Too Much Oxygen

 

Once upon a time, oxygen levels on Planet Earth hit 35%. This purportedly took place circa 300 billion years ago as the Carboniferous period was giving way to the Permian. At the same time carbon dioxide levels were falling. One explanation is that carbon burial (coal formation) was especially rapid, and thus there was less carbon to combine with atmospheric oxygen to form carbon dioxide. Today, humans are reversing the process by extracting the coal and combusting it for energy.

 

What was special 300 billion years ago to cause this? It so happens to coincide with the formation of the supercontinent Pangaea with its wet climate and vast flood plains that favor the formation of coal swamps. The rise of trees with woody lignin-containing stems meant slow breakdown to release carbon because decomposing bacteria have a particularly hard time digesting lignin. I’m reading all this in Nick Lane’s Oxygen, a fascinating treatise that connects oxygen to energy, life, death, sex, and aging. I first read Lane’s book almost two decades ago, but I’m re-reading it again to refresh myself on interesting oxygen factoids to use as a theme in my upcoming Quantum chemistry class – which culminates in the unusual chemical bonding situation of molecular oxygen.

 

But back to our story on oxygen levels. Can we measure them from so long ago? We can certainly measure the carbon content in rocks from that era. And it is high, even after accounting for erosion and metamorphic processes. We can also measure the contents of air trapped in microscopic bubbles of ancient amber. (In Jurassic Park, dinosaur DNA was extracted from insects trapped in amber.) As a third measure, the relative proportion of carbon-12 and carbon-13 isotopes in limestone tells us how enriched the atmosphere was with oxygen. The evolution of plants and their selectivity for carbon-12 corroborates the story. While all these measures are indirect, taken together they strengthen the hypothesis of such high oxygen levels in the past.

 

Chapter 5 of Lane’s book, from which I’ve taken this information, is titled “The Bolsover Dragonfly: Oxygen and the Rise of the Giants”. There were huge insects in the Carboniferous period! Dragonflies and mayflies had wingspans approaching 20 inches; there were meter-long millipedes, and scarily large spiders (though not quite the size of Aragog). Megafauna! Or perhaps I should say Mesofauna. Was this all because of elevated oxygen levels? More oxygen, more energy, faster growth? Speculations abound, but the one I found most interesting is that the large size lengthened the diffusion of oxygen through the organism so that by the time it reached the mitochondria, the concentrations were much lower. Otherwise, oxygen poisoning would result.

 

There was practically no free oxygen at the origin of life on Earth. We are descended from single-celled prokaryotic hydrogen-breathers. Living systems can’t get as much metabolic energy from hydrogen as they can from oxygen. Aerobes thrive energy-wise while anaerobes live on subsistence. Molecular oxygen is unique with its oddly weak double bond making it thermodynamically stable; yet it is oddly kinetically stable despite being a diradical (with two unpaired electrons). It’s much stranger than it looks at first glance, and I’m hoping to take my P-Chem students through that story this coming semester.

 

Oxygen might be good for life, at least we aerobes think so. But we’ve also evolved a bag of tricks not to be poisoned by it. That’s the topic of Chapter 10 in Lane’s book: “The Antioxidant Machine: A Hundred and One Ways of Living with Oxygen”. Oxygen loves to accept electrons. It does so one electron at a time, forming superoxide and then hydrogen peroxide (by also stealing protons). When oxygen steals an electron from another molecule, the latter now has an unpaired electron and becomes reactive (kinetically unstable). It then tries to steal an electron from some other neighbor, and so on, potentially resulting in a cascading chain reaction. Anti-oxidant molecules halt this process, often by donating an electron to stabilize the radical.

 

To counter the effect of peroxidation reactions that are ultimately due to too much oxygen, there are multiple antioxidant strategies. Heme proteins (similar to hemoglobin) detect oxygen levels, “binding to excess oxygen and releasing it only slowly, maintaining a constant and low concentration of oxygen in the immediate environment.” Mucus secretion is a very effective strategy. In bacteria, the negatively charged polymers in the mucus capture positive metal ions, and these react with the marauding radicals. Biochemistry utilizes sulfur-containing compounds to react directly with peroxides or indirectly by regenerating antioxidant molecules such as vitamin C. Recently my research has focused attention on the role of sulfur-compounds in proto-metabolism so I’m learning a lot about this area. Lane’s discussion of the enzyme superoxide dismutase is now much more fascinating, compared to two decades ago when I lacked appreciation in my first reading of his book.

