UNDERGRADUATE RESEARCH BLOGS
The Office of Undergraduate Research sponsors a number of grant programs, including the Circumnavigator Club Foundation’s Around-the-World Study Grant and the Undergraduate Research Grant. Some of the students on these grants end up traveling and having a variety of amazing experiences. We wanted to give some of them the opportunity to share these experiences with the broader public. It is our hope that this opportunity to blog will deepen the experiences for these students by giving them a forum for reflection; we also hope these blogs can help open the eyes of others to those reflections/experiences as well. Through these blogs, perhaps we all can enjoy the ride as much as they will.
EXPLORE THE BLOGS
- Linguistic Sketchbook
- Birth Control Bans to Contraceptive Care
- A Global Song: Chris LaMountain’s Circumnavigator’s Blog
- Alex Robins’ 2006 Circumnavigator’s Blog
- American Sexual Assault in a Global Context
- Beyond Pro-GMO and Anti-GMO
- Chris Ahern’s 2007 Circumnavigator’s Blog
- Digital Citizen
- From Local Farms to Urban Tables
- Harris Sockel’s Circumnavigator’s Blog 2008
- Kimani Isaac: Adventures Abroad and At Home
- Sarah Rose Graber’s 2004 Circumnavigator’s Blog
- The El Sistema Expedition
- The World is a Book: A Page in Rwand
6.24 – Burnham Nature Sanctuary (Chicago Park District)
This is my favorite site so far – absolutely gorgeous, lots of beautiful flowering plants, even though this site is right in Hyde Park!
Burnham Nature Sanctuary
The white flowers are Penstemon digitalis (Foxglove Beardtongue), a hardy native which I’ve written about previously. The purple blooms are the beautiful Tradescantia bracteata (Spiderwort). We found young Tradescantia too, which look like a hairy, fleshy grass. The yellow flowers are Rudbeckia hirta (Black-eyed Susan), which have distinctly hairy leaves.
Blooming Monarda fistulosa (Wild Bergamot)
I know this plant as bee balm from back home on the east coast. We hadn’t seen any blooming until we reached this site, but it sure is pretty! As you can see from the two pollinators in the picture, it lives up to its common name! It’s in the mint family, and like all mints has a square stem and opposite leaves. It is a native to the US, although sadly during this project I have realized that most of the wildflowers I grew up with, such as Daucus carota (Queen Anne’s Lace) are actually invasives 🙁
Rudbeckia hirta (Black-eyed Susan)
These two Rudbeckias are at two different stages in their life cycles: the left one still has anthers, and in the right one they have already withered away after use. The anthers are pollen-bearing segments that stick up, visible on the disk (central, dark brown) flowers here. You can see the anthers as dots on the disk in this picture from above, although they do stick upwards from the flower.
And to finish off this entry…
A mutant Rudbeckia hirta!
Pretty funny-looking, huh? Surprisingly common at this site!
The beginning of the end…
Today marks the beginning of the end of germination for the prairie restoration plants I will be working with this summer. Among the four species I am working with two are sufficiently planted and two have been partially planted in the hopes that other seeds with germinate.
These are the seeds in agar petri dishes in an incubator to induce germination.
Initially, two or three populations of four different species of seeds were placed on agar and have gone from cold to warm environments to start the germination process.
These are some of the different seeds on agar.
Today, most of the seeds have germinated and have been planted in cone-tainers. Already I have been recording first leaf dates as the seeds begin to grow.
The two above pictures show sections of the cone-tainers the hold the growing plants. The toothpicks indicate which ones have a first leaf date.
As the summer goes on the plants will continue to flourish and thirty-five days from their germination I will take functional trait measurements.
Shortening the Boot Time – Why Bother?
To give a better understanding of the “big picture” of my research, I’d like to talk about why I am doing this. Shortening the boot time of a computer seems nice, but not necessary. An important application that I’d like to focus is its application in data centers.
