The Tangled Tree

Before Darwin, the phrase “tree of life” conjured the image of an ancient grove in an Edenic location. To most biologists nowadays, and possibly a majority of scientists, the phrase brings up the image of evolutionary relationships from the origins of life to the present age. Before Harry Potter, the word “transfiguration” had something to do with a seemingly magical event of prophetic significance atop a mountain. To anyone who has read the Harry Potter books, it is the magical practice of changing one object into another. I would say that chemistry is about the transformation of one or more molecules into other molecules – it’s transfiguration at the molecular level. That’s the subject of another post. Today we’ll discuss the Tree. Or trees. Or maybe a tangle of bushes. Or a web.

I just finished reading The Tangled Tree by David Quammen. Personally, I think it is one of the best science-related non-fiction books I have read. This probably has much to do with my research interests related to the chemical origins-of-life. My love of history probably factors in somewhat. And Quammen is an excellent writer. He keeps the reader engaged with fascinating vignettes from his interviews with scientists all over the world. But he doesn’t lose sight of the science; and he builds the narrative one piece at a time into a glorious blend. A web perhaps. But that’s actually the point of the book.

The Tree story begins with Charles Darwin. But he didn’t really draw much of a tree. There is a “diagram of divergence” in his famous book, On the Origin of Species, which is wispy in a tree-like way. The famous depictions of “trees of life” in the nineteenth century are probably due to Ernst Haeckel. Much has been written about the life of Darwin, but I haven’t read many exposes of Haeckel, so I was pleased to learn more about him through Quammen’s book. Haeckel “leaned toward botany, but when he reached age eighteen, his father, concerned for the practicalities, pressured him to study medicine.” Sound familiar? That was back in the 1850s. “[Haeckel] hated the medical curriculum but stayed with it, stealing time to read more Humboldt and Goethe amid his studies.” You might say he forged his own liberal arts curriculum! He did however enjoy histology, and he “discovered an aptitude for drawing tiny structures in fine detail, one eye on the microscope eyepiece, the other on the page.” You’ve likely seen Haeckel’s famous illustrations somewhere even if you didn’t know they were his!

While Tangled Tree begins with Darwin, the main character in the book is Carl Woese. Both brilliant and odd, Woese is most famous for discovering the archaea. When I was in school, my biology class only taught us about bacteria/prokaryotes and eukaryotes. The latter have a cell nucleus, while the former do not. I had also learned about the five kingdoms: Monera, Protista, Fungi, Plantae, Animalia. That’s likely thanks to the strong evangelistic abilities of Lynn Margulis, famous for championing endosymbiosis against the disbeliefs of the scientific community back in the day.

Many other famous scientists enter and exit the narrative. I was particularly blown away by the stories of Fred Griffith and Oswald Avery. I had learned about their famous experiments as foregrounding the “discovery” of DNA as the genetic material which then led up to the Watson-Crick breakthrough. What I didn’t know, which Quammen makes very clear, is how important and strange their experiments were in relation to horizontal gene transfer (HGT). While Woese may be the dominant personality in The Tangled Tree, the main story is about HGT.  Quammen aptly subtitled his book “A Radical New History of Life”. Thanks to HGT, possibly very rampant in those origin-of-life early days, there really isn’t a Tree. A tangled web might be the more appropriate image.

The kicker of the story, though, is that HGT still takes place, and not just among bacteria and archaea. Genes are being transferred through “infective” heredity – a much faster evolutionary process than Darwinian heredity, the kind that we learn about in school. If you want to push evolution by leaps and bounds, HGT might be the main mechanism for wholesale significant changes. How do organisms best acquire the necessary adaptations? HGT might actually be the main and most significant driver. Those scary MRSA bacteria you’ve heard about – how did they evolve multiple-resistance so rapidly? And did you know that bacteria were discovered with resistance to modern drugs before those drugs were invented? There’s a nasty fight going on in the microscopic world, and you have to adapt quickly to stay alive.

