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? 











13 comments:

  1. I think the author is trying to explain how form and function are important in the building of structures. Different shapes, lengths and orientations are specific to different amino acids or proteins. Every polymer has slightly different characteristics and the tiny deviances in structure affect the whole. When trying to understand what we are looking at it is important to view the model from all sides and angles, not so much to see what we are looking at on a base level, but to understand where each individual section interacts with the whole. It is these subtle differences that make each polymer important and unique.

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  2. Nicole Doherty: I think the author is trying to visually demonstrate to students monomers and polymers. When we see the single Lego monomer we see a simple structure. When monomers are added to the single monomer we see a more complex structure forming. Although it appears more complex when you look at it closely you see just a pattern of monomers put together not some complicated incomprehensible structure.

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  3. I believe the author wants readers to think about the potential complexity of molecular biology. By comparing the legos to atoms and molecules we can see just how atoms and molecules can interact with each other. They can be split up or put together. By looking at the structures from many angles the reader can see how complex or organized the structure truly is.

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  4. The author is trying to teach us another way of learning biology that is different from the way we are taught (with memorization). This new view lets us observe monomers at different angles and see how each angle gives us different observations/information about the monomers. From the pictures on this post, I can observe that all the monomers share the same basic shape of two 2x3 blocks with three 2x2 blocks equally spaced on top. From here, unique polymers are form from the different combinations of monomers. It seems like the author is trying to convey to us that many unique and complex items are made of similar building blocks.

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  5. I think the author is trying to show how simple molecules, monomers, can be combined to create complex molecules, polymers. These polymers come in an array of sizes and shapes, made of different monomers that ultimately determine what kind of polymer there are. Some combinations can be lethal whereas others are harmless. It's interesting to see how easily a molecule can be changed just by the addition of one monomer to a complex polymer.

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  6. The author is saying that using a visual aid such as Legos helps with understanding the monomer and polymer structures. The Legos allow for a simplified visual to help understand the complex system.

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  7. Legos are a very original concept to introduce to science. As the polymer gets taller, it starts to seem more unstable as if it would tip over. However, in reality, as polymers grow, they become more stable because they act as a unit. The angle in which the polymer is looked at is very important. From the side, the tall polymer seemed very unstable, but from the top, it looked very neat and organized. The author helps students understand that although the polymer looks complex, it is actually made up of very simple molecules.

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  8. I think the author is trying to get across that biology or perhaps all sciences are best at a conceptual level, and it's easiest to understand the concepts of science through visual and interactive learning. By building it ourselves, we achieve a better understanding of the way in which the lego blocks interact and how a polymer forms, and better understand how molecules connect to one another.

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  9. I believe that the author's main point in this article is to show students that visual and hands-on learning experiments allow for a more in-depth examination of molecular structures. By simply adjusting the perspective of the legos or the colors of the blocks, a student is able to see that structures can differ. This, I think, shows that first-hand experimentation is better than textbook examples.

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  10. The author is trying to have his readers not only understand the difference between monomers and polymers but also visualize that difference. With visualizing monomers and polymers it is easier for students to understand how they work. The author is not being too complex or too detailed he is simply giving background information for future reference. The author is showing the difference between the simple and complex and uses difference angels to do so.

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  11. Michael Kapp
    The author is trying to explain the origins of life in a simple way to his audience. He uses legos as a way to describe monomers and polymers connecting and becoming increasingly more complex. He builds legos upon eachother creating more patterns and larger links between them as a way to link the legos to how polymers link together making increasingly more complex forms of life.

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  12. I think the author is trying to get the reader to understand the different factors that come into play as monomers become polymers. He uses visuals to display how different angles and different viewing distances show different patterns. The reader sees first hand what changes occur in the forming of polymers

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