BIOL368/F11:Class Journal Week 11

Alex A. Cardenas

1. I believe this paper was a discovery-driven paper because throughout the reading, there would be no reference back to anything in the beginning. It seemed like while they were finding out these different virulence factors and possibly different treatments of MRSA, they kept trying to find out more mechanisms that were being affected and anything else in relation to the exposure of ranalexin.
2. The advantages of both kind of research is that there are going to be findings no matter what. Although the findings that support a proposed hypothesis might be more rewarding. The disadvantage of discovery-driven research is the possibility of not being able to conclude anything substantial especially if you have nothing to go off of other than discoveries during research.

Alex A. Cardenas 17:49, 15 November 2011 (EST)

Robert W. Arnold

1. I would say this paper was very much discovery driven. It seemed like they grabbed an idea and ran with it. Instead of slowing down and making hypotheses, they seems to just continue running experiments and studying ranalexin effects.
2. I think they both need to be used together to really do good research. I think an overall hypothesis is good to have but sometimes if you get to nit-picky about the hypothesis you start to lose the big picture. Sometimes it is good get an idea of where you want to go and then see where you end up going. Hypothesis research may leave certain questions unresolved and discovery may lead you to discover things not pertaining to your research.

Robert W Arnold 19:50, 15 November 2011 (EST)

Nicolette S. Harmon

1. I think that the M. Smegmatis paper is more of a discovery-driven paper. This paper talks about what they feel the previous studies lacked in their findings, however they didn't know what they were looking for so I would say this paper is discovery-driven. I would say that the Markham paper was also discover-driven and that the Kwong paper was hypothesis-driven due to the fact that they were determining structure and function of gp120 in HIV-1.
2. Both are necessary to do proper research. When you do hypothesis-driven research, it is easy to dwell on why your data did not give you the results you expected. With hypothesis-driven research it is easy to overlook what you are studying as a whole, although having a hypothesis does give you a little more investment in the experimental process. Discovery-driven research is effiecient when you don't know what to expect from what you are trying to do, although it may be harder to draw a conclusion from you data since there was no previously established hypothesis.

Nicolette S. Harmon 23:16, 15 November 2011 (EST)

Samantha M. Hurndon

1. I believe this paper to be a discovery driven paper due to the fact that they based their research off of previous discoveries about flagellar genes.
2. With a discovery driven paper, one of the advantages is that you have some other relevant research use as a reference to your study. However, with this type of research an issue can be that you may not be able to conclude very much off your findings. With a hypothesis you can reject or accept which is a little more satisfying than concluding that your findings are inconclusive.

Samantha M. Hurndon 01:34, 16 November 2011 (EST)

Chris Rhodes

1. I would consider the Markham paper to be a discovery driven experiment. Although they had a lot of previous research to hypothesize with, there didn't seem to be clear expectations about what the lab was going to find in each of the patients. The grouping into progressor types was only done after the experiment was concluded and data analyzed and I don't think they could've have been looking for some specific something without defining their groups first. My Stanfield paper was clearly hypothesis driven as the lab was testing specific structures from their own previous research and indicated many times that they expected to see functional conservation of the GPGR region. My paper for this week is also very clearly discovery driven. The study was looking at the effects of oxygen and carbon limitation on bacterial cultures and looked at the entire genome suggesting there was no particular focus on any specific gene cluster or region.
2. Hypothesis driven research can typically focus on a particular area of study because they are more aware of what they looking for from their data or what experiments will give them the data they require to draw conclusions. Hypothesis driven research does have the disadvantage of having the potential for biased interpretation, researchers may purposefully or accidentally overlook data that doesn't agree with their original hypothesis or only interpret their data in terms of the original hypothesis rather than looking at all the potential options. Discovery driven experiments can sometimes lack a focus and often end up having to try and interpret a large amount of data where minor but critical details can be easily overlooked. However discovery driven experiments don't have the potential biases that come along with hypothesis driven research.

Chris H. Rhodes 02:10, 16 November 2011 (EST)

Isaiah M. Castaneda

1. Classify each paper as hypothesis-driven or discovery-driven and explain why you gave it this designation.

   • Markham: Discovery-driven. Markham did not indicate any hypotheses in the beginning of his paper, but rather appeared to be exploring evolutionary patterns while taking previous similar studies into consideration.
   • Stanfield: Hypothesis-driven. Stanfield already had done research on V3 peptide structures and was exploring hypothesis about V3 conformation changes and how they may or may not affect anti-body binding.
   • Douillard: Discovery driven. The research seemed to be based off of previous studies that Douillard wanted to further delve into. It may just be the way the paper was written, but there was no indication of hypothesis-based action being taken. However, by the end of the paper, clear hypotheses were made regarding future experiments. Therefore, future research done by Douillard & his colleagues may be classified as research-driven.

2. What do you see are the advantages and disadvantages to each kind of research?

   Discovery-driven research allows for refinement and correction of previous discoveries. They are easy to start because a foundation has already been created. However, research may not be as ground-breaking as hypothesis-driven research.

   Hypothesis-driven research is more original, yet more risky. The research can very possibly pioneer new findings and results, but there is also the chance that the results are inconclusive/insignificant, because the experiments were not based on previous, quality findings.

Isaiah M. Castaneda 02:51, 16 November 2011 (EST)