The demand for large data centers has been rising along with the Internet boom. Starting with the familiar consumer-facing social medias like Facebook, Twitter and Instagram to larger business-facing services like Amazon AWS and Akamai, services need a lot of servers to operate. These servers reside in a space called data centers, which consist of thousands of computers. Every time we post a photo on Instagram or watch a video on Youtube, we’re communicating with one of these servers.
One thing to note about servers in a data center is that they are left on all the time, even when they are not being used. On average, 90% of the servers in a datacenter are idle (not doing anything). The reason for this is mainly because of unpredictable peak usage from the consumer side. If 90% of these servers are turned off and then suddenly the number of users increases, the service cannot meet the needs of consumers. (Who wants to wait a minute for a Google search, or 3 minutes for a photo on Facebook, or 2 hours for a video on Youtube? Certainly not me) This can result in a serious damage to the company’s business, so data center operators are hesitant to turn off any servers even if they aren’t being used.
The result of idle servers lead to an enormous power consumption. A report from the Natural Resources Defense Council says that U.S. data centers consumed 91 billion KWh of electricity, which is enough to power all of New York City’s households twice over.
Researchers have been focusing on algorithms that try to turn off idle servers. An example is AutoScale, a policy based on leaving a “padding” of idle servers. Servers cannot be turned off easily because servers take a very long time to boot – usually around 300 seconds. In order to bridge this gap, AutoScale leaves on extra servers on and turns off the rest, and when there is an increase in the request, more servers than needed are turned on, while the excess servers are dealing with the increase in request.
The idea of my research is that if the long boot time of servers – 300 seconds currently – can be brought down to few seconds, fewer “extra” servers can be left on when adopting policies like AutoScale to actual mechanisms. Eventually this can lead to a more realistic and efficient adaptation of algorithms like AutoScale, contributing to saving energy consumption of data centers.
6.22- 6.23 – 41st St Bioretention (Chicago Park District)
First soil sampling site!
Soil corer and cooler containing sampling bags (plus our plant ID books)
A beautiful site (although we got rained out the first day of sampling.) Right between the beach and Lake Shore Drive, so I suppose only a beautiful view on one side, but still!
41st St Bioretention, Chicago Park District
You can see our transect tape running through the right side of the picture. This site is a pretty young restoration, which we could see by the clumping of the plant species which hadn’t had enough time to spread out. There were a whole bunch of Red-winged Blackbirds, who weren’t so happy that we were there but refrained from dive-bombing us. It was a small site and unfortunately had a lot of weeds, such as Medicago lupulina (Black Medick), a small clover with a little yellow flower.
My first soil samples were a success! Since this site was so close to the beach the layering in the soil is very clear in the corer. Cores are going to be 15 cm across all sites as a standard measurement.
Soil core from 41st St Bioretention
First soil sample!
And I found this little guy too! I keyed him out and he’s native from the midwest to the eastern United States.
Datana contracta (Contracted Datana)
Callaloo Country
After one week of interviews and 40+ hours of transcribing, I am nearer to answering my questions. And the answer may well be that there is no one answer. History is selective. Ask any Native. And narratives are also selective in what they reveal, but the people I have spoken to in and out of my research interviews each provide their own piece of the puzzle. As exhausting is it can be, I look forward to learning more, seeing more, and hearing more about identity in the Caribbean, indigenous islanders, and prospective research endeavors.
As I begin busting the black box of racial categories, indigenous identity is becoming important in the argument for cultural rather than racial or blood- linked categories. History did not begin in 1492, or 1498 in Trinidad’s case, and race does not start or end with my research, but I have to explore an immense terrain of literature and perspectives in order to understand where Trinidadian identities come from and where they are going.
A Day in the Life: We’re Not in Indianapolis Anymore
Since I last updated, I hopped on a bus to see Rio de Janiero, returned to Sao Paulo, had a three day lay over in Lisboa, and arrived at my next research site – Barcelona. I’ve been on the move a lot, and I wanted to paint a picture of what so much travel is like.
