cdkelly's blog

Side-by-side comparison of Figure 1. Spider Web Localized at the University of Massachusetts Amherst Student Union and Figure 2. Replicate Figure (See FIGURES section) led to the observation of differences. A total of 3 main differences were noted. They included sizing and orientation of figure markings, the surrounding scenery, and the area encompassed by the map. This section will describe these main differences in more detail.

The various markings of the figure including the labels, the indicating lines, the text, the quarter length line, and the the indicating circles differed in size and orientation. Each of the labels in the top left corner of each image had slightly smaller text compared to the original. Also, the labels were not placed in the exact corner and a lip was observed. In part A of the replicate, the line showing the length of the quarter for reference was longer and did not correspond with the length of the quarter. The number over the line was written in a larger font. Also, The red circle highlighting the location of the web in part B was larger in size, with a thinner line used.

    In Fall of 2018, I conducted an experiment for the class Writing in Biology at the University of Massachusetts. The project was a demonstration of the importance of clear, concise methods writing. I located a spider web on the University of Massachusetts campus and created a figure displaying a spider web and its relative location. Once completed, I shared it with another student in the class for the purpose of recreation. The student tasked with recreation did not see the original figure until submitting their version of it. The replicate version of the figure had variation in the size and location of certain components, different photographic elements, as well as map localization. The methods section included dimensions for all of the markings on the figure, but did not include any units of measurement. This caused the differences in size of markings and font in the replicate figure. The localization of the markings were different in the replicate as well because of missing details in the methods. Furthermore, the angle and location at which the photographs were taken differed in the replicate because of missing details as well. Weather and resultant conditions were different, but this was a factor that could not be controlled. The map image used in the replicate was zoomed out further than the original since the area encompassed in the original map image was not described in enough detail.

This project was a done as a demonstration of the importance of clear, concise methods writing. Each participant was instructed to create a figure displaying a spider web and its location. Once completed, a methods section was written and shared with another student in the class for the purpose of recreation. The student tasked with recreation did not see the original figure until submitting their version of it. For this paper, the figure was recreated relatively faithfully, but due to a number of missing details in the methods section, differences were observed. This demonstrated the importance of including any details within the methods section and the necessity of writing clearly and concisely. Eliminating as much room for error as possible is critical when synthesizing a proper methods section for empirical research.

The brain has fascinated me since high school, and taking classes at this University has only reinforced my interest. I have completed a number of biology, chemistry, and neuroscience courses that have all given me the skills needed to work in a lab setting. Said classes have regularly required me to use an array of biological and chemical apparatuses with a certain degree of precision and accuracy. Learning a number of different programs for data entry and brain imaging also became requirement for some of my classes and I believe I have learned a great deal from acquiring the necessary skills to operate them. I have TAed a neuroscience lab on campus, and in doing so I have become skilled with a number of laboratory techniques including usage of a cryostat, crystal violet staining, and fMRI data processing. Furthermore, on a number of occasions during my biology and chemistry labs I’ve had to take the lead in order to get my group going in the direction we needed to be proposing new approaches and diffusing tension among members. I know how to properly manage my time and think critically when it is necessary thanks to the experience that I have accrued at this University. But now I would like to move on to the next level and actually contribute something meaningful in the form of research,

The interesting thing about ligand-receptor interactions is the sheer number of different ligands and corresponding receptors. Each cell type has different receptors attached to its membrane and thus, many different ligands that can bind it. Each ligand-receptor complex sets in motion a series of chemical reactions in order to fulfill its specific role in the cell. A good example of this epinephrine (adrenaline) because it can interact with many different cell types and correspondingly receptors, but have much different effects from cell to cell.  

This is really cool, but I'm not sure I totally understand the concept. Does the biofilm encompass multiple bacterial cells? Perhaps if each bacterial cell is producing the material necessary for the biofilm, this acts as a form of quorum sensing and results in the local bacteria to begin production.

So when this specific type kinase receives the phosphate group addition, it becomes capable of catalyzing reactions. So as I understand, they are like enzymes that need an external energy source in the form of a phosphate group.

This fact highlights the importance of G-protein coupled receptors in the cell. Because G-protein coupled receptors are so critical in cell signaling, this makes sense. In addition, cellular signaling is a crucial and fundamental component of cellular function, furthering the importance of G-protein coupled receptors.

Are there situations in which the phosphate is removed from kinase A so that the active site is blocked? If the kinase A receives this phosphate group when it is synthesized, then does it have it all of the time? This section states that the subsequent activation by the secondary messenger is key to making the kinase really function, but it seems weird that it kinase A would always be in the primed state.

This reminds me of the way the neurotransmitters are released into the synaptic cleft. When calcium ions interact with specific channels on the terminal end of a neuron, a series of events occurs in which results in the membrane surrounding a given neurotransmitter and releasing into to the extracellular environment. In this case calcium elicits a change membrane rather than the calmodulin.

In tumorous cells, processes completed by RAS and other oncogenes are disrupted in a way that favors the tumors growth. Specific pathways in the cell are victims of this process and they become fundamentally altered as a result. Many drugs have been designed to target specific pathways and specific oncogene. Some of these drugs include bevacizumab and metformin. Although these drugs may have a beneficial effect at first, the cancerous cell soon finds a way to utilize another pathway for the same purpose. This is known as oncogene addiction. The mechanism of this phenomenon is rooted in the rapid evolution and resultant mutation that occurs in cancer cells. Therefore, targeting specific pathways or oncogenes has proven to be ineffective in that long-run. That's why current cancer treatment is focusing on the immune system instead.  

