Difference Dynamics

This post is Part 2 on Terrence Deacon’s Incomplete Nature (see here for Part 1). I’m now ten chapters in. The prose is still dense and repetitive, but I enjoy encountering interesting nuggets amidst the windy narrative. Deacon is also building up his case by introducing different levels of dynamics and making analogies to Aristotle’s Four Causes.

 

For most physical scientists, Aristotle’s efficient cause is our main focus, the process by which some physical interaction takes place. As a chemist, I’m also interested in the material cause: the identities of the molecular structures that are involved in these interactions. We chemists often think of these two causes in terms of the words ‘function’ and ‘structure’ respectively. The distinction is not always clear-cut.

 

Deacon begins Chapter 6 by discussing constraints. This, I think, is a very important feature. He exhorts his readers to think about what is absent when a constraint is in place, i.e., something couldn’t happen (which otherwise could have) if the constraint wasn’t there. It might seem odd to try and describe something by what it is not, but this is a time-honored practice that is simply practical when trying to describe seeming simple all-encompassing things: Energy, Life, God, and as mentioned in my previous post: Emergence.

 

This leads us to statistical thermodynamics – a course I regularly teach that students find painful. The beauty of statistical thermodynamics is that in a closed system (i.e., one with certain constraints), you don’t have to keep track of the individual movements and interactions of millions or zillions or moles of molecules. With the help of first-year college calculus, you can actually describe macroscale thermodynamic properties (that you can also measure experimentally) as averages of a zillion motions that are surprisingly easy to calculate. (At least they’re easy to calculate in idealized system, but there are many tricks one can use to handle non-idealized ‘real’ systems.)

 

Deacon argues that “where constraints at a higher level are linear extrapolations of those at a lower level… there is no loss due to reductive analysis. But where there is non-linear constraint… both physical and analytical decomposition eliminate the source of this constraint, and hence the source of its causal power. Such cases should therefore be paradigm examples of emergent transitions.” Essentially Deacon is saying that equilibrium thermodynamics is subject to reductive analysis – explaining a macroscopic property in terms of its tinier components – because of the linearity in constraint extrapolation. But this strategy of reductionism fails in emergent systems because it throws out the baby with the bath water.

 

Deacon’s dynamics paradigm has three levels: homeodynamics, morphodynamics, teleodynamics. Each ‘higher’ level is supervenient on its lower levels. Homeodynamics, the lowest level, is akin to equilibrium statistical thermodynamics. There is a tendency to reduce any asymmetries, i.e, the closed system will try to degrade any gradients that are present. Is there a difference that makes a difference? Get rid of it! Level the playing field! Equality for all!

 

There’s a nice nugget as Deacon discusses how Energy entered the lexicon, as introduced by the polymath Thomas Young in 1807. The Greek energia combines a prefix meaning ‘in’ or ‘to’ with a root word meaning ‘activity’ or ‘work’. In that sense, whenever my students define energy as the “ability to do work”, they’re not far wrong – but it’s superficial at best since we don’t really know what energy is. Deacon says: “… it might be more accurate to say that the capacity to do work is a gradient across which there is a tendency to even out and dissipate. Energy is more accurately, then, a relationship of difference or asymmetry, embodied in some substrate, and which is spontaneously unstable and self-eliminating… I suggest that the key to understanding what energy is is to stop focusing on the stuff that embodies it, and instead consider the form that is embodied… energy is a relationship of difference that tends to eliminate itself.” That’s the second law of thermodynamics in a nutshell and Deacon will attempt to connect this concept with Aristotle’s formal cause.

 

One has to slog through Deacon’s definitions of orthograde (with the gradient, go with the flow!) and contragrade (against the flow), but he needs these to set up his next level: morphodynamics. His essential argument is that the interplay of orthograde and contragrade processes at one level has an effect on constraints, and thereby allows (in the vicinity of an attractor) the emergence of supervenient levels. What is morphodynamics? In a nutshell, it has to do with the behavior of non-equilibrium thermodynamics and open systems. The Benard cell is Deacon’s prime example. Nothing new here. But he does have an easy to picture analogy of a building that’s hotter inside than outside, and how opening certain windows or doors removes a constraint for dissipating heat and can introduce new dynamical flows. But the winds could cause a door to slam shut thus adding a new constraint, and so on.

