Danger: Bodily Comfort

Unless I was a wealthy monarch, I would not want to have lived centuries ago. Most other people back then had difficult and uncomfortable lives. I enjoy today’s middle-class creature comforts. But maybe I shouldn’t, or at least not too much. I’m at the tail end of Daniel Lieberman’s The Story of the Human Body that traced early hominid hunter-gatherer bodily adaptations to the mis-adapted lifestyles of the twenty-first century.

 

In his chapter “The Hidden Dangers of Novelty and Comfort”, Lieberman explains why we
mistake comfort for well-being: “Who doesn’t love a state of physical ease? It is pleasant to avoid toiling for long hours, sitting on the hard ground, or being too hot or too cold… I am sitting in chair to write these words because it is more comfortable than standing… [when I] go to work, I can take an elevator to my office’s floor to avoid the stress of climbing the stairs. I can then sit in comfort for the rest of the day in another climate-controlled room. The foods I eat will require little effort to procure or consume, the water in my shower will be just the right temperature, and the bed in which I sleep tonight will be soft and warm.”

 

No, I’m not giving up my climate-controlled indoors, my warm showers, or my mattress. Nor would I want to hunt and gather food out in the wild. I wouldn’t survive. Or maybe I would and hunter-gatherer survival instincts might kick in. I recently replaced my ten-year old firm mattress with another firm one, because I think the old sagging one was exacerbating my lower back problems. Having a sedentary job where I sit in front of a computer most of the day is likely the root cause. It’s bad for my back, my shoulders, my eyes, and likely my muscles and bones which I don’t notice as much. I am trying to correct for this with daily stretching exercises and a regular walk (that is likely not long or brisk enough). My doctor told me that I needed to get more aerobic exercise walking uphill. I started doing that this year by parking further away from my building at the bottom of a hill. It has probably done me some good.

 

Reading Lieberman’s timeline of developmental bodily changes in children makes me thankful that I grew up in the twentieth century in a developing country where I was barefoot much of the time, didn’t spend all my time indoors, and ran around enjoying being outdoors even with crappy weather that today’s me thinks is darn uncomfortable. I did read a lot growing up but was lucky to only have mild myopia – I can only thank random gene assortment because two of my siblings have terrible myopia. We didn’t have comfortable sofas growing up and our mattresses were much, much thinner. Nor was there easy access to ultra-processed foods. And my bicycle was my main mode of transportation. Today’s kids are in a very different environment even in my home country. They spend most of their time indoors, ride in cars, spend gobs of time on mobile phones or tablets, and partake of the myriad conveniences of modern life.

 

Lieberman picks out three things to discuss: shoes (for feet) versus being barefoot and the nature of walking, how the shape of your eyeballs change with focused reading (be it a book or a screen) and not having diverse outdoor visual stimuli, and sitting too much thanks to the ubiquity of comfortable chairs. They were all eye-openers. As of yesterday I am now trying to look up and look outside while reading or being on my computer. I’m making sure I get up and stretch because I know I’m sitting for too long. I started going on extra walks and try to increase briskness. Now that my semester is ending I have to be even more cognizant about being active and looking away from a screen. Going to class and being in office hours helped with my being more active.

 

None of this is new. I had previous phases where I would be more mindful of my posture and being active. But after some time, I get lazy. And being older means I have less energy, and honestly, less of a desire to be active. I know I’m losing muscle mass and some days I do something about it, but other days I don’t. Why oh why do we default to ease and comfort? It’s just easier in the short-term even though I know it’s not good in the long-term. Good habits are so easy to break and much harder to re-form. I suppose I need constant reminders, and Lieberman’s book helps in this regard.

Fuzzy Meaning

Sometimes it’s good to revisit a paper I read a while back but did not appreciate. For today’s post, that paper is “The Meaning of Biological Information” (Koonin, E. V. Phil. Trans. R. Soc. A 374: 20150065, DOI: 10.1098/rsta.2015.0065). It’s not earth-shattering, but it more than meets the eye on my second read.

 

Koonin first distinguishes coming up with an equation to calculate information from the one used to calculate Shannon entropy. Then he (correctly in my opinion) emphasizes that what constitutes information is in the eye of the beholder. Where is this information stored? The genome. No surprises there. I’d argue it’s not just the genome but the entire cell, but that’s a discussion for another day. What type of information does the genome store? What does biology want to behold? Koonin says “information about the environment, allowing the organism to predict and exploit environmental changes”. I say Amen. He goes on to say “another key part is about the (nearly) universal aspects of cellular and organismal design”. Okay, I say. But I’d say the cell is responsible for this although the genome plays a tightly coupled role in the business of living.

