BIOL398-04/S15:Class Journal Week 2

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William A. C. Gendron


  1. What was the purpose of this assignment?
    • The purpose of this paper was two-fold. First, it was to help teach us how to read and approach a scientific paper so that we understand it and are able to discuss it. Second, it is to introduce us to the topic metabolic pathways and prepare us to look at chemostats for us to model.
  2. What aspect of this assignment came most easily to you?
    • Analyzing the charts was the easiest aspect of the assignment. These were relatively well made compared to the one I had to read for my presentation this morning so I was happy with that.
  3. What aspect of this assignment was the most challenging for you?
    • I am not as familiar with metabolic systems unfortunately so I had to read it carefully and make sure that I understood what was being referred to.
  4. What (yet) do you not understand?
    • I was unable to gain access to some of the papers that had the methodology for the enzyme detection, so I do not understand how they got that data.

[[William A. C. Gendron 02:33, 27 January 2015 (EST)]]

Alyssa N Gomes


  1. The purpose of this assignment was to learn how to deeply analyze a scientific paper, by breaking it down into several segments, going through the vocabulary first, and then re-reading to outline. Through this process, we can learn the importance of thinking critically and using the skills utilized in this paper toward our own work.
  2. Outlining this assignment came so easy to me. I was able to break it down into the segmented parts and determine which parts were important and which should be omitted. With scientific papers, there is great importance in being able to sift through the material and determine what parts contribute to the conclusion and which parts are too descriptive to need in a summary used to a wider audience.
  3. What aspect of this assignment was the most challenging for you? Understanding the paper as a whole came as quite the challenge to me. I think all of the complex names of genes, and nitrogen values contributed to the complexity of me trying to scan the paper easily. I had to slowly go over every sentence to make sure I could differentiate each specific RNA coding and gene-line. Reading the figures helped out a bit, but I have to admit, my lack of biology background made it difficult to process each scientific term.
  4. I still do not quite understand the actual processes used to determine the RNA expression levels and how to measure the transferase. I wish the paper had articulated more about what step-by-step means were used to put a number to these big ideas.

Alyssa N Gomes 00:14, 27 January 2015 (EST)

Lauren M. Magee


  1. What was the purpose of this assignment?
    • The purpose of this assignment was to expose us to scientific research and literature, so that in future weeks, we will be able to do our own literature reviews. Before starting any new research, you must first gain an understanding of what has been done on the topic previously. That is why literature reviews are important: to prevent us from repeating research and to assist in the development of new hypothesises. This assignment also focus on how to read research papers in order to fully understand the content.
  2. What aspect of this assignment came most easily to you?
    • I found the easiest part of this assignment to be finding words in the research article that you don't know. While I do have experience in both biology and mathematics fields, there are always different vocabulary words used that I usually use context clues to find the meanings for. I appreciate though that this assignment gave us the venue to further analyze the words we didn't know and confirm their definitions from an outside source.
  3. What aspect of this assignment was the most challenging for you?
    • I always find it difficult to read figures. It's not that I don't understand the information being presented, but often times the visual are hard to read and crammed into a small space of the paper. From writing my own research paper, I understand how hard it can be to include figures, because of the page limits some publications require. However, they often tend to make already challenging material even harder to interpret.
  4. What (yet) do you not understand?
    • Because the article was fairly dense with information, I could use some clarification on the processes of nitrogen metabolism and the application of the paper findings.

Lauren M. Magee 01:00, 27 January 2015 (EST)

Lucia I. Ramirez


What was the purpose of this assignment?

  • To see how math can be used to visualize the cause and effect between regulators

What aspect of this assignment came most easily to you?

  • Analyzing the graphs and seeing the correlation made between the concentrations being compared.

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

  • Trying to understand how these chemicals interact

What (yet) do you not understand?

  • The mechanics of the complex biology described in the text.

Lucia I. Ramirez 02:59, 27 January 2015 (EST)

Natalie Williams


  1. What was the purpose of this assignment?
    • This assignment is a precursor to what we will be doing for the rest of the semester. We will have to read different articles and journals as a class and on our own. By doing this together, we can discuss what we learned, see how interpreted the work, and better our skills for reading scientific articles and journals. Plus, by reading this articles, we can also learn lessons which will help us improve our own scientific writing skills.
  2. What aspect of this assignment came most easily to you?
    • The terms were not too difficult to understand for me. Just having taken Cell Function, some of the proteins and enzymes mentioned were very familiar such as NADPH and GDH. Plus, cell function looked at various pathways and how they are interconnected, and I could follow the concepts in this article.
  3. What aspect of this assignment was the most challenging to you?
    • For me, trying to summarize the article in my own words was more difficult. As a person who has had to read a lot of scientific papers, the language is something that you get used to; however, in summarizing the results and methods, it is hard to explain in laymen's terms.
  4. What (yet) do you not understand?
    • I am having trouble understanding specifically what each gene had to do with yeast and how its activity affected the overall organism.
Natalie Williams 16:42, 26 January 2015 (EST)

