BIOL398-03/S13:Class Journal Week 3

Reflection

user:Kevin Matthew McKay

• The purpose of the assignment was to familiarize us with scientific papers and specifically this scientific paper which we will be working with for part of this semester. It was meant to get us used to reading and analyzing data from experiments and graphs.

• It was easiest for me to understand the purpose and procedure of the experiment. I have referenced papers like this one for other work I have done and am familiar with the layout and many of the terms used in the paper.

• What was most challenging was really putting the heavy science of the paper into simpler form in my outline.

• I do not yet understand what a continuous culture is.

Kevin Matthew McKay 02:11, 30 January 2013 (EST)

Laura Terada Week 3 Journal

Laura Terada

Reflection

• What was the purpose of this assignment?
  • The purpose of this assignment was to help us to be comfortable with reading scientific papers and reports. Moreover, it allowed us to understand scientific data in the form of graphs. The questions we were required to answer in our assignment made us think about the overall purpose of the study, why it is relevant, and what implications it has for future research.
• What aspect of this assignment came most easily to you?
  • It was somewhat easy for me to understand the background information and the overall purpose of the experiment. I understood what aspects of nitrogen metabolism they were testing for and the reason for it.
• What aspect of this assignment was the most challenging for you?
  • The most challenging aspect was interpreting the data. There were a lot of variables being tested for (genes, enzymes, biomass, respiration, etc.), and so bringing all the data together to get a coherent conclusion was difficult for me.
• What (yet) do you not understand?
  • I'm still unsure how all the variables that were being tested for work together to get the conclusion. It seemed like the authors tested for different parts of nitrogen metabolism to show how ammonia concentration alters this process; however, I'm still unsure on how all the components relate to each other.

Laura Terada 19:08, 30 January 2013 (EST)

Paul Magnano Week 3 Journal

Paul Magnano

Reflection

• What was the purpose of this assignment?
• What aspect of this assignment came most easily to you?
• What aspect of this assignment was the most challenging for you?
• What (yet) do you not understand?

Paul Magnano 20:09, 30 January 2013 (EST)

Kasey E. O'Connor Week 3 Journal

Kasey E. O'Connor

Reflection

• What was the purpose of this assignment?
  • The purpose of the assignment was to make us familiar with reading and understanding scientific papers. This paper was not only good to give us experience and exposure to the proper paper layout and structure, but it was also relevant to the biological systems we are learning about. It also helped to teach us to how to read and understand graphs from specific reading.
• What aspect of this assignment came most easily to you?
  • Understanding the graphs in the paper was the easiest for me. Coming from a strong mathematics background, I have had a lot of experience with graphs, and these were relatively simple to understand.
• What aspect of this assignment was the most challenging for you?
  • The most challenging was trying to keep all of the different enzymes and other chemicals straight while I was reading and also trying to keep all the numbers and measurements straight.
• What (yet) do you not understand?
  • I still do not understand all of the ways the enzymes and gene activities were actually measured.

Ashley Rhoades Week 3 Journal

Ashley Rhoades

Ashley Rhoades Week 3

1. The purpose of this assignment was to familiarize ourselves with actively reading a scientific paper. Also this article introduces discusses concepts in our first project.
2. I took my time reading the paper and I took notes so I understood the article so for the most part comprehension came easily.
3. I still don’t have a full grasp of the cycle of nitrogen metabolism so some of those parts of the reading were more difficult.
4. Parts of the article discussing the enzymes in nitrogen metabolism I understand and parts I don’t and I think that’s because I don’t have the full cycle of nitrogen metabolism in my head.

Ashley Rhoades 23:41, 30 January 2013 (EST)

Helena Olivieri Week 3 Journal

Helena M. Olivieri

• What was the purpose of this assignment?

The purpose of this exercise was to introduce and familiarize ourselves with scientific journals that emphasizes the significance of modeling.

• What aspect of this assignment came most easily to you?

Most of the general concepts came easiest to me, as well as reading the graphs.