 

The next important observation Koonin makes is that animals and plants, the so-called ‘higher-complexity’ organisms have “the highest total information content but are also entropic genomes with a low biological information density”. Thus, prokaryotes are more information-dense. They have to be because selection is stringent for survival if you’re a bacterium or archaeum. Complex multicellular organisms on the other hand are only subject to “weak purifying selection and the high intensity of genetic drift preclude efficient purging of meaningless sequences and conversely allow proliferation of such sequence, in particular, various mobile elements”. But meaning is also in the eye of the beholder, and the question is what these mobile elements represent.

 

Koonin is going to endow such sequences with “fuzzy meaning”. Why are they fuzzy? These elements in the genome can be endowed with meaning at some point down the road evolutionary as they are transcribed. And some of them certainly are, not to make a distinct protein, but as some sort of regulatory element. This is where my limited knowledge of biochemistry hinders me from a fuller understanding. I know regulation is crucial in the living cells of extant life but I can’t quite comprehend its dizzying complexity – wheels within wheels turning every which way. Koonin helps clarify why these mobile elements might be important: “the sequences with fuzzy meaning form the material basis of plasticity from which functional molecules, primarily but not exclusively, regulators of various processes, are continuously recruited to assume better meaning.” And if you need information about changing environments around you to survive or thrive, the fitter organisms will have some plasticity as their back pocket ace.

 

What we thought of previously as junk DNA isn’t quite junk. But neither do we know exactly what it is for. It has the potential to be a useful adaptation. One example Koonin gives: “genes from selfish elements are often recruited by host organisms such that the specific activity of the encoded protein is modified and appropriated for host function”. The example I’m thinking about is how organisms coopt a poisonous molecule into a messenger molecule over time. That’s a big chunk of secondary metabolism in plants and insects, and likely many other organisms. There’s an arms race with different species employing poisons and protections. Many of the molecules we hear about that are chemically poisonous are found naturally in our body: cyanides, peroxides, hydrogen sulfide, and more. Koonin’s arguments make more sense to me now that I understand a bit more biochemistry, having forced myself to teach it last year.

 

To calculate information or ‘meaning’ in a genome, Koonin defines it as calculating the differences that could arise by comparing “an alignment of homologous sequences”. Thus, information density is relative, not absolute. I’ve been struggling to think about how to export this idea to the prebiotic molecules that I study. This is pre-genome so there’s nothing to align. But perhaps the (closed) autocatalytic set is analogous to the genome. Certainly we’d want to catalog the identities of the molecules and look at their diversity. But we’d also likely need an analog component to track concentrations of each molecule. I haven’t quite wrapped my mind around how to do this yet. It’s still fuzzy for me. And perhaps fuzzy meaning is the appropriate term to use here.

Food: Bipedalism, Teeth, Brain

Why does the human body look the way it is? While I suppose it could have magically appeared in its present form ex nihilo, it is more likely to have evolved from existing structures to adapt to the surrounding environment. Why am I thinking about this? Because I’m reading the fascinating Story of the Human Body by Daniel Lieberman, a professor of human evolutionary biology. 

 

The forerunners of the Homo genus show up in the fossil record some 6-7 million years ago. Then between 2-4 million years ago we have a bunch of Austropithecus fossils, of which Lucy is the most famous. Then comes Homo habilis somewhere around the 2 million year-old mark followed by its cousins. The last of these, Homo sapiens, shows up 0.2 million years ago thereabouts. The boardgame Origins How We Became Human begins somewhere in this time-frame leading up to modern day technological and polluting humankind, and you one can spend many hours simulating all of this in a fun yet challenging game.

 

Homo shows up as an ice age is beginning. Food is getting sparse. The climate is getting colder. While our close cousins, the chimpanzees, are still well-adapted to life in the trees and eating fruit, even they have to chew on bark and other plants in lean times. Homo starts to find a different niche. We are one of the few animals that spend much of our waking hours in the upright position, on two legs. And before comfy sofas, we walked a lot more. The savannas and grasslands require more walking and less swinging through the trees. Freeing our hands allows us to create better tools, whether it be digging for tubers or getting energy-and-nutrient-rich meat. It’s all about food. Eat or die. And most animals spend most of their lives looking for food and eating it.

 

We’re not as fast or as fierce as lions. We don’t have the speed to bring down a running antelope and rip its flesh with powerful jaws and teeth. But a group of us can run down an antelope eventually. We are one of the best long-distance runners in the animal kingdom, with thin hairs and sweat glands that allow us to keep going without overheating. And we have our hands free while doing it. Lieberman covers the wide range of anatomical adaptations from head to toe that allows us to do this. From the way our head sits and bobs around on our neck to the arch in our foot and the size of our big toe, we are long-distance running machines.

