Inorganic Organism

In his book Material World, Ed Conway suggests an analogy modern-man-made physical structures today and a living organism. “If steel provides the skeleton of our world and concrete its flesh then copper is civilisation’s nervous system, the circuitry and cables we never see but couldn’t function without.” And what gives these structures life comes from harnessing the long-dead. Black gold, or “[crude] oil is the food that sustains… it provides us with energy, with the chemicals from which we make the fertilisers that keep [us] alive.” Most of our electricity is generated by pumping out hydrocarbons from the bowels of the Earth, just as we have dug iron, copper, gold and other “precious” metals through mining – creating huge pits in the ground.

 

I learned that the quality of iron is dependent on how much carbon is present. To make ultra strong steel, “too much carbon and the structure of the lattice is easily imperfect, so the metal can easily shatter. Too little and the iron atoms slide over each other without much resistance.” But before modern science understood this, there were protocols and recipes developed by trial and error. The Hittites may have won many battles with their superior weaponry. Conway tells the story of steel through agriculture and improvements made to the plough. Mao’s Great Leap disaster makes an appearance. The steelworks of Azovstal is also discussed, with its history and present woes amid battle with Russia today and with Germany’s Hitler in the past. I also learned that a byproduct of the steelworks was neon which resulted in Ukraine becoming a major producer of this noble gas!

 

It also turns out that since the Manhattan Project and the detonation of nuclear bombs, the atmosphere is contaminated by trace levels of radioactive isotopes. And because making steel requires “spraying oxygen (from the air) into the lava mix”, if you wanted to make something called low-background steel, you could only obtain it from sources pre-1945. Apparently, this is why old sunken battleships are a great source, the Perth (near Jawa) and the Repulse and Prince of Wales off the coast of Malaysia. I also learned that steel is quite recyclable. It’s mostly iron, and you can sort it easily because it’s magnetic. I learned that “more than two-thirds of America’s steel is now made from scrap… old skyscrapers and cars are reconstituted”.

 

The advent of electricity completely changed human life. Copper is a major contributor to this story, and I’m amazed at the ingenuity and perseverance of the scientists and engineers involved. Conway traces the history of mining starting with Cyprus (from where we get the name) to Rio Tinto to Sweden and to the huge hole in the ground in Chuquimata, Chile – “the mine that ate a town”. I was staggered reading the size of the mining operation and had to look up pictures on the internet. I would probably be overawed and aghast if I saw it physically in person with my own eyes. Conway spends some time discussing deep sea mining and polymetallic nodules and the UN Convention on the Law of the Sea. Coincidentally, I had just read about the Philippines and Vietnam’s applications to have its continental shelf extended, amidst squabbles with China over who has rights to what zones. And there’s the brazenness of copper thieves in major metropolitan areas of the U.S. Clearly the industrial hunger for this metal has not abated.

 

In the chapters on oil, Conway discusses the different varieties of crude oil (based on its sulfur content and density), the transition away from coal to oil, and the present transition to natural gas. And while there are many advances in renewable sources, making solar panels or wind turbines or better batteries; all these require energy. Lots of it. I agree with Conway that we will be using these fossil-fuel products for a long time to come, certainly in the near future. Unless perhaps there is a significant shift toward nuclear power. I learned a little about oil refineries (they’re a complex complex!) And Conway discusses the many byproducts of the petrochemical industry and the ubiquity of plastics. Inorganic materials give you a lot to play with, but organic materials open up the toolbox to make pretty much anything you can imagine.

 

Conway’s book is a great reminder that our way of life and technology sits upon the bedrock of a physical material world. And although the ethereal world of the Internet beckons for our attention, none of it can be sustained without the physical. If not for steel, copper, fibreglass, or plastics, we wouldn’t have the cloud services and apps and devices that we glue our eyes on. One wonders if we’ve become willing slaves to the feeding of a huge inorganic-organic structure known as the modern way of life with its air-conditioned server rooms filled with blinking lights and computer chips. Artificial intelligence, we call it. Let’s hope it doesn’t subvert our intelligence any further. Because it has a limitless appetite and we will keep digging the materials out of the ground to feed it.

