Writing in Biology

African lungfish live in areas where there is a heavy wet season and a very dry season. When it is wet, the lungfish will live in, generally shallow water or very muddy, wet land. It is during this time the lungfish will reproduce. Female lungfish will make a burrow underwater, which it will fill with decaying plant material. The males then guard the egg chamber until the eggs hatch. During this period, the male lungfish will develop pelvic gills. Pelvic gills are very different from respiratory gills. In fact, they act in the opposite direction. Rather than taking in oxygen, they expel it. This is done to oxygenate the water surrounding the eggs, allowing the lungfish embryo’s to survive in stagnant water with their limited gills.

Once mating is over and the waters begin to recede, the lungfish will create a burrow in the ground for itself. While in this chamber the lungfish will excrete a large amount of mucus, filling the chamber and making a mucus cocoon. Lungfish can be sustained in this cocoon for months at a time, until the area in which it lives becomes wet again.

When writing reports it is important to be clear and concise in the methods section in order to facilitate replication. Many of the differences listed above could have been avoided with better descriptions. For instance when it comes to labeling the images, the font size looked to be much larger in the replicate. This may due to improper font size, or it may be because the images themselves are a different size, making the fonts seem different. The angle of the arrow could have been controlled by having an easier to draw arrow. That is to say, one not at an angle, or at an easy to determine angle. Additionally arrow keys could have been used to provide exact inputs to move the arrow from an easy to determine position to its final position. The line thickness differed on the arrow, though this was in the methods and was not followed. Specifying that the arrow head used was the “5^th one down” would have avoided the difference in arrowheads used to point to the web location. Unfortunately there does not seem to be much that can be done about the difference in map image, with the source used. The best that can be done is listing exactly everything visible in the image with the addition of dimensions of the image. Regardless this still leaves room for error.

When taking the photograph, the time of day and weather should have been accounted for in order to replicate the original image well. Since the lightpost and surrounding area was wet in the replicate we can assume it was raining. Also since the light was not turned on, this photograph was likely not taken at the same time. The addition of light shining down on top of the spiderweb would have likely produced a better contrast, allowing the spiderweb to be more visible in the photograph as well, as is true in the original.

Framing and instructions on framing could have been much better. In retrospect the original image of the surrounding area (Fig. 1:B) should have been directly centered around the lightpost, as is true in the replicate. The slight angle at which the original photograph was taken is difficult to describe and provides too much room for error. To go along with this, a specific distance from the lightpost to stand at and take a picture should have been specified.

Object used to provide scale was wrong. This may be due to a ruler just being unavailable at the time. Regardless however, it should have been mentioned that the ruler was to be held with the inches side closest to the lightpost. This point was not specified in the original methods.

Despite these differences, both the original and replicate images are very similar. This project has not only demonstrated the importance of a clearly written methods section but being mindful of how an experiment is performed. Keeping things reasonably simple, at least within the confines of the subject, will likely produce better results and enable easier replicability.

The formatting of the figure panels are different between the two figure panels. The three pictures in the replicated figure panel do not have any gap of space in between the photos. The three photos overlap on each side. Additionally, the labelling on each photo do not match to the original, as the labels are placed in the upper left corner of every replicated picture. The font of these labels is also smaller and more box-like. The thickness of the label font is also thinner in the replicate pictures. As for the red markings on the picture, the red boxes do not match in size between the original and replicated panels. The replicate panel has smaller boxes around the Lewis Hall and stair railing, and these boxes are not perfect squares unlike the boxes on the original figure. Figure A in the replicated panel is more zoomed in to the UMass Campus, whereas the original panel has a map that shows more of the outside area surrounding Lewis Hall.

While sitting down on the bottom step of the staircase, a picture was taken of the spider web in the hole of the stair railing. A UMass ID card was placed right beneath the spider web to act as a scale for the web size. The IPhone camera was tilted upwards so that the background of the picture was a green tree; this dark background created great contrast that could be manipulated to make the spider web show up, despite it being bright outside. After a picture was taken that captured the small spider web, another photo was taken 10 steps backwards from the Lewis Hall main entrance. This picture was angled slightly to the right, so that the Lewis entrance sign was at the top left of the picture, and the stairs and right side railing were at the bottom left of the picture. This picture would be used to understand where the spiderweb was located.

Assess and explain in an organized way the observed differences:

The first difference I observed between my figure and the replicate, was that the replicate was narrower and the red star indicating the location of the spider web was in the wrong place.

Regarding the differences in length and width between the original and the replicate figures, I did not specify in my methods how long it should be. Nonetheless, I did mention to place the red star over the location where the pictures were taken, which in this case was close to the furthest left corner of Franklin Permaculture Garden as you face it when coming from Morrill.

As well, the size of the letters was significantly greater in the replicate version, and the letters in the original are closer to the left upper corner than in the replicate.

I did mention to place the letters on the upper left corner of each image, but failed to specify that they should be closer to the corner. As well, I made no references to the size of the letters, which is the reason why in the replicate they are bigger than in the original.

Regarding picture A, the replicate version has more brightness and shows part of the ground behind the bush.

