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Anatomy of a Journal Article

Anatomy of a Journal Article
Labeled Test-Tubes (Kerry Lannert, Insta: k.lannert)

As demonstrated by the growing mistrust of scientists and medical professionals during the COVID-19 pandemic, the state of communication between researchers and the non-scientific audience is deteriorating. There are a number of reasons for this growing divide, including the archaic nature of published articles, research being held hostage behind ludicrous paywalls, and the proliferation of social media 'hot takes' that misconstrue findings or omit important details. There are no easy fixes for these issues, but a lot of the confusion and mistrust could be alleviated if scientists and the associated journals removed the institutional barriers they have constructed that disrupt or discourage accessibility to research.
I firmly believe that lack of a science degree should never prevent an individual from engaging with and benefitting from scientific research. Obviously reproducing the experiments in a journal article requires equipment and training beyond many readers but the data, findings, and conclusions should be accessible to everyone. For far to long the target audience for scientific papers have been other scientists and/or grant committees and I believe this much change if we as a scientific community wish to improve our relationship with society.
The goal of this blog is to provide a bridge between the academic world of scientific research and those who may be intimidated or feel underqualified to digest information and form their own educated opinions. Over time, I hope to breakdown complex topics (such as mRNA vaccines), decipher papers, and answer questions with an eye towards providing a safe and accessible space for anyone to engage with scientific research. This is intended to be a judgement-free zone, where anyone can ask questions without fear of mockery or a dismissive wave.
The first few posts on this blog are designed to provide a foundation with regards to how experiments are designed, data is interpreted, and the important concepts and terminology that are common in scientific reporting.
This initial post is a primer on the sections of a published scientific paper, from the title through acknowledgements. While not every paper will always include each of the following sections, generally the order of the sections and structure of a paper is standard across scientific disciplines, allowing readers to quickly find the important information such as the data or conclusions, without having to read through the entire experiment.

In every discipline, from sports reporting to covering political elections, the title of an article is critical as it serves as the first (and often only) impression an article may make on a reader. For this reason, many titles are written to grab attention, which has become a detrimental process for journalists as the headline is often written by someone other than the original author and can lead to misrepresentation of the associated reporting. In scientific writing, the title is just as critical but serves a different purpose than generating excitement or curiosity from a reader, specifically it must inform readers as to the experiment and findings present in the article.
A good scientific paper title will provide a very brief introduction to the paper and the authors' research. The can take a variety of forms and may include information about the experiment, its treatment group, the results, or the author's conclusions. For example, see the below headline:

In this title, the authors are describing their research and informing the reader that paper will be about the intricate relationship between the three noted items. From this, a researcher interested in any of these blood components or their complex interplay will immediately realize the importance of this work. Reading the full paper should then outline briefly was each of these items are and how the interact in a laboratory setting or a living organism. If the group wished to be more specific, they could have included even more information in the title, but in general brevity is good, so long as it doesn't risk misrepresentation of the experiment or outcome.

The abstract is the TLDR version of a full paper. It should succinctly provide a thorough overview of the experiment, its purpose, results, and conclusions. Typically, an abstract is just a paragraph or two and serves to expand upon the title, providing researchers more in-depth information about usefulness of the associated research. Since abstracts are often featured in databases, search results, or printed materials, they need to be brief enough to be digestible in these formats, while robust enough to ensure the reader can understand the scope and outcomes of the research.
Unfortunately, so many articles and journals exist behind paywalls that the only engagement a researcher may have with them is via the abstract. For this reason, the abstract also serves as a barometer for determining if a published article is worth the fees required to garner full access. Adding to the challenges of disseminating the information to the non-scientific community, these access fees can be quite high (for example an article I wanted to read about a knee surgery was $39 for one-time access or $119 for annual journal access) and these are in addition to the fees many journals charge the groups publishing the papers. These fees are often not prohibitive for scientists associated with universities or big companies as they have negotiated access.

