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? 











40 comments:

  1. I think the author is trying to make learning about the origin of life a little more comprehendible seeing as most people like to learn in a hands on way. As the author goes through explaining each different set of lego creations, the creations get larger and more complex. The more interactions the molecules have, the more complex the structure becomes and this is where the author would find it helpful for students. The more complex things get the easier it can be for a student to lose track of where they are so having a model can help remind the students of what is really going on and allows them to look at it more closely in a hands on way.

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  2. I think what the author is trying to get across here is that this exercise helps create a visual for analyzing monomer and polymer structures. These visuals show and example of how polymers are assembled and help put into perspective how different levels of complexity affect the stability, strength, and other aspects of polymer structures.

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  3. One thing that really stood out to me is that we as students have been conditioned to look at science through the lens of textbooks and assignments. But, as this post shows, science is not about meticulousness, necessarily. No, science is an endless cycle of processes, each bound together by its own laws yet constantly changing. This phenomenon can definitely be seen in the pictures above. Starts out simple, "here is a rule," we have a simple monomer. Clean, concise, and characteristic. However, as each monomer is added, a polymer immediately forms. This structure is now far more chaotic. Although each polymer is just a serious of monomers (or rules) as they grow and change they all become unique with their own outcome. Pretty indicative of the evolution of the natural world, in my opinion.

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  4. I think the author is trying to say that as things get more complicated, they become more stable and become a bigger structure. By using Legos in this case, the author is breaking down a very complex system into a system that isn't as complex anymore. The visual aid is used to help the reader visualize what the author is saying and what he is explaining. The molecules Re getting bigger because they are interacting with more and more organisms making it more complex for. The reader to understand, hence the visual aid.

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  5. 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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  6. 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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  7. 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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  8. 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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  9. 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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  10. I believe the author is trying to get across the point that science is not learned from a textbook. In order to fully understand a concept one must experience it with their own eyes and be able to ask questions. Through hands on experiments and experiences you can easily see patterns and shapes which may have been less clear in just the words of a text book. Because of these experiences we can then ask questions that will allow us to dive in further and fully understand the concept more than we would have before.

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  11. I think the author is trying to show the way a simple monomer can become complex. Viewing the structure at different angles also shows the complexity. The article allows students to see a monomer in its simplest form and its construction to a far more complex form. Being able to see the breakdown of how the structure is built is helpful to students because it shows the process, furthering understanding of the construction process.

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  12. The author is trying to help us students picture science in a different way than the way we were taught in schools. He emphasizes the importance of questioning science and interpreting science in different ways. It is fascinating to see a simple monomer interact with other monomers and become bigger and bigger and more complex. And in the end a polymer is formed from the interactions of many monomers.

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  13. 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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  14. I think that what the author is trying to get across is the idea that by creating a visual for something that may seem complicated, in this case the building of monomers and polymers, can make the process more understandable. Picture by picture we are able to see how something that starts off so simple, like a monomer, can actually gain structure and strength with the addition of more simple monomers. The visual aid helps the reader better understand the process.

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  15. The author would like readers to understand that science isn't all about getting to the answer, but questioning those answers as well. Using legos to represent monomers and polymers creates a whole new dimension to biology more so than simply just seeing the concepts on paper. The changes of the molecule structure are so much more apparent when you actively have to figure out, troubleshoot, rather, how these molecule structure are going to work together to represent the self-replication process. Ultimately the author wants readers to see that there is more to biology than a textbook definition and example.

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  16. 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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  17. 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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  18. The author is trying to show the link between simplicity, and complexity, especially in how they relate to the hierarchical order of life. It shows the simple monomer, transforming into a complex, sophisticated polymer. As it increases in complexity it also grows larger and larger.

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  19. The author is trying to give us visual examples of how to understand the complexity and organization that emerges as monomers interact with one another. By using this visual example we can see that orientation is a key feature that determines not only our understanding of the monomer or polymer itself but also how this effects the ways other monomers may interact with it. They are using simple terms to explain this complex connection between these polymers.

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  20. 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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  21. I believe that the author is trying to make something so microscopic and inaccessible, as some may say that monomers and polymers are accessible by using a physical model. Through modeling with Legos, students will be able to visualize how monomers connect to make polymers and polymers connect to become larger and larger. By viewing the Lego monomers and polymers from different angles, students are able to see how combining polymers has the ability to for and create all the aspects of our world.

