Writing in Biology

The background and scenery of part A and part B of the replicate figure had differences that resulted from the methods as well as differences that could not be controlled. The moisture and shadow position differences between the original and the replicate were due to the weather differences and the alloted time for replication. My methods stated the weather and time of day the photos were taken. In addition, the vehicle seen in the background of part B in the replicate was due to the same reason. On the other hand, the lack of the pipe extending from the electrical box in part A of the original was a result of methods omissions. I did not put enough detail into the way that the camera was held above the web in part A and used the word horizontal to describe the camera's orientation relative to the web. The pipe visible in the original figure is a result of the camera being at a slight angle; and its absence in the replicate is due to the camera angle being more horizontal. Furthermore, I mentioned that photo for part B was taken next to the second pillar of the bike rack structure. However, I did not mention that a portion of the structure itself was present in the original image. This explains why the structure was not seen in the replicate.

The map depicted in part C of both figures showed different levels of detail. In the original figure, the map was more zoomed relative to the replicate. The resultant extra buildings and map markings on the replicate arose because I did not describe the landmarks surrounding the Student Union in my methods section. I stated that the Student Union was at the center of the map image, but did not provide further information beyond that. Therefore, the person who replicated my figure had to approximate. In addition, the replicate lacked the scale marking and the logo seen in the bottom corners of part C of the original. These markings were not mentioned once in the methods. Thus, it is not surprising that they were not featured in the replication because the person could not have know about them in the first place. The lack of cropping instructions in the methods was another reason for this omission.

In conclusion, the replicate figure was similar in many regards to the original, but exclusions from the methods section made certain components vague for the reader tasked with replication. These exclusions led to all of the discussed differences between the two figures aside from the weather. This project emphasized the importance of paying attention to details when creating a methods section so that the replication process can proceed as intended in the original work.

The three main differences between the original figure and the replicate were the sizing and orientation of the markings of the figure, the surrounding scenery, and the area encompassed by the map. This section looks at these differences in more detail and makes inferences on what portion of the methods section caused them.

The size and thickness differences in the labels, indicating lines, text, length lines, the dot on the map, and highlight circles were all caused by the same facet of the methods. Not including units of measurement with all of the dimensions in the methods led to a vagueness in the original sizes. Dimensions were meticulously included with each part of the labeling on the figure, but there were no associated units. Thus, the person tasked with the replication of the figure did not know which of the number of possible units was used in the original, causing the size differences.

As for the orientation of the figure markings, the methods described the general location, but did not go into enough detail. This caused the labels in the top left corners of parts A,B, and C to be positioned slightly past the borders of the figure and resulted in a lip at all three locations. Also stemming from the lack of detail pertaining to orientation, the “location” box in Part C was found on the left side in the replicate. I only specified that the label box was off to the side of the red dot in part C, with the connecting line at an approximate 45 degree angle. I did not say which side it was on, which led to the replicate having it on the left. The connector line made contact with the red dot and the location box in the replicate because I only said that they were connected without elaborating in the methods. I didn’t say to which part of the location box the line connected, and I didn’t mention that the line did not actually make contact with either the box or the dot in the original. All of these missing details resulted in the different orientation of the markings in part C of the replicate.

In part C of the replicate, the text covering the student union was larger in font size and displayed in a straight line. As for the red dot marking the absolute location of the web, the replicate version was larger. The label box with the word “location” inside of it was positioned of the left side of the figure. Also, the thin line connecting the box to the red indicator dot made contact and was connected to the side of the box.  

The surrounding scenery of part A and part B of the replicate was subject to different weather conditions and contained objects not seen in the original. A pipe extending from the bottom of electric box next to the web was absent from part A of the replicate figure. For both part A and part B, the background had visible moisture. A lack of shadows was observed in part B of the replicate. A vehicle is visible in the background of part A. Also, the coloration and positioning of the leaves caught in the web were different across figures. The bike rack structure shown in part B was not seen in the replicate.    

