Drafts

There were control factors I had to consider when writing my methods. The first was the day of the week and time of day, due to Durfee Conservatory only being open Monday through Friday from 10AM to 4PM. The location of the photographer, orientation of the camera, and framing of the subject were also relevant factors, due to the various angles from which my species could be captured, necessitating that I be specific about where the photographs were taken from and how they were taken in order to ensure the replicate images would be as similar as possible. In addition, the particular digital program I used to create the figure needed to be relayed because so many of the details involved in the production were specific to inkscape, and would likely not carry over to a different program. Within the editing software, I had to control for the size, color, and placement of all of the components of the figure, including the photographs, the labels, the arrows, and the background.

The methods section of a scientific article allows researchers to determine the validity of a study based off of replicability. When developing an experiment, certain factors that may affect the replicability of a study should be controlled in an effort to minimize discrepancies between iterations. The Spring 2019 methods project in Dr. Brewer’s Writing in Biology class at the University of Massachusetts Amherst attempts to practice and develop these skills, as well as distinguish between observation and inference through the examination and replication of a multi-panel figure illustrating an interspecific interaction.

The destination of the cattails at UMass Amherst was at the campus pond in the center of campus. To obtain the picture, a student visited the UMass pond during daylight hours and walked down the grassy hill that leads to the pond from North Pleasant Street. The part of the pond where the width is the smallest was approached. This area is past the gravel path that runs along the side of the pond. From about 15 feet away from the pond water border, picture ‘A’ (Figure 1) was taken from shoulder height of the student, with a camera, of a cluster of about 15 cattail plants. The cattail is shown in the center and the background shows the pond water and other tall, yellow, string-like grass that surrounds the cattail and then the edge of the pond makes up most of the foreground.

          In James Cameron's film, Avatar, an alien tribe on the distant planet of Pandora fights the human invaders bent on mining their forest home. In The Nature of Things episode, titled the Real Avatar, the indigenous people of the Cordillera del Condor area of Peru face a similar predicament, as they fight against the Peruvian government and private mining and oil interests to defend their home, in an effort to preserve both biodiversity and their traditional way of life. Though there had been a previous agreement between the tribe and the government to establish a protected conservation area, the election of a new president, Alan García, led to the passage of new laws to open that land to privatization and development in the name of profit. These decrees disregarded the prior promises made to the indigenous people, and instead granted access to corporations, including a Canadian mining company and an American oil company, whose extraction activities threaten to pollute the area. The mountain range where many of these private development projects are meant to take place are comprised of a portion of the Amazon Rainforest, and also act as the sources from which rivers flow. The local tribes rely on these ecological features, traditionally viewing their environment as a living thing which provides for them and which they must protect. 

Fibroblasts, generally, are cells that synthesize extracellular matrix and collagen, thereby providing the structure for animal tissues.  Cancer associated fibroblasts (CAFs) are often present in the tumor microenvironment and have been implicated in angiogenesis.  The authors cite a study in which CAFs released CXCL12 into the bloodstream in a breast tumor xenograft model.  CXCL12 can recruit bone marrow derived cells to the tumor microenvironment. 

Pre-metastatic niches are essentially pre-determined cites that have no implanted tumor cells yet, but have been tagged with markers that will allow tumor cell localization and metastasis.  A study cited by McAllister and Weinberg showed that tumor-derived VEFG-A and P1GF could recruit bone marrow cells not only to the tumor sites, but also to the lungs, which in this case was tumor free at that point but later gained tumor cells.  Upon implementation of these bone marrow derived cells, the lung fibroblasts upregulated expression of fibronectin, thereby recruiting more bone marrow cells. 

Bright, colorful and lively is what I would describe the building if I was ever asked. The John W. Olver Design building that is located at 551 N Pleasent St. is one of my all time favorite buildings to study. The high ceilings, colorful walls and bright lights give the building a very "Ikea" feel to the building. The modern architecture is based off of new and innovative technologies of construction and embrases a sense of minimalism. 

The original figure was screenshotted with no space around the image. The replicate figure has a white border around the entirety of the figure. This could have been caused by taking a larger screenshot. The screenshot may have also captured part of the white microsoft word document, and therefore it could have resulted in the white boarder and white space above the textboxes. The original layout was also much smaller than the replicate layout. This could be due to an increased pixel count in the replicate figure. The original figure had a pixel count of 600, while the replicate figure had a pixel count of 1200. This could have caused the increased size of the figure when it was uploaded. 

Parts to control were the timing of the experiment and weather to make sure the waterfowl were present. Aspects of the condition of the environment were also controlled to minimize differences. The device on which the photos were taken was also controlled to ensure similar quality of images. The position of the waterfowl in relation to the camera and to each other were also controlled. This included the distance from the camera and from the other waterfowl in the image.  The food which they were given was controlled to ensure they would have the same response to the food they were given (this was cheerios). The amount and interval of time in which food was also controlled to make sure there was enough food to take the necessary photos. I noted how the waterfowl were lured together to take the photos to ensure the opportunity to take the photos were the same, considering the waterfowl are mobile. The method in which specific interactions such as when the geese bit one another was noted to ensure a similar image since such interactions were brief. This was done with the screenshot function of the iPhone after a video was taken. Construction of the panel itself was controlled with regard to color of the background for the photos to ensure similar results in the replication. It was noted that green was put to figure A, rose to figure B, purple to figure C, and turquoise to figure D. The labeling was also controlled, the location of the box (size 70x70 pix), as well as the font (Calibri size 20) were controlled too. 

On Wednesday afternoon, my Mammalogy lab section took a trip to Beneski Museum of Natural History at Amherst College. I had never been there before so it was exciting. On the main floor, there were huge skeletons of Ice Age era mammals. There was an irish elk, mastadon, sabertooth cats, dire wolf, cave bear, and a mammoth. They also had cases with skin and hair samples that had been preserved for thousands of years. We learned that many of the fossils there were found by Amherst College expeditions in the 1800s and 1900s. We had a worksheet to do while there looking at the exhibits. For the fossils we had to identify the scientific name (Genus and species) and make conclusions on diet and locomotion based on tooth shape and the proportion of limbs. 

The goal or the mission of this project was to create a figure that illustrated the interaction between the koi fish and plants in Durfree conservatory. The replicated figure completed that task but with small differences in format. In my methods I realized that I did not specify some key components that could have made both figures more identical. I did not specify how many koi fish were to be present in the frame when taking the photo, if it was supposed to be zoomed in or out, or the color of the koi. As for making the figure itself, I did state the scale of the border, but I did not indicate what scale and where to find it on the page. For the arrow, I stated I used “an arrow with a feathered end” and while at the time I thought that was specific, it really was not looking at the style of the other arrows. Overall, both figures used the arrows to point out plant and fish interacting.