After my last MUN conference at ASU, I actually managed to win best delegate or first place on my committee PEMEX as the Undersecretary of Hydrocarbons for the Ministry of Energy. It was a lot of fun, we even took over the Mexican government. But I still don't know what college I'm going to, and that's not a fun reality to be living in.
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| The person I was representing |
I am currently editing my paper, and the discussion section seems to be the thorn in my side (more like a gaping hole in my torso). The general feedback from my 2 peers was that my literature review provided significance and a decent background on my paper, but there needs to be a slight cleaning up of connections between using Lac1, folding mechanisms, and the actual research question. In addition I need to justify my gap more effectively. The methods section was relatively simple, there's only one real problem: technical terms. Looking back at it, I have defined only half the terms, and the terms I do define are often defined late. The results section was a worse version of this, as I basically hit the reader with a ton of technical jargon out of the gate. The visualization description was highly subjective, and I need to figure out how to phrase it in a more concrete way. The discussion interpreted the results, and completely forgot about the literature review, significance, and basically anything the reader would care about. I wrote it as if I was just publishing this for my peers in the biophysics field. I need to link the discussion to the lit review and tie the whole paper together.
As stated above, my strengths lie in the lit review and the results sections, and my weaknesses are technical terms, methods, and discussion. The main thing I'd like readers to search for is technical unclear terms, as I have lived in this paper for months and sometimes cannot convey terms simply.
The presentation for me should be interesting because I know everything about this paper, and frankly I explain things better while speaking over writing. My figures are exciting to discuss because I can physically point at them and identify regions etc... What I am nervous about is lapsing into technical jargon. My paper already uses a lot of diagrams, and it will be simpler to explain these in the presentation. 15 minutes will be a challenge, but I can always work around a time limit, and as technical as my project sounds, compared to other projects the amount of terms is smaller and more manageable.
The meme of this week is 322. 322 is term representing throwing a game. It originates from a Dota 2 match where professional player solo threw the game after making a bet against himself. The game score ended 3-22.
Shwath,
ReplyDeleteSo most of my comments are on your methods and discussion sections because you specifically asked for help on how to make those sections better. So before i dive into comments on those two, I'll just say that I thought your literature review was really strong and the only issues I saw with it were just a couple missing transitions and not fully explaining like one or two terms. Obv I commented on the doc so you can check them out there.
I'm just going to kind of lay it all out here and write out all the terms that I felt weren't explained sufficiently or some that you don't even begin to explain at all.
1. Chimera - i felt like this one had a decent definition, but it was a little more confusing just in the context of your paper. I understand that it's some sort of a combination of regions (I'm just going off of memory here) but what does that mean for the structure and the function of the protein? In other words, why is it significant that the proteins are chimeric?
2. Perturbations - I know what this meant in the context after reading it a couple times, but if you could just define it simply like "making the structural change to the protein" (I'm sorry that definition is probably so offensively horrendous and ignorant). I think it just comes off as weird to the reader to see "perturbations." Idk it's kind of a word that just throws you for a loop because you're not expecting it.
3. REMD Method - you tell me what the acronym means, but you don't really tell me too much else about it.
4. Linker sequence - this was one of those terms that just really came out of nowhere and you never provided me with an explanation of it
5. dfire - I have no idea
6. Likely structures - It's not that I don't know what this means, but you never specified why it was important that you find these likely structures.
7. PuR Regulatory body - I haven't the slightest idea of what this is
8. RIUDYG - same
9. Human ferritin protein - this really really came out of nowhere and it didn't seem to have any other relation in your paper except to one sentence. Either define it so i get it or get rid of it bc it doesn't seem to be anywhere else in your paper.
10. Residue, Flexibility, flexibility of residue
11. Isotropic perturbations - Ashwath please please please don't do this to me you neeeeeeed to at least give me a hint of what this is. If you're not going to tell me, at least let me figure it out in context. You didn't even give me enough context to figure it out
Also, you never tell me what the affect of temperature on proteins is and why you have to play around with temperatures. Then, you spend a decent amount of time talking about your first parameter (temp - still w/o telling me why it's important), but you don't spend nearly enough time talking about the parameter that is length of time. It's so vague to me.
OK last thing, make the question to your answer clearer. You restate the question, and right then should be when you clearly tell me the answer. Instead, you reiterate your methods briefly and then I'm looking for the answer somewhere within that paragraph.
Ok I'm sorry for my novel, but I hope this helps a little bit and I hope it helps alleviate some of the stress you're feelings. Final stretch! Keep the momentum!
Also, you don't have a section for future directions?
