First Week: Spring 2021 Edition

Yes, we’re still remote. No, I still don’t like Zoom.

 

I’m teaching just two classes this semester. Both are G-Chem 2 sections, but one is a small honors class and the other is a regular larger section. The gender ratio is completely skewed this semester. Across both my sections, I have 92% female students. While the honors section normally has a significant imbalance, this semester my regular larger section is similarly skewed. Not sure why.

 

While the subject matter is the same, I’ve decided to sequence some of the topics differently in each section. Hopefully I don’t confuse myself. The reason for this is that the large majority of my honors section students are also co-enrolled in the honors section of intro bio that focuses on bioenergetics. Over the break, I zoomed with my colleague in biology teaching that section, to find ways for us to align the material so the students see the synergy between the two classes. Thus, my honors section this semester will feature bioenergetics applications in chemistry. Content coverage is identical in both my sections this week, but they will begin to diverge next week. There will still be plenty of overlap but there will be differences in examples, assignments, and exams. We’ll see if I can keep everything straight in my head.

 

I suppose it’s not surprising that there were technological snafus. Thankfully not a campus-wide wifi outage which happened on the first day of class last semester. The problems this time around were linked to the Learning Management System and student access to the online textbook and homework system. I don’t completely understand what the problem was on the back end, but needless to say the signing up for access did not work as advertised. We were getting different instructions from day-to-day as the bookstore, I.T., and a third-party vendor were all involved in the mess – at least in my ignorant opinion. Instructions that worked for some students didn’t work for others, and students and faculty were understandably frustrated. I also had the video recording for my first class not show up until 24 hours later. No one knows why, but I had it all set up correctly and for subsequent classes, it shows up in about an hour after class ends which was the norm.

 

Preparing the course web sites was much quicker this time around since I’m now much more familiar with the LMS. I still don’t like it, but I don’t have much of a choice while we’re still remote. Can’t wait to be back in-person, hopefully next semester. I’ve tweaked my course setup a little. For my regular section, there will be three self-tests following my take-home annotated method, but two in-class midterm exams. My honors section will still do their midterms with the take-home annotated approach. I will have final exams rather than final projects - the final exam went fine last semester (in my opinion) and I don’t think there were academic integrity issues. The average on the final was just a tad lower than in a previous non-Covid year, but not too different.

 

Because of the long break between the semesters, my Zoom teaching is a little rusty. I didn’t do well on Monday, but my Wednesday and Friday classes ran more smoothly. One challenge is that the topics in G-Chem 2 require more complicated problem-solving calculations, and the limited viewing space via Zoom is therefore even more annoying compared to last semester. I might also be a little too ambitious in emphasizing the how and why of using models in thermodynamics, simply because I’ve been thinking a lot more about it because of research-related papers I’ve been reading. What I’m doing is good from a “scientific inquiry” perspective, but with the limited time and the loss in translation of the Zoom medium, maybe my time is better spent focusing on the problem-solving skills. I decided to schedule the first test in my regular section at the end of Week 3 (students get full credit for the attempt) just to see how much they’re learning.

 

It’s Friday afternoon. I feel tired. Probably also not used to expending the type of energy I do when I’m teaching. And my first several days felt very unproductive with lots of e-mails to answer and other administrative-type duties. It feels like the semester is back in swing, although I’d say it’s a bit of a rude awakening for me after the two months of doing research at my own uninterrupted pace. Okay, gotta make sure I’m ready for Monday of Week 2.

 

I wish it was the first week of Spring 2019.

Temporal Bandwidth

I don’t remember much of college, but I probably did not take advantage of being forced to take humanities courses. Coming from a country with a different education system where we were “streamed” early on (I was placed in the sciences) and had little choice in the classes we took, it was bewildering to be offered a smorgasbord of choice at the liberal arts college I attended here in the U.S. The college was also known for its core rigorous Western civilization course required of all first-year students.

 

Due to the oddity of being the first person from my country to attend said college, it was unclear how exactly some of my prior coursework might “transfer” (many countries have more extensive secondary education compared to the U.S.) After talking to a chemistry faculty member, it was decided that instead of taking General Chemistry, I should be placed directly into Organic Chemistry. Now it turned out that first-year students hardly ever wanted to take or be in O-Chem and so consequently the main O-Chem lectures were scheduled at exactly the same time as the core Humanities course. I received special permission to delay that Humanities core requirement.

 

But then the next year, I was enrolled in P-Chem which was, you guessed it, scheduled at exactly the same time because no one ever tried to take O-Chem and P-Chem simultaneously (O-Chem being a pre-requisite) and thus delayed my Humanities experience another year. Having figured out I could graduate in three years with some course cramming, I was finally enrolled in the intro Hum course, the only senior taking the class with a cohort of first-years. (I was careful not to reveal I was a senior and tried to blend in.) I was also writing my senior thesis in Chemistry at the time, and due to some unexpected things come up in research (which they often do), let’s say I devoted much more time to chemistry and um, skipped a bunch of Hum classes. (I had privately discussed this with the instructor who agreed it was okay.)

