sbrownstein's blog

In the Fall of 2018, as a part of the Writing in Biology Class at the University of Massachusetts Amherst, I conducted a project that used observation and inference skills to create a method that would be followed in order to recreate a multi-panel scientific figure. This project challenges the ability to examine and describe the procedure used to create a multi-panel scientific figure of a spider web found on campus. The description was detailed enough to direct the reader to recreate the figure as similar to the original as possible. I explained that the spider web used in the original figure was found on the third floor of the Morrill II building and how the pictures were taken. In addition, the methods section outlined how the figure was developed on the program, Inkscape. The replicate result had eight differences from the original figure. The replicate picture had been taken at a different location, at different angles and without flash. The map picture on the replicate had different navigation symbols. The lettered labels were different sizes, fonts, and were incomplete on the replicate. Lastly, the arrow was displayed differently between the two figures. I concluded that the different location was due to the unclear explanation of the location of the web. The variance in map symbols and size/font of the labels was a result of the absence of direction in the provided methods. The incomplete labels were a consequence of the reader not thoroughly reading the methods section. Ultimately, this project reveals how important precise observations and descriptions can be when explaining an experimental procedure. If clear directions are not given, the result may be different than the writer, or scientist, had intended.

In addition, I precisely described how to create the arrow label on the setting picture by using the marker feature on Inkscape. I can conclude that the arrow used in the replica was not constructed using this feature because it does not have the arrow marker at the end of a straight, bold line. Although the arrow was dissimilar, the reader angled the arrow in the appropriate direction. The changes I would make going forward would be to write a more precise description of the exact location the spider web, provide a more in depth explanation on the creation of the labels on the figure, and include every observation present on each picture in order to obtain an outcome similar to the original multi-panel scientific figure.

The differences observed between the two figures are partially due to the lack of detail explaining where the web was located, which symbols were present on the map, what font and size the lettered labels were. The differences among the arrow and lettered labels were due to the incomplete outcome based on the procedure given. The main difference between the two figures was that the web used by the reader was not the web used in the original figure. This may be due to the limited detail given in the methods section about the location of the web. The relative location on campus and the building was described in the methods section given to the reader. Yet, I could have explained which side of the hallway the groove of the wall was found depending on the staircase the reader approached from. This would have narrowed down the location of the web in the third floor hallway of Morrill II and reduced the chance of variability in the result. The specifications made in the Methods section as to what camera angle and settings, such as flash, were not very clear and may have led to some confusion for the reader when trying to recreate the figure.

The replicate figure, known as Figure 1, created by the reader had eight differences to the original multi-panel scientific figure, Figure 2. The main difference was that the reader did not find the exact location of the spider web I intended them to use. The reader took pictures in the same building and hallway, yet not the same corner/groove in the wall. Another difference is that the orientation of the web pictures in Figure 1 are different from the web pictures in Figure 2. The web pictures are slightly more offset to the right in Figure 1. The lighting in the web pictures of Figure 2 were brighter than those in Figure 1.

 One of the most important ways to credit a scientist’s work is through replication. Replicating a scientists’ work validates and reduces variability in experimental results. In the Methods project I conducted in the Writing in Biology Class at the University of Massachusetts Amherst in the Fall of 2018, the process of replication was used to evaluate observation and inference skills. The goal was to have a reader recreate a similar multi-panel scientific figure to the one that the writer had created, only using a description of the process used to develop it. The multi-panel figure contained at least three pictures: a close up picture of a spider web, a picture of the relative location or setting of the web, and a map of the area on campus that the spider web was found.

After collecting the pictures of the web and its location, I was required to find a picture of a map that would show my reader where my spider web was found on campus. My first instinct was to use the map on the “My UMass” App. This App has a feature to navigate campus via a map system. By searching for the building I found the spider in, Morrill II, I was able to screenshot its exact location. I kept both the Morrill II and the Morrill III buildings in the map to show that the hallway the spider was found in was connected both buildings. As a result of collecting all of the pictures needed to create my multi-panel figure, I downloaded the program Inkscape. This program required that I also downloaded the program XQuartz. I uploaded all of my pictures onto the Inkscape canvas and began to experiment with some possible orientations. I decided that having my location pictures on the left side and the spider web pictures on the right side would be the most aesthetically pleasing. First, I selected the hallway and map picture and set them both to equal width measurements of 106.6 mm. This was to create a straight midline within the figure. The hallway picture was placed on top of the map picture on the left side. The heights of the two pictures were slightly different because I wanted the map picture to be emphasized, therefore setting the height to be around 10 mm taller. The midline was offset to the right by about 3 mm in order to emphasize the location pictures. I stacked the three spider web pictures on top of each other on the right side, aligning all of their widths to be around 103.7 mm. The heights of the three pictures varied in increasing order down the figure. I believed this format was the most logical and easy to comprehend.

