Writing Exercise #13

Can experiments detect differences that matter?

This question is important when researchers carry out experiments. In this part, the author first talked about profiling a microbiome which is able to categorize at the level of phyla, species or genes. The disadvantage is from criterion which researchers used the different ratio of bacteria to distinguish microbes. For example, if an experiment was used to characterize animal communities, based on the ratio between an aviary of 100 birds and 25 snails and the ratio between an aquarium with 8 fish and 2 squids,  both an aviary of 100 birds and 25 snails were identical with an aquarium with 8 fish and 2 squids. However, it was not right because of the differences in stains in the genes which each species contain. Later, the modern technology provides a better way for distinction when they were able to study more genes in a sample. Nevertheless, if the networks are not characterized well, the outcome to any specific object is hard. In addition, the ability to identify functional differences in related genes play the important role to understand the genes or networks. Also, genomes are poorly understood with clues which can be true or false. Therefore, an experiment can detect differences or not play a significant role for researchers to understand fully about the subjects, especially topic related to genomes.

2. Does the study show causation or correlation?

In this part, the author discusses how an experiment was conducted in two directions, inverse and reverse directions in order to know if the study showed causation or just correlation. It’s so important to question when interpreting scientific literature. For example a study about gut microbiomes and diet in a 2012 article which was proposed a causal relationship after conducting a study between the gut microbiomes of old people living in care homes and old people living in the community. Though the data and proposal were fit together, the reverse causality, the potential for poor health to alter the gut microbiome, was not investigated. The less active immune system and differences in the digestion of frailer people could lead changes in the microbiome. In this case, the conclusion about the causal relationship was not correct. Thus, I think that this question helps researchers to have the overview and come with an appropriate proposal.

3. What is the mechanism?

This question helps researchers to have a deeper understanding of the subjects in their study. When there was a correlation which can contain a causal relationship also. However, the researchers do not know what makes the relationships. With the modern technology, the researchers are able to identify functional elements, different taxa, and specific characteristics. The experiment can be done to define actions of elements in microbiome related to the biochemical activity. This contributes to making a study become more convincing.

4. How much do experiments reflect reality?

This question focuses on examination the reflection of experiments to the reality. For example, the study about gut flora and weight gain. The researchers did the experiment on germ-free mice which did not represent the natural state of animals and do not have healthy owing. Thus, the study did not include the responses in animals with flouring microbiomes related to different adaption between mice and their microbiomes and human. Thus, the result may not generalize. This question provides researchers about their subject choices and evaluation if the result from their study is suitable and able to convince people in public including general readers and scientists.

5. Could anything else explain the results?

This question made me think of variables in a study. It’s necessary for researchers to think that there are other potential factors which could affect the results of their study and the way to analyze the data, make generate the hypotheses and evaluate the conclusion. For example, bacteria affects human but whether or not there are possible factors contributing to these effects. It is important to know about contributing factors in a study in order to make sure the results are not affected by these factors before coming to a conclusion.

** Overall, these five questions help the researchers to avoid hype. I think that question about the mechanism is the most helpful when discussing the controversy topic. As I understand, the controversy topic is from the disagreements among researchers on a topic. The researchers carry out different studies on the same topic, but they may have different results which may lead to opposite conclusions. For example, my final essay focuses on a question whether or not Helicobacter pylori eradication should be applied for GERD, Inflammatory bowel diseases (IBD), and allergy and asthma patients which researchers had different results from their studies to argue about this topic. The unclear part which was hard to explain the mechanism to support.

Source: Hanage, W. P. 2014. Microbiome science needs a healthy dose of scepticism. Nature, 512(7514), 247.