Writing in Biology

Once, I went home and upon entering my house, it smelled like vanilla. This smell is an observation and I inferred that someone had baked cookies. As it turns out, the smell was just a candle. Observations are things determined through the senses, how something looks or feels or smells or sounds. An inference then uses past knowledge to say something about that observation. An inference does not necessarily have to be correct, just a conclusion drawn from an observation. Observations are based in fact and describe how something is actually observed where as any processing of those observations are inferences.

Macromolecules are large molecules that make up everything around us. These macromolecules are composed of smaller subunits known as monomers. Monomers come together to form macromolecules which are polymers of their monomer subunits. These polymers are built from monomers through a process known as dehydration synthesis (1). This happens when one monomer forms a covalent bond with another, forming a chain and releasing water as a by product. There are four different classes of macromolecules. They are carbohydrates, lipids, proteins, and nucleic acids.

The first class, carbohydrates, is made up of monosaccharides, which form into long chains known as polysaccharides. Carbohydrates are important to the human body system because it is where the majority of the body's energy comes from (2). The body uses these foods to make glucose, an important energy source.

The second class, lipids, are molecules that contain hydrocarbons, which make up the building blocks of living cells. Lipids are important because they store the energy that our cells need to perform daily functions.

The next essential macromolecule, called proteins, basically dictate the function of the cell. Proteins can serve as a catalyst, transport and/or store other molecules, control growth and differentiation (3).

To identify the presence of different molecules, you can use a variety of tests. For this experiment, we used the Lipid Test which consists of determining if a certain liquid will leave a grease stain (indicating it is in fact a lipid), to test for lipids, The Simple Sugar Test to test for glucose using Benedict’s solution , and lastly, the Protein test using Biuret Reagent, to identify proteins. Unknown samples in this experiment were tested with different methods describe above to identify their contents.

Tidy datasets have a specific structure

• Each variable in a column
• Each observation in a row
• Each type of observational unit is a table

Data Semantics

• A dataset is a collection of values. Values are organized in two ways (every value belongs to a variable and an observation)

To compile my three pictures into one figure, I used the inkscape software. I imported all three images (spider web with water bottle, full image of the ISB wall and openstreet map of ISB) and resized them to fit each other better. To avoid stretching, I used the “lock” feature (as explained in Dr. Brewer’s video about compositing), and changed the height and width of pictures instead of using the arrows to drag the corners. The picture which displayed a close-up of the spider web with a water bottle for scale had the width x height dimensions of 200 x 357 mm. The openstreet map illustrating the location of ISB was 400 x 314 mm, and the photograph showing the setting (brick wall of ISB where the web was perched) was 200 x 357 mm.

To make my figure, I needed to get a high quality map illustrating the location. Thus, I went to openstreetmap.org and typed “Amherst, MA” into the search bar. Next, I zoomed till Integrated Sciences Building came to focus. I zoomed until the right side of ISB only showed Life Sciences Laboratory and the left only showed till the Campus Bookstore. The upper perimeter cut off at the East Experiment Station and the lower perimeter showed till Peet’s Coffee. When I had a zoomed-in version of the map that I wanted, I clicked on the link to share and downloaded the image in PNG format.

Observation and inference are two terms that are closely associated but should not be confused as synonyms. Whereas an observation is the direct relaying of what happened, inferences are possible explanations behind those observations. Observation is the direct information we have gathered, and inferences are what we can extrapolate from those information using prior knowledge. For example, if we see smoke wafting through the chimney, we can predict that someone has lit the fireplace. The smoke in the chimney is our observation. We don’t directly see the lit fireplace, so this is not our observation, merely an inference stemming from the fact that normally chimney smoke results from a fire.

For easy replicability, it was important that the camera position was something that anyone could achieve. The web picture was taken from between the break in the bushes. This area was used because it was the closest you could get to the web without disturbing it. To include the whole web and the gift card that was used for scale, the phone was held about 1.5 feet above the web. At 1.5 feet above, the gift card that was placed on the bottom right side of the photograph was easily seen. The phone was placed completely horizontal as the web was also flat against the bush. The photograph includes the whole web, but there is also a little bit of space around the edges where there is no web and only needles from the bushes. When it came to taking the picture of the environment, the camera position was at a 90-degree angle. The position it was taken from was about 4 feet right, and 3 feet backward from the web. From this position, the image was able to include the web, all the corner bushes, some of French Hall, a wooden structure that held saplings, and the Permaculture Garden shed in the background. This angle was chosen because it allowed for a lot of nature in the picture, and not only man-made structures such as buildings.

The picture of the spider web was taken on an overcast day. The time of day was 11:55am so the sun was overhead, but not shining bright due to clouds. Although clouds filled the sky, no precipitation had fallen. The air was still as there was no wind. It was chosen to take the picture during this weather because in the fall this weather is present a lot during the Fall. 

When categorizing animal behavior to make an ethogram, there are a few things to keep in mind.  Firstly, if a behavior happens only once or for a short duration of time it would be classified as an event. For example, if I were to do a single push up or throw a ball one time, these would be called events. However, if a behavior were to happen multiple times it would be known as a state. Let’s say I were to do 10 pushup or throw a ball five times, these would be sates since they are prolonged, repeated behaviors. The next important concept is that groups of behaviors can be brought together and called bouts. A bout is a series of movements or behaviors that ultimately reach the same goal. For example, a lion would stalk its prey, chase it down, attack it and eat it. All these behaviors are distinct and separate events, but when looking at the broad spectrum, they are all joined together to reach the goal of feeding and can therefore be classified as a bout. Lastly, it is empirical to make accurate observations and record the data thoroughly so that you can have as accurate an ethogram as possible. Programs like JWatcher allow you to enter behaviors as key codes so that the data collection process is fast and accurate.  

Before starting the exploration for a spider web, I brainstormed some locations that spiders may be present on campus. Initially, I thought to look in the old academic buildings on campus, such as Bartlett, Herter, or the Morrill Science Buildings. It was easiest for me to search in the Morrill Science Buildings first due to my class schedule, specifically Morrill II. When looking for a spider web in Morrill II, I knew to look in areas that were undisturbed. This was because undisturbed areas, such as corners and closets, would give a spider the opportunity to build a web without any complications. I slowly examined each hallway, looking in corners and stairwells. Finally, on the third floor, in the hallway connecting the Morrill II building and the Morrill III building, I came across a concaved rectangle in the wall. The groove in the wall looked untouched for a decent amount of time. I approached the bottom left corner of the groove and found a small spider sitting in the middle of a faint web. I took several pictures of the spider and its web with the flash on. Some pictures were facing down toward the web and some were taken against the left wall to display the definition of the web. The flash seemed to scare the spider further back into the corner, therefore I tried not to take excess pictures. In addition, I took a picture of the hallway the wall indentation was located to orient my reader as to where I found the spider web.