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Lesson 5

Scientific Questioning and Literature

In this last lesson of Module 1 we will talk about how scientists develop their questions and dive a little deeper into scientific literature.

Scientific Questioning

The scientific method - coming up with a question, performing background research, making a hypothesis, performing the experiment, making observations, and drawing and communicating conclusions - outlines the approach scientists use to develop specific questions and approaches to answering them.

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Perhaps one deviation from above is that you must first perform an extensive search of published literature before identifying your question and making your hypothesis. You don't want to ask a question that has already been answered (you might, however, want to repeat the experiments of other groups to make sure they are reproducible). The scientific method is also not linear. You might perform an experiment and realize it didn't give you as much information as you had thought, so you might need to go back and design a new experiment, or perform a second, complimentary experiment. 

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Developing scientific questions requires a bit of creativity. You might have a system or problem that you are interested in, but you must develop a scientific question that is testable by an experiment can be repeated and reproduced (by yourself and others). Read this journal article about how to develop good research questions. This article focuses on clinical studies with human subjects, however the same principles apply to "benchwork" studies. One disagreement I have with this article is that our studies do not always need to "make significant health impact in clinical and community practices". Both basic and applied science are important in the scientific community. Basic science are studies that produce new scientific knowledge while applied science are studies that build upon basic science in order to develop a new technique or technology. Basic science, which might not have an immediate application, is essential for future applied science discoveries.

 

Once you identify your scientific problem you must then develop your scientific study. Common types of scientific studies as identified by HHMI are:

  • Hypothesis-driven research

  • Measuring specific values

  • Measuring functions or relationships

  • Constructing models

  • Making observations and identifying patterns

  • Improving a product or process, including developing new scientific tools

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In practice, you would also consider your knowledge or that of your lab and mentors, as well as the scientific equipment available for use when developing your study. For example, in our lab we commonly use nuclear magnetic resonance (NMR), electron paramagnetic resonance (EPR), crystallography, and enzymatic activity assays (which we will learn more about in Module 3). If we want to develop a study using other approaches we will either have to learn them, or collaborate with other scientists who already have that expertise.

Scientific Literature

We introduced scientific literature in previous lessons. Primary literature (novel studies) are the main way scientists learn about their science. Authors submit their paper to a journal and it is then peer reviewed by three members of the scientific community. These reviewers look for any errors that might be in the paper and ensure that the conclusions the authors made are fully supported by their data. The reviewers can suggest that the paper be accepted as is, be accepted with minor revisions (generally formatting or small changes), be accepted with major revisions (often including additional experiments), or be rejected (not published). 

 

The formatting of scientific literature depends on the journal in which it is published but contain similar sections:

  • Title: The title should give you an idea of what the paper is about and if it might be of interest to you, but does not give too much information

  • Authors and affiliations: The authors who contributed to the paper are listed along with the institution from which they are from. The first author listed is the person who did most of the work, and subsequent authors are listed by how much they contributed. The last author is also important - they are the principle investigator (PI) who received funding for the project through grants and generally has a significant role in developing the studies. The corresponding author is denoted as well, and that is the person you should contact if you have any questions about the study. Generally the corresponding author is also the PI. The order of authors is different in different fields - some have the PI as the first author and other disciplines have the authors in alphabetical order.

  • Abstract: You have already looked at literature abstracts in lesson 2. The abstract should give you a complete, succinct summary of the paper in less than 250 words. Abstracts are usually a good place to start reading to see if the article is of interest to you.

  • Introduction: The introduction should give background on the system or problem studied in the paper including any previous literature that is of importance or which drove the scientific question. The hypothesis should be stated as well as the methods used to perform the experiments.

  • Methods: The methods section will explain how the authors performed the experiment including what supplies or instruments they used. There should be enough detail in the methods section that another group could repeat the experiments.

  • Results: The results section reports the data that was collected during the experiments, and can be considered the "meat" or "heart" of the paper. The results section also may contain tables or figures to better present the data collected.

  • Discussion: The discussion section presents how the authors interpreted their data reported in the results section. They also may compare their data to other studies, or suggest how this data fits into previously known information. In some papers the results and discussion sections are combined.

  • Conclusion: The conclusion section should briefly summarize what was found in the study and how it contributes to the larger field. Authors might also acknowledge future work that needs to be done.

  • Acknowledgements: In this section the authors acknowledge other people who contributed to the work but are not authors (for example they might have gifted supplies or given advice) as well as declaring any funding which helped fund the research.

  • Literature cited: Provides the sources cited throughout the paper. Could also be called a bibliography or references section.

Different scientists have different ways going about approaching a paper. Most will read the abstract first, some will read the conclusions first, some will look at the figures first. Read this Science article "How to (seriously) read a scientific paper" about how researchers approach reading papers, and their tips for doing so.

 

Note that these career scientists admit that they often get overwhelmed reading scientific papers! Papers can contain a lot of jargon, acronyms, and phrasing that is specific to a subfield. Thus, it is important to look up things you don't understand, or focus on the bigger picture if possible.

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In order for scientists, especially developing ones, to better understand scientific articles we often have what are called "Journal Clubs".  A journal club is a group which discusses an article. All members will read the article before coming to the group. Someone will start by summarizing the problem and hypothesis that the paper focused on. Then other members will take turns summarizing the results, generally by talking through the figures and tables. The members can discuss what they liked about the study, what was confusing, and what could have been done differently or better. They will then talk about the discussion and conclusion sections of the paper and if they agree or disagree with the authors. You would be surprised with how often we don't agree with something authors have said! Journal clubs also discuss what could have been done differently or what other methods could have been used to add additional data to support (or not) what the authors have published.

 

For your main assignment this week you will be reading a scientific article and we will have our own journal club. Again, there will be things you don't understand and that is to be expected. Google things you don't understand, especially methods that they used. Remember growth mindset - the more times you read a paper, the more you will understand and the easier it will get.  Be prepared to explain:

  • background, including previous studies

  • the problem (was this a good research question?)

  • the hypothesis

  • each of the tables and figures

  • the authors' main conclusions

  • do you agree with the author's conclusions?

 

We will take turns in the group discussing these things. It's ok to not fully understand, we will help each other out! To help you prepare, write down some thoughts about each of these and submit in your google doc for this week. 

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Since it is consuming our world currently, the paper we will discuss is about the novel coronavirus. It is important to be able to read scientific literature not only for developing your own scientific studies, but to also be knowledgeable about the world we live in.  

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