Workshop 2 Scientific Literature PDF

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BIOL 1103

Workshop 2 – Scientific Literature

Fall 2020

Workshop 2 – Scientific Literature Description and learning objectives This workshop will concern the scientific literature. You will learn how to find a specific article in the primary literature, use citations in an article to locate a reference, understand the composition of a journal article and how to find specific information in a journal article. You will also review what scientific journal articles are, how they are structured (with specific focus on the Methods section) and why they are important. In addition, you will learn how to properly cite and reference an article. Specifically, you will:      

understand the differences between primary, secondary and tertiary literature. find a specific article in the primary literature based on partial information (i.e., a clue). answer targeted questions relating to the composition of a proper methods section. review a sample methods section and critique for omissions and gaps in information. understand the structure and presentation of the results, including the presentation and description of data in scientific format. practice citing and referencing a scientific journal article.

Workshop Readings  Appendix 1: Word Processing  Appendix 2: Data Presentation and Analysis  

Appendix 3: Scientific Reports and Referencing Appendix 4: Electronic Submission of Assignments

Videos and Internet Materials  Writing Biology: http://writing2.richmond.edu/writing/wweb/biology/index.html  How to Seriously Read a Scientific Article: https://www.sciencemag.org/careers/2016/03/howseriously-read-scientific-paper  Organizing Academic Research Papers: https://library.sacredheart.edu/c.php?g=29803&p=185901  

Library Course Guide BIOL 1103: https://library.carleton.ca/research/course-guides/biol-1103 Kallet, R. 2004. How to write the methods section of a research paper. Respiratory Care, 49(10):1229-1232. https://pubmed.ncbi.nlm.nih.gov/15447808/

 Writing the Results Section: https://www.youtube.com/watch?v=dpWqcnxJF2E  Writing the Discussion Section: https://www.youtube.com/watch?v=-E5nqB0ugv4 Marked work associated with this Workshop session  Refer to Table A in the General Laboratory Introduction for the value of this assignment towards your final lab mark.  Complete the Lab 2 Workshop Assignment and submit it electronically via cuLearn before the deadline.

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BIOL 1103

Workshop 2 – Scientific Literature

Fall 2020

NOTE: Although you may discuss these questions communally, you must write and submit all your work individually. Write all answers in your own words and do not copy from the course materials, internet pages or from each other. DO NOT plagiarize!

Introduction Part 1 – Reading a Journal Article In this part of the workshop, you will be provided with a journal article (French et al. 2004 Methicillin Resistant Staphylococcus aureus (MRSA) in the Workshop 2 file). Read this journal article and answer the questions about the article in Part 1 of the Workshop 2 assignment. Part 2 - Finding a Specific Journal Article In this part of Workshop 2, you will be provided with a clue (a partial reference) allowing you to find a specific scientific journal article in the literature. The unique clue will be posted against your student number on the course page on cuLearn. Clues will be listed by lab section; ensure you are checking the section you are registered in for your student number and clue. The complete scientific journal article associated with your clue is freely available as an electronic document from the Carleton University library website. The article is also likely available through other websites (e.g., the publishing company, etc.), however it is likely that these other sources will not allow you access to the full article free of charge. Instructions about this are given below. Note: You are NOT required to pay for access to the article. All of the articles for this exercise may be accessed FREE OF CHARGE from the Carleton University library website. You are required to find the complete scientific journal article pertaining to the unique clue you were assigned on cuLearn. In some cases, you may locate a free preview of the article, consisting only of the abstract; such articles usually require a fee to access the complete article. This is NOT the article page you are looking for; DO NOT pay to access the complete article. You must access the entire article, consisting of an Abstract, Introduction, Methods, Results, Discussion and References sections. Once you have located the article identified by your clue, complete the questions in Part 2 of the Workshop 2 assignment. A Brief Introduction to Scientific Literature The most common method that scientists use to communicate their experimental findings is by writing journal articles (also called papers) that are published in scientific journals (periodicals). In most fields, these articles comprise what is known as the literature, which is the body of knowledge published on a specific topic. The literature can be divided into three groups or levels reflecting the different stages in the creation, discussion and reevaluation of scientific research. Primary literature contains information based directly on the experimental research conducted by the author(s). This level is also referred to as empirical research as it is based on measuring, evaluating and testing hypotheses. Articles in this group provide sufficient information for the research to be repeated

