Instructor: Dr. Marinella Sandros

Nanochemistry NAN 601 • Instructor: • Dr. MarinellaSandros How to Read a Scientific Paper?

Reasons To Read a Paper • You were told to • Describes current research Allows you to replicate/extend the results • Provides you with useful data Gives you “pre-digested” thoughts • To decide whether to publish it • Teaches you how to write. http://www.cbcb.umd.edu/confcour/CMSC838K-materials/how-to-read-a-paper.pdf

http://www.cbcb.umd.edu/confcour/CMSC838K-materials/how-to-read-a-paper.pdfhttp://www.cbcb.umd.edu/confcour/CMSC838K-materials/how-to-read-a-paper.pdf

Outline • Learn the basic structure of papers • Develop an approach to reading papers • Learn how to interpret an article citation

The Basic Parts • Title • Abstract • Introduction • Methods • Results • Discussion • References www.usc.edu/hsc/nml/portals/orientation/Intro-Scientific-Papers.ppt

Read In This Order • Title • Abstract • Introduction/ Discussion • Methods/ Results www.usc.edu/hsc/nml/portals/orientation/Intro-Scientific-Papers.ppt

The discussion section occurs before the author presents the results of the study. • True • False www.usc.edu/hsc/nml/portals/orientation/Intro-Scientific-Papers.ppt

Which occurs first in a scientific journal article? • Abstract • Discussion • Introduction • Methods • Results www.usc.edu/hsc/nml/portals/orientation/Intro-Scientific-Papers.ppt

Abstract • Generally, it gives a brief background to the topic; describes concisely the major findings of the paper; and relates these findings to the field of study. http://www.biochem.arizona.edu/classes/bioc568/papers.htm

Abstract • Summarizes • Often only part read • Don’t act on abstracts alone • Structured abstracts are norm • Background • Methods • Results • Conclusions www.usc.edu/hsc/nml/portals/orientation/Intro-Scientific-Papers.ppt

Introduction • In many journals this section is not given a title. As its name implies, this section presents the background knowledge necessary for the reader to understand why the findings of the paper are an advance on the knowledge in the field. • Typically, the Introduction describes first the accepted state of knowledge in a specialized field; then it focuses more specifically on a particular aspect, usually describing a finding or set of findings that led directly to the work described in the paper. http://www.biochem.arizona.edu/classes/bioc568/papers.htm

Introduction • If the authors are testing a hypothesis, the source of that hypothesis is spelled out, findings are given with which it is consistent, and one or more predictions are given. • In many papers, one or several major conclusions of the paper are presented at the end of this section, so that the reader knows the major answers to the questions just posed. • Papers more descriptive or comparative in nature may begin with an introduction to an area which interests the authors, or the need for a broader database. http://www.biochem.arizona.edu/classes/bioc568/papers.htm

Introduction • Context • What is known • Supporting literature (citations) • Gaps in literature • The research question • Newness • Relevance to field www.usc.edu/hsc/nml/portals/orientation/Intro-Scientific-Papers.ppt

Materials and Method • In some journals this section is the last one. Its purpose is to describe the materials used in the experiments and the methods by which the experiments were carried out. • In principle, this description should be detailed enough to allow other researchers to replicate the work. In practice, these descriptions are often highly compressed, and they often refer back to previous papers by the authors. http://www.biochem.arizona.edu/classes/bioc568/papers.htm

Methods • Steps taken to • gather data • analyze data • Statistical methods • Not a “cookbook” • Replicable www.usc.edu/hsc/nml/portals/orientation/Intro-Scientific-Papers.ppt

Results • This section describes the experiments and the reasons they were done. Generally, the logic of the Results section follows directly from that of the Introduction. • That is, the Introduction poses the questions addressed in the early part of Results. Beyond this point, the organization of Results differs from one paper to another. In some papers, the results are presented without extensive discussion, which is reserved for the following section. This is appropriate when the data in the early parts do not need to be interpreted extensively to understand why the later experiments were done. • In other papers, results are given, and then they are interpreted, perhaps taken together with other findings not in the paper, so as to give the logical basis for later experiments. http://www.biochem.arizona.edu/classes/bioc568/papers.htm

Results • Report of data • Tables and graphs • Statistical results • No interpretation www.usc.edu/hsc/nml/portals/orientation/Intro-Scientific-Papers.ppt

Discussion • This section serves several purposes. First, the data in the paper are interpreted; that is, they are analyzed to show what the authors believe the data show. Any limitations to the interpretations should be acknowledged, and fact should clearly be separated from speculation. • Second, the findings of the paper are related to other findings in the field. This serves to show how the findings contribute to knowledge, or correct the errors of previous work. As stated, some of these logical arguments are often found in the Results when it is necessary to clarify why later experiments were carried out. • Although you might argue that in this case the discussion material should be presented in the Introduction, more often you cannot grasp its significance until the first part of Results is given. http://www.biochem.arizona.edu/classes/bioc568/papers.htm

