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Scientific Writing: Sections of a Paper
- Sections of a Paper
- Common Grammar Mistakes Explained
- Citing Sources
Introduction
- Materials & Methods
Typically scientific journal articles have the following sections:
Materials & Methods
References used:
Kotsis, S.V. and Chung, K.C. (2010) A Guide for Writing in the Scientific Forum. Plastic and Reconstructive Surgery. 126(5):1763-71. PubMed ID: 21042135
Van Way, C.W. (2007) Writing a Scientific Paper. Nutrition in Clinical Practice. 22: 663-40. PubMed ID: 1804295
What to include:
- Background/Objectives: include the hypothesis
- Methods: Briefly explain the type of study, sample/population size and description, the design, and any particular techniques for data collection and analysis
- Results: Essential data, including statistically significant data (use # & %)
- Conclusions: Summarize interpretations of results and explain if hypothesis was supported or rejected
- Be concise!
- Emphasize the methods and results
- Do not copy the introduction
- Only include data that is included in the paper
- Write the abstract last
- Avoid jargon and ambiguity
- Should stand-alone
Additional resources: Fisher, W. E. (2005) Abstract Writing. Journal of Surgical Research. 128(2):162-4. PubMed ID: 16165161 Peh, W.C. and Ng, K.H. (2008) Abstract and keywords. Singapore Medical Journal. 49(9): 664-6. PubMed ID: 18830537
- How does your study fit into what has been done
- Explain evidence using limited # of references
- Why is it important
- How does it relate to previous research
- State hypothesis at the end
- Use present tense
- Be succinct
- Clearly state objectives
- Explain important work done
Additional resources: Annesley, T. M. (2010) "It was a cold and rainy night": set the scene with a good introduction. Clinical Chemistry. 56(5):708-13. PubMed ID: 20207764 Peh, W.C. and Ng, K.H. (2008) Writing the introduction. Singapore Medical Journal. 49(10):756-8. PubMed ID: 18946606
- What was done
- Include characteristics
- Describe recruitment, participation, withdrawal, etc.
- Type of study (RCT, cohort, case-controlled, etc.)
- Equipment used
- Measurements made
- Usually the final paragraph
- Include enough details so others can duplicate study
- Use past tense
- Be direct and precise
- Include any preliminary results
- Ask for help from a statistician to write description of statistical analysis
- Be systematic
Additional resources: Lallet, R. H. (2004) How to write the methods section of a research paper. Respiratory Care. 49(10): 1229-32. PubMed ID: 15447808 Ng, K.H. and Peh, W.C. (2008) Writing the materials and methods. Singapore Medical Journal. 49(11): 856-9. PubMed ID: 19037549
- Describe study sample demographics
- Include statistical significance and the statistical test used
- Use tables and figures when appropriate
- Present in a logical sequence
- Facts only - no citations or interpretations
- Should stand alone (not need written descriptions to be understood)
- Include title, legend, and axes labels
- Include raw numbers with percentages
- General phrases (significance, show trend, etc. should be used with caution)
- Data is plural ("Our data are" is correct, "Our data is" is in-correct)
Additional resources: Ng, K.H and Peh, W.C. (2008) Writing the results. Singapore Medical Journal. 49(12):967-9. PubMed ID: 19122944 Streiner, D.L. (2007) A shortcut to rejection: how not to write the results section of a paper. Canadian Journal of Psychiatry. 52(6):385-9. PubMed ID: 17696025
- Did you reject your null hypothesis?
- Include a focused review of literature in relation to results
- Explain meaning of statistical findings
- Explain importance/relevance
- Include all possible explanations
- Discuss possible limitations of study
- Suggest future work that could be done
- Use past tense to describe your study and present tense to describe established knowledge from literature
- Don't criticize other studies, contrast it with your work
- Don't make conclusions not supported by your results
- Stay focused and concise
- Include key, relevant references
- It is considered good manners to include an acknowledgements section
Additional resources: Annesley, T. M. (2010) The discussion section: your closing argument. Clinical Chemistry. 56(11):1671-4. PubMed ID: 20833779 Ng, K.H. and Peh, W.C. (2009) Writing the discussion. Singapore Medical Journal. 50(5):458-61. PubMed ID: 19495512
Tables & Figures: Durbin, C. G. (2004) Effective use of tables and figures in abstracts, presentations, and papers. Respiratory Care. 49(10): 1233-7. PubMed ID: 15447809 Ng, K. H. and Peh, W.C.G. (2009) Preparing effective tables. Singapore Medical Journal. (50)2: 117-9. PubMed ID: 19296024
Statistics: Ng, K. H. and Peh, W.C.G. (2009) Presenting the statistical results. Singapore Medical Journal. (50)1: 11-4. PubMed ID: 19224078
References: Peh, W.C.G. and Ng, K. H. (2009) Preparing the references. Singapore Medical Journal. (50)7: 11-4. PubMed ID: 19644619
Additional Resources
- More from Elsevier Elsevier's Research Academy is an online tutorial to help with writing books, journals, and grants. It also includes information on citing sources, peer reviewing, and ethics in publishing
- Research4Life Training Portal Research4Life provides downloadable instruction materials, including modules on authorship skills as well as other research related skills.
- Coursera: Science Writing Coursera provides a wide variety of online courses for continuing education. You can search around for various courses on scientific writing or academic writing, and they're available to audit for free.
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Scientific and Scholarly Writing
- PubMed and other NLM Literature Databases
- Tracking and Citing References
Parts of a Scientific & Scholarly Paper
Introduction.
- Writing Effectively
- Where to Publish?
- Avoid Plagiarism
Different sections are needed in different types of scientific papers (lab reports, literature reviews, systematic reviews, methods papers, research papers, etc.). Projects that overlap with the social sciences or humanities may have different requirements. Generally, however, you'll need to include:
INTRODUCTION (Background)
METHODS SECTION (Materials and Methods)
What is a title?
Titles have two functions: to identify the main topic or the message of the paper and to attract readers.
The title will be read by many people. Only a few will read the entire paper, therefore all words in the title should be chosen with care. Too short a title is not helpful to the potential reader. Too long a title can sometimes be even less meaningful. Remember a title is not an abstract. Neither is a title a sentence.
What makes a good title?
A good title is accurate, complete, and specific. Imagine searching for your paper in PubMed. What words would you use?
- Use the fewest possible words that describe the contents of the paper.
- Avoid waste words like "Studies on", or "Investigations on".
- Use specific terms rather than general.
- Use the same key terms in the title as the paper.
- Watch your word order and syntax.
- Avoid abbreviations, jargon, and special characters.
The abstract is a miniature version of your paper. It should present the main story and a few essential details of the paper for readers who only look at the abstract and should serve as a clear preview for readers who read your whole paper. They are usually short (250 words or less).
The goal is to communicate:
- What was done?
- Why was it done?
- How was it done?
- What was found?
A good abstract is specific and selective. Try summarizing each of the sections of your paper in a sentence two. Do the abstract last, so you know exactly what you want to write.
- Use 1 or more well developed paragraphs.
- Use introduction/body/conclusion structure.
- Present purpose, results, conclusions and recommendations in that order.
- Make it understandable to a wide audience.
What is an introduction?
The introduction tells the reader why you are writing your paper (ie, identifies a gap in the literature) and supplies sufficient background information that the reader can understand and evaluate your project without referring to previous publications on the topic.
The nature and scope of the problem investigated.
The pertinent literature already written on the subject.
The method of the investigation.
The hypothesized results of the project.
What makes a good introduction?
A good introduction is not the same as an abstract. Where the abstract summarizes your paper, the introduction justifies your project and lets readers know what to expect.
• Keep it brief. You conducted an extensive literature review, so that you can give readers just the relevant information. • Cite your sources using in-text citations. • Use the present tense. Keep using the present tense for the whole paper. • Use the same information that you use in the rest of your paper.
What is a methods section?
Generally a methods section tells the reader how you conducted your project.
It is also called "Materials and Methods".
The goal is to make your project reproducible.
What makes a good methods section?
A good methods section gives enough detail that another scientist could reproduce or replicate your results.
• Use very specific language, similar to a recipe in a cookbook. • If something is not standard (equipment, method, chemical compound, statistical analysis), then describe it. • Use the past tense. • Subheadings should follow guidelines of a style (APA, Vancouver, etc.) or journal (journals will specify these in their "for authors" section). For medical education writing, refer to the AMA Manual of Style .
What is a results section?
The results objectively present the data or information that you gathered through your project. The narrative that you write here will point readers to your figures and tables that present your relevant data.
Keep in mind that you may be able to include more of your data in an online journal supplement or research data repository.
What makes a good results section?
A good results section is not the same as the discussion. Present the facts in the results, saving the interpretation for the discussion section. The results section should be written in past tense.
• Make figures and tables clearly labelled and easy to read. If you include a figure or table, explain it in the results section. • Present representative data rather than endlessly repetitive data . • Discuss variables only if they had an effect (positive or negative) • Use meaningful statistics . • Describe statistical analyses you ran on the data.
What is a discussion section?
The discussion section is the answer to the question(s) you posed in the introduction section. It is where you interpret your results. You have a lot of flexibility in this section. In addition to your main findings or conclusions, consider:
• Limitations and strengths of your project. • Directions for future research.
What makes a good discussion section?
A good discussion section should read very differently than the results section. The discussion is where you interpret the project as a whole.
• Present principles, relationships and generalizations shown by the results. • Discuss the significance or importance of the results. • Discuss the theoretical implications of your work as well as practical applications • Show how your results agree or disagree with previously published works.
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- Research Guides
BSCI 1510L Literature and Stats Guide: 3.2 Components of a scientific paper
- 1 What is a scientific paper?
- 2 Referencing and accessing papers
- 2.1 Literature Cited
- 2.2 Accessing Scientific Papers
- 2.3 Traversing the web of citations
- 2.4 Keyword Searches
- 3 Style of scientific writing
- 3.1 Specific details regarding scientific writing
3.2 Components of a scientific paper
- 4 Summary of the Writing Guide and Further Information
- Appendix A: Calculation Final Concentrations
- 1 Formulas in Excel
- 2 Basic operations in Excel
- 3 Measurement and Variation
- 3.1 Describing Quantities and Their Variation
- 3.2 Samples Versus Populations
- 3.3 Calculating Descriptive Statistics using Excel
- 4 Variation and differences
- 5 Differences in Experimental Science
- 5.1 Aside: Commuting to Nashville
- 5.2 P and Detecting Differences in Variable Quantities
- 5.3 Statistical significance
- 5.4 A test for differences of sample means: 95% Confidence Intervals
- 5.5 Error bars in figures
- 5.6 Discussing statistics in your scientific writing
- 6 Scatter plot, trendline, and linear regression
- 7 The t-test of Means
- 8 Paired t-test
- 9 Two-Tailed and One-Tailed Tests
- 10 Variation on t-tests: ANOVA
- 11 Reporting the Results of a Statistical Test
- 12 Summary of statistical tests
- 1 Objectives
- 2 Project timeline
- 3 Background
- 4 Previous work in the BSCI 111 class
- 5 General notes about the project
- 6 About the paper
- 7 References
Nearly all journal articles are divided into the following major sections: abstract, introduction, methods, results, discussion, and references or literature cited. Usually the sections are labeled as such, although often the introduction (and sometimes the abstract) is not labeled. Sometimes alternative section titles are used. The abstract is sometimes called the "summary", the methods are sometimes called "materials and methods", and the discussion is sometimes called "conclusions". Some journals also include the minor sections of "key words" following the abstract, and "acknowledgments" following the discussion. In some journals, the sections may be divided into subsections that are given descriptive titles. However, the general division into the six major sections is nearly universal.
3.2.1 Abstract
The abstract is a short summary (150-200 words or less) of the important points of the paper. It does not generally include background information. There may be a very brief statement of the rationale for conducting the study. It describes what was done, but without details. It also describes the results in a summarized way that usually includes whether or not the statistical tests were significant. It usually concludes with a brief statement of the importance of the results. Abstracts do not include references. When writing a paper, the abstract is always the last part to be written.
The purpose of the abstract is to allow potential readers of a paper to find out the important points of the paper without having to actually read the paper. It should be a self-contained unit capable of being understood without the benefit of the text of the article . It essentially serves as an "advertisement" for the paper that readers use to determine whether or not they actually want to wade through the entire paper or not. Abstracts are generally freely available in electronic form and are often presented in the results of an electronic search. If searchers do not have electronic access to the journal in which the article is published, the abstract is the only means that they have to decide whether to go through the effort (going to the library to look up the paper journal, requesting a reprint from the author, buying a copy of the article from a service, requesting the article by Interlibrary Loan) of acquiring the article. Therefore it is important that the abstract accurately and succinctly presents the most important information in the article.
3.2.2 Introduction
The introduction section of a paper provides the background information necessary to understand why the described experiment was conducted. The introduction should describe previous research on the topic that has led to the unanswered questions being addressed by the experiment and should cite important previous papers that form the background for the experiment. The introduction should also state in an organized fashion the goals of the research, i.e. the particular, specific questions that will be tested in the experiments. There should be a one-to-one correspondence between questions raised in the introduction and points discussed in the conclusion section of the paper. In other words, do not raise questions in the introduction unless you are going to have some kind of answer to the question that you intend to discuss at the end of the paper.
You may have been told that every paper must have a hypothesis that can be clearly stated. That is often true, but not always. If your experiment involves a manipulation which tests a specific hypothesis, then you should clearly state that hypothesis. On the other hand, if your experiment was primarily exploratory, descriptive, or measurative, then you probably did not have an a priori hypothesis, so don't pretend that you did and make one up. (See the discussion in the introduction to Experiment 5 for more on this.) If you state a hypothesis in the introduction, it should be a general hypothesis and not a null or alternative hypothesis for a statistical test. If it is necessary to explain how a statistical test will help you evaluate your general hypothesis, explain that in the methods section.
A good introduction should be fairly heavy with citations. This indicates to the reader that the authors are informed about previous work on the topic and are not working in a vacuum. Citations also provide jumping-off points to allow the reader to explore other tangents to the subject that are not directly addressed in the paper. If the paper supports or refutes previous work, readers can look up the citations and make a comparison for themselves.
"Do not get lost in reviewing background information. Remember that the Introduction is meant to introduce the reader to your research, not summarize and evaluate all past literature on the subject (which is the purpose of a review paper). Many of the other studies you may be tempted to discuss in your Introduction are better saved for the Discussion, where they become a powerful tool for comparing and interpreting your results. Include only enough background information to allow your reader to understand why you are asking the questions you are and why your hypotheses are reasonable ones. Often, a brief explanation of the theory involved is sufficient.
Write this section in the past or present tense, never in the future. " (Steingraber et al. 1985)
In other words, the introduction section relates what the topic being investigated is, why it is important, what research (if any) has been done prior that is relevant to what you are trying to do, and in what ways you will be looking into this topic.
An example to think about:
This is an example of a student-derived introduction. Read the paragraph and before you go beyond, think about the paragraph first.
"Hand-washing is one of the most effective and simplest of ways to reduce infection and disease, and thereby causing less death. When examining the effects of soap on hands, it was the work of Sickbert-Bennett and colleagues (2005) that showed that using soap or an alcohol on the hands during hand-washing was a significant effect in removing bacteria from the human hand. Based on the work of this, the team led by Larsen (1991) then showed that the use of computer imaging could be a more effective way to compare the amount of bacteria on a hand."
There are several aspects within this "introduction" that could use improvement. A group of any random 4 of you could easily come up with at 10 different things to reword, revise, expand upon.
In specific, there should be one thing addressed that more than likely you did not catch when you were reading it.
The citations: Not the format, but the logical use of them.
Look again. "...the work of Sickbert-Bennett...(2005)" and then "Based on the work of this, the team led by Larsen (1991)..."
How can someone in 1991 use or base their work on something from 2005?
They cannot. You can spend an entire hour using spellcheck and reading through and through again to find all the little things to "give it more oomph", but at the core, you still must present a clear and concise and logical thought-process.
3.2.3 Methods (taken mostly verbatim from Steingraber et al. 1985, until the version A, B,C portion)
The function of the methods section is to describe all experimental procedures, including controls. The description should be complete enough to enable someone else to repeat your work. If there is more than one part to the experiment, it is a good idea to describe your methods and present your results in the same order in each section. This may not be the same order in which the experiments were performed -it is up to you to decide what order of presentation will make the most sense to your reader.
1. Explain why each procedure was done, i.e., what variable were you measuring and why? Example:
Difficult to understand : First, I removed the frog muscle and then I poured Ringer’s solution on it. Next, I attached it to the kymograph.
Improved: I removed the frog muscle and poured Ringer’s solution on it to prevent it from drying out. I then attached the muscle to the kymograph in order to determine the minimum voltage required for contraction.
Better: Frog muscle was excised between attachment points to the bone. Ringer's solution was added to the excised section to prevent drying out. The muscle was attached to the kymograph in order to determine the minimum voltage required for contraction.
2. Experimental procedures and results are narrated in the past tense (what you did, what you found, etc.) whereas conclusions from your results are given in the present tense.
3. Mathematical equations and statistical tests are considered mathematical methods and should be described in this section along with the actual experimental work. (Show a sample calculation, state the type of test(s) performed and program used)
4. Use active rather than passive voice when possible. [Note: see Section 3.1.4 for more about this.] Always use the singular "I" rather than the plural "we" when you are the only author of the paper (Methods section only). Throughout the paper, avoid contractions, e.g. did not vs. didn’t.
5. If any of your methods is fully described in a previous publication (yours or someone else’s), you can cite work that instead of describing the procedure again.
Example: The chromosomes were counted at meiosis in the anthers with the standard acetocarmine technique of Snow (1955).
Below is a PARTIAL and incomplete version of a "method". Without getting into the details of why, Version A and B are bad. A is missing too many details and B is giving some extra details but not giving some important ones, such as the volumes used. Version C is still not complete, but it is at least a viable method. Notice that C is also not the longest....it is possible to be detailed without being long-winded.
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In other words, the methods section is what you did in the experiment and has enough details that someone else can repeat your experiment. If the methods section has excluded one or more important detail(s) such that the reader of the method does not know what happened, it is a 'poor' methods section. Similarly, by giving out too many useless details a methods section can be 'poor'.
You may have multiple sub-sections within your methods (i.e., a section for media preparation, a section for where the chemicals came from, a section for the basic physical process that occurred, etc.,). A methods section is NEVER a list of numbered steps.