The differences between the original picture A and its replicate can be related to differences in image quality due to using different cameras, but mostly are due to not describing with further detail the positioning of the camera. The same holds true for picture B.

Picture B in the replicate was taken further away than the original so it includes more background and buildings, but it doesn't have the green sign to the right.

In the methods I mentioned that in order to take this picture the reader should take three steps backwards, but the difference in height and gait of each individual made this an inaccurate description, since the replicate was taken further away than the original. Nonetheless, I did specify to include the green sign to the right, which the replicate failed to do.

As well, picture B in the replicate was taken in a straight angle, while in the original ot was taken pointing down to focus on the bush with the web, which probably distorted the brightness of the picture too by making it brighter.

Once again, the differences in brightness and angles in picture B are due to not having described with more precision the positioning and settings of the camera.

Picture C in the replicate shows a larger area of the map than the original figure.

The replicate figure C encompasses all the buildings I described in the methods, but it covers a larger area than the original due to not specifying that once the screenshot covered my list of buildings, the rest of the picture should have been cropped.

Finally, there is a small gap between A and B in the replicate, which is filled in grey but is not part of either picture.

Regarding the small grey gap in the replicate figure between A and B, I did specify in the methods to display the elements so that they were touching each other, in which case there would be no gaps in-between the pictures.

Figure 1: Original multipanel figure displaying: A. close-up view of spider web; B. wider view of the spider web on the bush; C. OpenStreetMap screenshot of the location where the spider web was found.

Figure 2: Replicate multipanel figure displaying the elements described in Figure 1. This figure was made by following the Methods section of this paper without visualizing the original figure, for testing the replicability of the aforementioned section.

Describe and summarize the observed differences:

The first difference I observed between my figure and the replicate, was that the replicate was narrower and the red star indicating the location of the spider web was in the wrong place. As well, the size of the letters was significantly greater in the replicate version, and the letters in the original are closer to the left upper corner than in the replicate.

Regarding picture A, the replicate version has more brightness and shows part of the ground behind the bush. Picture B in the replicate was taken further away than the original so it includes more background and buildings, but it doesn't have the green sign to the right. As well, picture B in the replicate was taken in a straight angle, while in the original ot was taken pointing down to focus on the bush with the web, which probably distorted the brightness of the picture too by making it brighter. Picture C in the replicate shows a larger area of the map than the original figure. Finally, there is a small gap between A and B in the replicate, which is filled in grey but is not part of either picture.

Figure 1. Original Multi-Panel Figure of Spider Web. A. shows the spider web with a pencil for scale. B. shows the setting the spider web was located in. C. shows the location of the spider web on a map. The black star in C. shows the exact location of the spider web.

Figure 2. Replication of Original Multi-Panel Figure. This multi-panel was created after following methods describing the steps taken to take the photographs and edit them. A. shows the spider web with a pencil for scale. B. shows the hallway in Morrill IV that the web was located in. C. shows the location of the spider web with a black star on the UMass Amherst campus map. Figure 2 was used to test the replicability of the methods written.

Panel C in both Figures contains a map, but the maps showed discrepancies between them. The maps included a different range. For example, Figure 2 showed French Hall, while Figure 1 showed none of French Hall. In addition, Figure 2 included Thatcher Road and University Club, while Figure 1 did not. The maps included the same colors, but the colors are placed in different places. For example, in Figure 1 the Permaculture Garden is shown as beige on the map, while it is shown as green in Figure 2. In Figure 2 there are 2 white rectangles that do not exist in Figure 1. A red pin is placed in Figure 2 that is not in Figure 1. The keys placed on Figure 1 and Figure 2 are of different sizes. In addition, the black outline around the key is of different thicknesses. Figure 1’s key was labeled as “Key”, while Figure 2’s was not. The key in Figure 2 has black writing and the key in Figure 1 has red writing. The circle superimposed on the maps are different sizes, with Figure 2’s being larger. 

- Goals of the Methods Project:

The main goal of this Methods Project for Writing in Biology class is to reflect on the key components that a good Methods section of a scientific paper should have in order to convey its message. Scientific research must be easily replicated by others in order to prove its validity, that is the reason why this project includes following the methods of another student in order to replicate their figure as accurately as possible. As well, it is important to understand that inferences are conclusions that are made based on observing a phenomenon and formulating logical explanations for it, and that they should not be confused with observations. The last objective of this project is to identify the variables that must be controlled in order to be able to successfully replicate an experiment.

- Explain the subject of my figure

The subject of my figure was the web of a funnel weaver spider,  located on a bush in Franklin Permaculture Garden. In order to compose the figure I took a close-up photograph and another picture that showed its surroundings, and then I added a map marking the location of the spider web.

- Reasoning for selecting my figure

The reason why I chose to make this figure is because it can be easily replicated, since the spider web is clearly visible and located on an accessible area that many students know due to being close to Franklin Dining Commons and the BCRC.

- Factors I sought to control when I wrote my methods (but don't describe those factors)

When I wrote my methods I made sure to control the exact location of the spider web, as well as the spatial arrangements of the different elements of the figure, including the order in which the pictures were presented and their respective labels. As well, I described in detail other important features of the labels such as the colors of the letters and boxes in each image.