Quammen closes his story with contemporary examples. For the first time in the history of life, a “higher” organism is able to manipulate wholesale movement and modification of genes. That’s us. Humans! You’ve likely heard about CRISPR – but did you know that the reason those sequences exist are because organisms use them as a defensive mechanism against the invasion of infective heredity? I’ve talked a lot about the prominence of HGT and microorganisms in this post, but Quammen spends a chunk of his book talking about the different humans in the story – their foibles, their successes, their highs and their lows. They defend their intellectual territory and fight for recognition amidst a tangle of knotty scientific questions.

I highly recommend The Tangled Tree. It’s even better than the excellent I Contain Multitudes. And now I feel motivated to play some Bios Genesis, and pay closer attention to HGT abilities on the mutation cards! Here’s a recent example where my amyloid hydrolyzing marine bacteria also has evolved a homeobox with HGT capabilities.

Rewards and Intrinsic Motivation

Ideas surrounding intrinsic motion pop into my mind occasionally. For example, I’ve made several attempts at de-emphasizing grades in the hope of increasing intrinsic motivation, although it’s unclear if this has been successful. There might be an apparent relationship between creativity and intrinsic motivation, and that extrinsic and intrinsic motivation might compete. I’ve heard the meme that one should try to minimize providing rewards to students because it decreases intrinsic motivation, but apparently this assertion is questionable. At least that’s the claim of Cameron, Banko and Pierce in a 2001 paper.

The abstract essentially captures the main conclusions of the article. In many cases, providing rewards has a negligible or even positive effect on intrinsic motivation. However, rewards can have a negative effect if the task to be performed is “high-interest” and the rewards are both tangible and expected. Now, the conclusions drawn came from a meta-analysis, and the article essentially argues against the opposite results from a related meta-analysis in 1999, which argued against yet an earlier meta-analysis from 1994. I suppose that’s how research proceeds in some cases. Also note that the way most of these studies measured motivation is by comparing time-on-task with some sort of control. Spending less time on a task is the measured proxy for lower intrinsic motivation.

It reminds me as someone in the physical sciences, that things can be much more complicated in other areas particularly having to do with human behavior. The molecules I study behave much more consistently! Reading the article also made me think about three things related to teaching and student learning: (1) What are rewards? (2) Are my classes high-interest or low-interest? (3) Can I gauge intrinsic motivation in my students?

What are the rewards for the student? I suppose getting a degree and finding a job might count. Finding a fulfilling career could be a long-term reward. I suspect that getting an ‘A’ in my class is what most students would have in mind as a motivating reward. “If I work hard, I can do well in this class.” That’s the mantra of at least some students. There might be a few students who find reward simply in learning about chemistry. That’s as intrinsic as it gets, but I think these students would also have additional extrinsic motivations, which is not a bad thing. The article also suggests that verbal rewards have a positive effect in “high interest” situations.

Are my classes high or low interest? The two classes I teach practically every year are General Chemistry and Physical Chemistry. In General Chemistry, the majority of the students are not chemistry or biochemistry majors. I’d gauge 20% are our majors in my typical G-Chem class; some years more, other years less. I’d say that from the students’ point of view, interest is low. I don’t meet many students who find chemistry interesting but choose to major in something else. In P-Chem, all the students are our majors, however the majority are decidedly not interested in physical chemistry with all that physics and math. I would classify both these classes as “low interest”. I’ve also taught many sections of non-majors chemistry which also clearly fall in the low-interest category. By and large I would say that students in most of my classes are taking them to fulfil a requirement and they’re not all that interested in it. (In my special topics classes, most of the students are inherently interested!)

If my classes are “low interest”, then it seems that rewards of different sorts don’t have a negative effect on intrinsic motivation. Some might even have a positive effect, at least according to Cameron, Banko and Pierce. Students will almost always do something for extra credit, and everyone is always happy when there are “free points” for some activity. That’s the carrot approach. There’s also the stick approach – I’ve written about another article from the same journal on Emphasizing Grades and Aversive Control. When there’s little intrinsic motivation anyway, perhaps that’s where one needs extrinsic motivation.