 

I might have thought differently back then if I had read Alan Jacob’s new book Breaking Bread with the Dead. It’s a breezy enjoyable read, and I agree with much of what he writes. Of course I’ve had much more appreciation for the humanities since college, and I had read many of the ‘classics’ that he mentions ranging from the usual Greco-Roman antiquity stuff to more recent literature. Many, but not all, of his examples come from a standard Western civ canon, now no longer a given in such twenty-first century intro Hum core courses. Even my stalwart college has bowed to the pressure to include more diverse voices, not necessarily a bad thing.

 

Jacob values the classics, and he thinks we shouldn’t be too quick to dismiss them even in this day and age. While he provides memorable vignettes and arguments, the thrust of his book that caught my attention was that reading what seems like a foreign dead past (and as an international student, it was all foreign to me) is valuable for combating what he calls presentism – the ever-accelerating information-deluge age we are in right this moment. My present students have grown up in it, and I try to empathize with the pressures they face in this deluge so focused on the now, even when I don’t quite comprehend it. (I guess I’m a ‘slow professor’.)

 

Jacob makes the argument (with relevance to the social polarization in the U.S. where folks seem only to tune into ‘what their itching ears want to hear’ to quote the Bible, and old classic of sorts) that the sense that the ‘other’ might pollute oneself and should be avoided, is due to experiencing information overload. Here’s what he says: “information overload [is] a sense that we are always receiving more sheer data than we know how to evaluate – and a more general feeling of social acceleration – the perception that the world is not only changing but changing faster and faster. What those closely related experiences tend to require from us is information triage.” And how do you triage? As efficiently and quickly as possible, usually from close-to-instantaneous judgments without significant forethought. We’re doing this all the time these days, trying our best to avoid pop-ups trying to gain our attention through the world wild web.

 

How can we avoid being “tossed back and forth by the waves, and blown here and there by every wind of teaching and by the cunning and craftiness of people in their deceitful scheming”? (The Bible is very quotable!) Jacob suggests the idea of developing temporal bandwidth. The idea is that spending time living not just in the present, but infused by the past and future, increases your temporal bandwidth – and in doing so, gives you a heftier personal density. This density helps keeps you grounded when you are being buffeted by information overload, and you can do a better and more thoughtful job in your triage.

 

I find it amusing that bandwidth and density are terms most often used in science-technology settings. They may seem strange bedfellows – after all, if you literally increase your width without increasing your mass by a higher proportion (more than cubically!) your density will actually decrease. Jacob doesn’t address this because he uses these words to evoke an image of breadth, solidity, and firmness. To push his analogy a little further, I’d say he would advocate for significantly increasing your ‘mass’ of knowledge of the past, even if it is foreign to your ears. I think he’d say especially so. And he marshals vignettes throughout his book to support this argument.

 

Personal density isn’t something that bothers me, now that I’m old and stuck in my ways. I do see my students seeking and exploring who they are. Oh, the joys (and horrors) of youth! However, I think the idea of temporal bandwidth is interesting to consider. I happen to enjoy reading history. It’s what I read the most, outside of science. History of science is even better! Maybe that liberal arts education did help me gain an appreciation for the humanities and its intersection with the social and natural sciences. I do read very widely, and I read a lot. (If you follow my blog regularly you already know this since I regularly write about what I read.)

 

Have I developed temporal bandwidth? Maybe. I’m not sure how one measures one’s temporal bandwidth. Surely it can’t be just by counting the number of books I’ve read or coming up with some scale rating for the intellectual density of those books, as pretentious as that sounds. I’m much more comfortable thinking about complexity than I used to be; but maybe it’s because I study complex systems in chemistry so I happen to read a lot on the topic. The subtitle of Jacobs’ book is “A Reader’s Guide to a More Tranquil Mind”. Am I more tranquil? Compared to my younger days, certainly, but I don’t know if that’s attributed to reading voraciously. I also have what I think is a stable job doing what I enjoy, and I know that’s a rare and fortunate position to be in, especially these days. I suspect there are multiple routes to the tranquil mind, and they may not all pass through widening one’s temporal bandwidth. Prayer, meditation, focusing on a being who transcends time and space, may also be other avenues that lead to similar states. I don’t know. And I’m not worrying about it!

Things Fall Apart

I’m attracted to ancient civilizations and archaeology, but from armchair’s length. My latest reading combines archaeology, ecology, history, and politics. It has a curious and evocative title, Against the Grain. The writer, James C. Scott, claims his story is a “trespasser’s reconnaissance report” – perhaps all truly interdisciplinary work has this in common. Scott’s excuses for venturing far afield? Naivete and being surprised can yield insights when you correct your own misconceptions, and I daresay his broad interests come to fruition in this provocative little book. In Scott’s own words, it “creates no new knowledge of its own but aims, at its most ambitious, to ‘connect the dots’ of existing knowledge in ways that may be illuminating or suggestive.”

