Life in the Rocks: Cold Version

I vicariously followed the adventures of Tullis Onstott and his colleagues in Chapter Nine of Deep Life. Nunavut, Canada, is cold, cold, cold. Could there be life down in the rocks below the permafrost? If so, it might tell us how to hunt for life on Mars below its barren surface. While I mentioned the challenges of field work in my previous blog post, and how I am ill-suited to undertake such arduous, reading about it is exciting. I recommend Deep Life for the blow-by-blow accounts.

 

In this icy cold chapter, the scientific team successfully isolates a prokaryote that makes its living via chemolithoautotrophy. That’s chemistry in the rocks where you make your own food by using energy from the redox gradient from rock chemistry. The autotrophs we are most familiar with are green plants which are photoautotrophs. They make their own food with energy streaming down as photons from the sun. Trying to determine what this microorganism does or how it makes its living is challenging. You have to chop up its DNA, determine its sequence, then try and match it up to known sequences that code for proteins that do biochemistry you’ve seen before.

 

They got to name their organism: Desulforudis audaxviator. It lives through reduction of sulfur compounds (desulfo), it is rod-shaped (rudis), and it is a ‘bold traveler’ (audax viator) thanks to having genes that indicate flagella for motility. They even have a scanning electron microscope picture (read the book!). But what was shocking is that it also had the genes for a complete nitrogen-fixation pathway. That’s very expensive biochemically. Were these just a relic or does the microbe use them? I don’t know. It’s acetyl-CoA pathway also resembled that found in archaea. That’s of interest to me in relation to my origin-of-life research.

 

The author has a great cartoon picture (shown above) showing its potential biochemistry from the sequencing data. They have the audacious proposal that radiolysis provides energy that splits water producing H₂O₂ which oxidizes pyrite (FeS₂) providing sulfate for the microbe. H₂ is also a byproduct for more reducing power! Mineral transformations in the environment are included in the cartoon, which I thought was a very nice touch that you don’t see in a biochemistry textbook. This microorganism might have been able to make a wide range of co-factors including cobalamin (for vitamin B12). It has a typical wide range of transporter proteins providing info on what might go in and out, and it has the usual carbon fixation pathways that I’m interested in.

 

It’s amazing that micro-organisms are found in tiny cracks of rock in the tens of nanometers wide. Very little water can penetrate in, yet somehow enough does for it to make a living in thin films of water just nanometers thick. I’m dumbfounded. Life does find a way to adapt, even in the freezing cold below the surface where stones are turned into bread. Could something be found on Mars? I don’t know. But it will be very expensive to find out and you’ll need quick-thinking knowledgeable Swiss-army-knife folks who know how to adapt.

Armchair Science

My office chair has armrests. Yes, I’m an armchair scientist.

 

Why am I thinking about this? Because I am halfway through Deep Life by Tullis Onstott. It’s about the hunt for microbes miles below the earth’s surface. And how do you get there? Down the mines. The book introduced me to the field of subsurface geomicrobiology, but it’s not a typical science book. It’s more of a scientist’s adventure book that goes through the highs and lows of everything from the roulette wheel of grant funding, the whims of mine-bosses and customs agents, what it’s like to be sweating miles beneath the surface, and how to find MacGyver-skilled people. It’s about field work in the extreme.

 

I, on the other hand, as a computational chemist am as far away from field work as you can imagine. I sit comfortably in my office building and analyzing molecular structures from my desktop computer. All the number-crunching work is done by a high-performance cluster sitting in a cold room a building away that I can access via the internet with a few clicks on my keyboard. I’m an old-school command-line guy who uses the mouse as little as possible. I do regularly get up from my chair and walk two floors down to teach a class. (I eschew elevators.) I haven’t taught general chemistry lab in several years so I don’t even have an excuse to set foot in an experimental lab. However, I do go to our chemistry demo room a few times each semester to show off stuff in my chemistry lecture classes.

 

When you’re a field scientist who needs to collect living samples from deep-enough mines, your choices are constrained. You have to convince a mining company’s management that you’re not a spy or a saboteur, that you won’t slow them down, that you won’t cause an ‘incident’, and that it is to their benefit to let you go down their mines. To get good uncontaminated samples, you also need to scratch past a cave wall surface, and that means having the necessary equipment. And because these microbes are obligate anaerobes, you need to make sure they survive the trip to your makeshift lab so you can perform the analysis. The oxygen all around that’s life to us; it kills them. And some of them may be toxic. And you might need a laminar flow hood for your work, that somehow you have to get into your ramshackle on-site quarters.