I haven’t considered a formal assessment to gauge intrinsic motivation in my students, although this might be something interesting to try. I’m sure I could find some generic pre- and post- question sets that could be easily modified to gauge this. I suppose it will depend on what proxy is used and how much one trusts self-reporting from students. In any case, it’s not something I will be trying this semester because classes start on Monday!

Biochemistry Manga-style

While looking for a different book at my university library, I stumbled across The Manga Guide to Biochemistry. That’s the serendipity of browsing the library stacks, and I wasn’t expecting to find this in an academic library. That probably says more about my ignorance than about library collection strategies.

Since I’ve been teaching myself biochemistry, I checked out the book from the library. At a slim 250 pages comic-book style, this should be much less of a slog than the two thick biochemistry textbooks in my bookshelf. Certainly, the manga version will not include as much depth or breadth, but does it provide a decent overview with sufficient details?

The back cover tells you what to expect: “Science, Romance, and Robot Cats!” Here’s it’s self-synopsis.

Kumi loves to eat, but she’s worried that her passion for junk food is affecting her health. Determined to unlock the secrets of dieting, she enlists the help of her brainy friend Nemoto and his beautiful biochemistry professor, Dr. Kurosaka. And so the adventure begins… As Kumi explores the mysteries of her body’s inner workings. With the help of RoboCat, the professor’s friendly endoscopic robot, you’ll soar through the incredible machinery that keeps us alive and get an up-close look at biopolymers like DNA and proteins, the metabolic processes that turn our food into energy, and the enzymes that catalyze chemical reactions. As you dive into the depths of plant and animal cells, you’ll learn about:

·      The metabolism of substances like carbohydrates, lipids, proteins and alcohol

·      How the energy powerhouses known as mitochondria produce ATP

·      DNA transcription and the different types of RNA that work together to translate the genetic code into proteins

·      How enzyme kinetics are measured and how inhibition works

First of all, the manga is a breeze to read. And it does come chock full of details. Not to the depth of the biochemistry textbook, but certainly more fun to read. I suspect it would even beat a standard dry CliffNotes both in presentation. I think it provides a good overview of the main processes, and it has excellent diagrams. The explanations are clear. There’s also the sense of “this looks hard at first, but we’ll help you along the way and make things clearer”. While it mainly focuses on the basics, it also covers some applications. Two non-diet related examples include the ABO blood typing system and why mochi rice cakes have a springy texture.

It does not skimp on chemical structures, and you do get into the weeds of metabolic cycles. Here’s one example of Coenzyme A. I apologize in advance my poor photo-taking abilities. My hands shake and the lighting’s not great.

And when something complex is being presented, at first Kumi freaks out, but then she is helped along and comes to a better understanding. Here’s her initial encounter with the Krebs cycle. Yes, they do dive into all those details.

Here’s the beginning of a clear walkthrough of photosynthesis. They really do a good job walking the reader through the diagrams and highlighting the key aspects.

Last, but not least, they also go through equations, algebra and graphing. Here’s Kumi being very apprehensive in a section titled “Using Graphs to Understand Enzymes”. They do a thorough introduction of Michaelis-Menten kinetics and Lineweaver-Burk plots. Besides crunching the math, they also explain conceptually what they are doing and why. For example, why would you take reciprocals to construct the Lineweaver-Burk plot? Or how does understanding the plot help you distinguish competitive versus non-competitive inhibition? And what do those constants Km and Vmax mean anyway?

There’s even a tiny section on different types of RNA including ribozymes and self-splicing introns. I spent a chunk of time my previous sabbatical in a ribozyme lab studying the origin-of-life. I’m a theorist so I didn’t do any experiments, but I read a lot!

Overall, I really enjoyed reading The Manga Guide to Biochemistry. I would personally recommend students reading it before a college-level biochemistry course (rather than after) because it gives you an excellent overview overall. I certainly learned a few things that I didn't already know (although much of it was familiar). And it goes into details you would expect to see in standard post-O-Chem Biochem-1. It’s certainly much higher level than a GOB (General-Organic-Biochemistry) non-majors level course. Having an overview before taking a class is very helpful, in my opinion, and the manga guide makes the subject less scary than it might seem.

