Weekly MB 311 Blog

• Can experiments detect differences that matter?
  • Absolutely, this is the basis of all advancement that has been made in all areas of science. The ability to experimentally prove causation allows us to build off of other ideas and develop new ideas, methods and technology.
• Does the study show causation or correlation?
  • Causation occurs when the occurrence of something directly leads to an influence on something else. Correlation, on the other hand, just means that the occurrence of two things are somewhat linked. Correlation, at best, suggests a strong relationship between two variables while causation shows absolute linkage between two variables. As I read this question a quote from a previous stats course came to mind, “correlation does not imply causation!” It’s important to remember that while a correlation may insinuate a relationship, the presence of confounding variables is always possible.
• What is the mechanism?
  • Essentially, the mechanism mentioned in this paper revolves around the idea that once a relationship is found, the next step is to try to determine the mechanisms behind it, how they influence each other, and if the relationship is replicable .
• How much do experiments reflect reality?
  • This question is difficult to answer. The actual reflection on reality shifts between experiments and is a very important factor to keep in mind when reading any scientific literature. For example, reading a study about a biochemical reaction of a drug is informative, but considering the actual environment and other factors which could influence it within the human body is imperative before any human trials could occur.,
• Could anything else explain the results?
  • As mentioned above, confounding variables are always important to keep in mind as they could be influencing the results. In some cases, it may be difficult to fully explain the results. But being vigilant for potentially confounding factors and emphasizing replicability can help to reduce their impact.

Overall, I would say that #4 and #5 are the most important when discussing controversy surrounding scientific literature. Peers suggesting possible confounding variables, or alternate mechanisms in differing environments are important comments and things the researchers may not have properly considered initially. However, these are all important questions to consider during the scientific review process.

I found the article somewhat confusing and I had a difficult time initially taking in all the details and their meaning but I was able to understand the larger takeaways and their purpose. I then went on to read the review, and found that this helped me digest the content and better understand the paper. After reading both and having a good general understanding, I went back and read back over the areas which initially confused me with the aid of the review. Overall, I think the review helps to drive home the points and provides a more palatable approach to understanding the paper.

One main takeaway was the difference between our ability to sequence in this weeks classes versus the time period described in Fleischmann’s paper. Its clear to me that with our current technology genome sequencing has gone from taking six months to under an hour. This is an incredible advancement and made me feel very thankful for the developments in our field which make information so accessible. I am personally not a huge fan of the coding we’ve been doing, but it provides us with incredible information and ability.

(1) Adele Mennerat and Ben Sheldon in their review on PCR preparation effectiveness titled “How to Deal with PCR Contamination in Molecular Microbial Ecology.” (2014) explain the influence of Contaminants present within PCR primer reagents, influences of such contaminants and decontamination approaches to lessen the impact and improve data quality. (2) Mennerat and Sheldon provide evidence that enzymatic treatment does reduce contamination levels, but has the potential for adverse influence on microbial richness. (3) The purpose of this study is to provide analysis on potential decontamination methods for the Priming process, and test their influence on two enzymes (DNase 1 and Sau3AI) to determine if the ability to replicate and interpret the data collected from DNA amplification is improved or lessened. (4) Mennerat and Sheldon have developed an academic background in Biological laboratory practices, as well as other areas of study such as Zoology.

Prompt – Following our recent in-class tutorials where you worked your way through learning DNA sequence analysis and chimera detection through your use of the command line, reflect on this learning experience. For some of you, this is a practice you’ve done before – did you learn anything new to add to your knowledge base? Did you think of any work-around that you use that could be helpful to other students just learning this? If this is your first exposure to this, reflect on the process – what was the most intuitive (if anything) part of this process? What was the most difficult to understand? Did you have any “eureka” moments? In the end, does this make sense to you?

This was essentially my first experience with coding. Last term, I did a very small amount of data analysis using R studio in my stats course. However compared to the information and work we have done in the last few weeks in this class, that was nothing.

I found that initially, nothing was intuitive. I don’t have much computer experience, and until the pandemic hit, was not very literate in the abilities of my computer other than basic programs like google docs and some excel work. From the first assignment on, I struggled to understand what was happening. After only being able to complete the first assignment with the help of others at my lab bench, I decided I needed to sit down and just get practice using the interface. I pulled up our two tutorials we had at the time, a google doc and just tried to figure it out. I gained experience using basic commands, navigating between directories, reading actual sequences, etc. I felt I better understood the content and felt relatively confident in my ability to complete the next assignment.

