students have a sense of what energy means (even though it’s a slippery concept in truth), the words enthalpy and entropy are gobbledygook that we chemists infuse in meaning. Entropy is particularly trippy because there are multiple ways to think about it. But even enthalpy trips you up because its relation to ‘heat’ energy comes from calorimetry, and to make matters more confusing, heat is a verb and not a noun. Most reactions are not done in a calorimeter and we’re not measuring thermal energy being absorbed or released by a chemical reaction. Yet we retain the words exothermic and endothermic to classify whether these reactions have negative or positive values of delta-H. No wonder students have to do a lot of mental work keeping all this straight.

 

Early in the semester, I stress to the students the challenge of defining a cross-cutting ‘big’ concept such as energy or life. The way we get at the meaning of these concepts is through lots of examples. Hence, after calculating delta-S, the change in (nebulous) entropy of a chemical reaction, I recite what the value may signify. Is the system getting more ordered or disordered? Is there more or less available motion? Are there more arrangements or fewer arrangements? Is there a larger or smaller dispersal of thermal energy? Are molecular energy-level spacings getting closer and more densely packed? Is the ‘quality’ of the energy (in terms of ability to manipulate it further) getting worse? Hopefully by constantly repeating these mantras, the concept slowly takes root and the word takes a meaning that fits the circumstances.

 

I hardly ever use the word ‘spontaneous’ in regular everyday conversation. I might say ‘suddenly’ or ‘quickly’ or ‘without warning’ but I reserve spontaneous only for its thermodynamic context. I didn’t consciously do so, but I suppose that in making the effort not to confuse students, I subconsciously practiced the separation of meanings. But language and terminology evolve, and we adapt to bring new shades of meaning to words that we use. As someone who teaches G-Chem and P-Chem on a regular basis, I am hampered by the archaic and foreign words that have historically lodged into my field. It is still incumbent on me to ensure students know what to do with these words when encountering them in the internet wild. But at the same time, these words are used to get at large cross-cutting concepts that have no simple definition.

 

There may be a better solution, but for now I’m stuck with thermodynamic terminology. It is useful and powerful, when the students understand the models or constructs behind these words. Science is all about constructing (conceptual) models to understand the natural world, and to make useful predictions with these models, they should employ the language of mathematics. Without these underpinnings, we’d be wading through a morass of speculation, vagueness, and ignorance.

How Life Works

In college, I thought biology was interesting, but tedious with lots of facts to memorize. I was also doing poorly at experimental lab work. Cells died under watch and I couldn’t get the data I needed. Some of my lab partners were flaky. It wasn’t the most positive experience. At the same time, I was finding both organic and inorganic chemistry intellectually stimulating! It was a no-brainer. I chose to major in chemistry.

 

Thirty years later, I wonder what younger self was thinking. Biology is fascinating and remarkable! My segue into biology began when I got interested in learning more about the chemistry of the origin of life – a complex self-assembly problem. Before long, I started to read more papers in biochemistry and molecular biology. More recently, I’ve begun to appreciate the importance of systems biology and ecological thinking. To complement the scientific articles, I’ve also been reading more big-picture books that straddle into the philosophy of biology. My most recent foray is Philip Ball’s How Life Works, subtitled “A User’s Guide to the New Biology”. 

 

The New Biology isn’t all that new. Rather it’s a shift in perspective to a more holistic view. The discovery of the DNA double-helix set biology on a path that privileged genetics over other areas. This led to significant advances in our knowledge of biology, but it also revealed the dearth of what we know about how life works. Genes turn out to be a part of the story, but not the most important part. Nature is both more complex and subtle. Today’s post will be about things that jumped out at me in two chapters from Ball’s book, “Networks” (Chapter 5) and “Agency” (Chapter 9).

 

Ten years ago, I was a fly-on-the-wall of a back-and-forth argument among several biologists about the ENCODE project. I was surprised at the vehemence of folks who thought the project was one of the most worthwhile and important things to be doing, and others who thought it was useless bunk and a waste of resources. The inner workings of the cell are not just about DNA, but RNA (all sorts of different kinds), proteins, and a bunch of other biomolecules ‘talking’ to each other, and somehow in that glorious mess doing the business of living. Ball goes through that story, and I appreciate seeing the big picture now, which I didn’t see then. We also didn’t know as much then – the growth in new biological information has been tremendous over the last decade.

