Quantal Mysteries

I feel comfortable imagining atoms, the quantal units of matter. But I’m not sure how to think about photons, the quantal units of light. Things get stranger when quanta of light interact with quanta of matter. As Feynman says (in his famous QED): “Reflection and transmission are really the result of an electron picking up a photon, ‘scratching its head’ so to speak, and emitting a photon.”

 

This quote opens Chapter 6 of Sonke Johnsen’s Optics of Life. The opening paragraph is precious! “Light does not bend in a lens, it doesn’t bounce of the surface of glass, and it doesn’t spread out after passing through a small hole. It doesn’t even travel in a straight line. The happiest day of my scientific life came when I read Feynman’s QED and learned that refraction, reflection, and diffraction – things I had known since fifth grade – were all lies. More accurately, they were illusions. It appears that light bends, bounces, and spreads out. The illusion is so good that you can base solid mathematical predictions on them, but carefully thought and further experiments show that more is going on… They come from the fact that photons interact with one another in an unusual way. The interaction is often referred to as wave interference because it can be described mathematically much like the interference of water waves, but the reality of it is considered stranger.”

 

Johnsen will circle back to this strangeness in the final chapter of his book; but meanwhile he carefully goes through why we seem to observe light traveling in straight lines, and then bending, bouncing, or spreading out, under the appropriate conditions. I’ll say this. I wish I learned a bit more optics in high school physics (having never taken a physics college class). But it’s unlikely that learning it in school would have come with the interesting biological examples that Johnsen provides. So, if you ever wanted to learn some of these things, Johnsen’s book might at least be motivating. He tries to scale down the math to give you an intuitive feel for what’s going on. But some math is unavoidable, and for good reason: It’s dastardly useful.

 

In my P-Chem quantum chemistry course (and briefly without equations in G-Chem), I discuss the strangeness of the experiment where electrons are fired at a two-slit grating creating an interference pattern. We think of electrons as tiny particles (but not as waves) and therefore imagine we’re shooting tiny bullets through our electron-gun (or cathode ray tube, as found in old computer monitors and TVs). Maybe we’re firing them too fast and they’re bouncing off each other and thus “interfering”. But if we slow down the rate of firing electrons to essentially one at a time, we still get the build-up of the interference pattern (that you’d see if using light waves). This is very odd. Does a single electron go through both slits at once and interfere with itself somehow? Now, if we try to figure out which slit the electron is “passing through” by using a detector, the interference pattern disappears and the electrons “behave” like little bullets being shot out of a gun. Take away the detector and the interference pattern re-establishes. It’s all very mysterious! Students get a kick out of hearing this story – with no clear resolution other than making the point that the act of observation can screw up the experiment.

 

Light, on the other hand, is essentially treated as a wave, except when it interacts with matter. This is exemplified by the photoelectric effect, which I go through in great detail in G-Chem – although I’m convinced most of the students still don’t “get” it. Maybe it’s not their fault. This idea of light acting as quantal packets or photons is rather mysterious. And those equations in optics where light is treated as a wave are so much easier to work with, and the equations have awesome predictive power. The math always works out when you consider light to be a wave: it bends, bounces, and spreads out exactly the way we observe in nature. Johnsen considers the possibility that perhaps “photons are not a useful or accurate way to describe light” and he used the wave-related equations throughout the book. They work, and they work well! Using photons is “messier and far less intuitive”.

 

But since the interaction of light with matter is what chemists (and biologists) care about, where we observed quantal changes, we have to think about photons. Johnsen provides a memorable framework to think about this: “A sensitive light meter will record individual events, leading us to think of photons as insects flying into a bug zapper. However, just because something interacts with matter in a quantal fashion doesn’t mean that the thing itself is packaged in discrete units. Suppose you shake a crib with a sleeping baby. If you shake it hard, the baby always wakes up. However, if you shake it gently, the baby might wake up. The waking up itself is a quantal event – the baby is either awake or asleep – but the probability of this happening depends on how hard you rock. As a child, I remember a similar process working at the dinner table with my little brother. Kick him lightly under the table long enough and he would eventually blow his stack. You never knew quite when, though.”

 

Another reason why I’ve been thinking about the quantal nature of light is when I consider energy transduction and the second law of thermodynamics in the context of the biosphere. Ignoring the small amount of geothermal energy as a source for the moment, the vast majority of life on Earth is directly or indirectly supported by energy influx from the sun. I tell my students that these photons are high-quality energy, especially if they’re higher frequency and shorter wavelength. Ultra-violet and blue light are certainly high energy photons compared to red and infra-red. We typically treat infra-red and “heat” synonymously. I tell my students that “heat” is crappy low-quality energy. Technically, I will be more careful and say “thermal energy” rather than heat. Thermal energy is the kinetic energy of particles due to random motion, and as such, isn’t useful unless it can be directed in some way (which in itself will require some other energy source).

 

What does this have to do with the biosphere? Essentially, life absorbs a smaller number of high-energy photons (“light”), and then releases a larger number of low-energy photons (“heat”). Thus, entropy, if you were counting photons, increases in line with the second law of thermodynamics. (The Earth-Sun dyad can mostly be treated as almost a closed thermodynamic system.) Molecules and their electrons interact with photons. The photons are picked up, something is done, and photons are released. Sometimes the photons released seem to have the same energy as the original impinging ones. Sometimes they don’t. Usually the photons emitted are lower energy and larger in number, and they eventually dissipate into the coldness of space along a temperature gradient. Thus, the quantal nature of light, in obedience to the second law of thermodynamics, allows beautiful myriad structures to form, at least on Goldilocks-planet Earth.

