Enchantasy

I’ve been on a retro-gaming kick lately. Maybe it’s a nostalgic desire for when I was young, carefree, and had plenty of time to explore and ponder Ultima IV, which I revisited almost thirty years later. Another decade passed and in a second wave of nostalgia, I finally plunked down a little money during a sale to play Nox Archaist. I enjoyed it. Well-designed, well-paced, a good main-line quest with multiple interesting but not crucial side-quests, and the designer had streamlined gameplay – cutting out tedious parts and smoothening out flaws.

 

This year I stumbled upon the CRPG Addict blog and that led me to Antepenult, an obscure shareware game from the 1980s. It has its clever bits but also many flaws, but I still enjoyed it overall. Then the CRPG Addict started playing Enchantasy, another obscure shareware game (by Rick Abel, 1993). I waited until he finished to see his final rating, and I deemed it worth a try. Now that I’ve finished it, I think it’s better than Antepenult. While it shares similiarities to some of the Ultima games, I wouldn’t call it a clone. It had a different feel overall, and I enjoyed most of the game except the last stretch of the mainline quest felt tedious. I completed all the side quests, and the early ones were fun. But at some point, when my party of adventurers got a little too powerful, combat was just tedious. It was a while before I figured out that you could move and attack diagonally, and that you could explore the coasts and rivers with a boat. I would have avoided lots of tedious combat that way and my party would not have levelled up as quickly.

 

Good parts about the game: The interface was clean and easy to use. Having a map of the world was nice! The graphics were functional and over time I grew to like them better than the Ultima iconography. Early combat was a nail-biter and I enjoyed the early leveling up and skill-training. Conversations were guided and the NPCs emphasize the main point they want to get across. The world felt more interesting even with the generic find-magical-item and defeat evil main storyline. Each town felt unique. There were different grades of potions, weapons, and armor, including some interesting equipment. Monsters leveled up so that combat stayed interesting for a good chunk of the game. There was an interesting system where you had to know the names of some people before they would let you into their house and give you information. I took copious notes in this game, much more than in Antepenult or Nox Archaist. I also enjoyed visiting the Portsmith library!

 

There were houses off the beaten track, some had murdered people in them so there was a mystery as to who was killing them.

 

The caves and dungeons were straightforward to map and each had interesting features with secret passages and the like. The side quests were offbeat, and some of them quite amusing. I got to summon a white whale.

 

There was an abandoned alien base with a lonely robot who got left behind and wanted to be helpful.

 

 

 

Bad parts about the game: The early economy is very, very tight and I’m not sure I would have survived without the slot machines – a very incongruous feature of the game. It felt wrong to essentially rob every house or building I came across early on; I’m not sure if that was the intention. In the last bit of the game there seems to be needless running around from one town to another fetching items to give and receive to progress on your quest. After the excellent buildup in the early stages of the game, this last stretch felt tedious. It wasn’t until the end that I realized how unnecessary many of the side-quests were, even though I found the early ones fun and interesting.

 

There was a fun little end-sequence after the big boss battle. The game looked set up for a sequel. Like in Antepenult, an evil character gets away and lives to fight another day.

 

There was a nice celebratory victory where the people of the land congratulated and thanked me for saving them.

 

At some point, when I’ve forgotten the details I might replay it without the slot machines and using boats early, and perhaps not going through the cabinets and bookcases of the townspeople especially when they’re sleeping in bed and I’m rummaging their house. I went back and read the CRPG Addict’s entries and we did things in different sequences, although he finished the game in roughly half the time. Overall, it’s a good game and I enjoyed maybe a hundred hours of gameplay spread over two months. And the game kept me engaged for most of that time. I call that a win!

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.