 

I’m amazed by how all the different biomolecules interact with each other to do their thing. Not just one thing. Many things. Many different kinds of things. And it all looks like chaos! Molecules bump into each other, form transient complexes, and dissociate. Ball goes into detail discussing gene regulation and transcription, homing in on topologically associating domains (TADs). He calls them “ephemeral committees”. It’s as if “chromatin is a building with several floors (compartments), each with many rooms (TADs) containing separate committees. The committees have much the same membership in different cell types… molecules that are inclined to gather together. But exactly where they gather… varies between one cell and the next.”

 

It gets more complicated: TADS aren’t a “Lego-like assemblage of many molecules… like assigning everyone in a committee a specific place at the table and being unable to begin the meeting until all are correctly seated… it would take hours to get all the molecular members together in the same room and seated in the right place before any decision can be made. And this assumes that some members don’t drift away in the meantime, as perpetually restless molecules are apt to do.” Turns out the actual time spent is about six seconds, so “the committee needs to be very flexible. There might be no seating plan, nor any requirement that all members are present, so long as they have a quorum. The process may be literally rather fluid.”

 

The cell is not a factory running in what seems like organized lockstep; it’s a disorganized zoo with enclosures that are not totally enclosed. Ball highlights the potential importance of disordered proteins: “their propensity to form many indiscriminate and transient interactions with other molecules, seem to be ideally suited for promoting condensates.” I briefly discussed disordered domains in proteins when teaching biochemistry for the first time last semester, but I don’t think I really appreciate it due to my lack of knowledge. Further it highlights the incongruity between “digitally precise information [encoded] in the sequences of DNA, RNA, and proteins” that are then utilized in a “hazy environment… like telling each committee member exactly who may they talk to and what they may say, only to then create extremely lax rules about who comes to the meetings, how long they stay, and so on.”

 

Ball, however, sees an opportunity for this messiness: it’s what you need for a system to be robust instead of fragile. Ball compares it to a committee sufficiently diverse to include experts in specific areas, but also generalists, and mavens who are “good at connecting others and reconciling their points of view”. If you need “reliable generic decisions amid a tremendous diversity of experience and circumstance… lots of details [must] be weighed, filtered and integrated.” It comes down to information management and “not a concentration but a dispersal of power”. Those mavens? Their equivalent chemical skill is molecular promiscuity and leveraging combinatorial “fuzzy” logic. That’s why a “cell’s wiring can’t be compared to a complex electronic [computer] circuit”. Cell logic is wet and sloppy and needs to be!

 

Living seems to be an emergent process. Ball calls this causal emergence, and recapitulates the notion of biological relativity; no particular level of causality is privileged. The reductionist claims that all “macroscale causation is fully reducible to microscale causation”. The emergentist disagrees. One common thread in examples of causal emergence is noise reduction: “independence of the outcome on random fluctuations or chance events at the microscopic level”. The genetic algorithms and neural nets instantiated by 0’s and 1’s in a computer circuit are not like this – in fact we design them with high precision so the parts “don’t go wandering randomly out of place. But molecules do!” Ball compares the causal emergence we observe in living systems to human language, in which “meaning and indeed causal power… increase as we go up the scale from letter (or phonemes) to words, sentence, paragraphs… Zoom in on a text’s component characters and you lose all meaning.” But there’s more. Causal emergence leads to causal spreading, and Ball thinks that’s a key to how multicellularity emerged. The genomic expansion seems to be mostly in the regulatory elements. I admit that I don’t quite understand enough of the biology to grasp all this.

 

That brings us to agency. Ball’s definition: “the agent itself acts as a genuine cause of change: agents act on their own behalf.” Even in the chemistry classroom, I often use the language of agency when referring to a molecule: it wants to do something, it is attracted to something, it sees something in a neighboring molecule, it tries to lower its energy any way it can, it needs to pick up an electron, it is stable and “happy”. In the next breath, I warn my students about getting carried away with anthromorphizing molecules. Similar language is used in biology. I appreciated a footnote Ball provides from the philosopher Annie Crawford that “scientists who… consider their metaphors to be merely decorative additions that can be abstracted away from the meaning seem not to have thought very deeply about the nature of language… metaphors do real conceptual work.” I’ve become much more cognizant of this as my reading has branched into such philosophical realms.