While I think it’s fun and quick to read, it’s possible I’m biased because I already know a fair bit of chemistry, and I personally think biochemistry is very interesting. I’d be interested to know what students think. Maybe I’ll recommend it to one of my advisees who’s about to take Biochem-1, after I return it to the library.

What should I read next? The series has one on Linear Algebra. That might be useful for students before my Quantum class. Too bad my university library doesn’t have it. In fact, the only one they have in the series is the one on Biochemistry. I wonder why.

Student Experiences: Good and Bad

In preparation for the standard annual review, I’m re-reading student evaluations from my classes the previous calendar year. The new Student Evaluation of Educational Experience (SEEE) form, implemented this past fall semester, has more focused open-ended questions that also require the students to be more reflective.

·      What about this instructor/course was most beneficial for your learning?

·      What about this instructor/course could be improved to better your learning?

·      What advice would you give to another student who is considering taking this course?

I previously blogged about the advice question after reading the evaluations. I’m putting those comments on my course web sites this semester. I’m hoping it will help students get off to a better start!

In today’s post, I will be sharing some student open-ended comments. But I’m not going to be sharing them from the most recent semester because I taught two smaller classes and therefore the comments were particularly positive, and perhaps not reflective of the student population and experience at large in a chemistry course.

Instead I will be sharing from the previous spring semester when the old ‘teaching evaluation’ forms were being used for the last time. For the open-ended section, these old forms had the rather nebulous instruction “Make general specific comments about the instructor and the course.” What does the oxymoronic “general specific” even mean? As you can imagine, student comments are all over the place.

I’ve chosen a representative sample from my larger (non-Honors) sections of (second-semester) General Chemistry II. This selection includes some of the best and worst comments from that semester. They aren’t the superlatively best or worst comments I’ve had over a lifetime, but they do a decent job highlighting the student experience. It’s important to emphasize that student comments (positive or negative) don’t necessarily reflect whether I’m a capable and effective teacher if such a thing could be truly measured in any objective sense. Student comments are but one facet, but nevertheless an important one. Students are with you throughout the entire semester (as opposed to a drop-in observing colleague). Whether or not I agree with the substance of the student comments, they still have a perspective that I should take into account, for better or worse.

The comments in italics have only had very minor editions for punctuation and spelling. I’ve also removed identifying information and changed my name to HH (for Hufflepuff Hippo). My comments on their comments are interspersed.

·      Dr. HH is by far the most organized and put-together teacher I have ever had. He is made to only teach students that want to work hard. Warning: all the mean evaluations were done by lazy students! Dr. HH expects a lot of us and I loved that. Not easy by any means and so willing to help. Thanks for letting me come to every office hours! He serves as an example to other teachers! Give this genius man a raise please because he works so hard!

That was one of the most positive comments, but it highlights an interesting point. I’m supposedly good at teaching hardworking students, but it might also mean I’m only good at teaching ‘good’ students, and not so good with ‘not-so-good’ students. To put that in perspective, here’s one from a student who felt ill at ease with the pace.

·      Professor HH teaches extremely fast and does not slow down. It is very hard to keep up in class, and even in office hours. His exams are also extremely difficult. The homework and practice exams are nothing like the actual exam and it did not prepare me at all. I put so much hard work and effort into this class yet I still feel like it is not enough and that I will fail.

My class is clearly challenging. I’d say chemistry is inherently challenging. It does not come naturally to most of us. Me included, when I first started. You’ve got to work at it. (Also, my practice exams are from the previous year, and the exams have similar difficulty. However, some students will perceive them as more difficult. More on that later.)

·      Very difficult course and very demanding workload, but the instructor did an excellent job of teaching it and showed vast knowledge of the subject. Workload was necessary to understand the material.

·      Dr. HH was helpful in office hours but he is a very tough teacher. Last semester my teacher was willing to help students that did not really understand chemistry. I feel like I should have received more aid. I studied a lot.

I’m also apparently a ‘tough’ instructor and maybe not as helpful to all types of students. But at least the student above found me helpful in office hours. Others didn’t.

·      HH is very intellectual in his understanding of chemistry, however in his office hours, I often felt ridiculed for my inability to understand the material. The level of knowledge expected was way above an entry-level chemistry.