Discussion • Interpretation of results • Answer to research question • Goals met? • Often includes • relation to previous research • limitations • future directions www.usc.edu/hsc/nml/portals/orientation/Intro-Scientific-Papers.ppt

www.usc.edu/hsc/nml/portals/orientation/Intro-Scientific-Papers.pptwww.usc.edu/hsc/nml/portals/orientation/Intro-Scientific-Papers.ppt

Acknowledgements • Various contributions of other workers are recognized, followed by a Reference list giving references to papers and other works cited in the text. http://www.biochem.arizona.edu/classes/bioc568/papers.htm

References • List of sources cited in intro • Usually other journal articles • Previous studies in same field • Citation styles differ depending on • field of study (e.g. AMA vs. APA) • journal • EndNote and RefWorks www.usc.edu/hsc/nml/portals/orientation/Intro-Scientific-Papers.ppt

Understanding Journal Article References • Weiss, PA. Does smoking marijuana contribute to the risk of developing lung cancer? Clinical Journal of Oncology Nursing. 2008;12(3):517-519. • Journal • Volume Number • Issue Number • Researcher’s Article www.usc.edu/hsc/nml/portals/orientation/Intro-Scientific-Papers.ppt

Figures and Tables • These contain data described in the paper. The figures and tables also have legends, whose purpose is to give details of the particular experiment or experiments shown there. • Typically, if a procedure is used only once in a paper, these details are described in Materials and Methods, and the Figure or Table legend refers back to that description. • If a procedure is used repeatedly, however, a general description is given in Materials and Methods, and the details for a particular experiment are given in the Table or Figure legend. http://www.biochem.arizona.edu/classes/bioc568/papers.htm

Reading a scientific paper • Struggle with the paper • active not passive reading • use highlighter, underline text, scribble comments or questions on it, make notes • if at first you don’t understand, read and re-read, spiralling in on central points John W. Little and Roy Parker,University of Arizona

Reading a scientific paper • Get into question-asking mode • doubt everything • nit-pick • find fault • just because it’s published, doesn’t mean it’s right • get used to doing peer review John W. Little and Roy Parker,University of Arizona

Reading a scientific paper • Move beyond the text of the paper • talk to other people about it • read commentaries • consult, dictionaries, textbooks, online links to references, figure legends to clarify things you don’t understand John W. Little and Roy Parker,University of Arizona

Blame the authors if… • Logical connections left out • Instead of saying why something was done, the procedure is simply described. • Cluttered with jargon, acronyms • Lack of clear road-map through the paper • side issues given equal air time with main thread • Difficulties determining what was done • Ambiguous or sketchy description • Endless citation trail back to first paper • Data mixed up with interpretation and speculation John W. Little and Roy Parker,University of Arizona

What questions does the paper address? • Descriptive research • often in early stages of our understanding can't formulate hypotheses until we know what is there. • e.g. DNA sequencing and microarray • Comparative research • Ask how general or specific a phenomenon is. • e.g. homology searches, comparative genomics John W. Little and Roy Parker,University of Arizona

What questions does the paper address? • Analytical or hypothesis-driven research • test hypotheses • e.g. amino-acid composition can be used to predict thermophily • Methodological research • Find out new and better ways of doing things • Describe new resources • e.g. description of new homology search method, genome database • Many papers combine all of the above John W. Little and Roy Parker,University of Arizona

What are the main conclusions? • Look at Title and Abstract, then Discussion • Do they matter? • Of general relevance? • Broad in scope? • Detailed but with far-reaching conclusions? • Accessible to general audience? John W. Little and Roy Parker,University of Arizona

What evidence supports them? • Look at Results section and relevant tables and figures. • May be one primary experiment to support a point. • More often several different experiments or approaches combine to support a particular conclusion. • First experiment might have several possible interpretations, and the later ones are designed to distinguish among these. • In the ideal case, the Discussion begins with a section of the form "Three lines of evidence provide support for the conclusion that...." John W. Little and Roy Parker,University of Arizona

Judging the quality of the evidence • You need to understand the methods thoroughly • may need to consult textbooks • You need to know the limits of the methods • Separate fact from interpretation • Are the results expected? • Extraordinary claims require extraordinary evidence John W. Little and Roy Parker,University of Arizona

Judging the quality of the evidence • Look at details, assess them for plausibility • Where are the controls? • What is the gold standard? John W. Little and Roy Parker,University of Arizona

Do the data support the conclusions? • Data may be believable but not support the conclusion the authors wish to reach • logical connection between the data and the interpretation is not sound (often hidden by bad writing) • might be other interpretations that are consistent with the data John W. Little and Roy Parker,University of Arizona

Do the data support the conclusions? • Rule of thumb • If multiple approaches, multiple lines of evidence, from different directions, supporting the conclusions, then more credible. • Question assumptions! • Identify any implicit or hidden assumptions used by the authors in interpreting their data? John W. Little and Roy Parker,University of Arizona

Homework !!!!

Evaluating a paper • What questions does the paper address? • What are the main conclusions of the paper? • What evidence supports those conclusions? • Do the data actually support the conclusions? • Why are the conclusions important?

Instructor: Dr. Marinella Sandros