• What aspect of this assignment was the most challenging for you?

Slowing down to really comprehend the details of the article.

• What (yet) do you not understand?

I think I'm still a little confused by some of the molecular details. Helena M. Olivieri 23:49, 30 January 2013 (EST)

Anthony J. Wavrin Week 3 Journal

Anthony J. Wavrin

1. What was the purpose of this assignment?
   • The purpose of this assignment was for us to get experience reading a scientific paper and thinking about what was actually being done and why it was being done. This is important because it is a skill that has to be used in the real world of science when you do not have a professor to answer all of your questions. Also, it is the only way to keep up with the new discoveries of science.
2. What aspect of this assignment came most easily to you?
   • The actual reading and understanding of the paper. I have spent quite of bit of time reading scientific papers and this was a relatively simple experiment.
3. What aspect of this assignment was the most challenging for you?
   • The hardest aspect was the actual making of the outline. I am not used to organizing my ideas and making it understandable for others. Instead, I am use my own notation to remind myself.
4. What (yet) do you not understand?
   • In regards to the paper, the only thing that I did not understand completely was the RNA expression part. It was unclear to me of what the RNA they were isolating actually did, it only told me that it was associated with nitrogen in some fashion, or it was a control (either actin or histone).

Anthony J. Wavrin 00:33, 31 January 2013 (EST)

Matthew E. Jurek Week 3

Matthew E. Jurek

• What was the purpose of this assignment?
  • The purpose of this assignment was to introduce us to how to read a scientific paper. This is not the easiest thing to do, as these articles often involve a lot of unknown language. Outlining the article was meant to help us further understand this experiment. This is important as we will all be presenting a part of the paper in class. Learning how to read scientific papers will help in the future as we have more Journal Clubs.

• What aspect of this assignment came most easily to you?
  • Understanding the flow of this type of writing. Last semester I took a course where we read and discussed scientific articles each week. Because of that I was familiar with the various sections of this article (even though they weren't explicitly labeled).

• What aspect of this assignment was the most challenging for you?
  • Understanding what exactly was occurring in the experiment. It always takes me a few reads to fully understand the design and purpose of the experiment. I say this because I have to sift through all the specific details to get the larger picture. Also, the outline was difficult as it's hard to fully simplify the experiment for somebody else.

• What (yet) do you not understand?
  • I'm still trying to digest all the aspects of the experiment. In the enzyme part, the figure shows how enzymatic activity was controlled transcriptionally and post-transcriptionally. I'm still working on understanding how they reached these conclusions. Obviously it's dependent on the ammonia concentration, but I want to fully understand how they could tell this.

• Matthew E. Jurek 00:47, 31 January 2013 (EST):

James P. McDonald Week 3 Journal

James P. McDonald

1. What was the purpose of this assignment?
   • The purpose of this assignment was to familiarize ourselves and gain experience reading scientific papers. Scientific papers can be very dense and use complicated language so practice with these types of papers can be very useful. It is important to become skilled in reading scientific papers such as these as new discoveries are always being made in the science world. This assignment will also help us with reading more papers for future assignments we will have to complete in this class.
2. What aspect of this assignment came most easily to you?
   • Being able to read the paper and understand what is going on in it. I have had experience reading scientific papers so I have developed some skill in reading and understanding them. I know the sections that they are normally separated into and therefore I did not have any trouble finding the specific parts .
3. What aspect of this assignment was the most challenging for you?
   • Taking the information putting it into an outline. This process took a lot of time as I had a hard time translating the language used in the article, making it simpler so that other's can understand it and putting it in my own words. When I read a paper I have my own way of understanding and interpreting the information.
4. What (yet) do you not understand?
   • I still do not really understand the northern analyses section of the paper. I had a hard time understanding how they measured the RNA expression levels. I haven't seen a method similar to that used before so it was new to me and difficult to understand.

James P. McDonald 01:27, 31 January 2013 (EST)