 

I didn’t realize how much you can learn from fossil teeth. Lieberman goes through this in detail while keeping the reader engaged, which is no mean feat. And he does calorie counts to estimate how much our forebears might have to forage or hunt to stay alive. Processing our food to make it more efficiently digestible – by pounding, chopping, cooking – also led to adaptations in why our jaws and teeth are different from our chimp relatives. You can see the process of change through the fossil record from the various Austropithecus through the Homo hominids. And to have efficient energy stores, we need fat. We are fatter than most, even in the distant past, not to mention today – where our bodies still crave the fat and we get so much less exercise driving our cars to the supermarket and foraging in the aisles of abundance.

 

To get the meat, it is more efficient to hunt in groups. And men do this best since they don’t have to physically nurse children. But to communicate and coordinate and thrive as a social community, we need to expand our skill set beyond our dexterous hands. That requires growing our brain – an efficient prediction machine that helps us size up our immediate situation and act accordingly. I learned that our guts are about equal in relative weight to our brain, unlike our chimp relatives with much smaller relative brains. Our brain is energy-hungry and we have to keep it well fed. To do so, we store fat that we metabolize into glucose to keep the energy supply constant and reliable.

 

All this makes me think about my origin-of-life research and protometabolic systems. What do living systems need? Food to stay alive. And with a little more excess, organisms can grow and reproduce. Humans are particularly adept at accumulating more energy than we need for our daily sustenance, especially once better tools and hunting weapons, not to mention cooking, became part of our daily routine. Better to save up for those cold, icy days. Except for photosynthetic organisms that can transform carbon dioxide from the atmosphere, the rest of us have to get our carbon building blocks from other sources: plants, animals, fungi, and other organisms dead or alive. To survive and thrive, a metabolism needs to be efficient and the food gathering needs to improve. I need to think about this at a chemical level. It’s hard for me to imagine, but I can make analogies to what larger organisms do in their quest for food and nutrition. Ultimately it all comes down to grabbing energy to stay alive.

 

P.S. I also did not appreciate how good humans are at throwing objects with precision. Our arms, shoulders, hand-eye coordination, all kept in balance, are amazing!

Stoichiometry Blues

I don’t know why my G-Chem 1 students, on average, did much more poorly than expected on the most recent midterm that covered stoichiometry. While the midterm exam average for stoichiometry is typically lower than the other midterms, this year it was substantially lower, far outside the norm.

 

Last year, my G-Chem 1 exam averages were similar in the first three midterms, so I think the range of academic ability in chemistry is similar between the two classes. I also have all four midterms at the same point during the semester (although there was minor moving around of topics). So, it shouldn’t have been Thanksgiving break that caused students to forget everything they learned. And some students still aced the exam. I even made sure to cover the last bit of stoichiometry the Friday before Thanksgiving break so that the many students who chose to miss Monday’s class wouldn’t miss the last section on redox reactions.

 

What’s different? The main change I made in my G-Chem class was to ditch the online homework system and its accompanying textbook. Instead, I assign some homework and “collect” a subset of it to grade. What I collect is clearly less than what I had previously assigned in an auto-graded online homework system. It’s possible that students are not doing the other suggested problems that I don’t collect. (Some certainly do, when they come in with office hour questions or turn some of it in even if I didn’t assign those as part of what I collected. But others might not.) But the questions I do assign are written the way I would write an exam question, so I felt that was helpful to students. This is unlike the auto-graded online homework system that often phrases questions differently.

 

None of this seemed to be a problem through the first three midterms. Students were doing similarly as they did in the past. I even asked for feedback from the students about how they felt about the changes I made and the majority seemed to like them and thought my study guides were helpful to learning the material. My current hypothesis for the difference is that when it comes to stoichiometry, the students need much more practice problem solving, and the changes I introduced caused at least half (or more) of the class to practice less compared to previous cohorts. This wasn’t as big a deal in earlier topics. Even though there were calculation type questions earlier in the semester, they weren’t as concentrated as when we covered stoichiometry.

 

I think I need to assign more problems or provide more time in class to work through them if I don’t want to be doing more grading. And given that I’ve jettisoned the textbook, I should move stoichiometry earlier. (We’ve been using “atoms-first” textbooks for many years that shift stoichiometry to the last third of the semester. I didn’t want to make too many major changes compared to what I did last year.) I also think the Thanksgiving break causes students to forget what they learned, but I suspect this wreaks more havoc for stoichiometry than other topics, and this year there was a double whammy when the students didn’t practice enough.

 

Thankfully for the students, I drop the lowest of the four midterm scores, and that will be the case for the majority of students in my G-Chem class this semester. That was also true last year (stoichiometry always has the lowest average), but the average scores were nowhere as low as this year. So the overall student grade hasn’t been impacted yet, but it may mean that many students need to beef up their stoichiometry problem-solving skills before the final exam. While the final exam is cumulative, so stoichiometry might be 20-25%, that’s still a substantial portion. Some students have come by to talk, now that they realize what they missed so that’s a good sign. Hopefully more do so.

