Infectious Diseases: Real Science Review

A McDonalds cook’s product could be a McMuffin. A carpenter’s product may be a house. What might the product of a scientist be? It is a scientific paper published in a scholarly journal. When scientists complete a research project that explain the project and report the results in a report that they submit for publication in a scholarly journal. Upon receipt of the scientific paper, the journal editor sends the paper to experts for evaluation, a process called “peer review.” Peer review involves a detailed analysis by those experts of the strengths and weaknesses of the research addressed in the paper. Peer reviewers may approve the paper as written, may reject the paper as written but offer to review a revision, or completely reject it. If reviewers and editor approve the paper for publication after peer review, this published paper (also called a journal article) adds to the accumulating data and concepts in that area of research.

Articles like this are considered “primary sources” of research and are made available to scientists all around the world. All other sources of scientific information like reviews, textbooks, web sites, and lectures are called “secondary or tertiary sources” and lack the rigorous evaluation by experts that is given to original research papers.

You are now going to learn about “peer review” by doing it, using an actual original research report (scientific paper).

“What? I’m not a Ph.D.!
How do you expect me to do something so sophisticated?”

Slow down! No need to panic! It is not really all that sophisticated. You have the same kind of brain as a scientist! You are able to think critically and creatively.
You are able to determine good ideas from bad ideas and strong data from weak data. You can tell the difference between important findings and trivial findings. And you are capable of generating your own ideas. While you don’t yet have the formal training to be as good at this as real scientists, we all must start somewhere!

We are going to help you get started by giving you all the tools you need to conduct your own peer review of a scientific paper. First, we will give you key background information to help you understand more about both the peer review process and the specific research topic you will be considering. Finally, we will provide you with a version of the original research paper that we re-wrote so it is easier to understand. At the key points in the paper, we show a text box with questions you need to answer with critical and creative thought.

Through this activity, you will discover the thrill of realizing you too can think critically and conduct real scientific analysis when provided the tools, shown how and given the chance to practice! If your teacher allows several students to work together on this research review, you will also learn from each other how to think critically and creatively. Best of all, you will be learning science in the very same way as real scientists. That is what this experience is all about!

This learning activity aims to give you first-hand experience with the peer review process. We do not expect that you are experts in the field, but we are confident that you and your classmates will be able to successfully analyze the research report provided. You may need to ask an adult for assistance or look up a few things on your own, but that is perfectly okay.

In this activity, you will conduct the research review and then write a report that we will pretend will be sent to the journal editor. (In this case, others in your class and your teacher will be our imaginary journal editor.) Depending on instructions given by your teacher, you will either work independently or as part of a group to analyze each section of the research paper using the questions in the text boxes below as your guide. This activity is not meant to be performed all in one class period. Best results can occur if you can pool ideas from a well-working learning group.

It is important for you to know that you are not obliged to praise the article. Your job is to analyze it and if needed, even criticize parts of the rationale, experimental methods, results, or research discussion that seem deficient.

We expect you to think critically and creatively and share those ideas with others in your report.

A proper research report has four main parts, in this order: why, how, what and so what. Most research reports begin with an “Abstract” that summarizes the four main parts of the report.

Why. An introduction section (often called “Introduction”) of the report explains why the researchers wanted to invest time, money, and effort into this study. If the study is observational, the authors should explain why the scientific world would benefit from knowing about these observations. If the study is driven by a hypothesis, that hypothesis should be stated clearly along with an explanation justifying it.

How. The next section of the report (often called “Methods”) describes the experimental design, tools and equipment used, and details of the procedures used in the study.

What. The third section of the report (often called “Results”) presents the data generated by the study. Data are usually accompanied by statistical analysis. This analysis helps the reader know if the research results are likely due to chance or experimental manipulation.

So What. The last section of the report (often called “Discussion”) includes a discussion of the meaning of the research results. This includes analysis of the limitations of the research methods used, interpretation of the data, and discussion of the research relative to what other researchers have reported about the topic. This section also explores how the results from this study apply to the original need for the information or hypothesis. Finally, the authors usually suggest how their results might lead to new research projects to further extend the knowledge and understanding of the topic.

You will be addressing each of these four parts in your review.

You have probably learned about evolution of plants and animals. Why would evolution of bacterial or viral strains be any different? In principle, there would be no difference. However, infectious agents differ in several key respects:

1. Bacteria and viruses are a kind of parasite, and as long as there are plenty of susceptible hosts, they have a good chance of survival and proliferation.

2. We can try to eliminate infections, as with medical use of antibiotics, for example. However, a few organisms may survive because they have some biochemical pathways that protect them. These pathways may pre-exist the infection or may develop in response to continuous exposure to antibiotic.

3. One known pathway in bacteria is known as an “efflux pump.” The word “efflux” means moving outward. A bacterial efflux pump is a set of biochemical reactions inside certain strains of bacteria that eject antibiotics from inside the organism, which makes it resistant to antibiotic.

4. Bacteria divide rapidly, on the order of minutes to hours. Thus, a few bacteria that survive exposure to a given antibiotic will rapidly multiply as the rest of the susceptible and competing bacteria die. Then when those bacteria infect another individual, attempts to treat the patient with that same antibiotic will not be effective. You can see an example of rapid evolution of resistant strains at this web site: https://video.search.yahoo.com/yhs/search?fr=yhs-symantec-ext_onb&hsimp=yhs-ext_onb

5. All sorts of antibiotics have been in use since the 1940s, and thus it should come as no surprise that today many strains of bacteria are resistant to many different kinds of antibiotics. Resistant strains also develop in farm animals whose feed is laced with antibiotic to help them grow faster and more efficiently. Many resistant bacteria can infect both humans and animals.

6. The medical profession has found two ways to reduce this problem. One is to educate physicians and patients on proper use, which usually means to use a large enough dose of antibiotic over a long-enough time to wipe out an infection completely so there are no bacterial survivors. The other approach is to discover new antibiotics.

7. A third approach is the one you will analyze in the Real Science Review activity. Here the researchers are testing a drug that they think will inhibit the efflux pump mechanism of resistant strains. If the new drug works, it would mean the resistant organism would no long be so resistant, because inhibiting the efflux pump stops.

Download the adapted journal article and conduct a review of its contents.

Using guidance provided by your teacher and within the article, work individually or as a group to supply analysis for each indicated section within this article.

At different points in the paper you will see some questions. Cut and paste these questions into the report you are going to prepare on your local device. You should make notes on what you think the answer is for each question and later file a report of your answers to each of these questions to your teacher.

You will submit your report as directed by the teacher. If you are working in a group, develop a group answer. Google docs is useful platform where you can share your response with the group.

Download Article

You have now read an adapted scholarly journal article on axonal injuries. Before you begin the simulated peer review, let’s first check your understanding and knowledge about what you just read. 

Knowledge Check Question 1: What two words describe the mechanism of antibiotic resistance being studied in this experiment?

Knowledge Check Question 2: What three words describe how you can quantify the potency of an antibiotic?

Knowledge Check Question 3: If some drug or toxin or infectious agent attached to the extracellular part of integrin, could that affect what is going on inside the cell? Yes or no.

Knowledge Check Question 4: The evolution of bacteria compared to other kinds of organisms is that bacterial evolution is based on which of the following:

1. 1. 1. 1. Natural selection for adaptive features
         2. Competitive advantage
         3. Speed of reproduction
         4. Genes

For your convenience, here is the complete list of questions. You will complete this simulated peer review off-line. You can download this pdf and convert it to a text document where you can use whatever space needed to supply your answers. Or you can cut and paste from the screen display and create a fresh text document off-line.

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