Writing in Biology - Section 1

Panel A

Panel marker A is in the lower left-hand corner in Figure 1 while in Figure 2 it’s in the upper left-hand corner. The size of the letter in Figure 1 is larger and centered while the marker for Figure 2 is smaller and off-center. The image in Figure 1 is upright while the image in Figure 2 is sideways. The lighting in Figure 1 is brighter whereas the lighting in Figure 2 is darker. The leaf in Figure 1 is green and attached to a tree while the leaf in Figure 2 is brown and on the ground. The camera angle in Figure 1 is slightly downward while the angle in Figure 2 is directed straight downward.

Panel B

Panel Marker B is in the lower left-hand corner in Figure 1 while in Figure 2 it’s in the upper left-hand corner. The size of the letter in Figure 1 is larger and centered while the marker for Figure 2 is smaller and off-center. The image in Figure 1 is upright while the image in Figure 2 is sideways. The lighting in Figure 1 is brighter whereas the lighting in Figure 2 is darker. The size of the arrow in Figure 1 is skinny and long while the arrow in Figure 2 is short and wide. Lederle and the PSB are in the background of Figure 1 while Hotel UMass is in the background of Figure 2. The arrow in Figure 1 points upward, while the arrow in Figure 2 points downward.

Panel C

Panel marker C is in the lower left-hand corner in Figure 1 while in Figure 2 it’s in the upper left-hand corner. The size of the letter in Figure 1 is larger and centered while the marker for Figure 2 is smaller and off-center. The circle identifying where the plant was found is circular in Figure 1 and Ovular in Figure 2. The circle in Figure 1 is located in the upper-middle portion of the map, while the circle in Figure 2 is located in the lower left-hand corner of the map. The arrow pointing towards this circle is black in Figure 1 and red in Figure 2. Figure 1 includes landmarks such as the ISB, Hotel UMass and Hasbrouck while Figure 2 does not. Figure 2 includes landmarks such as the PSB, part of Lederle and part of Northeast Residential while Figure 1 does not. 

The find an example of phytophagy on campus, I tried to find a tree that was distinct and easy to locate. I used a tree that was right next to an intersection of two roads, and was not near other trees so that it was obvious which tree it was. I tried to make the leaf I photographed obvious by leaving paint on the leaf so that it would stand out among the other leaves on the tree. I used incskape and included the exact X and Y coodinates, and the width and height of the pictures so that the person replicating could have the same dimentions in their figures. I also included the zoom and the fartherest landmarks on the map so that the maps could have the same zoom and boundaries included. There are differences between the original and the replicate that can be explained by different times of day, different weather, different perspective of the pictures. The formatting differences can be explained by using different computer programs to make the figures.
 

A lab technique in genetics is insitu-hybridization. Insitu-hybridization is used to locate a specific gene in an organism. This technique uses a label to find an mRNA sequence because the mRNA does not leave the cell. The DNA is the same in every cell in the body, so highlighting the DNA would not tell you which cells express a certain gene. The proteins created by the mRNA sequence leave the cells, so this would not acurately tell you which cells are responsible for expressing that gene. Scientists use this method to locate tissues that produce a certain gene, this can be used for different medicines in research. There are other methods that can locate gene expresion, such as using immune cells with radioactive labels. This method does not target the exact cell that the gene is produced in, because the immune cells link onto the protein produced. Both are very useful methods of locating genes and gene expression of protiens.

Neurons are located throughout the entire body, sending electrical signals to trasnmit information to different organs, muscles, or tissues. These electrical signals are produced by the movement of different ions across the membrane of the neuron. Ions have different charges associated with them. Ions usually require different channels or pumps to move across the membrane. The sodium/potassium pump is essential to the movemen of sodium and potassium, obviously. There are various other channels or pumps that are utilized to transfer ions across the membrane. There are "leak channels" that allow ions to flow through the membrane and stay around their equilibrium. When there is enough ion movement to bring the membrane potential about about -40mV, then an action potential takes place. The action potential propogates charge down the neuron's membrane and sends the electrical signal. This happens in the central nervous system, as well as the peripheral nervous system.
 

