Writing in Biology

Figure 1 is the original figure panel that I created. The creation of this figure panel was described in the methods in order for someone to recreate. Figure 2 was the replicated figure panel that another student created using the methods. Looking at the format of the two figures, the letters labeling each image are different. In figure 1 they are much larger and easier to see than they are in figure 2. The location of the letters also seems to be higher in the original figure panel than they are in figure 2. Starting with image A in both images, the major difference is the map used. Although both are maps of the campus, figure 2 used an older map than figure 1. In figure 2, the design building is not included because the map is outdated. The map in figure 2 also has a black outline around the campus pond where figure 1 does not have this outline. Figure 2 also lacks the red circle and dot that show the location of where the images were taken that is seen in figure 1. Figure 2 also shows a less zoomed in version of the map. There is space shown above the ILC and below the FAC but these buildings are both slightly cut off in figure 1.  

    Looking at image B in both figures, one major difference is the black patch on the cement. In the original figure panel the black patch is only on the right side of the image but in the replicate the black patch touches both edges of the image. In figure 1, windows on the right side of Morrill can be seen but in figure 2, windows on the left side of Morrill can be seen but not on the right side of the building. The image of Morrill in figure 2 also seems to be taken from a head on view but there is a slight angle in image 1.  

The finer details of Figure Two were analyzed for differences. To start, there is a red UMOC sticker on the UCard in figure two that is not in Figure One. The labels of the images are different as well. The size of the circle in which the letters are placed is much larger than those in Figure One as well as the size of the lettering being larger. The images in Figure Two are labeled differently than those in Figure One. I noticed that the labels for picture of the environment and the map are reversed in Figure Two when compared to Figure One. Figure two also captures more of the surrounding environment including railings, more of the windows, a light post bulb, and the windows behind the air duct are closed whereas they are open in Figure One. Another difference was the red box used to highlight the location of the web within the environment. The box used for Figure Two has different dimensions thus making it more boxy and larger than that in Figure One. The map in Figure Two is also different in that it is more zoomed in than the map of Figure One. The dot specifying the location of the web is also in a different location. It appears to be more towards the front of the building where as my dot was more towards the middle.

 

The experiment required a photograph located at the W.E.Dubois library of a spider web on the left side of the indoor building's window. The experiment was intended to create a comparison between two figure panels the original and duplicate. To get the replicate photograph to be as exact as the original the experiment included a set of instructions with the location of the spider web, how to photograph the web, and what software was needed to present the panel. The instructions listed did not result in an exact replicate of the original copy, though the panels were in correct order small differences were noticeable such as the angle of the photographs including the spider web's distance from the camera lens and the format of the label borders. The results demonstrated that more accuracy in describing the instructions was needed to get the results wanted 

    The methods above are for the creation of Figure One. The methods were passed along to a peer who followed the methods as best as possible to create Figure Two. Upon receiving Figure Two it was now time to compare the two figures and make note of any and all differences.The differences can be categorized into two categories, differences in the photographs and differences in the details. To start, there are seven key differences with the photographs. Picture A, the photo of the spider web itself, has a different focal point than that in Figure One. Rather than the photo being taken from the side, the replicate was taken from a lower angle and focuses more on the bottom of the air duct. The scale used in Picture A of Figure One is more prevalent, the whole UCard is captured in the photo whereas the UCard in Figure Two is only half visible. This also causes the fingers to be more prevalent in figure one than they are in Figure Two. The second photographic difference is drawn form the picture of the environment in which the web is located. The replicate photo captures more of the background, it is brighter, and it was taken at a different height thus capturing more of the alley way and its surrounding. The last photographic difference comes from the picture of the detailed map. In Figure One, there is a pin drop beinhd the Student Union building which helped guide the program to zoom in on the address. This pin drop is not located in the picture of the map within Figure Two.

 

The differences in the map resulted from finding different maps in the online search for a campus map. Because the map in figure 2 lacks the design building, it is most likely that an old campus map was used and that it is outdated. The map is not as accurate of campus as the map in figure 1 because it is old and does not feature the new buildings on campus. The differences in the outlines around the campus pond and the cropping of the map could also relate to the fact that figure 2 used an older version of the campus map. The map in figure 2 also lacks the red circle and dot that show where the images were taken and this could be the result of the person recreating the map not having the same software used to add this to the original map. I used an iphone to edit the image and add these features so the person recreating the image might not have had access to an iphone to recreate these steps.    

