Wednesday, February 8, 2017

Molecular complexity: Complexity, symmetry, patterns, and the origin of life

My polymer was based on an asymmetrical monomer. I thought that I could create a spiral structure from these monomers, but their asymmetrical nature prevented a perfect spiral from happening. I decided to act like a monomer and just attach myself to the first thing I saw, and the polymer started to take shape. Though it wasn't the original design that I had intended to make, it did “spiral” in a way, making a new, unexpected pattern. This pattern worked better for the monomers than a traditional spiral would, making the emerging polymer easier to build on. If I continued to force a spiral pattern, my overall polymer would have suffered, so I had to think creatively and let the monomers do the work for me.

When I started my monomer, it was rather planar.  Initially, it started off symmetrical, but as I continued to build my polymer it became more asymmetrical. Rather than building upwards, I focused on expanding the width of it. It became very strong as I added more pieces because my structure had few gaps and was connected on all sides. Making the base strong was an important aspect of building this polymer as I observed that a weak base caused it to fall apart more frequently. I changed the shape multiple times, as it was difficult to find a pattern that supported the entire structure.

When I started my monomer I wasn’t sure how I should start to attach my monomers to form a polymer. At first, I randomly attached the monomers into a shape which was successful. However, I then googled images of RNA and DNA and found the strands fascinating and decided to try to create a strand of my own that reflected an RNA/ DNA strand. I created one long line of monomers and then attached separate monomers in an upside down “U” shaped form. I then attached the upside down “U”s to the base strand and kept attaching them until I ran out of legos. I found that the longer I made my polymer, the weaker it became. My polymer is a direct example of the article we read in the beginning of class. I made the invisible visible by creating a polymer, similar to DNA and RNA, both are invisible to the naked eye.

I started by creating a 3 piece, purple and pink monomer. I realized that this was too simple, and I was going to have problems building my polymer, so I then added a two more legos, of different colors, creating a 5-piece monomer. I created a bunch of these, and then started to add them together, to create a polymer. I kept running into problems, because my polymer was too vertical, and wouldn’t stand up without falling apart, so I had to create a more dense molecule. Thus, by the end of the building process, I was left with a polymer like the one pictured above: dense, vertical, not symmetrical, and relatively color-coded (purple and pink, with variations in color to account for variations in the molecule, or areas of positivity/negativity). Compared to the rest of my group, my polymer was the most dense and vertical, while, for example, Dani’s was extremely symmetrical and not dense. This lab was able to answer questions, such as how does complexity arise from simple systems. By building molecules out of legos, we were able to see how such a simple system (i.e. a 3, or 5 piece monomer made out of legos), can create a dense and large, complex molecule. This molecule was also able to be interactive. For instance, the polymer was only able to take form, if every lego piece was able to fit together well, with the others. Thus, the legos had to work together, to form a complex object.

In regards to the article that we read prior to the experiment, I found it quite relevant to how I came to make my polymer and make what seems to be the invisible, visible and aesthetically pleasing. I first started off my lab by making a 4 piece monomer and as I built up and wider, my model became more asymmetrical and visibly pleasing to the eye. At first it started out a simple monomer, the same monomer that I repeated to make over and over again to then use to create a wider and taller polymer. I stuck to a color combination of pink, red, yellow and orange to help make it look more identifiable. I came into problem when attempting to put all of the replicated monomers together. As I built it out wider however, my polymer became stronger and I was successfully able to connect the pieces together without it falling apart on me. It was interesting to see how something as small and simple as building legos, can turn into these beautifully arranged pieces that stand in to replicate molecules and RNA/DNA strands. Mine in comparison to the others at my table was about the same width but slightly shorter in height. It was interesting to see everyone’s variations of monomers constructed and see all the lego pieces come together to work as a cohesive unit of a polymer.

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