Scientific paper structure

why a scientific format?the scientific format may seem confusing for the beginning science writer due to its rigid structure which is so different from writing in the humanities. one reason for using this format is that it is a means of efficiently communicating scientific findings to the broad community of scientists in a uniform manner. another reason, perhaps more important than the first, is that this format allows the paper to be read at several different levels. for example, many people skim titles to find out what information is available on a subject. others may read only titles and abstracts. those wanting to go deeper may look at the tables and figures in the results, and so on. the take home point here is that the scientific format helps to insure that at whatever level a person reads your paper (beyond title skimming), they will likely get the key results and conclusions.top of pagethe sections of the papermost journal-style scientific papers are subdivided into the following sections: title, authors and affiliation, abstract, introduction, methods, results, discussion, acknowledgments, and literature cited, which parallel the experimental process. this is the system we will use. this website describes the style, content, and format associated with each section.the sections appear in a journal style paper in the following prescribed order:experimental process section of paper what did i do in a nutshell? abstract what is the problem? introduction how did i solve the problem? materials and methods what did i find out? results what does it mean? discussion who helped me out? acknowledgments (optional) whose work did i refer to? literature cited extra information appendices (optional) section headings:main section headings: each main section of the paper begins with a heading which should be capitalized, centered at the beginning of the section, and double spaced from the lines above and below. do not underline the section heading or put a colon at the end.example of a main section heading:introductionsubheadings: when your paper reports on more than one experiment, use subheadings to help organize the presentation. subheadings should be capitalized (first letter in each word), left justified, and either bold italics or underlined.example of a subheading:effects of light intensity on the rate of electron transporttop of pagetitle, authors' names, and institutional affiliations1. function: your paper should begin with a title that succinctly describes the contents of the paper. use descriptive words that you would associate strongly with the content of your paper: the molecule studied, the organism used or studied, the treatment, the location of a field site, the response measured, etc. a majority of readers will find your paper via electronic database searches and those search engines key on words found in the title.2. title faqs3. format:the title should be centered at the top of page 1 (do not use a title page - it is a waste of paper for our purposes); the title is not underlined or italicized. the authors' names (pi or primary author first) and institutional affiliation are double-spaced from and centered below the title. when more then two authors, the names are separated by commas except for the last which is separated from the previous name by the word "and". for example:ducks over-winter in colorado barley fields in response to increased daily mean temperatureima mallard, ura drake, and woodruff ducquedepartment of wildlife biology, university of colorado - bouldertop of pagethe title is not a section, but it is necessary and important. the title should be short and unambiguous, yet be an adequate description of the work. a general rule-of-thumb is that the title should contain the key words describing the work presented. remember that the title becomes the basis for most on-line computer searches - if your title is insufficient, few people will find or read your paper. for example, in a paper reporting on an experiment involving dosing mice with the sex hormone estrogen and watching for a certain kind of courtship behavior, a poor title would be:mouse behaviorwhy? it is very general, and could be referring to any of a number of mouse behaviors. a better title would be:the effects of estrogen on the nose-twitch courtship behavior in micewhy? because the key words identify a specific behavior, a modifying agent, and the experimental organism. if possible, give the key result of the study in the title, as seen in the first example. similarly, the above title could be restated as:estrogen stimulates intensity of nose-twitch courtship behavior in mice4. strategy for writing title.top of pageabstract 1. function: an abstract summarizes, in one paragraph (usually), the major aspects of the entire paper in the following prescribed sequence:the question you investigated (or purpose), (from introduction) state the purpose very clearly in the first or second sentence. the experimental design and methods used, (from methods) clearly express the basic design of the study. name or briefly describe the basic methodology used without going into excessive detail-be sure to indicate the key techniques used. the major findings including key quantitative results, or trends (from results) report those results which answer the questions you were asking identify trends, relative change or differences, etc. a brief summary of your interpetations and conclusions. (from discussion) clearly state the implications of the answers your results gave you. whereas the title can only make the simplest statement about the content of your article, the abstract allows you to elaborate more on each major aspect of the paper. the length of your abstract should be kept to about 200-300 words maximum (a typical standard length for journals.) limit your statements concerning