 |
| 3D Models of the Chimera and 1efa |
It's been a weird week, but I got the wheels back on the bus. I finally got my data back and my analysis back. The graphs are in and so are the structures. This week I was tasked with completing the paper! However, I only just got the results back this Sunday! I also have an extremely limited knowledge of what any of the DFI regions mean! Put those three things together and we now realize that I am very far behind. But if there's one thing I know about myself, the work will be done.
 |
| The comparison based on solely DFI values |
The name of the game is finish the results and discussion section in time for peer editing this Wednesday. I am going to meet with Professor Ozkan this Monday. I will comprehend what the covariance matrix is, what it did, and how I got this graph (I have a general understanding, but if there was ever a time to clear up misunderstandings with the one person who knows it best, now would be that time). The second step is the discussion. I am not exactly a graduate student majoring in Physics, so identifying the specific interactions between amino acids will be difficult for me (I can generalize and explain them). Dr. Ozkan and I will go through the protein and basically identify the "hooks" and "nonconserved" structures. The other papers I have looked at are highly specific and very brief in their discussion. I will try to expand upon that style and interpret my results.
A brief look at my data shows that both the chimera is lower in DFI when compared with Lac1 at the DNA binding sequences (indicating less flexibility) and more flexible in the nonconserved regions of the body. In general it seems that the body of the protein is affected by the changing of nonconserved regions.
Overall, I feel rather good about the direction my paper is going in. Hopefully the paper is completed by the middle of this week for editing. The strengths of my paper lie in the literature review and my baby birding (editing). The biggest weakness on the other hand is my technical language and my unwritten sections.
The meme of the week is Scott Sterling, an unfortunate soccer player who gets pegged in the face multiple times. He does block all the penalties though. Check it out
here.
I guess it's difficult for you to give feedback to your classmates on what to focus on, considering that you haven't written a good portion of the paper (and don't have a ton of clarity about what it'll look like), but I'd like to see you give a little bit more specific information to your peers.
ReplyDeleteEven if the wheels are back on the bus, it still doesn't mean the bus is running--it just means the bus can finally move. Big boy, your paper needs some work--not that this paper is bad, or anything. It just needs some work.
ReplyDeleteYour paper uses a lot of technical terms, but you don't always explain them, leaving the reader lost and confused. On the same point, you presume a lot of knowledge from your reader. A big part of this is probably because you yourself don't understand what is going on yet (not to bash on you or anything).
My biggest problem with your argument was that you did not clearly show the academic gap and why your research is important in filling said academic gap. Further, I think the word count limit is killing you here. The amount of information needed in this paper is enormous, and a 5,000 word count is not suitable for it. So, there were some points that you just did not even extrapolate. There were also other parts where you were too specific and you put in unnecessary information.
Right now, I think you are in a dangerous position: you know a lot more than the reader, however you still are not able to fully comprehend the material, so your paper is both confusing and hard to understand. Once you have sorted it all out, and clearly know what you want to talk about, I am confident your paper will be significantly improved.
Overall, I'm not saying it was a bad paper, it was just a bit confusing and disjointed, and it needs some work. But I believe in you and I know that your final paper will be a lot better.
Hey Ashwath!
ReplyDeleteI agree with Gursajan's overall feedback... I was getting the same vibes. Your research is fantastic, and your graphs and figures are extremely cool, but you seem to leave us with just results. What the reader is left with after reading your paper is just exactly what you observed about the chimera that you chose.
Unlike in your literature review, where you related it back to medical significance and some biology, you simply discuss features of the protein. In this way, your results section is solid, but I think your discussion section lacks a lot of interpretation. I see that you tried to connect it a bit to other sources, but the reader doesn't understand what all of it means. I think the best way to fix this might be a sit-down with Professor Ozkan to try to figure out how to connect your results to a solid interpretation where you are adding to the specific field of research, but not just stating facts for other researchers, like your boi Paul, but also for someone like an AP reader to understand. For this reason, your paper lacks punch because I don't really get the significance of what you're showing.
Stylistically, I'm not one who can complain about readability, but I definitely thought you threw around some terms in the results and discussion which were not introduced or introduced very briefly in the methods (e.g., DFI, REMD, etc.). I think your results and methods sections should be much more well-connected, especially considering your method was literally creating a model that spits out results for you. In this way (and perhaps with a few less acronyms), the reader can see what happened and understand the role you played in it. Some code screenshots may not be a bad idea. Lit Review was the strongest, but there are some places where you assumed knowledge (I pointed them out).
Good job overall, but make sure you are hashing out a better discussion with a greater significance. Because you did significant work all year, but it's lost on the reader.
Cheers,
Yash
(349)