Month: March 2021

This week in Class we had the opprotunity to sequence a whole genome from a Vibrio bacterium and see how complicated it is to piece a genome together. This was using modern technology, and the “difficulties” we had where nothing in comparison to those that first sequenced a whole genome. By reading both the highly technical scientific research paper by Fleischmann, and then a commentary that put things in to more general terms by Nowak on the initial sequencing of the Haemophilus influenzas genome, I was able to get a glismpe into the historical moment of sequencing full genomes.

It was incredible to see paper with a genome mapped out and possible functions of each gene mapped with it, but while the Fleischmann’s article was impressive, I didn’t fully understand until I read the Nowak’s review. In his review he states the incredible discovery of there being no citric acid cycle and the idea that influenzas can pick up genes from the environment from other influenzas. It also sates how incredible it is that this project took six months rather then three years. I read that and thought, six months? We just sequenced an entire genome in one class period. That was when it hit me that todays technological advancements are incredible, and something the past would have look at in awe.

This whole experience makes me certainly consider what I have to look forward too in my future as a scientist, what new technology will come out? And how will people in the future be looking at the scientific articles of today?

In W. P. Hanage’s article he uses human microbiome research as an example to discusses five questions we need to consider when reading scientific literature before we make any conclusions. The first question, “can experiments detect differences that matter?” is important because so many inaccurate conclusions are shown to the public before experimental findings are confirmed. Hanage describes this problem discussing how markets are manipulating published microbiome research from a single to a few studies to try to get products out to help control everything from mental health to diabetes. The reality is the gut biome is so complex that experiments have done little more than scratch the surface on the microbial diversity. 

Considering what research has actually shown leads us into the second question,“does the study show causation or correlation?”. It is difficult to know if the microbial composition can cause differences in human functioning or if the two (human health and microbiome diversity) fluctuate together because as the environment changes both will change but separately. Hanage’s makes a good point though, that correlation usually indicates a sort of casual relationship, and that is why the third question must be asked, “what is the mechanism?”. In order to determine how much one is related to another we need to lay out an exact mechanism that the interaction occurs through. 

The fourth question, “how much do experiments reflect reality?” is especially important in microbiology because so much of the work is done in a lab, in a controlled environment where the effects of the experiment are easily visible. For example, according to Hanage, gut microbiome changes have observable effects in diebetic lab mice, but in order to do these experiments the lab mice are germ-free and designed for lab work, not natural. Natures ever changing environment and hard to control factor, especially when examining the human microbiome that fluxuates per day per person, leads us to our fifth, and final question; “could anything else explain the results?”. This is extremely important to consider because we never want to draw permanent conclusions from data after an experiment that has all sorts of varying factors. I will discuss this more below, as I consider which questions to consider during scientific controversy. 

I would argue that “Can experiments detect differences that matter?” and “Could anything else explain the results?”, are the two questions that are helpful when discussing controversy. The former is important because it allows scientists to state whether there is even any point in examining an individual experiment, or if you can’t make a decision until multiple experiments have been done and recorded and duplicated. The latter is important because there are always many factors in science, no matter how much we try to control, that affect the result. This is particularly true when doing microbiology research, when even the tiniest contaminate can skew the results. Therefore when discussing controversial topics, we again need to identify if our results are valid and if there are other options, so no inaccurate conclusions lead to misinformed actions. 

Hanage WP. 2014. Microbiome science needs a healthy dose of scepticism. Nature 512:248. DOI: 10.1038/512247a.