Back to Individual Journal

Tessa A. Morris

  1. The purpose of this assignment was to become comfortable reading and understanding scientific papers. Being able to comprehend scientific papers is an important skill to have for scientists and mathematicians, because research involves discussion with peers as well as drawing on papers of the same topic.
  2. The aspect of this assignment that came most easily to me was reading the scientific jargon. I am becoming increasingly more comfortable reading scientific papers, even though the language used in the papers can make reading them unnecessarily difficult.
  3. The aspect of this assignment that was most challenging to me was summarizing the paper. It was such a short paper that ever sentence seemed important and I had trouble focusing my outline.
  4. I am still having trouble understanding the importance of each gene. There were a lot of different genes mention in the paper that were important enough to label, but I am having trouble understanding the function of each of the genes mentioned.

Tessa A. Morris 01:28, 26 January 2015 (EST)

Kristen M. Horstmann

  1. The purpose of this assignment was to help us create and refine critical reading skills for scientific articles. For the rest of the class, we will be reading and analyzing articles such as these, so this article was an introduction to that. It is important for us to strengthen these skills in order to be able to critically think about the topic presented, the findings, and the conclusion as we will likely have to sift through many articles such as this one for the rest of our scientific careers.
  2. Creating and defining a list of unknown words was the easiest aspect for me. I felt like I knew a good amount of the words in this article, and could have used context clues for the ones that I did not. However, by making a list and defining them, it ensured that I truly was understanding the words and not blindly thinking of something that I was remembering incorrectly.
  3. Understanding and sifting through the dense article overall was the most difficult part for me. I do not have a ton of experience reading scientific journals, only a few for chemistry and psychology. So being able to sift through the jargon, the wording, the acronyms, and different numbers was difficult the first time I read through it. This also applied to the figures. It is relatively easy to read figures and their explanations, but not so easy to understand how it applies to the article if I don't have an exceptionally strong biology background.
  4. I still do not fully understand the differences in function and importance of each gene and enzyme. With my limited understanding in molecular biology, I will need to refresh and continue learning the functions of the major enzymes, proteins, amino acids, etc. That would make reading articles- like this one- much more attainable to understand and analyze.

Kristen M. Horstmann 18:01, 26 January 2015 (EST)

Kara M. Dismuke

  1. What was the purpose of this assignment?
    • Besides understanding the specific results of the paper, I think the purpose of this assignment was to learn how to read a scientific journal article and analyze it’s findings. I think it helped to lay a foundation from which we will build upon in this course.
  2. What aspect of this assignment came most easily to you?
    • I do not know if there was one aspect that came easy to me as I have never really taken an in-depth look at a published scientific journal article before. While a closer reading allowed me to understand some of the material discussed, the article’s inclusion of graphical illustrations helped me to see trends and better understand what the article was discussing.
  3. What aspect of this assignment was the most challenging for you?
    • Because I am a math major with a limited background in biology, it was difficult for me to be able to understand the results presented in the paper as I struggled to understand the context of the material presented. Although looking up the definitions of many of the terms helped a little bit, it was challenging for me to apply these definitions while analyzing the experiment’s results.
  4. What (yet) do you not understand?
    • I think I understood the majority of the material as it relates specifically to the effects of increasing the ammonia concentrations, but I still do not understand the role that glucose (of various amounts) played in the experiment. While I could interpret the graphs to glean the various trends, I still feel like I do not understand the specific substances/chemicals that were discussed in the paper. I must admit though, I did understand more of the article’s material than I had anticipated.

--Kara M Dismuke 01:14, 27 January 2015 (EST)

Karina Alvarez

  1. What was the purpose of the assignment?
    • The purpose of this assignment was so that the we could have some experience in not only understanding scientific papers and becoming more comfortable in learning from them, but also learning to be more critical. As scientists, it is important to be able to critique one another's, and your own, work in order to come to results that are reliable.
  2. What aspect of this assignment came most easily to you?
    • The aspect of the assignment that was easiest for me was understanding the language of the article. Having researched nitrogen-fixing bacteria and legumes for a semester, I understood the role of limiting nutrients and could understand the methods used in the study.
  3. What aspect of this assignment was the most challenging for you?
    • The most difficult part of the assignment for me was being able to read the graphs. While I am comfortable making and reading graphs mostly, these had two Y-axes and were a bit more complex than I am normally accustomed to. While they were different, it only took a little extra time to understand them and the data they represented.
  4. What (yet) do you not understand?
    • I did not understand completely how NADP and NADPH signified increased growth or biomass. I would like to pursue this in class because it seems like an effective tool for understanding the growth and productivity of an organism.