 

Ball prefaces all this with a detailed discussion of Maxwell’s demon in the context of thermodynamics. This was familiar territory to me – an argument about the interconvertibility between information and thermodynamics. Ball then makes some intriguing and lucid statements (backed up by examples): “an organism can make use of the environment by becoming correlated with it… implying that they share information in common… such correlations become established in the process of evolutionary adaptation… [they] may also be engendered through learning from experience… it is shared information that helps the organism stay out of equilibrium… tailor its behavior to extract work from fluctuations in its surroundings… Life can then be considered as a computation that aims to optimize the acquisition, storage, and use of such meaningful information. And life turns out to be extremely good at it… The best computers today are far, far more wasteful of energy than [the Landauer] limit [apparently six orders of magnitudes more, compared to one order of magnitude in cells]… biology seems to take great care not to overthink the problem of survival.”

 

Mind blown.

 

Ball says that “having a mind is a good adaptive strategy for an organism that experiences a very complex environment”. The alternative of trying to “equip the organism with a suitable automated response for every stimulus it is likely to encounter”. That might work for something with limited functionality, but to be robust in a complex environment requires… well, you can see the challenges with automated-driving cars, and even then they only have a very limited function in the grand scheme of things. It’s amazing what our human minds can do. Ball thinks that it’s okay to bring the language of purpose back into evolutionary biology. He thinks the reason why biologists are uncomfortable is because biology “can’t deal systematically with agency and so has to infuse it into entities as a kind of magical capability… that arguments about human free will persist (often rather tediously) because we lack any account of how agency arises.”

 

It's clear I don’t really understand biology. Perhaps, like quantum mechanics, no one does. But I appreciate Ball provocatively pushing me to think both broader and deeper to do so. I think I understand a lot of chemistry, but maybe deep down I really don’t. The wonderful thing about being a teacher is that every now and then I have a small panic when I anticipate a profound question a student might ask in class (the reality rarely happens) and do a quick frenzied search about some conceptual underpinning. Inevitably, I learn that the concept is both complex and subtle; then I come up with a good-enough arm-wave explanation which I rarely have to use. But it’s the asking of deeper questions that matter, so I’m glad that I continue to ask them! How Life Works is thought-provoking in such a way that I will be re-reading it, just like Ball's book on quantum mechanics.

Enzyme Perfection

Since teaching biochemistry for the first time last semester, I’ve widened my reading to include general aspects of biochemistry that may help me see the big picture and educate myself! I just finished a short book by Athel Cornish-Bowden titled The Pursuit of Perfection. The author chooses interesting vignettes in biochemical evolution to probe the question of whether extant biochemistry is optimal in some sense. How and why did enzymes evolve to what they are today? Today’s blog post is on the first chapter, “Some Basic Biochemistry”.

 

Likely, the first thing that students learn about biochemistry even before they step into a formal biochemistry class, is about enzymes. Enzymes are crucial biochemical catalysts. Without them, biochemical reactions that involve making and breaking covalent bonds would be much, much slower! But why do we need enzymes? There are many other ways of increase the rate of a chemical reaction. You can heat it up, you can apply pressure, you can provide mechanical or electrical energy, and it works. But the problem with these approaches is that they often lack specificity.

 

The author puts it this way: “Why should we be impressed at the capacity of enzymes to do the same thing? The fact that an enzyme can do it at low temperatures is part of the answer, but the really impressive aspect of an enzyme is no that it is a good catalyst for a given reaction but that it is an extremely bad catalyst – no catalyst at all, in fact – for virtually every other reaction.” If you were at much higher temperatures, all sorts of unwanted reactions are also taking place, and achieving fine-tuned control is very difficult. That’s why biochemistry tends to only occur under a narrow range of “mild” conditions. Yes, there are some organisms that live in “extreme” environments, but from a universal perspective these conditions are still very narrow.

 

There is a conundrum, however. If enzymes are specific, they also have to be much larger in size than the reaction they are catalyzing. But why? First the author disposes of a misunderstanding stemming from our perception of “things we can handle”. We think linearly. His example: “If we say that a bed is a bit bigger than a person, we mean… that it is a bit longer than the person who sleeps in it. The fact that it is a lot higher and a lot wider, so that its volume is much larger than that of the person who sleeps in it…” He estimates that “an enzyme is typically 50-100 times larger than the combined volume of the molecules it acts on…” For comparison, “a volume ratio of 70” is typical for a car with a single passenger. For an office with a volume ratio of 70, it would feel tight – like a small closet or cubicle. A rough estimate of my office volume was 300 times my own volume, which was higher than the author’s average of a 200-fold volume ratio for a relatively comfortable office. I feel lucky!

