Xenonite

A month ago, in my quantum chemistry class, I did a “fun” segment on the ubiquity of hydrogen in the universe. We had finished solving the Schrodinger equation for the hydrogen atom, discussed the representation of orbitals, and talked about spin and the Zeeman lines. To wrap up, I told the students about SETI, the movie “Contact”, how we might talk to ETs on the hydrogen 21-cm line, and what information scientists from different worlds might communicate to each other to establish a baseline. After class, one of my students asked me if I had read The Three Body Problem (I had) and Project Hail Mary (I hadn’t). He said I’d really enjoy the latter without giving away the plot.

 

I looked up the book. The author is Andy Weir, and I enjoyed reading The Martian. The blurb sounded familiar – astronaut lost alone in the depths of space – which is why I hadn’t considered it previously. But after reading some reviews, I decided it might be interesting enough to give it a whirl. So I borrowed the book from the library, then waited for Thanksgiving Break to devote a block of time to immerse myself in a good book.

 

I’m pleased to say that Project Hail Mary is very good; better than The Martian given my research interests and spending much of my working hours prepping for biochemistry class. Yes, the protagonist is in a related situation. And yes, the protagonist has a personality similar to Mark Watney. But there are plenty of differences that make this an engaging story. I won’t give away the plot, but I will say that that Weir serves up interesting and thoughtful stuff on biology, chemistry, physics, mathematics, and climate science. The scientist in me loved geeking out on the material. The speculative biochemistry got the gears in my mind turning! More on that in a moment.

 

A chunk of the story has to do with what might happen when one comes into contact with an extra-terrestrial species. How might scientists from both realms communicate even though they may have different umwelts? Project Hail Mary is more well-grounded in science than The Arrival or Contact (my only experience is with the movies rather than the sci-fi novels they were based on). Weir does a good job here. But for me that wasn’t the best part of the book.

 

As a chemist, I was intrigued by a new material, xenonite. At least that’s what the human protagonist calls it because he could detect xenon as one of the heavy elements in it. Xenon, as my introductory chemistry students know, is a noble or inert gas. It shouldn’t do anything! But in G-Chem, I surprise them with a few noble gas compounds of xenon and krypton as they work on Lewis structures. While some of the physical properties of xenonite are described, Weir leaves the chemical properties a mystery although clues suggest that lighter elements with polymeric structure are part of it. It can be good storytelling to keep the science a bit vague.

 

Xenon means strange. Or fittingly: alien. Weir’s speculative descriptions of xenobiology were fun to read. What sort of body and what sort of biochemistry should the alien species have given the environment of its home? How might it have evolved? What are the possible building blocks at higher or lower atmospheric temperature? How might temperature affect the building and functioning of an organism? What about gravitational force? None of this speculation is new to sci-fi, but I could see where Weir started with reasonable biochemistry and then extrapolated to provide not unreasonable speculation. I’d say he does a good job overall in thinking about what chemical elements are important, how they might be acquired as food, the role of energy transduction, and how evolution plays into all of this.

 

All this got me thinking about what chemistries are available in different environments and where an organism might be able to exploit energy differentials. Is water required? What about ammonia? Or acetylene? Or cyano compounds? Or formamide? Why is phosphate the universal energy “carrier”? How about sulfur compounds? I could envision teaching a whole new class surrounding this question! But for now I think I will settle for coming up with some clever examples for my classes next semester – I’m teaching lots of thermodynamics and kinetics both at the G-Chem and P-Chem levels. I can expand on the examples I use when discussing fuels and energy transduction. I hope the students find such speculation fun. I certainly did. And that’s why Project Hail Mary was very well worth the read!

Track Changes

I’m typing the draft of this blog post in Microsoft Word on my laptop. I will then edit it by adding text, removing text, or moving text from one part of the document to another. This is easily done by using my trackpad to move the blinking line to the appropriate spot. Then I can type more text, or hit the backspace (delete) key to remove text, or I can highlight a bunch of text by dragging my finger across the trackpad, then cut and paste it to a different part of the document.