3.2.4 Results (with excerpts from Steingraber et al. 1985)
The function of this section is to summarize general trends in the data without comment, bias, or interpretation. The results of statistical tests applied to your data are reported in this section although conclusions about your original hypotheses are saved for the Discussion section. In other words, you state "the P-value" in Results and whether below/above 0.05 and thus significant/not significant while in the Discussion you restate the P-value and then formally state what that means beyond "significant/not significant".
Tables and figures should be used when they are a more efficient way to convey information than verbal description. They must be independent units, accompanied by explanatory captions that allow them to be understood by someone who has not read the text. Do not repeat in the text the information in tables and figures, but do cite them, with a summary statement when that is appropriate. Example:
Incorrect: The results are given in Figure 1.
Correct: Temperature was directly proportional to metabolic rate (Fig. 1).
Please note that the entire word "Figure" is almost never written in an article. It is nearly always abbreviated as "Fig." and capitalized. Tables are cited in the same way, although Table is not abbreviated.
Whenever possible, use a figure instead of a table. Relationships between numbers are more readily grasped when they are presented graphically rather than as columns in a table.
Data may be presented in figures and tables, but this may not substitute for a verbal summary of the findings. The text should be understandable by someone who has not seen your figures and tables.
1. All results should be presented, including those that do not support the hypothesis.
2. Statements made in the text must be supported by the results contained in figures and tables.
3. The results of statistical tests can be presented in parentheses following a verbal description.
Example: Fruit size was significantly greater in trees growing alone (t = 3.65, df = 2, p < 0.05).
Simple results of statistical tests may be reported in the text as shown in the preceding example. The results of multiple tests may be reported in a table if that increases clarity. (See Section 11 of the Statistics Manual for more details about reporting the results of statistical tests.) It is not necessary to provide a citation for a simple t-test of means, paired t-test, or linear regression. If you use other more complex (or less well-known) tests, you should cite the text or reference you followed to do the test. In your materials and methods section, you should report how you did the test (e.g. using the statistical analysis package of Excel).
It is NEVER appropriate to simply paste the results from statistical software into the results section of your paper. The output generally reports more information than is required and it is not in an appropriate format for a paper. Similar, do NOT place a screenshot.
Should you include every data point or not in the paper? Prior to 2010 or so, most papers would probably not present the actual raw data collected, but rather show the "descriptive statistics" about their data (mean, SD, SE, CI, etc.). Often, people could simply contact the author(s) for the data and go from there. As many journals have a significant on-line footprint now, it has become increasingly more common that the entire data could be included in the paper. And realize why the entire raw data may not have been included in a publication. Prior to about 2010, your publication had limited paper space to be seen on. If you have a sample of size of 10 or 50, you probably could show the entire data set easily in one table/figure and it not take up too much printed space. If your sample size was 500 or 5,000 or more, the size of the data alone would take pages of printed text. Given how much the Internet and on-line publications have improved/increased in storage space, often now there will be either an embedded file to access or the author(s) will place the file on-line somewhere with an address link, such as GitHub. Videos of the experiment are also shown as well now.
3.2.4.1 Tables
- Do not repeat information in a table that you are depicting in a graph or histogram; include a table only if it presents new information.
- It is easier to compare numbers by reading down a column rather than across a row. Therefore, list sets of data you want your reader to compare in vertical form.
- Provide each table with a number (Table 1, Table 2, etc.) and a title. The numbered title is placed above the table .
- Please see Section 11 of the Excel Reference and Statistics Manual for further information on reporting the results of statistical tests.
3.2.4.2. Figures
- These comprise graphs, histograms, and illustrations, both drawings and photographs. Provide each figure with a number (Fig. 1, Fig. 2, etc.) and a caption (or "legend") that explains what the figure shows. The numbered caption is placed below the figure . Figure legend = Figure caption.
- Figures submitted for publication must be "photo ready," i.e., they will appear just as you submit them, or photographically reduced. Therefore, when you graduate from student papers to publishable manuscripts, you must learn to prepare figures that will not embarrass you. At the present time, virtually all journals require manuscripts to be submitted electronically and it is generally assumed that all graphs and maps will be created using software rather than being created by hand. Nearly all journals have specific guidelines for the file types, resolution, and physical widths required for figures. Only in a few cases (e.g. sketched diagrams) would figures still be created by hand using ink and those figures would be scanned and labeled using graphics software. Proportions must be the same as those of the page in the journal to which the paper will be submitted.
- Graphs and Histograms: Both can be used to compare two variables. However, graphs show continuous change, whereas histograms show discrete variables only. You can compare groups of data by plotting two or even three lines on one graph, but avoid cluttered graphs that are hard to read, and do not plot unrelated trends on the same graph. For both graphs, and histograms, plot the independent variable on the horizontal (x) axis and the dependent variable on the vertical (y) axis. Label both axes, including units of measurement except in the few cases where variables are unitless, such as absorbance.
- Drawings and Photographs: These are used to illustrate organisms, experimental apparatus, models of structures, cellular and subcellular structure, and results of procedures like electrophoresis. Preparing such figures well is a lot of work and can be very expensive, so each figure must add enough to justify its preparation and publication, but good figures can greatly enhance a professional article, as your reading in biological journals has already shown.
3.2.5 Discussion (modified; taken from Steingraber et al. 1985)
The function of this section is to analyze the data and relate them to other studies. To "analyze" means to evaluate the meaning of your results in terms of the original question or hypothesis and point out their biological significance.
1. The Discussion should contain at least:
- the relationship between the results and the original hypothesis, i.e., whether they support the hypothesis, or cause it to be rejected or modified
- an integration of your results with those of previous studies in order to arrive at explanations for the observed phenomena
- possible explanations for unexpected results and observations, phrased as hypotheses that can be tested by realistic experimental procedures, which you should describe
2. Trends that are not statistically significant can still be discussed if they are suggestive or interesting, but cannot be made the basis for conclusions as if they were significant.
3. Avoid redundancy between the Results and the Discussion section. Do not repeat detailed descriptions of the data and results in the Discussion. In some journals, Results and Discussions are joined in a single section, in order to permit a single integrated treatment with minimal repetition. This is more appropriate for short, simple articles than for longer, more complicated ones.
4. End the Discussion with a summary of the principal points you want the reader to remember. This is also the appropriate place to propose specific further study if that will serve some purpose, but do not end with the tired cliché that "this problem needs more study." All problems in biology need more study. Do not close on what you wish you had done, rather finish stating your conclusions and contributions.
5. Conclusion section. Primarily dependent upon the complexity and depth of an experiment, there may be a formal conclusion section after the discussion section. In general, the last line or so of the discussion section should be a more or less summary statement of the overall finding of the experiment. IF the experiment was large enough/complex enough/multiple findings uncovered, a distinct paragraph (or two) may be needed to help clarify the findings. Again, only if the experiment scale/findings warrant a separate conclusion section.
3.2.6 Title
The title of the paper should be the last thing that you write. That is because it should distill the essence of the paper even more than the abstract (the next to last thing that you write).
The title should contain three elements:
1. the name of the organism studied;
2. the particular aspect or system studied;
3. the variable(s) manipulated.
Do not be afraid to be grammatically creative. Here are some variations on a theme, all suitable as titles:
THE EFFECT OF TEMPERATURE ON GERMINATION OF ZEA MAYS
DOES TEMPERATURE AFFECT GERMINATION OF ZEA MAYS?
TEMPERATURE AND ZEA MAYS GERMINATION: IMPLICATIONS FOR AGRICULTURE
Sometimes it is possible to include the principal result or conclusion in the title:
HIGH TEMPERATURES REDUCE GERMINATION OF ZEA MAYS
Note for the BSCI 1510L class: to make your paper look more like a real paper, you can list all of the other group members as co-authors. However, if you do that, you should list you name first so that we know that you wrote it.
3.2.7 Literature Cited
Please refer to section 2.1 of this guide.
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This document originally came from the Journal of Mammalogy courtesy of Dr. Ronald Barry, a former editor of the journal.
Structure of a Research Paper
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Structure of a Research Paper: IMRaD Format
I. The Title Page
- Title: Tells the reader what to expect in the paper.
- Author(s): Most papers are written by one or two primary authors. The remaining authors have reviewed the work and/or aided in study design or data analysis (International Committee of Medical Editors, 1997). Check the Instructions to Authors for the target journal for specifics about authorship.
- Keywords [according to the journal]
- Corresponding Author: Full name and affiliation for the primary contact author for persons who have questions about the research.
- Financial & Equipment Support [if needed]: Specific information about organizations, agencies, or companies that supported the research.
- Conflicts of Interest [if needed]: List and explain any conflicts of interest.
II. Abstract: “Structured abstract” has become the standard for research papers (introduction, objective, methods, results and conclusions), while reviews, case reports and other articles have non-structured abstracts. The abstract should be a summary/synopsis of the paper.
III. Introduction: The “why did you do the study”; setting the scene or laying the foundation or background for the paper.
IV. Methods: The “how did you do the study.” Describe the --
- Context and setting of the study
- Specify the study design
- Population (patients, etc. if applicable)
- Sampling strategy
- Intervention (if applicable)
- Identify the main study variables
- Data collection instruments and procedures
- Outline analysis methods
V. Results: The “what did you find” --
- Report on data collection and/or recruitment
- Participants (demographic, clinical condition, etc.)
- Present key findings with respect to the central research question
- Secondary findings (secondary outcomes, subgroup analyses, etc.)
VI. Discussion: Place for interpreting the results
- Main findings of the study
- Discuss the main results with reference to previous research
- Policy and practice implications of the results
- Strengths and limitations of the study
VII. Conclusions: [occasionally optional or not required]. Do not reiterate the data or discussion. Can state hunches, inferences or speculations. Offer perspectives for future work.
VIII. Acknowledgements: Names people who contributed to the work, but did not contribute sufficiently to earn authorship. You must have permission from any individuals mentioned in the acknowledgements sections.
IX. References: Complete citations for any articles or other materials referenced in the text of the article.
- IMRD Cheatsheet (Carnegie Mellon) pdf.
- Adewasi, D. (2021 June 14). What Is IMRaD? IMRaD Format in Simple Terms! . Scientific-editing.info.
- Nair, P.K.R., Nair, V.D. (2014). Organization of a Research Paper: The IMRAD Format. In: Scientific Writing and Communication in Agriculture and Natural Resources. Springer, Cham. https://doi.org/10.1007/978-3-319-03101-9_2
- Sollaci, L. B., & Pereira, M. G. (2004). The introduction, methods, results, and discussion (IMRAD) structure: a fifty-year survey. Journal of the Medical Library Association : JMLA , 92 (3), 364–367.
- Cuschieri, S., Grech, V., & Savona-Ventura, C. (2019). WASP (Write a Scientific Paper): Structuring a scientific paper. Early human development , 128 , 114–117. https://doi.org/10.1016/j.earlhumdev.2018.09.011
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Writing a Scientific Paper or Lab Report
Writing a scientific paper is very similar to writing a lab report. The structure of each is primarily the same, but the purpose of each is different
Lab reports are meant to reflect understanding of the material and learn something new Scientific papers are meant to contribute knowledge to a field of study.
Both are generally broken down into eight sections: title, abstract, introduction, methods, results, discussion, conclusion, and references.
- Ex: Determining the Free Chlorine Content of Pool Water"
- Abstracts are a summary of the research as a whole and should familiarize the reader with the purpose of the research.
- Abstracts will always be written last, even though they are the first paragraph of a scientific paper.
- Unlike a lab report, all scientific papers will have an abstract.
- Why was the research done?
- What problem is being addressed?
- What results were found?
- What are the meaning of the results?
- How is the problem better understood now than before, if at all?
Introduction
- The introduction of a scientific paper discusses the problem being studied and other theory that is relevant to understanding the findings.
- The hypothesis of the experiment and the motivation for the research are stated in this section.
- Write the introduction in your own words. Try not to copy from a lab manual or other guidelines. Instead, show comprehension of the research by briefly explaining the problem.
- Methods and Materials
- Ex: pipette, graduated cylinder, 1.13mg of Na, 0.67mg Ag
- List the steps taken as they actually happened during the experiment, not as they were supposed to happen.
- If written correctly, another researcher should be able to duplicate the experiment and get the same or very similar results.
- In a scientific paper, most often the steps taken during the research are discussed more in length and with more detail than they are in lab reports.
- The results show the data that was collected or found during the research.
- Explain in words the data that was collected.
- Tables should be labeled numerically, as "Table 1", "Table 2", etc. Other figures should be labeled numerically as "Figure 1", "Figure 2", etc.
- Calculations to understand the data can also be presented in the results.
- The discussion section is one of the most important parts of a scientific paper. It analyzes the results of the research and is a discussion of the data.
- If any results are unexpected, explain why they are unexpected and how they did or did not effect the data obtained.
- Analyze the strengths and weaknesses of the design of the research and compare your results to similar research.
- If there are any experimental errors, analyze them.
- Explain your results and discuss them using relevant terms and theories.
- What do the results indicate?
- What is the significance of the results?
- Are there any gaps in knowledge?
- Are there any new questions that have been raised?
- The conclusion is a summation of the experiment. It should clearly and concisely state what was learned and its importance.
- If there is future work that needs to be done, it can be explained in the conclusion.
- When any outside sources to support a claim or explain background information, those sources must be cited in the references section of the lab report.
- Scientific papers will always use outside references.
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Scientific Papers
Scientific papers are for sharing your own original research work with other scientists or for reviewing the research conducted by others. As such, they are critical to the evolution of modern science, in which the work of one scientist builds upon that of others. To reach their goal, papers must aim to inform, not impress. They must be highly readable — that is, clear, accurate, and concise. They are more likely to be cited by other scientists if they are helpful rather than cryptic or self-centered.
Scientific papers typically have two audiences: first, the referees, who help the journal editor decide whether a paper is suitable for publication; and second, the journal readers themselves, who may be more or less knowledgeable about the topic addressed in the paper. To be accepted by referees and cited by readers, papers must do more than simply present a chronological account of the research work. Rather, they must convince their audience that the research presented is important, valid, and relevant to other scientists in the same field. To this end, they must emphasize both the motivation for the work and the outcome of it, and they must include just enough evidence to establish the validity of this outcome.
Papers that report experimental work are often structured chronologically in five sections: first, Introduction ; then Materials and Methods , Results , and Discussion (together, these three sections make up the paper's body); and finally, Conclusion .
- The Introduction section clarifies the motivation for the work presented and prepares readers for the structure of the paper.
- The Materials and Methods section provides sufficient detail for other scientists to reproduce the experiments presented in the paper. In some journals, this information is placed in an appendix, because it is not what most readers want to know first.
- The Results and Discussion sections present and discuss the research results, respectively. They are often usefully combined into one section, however, because readers can seldom make sense of results alone without accompanying interpretation — they need to be told what the results mean.
- The Conclusion section presents the outcome of the work by interpreting the findings at a higher level of abstraction than the Discussion and by relating these findings to the motivation stated in the Introduction .
(Papers reporting something other than experiments, such as a new method or technology, typically have different sections in their body, but they include the same Introduction and Conclusion sections as described above.)
Although the above structure reflects the progression of most research projects, effective papers typically break the chronology in at least three ways to present their content in the order in which the audience will most likely want to read it. First and foremost, they summarize the motivation for, and the outcome of, the work in an abstract, located before the Introduction . In a sense, they reveal the beginning and end of the story — briefly — before providing the full story. Second, they move the more detailed, less important parts of the body to the end of the paper in one or more appendices so that these parts do not stand in the readers' way. Finally, they structure the content in the body in theorem-proof fashion, stating first what readers must remember (for example, as the first sentence of a paragraph) and then presenting evidence to support this statement.
The introduction
- First, provide some context to orient those readers who are less familiar with your topic and to establish the importance of your work.
- Second, state the need for your work, as an opposition between what the scientific community currently has and what it wants.
- Third, indicate what you have done in an effort to address the need (this is the task).
- Finally, preview the remainder of the paper to mentally prepare readers for its structure, in the object of the document.
Context and need
At the beginning of the Introduction section, the context and need work together as a funnel: They start broad and progressively narrow down to the issue addressed in the paper. To spark interest among your audience — referees and journal readers alike — provide a compelling motivation for the work presented in your paper: The fact that a phenomenon has never been studied before is not, in and of itself, a reason to study that phenomenon.
Write the context in a way that appeals to a broad range of readers and leads into the need. Do not include context for the sake of including context: Rather, provide only what will help readers better understand the need and, especially, its importance. Consider anchoring the context in time, using phrases such as recently , in the past 10 years , or since the early 1990s . You may also want to anchor your context in space (either geographically or within a given research field).
Convey the need for the work as an opposition between actual and desired situations. Start by stating the actual situation (what we have) as a direct continuation of the context. If you feel you must explain recent achievements in much detail — say, in more than one or two paragraphs — consider moving the details to a section titled State of the art (or something similar) after the Introduction , but do provide a brief idea of the actual situation in the Introduction . Next, state the desired situation (what we want). Emphasize the contrast between the actual and desired situations with such words as but , however, or unfortunately .
One elegant way to express the desired part of the need is to combine it with the task in a single sentence. This sentence expresses first the objective, then the action undertaken to reach this objective, thus creating a strong and elegant connection between need and task. Here are three examples of such a combination:
To confirm this assumption , we studied the effects of a range of inhibitors of connexin channels . . . on . . .
To assess whether such multiple-coil sensors perform better than single-signal ones , we tested two of them — the DuoPXK and the GEMM3 — in a field where . . . To form a better view of the global distribution and infectiousness of this pathogen , we examined 1645 postmetamorphic and adult amphibians collected from 27 countries between 1984 and 2006 for the presence of . . .
Task and object
An Introduction is usually clearer and more logical when it separates what the authors have done (the task) from what the paper itself attempts or covers (the object of the document). In other words, the task clarifies your contribution as a scientist, whereas the object of the document prepares readers for the structure of the paper, thus allowing focused or selective reading.
For the task,
- use whoever did the work (normally, you and your colleagues) as the subject of the sentence: we or perhaps the authors;
- use a verb expressing a research action: measured , calculated , etc.;
- set that verb in the past tense.
The three examples below are well-formed tasks.
To confirm this assumption, we studied the effects of a range of inhibitors of connexin channels, such as the connexin mimetic peptides Gap26 and Gap27 and anti-peptide antibodies, on calcium signaling in cardiac cells and HeLa cells expressing connexins.
During controlled experiments, we investigated the influence of the HMP boundary conditions on liver flows.