 

Now to the issue at hand. A smaller enzyme would require fewer resources to biosynthesize. It’s energetically costly to make bigger enzymes with more atoms! Why does it need to be so big? The author writes: “An enzyme is a precision instrument, capable of recognizing its substrates, distinguishing them from other molecules of similar size and chemical behavior, and transforming them in precise ways. In general, the more precise any instrument has to be the bigger it must be, and the relative size difference between an enzyme and the substance that it acts on, is not very different from what you would find if you compare a precision drill with the object to be drilled, if you include the clamps and other superstructure as part of the drill.” I had honestly not thought about it that way before, but it makes good sense, and I’m filing this mental picture for future reference!

 

But there’s more. An additional constraint is that the enzyme must be “extremely unreactive when not in the presence of the molecules they are intended to transform, to make sure that they do not undergo any unwanted reactions… This is much for difficult for working on a very small molecule than it is for a large one, and we sometimes find that the largest enzymes work on the smallest molecules, and vice versa.” Eeeks! I didn’t know this when I was teaching biochemistry and I wish I did. It makes sense to me, but I just never thought about it that way. Another factoid to be filed for future reference! The author uses the examples of pepsin and catalase to bring his point home.

 

And then I learned that the reason why we need catalase, and quite a bit of it, in our blood. It converts hydrogen peroxide (H₂O₂) back into water and oxygen gas. The author lucidly explains: “… any living organism needs to be able to destroy harmful chemicals… that get into cells. There are a great many potential hazards of this kind, and as the cell cannot prepare a separate solution to every conceivable problem that might arise, it deals with many unwanted chemicals by making them react with oxygen… This is a useful step, for example, toward making insoluble poisons soluble in water, so that they can be excreted…” Hence general-purpose (i.e. less specific) enzymes have evolved for this sort of business but they also oxidize water in the process turning it into H₂O₂, which can be toxic at higher concentrations, so catalase needs to get rid of it. (At lower concentrations H₂O₂ acts as a signaling molecule, which is what you might expect evolutionarily – poisons get co-opted into signalers.)

 

All this took the author just a few pages and I learned so much! I felt very humbled and reminded that I have a-ways to go before I start to think like a biochemist, but hopefully I’m on the right road. With help from others!

A Spherical Cow

Many years ago, I learned from physics colleagues that when asked to solve a ‘real-world’ problem, they begin with the statement: “Consider a spherical cow…” Little did I know that this is also the name of a book, and my university library had a copy (of the first edition published in 1985). Consider a Spherical Cow is written by John Harte, a professor at UC-Berkeley. It is subtitled “A Course in Environmental Problem Solving”.

 

The book presents 45 problems with worked solutions with interesting ‘real-world’ applications related to geoscience. Each of the ‘solutions’ discusses the approximations made when a simpler model is used (akin to the spherical cow) but also includes discussion and follow-up exercises (no solutions provided) if the model was modified to take more complicated features. Essentially, a cow isn’t really a sphere, so how do we account for that?

 

Chemistry features prominently in a number of the problems. There are problems of atmospheric chemistry, natural elemental cycles (carbon, nitrogen, sulfur, phosphorus). Some problems feature acid rain, trace metal mobilization, fossil fuel burning, and more; for example, “What is the pH in pristine precipitation?” No, it’s not seven. There are several thermodynamics and energy transfer type problems. There are also a number of ecology-type problems including an interesting one about how the population of China might change and when it might approach steady-state. It begins with 1980 data and predicts trends going forward in different age bands every decade through 2040. Today we can compare how well those initial models worked. The results are interesting, and Harte does a good job in discussing the caveats in any model.

 

The math is mostly algebra, albeit quite involved. There is a little bit of vector notation and the occasional differential equation, but these can essentially be transformed into algebraic problems. The appendix has data which students can draw from to solve these ‘real-world’ questions. Since I’d been thinking of transforming my G-Chem courses to include a chunk of data-science techniques, I found Harte’s approach helpful to think about even if I will likely not use many of the actual problems that he poses. It’s the habit of mind that we’re trying to inculcate in our students: how to approach a problem by constructing a simple (model) first and then iteratively improve upon that first guess.

 

I recommend Harte’s book if you are interested in seeing the workflow in his book starting with warm-up exercises and progressing to beyond back-of-the-envelope approaches. I’d also like to come up with the chemists’ equivalent of “Consider a Spherical Cow”. Any suggestions?

