slowly becoming an engineer

More than halfway through 20.109 at this point, I’ve gone from having Seamus Finnigan (the kid who keeps blowing stuff up in Harry Potter) as my 20.109 spirit animal to having Beaker as my spirit animal.

I feel like that’s an upgrade. Now, the article. The bane of my existence for the last week or so. Writing, editing, and going to office hours slowly became how I filled all my free time. The best part was trying to explain to non-109-ers how/why I was spending so much time writing this article. I think every other sentence I said this week hard the word “my research article” in it.

After putting a million and a half hours into the journal article, turning in the article was by far the most therapeutic and rewarding part of my week. I was trying to get my friends to read it and appreciate it in all its 14 page glory – which is kind of embarrassing in retrospect. Either way, now that I’ve turned it in and it is no longer running my life, the research article is kind of cool. I have this 14 page paper I wrote about experiments I did. I’m a real scientist! 

Spilling so much tea that I replaced my rug

Listen, I’m not going to lie. That was rough.

I don’t quite know how to feel about the research article. On the one hand, I am quite ecstatic about my performance. I feel as though I put in a lot of effort into learning what exactly happened in Module Two. On the other hand, that was insane. Like always, I didn’t realize just how “in-the-dark” I was until I started creating figures and interpreting the results. I honestly had little to no idea how to interpret the RNA sequencing data. To be quite honest, I didn’t even realize we had RNA sequencing data to interpret until the final lecture of Module Two. After many questions, some repeated multiple times, the lightbulb started flickering in my head. Granted, the lightbulb wasn’t fully lit, but something was definitely there.

So, I started. The methods section wasn’t too terribly difficult because of the comments and lecture discussion on editing our methods draft. Next, I wrote the introduction. This might have been out of order, but I wanted to achieve some narrative structure, and I had some ideas that I didn’t want to forget. Then I began writing the results and discussion. Even though I began to uncover what interpretations could be extrapolated from the figures I created, it was still difficult to articulate these ideas in a way that fit the narrative of my article. Once I ‘overcame’ this obstacle—as in I decided to just go with what I had—I finally wrote the abstract and the title. Then I was done.

Time for the true tea.

*A disclaimer, I do not mean to be rude or come off as extremely negative. I only mean to give my true and honest opinions about this article from my perspective.

1. The methods section. I do understand that the length of each section on the wiki was merely a suggested guideline, but I found it implausible for me to write the methods section in 3-4 pages. There were many experiments and procedures that needed to be written down that I found this expectation a tad questionable, at least for someone with little experience with scientific writing like myself. Again, I realize that I need to refine my skills in concise and efficient scientific writing, but I am only a beginner, so it was extremely difficult for me.
2. The discussion section. Or rather, the ‘future experiments’ discussion. This is where I find the class most troubling as someone with no previous lab experience. I feel as though there is an expectation to come into 20.109 with an understanding of experiments and assays done in research. I, unfortunately, do not meet this unspoken expectation. As such, I found it quite impossible, within the time frame of this assignment, to explore different types of experiments that could be relevant to this particular article. Because of this, I maintain that 20.109 should have a disclaimer stating previous laboratory experience is strongly suggested.
3. The time restraint. This is more of a personal issue. I had little to no time to complete this assignment. From the day I could start working on this assignment (Wednesday) to the due date (Saturday), I got a total of 9.5 hours of sleep. I spent all my time trying to complete this assignment along with my Biochemistry assignment. Despite my running on fumes, I still barely finished 30 minutes before 22:00. I still don’t know how I stayed awake in any of my classes.

Toward the end of this assignment, I was so over it. I really just wanted it to be done.

I am hopeful that Module Three won’t be so… Module Two-esque. Here’s to a possibly misplaced hope.

The Paper to End All Papers

I always figured I would have to write an actual scientific research paper sometime in my life. What I didn't figure is that I would be doing it so early. I guess I didn't really think this reality through very well - I just assumed that somewhere along the line in grad school I would just magically gain insight into writing a paper. Now that I've finished the first true research paper I've ever written in my life, I'm not sure how I feel.

All jokes aside, this assignment was just very intimating at first. There seemed to be a million things to do, and at times I thought there would be no way to every finish it. Even now, I feel like if I could just work on this paper until the end of the semester - refining the methods section, adding more references and future experiments, and discussing the results in greater and greater detail. One of the hardest parts of writing this paper was that the results were not very clear-cut and often contradictory with what was expected (particularly the Cell Titer Glo Assay).

