Writing in Biology

I entered Morrill 4 south and went up the flights of stairs to the second level. I walked into the hallway and turned to the right, where I saw doors that led to the bridge that connects Morrill 4 to Morrill 2. If you look out at the bridge, on the left there should be a blue sign that has “Morrill 4 South” written on it. Underneath this sign is a blue radiator, where I found the spider web. If you stand facing the Morrill 4 sign and the blue radiator, the spider web is located on the bottom left side of the radiator attached to the pipe and black part of the wall. I placed a ticonderoga pencil on the ground, angled at roughly 15 degrees from the wall. I then held my iPhone, with the bottom of it resting on the ground, about 6 inches from the wall and faced it towards the spider web. I then took a photo of the spider web and the pencil with my flash on. To get a photo of the environment, I stood about 5 feet away from the blue radiator, closer to the stairwell than the doors to the Morrill bridge. I then angled my phone so I captured the blue radiator, most of the rug on the floor, the blue Morrill sign, and the left door that goes out to the Morrill bridge.

The ability to replicate research is necessary in the scientific method as it allows for the validation of experimental findings. With replication research, one can further negate or question the results; this helps connect the research to real world situations. The methods of an experiment are the most important aspect in replicating an experiment, as they they outline the steps taken to reach an outcome. The learning goal in Writing in Biology class is to practice writing clear and concise methods in scientific structure.

In this experiment, students were asked to individually find one spider web somewhere on the UMass Amherst campus and photograph it. Two pictures were taken of the spider web; one picture of the spider web close up and another picture from far away to capture part of the location that the spider web was found in. These photographs were then imported onto a computer and edited into a figure panel that consisted of both pictures of the spiderweb and a third picture of a map indicating the spider web location. Following the figure panel, methods were written explaining the exact steps taken to arrive at the location photographed. Additionally, methods were written explaining the process of making the figure panel on the computer.  

Today in class we learned about the autonomic nervous system. This is the majority  of the nervous system and includes everything that you cannot control, which is most of your functions. The autonomic nervous system is made up of the parasympathetic system and the sympathetic nervous system. The parasympathetic nervous system is the rest and digest and the sympathetic is the flight or fight response. Your body does it's best to keep you centered between these two but different stimulus can alter your state. For example, when you're scared the flight or fight response takes over. Seeing a bear would stimulate the sympathetic nervous system and would lead to increased heartbeat, dry mouth, narrowed pupils, and this system is also linked to the gastrointestinal system. When you're relaxed, the parasympathetic system might take over. This state lowers your heartrate, makes you salivate, and in general you become calmer. The body tries to keep you inbetween these two systems. One of the only ways to affect the autonomic nervous system is breathing. Taking long, slow, deep breaths can lead to the parasympathetic nervous system. You can initiate this state and calm yourself down just by focusing on your breathing. Other than that, the systems are automatic and you cannot control. Like you cannot control what your response to a certain frightening stimulus would be, when scared you either run or try and defend yourself but it is an automatic response that you have no control over.  

Mammals use carbohydrates as a primary fuel during short periods of intense activity, but these reserves can not provide the energy required for travelling long distances like migratory hoary bats (Lasiurus cinereus) do. Instead, the flight muscles get powered by fat stores, which contain more energy per unit mass than carbohydrates and proteins. Bird migrations have been studied more extensively than bat migrations, and it is known that birds seasonally regulate fatty acid transport pathways and oxidative enzymes, increasing their activity during the time of migration. Based on the similitudes between migratory bats and birds, the researchers hypothesized that bat follow similar metabolic pathways and that fatty acid transport and mitochondrial enzymatic activity would be regulated seasonally as well.

The enzymatic activities studied were CPT, HOAD, and CS; while the fatty acid transport proteins studied (only looking at mRNA expression) were H-FABP, FAT/CD36, and FABpm in flight muscles.