 

But first we need to know the old story. The commonly held view is that early ‘civilizations’ (and there’s a reason to question this term in Scott’s book) followed this sequence: “domestication of plants and animals led directly to sedentism… fixed-field agriculture…  villages… towns… formation of states.” As a political science, Scott’s expertise is in the changing nature of statehood, be they nation-states, city-states, town-states, horseback states; and the blurring of distinctions between these categories as they come together and fall apart. But perhaps ‘falling apart’ and the notion of civilization ‘collapse’ is a highly biased view of us urbanists, comfortable in our milieu.

 

Scott turns the story on its head. His interpretation of the archaeological and ecological evidence suggests that “sedentism long preceded evidence of domestication” and millennia pass before we see towns, walled cities, nation-states. Perhaps these are dynamically forced together and drift apart as conditions change: ecologically, socially, politically. Scott writes: “State and nonstate peoples, agriculturalists and foragers, ‘barbarians’ and ‘civilized’ are twins, both in reality and semiotically. Each member of the pair conjures up its partner… born together as twins.”

 

Where does the grain come in? Wild cereal grains were present and utilized by hunter-gatherers especially in wetland areas. Climate and ecological forces may have played a role in the conversion of the wild type to the domesticated type, but the latter is more fragile and requires constant care and supervision to yield its harvest. Scott cheekily suggests that domestication may be a two-way street. Human sedentism and self-domestication come together. (In a time of Covid, it’s hard not to see the effects of sedentism in large scale.) Provocatively, Scott also suggests that the domestication of mass produced cereal grains allows for the stratification of society and a basis for tax-collection! How else could a city-state or nation-state survive or even thrive? Scott’s agro-ecological story is very interesting, and I recommend reading his book for the full story.

 

There are many other interesting threads in his book: the role of fire (à la Wrangham), the drudgery of the lower classes (à la Industrial Revolution), zoonotic plagues (à la Covid), and why raiding and piracy quite naturally arise with urban-ish centers that concentrate resources. While most of the examples come from Scott’s focus on Mesopotamia, he shows analogies to early civilizations across the globe. I found chapter six, “Fragility of the Early State: Collapse as Disassembly” the most interesting, and plays to Scott’s strengths. The factors are myriad. The dynamics are interesting. I think there are lessons to be learned about climate change, ecocide, war, slavery, trade, and trying to avoid taxes. I find his take on ‘collapse’ intriguing. I’ll explain in a moment, but first some quotes from the chapter.

 

“Why deplore ‘collapse’ when the situation it depicts is most often the disaggregation of a complex, fragile, and typically oppressive state into smaller, decentralized fragments? One simple and not entirely superficial reason why collapse is deplored is that it deprives all those scholars and professionals… There are fewer important digs for archaeologists, fewer records and texts for historians, and fewer trinkets… to fill museum exhibits… one will search in vain for a portrayal of the obscure periods that followed them… Yet there is a strong case to be made that such ‘vacant’ periods represented a bolt for freedom by many state subjects and an improvement in human welfare… The irregular cycles of aggregation and dispersal hark back to patterns of subsistence that predate the first appearance of states.”

 

As I study complexity and the origin of life, and therefore death, a similar dynamic comes into play. Things come together, things fall apart. Or in more neutral tones, assembly and dissembly – part and parcel of life and death. Over the years I’ve become more sympathetic to some version of Gaia hypotheses, that one can think of larger systems and structures as being organism-like. What we think of as life and biology, away from the constraints of reductionism, might teach us some new things as scientists exploring the ‘natural’ world. Or perhaps complexity and catastrophe are two sides of the same coin.

 

As I prepare for a semester discussing thermodynamics and equilibrium, and that strange concept called entropy that might arise because of our closed thermodynamic models, perhaps my students and I will be illuminated with some new ideas, maybe even ones that go against the grain and supplant some old ideas. Things fall apart. And they come together again.

 

P.S. Reading this book also made me want to play Origins again!

Feedback

I’ve been thinking about feedback and feedforward loops as I read about the origin of life and the emergence of dynamical control systems to optimize robust behavior. Much of it is abstract, and sometimes I get lost in the math. I consider myself a beginner in these areas, and I’m experiencing the challenge and frustration in my lack of ability to teach myself efficiently. It’s taking time and concentration that I can no longer spare as teaching and the new semester begins. Now if only I had a good teacher that can help guide me along the path, helping to predigest some of the material and providing feedback so I don’t go around in circles.

 

All this is, however, an excellent reminder of why feedback is important to learners. And while the basics of college chemistry is old hat for me, it is new to most of my students. In the same way that I feel like I’m fumbling around systems-theory, my students will likely be fumbling around thermodynamics, kinetics, and equilibria. My job as a teacher to help their learning is to predigest and sequence the material in a way that aids the student to begin to get a grasp of the material. I say “begin to get a grasp” because learning new things (you are not evolutionarily pre-adapted to learn) is an iterative process. You can’t magically understand this knowledge without the work and effort. So, yes, the learner needs to contribute substantially to the effort. And it helps to get regular useful feedback along the way, to help ease the difficult journey.