Tech Tree

In the 1980s, I discovered Civilization, the boardgame (Avalon Hill), and saved up enough money to buy the game. I had always been enamored reading about ancient civilizations, but to be able to rule one of them and decide its fate was a revelation! You had to manage the economics of trade and war, keep your citizens fed, make alliances, undermine your enemies, and gloriously advance in the technology tree. It was probably my first encounter with the tech tree in a game and I loved it!

 

I still have my old copy of Civilization. It has sat unplayed in a box for some three decades or more. (I also have a pristine copy of its expansion, Advanced Civilization, that I snagged from a game store going out of business in the early 2000s. Computer and video games were ascendant; board games were only just beginning their rebirth.) But the problem with Civilization, the boardgame, is that to truly shine you needed to find six other players willing to spend 10+ hours to play what seems like an archaic boardgame. I’ve since played many other 2-4 hour games with decent tech trees (such as Through the Ages), but they don’t quite have that same heft as their progenitor.

 

Civilization the boardgame was also the inspiration for Sid Meier’s Civilization, the computer game. I was no longer playing computer games in the 1990s, partly because I didn’t own a computer (laptop or desktop) until I started my job as a faculty member and I certainly wasn’t going to use my office desktop to play games. When my brother gave me his old ThinkPad, it had Civilization installed. I enjoyed several games at the easy Chieftain and Warlord levels. But because I didn’t have the manual, I didn’t know how the tech tree worked, and I had no focused strategy. I built up my cities, warred with neighbors, and advanced higgledy-piggledy through the tech tree, choosing what I think sounded good at the time. I didn’t understand how the scores were calculated, and I never changed my tax rate. It was somewhat fun to win at the lower level, although my winning percentages were never very high. After a few losses at a higher level, I gave up.

 

Fast-forward twenty-five years. I am rediscovering old computer games that are free to download and run on an emulator. I still can’t find six other human players willing to devote gobs of time to a Civilization boardgame. I decide to read the Civilization manual and look at the tech tree for the first time. I was hooked. With fresh eyes, the game looked much more interesting and I learned many things I didn’t know and mostly didn’t remember. Time to give it a whirl.

 

I romped through my first game at Chieftain level. Then I proceeded to win a couple of games at Warlord level, with higher percentages, but still not great. Then I moved on to Prince level, and then realized that I could get much higher scores by focusing on conquering the world as soon as possible. I always played with seven civilizations so it takes a while to find them all and do this. But how could I do this as efficiently as possible? I started to realize for the first time, that the strategy is not to advance too far in the tech tree. I needed to quickly get The Wheel to build chariots, Mathematics to build catapults, Writing to build diplomats, and Navigation to build sailing ships. At higher levels, I needed to build temples to keep my populace content while I built up a massive army. Previously I always prioritized Pottery to build a granary (just like I would in the boardgame).

 

At King level, I started to break the 100% rating. In my third game, as the French, and being fortunate to start with two settler units, I was able to remain as a Despot and conquer the world in 580 A.D. for a final score of 1642 and a rating of 131%. The only problem was that I mostly ignored the tech tree. Could I get a higher rating by shifting to science and focusing on Future Technologies? Since I had saved the game just before my military victory, I decided to resume at that point without conquering the hapless Babylonians who were down to their last city on a small island, and I had their city surrounded by diplomats. I switched to prioritizing science, switched governments to a Democracy, built the largest spaceship possible, but the plan was not to launch it but march through Future Technologies until close to the end-year before sending out my spaceship. It was really, really boring. I was essentially building and selling Courthouses and SDI Defense systems almost every turn. I finally caved and launched my spaceship, finishing the game in 1885 A.D. with a final score of 2293 and a rating of 183%.