 

But apparently this is not enough, and there needs to be another supervenient level. The orthograde and contragrade at the morphodynamics level allow the emergence of teleodynamics. You can sense Aristotle’s final cause lurking here. Deacon has a nice little chart that distinguishes the three. I’ve put them in the bullet points below.

 

·      Homeodynamics (e.g. thermodynamics): the orthograde is an increase in entropy, the removal of constraints, and moves towards equilibrium

·      Morphodynamics (e.g., self-organization): the orthograde is an amplification of constraints leading to dynamical regularization and metastability

·      Teleodynamics (e.g. life): the orthograde is reproduction and repair of systems, i.e., preserving constraints and allowing them to correlate

 

Honestly, I’m not sure why there aren’t more levels. It could just as well be turtles all the way up. Autocatalysis and self-assembly are thrown together to make something that is sorta like life, but not quite. A negentropy ratchet is thrown in. You can tell that I’m finding this all to be obfuscating rather than clarifying. Deacon seems to promise that we’ll get to some useful examples, but I’ve yet to see them. But I’m hoping Chapter 11 (“Work”) will tie some of these threads together. That’s my work for tomorrow morning!

Heteropathy

Emergence is a buzzword in the study of complex systems. Its new life came into being as experimental scientists delved into self-assembled molecular systems. Parallel to these discoveries were advances in computational capabilities allowing for the simulation of non-linear dynamics at longer timescales. I guess I’m in the right era to be studying the origin-of-life and possibly make headway. That being said, emergence is an old idea, but only now coming into its own.

 

I’ve read many takes on the notion of emergence. My most recent foray is Terrence Deacon’s Incomplete Nature. It’s a thick book. The prose is dense although repetitive, making it tedious to read. It’s also ten years old – which is getting old when you’re at the cutting edge of experimental and computational science. I’m five chapters in. Chapter 5 is appropriately titled “Emergence” and ties together the (tiresome) threads together of the first part of his book. I’m glad I made it this far because I enjoyed the historical perspective that Deacon narrates. And I think I’ll keep going to see if there are any nuggets to glean. (I wasn’t so sure as I slogged through the first four chapters.)

 

Deacon thinks the two outstanding problems that defy the reductionism of established science are the origin of life and the nature of mind. His expertise in biological anthropology and neuroscience speaks to the latter. I’m interested in the former, but I agree with him that there are many parallels in the two cases. I personally think the origin-of-life problem might be the more tractable of the two, but it’s too early to tell.

 

The historical perspective that Deacon takes begins with the philosophers John Stuart Mill and George Henry Lewes. Mill makes reference to an example that my introductory general chemistry students encounter – the formation of table salt (useful and beneficial to us) from two seemingly dangerous substances, sodium metal and chlorine gas. The heart of chemistry is Atomic Theory, and students in my chemistry class (hopefully) learn to use the model of ‘invisible’ atoms as the constituents of matter to explain all manner of interesting macroscopic observations.

 

Mill thinks there’s something different about organisms that distinguishes them from mere machines. Quoting Mill: “To whatever degree we might imagine our knowledge of the properties of the several ingredients of a living body to be extended and perfected, it is certain that no mere summing up of the separate actions of those elements will ever amount to the living body itself.” The essential point Deacon makes is that there is a “discontinuity of properties despite compositional continuity” when one crosses ‘levels’. How those levels are divided from each other is still contentious, but this idea gibes with ‘biological relativity’ arguing that no explanatory level can be privileged over others.

 

Within a level, reductionism works, i.e., the whole is the sum of its parts. Mill calls these homopathic laws. Don’t confuse homopathy with homeopathy (as my Spellchecker keeps doing and there’s one typo in page 155 of Deacon’s book that demonstrates its insidiousness); the latter makes no sense chemically is all I will say about it in this post. But back to the topic at hand. When levels are crossed, heteropathic laws operate. What are these heteropathic laws? There’s the rub. We don’t quite know, but this is what we’re trying to discover. In a sense, we haven’t answered the age-old question of what an Element or a Substance is, even though both words show up on the first day of my general chemistry class. They’re slippery concepts going back to the ancient Greek philosophers.