 

In days of yore, constant feedback was provided one-on-one through apprenticeships over years – the artisanal model. There was no other way to learn expertise in such skills, at least to a high-enough level to make a living as a specialist of some sort. Nowadays, education is mass produced. This isn’t necessarily a bad thing – many basics of the basics we learn in school can be taught reasonably in a classroom with many students. Hopefully not too many, because feedback, and individual feedback in particular, takes time and energy. Let me put it this way: There are many commonalities in how students learn (which lend themselves to mass methods) but when a student isn’t “getting it”, this failure comes in a variety of forms less common to each other. It’s somewhat like the adage that “all happy families are alike, but every unhappy family is unhappy in its own way”.

 

Class sizes have slowly been creeping up, at least in my department at my college because student numbers are increasing but faculty numbers not so much. Not only do I know my students less well on average in a larger class, the time required for optimal individual feedback scales with class size. (Not to mention, a faculty member will feel increasing time pressure with higher administrative burdens and research expectations as the years pass.) What has happened in my general chemistry classes? My colleagues and I made the transition to “smart” online homework systems that are packaged with any standard G-Chem textbook. The system gives them hints and feedback if they get an answer wrong and tries to nudge them along the path. A provider might make claims about how smart the system is in individual targeted-ness, although this is mostly a mirage.

 

I’m not all that happy with this state of affairs, which is why when I get to teach smaller G-Chem classes (e.g. Honors), I write my own problem sets in addition to the online homework. In office hours, most of the questions I get are on the problem sets (rather than the online homework), and I get to engage in feedback when answering questions, and when I eventually grade them. These conversations allow me to get to know individual student quirks and who might stumble how and where. But I don’t do this for my larger G-Chem sections. Call it laziness. Call it prioritizing. I’m not satisfied with this situation, and I have tried to mitigate that loss with frequent low-stakes quizzes (with in-class immediate feedback) and other measures.

 

The challenge with computer-based feedback is that it ultimately relies on algorithms honed through mass production. This means that it’s good for a subset of things you’d want your students to learn to do, but not everything, and possibly not even the lion’s share. I recognize that with advanced parsing techniques and machine-learning methods, algorithms will make more headway and be able to adequately cover a larger subset, but there may still be much that’s missing. I do some Duolingo every day, and I can see how the techniques they use leverage the science of learning, I would likely still not do great if you plopped me into an environment solely with native speakers. I suspect there’s a fundamental limitation to computer-based approaches because complex systems are likely non-simulable, non-computable.

 

I don’t know the solution out of education’s iron triangle. But one thing I do know is that if I want to help my students learn, I need to spend the time and energy giving them good feedback. I have a suspicion that over the years I have lagged in that area as other things started to make demands on my time. I suppose I’m writing this to remind myself of the importance of giving timely and sufficiently detailed feedback.

Archaeology From Space

I don’t personally know any archaeologists. But if I could single out one who is an unapologetic apologist for archaeology, it would be Sarah Parcak. Her book, Archaeology From Space, won the most recent Phi Beta Kappa Book Award for Science. I heard about it when I tuned in to the online awards ceremony. Parcak’s brief remarks about her book were all that was needed for me to add it to my must-read list. I was not disappointed.

 

I’d heard of using LIDAR mapping to discover archaeological sites through perusing the occasional news article. What I didn’t know was that prior to LIDAR, older eye-in-the-sky technologies were already aiding archaeologists. I also didn’t know that you and I can aid archaeology from the comfort of our homes and an internet connection through Global Xplorer, launched by Parcak and her team after she received the 2016 TED million-dollar prize for her dream-big audacity. I’m looking forward to seeing Peru from Space!

 

Satellite imagery gives you a starting point, a narrowing down of possibilities. Then comes the hard work of dig-in-the-dirt archaeology. Parcak goes into fascinating detail focusing on some well-chosen examples in her career; successes and failures both get the royal treatment. Her story-telling is brisk and bursting with enthusiasm; reading it I felt like I was right there in the thick of things. And she’s funny. Humorous asides punctuate the text all over. I believe her when she thanks her editor in her acknowledgement for the “tough love and for reading early drafts containing terrible jokes that needed to be buried in tombs forever. May they never resurface.” Well, the jokes that she did leave in bring joy to this reader!

 

While Parcak is an Egyptologist by specialty, and she goes into fascinating detail in this area, her many collaborations lead to projects in North America, Europe, and South America. I enjoyed reading about different archaeological sites, different concerns, different challenges, and how much we can learn about the past. The chapter on looting and the trade in antiquities is heartbreaking. Many people involved are caught in a system fueled on the one hand by greed, and on the other hand by poverty. Not knowing much about this area, I found it particularly eye-opening.