The differences in image B are most likely the result of taking the pictures from a different angle or from the person taking the image standing in a slightly different position. The image features the same building and the same doorway but the angle at which the picture was taken resulted in a slight difference in the picture. The image in figure 1 shows more of the right side of the building and the image in figure 2 shows more of the left side of the building, so the position of the person taking the pictures might have been different. The angle at which the phone was held might also account for these differences.

When studying histology, staining is a procedure that allows scientists to identify and observe different structures. One of the most common stains for histology is the hematoxylin and eosin stain. Hematoxylin is a basic dye. Since it is a basic dye, it has the ability to stain acid structures in the cell. DNA and RNA in the nucleus or cell are often dyed by hematoxylin. Hematoxylin dyes these structures a purple/blue color. For contrast in staining, eosin is a pink acidic dye used to stain basic structures. Proteins are the most common structures stained by eosin. The contrast between the two dyes makes it easier for individuals to find and identify certain structures in the cell efficiently.

When choosing a spider web to photograph and create a figure from, there were six factors I considered for replicability. I considered the angle of the camera, positioning of the photographer, the lighting, the type of pencil used, and my directions when capturing the spider web and its environment. I chose a spider web located indoors to avoid the factor of weather. For the formatting and editing of the multi-panel, I considered the clarity of my methods.

I observed a total of four main differences between my original multi-panel figure (Figure 1) and the replicated figure (Figure 2). I observed differences in the original photographs taken and the replicated photographs. First of all, it is difficult to see the spider web in the close up photograph of the spider web. In the replicated Figure A, I mostly see the pipe of the radiator rather than the web. I also observed that the color and positioning of the pencil used in the replicated photo is different from my original. The pencil I used was yellow while the replicated photograph has a red pencil. For the replicated Figure B, I noticed that the photograph did not include the same amount of the rug, doorway, or wall as my original Figure B.

In the Fall of 2018, as a part of a Writing in Biology class at UMass Amherst, I conducted a project where I created a scientific figure, wrote the methods for creating said figure and passed the methods along for somebody else to replicate. The purpose of this was to show how much detail plays a factor when writing a methods section. The methods should be clear and easy to follow, like a recipe of sorts. Science, in and of itself, is about imperfections and this project highlights that. Blindly assembling a scientific figure using someone else's methods is a daunting task and is sure to generate interesting results  similar to those put forth later in this paper. After receiving the replicate figure, it was evident that the differences between the two figures were due to a combination of  human error and natural differences. Inferences were then drawn from the differences and a list of potential factors was generated as a means of explanation. 

The pituitary gland is a major player in the endocrine system, the system that controls hormones in the body. The pituitary gland is often referred to as the master gland because it controls the other glands in the body. It used to be widely thought only that the pituitary gland controlled the brain, but interestingly, the brain controls the pituitary gland. The brain secretes neurotransmitters which control hormones. The pituitary has two different regions: the posterior pituitary (neurohyphosis) and the anterior pituitary (adenohyphosis). The hypothalamus (a region of the forebrain) produces the neurotransmitter oxytocin and antidiuretic hormone (also called vasopressin) inside of its neurons, and passes them along to the posterior pituitary, which secretes them into the body. Antidiuretic hormone targets the kidneys, especially its tubules, and regulates water levels. Oxytocin targets the mammary glands, facilitating lactation, as well as the uterus, controlling contractions. The hormones are made in the hypothalamus, the posterior pituitary only secretes them. In contrast, the anterior pituitary gland synthesizes its own hormones, but they cannot be released unless regulatory hormones released from the hypothalamus signal them to do so. The anterior pituitary gland secretes prolactin which targets the breasts for milk production, ACTH which stimulates cortisol release, growth hormone which acts on bones, gonadotrophic hormone which acts on sex organs, and thyroid stimulating hormone. 

Many of the differences that are seen between the two figures are results of different camera angles, different cameras, different people taking the images, different positioning of the person taking the images as well as different software available. This assignment was relatively successful because the recreated figure panel is pretty similar to the original, most of the differences come from uncontrollable differences such as camera and software used as well as the angle at which pictures were taken. There are however a lot of differences that could have been prevented with a more clear methods section or by the methods being followed more precisely. This assignment really demonstrates the importance of needing a clear and descriptive methods section in order for something to be recreated exactly or accurately.

Acknowledgements

    The figure 2 was recreated by classmate “curbano” who followed my methods and recreated their own figure panel based on my methods. Their work allowed me to analyze the differences and to assess the success of this assignment.