 

Deacon introduces a triad of philosophers known as the “British emergentists” that build on the work of Mill and Lewes. One of the arguments made is the inability to predict properties at one level from laws or properties at a ‘lower’ level. (By ‘lower’, one means a smaller lengthscale.) This led to two camps: Folks that emphasize the ontological nature of emergence, and folks that emphasize the epistemological nature. Both concepts have their problems. Deacon also discusses ‘weak’ versus ‘strong’ emergentist views depending on how severe one thinks about the ontological discontinuity between levels. My chemistry students by the end of the semester would think this discontinuity odd. They’d argue that we just don’t know enough yet to be able to make predictions, but that ‘hidden variables’ will eventually come to light.

 

Quantum mechanics gets dragged into the picture by the American philosopher Paul Humphreys. The idea is that because of wave-particle duality and other seemingly strange interpretations of the quantum world, “the individuation of events and objects is ambiguous… to circumvent the problem of double-counting causal influences at two levels… by arguing that fusion results in a loss of some constituent properties. They literally cease to exist as parts are incorporated into a larger configuration.” I’m somewhat sympathetic to this muddy view – an oxygen atom in the oxygen molecule differs greatly from an oxygen atom in the water molecule from my perspective as a quantum chemist. This is akin to the Humpty Dumpty problem. If you take H.D. apart, you can’t quite put him back together again.

 

Throughout the first several chapters, Deacon hints at the role of constraints in the process of emergence. He also weaves in and out discussing its time-dependence. I suspect that these two pieces are vital in conceptualizing what emergence is. But just like those other big words (Energy, Mind, Life), I don’t think we will easily be able to define Emergence. Rather, we’ll try to get at it conceptually with myriad examples. Somehow we’ll have to figure out Heteropathy works. Is it Work? I’ll know what Deacon thinks when I get to Chapter 11. Hopefully it won’t be a bankrupt idea.

A Year Back

I missed the Great Pivot of March 2020. Because I was on sabbatical, it gave me the time and space to think about how I would offer my courses remotely. While some of my other sabbatical plans were squashed, I was still able to make good progress on one of my research projects. Being a computational chemist, I just needed an internet connection to VPN into my institution’s computing cluster.

 

We were remote both semesters of the 2020-2021 academic year. I didn’t like it, but it wasn’t as bad as I had anticipated. (Here’s my roundup for Fall 2020 and for the year as a whole.) In short, my upper-division special topics class translated well into the remote environment because we discussed the primary literature. I hardly had to “draw” anything on a whiteboard (viewed through Zoom). The rest of my classes were general chemistry extensively used the white board, but I think I managed fine, and so did the students. I’m glad I wasn’t slated to teach physical chemistry during the remote year.

 

I was glad to be back in person for the 2021-2022 academic year. I think most of the students were too. We had a short remote stint at the beginning of the spring semester because of the Covid winter surge, but that was only for a couple of weeks. Teaching while masked wasn’t terrible since our classrooms are not large. Student participation didn’t seem diminished compared to pre-Covid times. One thing students were not used to: taking exams in-person in a classroom once again. The first exam in my fall semester classes felt stressful for the students. I think they got used to it pretty quickly. I also feel that my weekly meetings with my research students were more efficient in person, and I’d like to think I was able to convey my excitement about their projects better in person.

 

This past year I maintained hybrid office hours, i.e., I had my Zoom open during office hours but also encouraged students to visit in-person (masked) especially if their questions involved diagrams or math. Physical chemistry is full of math, and my P-Chem students always visited in person. It was much easier to work through problems together that way. While I had a few G-Chem students visit via Zoom, those that chose to come to office hours mostly came in person. I did notice that fewer unique students came to office hours this past year compared to when we were remote. I suspect it’s because students (especially first-years in my G-Chem classes) didn’t know their classmates and so many of them were working alone on homework rather than with others.

 

During the remote year I was just trying to keep up with adjusting to Zoom and Blackboard. This past year back in-person, feeling a sense of normalcy, I had time and space to think about how to improve my classes. I overhauled my quantum chemistry course, ditching the textbook and making worksheets for each class meeting. This was a lot of work but I’m happy with the effort I put in because I can build on it the next several times I teach the course. I made some improvements to my statistical thermodynamics worksheets with some new things I tried in quantum. Overall, I felt my stat therm class was more streamlined this year. I had students submit their problem sets and mock exam questions through Blackboard and that worked well. In my G-Chem classes, the self-tests were delivered and submitted through Blackboard too – a practice I retained from the remote year that worked well. Overall, I handed out less paper in class than I used to, and I made more pdf files. So even though we’re back in-person, I now use Blackboard for material delivery and assignment submission, something I hardly used pre-Covid.

