Saturday, December 31, 2016

Abstract reasoning-it's not the facts that matter

We've been discussing for decades how important it is to inculcate our students with critical thinking skills. In recent years I sense that we've backed off from that lofty goal (and wrongly so) in the academic world, in favor of a narrowly conceived push for "quantitative reasoning." Whatever this small-minded objective is supposed to accomplish, at its heart it aims desperately to rationalize, pin down, or somehow pigeon hole the rambling, ambiguous, multi-colored blanket of critical analysis. Perhaps this is due to the frustration we experience teaching critical thinking. It's arguable that our first- and second-year undergraduates are at the entryway to critical thinking. They're too young to embrace it fully let alone use it, and with time, another half decade or so, they will be cognitively prepared for critically taking apart problems and analyzing them from a mature perspective. But our students' readiness shouldn't deter us from hammering home critical thinking through example, discussion, reading, and practice. Critical thinking means getting some separation between the problem at hand and taking, all at once, a deeper look and a look from 30,000 feet. It's a lot more complicated than learning to spot a lie through statistics but it's a lot more useful. 

I've taught cellular and molecular evolution for over twenty years and about halfway through struggling with the material I came to realize that it's not the "facts" that matter. Students tend to believe what we say, or at least they try to memorize our "facts" for the next exam. But as we conceptualize nano-scale phenomena it becomes apparent that it's what's happening around the edge of the "facts" that really makes a difference. And I think grappling with this means reasoning in an abstract manner. 

Here's a simple example. We teach the characteristics of water and how these characteristics influence living systems. This bolus of information is a bit abstract in its own right because we don't "see" surface tension or cohesion. And we don't readily see them in action, for example in the xylem tissue of a plant or the formation of a raindrop. Teaching this material is, in a sense, making the invisible visible. But it goes deeper. To get at the core of understanding the behaviors and properties of water it helps to understand the nature of the molecule. Literally, how do the three atoms interact? How does the electron cloud establish and behave itself? How is polarity the end result and what does this mean? If we can help students grasp these deep abstractions we can help them see more clearly (more analytically) the behaviors of water. 

But when we delve into these mysterious (if basic) facts about water we are wading into depths that may take us to a different place than we expected. All of a sudden we're in the territory of how-things-work-and-why. We are in a deeply abstract mindset where a whole new set of connections can be set up. For example, as we consider hydrogen bonds in water we are free to construct a hydrogen-bond model of proteins. And we may see how hydrogen bonds and their behaviors influence not only protein folding and prtotein surfaces, but the complex behaviors of protein molecules. From this vantage point we may understand better, if not fully, the interactions between embedded proteins and the phospholipid bilayer membrane. We free ourselves gradually from "facts" and encounter a world of analogies, connections, and speculative reasoning. I call this wonderful place abstract reasoning. It's a branch of critical thinking that requires a cognitive leap away from textbooks and flash cards. Using it engenders high-level brain function but it also prepares students for future encounters with the abstract, something they will have to deal with the rest of their adult lives. 

OK. This was a kind of introduction to abstract thinking, something I hope to pursue in future writing. It's key I think to critical thinking, which demands similar cognitive investment as well as a healthy dose of getting "above" the problem, that is, speculation. I hope to write about the challenges posed by abstract thinking. And most important, this is the first year I'll approach the topic of cellular and molecular evolution by fully embracing this challenge. 

Friday, December 30, 2016

Constant Reinvention

We know that things like the human skin are in a constant state of regeneration. Old cells die and are sloughed off and new cells arise in their place. This is the case with organs, bones, and many other tissue systems in our bodies. Reinvention is part of biology. The past couple of decades have brought a focus on a locus of reinvention in animals--stem cells, which are omnipotent regions that can regenerate and differentiate into other kinds of cells. As a plant biologist I've been greatly interested in meristem cells, which are analogous to stem cells in animals. Botanists have studied meristem cells and meristematic regions of plants for well over 100 years. The question of reinvention and regeneration in the plant body is, if not fully understood, at least very well researched. 

What's less well researched I think is the question of molecular and cellular space in both biotic and abiotic systems. Looking at molecular structure and its attendant electron cloud, one is struck by the idea that the electrons are not actually "in place." They are present statistically but never for long enough to be detected in any physical location. It follows that the "surface" of a molecule is an environment that's in a state of constant reinvention and regeneration. As its electrons orbit there are slight changes that occur on this "surface." They occur constantly and they affect more than the physical shape of the molecule. They influence its chemistry and electromagnetic state as well. They make this solid idea of a bit of matter something malleable and ever-changing. Further complicating the matter, a molecular surface doesn't actually exist in a physical sense. It is an ambiguously defined region of unambiguous interaction with other molecules. This issue, which overflows with uncertainty, is indeed, an idea that was named the uncertainty principle. It was introduced in 1927 by Heisenberg, and perhaps not coincidentally it is a product as well as a driving force of modern thought. If matter is not "real" in some familiar physical sense, can it be considered real in the perspective of a non-conventional physicality? Or must we encounter matter in a different sense altogether? 