 

Before word processors, I would have to write out my thoughts with pen on paper. (I was taught in school that you had to use the pen and not the pencil.) I would then use a different coloured pen to mark-up my edits. And after I was happy with everything, I would slowly type it out on a typewriter, taking care not to make any mistakes because I hated using white-out. (I did not know of “correction tape” back in the old days.) Have word processors change the way I approach writing a document? I think so. But it has felt more like a gradual shift because I only moved to word processing in fits and starts.

 

Why am I thinking about this? Because I’m reading Matthew Kirschenbaum’s Track Changes, which is a history of word processing. Kirschenbaum digs up all manner of interesting details on the advent and evolution of word processors. There are stand-alone word processors like the Wang, much used by many authors in the 1980s. Some writers started using microcomputers with programs such as Wordstar, followed by WordPerfect. Other writers refused to use an electronic device and would use their favorite typewriter, or write longhand and hire a typist. There are fascinating tidbits in the wild and open early days of word processing, unlike the consolidation we see now where Microsoft Word and Google Docs are pretty much all my current students have ever encountered.

 

Memories. They’re mostly hazy. But I do remember using a typewriter as a child. My mother, a schoolteacher, would type out exams for her class. Sometimes I was the free labour typist. Because I had weak fingers, my technique was a strange double-finger tap – my second finger atop my third to provide the extra strength – only with my right hand. My left hand was used to hold down the shift when capitalization was needed. I was pretty quick for a “one-finger” typist.

 

In the mid-to-late 1980s, we got an Apple II clone. (The actual Apple II would have been very expensive in the country where I grew up, far from the United States.) I learned how to use Wordstar. With a much easier-to-press clone keyboard, I was able to utilize all my fingers for typing. I even practised on a simple typing computer program whose name I can’t remember. There was no mouse to point-and-click. Keyboard commands were used to navigate the document or to cut and paste. I’d like to think this prepared me when I eventually learned to use the vi text editor as a computational chemist in graduate school.

 

My first two papers in graduate school were written in TeX with an emacs editor. All subsequent papers were written with Microsoft word because we had industry collaborators and I needed to read and write research updates. When I put together my thesis, reformatting the two TeX papers into thesis chapters was very annoying with many hours spent getting things to look right. I had used Microsoft Word sparingly as an undergraduate, to write papers or lab reports when required, and for my undergraduate thesis. I carried disks around. I made backup copies because you never know when your data becomes “corrupt” and you get a disk-read error.

 

When I started as a professor, I wrote out my lecture notes longhand in pen with multiple colors for emphasis. I had access to Microsoft Word, which I used to write a problem set or an exam. I still wrote out the solutions longhand, a practice that continues to this day which my students find surprising. I explain to them that I actually take my own exams to make sure they are suitable in length and difficulty. I think the students appreciate this even though some still comment that my exams are too long and too hard.

 

My first switch to partial lecture notes in word-processor format came when I ditched the textbook for P-Chem II more than fifteen years ago. I made Word-processed worksheets with blank spaces for students to write notes. For my own lecture notes, I’d write longhand on those worksheets with multi-colored pens, as I did before. Four years ago, I did the same for P-Chem I. Just under ten years ago, I started transcribing my G-Chem lecture notes into Microsoft Word. The students don’t see these notes. I still write out all relevant information on the whiteboard in class. Except for a few topics (stoichiometry, nuclear chemistry, electrochemistry) where I still use my longhand notes, the conversion is almost complete. This semester, teaching biochemistry for the first time, I made all my notes on Word. No longhand. My conversion is complete.

 

But I wonder if something has been lost in the process. Reading Kirschenbaum’s book made me think about my thought process when preparing my lecture notes. It feels different to use a word processor compared to writing longhand. I have this nagging feeling that I was more thoughtful when I wrote longhand, because I wanted to keep my notes as clean-looking as possible – otherwise it would be hard to decipher my own scrawling in the margins accompanied by cross-outs, carets, and arrows. There’s also something about the layering of these edits that preserves the original, so unlike Word where I delete some text and it disappears into oblivion. Every semester that I re-teach a class, I always make a new copy to preserve the previous one – but to be honest I hardly look back at the earlier versions.

