Are we in the Smith River Allochthon?: A geologic trope through Gladstone

This week I posed as a Gladstone Gladiator (my research advisory cohort of 4 structural geologists) in the Gladstone quadrangle to gain field experience and help with data collection for their USGS EDMAP project. The Gladiators’ goal is to map the 7.5 minute quadrangle’s geologic components over the course of the next year, and my goal was to practice my field methods over the course of a week. There was no diamictite evident, but most rocks exhibited a fair amount of strain and that satisfied my research theme of the summer just fine.

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Week 3: Sales

On Monday I went to the BayaniBrew Manila office, a rustic two story configuration by the river in Makati. I went over my work schedule with one of my supervisors, Erwin, and then headed back to my apartment to work on the big deck I have due at the end of my internship. The next day I shadowed Joy, a saleswoman, around the city. We stopped at around 20 stores checking the stock, taking pictures of the displays, checking the dates on the available supply, and then distributing reorder suggestion forms. Unfortunately I had to end early that day due to being sick the entire previous night, which I suspect was from a milk tea place I’d tried next to my apartment. Wednesday was a Muslim holiday and I went to Shake Shack with Matt and JD and we spent more time on High Street. Thursday I was shadowing Joy again but this time we spent the day at a newly opened grocery store distributing samples to customers. Joy’s method was working harder not smarter which was frustrating to observe. I also realized how strongly the Philippines represents organized chaos. There are police or guards outside most establishments and you usually have to go through a metal detector and get your bag searched at malls, but they’re not thorough. The traffic takes hours to get through but I haven’t yet seen an accident. And finally, the cleanliness. When we were preparing samples to distribute, I had to suggest the use of gloves, which seemed like second nature to me as we would be handling other people’s drinks. There we were, in a nice, renovated grocery store with meticulously organized shelves and there was no soap in the bathroom.

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Week 2: The Farm

This past week I’ve spent at the GK Enchanted Farm where Bayani Brew resides. I arrived Tuesday and took a tour to learn about the various businesses that the farm supports and what “GK” means- Gawad Kalinga. They’re communities that promote collective involvement and work to reduce farmer poverty. They do this by buying products directly from the farmers at around 2-3x the cost, reducing the middleman and therefore putting money directly in farmer pockets. At the farm I had French roommates who were heading off to spend time in various communities in the Philippines to build for them. Wednesday I shadowed Jules, the production manager at the farm, and observed how the tea is made and the product tasks that contribute to its making. I spent time with the brewers and helped add sugar to the tea, clean pandan, and cap and label bottles. The BayaniBrew brewing method involves cleaning plants, boiling water and leaves, adding sugar, filtering out natural contaminants (like soil and bugs) at least three times, filling bottles, checking the bottles to make sure there isn’t overwhelming residue at the bottom of the bottle, and then finally labeling and boxing. Thursday I spent more time in production and got to see the part of the farm where the tea ingredients are actually grown, then I spent more time in production and then attended a team dinner at Jollibee. Filipinos are OBSESSED with Jollibee. I’d never heard of it but it’s apparently where every kid goes on their birthday, and it’s many people’s favorite restaurant. I played it safe and got a cheeseburger because I don’t like spaghetti or bone-in fried chicken and got many disgruntled looks for not getting something more traditional- they take Jollibee very seriously. That night I went to karaoke with Jules and some French interns and stepped out of my comfort zone and rapped No Diggity. Friday morning I helped Jules with an experiment she was doing to see if they could use a double brewing method, which would save time, energy, and money. I was then off to Manila. 

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Week 3: Modifying the sequences by removing the overlaps and making spatial density plots of TEs across the chromosome

Last week, I generated many histograms of matching ratio of TEs in different families. However, the sequences were mostly fragmented, because there were many insertions inside TEs. Thus, I ran a python script named one-code-to-find-them-all to generate a csv file, containing all the consolidated TE sequences. From there, I calculated the new ratio that the query sequences matched the referential ones. And according to the matching ratio, I categorized intact and fragmented DNA and LTR. DNA transposons with a matching ratio higher than 90% would be considered as intact ones; otherwise, they were fragmented ones. The threshold for LTR was 50% instead. Although the data were from a consolidated TE file, there were still overlaps in the sequences. The overlaps prevented me from getting the precise density of TEs within a certain region of the chromosome. Thus, I wrote a python script to remove all the overlaps. After that, I regenerate the files for intact and fragmented DNA and LTR, and further divided them according to their families. Then I was interested in the density of the intact and fragmented TEs across the genome. That was to say, I wanted to see whether there was a pattern for the distribution of the intact and fragmented DNA and LTR transposons. Thus, I calculated the density of all the DNA and LTR inside each of the windows on the 14 chromosomes separately. I also did the same thing for every TE family. Then I wrote python programs to plot the density plots for all the categories mentioned above. Therefore, for each chromosome, I made a density plot of all DNA and another for all LTR. Furthermore, I also made density plot of each of the 6 families of DNA transposons and that of each of the 3 families of LTR transposons.

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Week 1: Hong Kong and Singapore

This week I arrived in Asia- my very first time on this continent. Within 24 hours of landing in Singapore from the U.S., I was already on my way to Hong Kong with my boss. He introduced me to the employees of his venture capitalist firm and showed me their shoebox of an office in the central part of the city. I was then left to my own devices and explored a little bit of the city. I walked to the botanical gardens and spent some time people-watching in the park. The botanical gardens have an impressive fountain surrounded by benches for those seeking refuge from the clustered city. It was there that I was able to breathe in the Asian air and take a moment to appreciate how far I’d come and the new culture that I had begun to dive into. 

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