In part C of the replicate, the map encompassed a larger region of the campus. Compared to the original, part C was more congested with labels on the map itself. It showed nearly the entire campus pond as well as more of the local buildings.

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.

The map in Figure 1 had a red circle and dot indicating where the images were taken that are not present in Figure 2, likely because of different technology available. The person who recreated the figure panel may not have had access to an iphone, which was used in creating the marks on Figure 1. The map in Figure 2 is an older version than the map used in Figure 1, indicated by the lack of the Design building. Figure 2 used an older map, result of finding different images when searching for a campus map online. The pond in figure 2 has a black outline which is a result of a different map.

Image B in Figure 1 had the windows on Morrill on the right side of the door where image B in Figure 2 had them on the left and the black spot of cement touched both sides of image B in Figure 2, it is only on the right side of the image in Figure 2. The two people who took these images were likely standing in different areas or had the cameras facing a different angle. A different type of camera could have resulted in these differences. The  

Image C in Figure 1 showed the corner of the glass panel with the ucard in the middle of the picture on the left side. Figure 2 showed the front of the glass panel with the ucard toward the bottom of the picture.The angle at which the person who took the picture was different relative to the building.The ucard was held at a different height. The reflection of the person who took image C in Figure 2 is seen and this finger did not have nail polish. In image C of Figure 1, only the reflection of the arm is seen and there is jade nail polish on the finger. The two people were standing at different angles relative to the building, the person who created Figure 2 was head on where the person who created Figure 1 was on an angle. The difference in nail polish is a result of the two figure panels being created by different people.

The factors listed above resulted in the differences found between Figure 1 and Figure 2, because of these reasons the original figure panel was not recreated identically.

Results

    There are many differences in all the figures in the panel.  The differences noticed first were in the actual pictures of the spider web and its habitat.  The spider webs and the trees that the webs were located are completely different. In figure B the original was much larger and easier to see as it contained a leaf and some other debris while the replicate web was clear of debris, much smaller and almost not visible.  The original picture also contained a purple folder with a thumb visible on one side as it is being held up behind the web, the replicate has no background and also no thumb. The trees in which the webs reside are also very different, in figure B and C, the original tree can be seen to be a tree with a trunk and many branches while the replicate tree is more of a tall hedge. The web of the original in figure B is found in the fork of a tree while the replicate web is found on the side of the hedge.  In the original figure B you can also see the setting behind the web a little bit which is not visible at all in the replicate. Figure C original is different too because the replicate picture is taken from a paved lot as opposed to the grass next to mahar.

    More differences were also seen between the editing and the presentation of the map and the entire panel.  Moving to figure A the maps, they are different in size, the original being zoomed in more and lacking a key.  The area circled in the replica is smaller than the original and black font is used as opposed to red in the original.  The letters used to distinguish each figure are large black text in the original while the replica used thin drawn black letters.  The positioning of these letters in the corner of each figure is different between the two figures. The entire panel of the original creates a tall rectangle that has each figure outlined in white.  The replicat is not outlined and creates an elongated rectangle as the images are just placed in a row as opposed to figure A as a tall rectangle and B and C two squares stacked on top of eachother.

Additionally, flooding as a result of hurricanes has become worse in recent years due to climate change. Sea levels have been rising and Houston sits barely above sea level to begin with, so now there is more water creating larger stormsurge potential than there was 100 years ago (Associated Press). The air and water are also warmer, and warmer water leads to increased evaporation occurring. Increased evaporation leads to a rise in air humidity; the amount of water that sits in the atmosphere. When there is more water in the atmosphere, there is more potential water to be collected by hurricanes and then come down as rain when the hurricane makes landfall. This was a key factor in the massive amounts of flooding that occured in Houston after Hurricane Harvey (Associated Press).

Being a city near the coast, Houston has fallen victim to many hurricanes and most recently was devastated by Hurricane Harvey. Harvey tore through the Gulf of Mexico in and made landfall in late August of 2017. It inflicted $125 billion dollars worth of damage, most taking place in the catastrophic amount of rainfall that took place in downtown Houston, which received upwards of 40 inches of rain in just 4 days (Costliest Tropical Cyclones).