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BIOL 1103

Workshop 2 – Scientific Literature

Fall 2020

by another researcher. Before any article is published as primary literature, it goes through the peer review process. This means that it is reviewed by at least two other scientists having the expertise to evaluate the quality of the research and validate the interpretation of the results. While this does not preclude errors or protect against fraud, it does eliminate the dissemination of incorrect information based on poorly conducted research. Once a significant amount of information on a single topic has accumulated in the primary literature, the findings are often analyzed and summarized in a review paper by a scientist who works in that area of research. As a review paper does not report original research, it is not considered primary literature. This type of article, based on a synthesis of primary research is secondary literature. Review articles are published in the same journals as primary literature, are also peer reviewed, and may draw new conclusions, or repackage the data in a new form. Other forms of secondary literature include books and annual reviews. As the information from primary literature and reviews disseminates through the scientific community and becomes accepted as valid (i.e., is reproducible) it gradually finds its way into tertiary literature (textbooks, magazines, newspapers, etc.) that are written for students or the public. Tertiary literature may or may not be written by scientists and does not usually provide any new information. The tertiary literature is usually oriented towards non-specialists by providing a summary in non-technical language (i.e., reducing or eliminating scientific jargon). As tertiary sources are not peer reviewed and can be written by authors who may be unfamiliar with the topic material, some tertiary literature may be less reliable than other sources. This requires that the reader examine the credentials of the source closely before using the information. In general, secondary and tertiary articles assist a student to locate and understand the primary literature. However, primary literature is the best source for the most current information on a research topic. Every year thousands of articles are published in periodicals on all aspects of science. As a result, it is not always easy to locate a specific article, or one about a specific subject. Fortunately, most journals make their articles available through the internet and there are searchable databases for most of the primary literature. Knowing how to locate a specific scientific article or articles on specific topics represents a potential gold mine for students working in biology (or any scientific discipline) for preparing essays, laboratory write-ups, etc. Finding Scientific Journals through a Database Search or by using Google Scholar Many scientific journals are now published only in electronic formats, although some journals also publish a hard copy (paper) version. Both versions are usually identical, can be accessed via the internet, and downloaded as a PDF (Portable Document Format) files. Many journals have electronic articles archived as far back as the early 1900's.

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Electronic access to most journals requires a paid subscription, although some journals provide free access one year from first publication. The Carleton University Library purchases site licenses for many different journals, which allows students to download articles free from computers on campus or from home via a remote login through the library website. If you are unable to access the library website from home, contact the Library for assistance with connection problems. Several different journal databases can be searched by topic(s), author(s) name(s), journal, date, etc. to find relevant papers. One of the most comprehensive is the Web of Science (search for Web of Science in the Database search on the library website) containing articles from a wide range of disciplines. Searches of this database will retrieve the title, author(s), journal and abstract of any papers matching the search parameters, and a link to the paper if an electronic copy exists. To help you with your search, an internet course guide has been set up by the Carleton University Library specifically for this course, which gives instructions on how to conduct a database search to find a journal article; or search the Library website using ‘BIOL 1103’ as the keyword. These instructions will inform you how to search the electronic database, Web of Science, using the partial reference (clue) you were assigned and find the specific paper. You may have to search more than one database in order to find your article, so do not give up if your first search is unsuccessful. Although you may contact the library for assistance if you have a general question that cannot be answered using the online information, library staff will NOT find your paper for you. Another option is to use Google Scholar to search for your journal article. Google scholar is used in the same manner as you would use Google search for a topic. When deciding what to search for, remember the information contained in your clue and consider what information is the most important to locate the specific journal article corresponding to your clue (the author(s), year of publication and the exact article title). An author may publish several dozen (or even hundreds) of journal articles throughout their career. This means that a search in Google scholar using the author’s name as the sole search criteria will likely yield abundant results. This may not be the most efficient way to search for your specific journal article as you will have to sift through all of the journal articles written by that author, or authors with the same name. As you may suspect, performing a Google scholar search using the year of publication as the sole search criteria would not be very useful in terms of finding your specific journal article. For example, a search for ‘journal article 2019’ in Google scholar produced 1.9 billion results. The only other piece of information provided to you in your clue is the title of the article. This information is likely the most helpful in terms of searching for the article using Google scholar as it is extremely rare that two or more journal articles have exactly the same title. As most researchers spend the majority of their careers working on a single topic of research, they will likely publish multiple journal articles on a similar subject. This means that when performing your search you need to watch out for journal articles with similar titles. Many articles may even have the same author and/or year of publication as the article for which you are searching. If you are not paying close enough attention when performing

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your search, you may end up locating an incorrect journal article. Once you have located the exact journal article you were assigned, based on the clue provided to you, you will need to access it. From outside the Carleton campus, or if you are unable to access the journal article free of charge, note of the citation information (i.e., the citation information that was missing from your clue such as journal name, volume, page numbers, etc.); you can then log into the Carleton University Library website (using your Carleton username and password) to locate the journal article. All journal articles matching the clues are accessible using the Carleton University Library and can be accessed free of charge. We do not expect you to pay to access any article for this assignment. If you cannot access a free copy, please contact your TA.