That's exactly like real life though. In my UROP we often get contradictory or unsatisfactory results as well. Usually, this results in repeating the experiment, but when these results start to repeat you begin to question whether your own model is correct and dive back into the literature. Thankfully, there was some precedent for our unusual results, which I made sure to address in the paper. Looking back on the very first few homework assignments for 20.109, I realize my paper-writing skills have improved significantly, especially in writing up methods. I could probably whip out another paper if needed to, but I think if I had to do another of this scale before the semester ends my brain just might die. It would be nice to go curl up and hibernate for a couple of months, but the science must go on! (Actually, probably just going to take a nap anyway)

Traumatic life experience

Writing a scientific research paper is necessary to grow as a scientist.

... I told myself around hour 15 of working on my paper.

This research paper was very, very difficult for me to write. When I sat down to start it, I felt very lost. Maybe it was because of our Spring Break in the middle of the module. Maybe it was due to my own negligence at not focusing. Maybe it was because there were so many different things happening, all overlapping on different days. I'm not really sure what the reason was, or if it was even any of these things. But in the end, when I started writing my paper, I had a very poor idea of what actually happened in the module.

From there, I spent quite a bit of time reading a lot, and I mean a lot, or research papers. I started off by writing my introduction. While I think it's easier to generate figures based on data, or a results section based on figures/data, the introduction of the paper is the most logical place to start. The introduction is a hour glass story. It starts from general, moves on to specific, then on to the question. That is exactly what I needed to do to reorganize my thoughts, and to parse what actually happened the past few weeks.

Writing the introduction first meant finding a lot of resources. Finding resources meant reading a ton of papers. This was the most useful thing I did to prepare for my paper. Tackling separate research papers on PARP inhibitors, compound 401, etc. really helped me piece together the picture we were expecting to see in our data. Which, of course, as science goes, was not at all the picture we saw. However, having all of these sources ready helped me go back and say: okay, we found this problem here.. so what did this person do to test something similar?

Once I had my introduction finished up until the 'here we show' chunk, I really felt prepared to write my paper. I moved in between figures and results, a little bit of editing methods, and on to discussion. The discussion was the most exciting. I felt that in writing my intro, I had read enough papers to find discussion points and plausible future experience to test theories. It was really rewarding to feel like I had actually gained knowledge from scientific literature, as I had never seriously read extensive (and by that I really mean semi-extensive, as there's no way you can compare the literature I read to something a PhD candidate reads) scientific literature on one topic.

After approximately 24 hours of writing, I finally had a final product. There was a lot of tweaking. A lot of things I thought I knew, came to office hours to ask a question, and realized I didn't understand. A few things that I spoke to peers about, only to find out that there is actually a 'correct' way to do something. But after the entire roller coaster, I was finally finished.

Then stellar crashed at 9:54 pm. A very anti-climatic end, to a very high-stress experience in my life.

And yet, I wrote my very first official scientific paper- and that's exciting. :)

IT JUST GOT REAL

This research article was probably one of the most difficult writing assignments I have had to date. I cannot remember a time when I spent so much time looking over every little detail possible in a paper. From figuring out how to make a decent title, to figuring out how our data made sense, to syntax and formatting, I was definitely pushed in this assignment. Nevertheless, I think I am quite satisfied with the results.

Looking back at the Mod 2 paper I think the idea that we had no revisions and no partner to help us out made the assignment seem very real. You had to figure out how everything worked and how it would be presented, and you didn't really have anyone to look over your shoulder and tell you you made a mistake. I think given that as we go through our career as biologists this will become more and more our reality, I believe that it was very necessary to make this jump and I believe it made for a very interesting assignment.

All in all, I am tired haha. It was a good assignment and I feel like I learned a lot about how papers are written. I now have a much greater respect for every figure I see in a paper I may be reading, but for I think I am going to go take a nap :P

Maybe I should change my major to literature with a focus in Kurt Vonnegut (not really)

The Research Article was tougher than the Data Summary. Like....a lot tougher. I struggled despite doing more things right than I usually do. I thought it was going to go really well because I did some things right:

I started A FULL WEEK before it was due. I'm not sure I've ever done that before this assignment. I was home in Indy on Saturday the 15th and was like 

So off I went. Wrote up the results. That was easy...I just put all the figures in and talked about them. 

Wrote the discussion. Not too difficult either...there were a few surprises in the figures, but generally the data made sense and lead to some reasonable suggestions. I handled the methods on Sunday night and took a break on Monday because I was so ahead. Then most of Tuesday...but it's fine. I'm almost done! No worries. 

Tuesday night I got to the introduction. Started with cancer. Easy. Started drafting up some sentences about the cell lines, the treatments, what we did...

ITS SUPPOSED TO BE A COHERENT STORY. My report wasn't. It was a collection of figures and an explanation of what they say...a REPORT, not an article. So now I've got a bunch of writing (50% of which is about to be slashed) and figures and no message. And I read back through the results and discussion to see what my message is...

Yep. There's nothing there. 