Simply put, a paper's introduction serves to answer the question of why. Specifically, why is the following experiment and its findings important or valuable? In the introduction, the authors should explain and cite the relevant background information that aided in their decision-making for the included line of experiments. They should also state their research questions and hypothesis.
We will discuss the meaning of a research question versus a hypothesis in greater detail in a future post, but for now in brief:
1. Research Question: Simply a question you seek to answer. "If we treat this rosebush with this plant food, what are the outcomes?"
2. Hypothesis: Must be more robust and able to be subjected to statistical analysis. "We predict that adding this plant food to our rosebushes will result in longer lasting flowers." This can then be tested against a control group and run through hypothesis testing (using P-Values, more later) to determine if the result is statistically significant. Simply put, is the observed outcome likely a result of the treatment or random chance?
Both the research questions and hypothesis are important, but the hypothesis allows for actual statistical analysis and a result that can be repeated by another research team.

Materials and Methods
If the introduction is the why of a scientific paper, the materials and methods is the how. In this section, researchers will explain how they conducted the experiment, including the treatment group, how treatments were administered, what reagents (chemicals, biologicals, etc) were used, and details about the protocol and equipment.
In the past, these sections used to contain in-depth protocols, but often now simply cite the papers the new experiments are built upon and include only the new or unique aspects of the experiment. For example, if a lab was going to develop a PCR test for a new COVID variant, they may cite the previous experimentation and only include their template in their paper. The idea is to keep the section brief and focused on the work done by the paper's authors, while ensuring any other lab would be able to reproduce their experiments using this section and the cited materials and methods from previous work.

The results section is where the data collected from an experiment is disclosed to the reader. This is typically presented as a mix of written paragraphs, data tables, and plots designed to show the collected results and allow the reader to process and form their own opinions.
A key thing to remember about the results section is that it should be written without bias and not contain the authors' explanations or feedback on the data. The data (and the methods chosen to present it) should accurately reflect the outcome of the experiment, even if it doesn't match the expected results. A scientist formulated their conclusions after the data is collected, otherwise it becomes very easy to introduce bias, even through subconscious methods.
An experiment is designed with a testable hypothesis that is informed by previous experimentation, but if the data does not support this hypothesis, the must be accurately reported and the hypothesis rejected.
We will discuss data collection and reporting in-depth in a later post, but for now just think of this section as an objective reporting of results that does not contain commentary from the authors.

The discussion section is where the authors make their case for their interpretations of the experimental results. In this section, the authors will describe their findings and use statistical analysis and other methods to lend supporting evidence to their interpretations.
The breadth of this section depends on the experiments the potential impact they may have on their authors' field of work. If the experiment didn't show a difference between a treatment group and a control group, it may be a pretty short section, however if the differences observed were robust and could impact human health, the section and its impact could be great.
*A note about negative results: A negative result is not a failure and often merits reporting so that other groups do not conduct the same experiments. They can also provide valuable information to inform the next round of
experimentation. In general it is good practice to design experiments where a negative result is still important.
Ideally, authors will state their conclusions based on the data, provide the evidence that supports these conclusions, and then explain how these findings can be applied to other rounds of experimentation or incorporated into their field.

Even though the list of authors at the beginning of a paper can be exceedingly long, it is rarely exhaustive. The acknowledgement section allows for credit to be given to others who contributed to a project, but not to the level warranting authorship on the paper. This can include things such as outsourced testing or providing unique supplied.
This section also provides a location to disclose funding sources (such as federal grants or funding from industry groups) and address potential conflicts of interest.

Literature Cited
Any information provided in a scientific paper that is not a direct result of a the current experiment, even if it is from a member of the paper's authorship team, must be cited. The citation method can vary, but typically citation in the paper includes the name of the first author and the year (example: Walsh, et al. 2021).
At the end of the paper in the literature cited or reference section, a full account of papers, books, or other sources cited within the paper must be included. This does not only serve to provide the appropriate credit for previous work, but provides a collated group of resources for the reader to learn more about the subject.