BE 20.109(F20) Class blog

Dear Diary, Today I met someone. Virtually only, yes. You know what I was wondering about the whole time? I was thinking about how a person can comprehend the other person's week-long work product in less than 10 mins. And understand it to the level of being able to comment on it, suggest scientific and technical edits and also give tips on presenting the work. I usually get lost in seminars and talks because of the time frame in which I am supposed to understand what is being told, even though the speaker is making all efforts to actually explain it, unlike what happened in the meeting today. No, it was not a date. But it was special, really special. Have you heard of the rubber duck debugging method used by programmers? You basically place a cute little Duckie. It doesn't have to be cute, it can have any expression you want like. It can be aggressive to keep reminding you of your mom, just kidding. Right, so you place the fake duck bead your laptop and assume it is humanised ...

At a recent job interview, I was asked the question, "what are some ways you can think of to improve the brute force techniques used in drug discovery?" The question had an implicit bias, that brute force approaches to solving problems are less preferable to a well thought out alternative. The same bias is built into the philosophy of this school. At MIT, a seldom spoken set of rules guides the actions of some of the most industrious nocturnal students. The Hacking Ethics is a set of 13 rules that encourage safety and respectful behavior of hackers, but the philosophy which crafted it also applies to real life. My favorite Ethic is rule 3: "Brute force is the last resort of the incompetent." This has a clear important application to hacking: don't break a window when you can open a door. There's often a smarter strategy than using force to accomplish your goal. This conventional wisdom applies to many aspects of life, but does it apply to pharmaceutical rese...

The research article was an incredibly long, but rewarding, piece of work. All the homework leading up to the assignment was super tough too, but I took a lot of the feedback from the instructors directly into writing the paper!  Second, I ended up reading a lot of the material through online journals like Cell, Science, NCBI, and others to get a good idea of what this article would look like in real life. To somewhat pick the brain of other scientists, how would other people present results from an SMM screen? How would their molecules look? Would they present one representative molecule or the whole list of binders? What would they propose to be done to the small molecules identified? Does the screen even mean anything significant by itself without confirmation? And a bunch of things that were important in writing the paper from a scientist's side.  The most useful resource was for sure using the BE Comm Lab. I feel like going to the Comm Lab was super helpful and their pers...

  In preparing my research article, I relied mostly on feedback from past assignments as well as notes taken during CommLab presentations. Feedback from past assignments was very helpful in showing me where I had gone wrong and in what direction I should take each component. Unfortunately, we did not cover every section in a prior assignment/I also really missed the mark on a few of them, which was where the CommLab notes proved very helpful. The notes provided good information regarding the structure of the sections as well as how I should go about writing them. Unfortunately (yes, again), as vary the days so, too, my note-taking ability, so my CommLab notes were not always the most thorough. I revisited some of the presentation slides and learned the hard way that, while these were great presentations, they make for less great reading material as, well, that wasn’t their intended medium. This wasn’t too harrowing a difficulty though, as they provided some useful information and...

 Writer's block, public enemy number one. I assumed that it was only for authors; little did I know that writing this research article would make me an author and liable to writer's block. When I first heard of the assignment, I was excited to write the article, but extremely nervous. I tried to start early, but I became paralyzed every time I sat down to write it. What do I write? What goes into the discussion or results section? What's an overreach? The wiki page both eased and exacerbated my fears; the description of each section was super informative but seeing how many pages everything had to be was intimidating. 14 pages. Wow. Rationally 14 pages are not that long, but it feels like a million when you have to sit down and write. Luckily, I remembered from the Comm Lab; the best thing to do was not worry about order and start writing anything. I started with the methods section because we had done most of it in a homework assignment. It helped break me out of my writ...

 A key thing I picked up on in this research article: it's always ok to rewrite everything. For the last 2 days of module 2 (and the first 2 days of module 3), I came to the conclusion that my research article would conclude that my identified small molecules were only related by an amide, imino, or azido group, and there was nothing else that was interesting about them. To be fair, there are rather a lot of things that go into a molecule, and seemingly minor changes in a molecule (shift of a nitrogen atom from one carbon to the next one over) can seriously impact the biochemistry of a molecule. There's also the minor issue that interpreting the small molecules was the very last thing we did in the module, and therefore I spent more of my time fixing up the parts of the article that we had already done for homework. Also, it's generally hard for me to get into writing something without the enormous shadow of an imminent looming deadline. But I digress. The point is, I was r...

Embarking on the journey to write the research article was incredibly daunting. I could barely read through a reputable, published paper without getting stuck on every paragraph. How in the world was I supposed to write my own research article? And while this was certainly no easy feat and certainly time consuming (I think I spent 5 hours today simply editing the 17 pages I had), it came together much smoother than I had previous thought. The best thing I did for myself in writing this research article was starting early. I must admit, I cannot take full credit for this proactiveness. I had a very busy weekend planned for the last weekend before this Wednesday deadline, and had another paper due Thursday. Thus, I had to make sure I started early, and thank goodness that I did. I still ended up working up until the deadline, and even after I felt like I was done, I put in another two hours of editing, and this endless cycle continued on and on until I was blind to my own writing. In ter...