Lonely Hobbit, Victory Rout

This year I’m having another resurgence in playing Origins: How We Became Human. I had gotten into it back in 2021 and wrote a couple of blog posts. If you’re unfamiliar with the game, I suggest reading this overview. For today’s session report, I took fewer notes. I was playing Hobbit and I thought I would do poorly given an unfavorable climate change causing me to be isolated with little room to expand or build. But I managed to turn things around and romp to victory. You can also read a more flavorful session report with a global view (where I came in second place as Hobbit). But on to the action!

 

Back maybe a hundred thousand years ago…

 

Turn 1: A diminutive tribe imitates group mating rituals from their taller northern neighbors. In addition, they learn to scrape hides and a new profession emerges: the leatherworker! Something opens up in the limbic system of their brains – technical knowledge!

 

Turn 2: Some astronomical event triggers climate change, and impassable and dangerous jungles expand all around. The ‘hobbits’ are hemmed in with nowhere to go. But their brains expand to acquire natural knowledge and the rudiments of language. Basket-weaving becomes a major activity.

 

Turn 3: A Milankovitch cycle triggers a tropical age with a rise in ocean levels. There is little land and the new species are hemmed in on a tiny tropical island. [Pictured: The green cube on the Hobbit starting spot is isolated because of the two climate changes. Can’t move. Can’t expand.]

 

Turn 4: Inexplicably, sudden global cooling occurs and an ice age returns! [This is very rare! It requires a six to be rolled the turn before due to a climate card being drawn, and another in this turn. There aren’t that many of these cards.] The hobbits quickly expand into Sulawesi and are able to domesticate the water buffalo, but they catch a zoonotic disease and develop child swaddling.

 

Turn 5: Land south beckons as the hobbits discover land in a large continent to the south. [Pictured below: Australia!]

 

Turn 6: Kayaks are developed and fishing becomes a huge industry. The hafted thrusting spear is invented and hobbits enter the Copper Age. Using a hammer and anvil to crack nuts brings more nutritional access.

 

Turn 7: The diprotodon wombat in the Australian desert is domesticated into a warbeast! Hobbits enter the Bronze Age [ahead of the other players].

 

Turn 8: [Neanderthals cultivate wheat and advance to Era II and the Bicameral Age first.] Hobbit women begin to practice sham menstruation to reduce the number of children. With kayaks and bronze tools, adventurous groups hack their way through the jungles to the north into China.

 

Turn 9: Millet is cultivated but at low protein value. However, Hobbit society is doing well and productive overall. [My innovation level is at 4 even while I’m still in Era I; I had never achieved this before.]

 

Turn 10: [Cro-Magnons advance to Era II, Peking Man who has been doing poorly enslaves themselves to the advanced Neanderthals so they can quickly increase their footprint.] Hobbits fail to cultivate soybeans (twice)!

 

Turn 11: [Cro-Magnons and Neanderthals advance to Era III, Peking Man freed and quickly acquires a metropolis.] Hobbits finally cultivate soybeans but it is also low protein. They begin to practice burials and expand their language finally moving into Era II. It’s the bicameral age and we are starting to develop more self-awareness.

 

Turn 12: Culturally, body paint and shell necklaces become a new status symbol. The climate becomes mild becoming more of a Parkland – the jungles disappear. We start to build ziggurats and can boast of a rich culture.

 

Turn 13: A group of adventurers makes it to the Maldives but then are infected by diphtheria from the Africans in the continent west of us. We learn new food storage techniques. We are able to cultivate coconuts [thereby getting to the important Footprint level 3]. Temple administrators become the governors in our society. We move into Era III, the Age of Faith.

 

Turn 14: We develop the iron ploughshare and become the first to reach the Iron Age. This superior metallurgy puts all other nations on notice. We develop public baths and the new professional class of architects is held in high esteem!

 

Turn 15: The outrigger canoe is invented and our adventurers discover a new world across the Bering Straits.

 

Turn 16: The Africans hit with a barbarian raid on the Maldives. A serious drying and desertification takes place all over the globe. Our spies practice espionage on our enemies. Islam becomes our dominant religion.

 

Turn 17: The volcano Kikai erupts. It is felt by our metropoli in the northeast but there is no severe damage or loss of life. Our spies help us to develop hieroglyphs. Our engineers build trireme galleys. We take mathematics seriously and build Aristotelian schools. A new settlement is founded in Hawaii.

 

[I stopped to take photos at this point. I’m Player Green with metropoli in Asia, Hawaii and the Maldives. Neanderthal is Player White and occupies western Europe and Africa. Peking Man is Player Red in Central Asia. Cro-Magnon is Player Black in East Africa.]