 

One thing you might be wondering: If oxygen levels were so high, shouldn’t there have been massive forest fires? And wouldn’t these have consumed the oxygen thereby maintaining balance? Lane tackles this head-on by estimating what would be needed to maintain the balance – the unrealistic total vaporization of all the forests. It turns out that forest fires tend to promote the burial of carbon and coal formation. Also, the previous estimates that oxygen levels above 25% would cause conflagration were dependent on setting moistened paper on fire. Paper has little lignin, and furthermore real plants accumulate silica which acts as a fire retardant. Turns out that more shiny coal indicates it was formed at higher temperatures likely with more oxygen in the atmosphere. The coal from the Carboniferous is particularly shiny, further evidence of high oxygen levels.

 

Oxygen is an enigmatic molecule. We aerobes can’t live without it, but it’s killing us at the same time it’s fueling our way of life. Lane spotlights this tension in his engaging and very readable book, peppered with fascinating anecdotes. Did you know that silica was used in paints as a fire retardant during the Second World War? Or that the males of many ants and bees are haploid possibly for similar reasons as human sperm? And if not for skin pigments such as melanin, you’d change from red to a blue hue when you engaged in vigorous bodily exertion? Lane provides memorable and colorful analogies. My favorite is his description of the Fenton reaction: “Hydrogen peroxide is a gangland thug. Normally quiet, posing little danger to casual passers-by, it turns violent on meeting a rival gang member. Damage to proteins containing embedded iron can be as swift and specific…” More importantly, I was reminded of how biochemistry tunes itself to avoid redox catastrophe. Living with oxygen is a fine balance indeed.

Sleep Anxiety

I used to have insomnia. For two decades. Then sometime after turning forty, my sleeping problems diminished. I’m not sure why. Probably a combination of factors, foremost of which might simply have been the slow shift of my circadian rhythms over time. I was a late night-owl as a teenager, but made an abrupt shift to an earlier schedule when I arrived in the U.S. as a college student in my early twenties. In my tropical home country, we ate dinner later and there was a tradition of a late-night supper when the weather was cooler.

 

Because of my insomnia, I have read many books and articles on sleep over the years. I continue to do so as a matter of habit, and simply because sleep still remains mysterious even though scientists have amassed a lot of interesting data and we now know much more than we used to. I didn’t experience significant sleep anxiety during my two decades of insomnia; I just got used to it and it didn’t significantly impair my work performance. Napping helped. And I have significant chunks of time to myself, which is a great boon as an introvert.

 

The Sleep Prescription is a mini-book by Aric Prather, a sleep scientist at UCSF. Published last year, its tagline is “7 Days to Unlocking Your Best Rest”. The author provides a good mix of the scientific underpinnings of sleep along with engaging anecdotal stories of anxious insomniacs trying everything they can to improve their sleep. I was familiar with much of the science, but I still appreciated Prather’s approach in this book – very practical with easy-to-remember tips. Here’s my summary of his seven points for seven days.

 

#1. Set your wake-up time and stick to it! Yes, even on the weekends. I used to sleep in on weekends to catch up on my deficit. I stopped doing so a long time ago. It helped. I no longer confuse my circadian rhythm. At least until I travel internationally and my body clock gets messed up. But that’s okay because I give myself time to readjust.

 

#2. Sleep problems are often tied to waking life problems. Particularly stress. Prather discusses the role of cortisol in the sympathetic nervous system and its role in waking you up from sleep. I am blessed to have led a relatively stress-free life. I didn’t feel the pressure to “get all A’s” as a college student. Early on in my career as an academic, I decided I didn’t need to be a star, and I instituted strong work-life boundaries. I’d say work stress wasn’t much a factor in my insomnia. Although sometimes I would lie awake thinking about work-related ideas in my teaching and research. (These were positive thoughts but still kept me awake.) Prather’s advice is to “ease off the gas” and schedule micro-breaks from work stress. I already take regular breaks mostly so I’m not sitting for too long.

 

#3. Energize when you need to during the day. Prather mentions sticking your head in the freezer for cold shock. I’d heard this before, but I don’t do it. He also discusses managing your caffeine. I avoid caffeine so that’s not an issue. Is it okay to nap? Yes, but not for too long. Prather explains the sleep cycle and how to relieve sleep pressure without getting into the phase where you wake up groggy. Turns out forty winks is a good measure. I lie down for forty minutes. I might not fall asleep but if I do so, it might be for twenty or thirty minutes. It works. But you must set an alarm and not hit the snooze button.