I wonder whether these kinds of questions of ambiguity are worth posing to my undergraduates. They like the cold hard facts from their professors. So are these the kinds of intellectual concerns that young people want to be involved with? Do they matter? I think they do. The past few days and weeks in this tumultuous historic moment have stood convention, in its social and political sense, on its head. perhaps more than 1927, these are times of huge uncertainty. Social and political norms, even the nature of information itself, seem to be reinventing themselves whether we like it or not. And I know how deeply this affects my students. Their response on the day after the election was momentous and heartfelt. So maybe addressing questions of regeneration, reinvention, and uncertainty, all of which lie at the heart of scientific thought will resonate with my students next semester. 

One thing I'm sure of. As they go out into the world and start to work and function as adults they will find themselves reinventing their identities, their behaviors, and their ways of thinking as they move forward through life. For a long time now I've wanted to teach a science course that involves the exercise of reinvention. While the scientific facts themselves are interesting, it's the abstractness of them and the cognitive innovations that can arise from them that may be of great utility to my students in the future. 

Thursday, December 29, 2016

Playing around to survive

It's perhaps a not-so-well-known fact that evolution is a game, putting together diverse components to make survival happen. The fancy word is "bricolage" and I ran across it the other day while researching explanations for the origin of life on earth. How I will bring this particular idea back to my students is still not clear. The "RNA world" hypothesis is not an easy one to explain. But the concept of bricolage, or tinkering, something that I expect we will do every week this semester in lab, is a driving factor in evolution as well as a central practice of the course in bioinspiration that I'm developing. 

I think even among scientists we may not spend enough time thinking about the playful aspect of evolution. We should consider it more. Visualize photosynthesis. The random walk of a photon along an array of chlorophyll molecules in a photosystem is emblematic of a kind of physical "play" that results in very real physical benefit to the plant. Certainly in evolutionary biology, the randomness of phenotypic variations in a population and the randomness of environmental conditions the population experiences is part of a  random walk through time, space, physical characteristics, and speciation. In another example, yesterday I wrote about electron clouds, a stochastic phenomenon with very real implications for how life functions. These phenomena point to a perhaps unsettling uncertainty that underlies all biological processes. 

This came home to me after a short discussion with a young man, just a little older than my students, whom I've known for many years. He's just finishing up his undergraduate studies at a large Ivy League university and he is busy launching himself into a budding career that will make him a high power attorney, same as his parents. He was groomed for this kind of "success" but if you ask me it's all a little bit dismal. A young person of 20 or so has to do some experimenting. Or maybe a lot. There needs to be healthy uncertainty, not just about which law firm you'll end up in, but about life itself. What are you cut out to be? Who will you become? In contrast, this highly directed march toward a career goal precludes the kind of "getting lost" that teaches us so much. He's a nice enough kid and he'll end up making a lot of money, and there's nothing wrong with that, but it all seems like a strange expenditure of a life, a kind of one way track. It's as if his parents, who brought him up to be this person somehow didn't trust their child's ability to direct his own intellectual and career development. He does seem to have been produced in a cookie cutter. I'm much prouder of my own adult children who have pursued work that is far off the conveyor belt but at the same time productive and positive. They make life better for people-what can I say? They had to play around to figure out what they'd do in life. They ran into some disappointments, some dead ends, but they made their own way in an original, self-defined way. 

What is this all has to do with evolution? I think at its core the human spirit is a diverse and creative environment. At the same time, we humans tend to crave order, hierarchy, and predictability. How do we strike a balance between these conflicting impulses? I think whether we study the random walk of photons, population ecology, or electron clouds we can detect a kind of "order" that keeps things together. These underlying patterns that science can elucidate have a lot to offer us. They represent a kind of serious play, high stakes (survival) but high-yielding (innovation). At the same time they can direct our thoughts about evolution. In particular they may be able to encourage us to play around just a little bit as we move forward in life. 

Wednesday, December 28, 2016

Electron Clouds: A study in uncertainty

So it's pretty amazing to be preparing for next semester's course in cellular and molecular evolution. I told my dean earlier this year that I obsess about the way my students learn and experience science. Here it goes again. Even though I've taught this course or some variant of this course for more than 20 years I keep thinking about new angles. 