To tackle this problem, we developed a new software verification technique called oblivious hashing, which calculates the hash values based on the actual execution of the program.
The list below provides examples of verbs that express research actions:
apply | We applied Laklöter's principle to . . . |
assess | We assessed the effects of larger doses of . . . |
calculate | We calculated the photoluminescence spectrum of . . . |
compare | We compared the effects of . . . to those of . . . |
compute | We computed the velocity predicted by . . . |
derive | We derived a new set of rules for . . . |
design | We designed a series of experiments to . . . |
determine | We determined the complete nucleotide sequence of . . . |
develop | We developed a new algorithm to . . . |
evaluate | We evaluated the efficacy and biocompatibility of . . . |
explore | We explored the relationship between . . . |
implement | We implemented a genetic algorithm for . . . |
investigate | We investigated the behavior of . . . |
measure | We measured the concentration of cadmium in . . . |
model | We modeled the diffraction behavior of . . . |
For the object of the document,
- use the document itself as the subject of the sentence: this paper , this letter , etc.;
- use a verb expressing a communication action: presents , summarizes , etc.;
- set the verb in the present tense.
The three examples below are suitable objects of the document for the three tasks shown above, respectively.
This paper clarifies the role of CxHc on calcium oscillations in neonatal cardiac myocytes and calcium transients induced by ATP in HL-cells originated from cardiac atrium and in HeLa cells expressing connexin 43 or 26. This paper presents the flow effects induced by increasing the hepatic-artery pressure and by obstructing the vena cava inferior. This paper discusses the theory behind oblivious hashing and shows how this approach can be applied for local software tamper resistance and remote code authentication.
The list below provides examples of verbs that express communication actions:
clarify | This paper clarifies the role of soils in . . . |
describe | This paper describes the mechanism by which . . . |
detail | This paper details the algorithm used for . . . |
discuss | This paper discusses the influence of acidity on . . . |
explain | This paper explains how the new encoding scheme . . . |
offer | This paper offers four recommendations for . . . |
present | This paper presents the results of . . . |
proposes | This paper proposes a set of guidelines for . . . |
provide | This paper provides the complete framework and . . . |
report | This paper reports on our progress so far . . . |
summarize | This paper summarizes our results for 27 patients with . . . |
Even the most logical structure is of little use if readers do not see and understand it as they progress through a paper. Thus, as you organize the body of your paper into sections and perhaps subsections, remember to prepare your readers for the structure ahead at all levels. You already do so for the overall structure of the body (the sections) in the object of the document at the end of the Introduction . You can similarly prepare your readers for an upcoming division into subsections by introducing a global paragraph between the heading of a section and the heading of its first subsection. This paragraph can contain any information relating to the section as a whole rather than particular subsections, but it should at least announce the subsections, whether explicitly or implicitly. An explicit preview would be phrased much like the object of the document: "This section first . . . , then . . . , and finally . . . "
Although papers can be organized into sections in many ways, those reporting experimental work typically include Materials and Methods , Results , and Discussion in their body. In any case, the paragraphs in these sections should begin with a topic sentence to prepare readers for their contents, allow selective reading, and — ideally — get a message across.
Materials and methods
Results and discussion.
When reporting and discussing your results, do not force your readers to go through everything you went through in chronological order. Instead, state the message of each paragraph upfront: Convey in the first sentence what you want readers to remember from the paragraph as a whole. Focus on what happened, not on the fact that you observed it. Then develop your message in the remainder of the paragraph, including only that information you think you need to convince your audience.
The conclusion
At the end of your Conclusion , consider including perspectives — that is, an idea of what could or should still be done in relation to the issue addressed in the paper. If you include perspectives, clarify whether you are referring to firm plans for yourself and your colleagues ("In the coming months, we will . . . ") or to an invitation to readers ("One remaining question is . . . ").
If your paper includes a well-structured Introduction and an effective abstract, you need not repeat any of the Introduction in the Conclusion . In particular, do not restate what you have done or what the paper does. Instead, focus on what you have found and, especially, on what your findings mean. Do not be afraid to write a short Conclusion section: If you can conclude in just a few sentences given the rich discussion in the body of the paper, then do so. (In other words, resist the temptation to repeat material from the Introduction just to make the Conclusio n longer under the false belief that a longer Conclusion will seem more impressive.)
The abstract
Typically, readers are primarily interested in the information presented in a paper's Introduction and Conclusion sections. Primarily, they want to know the motivation for the work presented and the outcome of this work. Then (and only then) the most specialized among them might want to know the details of the work. Thus, an effective abstract focuses on motivation and outcome; in doing so, it parallels the paper's Introduction and Conclusion .
Accordingly, you can think of an abstract as having two distinct parts — motivation and outcome — even if it is typeset as a single paragraph. For the first part, follow the same structure as the Introduction section of the paper: State the context, the need, the task, and the object of the document. For the second part, mention your findings (the what ) and, especially, your conclusion (the so what — that is, the interpretation of your findings); if appropriate, end with perspectives, as in the Conclusion section of your paper.
Although the structure of the abstract parallels the Introduction and Conclusion sections, it differs from these sections in the audience it addresses. The abstract is read by many different readers, from the most specialized to the least specialized among the target audience. In a sense, it should be the least specialized part of the paper. Any scientist reading it should be able to understand why the work was carried out and why it is important (context and need), what the authors did (task) and what the paper reports about this work (object of the document), what the authors found (findings), what these findings mean (the conclusion), and possibly what the next steps are (perspectives). In contrast, the full paper is typically read by specialists only; its Introduction and Conclusion are more detailed (that is, longer and more specialized) than the abstract.
An effective abstract stands on its own — it can be understood fully even when made available without the full paper. To this end, avoid referring to figures or the bibliography in the abstract. Also, introduce any acronyms the first time you use them in the abstract (if needed), and do so again in the full paper (see Mechanics: Using abbreviations ).
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Writing a scientific paper.
- Writing a lab report
- INTRODUCTION
Writing a "good" methods section
"methods checklist" from: how to write a good scientific paper. chris a. mack. spie. 2018..
- LITERATURE CITED
- Bibliography of guides to scientific writing and presenting
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The purpose is to provide enough detail that a competent worker could repeat the experiment. Many of your readers will skip this section because they already know from the Introduction the general methods you used. However careful writing of this section is important because for your results to be of scientific merit they must be reproducible. Otherwise your paper does not represent good science.
- Exact technical specifications and quantities and source or method of preparation
- Describe equipment used and provide illustrations where relevant.
- Chronological presentation (but related methods described together)
- Questions about "how" and "how much" are answered for the reader and not left for them to puzzle over
- Discuss statistical methods only if unusual or advanced
- When a large number of components are used prepare tables for the benefit of the reader
- Do not state the action without stating the agent of the action
- Describe how the results were generated with sufficient detail so that an independent researcher (working in the same field) could reproduce the results sufficiently to allow validation of the conclusions.
- Can the reader assess internal validity (conclusions are supported by the results presented)?
- Can the reader assess external validity (conclusions are properly generalized beyond these specific results)?
- Has the chosen method been justified?
- Are data analysis and statistical approaches justified, with assumptions and biases considered?
- Avoid: including results in the Method section; including extraneous details (unnecessary to enable reproducibility or judge validity); treating the method as a chronological history of events; unneeded references to commercial products; references to “proprietary” products or processes unavailable to the reader.
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Online Guide to Writing and Research
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- Online Guide to Writing
Structuring the Research Paper
Formal research structure.
These are the primary purposes for formal research:
enter the discourse, or conversation, of other writers and scholars in your field
learn how others in your field use primary and secondary resources
find and understand raw data and information
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For the formal academic research assignment, consider an organizational pattern typically used for primary academic research. The pattern includes the following: introduction, methods, results, discussion, and conclusions/recommendations.
Usually, research papers flow from the general to the specific and back to the general in their organization. The introduction uses a general-to-specific movement in its organization, establishing the thesis and setting the context for the conversation. The methods and results sections are more detailed and specific, providing support for the generalizations made in the introduction. The discussion section moves toward an increasingly more general discussion of the subject, leading to the conclusions and recommendations, which then generalize the conversation again.
Sections of a Formal Structure
The introduction section.
Many students will find that writing a structured introduction gets them started and gives them the focus needed to significantly improve their entire paper.
Introductions usually have three parts:
presentation of the problem statement, the topic, or the research inquiry
purpose and focus of your paper
summary or overview of the writer’s position or arguments
In the first part of the introduction—the presentation of the problem or the research inquiry—state the problem or express it so that the question is implied. Then, sketch the background on the problem and review the literature on it to give your readers a context that shows them how your research inquiry fits into the conversation currently ongoing in your subject area.
In the second part of the introduction, state your purpose and focus. Here, you may even present your actual thesis. Sometimes your purpose statement can take the place of the thesis by letting your reader know your intentions.
The third part of the introduction, the summary or overview of the paper, briefly leads readers through the discussion, forecasting the main ideas and giving readers a blueprint for the paper.
The following example provides a blueprint for a well-organized introduction.
Example of an Introduction
Entrepreneurial Marketing: The Critical Difference
In an article in the Harvard Business Review, John A. Welsh and Jerry F. White remind us that “a small business is not a little big business.” An entrepreneur is not a multinational conglomerate but a profit-seeking individual. To survive, he must have a different outlook and must apply different principles to his endeavors than does the president of a large or even medium-sized corporation. Not only does the scale of small and big businesses differ, but small businesses also suffer from what the Harvard Business Review article calls “resource poverty.” This is a problem and opportunity that requires an entirely different approach to marketing. Where large ad budgets are not necessary or feasible, where expensive ad production squanders limited capital, where every marketing dollar must do the work of two dollars, if not five dollars or even ten, where a person’s company, capital, and material well-being are all on the line—that is, where guerrilla marketing can save the day and secure the bottom line (Levinson, 1984, p. 9).
By reviewing the introductions to research articles in the discipline in which you are writing your research paper, you can get an idea of what is considered the norm for that discipline. Study several of these before you begin your paper so that you know what may be expected. If you are unsure of the kind of introduction your paper needs, ask your professor for more information. The introduction is normally written in present tense.
THE METHODS SECTION
The methods section of your research paper should describe in detail what methodology and special materials if any, you used to think through or perform your research. You should include any materials you used or designed for yourself, such as questionnaires or interview questions, to generate data or information for your research paper. You want to include any methodologies that are specific to your particular field of study, such as lab procedures for a lab experiment or data-gathering instruments for field research. The methods section is usually written in the past tense.
THE RESULTS SECTION
How you present the results of your research depends on what kind of research you did, your subject matter, and your readers’ expectations.
Quantitative information —data that can be measured—can be presented systematically and economically in tables, charts, and graphs. Quantitative information includes quantities and comparisons of sets of data.
Qualitative information , which includes brief descriptions, explanations, or instructions, can also be presented in prose tables. This kind of descriptive or explanatory information, however, is often presented in essay-like prose or even lists.
There are specific conventions for creating tables, charts, and graphs and organizing the information they contain. In general, you should use them only when you are sure they will enlighten your readers rather than confuse them. In the accompanying explanation and discussion, always refer to the graphic by number and explain specifically what you are referring to; you can also provide a caption for the graphic. The rule of thumb for presenting a graphic is first to introduce it by name, show it, and then interpret it. The results section is usually written in the past tense.
THE DISCUSSION SECTION
Your discussion section should generalize what you have learned from your research. One way to generalize is to explain the consequences or meaning of your results and then make your points that support and refer back to the statements you made in your introduction. Your discussion should be organized so that it relates directly to your thesis. You want to avoid introducing new ideas here or discussing tangential issues not directly related to the exploration and discovery of your thesis. The discussion section, along with the introduction, is usually written in the present tense.
THE CONCLUSIONS AND RECOMMENDATIONS SECTION
Your conclusion ties your research to your thesis, binding together all the main ideas in your thinking and writing. By presenting the logical outcome of your research and thinking, your conclusion answers your research inquiry for your reader. Your conclusions should relate directly to the ideas presented in your introduction section and should not present any new ideas.
You may be asked to present your recommendations separately in your research assignment. If so, you will want to add some elements to your conclusion section. For example, you may be asked to recommend a course of action, make a prediction, propose a solution to a problem, offer a judgment, or speculate on the implications and consequences of your ideas. The conclusions and recommendations section is usually written in the present tense.
Key Takeaways
- For the formal academic research assignment, consider an organizational pattern typically used for primary academic research.
- The pattern includes the following: introduction, methods, results, discussion, and conclusions/recommendations.
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Table of Contents: Online Guide to Writing
Chapter 1: College Writing
How Does College Writing Differ from Workplace Writing?
What Is College Writing?
Why So Much Emphasis on Writing?
Chapter 2: The Writing Process
Doing Exploratory Research
Getting from Notes to Your Draft
Introduction
Prewriting - Techniques to Get Started - Mining Your Intuition
Prewriting: Targeting Your Audience
Prewriting: Techniques to Get Started
Prewriting: Understanding Your Assignment
Rewriting: Being Your Own Critic
Rewriting: Creating a Revision Strategy
Rewriting: Getting Feedback
Rewriting: The Final Draft
Techniques to Get Started - Outlining
Techniques to Get Started - Using Systematic Techniques
Thesis Statement and Controlling Idea
Writing: Getting from Notes to Your Draft - Freewriting
Writing: Getting from Notes to Your Draft - Summarizing Your Ideas
Writing: Outlining What You Will Write
Chapter 3: Thinking Strategies
A Word About Style, Voice, and Tone
A Word About Style, Voice, and Tone: Style Through Vocabulary and Diction
Critical Strategies and Writing
Critical Strategies and Writing: Analysis
Critical Strategies and Writing: Evaluation
Critical Strategies and Writing: Persuasion
Critical Strategies and Writing: Synthesis
Developing a Paper Using Strategies
Kinds of Assignments You Will Write
Patterns for Presenting Information
Patterns for Presenting Information: Critiques
Patterns for Presenting Information: Discussing Raw Data
Patterns for Presenting Information: General-to-Specific Pattern
Patterns for Presenting Information: Problem-Cause-Solution Pattern
Patterns for Presenting Information: Specific-to-General Pattern
Patterns for Presenting Information: Summaries and Abstracts
Supporting with Research and Examples
Writing Essay Examinations
Writing Essay Examinations: Make Your Answer Relevant and Complete
Writing Essay Examinations: Organize Thinking Before Writing
Writing Essay Examinations: Read and Understand the Question
Chapter 4: The Research Process
Planning and Writing a Research Paper
Planning and Writing a Research Paper: Ask a Research Question
Planning and Writing a Research Paper: Cite Sources
Planning and Writing a Research Paper: Collect Evidence
Planning and Writing a Research Paper: Decide Your Point of View, or Role, for Your Research
Planning and Writing a Research Paper: Draw Conclusions
Planning and Writing a Research Paper: Find a Topic and Get an Overview
Planning and Writing a Research Paper: Manage Your Resources
Planning and Writing a Research Paper: Outline
Planning and Writing a Research Paper: Survey the Literature
Planning and Writing a Research Paper: Work Your Sources into Your Research Writing
Research Resources: Where Are Research Resources Found? - Human Resources
Research Resources: What Are Research Resources?
Research Resources: Where Are Research Resources Found?
Research Resources: Where Are Research Resources Found? - Electronic Resources
Research Resources: Where Are Research Resources Found? - Print Resources
Structuring the Research Paper: Formal Research Structure
Structuring the Research Paper: Informal Research Structure
The Nature of Research
The Research Assignment: How Should Research Sources Be Evaluated?
The Research Assignment: When Is Research Needed?
The Research Assignment: Why Perform Research?
Chapter 5: Academic Integrity
Academic Integrity
Giving Credit to Sources
Giving Credit to Sources: Copyright Laws
Giving Credit to Sources: Documentation
Giving Credit to Sources: Style Guides
Integrating Sources
Practicing Academic Integrity
Practicing Academic Integrity: Keeping Accurate Records
Practicing Academic Integrity: Managing Source Material
Practicing Academic Integrity: Managing Source Material - Paraphrasing Your Source
Practicing Academic Integrity: Managing Source Material - Quoting Your Source
Practicing Academic Integrity: Managing Source Material - Summarizing Your Sources
Types of Documentation
Types of Documentation: Bibliographies and Source Lists
Types of Documentation: Citing World Wide Web Sources
Types of Documentation: In-Text or Parenthetical Citations
Types of Documentation: In-Text or Parenthetical Citations - APA Style
Types of Documentation: In-Text or Parenthetical Citations - CSE/CBE Style
Types of Documentation: In-Text or Parenthetical Citations - Chicago Style
Types of Documentation: In-Text or Parenthetical Citations - MLA Style
Types of Documentation: Note Citations
Chapter 6: Using Library Resources
Finding Library Resources
Chapter 7: Assessing Your Writing
How Is Writing Graded?
How Is Writing Graded?: A General Assessment Tool
The Draft Stage
The Draft Stage: The First Draft
The Draft Stage: The Revision Process and the Final Draft
The Draft Stage: Using Feedback
The Research Stage
Using Assessment to Improve Your Writing
Chapter 8: Other Frequently Assigned Papers
Reviews and Reaction Papers: Article and Book Reviews
Reviews and Reaction Papers: Reaction Papers
Writing Arguments
Writing Arguments: Adapting the Argument Structure
Writing Arguments: Purposes of Argument
Writing Arguments: References to Consult for Writing Arguments
Writing Arguments: Steps to Writing an Argument - Anticipate Active Opposition
Writing Arguments: Steps to Writing an Argument - Determine Your Organization
Writing Arguments: Steps to Writing an Argument - Develop Your Argument
Writing Arguments: Steps to Writing an Argument - Introduce Your Argument
Writing Arguments: Steps to Writing an Argument - State Your Thesis or Proposition
Writing Arguments: Steps to Writing an Argument - Write Your Conclusion
Writing Arguments: Types of Argument
Appendix A: Books to Help Improve Your Writing
Dictionaries
General Style Manuals
Researching on the Internet
Special Style Manuals
Writing Handbooks
Appendix B: Collaborative Writing and Peer Reviewing
Collaborative Writing: Assignments to Accompany the Group Project
Collaborative Writing: Informal Progress Report
Collaborative Writing: Issues to Resolve
Collaborative Writing: Methodology
Collaborative Writing: Peer Evaluation
Collaborative Writing: Tasks of Collaborative Writing Group Members
Collaborative Writing: Writing Plan
General Introduction
Peer Reviewing
Appendix C: Developing an Improvement Plan
Working with Your Instructor’s Comments and Grades
Appendix D: Writing Plan and Project Schedule
Devising a Writing Project Plan and Schedule
Reviewing Your Plan with Others
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HOW TO WRITE A SCIENTIFIC ARTICLE
Barbara j. hoogenboom.