Living out of one bag (the Osprey Porter 46) in hostel dorms in different cities with different languages is much different than the life I normally lead. Go figure. I have much less privacy, everything takes more effort than it usually does, and I am constantly exhausted. The hostels I’ve stayed in have all been fine (the online reviews I have provided range from 84–97 percent). For those who are unfamiliar with hostels, they are basically hotels but instead of providing a room, they provide a bed in a dormitory that has anywhere from 4-12 beds, a shared bathroom, and a locker for your things. They usually cater to younger people (groups of backpackers, gap year students, and young couples) and often arrange tours and other activities for travelers. Here are a few entertaining tidbits from my travels so you can get a glimpse of what life traveling alone is like.
Here I am on Pão de Açúcar, with Christ the Redeemer in the background.
– One morning I was awoken to a 300 pound construction worker climbing onto my bed because he didn’t think it was important to use the ladder that was six inches away from his feet.
– Aforementioned construction work was part of a group of six 300 pound construction workers who drank heavily and snored even more heavily. Ear plugs are a must every night in a hostel.
– Getting around cities can be hard (especially Sao Paulo) so I spend at least 27% of my time working on transportation. This includes finding WiFi to use Google Maps, buying tickets for the metro, asking for directions, checking maps, and locating street names. Of this 27%, I would say 60% of that I have next to no idea where I am. It’s an adventure.
– I’ve become very good at asking for directions in Spanish and Portuguese. Unfortunately, I am much less skilled at understanding the response. For instance, I’m in a coffee shop right this very moment that may or may not have been recommended to me by the woman at the front desk of the hostel. She said it was to the left and on a corner (A la izquierda y está en la esquina). So I am nearly certain I’m at the right place. Regardless, good coffee.
– Even now that I’m in a Spanish speaking culture, I still haven’t broken the habit of saying “Thank you” in Portuguese. I have confused a lot of people here when a clearly American traveler speaking a moderate level of Spanish replies to something in Portuguese.
– Walking around cities, I have frequently been offered illicit substances for my consumption. A quick step and a firm “no” usually takes care of this. But it is impressive how bold these business people are.
– I take a lot of selfies.
– This morning, a loud Australian man walked into the dorm fifteen minutes before noon. His friends all exclaimed “Oh you made it back! We were a bit worried about you.” He’d been out all night. Upon his return, he suggested they go to the casino tonight.
– Finding food often takes the most effort. If I’m going out to eat, I don’t want to end up a tourist trap or get a bad meal, so research (often in a foreign language) is required. If I ask for a recommendation, it is always possible that I ended up somewhere else accidentally if there was a breakdown in communication. (Definitely happened in Portuguese, but I’m much more competent in Spanish.) If I want to make food, I have to find the grocery store (Onde fica o supermercado mais preto de aqui?) There’s limited storage space in hostels, so I only buy for one or two meals, and there’s also high demand for kitchen space.
One of the wow moments – a view of Copacabana Beach, Rio de Janiero during my morning run.
I may have illuminated some of the struggles of traveling above – and there are struggles – but the trip has been amazing thus far. I’ve learned countless things being in these cities and getting to converse with people from different cultures. I could (and will!) provide a post with a long list of the highlights and the wow moments, but I thought some of the mishaps may be more humorous and more insightful.
I’ve just scheduled my next interview in Barcelona for this week, where I’ll be meeting with a group of professors who are working on gender issues on their campus.
Newcomer’s Nerves
As with anything, approaching something new is always difficult; whether you welcome the difficulty is a different matter. I, for one, was anxious for essentially an entire quarter about starting science research. So anxious in fact that I came in a few days before I was supposed to start to fill out two sheets of paperwork that easily could have been handled in the first hour. My friends had already began research during the school year and felt comfortable in their labs, taking their own lunch breaks, doing whatever processes were necessary for their experiments. But, I still had/have worries over beginning my experiment. Where do I begin? Where do I order mice from? Where do I order their chow from? How do I weigh them? I haven’t even touched a mouse yet.