 

[I’m the only player in the New World. You can also see in the Development tree that I’m on par with Neanderthal in all areas. In some areas, Cro-Magnon and Peking Man are slightly behind.]

 

[Here’s my player board. My innovation is at 3 which is pretty good and I have three producers and one consumer. I need to increase this.]

 

Turn 18: Biofuel extraction in Hawaii is successful! [I’m the first to advance to Energy level 2, a sign that I’m now in the lead, which means the other players might start collaborating.] We quickly expand into Venezuela and establish a metropolis to prospect for oil.

 

Turn 19: Thera erupts in the Mediterranean. We develop terraced agriculture [moving to Footprint level 4]. Our society enters a golden age of feudalism. [We must be in the Middle Ages now?]

 

Turn 20: Yellowstone erupts. [That’s a lot of volcanoes in the last several turns! Not so common.] There is also significant climate change causing deserts to retreat and reestablishing a milder savanna climate. We domesticate the Camelops in North America and develop a battering ram tank for war. Attempts to extract for oil fail. [I need to roll a six on each attempt.]

 

Turn 21: Our society is struck by bubonic plague, we start to develop drugs and medicines. We’re the first to advance into Era IV, the Age of Reason. It’s a renaissance!

 

Turn 22: Many social changes come about: humor becomes popular, courtesans become active, marriage dowries are practiced, and monogamy becomes dominant. We strike oil in Venezuela! [This brings me to Energy level 3 and Metallurgy level 4, the Gunpowder Age. I can now easily siege and take over metropoli from other players.]

 

Turn 23: [Neanderthal makes it to Era IV] A court system is developed and lawyers abound throughout our society. We turn to world conquest, besieging other cities, and foreign workers fill our pool of laborers and artisans.

 

Turn 24: Our society undergoes a revolution from a social equity society to one that favors individual freedom. We enter a golden age of entrepreneurship.

 

Turn 25: [I reach Energy level 4] So many things are invented: steam engines, pharmaceuticals, aluminium smelting and plastics. [I also advance my Maritime and Metallurgy levels.] Broadcasting takes root and ‘couch potato’ becomes a new phrase in our vocabulary. We also invent the personal computer and software programmers are highly sought after. Videogames become popular. [These last few cards are ‘Utopia’ cards that help me trigger the Game End by modifying a die roll. I am successful and the game ends.]

 

[I rule most of the world and have hemmed in my opponents.]

 

[In advancements, I’m clearly ahead in Energy, Maritime and Metallurgy.]

 

[I have lots of producers with lots of foreign workers, the non-green cubes. My innovation and population are at their maximum.]

 

I win the game with a final score of 48 points. This is very high in my experience of 4-player games. The other players are far behind (Cro-Magnon 14, Peking Man 8, Neanderthal 13) so my victory was a rout. Some games are like that, others are much closer.

 

P.S. If you liked reading these session reports, here’s one on boardgamegeek.com where I came in second as Neanderthal.

The Expanse

A while back, I read the first three books of The Expanse series, which I enjoyed and is a good temporary stopping point. Several months ago, I discovered that my local library was ordering the DVD box set of the full six-season TV series. I’d heard good things about it. I decided to first read Books 4-6 before starting on the TV series. Then my spouse and I slowly watched our way through the visual version of The Expanse.

 

Overall, I would give two thumbs up to the TV series. They did a good job adapting the books to the visual medium. This is always a challenge. I felt there was a bit of a rough start to Season 1. My wife, who had not read the books, was confused in the first several episodes. Even though I knew the story, I still found the presentation confusing. I understand the strategy of plopping the viewer dab smack in the middle of the action without much explanation (some scifi revels in this), but in this case I thought it was less than effective. Thankfully, things started to cohere as the season progressed and I feel that a certain consistency emerged over time.

 

[SPOILERS from here on…]

 

The TV series blends in background information and characters from future books by introducing them earlier in the season. Avasarala who only shows up in Book 2 begins to be featured in Season 1, and I think they did this effectively. Havelock also showed up in Season 1, but was inexplicably absent in Season 4. I can see why they cut out chunks of that story to concentrate on what was happening in Ilus. You have to make choices of what to keep and what to cut. Overall, the TV series has fewer characters from the book, as expected. Some are composite characters. For me, the most interesting choice was to introduce Drummer early and progressively make her a single main character by taking on the roles of other key characters. This was very well done, and the show-writers did an excellent job in using their freedom to create a compelling character.

