1 How to Read a Scientific Paper What is a scientific paper? Scientific papers are peer reviewed Anatomy of a scientific paper... 4 How to read a scientific paper 5 Ethics in research and publishing... 6 Understanding numerical data.. 7 What does statistical significance mean?... 8 Case study: Buy My Oranges....9 Appendix: Numerical analysis Additional resources and credits 13
2 What is a scientific paper? Scientific papers go straight to source If someone asks you about a new movie you haven t seen yet, what do you say? Maybe, I haven t seen it, but I ve heard it s good. We generally try to distinguish first-hand from second-hand use in new ways to address different questions. The authors of scientific papers also provide an interpretation of what y think ir new information means and how it contributes to our understanding of how natural world works. By presenting data itself as well as analysis, or authors can evaluate se interpretations for mselves. Because our understanding is always changing, sometimes interpretations of data can be reevaluated in light of new ideas and new data. information. Like children s game of telephone, information can change as it is passed along. To get real story, wher a film review or results of a new research study, go to source. Scientific papers present data and interpretations Scientists report results of ir research by writing and publishing scientific papers, which are written in a very formal style. One of objectives of a scientific paper is to make available data from a set of studies so that ors can learn from m and build on m to address new questions. By publishing and sharing data, scientists work toger to advance our understanding. Some articles include results from a few targeted studies, and ors present large datasets that or scientists can Society needs scientific literature Much scientific research is publicly funded, and knowledge and technologies that emerge from research have social impacts. Traditionally, output from scientific research has been published in journals that are not widely available outside of university libraries, but in past decade re has been a trend toward increasing openness in science and a desire to make research articles more broadly available. However, it is not sufficient to make se resources available, as in many cases y are written for experts and practicing scientists and refore not readily comprehensible to those who haven t been trained in discipline. We ve written this article as a guide to help people learn to read scientific literature, with goal of increasing access to science and communication about science. Copyright 2013 American Society of Plant Biologists.
3 Scientific papers are peer-reviewed Peer review is a tradition in scholarly publication. Prior to publication, an article is evaluated by or experts, usually anonymously, and se evaluations are used to improve paper. The reviewers may recommend that additional data be collected and analyzed or thatt claims not well supported by data be removed. In standard process, shown to right, authors submit ir paper to a journal editor, who evaluates wher topic is a good match for journal. If so, paper is sent to two or more experts, who read it and provide ir frank evaluations, including wher conclusions are supported by evidence and wher study is novel, important, and interesting. The editor forwards comments to authors, along with a decision to accept paper, to request revision, or to reject it. The role of reviewer is to evaluate experimental design and data presented, as well as interpretation of results. Sometimes, reviewer will find that experimental design was not rigorous enough to support interpretations made by authors, in which case reviewer might recommend that additional experiments be performed or that analysis of results be revised. Most of articles of masss media (newspapers, magazines, and blogs) are not subject to peer review. Although y can be effective at introducing scientific topics to a broader audience, y are not always sufficiently cautious in ir analysis of results of study and sometimes overstate conclusions. For example, mass media often states that high fructose corn syrup causes obesity, although ree is little convincing data to support this claim. Similarly, a research report might show that under laboratory conditions, a new drug slows rate of growth of cultured cancer cells, but media may describe it as a new cure for cancer. If you want to know more about a news report on a scientific breakthrough, find original, peer-reviewed article and read what researchers actually discovered.
4 Anatomy of a scientific paper TITLE AUTHOR INFORMATION ABSTRACT: A summary of study and findings, written by author. INTRODUCTION: A statement of what is currently known about study subject that articulates questions being investigated. It cites or scholarly works, lays foundations for study, and sometimes states a hyposis to be tested. RESULTS: A description of research conducted and results obtained. Results are presented as tables, large datasets, and figures, which can include graphs, videos, diagrams, and photographs. Figure legend Some papers include additional supporting data as a supplement. DISCUSSION: An analysis and interpretation of data presented that integrates new information with prior findings, states implications of work, and sometimes generates new hyposes tobe tested. METHODS: A description of how studies were conducted, with sufficient detail so that ors can repeat m exactly. REFERENCES: The list of articles cited in paper that provide information on research topic and methods used.