 

There are two other possibilities for the lower-than-expected exam scores. It’s possible the exam was harder this year. I don’t actually think so, but since instructors are inflicted with the curse of knowledge, I can’t say for sure. I’ve been writing exams for many years and I’m confident that the exam I wrote was about right, but it could have been a tad harder – certainly not so much more difficult to cause the substantial drop in scores. It’s possible I have an academically weaker class this year when it comes to stoichiometry and math-related chemistry problems. My G-Chem classes are small, often less than 30 students (although it can be as high as 40) so there can be substantial differences from one group of students to another.

 

In any case, I need to think about some changes I’d like to make to my G-Chem 2 class next semester that is certainly more math-heavy. I am teaching the Honors section and the students who register for that class are self-selecting so I might not run into the same issue. Certainly I need to make changes to my G-Chem 1 class next year if I continue not to use an online homework system and textbook.

Learning by Imitation

Chunks of time in my chemistry classes (G-Chem and P-Chem) are spent working through examples on the white board. Students write along with me as the solution unfolds. Essentially, they are copying or imitating my answers. I think this is a key way for students to learn chemistry efficiently. When they haven’t yet acquired the experience of solving many, many different kinds of chemistry problems, the entry point is to go through worked examples of increasing difficulty. Then I let them loose on homework problems for further practice, but this usually takes place outside of class. There’s only so much time available in the classroom, and I prefer to spend it going through the nuances of worked examples while answering questions synchronously in real time.

 

I suspect this process of imitation is how I learned most of what I know today, be it chemistry or cooking or useless trivia. Scientists are starting to notice more examples of learning by tool-making in other animals, particularly primates. And it seems that they are learning by imitating each other too. We humans are particularly adept at imitation. Is this how we became so much more technologically advanced compared to our animal cousins? In the boardgame Origins: How We Became Human, the most important action in the Age of Instinct is Imitation. After that first age, this action is now called Education, but is essentially the same thing – you can take cards played into the discard pile by other players.

 

The idea of copying gets a bad rep in education. It’s often associated with mindless imitation without learning. I have no doubt this happens sometimes in my classes, especially if students didn’t do the assigned reading before coming to class. Then they’re lost and sometimes they copy what’s on the whiteboard without understanding. But even for students who are following along, they don’t fully understand why the protocol I am leading them through works. I talk my way through why I do each step, not just how, but the reality is that until they see a lot more examples and do the homework, they won’t necessarily appreciate the efficient process I’m taking them through. But that’s okay, because imitation and comprehension support each other.

 

Pondering the importance of imitation, I’m wondering if I should go back to providing full worked-out solutions to homework problems in G-Chem. (I’ve always provided full solutions in P-Chem.) I used to do this in my early days of teaching G-Chem. Then I stopped doing it because students would just look at the answers without struggling through the problems and then do badly on the exams. They deceived themselves into thinking they knew the material by short-circuiting the learning process. At present I provide answers to numerical problems without the full-worked out solution, but I’m starting to think I need to provide more guidance in how to explain conceptual answers. They see it in class. They imitate it in class discussion. They are partially found in my Class Notes handouts. The most capable and well-prepared students do very well on the exam with these, but there’s a large gulf compared to the least-prepared students who essentially write nonsense or leave chunks of the exam blank because they have no idea.

 

Finding the right balance will be tricky. I don’t collect student answers to all the questions I recommend they try after each class. It would be nigh impossible for me to grade them all. (Right now, I collect a subset.) Do students try everything I assigned them to practice if I don’t grade it? Some do, and they benefit from it. Others don’t. The adage of leading the horse to water may apply here, and maybe I shouldn’t worry so much and let the students choose if they want to do the work or not. Since I’ve moved away from the online homework system that gives immediate feedback to the student (although not always the best worked solution), I’m grappling with what to do about providing solutions. For some of the easier and more straightforward questions, ChatGPT does decently at providing a worked solution, but not for more challenging ones. And nuance is important in chemistry which present A.I.’s fail to capture.

 

Learning is still a mysterious thing. But I’m beginning to think that imitation is surprisingly effective. How best can I leverage it? That’s the question.

Adventure Creation Kit

Two adventure-themed computer games I played back in the ‘80s had a unique style that I would call fast-and-furious in a mythological milieu. They were Ali Baba & The Forty Thieves and Return of Heracles, both programmed by Stuart Smith. While there were similarities to other adventure games, there wasn’t anything quite like them – strange and strangely addictive. Wandering creatures and NPCs (non-player characters) had a strange life of their own; they weren’t just there to interact with you. Sometimes they would fight each other for no seeming apparent reason while you picked up the spoils.

 

Like other kids who were exposed to computer games, I wondered what it would be like to create my own fun computer game. I had time on my hands. I learned BASIC by reading books in a bookstore or from the library and taking notes. I went to a friend’s house to practice my skills (because we didn’t own a computer). But all I could manage were some simple Lemonade style text-games. Then I discovered Adventure Construction Set, also by Stuart Smith. (Back in the day of pirated disks with no manuals I didn’t realize all these were by the same author.) It had a built-in game Rivers of Light, but I was most excited about making my own games. I gave up after a while. It felt very tedious.