 

An engaging scifi book is often more about probing the social science aspects rather than getting into details of the ‘hard’ science. This, I think, is a very effective approach. You need to provide enough to make the world feel realistic, but be vague enough so that your reader doesn’t suffer from disillusionment because you introduced something more ridiculous than fantastic. You can be vague in a book and leave imagination up to the reader but this is not so easy in the visual medium where you now have to decide how you will represent the technology. The Expanse TV series is a mixed bag. Some of the visuals are absolutely spot-on and I felt immersed in their world. Others were more meh and broke the spell of illusion. But overall, I like their representations of the Belt space stations, and the PDC countermeasures against torpedoes made for exciting visuals. Seeing the Nauvoo first get towed out was awesome.

 

I didn’t recognize any of the actors in the series. That was a good thing. Most of them did not look like what I might have imagined when reading the books, so while I experienced some cognitive dissonance in the early goings, eventually I felt that the main-billed actors inhabited their characters and I think they made excellent choices overall. No one was a dud. Drummer was superbly portrayed and one of the most engaging presences on-screen, which I find interesting given that she was a composite of multiple characters in the books. I suspect that going forward when I read Book 7, I will start to picture the TV series actors instead of what I had imagined previously in my mind’s eye. Not sure if this is a good or bad thing.

 

Finally, as a chemist who studies the origin of life, the protomolecule is of particular interest to me. I was less impressed by the visuals involving the protomolecule. And now that I think about it, the name is highly misleading. There’s no way a single molecule (even one that is large and multifunctional) can do what it purports to do – feed on organic matter and activate it into something life-like that straddles the boundary between machine and organism. It has to be a protomolecule system. But adding the word system would sound clumsy. Mixture? Composite? I can’t think of a better word, but the use of the singular-sounding protomolecule entrenches a wrong conception of how chemistry works. And the protomolecule’s action is all about chemistry.

 

Maybe after finishing Books 7-9, I will revisit what I think the protomolecular system needs to consist of. I study protometabolism. Maybe that’s what they should have called it: the protometabolism – but that would likely have been confusing. But that’s for another time. Watching the series also made me think of the “curse of knowledge” that inflicts all teachers. We have to constantly try our best to put ourselves in the shoes of our students to anticipate what will be confusing to them. If you haven’t read the books, parts of The Expanse TV series will be a bit of a muddle. My spouse would still say she found it engaging, and she was able to follow most of it with no problems. I did clarify some of the parts she found muddled, but overall that was minimal except for the early going in the first season. I am happy to recommend The Expanse TV series if you’re looking for engaging characters and an interesting multifaceted story.

Ends and Odds

If you wait long enough, everything goes to equilibrium – a strange state of balance where it looks like nothing is changing. But look more closely and you see a frenzy of activity that seems to go… well, nowhere. Why?

 

A macroscopic process seems irreversible. A drop of ink in water spreads out and smears until it uniformly colors the liquid. You’ll never see the colored liquid turn back into colorless water and an ink droplet. But at the microscopic level (actually nanoscopic), the motion of jittery molecules does not distinguish between forward and reverse. Molecules just keep moving back and forth, and forth and back. Our experience is that macroscopic processes are unidirectional along the flow of time, while microscopic processes are time-reversible – you can’t tell if it’s going forwards or backwards and it makes no difference.

 

I’ve been reading Knowing by Michael Munowitz and enjoying his lucid explanations into the nature of… well, nature. Today’s post is about Chapter 10, aptly and cleverly titled “Ends and Odds”. It’s about thermodynamics. It’s about the fate of all macroscopic processes (to reach equilibrium!). It’s about the elusive nature of time, flowing unidirectionally toward greater and greater entropy. It’s about statistics. What makes the time-agnostic microscopic world into the one-way flow of the macroscopic world is a matter of odds. Munowitz declares this is about freedom. While the frenzy of the jittery microscopic motion never stops, this “freedom [of motion] leads to equality: freedom of position, equality of distribution.” This is what it means to be at equilibrium.