Students of Dr. Brewer’s Writing in Biology class were assigned to locate and photograph a spider web and its environment on the UMass Amherst campus. Students then created a multi panel figure including a photograph of the spider web with an object for scale, the environment the web was in, and a map showing the location of the web on campus. Once the multi-panel figure was completed, each student wrote a detailed methods that described the steps taken for capturing their photographs and creating the multi-panel figure. Finally, the methods written were given to another student and that student attempted to make the same multi-panel of the original student. The purpose of this experiment was to see how close the multi-panel figures were and observe the differences between the two.

There are several objectives for this activity. The main goal of this activity was to practice scientific writing, specifically the methods section. Especially in the world of science, it is important for students to have clear, detailed methods. This allows other people to replicate activities and experiments correctly. Additionally, this activity taught students how to make organized multi-panel figures. The overall aim of this exercise was to have students practice writing a clear and understanding scientific paper.

When choosing a spider web to photograph, there were many factors to consider for replicability. Things such as weather, time of day, and lightning had to be considered.

Students in Professor Bergan’s Writing in Biology class were tasked with finding a spider web somewhere on the UMass Amherst campus and photographing it. Students then created a figure including the photographs of the spider web and a detailed map to show its precise location. When the figure had been created, a detailed methods section was written that outlined the steps taken to obtain the photographs and create the figure. Next, the methods were given to another student who was instructed to follow them in an attempt to create a replicate of the original figure. The goal of this experiment was to compare the two figures that had been created by two different students and observe the differences between them.

The main objectives of this task were to practice writing different sections of a scientific research paper, creating clear and accurate figures that could be replicated, and following detailed methods written by someone else in hopes of obtaining the same result. Writing a detailed and accurate methods section about how the figure was created was crucial, and showed just how specific researchers need to be when writing methods sections that will be submitted for publishing. This exercise was aimed to show students how proper writing techniques are both valuable and necessary in the scientific community.  

When choosing a spider web to photograph, several factors had to be considered to ensure the proper recreation of the figure. These included the time of day, lighting, weather, and the type of camera used. The use of an object to represent scale as well as the orientation of the camera at the time of the photograph were key components of the experiment. Also important was the distance at which the camera was held in relation to the spider web and where the person was standing when they took the photo.

When outlining how the figure was digitally created, there were also factors that had to be accounted for to ensure that it could be replicated. The arrangement of the photographs in relation to one another, the borders separating them, and the use of letters to distinguish one photograph from another all had to be described.     Accuracy and attention to detail were essential for this experiment to be successful.

    In this lab, the feeding habits of tetrahymena thermophila were observed. Tetrahymena are unicellular predatory ciliates that live in fresh water everywhere. They feed on bacteria and reproduce both sexually and asexually. In order to examine the feeding rates of the tetrahymena, five samples of glutaraldehyde were prepared. Glutaraldehyde is a solution that kills the tetrahymena without harming their tissues. Five samples were prepared in order to collect samples of the feeding tetrahymena at time zero, ten, twenty, thirty, and forty minutes. After the tetrahymena were submerged into the India ink, samples of the tetrahymena feeding on the ink were put into the glutaraldehyde at those given time periods. After the experiment was finished, the feeding tetrahymena were observed under the microscope at four times magnification. Within each sample, ten different cells were observed and the number of dyed food vacuoles within each cell was recorded. The dyed food vacuoles within the cell show that the India ink was consumed by the cell due to the process of endocytosis that was performed in order to obtain food. As the forty minutes progressed, we noticed that there were more dyed food vacuoles within each cell than in the earlier observed time periods.

Students were tasked with finding a spider web somewhere on the University of Massachusetts campus and photograph it. In addition to this, students were tasked with creating a figure using these photographs, which included a map for reference. A detailed methods section describing where the spiderweb was photographed and the specific approach used to photographing and editing figures needed to be written. These methods were to be followed by another student, with the attempt to recreate the original figure. Once a replicant was created, students had to observe differences between the figures.

The goal of these tasks was to simulate a research report, giveing students practice at writing them, as well as creating figures for the report. Following another students methods demonstrated the need to be highly specific and precise when describing what is done. Overall, this project was designed to help students understand how to more accurately present and describe their methods in a well written research report.