Four Material Pillars

Do you want to know How the World Really Works? It’s the title of Vaclav Smil’s latest book. Unlike his previous tome that I read, this book is a brisk read. Each of the seven chapters begins with the word “Understanding…” and the seven things we should understand are (1) energy, (2) food production, (3) our material world, (4) globalization, (5) risks, (6) the environment, and (7) the future. Today’s blog post focuses on #3, subtitled “The Four Pillars of Modern Civilization”.

 

Smil grounds his data analysis in quantifying energy; I find this particularly appealing as a physical chemist. While most of the twitter and chatter of our modern world focuses on the internet-web-cloud that is based on silicon, Smil argues (convincingly) that this isn’t a crucial pillar. As physical beings, with physical needs (food being foremost!), what has built modern human society are the following four pillars (in alphabetical order): ammonia, cement, plastics, steel.

 

Ammonia feeds the world. Smil’s analysis shows that without synthetic ammonia for fertilizer, we would not be able to feed half the present world’s population of 8 billion people. Globally there is actually a surplus of food, but it is not distributed equally. Rich countries waste food, poor countries need more of it. Why is ammonia crucial? Because we need nitrogen, a key component in proteins and nucleic acids. There’s plenty of nitrogen in our atmosphere in the form of N₂ gas. But most living things can’t use it because of the very strong triple bond between the nitrogen atoms that make N₂ an inert gas. Some bacteria can “fix” this nitrogen, but only in a limited number of crops, mostly legumes. Manure or wood ash also provide nitrogen, but you’ll need heaps of it to cultivate crops on a large scale.

 

Enter the Haber process: N₂ + 3 H₂ à 2 NH₃ (ammonia). Students in chemistry classes see this example repeatedly because it’s useful for exercises in stoichiometry and equilibria, and discussing catalysis. 80% of ammonia produced is used for fertilizer, but ammonia is a gas, so spraying the gas on your field does you no good. Solubilizing it in water can work, but there’s also an issue with runoff. The dominant useful form is as solid urea, although ammonium salts are also used. The tough part about making ammonia: What’s your source of H₂? Right now it’s natural gas in the steam-methane reforming process. That’s an energy-intensive process, so we’re not weaning ourselves off hydrocarbon fuels anytime soon.

 

Concrete has gotten attention recently because it is a significant contributor to rising CO₂ levels in the atmosphere. Why? You need high temperatures and fuel to make it. And we make lots of it – billions of tons per year. It’s a bedrock of construction. Not just for tall urban buildings but for large sewer pipes, subway foundations, airport runways, bridges, sidewalks. You need something that’s strong, durable, and relatively cheap to make from sand, rock, and water? Concrete is what you want. The Pantheon in Rome, constructed two thousand years ago, still stands today. The “Roman cement” was made using gypsum (mostly CaSO₄), quicklime (mostly CaO), and volcanic sand (mostly SiO₂).

 

Plastic is amazing. While we easily identify its presence in plastic bags and Tupperware, the range of plastics we utilize today is staggering. It’s lightweight, durable, and can easily be shaped and tuned to whatever properties you need! Pipes, fabrics, plexiglass, rubber, insulation, packaging foam, adhesives, optical lenses, liquid crystal polymers, Kevlar, upholstery, the keys on your laptop, hospital feeding/IV tubes, toys, office supplies, and your credit card. Where do plastics come from? Petroleum materials, hydrocarbons, fossil fuels. I’m not sure much of modern society can live without plastic; it would be a very hard transition into a plastic-less world.

 

Steel is a partner to concrete in many of our large-scale engineering wonders today, but it is also used ubiquitously in smaller items: tools, cutlery, pots and pans, small appliances, ground-based vehicles, cargo containers, and most unfortunately, weapons. Steel is mostly iron, with some carbon and silicon, but as you can imagine, is also energy-intensive to make. We’re also making billions of tons. And yes, it’s also contributing to the rising CO₂ levels in our atmosphere.

 

You can sense a trend here. With climate change politics focusing on CO₂ levels and fossil fuel use, and the search for alternative “renewable” energy resources, carbon has gotten a bad rap. Smil makes the argument that we aren’t going to move away from hydrocarbons anytime soon, certainly not in a very big way, because it is underpinned by energy usage. Electrifying vehicles and making/recharging batteries is also energy-intensive and that energy has to come from somewhere. There’s no free lunch. Not to mention that you need physical materials to power the virtual world run on electricity. This is sobering but true. I know I personally would not want to go back and live in pre-industrial times. Unless you were a monarch or a rich nobleperson, life was subsistence and probably quite miserable – although you might not realize it if a subsistence life is all you ever know and you never see anyone in a different situation. Not to mention, there’s no way to support billions of humans on the planet. For both good and ill, we have transformed our world with modern materials and there’s no turning back.

Blue Planet

This past month, I’ve been watching BBC’s Blue Planet and Blue Planet II. As the narrator David Attenborough reminds his viewers, we know more about the surface of the moon and possibly Mars than about the seabed on our own planet. I’m amazed by the diversity of aquatic life, but perhaps this should not be so surprising if life on Earth began and evolved first in the waters before venturing on to dry land. I was also amazed at how underwater filming technology had progressed by the sharpness of the images in Blue Planet II. It wasn’t just more of the same, it was spectacular.