There were things, but there wasn't anything I could really get excited about writing. Eventually I picked a story that I found a bit boring and a bit of a stretch and rolled with it, but I needed to double check one thing on a lab computer and incorporate that into a figure. That was Wednesday night I think, and it turns out THAT'S when the project began. 

Since the heatmap showed some unexpected differences between DLD1 and BRCA2- cell lines, I wanted to make sure they were at least responding to the etoposide the same way in the RNA-Seq. But when I looked at the data...

(Favorite meme ever maybe). There was one really pervasive difference in response. I wanted to restructure my paper around this difference because I thought it was cool and unexpected and could make for some interesting discussion. The problem with that? 

I'm not nearly experienced enough to explain what I saw. But you know what? I had a ton of fun trying. I thought and read carefully and was grateful to have a project to really invest myself in. I came up with some ideas I was pretty happy with, finished my coherent story on Saturday around 7pm, proofread, and got it in!

Then I went to lecture for 20.330 on Monday and heard something that debunked all of my ideas as to what was actually happening. In the wise words of a famous pessimist from my home state...

Decisions, decisions in 20.109

I came into this research article with methods, a figure, and an outlined introduction already complete (thank you, 20.109 homework. I never thought I'd be so thankful for homework, but here I am, retracting all feelings of animosity towards my prior assignments). My attitude at first was very much as follows: "figures, results, and discussion? Pfff, it'll be smooth sailing from here." Okay, I wasn't that flippant, but I felt at least 50 notches more relaxed on the "panic-because-everything-you've-done-feels-awful" scale than I did towards the end of the writing process.

What I didn't anticipate was the overwhelming numbers of decisions I had to make while presenting the research story. Decisions included what information belonged in each section (I agonized over the divisions between results and discussion especially), which figures I wanted to present and how to present them, how much information to include in my captions, the order and way in which I explained my results and interpreted them, and so on. The paper felt less like a continuous sprint and more like an agonizing crawl from detail to detail.

One of my biggest regrets is that I didn't go to any of the many office hours offered throughout the week. I should have grabbed my laptop and worked on the paper in the presence of instructors who could alleviate my fears by answering my questions, but each time, I was convinced my paper wasn't close enough to the final draft. I opted to go it alone, which in retrospect, caused me more anxiety. Lesson very much learned for our next major assignments...

In the end, though, I appreciated the assignment. Science is not useful without clear communication of results and its implications, and writing this research article gave me a taste of what all those people in the lab do when they want to publish findings. It was interesting to really dive into the material and find potential solutions to experimental mysteries--it made me feel like a real scientist.

Research Article Regrets

I'm so glad I'm finally done with the Mod 2 Research Article. I think the homework and feedback definitely helped prepare us, but writing the research article was definitely still a challenge. Thinking about our confounding results and what could be happening, and thinking of future experiments to test these hypotheses was definitely interesting.

I regret not starting earlier on this assignment. I think I should have started at least a week earlier so I could feel less pressed for time at the end. Also, I feel like I was relatively inefficient when working. In the beginning I felt less pressured so I got things done really slowly. 

Me: 

My goal is to be more on top of things for the rest of this semester (which is only a month, but still). I feel frustrated because of my bad procrastination habits. I really regret not being more on top of this assignment.

 On a different note, thanks so much Noreen for all the help in office hours (: Thank you so much for answering all of my questions, and for having more office hours on Saturday. We really appreciate it (: Also, thanks for feeding us! (: Although this assignment was stressful, it was fun to commiserate together with all the other 109-ers in office hours and joke around. 

Also, writing the research article made me really think about all the experiments we've been doing and the results we generated. I think this module is really cool and it introduced me to a lot of new concepts and tools (such as RNA-seq). Writing this research article was a good way to wrap up this module and really think about what the results of our experiments mean in a broader context. Although it was stressful, I think this assignment is very useful.

Looking back on this module, I think for the two major assignments, journal club presentation and this research article, I feel regretful. For the journal club presentation, I wish I hadn't let nerves get the best of me, and for this assignment I wish I started earlier and also worked more efficiently and quickly (I also regret not starting earlier because if I finished earlier I could have gone to the march ): ). I've been really frustrated this past semester with myself in general actually, but I want to do better from now on. Like I said/wrote in my last post, these "failures" may sting, but they only motivate me to do even better in the future. Also, I know this entire post is ironic because I forgot to write my blog post on time. 

That was fun, I think

Writing this paper was really different from what I expected. Initially, I thought it was just going to be a really long paper and I was starting from square one. So when I first started I just opened a word document and started typing the introduction. I got about halfway through it before I realized we had basically already written half the paper and outlined the rest. So, I pulled all the homework assignments and outlines together and had 8 pages right off the bat. Great! This is going to go by so much faster than I thought. Boy was I wrong.

