crmckenzie's blog

    This project focused on the Methods section and the aim was to walk through the creation of a multipanel figure in such a way that it could be replicated. The three pictures that had to be included were a picture of a plant found on University of Massachusetts Amherst’s campus, an up close pictures of that plant’s flower or leaf, and a map depicted the plant’s origin. The findings of this project revealed the areas that this Methods section was lacking in and where it lacked clarity, such as in angle and distance from camera to plant. Other factors such as time and tamperability in the greenhouse were also found to cause differences in the two figures. These factors aside, these findings reveal that it is crucial to provide a clear and detailed Methods section in all scientific papers.

Due to the fact that the exact sizes of the images were specified in the Methods, the sizes of the images are in scale with one another. However, relative to Figure 1, Figure 2 appears to be stretched based on the width of the plant in Panel A. Panel C is also visibly out of proportion when compared to Panel C of Figure 1, and from this it can be inferred that there was difficulty with the lock feature that was explained in the Methods. The Methods did not specify what time of day the pictures were taken at, so there are far more shadows in Figure 2 than in Figure 1. The Methods also did not specify exactly how far away from the plant to take the pictures from, or at what angle, and this is why there are far more plants visible in Figure 1 in the background. The Methods also did not specify how to center the picture in relation to the white tag which may have been helpful. Panel B varied drastically between the pictures which means that the Methods may not have been clear enough in this area. Panel C does not have the same tone of pink to fill in the countries even though it was specified, however it may not have been clear enough as there were many different colors. The backgrounds of the maps are also different but this is because this was not specified in the Methods. The largest difference between the two figures is that there are no orange flowers in Figure 2, and this must be due to timing.

Once in Inkscape, I went to file > import and imported all three of my images. I used the lock feature to ensure that when I was resizing the images the proportions would stay the same and the pictures would not stretch. I decided that I wanted the full sized picture of the plant to be on the top and the up close picture and the map to be below it. The full sized picture would be “a”, the close up “b”, and the map “c”. To accomplish this, I resized the images so that they all fit together with no spaces in between them. The top picture ended up being 266.530 millimeters long and 199.898 millimeters  tall. The up close picture of the flower ended up being 128.298 millimeters long and 158.773 millimeters tall. The map picture, directly to the right of the up close flower picture, was 138.232 millimeters long and 158.773 millimeters tall. I used the text tool in the “Times” font to create letters a through c and the box tool to create a small white box which I then duplicated until there were three. I placed each square in the top left hand corners of the images and centered letters a through c in their respective boxes. I then selected the “Export PNG Image” option and named the file “mckenzie-original.png”.

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.

    Scientific writing is a skill all scientists must possess in order to communicate their research and findings in an effective manner. The Methods section of a scientific paper describes the process the author went through to uncover their findings and to create their figures. This project was primarily focused on the concept of replication and the ability to reproduce a figure using a peer’s Methods section. The assignment called for the creation of a multi panel figure of a plant found on the University of Massachusetts Amherst campus that included a picture of the plant, a close up of a leaf or flower, and a geographical figure indicating the plant’s natural origin. The figure created for this experiment was about the Cattleya ‘War Paint’ orchid. The figure has three panels. The first is the full picture of the plant, the second an up close picture of one of its flowers, and the third a map of its origin, which includes Mexico and several countries in Central and South America. This figure was then replicated using the Methods section below to test the clarity and effectiveness of the section.

            I believe that Dr. Farkas’ work could do wonders for cancer research. All three areas of research have an untapped potential, especially that of the macrophage research as once it is perfected, it is an area of immunotherapy and thus is a widely reliable method. I do, however, anticipate room for error in this method even once the process and the molecules involved are identified, as different types of cancer may behave in different ways. It is this variable that could set this research back. I also believe that a lot of the inspiration for these methods of research came from the novel idea of ADCs and their success thus far. The delivery system nucleic acid research is a direct application of this, and depending on the effectiveness of the materials, it could prove to better this idea. The circadian rhythm research can serve not only as a method to discover potential treatment processes for cancer, but also as a warning or a cause to increase mindfulness for circadian rhythms. All of these processes, if successful, would be long lasting and extremely significant to cancer research.

            Since Dr. Farkas studies three different areas of research, three different approaches are being taken, though all are connected in the sense that all are meant to further understand the causes of cancer and to lead to potential treatment. First is the study of the altered circadian rhythms, as they have been found to match up with drug resistance during cancer treatment and to in general cause more aggressive cases of cancer. In this research, detectable entities, or luciferase reporters, are being developed for proteins essential to the circadian clock and for the cancer proteins involved. The reporters are to be used to detect change in rhythm. One potential obstacle is the comparison and relationship of this process in different types of cancer, as they may all not be able to be treated in the same way. Next, the study of modified macrophages as targets for cancer is equally as promising. In this research macrophages are targeted so that the macrophages that are recruited for the toxic sites of cancer can be harnessed and used for good instead (attacking the cancer), rather than in other cancer research where they are outright killed. This research is creating macrophages that have reporters that can distinguish between phenotypes so that they can attack only at unhealthy tissue. Finally are the capsules for therapeutic delivery that are being studied in the hopes that co-delivery enhances the effectiveness of cancer treatment. All of these processes involve the understanding of targets and antibodies which is a long studied field in cancer research.

First, I traveled to the Durfee Conservatory located behind the Morrill buildings to find a plant to photograph. After walking through the first room of plants from the front of the greenhouse and into the second room, I began to assess which plant stood out to me the most. On the far left in the middle of the wall, I found a flowering potted plant. One type of flower was white and pink, and the other was light orange and pink. I used a ruler to measure the proportions of the different areas of the plant. The plant had thick stems approximately 25 centimeters long that were partially white. The leaves were approximately 20 centimeters and the flowers themselves varied in size but averaged at 12 centimeters. From the tag in the soil, which was placed backwards in the pot so that the name was not showing in the picture, I discovered that the plant was the Cattleya ‘War Paint’ flower. I then took two different pictures. The first was a picture of the entire plant and its pot and the second was an up close picture of a white and pink flower with some leaves and petals of other flowers in the background. I then left to create my figure at home.

Both of these figures display two pictures of a building, pictures A and B, and one of a tree, picture C. They are fairly similar upon first impression. They are both aerial views of a building that appear to have been taken during different seasons and this may have been an instruction in this person’s methods section. This is an inference based upon the observation that the trees are fuller in one of the aerial pictures, however in Figure One picture A has full trees, whereas in Figure Two, picture B has full trees. Pictures A and B in Figure One appear have been taken at a farther distance as opposed to Pictures A and B in Figure Two. Picture C in Figure One features a bright and greener tree with a bluer sky, whereas Figure Two’s Picture C appears to be in less sunlight. One inference I could make from this is that Figure One’s Picture C was taken earlier in the day than Figure Two’s Picture C. The building featured in Figure Two’s Picture A and B appears to be animated and the building does not seem to fit in with the background of the picture which appears to be more natural. An inference I could make is that this person photoshopped or edited the image. Figure Two Picture A has an arrow pointing to the tree and Figure One does not have any arrows.

An example distinguishing between an observation and an inference would be observing a neighbor's yellow lawn and making assumptions based off of this observation. One could assume that the neighbor does not take care of their yard, or that snow killed the grass, or that their dogs ruined their lawn, but these are not proven facts, they are educated guesses. An inference is a conclusion drawn from an observatino that may or may not be correct.