eehardy's blog

When I began the “METHODS” assignment, I initially underestimated how much work it would be. In terms of most things, I am not very detail-oriented, and this project required high levels of attention to detail. In addition to that complication, I encountered a few random obstacles. It was actually more difficult than I had imagined to find a spider on campus in the first place. I looked in several corners and crevices indoors, before I finally headed outdoors and found one nested in its web on a plant pot outside of a central building on campus. When I was doing my write up initially, I was describing things pretty vaguely, jotting down my description as the way that I had the steps listed in my head. However, as I edited it and tried to think about it from an outsiders perspective, I realized that I was missing several details that were necessary for someone following my methods to get to the right place to find the spider. The way that I recalled things in my head was not naturally that detailed, although I did remember the details, I would not originally think of saying them, so I had to focus extra on that. I tried to put in every detail that I could think of so that the person following in my Methods would be able to obtain similar results. This is very important in a scientific Methods section: replicability is key. If a person cannot utilize a scientific methods section to repeat the experiment, the results cannot be tested a second time and thus cannot be verified. Even after adding all of the details that I could think of, when one of my classmates repeated my experiment there were still some differences between their end product and mine due to a few key details missing from my Methods that I had not thought of. In the end, this project really taught me and reiterated the importance of a very detailed scientific Methods section. I learned that the more detail, the better.

My teammates and I underestimated how much planning we should have done when working on the PROPOSAL. We did spend a solid amount of time doing the actual writing, but we did not read enough into how our PROPOSAL should be written so that we could plan accordingly. We did not read enough into how each section should be structured, and we did not collect enough background information before we started writing it. Our abstract ended up being much too long and our background information section was much too short. Our paragraphs were also not structured very well. We were a bit surprised when we got a grade lower than what we wanted, but looking back we had done a lot of things incorrectly and not planned well. It was unfortunate, but it it drove us to put a lot of extra effort into the PROJECT and learn from our mistakes.

In completing the assignment, “PROJECT,” I sharpened my skills in time management, team work, and scientific writing. Initially, I felt overwhelmed at the prospect of completing the research aspect as well as the write up, but that feeling dissipated soon after my teammates and I developed a solid plan. One reason that we felt particularly stressed in the beginning was because we realized that our recent assignment that we had completed, our “PROPOSAL” was insufficient. This meant that we had extra work to do on the “PROJECT,” since we could not extract much of our text directly from our flawed Proposal.  However, this extra demand prompted us to tap into our time management skills, which I think was a process of growth for all of us. We had to focus extra energy on planning, designating specific days to work on specific tasks, and setting ourselves mini-deadlines. We had to plan what were appropriate times to use the necessary equipment, like the high technology microscope, based on when it was available, and then leave ourselves sufficient time to do the write up. 

This project also drove us to further develop our teamwork and communication skills. We had to revise our initial teamwork strategy of splitting up the work and simply reviewing each others parts, to a strategy where all of us did each part separately, then combined them for the best end product. Sometimes I am quiet and do not voice all of my thoughts, but I think that I did a good job pointing out when something needs to be changed, and I think that I did a good job listening to my teammates as well. I also learned more about scientific writing. I read guides to writing the different subsections of the project in the book “Writing in the Biological Sciences.” I learned useful information about how the subsections should be structured, like for example how scientific introductions should have a funnel structure, starting with general background information and ending with the experimental approach. All of this hard work and learning payed off, because in the end we were all very satisfied with our poster. We were able to effectively measure the spider webs, complete the writeup, and create an aesthetically pleasing and informative poster. We were all very proud of our work, and I am proud of all that I have learned, as well.

Entering the class project titled “PROJECT,” I was feeling overwhelmed. My  group realized that our Project Proposal, which laid out all of the details of our project, and much of which could be used for the project itself, was insufficient, meaning that we would have to do extra work on our project since we couldn’t extract much of it from the proposal. The first time we met up to discuss the Project, we were all feeling overwhelmed, knowing we needed to work on the write up and do the actual research of measuring the spider webs itself.

We tried to work things out and made a little bit of progress. After meeting a couple more times and developing a solid plan, we were feeling a lot better and realized that the Project was not as much work as we had thought that it was. Planning out the project with my team helped me develop and learn about some time management and organizational skills. We had to plan what were appropriate times to use the necessary equipment, like the high technology microscope, based on when it was available, and then leave ourselves sufficient time to do the write up. I also learned to collaborate better and communicate effectively as a teammate. Sometimes I am quiet and do not voice all of my thoughts, but I think that I did a good job pointing out when something needs to be changed, and I think that I did a good job listening to my teammates as well. We were all very satisfied when we were able to effectively see and measure the spider webs under the microscope. I also learned a lot about how to consolidate information, because we had to cut down the text on our poster. Over all, I learned a lot doing this project and was very satisfied.