1 Grand Valley State University, Grand Rapids, MI, USA
Robert C. Manske
2 University of Wichita, Wichita, KS, USA
Successful production of a written product for submission to a peer‐reviewed scientific journal requires substantial effort. Such an effort can be maximized by following a few simple suggestions when composing/creating the product for submission. By following some suggested guidelines and avoiding common errors, the process can be streamlined and success realized for even beginning/novice authors as they negotiate the publication process. The purpose of this invited commentary is to offer practical suggestions for achieving success when writing and submitting manuscripts to The International Journal of Sports Physical Therapy and other professional journals.
INTRODUCTION
“The whole of science is nothing more than a refinement of everyday thinking” Albert Einstein
Conducting scientific and clinical research is only the beginning of the scholarship of discovery. In order for the results of research to be accessible to other professionals and have a potential effect on the greater scientific community, it must be written and published. Most clinical and scientific discovery is published in peer‐reviewed journals, which are those that utilize a process by which an author's peers, or experts in the content area, evaluate the manuscript. Following this review the manuscript is recommended for publication, revision or rejection. It is the rigor of this review process that makes scientific journals the primary source of new information that impacts clinical decision‐making and practice. 1 , 2
The task of writing a scientific paper and submitting it to a journal for publication is a time‐consuming and often daunting task. 3 , 4 Barriers to effective writing include lack of experience, poor writing habits, writing anxiety, unfamiliarity with the requirements of scholarly writing, lack of confidence in writing ability, fear of failure, and resistance to feedback. 5 However, the very process of writing can be a helpful tool for promoting the process of scientific thinking, 6 , 7 and effective writing skills allow professionals to participate in broader scientific conversations. Furthermore, peer review manuscript publication systems requiring these technical writing skills can be developed and improved with practice. 8 Having an understanding of the process and structure used to produce a peer‐reviewed publication will surely improve the likelihood that a submitted manuscript will result in a successful publication.
Clear communication of the findings of research is essential to the growth and development of science 3 and professional practice. The culmination of the publication process provides not only satisfaction for the researcher and protection of intellectual property, but also the important function of dissemination of research results, new ideas, and alternate thought; which ultimately facilitates scholarly discourse. In short, publication of scientific papers is one way to advance evidence‐based practice in many disciplines, including sports physical therapy. Failure to publish important findings significantly diminishes the potential impact that those findings may have on clinical practice. 9
BASICS OF MANUSCRIPT PREPARATION & GENERAL WRITING TIPS
To begin it might be interesting to learn why reviewers accept manuscripts! Reviewers consider the following five criteria to be the most important in decisions about whether to accept manuscripts for publication: 1) the importance, timeliness, relevance, and prevalence of the problem addressed; 2) the quality of the writing style (i.e., that it is well‐written, clear, straightforward, easy to follow, and logical); 3) the study design applied (i.e., that the design was appropriate, rigorous, and comprehensive); 4) the degree to which the literature review was thoughtful, focused, and up‐to‐date; and 5) the use of a sufficiently large sample. 10 For these statements to be true there are also reasons that reviewers reject manuscripts. The following are the top five reasons for rejecting papers: 1) inappropriate, incomplete, or insufficiently described statistics; 2) over‐interpretation of results; 3) use of inappropriate, suboptimal, or insufficiently described populations or instruments; 4) small or biased samples; and 5) text that is poorly written or difficult to follow. 10 , 11 With these reasons for acceptance or rejection in mind, it is time to review basics and general writing tips to be used when performing manuscript preparation.
“Begin with the end in mind” . When you begin writing about your research, begin with a specific target journal in mind. 12 Every scientific journal should have specific lists of manuscript categories that are preferred for their readership. The IJSPT seeks to provide readership with current information to enhance the practice of sports physical therapy. Therefore the manuscript categories accepted by IJSPT include: Original research; Systematic reviews of literature; Clinical commentary and Current concept reviews; Case reports; Clinical suggestions and unique practice techniques; and Technical notes. Once a decision has been made to write a manuscript, compose an outline that complies with the requirements of the target submission journal and has each of the suggested sections. This means carefully checking the submission criteria and preparing your paper in the exact format of the journal to which you intend to submit. Be thoughtful about the distinction between content (what you are reporting) and structure (where it goes in the manuscript). Poor placement of content confuses the reader (reviewer) and may cause misinterpretation of content. 3 , 5
It may be helpful to follow the IMRaD format for writing scientific manuscripts. This acronym stands for the sections contained within the article: Introduction, Methods, Results, and Discussion. Each of these areas of the manuscript will be addressed in this commentary.
Many accomplished authors write their results first, followed by an introduction and discussion, in an attempt to “stay true” to their results and not stray into additional areas. Typically the last two portions to be written are the conclusion and the abstract.
The ability to accurately describe ideas, protocols/procedures, and outcomes are the pillars of scientific writing . Accurate and clear expression of your thoughts and research information should be the primary goal of scientific writing. 12 Remember that accuracy and clarity are even more important when trying to get complicated ideas across. Contain your literature review, ideas, and discussions to your topic, theme, model, review, commentary, or case. Avoid vague terminology and too much prose. Use short rather than long sentences. If jargon has to be utilized keep it to a minimum and explain the terms you do use clearly. 13
Write with a measure of formality, using scientific language and avoiding conjunctions, slang, and discipline or regionally specific nomenclature or terms (e.g. exercise nicknames). For example, replace the term “Monster walks” with “closed‐chain hip abduction with elastic resistance around the thighs”. You may later refer to the exercise as “also known as Monster walks” if you desire.
Avoid first person language and instead write using third person language. Some journals do not ascribe to this requirement, and allow first person references, however, IJSPT prefers use of third person. For example, replace “We determined that…” with “The authors determined that….”.
For novice writers, it is really helpful to seek a reading mentor that will help you pre‐read your submission. Problems such as improper use of grammar, tense, and spelling are often a cause of rejection by reviewers. Despite the content of the study these easily fixed errors suggest that the authors created the manuscript with less thought leading reviewers to think that the manuscript may also potentially have erroneous findings as well. A review from a second set of trained eyes will often catch these errors missed by the original authors. If English is not your first language, the editorial staff at IJSPT suggests that you consult with someone with the relevant expertise to give you guidance on English writing conventions, verb tense, and grammar. Excellent writing in English is hard, even for those of us for whom it is our first language!
Use figures and graphics to your advantage . ‐ Consider the use of graphic/figure representation of data and important procedures or exercises. Tables should be able to stand alone and be completely understandable at a quick glance. Understanding a table should not require careful review of the manuscript! Figures dramatically enhance the graphic appeal of a scientific paper. Many formats for graphic presentation are acceptable, including graphs, charts, tables, and pictures or videos. Photographs should be clear, free of clutter or extraneous background distractions and be taken with models wearing simple clothing. Color photographs are preferred. Digital figures (Scans or existing files as well as new photographs) must be at least 300dpi. All photographs should be provided as separate files (jpeg or tif preferred) and not be embedded in the paper. Quality and clarity of figures are essential for reproduction purposes and should be considered before taking images for the manuscript.
A video of an exercise or procedure speaks a thousand words. Please consider using short video clips as descriptive additions to your paper. They will be placed on the IJSPT website and accompany your paper. The video clips must be submitted in MPEG‐1, MPEG‐2, Quicktime (.mov), or Audio/Video Interface (.avi) formats. Maximum cumulative length of videos is 5 minutes. Each video segment may not exceed 50 MB, and each video clip must be saved as a separate file and clearly identified. Formulate descriptive figure/video and Table/chart/graph titles and place them on a figure legend document. Carefully consider placement of, naming of, and location of figures. It makes the job of the editors much easier!
Avoid Plagiarism and inadvertent lack of citations. Finally, use citations to your benefit. Cite frequently in order to avoid any plagiarism. The bottom line: If it is not your original idea, give credit where credit is due . When using direct quotations, provide not only the number of the citation, but the page where the quote was found. All citations should appear in text as a superscripted number followed by punctuation. It is the authors' responsibility to fully ensure all references are cited in completed form, in an accurate location. Please carefully follow the instructions for citations and check that all references in your reference list are cited in the paper and that all citations in the paper appear correctly in the reference list. Please go to IJSPT submission guidelines for full information on the format for citations.
Sometimes written as an afterthought, the abstract is of extreme importance as in many instances this section is what is initially previewed by readership to determine if the remainder of the article is worth reading. This is the authors opportunity to draw the reader into the study and entice them to read the rest of the article. The abstract is a summary of the article or study written in 3 rd person allowing the readers to get a quick glance of what the contents of the article include. Writing an abstract is rather challenging as being brief, accurate and concise are requisite. The headings and structure for an abstract are usually provided in the instructions for authors. In some instances, the abstract may change slightly pending content revisions required during the peer review process. Therefore it often works well to complete this portion of the manuscript last. Remember the abstract should be able to stand alone and should be as succinct as possible. 14
Introduction and Review of Literature
The introduction is one of the more difficult portions of the manuscript to write. Past studies are used to set the stage or provide the reader with information regarding the necessity of the represented project. For an introduction to work properly, the reader must feel that the research question is clear, concise, and worthy of study.
A competent introduction should include at least four key concepts: 1) significance of the topic, 2) the information gap in the available literature associated with the topic, 3) a literature review in support of the key questions, 4) subsequently developed purposes/objectives and hypotheses. 9
When constructing a review of the literature, be attentive to “sticking” or “staying true” to your topic at hand. Don't reach or include too broad of a literature review. For example, do not include extraneous information about performance or prevention if your research does not actually address those things. The literature review of a scientific paper is not an exhaustive review of all available knowledge in a given field of study. That type of thorough review should be left to review articles or textbook chapters. Throughout the introduction (and later in the discussion!) remind yourself that a paper, existing evidence, or results of a paper cannot draw conclusions, demonstrate, describe, or make judgments, only PEOPLE (authors) can. “The evidence demonstrates that” should be stated, “Smith and Jones, demonstrated that….”
Conclude your introduction with a solid statement of your purpose(s) and your hypothesis(es), as appropriate. The purpose and objectives should clearly relate to the information gap associated with the given manuscript topic discussed earlier in the introduction section. This may seem repetitive, but it actually is helpful to ensure the reader clearly sees the evolution, importance, and critical aspects of the study at hand See Table 1 for examples of well‐stated purposes.
Examples of well-stated purposes by submission type.
Type of Submission | Example purpose |
---|---|
Original Research | Therefore, the purpose of this study was to describe the volume of pitching for pitchers from multiple college teams at the Division I level. |
Systematic Review of the Literature | Therefore, the purpose of this systematic review was to investigate the association between training characteristics and running related injuries. |
Clinical Commentary/Current Concepts Report | The purpose of this clinical commentary is to examine the risk factors contributing to the high recurrence rate of hamstring injuries, and propose a unique rehabilitation strategy addressing these factors in order to decrease the rate of reinjury. |
Case Report | The purpose of this case report is to describe the non-surgical management of a professional athlete with the characteristic signs and symptoms of a sports hernia. |
Clinical Suggestion | The purpose of this clinical commentary is to review types of integumentary wounds that may occur in sport, and their acute management. |
The methods section should clearly describe the specific design of the study and provide clear and concise description of the procedures that were performed. The purpose of sufficient detail in the methods section is so that an appropriately trained person would be able to replicate your experiments. 15 There should be complete transparency when describing the study. To assist in writing and manuscript preparation there are several checklists or guidelines that are available on the IJSPT website. The CONSORT guidelines can be used when developing and reporting a randomized controlled trial. 16 The STARD checklist was developed for designing a diagnostic accuracy study. 17 The PRISMA checklist was developed for use when performing a meta‐analyses or systematic review. 18 A clear methods section should contain the following information: 1) the population and equipment used in the study, 2) how the population and equipment were prepared and what was done during the study, 3) the protocol used, 4) the outcomes and how they were measured, 5) the methods used for data analysis. Initially a brief paragraph should explain the overall procedures and study design. Within this first paragraph there is generally a description of inclusion and exclusion criteria which help the reader understand the population used. Paragraphs that follow should describe in more detail the procedures followed for the study. A clear description of how data was gathered is also helpful. For example were data gathered prospectively or retrospectively? Who if anyone was blinded, and where and when was the actual data collected?
Although it is a good idea for the authors to have justification and a rationale for their procedures, these should be saved for inclusion into the discussion section, not to be discussed in the methods section. However, occasionally studies supporting components of the methods section such as reliability of tests, or validation of outcome measures may be included in the methods section.
The final portion of the methods section will include the statistical methods used to analyze the data. 19 This does not mean that the actual results should be discussed in the methods section, as they have an entire section of their own!
Most scientific journals support the need for all projects involving humans or animals to have up‐to‐date documentation of ethical approval. 20 The methods section should include a clear statement that the researchers have obtained approval from an appropriate institutional review board.
Results, Discussion, and Conclusions
In most journals the results section is separate from the discussion section. It is important that you clearly distinguish your results from your discussion. The results section should describe the results only. The discussion section should put those results into a broader context. Report your results neutrally, as you “found them”. Again, be thoughtful about content and structure. Think carefully about where content is placed in the overall structure of your paper. It is not appropriate to bring up additional results, not discussed in the results section, in the discussion. All results must first be described/presented and then discussed. Thus, the discussion should not simply be a repeat of the results section. Carefully discuss where your information is similar or different from other published evidence and why this might be so. What was different in methods or analysis, what was similar?
As previously stated, stick to your topic at hand, and do not overstretch your discussion! One of the major pitfalls in writing the discussion section is overstating the significance of your findings 4 or making very strong statements. For example, it is better to say: “Findings of the current study support….” or “these findings suggest…” than, “Findings of the current study prove that…” or “this means that….”. Maintain a sense of humbleness, as nothing is without question in the outcomes of any type of research, in any discipline! Use words like “possibly”, “likely” or “suggests” to soften findings. 12
Do not discuss extraneous ideas, concepts, or information not covered by your topic/paper/commentary. Be sure to carefully address all relevant results, not just the statistically significant ones or the ones that support your hypotheses. When you must resort to speculation or opinion, be certain to state that up front using phrases such as “we therefore speculate” or “in the authors' opinion”.
Remember, just as in the introduction and literature review, evidence or results cannot draw conclusions, just as previously stated, only people, scientists, researchers, and authors can!
Finish with a concise, 3‐5 sentence conclusion paragraph. This is not just a restatement of your results, rather is comprised of some final, summative statements that reflect the flow and outcomes of the entire paper. Do not include speculative statements or additional material; however, based upon your findings a statement about potential changes in clinical practice or future research opportunities can be provided here.
CONCLUSIONS
Writing for publication can be a challenging yet satisfying endeavor. The ability to examine, relate, and interlink evidence, as well as to provide a peer‐reviewed, disseminated product of your research labors can be rewarding. A few suggestions have been offered in this commentary that may assist the novice or the developing writer to attempt, polish, and perfect their approach to scholarly writing.
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Educational resources and simple solutions for your research journey ![]() ![]() How to Write the Methods Section of a Research Paper![]() Writing a research paper is both an art and a skill, and knowing how to write the methods section of a research paper is the first crucial step in mastering scientific writing. If, like the majority of early career researchers, you believe that the methods section is the simplest to write and needs little in the way of careful consideration or thought, this article will help you understand it is not 1 . We have all probably asked our supervisors, coworkers, or search engines “ how to write a methods section of a research paper ” at some point in our scientific careers, so you are not alone if that’s how you ended up here. Even for seasoned researchers, selecting what to include in the methods section from a wealth of experimental information can occasionally be a source of distress and perplexity. Additionally, journal specifications, in some cases, may make it more of a requirement rather than a choice to provide a selective yet descriptive account of the experimental procedure. Hence, knowing these nuances of how to write the methods section of a research paper is critical to its success. The methods section of the research paper is not supposed to be a detailed heavy, dull section that some researchers tend to write; rather, it should be the central component of the study that justifies the validity and reliability of the research. Are you still unsure of how the methods section of a research paper forms the basis of every investigation? Consider the last article you read but ignore the methods section and concentrate on the other parts of the paper . Now think whether you could repeat the study and be sure of the credibility of the findings despite knowing the literature review and even having the data in front of you. You have the answer! ![]() Having established the importance of the methods section , the next question is how to write the methods section of a research paper that unifies the overall study. The purpose of the methods section , which was earlier called as Materials and Methods , is to describe how the authors went about answering the “research question” at hand. Here, the objective is to tell a coherent story that gives a detailed account of how the study was conducted, the rationale behind specific experimental procedures, the experimental setup, objects (variables) involved, the research protocol employed, tools utilized to measure, calculations and measurements, and the analysis of the collected data 2 . In this article, we will take a deep dive into this topic and provide a detailed overview of how to write the methods section of a research paper . For the sake of clarity, we have separated the subject into various sections with corresponding subheadings. Table of Contents What is the methods section of a research paper ?The methods section is a fundamental section of any paper since it typically discusses the ‘ what ’, ‘ how ’, ‘ which ’, and ‘ why ’ of the study, which is necessary to arrive at the final conclusions. In a research article, the introduction, which serves to set the foundation for comprehending the background and results is usually followed by the methods section, which precedes the result and discussion sections. The methods section must explicitly state what was done, how it was done, which equipment, tools and techniques were utilized, how were the measurements/calculations taken, and why specific research protocols, software, and analytical methods were employed. Why is the methods section important?The primary goal of the methods section is to provide pertinent details about the experimental approach so that the reader may put the results in perspective and, if necessary, replicate the findings 3 . This section offers readers the chance to evaluate the reliability and validity of any study. In short, it also serves as the study’s blueprint, assisting researchers who might be unsure about any other portion in establishing the study’s context and validity. The methods plays a rather crucial role in determining the fate of the article; an incomplete and unreliable methods section can frequently result in early rejections and may lead to numerous rounds of modifications during the publication process. This means that the reviewers also often use methods section to assess the reliability and validity of the research protocol and the data analysis employed to address the research topic. In other words, the purpose of the methods section is to demonstrate the research acumen and subject-matter expertise of the author(s) in their field. Structure of methods section of a research paperSimilar to the research paper, the methods section also follows a defined structure; this may be dictated by the guidelines of a specific journal or can be presented in a chronological or thematic manner based on the study type. When writing the methods section , authors should keep in mind that they are telling a story about how the research was conducted. They should only report relevant information to avoid confusing the reader and include details that would aid in connecting various aspects of the entire research activity together. It is generally advisable to present experiments in the order in which they were conducted. This facilitates the logical flow of the research and allows readers to follow the progression of the study design. ![]() It is also essential to clearly state the rationale behind each experiment and how the findings of earlier experiments informed the design or interpretation of later experiments. This allows the readers to understand the overall purpose of the study design and the significance of each experiment within that context. However, depending on the particular research question and method, it may make sense to present information in a different order; therefore, authors must select the best structure and strategy for their individual studies. In cases where there is a lot of information, divide the sections into subheadings to cover the pertinent details. If the journal guidelines pose restrictions on the word limit , additional important information can be supplied in the supplementary files. A simple rule of thumb for sectioning the method section is to begin by explaining the methodological approach ( what was done ), describing the data collection methods ( how it was done ), providing the analysis method ( how the data was analyzed ), and explaining the rationale for choosing the methodological strategy. This is described in detail in the upcoming sections. How to write the methods section of a research paperContrary to widespread assumption, the methods section of a research paper should be prepared once the study is complete to prevent missing any key parameter. Hence, please make sure that all relevant experiments are done before you start writing a methods section . The next step for authors is to look up any applicable academic style manuals or journal-specific standards to ensure that the methods section is formatted correctly. The methods section of a research paper typically constitutes materials and methods; while writing this section, authors usually arrange the information under each category. The materials category describes the samples, materials, treatments, and instruments, while experimental design, sample preparation, data collection, and data analysis are a part of the method category. According to the nature of the study, authors should include additional subsections within the methods section, such as ethical considerations like the declaration of Helsinki (for studies involving human subjects), demographic information of the participants, and any other crucial information that can affect the output of the study. Simply put, the methods section has two major components: content and format. Here is an easy checklist for you to consider if you are struggling with how to write the methods section of a research paper .
