• Can experiments detect differences that matter?
• Does the study show causation or correlation?
• What is the mechanism?
• How much do experiments reflect reality?
• Could anything else explain the results?

The questions above are all important questions when reading, writing, or performing scientific research.

One, it is important for research to detect differences that matter. This is very important as it is really the point of research, to find differences between groups and discover what causes the difference.

Two, it is important to know if a study is pointing to causation or correlation. In a lot of observational studies we can discover correlation, but we can never say there is causation (yes, I learned this in stats… Thank you Jeff).

Three, what was the mechanism that was used to create this different? After a pattern is recognized the next step is to figure out what is creating it and how.

Four, when reading scientific articles it is crucial to decipher how representative the study is of the actual environment. For example does an in vitro study represent what would happen in a human body?

Five, is the result we are seeing caused by what we think it is? In some studies there are too many variables at play to confidently say that A causes B. This is why a good experimental design is important, so that variables can be removed from the equation.

All of these are important, but as for which one is the most helpful for discussing controversies I don’t know if there is an answer that fits every situation. I truly think it depends on the study. I think generally the last two are the most applicable though. Because often studies are too broad and their results could have been caused by an number of things, or they are to narrow don’t represent reality. Really though all of these are important when reviewing science and for interpretation.

The summary article this week was very helpful to understand the information in the full article as well as its significance. This is especially necessary considering the information being covered is about 26 years old from the publish date.

I think the most interesting thing to me was the length of time it took to sequence genomes and the cost involved. Our technology now is exponentially faster and more cost effective, but we would not be where we are today without predecessor tech like the ones discussed in these papers.

Another cool thing is seeing how computing helped to really push genome sequencing forward. I think this trend will continue for ever. As technology improves we will continue to see advancements in scientific techniques as a whole.

(1) Adèle Mennerat associate professor of evolutionary ecology at the University of Bergen in her research article entitled “How to Deal With PCR Contamination in Molecular Microbial Ecology” (2014) asserts that the addition of DNase in PCR mixes can reduce the number of contaminants in PCR mixes. (2) Mennerat provides evidence by performing PCR techniques with a known contaminated PCR mix, but with the addition of DNase that is heat deactivated prior to replication, and shows the reduction in contaminants. (3) Mennerat purpose is to create a solution to PCR contamination in order to improve PCR purity and fidelity. (4) The intended audience is other lab scientist that work with PCR

Working in command line has been both grueling and enjoyable. There have been tons of points that have been frustrating and confusing, but when you finally get your code to run and it does what you want it to do it is the most amazing feeling. It reminds me a lot of how I feel when I learn a new skate trick. Some of the hardest things are the most rewarding and enjoyable.

Coding is relatively new to me. I have done some R coding, html, and a tiny bit of python. Command line is relatively straight forward and is much easier to debug than html, that is the absolute worst. I have had some pretty frustrating moments though mostly with the software itself, both Cyber Duck and command line have crashed on me or flat out would not accept my password, which set me back a day or two, because I can’t do work if I can’t get in.

One thing I found extremely helpful is to have Cyber Duck open when trying to navigate my files, and also to compare to my code to find typos. Another thing that is very helpful is to have another monitor for directions. This is of course money dependent, but I found it extremely helpful to not have to jump around windows. It could also help to just put it on a bigger screen to more easily view your code, even going to the library and using a monitor their or hook your laptop up to a tv.

I had a few moments that really made me feel like I was getting it. The most exciting ones were when I had made a mistake and I knew exactly what I did and new how to fix it, or new how to move about the files without having to references the notes. I have learned a lot over a short period of time, and I am proud myself and the rest of the class.

Being able to read and critique my peers’ writing was very valuable. We didn’t get to do the full panel format but my group of three discussed the papers we were assigned in our small group. I really enjoyed this format. I always enjoy when I can hear other people’s point of view. It always presents new ways of approaching writing and interpreting scientific writing.

My biggest take away was how important it is to expand on my experimental design. The best papers I read had very explicit steps, expected results and well chosen controls. I think my writing tends to be either way to detailed or very vague. For proposals a balance of the two is needed. For my lab report I will be expected to be more detailed which I don’t expect to struggle with as much, but it is a great lesson to learn.

My other take away was how very creative scientific minds can be and how important that is. I read some very interesting and creative papers. This is more of a cool thing, not really a lesson. I was just very impressed. I will try to remember to be creative in my future DOI’s. It is always good to come at scientific questions from a lot of angles.

In “Identification of Household Bacterial Community and Analysis of Species Shared with Human Microbiome” (2013), Yoon-Seong Jeon a bioinformatic scientist, studies and identifies common household bacteria so that household safety can be better achieved. Jeon achieves this by sampling various surfaces in ten households, and through the use of high throughput sequencing identifies the bacteria in the environments. Jeon performs this research in order to inform and improve public health. The audience is public health workers with a science background.

In the science community it is common practice to have your scientific writing peer reviewed. What is peer reviewing? Its pretty simple, basically you submit your paper to a publication and that publication requests other scientists to review your document. Then they report back to you and the publication on their edits and thoughts. This is meant to improve your paper.

Peer reviewing is an important part of the scientific writing process. It helps to improve the integrity of published papers and guards against mistakes. There are of course flaws in the system. For instance the writer can request certain people to review their document which can give an advantage. Another example is if someone who knows of you and does not like you, then they may be overly critical of your work. Even scientists can be petty.

Even with these issues the process of peer reviewing is important and is likely to be the industry standard for generations to come.

I found the process of peer reviewing to be very beneficial for me, it made me reflect on my own proposal. One thing in particular was my explanations of terms and processes. I read one paper that did very well in defining all the pertinent items. This made me think about my own and re-access the quality of my work.

I think it is also helpful to get feed back from your peers before turning in a final. It makes it feel less stressful for me. I should mention though that I do not mind being critiqued or critiquing others.

Lastly, I enjoyed seeing the very broad range of interests between my peers. I like expanding my understanding of the microbial world and this really helps to get exposed to more fields.

The phrase “microbial population” describes a single species of microbe that inhabits a specific ecological area. This population will look different depending on the microbe in the population. This is generally dictated by the morphology and behavior of me the microbe. In contrast a microbial community is made up all microbes in a given ecological area. Like a population, a community will vary in its behavior based on the microbes present.

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