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The Methods section of a scientific paper allows for the reproduction and verification of any given experiment. In order to do so, a carefully thought out narrative must be developed with clear explanation of materials and subjects, as well as experimental design including variables and controls and procedure. In this study we examined how to write an accurate methods section by having a peer follow a set of methods detailing the construction of a figure and subsequently comparing the two figure in order to determine the clarity and accuracy of the provided methods section.  Our findings show that small details, variables and controls not accounted for in the methods section of a paper can lead to deviations in the reproducibility of a given experiment. This is important for any scientific paper and provides it with legitimacy.

When looking at the entire figure, the font and size of the panel labels are not the same. The labels in figure 1 are bigger, bolder, and to the left of the pictures. The labels in figure 2 are smaller, in a different font, and on top of the pictures. The pictures in figure 1 also seem to be clearer than the pictures in figure 2. In addition, the pictures in figure 1 are more flush to the top and bottom of the figure and there is no horizontal space between figures A, B, and C. In figure 2, the pictures are not flush with the top and bottom of the figure and there is a horizontal space between figures A, B, and C.

    We tested the hypothesis that given a detailed and accurate methods section the construction of a figure could be repeated with precision. In order to test this, methods were provided for the construction of a figure to a peer without knowledge of the original figure in order to determine the efficacy of the methods in providing an accurate template for exact replication. We observed differences between the overall structure of the replicated and original figure in multiple areas. These results suggest that the provided methods did not take into account all possible variables as well as controls for the reconstruction of the figure.

Every experiment contains a method section, where the scientist records the steps and describes the process of the experiment that yielded the observed results. The methods section allows other scientists to replicate the experiment and furthermore, it provides the experiment with validity. The purpose of the methods project is to understand and develop a methods section of our own. To achieve this, we created a multipanel figure containing three pictures: one picture of the entire plant, a close-up of the flower, and a map of the origin of the species. For this project, the Camellia Japonica Napoleon was the plant being observed. The Camellia Japonica Napoleon is a plant that has beautiful multilayered pink flowers which begin blooming from January to March. This plant’s origin can be traced back to China, Japan, South Korea, and Taiwan, but they are now sold and grown in many places across the world, such as the United States. This plant was chosen because the plant was easily accessible and it was starting to bloom. In the methods section, the main focus was getting the student to the right place and to the correct plant. The angle in which the picture was taken was also a focal point of the methods section. Lastly, the way the multipanel figure was constructed was carefully explained in the methods project to ensure the right figures were put in the correct positions.

Retrievers are either black or brown depending on whether TRP-1 and TRP-2 are synthesized. If TRP-2 and TRP-1 are synthesized then the retriever is black, but if only TRP-2 is synthesized then the retriever is brown. In the case of a yellow lab however, neither TRP-1 or TRP-2 are synthesized. This is due to a mutation in the MSH gene that changes its conformation. Because of the change in conformation, the MSH can no longer bind to the MSH-R. The MSH-R is what signals to produce the TRP-1 and TRP-2 that causes pigmentation. This is what causes the hair of the yellow retriever to never become pigmented.

The differences between Figure 1 and Figure 2 are immediately apparent, however there are several similarities as well. The figures share proportions in that Panels B and C are the same approximate size to each other and in each while Panel A is the same approximate size in each. The lighting is more evenly distributed in Figure 1 than in Figure 2 and there are less shadows. Figure 1 is taken slightly higher and angled slightly more in Panels A and B. In Figure 1’s Panel A, there are more pots and plants visible in the background, while in Figure 2’s Panel A, the top ledge of plants is not visible and only one pot is in good visibility. Figure 2 Panel A’s plant is wider in relation to the rest of the picture. The white tag leans left to the midline of the plant in both figures. Panel B of each of the figures varies in that Figure 1’s Panel B depicts one pink and white flower with a couple others in the background, while Figure 2’s Panel B depicts the entire plant at a different angle with the tag to the left of the midline of the plant. There are also many differences in the Panel C’s. Figure 1 includes South America and North America with a portion of Greenland, while Figure 2 omits everything north of the U.S. and adds a portion of Africa. The background of the map is gray is Figure 1 while in Figure 2 it is blue and green. In each, pink is used to fill in individual countries, however it is slightly more purple in tone in Figure 2. The continents appear to be slightly skinnier in Figure 2.

         Sub-Saharan Africa is home to a wide variety of insects. One in particular standing out from the rest, taking a human characteristic and imbedding it in themselves, heroism. The termite eating African Matabele ant, or the Megaponera analis, embrace the sayings “never leave a fallen comrade”, providing purpose and value of each individual ant. During invasion of termite nest in an effort to feed, many ants sustain a certain level of injuries, which they have adapted to overcome. If injured, they are shown to bring back these injured ants to their colony and provide aid for their recovery. In a study in 2017, these ants have been observed carrying all non-fatally injured ants back to their nesting areas in an effort to save the injured. In an experiment, scientists removed legs of some ants and notices a spike in response of their comrades. Their comrades quickly returning them to the artificial nest, where they began to clean the wound using their mouths for up to 4 minutes. This cleaning is believed to clear any dirt in an infection prevention effort, their saliva also believed to contain antimicrobial chemicals. Ants treated are shown to have a 90% 24-hour survival rate as oppose to a 20% survival rate if left untreated.

Retriever dogs have three distinct phenotypes. There is the black phenotype, the brown phenotype, and the yellow phenotype. The difference in expression between the black and brown phenotype comes down to the production of two enzymes: TRP-1 and TRP-2. All retrievers produce tyrosine, which when reacted with tyrosinase forms dopaquinone. TRP-2 then reacts with the dopaquinone to create the brown pigment, which then reacts with TRP-1 to form the black pigment. Black is the dominant color of the two because it takes only one signal to produce both TRP-1 and TRP-2. There is a mutation in the recessive allele that causes only TRP-2 to be produced, causing the pigmentation to halt once it reaches the brown pigment. 

Inferences can be made regarding the differences observed between these two figures due to how the methods were written.  The differences in fonts, bolding, and location of panel labels are due to there not being a precise description of how these should look.  There is only a description of which figures are labeled with which letter, allowing room for error.  Both figures contained panel labels that were in black, potentially due to black being the most common font color.  There is also a color difference in parts A and B of both figures.  This may be due to the differences in cameras used, or differences in day time when the pictures were taken.

In part A of both figures, the camera angle and orientation of the sign in front of the orchid differed.  There was explanation of how to orient the plant using the sign as a reference in the methods, but these instructions were followed more closely in the second figure.  The picture was initially taken,then the methods written, making the methods conform less to the picture.   There was also less description about the distance between the orchid and the photographer which could account for there being more of the bench and surrounding plants included in figure 2.

Results

Both figures showed the natural range of C. japonica labeled as part A, and both maps showed the same locations, China, North Korea, South Korea, and Japan as where the plant can be found naturally. Both the original and the replicate figure had two images with a single flower as the subject. Both figures also had an image of the entire plant. The main differences between the figures appears to be the lighting in the images of the flowers, and the distances at which the camera was from the subject of the pictures. The original images are brighter than the replicate. The content of the images in the original and the replicate is nearly identical. Another purely aesthetic difference is how the images are arranged, with the original having transparent space between the images, and the replicate having no empty space at all.