each segment of the paper (i.e. purpose, methods, results, etc.) to two or three sentences, if possible. the abstract helps readers decide whether they want to read the rest of the paper, or it may be the only part they can obtain via electronic literature searches or in published abstracts. therefore, enough key information (e.g., summary results, observations, trends, etc.) must be included to make the abstract useful to someone who may to reference your work.top of pagehow do you know when you have enough information in your abstract? a simple rule-of-thumb is to imagine that you are another researcher doing an study similar to the one you are reporting. if your abstract was the only part of the paper you could access, would you be happy with the information presented there?2. style: the abstract is only text. use the active voice when possible, but much of it may require passive constructions. write your abstract using concise, but complete, sentences, and get to the point quickly. use past tense. maximum length should be 200-300 words, usually in a single paragraph.the abstract should not contain:lengthy background information, references to other literature, elliptical (i.e., ending with ...) or incomplete sentences, abbreviations or terms that may be confusing to readers, any sort of illustration, figure, or table, or references to them. top of page3. strategy: although it is the first section of your paper, the abstract, by definition, must be written last since it will summarize the paper. to begin composing your abstract, take whole sentences or key phrases from each section and put them in a sequence which summarizes the paper. then set about revising or adding words to make it all cohesive and clear. as you become more proficient you will most likely compose the abstract from scratch.4. check your work: once you have the completed abstract, check to make sure that the information in the abstract completely agrees with what is written in the paper. confirm that all the information appearing the abstract actually appears in the body of the paper.top of pageintroduction[ strategy | faqs | style | structure | relevant literature review | statement of purpose | rationale ]1. function: the function of the introduction is to:establish the context of the work being reported. this is accomplished by discussing the relevant primary research literature (with citations) and summarizing our current understanding of the problem you are investigating; state the purpose of the work in the form of the hypothesis, question, or problem you investigated; and, briefly explain your rationale and approach and, whenever possible, the possible outcomes your study can reveal. quite literally, the introduction must answer the questions, "what was i studying? why was it an important question? what did we know about it before i did this study? how will this study advance our knowledge?"2. style: use the active voice as much as possible. some use of first person is okay, but do not overdo it.top of page3. structure: the structure of the introduction can be thought of as an inverted triangle - the broadest part at the top representing the most general information and focusing down to the specific problem you studied. organize the information to present the more general aspects of the topic early in the introduction, then narrow toward the more specific topical information that provides context, finally arriving at your statement of purpose and rationale. a good way to get on track is to sketch out the introduction backwards; start with the specific purpose and then decide what is the scientific context in which you are asking the question your study addresses. once the scientific context is decided, then you'll have a good sense of what level and type of general information with which the introduction should begin. here is the information should flow in your introduction:begin your introduction by clearly identifying the subject area of interest. do this by using key words from your title in the first few sentences of the introduction to get it focused directly on topic at the appropriate level. this insures that you get to the primary subject matter quickly without losing focus, or discussing information that is too general. for example, in the mouse behavior paper, the words hormones and behavior would likely appear within the first one or two sentences of the introduction. top of pageestablish the context by providing a brief and balanced review of the pertinent published literature that is available on the subject. the key is to summarize (for the reader) what we knew about the specific problem before you did your experiments or studies. this is accomplished with a general review of the primary research literature (with citations) but should not include very specific, lengthy explanations that you will probably discuss in greater detail later in the discussion. the judgment of what is general or specific is difficult at first, but with practice and reading of the scientific literature you will develop e firmer sense of your audience. in the mouse behavior paper, for example, you would begin the introduction at the level of mating behavior in general, then quickly focus to mouse mating behaviors and then hormonal regulation of behavior. lead the reader to your statement of purpose/hypothesis by focusing your literature review from the more general context (the big picture e.g., hormonal modulation of behaviors) to the more specific topic of interest to you (e.g., role/effects of reproductive hormones, especially estrogen, in modulating specific sexual behaviors of mice.) top of pagewhat literature should you look for in your review of what we know about the problem? focus your efforts on the primary research journals - the journals that publish original research articles. although you