When taking photographs of the spiderweb, there were a number of factors to control for in order to obtain similar pictures. Things such as the time of day, amount of light, and weather needed to be accounted for. In addition to this, the object used for accurately representing scale had to be noted, as well as where it was held in relation to the spider web. Furthermore, distance from the spiderweb, and the angle at which the photograph was taken had to be taken into account.

Similar factors had to be controlled when describing the editing done to create the figure. The size the photographs were scaled to was noted, as well as their general arrangment. How labeling was implimented on the figure was to be controlled. This included the color, font sizes, and location of the labeling.

To find the spiderweb, I left class on Friday afternoon around 4pm and took a left out of the doorway, walked to the end of the hall, and took another left towards the stairs. Friday was a sunny day with a high temperature around 60 degrees Fahrenheit.  I walked down one flight of stairs when I came to the back entrance of the Morrill Science Center. I took a left out of the doors and walked in the parking lot between shade tree lab and Morrill until I passed Morrill 2 and was in the small parking lot across from Morrill 4 South.  On the opposite side of Morrill 4 South, there were 4 parking spots with a brown rock wall on one side. About 75% up the wall above the curb that lines the right side of the parking lot there was a spider web between two stones. The spiderweb was between the 9th and 10th stones, counted up from the curb.  The spider web was attached to three smaller rocks and one bigger rock. There was a piece of tan material stuck within the spider web, making it stick out.

To take the first vertical picture, I got much closer to the web. Only the 4 rocks surrounding it and the full length of the web were shown in my photo I angled my phone’s camera directly at the web, from the left side.  I made sure my phone was focused on the web and not on the rocks, so the left barrier rock was blurry in my image. Directly in the middle of the top quarter of the picture was the small tan filament. Where the middle rock in the photo turned was slightly right to the direct middle of the frame.  The angle my camera was at makes the rocks look like they are pointing at about a 15 degree slant above the horizontal. The lower right hand side of the web has a light brown coating over part of the web.

I then began to make the  map. Using scribblemaps.com I located the parking lot in which I found the spider web. I then began to label “Morrill IV South” at 42.390238005 degrees North and -72.524533868 degrees West.  I did this by clicking the “abc” button in the top left corner and then putting the label in around the place I wanted it. Then, I clicked on the label and entered desired latitude and longitude.  I followed the same process to label “Wilder” at 42.390352903 degrees North and -72.523756027 degrees West. I then labeled “Morrill II” at 42.389915101 degrees North and -72.524363548 degrees West.  And finally I labeled “The University Club” at 42.389897272 degrees North and -72.523683608 degrees West. The resulting shape was a horizontal rectangle.

I then labeled the place in which I found the spider web. I searched for the University Club and a map of the area came up.  I placed the gray cross directly in front of the red car in the set of 3 cars on the map. I then selected the small circle tool in the top left toolbar on the website.  The area of the circle I put on the map was 85.71 meters squared with a radius of .01 km and a circumference of .03 km. At first, the circle showed up with a red outline and filled in green.  I selected the eraser tool and clicked on the middle of the circle to erase the green and leave a red outline. To obtain the map I kept the cross directly in the middle of the circle and zoomed in all the way to that point. From there, I clicked the negative zoom button twice.

I then started the screenshot of the map by clicking Control+Command+4.  I started my mouse in the top left corner just under the settings box and between North pleasant street and the sidewalk.  I then dragged the mouse to the right over to Stockbridge Road. I then dragged the mouse down past the lower labeling of Stockbridge Road on the map.  That saved the image to my desktop.

To take the third picture, I put my black sweatshirt down on top of the ledge and focused the camera so that the University Club was in the top right corner of the frame.  The picture was vertical. The 5 windows on the northern facing side of the building were visible in the shot, but only one second floor window and one first floor window were visible on the Western facing side.The fence was also visible in the frame.  While there was some space between the right end of the fence and the edge of the picture, the left side of the fence was not visible in the picture. There were 15 black fence posts visible in the frame with my black sweatshirt folded partially blocking the view of the bottom of two leftmost posts.  Since I took the picture at a slight angle, the right hand side of the frame goes up to about the middle second floor window. The left hand side of the frame only goes up to what would be the equivalent of the top of the first floor of the University Club if a line had been drawn from the left top corner of the picture over to the house, running parallel to the brick wall. The bottom left hand corner of the picture was almost touching the bottom of the brick wall on that side.