In the future, I would like to use my biology degree to pursue a career in medicine. With that in mind, bioethics must be considered when approaching life science in the real world. Bioethics is the ethics of medical and biological research. Ethics drive the way we are allowed to behave in different settings, and the science field is no exception. One article illustrates the consideration of bioethics, where five couples are currently lined up for CRISPR babies to avoid deafness. The CRISPR-Cas9 system is a modern gene-editing technique that has not been well tested. It primarily causes a mutation in the germ-line cells, creating a heritable sequence for future generations. There are guidelines in place to make sure that CRISPR is not abused and tested on humans without proper conditions. One such condition is the inevitable death of some diseases. An example includes the editing of HIV-resistant infants. In this case, I think that the editing of infants to get rid of deafness is not life-threatening, so it should not be used and should be considered invasive, palliative surgery. However, moral guidelines may vary from country to country. Russia may have different protocols that may allow them to bypass this issue.

There are many possible explanations for the differences between Figure 1 and Figure 2. The orientation and placement of the images within the figures were different. I did not specify the exact location of each panel within my original scientific figure, Figure 1. I also did not mention labeling each panel, A, B and C, so that may explain the lack of labels within Figure 2. The arrows of each figure also differed in color and placement. This may be due to the fact that I created one of the arrows, the white one in Figure 1, on a different software than the usual editing software, Inkscape. I did not include the fact that I did this in my methods description. 

In the first image, panel A in Figure 1, the original and replicate look differently. This may be due to the fact that the replicate camera was held closer to the leaf than I had originally, or perhaps the student zoomed in their camera to capture the photo while I kept mine zoomed out. The difference in phytophagy spots and leaf shape may be because different leaves were used. It could also be because the replicated photo was taken over a week after my original photo. The leaf could have decomposed slightly or been weathered more during that time, explaining the brown spots on the leaf in Figure 2.

In the second image, the frame was different among figures. This is probably because the replicated photo was taken from a different spot. I specified the direction from which to take the photo in my methods section, but did not specify how far away the photo should be taken from. The person used for reference in this second image was also a different person, a factor that was difficult to control. 

    The third panel of the figures was a map pointing to where the phytophagy was found. It seems that the same map was used for both, but thy were cropped differently which would explain the different frames among the figures. I did not mention how I cropped the map when writing my methods section. The arrow difference between this media in the figures could be because we used different dimensions and drew the arrows differently in Inkscape. 

The orientation of the different images within the figures were different. I did not specify the exact location of each panel within my original scientific figure, Figure 1. I also did not mention labeling each panel, A, B and C, so that may explain the lack of labels within the Figure 2. The arrows of each figure were different. This may be due to the fact that I created one of the arrows, the white one, in my original figure on a different software than the usual editing software, Inkscape. I did not include the fact that I did this in my methods description. 

    In the first image, panel A  in Figure 1, the original and replicate look differently. This may be due to the fact that the replicate camera was held closer to the leaf than I had originally, or perhaps the student zoomed in their camera while I kept mine zoomed out. The difference in phytophagy spots and leaf shape may be because different leaves were used. It could also be because the replicated photo was taken over a week after my original photo. The leaf could have decomposed slightly or been weathered more during that time.

To capture my example of phytophagy, I began at the bus stop directly in front of the Integrated Learning Center (ILC) on the UMass campus. I began walking south down the sidewalk of North Pleasant St, and took a right turn down the path heading toward the W.E.B. Du Bois Library. I walked until I reached the path on the east side, or the side closer to North Pleasant Street, of the campus pond. I turned left onto this path and walked for a bit until I encountered the 3rd tree on the right that has 2011 plaque on the ground in front of it and a label on the trunk reading “Swamp White Oak”. This is the tree I chose. 

I stood on the far side of the tree, closer to the Fine Arts Center, and stood facing the tree and the ILC. Toward the bottom of the branched part of this tree is a bundle of leaves, but not the bundle closest to the ground. This bundle has leaves with little holes eaten out of them, an example of phytophagy, the eating of plants. I oriented my camera so that these holes could be clearly seen and took a picture. I also stepped back toward the Fine Arts Center and took another picture of the tree, in portrait landscape, so that the entire tree could be seen in the frame. I had a person stand beside the tree for size reference. I created a map, with an arrow pointing to the spot of phytophagy I found. After I had my three forms of media, I compiled them into a multipanel scientific figure. 

The goals of the Methods project are to practice observation versus inference, practicing how to write and describe an experiment done so it can be exactly replicated, and identifying and addressing factors that need to be controlled during an experiment. In order to complete all these goals, the student has to create a multi-panel scientific figure demonstrating an example of phytophagy, the eating of plants. This figure includes one close up image of an example of phytophagy, a zoomed out image of the same example, and a map that illustrates where the example was found around Amherst. The student then must document their exact methods and have another person follow and replicate those methods