 

After finishing Antepenult, I mused about whether I would create its sequel. Was there something out there like Adventure Construction Set but updated for the Ultima series? Turns out there was. Thus did I discover Adventure Creation Kit by Chris Hopkins, originally written in the ‘90s with patches up to 2009. I downloaded it and fired up DosBox. It has a tutorial and two-built in adventures. I ‘played’ the tutorial and the shorter Brigands adventure. Then I read the manual. It looked like quite a robust engine which supported BASIC-style macros that expanded all manner of things you could potentially do. It also had an Ultima V tileset. If I’m going to create an Ultima-clone, I might as well just use the tileset.

 

After creating a sandbox and playing around with it for several sessions, I felt ready to create my first game. It featured a 64 x 64 world map, three towns (one medium 32 x 32 and two small 16 x 16). The fifth map was a series of a dozen interconnected dungeon-style rooms. There were over 25 separate dialogues and I created some new icons for characters and some new special items. Creating the game took me 10-12 hours. I made it for my spouse who had never played such adventure games before but has heard me reminisce about them. Here’s a screenshot at a shoppe in one of the towns.

 

Adventure Creation Kit has a reduced command interface compared to Ultima, helpful to the new player, and these are listed on the right-hand panel. Dialogue with the townsfolk allows for plenty of interesting options, but I haven’t figured out if the dialogue can be scrolled rather than the screen-clear with each new prompt. There is no party – just the sole adventurer (like both Ultima II and Antepenult) which simplifies things such as no additional combat screen. Spellcasting utilizes simple generic reagents but it looks like I can modify how these work through macros. Here’s a picture just outside the start town.

 

 

It was interesting to see how my spouse interacted with the system. Things that were obvious to me as someone who played these types of ‘80s games were not at all obvious to her. She found the iconography unfamiliar. I advised her to ‘Look’ at anything she wasn’t sure of. She was also initially confused by the world-map wraparound. I had an NPC hint that the “world was small and round” but she didn’t quite get the reference. Eventually she figured out how to navigate around, but she went through great lengths to avoid combat unless it was inevitable. I did help her get suitable weapons and armour at the shoppe.

 

Even though an NPC had told her to be careful of the poisonous marshes and their ‘pink flowers’ outside, she still blundered into it and her character got poisoned. I had to direct her to go back to the shoppe to get a curing potion. (Her character hadn’t yet learned how to cast a Cure spell.) Again, this would have been obvious to me but I had forgotten to have an NPC explain it to a newbie. The original marshes tile did not have the pink tinge as you can see in the screenshot above. I had added those to the tiles to make them more obvious.

 

Overall, she enjoyed learning and playing the game, although I learned more just watching how she navigated the system. To me that’s a win and the hours I spent created the game were worth it. Clearly one should highlight keyword text in dialogues (I didn’t, but Nox Archaist did, which is extremely helpful to new players). It also made me aware of some odd issues in the game such as line-of-sight when dealing with opaque tiles and which regions of a map get illuminated. I have grandiose ideas of creating an Antepenult sequel but it would require much more time and effort, and I don’t think she would play it. I looked around to see if there is an active community still using Adventure Creation Kit but I haven’t come across it. I expect to play around with the kit a little more, but I think what is needed is a more modern base code. So if anyone out there who likes programming wants to create a modern version of the kit, I will be happy to write some (hopefully) engaging Ultima-style adventures!

 

P.S. To learn more about the Stuart Smith style, I highly recommend this article by the CRPG Addict. I think it does a great job capturing the essence of Smith’s games.

A Sign in Space

Back in the third week of October, we were finishing up solving the Schrodinger equation of the hydrogen atom in my quantum chemistry class. I end that module with a brief discussion of hydrogen’s role in mapping the universe – its abundance, and why it might be used to communicate messages with extra-terrestrials. It’s a variation of my Star Wars Day class in G-Chem, but my P-Chem students have just seen the Zeeman splitting and understand where the 21-cm wavelength line comes from. I showed the students the SETI message that was beamed out from the Arecibo telescope.

 

One of the students asked how anyone would know how to interpret the data if you didn’t have any idea what the content would be. In the movie Contact, computers solve this presumably by running all manner of decoding algorithms on the detected message. But that’s a mighty big handwave. Humans write algorithms, and they are based on having some preconceived notion of the problem we are trying to solve. But if you have no idea where to start, what do you do? You could easily misinterpret the “code” in so many ways, most of which will just be garbage.