Biological factors are usually the most obvious and well-known factors involved in diseases. There are many different biological factors that can increase the risk of obesity for individuals. Although genetic factors have been linked to obesity, this does not seem to explain the sudden proliferation of obesity that we are seeing today. There is another factor, however, that seems to connect quite perfectly in the scheme of our current generation and obesity: sleep deprivation. Over the past century, the average amount of sleep per night in the United States has plummeted from 9 hours to about 6.5 hours, and seems to be decreasing even more. Recent studies have suggested that maybe the coinciding of the current sleep deprivation epidemic and the obesity epidemic is really no "coincidence" at all. Sleep deprivation has actually been linked to obesity. The research done has not only identified correlation, but specific factors caused by sleep deprivation that can cause obesity. In a study where subjects received 4 hours of sleep, remarkable changes in their hormone levels were noted and their glucose tolerance was impaired (this can be a marker of insulin resistance and diabetes). Sleep deprivation reduced levels of the hormone Leptin by 18%. Leptin is key for the regulation of energy and hunger. Leptin sends signals to the hypothalamus that suppress appetite, so when levels of Leptin are reduced appetite and cravings increase. While Leptin decreased with sleep deprivation, another hunger-regulating hormone, ghrelin, actually increased. Unfortunately, the increase of ghrelin actually has just about the same effect as the decrease of Leptin: an increase in appetite. Ghrelin is a hormone made in the stomach that sends a message to the brain that increases appetite and actually increases cravings for high carbohydrate, high-calorie foods. The craving of these fattening foods caused by ghrelin is likely adaptive and related to evolution and the foods that once kept our ancestors alive and provided them with enough energy, but today these excessive cravings induced by extra ghrelin are certainly not favorable. Not surprisingly, the subjects who were sleep deprived and subsequently had fluctuations of these hormones gained weight. Another study using brain scans further supports the link between sleep deprivation and obesity. A group of neuroscientists and psychologists used functional magnetic resonance imaging (fMRI) to study the brains of two groups of individuals: one who had been sleeping well and one who had not. For those who were deprived of sleep, the fMRI showed increased activity in the more primitive areas of the brain, such as the amygdala. These areas regulate the desire to fulfill the base biological needs: food, sex, and sleep. The more “higher order” areas of the brain controlled in decision making, like the frontal and insular cortexes, showed significantly less activity. So with an increased desire for food and decreased reasoning and decision-making abilities, the outcome is pretty clear. The sleep-deprived subjects wanted junk food. With the ridiculously jam-packed schedules of both adolescents and adults these days, sleep is declining, and clearly at a price. Sleep deprivation and the following hormonal changes clearly illustrate the roles biological factors play in obesity. Hopefully, people can learn from these studies about the importance of sleep and reduce obesity and the various other damaging effects of sleep deprivation.

    For the research I am working on, I am analyzing the physical behaviors of actin and microtubules when cross-linked in various combinations and ratios. I analyze actin cross-linked to itself interacting with microtubules, microtubules cross-linked to themselves interacting with actin, actin and microtubules cross-linked to each other interacting, and actin and microtubules interacting with each other with no cross-linkers. I analyze how these differing combinations influence the behaviors of the actin and microtubules. The ratio of cross-linker used varies from 0.02 to 0.08.    

    In my analysis, I utilize FFTs (Fast Fourier Transform) of the microtubules and actin, and I analyze the data graphically and numerically using Excel and the data analysis application KaleidaGraph.

The results of our experiment testing whether or not a relationship exists between the body weight and the average web thickness of a spider indicated a negative correlation, but likely were unreflective of reality. We hypothesized that spider body weight would be positively correlated with web thickness, speculating that a heavier spider would need a thicker web to support its weight. Before we began our experiment, we found another study that investigated this same subject and found that there was no correlation. We wanted to see if our results would be the same, or if they would be different. We photographed 3 spider webs under a microscope, and for each spider we measured and averaged 10 different threads of its web, then compared them to its body weight. The spider with the lowest weight (Spider 1) had the highest average web thickness, whereas the spider with the highest weight (Spider 3) had the lowest average web thickness. Both measurements of weight and average web thickness of Spider 2 were in between Spiders 1 and 3. However, our results are unlikely to be representative of reality for two main reasons. First, our sample size was very small since only 3 of the spiders we selected for our study produced webs in the experiment time. A small sample size leaves the differences between the measurements up to chance. Second, there was a high standard deviation within each spiders ten individual web strand width measurements; they varied greatly from the “average.” Thus, the average, which was used to identify the trend of negative correlation, is unreflective of the full data scope and thus not a meaningful measurement when plotted against spider body weight. To further this point, one can see in our graph that Spider 2 had a web width average that was in between the averages of spiders 1 and 3. However, looking at all of the individual web strand measurements of Spider 2 that went into the average, one of it’s values is the highest value of all 3 spiders, and another one of it’s values is the lowest of all 3 spiders. It is the spider with the most moderate weight, but it has the largest range of web widths. Since the measurements based on Spider 3 are from the same spider, they are all have the same weight, yet their width varies so largely, so it must be highly influenced by some other factor external to weight.  In conclusion after reanalyzing the data, it is unlikely that spider weight has an effect of spider web thickness.