may read some general background references (encyclopedias, textbooks, lab manuals, style manuals, etc.) to get yourself acquianted with the subject area, do not cite these, becasue they contain information that is considered fundamental or "common" knowledge wqithin the discipline. cite, instead, articles that reported specific results relevant to your study. learn, as soon as possible, how to find the primary literature (research journals) and review articles rather than depending on reference books. the articles listed in the literature cited of relevant papers you find are a good starting point to move backwards in a line of inquiry. most academic libraries support the citation index - an index which is useful for tracking a line of inquiry forward in time. some of the newer search engines will actually send you alerts of new papers that cite particular articles of interest to you. review articles are particularly useful because they summarize all the research done on a narrow subject area over a brief period of time (a year to a few years in most cases). top of pagebe sure to clearly state the purpose and /or hypothesis that you investigated. when you are first learning to write in this format it is okay, and actually preferable, to use a pat statement like, "the purpose of this study was to...." or "we investigated three possible mechanisms to explain the ... (1) blah, blah..(2) etc. it is most usual to place the statement of purpose near the end of the introduction, often as the topic sentence of the final paragraph. it is not necessary (or even desirable) to use the words "hypothesis" or "null hypothesis", since these are usually implicit if you clearly state your purpose and expectations. top of pageprovide a clear statement of the rationale for your approach to the problem studied. for example: state briefly how you approached the problem (e.g., you studied oxidative respiration pathways in isolated mitochondria of cauliflower). this will usually follow your statement of purpose in the last paragraph of the introduction. why did you choose this kind of experiment or experimental design? what are the scientific merits of this particular model system? what advantages does it confer in answering the particular question you are posing? do not discuss here the actual techniques or protocols used in your study (this will be done in the materials and methods); your readers will be quite familiar with the usual techniques and approaches used in your field. if you are using a novel (new, revolutionary, never used before) technique or methodology, the merits of the new technique/method versus the previously used methods should be presented in the introduction. top of pagematerials and methodsthis section is variously called methods or methods and materials.1. function: in this section you explain clearly how you carried out your study in the following general structure and organization (details follow below):the subjects used (plant, animal, human, etc.) and their pre-experiment handling and care, and when and where the study was carried out (if location and time are important factors); if a field study, a description of the study site, including the physical and biological features, and precise location; the experimental or sampling design (i.e., how the experiment or study was structured. for example, controls, treatments, the variable measured, how many samples were collected, replication, etc.); the protocol for collecting data, i.e., how the experimental procedures were carried out, and, how the data were analyzed (statistical procedures used). organize your presentation so your reader will understand the logical flow of the experiment ; subheadings work well for this purpose. each experiment or procedure should be presented as a unit, even if it was broken up over time. in general, provide enough quantitative detail (how much, how long, when, etc.) about your experimental protocol such that other scientists could reproduce your experiments. you should also indicate the statistical procedures used to analyze your results, including the probability level at which you determined significance (usually at 0.05 probability).2. style: the style in this section should read as if you were verbally describing the conduct of the experiment. you may use the active voice to a certain extent, although this section requires more use of third person, passive constructions than others. avoid use of the first person in this section. remember to use the past tense throughout. the methods section is not a step-by-step, directive, protocol as you might see in your lab manual.3. strategy for writing the methods section.4. methods faqs.top of pagedescribe the organism used in the study. this includes giving the source (supplier or where and how collected), size, how they were handled before the experiment, what they were fed, etc. in genetics studies include the strains or genetic stocks used.describe the site where your field study was conducted. the description must include both physical and biological characteristics of the site pertinant to the study aims. include the date of the study (e.g., 10-15 april 1994) and the exact location of the study area. location data must be as precise as possible: "grover nature preserve, ? mi sw grover, maine" rather than "grover nature preserve" or "grover". when possible, give the actual latitude and longitude position of the site (the www has sites which provide this service). it is most often a good idea to include a map (labeled as a figure) showing the location in relation to some larger more recognizable geographic area. someone else should be able to go to the exact location of your study if they want to repeat or check your work, or just visit your study area.note: for laboratory studies you should not report the date and location of the study