 

It was time to try Emperor level. I was unable to finish the first game because of a glitch in the game where even though I conquered all the civilizations, the game didn’t end because a civilization likely got destroyed before it built its first city. I discovered this glitch in an earlier Prince-level game. Yes, I could have gone for the highest score ever with a future technology approach, but it would be too boring. Instead I played a second game, and as the Chinese, I was able to win in 1340 A.D. with a final score of 1532 and a rating of 153%. Wiser than Solomon apparently. But the game itself was a grind. The joy of the tech tree had been lost, and while I enjoyed being extremely efficient in having lots of small cities to keep up production, it became less interesting. I don’t feel attracted to trying the sequels to Sid Meier’s original Civilization. I’m an old-school computer gamer used to simple blocky graphics and not too many options. Maybe I’ll find something that’s in my sweet spot, and at least Sid Meier’s original scratched the itch of not having played the boardgame in a long, long time. But I do miss the tech tree!

Purifying Sand

There are many grades of sand. I’m learning this from Ed Conway’s Material World where sand is the first of “the six raw materials that shape modern civilization”. The story begins with glass. Pliny the Elder claims it was the Phoenician sailors and traders who, in the evening, “lit a fire on the beach, and in the absence of anywhere else to rest their pots, they perched them on some of the natron blocks”. Natron is rich in sodium carbonate, and combined with seashore sand and high temperatures, makes glass. Or at least a type of glass. There are many different types.

 

Glass is mostly silicon dioxide (SiO₂), commonly known as silica. But it has a very high melting point, and will only melt in a simple open furnace if impurities such as sodium are present, because these impurities lower the melting point – as my G-Chem students have learned. But this also affects the quality and type of glass produced. Now if you can find sand that is over 95% silica, you can make useful stuff such as water filters, or you can make “the very clearest, finest glass”. There are some specific locations around the world, and Conway discusses a visit to Scotland to a rock mine with 99% pure silica. Conway then tells a fascinating story about the importance of field glasses (binoculars) requiring really high-quality glass and the key role they played in the first world war. Call it the early tech information support that is crucial! Nowadays we use satellites and drones.

 

Concrete is the second product of sand that Conway discusses. I had previously read about the Roman aqueducts and the discovery of Portland cement so much of this chapter was familiar. But Conway also discusses land reclamation projects all over the world, and I was staggered by how much earth has been moved both to make concrete for buildings, and to make new ground where there once was sea to place such buildings. I learned about governments playing cat-and-mouse with “sand mafia” gangs who would perform bloody murder to keep their illegal trade going. Conway also discusses new concrete-like materials that have a lower carbon footprint. Some are based on hemp. Some on graphene. And there’s even one designed to absorb carbon dioxide over time.

 

Most eye-opening to me was the production of ultra-pure silicon. It needs to be 99.9999999% pure to be nanocrystal-grade. You need it for your latest and greatest computer chips that are powering the A.I. revolution. Conway traces the supply chain, from raw materials, to multiple factory-industrial stages, before you get those Nvidia or AMD branded ones that are in high demand. The manufacturing process is so demanding that I was in awe of everything that has to go right when so many things that can go wrong. And these companies in the supply chain have perfected the techniques for mass production. They are all over the world and except for TSMC and ASML that have been in the news recently, I hadn’t heard of the many others that Conway listed. All of them are crucial cogs and the supply could easily be cut off. Scary, now that we’re so dependent on computer chips in everything.

 

Reading Material World reminded me of how I’d like to re-theme my G-Chem class to focus on materials. I haven’t figured out exactly how to do that yet, but I have some fresh ideas to chew on. Up next in my reading: Salt.