 

My year back isn’t quite over. We’re just starting Finals Week. Hopefully none of my students catch Covid and are able to take their final exams on time. Last semester, I count myself fortunate that there were no issues in all three of my classes. But you never know. The U.S. is seeing an uptick in cases again. All in all, it’s nice to have a year back. It passed quickly, and I’m already starting to think about my classes next academic year. But first I need to finish the semester, and gear up for summer research!

Write Your Own Assessment

A math colleague recently shared her endeavor to getting students comfortable writing their own questions (and answers) as part of the learning process. I haven’t personally done much in this area other than my Mock Exam Question assignment in P-Chem; which I’ve been running for a few years with only minor changes. My colleague’s approach is much more extensive and likely to see more gains than my surface-level approach, so I was happy to learn what she was doing. Essentially, she scaffolds the assignments, getting students started on writing a question for a quiz, then a midterm, then a final. She calls this “Write Your Own Assessment” and has been refining it in an introductory-level college algebra course.

 

After the students have taken several short quizzes, the first assignment is “Write Your Own Quiz”. The guidelines students are given have been exemplified by previous weekly quizzes that they’ve taken. One question can be easy to answer, but a second one must be of at least moderate difficulty. Students must also include a detailed answer key to their submission. She then “grades” their efforts by providing feedback on the quality of their submission.

 

A month later, the next assignment is Write Your Own Midterm, and provide an answer key. There are similar guidelines to the Write Your Own Quiz assignment in terms of what is expected. And towards the end of the semester there is Write Your Own Final. Students are allowed to include similar, but not identical, previous questions they’ve written for the Quiz or Midterm assignments. In addition, the students also write a paper reflecting on what they have learned through the process of writing their own assignments. I mulled a similar reverse final because of the pandemic but ultimately did not follow through. I certainly had not put in the scaffolding for it.

 

My approach falls far short of this. I do tell the students how to go about writing a Mock Exam Question based on the Problem Set questions they’ve seen in P-Chem. They each have to submit at least one question, and they work in groups of four with the stipulation that the range of questions submitted covers some breadth. (They can’t all write a question on the same topic.) I did not provide any feedback on their submissions nor did I ask for a detailed answer key. I did tell them that they should know the answers to their questions, and I expected that after taking the exam they would have a sense of whether their question was well-posed. Honestly, I was lazy and didn’t want to do a bunch more grading beyond looking to see that students followed the parameters. I provided a small incentive of unspecified extra credit for particularly good submissions (as subjectively judged by me for relevance and creativity).

 

I gave full credit (1% of the overall course grade) for each assignment. There were three – and each of them was due the day of the midterm (thus students who did the assignments would get 3%). A small number of students simply don’t do them (or forget) but the majority do so. Typically, one or two students get the extra credit for one of the assignments per semester. Overall, this is a very low stakes assignment that I hoped helped them as they were studying for the midterms.

 

Listening to my colleague’s approach and seeing her assignment instructions reminded me how poor my version was compared to hers. I haven’t sufficiently leveraged the power of Write Your Own Assessment assignments and I could do better in this area. In her instructions, she also tells the students that they will find the assignment difficult at first and resort to using a known problem and just changing the numbers or making a minor modification. She exhorts this initial approach as “a great way to start”, but expects that as they approach the final assignment, they will start to write more creative and interesting problems. My students mostly stay at the initial approach because I haven’t provided guidelines or feedback to push the more creative aspects of writing good problems. This is something for me to think about and ponder now that the semester is ending, as I start to think about next semester’s classes!

A Dark Room

I have recently become intrigued by interactive fiction, although I have yet to try it out. The semester isn’t over yet, and I don’t want to get distracted by what might be an immersive process. I should be focused on teaching my students to the best of my ability! To keep myself thinking about teaching in fresh ways, I read widely about education, teaching and learning. That’s how I stumbled on A Dark Room. (Warning: it could be an aptly-named black hole on your time!)