In our research project, we analyzed the correlation between body weight of a spider and the thickness of its web. We were only able to obtain 3 spider webs from our population of six spiders. To get a fuller picture of weight vs thickness, we also compared our results to the results of another study which examined the same hypothesis, but had a greater sample size and used multiple species whereas we used one species. Our results of the average web thicknesses of each spider plotted against their weight were a negative nonlinear correlation. The results of the other study showed no correlation. Our results probably did not show the full picture of reality. We only had a sample size of three, which is a very small number. Also, although the average widths plotted against the weights showed a negative correlation, there was a high standard deviation in the individual measurements, so the average probably does not mean that much. Spider number 2 that we measured had a weight that was in the middle of spider 1 and 3, as well as an “average” width that was in between 1 and 3. However, as our graph shows, looking at the individual data points spider number 2 actually had both the highest and the lowest observed single strand diameter, with individual points scattered on both the very high and the very low points of the plot. Thus, the average is not a very effective measurement. The spider’s body weight is constant, yet its strands have a large variation. It is likely that in reality, spider body weight does not play a role in determining web thickness, but rather other factors, such as the type of the web itself and its purpose. 

2-naphthol was reacted with sodium hydroxide and n-butyl iodide via an SN2 reaction and butyl naphthyl ether was obtained in 5% yield. The product yield was very low due to incorrect use of the suction filtration machine by the student. The product was identified as butyl naphthyl ether via TLC analysis with correct data from the student’s partner, as well as from using the melting point of the small amount of product that did form. The first plate did not have applicable data because the amount of product formed was too small to make a significant difference between A, B, and C. The spots were all almost entirely equivalent to the A spot (the 2-naphthol solution) because the amount of product (C ) was so low, thus making the C spot ineffective and the B spot essentially just the same as the A spot. However, the plates of the student’s partner, which had the better ratios of hexane to EtOAc sufficed for the date for the rest of the Rf values. On plate 3, substance C travelled farther than substance A, which tells that the final product of the reaction is much less polar than the starting material. This makes sense in accordance with the reaction scheme because 2-naphthol is more polar than butyl naphthyl ether. Of the three solutions used, the best separation of substances was obtained with the solution ratio 60:40 hexanes:EtOAc. The solution with 25:75 hexanes:EtOAc was too polar to get a sufficient separation and the solution with 75:25 hexanes:EtOAc was not polar enough to get a sufficient separation of the substances present. By adding more EtOAc, the solution became more polar so that both the starting material and product had sufficient separation. The hexane composition of this solution agrees with the assumption that the product was less polar than 2-naphthol because butyl naphthyl ether is less polar than 2-naphthol The identity of the product was shown by the sample’s melting point of 33 °C, which fits with butyl naphthyl ethers melting point  of 33-35 °C.

The first recrystallization had a 30.02% recovery.  While this percent recovery is rather low, this recrystallization likely got rid of a significant amount of impurities that were incorporated in or on the crystals after the crude weight was obtained.  From the first recrystallization to the second recrystallization, a 72.4 3recovery was obtained.  In comparison to the percent recovery obtained from the first recrystallization, this yield is quite high.  This second recrystallization likely got rid of any remaining impurities, and product may have also been lost during the transfer of materials. 

            While the percent recovery of the first recrystallization was low, the melting point obtained from this purified sample, 52-54 °C, was not too far from the standard melting point, 56-57 °C.  The melting point obtained from this first recrystallization was indicative that the sample obtained was impure as the melting point obtained was greater than 2 °C lower than the standard melting point.  However, after the second recrystallization was conducted, the melting point of was 55-57 °C.  The melting point found experimentally aligns nicely with the expected melting point, meaning that these crystals were very pure.  Not only does this second recrystallization affirm the fact that multiple recrystallizations yield purer products, but it also confirms the identity of the extracted product since melting point is a physical property of a substance.

The air condenser was attached to the round bottom flask, and the solution was placed on the sand bath.  The flask gently boiled for 10 minutes and was then removed from the heat, allowing the solid within the flask to settle to the bottom.  During this time, a pressure filtration was set up.  Once the solid in the flask had settled to the bottom, the condenser was removed from the flask, and the liquid within the flask was transferred to a 25-mL Erlenmeyer flask (25.5g) by pressure filtration.  To the remaining solid in the round bottom flask, 2 mL of fresh TBME was added, and the flask was reheated for an additional three minutes on the sand bath.  The liquid in the round bottom flask was again removed via pressure filtration and placed into the same 25-mL Erlenmeyer flask.   The solvent in the Erlenmeyer flask was evaporated by passing a stream of air over the flask while the flask was also being warmed.  A pale yellow product remained in the flask once the solvent had evaporated, and the flask was allowed to sit and dry for an additional five minutes.