 

My favorite chapter in her book is “The Future of the Past”. (This reminds me I should re-read Alexander Stille’s excellent book of the same name. I see it on my bookshelf beckoning!) Parcak begins by imagining a future archaeotechnician in the year 2119 acquiring data with the help of several scanning bots. She then ties the different activities to what’s possible now, what’s in the near-future, and what’s not so easy to achieve. She also makes what I think is a prescient prediction: “In the future, I think it’s very likely that all archaeologists will develop an additional primary expertise within the sciences… [those] with strong scientific and interdisciplinary backgrounds have a far greater chance of employment… we have to ask ourselves whether archaeology will become a sub-focus within the sciences.”

 

What got me really excited was reading about hyperspectral imaging in archaeology. As a chemist attempting to get students interested in making visible the invisible (via the interaction of “light and matter”), I’m starting to re-imagine different aspects of my G-Chem 1 class to make it archaeologically-themed. We already talk about different types of spectroscopy to identify the structures of atoms, molecules, and crystalline solids, but I hadn’t connected this to a larger systemic context; maybe archaeology could be the link! I could even tie it to space exploration, as Parcak does with both wit and aplomb. Why is it that I’m always excited about revamping a class shortly after I’ve finished teaching it? I’ll need to wait until next fall. Right now I need to focus on G-Chem 2 as the spring semester is about to begin.

 

While I find archaeology fascinating, I’ve never pictured myself as an archaeologist because I don’t think I could survive the hard, painstaking, outdoor work in terrible weather. I much prefer reading from my armchair. A number of years back, I did incorporate a book by archaeologists into a first-year living-learning-community that my G-Chem class was a part of. Perhaps I could do something similar with Parcak’s book, but I’ll have to think more about how exactly this might work. Oh, so many ideas, so little time! At least Parcak’s book motivated me to play Thebes this weekend. That’s the closest I get to being an archaeologist. Until I get going on Global Xplorer. I’m holding off for at least a month because early in the semester is not a good time to potentially get addicted, and not put in the time doing my actual job as a chemistry professor.

Systems Chemistry Education

I recently attended an American Chemical Society sponsored webinar on “Systems Thinking in Chemistry Education”. Since my area of research involves complex systems, and I get paid to be a chemistry educator, you might think that I’d automatically incorporate systems-thinking into teaching my chemistry classes. Well, I do and I don’t. Mostly because I haven’t spent the time seriously thinking about how the two should complement each other in my classes. So this was an opportunity to learn from others who have been thinking about the issue.

 

The presenters provided an overview, some specific examples of how systems thinking might be incorporated into General Chemistry, potential future directions, and some resources. I learned that the Dec 2019 issue of the Journal of Chemical Education is devoted to this topic. I read three papers highlighted by the presenters in their examples, and today’s blog post will focus on one of them – the overview introductory article that sets the stage. (Abstract and citation shown below.)

 

The article begins by recognizing the useful role of reductionism in both scientific discovery and science education. Reductionism has its limitations, and often is contrasted with Emergence. While the two might be inverses of each other in complicated systems, this is not true for complex systems. And many systems that we deal with are complex. I’m pleased that Ludwig von Bertalanffy’s contributions are prominently highlighted in the article, and that the way systems thinking is described was not overly-simplistic (which I feared it might be before reading the article fully). In particular, systems thinking was not pushed as the panacea nor a substitute for present approaches that have worked well over the years, but rather as a potential enhancing complement in appropriate areas.

 

Systems thinking is defined as “the ability to understand and interpret complex systems and involves the following…”

·      Visualizing the interconnections and relationships between the parts of the system

·      Examining behavior that changes over time; and

·      Examining how systems-level phenomena emerge from interactions between the system’s parts.

I also found the “Systems Thinking Hierarchical Model” (the triangle shown with the abstract above) useful as a guide to seeing the different aspects at which a student might engage in systems thinking.

 

From the examples provided, the second semester of G-Chem (covering thermodynamics, kinetics, and equilibrium) seems to be a good place to incorporate systems thinking. The sense that I get from the examples is about seeing the chemistry in context by highlighting the systems-level features. Most of us already provide application-examples for context in our classes, but these are usually discussed briefly and anecdotally rather than probed more carefully for those systems-level features. Environmental science and sustainability seem to be the prime contextual targets, and the aim seems to be “educating future global citizens”.

 

Incidentally, in preparing for my upcoming G-Chem 2 class, I had been thinking about how science builds limited models as a way of studying systems via reductionism. Thermodynamics provides a prime example. By defining closed systems with particular idiosyncratic boundaries between subsystems, we’ve stripped out the complex parts, and over-simplified the system such that it no longer behaves as a complex system. That’s partly why entropy has to be introduced as a separate concept. We do this all the time in science, and we’ve similarly done so in science education especially as we moved towards mass education. Build a box. Reduce the systems. Make machines. Convince yourself that what you’ve made is similar enough to the real thing.