Now that you know how to write the methods section of a research paper , let’s address another challenge researchers face while writing the methods section —what to include in the methods section . How much information is too much is not always obvious when it comes to trying to include data in the methods section of a paper. In the next section, we examine this issue and explore potential solutions. ![]() What to include in the methods section of a research paperThe technical nature of the methods section occasionally makes it harder to present the information clearly and concisely while staying within the study context. Many young researchers tend to veer off subject significantly, and they frequently commit the sin of becoming bogged down in itty bitty details, making the text harder to read and impairing its overall flow. However, the best way to write the methods section is to start with crucial components of the experiments. If you have trouble deciding which elements are essential, think about leaving out those that would make it more challenging to comprehend the context or replicate the results. The top-down approach helps to ensure all relevant information is incorporated and vital information is not lost in technicalities. Next, remember to add details that are significant to assess the validity and reliability of the study. Here is a simple checklist for you to follow ( bonus tip: you can also make a checklist for your own study to avoid missing any critical information while writing the methods section ).
What NOT to include in the methods section of a research paperTo address “ how to write the methods section of a research paper ”, authors should not only pay careful attention to what to include but also what not to include in the methods section of a research paper . Here is a list of do not’s when writing the methods section :
We hope that by this point, you understand how crucial it is to write a thoughtful and precise methods section and the ins and outs of how to write the methods section of a research paper . To restate, the entire purpose of the methods section is to enable others to reproduce the results or verify the research. We sincerely hope that this post has cleared up any confusion and given you a fresh perspective on the methods section . As a parting gift, we’re leaving you with a handy checklist that will help you understand how to write the methods section of a research paper . Feel free to download this checklist and use or share this with those who you think may benefit from it. ![]() References
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Parts of a Technical PaperThe basic parts of a scientific or technical paper are: Title and Author Information Abstract Introduction Literature Review Methods Results Discussion Conclusions References and Appendices Detailed Explanation for Each PartTitle and Author Information: The title of your paper and any needed information about yourself (usually your name and institution). A short (usually around 250-400 words) description of the paper. Should include what the purpose of the paper is (including the basic research question/problem), the basic design of your project, and the major findings. Introduction: A general introduction to your topic and what you expect to learn from your project or experiment. Your research question should be found here. Literature Review: An analysis of what has already been published about your chosen topic. Should be able to show how your research question fits into the context of your field. A description of everything you did in your experiment or project, step-by-step. Needs to be detailed enough so that any reader would be able to repeat each step exactly on their own. What actually happened during your project or what you found at the end of your experiment. This is usually the best part to include the majority of your graphs, photos, tables, and other visual aids, as long as they help explain the results of your work. Discussion: An analysis of the results that integrates what you found into the wider body of research in your field. Can also include future hypotheses to be tested or future projects to build from your own. Conclusion: Can be included in the discussion if necessary. A final summary of the paper, including whether or not you were able to answer your original research question. References and Appendices: The reference page(s) is a list of all the sources you used to research and create your project/experiment, including everything cited in the literature review and methods sections. Remember to use the same citation style throughout the paper. An appendix would include any additional information about your work that you were not able to include within the body of your paper (like large datasets and figures) that would help readers better understand your results.
Scientific Writing
Example Paper
Introduction
Typically scientific journal articles have the following sections: Materials & Methods References used: Kotsis, S.V. and Chung, K.C. (2010) A Guide for Writing in the Scientific Forum. Plastic and Reconstructive Surgery. 126(5):1763-71. PubMed ID: 21042135 Van Way, C.W. (2007) Writing a Scientific Paper. Nutrition in Clinical Practice. 22: 663-40. PubMed ID: 1804295 What to include:
Additional resources: Fisher, W.E. (2005) Abstract Writing. Journal of Surgical Research. 128(2):162-4. PubMed ID: 16165161 Peh, W.C. and Ng, K.H. (2008) Abstract and keywords. Singapore Medical Journal. 49(9): 664-6. PubMed ID: 18830537
Additional resources: Annesley, T. M. (2010) "It was a cold and rainy night": set the scene with a good introduction. Clinical Chemistry. 56(5):708-13. PubMed ID: 20207764 Peh, W.C. and Ng, K.H. (2008) Writing the introduction. Singapore Medical Journal. 49(10):756-8. PubMed ID: 18946606
Additional resources: Lallet, R. H. (2004) How to write the methods section of a research paper. Respiratory Care. 49(10): 1229-32. PubMed ID: 15447808 Ng, K.H. and Peh, W.C. (2008) Writing the materials and methods. Singapore Medical Journal. 49(11): 856-9. PubMed ID: 19037549
Additional resources: Ng, K.H and Peh, W.C. (2008) Writing the results. Singapore Medical Journal. 49(12):967-9. PubMed ID: 19122944 Streiner, D.L. (2007) A shortcut to rejection: how not to write the results section of a paper. Canadian Journal of Psychiatry. 52(6):385-9. PubMed ID: 17696025
Additional resources: Annesley, T. M. (2010) The discussion section: your closing argument. Clinical Chemistry. 56(11):1671-4. PubMed ID: 20833779 Ng, K.H. and Peh, W.C. (2009) Writing the discussion. Singapore Medical Journal. 50(5):458-61. PubMed ID: 19495512 Tables & Figures: Durbin, C. G. (2004) Effective use of tables and figures in abstracts, presentations, and papers. Respiratory Care. 49(10): 1233-7. PubMed ID: 15447809 Ng, K. H. and Peh, W.C.G. (2009) Preparing effective tables. Singapore Medical Journal. (50)2: 117-9. PubMed ID: 19296024 Statistics: Ng, K. H. and Peh, W.C.G. (2009) Presenting the statistical results. Singapore Medical Journal. (50)1: 11-4. PubMed ID: 19224078 References: Peh, W.C.G. and Ng, K. H. (2009) Preparing the references. Singapore Medical Journal. (50)7: 11-4. PubMed ID: 19644619 The link below includes more detailed descriptions for each section along with examples of a scientific paper. Guide from Scitable by Nature Education ![]()
Organizing Your Social Sciences Research Paper
The purpose of the discussion section is to interpret and describe the significance of your findings in relation to what was already known about the research problem being investigated and to explain any new understanding or insights that emerged as a result of your research. The discussion will always connect to the introduction by way of the research questions or hypotheses you posed and the literature you reviewed, but the discussion does not simply repeat or rearrange the first parts of your paper; the discussion clearly explains how your study advanced the reader's understanding of the research problem from where you left them at the end of your review of prior research. Annesley, Thomas M. “The Discussion Section: Your Closing Argument.” Clinical Chemistry 56 (November 2010): 1671-1674; Peacock, Matthew. “Communicative Moves in the Discussion Section of Research Articles.” System 30 (December 2002): 479-497. Importance of a Good DiscussionThe discussion section is often considered the most important part of your research paper because it:
Annesley Thomas M. “The Discussion Section: Your Closing Argument.” Clinical Chemistry 56 (November 2010): 1671-1674; Bitchener, John and Helen Basturkmen. “Perceptions of the Difficulties of Postgraduate L2 Thesis Students Writing the Discussion Section.” Journal of English for Academic Purposes 5 (January 2006): 4-18; Kretchmer, Paul. Fourteen Steps to Writing an Effective Discussion Section. San Francisco Edit, 2003-2008. Structure and Writing StyleI. General Rules These are the general rules you should adopt when composing your discussion of the results :
II. The Content The content of the discussion section of your paper most often includes :
III. Organization and Structure Keep the following sequential points in mind as you organize and write the discussion section of your paper:
IV. Overall Objectives The objectives of your discussion section should include the following: I. Reiterate the Research Problem/State the Major Findings Briefly reiterate the research problem or problems you are investigating and the methods you used to investigate them, then move quickly to describe the major findings of the study. You should write a direct, declarative, and succinct proclamation of the study results, usually in one paragraph. II. Explain the Meaning of the Findings and Why They are Important No one has thought as long and hard about your study as you have. Systematically explain the underlying meaning of your findings and state why you believe they are significant. After reading the discussion section, you want the reader to think critically about the results and why they are important. You don’t want to force the reader to go through the paper multiple times to figure out what it all means. If applicable, begin this part of the section by repeating what you consider to be your most significant or unanticipated finding first, then systematically review each finding. Otherwise, follow the general order you reported the findings presented in the results section. III. Relate the Findings to Similar Studies No study in the social sciences is so novel or possesses such a restricted focus that it has absolutely no relation to previously published research. The discussion section should relate your results to those found in other studies, particularly if questions raised from prior studies served as the motivation for your research. This is important because comparing and contrasting the findings of other studies helps to support the overall importance of your results and it highlights how and in what ways your study differs from other research about the topic. Note that any significant or unanticipated finding is often because there was no prior research to indicate the finding could occur. If there is prior research to indicate this, you need to explain why it was significant or unanticipated. IV. Consider Alternative Explanations of the Findings It is important to remember that the purpose of research in the social sciences is to discover and not to prove . When writing the discussion section, you should carefully consider all possible explanations for the study results, rather than just those that fit your hypothesis or prior assumptions and biases. This is especially important when describing the discovery of significant or unanticipated findings. V. Acknowledge the Study’s Limitations It is far better for you to identify and acknowledge your study’s limitations than to have them pointed out by your professor! Note any unanswered questions or issues your study could not address and describe the generalizability of your results to other situations. If a limitation is applicable to the method chosen to gather information, then describe in detail the problems you encountered and why. VI. Make Suggestions for Further Research You may choose to conclude the discussion section by making suggestions for further research [as opposed to offering suggestions in the conclusion of your paper]. Although your study can offer important insights about the research problem, this is where you can address other questions related to the problem that remain unanswered or highlight hidden issues that were revealed as a result of conducting your research. You should frame your suggestions by linking the need for further research to the limitations of your study [e.g., in future studies, the survey instrument should include more questions that ask..."] or linking to critical issues revealed from the data that were not considered initially in your research. NOTE: Besides the literature review section, the preponderance of references to sources is usually found in the discussion section . A few historical references may be helpful for perspective, but most of the references should be relatively recent and included to aid in the interpretation of your results, to support the significance of a finding, and/or to place a finding within a particular context. If a study that you cited does not support your findings, don't ignore it--clearly explain why your research findings differ from theirs. V. Problems to Avoid
Analyzing vs. Summarizing. Department of English Writing Guide. George Mason University; Discussion. The Structure, Format, Content, and Style of a Journal-Style Scientific Paper. Department of Biology. Bates College; Hess, Dean R. "How to Write an Effective Discussion." Respiratory Care 49 (October 2004); Kretchmer, Paul. Fourteen Steps to Writing to Writing an Effective Discussion Section. San Francisco Edit, 2003-2008; The Lab Report. University College Writing Centre. University of Toronto; Sauaia, A. et al. "The Anatomy of an Article: The Discussion Section: "How Does the Article I Read Today Change What I Will Recommend to my Patients Tomorrow?” The Journal of Trauma and Acute Care Surgery 74 (June 2013): 1599-1602; Research Limitations & Future Research . Lund Research Ltd., 2012; Summary: Using it Wisely. The Writing Center. University of North Carolina; Schafer, Mickey S. Writing the Discussion. Writing in Psychology course syllabus. University of Florida; Yellin, Linda L. A Sociology Writer's Guide . Boston, MA: Allyn and Bacon, 2009. Writing TipDon’t Over-Interpret the Results! Interpretation is a subjective exercise. As such, you should always approach the selection and interpretation of your findings introspectively and to think critically about the possibility of judgmental biases unintentionally entering into discussions about the significance of your work. With this in mind, be careful that you do not read more into the findings than can be supported by the evidence you have gathered. Remember that the data are the data: nothing more, nothing less. MacCoun, Robert J. "Biases in the Interpretation and Use of Research Results." Annual Review of Psychology 49 (February 1998): 259-287; Ward, Paulet al, editors. The Oxford Handbook of Expertise . Oxford, UK: Oxford University Press, 2018. Another Writing TipDon't Write Two Results Sections! One of the most common mistakes that you can make when discussing the results of your study is to present a superficial interpretation of the findings that more or less re-states the results section of your paper. Obviously, you must refer to your results when discussing them, but focus on the interpretation of those results and their significance in relation to the research problem, not the data itself. Azar, Beth. "Discussing Your Findings." American Psychological Association gradPSYCH Magazine (January 2006). Yet Another Writing TipAvoid Unwarranted Speculation! The discussion section should remain focused on the findings of your study. For example, if the purpose of your research was to measure the impact of foreign aid on increasing access to education among disadvantaged children in Bangladesh, it would not be appropriate to speculate about how your findings might apply to populations in other countries without drawing from existing studies to support your claim or if analysis of other countries was not a part of your original research design. If you feel compelled to speculate, do so in the form of describing possible implications or explaining possible impacts. Be certain that you clearly identify your comments as speculation or as a suggestion for where further research is needed. Sometimes your professor will encourage you to expand your discussion of the results in this way, while others don’t care what your opinion is beyond your effort to interpret the data in relation to the research problem.
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How to Write the Results/Findings Section in ResearchWhat is the research paper Results section and what does it do?The Results section of a scientific research paper represents the core findings of a study derived from the methods applied to gather and analyze information. It presents these findings in a logical sequence without bias or interpretation from the author, setting up the reader for later interpretation and evaluation in the Discussion section. A major purpose of the Results section is to break down the data into sentences that show its significance to the research question(s). The Results section appears third in the section sequence in most scientific papers. It follows the presentation of the Methods and Materials and is presented before the Discussion section —although the Results and Discussion are presented together in many journals. This section answers the basic question “What did you find in your research?” What is included in the Results section?The Results section should include the findings of your study and ONLY the findings of your study. The findings include:
If the scope of the study is broad, or if you studied a variety of variables, or if the methodology used yields a wide range of different results, the author should present only those results that are most relevant to the research question stated in the Introduction section . As a general rule, any information that does not present the direct findings or outcome of the study should be left out of this section. Unless the journal requests that authors combine the Results and Discussion sections, explanations and interpretations should be omitted from the Results. How are the results organized?The best way to organize your Results section is “logically.” One logical and clear method of organizing research results is to provide them alongside the research questions—within each research question, present the type of data that addresses that research question. Let’s look at an example. Your research question is based on a survey among patients who were treated at a hospital and received postoperative care. Let’s say your first research question is: ![]() “What do hospital patients over age 55 think about postoperative care?” This can actually be represented as a heading within your Results section, though it might be presented as a statement rather than a question: Attitudes towards postoperative care in patients over the age of 55 Now present the results that address this specific research question first. In this case, perhaps a table illustrating data from a survey. Likert items can be included in this example. Tables can also present standard deviations, probabilities, correlation matrices, etc. Following this, present a content analysis, in words, of one end of the spectrum of the survey or data table. In our example case, start with the POSITIVE survey responses regarding postoperative care, using descriptive phrases. For example: “Sixty-five percent of patients over 55 responded positively to the question “ Are you satisfied with your hospital’s postoperative care ?” (Fig. 2) Include other results such as subcategory analyses. The amount of textual description used will depend on how much interpretation of tables and figures is necessary and how many examples the reader needs in order to understand the significance of your research findings. Next, present a content analysis of another part of the spectrum of the same research question, perhaps the NEGATIVE or NEUTRAL responses to the survey. For instance: “As Figure 1 shows, 15 out of 60 patients in Group A responded negatively to Question 2.” After you have assessed the data in one figure and explained it sufficiently, move on to your next research question. For example: “How does patient satisfaction correspond to in-hospital improvements made to postoperative care?” ![]() This kind of data may be presented through a figure or set of figures (for instance, a paired T-test table). Explain the data you present, here in a table, with a concise content analysis: “The p-value for the comparison between the before and after groups of patients was .03% (Fig. 2), indicating that the greater the dissatisfaction among patients, the more frequent the improvements that were made to postoperative care.” Let’s examine another example of a Results section from a study on plant tolerance to heavy metal stress . In the Introduction section, the aims of the study are presented as “determining the physiological and morphological responses of Allium cepa L. towards increased cadmium toxicity” and “evaluating its potential to accumulate the metal and its associated environmental consequences.” The Results section presents data showing how these aims are achieved in tables alongside a content analysis, beginning with an overview of the findings: “Cadmium caused inhibition of root and leave elongation, with increasing effects at higher exposure doses (Fig. 1a-c).” The figure containing this data is cited in parentheses. Note that this author has combined three graphs into one single figure. Separating the data into separate graphs focusing on specific aspects makes it easier for the reader to assess the findings, and consolidating this information into one figure saves space and makes it easy to locate the most relevant results. ![]() Following this overall summary, the relevant data in the tables is broken down into greater detail in text form in the Results section.