 

#4. Set aside time blocks to worry and not too late in the day. The strategy behind this is to reduce anxiety because you can tell yourself that you have time to worry. It sounds weird, but Prather assures the readers that it works. He provides several “levels” of doing this. I’m thankful I don’t feel the need to do this, but I can see its usefulness for folks who are in much more stressful situations.

 

#5. You are not a computer, you can’t just shut down. That’s the title of chapter five. When I had insomnia, I learned the importance of having a wind-down routine. I do many of the things you’ve likely heard about. I have relaxing activities. I take a warm shower. I have a tiny cup of cereal with milk. And I’m adamant about not doing any work in the evenings, which also means I hardly use my computer then. When I was younger and my insomnia was worse, having the routine helped. I also kept a sleep diary (as Prather recommends) to help me discover what worked and what did not. I stopped doing so in my early forties; I no longer needed the diary. But the routines have stayed.

 

#6. You can retrain your brain. Prather has a number of good tips, including “do not get into your bed until you’re sleepy.” This is a tough one for me because I like lazing in bed. It’s physically soothing and I feel happy when I’m in bed with my pillows. It doesn’t help my sleep though. Prather also says that if you don’t fall asleep after 20-30 minutes, get up and do something else that’s still relaxing. And don’t bring your book or laptop into bed. If you have to, do it differently – in a different position, at a different corner of the bed, etc. I like to read in bed and it is part of my wind-down routine. Prather understands these things and discusses compromises. While I don’t necessarily follow his advice here, I’m reminded of his suggestions and I found myself readjusting to them.

 

#7. Stay up late to build up sleep pressure if needed. Prather has a scheme for doing so and provides appropriate guidelines. While I would use this strategy when shifting time zones, I wasn’t always consistent. I like Prather’s approach and I will try it the next time I need to get over jet lag. I was also reminded, not just in this chapter but throughout the book, that the goal is not perfect sleep, but good-enough sleep. What is good enough? Prather has a straightforward scheme for you to calculate this from a 7-day log of your sleep. I like his guidelines and his approach of keeping all these strategies low-stress.

 

If you are anxious about your sleep issues, I highly recommend Prather’s book. I find it practical and research-informed. Sleep anxiety should not rule your life. Your body is built for sleep and wakefulness. Prather recognizes that individuals have different sleep needs and his book might help you find a happy medium.

Skinny Core

I just returned from a LABSIP workshop. What is LABSIP? Lowering Activation Barriers to Success In P-Chem. While the acronym doesn’t roll off the tongue, I find the name amusing. Then again, I once gave a talk at a chemistry conference titled “Getting Over the Curve”, a subtle reference to the same “energy diagrams” that those of us who teach P-Chem agonize over, because our students are frequently confused by the graph axes among other things.

 

The workshop was a blast. There was plenty of nerdy P-Chem humor. I met old friends and acquaintances, and made new ones. It was a targeted small in-person workshop with just 25 invited participants with a packed schedule. I was not involved in organizing it, and was able to fully enjoy the time without worrying about administrative details. In today’s blog post, I will discuss one of the activities we attempted: Can we agree on and distill a “skinny core” list of topics that should be in physical chemistry courses?

 

Before this in-person group meeting, there had been a Zoom meeting with a few hundred participants. From the AllOurIdeas online polling system (here are the Quantum results), the group found that there was actually a good consensus on what the community of physical chemists thought was important in a potential two course outlay dubbed Quantum and Thermo. One of our jobs in the small workshop was to hash out a “skinny core” that provided a guideline for instructors who teach a wide variety of P-Chem courses. Some of us teach the standard two-semester sequence for chemistry majors. Others teach it in three-quarters. Others squeeze it into two. Yet others teach a one-semester grab bag that includes both broad areas. Some teach P-Chem for engineers, or biochemists, or some other subgroup.

 

What should the core ideas be? We came up with an initial set which still needs more discussion, refinement and editing. Eventually it will be published by LABSIP and hopefully this provides a service to the community of P-Chem instructors regardless of the flavor of our classes. A little later in the post, I will reveal my personal version for the Quantum half based on the discussions I participated in. It does not reflect the group consensus although there is significant overlap. I’m teaching Quantum in the upcoming fall semester so this exercise felt timely for me.