 

I don’t think what I’ve described is what most chemical educators have in mind even if that’s what we’re all engaging in, and I’m not sure that is the systems thinking suggested by the articles I read and the presentations I saw. That being said, I will be trying to introduce a bit of systems thinking into my Honors G-Chem 2 class this coming semester, by meshing what we’re learning to the material students will encounter in a bioenergetics intro-Bio level Honors class that most of them are also enrolled in. I’m not going to do too much this semester because we’re still in a pandemic and I’m teaching online. We all have enough to deal with already so I’m not doing any major overhauls. But I’d like to think about these matters more carefully this summer as I look forward to next year. It will also give me time to read more articles in that Dec issue so I can come up with something that works well!

Slicing the Chemistry Pi(e)

Prompted by a colleague to ponder the unity and diversity of chemistry, I’ve been imagining Venn diagrams. For some reason, they come in threes.

 

Let’s start by considering the three traditional science disciplines and their mutual overlaps. The following diagram which I’ve previously introduced to introductory students when discussing the definition of life. 

 

I’ve labeled the overlaps from a chemist’s perspective. Physical chemistry is where physics and chemistry overlap (a physicist might call it chemical physics); that’s formally how I’m classified within the world of chemistry. I teach the dreaded P-Chem (Advanced Arithmancy!) and within the American Chemical Society (ACS), I’m part of the PHYS (physical chemistry) division. Biochemistry is where biology and chemistry overlap. And all three might come together in an area I’ve called biophysical chemistry. This way of slicing the chemistry pie visualizes its relationships (and lack thereof in non-overlapping areas) with its sister sciences, physics and biology.

 

The ACS curriculum identifies five areas within chemistry: Analytical, Biochem, Inorganic, Organic, and Physical. To certify that our graduates have gone through the ACS-certified curriculum, our department has to show ACS that our students have covered material in these five areas, usually logged as class hours spent in both lecture and lab across these areas. This classification can be traced historically as chemistry began to specialize into these domains. Nowadays we might also discuss further specialization in areas such as materials chemistry, environmental chemistry, polymer chemistry, nuclear chemistry, solid-state chemistry, or my area of expertise – computational chemistry. You could represent these in a sliced-up pie chart, but I prefer the Venn diagram because it highlights the overlap between boundaries.

 

How might we make sense of all these different subfields and their relationships? Let’s try to group things by category. Here’s one possibility: Geochemistry, Biochemistry, Astrochemistry. These are three distinct areas of chemistry, but they also potentially overlap in interesting ways. You could further subdivide geochemistry into its three spatial realms: lithosphere, hydrosphere, and atmosphere. Once again, the boundary zones are of great interest, chock-full of complexity, and likely to enlarge our understanding of chemistry.

 

When I chat with students about what they might find interesting in chemistry, we discuss what classes they enjoyed, but I also talk to them about two main activities of chemistry: Making and Measuring. While not exclusive to each other, different laboratory activities tend to focus either on one or the other (although we do bring them together at the end). If I was looking for a trinity of chemistry applications, I could perhaps choose: Materials, Medicine, and Manufacturing, for my three Venn circles. Once again, the overlaps might be where interesting action may be found.

 

What unites all these different slices of chemistry? Today I’d say that chemistry focuses on the Molecular level, and translates what’s going on there to the Macroscopic human-sized world where we operate. We’ve used a lot of M-words in the last paragraph, kinda like an M-Theory. All these M-words are anthropocentric to us humans who are practicioners of chemistry.

 

What my colleague actually asked me is whether there are cross-cutting concepts across the different areas of chemistry, or perhaps what unites the slices of the pie. That they’re all pie? Maybe I should ask what are the ingredients of the pie? Or the pi? What does pi have to do with the pie? We’ll get to that.

 

The slices and Venn circles are labeled in ways familiar to chemists. They help us distinguish differences. But what unites them? In the spirit of threes and the anthropocentric “I”, may I suggest the following three concepts: Identity, Interaction, Information. There, I made a Venn diagram!

 

I chose not to use the more familiar structure-function dyad, because I think it’s too limiting, and we’re too used to the mantra that structure dictates function. This limitation is especially apparent in the growing field of Systems chemistry. I haven’t fleshed out my three I’s, but here’s what I can say broadly or vaguely. I think a truly cross-cutting concept should be more generic, and may manifest itself in potentially different but related forms across the different slices of the chemistry pie. (1) While Identity is most easily associated with individual molecular structure, it might encompass more abstract concepts such as familial relationships, classification, and macroscopic views of matter. (2) Interaction isn’t just about intermolecular forces and chemical reactions, and should not just be subsumed into Identity, but may encompass other types of dynamics that chemists are not used to contemplating. (3) Information, the slipperiest of the three, should not just be relegated to cheminformatics or Shannon entropy; I haven’t yet grasped how to think about it in a broader sense beyond the analogy that semantics, and not just syntax, is key to the understanding of language. Information could also encompass other I’s such as Imagination or Interpretation, that highlight the Interaction between observer and observed, a boundary that might prove non-trivial.