The thing is, the people in my lab, and any lab, are extremely great resources. Though I still have all those questions, they make sure I practice techniques (such as using the micropipette), learn new processes I am unfamiliar with (PCR and qPCR), and they continue to make sure I am going in the right direction. After all, I have 8 weeks to learn everything I need to for my experiment. I have my first in-person animal training tomorrow and though I am nervous the mice won’t like me, I have come to terms with the fact that I probably won’t be the next mouse-whisperer because I know I am in good hands no matter what I’m doing.
On a different note, I feel like I would enjoy writing about the different processes I learn. After all, it is a science blog. For any prospective researchers, maybe this will give you an idea of the things you might learn in lab, and labs you might be interested in. This past week has consisted mostly of learning how to do several processes, mainly PCR and real-time PCR. For anyone who has taken the genetics course in the biology sequence, PCR is used to amplify DNA. In my case, we amplified the DNA in mice tail tips to determine their genotype.
First, we have to extract the DNA from the tips. Then, once we have the DNA, we can run either a PCR or a real-time PCR (qPCR). qPCR differs from PCR in that we can detect amplification much earlier (thus, real time) rather than after the entire process is completed. Both use primers, dNTP’s, a buffer solution, and DNA polymerase. For regular PCR, we use master mix (DNA polymerase), a forward primer and reverse primer (to initiate replication of both strands), and water. Another very important part of any science research is concentrations of the solutions you are using. After putting our solution together, we pipette the master mix solution into each DNA sample. After vortexing and centrifuging the DNA samples, we let it run in the thermal cycler, which actually carries out the amplification process. While that’s happening, we make the gel for the gel electrophoresis. Something I realized very quickly was that we have to actually make most of the things we simply read about in the textbook. We use a previous gel and heat it up until it is a clear liquid and add in ethidium bromide (carcinogen, aka use gloves!). Then, we pour the gel into the electrophoresis apparatus with two plastic combs with teeth to create wells. After a lot of waiting, we take out the combs and add the buffer and DNA. We let the machine run voltage through our samples to separate the DNA into strands of different sizes and, again, wait. After that’s done, we have the completed product. Now, all that’s left is to look at the gel with a UV light to see the bands and from there we can determine the genotypes of each sample. Though qPCR is very similar, it presents its own learning curve and challenges, so I’ll probably write about this next time. For now, I am going to take a lunch break with my friends and fellow summer science researchers.
Getting started
Not many know what goes behind the scene when we press the power button on our computer. Fewer people know that the time it takes to fully boot a computer is affected by legacy code in the BIOS, making our brand new machines to go through through the very same steps that early computers in the 70s went through. Regardless, our personal computers boot fast enough – perhaps a minute or two at the maximum. However, the story becomes different when we’re talking about huge server racks in data centers. Bringing down the boot time of the servers has a range of applications, one of them being a potential reduction in the power consumption of large data centers.
This summer I will be conducting a research to prove that it is possible to bring down the boot time through virtualization. More specifically, by replacing the BIOS firmware with a kernel that is small enough to fit in the ROM where the BIOS usually resides but capable enough to launch a virtual machine monitor, which will run the server OS as its hosts.
I anticipate this blog’s posts to be little more technical/jargonish than what most people are used to, so I will try to not only post the progress of my research but also background information on the topic from time to time.
