BIOL368/F14:Class Journal Week 11

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Chloe Jones

  1. Classify each paper as hypothesis-driven or discovery-driven and explain why you gave it this designation.
    • I think that the paper that I am doing for this week’s journal club was discovery driven, because in the paper they never discussed previous studies or other findings. Throughout the paper if they found a mechanism or a module that was influential to the mechanism of MRSA they would then work upon that and try to build new cases to find therapeutic strategies. Antimicrobial peptides were a potential source, and they were the first ones to really analyze it as an antibiotic for MRSA. I would classify the Markam et al. paper as a discovery paper as well because he did not introduce his hypothesis in the beginning of the paper and he too had no idea what the outcome would be. He had some idea that a lower T-cell count was indicative of a person with a more progressive form, but he had no prior evidence or knowledge that diversity and divergence would be traits of progressiveness as well. As for the Huang et al. paper I would have to say it was discovery driven as well because although they had some knoweldge of he gp-120 protien the V3 region had not been analyzed to an exent that would allow them to have an idea that it aided in neutralization.
  2. What do you see are the advantages and disadvantages to each kind of research.
    • Hypothesis-driven papers allows you to use information that is already available, and make an educated guess at to what is going to occur in your experiment. The advantages of this is the fact most of the time you have background information which is helpful. The disadvantages may be that sometimes you limit yourself to building on somebody’s else’s project, when your original ideas for experiment may be better suited or your data may be dissimilar to original data that project was built off of. Discovery-driven papers allow you to create your own experiment and not have to incorporate other findings and try to make sense of the data. However, it’s a disadvantage because you don’t know what to expect from the experiment, and the conclusion may be harder to interpret with no previous finding so it makes it not as supported.

Electronic Lab Notebook

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Class Journals


Chloe Jones 03:46, 15 October 2014 (EDT)Chloe Jones

Isabel Gonzaga

  1. Classify each paper as hypothesis-driven or discovery-driven and explain why you gave it this designation.
    • Markham et al: Markham et al. was largely discovery driven, as he did not explicitly state a hypothesis for his findings. The researchers' goals were just to expand their knowledge of the HIV virus and its diversity in individuals from the various progressing groups
    • Huang et al was primarily discovery driven. Their research was focused on finding out anything they could about the V3 region functioning. Although they hypothesized about the V3 region structure, their findings regarding its mechanism and flexibility are primarily discovery based, and were not anticipated clearly at the beginning of their experiment.
    • Voskuil et al combined both of the two types of research. In this article, they started with one hypothesis and performed a hypothesis-driven research. Then, using those findings, they would propose a new hypothesis to further expand on the scope of their research as they discovered more and more about the topic. The sequential use of various experiments make it discovery-driven. However, I think that Voskuil et al. was primarily hypothesis driven, as each experiment and test ran had a clear hypothesis and expectation.
  2. What do you see are the advantages and disadvantages to each kind of research.
    • Hypothesis-driven research allows for a very clear framework for one to work in. The entire experiment protocol may be written out before hand, with the anticipation of certain results. In understanding what results will be seen, it makes it easier for the researchers to know exactly what to look for in the experiment, and devise a method to accurately measure that specific variable. A downside of this, however, is that there is potential for bias to be introduced in the research. As other variables are isolated, other necessary factors may not be considered in the final results determined for the experiment.
    • In contrast, discovery-driven papers allow for a lot more freedom in experimental design. More qualitative research is able to be used, so the researcher is not limited to quantitative results. Bias is also reduced. It also allows the researcher to look at the issue in a greater context, rather than isolating out the variables, and thus they might be able to see a more holistic view of the problem at hand.

Isabel Gonzaga 02:28, 12 November 2014 (EST)

Weekly Assignments

Class Journals

Electronic Lab Notebook

Nicole Anguiano

  1. Classify each paper as hypothesis-driven or discovery-driven and explain why you gave it this designation.
    • I would classify the Markham et al. and Huang et al. papers as discovery-driven. The Markham et al. paper did not state any hypothesis or predict a result at the beginning, but aimed to see if any correlation between progressor group and other factors such as diversity and divergence existed. The Huang et al. also did not state any hypothesis or predict a result, but simply aimed to see if the crystal structure of the V3 protein, as well as any knowledge of its function could be discovered. Neither worked off of a hypothesis. The paper that I analyzed for the presentation, by Fontan et al, is discovery driven. It didn't aim to prove any hypothesis, but merely sought to see if there is any correlation between the σB regulon and oxidative stress.
  2. What do you see are the advantages and disadvantages to each kind of research?
    • Hypothesis driven research has enough background to provide an educated guess on what the result will be. Because the result is likely already known, the experimental design becomes much easier to create. However, there can be a potential to bias the experiment towards what is already known due to the research that is already out there. It can be more difficult to come up with fully original experiments when dealing with pre-existing data and information. Discovery driven research comes from a lack of knowledge about the topic. In thus, it allows for full creativity in creating an experiment. While this can also make things more difficult, it allows for varying experiments around the same topic that may approach it in different, more effective ways. However, as there is little background information on the topic, the results can be difficult to interpret. It can be difficult to draw any concrete conclusions from the results, as it is possible that other unseen factors could be at play, so further research is often needed to find a more concrete conclusion.

Nicole Anguiano 01:15, 19 November 2014 (EST)

Nicole Anguiano
BIOL 368, Fall 2014

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