5 How to read a scientific paper Although scientific papers seem short, of Results. Once you ve read y are quite dense, and it takes a bit of authors conclusions and interpretations, time and effort to read one! Here are a go back to Resultss section to examine few tips to help you get used to format data on which y based ir and make sense of paper. conclusions. Read Title The title should indicate topic of research, including name of subject organism. Read Abstract The abstract should summarize question being addressed, approach taken, and major findings and ir significance. Read Introduction The Introduction section of paper will provide necessary background information to help you understand goals of study and why study is important and interesting. It also will cite references to previous publications and or relevant work. The references within text are often cited by author and year, but sometimess by a number. The complete citation for each reference is found at end of paper. If you are reading paper online, ree are often hyperlinks to cited references. Read Discussion Most people find that paper is easier to understand if y read it out of order and read Discussion section of paper before Results section. The Discussion summarizes findings of research and explores implications Read Results and Methods The Resultss section describes experiments carried out and data obtained. Be sure to examine figures and tables as you read through text. Do data support authors conclusions? The Methods section provides more information about experiments and statistical methods, ncluding citations to or papers that describe standard methods. Some of methods and terminology in se sections may be unfamiliar, but you can often find more information in or online sources or a textbook. Look at References The cited eferences can lead you to additional information that may help you understand paper. Often se eferences can be found throughh a hyperlink in online article. Look at Citing Articles An online article that has been published a year or more ago usually lists links to articles that have cited it. This information is useful because from se papers you can find out how or authors interpret results and conclusionss of paper you are reading and how or studiess have extended se findings.
6 Ethics in research and publishing Scientific research and publishing are governed by ethical principles and a code of conduct. Researchers and authors must carry out ir work with honesty, integrity, fairness, and respect. Serious misconduct, such as data fabrication, falsification, or plagiarism, is rare, but can make headlines. Journal editors and reviewers are held to a code of conduct that requires y suspend ir personal biasess and act as objectively as possible. For example, a reviewer has to treat unpublished work as confidential and cannot pass along information to ors. The reviewer also has to fairly evaluate work in paper, even if it threatens to scoop or contradict reviewer s own work. Scientific misconduct undermines public s trust, disrupts progress of research, and if undetected, can lead to wasted efforts as ors try to build on unsubstantiated, false, or fabricated claims. Many organizations have developedd materials that explicitly definee ethical guidelines and that can be used for training young scientists; a few of se are listed below. Resources The American Society of Plant Biologists has developed a suite of policies for ethics in publishing: (http://www.aspb.org/publications/editorialee thics.cfm). The US Office of Research Integrity (ORI; One of many training tools ORI has developed is an interactivee video drama called The Lab, in which viewer selects a character and makes choices as an issue of research misconduct unfolds (http://ori.hhs.gov/thelab/thelab.shtml). The Committee on Publication Ethics (COPE; provides guidelines, training, and codes of conduct for editors and publishers of peer- Xi reviewed journals. The Scientificc Research Society Sigma has a wealth of resources about ethics in research and publishing (http://www.sigmaxi.org/programs/ethics/in dex.shtml). A set of six essays on ethics published in its journal American Scientist is available as a free PDF (http://www.sigmaxi.org/programs/ethics/f ortherecord.pdf). The U.S. National Academies of Sciences has published a book called On Being a Scientist: A Guide to Responsible Conduct in Research, which is free to download and includes nteresting case studiess for discussion (http://www.nap.edu/ catalog.php?record_idd =12192).
7 Understanding numerical data Scientistss use many complementary and distribution of values are very methods in ir investigationss and often different in each sample. (These data are include numerical data. For example, a represented as a histogram, in which scientist who wants to develop drought- x-axis showss value of tolerant soybeans might count number measurement, and y-axis shows how of seeds produced by standard and many times that measurement was drought-tolerant variety, or might quantify counted). amount of oil or protein contained in those seeds. The standard deviation of mean The standard deviation of mean (often Numerical data are very powerful but can simply called standard deviation) is a be easily misunderstood or measurement of how much misrepresented. The methods used to set of data varies analyze numerical data must be around mean. The appropriate for method used to collect standard deviations of data, distribution of data data sets below are 3.2, values, and parameters measured. 13, and 23, from left to When measurements are collected from right. The more spread out independent samples, values can be data, larger used to determine averagee value and standard deviation. On also how much variation ree is in right, we ve represented sample population. mean of each sample as a bar of height 10, with The arithmetic mean an error bar that extends The arithmetic mean is value we beyond mean by one usually have in mind when we talk about standard deviation. an average. It is calculated by adding up value of each measurement and The simplest way to dividing sum by number of calculate standard deviation is to use measurements. a spreadsheet program like Excel (see Appendix for more information). Sometimes mean value can also Clearly, a single value such as mean coincidently be most common value does not convey enough information to be ( mode) or fall right in middle of informative on its own. A measure of range of values ( median), but not variation of data, such as standard always. For example, mean of each of deviation, is also necessary and should be three datasets shown below is 10 included in a research article. (indicatedd by a red arrow), but range