 

Overall, I had the same feeling as when I watched Planet Earth and Planet Earth II. If I had encountered these documentaries earlier in my life, I might have become a biologist or an ecologist. And because I’ve also been reading The Optics of Life, it made me think about an interdisciplinary elective class I could put together on the interaction of life and matter – underwater! I don’t know what I’m thinking; I can’t even scuba-dive and going to the beach or into the ocean doesn’t hold any interest for me. But I do know about photons and electrons and the idiosyncracies of the chemical world.

 

Why have the deep seas and oceans remained mostly unexplored? I don’t know. The cost can’t be higher than for space exploration. There’s so much of interest that’s alive and kicking; and the Blue Planet documentaries highlight how life is stranger than fiction. I had some notion that many creatures are purposeful and intelligent, but seeing the intricate web of behaviors was astounding. I’m thankful to the patient camera operators who must have spent hour after hour getting footage that could be edited into an engaging story. Real life is stranger than fiction.

 

My favorite episode is “The Deep”, #2 on Blue Planet II. Given my interests in the chemical origins of life, it was cool to see the sharp images of life in hydrothermal vents. I’d seen some online videos and Blue Planet does show some of these, but the images in “The Deep” wowed me. I’m also happy that they had footage of Lost City, an example of alkaline hydrothermal vent with conditions that might have been suitable as the cradle of life. I’d known about methane bubbles from the ocean floor, but I found the footage especially striking. Wow!

 

I briefly lamented being a theorist rather than an experimentalist, although I know I’m well-suited to being a computational scientist rather than one who works in a wet lab or out in the field. Johnsen’s penultimate chapter in The Optics of Life reminded me that there’s no substitute for experience if you’re a field scientist. You might know gobs of theory but if you don’t have practical experience, your experiments and measurements could just as well turn out to be useless junk. As a theorist, I am good at some things, but I’m glad that I’m also surrounded by colleagues who have experimental expertise. I suppose I do have some practical experience as a chemistry instructor. I know where the tricky parts are and I do have an arsenal of approaches to help students understand the material. And I guess I’m satisfied with being an armchair viewer of the beauty of life in the oceans.

Prout's Hypothesis

Alchemy became a bad word. Alchemists were recast as frauds, charlatans, and tricksters, claiming to tell you the secret to unlimited wealth and health – for suitable payment. History is glossed over and framed from the point of view of the winners – the modern chemists. We do real chemistry! The dark magic of alchemy is merely an illusion that dissolves in the light of true science.

 

But reality is much more complicated. In his 2014 Dibner Library Lecture, Lawrence Principe tells a surprising story, not known to most chemists. The lecture is titled “Alchemy and Chemistry: Breaking Up and Making Up (Again and Again)”. Principe is both a chemist and a historian. He’s written the landmark book about the history of alchemy. And in my last blog post, I discussed his investigation into the phosphorescence of the Bologna Stone. Having read a number of his works, I thought I was well versed in the (hi)story of alchemy, but I gained some new insights from reading the text of his Dibner lecture.

 

I had thought that alchemy essentially died when modern chemistry was ushered in by Lavoisier and his contemporaries towards the end of the 18^th century. But I was wrong. Alchemy’s name had been sullied, but it was still alive and kicking, biding its time quietly. The new reigning paradigm was that once you distilled substances to their most fundamental, these “elements” were fundamental. You couldn’t transmute or change one element to another. But in the 19^th century there came three new developments that questioned whether indeed elements were immutable.

 

The first of these, thanks to Lavoisier’s insistence of very careful measurements of atomic weights, was the following observation (in Principe’s words): “the atomic weights of nearly every known element, about fifty at that time, turned out to be integral multiples of the weight of the lightest element, hydrogen. Carbon weighed exactly six hydrogens – oxygen eight, sulphur sixteen. There was no reason to expect this striking regularity… This strange outcome led William Prout (1785-1850) to propose in 1817 that all the known elements were actually condensations of hydrogen, such that hydrogen was the unique material building block of everything.”

 

Determining the fundamental building block of all matter was an old philosopher’s trade going back to the sixth century BCE. Thales thought it was water. Anaximenes thought it was air. Heraclitus thought it was fire. Xenophanes thought it was earth. Empedocles brought them together as the Four Elements theory, later championed by Aristotle, and it was a fundamental building block for the early alchemists. I tell this story on the first day of class before moving on to Lavoisier and Dalton (he of atomic theory fame). I’ve known about Prout’s hypothesis, but hadn’t figured out how to discuss it effectively in class; I used it once (but students just seemed puzzled) a number of years ago but have since left it out. I have written about pantogen.

 

Prout’s hypothesis had its detractors and supporters. Berzelius, who was integral to transforming the alchemical mess of elemental symbols into the standard ones we use today, was against the hypothesis. Berzelius argued that some elements, notably chlorine and copper, had masses that could not be a multiple of hydrogen. (A quick look at the periodic table will show you that most of the elements have atomic masses close to an integer value, but there are some exceptions, including chlorine and copper.) Dumas, on the other hand, was a supporter of the hypothesis because of the discovery of isomerism. As Principe says: “Isomerism implied that some unsuspected internal arrangement of their common components determined the properties of these substances, rather than merely the kind and number of atoms they contained. A similar dependence of properties on internal structure rather than on composition appeared in the phenomenon of polymorphism…”

 

The third observation came from the “radical theory” of organic chemistry. A notable example is ammonium (shown to contain one nitrogen and four hydrogens) which moved as a cluster (“radical”) or a unit. In particular, ammonium could substitute for the metal in a salt. Principe explains that this was “a type of substitution reaction that had long been recognized to occur among various metals, but only among metals. The implication was that ammonium was itself a metal composed of two nonmetals… that metals could be compounds after all, just so tightly bound that the means of decomposing them had simply not yet been found.”