Scent of Death

Chemists think about poisons. And students seem to perk up when I mention examples of such substances in class. I enjoyed learning more about them by reading Most Delicious Poison, written by evolutionary biologist Noah Whiteman. There is significant overlap to the book I just read about flavor molecules since they are secondary metabolites produced by plants. Just like many poisons! Whiteman’s book is a little more dense, but just as interesting. Today’s post features Chapter 6, “Abiding Alkaloids”. It begins with the scent of death.

 

When an organism dies, it’s a feast for microbes acting as decomposers. Many of the compounds released that your nose knows are amines – they have nitrogen in them. Cadaverine and putrescine are two examples that you’d guess are stinky. Skatole is a less obvious name, but it has the odor of feces at higher concentrations, and oddly has a flowery smell (including jasmine) at low concentrations. A perfume that has an intoxicating smell? Whiteman reminded me about the root word ‘toxic’. To be intoxicated used to mean that you got poisoned. Now it means you’re drunk or high.

 

Since nitrogenous compounds are alkaline, these compounds are also called alkaloids. I was surprised to learn that “our (living) bodies produce endogenous cadaverine, putrescine, and spermidine because these molecules serve critical roles in our cells. Spermidine is particularly interesting. Adding it to the diets of laboratory animals extended their life spans by 15 to 30 percent. In human cells bathed in spermidine, aging also slowed… One effect of spermidine is that it helps keep our genes switched off. As cells age, more and more genes get turned on willy-nilly… Spermidine may also enhance the removal of damaged cells, including those containing beta-amyloid plaques…”

 

Whiteman goes on to discuss the co-evolution of plants and insects and the role of specific secondary metabolites that act as signals and poisons. Plants evolve defense mechanisms against hungry insects. The insects evolve resistance to those poisons. Stinky plants such as the famous corpse flower trick specific insects to visit and in doing so help to distribute pollen. This is how niches develop. Whiteman believes this is why “there are so many toxic plants and toxin-specialized herbivores… the chemical war of nature… has also given rise to much of the pharmacopeia that we use and abuse.”

 

Skatole is an example of an indole. Related molecules with an indole chemical skeleton include a range of mind-altering drugs. Whiteman discusses DMT (N,N-dimethyltryptamine) found in a variety of tropical plants, and psilocybin found in magic mushrooms. Interestingly, our neurotransmitters have similar chemical structures. Serotonin looks very much like psilocin. Lysergic acid or LSD is also an indole, albeit a more complicated looking one with four fused rings. I also learned that “when a chain of psilocin molecules become bonded to one another… [they] act much like tannins which also turn blue when oxidized.” It reminded me about the quest to find inks and paint pigments!

 

I can’t help but also mention tubocurarine, the poison known as curare, which also has quite the complicated chemical structure. By the way, there are beautiful illustrations of plants paired with the chemical structures of molecules in this book. Indigenous hunters in the tropics tipped their arrows or blow-darts with curare. It’s a silent and effective killer, paralyzing the prey by blocking the activity of the neurotransmitter acetylcholine. (Once upon a time, I studied the enzyme responsible for breaking down acetylcholine.) Tubocurarine, I learned, was also “the first muscle relaxant used in general anesthesia”. Whiteman discusses this alongside cocaine and other drugs from plants with names such as mandrake, devil’s snare, moonflower, in Chapter 8, “Devil’s Breath and Silent Death”.

 

There’s so much more I could discuss from this book. Instead I’ll end by saying that if I ever teach a medicinal chemistry class (a doubtful prospect given I’m not an organic chemist), I will be drawing inspiration from Most Delicious Poison. I particularly enjoyed the later chapters on “The Herbivore’s Dilemma” and “The Spice of Life” (which discusses flavors) but I encourage you to read Whiteman’s book if any of this interests you!

All About Flavor

Do you enjoy spicy food? Where do all those spices come from? I grew up in the tropics where a smorgasbord of spices is abundant in many of my favorite dishes. Warmer temperatures, lots of rain, and lots of sun, are great for growing flora. Competition is fierce for nutrients and energy – it’s literally a jungle out there!