Captioning and Referencing Tables and FiguresTables and figures are central components of your Results section and you need to carefully think about the most effective way to use graphs and tables to present your findings . Therefore, it is crucial to know how to write strong figure captions and to refer to them within the text of the Results section. The most important advice one can give here as well as throughout the paper is to check the requirements and standards of the journal to which you are submitting your work. Every journal has its own design and layout standards, which you can find in the author instructions on the target journal’s website. Perusing a journal’s published articles will also give you an idea of the proper number, size, and complexity of your figures. Regardless of which format you use, the figures should be placed in the order they are referenced in the Results section and be as clear and easy to understand as possible. If there are multiple variables being considered (within one or more research questions), it can be a good idea to split these up into separate figures. Subsequently, these can be referenced and analyzed under separate headings and paragraphs in the text. To create a caption, consider the research question being asked and change it into a phrase. For instance, if one question is “Which color did participants choose?”, the caption might be “Color choice by participant group.” Or in our last research paper example, where the question was “What is the concentration of cadmium in different parts of the onion after 14 days?” the caption reads: “Fig. 1(a-c): Mean concentration of Cd determined in (a) bulbs, (b) leaves, and (c) roots of onions after a 14-day period.” Steps for Composing the Results SectionBecause each study is unique, there is no one-size-fits-all approach when it comes to designing a strategy for structuring and writing the section of a research paper where findings are presented. The content and layout of this section will be determined by the specific area of research, the design of the study and its particular methodologies, and the guidelines of the target journal and its editors. However, the following steps can be used to compose the results of most scientific research studies and are essential for researchers who are new to preparing a manuscript for publication or who need a reminder of how to construct the Results section. Step 1 : Consult the guidelines or instructions that the target journal or publisher provides authors and read research papers it has published, especially those with similar topics, methods, or results to your study.
Step 2 : Consider your research results in relation to the journal’s requirements and catalogue your results.
Step 3 : Design figures and tables to present and illustrate your data.
Step 4 : Draft your Results section using the findings and figures you have organized.
Step 5 : Review your draft; edit and revise until it reports results exactly as you would like to have them reported to your readers.
One excellent option is to use a professional English proofreading and editing service such as Wordvice, including our paper editing service . With hundreds of qualified editors from dozens of scientific fields, Wordvice has helped thousands of authors revise their manuscripts and get accepted into their target journals. Read more about the proofreading and editing process before proceeding with getting academic editing services and manuscript editing services for your manuscript. As the representation of your study’s data output, the Results section presents the core information in your research paper. By writing with clarity and conciseness and by highlighting and explaining the crucial findings of their study, authors increase the impact and effectiveness of their research manuscripts. For more articles and videos on writing your research manuscript, visit Wordvice’s Resources page. Wordvice Resources
Click through the PLOS taxonomy to find articles in your field. For more information about PLOS Subject Areas, click here . Loading metrics Open Access Peer-reviewed Research Article On the possible use of hydraulic force to assist with building the step pyramid of saqqaraRoles Conceptualization, Data curation, Investigation, Methodology, Project administration, Resources, Supervision, Validation, Visualization, Writing – original draft, Writing – review & editing * E-mail: [email protected] , [email protected] Affiliation Paleotechnic., Paris, France ![]() Roles Conceptualization, Data curation, Formal analysis, Investigation, Methodology, Project administration, Software, Validation, Visualization, Writing – original draft, Writing – review & editing Affiliation Univ. Grenoble Alpes, INRAE, CNRS, IRD, Grenoble INP, IGE, Grenoble, France Roles Conceptualization, Investigation, Methodology, Software, Visualization Affiliation Sicame Group, Arnac-Pompadour, France Roles Conceptualization, Investigation, Methodology, Validation, Writing – review & editing Affiliation CEDETE—Centre d’études sur le Développement des Territoires et l’Environnement, Université d’Orléans, Orléans, France Roles Conceptualization, Investigation, Methodology, Validation Roles Conceptualization, Investigation, Methodology, Visualization Affiliation AtoutsCarto, Bourges, France Roles Methodology, Project administration Affiliation Verilux International, Brienon-sur-Armançon, France Roles Conceptualization, Investigation, Validation, Writing – review & editing Roles Conceptualization, Data curation, Formal analysis, Investigation, Methodology, Software, Validation Roles Conceptualization, Investigation, Methodology, Supervision, Validation
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The Step Pyramid of Djoser in Saqqara, Egypt, is considered the oldest of the seven monumental pyramids built about 4,500 years ago. From transdisciplinary analysis, it was discovered that a hydraulic lift may have been used to build the pyramid. Based on our mapping of the nearby watersheds, we show that one of the unexplained massive Saqqara structures, the Gisr el-Mudir enclosure, has the features of a check dam with the intent to trap sediment and water. The topography beyond the dam suggests a possible ephemeral lake west of the Djoser complex and water flow inside the ’Dry Moat’ surrounding it. In the southern section of the moat, we show that the monumental linear rock-cut structure consisting of successive, deep compartments combines the technical requirements of a water treatment facility: a settling basin, a retention basin, and a purification system. Together, the Gisr el-Mudir and the Dry Moat’s inner south section work as a unified hydraulic system that improves water quality and regulates flow for practical purposes and human needs. Finally, we identified that the Step Pyramid’s internal architecture is consistent with a hydraulic elevation mechanism never reported before. The ancient architects may have raised the stones from the pyramid centre in a volcano fashion using the sediment-free water from the Dry Moat’s south section. Ancient Egyptians are famous for their pioneering and mastery of hydraulics through canals for irrigation purposes and barges to transport huge stones. This work opens a new line of research: the use of hydraulic force to erect the massive structures built by Pharaohs. Citation: Landreau X, Piton G, Morin G, Bartout P, Touchart L, Giraud C, et al. (2024) On the possible use of hydraulic force to assist with building the step pyramid of saqqara. PLoS ONE 19(8): e0306690. https://doi.org/10.1371/journal.pone.0306690 Editor: Joe Uziel, Israel Antiquities Authority, ISRAEL Received: December 7, 2023; Accepted: June 22, 2024; Published: August 5, 2024 Copyright: © 2024 Landreau et al. This is an open access article distributed under the terms of the Creative Commons Attribution License , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Data Availability: All relevant data are within the manuscript and its Supporting Information files. The computer codes are available upon request. Funding: The Sicame Group, The Atoutscarto Company and The Verilux Company provided support in the form of salaries for GM, CG and J-CM, respectively. The specific roles of these authors are articulated in the ‘author contributions’ section. Competing interests: The authors have read the journal’s policy and have the following competing interests: GM, CG and J-CM are paid employees of The Sicame Group, The Atoutscarto Company and The Verilux Company, respectively. There are no patents, products in development or marketed products associated with this research to declare. This does not alter our adherence to PLOS ONE policies on sharing data and materials. 1 IntroductionThe funerary complex of King Djoser, built at Saqqara in Egypt around 2680 B.C., is considered a significant milestone in monumental architecture. It is the first to disclose two crucial innovations: a pyramid shape for the pharaoh’s grave and the exclusive use of fully dressed stones for masonry. In practice, it is also revolutionary in the ability to extract and raise stones by millions before stacking them with precision [ 1 ]. Djoser’s complex visible achievements are such that its architect, Vizier, and Great Priest of Ra, Imhotep, was deified by the New Kingdom. The knowledge and innovations implemented in the Djoser mortuary complex profoundly influenced future developments and were widely perfected throughout the Old Kingdom’s III rd and IV th Dynasties, i . e . circa 2680–2460 B.C. These developments resulted in a substantial increase in the megaliths’ size [ 2 ], leading to pyramids of spectacular dimensions, such as those of the Meidum, Dahshur, and Giza plateaus. In less than 150 years, the average weight of the typical large stones was thus multiplied by ≈8 and went from ≈300 kg for Djoser’s pyramid to more than 2.5 tons for Chephren’s pyramid’s structural blocks [ 3 ]. For the largest lintels, the weight increases by two orders of magnitude, with several blocks of ≈50 – 100 tons for Cheops’ pyramid. On this short timeframe on the scale of human history, Egyptians carried and raised some 25 million tons of stones [ 4 ] to build seven monumental pyramids. Assuming an annual work schedule of 300 days at a rate of 10 hours/day, meaning 450,000 hours spread over less than 150 years, this requires a technical and logistical organization capable, on average, of cutting, moving, and adjusting about 50 tons of stone blocks per hour. Even if one admits that not every pyramid’s blocks are fitted with millimeter precision, the amount of work accomplished is truly remarkable. Interestingly, the pyramids later built in Egypt tended to be smaller with time and never reached the volume of the Old Kingdom’s monumental structures again. As authentic sources from the working sphere of pyramid architects are currently lacking, no generally accepted wholistic model for pyramid construction exists yet. Although many detailed publications dedicated to pyramid-building procedures have given tangible elements [ 5 , 6 ], they usually explain more recent, better documented, but also smaller pyramids [ 7 ]. These techniques could include ramps, cranes, winches, toggle lifts, hoists, pivots, or a combination of them [ 8 – 10 ]. Studies of the pyramid’s construction sites also revealed a high level of expertise in managing the hydraulic and hydrological environment, such as utilizing waterways to deliver materials, constructing ports and locks, or setting up irrigation systems [ 11 , 12 ]. These achievements have led some scholars to refer to ancient Egypt as an ‘early hydraulic civilization [ 11 ].’ However, there is actually very little multidisciplinary analysis combining the rich archaeological findings on pyramids with other disciplines such as hydrology, hydraulics, geotechnics, paleoclimatology, or civil engineering [ 9 ]. Therefore, the topic of water force in the context of pyramid construction remains insufficiently addressed in the academic literature. Moreover, a second question accentuates the enigma: the Pharaohs who built these pyramids are missing. Until now, neither written record nor physical evidence reports the discovery of one of the III rd and IV th Dynasties’ Pharaohs. Old Kingdom’s ‘big’ pyramids’ rooms were allegedly plundered [ 13 – 15 ] during the millennia that followed the construction of the pyramids, leaving little evidence behind [ 12 ]. The III rd and IV th Dynasties’ rooms present little or no funerary attributes, such as those observed in other high-dignitary figures’ tombs contemporary to the period [ 16 , 17 ], with no King’s remains found inside. In addition, the walls of the pyramids’ chambers do not exhibit any hieroglyphs, paintings, engravings, or drawings, which would allow us to qualify them as funerary with certainty. Despite this lack of evidence, many authors [ 18 ] still support that these rooms can be attributed to Pharaohs’ burials mainly based on royal cartouches or Kings’ names found elsewhere within the pyramid or nearby temples. Over the recent years, Dormion & Verd’Hurt [ 19 , 20 ], Hamilton [ 21 – 24 ] or others [ 1 , 25 ] were among the first to consider possible non-funerary functions of pyramids’ internal layouts by pointing out some architectural inconsistencies and highlighting the high degree of complexity of several structures, irrelevant for a burial chamber. Their analysis provided both chambers and gallery systems with a technical dimension, emphasizing a level of engineering on the part of the ancient builders that is quite remarkable and sometimes challenges any apparent explanation. This technical level is at once reflected in the geometry of the rooms and ducts, as well as in the stonework, which includes materials selection, extraction, cutting, and then assembling with exceptional accuracy [ 20 ]. This precision involved several advanced sub-techniques, such as inter-block mortar joint realization [ 26 – 29 ] or stone polishing with flatness and roughness values that reach levels of contemporary know-how. Apart from surfaces and interfaces, the builders’ technical ability is also evident throughout sophisticated mechanical systems set up in the pyramids [ 30 ], as swivel stone flaps’ designs in the Meidum and Bent pyramids [ 21 , 24 ] or tilted portcullises found in the Bent pyramid, as well as at Giza [ 20 ]. These elements suggest that, rather than an aesthetic rendering or a funerary use for these layouts, ancient Egyptians intended technical functions for some walls, tunnels, corridors, shafts, and chambers where more straightforward existing techniques were insufficient. In summary, the analysis of the pyramids’ construction and the investigation of their internal layouts seem to require more research to provide a wholistic explanation to their purpose. This study aims to provide a fresh look at these topics by applying an alternative, multi-disciplinary, wholistic approach. It revisits the Old Kingdom’s pyramids’ construction methodology and seeks to explain the significance of internal layouts during construction. Based on current archaeological knowledge, we demonstrate that the Saqqara’s topography and the layout of several structures are consistent with the hypothesis that a hydraulic system was used to build the pyramid. The paper is divided into three main sections that analyze the current scientific literature to address the following inquiries: (i) Was the plateau of Saqqara supplied with water? (ii) If so, how was it possibly stored and treated? and (iii) How was it used to build the pyramid? A discussion and some concluding remarks and perspectives follow. 2 The saqqara’s hydrologic networkOur study began with the postulate that the larger Cheops’ and Chephren’s pyramids of Giza plateau were the outcomes of technical progress from previous pyramids, with the Step Pyramid as a technological precursor. While many literature studies focus on the construction of Cheops’ pyramid, we found it more relevant to examine the building techniques used for the Step Pyramid first. This would provide insight into the processes used by ancient builders that were later refined in subsequent pyramids. As a first approach, we analyzed potential reasons for the specific building of King Djoser’s Complex on the Saqqara Plateau. 2.1 Water resource from the desert wadisAlthough detailed measurements of the Nile flood levels have been reported since the V th Dynasty (2480 B.C.) [ 31 – 33 ], there is very little information available about the hydrology of its desert tributaries, known as ’wadis’, in ancient Egypt. Sedimentological evidence of heavy rainfalls and flash floods exists [ 31 , 34 ] but little is known beyond that. Determining the rainfall regime that the Saqqara region experienced about 4,700 years B.P. is challenging and uncertain. Past studies demonstrated that, from about 11,000 to 5,000 B.P, during the so-called ‘Green Sahara’ period, the whole Sahara was much wetter than today, and the landscape was savannah rather than desert [ 35 , 36 ]. Around 4500–4800 years B.P. too, the Eastern Mediterranean region was wetter than it is now, despite drying up later [ 37 – 39 ]. A range of annual precipitation value of 50–150 mm/year is assumed in the following calculation to perform crude computations of water resource. It covers the range between the >150 mm/year suggested by Kuper & Kropelin [ 40 ] for the end of the Green Sahara period, before the subsequent drier period, during which rainfall decreased to <50 mm/year. The range of variability, i . e . 50 to 150 mm/yr is also consistent with the typical inter-annual rainfall variability observed in the region [ 38 ]. Then, current hydrological monitoring on Egyptian wadis located further to the north and experiencing comparable annual rainfall ( i . e ., 100–200 mm/yr) showed that only 1–3% of this mean annual precipitation was measured as runoff, i.e., surface flows [ 41 ]. This average range is hereafter used for conservative, first-order estimations of available water volume, referred hereafter to as the ‘water resource’. Note that the infrequent, most intense events can reach 50 mm of rainfall and trigger devastating flash floods where the runoff coefficients have been measured up to 30%, i . e ., one order of magnitude higher than the mean annual [ 41 – 43 ]. Note that these water resource and flash flood hydrology estimates neglect that the soils were probably richer in clay and silt just after the Green Sahara period, with several millennia of a wetter climate and savannah landscape [ 35 , 36 ], which would increase the runoff coefficient and available surface water resource in the wadis. 2.2 The Saqqara site: a plateau with a water supplyThe Saqqara necropolis is located on a limestone plateau on the west bank of the Nile River, about 180 km from the Mediterranean Sea ( Fig 1 ). The entire site lies in the desert, less than two kilometers from the plateau’s edge (elevation 40–55 m ASL— Above Sea Level ), which overlooks the Nile floodplain (height ≈ 20 m ASL). Further to the west, the desert rises gently for about 20 km (hills’ top elevation ≈ 200–300 m ASL).