I ended up finishing the first draft pretty quickly, or at least faster than I thought. I believed I was on the home stretch then, I just have to go through and edit the paper and the figures and I’ll be done! So I started editing and it was bad.

So I just kept going. I red through the paper about 15 times and basically rewrote it each time. Each time the paper got better, but was liking it less and less. I think I got so familiar with the paper that the scientific language started to seem colloquial and informal. I’m so used to reading scientific papers and being very confused that reading through a paper and understanding it was unsettling. It made all the language seem simple and unnecessary. So I was really worried, but then I realized that maybe that's exactly how I should feel. The paper should ideally allow me to perfectly understand the material, and vis versa, writing a good paper pretty much requires good knowledge of the material. So maybe my paper was good! Probably not though…. I guess we’ll see.

How to Run a Marathon (20.109 Edition)

We had only been back in class for two weeks after spring break last weekend, but I was already desperately in need of a break. With the due date for the module 2 research article fast approaching, though, it seemed unlikely that I would get to take much time off over the long weekend, but after working almost all day Saturday and Sunday, I felt like I had made enough progress to take Marathon Monday off. It was probably the first day the entire semester that I did literally zero work, and the most stressful thing that happened to me the entire day was that I somehow managed to lose my sunglasses twice within two hours without even leaving the house, only to find them on my desk both times. 

I didn’t actually watch any of the marathon runners that day, but after finally submitting the module 2 research article, I definitely feel like I’ve been running my own marathon these past few days. It was incredibly satisfying to finish all of the writing, though, especially since it looked really official by the time it was finished, and the best part is that I finally have time to pay attention to the work I have for other classes. If only I could stop playing with my ring and actually focus.

There are a few really important things that I did while I was writing the article that helped me a lot through the process. The first was that before I even started writing, I made sure I understood everything that was going on. I was pretty confident that I knew what happened in most of the experiments, but there were a few that took a lot of staring at the figures to figure out. And some that I just had to ask Leslie to explain. Knowing what I was talking about made writing my results section much more straightforward.

The second was that I did the majority of the writing over the long weekend, so by the time the teaching faculty were holding extra office hours, I had a really good idea of what I needed to ask questions about. I probably spent more than 10 hours in office hours this past week, but it was definitely worth it - even when there were so many people there that it became difficult to find opportunities to ask questions, it was a good place to work on the article without too many distractions. While the assignment was required a lot of effort, I think the time spent together in office hours working on it has really brought us closer as a class. This has been particularly important for me since I was one of the few (if not the only) members of my Course 20 class who did not take 20.110 last semester, so I hadn’t really had the chance to get to know most of the other Course 20 2019s yet.

The third thing was that I made sure to remember that the goal of the paper is to tell a story. Unlike many of the writing style techniques I learned in high school English, this idea applies even to scientific writing, where being concise and objective is more important than being creative and eloquent. It really helped me keep my ideas in a logical order and remember to go through my results, introduction, and discussion multiple times to make sure they were consistent. It’s nice not having to discard everything I learned in high school.

And finally, as is equally important when running an actual marathon, I paced myself. While my actual reason for starting early on the assignment was seeing that I had an exam in 6.004 two days ago and another in 7.05 tomorrow and mildly panicking, it allowed me to spend the first few days working only as much as I felt like, which made it much less stressful. And that reminds me, I should probably get back to studying for my 7.05 exam tomorrow. My marathon isn’t over yet.

Connecting the Points

This writing assignment would have been more fun if I have spread out the assignment throughout the week. 

Writing the report felt right. It felt like I was writing an ending to a chapter. The connections I did not see before, where suddenly laid out with each graphs and paragraph that I wrote. 

I wished I had finished the report at the due date, but perfectionism has no limits, especially when every point counts. Either way, it is gratifying to write this report because regardless of the grade on the paper, I feel like I understood what the point of this module was, and appreciate the “cutting-edge” research I performed.

I was never a fan of genomics, and I did not know much about cancer besides whoever solves it will be famous. I was optimistic, but I was definitely lost in an ocean of facts. I would hear the reason behind every experiment. However, instead of constructing bridges, each fact became a lone island. I had all of the information, but never really grasp the big picture. 

So, when I started to write the report, I was too intimidated to write anything because I did not know where to start. I heard snips and hints of what to focus on, but the connections were never solidified. Luckily, I slowly found the connections, stringing the scattered days of lab and data into a story. I am glad I left this module with a good idea of what was going on. I feel like I can talk about, and know how to approach topics related to it. Taking the time to observe the data and results and see what other people found was exhilarating. It reminded me of why I like archaeology so much. I like reading papers and seeing the conclusions they see from a few pieces of data. I like compiling different ideas to support my idea. I wished I had the courage and confidence to confront the report earlier on. Nevertheless, I feel proud of what I have written so far.

What just happened?!