 

Spices were so desired and so valuable that the Western powers fought their way to establish overseas colonies so they could control the spice trade. They left devastation in their wake, not just to the people and economies of those countries, but to the very nature of food. The story of flavor in our food is enigmatically told by Mark Schatzker in The Dorito Effect. Reading it makes me long for the old days where maybe vegetables, meat, and fruit, was tastier and more flavorful. But I might be misremembering and over-romanticizing.

 

The monstrous agricultural industry, with its focus on mass production and efficiency, has essentially made food blander. In the supermarket, the chickens or tomatoes are larger and plumper, but at a cost of flavor. What do we do? We mask it in spices, sauces, and other strong flavors. I haven’t eaten plain chicken breast meat in ages; it’s tasteless. And with the increasing convenience of spice pastes and mixes, we now flavor our food with molecules that fool us into thinking our food is tasty, without the accompanying nutrition that would have come without including the source ingredients.

 

Schatzker discusses the thesis that our bodies know what is good for us, at least in the distant old days before the agricultural revolution. We still observe this in animal behavior, where they may choose to eat different foods depending on what nutrients they may be short of in their diet. Scientists can trick those animals with flavoring molecules – that’s how we get chickens to be so plump and put on weight quickly. Without the sleight of taste, the chickens would stop eating the quick-fattening food after a while, as their bodies tell their taste buds they are missing something! We’re doing the same thing to ourselves.

 

The flavors of food come from secondary metabolites. Primary metabolism refers to the core processes of interconverting energy and biomass. Those are the chemical pathways I study in the origin of life. But the more I look at secondary metabolism, the more fascinating it seems. In flora, the chemical molecules may be related to smell, taste and flavor as a whole. Fruity odors are attractive to fauna that may help disperse seeds or their equivalent. Bitter tastes tell pests to stay away from the poison. It’s the dose that makes the poison, and relatively large organisms such as ourselves will happily consume these bitter tastes for medicine, or for the buzz it gives us in caffeine or cocaine. And now food chemists, by extracting or synthesizing flavor molecules, have messed up our habitual pathways honed by evolution.

 

Schatzker discusses the “flavor problem” in the following way: “For half a century, we’ve been making the stuff people should eat – fruits, vegetables, whole grains, unprocessed meats – incrementally less delicious. Meanwhile, we’ve been making the food people shouldn’t eat – chips, fast food, soft drinks, crackers – taste ever more exciting.” Here are his three “Rules of Flavor”:

 

1.     Humans are flavor-seeking animals. The pleasure provided by food, which we experience as flavor, is so powerful, that only the most strong willed among us can resist it.

2.     In nature, there is an intimate connection between flavor and nutrition.

3.     Synthetic flavor technology not only breaks that connection, it also confounds it.

 

What can we do? Evolution is not going to help us veer from Rule #1 anytime soon, because that’s a long and slow process of adaptation. Rule #3 has been so co-opted by the food and beverage industry that it’s unclear what can or will be done when profits and costs and competition rule. We’ve been doing Rule #2 to spice up our bland mass-produced food. Can food scientists pivot to growing food or producing livestock that is both tasty and nutritious? Schatzker seems to think so and provides a few examples of people doing so, but they’re in the minority, and the cost is high. My suspicion is that the divide between the have and have-nots will continue to increase and those that can pay for more nutritious food will do so, while the masses will continue to suffer from a host of increasing health issues.

 

Reading The Dorito Effect was both depressing and enlightening at the same time. I’m depressed by the state of food and nutrition in the twenty-first century. As someone increasingly interested in biochemistry, I was enlightened by the complex relationships between flora, fauna, biological niches, ecology, and how that plays out in the variety of secondary metabolites being released by plants – such amazing organisms! I feel there is so much more to learn and I’m just barely picking at the surface.