Perfect Paragraph

In the fall semester of 2018 in my Writing in Biology Class, I conducted a project where the purpose was to take a picture of a spider web, it’s habitat, and a map of the area.  Then I had to write a methods section being precise enough so that someone else could attempt to replicate my image exactly. After my procedure was followed there were many differences in the original vs the replica.  In Figure A and B they are entirely different as the spider web and the tree itself were different, most likely because of the foul weather all that week. The panel itself was also different in the text used and the shape and size of each picture in the collage.  Figure C, the map, also differed as the replica was the entire map and the original was zoomed in around the area searched. These differences can be attributed to lack of precision in the methods section. The overall panels were very different in the way they were presented and edited.  

When taking the pictures for the figure panels I used 4 elements as controls. The time of day when the pictures were taken at 9:55 in the morning, the ucard was used for scale, the orientation of the ucard was vertical and backwards, and the location of the images was set. A time was given so that the pictures would have similar lighting. The ucard was used for scale because all students are UMass are issued a ucard, so whoever recreated the figure would have one. The orientation and the direction of the ucard was also a control so that the scale would be the same. The location of the figure panel images was also controlled and Morrill was used because this is a building all students in the class know since this is where class is held. Some variables that I identified that could not be controlled include weather, type of camera, platform used to create figure panel, and distance and angle of the photographer relative to the building. Weather is uncontrollable and different weather could affect the quality of the images. The type of camera is also an uncontrolled variable because a standard camera was not used. This also applies to the platform used to create the figure panel. The exact location of the person taking the images is also a variable because the positions were not marked.  

"Sea star wasting syndrome" (SSWS) is a disease that affects many species of sea stars, causing them to lose turgor pressure until they eventually rip apart and turn into white puddles of goo. The origins of this disease are still uncertain, and while most researchers suspect that it is caused by a virus, other scientists like Melissa Pespeni from the University of Vermont think that SSWS is caused by a combination of environmental and genetic circumstances. Pespeni and her team studied the genome of the microbiota present in healthy and sick sea stars, and exposed a group of 37 healthy sea stars to SSWS in order to record the progression of the disease. Only 8 sea stars remained healthy after the experiment, and the results showed that their microbiomes change as the disease settles in, decreasing the numbers of beneficial bacteria in the Pseudoalteromonas genus and leading the way for opportunistic pathogens to cause more damage in the tissues. Pespeni argues that SSWS is most likely caused by pollution particles that disrupt the microbiome of healthy sea stars, allowing for the virus to attack their weakened immune systems.

The project focused around the photography of a spider web, which is why some of the biggest factors in causing discrepancies were camera settings. Figure 2 included more of the environment than Figure 1, which can be seen by more of French Hall showing. The number of feet was given as to where to take the picture of the environment from, so it is possible that the phone used for Figure 2 had a different focal length. If it was specified to use an iPhone 7 plus, this could have been avoided. In addition, in Figure 1 the bush appears to be darker. This was most likely because the flash was on when the photograph was taken for Figure 2. When the photo for Panel A in Figure 1 was taken the camera was on 1% zoom, in the second figure the web appears closer which suggests that the camera was zoomed in.

To better understand how methods are written in the scientific community, a project was undertaken for my Writing in Biology course at the University of Massachusetts Amherst in the fall of 2018. A figure was built consisting of two photos of a spider-web on the UMass campus, along with a map of the location of the spider web. A methods section was written for this process, and fellow classmate followed this. A replicated image, solely based on the methods section was created, and then compared to the original figure. It was found that unless a methods section is explicit on important factors such as the number of pictures, labeling, and figure size specifications, it is difficult to replicate a figure or process. Regardless of this, small differences will be present, highlighting the importance of being explicit in every way possible when writing a methods section.

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.

ABSTRACT

As a part of my Writing in Biology class in the Fall semester of 2018 at the University of Massachusetts Amherst, I conducted an experiment to test the reproducibility of a multipanel scientific figure based solely on the methods I wrote while conducting the experiment. In order to increase reproducibility, I sought to control as many variables as possible while creating my multipanel figure. While writing the METHODS section, I recorded my steps with detail to allow for simpler replication.  The results exhibited variation in areas such as the format of the figure itself, markings on the pictures within the figure, and the content of the pictures. The factors that caused the disparities include differing programs used to create the figure, differing conditions on the two days, and the original spider web no longer being available for photography. The original multipanel scientific figure was not reproduced exactly causing disparities between the replicate and original figure.

One of the new techniques that has revolutionized the genetics field is CRISPR-Cas by cutting DNA. This important discovery provides a way of editing the genome that was applied to DNA in many organisms such as bacteria, fruit flies and yeast. There is an immunity that CRISPR-Cas has by being in bacteria and archaea and are used to defend these organisms against invaders. Scientists have invented a system known as CRISPR-Cas 9 that requires two RNA molecules, crRNA and tracrRNA. At the end it will facilitate the use of gene editing and by recognizing the specific sequence of DNA that works better than restriction enzymes. 

The layout of the pictures and the labels is one of the most obvious differences presented in the figures. This is from a lack of exact actions and clarity in the methods section. The methods said that the images should be “adjusted to about equivalent sizes”, when in actuality, they should have been the exact same sizes. Furthermore, the exact width and height of each picture is provided by the inkscape program and should have been provided to remedy this inconsistency. As far as the labelling, the methods section provides that a red box should be made for each of the labels and a lowercase letter used. It is true that a color was not specifically given for the text. Additionally, the methods section provided where the location of the box and letter labels should go. However, given that the pictures of figure 2 were not the same size, the final adjustment given in the methods section may have distorted the picture further from the original Figure 1. This could also be fixed if the exact sizes of the images were provided.

The very first thing that I did was look up where spiders like to make their webs. I searched "where do spiders make their webs in northeast America. It gave me limited information basicallt saying that depending on the type they can live in many different places from trees to grass to manmade things.  This led me to begin my search in my backyard which is the Newman center and the trees next to the mahar lecture hall. I looked in the volleyball court net next to Newman center and the bulletin board by the entrance of mahar, I found nothing. I then looked in the trees and found a few webs and used a measuring tape to compare the size of each web. The first two were about 5 inches in size and the third one I found was about seven to eight inches in diameter.  I then used the camera app on the iPhone to compare how each web looked in through the camera lens initially without any effects. The third web contained a leaf in it which helped as a reference for size and to help display the web itself. The third web was clearly the best web for the picture so I chose to move forward with that one.