 

Last weekend I stumbled across A Sign in Space. It’s a clever experiment. A media artist, Daniela dePaulis, in collaboration with space agencies and observatories, designed a message that was then transmitted a signal from a spacescraft which was then picked up by our ground-based telescopes, similar to those that Jodie Foster used in Contact. As to the interpretation of the stream of zeros and ones, that was turned over to the public. Citizen scientists were going to try and make sense of the data. It took a year before a father and daughter team finally cracked the code. But what was most interesting was looking through the process in which people with different expertise and all walks of life, not only speculated, but did some hard work in trying to make sense of it all. There were plenty of false trails, clever ideas, lots of humor, and I was impressed by the shared sense of people who didn’t know each other all helping solve an interesting problem.

 

The actual solution isn’t as interesting, although it continues to spark lively discussion on a Discord thread devoted to this project. The message provided a visual image of five amino acids. None of them were “canonical” amino acids and some (if not all) of them have been discovered on meteorites. They were all alpha-amino acids. It wasn’t clear if they were all-D or all-L, but folks on Discord thought they were the L optical isomer (similar to life on Earth). Three were hydrophobic with linear alkyl side chains of 2, 3 and 4 carbons respectively. One had an amine group (a “basic” amino acid) and one had a carboxylic acid group (an “acidic” amino acid). All were depicted in their non-zwitterionic form.

 

From an origins of life point of view, the basic amino acid (2,4-diaminobutyric acid) has several possible roles. As to the three hydrophobic amino acids, there are reasons why they would not have been selected for from the point of view of chemical evolution if one wanted to have a limited yet diverse set of amino acids. The branched acidic one is interesting, but more costly from a synthetic point of view. As to whether these would form some sort of code, it would be inefficient. I don’t think the artist who put this together was thinking along those lines. While we don’t know exactly how alien scientists would think and approach a problem, we human scientists can likely come up with some reasonable scenarios. If this were an actual transmission from E.T., and the message did show these five amino acids, my speculation is that they know the makeup of our proteins and are telling us that they have some additional ones we don’t have.

 

Science content aside, what I really liked about this project was the test-like conditions of what citizen science might look like if alien messages were received from outer space. There was a vast open-endedness to the possibilities even though the final “solution” was very narrow and not particularly meaningful from a natural science point of view. From a social science point of view, I think this was a creative experiment! I look forward to being surprised by the ingenuity of how to get society at large to care about science, dive into it, and experience what it’s like to solve an interesting intellectual problem collectively.

Ten Years

It’s hard to believe I made it to ten years. But my interest has waned, no thanks to data-scrapers vacuuming up writing to train their large language models. My number of blog posts has dropped by twenty percent the last two years and I expect it to dip further. Today is the day I will give myself permission to no longer feel obligated to keep up. I will probably write occasionally when the fancy strikes me, but I have other interests to take up my time.

 

Looking back at my mid-decade post, I would agree with past self. My writing in this format has gotten a little stagnant; that’s the diminishing returns part. I do still write primarily for myself, and to some extent my students. I have a few links as optional reading for students who are interested to get a slightly different perspective on some of the topics they see in class. My sense is that students who’ve read these optional posts found them helpful or at least amusing.

 

Have the things I write about changed?

·      Book reviews are now at 49%, up from 43%. I don’t think I’m reading more. I’m just blogging less about other things.

·      Teaching is at 33%, a slight drop, but not by much. I love thinking about teaching and learning. That won’t change – even when I retire from my full-time job as a professor.

·      Research dipped a little from 8 to 6%, although origin-of-life posts maintained steady at 11%.

·      Magic also dipped from 12 to 10%. I certainly think less about magic these days. And it’s been a while since I re-read Harry Potter or any other magic-related fiction. I’ve been reading sci-fi a little more; I suppose technology is a sort of magic but I haven’t labeled the posts as such.

 

Halloween does make me think of magic. Today, I read an article about the history of how Halloween is celebrated in the United States and how that has changed over time. It was both thoughtful and interesting. I have gotten into retro-gaming (computer games from the ‘80s) and some of the fantasy-themed role-playing-ish games feature magical systems. I haven’t written about them much, and the latest one I played hardly used it. [LINK] But I’ve started thinking about whether I could create a game and what a suitable magic system might look like. Maybe some of those thoughts will make it to future blog posts.

 

In any case, Happy Halloween, and to my readers, I hope at least some of the past blog posts have delighted or amused you, or even better – you learned something from them!

Astrobiology Frontiers

Mars gets a lot of press as the frontier in the search for extraterrestrial life on another orb. We Earthers have landed a bunch of probes, taken lots of pictures, and performed some in situ chemical analysis. We don’t know whether life existed once on Mars, although the working hypothesis is that early Mars was quite hospitable to life. The present red and rocky desert isn’t; but maybe life clings to existence in the subsurface. We have some very interesting and largely unexplored subsurface life right here on planet Earth.