 

Threading through Principe’s lecture is the story of an individual I had never heard of: Cyprien-Theodore Tiffereau (1819-1909), later known as “the alchemist of the 19^th century”. Alchemy wasn’t dead, but it had gone underground. Principe argues that, in France, shortly after its premier scientific academy was founded, political figures and administrators forbade members of the academy from studying the transmutation of metals, characterizing such activity as both futile and fraudulent. However, according to Principe: “The Academie’s chymists, however, acted the way all academics should towards administrators. They ignore them.” Principe provides several examples leading up to the late 18^th century when alchemy peters out with the theories of Lavoisier and Dalton.

 

Tiffereau is an interesting character. He goes to Mexico to learn more about making daguerreotypes (forerunners to photography), but what’s he’s really interested in is metals and their ores, and the possibility of transmutation. Principe writes that in 1846, “he achieved a result that would inspire (or haunt) him for the rest of his days. After exposing nitric acid to strong sunlight for several days, he poured it over filings of a silver-copper alloy and left the mixture in the sun. A portion of the filings dissolved. He then boiled the mixture to dryness and added more acid. Upon repetitions of the process, the initially greenish-black residue grew increasingly lighter in color, and finally turned a brilliant metallic yellow. His tests (and those done by others later) showed the yellow material to be gold.” He was successful three times. The ores he obtained came from mining operations where gold was also found. Tiffereau’s explanation builds off Prout’s hypothesis: He thinks that copper is converted to silver by incorporating oxygen, and then in turn, the silver is converted into gold. Nitric acid acts as an oxidizer.

 

The Mexican-American war forces Tiffereau to return to France. But he is not able to replicate his experiments, and he beseeches the Academie for funds (and help) to do so. And thanks to the work of Dumas, they seemed at least open to the possibility, although ultimately no help was forthcoming. Tiffereau thought the problem might be the weaker sunlight in France compared to Mexico. A similar argument was made by John William Draper (who became the first president of the American Chemical Society). Draper made a claim that he had succeeded in converting silver into something with similar properties to gold when he did his experiments in America, but they failed in the weaker sunlight of England. These arguments might sound spurious to us today, but I’m now more circumspect given that the difference in light can lead to very significant differences in the wide world of biology that I’ve been learning from The Optics of Life.

 

By the late 19^th century, alchemy and the transmutation of metals had fallen out of favor again. Principe argues that this was because “the occultist revival and its radical interpretation of alchemy… had now made the subject more distasteful, even embarrassing, to scientists. Many occultists set themselves in explicit opposition to the scientific establishment, decrying chemistry as mechanical and lifeless and chemists as blind… In the context of the occult revival, it was now alchemy’s turn to spurn chemistry.” Meanwhile, Tiffereau shoulders on, now thinking that the missing link could be the (recently discovered) nitrogen-fixing bacteria present in the soil and the ore. He called them “mineral microbes”.

 

But in the 20^th century, the twin discoveries of radioactivity and the internal structure of the atom would revive transmutation. With more modern apparatus that could alter the composition of the atomic nucleus (usually with neutron bombardment), scientists would successfully convert platinum or mercury into gold. (Platinum and mercury are the left and right neighbors of gold on the periodic table.) Chemistry classes all over the world now teach that elements are uniquely defined by the number of protons in the nucleus (known as the atomic number). Hydrogen’s atomic number is 1 and its most common isotope only has a single proton in its nucleus. In a way, one might say Prout’s hypothesis has been revived – different elements can be formed by adding protons or hydrogen nuclei. However, the energies required to effect this transformation are huge, and most of what we call chemistry – involving the movement and transfer of valence electrons far outside the nucleus – takes place at more accessible lower energies.

 

Principe says in his conclusion: “The successive making-up and breaking-up of alchemy and chemistry underscores the commonality of goals and practices expressed by the word chymistry when speaking of the early modern period. The desire to understand and control matter and its transformations lies at the heart of both alchemy and chemistry… The story also underscores how difficult it really has been (and remains) to understand the microstructure – indeed the very nature itself – of matter, a realm forever beyond the limits of human sense perception.”

 

This blog post is just a small excerpt from a wealth of interesting information provided by Principe in its lecture. Do an internet search and read it in full for yourself!

Bologna Stone

Today, if you encountered a glowing rock, you are likely not to touch it with your bare hand. Who knows what it might do to your flesh? It might be radioactive. It might be an egg of a dangerous alien species, ready to emerge and gruesomely kill you. Modern science and sci-fi have conditioned our response to be cautious about glowing rocks. But you’d still be curious about it. Very curious. You might contact NASA – maybe it fell from the sky? Or perhaps a scientist at the local university? All this assumes you’ve taken pictures and video with your smartphone, all at arm’s length, to document your find!

 

Back in 1602, a cobbler found that certain stones, after being roasted in a furnace, could glow in the dark. These stones only came from a specific location: along the slopes of Monte Paderno near the city of Bologna, Italy. These stones were phosphorescent; they absorb light, and then emit light for some period of time before the effect fades away. (Not to be confused with fluorescence which is closely related, but the light emission is much quicker and is not persistent. Also not to be confused with chemiluminescence where chemical energy is converted into light emission.) This became known as the Bologna stone. It only worked with the stones from this particular region.