(Satellite image: Airbus Pléiades, 2021-07-02, reprinted from Airbus D&S SAS library under a CC BY license, with permission from Michael Chemouny, original copyright 2021). https://doi.org/10.1371/journal.pone.0306690.g001 The reasons behind the construction of the Djoser complex at Saqqara remain unclear. The contribution of economic, socio-political, and religious factors was previously highlighted [ 44 , 45 ], but environmental factors were also possibly influential. In 2020, Wong provided evidence that the climate, geology, and hydrology would have influenced building choices and may have contributed to, or perhaps accelerated, the emergence of stone architecture on the Saqqara plateau [ 37 ]. From a geological standpoint, the layered structure of the limestone at Saqqara was indeed stressed as a favorable factor for excavating large amounts of construction stones [ 46 , 47 ]. These layers, which consist of 30–60 cm thick sand-rich calcareous beds alternated with calcareous clay and marl layers, made it easy to extract the limestone blocks from their parent beds by vertical cuttings, the original thickness being reflected in the building stones’ thickness of Djoser’s complex. From a hydrological standpoint, the Abusir wadi is considered a second environmental factor that strongly influenced the Early Dynastic development of the Saqqara necropolis at least [ 45 , 48 – 50 ]. The Abusir wadi is the ephemeral stream draining the hills west of Saqqara ( Fig 1 ) . Before this study, academic research mainly focused on the downstream part of the wadi [ 45 , 48 – 50 ], namely the Abusir Lake [ 51 ] located north of Saqqara Plateau. However, the upstream portion has remained undocumented. In order to analyze the relationships between the Abusir wadi and the Step Pyramid’s construction project, the drainage networks west of the Saqqara area were mapped for the first time to the best of our knowledge, using various satellite imagery ( Fig 1 ) and Digital Elevation Models (see S1 Fig in S2 File ). A paleo-drainage system can be identified upstream of the Gisr el-Mudir structure as the origin of the Abusir wadi ( Fig 1 , pink line). The boundaries of this runoff system form a catchment area never reported so far, although easily recognizable from the geomorphological imprints of surface paleochannels in the desert and on historical maps [ 52 ]. Although it currently has a 15 km 2 surface area, we cannot rule out the possibility that the drainage divides shifted and changed due to land alterations and aeolian sand deposits over the past 4,500 years. The current catchment summit is about 110 m ASL, giving the Abusir wadi a 1% average slope over its slightly more than 6 km length. In the field of hydrology, a 1% gradient is described as ‘rather steep’. With such steep slopes, transportation of sand and gravel is expected during flashfloods, which can cause severe downstream damage (scouring or burying of structures, filling of excavations and ponding areas). In comparison, irrigation channels are rather at least ten times less steep (about 0.1%), and the Nile slope is less than 0.01% (less than 200m of elevation gain between Aswan and Cairo). 2.3 The Wadi Taflah: A possible complementary water supplyReported since the early 1800s, a former tributary to the Nile called the Bahr Bela Ma [ 53 , 54 ] or ‘ Wadi Taflah’ flowed parallel to the Abusir wadi catchment, less than two kilometers south of the Saqqara plateau. From satellite imagery, we identified that the Wadi Taflah arises from a drainage area of almost 400 km 2 and consists of three main branches ( Fig 2 , numbered black dots) still visible from the desert’s geomorphological marks. This network is also visible on the radar imagery provided by Paillou [ 55 ] that can penetrate multiple meters of sand ( S2 Fig in S2 File ). The similarity of the optical and radar drainage patterns confirms the existence and old age of this hydrological network. https://doi.org/10.1371/journal.pone.0306690.g002 Although no canal was detected from the satellite data, the close proximity of Abusir wadi with the Wadi Taflah ( Fig 2 ) is intriguing and raises the question about a potential ancient, artificial connection between them. According to the 18 th -century maps published by Savary [ 54 ], the Wadi Taflah was ‘closed by an ancient King of Egypt.’ Such a testimony, although imprecise, could suggest the construction of a water diversion by a former ruler. A geophysical investigation could help to find such a structure if existing. The drainage area of Wadi Taflah covers nearly 400 km 2 at an elevation >58 m ASL. This elevation is high enough to allow the diversion of the drainage area toward the Abusir wadi. This would result in an increase in the drained area and associated availability of water resources by a factor of >25 times. Based on the hydrological conditions described in section 2.1, the estimated water resource from Abusir wadi and Wadi Taflah is crudely between 7,500 to 68,000 m 3 /year and 200,000 to 1,800,000 m 3 /year, respectively. 2.4 The Abusir wadi: A structural element in the early dynastic Saqqara’s developmentAccording to the Saqqara topography ( Fig 3 ), the Abusir wadi flowed through the Gisr el-Mudir enclosure before heading north towards the Nile floodplain, where it used to feed an oxbow lake, the Abusir Lake [ 51 ]. With such a localization, the Gisr el-Mudir walls literally dam the Abusir wadi valley’s entire width. The sparse vegetation only growing in the valley bottom upstream of Gisr el-Mudir and not elsewhere in the area evidences this damming and interception of surface and subsurface flows ( Fig 4A , green line). This slight moist area is dominated by plants commonly found in desert margins and wadis, such as Panicum thurgidum and Alhagi graecorum [ 56 ], and is typical of hypodermal flows. Contour lines extracted from the 1:5,000 topographical map [ 52 ] “Le Caire, sheet H22”. https://doi.org/10.1371/journal.pone.0306690.g003 a. The Gisr el-Mudir check dam (Satellite image: Airbus Pléiades, 2021-07-02, reprinted from Airbus D&S SAS library under a CC BY license, with permission from Michael Chemouny, original copyright 2021); b.: Digital Elevation Model generated from the 1:5,000 topographical map “Le Caire, sheet H22”. https://doi.org/10.1371/journal.pone.0306690.g004 Downstream of the Gisr el-Mudir, the Abusir wadi joins the Saqqara Plateau. Its boundaries are defined to the south by an outcropping limestone ridge and to the east by the Sekhemkhet and Djoser’s enclosures ( Fig 3 ). The landform of this area seems inconsistent with a pure fluvial formation. Instead, the very flat topography on about 2–2.5 km 2 , according to the Saqqara Geophysics Survey Project (SGSP) [ 57 – 60 ] and possibly allowed some ephemeral ponding water which may have resulted in an episodic upper Abusir lake after the most intense rainfalls. However, due to the several-meter deep wind-blown and alluvial sand cover accumulated over the past millennia [ 57 ], the riverbed altitudes during Djoser’s reign are challenging to establish without further investigations, and only broad patterns can be determined from the local topography [ 52 ]. As with many other small wadis, the Early Dynastic hydrology of the Abusir wadi remains largely unknown. According to fluvial sediment analysis in the Abusir Lake area, the Abusir wadi was probably a perennial stream during the Old Kingdom period [ 51 ]. Although the climate is hot and arid nowadays, several studies support a more humid environment during the Old Kingdom [ 34 ] . Multiple strands of evidence indeed suggest that Egypt experienced considerable rainfalls around the reign of Djoser, resulting in frequent flooding and heavy runoffs on the Saqqara Plateau. This climatic feature is supported by sedimentary deposits resulting from flowing water of ‘considerable kinetic force’ contemporary to Djoser’s reign [ 61 , 62 ] . According to Trzciński et al.[ 34 ], the strongly cemented structure L3 found in the Great Trench surrounding the Djoser Complex was due to cyclical watering while the high content of Fe3+ indicates that the region experienced intensive weathering in a warm and humid environment. In 2020, Wong concluded that the ‘ intriguing possibility that the Great Trench that surrounds the Djoser complex may have been filled with water ’ during Djoser’s reign [ 37 ]. If so, this might explain why tombs were built on the northern part of the Saqqara plateau which has a higher altitude [ 45 ] and nothing was constructed inside the Trench until the reign of Userkaf and Unas (V th Dynasty). 3. The saqqara’s water management system3.1 the gisr el-mudir check dam. Reported at least since the 18 th century [ 63 ] and extensively described within a decade of a geophysical survey by Mathieson et al ., see also [ 45 ] for a summary, the Gisr el-Mudir is a rectangular enclosure located a few hundred meters west of the Djoser’s complex ( Fig 3 , Fig 4A & 4B ). This monumental structure has a footprint of about 360 m x 620 m, i . e ., larger than the Djoser complex (545 m x 277 m). The walls have an estimated volume of >100,000 m 3 (SGSP, 1992–1993 report), meaning about one-third of the Step Pyramid’s volume. Field inspection and geophysical results from the SGSP [ 57 ] found no construction inside except for a couple of more recent, small graves, thus confirming that the enclosure is mainly empty. Moreover, several elements in the building suggest that this structure predated the Step Pyramid’s complex and was tentatively dated to the late II nd or early III rd Dynasty [ 57 , 64 ], which might turn it into the oldest substantial stone structure in Egypt discovered so far. Before this study, several conflicting theories about the Gisr el-Mudir’s purpose were put forward [ 59 ]: e . g ., an unfinished pyramid complex (but the lack of a central structure made it improbable to be a funerary monument), a guarded fortress [ 65 ] protecting the Saqqara necropolis from nomadic Bedouin incursions, an embankment to raise a monument to a higher level [ 66 ], a celebration arena [ 64 , 67 ], or even a cattle enclosure. However, given the low level of exploratory work afforded to the structure, no generally accepted explanation exists yet, and its purpose has remained more conjectural than substantiated. In light of the upstream watershed and its transversal position across the Abusir River, the Gisr el-Mudir’s western wall meets the essential criteria of a check dam, i . e ., a dam intending to manage sediment and water fluxes [ 68 , 69 ]. This comparison is particularly striking regarding its cross-section ( Fig 5 ). According to Mathieson et al . [ 59 ], the basic structure of this wall consists of a hollow construction of two rough-hewn limestone masonry skin-walls, ≈3.2 m high, separated by a 15 m interspace filled with three layers of materials extracted from the surrounding desert bedrock [ 70 ] and cunningly arranged. The first layer ( Fig 5 , ‘ A ’ dot) is made of roughly laid local limestone blocks forming a buttress against the inside of the facing blocks. The secondary fill ( B ) comprises coarse sand and medium to large limestone fragments. Then, the third fill ( C ) consists of rough to fine sand and silt, small limestone fragments, and chippings with pebble and flint nodules. Finally, these A, B, and C backfill layers are positioned symmetrically to the median axis of the wall. Figure adapted from [ 58 ]. https://doi.org/10.1371/journal.pone.0306690.g005 Civil engineering was used during the Old Kingdom to protect settlements from flash floods, such as the Heit el-Ghurab (’Wall of the Crow’) safeguarding the village of the pyramid builders at Giza [ 71 ]. Regarding the Gisr el-Mudir structure, the abovementioned elements strikingly echo the transversal profile and slope protection of another famous Old Kingdom structure: the Sadd el-Kafara dam built on the Wadi al-Garawi , a colossal building found to be contemporary to that of the Gisr el-Mudir [ 72 – 74 ]. Both structures present the technical signature of zoned earthen dams: a wide embankment made of a central impervious core surrounded by transition filters, i . e ., filling material with coarser grain size, preventing erosion, migration, and potential piping of the core fine material due to seepage. The semi-dressed limestone walls stabilized the inner material and protected it against erosion when water flowed against and above the dam. Both dams have much broader profiles than modern dams. This oversizing could be due to the unavailability of contemporary compaction systems or an empirical and conservative structural design. They both have narrower cores of fine material at the bottom of the dam than at their crest, contradicting modern design [ 75 ]. This can be attributed to the construction phasing that would have started by raising the sidewalls buttressed against the coarse and intermediate filling ( B and C fills in Fig 5 ), followed by a phase of filling the wide core with finer, compacted material [ 72 ]. Finally, the eastern wall’s north-south profile ( Fig 6 , line A-B ) presents a parabolic profile relevant to guide the flows to the basin’s center formed by Gisr el-Mudir. This guidance would have prevented the dam failure by outflanking during flooding events when the dam outlet was saturated. We estimate that the accumulated water crossed the dam through an outlet likely located at the valley’s lowest elevation, i . e ., near 48.7 m ASL ( G1 in Figs 4B and Fig 6 ). In summary, the Gisr el-Mudir’s western wall likely acted as a first check dam to the Abusir wadi flows. https://doi.org/10.1371/journal.pone.0306690.g006 The excavations performed on the eastern wall of the Gisr el-Mudir highlighted a lower structural quality [ 45 ]. Its shape is similar to that of the western wall, with a distinctive parabolic profile ( Fig 6 , line C-D ). Furthermore, it discloses two topographical singularities: first, its overall altitude is a few meters lower than the western wall ( Fig 7A ). Then, in the southern part of the eastern wall, a geophysics anomaly ( G2 in Figs 4B and Fig 6 ) was found to be a series of massive, roughly cut, ‘L’-shaped megaliths [ 45 , 66 ]. Before our study, these megaliths were thought to possibly be the remains of a monumental gateway–due to their similarities with the Djoser’s complex enclosure’s entrance–but their purpose was not specified [ 66 ]. According to our analysis, these megaliths could be the side elements of the water outlets, possibly slit openings [ 76 ] that were likely closed off by wood beams but could be opened to drain the basin. They are consistently found near a trench that is 2.2 m deep [ 45 ], which we believe is possibly the canal that guided outflowing water. In a nutshell, the eastern wall likely acted as a second check dam to the Abusir flows. a. West-east elevation profile of the Gisr el-Mudir structure. b: Schematic reconstitution of the profile with water flow. https://doi.org/10.1371/journal.pone.0306690.g007 In addition to the two dams formed by the western and eastern walls, the Gisr el-Mudir enclosure forms a basin ( Fig 4 ). It is closed to the north by another wall made of limestone blocks, though not very tall (likely <2m) because it is built on a natural ridge [ 45 ]. The basin’s southern boundary is also mostly made of a natural ridge. The possible absence of a masonry wall on certain portions on this side was unexplained by previous analyses [ 45 ]. However, it makes perfect sense when considering a reservoir function. Anchoring dams against side slopes is indeed the standard approach to guide flows and prevent outflanking [ 68 ]. In essence, the Gisr el-Mudir enclosure exhibits the defining features of a check dam ( Fig 7B ). The catchment it intercepts is large enough (15 km 2 ), plus eventual water derivation from the Wadi Taflah to produce flash floods transporting significant amounts of gravel, sand, mud, and debris due to its slope during intense rainfalls. The valley upstream of the western wall likely served as a first reservoir where the coarsest gravels tended to deposit. The overflowing water then filled the inner basin of the Gisr el-Mudir, where coarse sand would again deposit. Assuming a storage depth between 1 and 2 meters, the retention capacity of the basin would be approximately 220,000–440,000 m 3 . This volume is in line with the overall water volume of a flash flood that could be produced by the Abusir wadi, which is estimated to be about 75,000–225,000 m 3 , assuming 50 mm of rainfall and a 0.30 runoff coefficient. This key, first structure of the Saqqara hydraulic system would have then delivered clear water downstream in normal time, as well as muddy water with an eventually suspended load of fine sand and clay during rainfall events. 3.2 The deep Trench’s water treatment system3.2.1 general configuration.. The Djoser’s Complex is surrounded by a vast excavation area, commonly referred to as the ’Dry Moat’ since Swelim spotted its outlines [ 77 , 78 ] ( Fig 3 , blue strip). The Dry Moat is alleged to be a continuous trench cut in the bedrock, up to 50 m wide and ≈3 km long, enclosing an area of ≈600 m by ≈750 m around the Djoser complex [ 77 , 79 , 80 ]. When considering an average depth of 20 m for the four sides of the trench [ 61 ], the total excavated volume is estimated at ≈3.5 Mm 3 , approximately ten times the Step Pyramid‘s volume. Due to the thick cover of sand and debris [ 61 ] accumulated over the past millennia, its precise geometry is incompletely characterized. The moat’s east and south channels are particularly debated [ 61 ]. According to Swelim, the moat’s south channel probably split into two parts, known as the Inner and Outer south channels [ 78 ] ( Fig 8 , blue strips). The Inner south channel is relatively shallow (5–7 m deep), 25–30 m wide, and spans approximately 350 m parallel to the southern wall of Djoser’s complex. Water from the Abusir Lake can follow two parallel circuits. https://doi.org/10.1371/journal.pone.0306690.g008 The ‘Deep Trench’ [ 81 ] ( Fig 8 , red rectangles and dotted lines) is built inside the Inner south channel, along its south wall. It is a ≈27 m-deep, 3 m-wide, and hundreds of meter-long rock-cut channel with several ‘compartments’. So far, only about 240 m [ 78 ] of its probable 410 m length have been subject to archaeological excavations in 1937–1938 [ 78 ], 1937–1945 [ 81 ], and 1975 [ 82 ]. Consequently, approximately 170 m remains unexplored, mainly due to the presence of the later Old Kingdom two groups of mastabas built above the trench and at risk of collapse if submitted to underground excavation (transparent grey parts in Fig 8 ). Generally, two leading theories are highlighted in the literature to explain the purpose of the trench: (i) a quarry for the Djoser’s complex [ 47 , 83 ], or (ii) a spiritual function [ 78 , 84 , 85 ]. However, over recent years, authors have pointed out several specificities in the trench’s architectural layout, which seem irrelevant in a religious or mining context [ 1 , 86 , 87 ]. In particular, on the mining aspect, several authors estimate [ 45 , 86 ] that the form of the track suggests that the extraction of stones was not its sole or even primary function, as it does not match with the ancient Egyptian quarrying methods. Reader also considers that some parts of the trench which are ~27 m deep and covered with a rocky ceiling, are wholly unrealistic for quarrying operations and unlikely to have required the paving found near the trench’s bottom [ 45 ]. This point is further emphasized by the narrow width of the excavated Deep Trench (3m), which is impractical in a mining scenario. On the spiritual aspect, Kuraszkiewicz suggests that the trench may have developed a ritual significance as a gathering place for the souls of the nobles to serve the dead King [ 86 ]. Monnier [ 1 ] considers that the discovery of several niches in the channel does not fully demonstrate the moat’s religious purpose and considers it secondary. The trench’s ritual significance is also regarded as secondary by Reader [ 45 ], who suggests the ritual aspects developed only after the complex’s construction and do not reflect the original function of the structure. In 2020, based on the archaeological, geological, and climatic evidence, Wong was the first to introduce the idea that the trench may have had a completely different function, being filled with runoff water following downpours [ 37 ]. If so, this would explain why it was not until the reigns of Unas and Userkaf (V th Dynasty) that new graves occupied the moat. The onset of drier climatic conditions [ 31 , 88 ] around the end of the IV th Dynasty would have created more favorable conditions for new constructions inside the moat. Despite the potential impact of Wong’s assumption, it did not receive much attention in the literature. Nonetheless, the current authors believe that Wong’s conclusions make sense when considering Saqqara’s downstream localization of a watershed. 3.2.2 The deep Trench: A series of rock-cut compartments built in a hydrological corridor.The Inner south channel and the Deep Trench are built inside the Unas Valley, a hydrological corridor connecting the Abusir wadi plain to the Nile floodplain ( Fig 3 ). Both were thus possibly submitted to (un)controlled flooding [ 34 , 61 ] from the Abusir wadi plain. The Deep Trench connects at least three massive subterranean compartments [ 45 , 47 ] ( Fig 8 , red parts) meticulously carved out with precisely cut surfaces [ 78 ] ( Fig 9 ) and joined by a tunnel [ 77 ] . A fourth compartment, retroactively named compartment-0 ( Fig 10 ), likely exists [ 45 , 78 ]. On a large scale, the perfect geometric alignment of these compartments is remarkable, as well as their parallelism with the Djoser’s complex and their bottom level similar to those of the southern and northern shafts (≈27 m ASL). These spatial relationships have led some authors to consider that the trench was created as a part of Djoser’s Complex [ 86 , 89 , 90 ]. This assumption has been reinforced by Deslandes’ discoveries of at least two east-west pipes, about 80 m long, connecting the Djoser’s Complex’s subterranean layouts to the Dry Moat’s eastern side [ 91 ]. a: View from the west; b: View from the east. The workers in the background provide a sense of the structure’s immense scale and technicity. https://doi.org/10.1371/journal.pone.0306690.g009 View of the south face. https://doi.org/10.1371/journal.pone.0306690.g010 Taken together, the Deep Trench architecture highlights technical proficiency and suggests that the ancient Egyptians intended a technical function rather than a spiritual one. Surprisingly, despite the available clues, the Deep Trench has never undergone detailed engineering studies to analyze its features and identify its purpose. The following sections suggest a hydraulic rationale behind the trench’s internal layout (more details in the Supplement ). 