Writing in Biology

Writing clear and informative methods allows scientists to replicate experiments effectively. In the Writing in Biology course at UMass Amherst in Fall 2018, I conducted a project to observe and analyze the differences between an original multi-panel figure and a replicated version made by another student. Students in the course created multi-panel figure of a spider web on campus and wrote methods on how they captured and edited the photographs to make the finished figure. Each student switched their methods with another to try to duplicate the other student’s multi-panel figure. I found six differences between my original multi-panel figure and the replicated figure. I observed differences in the photograph of the spider web, the location of the pencil in the photo, the formatting of the figure, the text size, and the placement of the black star between the original and the replicate. Factors such as the angle of the camera, the positioning of the photographer, lighting, the type of pencil used, the interpretation of the methods, and nonspecific instructions led to the differences observed in the two multi-panel figures.

Protostomes includes organisms such as annelids, molluscs and insects. During protostome development the first opening to appear in a blastopore becomes the mouth of the organism. This pore deepens, forming the gut and eventually the anus. Protostomes exhibit spiral clevage in their cells, since each layer is offest slightly. Additionally the cells roles (ie: this cell will be a neuron) are determined very early on in development. The role is chosen, and stays as such in the organisms adult form. The coelom of the organism develops through a process called schizocoely, in which masses from the mesoderm migrate and form the coelom.

Deuterostomes include organisms such as echinoderms, hemichordates, chordates and vertebrates. Unlike the protostome, rather than forming the mouth furst during blastulation, the anus forms first. Furthermore, deuterostomes exhibit a radial clevage, as cells are not offset with each layer. These cells fate and role are also indeterminate. Rather the cells role in the body of an adult will be determined at a later time, usually though stem cells. The coelom of a deuterostome is developed through a process called enterocoely, where the mesoderm folds and pinches to form the coelom.

The causative agent in prion disease is a misfolded protein that causes normally folded protein to misfold and aggregate. This aggregate of proteins leads to brain cell damage and death, although the exact mechanism is not known. This makes prion disease the only known type of infectious agent in which the causative agent is not based in genetic information in either the form of DNA or RNA. One of the commonly known examples of prion disease is Mad-Cow disease, and though there are different types for different species, in humans it is known as CJD. Prions cause whole areas of brain cells to die, which gives the brain the appearance of a sponge and therefore a “spongiform” phenotype.

The term prion, also known as PrP, comes from the combination of the term “proteinaceous infectious only”. It is especially hard to prevent prion disease by any sterilization means because most sterilization techniques are targeted towards DNA and RNA, such as chemical reagents or by heating. This leads to the most common way of contracting the misfolded protein. Although it can spontaneously misfold on its own, the prion is often inducted into a system and then causes other proteins to transform and collect together.

Scientists today still have a difficult time categorizing aggressive behavior in psychology and biology. It is often wondered is aggressiveness is a learned behavioral and emotional trait, or if these chemicals are innate from birth. The social learning theory is a way that scientists try to understand where aggressive behavior comes from; it is known that behavior can be shaped by many different factors. Researchers identified that children would often imitate parents or elders in their actions; for example, if a parent engaged in an aggressive behavior, the child would be more likely to have aggressive tendencies and vice versa. Additionally, they found that children are more likely to imitate behaviors from the parents of their same sex. That being said, boys were more likely to imitate aggressive behaviors to a higher degree. This is most likely due to a mixture of hormones and societal stresses; masculinity plays a big role in how boys gain aggressive behaviors. As girls are less likely to be expected to have aggressive tendencies, they follow their mother’s aggressive behaviors to a weaker degree than males. This theory was tested in an experiment conducted by Ross Bandura. These experimental findings are crucial to understanding how behaviors are learned throughout childhood. This research has opened the door to many other research projects regarding behavior in the future. 

The goal of this project is to describe the procedures used to write a research project paper. The main concept to be gained from this project is the process of producing something and then giving clear and concise instructions on how to reproduce it. The goal should be that someone can pick up your instructions and replicate the experiment you did, if not to the exact detail, then very close. The importance of this concept can be seen in any scientific experiment. Without a replicable “methods” section, a research project is unverifiable. For example, what if Mendel did not give clear instructions on how to reproduce his experiment with peas and traits? There would not have been any validity to his experiment because it is not reproducible (one of the fundamental parts of research).  

A secondary goal for this project is the ability to differentiate between observation and inference. Observing specific details about something, as well as the overall picture is an essential part of science. Distinguishing on whether it is appropriate to make an observation or inference on a situation by situation basis provides a scientist with the tools to figure out what to study/experiment on, and what to just use the simple tool of inference on.

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.

TITLE- 

Reproduced Multipanel Scientific Figure of Spider Web Contains Disparities from Original Figure

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.

The photograph of the close-up spider webs placed in Panel A in the figures are not identical. In Figure 1 a gift card was used for scale, but in Figure 2 a Ucard was used. In Figure 2 the Ucard was placed on the left side of the web, instead of near the bottom of the web like it was Figure 1. In addition, the spider web in Figure 2 was took up less of the figure than In Figure 1 the bush appears darker than it does in Figure 2. Another observed difference in this panel is the web. In Figure 2 the web is more visible than it is in Figure

The figures also included differences which were caused by not specific enough methods. For example, the methods did not mention that a person was walking in the crosswalk in the background. The methods also were not extremely specific when it came to creating the figure. This caused differences in label size, key size, and font size. In addition, it was not specified whether to create a border around the figure like seen in Figure 2. The methods said to create a key, but the font color, size or border thickness were not mentioned which played a factor in the differences between the figures. In addition, the methods mentioned that the location of the web was circled on the map, but it did not say how large the circle was.