One of the most important ways to credit a scientists work is through replication. Replicating a scientists’ work validates and reduces variability in experimental results. In this project, the process of replication was used to test observation and inference skills. The goal was to have a reader recreate a similar multi-panel scientific figure to the one that the writer had created, only using a description of the process used to develop it. The multi-panel figure contained at least three pictures: a close up picture of a spider web, a picture of the relative location and setting of the web, and a map of the area on campus that the spider web was found. Precise observations result in more accurate outcomes in an experiment. This project required proficient observation and writing skills in order to obtain a similar replicate of the original figure. A detailed procedure on how the pictures were taken and the development process of the figure were needed to obtain an accurate result. I chose the spiderweb I found in Morrill II because I believed it was a good location, it was a faint, complex web, and it obtained a spider on it. Choosing this web allowed me to give my reader an accessible location to find and take the same pictures and enabled me to elaborate on the fine details of the web itself and the process I used to create my figure. The groove in the wall I found my web gave me an opportunity to use the program, Inkscape, to enhance my figure inserting additional features such as arrows. Some of the controlled variables in this project include the location of the web, the types of pictures used in the figure, and some of the finalizing features on the figure. Every project must describe web that is on campus, consist of at least three pictures of the web and its location, and the finalized figure must include labels, be the sized to a sheet of paper, be 1200 pixels and be exported as a “png” file. Between detailed observations and specific controlled variables, the project should result in a similar replica of the original multi-panel scientific figure.

This is demonstrated in Table 1 when the number of dyed food vacuoles within each cell increased as the time periods got larger. This was also proven in Graph 1 because the curve of the average number of dyed food vacuoles within each cell increases as the time advances. This reveals that the feeding rate of the tetrahymena increases as time progresses. After collecting all of the data, the average number of dyed food vacuoles per cell within each time period was able to be calculated by finding the mean. In addition, the standard deviation was able to be calculated for each time interval. This determines how far away the data was from the mean. Most of the standard deviations were relatively low numbers, showing that the data was accurate.

    In this lab, the feeding habits of tetrahymena thermophila were observed. Tetrahymena are unicellular predatory ciliates that live in fresh water everywhere. They feed on bacteria and reproduce both sexually and asexually. In order to examine the feeding rates of the tetrahymena, five samples of glutaraldehyde were prepared. Glutaraldehyde is a solution that kills the tetrahymena without harming their tissues. Five samples were prepared in order to collect samples of the feeding tetrahymena at time zero, ten, twenty, thirty, and forty minutes. After the tetrahymena were submerged into the India ink, samples of the tetrahymena feeding on the ink were put into the glutaraldehyde at those given time periods. After the experiment was finished, the feeding tetrahymena were observed under the microscope at four times magnification. Within each sample, ten different cells were observed and the number of dyed food vacuoles within each cell was recorded. The dyed food vacuoles within the cell show that the India ink was consumed by the cell due to the process of endocytosis that was performed in order to obtain food. As the forty minutes progressed, we noticed that there were more dyed food vacuoles within each cell than in the earlier observed time periods.

As the temperature is increased in a reaction, the reaction will proceed faster. This is due to the increased collisions of molecules within the solution that is undergoing the reaction. When the temperature is increased, the kinetic energy of the molecules is increased and causes more collisions to occur. This allows the reaction to occur faster. The activation energy is decreased when the temperature is increased. The activation energy is the minimum amount of energy to start a reaction. This is because the increased amount of collisions between molecules allows bonds to break easier and the reaction to proceed at a faster rate, requiring less energy for the reaction to start. According to the graph that was created with the data collected in experiment four (the natural log the the rate constant k, over the inverse of temperature in kelvin), the activation energy can be found through the slope of the graph. In this case, the slope is negative. This demonstrates that as the temperature is increased, it takes less energy required to start the reaction. The Arrhenius plot is an accurate way to solve for variables in the Arrhenius equation. Some possible variables one could solve for is the activation energy (slope equals the  negative value of the activation energy divided by the gas rate constant) and the natural log of A (the y-intercept of the graph). The rate constant is increased as the temperature is increased. The rate constant is solved by dividing the rate of the reaction by the multiplication of both the concentrations of each solution used. Due to the fact that the rate had increased as the temperature was increased, the rate constant value increased as well. This is because the the rate was in the numerator of the rate constant equation. As the numerator got larger, so did the rate constant.