Writing Exercise #13

In this post, I’ll be discussing the significance of five important questions which one should consider while interpreting scientific literature.

  • Can experiments detect differences that matter?

This point is important, because it’s these differences which allow results to produced and made apparent through empirical study. Without the inclusion of statistically significant deviations from one group to another, any claims laid are unsupported conjecture, and may be considered next to useless in many forums.

  • Does the study show causation or correlation?

The distinction between these two terms is crucial for determining the effects which things have on one another, and is as important to understand as the closely related distinction between fact and superstition. For example, every adult in the history of the world who has died has consumed water, but this doesn’t mean that water is responsible for their deaths.

  • What is the mechanism?

This question looks more closely at the connections between observations and their results, and considers the physical conditions and process which lead to the reproducible observations under question. Ultimately, it lends deeper understanding to perceived connections.

  • How much do experiments reflect reality?

The importance of this question almost goes without saying. After all, what’s the point of performing an experiment with nigh on useless results? I sure wouldn’t want a child who’s only medical experience was playing the game “Operation!” (adept as they may be at it) to start cutting things out of me. This is the same Idea.

  • Could anything else explain the results?

Finally, This is a condition that has been analyzed in statistics and many other fields for quite some time. At its core, this question is related to many others, like determining causation vs correlation, or finding the mechanism. As such, I believe it is likely the most important question to consider while interpreting scientific literature. No matter how many of the other questions are adequately answered by a study, if there’s something else out that there that is equally or more likely to produce the same results, more experiments need to be performed, and more data obtained.


Writing Exercise #12

While it may initially seem absurd to think that the brain and microbiome of the gut could have an intimate connection ( I was skeptical coming in to the idea, to say the least), there are actually many different connections that allow this relationship to be possible, as the gut is considered to be the “second brain” and is wrought with neural connections.

Looking more towards the practical applications of this axis,  the microbiome affects brain function by:

  • Triggering the release of cytokines by affecting immune cells
  • The direct production of corticosteroids and neurotransmitters
  • Other small materials, and enzymatic products may affect the brain via nerves

In return, the brain can adjust the microbiota via the release of hormones and steroids capable of affecting it. For example, during times of stress, the environment of the stomach may become much more acidic, and this could ultimately result in a population shift along the microbiome towards more acid-tolerant microbes.

In terms of mental health, these brain affecting capabilities can actually have quite the effect. For example, the addition of Lactobacillus rhamnosus to the microbiome was shown to reduce the observable effects of depression in mice, but only when there was an appreciable nerve connection between the gut and brain. Research has also shown that the presence of a microbiota may have a hand in reducing the effects that stress exerts on a body.

With all of that said, turnabout is fair play, and mental health can be readily affected by the microbiome as well. Besides the simple case of having the brain and autonomic responses themselves adjusting microbiota, there are multiple examples of mental conditions which adjust behavior. Lesch-Nyhan syndrome is a particularly devastating example which compels an inflicted individual to eat his own fingers and lips. Conditions such as this could readily introduce new organisms into a microbiome, and could also upset the relatively well maintained environment found therein.

All of these effects come together in a roiling stew of situations and conditions that can dramatically affect human health as a whole, in both positive and negative ways.

Writing Exercise #11

Through the precess of peer reviewing, I’ve learned several ways in which to better review my own writing, by holding myself to the same standards of those who I’ve passed my own judgement on. The opportunity to look over the best work of others also gave me a chance to learn from their writing styles and notice tools or abilities that I’d like to emulate in my own work.

With all that said, the process of pouring over somebody else’s work and looking for errors or missteps was strange, as I’m not one who usually critiques the works of others. Another issue with the process of peer reviewing is that it’s incredibly difficult to stay enthusiastic and engaged with someone else’s work on a topic you may not be familiar or interested with, all in an effort to examine the minutia of what they’re saying. This makes it necessary to take several breaks while reviewing in order to keep a fresh mind, but also results in a general dilution of early information as you progress with your review.

All in all, peer review seems like an important process which can be trying to the reviewer, but ultimately results in a generally higher caliber of work for everybody involved.

Writing Exercise #10

In peer review, articles which authors want to publish in scientific journals are examined by researchers in the field on which the article is founded. Through the process, the author sends his article into the editor of a paper of his choice, this editor then decides wether to reject the article or send it out to the reviewers who will submit their recommendations back to the editor. On these recommendations, the editor then decides if he wants to accept the article, require further revision, or reject it outright.

These steps allow for interactive and constructive discourse between members of a specified scientific community that may otherwise never have had any contact. This system means that there is a level of accountability and accuracy in papers now which never could have existed before. With multiple individuals who are well familiarized with the field looking over each piece, rather than one editor who may or may not be an expert, the quality of the writing is likely to increase. Unfortunately, having so many individuals looking over a piece of writing in a single blind style makes it easy for disagreements and misunderstandings to butty an otherwise revolutionary discovery, which is why many have pressed for much more transparent peer review processes.

Writing Exercise #9:


-Never eating raw food, bathing multiple times a day, washing one’s hands, never going outside, always wearing a particulate-filtering mask, wearing gloves all the time, minimizing contact with other people, refusing to come into contact with animals, never touching dirt, only drinking clean and sterilized water, undergoing medical procedures observing strict aseptic techniques, etc.

Writing Exercise 8:

Free Write 1 – 5:15

I feel like this is a class where we cover things that most people at our standing in school are aware of, and maybe even think a fair amount about. But what makes this course so different is its way of framing topics and analyzing connections between circumstances that we may never have considered before in classes that only pay the microbiome the attention of a side subject. I think it’s this deep dive into an otherwise fringe topic that has really surprised me. From claims of the microbiome being an additional endocrine organ (which is a claim so bold that it still blows me away), to the idea that gingivitis or periodontitis can be closely connected to coronary heart disease , I think the newly emerging importance of the human microbiota is fascinating.