Many components of the figure were like the original, but there were numerous differences. These differences highlighted details that were missing from the methods section or not written clearly enough. One oversight at the root of a number of the differences was the lack of units of measurement. Each component of the original figure was described with the dimensions in terms of the width and height, but none of them contained the type of unit being used. This resulted in the smaller font in the component label boxes. Had I designated that the entire figure utilized millimeters as the unit of measurement, then the three label boxes would have had a font size that resembled the original more closely. Furthermore, the length and thickness of the red line over the quarter would have also been more like the original. More clearly stating that the line was meant to encompass the diameter of the quarter would have also increased similarity. The objects in the background were more difficult to control because of the weather during the week the replicate was created. Thus, the moisture seen in the replicate was not necessarily due to the instruction of the methods because the weather and time were clearly stated. But, the images showing the location did not include the bike rack structure due to it not being mentioned in the methods that it was in the figure. I only stated the location from where the photograph was taken, not the details of the scenery.

 

Many components of the figure were like the original, there were differences. These differences highlighted details that were missing from the methods section. One oversight that was at the root of a number of the differences was the lack of units included in the methods section. Each component of the figure was described with the dimensions in terms of the width and height, but none of them contained the type of unit being used. This resulted in the font appearing smaller in the component labels. Had I designated that the entire figure utilized millimeters as the unit of measurement, then the three label boxes would have had a font size that resembled the original more closely. Furthermore, the length and thickness of the red line over the quarter would have also been more like the original. More clearly stating that the line was meant to encompass the diameter of the quarter would have also increased similarity. The objects in the background were more difficult to control because of the weather during the week the replicate was created, thus the moisture seen in the replicate was not necessarily due to the instruction of the methods because the weather and time were stated. But, the images showing the location did not include the bike rack structure due to it not being stated in the methods that it was in the figure. I only stated the location from where the photograph was taken, not the details of the scenery.

    Since the map portion contained the most differences, the part of the methods discussing its creation was not detailed enough. I did not clearly state the area shown in the map with other buildings or landmarks, and the resultant recreation was more zoomed out as a result. The abundance of labels on the replicate map also were also related to this because it showed a larger area. The text labeling the student union was written in a straight line in the replicate because I did not mention that wrote it on two separate lines in the methods. Much like the other labels and markings on the replicate, the red dot placed on the map was larger because I did not specify the units. Although the location box was correctly recreated, it extended to the left at a roughly 45 degree angle rather than the right because its directionality was not discussed in the methods. Similarly, the thin black line connecting the location dot to the location box was connected and overlapping in the replicate because I didn’t mention its connectivity.

    In conclusion, the replicate figure was similar in many regards to the original but a number exclusions from the methods section made certain components vague. This vagueness led to the discussed differences between the two figures. Mainly, not including the units of measurement with all of the dimensions in the methods. The lack of detail in the map portion of the original was also highlighted by the resulting replicate figure. This projects certainly emphasized the importance of paying attention to details when creating a methods section so that the replication process can proceed as intended.

Upon side-by-side comparison of the two figures, a number of similarities and differences were observed. Firstly, the web at the center of the original figure was successfully located and the correct images were obtained. Moreover, the overall orientation of the three images contained within the original figure were faithfully reproduced. In addition, the format of the three figure labels were the same and placed in the same locations as the original. The box labeling the location was the same dimensions and the line extended to it was the same thickness. As for the other labels on the figure, the correct colors were used in the replicate and the general use of them was recreated correctly for the most part.

    Although many components of the replicate were similar to the original, a number of dimorphisms were observed as well. Each of the labels in the top left corner of each image had slightly smaller text compared to the original. In the image of the web, the line showing the length of the quarter for reference was longer and did not correspond with the length of the quarter. In addition, the number over the line was written in a larger font. For both the photograph of the web and the location, the background was slightly different and moisture was visible in the replicate. Next, the circle highlighting the area of the web was larger and covered a wider space.

    The map portion of the replicate contained the most differences. Firstly, it encompassed a larger region compared to the original and was more congested with labels. The text covering the student union was larger in font size displayed in a straight line. As for the red dot marking the absolute location of the web, the replicate version was larger. In addition, the line extending to the box labeled “location” extended off to the left rather than the right. The line also connected to a different part of the location label box and made contact with the dot and the label.

Each figure was intended to show a spider web somewhere on the University of Massachusetts campus, its relative location, and a map marking its absolute location. For the purpose of replicability, many factors needed to be controlled and clearly described in the methods section. The featured web was chosen because it was substantially sized, relatively easy to locate, and in an area that allowed for photography. Moreover, the methods were created with specific details in mind to increase similarity between the original and the replicate. These included the location of the web based on nearby geographical features, utilization of specific dimensions for both the images and the labels, and description of how each of the three images were obtained and oriented. Within this paper, the original methods, the original figure, the resultant replicate, and the consequential differences and similarities will be examined.

This project was conducted by the students in Writing in Biology 312 under the instruction of Dr. Steven Brewer. It consisted of each student collecting a series of images and putting together a figure while simultaneously writing a methods section detailing its construction. The objective was to create a replicable set of methods so that another student in the class could recreate the figure prior to seeing the original. Each figure was intended to show a spider web somewhere on the University of Massachusetts campus, its relative location, and a map marking its absolute location. By having another student in the class follow the set of methods detailing the synthesis of the figure, we could infer what portion of the methods needed improvement or more clarity. These inferences were based on observations of dimorphisms between the original figure and the replicate. This paper covers a specific set of methods and the resultant replicate figure.