I worked on Assignment #3 with a few people from my lab bench, and was able to contribute and somewhat understand the purpose/ application of the work. I wasn’t able to keep up on the graph creation we did in class, but plan on going back through the lecture and following along soon.

Overall, I think I get the “main points” but am worried about how specific we should be in our report. I understand the overarching themes and why we did the work that we did, but don’t feel I could accurately articulate the finer details of the process.

The ability to review others ideas and methods in writing on the same prompt was extremely valuable and allowed me to gain new insight into my own writing’s format. In all of my experience peer reviewing, I have found it is easier to see errors in someone else’s work over your own. Perhaps this is because you’re invested in your own work, and know the thoughts behind each statement, rather than reading it at “face value.” However, after reading through and editing other’s work, it is always far easier to then notice errors or inconsistencies in my own. After peer reviewing papers a few weeks ago, I went back and read through my own paper. I noticed several errors and a conceptual miscommunication that I had not picked up on after several readings. I believe exercising this helped me get a higher score and review my own work with a fresh perspective.

Additionally, I feel reading others ideas helps me to become inspired in working on my own. Each paper I have read had fresh, unique ideas which I was, one way or another, able to apply to my own writing. Even if not directly, it allowed me to read my own writing with another “voice” in mind. I think that perspective shift is extremely valuable in exercises like this regardless, but especially during COVID when it is difficult to interact and get others perspectives.

(1) Dr. David Morens, an expert and esteemed author in the field of immunology, in his article for the 103rd volume of The American Journal of Tropical Medicine and Hygiene titled “The Origin of COVID-19 and Why it Matters” (2020) discusses the evolution of the SARS0-CoV2 virus which has started the Coronavirus pandemic. (2) Morens examines the progression of two groups of viruses; the sarbecovirus and β-coronaviruses for parallels as well as their presence in mammals (bats and pangolins) considered “virus reservoirs” with extreme potential for viral transfer to humans. (3) The purpose of this publication is to provide an evolutionary and transmissive history of the family of virus’ behind the current pandemic, in order to help prevent future outbreaks of the same nature. (4) Dr. Morens and his team attempt to exchange vital information to the readers of the scholarly journal, which are generally other professionals involved in research or healthcare as well as to scientifically literate individuals interested in bettering their understanding of the challenge which we all currently face.

Citation:

Morens D, Breman J, Calisher C, Doherty P, Hahn B, Keusch G, Kramer L, LeDuc J, Monath T, Taubenberger J. 2020. The Origin of COVID-19 and Why it Matters. American Journal of Tropical Medicine and Hygiene 103(3): 955–959.

Describe the process of peer review to someone who does not frequently read scientific articles. In your response, consider the pros and cons of peer review and how that might impact the credibility of the results that come from that scientific article.

“Peer Review” refers to the process of critiquing a scientific article before its formal publication in a academic journal. This is required for an article or study to be considered accurate and genuine. Generally, the article is viewed by other professionals in the field. The editors carry out many important functions, such as ensuring that the author used accurate and up to date information, that the study was carried out following the scientific method and is replicable, and that data was correctly analyzed and was not used to make false or untrue claims.

Once the editors have completed their analysis of the paper, it is returned to the original author who then reviews any critiques or suggested changes . Once the author has finished the editing, the paper is returned to the editors for a final review. If the paper is deemed accurate and well executed, it may be published.

As with any system, the peer review process has a mix of benefits and drawbacks but is a pivotal process in ensuring the information available is accurate to the best of our knowledge. On such drawback of the system is the innate presence of bias. For instance, in any professional field there is competition. Where competition exists, so do rivalries. Therefore the process is subject to the opinion and prejudice of the reviewer(s). Which is why it is beneficial to have the material reviewed by several professionals, preferably from different backgrounds..

A major benefit of the system, however, is the expertise that is inferred whenever a piece holds the title of “peer reviewed.” This tag allows those who cite the source, or just use it to improve their knowledge of a topic to feel confident in the authenticity of the information.