 

What is A Dark Room? Well, it’s hard to describe. I couldn’t do better than this 2014 New Yorker article titled: “A Dark Room: The Best-Selling Game That No One Can Explain.” According to the article, its forerunners are Colossal Cave (Adventure) and Zork, the landmark works that launched interactive fiction. There’s something mysterious yet addictive about it. One part resource management – you’re building up a village and its economy – and one part exploration which resembles a more open-ended version of a Choose Your Own Adventure book with simple battles and finding items. I haven’t gotten that far yet, so I don’t know what the goal of this game is.

 

I like the simplicity of an all-text game that harkens to the computer games I encountered in the 1980s – the only decade in which I played such games actively. I’ve never taken to the more complex graphics-intensive games from 1990 onwards, except for a stint with Sid Meier’s Civilization, the original version. Ironic perhaps because I study complex systems in my research using computational methods, but I shy away from complexity in other areas of my life. Neither have I understood the draw of the Tamagotchi or the obsession with Farmville, which require your constant attention to keep your pet alive/happy or build up your thriving farm. Yet A Dark Room uses a similar strategy to keep you engaged – you just want to press the buttons to gather wood and check the traps you have set to obtain meat, fur, and other goods that can be turned into other goods. There’s also the feeling of wanting to build bigger barns and optimize your resource production.

 

I was only planning to check out A Dark Room (on a web server) and before I knew it, thirty minutes had passed. In my second session, an hour flew by. I’ve played several more sessions although I don’t know how long I will continue. The village-maintenance repetition does get a little old, but I haven’t gotten very far in exploring yet; about twenty clicks from the main village in most directions. I’m not even sure how big this world is. That being said, I’m very impressed by the simplicity of the interface. There’s no rulebook. It’s not clear exactly how things work, and there’s a joy in discovering this for oneself. When educators talk about engaging through gamification, this might be the sort of experience they’re thinking about. It looks simple, yet it may belie layers that you, the reader or explorer, just can’t wait to peel off. Or I might be wrong, and this might be a shallow world.

 

I’m still entertaining the idea of creative an interactive fiction world about learning magic while teaching concepts of science, and especially chemistry since that’s the area of my expertise. A Dark Room has opened up my perspective of what one can achieve in a simple text-based creative work. It’s clever, at least that’s my assessment for now.

Metal Muncher: Ghost Version

Yet another Ghostbusters movie. Yet another Ghost-related blog post. I enjoyed Ghostbusters Afterlife. It’s not mainly about ghosts or ghostbusting but about family and friendships – relationships by blood or forged by working closely together. The kids who helm the movie give it a touch that’s missing from the previous movies in the franchise. The narrative of the movie unwinds slowly, but keeps the viewer engaged. There are hokey parts that pay homage to the original movie, but are overall well done.

 

I won’t say much more about the story arc of the movie, so as not to spoil it. Instead I will focus on a side character, the ghost known as Muncher. Unlike Slimer, Muncher doesn’t have much personality. Muncher just munches on stuff, particularly if it’s metallic. It allows Muncher to shoot bullets in self-defence when threatened. Instead I’m interested in mulling over the corporeality of Muncher and iron, complementary to my previous posts on the interaction of ghosts and matter.

 

Ghosts are thought of as ghostly, typically interacting little with matter as we experience it. This is true of the Harry Potter ghosts who glide through walls, people and other seemingly solid objects. Interacting with matter might be possible although difficult, as illustrated by the pantless politician in the comedic BBC series Ghosts. In Ghostbusters, such interaction is not a problem. Muncher does not fly through any walls, and in fact, carefully avoids running into solid objects at high speed. The ghostly entities in this movie seem to be able to wear material corporeality like a garment. They sort of dissolve when forced into a Ghostbuster trap. They seem to travel either as smoke or as photons of lights or some combination thereof.

 

Muncher seems to have an appetite for metal, eating through it faster than a strong acid can dissolve it. Why? I don’t know. While Muncher is luminous, Muncher’s body is not transparent so it’s unclear where the metal goes. At the very least, it gets broken into smaller pieces that can be egested like shrapnel. Is it waste? Can Muncher transform one metal into another type of metal? Can Muncher break down a chunk of metal all the way down to the atomic level, and what happens then? I don’t know. These are perhaps questions a Ghostscientist might try to answer. Hopefully as Phoebe, the protagonist of Afterlife, grows up, she could pursue such questions.