 

I learned about the Bologna stone reading Peter Wothers’ book on the origin of element names in today’s Periodic Table. The cobbler, Vincenzio Cascariolo, who discovered the stones’ phosphorescence didn’t know anything about its chemistry. He called it spongia solis, meaning ‘sponge of the sun’, thinking that the stone soaked up the rays of the sun akin to a sponge. The famous scholar and polymath Athanasius Kircher thought that “the stone was a kind of magnet acting on light in the same way that an ordinary magnet acts on pieces of iron.” Turns out that moonlight can also be sponged up by the Bologna stone, and it became known by many names including lapis phosphorus, meaning ‘the stone that carries light’.

 

It turns out that the Bologna stone has no phosphorus. To learn more about the history and chemistry, I read Lawrence Principe’s article, “Chymical Exotica in the Seventeenth Century, or, How to Make the Bologna Stone” (Ambix 2016, 63, 118-144). Principe has also written a superb book on the history of alchemy that is now on my bookshelf, one of the rare instances where I buy the book after reading a copy from the library.  In the Ambix article, Principe details the investigations of Wilhelm Homberg on the Bologna Stone. But Principe isn’t just an armchair historian, and he goes through the process of trying to reproduce the lost art of making these stones phosphorescent. In the process, he discovers that it’s not just the particular type of ore (chemically-speaking) that you begin with, but impurities present in the preparation can enhance or inhibit the phosphorescence.

 

The story takes many twists and turns. To acquire his vast expertise in these ‘chymical exotica’, Homberg trades in chemical secrets. I’ll tell you a secret preparation that I know if you tell me one that you know. No one outside of Bologna could prepare these stones, so Homberg travels there and learns. Eventually the methods were published, but they were hard to reproduce. One might suspect that perhaps a crucial step or ingredient was purposefully left out in the published procedure to maintain the value of the secret, but this does not seem to be the case. Homberg himself was very confused when after being successful in Italy, he was unable to reproduce the effect in Paris where he now had a prestigious position in the Academie Royale des Sciences. After failing over and over again, and trying to avoid his imploring fans and colleagues to show them the process, he stumbled upon success in a fascinating tale that Principe elaborates. Here’s an excerpt with Homberg as narrator.

 

What chagrined me more was that I had promised to teach one of my friends the method of making the stones luminous, and he was pressing me strongly to keep my word to him. After many excuses, I ran into this friend one day on the street in his neighbourhood, and he led me to his house and showed me some raw Bologna stones and a furnace which he had had made expressly for this calcination according to the design I had given him… Being thus pressed, I began again the operation which had so often failed, and to speak the truth, I was trembling all the while, for I had not told him that I had always failed at it in Paris. When the operation was finished I found the stones the most brilliant and luminous that I had ever seen. My astonishment was enormous, for I had changed nothing in the operation. These were the same stones as mine, for I had given them to him. After having examined everything well, I found no difference except that in this last operation I used a bronze mortar… in place of the iron mortar which I had used in my laboratory in Paris.

 

The primary ore of the Bologna stone is barium sulfate (BaSO₄) which does not exhibit phosphorescence. Roasting in the furnace drives off the oxygen turning it into barium sulfide (BaS). For that, you need both a reducing agent and the right (high) temperature to facilitate the chemical reaction. But the key to phosphorescence is the impurity of the Bologna stone. It contains trace amounts of copper(I). Wothers explains: “During exposure to light, electrons in the copper ions become energetically excited and trapped in defects in the barium sulfide crystal. Over time, the electrons return to their lower-energy tate, emitting the stored energy as light once again.” The presence of iron significantly inhibits the phosphorescence, which is why Homberg failed in his Paris laboratory. Bronze, on the other hand, is an alloy containing almost 90% copper. Thus, the grinding in the bronze mortar introduces more copper impurities and the brighter glow!

 

Principe learns much more from his process. It begins with going to Bologna to look for the stones and finding that no one sells them, he has to make use of the seventeenth century accounts to find them in nature. It is a credit to the early writers in their specificity and a wonder that modern development had not destroyed the original site that Principe was able to find the right ores. Many crystalline ores in the vicinity looked similar, but Principe knew that the barite (common name of BaSO₄) would feel much heavier in the hand. Getting the furnace with the right conditions is also tricky. The standard chemical explanation that you just need to burn it with charcoal (elemental carbon) as the reducing agent will work. We can even write a balanced chemical equation for it (BaSO₄ + 2 C à BaS + 2 CO₂). I even used this equation in a stoichiometry G-Chem exam question some years ago.

 

When Principe designed the furnace according to Homberg’s description, he figures out that there won’t be complete combustion because the vents are too small. He also notices that the flames have a purplish hue just outside the vent (but not inside the furnace). Thus, the reducing agent acting on barite at the furnace temperature is actually carbon monoxide. If there was complete oxidation within the furnace, carbon dioxide can instead react with the ore to form barium carbonate (BaCO₃) instead of the desired BaS. In his conclusion, Principe notes that “chemical processes, even the ‘simple’ ones, frequently turn out to be far more complicated in practice than one would imagine, and this is often the case because of subtle or unnoticed differences in materials… [These materials] have their own histories, which include the problems of finding starting materials that are correct and consistent, and developing methods of preparation, many (perhaps most) of which will fail, more often with some practitioners than others… Considering the enormous variation in materials such as purity, particle size, and origin, as well as more obscure factors like scale, climate, and the reactivity of vessels and instruments, it is amazing that anything beyond the most tri vial chemical reaction actually works the same way twice.” There is also a visceral feeling that you can only get when you repeat the experiment, and not as an armchair theoretical chemist. The stones, when correctly prepared, stink. Principe finds that he “could accurately predict how brightly a stone would glow based on how strongly it smelled… when the calcined Bologna Stone ages and ceases to luminesce, the odour of Sulphur likewise vanishes.”