That. Was. Emotional.

It truly was.

I finished my research article about an hour ago (late day), and I am still reflecting about what just happened. Writing the Module 2 Research Article was a transformative experience. Like, I am a new person. I want to say I am exaggerating...but I'm kinda not. To say that I just wrote a 13-paged research article...honestly, I don't believed I just typed that, let alone say out loud... powerful.

I am 100% sure that I felt every single emotion writing the Module 2 research article. Not gonna lie, at first I was scared. The first day the research article was assigned, I remember Maxine saying that it should be anywhere were 12 to14 pages, and I was like ....

But I couldn't have that mindset for long because, well you know, I had to actually write the Research Article. Next, I was "chillin," just working along, doing the homeworks (which were very helpful in completing the Module 2 Research Article),  and I as like "wow, this is great." 

Then next thing you know, I had midterms left and right, extracirruclars starting ramping up, and everything was happening all at once. Nothing really going my way. My nice, relaxed, we are doing this mindset, QUICKLY changed. I thought to myself, "OMGOMGOMGOMG. HOW IS THIS GETTING DONE? WHAT AM I DOING? SHOULD I BE COURSE 20? WHY AM I GOING TO THIS SCHOOL? WHO AM I?" (yes, it really did escalate that quickly)

After a good night's rest, I was back. I was determined. I was focused. And I was finishing up today, I kept thinking, "Wow. I am such a scholar." (which I thought so humbly - just to note).

And then I was done. Over. Finished. Complete. The 20.109 Module 2 Research Article is hands down the longest thing I have ever written. It is so amazing to put in that kind of work a, and really understand what you are doing.

 #BLESSED

Woo!

Am I still alive??

Disclaimer: although I got pretty close, no all-nighters were pulled in the making of my report.

I think I wrote so much for the report that I never want to see my keyboard again. But in typical 109 fashion, the writing is never done!!! Yay for blog posts and further procrastinating my studying for 7.05…

Anyway, I started this report as early as I possibly could, and still somehow managed to work on it until 7 pm on the due date...not really sure how that happened, but I think a lot of that comes from the fact that I never really feel like I'm done with writing. Plus, this report was literally never ending- I've never written a paper this long before, much less a paper about science that I wasn't totally sure even connected until about halfway through writing. I think the most difficult part of this report for me was actually connecting all the experiments in this module...to be completely honest I didn’t really understand why the RNA-seq and cell viability data were connected until really late in this process. I understood how each experiment worked as we went through Mod 2, but for some reason that didn’t really translate to a full understanding of the project as a whole, and this made it difficult for me to finish the paper.

I started out with the intro and methods, because I understood the larger motivating questions for this module and the physical experiments we did, but moving into results definitely had a pretty big activation energy. Then when it came time to write the discussion, I felt like I was just repeating myself, and had to totally backtrack what I was writing after feedback from the instructors on what a discussion should actually include. I finished out with title and abstract, but I think I was barely breathing at that point so it was kind of a blur (maybe I should graph coherence of language with sleep deprivation for our independent Mod 3 project??). Last blog post, I made a joke about spending more time in office hours than sleeping in preparation for my presentation, but this week I think that was actually true.

That being said, I realized how amazing all my fellow 109ers are during the endless office hours we spent in building 56. I laughed along with everyone when we talked about all sharing a variation of the same title, ate snacks when we were all too hungry to function, and talked about papers we found as useful references. So at least through all my sleep deprivation, stress, and lack of hope for ever finishing, I was able to have a little fun with some cool people. And thankfully, I got it all in under 14 pages, because as Noreen said “Nothing over 14 pages could be that compelling,” and I didn't want to take her up on that challenge.

Thanks so much to all the instructors for your help throughout this process. Even though it was sometimes painful, I think it was cool to be able to say that I’ve written a paper-esque report for a class- it has definitely taught me a lot about what it will mean if I choose to pursue more research after graduation.

As I was beginning to work on this project, I realized that this was the first time that I had written a full-paper paper since my writing about sports class in my freshman fall semester. As I have enjoyed writing but substituted those classes for economics classes recently, I entered this assignment with the excitement of refining those skills. I was also excited to explore the new field of scientific writing, as I had not written any papers on scientific topics before.

I thought that writing a research article was going to take a long time, and I was definitely right. Having written all the sections of my paper and reviewed the majority of them with Maxine by Friday night, I was prepared for a busy Saturday afternoon with a tennis match and low expectations for the number of final edits on my paper. After I discovered that my match was canceled, I ended up going to office hours. I quickly discovered that I had minor improvements to make for most of the sections of my paper, as small additions, more citations, and minor inaccuracies had to be fixed. I came to understand that a research paper can always be refined and changed and that I had to accept my work at a certain point. Realizing that I needed to leave for the ZBT semiformal I was in charge of, I ended up running towards our van and asking the driver to wait to give me time to turn in my research article while I still had Internet access. This was an unusually stressful several minutes, as I am not normally worried by school work.

