These days, it seems like every day we learn of a new variant of SARS-CoV-2 (the virus that causes COVID-19). However, it’s hard to understand what a variant is and how it changes the virus. In this post, I wanted to introduce PyMOL, a program that students have access to through the University. This program can be used to see what the spike protein and its mutations actually look like.
But first, here’s some background on SARS-CoV-2: COVID-19 is a disease caused by a strain of coronavirus called SARS-CoV-2. This virus gets inside the human cells by using something called a spike protein. This spike protein binds to a receptor on the human cell called the ACE2 receptor, and this allows the virus to infiltrate the cell. The variants of SARS-CoV-2 that we keep hearing about typically have different mutations on the spike protein. In the case of the B.1.1.7 variant, which is a variant that is thought to be 30-50 percent more infectious than other variants in circulation, the mutations are at a location that allow the spike protein to bind better to the ACE2 receptor. If you bind better to the receptor, you’re better at infiltrating the cell. The spike is also the target of the vaccine and our natural immune system.
Now, let’s try and look at where these mutations actually are.
Due to the Covid-19 pandemic, a lot of in-person internships and research positions for students have been transitioned to remote opportunities. Last summer after my first year of college, I opted to take online classes over the summer because in-person opportunities were not a possibility. For this upcoming summer, I was hoping to gain laboratory experience in person, but my internship was also transitioned online. With only one summer left before I apply to graduate school, this left me with a looming question: will I have enough in-person research experience before I apply to graduate school?
Although this question bothered me for a while, I realized that I was approaching this issue from the wrong perspective. I feel as though many students are probably dealing with similar issues now that many summer opportunities have been canceled or moved online due to the pandemic. In this article, I am going to walk through the reasoning behind why you should not worry too much about lacking in-person research experience and also include some additional opportunities you should be on the lookout for.
An amusing remark on academics, itself attributed to several different academics, goes something like this: In academia, disputes take on such huge proportions precisely because the stakes of them are so small. Whether this observation is or is not true, I have found that its general sentiment is passed down to undergraduates, if inadvertently so. Of course, there are pedagogical reasons for instilling this impression; when we are learning about debates on a given subject within a discipline, it can help to read the most absolute positions on either side, if only to distill the terms of argument.
But the impression that such debate must necessarily be black and white, and must be of great intensity, can be daunting to accept as an undergraduate writer. Who am I, I wonder to myself, to so totally challenge the work of an established academic researcher? Even if I might disagree with their broader argument, have they not done far more research than I have? Relatedly, what if their research offers some quite usable background information– am I not just a little hypocritical to use it while arguing against the position it was intended to support? Or, what if I agree with smaller asides or observations by the researcher, but not the thrust of their whole argument? In a word, need the division be so absolute within the scholarly conversation?
When writing a research manuscript or a lab report, I have been conditioned to complete all of my experiments first and then start by writing the results section. My mentors have always encouraged me to start with the section that ‘writes itself’, given that when you obtain your experimental results, you cannot alter them. I started the school year thinking I would use this approach for my thesis – focus strictly on experiments during the fall and the start of spring semester and transition into the written portion of the thesis during late spring semester. However, while I was at home and outside of the lab between Thanksgiving break and early February, I knew I could not spend more than 2 months without thesis progress. Although I did not have my results nearly ready by that point, I began to brainstorm different ways in which I could work on my lab-based thesis without access to the lab. In this post, I will highlight ideas and resources that can help you make progress on your thesis, even while you are outside of the lab.
Last school year, during my first year at Princeton, I rarely ventured out to study in the libraries, instead preferring to stay in the comfort of my dorm room. However, after spending the fall semester at home, I realized just how much I missed the Princeton libraries, and I regretted not taking advantage of this amazing resource more often while on campus.
Going into spring semester, I challenged myself to explore the many incredible study spaces on campus that I had never been to. I was partly inspired by this post on the best study spaces on campus, and I wanted to provide an update on how studying on campus during a pandemic is like. A lot of the logistics around studying in the libraries have changed due to new Covid-19 regulations. So, in this article, I am going to lay out the changes to the Princeton library system and provide an update on some of the best new study spaces on campus.
For better or worse, the university is internally cloistered as an academic institution. Walls literal and metaphorical separate the departments. This is perhaps most apparent to students on an administrative level; each department has its own academic guidelines, grading policies, and research expectations. Deeper differences, though, may present in modes and content of knowledge production. Disciplines often preclude interdisciplinarity. Divergent methodologies might be applied to the same subject matter to produce different results; within a department, the range of expertise might end up applying similar methods to wildly different subjects.