 

I wouldn’t survive in the field. I have poor hands in lab that also regularly shake due to a neuromuscular issue. There’s a reason I am a theorist. I also thrive on having an organized schedule, having control over my time, and not constantly being thrown into chaotic situations. I have little in the way of MacGyver skills. When you’re out in the field, unpredictability is the name of the game. You have to adapt. It’s something I don’t think I’m good at. If the zombie holocaust descends, I will probably perish quickly, or join the robotic horde depending on what type of zombie-virus we’re talking about.

 

I do enjoy discovering new things though! If I didn’t, I probably wouldn’t be an academic. But I do it through reading and running calculations, at least in my work life. I like learning new things even though I may not have the physical dexterity or strength to perform them. And discovery is always exhilarating! Now that I’m older and well aware of my physical limitations, I see many advantages of my life as an armchair scientist. And I’m happy to live vicariously through reading the adventures of folks out in the field and in the deep.

Bending the Elements

When discussing Aristotle’s elaboration of the four elements as the foundation of matter in my first day of an introductory chemistry class, I used to spend five seconds poking fun at the 2010 movie The Last Airbender. I only watched it once (for free on DVD) and I thought it was very poor. I had high expectations. An interesting theme that incorporated Earth, Water, Air, Fire, into daily life. A famous director. What could go wrong? It was a disappointing mess. Elemental was not great, but much better. And I had recently proposed teaching a non-majors class titled Earth, Water, Air, Fire, Life!

 

Then several years ago, a student suggested that I watch the Nickelodeon animated TV series that the movie was based on: Avatar, the Last Airbender. A second student piped up to support the first one and both thought the TV series was very well done. I’m very glad that two brave students on the first day of class were willing to challenge me on my poking fun at The Last Airbender. I should say they didn’t think the movie was all that good either, so we were in agreement there, but they encouraged me to give the TV series a chance given my interests in ancient ideas about elements. I nodded politely in response. But in my mind, I was skeptical. I associated the name Nickelodeon with children’s cartoons. (I didn’t watch these growing up in a different country.) Could anything good come out of there particularly when I associated it with Sponge Bob Square Pants (which admittedly I haven’t watched either).

 

Some years passed. I forgot about it. But then this summer something prompted me to watch the TV series. Maybe it was a conversation with my summer research students or maybe prompted by something I read, I don’t remember why. Anyway, I look at my local library catalog and they had the DVDs of almost the entire series (missing one disc in Season 3). So, I settled down to watch Season 1. Episodes are just 20 minutes long, and they were good! The main protagonists were interesting characters and I found the story engaging. I also cheered whenever Appa, the flying bison, got something interesting to do. Appa reminds me of the enigmatic Cat-Bus in My Neighbor Totoro.

 

I’m most of the way through Season 1. My quick synopsis: there are four nations and each of them has practitioners in the art of manipulating their associated element. The Fire nation has attacked the other three and has been dominant. Remnants of the Earth and Water nations have fled or are in hiding, protecting themselves from the conquering Fire nation. The Air nation seems to have mostly disappeared. The main protagonist, Aang, is the reincarnated Avatar who supposedly can be a master of all four elements and end the war. But he’s only twelve years old, and having learned air-bending skills when he was young, still needs to master the other elements. Hence: Avatar, The Last Airbender.

 

The most visual aspect is how to manipulate the element of your specialty to do your will. Earth-benders manipulate the stuff of earth from the ground itself. Water-benders can move water to do their will. Fire-benders seem to mostly create fire and launch them as fireballs (great for war). Air-benders can move air and utilize its currents in their own movement. Three things seem to be needed to manipulate an element: innate propensity, the movement of your arm, and mental focus. Not everyone in a nation has the ability to bend matter. Those that do undergo training to learn the mental focus and the arm movements. Manipulating matter mainly consists of being able to collect it, shape it, and throw it, often against the force of gravity. It’s similar to magic.

 

Of the four elements, air is the lightest and should be the easiest to manipulate against gravity. From a molecular perspective, you need to apply higher pressures in one vicinity to channel the molecules into a lower pressure area. It’s not obvious how one would do that, but a skilled air-bender can generate powerful winds and cyclones suggesting that quite a bit of energy may be involved. Since N₂ makes up almost 80% of our atmosphere, perhaps an air-bender has a special connection to these molecules in their gaseous form and can magically command or will them to move in a particular way. Essentially the air-bender needs to overcome the entropy and cause these molecules to take a low probability macroscopic arrangement.

 

For water, only one substance is involved: molecular H₂O. Perhaps water-bending is similar to air-bending in this regard. The water-bender has an affinity to manipulate the movements of this molecule and overcome gravity. I’ve seen water benders create waves, push water, pull water, and turn it into ice. So the water-bender needs to also have the magical ability to control the hydrogen-bonding between water molecules. Essentially the water-bender uses arm movements that cause bulk water to mimic that same movement. Maybe there’s a hidden force that can be turned on and off by focusing the mind that provides an unseen action-at-a-distance relationship between the arms/hands and the substance H₂O.