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  22. In this piece, the author conveys the importance of special recognition, proper assembly, and personal perspective are in using simple plastic pieces in such an elaborate way. My own personal thought is that hands on approach to molecular biology will be extremely beneficial to visual learners like myself, and that all students will gain valuable perspective through metaphorically assembling the building blocks of life.

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  23. I believe the author is trying to demonstrate to its readers that the complexity and hierarchical order of life can be viewed in a much simpler way when broken down into the individual steps. When you look at how a monomer can develop into a polymer it shows the complexity of the polymer, but in a way that is easier to comprehend rather than just memorizing the terms. As a result of breaking it down, you are really able to understand the process.

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  24. I think the author is trying to make it easier to visualize monomer and polymer structures as they grow increasingly complex. The author is trying to demonstrate how the complexity and changes in structure add to the stability and strength of the structure as a whole.

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  25. What this article is trying to get across is the complexity and significance of the formation of monomers, polymers, and ultimately organisms. However, by using legos as a representation of the formation, it allows the reader to easily understand throughout the process. This week we looked at the origin of life and how the environment evolved from microscopic organisms. This article gives us a look of that in an easy hands on way.

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  26. I believe the author's main objective is to explain how something so complex as polymers and monomers can be broken some into simpler terms by using Legos. As a children, we all played with Legos and remember our parents screaming when they stepped on one so by using them later in life, we build familiarity with them. I also think that the author is trying to show that one thing can be interpreted differently, just by the way and angle it's viewed at. If you don't understand a complex concept, step back and try to understand it from another point of view.

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  27. 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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  28. It is definitely strange to have a lab where legos are involved. Even though I believe that science is something you do, not something that you read from a $300 textbook, most sciences class I’ve taken portray science as the latter. In order to imagine the making/synthesis of complex systems, I think it’s logical to subject students to their own little synthesis in a macro scale.

    (Alejandra Rodriguez)

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  29. This article is trying to give a visual representation of polymers and monomers. It shows their impact on one another and how they affect each other. The legos show the difference between complexity and simplicity. The legos show polymers and monomers form and function.
    Ashley Toppel

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  30. I think the author is trying to break down the difficult parts of science and explain that it is easier to comprehend than it may seem at first. Through the use of patterns, visual experimentation, and other ideas, we can be able to understand and better be acquainted to the way things work scientifically.

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  31. I think the reader is trying to show us the structure of a monomer through the visuals of legos. Through this visual concept, it is much more easier to understand the way that monomers form together to create polymers. The visuals show how polymers can grow larger in both size and complexity.

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  32. I think the author aims to show visually that even complex structures can be broken down into "building blocks". The legos allow us to look at a complete building and dissect it, to see the components that make up this complex structure.

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  33. I think the author is trying to convey that the only way for us to understand the complexity of science (monomers, polymers...) visual and interactive systems will help us learn and understand the structures of how things truly connect with each other. As each monomer structure builds on top of the other, it gets more and more complex which ultimately helps us analyze how each structure is affected by its interactions.

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  34. 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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  35. The author is showing us how we are able to simplify biology by breaking down complex structures. He visually depict how we can break these down by using something as common as legos. This hands on way of building monomers and polymers makes us experiment and "play" with biology.

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  36. Content. Content. Content. This is what has been ingrained in us since elementary school. The author of this article is enlightening us with a different (almost foreign) perspective: discovering the actual process. Through the polymer/monomer visual example, we are shown that the little pieces play a unique role in the whole structure.

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  37. The author discusses how, throughout their academic careers, have been taught that science is about defining, memorizing, and regurgitating." The author argues however that science is indeed a field open to "exploration and interpretation." Similarly, the author discusses how chancging our perspective of these lego "monomers" and "polymers" will change our analysis of them. Therefore, the may be implying that in changing our perspective of what science entails, we may be able to analyze it in a new light.

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  38. 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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  39. The author is swaying away from traditional means of learning new and complex material. Rather than have students memorize content that will likely be forgotten after an examination, the author attempts to visually stimulate the learners mind by physically representing complex monomers and polymers with the lego pieces. The legos allow for an easier understanding of the process and formation that takes place when atoms turn into monomers, less ordered structures, into polymers, more ordered structures.

    Matt Almengor

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