·      HH goes very fast in his lectures, but it is generally understandable. Sometimes during office hours, I would get responses like “Read the book” which I find to be generally unhelpful especially if I don’t understand something, an explanation would be nice. Overall I like this course and would recommend.

Honestly, I don’t think I ever ridicule a student – but that’s my perspective. I am however known to be very direct when I’m trying to help a student. If the student comes unprepared to office hours and hasn’t put in some amount of work beforehand, I refuse to spoon-feed. I suppose that makes me tough and lacking in empathy, both of which might well be true. I’m not the nicest person around, although I’d like to think I’m generally well-mannered. I do have high expectations and I do go at a fast pace to keep students on-their-toes and (hopefully) learning, consistent with Vygotsky’s zone-of-proximal development. The student however felt ridiculed from his or her perspective, and I acknowledge this even if it was not my intention.

Here’s one more about my speed from a student anticipating a C grade before the final exam. I do get a fair share of positive comments from students who aren’t doing great in the class.

·      Best chem professor I’ve had, explanations are deep and thorough, he just explains things really fast.

Besides my fast pace (which comes up in many comments I haven’t shared), the other common thing students remark on is that I’m organized in class, and knowledgeable about my field.

·      Dr. HH is the most organized and efficient professor I’ve ever had. He never falls behind in his lectures and is always willing to help his students.

·      Dr. HH knows much about his field. He was very organized and prepared for each class. However I think tests were unfair in that it is only out of 25 points.

Being knowledgeable or ‘intellectual’ (from a previous comment) can also be a negative when it is combined with a ‘but’.

·      Dr. HH is very knowledgeable about chemistry, but he’s not very good at clearly explaining concepts. When I read the book I find it to not make sense even with his lectures. He also does not give enough examples outside of class.

And here’s a contrasting comment that says the exact opposite.

·      Dr. HH is an amazing professor. He explains topics in class very well and gives plenty of examples. The exams are difficult, but everything can be found from the class notes and his explanations in lecture follows the material in lab.

Students think my exams are difficult. (It would be a problem if they found them easy.) Yet the strong students still do very well and my grade distribution looks pretty normal. They are also not inflated. (The mean and median in G-Chem 2 is usually a C+ and occasionally a B-.) I do provide previous year exams (of similar difficulty) to the students for practice – but (shockingly) many students don’t take advantage of them. I tell students how to take a practice exam (i.e., under exam conditions) – many students don’t follow this and thus perceive the past-year exam to be easier because they have their notes close by for reference. At least one student thought my exams were impossible.

·      His tests are impossible. I’ve never tried so hard in a class before. He does not have much empathy and always kicks me out during office hours. His tests are way harder than what’s taught in class.

That being said, if a student comes close to the end of office hours, I usually let it run over and answer any direct questions a student has. However, I don’t allow students to ‘work in my office’ beyond office hours if they don’t have immediate questions. I’ve never kicked out a student during scheduled office hours. The student however perceives being kicked out of office hours. (Most students are very respectful of my time so this is not a common that I face.)

Some of my G-Chem 1 students follow me into G-Chem 2, and those almost always have positive comments. This is not surprising since a student who didn’t like having me as an instructor the first semester would avoid me for the second semester. We teach multiple sections so students can pick and choose.

·      I think this course flows very well with G-Chem 1. Dr. HH was my professor for both courses and I felt more prepared this semester. Dr. HH is always willing to host office hours and is very helpful whenever I have questions. I liked this course and that is solely because of Dr. HH.

·      Dr. HH is very good at teaching gen chem. I’ve had him for 2 semesters and I feel that he is extremely clear with his teaching. He provides many opportunities for help and knows a lot about chemistry. He teaches in a way that really helps you visualize and understand how and why chemistry works.

I liked that these two students highlighted things that I consciously try to do. I constantly make reference to what students have learned in G-Chem 1 and make connections. I also talk constantly about models and how they help illuminate chemistry (although they have limitations). Yes, the student actually underlined how and why in the comment above for emphasis.