I, for one, think that these disciplinary divisions often do more to stifle than to encourage intellectual growth or humanistic inquiry (on the problems and politics of the academic disciplines, see my interview with Daniela Gandorfer here). But, as things are, attempting to explain research across disciplines can be quite difficult– like speaking to someone in a different language without a translator. Seniors writing their theses are certainly familiar with this issue when trying to explain their work to people outside their department, or in some cases, anyone other than their adviser. When it comes to feedback on thesis work, then, it makes immediate sense to gravitate towards people with background in whatever you are writing about. They indeed might be able to give very pointed advice.
That said, there is still great value to turning towards those beyond the official borders of your discipline. A lack of familiarity with the subject matter can indeed be an asset– especially in terms of providing feedback on your writing and your writing/research process.
Haider Abbas ‘17 is a Princeton alumni who recently published his inspirational senior thesis which he created while in the Princeton School of Public and International Affairs. Many Princeton seniors are now beginning to dive deeper into their theses, therefore I think that hearing from Abbas would be very helpful. Thankfully, a few weeks ago, I was able to interview Abbas and he offered key insight into why he chose his thesis topic, how he was able to produce his thesis, and most significantly the impact that his thesis will have beyond his years at Princeton. I hope that you can learn from his experience and develop a thesis that you feel passionate about!
This interview has been edited for length and clarity.
Oh, it’s unfortunate that your classes are all online now… But all the extra free time must be nice, right?
Actually, no. Somehow, I have ended up in a place where I’m busier than I was back when school was offline. And that’s without Powerlifting Team practices, the thirty-minute dinners that consistently turned into three-hour-long social gatherings, and all of the hours I spent working on-campus jobs.
I’ve realized it has to do with my relationship with time. In the past, I didn’t need to be very intentional with my free time: it always just happened. Nowadays I think back fondly to my naïve visits to the Rocky Common Room for pre-bedtime cereal-breaks, only to end up practicing handstands on the rug by the piano with my friends until 2 am.
Without spontaneous social interaction, I ended up filling up all of my time with work, clubs, projects, and research. Unfortunately for first-year students, these challenges are only compounded by the transition to college academics in general. Whether or not you feel like you’re busier this semester, I believe we can all benefit from evaluating how we make time for ourselves: below are five tips I’ve implemented to help facilitate a productive and sustainable semester this fall.
When I first applied for departmental senior thesis funding early this spring, everyone was still uncertain about how long the effects of the COVID-19 pandemic would last. It seemed departmental administrators were optimistic: funding requests could still be made for summer travel. In my application, I detailed my intent to travel to university and state archives throughout the U.S. south for a thesis examining how antebellum Mississippi Valley planters conceptualized the idea of labor. But before I even heard back about whether I was to receive support, the department updated its funding parameters to prohibit summer travel and I had to redo my application in turn. My summer plans, of course, were not the first academic casualty of the strange 2020 world; nor would they be the last. Fortunately, though, there were ways to work around my newfound limitations: all of the archives that I wanted to visit offered services for resident librarians to scan and send materials from their collection, so I updated my application to ask for funds to pay for associated fees. Here, I’ll be sharing some tips for requesting archival materials to be scanned, which I hope will be helpful to any researcher unable to travel (pandemic or not).
This year, as we prepare to write our final papers in quarantine, it will be extra tough to locate the sources we need for our research. Without in-person access to campus libraries, this Dean’s Date will require some new strategies for accessing research materials. To help with this process, I’ve collected a few virtual research resources from my weeks of quarantine thesis work, as well as the beginnings of my Dean’s Date research (also check out Alec’s recent post for more tips):
Do not underestimate the library catalog. A lot of sources are available online, especially with the University’s new partnership with the HathiTrust Digital Library. Through this partnership, millions of scanned books have been made temporarily available to students—in addition to Princeton’s many existing online holdings. To see if a book is available online, just search for it in the Princeton library catalog. If you don’t see a digital edition listed, try clicking on a print edition and seeing if a scanned version is available through HathiTrust (if it is, there will be a link just below the book’s title and general information). You can also click the “Request” button under “Copies in the Library,” then “Help Me Get It” and a librarian will do their best to send you a digital copy—if it’s available—within a few days.