Introduction
The circadian rhythm is a mechanism that allow organisms to synchronize their internal physiological systems to their external environment. Our brain has an internal biological clock that synchronizes other biological clocks in our bodies, such as in our heart, pancreas, fat tissue, kidney, and liver. In 2009, researchers in the Turek Lab discovered that mice fed a high-fat diet during the light phase (mice’s irregular feeding phase since mice are nocturnal) gain significantly more weight than mice fed a high-fat diet during the dark phase. However, the experiment only tested male mice. In 2015, researchers found no significant difference in weight gain between daytime-fed female mice and night-time fed female mice. My project aims to identify a cause for the difference in how male and female mice gain weight by testing the effect of estrogen. Estrogen is a hormone that reduces food intake and body adiposity while increasing energy expenditure. Previous research has shown that a decline in estrogen levels may be associated with irregular internal circadian rhythms. Furthermore, studies have shown that ovariectomies have shown an increase in body weight while estrogen treatment after an ovariectomy showed a decrease in body weight. To study the effect of estrogen, I will study the weight gain in normal female mice compared to ovariectomized female mice on different feeding times to see how estrogen and circadian timing of feeding affect weight gain together.
This blog will likely be a place for me to share experiences of working in a science lab for the first time, learning new procedures, and any other challenges that may come my way.
Some of my Favorite Things
Note: I wrote this post Monday, but I’m posting it on Wednesday. Adding pictures takes a surprisingly long time, and I ran out of time to add pictures on Monday. I’ll write another (more up-to-date) post soonish maybe! But it might not have pictures, haha.
Since today (Monday) marks the first day of the first full week of classes, and I will have more homework than I had anticipated based on Friday’s classes, in this post I will only talk about my favorite parts of each of the past few days. As promised, I will talk about what I’ve been learning and the beauty all around me that I’ve been lucky enough to enjoy. I’ll start with this past Saturday.
Saturday morning, a couple friends and I walked from our dorm to a famous brunch place near Rümeli Kale (Castle), aka Rümeli Hisarı (Fortress), a fortress built by Ottoman Sultan Mehmed II between 1451 and 1452 that helped him conquer Constantinople in 1453. (Thank you, Wikipedia, for the knowledge, and thank you, this blog, for motivating me to look up the histories of places I visit.) George tried to take a selfie with the castle, but he’s not very good at it yet. 🙂 The brunch place had an amazing view of the Bosphorus, and even more importantly, it had amazing food. Turkish breakfasts normally consist of lots of bread with various things you can put on top, including different cheeses and jams; a plate of cucumbers and tomatoes in olive oil and salt; if you want to be fancy, egg dishes such as socuklu yumurta (eggs with special Turkish sausage) and menemen (soft scrambled eggs with lots of tomatoes, spices, and some other vegetables); and, of course, Turkish tea! After breakfast, we walked along the Bosphorus from Rümeli Hisarı back to Bebek and took a ton of pictures. It was a beautiful day – sunny and warm after a cool and rainy week, and thankfully not too hot. The Bosphorus sparkled in the sun, gorgeous yachts and sailboats were docked at shore, and quaint cafes and impressive houses lined both sides of the water.
My second favorite part of Saturday was walking from Bebek to Ortaköy (still along the Bosphorus, but in the opposite direction of Rümeli Hisarı) in the evening for dinner. I mentioned this trip in my previous post, but only in the context of feeling unsafe as a young woman in a small group of young women walking around Istanbul at night. But besides from feeling slightly unsafe at times, it was a wonderful evening. The Bosphorus was just as beautiful as it had been earlier that day, but in a different way – mini cruise boats with sparkling lights dotted the length of the canal, and beautifully-lit buildings sprinkled the dark hills on either side of the water. It was invigorating, albeit tiring, to walk the three miles from Bebek to Ortaköy, and we were rewarded at the end with a dinner of kumpir, the Turkish version of a baked potato. We ate and sat right next to Ortaköy’s famous mosque, and then we headed back to our respective neighborhoods.