Having taught for many years, there isn’t much that’s new in the evaluations that I haven’t heard before. Similar comments show up every year, and the above is a pretty good representative sample from G-Chem. (Comments from other classes have their own representative sets.) It will be interesting to see if the new forms that encourage more student reflection will provide varying perspectives. (I’m biased because I helped to design the new forms.) We’ll see!

P.S. My institution seems to have this culture where most students address their professors with the “Dr” honorific. I neither encourage nor discourage this.

Annotated Self-Grading

The past Fall semester I experimented with student annotated “self-grading” in two classes. This was Idea #1 from my Three Fall Ideas over the summer.

In General Chemistry, my students had take-home midterm exams. These would be handed out in class on Friday and students would turn them in on Monday. The following instructions were on the cover page.

·      After you’ve finished studying, find a quiet spot and take the exam (closed-book, closed notes, etc) on your own. It’s just you, the exam, and a calculator! TIME LIMIT: 1 hour.

·      After the hour is up, you are allowed to make annotations to your exam in a different color. This includes corrections, clarifications, and anything you think makes your answer more accurate or easier to understand. You may consult your notes, the textbook, and even your classmates.

To encourage student adherence to the “closed” nature of the first hour, I told the students that if they made a good-faith effort to follow the two-color scheme, I would give them full credit on the exam regardless of how they actually did (pre-annotated or post-annotated). These midterm exams were worth 20% of the total grade in the class. (In previous years, these are worth ~50%). I also stressed the importance of following the instructions with a warning that it they didn’t adhere, it would give them a false sense of their knowledge of the material, and that it would come back and bite them on the higher stakes closed-book final exam, now worth 50% of the grade (instead of ~33%). This caused a slight uptick in stress approaching the final exam, but the students on average did just fine.

I am very pleased that all my students adhered, as far as I could tell, this past Fall. Because I was giving the students more “free points” during the semester, I had rescaled my grading bands into 10% increments per letter grade rather than my typical 15% increments. The end result: The class on average performed the same as the previous year. The slight difference could be attributed to all sorts of factors, but my sample sizes are too small to tell. I’d like to think that the act of annotating forced the students to think carefully about their answers and whether they could improve on it – an act of metacognition, so to speak. But it’s hard to say at this point. I did use the same final exam as last year with minor modifications and student performance was about 1% higher, not significantly different given my small class size. (I can reuse a final exam that I’ve never provided as a sample exam, and in my many years of teaching there has never been a problem.)

Several years ago, when I tried take-home exams without self-annotation, some students didn’t adhere which resulted in them doing terribly on the final exam. I’d like to think that allowing the self-annotation increased adherence. Another factor is that I was teaching a small Honors section composed of only first-year students (I did the same last year but without the take-home self-annotated exams). Honestly, these first-year Honors students tend to be good at following instructions, in my experience – which is why I was willing to try this experiment.

My grading time didn’t decrease significantly because I still went through the student exams carefully and made comments when students were missing something or if I thought the student did a particularly good job. No grade was provided by me on the exam. When I handed the students exam back to them, I included a detailed Answer key so they could make a comparison to one set of “ideal” answers. (There are often multiple ways to answer a question correctly on my exams.)

After reflecting on all this, I’ve decided to repeat this same experiment in my upcoming Spring second semester General Chemistry course. This is also a smaller Honors course, although there are more students (filtered in from different first semester sections) and they might not all be first-year students. One thing I will be adding to the midterm exam instructions is that after annotating their exams, students will estimate the grade on their exam before they put in the annotations. While this sounds counter-intuitive for someone who generally tries to de-emphasize grades, in this case I think it will be helpful as the students approach the final exam and reduce some stress. This is based on feedback from my students from last semester. But I don’t know for sure, so I’ll have to do the experiment.

In my Physical Chemistry I (Quantum) class this past Fall, I had students annotate their problem sets. There are seven problem sets during the semester (each worth 2% of the total grade). The problem sets are long and challenging for the students, but that’s where a lot of the actual learning happens. Students who don’t work at the problem sets tend not to do well. I encourage students to collaborate on problem sets. In their end-of-semester evaluations, students recognize the importance of the problem sets.

