How to Read a Scientific Paper Adapted from notes made by: Warwick Allen and Arundhati Bakshi

How do we communicate Science?  Multiple mediums to communicate science: Journal articles Presentations Reports Posters Books Blogs News networks Social networks

Journal Articles  Journals  Science, Nature, PNAS, TRENDS, Genes & Development,... ... and many many more!  Peer-reviewed: critiqued and analyzed by other scientists in the field  General Structure (with some variations): Title, Abstract, Introduction, Materials & Methods, Results, Discussion, References  Best way to keep up with the newest, most cutting-edge developments in your field of interest

How to Read Journal Articles Decode Understand Evaluate & Critique Extend Undergraduate students Upper-level undergraduate & graduate students Graduate students & professional scientists

How to Read Journal Articles Decode Understand Evaluate & Critique Extend What do the terminology mean? What is the overall idea of this paper? What did the authors do? Why – what was the motivation? What did they find? What does it mean? Did the authors do the right thing? Did they interpret their findings appropriately? Do the data/evidence support their conclusions? How can you further the work presented in this paper by future experimentation?

DECODE Journal Articles in 6 Easy Steps! Decode Understand Evaluate & Critique Extend 6 steps

DECODING Journal Articles 1)Start with the TITLE. 2)Ask yourself: Do you have a broad idea of what this paper is going to be about? 3)If yes: skip to slide 10. 4)If no (which is much more likely actually!): skim the INTRODUCTION and identify the main KEYWORDS. 5)Look up the meanings of these keywords and a brief background on them: a quick Google search or Wikipedia reading would suffice! 6)Then try to answer the question again: What is the paper about?

Can you summarize the broad idea for what this paper is going to be about, given the title below? A.Yes B.No

Skim through the INTRODUCTION and identify a few KEYWORDS.

Match the keywords with their meanings. Take your best guess! KEYWORDS 1.Repression 2.Ribosomal proteins 3.Cell cycle 4.Phenotypes 5.Ribosomal biogenesis 6.Nucleolar stress MEANING A.The making or building of a ribosome B.Stages of growth that a cell goes through ultimately leading to cell division C.Outwardly observable characteristics or traits of an organism D.Several proteins that make up the ribosome, i.e. the protein-makers of the cell E.Stresses that a cell undergoes due to improper ribosome biogenesis F.Shutting down or decreasing the production of something

Now try to summarize the major idea of what the paper is about using the information from the TITLE. If you reduce the production of the proteins that make up the ribosome (repressed synthesis of ribosomal proteins), it has an effect on what the cell looks like in terms of its shape (morphology), and how it grows and divides (cell cycle) with the exact observable effects being dependent on which protein was “messed up” (protein-specific…phenotypes)

UNDERSTAND Journal Articles in 6 Easy Steps! Decode Understand Evaluate & Critique Extend 6 steps Undergraduate students

Now that you have identified the major idea of the paper, we are back in business! 1.Now read the INTRODUCTION again, but this time, more actively.  Read critically and try to connect it with other information you already know. You’ve already done some of this when you guessed the meanings of the keywords correctly! So don’t let terminology fool you into thinking you don’t know something when you actually probably do. Keep a list of words you don’t understand and look up the meanings, then write that down in your own words. Keep this piece of paper at hand! UNDERSTANDING Journal Articles involves ACTIVE READING

Now that you have identified the major idea of the paper, we are back in business! 1.Now read the INTRODUCTION again, but this time, more actively.  Read critically and try to connect it with other information you already know.  Try to identify the answers to the following questions as you read along – keep a pencil & highlighter handy… take notes and annotate! What is the motivation for this study? What does this study seek to understand? What is the model organism/system? Know both common and scientific names! UNDERSTANDING Journal Articles involves ACTIVE READING

Identify the MOTIVATION for this study and the MODEL ORGANISM used from the fragment of the introduction below. A drive to find out what is currently unknown is usually the motivation for almost any research (paper)! Common name Scientific name Use “normal” English language cues to guess... Don’t get hung up on words you don’t understand!

Choose the response that best describes the statement below that is highlighted in blue, taken from the Introduction. A.Motivation for the study B.Major objective of the study C.A key result from the study D.It is only meant to introduce the main model organism used in the study Can you identify statement(s) that would be an appropriate indication of one of the motivations for this study? “Nucleolar stress” is not well understood. Use “normal” English language cues to guess... Don’t get hung up on words you don’t understand!

Now that you have identified the major idea of the paper, we are back in business! 1.Read the introduction again, but this time, more actively. 2.Now move to the ABSTRACT.  What’s in an abstract? o Summary of the entire article that includes the following: Purpose or rational of the study or why they did it (expanded in the Introduction) Methodology or what they did and how they did it (expanded in the Methods) Results or what they found (expanded in Results) Conclusion or what the results mean (expanded in Discussion) UNDERSTANDING Journal Articles involves ACTIVE READING Identify these points and annotate! Use it to summarize the abstract at the end!