Free Write 2- 5:03

What makes this course so different is its way of framing topics and analyzing connections between circumstances that we may never have considered before. I know I’ve already mentioned it several times, but the claim that the microbiome is important enough to be considered an additional endocrine organ is a perfect example of this. With all of my studies so far being centered around medicine and the tangible causes of disease or physical complications, I’ve always had the mindset of finding one particular issue that is causing havoc on a much larger scale, but this course has made me start thinking about how minor imbalances in systems that most people consider largely unimportant (ie disbiosis in the microbial community) can open the door for exceedingly awful chronic conditions for which there is no known cure or clearly defined causative agent. It’s an interesting field that opens so many new avenues of consideration for me, and I’m really appreciating my new viewpoint on disease.

Looking at everything I’ve written hear and that has gripped me in the class so far, I think that the controversial issue I’m going to want to cover is whether or not the human microbiota can actually be considered an additional endocrine organ. If that doesn’t feel right, I’ll start researching phenomena where the microbiome is being connected to physically presenting symptoms (like a cardiovascular incident.)

Writing Exercise #7

During pregnancy and birth, The body of a mother undergoes exorbitant amounts of stress. Several stressors, ranging from the ingestation and injection of various drugs, to the physical distortion of carrying and forcing out a creature about as ergonomically designed as a Ford pinto, to the possibility of an active and surgical removal can all work together in forming inflammation and other environmental changes throughout the body. If last week’s readings taught me anything, it’s just how devastating critical conditions created by actions like those above can be on the microbial community in an individuals body, often resulting in disbiosis as the microbe balance is flipped on its head.

As far as the infant is concerned, its entire development thus far has involved floating in a hermetically sealed sac and absorbing nutrients that are identical to those being used by its mother. At the time of birth, this carefully maintained environment is finally shed, and the infant is exposed to an entire world of microbes just waiting to assimilate into his blossoming microbiota. At this point, unburdened by the large number of microbes that will follow him through the rest of his life, the infant is capable of hosting flourishing microbial communities, as they have little competition at the start of life.

As a side note, the place that an individual is born can also have a great influence on how their microbial balance is adjusted. In a sterile hospital setting, there may be very little transmission of outside organisms to the new mother and child, however, the same precess (involving two severely immunocompromised individuals I ay ad) taking place in an unclean and/or pathogen ridden place can have the opposite effect.

Writing Exercise 6:

Antibiotics and their appropriate uses are something that have been drilled into me at every stage of life. Growing up wanting to be a physician, I’ve always had a soft spot in my heart for medicine and its use. As such, I think that the discovery and production of antibiotics are some of the most miraculous achievements in human history, saving countless lives and the world of health all together. It’s my philosophy to only take antibiotics when I know that I’m infected with a bacteria, and not a virus. I also make it my personal mission to finish every course of antibiotics that I receive following any and all directions provided to me.  I know and have seen in hospitals just how dangerous antibiotic resistant diseases can be, and I also know that the overuse of antibiotics can greatly decrease their effectiveness, even on a society-wide level. Both of these are issues that can have deadly consequences.

Writing Exercise 5:

There are so many choices throughout the day and in one’s diet that can affect the microbial communities and balance in an individual’s body. One which I think many people at this university may partake in in alcohol consumption. This is an activity that could very well hill many bacteria present in the gut, and could potentially result in the increase in abundance of any species which survived or thrived in the newly hostile environment, potentially resulting in a microbial imbalance (disbiosis). Additionally, I should probably do more than I already do to consume a more probiotic diet. With so many options out there tat fit the bill (from yoghurt to kombucha), I’m sorely lacking by only eating sauerkraut as a microbe-laden supplement.

All in all, I do little of what I should (diet-wise) to promote a healthy gut microbiome. I also have a penchant for fatty and unhealthy foods, which surely cause inflammation and irritation along my intestinal tract, causing damage to local bacteria. Fortunately, I’m also a fan of raw vegetables, which can be a source for consuming microbes and expanding microbial diversity.

Writing Exercise #4

List of behaviors that could change a gut microbial community:

Drinking bleach: would vastly reduce the number of microbes present in the gut community. This could result in a reduction in the number of microbes responsible for: maintaining the structural integrity of gut tissues, fighting off pathogenic organisms, or aiding in digestion; which would ultimately lead to a decline in health. Additionally, any surviving bacteria may be able to grow out of control due to the vastly reduced competition, resulting in disbiosis. (PS This is all assuming that drinking bleach didn’t kill you in the first place.)

Eating sugar-laden foods: The sudden bump in glucose levels would likely provide the gut bacteria with an increased food supply. An increase in local resources could cause a population boom throughout the microbial community due to the lessened stresses of competition. This increase in population may cause a dramatic change in microbe proportions, resulting in disbiosis and possible pathogenic effects. As a side note, the subsequent die-off of microbes after a reduction in glucose presence may have toxic effects on the human host.

Taking a probiotic supplement: Could increase the diversity of microorganisms present in an individual’s gut. According to lecture, this increase in microbiota diversity can result in a more stable and resilient microbial community, capable of resisting disbiosis and preventing negative effects on the human body and its health.

Walking around licking every surface in sight: Through oral contact with a wide array of microbial communities, the micro-biome of the gut would likely blossom with new species and  great diversity. Unfortunately, indiscriminately loading on new bacterial species makes it incredibly likely that there will be conflict between organisms in the gut, and even more likely that one of the organisms consumed would be pathogenic, subsequently hurting the health of the individual.