This assignment definitely helped me realize the importance of the argument to the overall paper. Trying to connect all of the different experiments that we completed as well as establishing the benefits of our research to the field was very challenging. I had presented numerous points in my discussion, so it was an interesting task of tying all these ideas together. While I thought I was able to successfully reach my conclusion and bring everything together in a succinct several sentences for my abstract, I ended up with a title that was definitely a little long (so hopefully that turned out all right). 

Overall, writing the research article made me feel like an actual scientist. While I have felt like I am building up my knowledge base through numerous classes here at MIT, I felt somewhat of a disconnect from my work in the classroom and the research field as a whole. Completing our projects in the lab and actually having to document our experiences made me feel like I was actually working towards scientific improvement. Instead of just knowing more about organic chemistry, thermodynamics, or genetics, I was actually applying my knowledge and seeing what I could do. Despite the difficulty and large amounts of work, I really appreciated completing this assignment. 

So many words

After writing 5000 words for the research article, I'm going to follow Noreen's advice and keep it concise. The biggest thing I learned while writing this paper was that you need to know what you want to conclude from the data before you start writing. This was hard for me because I like to do things from start to finish. I guess it's time to adapt because that doesn't work for research papers. Results and discussion are the most important parts of the paper because, as it turns out, data analysis is the hardest part. It's relatively straightforward to detail methods and write about background, but pulling meaning out of data and sorting out the facts takes patience, time, and lots of help from everyone in 20.109. It was stressful and definitely overhwelming at times, but this assignment ultimately has given me confidence that when I set out to write my first real research paper it will be successful because of all of the guidance I received with this assignment. I guess that's why we have to take CI-Ms! I think we can all agree that the key-word from that acronym is INTENSIVE.....

No One Likes Low Qual Scientific Stories

After drafting the Mod 2 Research Article, I felt a little like this:

To be honest, I wasn’t sure how to start writing this journal-like article. The idea of it seemed very daunting, considering this was a solo-project (RIP teamwork for this module D:) and no revisions could be made this time.

The hardest part for me was crafting the story for my research article. While analyzing my data wasn’t the hardest part, trying to piece together the different parts of my research left me a little like:

but when I was in a very work heavy mood:

This wasn’t because of the research article itself. It’s because I’m just bad at organizing my material. I went to office hours constantly to ask for small things on how I should format my data for the story. I asked Leslie (still the MVP) to look over my abstract. I asked friends to clarify aspects of each experiment so I could try to piece the important parts together for my story on synthetic lethality. Even until the last moment, I was trying to make sure everything made sense.

Overall, although I realized that scientific writing is hard, the experience was totally worth it because I feel like I can make a cool story out of scientific data and explain it (maybe somewhat haha). I’m hella excited to build a biological battery.

When the research article was completed:

I Feel Like A Scientist... Kinda

It took me until I began to write the article to realize that I had just spent an entire module without connecting the things I was learning.

As questions popped up, with the answers not far behind, I had to take a moment just to let everything come together. And another moment. And:

It's at the point in the semester when I realize that taking two lab classes was likely not the best idea. (Something I hope will turn around by the end.) 

I read through all of my lab and lecture notes and wrote up some of the things I continuously forgot, like what delta CT, p21, and compound 401 (and a plethora of other words I had disconnected from its meaning) were.

Getting myself started on each topic was the hardest part. After I knew where I was and where I wanted to go I could write out the pathway. (As long as I didn't have to cite a manufacturer...)

I'm just happy I finished and could actually put together a research article. I feel like a real researcher- which I expect to be a lot of trying to explain your ideas and conclusions rather than a lot of blowing things up in lab.

You Gotta Have A Good Story

One of the hardest things I've had to deal with in this class is learning how to write scientifically, which is very much easier said than done.  It goes against every writing convention I've ever been taught, and yet it's so widely accepted to just always write passive sentences and simply run on and on about data.  Compiling the data itself wasn't particularly hard, it was putting everything together in a way that made sense, even if it didn't really make sense to me.  So, putting all that together into one paper, I'm sure we all had a rough time trying to make heads or tails of what does and doesn't need to be in our paper.

One of the most common things I heard while trying to write this was the fact that it needed to tell a story.  It wasn't enough to simply word vomit a bunch of numbers and figures onto a piece of paper and submit it as scientific research.  Keeping everything concise and direct while at the same time portraying a story of what exactly we did ultimately turned out to be the biggest struggle of this paper.  How were we supposed to keep everything bare-bones with little to know bias and still keep the literature interesting enough to actually be readable.

