Episode 23: Scripting and Sliding

It's been an exciting week, of research. The editing got intense this week with revised papers. Everyone had to go the extra mile to give good feedback. Sad to see some teams NCAA bracket, Calais Campbell is gone from the Cardinals. Also the presentation is in 2 weeks, so that's creeping up on us.

The meme of the week is an old one, Supa Hot Fire. It is a character in a series of satrical YouTube videos, parodying battle rap. The videos consist of rapper Supa Hot Fire battling multiple rappers. The videos revolve around the crowd biasing around Supa Hot, overreacting to the extreme when he finishes his verse. Here's an example.

This week we were tasked with slides and scripts, and understanding the presentation rubric.

The first rubric row talks about the research question and the reasoning behind it. Being worth only 3, it is not a hard row to knock out of the park. I feel like my script adequately responded to this row. Row two is about the implications and limitations of my results. By conveying my results and discussing significance, implications, and limitations, I can attain the 6 points here. It is important to notice that the lit review has very little importance in this section, and that my focus should be on the methods and results.

The third row connects the hypothesis from the lit review to the conclusion arrived by the paper. I need to explain what I thought at first, what I arrived at in the conclusion, and what from my findings confirmed the hypothesis or not. Using Swint-Kruse as my hypothesis and initial thoughts will help me out in the presentation. I did a decent job of row 3 when arriving at my question and discussion. At a meager 3 points the row should not be difficult to achieve.

Now row four is my battle ground. The ability to present, speaking style, and presentation tools give this row a 6 point evaluation. As a veteran debater and public speaker, running my ideas past in a confident presentable way is not very difficult. My slides are simple and easy to understand.

I placed a lot of confidence in my ability to explain the graphs. It will be a lot easy to point and interact with tables and graphs as opposed to explaining things in a painstaking manner in my paper.

Till next week,

Ashwath V.

Episode 22: Revisiting a Paper

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.

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.

Episode 21: GRAPHS ARE IN

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.

Episode 20: Discussion and MUN

This week I attended a Model United Nations conference where I was Venezuela working with the Security Council on issues such as the South China Sea and Syria. It was a double team event, so I had a partner. His name was Amaan. I basically did all the talking, and Amaan did the writing.

When you hate the errors in CPUs holding you back

In terms of my research,  I am still waiting on my min12 results. The final step is just not coming together for whatever reason. Hopefully I can get it fixed in a timely manner. In preparation of a late arrival, I will write a results section based on the Lac1 data I have prepared. JUST KIDDING I JUST CHECKED IT AND I HAVE THE RESULTS BACK!!!!!!!!!!!!!!!

For the topic of this blog post, I was tasked with analyzing the discussion sections of my discipline. The three papers I decided to look at were Subdividing Repressor Function: DNA Binding Affinity, Selectivity, and Allostery Can Be Altered by Amino Acid Substitution of Nonconserved Residues in a LacI/GalR Homologue, The Role of Conformational Dynamics and Allostery in the Disease Development of Human Ferritin, and Rheostats and Toggle Switches for Modulating Protein Function.

The first paper delved into the evidence by analyzing the flexibility of the linker region of Lac1. It talked about locking, binding affinity, and overall 3D descriptions. Then the writers moved into more theoretical extrapolations about reverse evolution. It seems to analyze the effects of their trials to each of the 3 regions of Lac1. It may be easier to explain if I walk through all 3 sections of a chimera in a similar fashion. But even after that it talks about future applications like Protein Engineering and in Vivo and in Vitro Functions. These really hook the reader, so it will be useful to add the analysis in.

The second paper was very focused on the use of DFI. The discussion was heavily linked to the DFI evaluations. I think I should try to combine the DFI analysis from the second paper with the extrapolations from the first.

Finally the third paper was extraordinarily technical in its discussions. Similarly to paper one, it did look into several different extrapolations. But the literature was so technical that the average reader would get lost in trying to understand the reading.

So my discussion section will focus on the DFI for each of the three protein regions first with 3D protein descriptions, then it will delve into the implications for the analysis.

And before I leave, let me hit you with the To Be Continued meme. It basically stops a situation right and the climax, leaving you wanting more. The origin is from the Jojo's Bizarre adventure cliffhangers. Check a compilation out here.