 

I learn from Wothers that while the Bologna Stone was unique when first discovered, eventually more glow-in-the-dark were discovered. Seventy years later, in a serendipitous discovery Balduin’s Phosphorus – a preparation of calcium nitrate that contained no phosphorus whatsoever – was discovered. It gave rise to the word ‘phosphoresence’. Around the same time, phosphorus was discovered and purified. The light emitted from phosphorus does not come from phosphorescence. Rather it is chemiluminesence. Phosphorus (the ‘white’ version that is molecular P₄) oxidizes quickly and flashily and is dangerous to handle. And in the eighteenth century, fluorite (calcium fluoride ore, CaF₂) was found to emit light, but it does so only when heated up, having absorbed radioactive rays over a long period of time that have trapped excited electrons in the crystal. Once the emission is over, the fluorite cannot easily and quickly be recharged (unless exposed to a strong radioactive source). Turns out this is a great way to carry out ‘thermoluminescent dating’ of ancient pottery and ceramics.

 

Today, modern chemists can easily make glow-in-the-dark novelties that employ a variety of physicochemical mechanisms. They’re so common now, perhaps they are no longer novelties. But back in the day when the Bologna Stones were ‘discovered’, it must have been an enigma to experience.

Chemist's Basilisk

The element bismuth (#83 on the periodic table) was also known as the chemist’s basilisk. I learned this reading Peter Wothers’ book on the naming of chemical elements, aptly titled Antimony, Gold, and Jupiter’s Wolf. What is a basilisk? If you’ve read Harry Potter and the Chamber of Secrets, you’d know that it was a serpent that turned you into stone if you looked into its eyes. Hermione cleverly figures out that this king of serpents was making use of pipes (or the plumbing system) to travel through Hogwarts.

 

Why would bismuth be connected to the basilisk? Turns out that artisans making pewter would mix bismuth with tin “that it may confer splendor and hardness to it… bismuth hardens and gives a shine to tin”. That’s why bismuth was also known as tin-glass. The German chemist Rudolf Glauber referred to bismuth as a Demogorgon, “named after the dreadful snake-haired sisters whose look turns the beholder to stone.” (This is not to be confused with the Demogorgon of Stranger Things, although it is likely related.) Apparently, bismuth also strengthens silver (with the side effect of turning it black) and apparently also hardens gold. Glauber, who lived in the 17^th century, apparently suggested that “Great Princes also might have Armour and Arms made of this hardened Sol, which would be much better than any of Iron or Steel, which easily take rust, to which Sol is not subject.”

 

You’ve likely guessed that Sol refers to the sun. Indeed, in the ancient world, the seven known metals were associated with the seven known heavenly bodies. In the Earth-centric astronomy of the day, from closest to furthest, these would be the Moon (silver), Mercury (mercury), Venus (copper), the Sun (gold), Mars (iron), Jupiter (tin), Saturn (lead). Way back then, shiny liquid mercury was called quicksilver. The alchemists, in their secret recipes for the philosopher’s stone, would allude to the ingredients in a cryptic manner. Thus, one would read allusions to the sun or the moon or the gods, when what they were really referring to was chemical substances.

 

I also learned from Wothers’ book that metallic bismuth and antimony share with water the rare property that the liquid form is denser than the solid form. Just like ice floats on water, solid bismuth floats on liquid bismuth. For the vast majority of substances, the solids are denser than the liquids, and thus the solids sink. Antimony (#51) is in the same column and just above bismuth on the periodic table. It was often confused with bismuth because of their similar chemical properties. Antimony has the symbol Sb referring to the Latin stibium – apparently related to an Egyptian word that refers to eyeliner. Scarily, it was in ancient times as an eye dilator, part of beauty preparations for women. That sounds like a bad idea to the chemist in me.

 

Antimony was used to purify gold. In another 17^th century text, antimony is known as the ‘Wolf of Metals’ because it ‘devours all Metals but God’. I take this to mean that it preferentially reacts with other metals in a mixture that contains gold, thus allowing the gold to separate from the mixture. Once again, the alchemists couch this in cryptic language: “Take the most ravenous grey Wolf, which by reason of his Name is subject to valorous Mars, but by the Genesis of his Nativity he is the Son of old Saturn, found in Mountains and in Vallies of the World: He is very hungry, cast unto him the Kings, body that he may be nourished from it; and when he hath devoured the King, make a great fire, into which cast the Wolf, that he be quite burned, then will the King be at liberty again.” Wothers provides the picture of a 17^th century engraving.

 

Lead (#82) is just to the left of bismuth in the periodic table. In ancient times, it was also used to purify gold. Wothers describes the process “known as cupellation, the impure gold would be roasted with lead in a porous vessel known as a cupel. Remarkably, this process, relatively unchanged over the centuries, is still carried out today during the assaying of gold. Perhaps through analogy with Saturn consuming his children, the lead is said to devour all the metallic impurities. In the high temperatures of the assay furnace the lead and impurities form molten oxides which are absorbed into the cupel itself, leaving the gold behind.” Saturn is the Roman name for the Greek Titan Kronos, father of Zeus. Jupiter is the Roman name for Zeus. I’m not sure exactly how antimony is Jupiter’s Wolf in particular. Zeus did not eat Kronos. Before dispatching Kronos, Zeus feeds him an emetic so that all those who were previously eaten are disgorged. Yuck. Turns out antimony is an emetic because it’s poisonous and therefore your body tries to get rid of it. You could add powdered antimony oxide to wine (it was known as vinum emeticum) or you could make an antimony glaze on your cup (known as the ‘emetic cup’) to help you vomit.

