ekirchner's blog

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

Figure Format

• Descriptions inside frame of figure vs. hanging outside
• Border between pics vs. no border
• Aligned images vs. not aligned
• A, B and C labels consistently placed vs. not
• Good arrow color contrast vs. blending of arrow into image

Image Quality

• Consistent lighting vs. sun spots
• No glare vs. glare
• Contrasting zoom and frames between images vs. similarity among images within one figure

Camera angle

• Panel A: One individual leaf vs. bundle
• Panel B: Camera pointed at trunk vs. pointed more upward
• Panel C: Smaller frame of trunk vs. including surrounding ground and separate trees

Wheat is a grass grown throughout the world for its seed, and it makes up the genus Triticum. Three commonname types of wheat are Einkorn, Durum, and Bread Wheat. Einkorn, sicentific name being Triticum monococcum, is a wheat that has one seed per spikelet. A spikelet is teh absic unit of a grass flower with one or two florets on the tip. Einkorn wheat is not widely cultivated, and the glumes fit tightly around the seed, providing a seed covering. Durum wheat, scientific name being Triticum durum, is grown in Spain, Italy, and the US. Unlike Einkorn, Durum has naked seeds with no covering, and it is good for making pasta. Bread wheat, scientific name being Triticum aestivum, has several different subspecies and is used for making bread. A big difference between these three types of wheat is that they all have different chromosome counts. Einkorn has 7 pairs of chromosomes, Durum has 14 pairs, and Bread wheat has 21 pairs. 

Recently in my Animal Behavior class, we were required to listen to a podcast that discussed the bias of scientific research being done. The man speaking was speaking on behalfs of biologists that studied invertebrates. He said that when someone he knew submitted a grant proposal for an inverterbate subject, it got denied. Another scientist then replied to this news saying that it was much harder to get a grant approved when working with invertebrate organisms as opposed to vertebrates, which got a lot of immediate backlash from the surrounding researchers. The speaker said he looked into this and found a very clear-cut gap in the amount of research being done on invertebrates vs. vertebrate organisms. So much research was being performed on vertebartes because scientists feel it relates more to humans and they only care about the scientific development in relation to our own species. The podcast the went on to talk about his story and how he attempted to bring light to this issue. I do not think he got very far in his case, but it is still an issue that needs to be addressed and re-assessed. 

Plants are photosynthetic eukaryotes. Photosynthesis is the act of coverting light energy to chemical energy. Phtosynthesis evolved in bacteria, speficially cyanobacteria, and plants and algae are responsible for most of the transfer of energy in the biosphere. Photosynthetic eukaryotes first developed when an archae-like cell engulfed an aerobic bacterium. This is known as endosymbiosis and created a proto-eukaryote. This eukaryote then englufed cyanobacteria, a photosynthetic prokaryote, which then turned into a chloroplast to produce a photosynthetic eukaryote. The first cyanobacteria were like completely identical to modern-day cyanobacteria because they first used electrons from hydrogen sulfide, which later produced our oxygen-rich atmosphere. 

What is and what is not a plant is very unclear and debated. The main criteria of plants are cellulose in the cell wall, they store food as starch in plastids, they have phragmoplasts and plasmodesmata, and they photosynthesize. This creates a general idea of what is a plant, but there are some algae we consider plants that do not fit all this criteria. Nowadays, what people consider plants are mostly our modern-day land plants and green algae. 

Today I chose my example of phytophagy on campus fo the methods project. Although there will be many factors when directing someone to the phytophagy, there are only a few I can control. For example, the weather was nice today and I went outside at 12 pm to view the plant I am using. I can control the time at which to look for my plant, but I cannot control the weather on any given day. I can also control the exact coordinates of my plant, as well as the angle from which a person views it. I was able to clearly see the phytophagy when standing facing the northeast direction, but standing in front of the plant facing south would not be effective. I can also control the amount of confusion by referencing items around my plant, like the campus pond or the ILC. There are only a few factors I am in control of, so I am hoping that my photos and map will help me out a bit more. 

Today I had a quiz in Bio285, Cell and Molecular Biology I, a class I am in as a senior amongst many sophomores and juniors. The quiz was on basic protein structure and folding, but some of the questions were pretty tricky. The primary structure is the first level of proteins, and it is the sequence of amino acids in a polypeptide held together by peptide bonds. The second level is the secondary structure, which is the folding of the backbone. Secondary structure is held together by hydrogen bonds between amino and carboxyl groups of different amino acids. The third level is the tertiary structure, which is the interacting and folding of R groups. Tertiary structure can be influenced by many types of bonds, covalent and non-covalent, including disulfide, hydrogen, Van der Waal’s interactions, electrostatic interactions, and hydrophobic interactions. The type of bonds formed depends on the polarity and charge of the R groups. The fourth and final level of protein structure is the quaternary structure. This consists of multiple polypeptides interacting together, and they can be different polypeptides or multiple of the same. These are held together by all the bonds mentioned in tertiary structure bonding.