I took the vertical pictures on an iPhone 6.  I created the map with scribblemaps.com. I made the .png file with the pictures in Powerpoint.

Using Powerpoint, I dragged the three pictures onto one slide and organized them in the following order left to right: zoomed in web photo, map, and surroundings of web.  I then deleted the existing text boxes. The pictures were aligned so that their size could be maximized while still being next to each other with a small margin. I made the two vertical photos the same size and centered them to the horizontal photo and I centered all of them to the middle of the slide.  I then added small text boxes to the lower left hand corner of each photo. I made the zoomed in photo: A, the map: B, and the surroundings photo: C. I then highlighted each of the letters and clicked on the black A with the red line under it, making the letters red. I then clicked the insert tab and then shapes button to select the “right arrow” to point from the left side to the web.  The size of the arrows in my photo was comparable to the size of one of the stones. I then selected the “down arrow” to point to the location of the spider web from above. I made the “down arrow” about the same size as the “right arrow”.

In the two figures I was given to examine (#15), there were several differences.  I can infer that the differences that I observed were most likely caused by a minor lack of detail in the original methods causing the replica to be slightly different.  

The largest difference that I noticed involved the flower.  I observed that the flowers had different stems: one curled up and away from the main stem and the other came from the stem at an almost 90 degree angle. I can infer that the methods must have not included the angle of the stem.  In the original picture, I observed that that the orientation of the flower to the stem was stem on the right and flower on the left of the picture, but the replica picture had the opposite. I can infer that the orientation of stem to flower was not detailed in the methods.  In the background of the first picture there are several large flowers at the top, but in the second picture the flowers in the background are mostly below. I can infer that the methods did not include the angle at which the picture was taken or what the background would look like.

In the second picture, the results are strikingly similar.  Since the tree is the same exact tree and both pictures were taken in daylight, I can infer that these were well illustrated in the methods.  The one difference I observe in the pictures is the amount of water on the wall. I can infer that that was probably not an error in the methods, but just a product of chance that it rained that day.  

The third picture is a map highlighting the countries in which these species are found.  The first map highlights Florida, but the second does not and the second highlights Belize and Guatemala, but the first one does not.  A factor that caused the difference in the two maps is a difference in research.

In the two figures I was given to examine (#15), there were several differences.  I infer that the differences that were observed were most likely caused by a minor lack of detail in the original methods causing the replica to be slightly different.  

I observed that the flowers had different stems: one curled up and away from the main stem and the other came from the stem at an almost 90 degree angle.  In the original picture, I observed that that the orientation of the flower to the stem was stem on the right and flower on the left of the picture, but the replica picture had the opposite.  In the background of the first picture there are several large flowers at the top, but in the second picture the flowers in the background are mostly below.

In the second picture, the results are strikingly similar.  Since the tree is the same exact tree and both pictures were taken in daylight,  The one difference I observe in the pictures is the amount of water on the wall.  

The third picture is a map highlighting the countries in which these species are found.  The first map highlights Florida, but the second does not and the second highlights Belize and Guatemala, but the first one does not.

Inferences

The areas that I believed had the most discrepancies were the flower, the angle and background of the photos, the differences in countries filled out in thedescribing the flower, explaining the angle and background of the flower, and

I can infer that the methods must have not included the angle of the stem.

I can infer that the orientation of stem to flower was not detailed in the methods.

I can infer that the methods did not include the angle at which the picture was taken or what the background would look like.

    I can infer that these were well illustrated in the methods.

I can infer that that was probably not an error in the methods, but just a product of chance that it rained that day.

A factor that caused the difference in the two maps is a difference in research.