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?