 

As chemists, we want students to learn how the quantum world applies to chemical questions; this means we are interested in things at the scale of atoms and molecules. Solving the Schrodinger (wave) equation is at the heart of quantum chemistry. This requires learning about eigenvalue equations and using operators. It also means coming to grips with the strange nature of quantum measurement, the ideas of wave-particle duality, and the Heisenberg Uncertainty Principle. As instructors, many of us use both historical and more recent research to highlight what’s cool about the quantum, but we don’t all use the same examples.

 

In my opinion, what science does to elucidate how the natural world works, is to build models. Models, by their very nature, cannot capture all aspects of a complex system. But by constructing a model, we can test our understanding of nature, make predictions, and thus refine our theories. In P-Chem, these models are grounded in mathematics. There was very broad consensus that as chemists we should cover the particle-in-a-box, harmonic oscillator, and hydrogen atom models. Some of us discuss the rigid rotor as an additional model, others fold it into the hydrogen atom or cover particle-in-a-ring models. Everyone agreed that there should be some mention of electron spin. We also agreed that one should go beyond the hydrogen atom and discuss models relevant to chemistry where the Schrodinger equation cannot be solved exactly. Thus approximate methods and their accompanying theories and models should be included. I think all of us covered at least the helium atom and the Born Oppenheimer approximation, i.e., cases with multiple electrons and multiple nuclei respectively. For me, that’s a core that covers 7-10 weeks, suitable for a half-semester or quarter-long quantum course. Most of us include a bit of spectroscopy, but I think it could also be done in a separate course (e.g. P-Chem lab).

 

Here’s an outline of my semester-long quantum course. My version of the skinny core is in bold, what I think is common consensus but I left out of the core is in italics, and things where there is less agreement is in unaccented text. As a computational chemist who is also interested in chemical bonding, there are certain things I want the students to appreciate in my Quantum course that are unique to me, and these optional items are also in unaccented text. (In my early days, I taught computational chemistry as an elective, but I have pivoted to origin-of-life which is a topic of broader interest to students.) Our LABSIP group did not specify an order that topics should be covered; I think there are different ways to skin the quantum cat, so the following order is my own. It’s somewhat close to a “traditional” sequence, but there are good reasons for doing so to take advantage of topics building on each other.

 

·      Dawn of the Quantum (bits of history)

·      De Broglie Hypothesis and the Heisenberg Uncertainty Principle

·      The Bohr Atom

·      Classical wave equation (to teach some differential equations)

·      Schrodinger Equation and Particle-in-a-Box models

·      Operators, Expectation Values, Commutators

·      Postulates of Quantum Mechanics, wavefunction properties

·      Quantum Tunneling

·      Harmonic Oscillator model

·      Infrared Spectroscopy, Normal Modes, Anharmonicity

·      Rigid Rotor Model, Rotational Spectra, Rovibrational Coupling

·      Spherical Harmonics and the Hydrogen Atom model; Atomic Orbitals

·      Electron Spin, Term Symbols

·      Helium Atom and the Variational Principle

·      Alternative Orbital Wavefunctions, Basis Sets, Hartree-Fock Theory

·      Perturbation Theory

·      Pauli Exclusion Principle

·      Multi-Electron Atoms and Hund’s Rule

·      Born Oppenheimer Approximation, Molecular Hydrogen Cation Model

·      Molecular Orbital Theory (Diatomics)

·      Electronic Transitions, Franck-Condon Principle

·      Polyatomics and Hybridization Theory

·      Huckel Theory

·      Advances in Valence Bond Theory (beyond the 2c-2e Heitler-London bond)

 

Whew! We get through a lot, but I hope at the end of the course, the students have a newfound appreciation for the importance of the quantum to fundamental questions in chemistry, and that what we call the chemical “bond” is a strange beast that’s largely imaginative (although grounded in different theories). I’ve rearranged my course over the 20+ years I’ve taught P-Chem. Topics such as group theory, lasers, NMR spectroscopy, have rotated in and out. I expect my class will continue to evolve, and I think that’s a good thing. But I also expect to preserve the skinny core.

Bios Mesofauna

The Cambrian “Explosion” led to a diversity of creature body types. Could the trilobites have persisted? Will the arthropods colonize more territory than the crustaceans? What features may have led to the wide range of successful insects? All this and more can be explored in Bios Mesofauna, the latest chapter in the Bios series of games designed by Phil Eklund with streamlined new versions courtesy of Ion Game Design. 