This year I want to go highly experimental in my approach. And by "experimental" I don't mean making students do experiments. Instead, I want students to experiment with new ways of looking at science. I want them to grapple with molecular structure and behavior. I want them to think about the way molecules and their workings affect living systems. And I want them to have fun--modeling molecules, modeling biological shapes and patterns, and modeling biological process. 

In preparing my first week's lectures for next semester I am confronted with an old friend that also presents an old problem. Wonderful water. We take it for granted. All living systems are made from it. We see it, touch it, experience it every day. And we are built from it. As scientists we take water and its characteristics for granted. Now, I could list out the properties and characteristics of water for my students. I could also, as I've done in previous years, explain the formation of the electron cloud around each water molecule, which contributes to its polarity. Of course, these features will be included in the first lectures of the semester.

But what about the phenomenon of the electron cloud itself? I have to ask, why do we tend to stop teaching about this phenomenon once we've finished teaching about water? Certainly electron clouds feature in every molecule large and small (consider proteins), and in multi-molecule systems like the phospholipid bilayer membrane. If we put aside the conventional "science" that students have had drilled into them since their days in junior high school, can we start to approach biology as a science of shape and conformation? Can we begin to explore biological interactions from the standpoint of perceivable form, working from there to stretch our perceptions past what is typically offered in textbooks? Can non-major undergraduates do conceptual work that's at the level of a speculative, highly exploratory doctorate? I think they can. 

I'm toying with the idea of having my students model a hypothetical electron cloud around a hypothetical atom or molecule. Usually for exercises like this I ask them to find Google images of the phenomenon they will model. Usually this works pretty well. But in previewing images of electron clouds I find that the number and variety of images are fairly limited. The last thing I want my students to do is to develop models that they copy from the typical organic chemistry schematics. More important than understanding orbital shells or p-levels, I want my students to think, rather deeply, about what an electron cloud is and how they might perceive it for themselves. 

A lesson like this might have more than one outcome. For example, electron clouds are all about uncertainty. We hypothesize about electron clouds based on statistical calculations--what is the chance that a certain electron will be in a particular position at a given time? Fairly complicated stuff. If we consider this at its deepest level we can conclude that matter itself is uncertain. Or at least, not "solid." Can we take this a step further and through it, suggest to students that perhaps their best laid plans about majors and careers are also a bit up in the air? As you can see, part of my ambitious goal is to use the models we build in science to help elucidate problems that are considered to be very much outside of science. 

It promises to be an interesting and engaging semester. Unfortunately, spring semester is always a bit short. And always there's a huge question to me whether my second-year undergraduates can really appreciate or even benefit from the thought I put into these questions about their learning. I guess I'll just keep at it and wait for their responses as the semester moves forward. 

Monday, December 26, 2016

An introduction to bioinspiration

This is the blog of my NS202 Natural Sciences course at Boston University's College of General Studies. We are taking a new approach to studying cellular and molecular evolution, with a focus on modeling nano systems. We will make our models by hand and at the same time, explore our learning process as we derive inspiration from the workings of cells, molecules, and biological systems. Each week students will submit posts to the blog, which will provide a platform for us to communicate our questions, impressions, and discoveries. 

In this course, students will go beyond traditional "textbook" biological models to explore the evolution of cellular and molecular phenomena at the nano level. By building models, literally with their own hands, students will be introduced to concepts and consequent functionalities that arise through evolutionary constraints such as symmetry/asymmetry, uneven planar surfaces, and junctures of interaction. We will apply these nominally "biological" concepts to the arts, society, finance, and other topics related to students' majors. The course is part of a multidisciplinary team endeavor among three CGS professors (I'm working with colleagues from the Social Science and Humanities Divisions) that will conclude with a capstone project titled "Making the invisible visible."

What I love about the course we are now embarking on is that we are taking a wholly new approach. I consider this course to be an incubator for new ways about thinking about science, just as my faculty team is an incubator for new ways to approach the year-end capstone project. It's an honor to have the opportunity to work creatively with the intelligent and creative people on my team. It will be a lot of hard work but I know we're up to it. 

A final word for my students. While lab and lecture are very much connected, they represent different narratives of the same story. Much of the lecture material will come across as factual (though very visually-oriented) while lab will really and truly be a place of play. Connecting these approaches will be part of our challenge this semester. Hopefully the playful aspect of lab will "loosen people up" for lecture, while the "facts" of lecture will inform the way we build and play in lab. This blog, which students will contribute to weekly as part of their group lab work, is where we'll record our impressions of the process. I'm so excited for the semester to begin!