A methods section of a scientific paper has the potential to have the greatest impact on the lasting legacy of a scientific paper. The methods section is what is used to replicate a paper’s experiment and serves to try and replicate the results. In the fall 2018 Writing in Biology class offered at the University of Massachusetts, Amherst, a project was assigned to demonstrate this point.  I conducted this project by first writing a methods section that included how to find a previously discovered spiderweb, photograph it and then turn the images into a multi-paneled figure.This was followed by another student in the class being given the methods section with the task of following as best as possible so as to try and produce an identical replicate of the final multipanel figure. Once a duplicate figure was made, I set out to identify observable differences between the two figures and from that, infer what could have caused the differences. I noticed that the figures had differences in the layout and size, the panels had differences in the location of the labels as well as the label’s color, capitalization and border, and there was a difference in the map type that was used. There were differences in the objects in the photos, such as a leg in the replicate, the pen that was used for scale, the amount of visible floor and wall tile, a wooden door in the corner of the photo and how much of the heating duct could be seen. From the observable differences, factors could be identified that may have led to the differences seen. The factors identified were the familiarity with the Inkscape program for composing the figures, the angle of the camera, the distance of the photo taken from the object, and the availability and access to resources. Being able to identify differences in an end product and what may have caused them will be an important part in understanding not only the data that this experiment generated, but data that any experiment may produce. Even if the methods section is written as precisely as possible, small variables may still cause an end product to be different and the ability to recognize what is different and why is how best to understand what the experiment’s results mean.

 

Three main steps were involved in the mutagenesis of the yeast cells. A mutation was induced using UV radiation, initiating the experiment. Mutation was induced on wild-type yeast cells, a andα, which under normal conditions are able to synthesize the important molecules required for survival. Secondly, the yeast cells were selected for and screened for mutations. Screening was done by plating the original Yeast cells onto YED media. These plates were then exposed to UV light, damaging the cell’s DNA. Lastly, the mutants were categorized using complementation. 

In order to observe the effects of mutagenesis, dilutions of yeast cells were placed on a YED plates. The control plate contained a 10⁵dilution of cells to allow for comparison. A second plate, to be exposed to UV radiation contained a 10⁴dilution of cells. The plate containing a 10⁴dilution was then exposed in a UV irradiator for exactly twelve seconds. These plates were then incubated for a week at 30°C. Exactly one week later, to observe the effects of the induced mutagenesis, four mutant samples aW, aX, αy, and αZ and four known mutants, ADE1a, ADE2a, ADE1α, and ADE2α were obtained and streaked onto a YED plate. These were then crossed as shown in Figure 3. The plate was then placed in an incubator at 30°C for one day. After two days, the plate was replicated onto two MV media plates (one containing adenine and the other not containing adenine), and incubated for one day at 30°C. 

The kingdom of animalia may be seperated into protostomes and deuterostomes. Protostomes includes animals such as annelids, molluscs, and insects, while deuterostomes includes organisms such as the echinoderms, hemichordates, chordaes and verebrates. There are 5 main characteristics which separate the protostomes and deuterostomes. During protostome development, the first opening to appear in the blastopore becomes the mouth of the organism. This pore deepens, eventually reaching through the organism, forming the gut and exiting at the anus. In contrast, during deuterostome development, the anus will form first, followed by the mouth. Protostomes cell layers develop slightly offset from one and other. This produces a spiral cleavage pattern. This is unlike deuterostome development, which has a radial cleavage, where the cells are stacked on top of each other. Furthermore cell role is determined very early on in protostome development, while deuterostome cell role is indeterminate. Lastly, the method of coelom development differs between protostome and deterostomes. Protostome coelom development proceeds through a process called schizocoely. During this method masses of the mesoderm migrate and form the coelom. However, deuterostomes perform enterocoely, where the mesoderm folds and pinches off to form the coelom.