 

In her recent book The Secret Life of the Universe, Nathalie Cabrol, director of the Carl Sagan Center at the SETI institute helped me broaden my frontier as to what’s interesting and potentially investigable in addition to Mars. She addresses the “veil of secrecy” of Venus and discusses possible habitable scenarios. I learned about new missions on the slate from NASA and ESA. She covers Mars, of course. But then she spends some time discussing Titan, Europa, Enceladus, Callisto and Ganymede. They’re all different, and each is uniquely interesting. I had previously heard or read about the first three as being interesting sites for finding life, but not the latter two.

 

But her book goes further afield. Ceres turns out to be quite interesting; it has geological seismic activity and possibly a liquid briny ocean beneath the ice. Pluto has “mountainous and glacial” terrain, and its partner Charon may have had a subsurface liquid ocean, I’m guessing made up of nitrogen and possibly ammonia (based on Pluto’s glaciers). I was previously under the impression that only planets in the “Goldilocks zone” of habitability where you were about the right distance from your sun to support liquid water were possible candidates for life. But Cabrol opened my gaze further afield. There could be very interesting and unique activity on a planet on a moon due to many factors, some of which might be conducive to complex chemistry arising.

 

One chapter is titled “Visions of Tatooine and Mordor”. Cabrol classifies the different exoplanets (over 5,500 and counting) into five categories, and then picks out specific examples of interest to astrobiologists. Kepler-16b is Tatooine – it has two suns. The gas giant Bespin could be Cloud City. And the ocean-world Kepler-22b could be Kamino. The interesting TRAPPIST system is also discussed. Cabrol discusses these many interesting orbs in the context of the Drake equation. Our ever-growing knowledge and discovery of so many planets, coupled with the possibility of the habitable zone being widened beyond the traditional Goldilocks parameters, suggests that E.T.’s existence is that much more likely.

 

I was particularly struck by her suggestion that “explaining the origin of life might not be enough to define it”. We’re blinkered by life-as-we-know-it, and it’s very difficult to imagine how else life might manifest. As to what it means to demonstrate the tasks of living, it may also be that “what life does is not what life is”. More questions, few answers. But it made me excited about potentially offering a course in astrochemistry. I’m certainly no expert, but it would be a great way to motivate myself to learn the material!

Happy Mole Day

It’s the middle week of the semester. We don’t have a mid-semester Fall Break. And this year mole day is smack in the middle of the week. Our department student affiliate chapter has organized several fun activities. Liquid nitrogen ice-cream is quite popular. (I was in a meeting so I missed it.) There’s also lab-coat tie-dyeing. Personally, I prefer my pristinely white lab coat. As a computational chemist I don’t spend any time in lab running chemical reactions, although I have taught general chemistry lab and I have on occasion subbed in an advanced lab class for several hours.

 

I don’t have any mole-specific thoughts today. In G-Chem 1, we’re smack in the middle of chemical bond. I’ve been thinking about what we might omit if we moved thermochemistry from G-Chem 2 to G-Chem 1. Do we need to discuss the exceptions in electronic configurations? Do we need to discuss the kinks in the trend of first ionization energy across the row in the periodic table? Do we need to discuss hybridization of orbitals? Can we omit the photoelectric effect? In addition to discussing wave-particle duality, I use it as a springboard to introduce energy diagrams. I’ve been trying to include energy diagrams as much as possible: hydrogen atom (and Bohr model), photoelectron spectroscopy, electron configurations, and bond energy curves.

 

In P-Chem 1 we have just finished the hydrogen atom. I promised the students we’d be there by mid-semester so that we can get to molecules! With more electrons! Many of the students will also be happy to see the math load decrease. The next problem set will still be math-ugly (or math-elegant, depending on your point of view) because we’ll be covering the variational principle and perturbation theory. Once we get past the Born-Oppenheimer approximation, the problem sets will get much less math-intensive. We’ll draw pictures of models and try to extract conceptual information from them. But first students will need to get pass the dreaded Exam 2 coming up on Friday.

 

September was for getting settled in (and ahead) in my classes. October was when I wanted to start working on a research article. I have gotten started but it’s slow-going. I think I have most of the data tables done and I’ve outlined the key figure for the paper with lots of chemical structures and a bunch of arrows. But there’s still quite a-ways to go and it’s been hard for me to get motivated to write. I’d much rather spend time thinking about my classes, or two side-projects that I’ve been exploring that may turn into collaborations with experimentalists. So I am getting some research done, but it’s slow. I did spend a chunk of September training two new research students; the first month is full of “how do I do that again?” but I think they’re getting the hang of it now and are starting to produce their first tranche of results.