 

Mesofauna shares many of the game mechanics with the second edition of Megafauna, but it is even more streamlined. It’s easier to teach and to learn – a major plus for introducing newer gamers to the Bios series. Gone are some of the more fiddly rules, although at the expense of scientific realism. While I personally miss factors related to sea level and amount of CO₂ in the atmosphere, a full game of Mesofauna retains shifting continents and cosmic environmental events. There are two introductory levels you can attempt before sinking your teeth into the full game. I felt that the introductory versions worked well for introducing new players to the feel of the game before layering on more complexity.

 

The game can be played with 1-4 players (yes, there’s a solitaire scenario) and can even be combined with Megafauna, if you want some extra competition and more players. The heart of the game comes from acquiring mutation cards that provide new organs for your growing organism! These come in four colors: red for sensory, blue for reproduction, yellow for respiratory, green for digestive. The green and yellow organs are helpful to herbivores, the red ones for carnivores, and the blue ones allow you to spread more quickly. But the faster you spread, the less choice you have in acquiring new mutations.

 

Mutations can be “promoted” by flipping the card over allowing the formation of new species or the further complexification of your organisms. The lopopod player (purple) has two species in the mid-game snapshot below. In the top row, the primitive Aysheaia has three basal organs (one yellow and two green cubes), a crop (green card with two yellow cubes) which is a foregut for predigestion, and male contest behavior (blue card with cubes).  The Tully Monster also has three basal organs, and in addition you can see a profile of the creature composed of three cards: book gills for swimming, a web-spinner tarsus, and Batesian mimicry. This “portrait” contains two “pheromones” (one yellow and one blue in its shilouette) which provide protection against mutagenic events and score points. There’s something very satisfying about building up your organisms this way!

 

While the game begins with a single supercontinent (Pangaea), events may cause the land masses to break up or recombine. In the three-player mid-game shown below, the lopopods (purple) occupy the eastern continent. The crustaceans (light blue) are spread out over two continents although predominantly in the northwest. The arthropods have representation on all three continents. The wooden pieces are dubbed “creeples” and have aesthetic bug-like shapes. Most are terrestrial, some can swim, some can fly.

 

On your turn, each of your species you have can only take one action. There aren’t many to choose from, which keeps the game streamlined. You can “purchase” a mutation card. You can “promote” a mutation card by flipping it over either adding to your portrait or to create a new species. Or you can “populate” by dispersing creeples of your species across the lands (and lakes). There are two others mentioned, but the aforementioned three P’s constitute what you’re doing most of your turn. When creeples advance into each other’s territory, there’s a simple way to determine the winner. Each mapboard hex is divided into a lower trophic half for herbivores and an upper trophic half for carnivores. There are a few other special features and rules, but that’s the gist of it. What I haven’t told you is the range of sneaky strategies you can employ. Evolution and adaptation are at the heart of Bios games – you have to keep an eye on what your opponents are up to. And a change in the environment, outside of anyone’s control can wreak havoc on the best plans.

 

Above is the end-game map. The southwest continent is solely occupied by the arthropods, a combination of venomous firebrats, millipedes and spiny caterpillars. On the large northern continent, the arthropod player has a small colony of dragonflies in the west; the lopopods and crustaceans fight for dominance. A small group of blood-feeding trilobites has survived, while their descendants the sand crabs occupy much more territory. Not shown is a small continent in the southeast, also contested by both the purple and blue players.

 

End-game scoring comes from adding up the number of creeple counters in play, the number of pheromones in portraits, and fossil scoring markers that are awarded periodically during game events. Scores were close in this three-player game. The arthropods (grey) won with 19 points, while the other two players had 15 points apiece. Here’s a picture of three of the four arthropod species in play. The firebrats (top row) have evolved silk ballooning, a head that sprays venom, and yolk proteins. The millipedes (middle row) have muscle shivering for warmth, hinged wings, and are slavers. The spiny caterpillars have evolved kidney-like nephridia and claws. Not shown are territorial dragonflies with jumping legs and a central brain.

 

Overall, I think Mesofauna is an excellent addition to the Bios series. With its streamlined rules and decent introductory games, it is probably the easiest to learn for new players. The full game has enough meat to satisfy the gamer looking for more oomph and flavor. The variety of map combinations and different tactical moves should keep the game fresh over multiple plays. What remains to be seen is how much staying power the game will have over the long haul. But then one can try the other Bios games and combine them into one huge super-game. I’m still partial to the first edition of Origins (How We Became Human) since it’s the one I’ve played the most. And while I rarely play Bios Genesis much anymore (it’s brutal and unforgiving), it still has a place in my heart because it’s about the origin of life – my area of research!