 

That’s probably more than you wanted to know about antimony. Turns out there are many other speculatory guesses about where it got its name. Besides the eyeliner theory, there is the monk-killer theory, the ‘enemy of solitude’ translation, and more. But for all this wonderful detail, I’d recommend you read Wothers book. It’s a little dry in parts, and not as engaging as Periodic Tales. But for someone like me who’s interested in the alchemical connections, I’m enjoying Antimony, Gold, and Jupiter’s Wolf.

Umwelt

Back in 1974, the philosopher Thomas Nagel wrote an article titled “What is it like to be a bat?”. Back then, he was probing the question of consciousness.

 

The answer fifty years later is that we still don’t know. We’ve learned a lot about bats since then. We’ve also learned a lot about various creatures large and small, and scientists now realize we don’t know what it’s like to be a bat or a cat, an owl or a fowl, because we humans rely mostly on one of our five senses: vision. Our vision is acute and we’re good at distinguishing colors. Some birds have better vision than us, but most creatures of the animal kingdom do not. This is the subject of Ed Yong’s marvelous new book, An Immense World, subtitled “How animal senses reveal the hidden realms around us”.

 

While vision is the primary sense utilized by humans as we go through our motions in everyday life, we also smell, taste, hear, and touch. But for a mole in a hole, vision isn’t important at all. Some moles are blind, and those that are not have poor vision. But moles have other senses enhanced. The star-nosed mole, a remarkably strange creature, has a snout covered with sensitive mechanoreceptors that relays detailed information to its brain of what it encounters. How the mole decides what is food and what is not, just from the sensation of touch, is so quick that it can only be captured with high-speed cameras.

 

We have an anthropocentric view of our five senses. Thus, we think that other creatures use their senses the way we do and pay attention to the same things that catch our attention. This is almost never the case! I had long thought (because I read it somewhere) that the zebra has stripes so it can camouflage itself in the savanna, especially in a group setting, and thus confuse lions. Turns out lions have rather poor vision and do not notice the stripes that we think are significant. The zebra might look just like a horse or a donkey to a lion. Why the stripes? Turns out that the stripes are to ward off bloodsucking insects that carry disease like the tsetse fly.

 

We also artificially classify the senses based on where our organs of perception are located. The eye sees. The nose smells. The tongue tastes. The ear hears. The skin touches. Depending on the stimulus, one or more of our senses may pick it up. We’re familiar with the close relationship between smell and taste. When you have a bad cold and can’t smell much, food tastes much blander. Or you pick up something from one sense and shift to another. You hear a noise, and you turn your head so you can see where it comes from. How we perceive the world as humans is based on the particular sensory organs we have and use. Ed Yong calls this the Umwelt – a word first used by a zoologist Jakob von Uexkull. Here’s how he describes the feeling of it.

 

Earth teems with sights and textures, sounds and vibrations, smells and tastes, electric and magnetic fields. But every animal can only tap into a small fraction of reality’s fullness. Each is enclosed within its own unique sensory bubble [the Umwelt], perceiving but a tiny sliver of an immense world… Uexkull didn’t use [Umwelt] simply to refer to an animal’s surroundings. Instead, an Umwelt is specifically the part of those surroundings that an animal can sense and experience – its perceptual world... Creatures could be standing in the same physical space and have completely different Umwelten.

 

Yong’s book is a marvelous exploration into the Umwelten of different creatures. All I can say after reading his many examples is that evolution has tuned the remarkable sense-abilities of different creatures based on their surrounding environment and ecology. Yong is also one of the most engaging science writers I’ve had the privilege of reading. His book is a page-turner and you’ll want to read every footnote. Nature is strange and fascinating. I’m sure I would have become a biologist had I read An Immense World at an early age or seen the Planet Earth series. Living creatures are amazing! I’m making up for it as a chemist by studying the origin of life.

 

Chapter 1 of Yong’s book is titled “Leaking Sacks of Chemicals”. By grouping smell and taste together, he emphasizes the uniqueness of these two senses – they sense chemical substances at the individual molecule level. Yong writes: “Many living things can sense light. Some can respond to sound. A select few can detect electric and magnetic fields. But every thing, perhaps without exception, can detect chemicals. Even a bacterium, which consists of just one cell, can find food and avoid danger by picking up on molecular clues from the outside world. Bacteria can also release their own chemical signals to communicate with each other…” I’d call this the First Sense! How appropriate that it is chemical in nature!

 

I learned about the exquisite nature of the dog’s nose. It’s a marvel! (You’ll have to read Yong’s book to find out more.) And it turns out the human nose is also quite impressive and can be trained. Those books that say our sense of smell is poor in the animal kingdom are very wrong, says Yong. And he provides examples to back up his claim. It’s tough to study taste and smell. Yong writes: “Scientists who work on vision and hearing have it comparatively easy. Light and sound waves can be defined by clear and measurable properties like brightness and wavelength, or loudness and frequency… Such predictability simply doesn’t exist in the realm of smells. To classify them, scientists use subjective concepts like intensity and pleasantness, which can only be measured by asking people. Even worse, there are no good ways of predicting what a molecule smells like – or even if it smells at all – from its chemical structure.” Sounds like a challenge for chemists!