 

I also have this nagging feeling that the ease of word processing and editing has made my thought process more meandering. I used to have tightly choreographed lectures. Every word was chosen carefully. Now with my poorer eyesight and reading formatted Times New Roman instead of my own handwriting, I wonder if I’m starting to do a poorer job in my teaching. Yes, I’ve gained a lot of experience over the years knowing where the tricky spots are for students. But I suspect I’m less focused in my lectures than I was before. Having attained the sought-after rank of full professor some years back, no colleagues visit my classes anymore and I don’t get any peer feedback. Students still write their comments in their evaluations, although these are now electronically dashed off rather than handwritten. But the students don’t know how I have evolved as a teacher – they only see the here-and-now.

 

Track Changes is a wonderfully apt name for Kirschenbaum’s book. It reminds me that I should take some time to track the changes in my teaching and think about where I want to go with it. It also made me nostalgic for old Apple II games (I had a tiny bit of fun on an emulator). I began to wonder how other parts of technology change the teaching and learning experience, especially now that many of my students have tablets with a stylus that they use for note-taking and to write out their problem sets. I started to think about how one’s visual field, be it a tablet screen, 8x11-sized paper, a full-sized monitor, or looking up at a white-board – how does this impact teaching and learning? And the only way to learn how to improve the educational experience is to track changes!

Body Electrolytic

We living organisms are sacs of salty solution. That’s why we can be electrocuted. In my G-Chem class yesterday, we discussed electrolytes – solutions that conduct electricity. What do electrolytes have? Mobile charged particles, in this case ions from a dissolved soluble salt.

 

The black ghost is a knifefish – one of several species that include the electric eel in this family of electric fish. You can listen to the “sound” it makes by dipping an electrode in water set to detect the right frequency (~900 Hz). The black ghost generates an electric field which can be distorted by objects that have different conductivity compared to water. Thousands of electroreceptors on the body of the black ghost “listen” for these distortions. That’s how it detects its prey – the sacs of salty solution!

 

Perhaps “listen” is the wrong word. Should it be “see”? Our eyes detect electromagnetic radiation in the form of photons, although this isn’t akin to the electric field. Or maybe it should be “touch”. We have touch receptors all over our body, and essentially the black ghost extends its sense of touch when it generates the surrounding field. It costs valuable energy to generate an electric field so it doesn’t extend very far and quickly dies off with distance. You’re potential prey only if you get too close.

 

I’m learning all this re-reading An Immense World by Ed Yong, the best non-fiction book I read last year. Most of what I read is borrowed from the library. After my first read (last November!), Yong’s book is one that I knew I would return to on multiple occasions so I bought my own copy. (It’s the first non-work-related book I’ve bought in a decade.) Today’s post is from Chapter 10, “Living Batteries”.

 

What are the advantages of generating an electric field to detect prey? Yong writes: “It might be that electric fields are more reliable than almost any other stimulus. They aren’t distorted by turbulence… in fast-flowing rivers, where torrents and eddies befuddle the lateral line. Electric fields aren’t obscured by darkness or murkiness, so electric fish can stay active in turbid waters and nighttime hours. Electric fields aren’t blocked by barriers as light and smells are, so electric fish can sense through solid objects… it’s very hard to hide from these animals. They are sensitive to… capacitance… [an object’s] ability to store a charge.”

 

I also learned that these marvelous creatures turn their electric fields on and off to generate a particular rhythm – it’s akin to the “sound of their voice”. But this steady beat can also be modulated to communicate other sorts of information. Essentially living batteries are talking and listening to each other through pulsed electric fields. Yong writes: “These animals can’t hide from each other… A river full of electric fish must be like a cocktail party where no one ever shuts up, even when their mouths are full.” And some species, such as the elephantfish, have significantly sized oxygen-guzzling brains (as a percentage of body weight).

 

Reading Yong’s book inspired me to imagine teaching a class on the “Chemistry of Sense”. I already talk about photons in my G-Chem class and how we use them to “see”. I could bring in smell and taste by discussing molecular recognition and interactions. It requires molecules to “touch”, so to speak. While I hadn’t thought much about sound, I was reminded by our human limitations of hearing (20 Hz to 20 kHz) and what we might be missing, analogous to vision where I already discuss how organisms in other environments may have evolved different photoreceptors to detect different dominant wavelengths. And we could even speculate about sixth or seventh senses with electric fields as one possibility. After all, our electrolytic bodies are sacs of salty solution!