8 What does statistical significance mean? which is probability that null Significant, but statistically significant? When comparing samples or populations, differences in measured values can be small but neverless meaningful. To determine if observed differences are meaningful, scientists use statistical tests. If hyposis is true. By convention, biologists typically reject null hyposis if p<0.05. That is, unless p<0.05, re is no differencee between samples, and alternative hyposis (that samples are different) is rejected. a measured difference is supported by statistical test, it can be said that difference between sampless is statistically significant. Note that this does not mean that difference is real, just that re is a strong probability that samples are different. When we apply t-test on our height samples, calculated p-value is 0.5. Therefore, we do not reject null hyposis, and we conclude that re is no statistically significant difference between heights of people at west-side restaurant (WR) and east-sidee Taller, or not? restaurant (ER). As an example, let s see if people who live on east side of town are taller than those on west side of town. It would be extremely difficult to measure height of every person in town, so instead we will measure a subset of people and n apply a statistical test to help us interpret data. We can also measure height of people in a school cafeteria in west side of town (WS). In this sample, mean and standard deviation of heights measured at school are cm (18). We can compare se values to those measured at west-sidee restaurant, which had a mean We measure height of 20 people at fast- of food restaurants on east or west side town and calculate mean and standardd deviation of each sample ( standard deviation is often indicated in parensess of cm (11). Now when we apply t- test to se samples, result is p<0.05. Therefore, we reject null hyposis and say that difference in height between people at WR and at WS is following mean). On west side of town, mean of measured heights is cm (11) and on east, cm (11). They don t look different, but are y? To find out, we can use a statistical test that is commonly used to compare two sets of related but unlinked data, called a Student s t-test (which can be done in Excel; seee Appendix). statistically significant. In graph to right, mean values and standard deviations for three samples are shown. To indicate that measured values in WS sample differ significantly, we highlight m with a star. Statistically significant, but significant? * By convention, a t-test calculates probability that null hyposis is true. The null hyposis states that two samples are same. The alternative hyposis is that two samples are different. The outputt of a t-test is a p-value, Just becausee a result is statistically meaningful doesn t make it important. Is it newsworthy to find that school kids are shorter than adults?
9 Case study: Buy my oran ges You like fresh orange juice, and you also If I haven t convinced you to buy like to get some vitamin C in morning. my oranges, how can I convince I have developed a new variety of you? What or questions do oranges, BETTER ( B), that I m marketing you have? How would you get based on ir higher-than-usual vitamin C content. your questions answered? You ve always bought AVERAGE (A) oranges, but when you go to farmers market, you notice me selling new variety. To show you how amazing my oranges are, I squeeze juice from an A and a B orange and let you taste m both. They re both delicious, and you don t notice any difference in ir flavor. They also produce exactly same volume of juice per orange. Now I use my portable spectrophotometer and an indicator dye, which reacts with vitamin C to give a color that indicates amount of vitamin C in juice. I show you results. The data show that A has 18.3 mg of vitamin C per 100 ml juice, and B has 19.8 mg of vitamin C per 100 ml juice. Given that juice from B tastes just as good, and oranges produce same amount of juice, but B produces more vitamin C, will you start buying B instead of A? Why or why not?
10 Are y really different? You probably are concerned that differencee between amounts of vitamin C in two juices is fairly small (B has about 8% more than A) and wonder if that difference is real or random. Maybe I just got lucky and picked a B orange with a slightly higherthan-average level of vitamin C. You probably want to know if difference I observed is repeatable and wher a small difference of less than 10% has any real meaning. It is possible to answer both se questionss by measuring vitamin C content from several oranges of each variety and analyzing mean and standard deviation of both datasets. Let s look at two scenarios. In one, two types of oranges are not really different and I just got lucky. We ll call that null hyposis, meaning that re is no difference. In alternative hyposis, two types of oranges are different. If we measure vitamin C content of lots of different oranges, we can begin to figure out which of se scenarios is supported. A histogram plot showing measured vitamin C values from type A (blue) and type B (orange) for two different scenarios is shown below. Just looking at data, we can get a sense that values for B tend to be higher than values for A in bottom plot, but we can actually assign a certainty to this interpretation by analyzing numbers. In first dataset, mean (with standard deviation shown in parenses) of A and B respectively are (0.67) and (0.67). In second dataset, values are (0.39) and (0.35). The * Student s t-test confirms that second dataset really is different: p< <0.05, whereas for first set, p= =
11 Therefore, by repeating measurement, we can work out wher two samples are different or same. Because scientists regularly measure small but meaningful differences, replication, numerical analyses, and statistical testing are essential tools for scientists. Or considerations Which of se statements are supported by this study? B oranges are healthier. If I eat B oranges I will get fewer colds. B oranges are a better value. B oranges always have more vitamin C. The answer is that none of se statements are supported by data presented in this study. Based on distribution of values shown in second, alternative hyposis, dataset our study showed that re is slightly more vitamin C on average in B oranges, but any claims beyond that are unjustified extrapolations. To investigate se issues, we would have to design and perform additional experiments. We could also examine scientific literature to investigate relationship between vitamin C consumption and incidence of colds. Furrmore, characteristics of a fruit are somewhat variable and depend on conditions in which it was grown. Perhaps next year vitamin C level will not be different between A and B. It would be nice to see a difference that extends over more than one harvest season and more than one growing region. Science provides us with a set of very powerful tools with which to understand world, but our knowledge accrues in small steps. Any single study provides an incremental advancement, but also lays groundwork for furr studies. Caveat emptor If you wanted to buy a car, you wouldn t take advice of salesperson on car lot, would you? You would first do a side-by-side analysis of cars you like to compare fuel efficiency, safety ratings, and reputation of manufacturer. An educated consumer makes good choices by looking at evidence. We are all consumers of science, wher it informs our decisions about voting, health care, eating, purchases, energy use, or merely how we understand world. Although scientific literature can be a bit daunting, it is an important resource. Learning to read scientific papers empowers you to cut through hyperbole and hype, to see for yourself evidence that lies behind claims, and to draw your own informed conclusions from studies.