It's unfortunate that don't get to submit a draft before we get our final grade for this seeing as how I'm sure many of us made some fairly simple errors that we really couldn't have accounted for.  Unless someone has written as scientific journal article before, I doubt anyone would be able to get it right on their first try.  However, I did appreciate being able to talk to my peers and ask other people for advice on how I should go about writing any one particular detail (not too much advice of course, but you get the idea).  It will definitely be harder in the future when really I'm the only one who understands what I'm going to write about.  I won't be able to ask anyone for help since I alone did the research.  Then writing the article will be a huge job in itself that I won't be able to get very much help with.  At the very least, that's why there are editors to these journals and more people to read the paper, but even then it's still a very daunting idea.  I'm glad I was able to experience this now with multiple people to assist me as opposed to by myself in the middle of a grad level research project or something.  It was a great learning experience as far as time management and how to plan out writing a fairly large paper in a style that was completely foreign to most.

Words are hard

Constructing the research article was a rough time. Every element on its own had its own difficulties. Even from the start, when planning out the narrative for the research article to follow, it was initially hard to see the big picture and understand where the data from our experiments contributed to the pool of knowledge in the universe. We received the data and had to try to comprehend what it meant, especially when the results didn’t align with our expectations. Then came the magnanimous task of writing up the entirety of the experiment, which involved a writing out a long methods section, and synthesizing established science from literature with new information from our results, to come to a conclusion. And even after the individual parts of the paper were done, we had to make sure that the paper flowed coherently, with proper transitions, to tie into the big picture.

It was challenging, but all the resources we were provided definitely helped make it a fulfilling experience and learning opportunity. Professor Samson’s lectures ingrained the foundations of DNA repair and established the pathways of homologous recombination and NHEJ and how they affected each other. The in-depth feedback on our methods, first figure, and intro were very helpful as always. I know that Noreen and Leslie told us from the beginning of the semester that the communication lab would be a good resource, and I definitely should have gone, especially when I was unsure about framing the overall question, and whether I was introducing enough information and hitting on enough points of discussion. As usual, for me it was an issue of not completing everything on time.

Also, in terms of the experiments we did, it was interesting to see the different angles we could take in probing the DNA damage response of the BRCA2 null cells. It made sense to use an assay that counted how many cells survived after being treated with the different drugs. The RNA-seq was a different angle in approaching the question that I was never exposed to before. It was cool to be able to compute statistics and upregulated and downregulated genes from the RNA-seq data, and actually be able to connect the most down/up-regulated genes to their functions. I know we probably barely touched the surface of what kind of information you can learn from an RNA-seq, and I wonder what other kinds of data analysis you can do.

Writing this research article made me confused about my major/ life plans again. I thought I was planning on going to grad school, but that will involve lots of writing proposals, grants, papers, presentations, and all that. If it took me this long to write lab report which we were given all the details of and resources for, I can only imagine how hard it would be to write one on my own. I know it takes practice, but practice takes motivation. Ah. 

Be Prepared!

Though there are many life lessons that can be learned from the research writing article , the one that sticks out to me is the old Girl Scout adage of ‘Be prepared’.  

I don’t need to tell anyone here about how daunting the project was, or about sleepless nights spent frantically editing figures as these are fairly common experiences.  However, I’m sure each of us had our own unexpected issues pop up.  Some of these issues were probably avoidable and can be used in the future.  For instance, I learned that you should check the page limit before you write the whole assignment and go significantly over because you like run-on sentences. Others could not be predicted, like a computer crash that destroys your all your figures a few days before the deadline.  (The life lesson here is back up your files.)

No matter what the problem I encountered along the way, I found that certain precautions helped me get over these hurdles. One was starting early, as that gave me a time buffer close to the deadline.  It also gave me time to fully develop the story I wanted to tell in my research article, as that changed drastically through the writing process. Another was going to lecture, which gave a lot of incredibly useful information for explaining processes and figuring out exactly what was happening with our data.  Though it pains me to admit, the homework was also very helpful in starting the research article and figuring out exactly what to include.  Finally, office hours were a great way to clarify information, check my conclusions, and figure out how to represent data.

With this information and these resources, any problem that came up was more or less manageable.  Overall, though the writing process was stressful and rocky at times, it was okay with the proper preparation. My old troop leader would be proud.

What Point am I Trying to Make?

The Mod 1 report seemed difficult at the time, but then I started writing the Mod 2 report. I had my methods section done from our previous assignment, as well as a start to my introduction, discussion, and results sections. But I still had to put everything together, and finish several sections.

But I had already done all of this in Mod 1, so I could just follow the same procedure and it would be easy, right?

Wrong.

The Mod 1 experiments had been fairly linear. Mod 2? Not so much. We had multiple experiments running in parallel, which made writing about the results, and then later discussing the results, difficult.