On Sunday I spent most of the day alone, practicing flute, doing homework, and relaxing. My favorite part of the day was when I got back from shopping, sat on my balcony, and ate chocolate ice cream while reading a book for fun. Because it was a more solitary and laid-back day, I had time to reflect on all the socializing with new people I’ve been doing. Although I’m 21 and have been in a fairly large number of situations where I’ve had to build an entirely new group of friends, it still surprises me to notice patterns in the types of people I most gravitate towards. In other words, no matter how old I get (though I know I’m still pretty young), I don’t think I’ll ever stop learning things and being reminded of things about myself. I’ve ended up spending most of my time with very nice people. They are many things other than nice – including smart, funny, weird, cynical, optimistic, extraverted, introverted, etc. – but the characteristic that they all most obviously share is their kindness, or specifically, the fact that they immediately appear warm to others. (Many people who are more reserved than warm upon first encounters are quite kind, but they are not the people with whom I spend most of my time.) This shouldn’t surprise me, because when I think about my best friends in other walks of life (high school, college, etc.) they are also all very kind people. However, I am still a bit startled by this trend I notice in myself, and perhaps a bit unsettled. I think the unsettled feeling comes from a stereotype that very nice people are either not too smart or not too interesting. And I think this feeling is exacerbated by my own insecurities regarding how smart, interesting, etc. I appear to other people, since in my experience the first thing people comment on in regards to my personality is my kindness. Furthermore, I am insecure about the fact that I get along best with initially-warm people. Does this mean I have too thin a skin and am not strong enough to handle people with slightly colder exteriors? Does this mean I am weak and limited in my interactions with others? But of course then I remember that most people do have a “type,” and the ones who feel extremely comfortable with most types of people are few and far between. Furthermore, I do not wish to indulge my insecurities, and in fact I do get along well with most of the people I’m meeting, even if I don’t feel super comfortable around all of them. Finally, despite some of the less-than-positive thoughts that this new experience is inspiring, I am still glad for the opportunity to reflect and learn about myself.
Relaxation/Reflection time:
Last thing for today: My favorite part of Monday was the Tanışma Kokteyli, aka a Getting-to-know-people Cocktail Hour (rough translation). The TLCP hosted it on the university’s South Campus at Kennedy Lodge, an absolutely beautiful building with even-more-breathtaking views of the Bosphorus (from a hill, not from water-level like the views in Bebek, Ortaköy, Rümeli Hisarı, etc.). The program paid for an open bar (the drinking age in Turkey is 18, no surprise there) and very delicious hors d’oeuvres. It was lovely getting to talk to many people in the program, not just those limited to my class of 11 (11, not 9, for those keeping track, now that two people joined us who weren’t in class Friday). One of my friends got rather drunk, but he was the kindest, most good-natured, and most entertainingly-philosophical drunk I’ve ever known. (He is a very kind and good-natured person, so it makes sense.) The most interesting thing he said was that although he doesn’t agree with Turkish President Erdoğan and Prime Minister Davutoğlu’s politics (conservative and non-secularist, in case anyone is wondering), he admires them in some way for their intelligence, hard work, and devotion of their lives to their country and to a cause greater than themselves. (He was especially talking about Davutoğlu, who graduated from Boğaziçi Üniversitesi, one of the best universities in Turkey, and is very smart and accomplished.) I don’t know if I agree with him – if I had thought of this argument at the time and not 30 minutes later, I might’ve pointed out that although they may partly aim to serve a cause greater than themselves, they also probably works toward self-serving goals like greater personal success and power. After all, as we all know, power corrupts. However, I mention this issue here because it is an interesting thought that I think too many of us forget in today’s ever-more partisan world of politics: people are more than their party, and they are not black and white. Most of us have done things that deserve both respect and admonition, although of course this is no excuse for political beliefs that impinge on basic human rights such as freedom of religion.
This cat’s just chilling outside the Kennedy Lodge:
Okay, that is more politics than I ever expected to discuss in my blog. I think I should stop there! As always, thanks for reading, and iyi akşamlar!