unless it is relevant. most often it is not. top of pagedescribe your experimental design clearly. be sure to include the hypotheses you tested, controls, treatments, variables measured, how many replicates you had, what you actually measured, what form the data take, etc. always identify treatments by the variable or treatment name, not by an ambiguous, generic name or number (e.g., use "2.5% saline" rather than "test 1".) when your paper includes more than one experiment, use subheadings to help organize your presentation by experiment. a general experimental design worksheet is available to help plan your experiments in the core courses.describe the protocol for your study in sufficient detail that other scientists could repeat your work to verify your findings. foremost in your description should be the "quantitative" aspects of your study - the masses, volumes, incubation times, concentrations, etc., that another scientist needs in order to duplicate your experiment. when using standard lab or field methods and instrumentation, it is not always necessary to explain the procedures (e.g., serial dilution) or equipment used (e.g., autopipetter) since other scientists will likely be familiar with them already. you may want to identify certain types of equipment by brand or category (e.g., ultracentrifuge vs. prep centrifuge). it is appropriate to give the source for reagents used parenthetically, e.g., "....poly-l-lysine (sigma #1309)." when using a method described in another published source, you can save time and words by referring to it and providing the relevant citation to the source. always make sure to describe any modifications you have made of a standard or published method.describe how the data were summarized and analyzed. here you will indicate what types of data summaries and analyses were employed to answer each of the questions or hypotheses tested.the information should include:how the data were summarized (means, percent, etc) and how you are reporting measures of variability (sd,sem, etc) this lets you avoid having to repeatedly indicate you are using mean ± sd. data transformation (e.g., to normalize or equalize variances) statistical tests used with reference to the particular questions they address, e.g., "a paired t-test was used to compare mean flight duration before and after applying stablizers to the glider's wings.""one way anova was used to compare mean weight gain in weight-matched calves fed the three different rations."any other numerical or graphical techniques used to analyze the data top of pagehere is some additional advice on particular problems common to new scientific writers.problem: the methods section is prone to being wordy or overly detailed.avoid repeatedly using a single sentence to relate a single action; this results in very lengthy, wordy passages. a related sequence of actions can be combined into one sentence to improve clarity and readability: problematic example: this is a very long and wordy description of a common, simple procedure. it is characterized by single actions per sentence and lots of unnecessary details."the petri dish was placed on the turntable. the lid was then raised slightly. an inoculating loop was used to transfer culture to the agar surface. the turntable was rotated 90 degrees by hand. the loop was moved lightly back and forth over the agar to spread the culture. the bacteria were then incubated at 37 c for 24 hr."improved example: same actions, but all the important information is given in a single, concise sentence. note that superfluous detail and otherwise obvious information has been deleted while important missing information was added."each plate was placed on a turntable and streaked at opposing angles with fresh overnight e. coli culture using an inoculating loop. the bacteria were then incubated at 37 c for 24 hr."best: here the author assumes the reader has basic knowledge of microbiological techniques and has deleted other superfluous information. the two sentences have been combined because they are related actions."each plate was streaked with fresh overnight e. coli culture and incubated at 37 c for 24 hr."top of pageproblem: avoid using ambiguous terms to identify controls or treatments, or other study parameters that require specific identifiers to be clearly understood. designators such as tube 1, tube 2, or site 1 and site 2 are completely meaningless out of context and difficult to follow in context. problematic example: in this example the reader will have no clue as to what the various tubes represent without having to constantly refer back to some previous point in the methods."a spec 20 was used to measure a600 of tubes 1,2, and 3 immediately after chloroplasts were added (time 0) and every 2 min. thereafter until the dcip was completely reduced. tube 4's a600 was measured only at time 0 and at the end of the experiment."improved example: notice how the substitution (in red) of treatment and control identifiers clarifies the passage both in the context of the paper, and if taken out of context."a spec 20 was used to measure a600 of the reaction mixtures exposed to light intensities of 1500, 750, and 350 ue/m2/sec immediately after chloroplasts were added (time 0) and every 2 min. thereafter until the dcip was completely reduced. the a600 of the no light control was measured only at time 0 and at the end of the experiment."top of pageresults1. function: the function of the results section is to objectively present your key results, without interpretation, in an orderly and logical sequence using both illustrative materials (tables and figures) and text. summaries of the statistical analyses may appear either in the text (usually parenthetically) or in the relevant tables or figures (in the legend or as footnotes to the table or figure). the results section should be organized around