 

The slices we have made are human conveniences to corral what might be a huge area into more manageable ones. We may specialize and self-identify (or be identified) with certain slices. But we should be continuously aware that by reducing our field of vision – for good reason, to learn some new things! – we also blinker ourselves from the richness of the whole. In a previous post, I quoted Rosen’s description of that funny number pi – yes, the one that shows up in pies, and that we celebrate by eating said pies on Pi Day. Those seemingly thin boundaries along slices of pie, might actually be broad rich areas of investigation, fractal-like as you look closer, but more complexly so, and certainly not captured by simple Venn diagrams.

 

Identity, Interaction, Information. Perhaps that’s one way to think about the Chemistry Pi.

 

P.S. For other Pi-related posts, see Abstraction or Happy Pi Day!

Making an Impact

I tell my students that one of the best things about being a professor is when my former students come back and tell me what they’re up to in life! While travel is much reduced because of Covid, I had a number of former students out-of-the-blue e-mail me this past week to say hello, give me an update, and thank me for the impact I made in their lives. It’s very heartening and I’ve felt encouraged, and (almost) ready for the new semester.

 

I get to know students in different ways, and a selection of students I heard from this week will illustrate these different relationships. One was an academic advisee letting me know of successful post-graduation plans. One was a student in two of my classes who is finishing up one successful post-doctoral research stint and moving on to the next opportunity. One was a research student (but had not taken a class with me as an undergraduate) who was going through a difficult time, but was reminiscing about the positive experience working in my lab. And one was all three – an academic advisee, a student in one of my classes, and a research student – who is on track to finish her PhD this year.

 

I spent a fair amount of time chatting with these students during their undergraduate days, be it in office hours, in lab, or in the hallway. While I try to get to know students in my classes, there’s little time to actually do so in class or the five minutes before class begins. So I tell students in my classes that one of my favorite times is office hours. Come visit, come get to know me, and give me the opportunity to get to know you. This happens as a matter of course for my academic advisees and my research students, but not necessarily for students in my classes who aren’t my advisees or working in my research lab. Not many take me up on the opportunity, although I was interviewed by a student a couple of years ago.

 

I am not like most of my students. I don’t look like them. I don’t talk like them. I grew up in a very different country, and have an accent strange to their ears. And my teaching style is a bit more “authoritative” (the dominant style where I grew up) so it might feel intimidating to the student. It doesn’t help that I teach P-Chem, the toughest and least-liked class of our majors. I try to be friendly and amiable, but my introverted slightly guarded personality might get in the way. So sometimes I’m not sure if I’m making an impact, although I keep trying. This week I got a precious reminder that I do make an impact, not on everyone and not all the time, but it does happen and it’s a great reason to keep at it.

Irreducible Complexity

It’s unfortunate that the phrase irreducible complexity is most commonly known nowadays as the failed idea of creationists arguing against neo-Darwinian evolution. I’m greatly over-simplifying the story here because today’s blog post is not about this popular “controversy” between science and religion.

 

Instead I’m going to discuss some thoughts from reading Robert Rosen’s Essays on Life Itself, in particular focusing on the relationship between physics and biology. I’d like to think I have special insight as a chemist sitting between these two fields, but maybe I don’t, and maybe it’s an open question whether or not these fields are sequentially linked. The Venn diagram I have used with my students to discuss definitions of life may not be accurate either.

 

I discovered Rosen’s work after stumbling on Mikulecky’s definition of complexity, which implicitly contains the idea of the irreducible. This is distinguished from something that is “merely” complicated, which is reducible to its parts even if the disentanglement process is super-complicated. Rosen begins with Schrodinger’s What is Life? and argues that most contemporary physicists and biologists ignore a deeper fundamental question about the relationship between the two areas.

 

Schrodinger argued that we might need a “new physics” to characterize life. In the present reductive model, familiar to scientists and students of science, biology can be implicitly reduced into chemistry, which can then be reduced to physics. Living organisms are a subset of the larger “world” of non-organismic materials and forces; they are a special and perhaps even rare case – rare in the physical universe because of the special Goldilocks conditions of planet Earth. Rosen turns this idea around, making the enigmatic proposal that “organisms are more general than the non-organisms in the old physics, and that their apparent rarity is only an artifact of sampling.”

 

An argument made against modern-day proponents of irreducible complexity from scientific creationists affiliated with the IDEA institute and the Intelligent Design movement is that they are reviving the failed idea of vitalism, and attempting to smuggle in God as its sustainer – thus we can’t explain life without God, the author and creator of life. I find this view theologically impoverished; it seems like a God-of-the-gaps argument that relegates the supreme being to a tinkerer of parts within the “old physics”.