In previous years, I would see weaker students ‘copy’ the problem sets of stronger students when they worked together. Yes, they wrote up their own work, but how many of them really grappled with the problem set? My hope is that the self-annotation would take the pressure off having to turn in a “perfect” problem set (to get as many points as possible) and more importantly, encourage the students to look closely on what they understood and what they did not, where they got stuck, and how they can improve.

My problem sets had a “Finish By” date, although in every class I emphasize which problems students should attempt before the next class so they keep up with the material. On the Finish date, I hand out the Answer Key. Students then have to annotate their problem sets in a different color based on the solutions and turn them in on the “Due Date”, typically the next class period. At first some students would simply copy down parts that they got wrong, which required me to emphasize that annotating the exam might require making corrections in minor cases, but then in major cases the student should instead discuss where they went wrong and why, and not copy out large chunks of the Answer Key. I was more interested in seeing what they learned rather than a repeat of my Answer Key. After several reminders, the students by and large followed through.

My incentive to the students was that if they made a good-faith effort to follow the two-color scheme, I would give them full credit on the problem sets regardless of how they actually did pre-annotation. I’m pleased to say that students got better at annotating as the semester progressed. One disadvantage, in my opinion, is that fewer students came to office hours to get help (because they knew they would ‘get the Answer Key’ and not be penalized for an incomplete problem set pre-annotation). Students also have the option of not turning in a problem set at all and the 2% is then lumped in with their next exam. I’d done this for years to discourage students blindly copying other students and just submitting something for the sake of turning it in, thus increasing my grading time for no particular value. Every year a student or two would do this later in the semester; that was also true this semester (one student did this per problem set, although not always the same student).

As in my General Chemistry class, I changed my grade bands to 13% increments rather than 15% increments. This was based on rescaling how the 7 x 2% = 14% on problem sets would now be essentially “free points”. The overall average grade was comparable to previous years, as were the overall average grades in each exam. Actually, the average grades were marginally higher, but I had an unusually small class last semester of only fifteen students and these don’t always adhere closely to the norm. I also had a crop of very strong seniors in that class. Once again, I’d like to think that annotation helped with meta-cognitive aspects of student-learning, but it’s very difficult to measure how and what students are actually thinking. You can ask them in surveys, but that’s a proxy – not always reliable.

This coming Spring semester, my Physical Chemistry II class (Statistical Thermodynamics and Kinetics) will be more than twice as large. I definitely plan to have self-annotated problem sets again  because in P-Chem, the grading time decreases significantly. I no longer have to look for hard-to-find math errors and can concentrate on the conceptual parts. I still make comments on student problem sets as I go through them, but it’s a huge time-saver. I am, however, concerned about the weaker students not coming into office hours for help. (In the past, many of the weaker students didn’t come anyway. Typically, it’s the stronger students and mid-range conscientious ones that show up.) I’m not sure how much of a difference it makes; I didn’t see worse fallout from the lower end – although a small number of students still did quite poorly (which happens every year). I have been considering an assignment encouraging students to group-study for exams by asking them to write potential exam questions. I’m still working on my syllabus and need to give this a bit more thought.

Overall, I’ve been happy with introducing self-annotation in my General Chemistry I and Physical Chemistry I classes. We’ll see how they fare in General Chemistry II and Physical Chemistry II this coming semester.

P.S. As to my Idea #2 for Magic Hour usage, I think I did well. Here are two examples I blogged about: Connecting the Liberal Arts and Magic & Chemistry.

P.P.S. My Idea #3 for a student creative project to replace an exam in Physical Chemistry didn’t work as well. A couple of students attempted this – one attempt was middling at best, the other was poor. And it was a lot of extra reading for me. I’m not sure how much it helped the students consolidate the material they missed. Instead I think I will go to an option I’ve tried several times: If the grade on the final exam is higher than the student’s grade thus far in the class, then the overall grade is replaced by the final exam grade.