But the hardest part was deciding on what main point to make through the research article, and trying to create a cohesive story around it. In fact, I ended up sending a panicked email to the instructors just over an hour before the paper was due, trying to make sure I understood how I could tie all of the pieces of the module together.

Overall, I think I would have struggled a bit less if I had chosen a specific point to make in the paper as a whole as soon as I had started writing the article, rather than trying to cohesively tie everything together at the end. It would have allowed me to have a better idea of which results to focus on throughout the writing process, which in retrospect, would have been very helpful.

Looking ahead, I am excited for Mod 3. I have a strong interest in the intersection of biology and energy, especially as related to sustainability, and I think this will fit in very well with my interests.

14 pages later...

Coming to you live right after turning in my first ever research article! Wow, what a rush. I waited a day to hand in the final product, but it's been submitted and I can officially say that I wrote something longer than 15 pages (not even including the figures!!). I'm really proud of the work that I did, re-reading my article after thinking about how nervous I was to write it at the beginning of the module makes me really happy.

For me, the best part about this report was creating the figures. I had gotten a taste of the figure-making process during the mini report from the first module, but I've learned that I really like using manipulation of photos and data to tell a story about what I've done. Even when just making these little figures for this reports, I tried to take up as much space on the page as possible, and had to edit them down because I was worried they were showing too much information. I just liked the way they looked on the page, and how they represented the data that I had collected to its' full extent. I'm anxious to get feedback on them, but if I get good responses then I'll be more confident in my figure making abilities for the future, and hopefully continue to improve.

In addition, I liked being able to craft my own story in a way through the interpretation of the data. while this was daunting at first (it would have been a lot easier if I had just been told the end goal, like the previous module), once I had figured out my story and knew where to go with it, I felt really confident about it. I think it mimics the natural research process anyway, because even when you plan ahead to attempt to get a certain result, sometimes you don't get what you're expecting to see and have to change up your story or research plan to account for your findings. Therefore, while this part was initially a little frightening, it ended up being very rewarding.

Overall I had a very positive experience with this module, but it was a fairly long one and so I'm ready to put it to rest and move on to the next! <3

2 down, 1 to go!

It's pretty crazy to think we're more than 2/3 of the way done at this point, and the Mod2 research paper was a pretty good culminating assignment to signify everything we've learned about scientific writing this semester so far. But now we're in the home stretch!

If anything this paper has proven that writing a scientific paper is hard, and you'll never ever feel like it's totally finished and you've done everything you could, even if it's your 50th time reading it through. The page limit was surprisingly such a struggle to fit into, and I definitely spent nearly as long shortening my paper as actually writing it. And even more so with the full-length paper than with the data summary, it's surprising how everyone's paper can be so different, even though we all did the same experiments and analysis, based on what points people choose to focus on and what stories different people tell. Something I definitely got from this assignment is that you can't use every bit of information in the final paper, and that's okay.

Time management around such a huge assignment was definitely really stressful (ahhhh), but thanks to all the teaching staff for all their extra office hours and help :')

Going into Mod3, I'm really excited to build our own biological batteries (obviously) and to have a completely different final assignment format that lets us present our own research ideas, which is equally good practice as writing up our results in a paper. One more module to go, we can do it!!!

(also, writing/seeing these blog posts has seriously enlightened me on the number of memes in existence on the internet?? Clearly I'm not accustomed to blogging)

Almost to the end!

I both loved and hated writing this research article for Mod2. I had a lot of work leading up to the due date, so I planned to finish my intro, results, and discussion Friday night and then fix them up Saturday during office hours… Except that trying to get work done in my bed late at night is always a bad idea… so this happened:
 

It left me with a lot of work to finish on Saturday, but overall I’d say I’m pretty satisfied with the results! The research article was a lot of work and required a lot of thinking and planning, but I really liked our experiments in Mod2 and then having to think of a way to frame it as a story. Here are some of my thoughts:

• I really liked Mod2 because of the different experiments that we did. I think that it’s really cool to see how we approached one central idea with multiple experiments.

• Science as storytelling is really cool because you can choose how to explain that one experiment led to the next and then plan how to order your figures and writing to show that.

• The homework assignments proved to be a really helpful starting point. Although I changed a lot from my discussion outline, it was nice to see what my original ideas were and build off of that.

• The methods section was really difficult, but it was the only one I felt satisfied with upon completing it. Once I made all my methods corrections, I could move on, whereas I kept going back to the rest of the sections and adding more when I had new ideas.

• I’m so thankful to Noreen for having office hours on Saturday :) 

• I really struggled with the title and abstract on this one because I had trouble identifying the main conclusions that we came to. There were a lot of things we found out, and some of our results were surprising.

 Overall, I really liked this module and feel like writing this research article was helpful preparations for future papers that I will write!

Yay for almost being done with this semester!