Answer the questions given the abstract below. Identify a statement which discusses the: Purpose or rational of the study or why they did it Methodology or what they did and how they did it Results or what they found Conclusion or what the results mean

Answer the questions given the abstract below. Identify a statement which discusses the: Purpose or rational of the study or why they did it Methodology or what they did and how they did it Results or what they found Conclusion or what the results mean

Answer the questions given the abstract below. Identify a statement which discusses the: Purpose or rational of the study or why they did it Methodology or what they did and how they did it Results or what they found Conclusion or what the results mean

Answer the questions given the abstract below. Identify a statement which discusses the: Purpose or rational of the study or why they did it Methodology or what they did and how they did it Results or what they found Conclusion or what the results mean

Answer the questions given the abstract below. Identify a statement which discusses the: Purpose or rational of the study or why they did it Methodology or what they did and how they did it Results or what they found Conclusion or what the results mean

Now that you have identified the major idea of the paper, we are back in business! 1.Read the introduction again, but this time, more actively. 2.Now move to the abstract. 3.Skim through the METHODS.  Identify key techniques used in the paper (usually the sub-section headings within the Methods section) and what they were used for. Fill out a chart! Don’t spend too much time here… these techniques will make more sense by the end of the semester! UNDERSTANDING Journal Articles involves ACTIVE READING

In which section of the paper would you expect to find the answer to the question displayed below? A.Abstract B.Introduction C.Methods D.Results E.Discussion F.References Question: Name two types of microscopy used in this study.

Now that you have identified the major idea of the paper, we are back in business! 1.Read the introduction again, but this time, more actively. 2.Now move to the abstract. 3.Skim through the methods. 4.Move to the RESULTS.  Results sections have both figures and text. Approach one figure at a time and find the relevant text supporting that figure. As you read, try to answer the following questions about that figure: What question is this figure trying to address? What is the answer to that question? Briefly summarize the title of the figure and relevant information in your own words. UNDERSTANDING Journal Articles involves ACTIVE READING

Now that you have identified the major idea of the paper, we are back in business! 1.Read the introduction again, but this time, more actively. 2.Now move to the abstract. 3.Skim through the methods. 4.Move to the RESULTS... Jot down key results from ABSTRACT!  Focus on understanding one figure at a time...  But if it is using too many words you don’t understand that are bogging you down, skip it!  Go back to the abstract and jot down key results stated in the abstract. Then only focus on decoding the fewer words that you don’t understand from there. UNDERSTANDING Journal Articles involves ACTIVE READING

What would be some terminology you would need to look up in order to understand the Results? Identify a statement which discusses the: Purpose or rational of the study or why they did it Methodology or what they did and how they did it Results or what they found Conclusion or what the results mean

Can you answer the following questions after understanding the results from the abstract?  What changes were observed in bud morphology/shape?  How was cell cycle affected?  Were the changes observed uniform for all r-genes or were specific changes observed for specific genes? Were there shared features?

Now that you have identified the major idea of the paper, we are back in business! 1.Read the introduction again, but this time, more actively. 2.Now move to the abstract. 3.Skim through the methods. 4.Move to the results or get a summary of the key results from the abstract. 5.Spend some time reading the DISCUSSION. This is where the authors break down each piece of their result and try to explain it. This section should be the most helpful in truly understanding the content of this paper! UNDERSTANDING Journal Articles involves ACTIVE READING

After reading the ABSTRACT, what would be the best section to read in order to answer the questions below?  What changes were observed in bud morphology/shape?  How was cell cycle affected?  Were the changes observed uniform for all r-genes or were specific changes observed for specific genes? Were there shared features? A.Introduction B.Results C.Methods D.Discussion

Now that you have identified the major idea of the paper, we are back in business! 1.Read the introduction again, but this time, more actively. 2.Now move to the abstract. 3.Skim through the methods. 4.Move to the results or get a summary of the key results from the abstract. 5.Spend some time reading the discussion. 6.And finally, solidify your understanding: SUMMARIZE!!! UNDERSTANDING Journal Articles involves ACTIVE READING  Using your notes and annotations from throughout reading the paper, create a short summary in your own words of what the article is generally about.

Summary: DECODING and UNDERSTANDING DECODE: Title and Keywords (skim the intro) UNDERSTAND: Introduction UNDERSTAND: Abstract UNDERSTAND: Methods (skim!) UNDERSTAND: Results (Abstract) UNDERSTAND: Discussion SOLIDIFY: Briefly summarize the article/abstract in your own words

References  Sally G. Hoskins, David Lopatto and Leslie M. Stevens (2011) The C.R.E.A.T.E. Approach to Primary Literature Shifts Undergraduates’ Self-Assessed Ability to Read and Analyze Journal Articles, Attitudes about Science, and Epistemological Beliefs. CBE Life Sciences Education, 10(4): 368–378.  John W. Little and Roy Parker. University of Arizona. How to Read a Scientific Paper. ( )  Dr. Mary Purugganan and Dr. Jan Hewitt. Cain Project in Engineering and Professional Communication, Rice University. How to Read a Scientific Article. (  Susan Carson and Eric S. Miller. North Caroline State University. Introducing Primary Scientific Literature To First-year Undergraduate Researchers.

Summary: DECODING and UNDERSTANDING Title & Intro Identify and find meanings to keywords. Rephrase the title in your own words What is this paper about? Introduction Identify the motivation for the study and what it seeks to understand Highlight and take notes! Abstract Get the overall summary of the paper. This will tune you in for the details in later sections. Methods Skim! Do not spend too much time for now. Make a chart for the key techniques used and what they were used for. Results Go one figure + accompanying text at a time. Identify what question the figure is trying to address What is the answer to that question? Discussion MOST IMPORTANT!!!! Authors break down and explain their results. Read carefully and annotate, take notes, highlight. Summarize! Using your notes and annotations create a short summary of the paper in your own words. This will SOLIDIFY YOUR UNDERSTANDING of the paper!