Bios Megafauna 2nd Edition

Over winter break, I learned how to play the second edition of Bios Megafauna. While it retains some flavor of the first edition, the second edition plays very differently. Overall, there is more to do each turn and the game seems a little more forgiving overall so you don’t get wiped out too easily. It can still happen with bad luck and bad play, but you did not get stuck on a single square which would happen occasionally in the first edition.

The second edition of Bios Megafauna was also designed to serve as a sequel to Bios Genesis. Hence, the two games share many commonalities. The mutation cards now come in the same four colors. Mutations can be promoted, and mutation cubes turned into basal organs. There is an Event card deck that simulates the changing roller-coaster climate and the possible disasters that your organisms will have to face. The climate now features three different tracks that can be manipulated due to environmental changes: oxygen level, cloud cover, and overall temperature. Green, white and black disks can be moved between the reservoir board (shown below) and the playing area.

Of the four players in the game, three of them are fauna-ish phyla and the oxygen level determines the number of actions (number in the black gear) each player can take along with the number of mutations (number in red heart chamber) each fauna-species can sustain if there was a serious mutagen-causing event. The fourth player (Player Green) is different, just like in Bios Genesis. Suitably, Green represents flora-ish phyla. In the hotter atmosphere, Green gets more actions (number in the green gear) while it’s protection against mutagens varies with cloud cover with a maximum in the middle of the reservoir.

The four players start on cratons representing separated landmasses at the beginning of the Ordovician Era: Laurentia, Baltica, Siberia, Gondwanaland. As the game proceeds, these “cratons” may move due to Event cards, and they might even collide with each other to form a larger continent. Above is a snapshot from one of my games where Siberia and Gondwanaland have crashed into each other. Players Black, White and Orange are battling for space. Each player has five “creeple” species represented by different shapes. The “blob” is the starting archetype but speciation can result in swimmers (“fish”), armored creatures (“snails”), burrowing creatures (“worms”), and flying creatures (“insect-looking flyer”). On the craton, the green disks represent forests, the black disks mountains, and the white disks ice or desert. Hexes with no disks may be weeds, swamp or sea.

Below are two player tableaux of the same game. I apologize for the quick, poorly taken, blurry pictures. (My hands shake!) Player Black representing an arthropod archetype also has speciated to a species with a horned shield and a swimmer equipped with a salt-exposed tubenose, but not much else in terms of advanced beneficial mutations. The cubes represent basal organs (blue for genes, yellow for metabolism, etc., similar to Bios Genesis). Player Green at the moment only has an archetype species but it seems quite advanced having a lure, flushing capability and bone marrow. It also has developed a primitive “anger” emotion.

The picture below shows the Laurentia craton occupied exclusively by Player Orange. The brown dice shows its latitude which can change. Above you can see several purple Event cards. The most recent significant event is a Chicxulub Class Comet that caused a crater. It also causes other environmental changes. Weeds climax into forests. There is also a deluge and mutagenic activity. The comet comes along with a Hypercapnia that causes offshore carbon to go into the atmosphere. Black disks to the right of each craton are moved back to the atmosphere reservoir and any offshore bloom (a green disk on top of a black disk) get moved to the oxygen reservoir. These are large scale climate changes! They have caused it to suddenly get much hotter on planet Earth.

The iconography takes a little getting used to. In the first game, referring to the rulebook to figure out what each icon meant was a constant. That being said, I felt the second edition rules to be streamlined. There were fewer exceptions, which is saying a lot given that Phil Eklund’s games tend to have many, many rule exceptions thanks to the idiosyncracies of evolution and the diversity we see on our wonderful planet. I was able to learn the game much faster than previous Eklund games, although it likely helped that I had played both the first edition of Bios Megafauna and Bios Genesis multiple times. It’s easier to teach, and being more forgiving of a game (you don’t keep dying), I think it will likely see more play time overall. One thing I did miss from the first edition was seeing the evolution of the different supporting flora. Much of that is gone from the second edition, but the increase in playability more than makes up for it.

In conclusion, this is a nice way to get introduced to an Eklund game if you’ve never played one. And it has creeples!

P.S. I also feel more motivated to learn High Frontier, which has been sitting in my shelf for years. (I also have the expansion.)