 

It’s hard for us to get out of the mindset that life seems rare and special. Perhaps that’s because we modern folk think in terms of material substances rather than functionality. To think of functionality smacks of teleology and the smuggling in of purpose. We the scientific-literates focus on the syntax but not on the meaning. Information is reduced to bits, bytes, and Shannon entropy. We’re all about counting backwards and forwards in precise discrete addition and subtraction, each piece independent from each other. We do acknowledge mysteries such as the nature of energy – we don’t know what it is but we can count it – but that’s only because we haven’t gotten through the process of disentangling its complications.

 

Rosen has many analogies as to why this sort of thinking is flawed. Here’s my favorite one that serves as an analogy to why the “old physics” might be a subset of unruly biology, rather than the other way around of subsuming biology within the larger realm of physics.

 

“This kind of argument rests on a confusion about, or equivocation on, the term rare, and identifying it with special. An analogous argument could have been made in a humble area like arithmetic, at a time when most numbers of ordinary experience were rational numbers, the ratios of integers. Suddenly a number such as π (pi) shows up, which is not rational. It is clearly rare, in the context of the rational numbers we think we know. But there is an enormous world of ‘new arithmetic’ locked up in π, arising from the fact that is much too general to be rational. This greater generality does not mean there is anything vitalistic about π, or even anything unarithmetic about it; the only vitalistic aspects show up in the mistaken belief that ‘number’ means ‘rational number’.”

 

There are many other thought-provoking ideas just in the first fifty pages of Essays on Life Itself, I could spend the rest of my lifetime exploring them in detail. As a reminder to myself, since my blog is a cyborgian extension of my otherwise poor memory, I will briefly note a few of these here in the hope that I will get back to them at some point.

 

Rosen grounds his definition of complexity by thinking about the non-commutability of relationships, and that analysis and synthesis are not exactly opposite processes. I’m reminded of when I discuss Hermitian operators and Heisenberg’s Uncertainty Principle in my quantum chemistry class, and it seems like there’s some quantum astrology going on. Rosen regularly refers to the difference between inertial and gravitational mass, with a hint to why the N-body problem exists. Most of us (me included) don’t think about the difference between these two types of mass because they are numerically equivalent. But they are not the same.

 

This brings me to Rosen’s thoughts on biomimesis and simulation. Can mind be reduced to machine? If an artificial intelligence passes the Turing test, does it mean it is alive? Does it matter if we humans can’t tell the difference? Rosen marvelously connects science and magic as he ponders the nature of objectivity: “[Mimesis] is animated by an idea that things that behave enough alike are alike, interchangeable. In biology, such ideas go back to the earliest historical times and, indeed, are intimately related to the archaic concept of sympathies as in ‘sympathetic magic’ … if we can produce a system manifesting enough properties of an organism, i.e., it behaves enough like an organism, than that system will be an organism… Indeed, mimesis treats such individual behaviors as a reductionist treats atoms, as syntactic units… [that] can be reduced and then recombined...”

 

I’m reminded of the parallel work in origin-of-life research that studies artificial life, some through carefully designed biophysical systems such following GARD, but more often through simulation – with the underlying assumption that software and hardware can be treated independently from each other. As a computational chemist, I also wonder if my particular approach to tackling origin-of-life questions is doomed to failure, given that one aspect of the complexity of biology, according to Rosen, is that it is non-computable. The irreducibility of life makes it so. I’m also reminded of one tricky aspect that most students don’t notice on the first day of my introductory chemistry class when we discuss the definitions of element, atom, molecule, compound. There’s a certain circularity to those definitions, and I feel a slight pang of helplessness every time we go through it, because the occasional student (one who has had little background in chemistry) will for good reason that they cannot easily articulate find the definitions confusing, and I will provide pat answers in class so we can move on.

 

Rosen employs notions of graph theory as he ponders how to think relationally about forces acting on materials which are themselves sources of forces. I’ve been thinking along these lines in my current research as I struggle to conceive the limitations of differential equations in studying the kinetics of autocatalytic systems and how they evolve. There’s a strange (by which I mean I don’t understand it) recursive relationship going on, that might lead to infinite regress on the one hand – you might need a larger system to explain what’s going on in your subsystem – and yet “infinity is not the same as large finite” as Rosen states, and it boggles my mind how to think about this. Even more mind-boggling, Rosen suggests a possible way out through replication as some way to stabilize open systems such that somehow the recursive loops close back into some sort of discrete entity (an organism!) with boundaries that remain fuzzy.

 

Murkily, rather than clearly, the approach to understanding complexity will not adequately proceed through pure reductionism. Reductionist models can give us partial understanding of the part, not the whole, and we need to remember the limitations of our model whereby we’ve conveniently hidden or ignored the irreducible parts. To grasp that whole, maybe a “leap of faith” is required. Not because of small gaps because the “old physics” is starting to see widening chasms as it explores complexity theory, but large gaps that Schrodinger began to ponder when he suggested a new physics is needed. Those lessons may come from life itself.