12 Appendix Numerical analysis Here are numbers graphed on page titled Understanding numerical data. Graph 1 Graph 2 Graph Here are numbers used on page titled What does statistical significance mean? West East Rest. West Rest. School Mean StDev The mean and standard deviation were calculated using functions in Excel (2010). To calculate mean of a group of numbers, in an empty cell below m, type =average( ). The space between parenses is filled with first and last cell in column for example, (A6:A29). After you type left parensis, you can use your mouse to draw a box around column of numbers and n type right parensis. To calculate standard deviation, type into an empty cell =stdev(a6:a29). Mean StDev t test (ER vs. WR) (WS vs. WR) The mean and standard deviation were calculated as described previously. The t- test was also calculated using a function in Excel. Click on function box (fx) icon at top of page. In pop-up window, select category statistics and n T.Test. In pop-up box, select one set of numbers for Array 1, second for Array 2. For this kind of data, (independent, Gaussian distributed), select 2 for tails and 2 for type.
13 Additional Resources and Credits Additional Resources American Statistical Association: Education. (http://www.amstat.org/education/onlineresources.cfm) Benchpress Project. (2012). Resources to teach journalists about scientific papers and statistics (http://www.benchpressproject.org.uk/) Hans Rosling. (2010). The Joy of Stats (Video) (http://www.gapminder.org/videos/-joy-of-stats/) Sense About Science Making sense of statistics (http://www.senseaboutscience.org/resources.php/1/making-sense-of-statistics) Peer review: The nuts and bolts (http://www.senseaboutscience.org/resources.php/99/peer-review--nuts-and-bolts) I don t know what to believe: Making sense of science stories (http://www.senseaboutscience.org/resources.php/16/i-dont-know-what-to-believe) University of California Museum of Paleontology Understanding Evolution The journal club toolkit Understanding science: How science really works The social side of science: A human and community endeavor (http://undsci.berkeley.edu/article/0_0_0/socialsideofscience_01) Publish or perish? (http://undsci.berkeley.edu/article/0_0_0/howscienceworks_15) Scrutinizing science: Peer review (http://undsci.berkeley.edu/article/howscienceworks_16) A blueprint for scientific investigations (http://undsci.berkeley.edu/article/0_0_0/howscienceworks_03) Visionlearning Scientific communication: Understanding scientific journals and articles (http://www.visionlearning.com/library/module_viewer.php?c3=&mid=158&l=) Scientific communication: Peer review (http://www.visionlearning.com/library/module_viewer.php?mid=159) Scientific communication: Utilizing scientific literature (http://www.visionlearning.com/library/module_viewer.php?mid=173&l=) Scientific research: The case of ivory-billed woodpecker (http://www.visionlearning.com/library/module_viewer.php?mid=174&l=) Produced by Mary Williams for American Society of Plant Biologists (www.aspb.org). About American Society of Plant Biologists (ASPB) WHAT IS ASPB? ASPB is a professional society devoted to advancement of plant sciences. It publishes two world-class journals and organizes conferences and or activities that are key to advancement of science. Membership in American Society of Plant Biologists is open to anyone from any nation who is concerned with physiology, molecular biology, environmental biology, cell biology, and biophysics of plants and or related matters. WHAT IS A PLANT SCIENTIST? A plant scientist specializes in scientific study of plants. Within plant biology re are many areas of interest, including cellular and molecular biology, genetics, development, evolution, physiology, and biochemistry. Plant scientists are working worldwide in nearly all sectors including academia, corporations, pharmacology, research, nonprofits, and government.
The American Society of Plant Biologists (ASPB) is a professional society devoted to the advancement of the plant sciences. It publishes two world-class journals and organizes conferences and other activities
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Module 5: Statistical Analysis To answer more complex questions using your data, or in statistical terms, to test your hypothesis, you need to use more advanced statistical tests. This module reviews the
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