 

As we head towards cooler temperatures, and with thermochemistry still on my mind, I’ve been musing about the nature of hot and cold. What is cold? The absence of heat, I suppose; although heat is not a noun. Let’s just say that when heat flows out of the system, if that leads to a loss in thermal energy, then the system gets colder. The zeroth law is constantly trying to make the temperature uniform everywhere. That makes refridgeration a neat trick when you don’t want to be using blocks of ice to cool stuff down. I grew up with a refridgerator in the house so I don’t know what it felt like to be without one. You’d have to eat up your fresh produce quickly enough so it wouldn’t spoil. Higher temperatures mean chemical reactions are occurring more quickly on average! And what is temperature? It’s a statistical average of the thermal energy of gazillions of molecules – six gazillion if it’s a mole of molecules. Aha, I was able to tie this back to the mole. Happy Mole Day!

Antepenult

Antepenult is an obscure Ultima clone, created for the Amiga in the 1980s by Paul Falstad, and distributed as shareware. This summer, I learned about it by stumbling onto the CRPG Addict blog; the writer Chester Bolingbroke is playing his way through old computer games in the role-playing-game genre. He’s an excellent and engaging writer, and my quick skim of his first two articles convinced me that I should give it a try. I did not read these closely so I would avoid detailed spoilers. After all, the fun part is solving the puzzles for yourself!

 

Unlike Nox Archaist, which pays homage to the Ultima series, but is much more streamlined with modern design sensibilities, Antepenult is indeed a child of the 1980s. And it really is an Ultima clone – down to most of the graphics and much of the gameplay. I’d classify it as a mishmash of Ultima II, III, and IV. You’re a single player; there is no party. You consume food. There are basic weapons, armor, and supplies (torches, keys, gems). You can obtain other special items, some of which provide the equivalent of magic. You get gold by fighting the same denizens you’d see in Ultima. It feels very familiar. You begin near a castle and a town; and the ruler of the castle sets you on your quest. Basically, you need to conquer evil and save the world. Nothing new there.

 

You begin in the land of Havilah. If you’ve read the bible, some of the non-player characters (NPCs) have biblical names, some are the early church fathers, and then there’s a whole bunch of Greek mythology thrown in. I met Homer and Asaph in the same hallway of a city. They were composing songs and poems about the evil that had come and my eventual victorious quest. To complete said quest, I needed to explore different towns and worlds and talk to NPCs. I was given a list of items to collect, and many of the NPCs strung me along by telling me the next person to talk to. The four elements of Earth, Water, Air, Fire, feature prominently. I had to discover how to access these different worlds. And if you guessed it, the waterworld is called Atlantis and its king is Neptune. Two towns in that world were Tyre and Sidon. Yes, it’s a mishmash. And the special items you collect are Ultima-cloney. I won’t say much in case you ever want to try the game yourself.

 

I’d never used an Amiga before but I was able to eventually get FS-UAE working several moons ago. So as not to interfere with my workweek, I only played Antepenult for some number of hours each weekend. I took copious notes and I started to make maps. When I really got stuck, I would skim the CRPG Addict’s articles and get a clue as to how to proceed. This didn’t happen very often and it has been interesting to compare Bolingbroke’s play-through with my own. We used similar strategies overall, and occasionally got stuck in the same spaces. But any seasoned old-school Ultima player would probably do the same things. Some patience is needed. A teenager today would probably find it b-o-r-i-n-g. But someone who played Ultima as a teenager will feel the nostalgia when discovering some clever and amusing parts in the game.

 

Here I am at the final castle of the big bad boss.

 

After defeating him, instead of getting a “Congratulations! You won!” message, I got confused as fire and black spots suddenly started appearing and I wasn’t sure what to do and whether I needed to run out of the castle. Everything goes black.

 

I wake up in a restored castle Pergamum and as I walked through the hallways I am thanked by its many inhabitants for saving the world. Asaph was one of them. As were a number of the church father namesakes who gave me clues for my quest. One character who I saved from a high school in hell sets up a possible sequel. (I thought I killed the hag, but apparently she got away. I must have just killed the daemon inhabiting a body that claimed her name.)

 

The king of Havilah, Lord Hypnos, tells me how to return to my own world. Very Ultima. When I enter the portal to do so, there’s an amusing sequence at the very end. Another hint of a possible sequel. No sequel ever came. According to Bolingbroke, this was Falstad’s only game and he programmed it when he was young, and before adulting became a fulltime job.

 

I’ve now read in detail all Bolingbroke’s Antepenult articles. If you’d like to just get a sense of the nostalgia by living vicariously through his playthrough, you won’t be disappointed by his articles. If you want the full experience, get an Amiga emulator and give it a go. My copy was unregistered which makes the game harder when you’re in Tartarus, but not insurmountable. In his articles, Bolingbroke provides enough information whenever you’re stuck. My overall rating of Antepenult? It’s not as good as Nox Archaist, but it has some very clever bits. When I finish my adulting phase-of-life, maybe I will take up writing a retro-game themed on the four elements. I have imagined some of my own clever bits. Maybe my game will be the Antepenult sequel.