 

Earth is a little trickier since there are a whole bunch of substances that make up the earth. Sand is mostly silica but rocks can be made up of all sorts of elements. The primary distinction between Earth and its Water and Air counterparts is its solidity. Air-benders manipulate the gaseous state. Water-benders manipulate the liquid state. Earth-benders manipulate the solid state. But there seem to be limits. Earth-benders don’t manipulate all solid substances. They seem to certainly move ‘natural’ non-man-made stuff, but there is some inconsistency on whether they can manipulate man-made solids: concrete, metal alloys, and the like. So are they limited to some elements but not others? I don’t know. Could water-benders manipulate pure ethanol or mercury which are also liquids? Or are they restricted to H₂O? An air-bender who manipulates O₂ could be a killer. Can Aang move different gaseous substances in different ways? I don’t know.

 

The fire-benders seem to mostly use their art to create fire and launch it as a projectile. Chemically to make ‘fire’ you just need a combustible material and energy to get the chemical reaction started. There are small amounts of methane and other combustible gases in the atmosphere. Do fire-benders essentially manipulate the reaction of methane with oxygen? That might be a sort of air-bending? There’s no sign that they start using a solid combustible. And water seems to put out their fire. Or maybe they use friction as an energy source? Again, I don’t know.

 

The chemist in me seems to be trying to peg element-bending abilities with the chemical substances most involved. But maybe there’s a better way to think about it that I haven’t stumbled upon. Regardless I’m still enjoying the TV series and I’m glad my students encouraged me to give it a chance!

First Week: Fall 2024 Edition

I just have two classes this semester, my usual General Chemistry 1 and Physical Chemistry 1. Once again, I am teaching the Honors preceptorial, but with the smaller incoming class at my university (probably impacted by FAFSA woes), I only have fifteen new academic advisees instead of the usual twenty in my G-Chem 1 class. This morning, I recited all of their names correctly in class. Hooray! Like last year, I’m having each of them visit me during my drop-in (office) hours so I can learn a little more about each of them as individuals. I’m always delighted to get to know new students and they seem like a good bunch!

 

The one major change I’ve made to my G-Chem class is ditching the textbook. While I have chosen a decent online textbook as a reading reference that also has relevant practice exercises, I am supplementing the reading by providing Class Notes for every lecture. These do not recap the lecture in detail, but rather note the key concepts. Students still have to come to class to see the examples and engage with the explanations of the conceptual material. I will also continue to employ Study Guides. I’ve made some minor rearrangements in content. Nuclear chemistry has been moved back to early in the semester. I chopped up the standard chapter on liquids and will sprinkle it throughout the semester, and intermolecular forces has moved up earlier. I’m also making some minor moves in the chemical bonding section and stuff related to wave-particle duality. So there’s some amount of work on my part, but it’s not a major overhaul. The big question is whether the students are sufficiently prepared for the exam without the usual online auto-graded homework. First exam is at the end of the third week, so we’ll see.

 

I am not making many changes to P-Chem, just minor tweaks to most of the material with some minor rearrangements to the last two weeks where I go into different chemical bonding theories. Last year, I did expand Valence Bond Theory and I did culminate the class by examining why triplet molecular oxygen is such a strange molecule. But it didn’t feel as streamlined so I need to figure out how to do this better. I only have eight students, and I had five of them in G-Chem 1, G-Chem 2 or both. Most of them know each other, and that’s a good thing because I tell them that P-Chem is a team-sport. I’m encouraging them to work with each other on problem sets, visit me often to ask questions, and study together for exams.

 

On the first day of P-Chem, I couldn’t get through the material I had prepared. On the first day of G-Chem, I barely got through but rushed a little at the end. It could be that both classes were a little more interactive – perhaps students are more willing to speak up in smaller classes? But the other thing I’ve noticed over the years is that I tend to spend a little more time pontificating early-on about the nature of chemistry, science, and model-building to understand the natural world. I think this approach pays dividends later, or at least I hope so.

 

It was a busy week because in addition to a bunch of first-week administrative meetings, I also trained two new research students. Because of differing class schedules, I wasn’t able to train them together, but that’s okay. I did spend time last week putting together tutorials for the new research software we’ll be using. I think I did a relatively good job because there weren’t many typos and the two students (when asked) said they thought the guides were clear. I have two returning students (from summer research), one of whom has learned the new software and the other one will do so this afternoon. The semester will be less productive than the summer research-wise, but I’m looking forward to writing up the good work that my students did this past summer. I also have a potential new collaboration but I’ll need to delve in a little more to see if it will be a good fit.

 

Whew! It’s been a great first week. Tiring, but it’s so nice to feel the energy of being back on campus with students who are excited to embark on their first semester of college or coming back from the summer and reconnecting with their friends.