ReplyDeleteHey Shwath! I really enjoyed learning more about your project and seeing everything come together in your paper. Also, supercomputers... COMP BIO leggo!!! Ok, so here's my general thoughts about each section.
ReplyDeleteLiterature Review: I thought this was the strongest part of your paper. I provided some suggestions to tighten up the writing style. I also think it is imperative that you provide a clear, concise definition of "protein folding" up front when you first mention it, because this is so fundamental to your entire literature review. Further, you will see areas in your lit review where I think it will be key to tie the concepts you bring up back to the overarching significance of your paper: understanding protein characteristics to combat deadly diseases. There are a few instances where I think that transitions between subsections can be improved as well to maintain a direct organization that is easy to follow for readers. Lastly, there are some key definitions which you need to improve on when you talk about the building blocks of proteins, so that non-bio people can have a picture in their head of how the RNA relates to codons relates to amino acids relates proteins. I do think that you need to restructure your last paragraph so that everything before the question is moved to the previous subsection, and rather this subsection is just devoted to the question, your hypothesis, and the implications of your research. But I think these are relatively minor changes, and overall the section is strong.
Methods + Results: I agree with you that both sections have similar errors: brushing over of technical terms. Honestly, while you had a clear structure, I got really lost because you didn't provide an understanding of the different factors you were assessing such as perturbations, DNA-combining sequence, the linker sequence, and the body sequence. The other main issue I saw was for the subsections about Refinement, REMD Simulations, etc. there was no statement of purpose. I think you need to have a sentence for each of these subsections saying what the purpose of each part of your methods is and how that step will lead you closer to answering your question. Kind of related to that, I think you should include a sentence at the beginning of your results restating the purpose of your research and how your methods contributed to answering your question. The more times you can relate back to purpose / significance, the more invested readers will be in your paper. The same terms that you didn't adequately define in the methods, were equally confusing in the results sections. For example, when discussing the Chimera sample in the results, I didn't really have a grasp of what happened in each trial. Without a mental picture of what was going on, it was hard to follow this section.
Discussion: So I made sure to look out for the concerns that you voiced in your blog. One thing that I believe can be improved is the way you relay your findings. While you try to put the various findings in conversation with each other, I think you still need to work on making the links in the findings more apparent. For example, I think you need to do a better job of exploring the relation between binding site and linker and protein function. These are hard to grasp terms / concepts, so the more explicit you can make the connections in your findings, the better. I do want to say that I really liked your interpretation of the results in the second paragraph. I thought it linked everything together in a way that made sense and was not overwhelming. Use that sections as an example for adjusting your first paragraph. While you have significance, this subsection would be strengthened if you fully expanded on how protein flexibility / new proteins can contribute to curing diseases (while it's probably in your head, the connections are not clear for the reader).
Overall, you are on the right track! I see that your motivation to perfect this paper is not 'lac1'ing, so I know that your final product is going to phenomenal!
Hi Ashwath,
ReplyDeleteOverall: You need to explain a lot more and use transitions. When I was reading through the LR, I was excited as a non-bio person that I could understand what was happening, but as the paper progressed you lost me a lot. It all stems for the end of the LR and your methods because they fail to define things and explain their significance. Fixing this would vastly improve your paper and make it easier to follow. Additionally, you tend to use 3-4 sentences to explain one point (especially with the limited definitions you provide). This led me to when reading the first sentence of the sentences that should be combined to questioning what is the purpose of this topic.. what even is this topic. Use appositives and "to" clauses to make you paper flow better. Also, you uses so many sentences that start with "the" next to each other. This indicates that you need to use transitions and combine sentences.
Literature Review: This was definitely the best part of your paper. For 3/4ths you defined everything, made it easy to follow I have no real huge critiques. The major thing is you are missing a hypothesis, which would be helpful for developing your conclusion. Additionally, you seem to go on tangents, but I know they aren't tangents, but that is how they come across. Please be sure to tie everything back to the purpose.
Methods: This is when you stop defining everything and I died trying to read it. I commented on everything you lack a definition for on the paper. Additionally, you have 2 figure 3s. In addition to lack of definitions, I didn't see a lot of importance. YOU NEED TO SHOW PURPOSE.
Results: Again, huge lack of definitions. I also didnt realize I left the methods section, you need a more clear transition into the results. The lack of definitions from the methods left me confused in the results.
Discussion: First you need to add future directions. Second, this section is lacking (you only have 2 paragraphs on your actual results). Also, you refer back to the diseases this research would help and I was like lol so thats what the purpose of this entire paper was. I should not have thought of that. This shows you need to keep the purpose of this paper weaved throughout.
Everything is there for the first 3 sections, it just needs more explanation and the discussion section needs to be greater.