 

I learned about moths. I learned about ants. I learned about elephants. I learned about birds – vultures, migrating seabirds, homing pigeons. I learned about snake tongues. Then I learned that bees and flies and wasps have their taste sensors on their feet and legs. Who would have thought? I learned that the catfish probably has the best sense of taste in the animal kingdom: “They have taste buds spread all over their scale-free bodies, from the tips of their whisker-like barbels to their tails. There’s hardly a place you can touch a catfish without brushing thousands of taste buds. If you lick one of them, you’ll both simultaneously taste each other!”

 

And that was just the first chapter. I could probably write a blog post on each chapter. I might at some point when I go back and re-read the book. There are so many nuggets I’d love to explore further, and Yong provides an extensive bibliography to do so. I’ve already started on one of the books he cites, and have several others on my to-read list. I borrowed An Immense World from the library. But I know I’ll be reading it again so I’ll be purchasing my own copy. It’s that good!

 

P.S. Here’s my blog post on Yong’s previous book.

Absorption Log

Light meets biology in The Optics of Life by Sönke Johnsen. It’s a useful primer for anyone who wants to learn more about photons and the cells that detect them. Biology, chemistry, and physics are rolled into one served alongside just a few mathematical equations, and a sprinkling of wry humor. Yes, the book is science-nerdy. Yes, the second chapter is all about the importance of units and how not paying attention to wavelength versus frequency can really screw you up. But there are so many great nuggets, be they factoids or quotable jokes, that I’m quite willing to plow through the denser sections. Most important to me, reading it makes me think about all manner of interdisciplinary things!

 

I’ve just finished the fourth chapter, titled Absorption. Here’s the opening paragraph for a taste: “Absoprtion has been called the ‘death of photons’ (Bohren and Clothiaux, 2006). While the energy of a photon is never truly lost (reincarnation is a fact in physcis), most people find the conversion of photons into heat and chemical reactions less appealing than their original emission. I admit that I enjoy watching bioluminescent plankton more than contemplating the blackness of my T-shirt. Without absorption though, the earth would be a far less colorful place, with no paintings, flowers, leopard spots, or stained-glass windows.”

 

Johnsen will go on to cover paints, windows, the coloration in all manner of species. But first one has to learn about resonance, antennae, and how electromagnetic “signals” are propagated. Eventually he gets to the difference between absorptivity and absorbance. Our G-Chem students are introduced to this in their first semester of lab where they do some experiments to determine the concentration of an unknown dye with the help of a spectrometer. Absorbance is a funny thing, though. It is defined as the negative (natural) logarithm of the fraction of light that is transmitted. In equation form, this is A = –ln(f_T).

 

Natural logarithms show up in a variety of situations. Whenever you have a large enough sample of particles that can randomly do something or not do something, you observe macroscopic behavior that corresponds to an exponential decay curve. In the case of absorbance, this has to do with whether a photon hits a molecule and gets absorbed. In radioactive decay, it’s related to when an atomic nucleus might transform into another by emitting radiation. In chemical kinetics, a first-order reaction has a rate that is proportional to its concentration. We’re not used to thinking about exponential decays. We think linearly. It takes a bit to get my G-Chem 2 students to see that if rate is linearly proportional to concentration, then the concentration changes exponentially with time.

 

Johnsen explains why absorption and absorbance are often confused, pointing out that it’s partly because when the fraction of light absorbed is small, then absorbance takes approximately the same value. An equation that helps you see this: ln(1 + x) is approximately equal to x when x is small. Johnsen then explains what the absorption coefficient is and why it’s useful especially if you were a biologist trying to determine what the photoreceptors of marine creatures are detecting. Colors and light in the sea are an interesting business to the denizens of the deep especially since longer wavelength (redder) light is more easily absorbed by water, i.e., the bluer light has more penetrating power. All manner of adaptations arise, and Johnsen deftly explains the preponderance of different kinds of reds in many marine invertebrates.

 

I found the discussion on paints enlightening. Apparently “many oil paints look nearly black when they come out of the tube. It’s not until they are mixed with white paint that they look like the color on the label. White paint (and white in general) is more special than it looks. Rather than simply being paint without pigment, it is actually a mixture of a transparent latex or oil base and powdered titanium dioxide.” The key here is that TiO₂ has “a high refractive index in the visible range (~2.5), about the same as diamond… and scatters a lot light.” Artists have to know how much white to mix into their oils to get what they need. This same interplay of absorption and scattering is also true for colors of organisms. Johnsen goes through a series of examples and adaptations in cephalopods, birds, and more.

 

This is followed by another interesting discussion of Easter egg dyes, and he smoothly pivots into the odd case of green. Green dyes transmit in the green range, or more pertinently, they have pigments that strongly absorb the red and the blue. But yellow, orange or red dyes essentially just have a step function with low transmittance at short wavelength and high transmittance at longer wavelength. (For blue dyes, the step function is in the opposite direction.) We also observe these features in the molecules of color that living organisms use – the carotenoids. I find this odd and intriguing. Surely there are molecules that can provide the color peaks exactly where needed in the spectrum, but maybe there’s a limit to what can be biosynthesized that lead to the asymmetry. There’s something strange about all of this. It’s certainly opened my eyes to how much I don’t know about vision, color, and light, as it pertains to biology (and not just its simple physics). I’m tempted to pitch teaching a class about the “Chemistry of Living Color”, and add it to the list of courses I might want to do one day that will give me an excuse to delve deeper!