How did it feel to read and critique someone else’s writing?

I have peer reviewed many times in my life, both formally and informally. I have gained experience with this since my freshman year, with everything from writing courses to science classes. When I first started peer reviewing, I was uncomfortable giving others advice and breaking down aspects of their papers which, in my opinion, needed work. But as I progressed through my major, I was exposed to the experience again and again. One experience that sticks out to me is advice I got on a lab report in a general Chemistry course. The comment essentially told me to save a few aspects and otherwise start from scratch. At first I was defensive, but eventually decided the reviewer was right and took his advice. Due to this, I got an A on the report and in the class overall.

Over time, I gained an appreciation for others opinions on my work, whether or not I decided to apply them. This helped me realize that others likely feel the same way. Since this realization, I have been honest in my reviews without the fear as coming off as harsh. Especially since my experience with my lab review. A component of the peer review which can help reduce this fear is making the process anonymous, which this course did. That way there is no concern over judgement from the author or reviewer.

I am especially excited to receive reviews on my proposal as I was concerned with the structure of my study. I believe I did well, but having a peer’s opinion is invaluable. While I have felt that other reviews I have received have been valuable, I believe the reviews for this project will be immensely helpful.

What did you learn that you can apply to your own writing?

I learned a great deal from the peer review process. While I have not yet received reviews on my own project, I believe that simply reviewing others gave me a lot of useful information. For example, both papers I reviewed contained a similar amount of background information / explanation of the purpose as my own paper. This was excellent as I was concerned that I focused too heavily on that and not enough on the experimental design. Furthermore, I realized that I went more in depth on the method than either paper I reviewed, and have decided to reduce that section as a response. This will allow me to fit more into areas I felt I was lacking.

Overall, simply reading others ideas and seeing how they went about planning their study helped me feel more confident in my own proposal. In a way, we went about this project blind. Just seeing other examples created by my peers helped me know I was on track.

List Characteristics of a Microbial Population.

What comes to mind initially regarding a microbial population are the species’ sources of Energy and Carbon. For example, a population which derives its Energy and Carbon from organic sources would be termed a “Chemoheterotroph”. Breaking this down, Chemo signifies the organisms receive their energy from chemicals, while Heterotroph indicates that the organism must consume others to fulfill its nutritional requirements. Conversely, a Population could be designated as a Photoautotroph. The components of this name are broken down into “Photo” which means they capture energy from the suns light (photons) to produce necessary organic compounds and “Auto” which means they are able to synthesize their own food from simple organic substances. All variations of these arrangements exist, as organisms, especially microbes, show incredible diversity. Some are even categorized as “mixotrophs” and are able to take advantage of a range of metabolic options depending on the most advantageous in their current environment.

While these categories are helpful, their classification still leaves many questions. Further characteristic determinants of microbials include environmental aspects such as: pH range, temperature, prevalent gasses, osmotic pressure, nutrient availability, water availability, etc. It is important to note, however, that each population has varying acceptable ranges for each of these and some are more “sensitive” to changes than others. These environmental characteristics are valuable to researchers in many ways. Collecting this information allows them to make generalized assumptions as to the various populations which are likely present in a given environment.

How does this differ from a Microbial Community?

As mentioned, the previous environmental characteristics can be very helpful in making assumptions regarding the populations likely present. However, when discussing communities the focus is larger and encompasses many populations, their interactions and the environmental influence. According to Nature Research, a microbial community is simply defined as the groups of microorganisms which share a living space and interact (Nature 2021). The analysis of a community brings important new questions to the table. One such question, how do these various populations interact, is vital in understanding the dynamics of the community, For example, some populations may be predators of another, or conversely, one community may be reliant on the byproducts of another. Interactions from parasitism to symbiosis are present and important factors of all communities.

Analysis of the communities characteristics through various means has proven to be pivotal in bettering our understanding of the natural world, as well as increasing our ability to manipulate it to better our needs. A great example of this is soil microbiology research and its contribution to farming. Without working to better understand populations interactions and beneficial species preferred conditions, progressing our farming practices would likely not have proven to be so successful.

Citation:

Springer Nature Limited. Microbial Communities. Nature Research, 2021. Retrieved From:

https://www.nature.com/subjects/communities