Part 1: Reading a Journal Article After carefully reading the journal article provided to you, review Appendix 3 (Scientific Reports and Referencing). Answer the questions in the Workshop 2 assignment concerning the content of this journal article and presentation format.

Part 2: Scientific Journal Articles: Structure, Citation and Referencing You were provided with a unique clue (a partial scientific reference) on cuLearn. You are to locate the journal article that corresponds to this clue. The article title, authors’ names and date of publication should all match exactly. You will use this journal article to answer the questions in Part 2 of the Workshop 2 assignment. Once you have found the journal article that corresponds to your unique clue from cuLearn, you should scan through it. Scientific Journal articles are sometimes long and quite often complicated – unfortunately there is no getting around this! You may choose to read an article from beginning to end but often, it is not necessary. Begin by examining the basic components of a journal article (often called a ‘paper’). Refer to the journal article you found while you read through this information. This comparison should help you get a feel for where specific information is found in the article. Starting at the top: Title: This is a short label (usually fewer than 10 words) stating the content of the article to the reader. The title contains keywords, which alert the reader to what is in the article. The title will usually include the scientific name of the study organism(s), if applicable. A title does not usually contain abbreviations. List of Authors: Only those who have actively contributed to the design, execution, or analysis of the experiment are listed. The order in which the names appear is important. The lead or primary author is always listed first. Names then follow in sequence, based on the level of contribution each person made to the paper. The greater the contribution made, the closer the name will appear towards the front of the list.

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Abstract: The abstract is a short description of experimental objectives, the problem being investigated, methodology, results, and conclusions. This is often the most useful section of a paper for you as it provides a general, yet detailed, overview of the entire paper; this allows you to decide if you are interested in reading the rest of the article. References are not normally included in the abstract. Introduction: Background information is included in the Introduction to enable a person not familiar with that field of research to inform themselves about the topic. Since the author has only a limited amount of space, concise historical reviews are usually cited. This section contains a statement of the purpose of the research (e.g., nature and background of the problem) and may state any research hypotheses. Methods: This section contains the technical information and procedures that were used to obtain the results. This section contains detailed procedural information that should allow the experiment to be repeated by another scientist in order to reproduce the results or judge the overall validity of the research. Results: This is usually a technical presentation of the experimental data and/or observations. The results are described in words, in paragraph form. Tables and/or figures summarizing data, statistical test results, and figures or diagrams may also be included, as necessary. Discussion: In this section the author(s) analyze(s) and interprets the experimental data or observations and brings the results into context of what is known about the subject. The authors must convince the reader of the validity and importance of the results. Future research about further studies that could extend the current research may also be included. References: Scientists rely heavily on information presented in scientific papers written by other scientists. The Introduction and Discussion sections of a scientific paper often contain many citations concerning publications of related work and findings. The format of these citations varies in different biological journals but generally contains the same components: a citation in the text listing one or more of the authors and the year of publication, and a complete listing for this paper (all authors, year of publication, full title, journal, etc.) in the References section. You will learn more about these components when you complete your Scientific Literature Take-Home Assignment. Acknowledgements: It is customary for the authors to thank colleagues who, while not contributing enough to warrant co-authorship, have nevertheless helped in the work. Institutions that have provided funding for the study are usually included in this section. When reading a scientific journal article, you should begin with the Abstract. The Abstract will tell you if the topic examined and the results obtained in the paper are of interest to you or apply to the research you are conducting. Next, read the Introduction and parts, or all, of the Discussion, since they constitute the remainder of the information necessary for a general view of the topic. If you need to know the experimental methodology, the Methods section will provide these details. This section usually contains technical descriptions and is often, for non-specialists, the most difficult 6

BIOL 1103

Workshop 2 – Scientific Literature

Fall 2020

section to read. If the paper is being read for technical reasons, this section should be studied carefully, since small details are often important for reproducing or revising the experiments. Finally, the Results can be read and evaluated. Scientific Literature Assignment The purpose of this assignment is to introduce you to scientific journal articles, citations, references and to practice accessing these articles. After completing this assignment, you should be able to access scientific journal articles and be familiar with locating key/specific information within an article. This skill will benefit you when you are required to search the literature when writing scientific reports throughout your University career. It is recommended that you review Appendix 2 - Scientific Reports and Referencing and the relevant information in the Videos and Internet Materials section above; there are also short videos posted in Workshop 2 about finding scientific articles and information. A Series of Citations 1. In the Workshop 2 folder on cuLearn there is a folder titled Student Clues. This folder contains PDF documents b...