Sunday, November 16, 2014

Capturing Movement in Mexico City

Mexico City, Tenochtitlan, a huge living sculpture, a built environment whose immediacy sits on the surface of a dense and teeming historicity. The land, a bowl surrounded by mountains, sinks as it evolves, sculpted by tectonic and human forces that slide, accrete, press, and tunnel. South: Chinampas, a living collaboration of humans and nature. North: Teotihuacan, the collaboration of humans and heaven. In the Centro Historico the monumental Zocalo lies juxtaposed, pulsing between palaces and ruined temples, teeming markets and packed streets.

People here join and shape the living urban sculpture, a millennial continuum of movement: Hurried, clustered, selling, strolling, digging, parking, building. Climbing the stairs of innumerable churches, government buildings, markets, monuments, subways. opening and closing a million windows and doors of a million apartments and cars. Green spaces, plazas, fountains, roadways, murals, graffiti, all moving through growth, flow, stretching, covering, adding to the fabric of the city. And always, the slow movement downward of a city sinking into the lake that is its foundation.

Movement has always been a part of this city. The God of Earthquakes, Olin, is also the god of movement. The symbol for Olin, which is also the symbol for earthquakes and movement, can be found in all kinds of iconography in and around Mexico City. As we learn more about how this city moves, it is fascinating to see that an understanding of movement has always been important to the people living here. 

Thursday, May 22, 2014

Nano modeling with lego bricks

Working on a lab for next year's introductory biology course (non-majors). This could fit in at the beginning when we discuss the origin of life (increasing complexity leading to increasing order). Maybe students would challenge this because increasing complexity in these lego models looks more chaotic (!) or the exercise could fit later in the semester when we study polymers (polypeptides, polysaccharides, etc.). Deciding where it would make the most impact depends on a lot of factors, almost all of them external to the content of the course! 

The key is to keep my students engaged in the process of studying, to think about questions and permutations of questions, and to encourage them to develop ideas. Congruent to this is that I want them to see the lego structures less as "built" objects but "developed" objects...structures that tend to function in certain ways depending on how they are organized...not necessarily things that have to be "big" or "long" (or any particular quality of a polymer)...just things to contemplate. This is one of the great beauties of teaching science to non-majors. The content is less important than the process. But it's also a challenge. Students have been taught that science is about defining, memorizing, and regurgitating. So much different from the way we scientists see things, which is that the natural world is a space open to exploration and interpretation. Asking questions about form in space is the goal of this lab. This is the rigor that I want to impart. 

So let's look at a simple "monomer" (molecular building block) made from lego bricks. Keep in mind that color is irrelevant here, at least in this first attempt. 

Next let's look at a couple of monomers assembled together. 

How do they look from another angle (below)? What, if anything, does this tell is about spatial orientation in this structure?

What happens when we add more series of monomers? While assembling this structure what happens to its stability? How do different parts of the structure seem to relate to one another? What patterns emerge that we didn't see with just one or two monomers?

What does the angle we view this polymer at tell us? Does it matter which angle we view it from? Might it make a difference to another molecule trying to interact with this one?

Now let's pretend there there is some kind of interaction with an identical molecule or molecules. How does this change the picture?

And how do things change when we look at a close-up of this interaction? What kinds of changes are taking place at the surface, where pieces of the molecules connect to one another? Has the structure "changed" or is it the "same?" Is there something qualitatively different about this combination of identical monomers when we compare it to a single monomer?

And what happens when we view this structure from another angle? What are implications for further interactions when we look at the molecule from a new angle? What do we learn about the form of this thing when seen from a new angle?

Are there other patterns we can detect when we look further? Anything that might make a difference if you were trying to characterize this interaction or compare it to others?

Well that's a lot of work I think. Also introducing students to questions of stability, strength, etc. might be possible. We can also ask questions about simplicity vs complexity. Are these relative terms? How do we interpret them in the context of this exercise? What do they mean when we are analyzing biological systems, not just at the molecular level? 

Saturday, April 26, 2014

Evolution, Constraints, and Legos.

I spend a lot of time teaching my undergraduates about how constraints in the environment influence biological processes. From an evolutionary perspective we can call these constrains "selective pressures." In class I ask the students to brainstorm what these selective pressures might be. In students' minds it pretty much boils down to the availability of resources, through there are many other environmental constraints as well, such as climate, pathogens, and symbionts. 

But what bothers me about this exercise is that it's all pretty abstract. We can talk about resources and even think of examples. But it remains a kind of thought exercise without a compelling hook into the reality of biological systems. 

So the other day I picked up some Legos and started to model a termite mound, which incidentally is my favorite example for discussing environmental constraints with students. What looked like thousands of blocks began to appear quite inadequate by the time I had started an outer chamber to surround the inner chamber of my termite mound. I realized I would have to build more efficiently or much, much smaller as my supply of lego bricks dwindled. What would a termite colony do?

Aha! A way to teach about how constraints limit biological processes! Maybe I shouldn't order all those extra bricks after all. 

My barely started termite mound model. About at this point I ran out of bricks

Looking up into my termite mound, visualizing air flow. 

Friday, April 25, 2014

Legos for modeling science ideas

Teaching non-majors science I've always been interested in how we represent science ideas. My goal is to give students a chance to visualize and express science ideas on their own. There are so many ways to go about this. 

Just before YouTube got started I devised a "metavisualization" curriculum based on metacognition and visualization. My objective for that project was to engage students in making videos that conveyed scientific ideas. Some of the vids were great. Most of them reflected the last-minute effort that undergraduates put into assignments. I decided to drop the project after watching too many bad videos. 

Last year I got an arts initiative grant from my school. I used it to get students to do more hands-on, less cookbook labs. Some of the labs involved experiments the students made themselves, like seeing how water behaved in various situation. Others involved building with zometools, a simple yet sophisticated, infinitely flexible building set. All of the labs asked students to observe and reflect mindfully on what they were experiencing. 

I want to build on these labs next year. I did some research into the work they're doing at the MIT Media Lab and found the philosophies of learning coming out of there in coherence with mine. Ideas like "serious play" and "lifelong kindergarten" appeal to exactly the kind of learning environment I'm trying to build. The Media Lab is also a proponent of Legos. 

So I ordered a couple if lego sets to see if I could build some models with them. I unpacked the sets yesterday and experimented with a few ideas I'd like my students to pursue. One was a model of a termite mound. I had enough blocks to do a partial model. 

Then I worked on a couple of ideas for modeling polymers. I guess the possibilities are endless but here are a couple. 

Finally, I did a little experiment with genetic drift in two populations. I think it worked pretty well. 

1. A single population with randomly distributed variations. 

2. Two populations randomly isolated from one another. 

3. The process of genetic drift over a period of time. (Surviving populations in front).  The result: new species?

If you've worked with Legos in a university setting I'd love to hear your experiences. Most important, how did students respond?