 

Munowitz walks the reader through three examples: pressure, temperature, and distribution. Molecules freely move until all pressures equalize, all temperatures equalize, and all concentrations equalize. It all comes from statistics. Considering pressure, Munowitz writes that it “arises from the impacts of individual molecules against the walls of a container. Each single impact is small, yet there is strength in numbers. The collisions come rapidly and in tremendous quantity, averaging together to produce a steady macroscopic pressure at equilibrium: a statistical average, emerging clear and sharp from the microscopic confusion. Microscopic randomness gives way to macroscopic reliability.” The same thing happens for temperature and distribution (concentration). Macroscopically there is a reliable one-way gradient. Heat flows from hot to cold. Solute molecules flow from a more concentrated area to a less concentrated one.

 

Here are a few more quotes from Munowitz that I liked:

·      “Always in motion, microscopic particles exchange energy and influence as they slip into a state of equilibrium… We need to understand particles as crowds, and we need to understand them as individuals and small groups. For the many, we need statistics.”

·      “To be in equilibrium is to lose track of time, to disappear the into the gray sameness of an unchanging macroscopic state… Without change, time disappears. The clock ceases to tick.”

·      “Once a system attains equilibrium, all memory of the past is gone. Looking at the present, nobody can say when the system got, how it got there, why it got there… The scant macroscopic information to be gleaned (… constant this, constant that) provides no clue to what came before. It Is, at least for the present, the end of history.”

 

An equilibrium can be stable; it can be unstable; or it can be metastable, as shown by these three pictures from left to right.

 

Munowitz writes: “a stable equilibrium need not last forever, because stability is always a matter of where one sits in relation to some other possible state… Hit any equilibrated system hard enough, and it will awaken as if from a slumber… there can be a second at after equilibrium, and more than that, too: there must be activity during equilibrium. How else could a quiescent system, lost in the macroscopic timelessness of equilibrium, be able to accept a better offer and embark on a new history? To do so, it must tap a power that comes from within. It must draw upon a microscopic power belied by an overall macroscopic calm.” Munowitz will explain this with the help of two friends, Mack and Mike, and their glaringly different perspectives. I encourage you to read Knowing for the full glory of his prose, here are just snippets:

 

“To Mack, our macroscopic observer, equilibrium is a static affair: a tableau, timeless and unchanging, a still photograph rather than a movie. Except for the occasional fluctuation, which flickers briefly and then disappears, there is nothing to report…”

 

“To Mike, a microscopic observer, equilibrium offers a restless, dynamic picture of infinite variety. Atoms and molecules move this way and that… Some speed up, and some slow down. They smash together an come away with new structures… Microscopic equilibrium is a movie with a cast of zillions, and every frame is different…”

 

“But even as Mike’s fine-grained movie plays on, with one inexhaustibly rich image giving way to another, Mack still sees the same scene frozen in time… with one macroscopic state... Run the tape backward, forward, in random sequence, in whatever way you like – it makes no difference… Meanwhile the microscopic actors work furiously only to have the system stay in place. Atoms and molecules, colliding unceasingly, exchange energy… they vibrate…  interact with fields… reconfigure their electrons… break into bits… react chemically… The give and take of energy never stops, but at equilibrium only the one microstate endures. The microstates partition the total energy in different ways, yet still the equilibrium microstate remains the same.”

 

Mack is amazed by the rich world of interactions that Mike describes. Mack wants to know what is “the special force that guides a system unerringly (almost eerily) to equilibrium and subsequently defends the stable state so stubbornly against small fluctuations.” It’s a mystery to Mack and wants Mike to explain. Mike is confused and says “What mystery? What special force? I see nothing but a lot of little molecules obeying the ordinary laws of mechanics exactly as they should. Believe me, there is nothing unusual going on here.”

 

Maybe not unusual, but something is going on. Munowitz calls it “the law of the land in the Land of the Big, the Many, and the Simple.” It’s statistics. The odds are what leads to the end. But if there’s an end, there’s a beginning. Time moves in one direction, at least that’s our experience as macroscopic organisms. The freedom that leads to equality of distribution drives this process inexorably forward. Entropy reigns supreme over large time scales. Munowitz writes: “Later means a world in which a fixed quantity of global energy has spread to a large number of recipients. Later means a world in which useful energy… has become just a little bit harder to find, a world that has yielded just a little bit more to the relentless pull of statistics.”

 

Today in my statistical thermodynamics class, I waxed poetic about fate and destiny. I derived the equations showing how and why chemists introduce the Gibbs Free Energy. I drew pictures. I grimly talked about the entropy tax that must be paid for any chemical reaction being leveraged to do useful work. I’m not sure if the students shared my rhapsodizing enthusiasm. I’m thinking of assigning them Chapter 10 since Munowitz says it all much better than I do. It’s all about Ends and Odds.