a series of tables and/or figures sequenced to present your key findings in a logical order. the text of the results section follows this sequence and highlights the answers to the questions/hypotheses you investigated. important negative results should be reported, too. authors usually write the text of the results section based upon this sequence of tables and figures.2. style: write the text of the results section concisely and objectively. the passive voice will likely dominate here, but use the active voice as much as possible. use the past tense. avoid repetitive paragraph structures. do not interpret the data here. the transition into interpretive language can be a slippery slope. consider the following two examples:this example highlights the trend/difference that the author wants the reader to focus: the duration of exposure to running water had a pronounced effect on cumulative seed germination percentages (fig. 2). seeds exposed to the 2-day treatment had the highest cumulative germination (84%), 1.25 times that of the 12-h or 5-day groups and 4 times that of controls.in contrast, this example strays subtly into interpretation by referring to optimality (a conceptual model) and tieing the observed result to that idea: the results of the germination experiment (fig. 2) suggest that the optimal time for running-water treatment is 2 days. this group showed the highest cumulative germination (84%), with longer (5 d) or shorter (12 h) exposures producing smaller gains in germination when compared to the control group.3. strategy for writing the results section4. frequently asked questions (faqs).top of pagethings to consider as you write your results section:what are the "results"?: when you pose a testable hypothesis that can be answered experimentally, or ask a question that can be answered by collecting samples, you accumulate observations about those organisms or phenomena. those observations are then analyzed to yield an answer to the question. in general, the answer is the " key result".the above statements apply regardless of the complexity of the analysis you employ. so, in an introductory course your analysis may consist of visual inspection of figures and simple calculations of means and standard deviations; in a later course you may be expected to apply and interpret a variety of statistical tests. you instructor will tell you the level of analysis that is expected.for example, suppose you asked the question, "is the average height of male students the same as female students in a pool of biology majors?" you would first collect height data from large random samples of male and female students. you would then calculate the descriptive statistics for those samples (mean, sd, n, range, etc) and plot these numbers. in a course where statistical tests are not employed, you would visually inspect these plots. suppose you found that male biology majors are, on average, 12.5 cm taller than female majors; this is the answer to the question.notice that the outcome of a statistical analysis is not a key result, but rather an analytical tool that helps us understand what is our key result. top of pageorganize the results section based on the sequence of table and figures you'll include. prepare the tables and figures as soon as all the data are analyzed and arrange them in the sequence that best presents your findings in a logical way. a good strategy is to note, on a draft of each table or figure, the one or two key results you want to addess in the text portion of the results. simple rules to follow related to tables and figures:tables and figures are assigned numbers separately and in the sequence that you will refer to them from the text. the first table you refer to is table 1, the next table 2 and so forth. similarly, the first figure is figure 1, the next figure 2, etc. each table or figure must include a brief description of the results being presented and other necessary information in a legend. table legends go above the table; tables are read from top to bottom. figure legends go below the figure; figures are usually viewed from bottom to top. when referring to a figure from the text, "figure" is abbreviated as fig.,e.g., fig. 1. table is never abbreviated, e.g., table 1. top of pagethe body of the results section is a text-based presentation of the key findings which includes references to each of the tables and figures. the text should guide the reader through your results stressing the key results which provide the answers to the question investigated. a major function of the text is to provide clarifying information. you must refer to each table and/or figure individually and in sequence (see numbering sequence), and clearly indicate for the reader the key results that each conveys. key results depend on your questions, they might include obvious trends, important differences, similarities, correlations, maximums, minimums, etc.some things to avoid:do not reiterate each value from a figure or table - only the key result or trends that each conveys. do not present the same data in both a table and figure - this is considered redundant and a waste of space and energy. decide which format best shows the result and go with it. do not report raw data values when they can be summarized as means, percents, etc.top of page statistical test summaries (test name, p-value) are usually reported parenthetically in conjunction with the biological results they support. always report your results with parenthetical reference to the statistical conclusion that supports your finding (if statistical tests are being used in your course). this parenthetical reference should include the statistical test used and the level of significance (test statistic and df are optional). for example, if you found that the mean height of male biology majors was significantly larger than