3.2.3 Consistency of the Deep Trench architecture with a water treatment system.Being largely described in the literature [ 77 , 86 , 92 ] , the compartments’ layouts are presented in detail in the Supplement . Considering its architecture and geographical location, the Dry Moat’s southern section combines the technical requirements of a water treatment system, including sedimentation, retention, and purification. Fig 10 illustrates a comprehensive outline of the installation’s functioning process. Similarly to the Gisr el-Mudir, we found that the Deep Trench compartments likely served to transfer water with low suspended sediment concentration to the downstream compartments by overflowing. The process of using a series of connected tanks to filter water and remove sediment is an ancient technique that has been extensively documented in archaeological and scientific literature [ 93 – 96 ]. This method has been employed for centuries to clean water and has played a significant role in the development of water treatment practices. Compartment-0 presents the minimum requirements of a settling basin (considerable length and width, low entry slope, position at the entry of Unas hydrological corridor) whose purpose is to facilitate the coarse particles’ settling that would overflow from Gisr el-Mudir during heavy rainfalls. The descending ramp along the south wall identified by Swelim [ 97 ] may have permitted workers to dredge the basin and remove the accumulated sediments along the east wall ( Fig 10 ) . The very probable connection [ 45 , 97 ] between compartment-0 and compartment-1, blocked with rough masonry ( Fig 9B and S3 Fig in S2 File ), is consistent with an outlet overflowing structure. Additionally, when the flow rate in compartment-0 was too high, the tunnel or even the northern portion of the trench may have been used as a spillway bypass to evacuate excess water toward the eastern portion of the Unas wadi valley ( Fig 8 , safety circuit). Compartment-1 is then consistent with a retention basin with > 3000 m 3 capacity ( Fig 10 , left part). The bottom stone paving with mortar joints probably limited water seepage through the bedrock. Its eastern end could go until the compartment-2 [ 45 ] to form a single compartment, but this point remains debated [ 78 , 97 ] . Compartment-2’s is, unfortunately, largely unexplored ( Fig 10 ). Its downstream position might indicate a second retention basin or possibly an extension [ 45 ] of the first one. The western part of this compartment (stairs area) perfectly aligns with the base levels of the Djoser’s complex south and north shafts, which points towards a connection between the three [ 86 ] . If so, it would be aligned with the recently discovered pipe of a 200 m-long tunnel linking the bottom of Djoser’s Complex’s southern and northern shafts [ 91 ] (see next section, Fig 11 ). Compartment-2 would then be another, or an extended, retention basin equipped with a water outlet toward the north. https://doi.org/10.1371/journal.pone.0306690.g011 Compartment-3 ( Fig 10 , right part) is likely a side purification basin for drinking water. Its position as an appendix of the primary water circuit connecting Gisr el-Mudir to Djoser’s complex seems optimal to minimize water circulation and maximize water-settling time, thus increasing its purification. The second and third sections likely allowed further settling of particles and would have served as reservoirs during dry periods. The relatively smooth walls of the whole structure would have hindered the growth of microbes, plants, and other contaminants, thereby helping maintain the water’s cleanliness [ 98 ] . Four surface wells allowed access to the end of the last compartment where the water, kept clear and fresh in the shadow of this subterranean monumental cistern, could be used by the building site workforce [ 99 ] . The excavated volume of the Deep Trench is greater than 14,000 m 3 [ 77 , 86 , 92 ]. If we assume that most of the water available in the Wadi Taflah was diverted toward Saqqara, this volume could be filled about a dozen to more than one hundred times per year on average. We hypothesize a typical filling level of 45 m ASL in the Deep Trench, but an accurate topographical survey is lacking, and the maximum water level could vary between 40–52 m ASL, according to the surrounding terrain elevation. In essence, we discovered and highlighted for the first time that the Deep Trench’s position and design are consistent with possible use as a water treatment and storage system capable of cleaning and storing thousands of cubic meters of water. 4. The central hydraulic lift system4.1 overview of the djoser’s complex’ substructure. The internal and external architecture of the Djoser’s Complex is thoroughly documented [ 1 , 3 , 100 , 101 ]. The Supplement provides an overview of this structure. Basically, the six-step Step Pyramid itself stands slightly off-center in a rectangular enclosure toward the south and reaches a height of approximately 60 m ( Fig 11 ). The pyramid consists of more than 2.3 million limestone blocks, each weighing, on average [ 2 ], 300 kg, resulting in a total estimated weight of 0.69 million tons and a volume of ≈330,400 m 3 . The substructure features at least 13 shafts, including two significantly sizeable twin shafts located at the north and south of the complex ( Fig 11 , insets 3&4), and an extensive and well-organized network of galleries descending up to 45 m below ground level [ 102 ]. The north shaft is surrounded by four comb-shaped structures distributed on each side and angled 90° apart. Ground Penetrating Radar (GPR) revealed that the twin shaft layouts are connected [ 91 , 102 ] by a 200 m-long tunnel. Moreover, at least two of the twelve shafts on the pyramid’s east side are connected to the supposed eastern section of the Dry Moat by two 80 m long pipes ( Fig 11 and Supplement ). From our 3D models, we estimate that ancient architects extracted more than 30,000 tons of limestone from the bedrock to dig the whole underground structure. The total length of the tunnels and subterranean rooms combined is ~6.8 km. However, its layout and purpose remain primarily poorly known and debated [ 6 ]. 4.2 The connected twin shaftsThe ‘north shaft’ is located under the pyramid of Djoser and is almost aligned with its summit. This shaft is ≈28 m deep and has a square shape with 7 m sides. Its bottom part widens to ≈10 m on the last, deepest 6 m, forming a chamber ( Fig 12 and S6 Fig in S2 File ). On its upper part, the shaft extends above the ground level by at least four meters inside the Step Pyramid in the shape of a hemispherical vault that was recently reinforced ( Fig 11 , inset 5 ). This upper part inside the pyramid body remains unexplored. However, as noticed by Lauer, the shaft sides above ground level display comparable masonry to that of the southern shaft, indicating a possible upward extension [ 3 ]. On the pyramid’s north side, a steep trench with stairs provides access to the shaft. a.: Granite box of Djoser’s complex north shaft serving as an opening-closing system for the water flow coming from side tunnels -source: [ 113 ]. b.: Limestone piles supporting the box - source: [ 3 ]. c: Diagram of the North Shaft plug system. Redrawn from Lauer sketches [ 108 ]. https://doi.org/10.1371/journal.pone.0306690.g012 The ‘south shaft’ is located ~200 m south of the north shaft, close to the Deep Trench ( Fig 11 , inset 1 ). Its dimensions and internal layout are broadly similar to the north shaft’s. The substructure of the south shaft is entered through a west-facing tunnel-like corridor with a staircase that descends about 30 m before opening up inside the shaft. The staircase then continues east and leads to a network of galleries whose layout imitates the blue chambers below the Step Pyramid. As mentioned earlier, a 200 m-long tunnel connects the lower part of the north and south shafts ( Fig 11 , orange pipe). A series of deep niches located on the south face of the south shaft [ 97 ], the shape of which resembles that of the Deep Trench’s compartments 1 and 2, might indicate a former connection between both. This point remains to be confirmed by additional investigation. The south shaft is connected to a rectangular shaft to the west via a tunnel-like corridor with a staircase that descends approximately 30 meters before opening up into the south shaft ( Fig 11 , inset 2 ). At the corridor level, a chamber has been cut into the bedrock parallel to the descending passage [ 3 ], towards the south. This chamber features several incompletely excavated niches on its south wall, which could extend under the south wall of the Djoser complex ( Fig 8 ). Pending further excavations, they might indicate a connection with the Deep Trench. 4.3 The twin shafts’ internal layout: two plug-systems topped with maneuvering chambersThe initial purpose of the twin shafts’ granite boxes has been largely debated [ 15 , 100 ]. The presence of two shafts with two similar granite boxes and almost identical substructures was previously explained as a separation of the body and spirit of Djoser [ 100 ]. However, the Pharaoh’s body is actually missing and was not found during modern excavations. Several authors and explorers excluded the possibility of King Djoser’s burial in the north shaft [ 15 , 103 ]. Vyse claimed [ 15 ] that the box’s internal volume was too narrow for moving a coffin without breaking the body. Firth and Quibell considered [ 103 ] the fragments found by Gunn and Lauer [ 104 ] to be of mummies of ‘late date’, possibly belonging to the Middle or New Kingdom. Finally, a thorough radiocarbon dating [ 105 ] on almost all retrieved remains [ 104 , 106 , 107 ] located near the granite box excluded the possibility that ‘ even a single one of them ’[ 105 ] could have belonged to King Djoser. Therefore, although the northern shaft had clear funerary significance much later, its original purpose during the time of Djoser may have been different. Unfortunately, the main part of the materials that filled the twin shafts was removed during past archaeological excavations, mainly in the 1930s [ 108 ], leaving only the two granite boxes at their bottom ( Fig 11 , insets 3 and 4 ). Therefore, the shafts’ internal layout description is mainly based on the explorers’ archaeological reports and testimonies[ 109 – 111 ]. The two granite boxes are broadly similar in shape and dimensions. Both are made of four layers of granite blocks and present top orifices closed by plugs that weigh several tons ( Fig 12A ). The southern box is slightly smaller, with a plug made of several pieces, making it less versatile. The north box does not lay directly on the underlying bedrock but is perched on several piles of limestone blocks supporting the lower granite beams ( Fig 12B ), tentatively attributed to robbers by Lauer [ 3 ]. The space around the box is connected with four tunnels arranged perpendicularly on each side of the shaft (see Supplement ). This space was filled with several successive layers [ 108 ] ( Fig 12C , grey parts). The lowermost layer consisted of coarse fragments of limestone waste and alabaster, making it permeable. Meanwhile, the upper layer, going up to the box ceiling’s level, was made of limestone jointed with clay mortar [ 108 ], i . e ., less permeable [ 112 ]. This ceiling was itself covered by a 1.50 m thick layer of alabaster and limestone fragments plus overlying filling ( Fig 12C , blue part), except around the plug hole, which was encircled by a diorite lining, a particularly solid rock ( Fig 12C , green part). Directly above the granite boxes were ‘maneuvering chambers [ 108 ]’ that enabled the plug to be lifted. The plug closing the north shaft’s box has four vertical side grooves, 15 cm in diameter, intended for lifting ropes ( Fig 12C ) and a horizontal one, possibly for sealing. Below the chamber ceiling and just above the orifice, an unsheathed wooden beam was anchored in the east and west walls ( Fig 12C ). This beam likely supported ropes to lift the plug, similar to those found in the south shaft with friction traces [ 108 ]. Interestingly, the granite stones forming the granite box ceiling were bounded by mortar ( Fig 12A ), creating an impermeable barrier with the shaft’s lower part and leaving the plug’s hole as the only possible connection between the shaft and the inside of the box. Conversely, most joints between the box’s side and bottom stones, connected with the permeable bottom layer, were free from mortar. These details, thoroughly documented during Lauer’s excavation [ 3 , 108 ] and visible on pictures ( Fig 12A and 12B ), clearly point to technical rather than symbolic application. Taken together, the granite box’s architecture and its removable plug surrounded by limestone clay-bound blocks present the technical signature of a water outlet mechanism. When opened, such a plug system would have allowed the north shaft to be filled with water from the Deep Trench or, in another scenario, from the Dry Moat’s eastern section. The permeable surrounding filling would have permitted water discharge control from the four side tunnels. Then, the water could only seep through the granite box’s lower joints. This design would have prevented water from rushing through the system at high speed and with pressure shocks. Considering water coming from the Deep Trench (elevation delta: 10–20 m), the retaining walls and the many layers’ cumulated weight stacked over the granite box acted as a lateral blockage and would have prevented the box ceiling from being lifted due to the underlying water pressure. 4.4 Consistency of the internal architecture of the Djoser’s complex with a hydraulic lift mechanismAfter gathering all the elements of this study, we deduce that the northern shaft’s layout is consistent with a hydraulic lift mechanism to transport materials and build the pyramid. Elements at our disposal indicate that the south and north shafts could be filled with water from the Dry Moat. A massive float inside the north shaft could then raise stones, allowing the pyramid’s construction from its center in a ‘volcano’ fashion ( Fig 13 ). https://doi.org/10.1371/journal.pone.0306690.g013 Although a connection between the Compartment -2 and the Djoser shafts has yet to be identified, it is highly probable that sediment-free water from the Deep Trench was used in this system ( Fig 13 , disk ‘ 1 ’). This water quality would have reduced the risk of fouling and malfunction because it minimizes the presence of sand and clay that feed into the north shaft. This would prevent the deposition and progressive filling in the tunnels and connections, as well as the clogging of the joints between the bottom and side granite blocks of the box. The 200 m-long underground pipe [ 91 ] that connects the north and south shafts is then consistent with the transfer of water from the Deep Trench’s water treatment system to the north shaft, possibly via the south shaft. Furthermore, there is a proven connection between the tunnels surrounding the north shaft and the Dry Moat through the Deslandes’ pipes [ 91 ] on the eastern side of the complex ( Figs 11 and 13 ). Pending further investigation, we hypothesize that the water inlet was located to the south ( Fig 13 , disk ‘ 1 ’), with the outlet(s) sending water toward the east through two juxtaposed pipes (disk ‘ 2 ’). Several horizontal galleries connected to these two pipes were acacia-cased [ 3 ], a technique commonly used to safeguard the walls in hydraulic works in ancient Egypt. A large stone portcullis [ 108 ] found in one of these galleries may have served as a versatile gate closed during the water filling of the north shaft. In another scenario, the Deslandes’ juxtaposed pipes ( Fig 13 , disk ‘ 2 ’) could be considered as a water inlet for unfiltered water. Finally, we hypothesize that a hydraulic lift, a massive float that was possibly made of wood and weighed several tons (see Supplement ), should run slowly inside the shaft to prevent instabilities and friction with the sides. The stones could have been elevated by filling and emptying cycles, allowing the lift to move up and down with stones ( Fig 13 ). These stones could have passed along the northern entrance until the central shaft. Recent discoveries have shown that this gallery was kept open until the very end of the pyramid’s construction, after which it was closed [ 1 , 91 ]. In our scenario, the stones could have been transported directly at ground level, corresponding to the pyramid’s first course, or slightly higher through a ramp penetrating in a (currently sealed) corridor some meters above the ground level. This configuration would have had the particular advantage of minimizing the elevation gain for which the hydraulic lift would be required. The stones could have been transported via the so-called ‘Saite gallery [ 114 ]’ in a final scenario. Although Firth [ 114 ] considers this gallery to postdate the III rd Dynasty, it remains possible that it was recut on the basis of an earlier gallery. 4.5 Modelling the hydraulic lift mechanismWe developed a simple numerical model of the hydraulic lift to study its water consumption and loading capacity (see Supplement ). The model was kept as simple as possible to be easily checked and only intended to give relevant orders of magnitudes. The hydraulic lift is modelled as a float loaded with stones to build the pyramid and with a vertical extension to raise this material at the necessary level. Based on the initial altitude of the lift, Z m , which cannot be below 17m from ground level (the bottom of the shaft was filled with the box and overlying rocks, see Fig 12C ), and assuming a loading of the material on the lift at the ground level, the maximum height that can be reached in one cycle is <17m. To achieve greater heights, we hypothesize that the lift platform was blocked during the float descent, e . g ., using beams (see Fig 14 ). This modification would have allowed the platform to reach higher altitudes by adding or unfolding an extension. For the top of the pyramid, the float could be conversely used as a counterweight when descending, pulling on ropes that would haul the platform after passing over pulleys above the shaft head. A dual-use method involving hauling during shaft draining and elevating during water filling would have been the optimal management approach. The lift platform (red line), and extension support (orange line) during the unfolding of the lower element are represented. The associated holes are to be localized in further excavation of the upper part of the shaft. https://doi.org/10.1371/journal.pone.0306690.g014 The beginning of the pyramid building was most probably performed using ramps prolonging the path from the local quarry, possibly the Dry Moat [ 44 ]. To provide an upper bound of water consumption, we modelled the pyramid building using the hydraulic lift from the first layer at ground level. Our model suggests that this upper bound value is 18 Mm 3 of water required to build the whole pyramid using the float to lift stones only when the shaft is filled (see Supplement ). A few million were required to build the first 20 m and could be saved if ramps were used instead. The total amount of water needed would have been reduced by about one-third if the float had been used as a counterweight, pulling on ropes to haul stones on a platform suspended in the top part of the shaft rather than being located on a wooden frame extension attached to the float. Finally, if both lifting (when filling the shaft) and hauling (when draining the shaft) were used, the water consumption would decrease by two-thirds. If the loading was not performed at ground level but rather through a ramp and gallery above ground level, about one-quarter of the water would be saved if, for instance, using a 5 m-high ramp and 43% for a 10 m-high ramp. Further investigation above the vault and on the pyramid sides could help to identify such an eventual gallery. If, conversely, the loading was performed about 13 m below ground level in the top part of the northern gallery ( S6 Fig in S2 File ), the water consumption would typically increase by two-thirds. On the other hand, through our research and calculations, we have determined that the Wadi Taflah catchment had the capacity to supply 4–54 Mm 3 over 20–30 years of construction, therefore not enough when assuming only pessimistic values (lower bound for rainfall and runoff coefficient, fast construction and sub-optimal use of the lift just using it when water rose), but sufficient when assuming intermediate values, and eight-times enough water to meet this demand when assuming optimistic values (upper bounds of parameters and dual lifting-hauling functioning). If further research demonstrates that the higher clay and silt content possibly present at that time shortly after the Green Sahara period probably led to increased runoff coefficients by a factor of 2–3 or even more, the resource would be increased by the same factor. The climatological conditions on the Saqqara plateau during the III rd Dynasty are still not well understood [ 37 ]. As a first assumption, we estimate that the water supply may have been continuous even without an upper Abusir lake’s permanent existence, thanks to the flow from the wadi Abusir and, more significantly, through a probable derivation system from the nearby Wadi Taflah, assuming this large catchment had a more perennial runoff regime. Pedological investigations would be worthwhile in the plateau area and in the talweg of both wadis to look for evidence of more frequent water flow. As a result, the hydraulic mechanism may have only been usable when sufficient water supply was available, so it may have only been used periodically. Other techniques, such as ramps and levees, were likely used to bring the stones from the quarries and adjust their positions around the lifting mechanism or when it was not in operation. 5. DiscussionA unified hydraulic system. Based on a transdisciplinary analysis, this study provides for the first time an explanation of the function and building process of several colossal structures found at the Saqqara site. It is unique in that it aligns with the research results previously published in the scientific literature in several research areas: hydrology, geology, geotechnics, geophysics, and archaeology. In summary, the results show that the Gisr el-Mudir enclosure has the feature of a check dam intended to trap sediment and water, while the Deep Trench combines the technical requirements of a water treatment facility to remove sediments and turbidity. Together, these two structures form a unified hydraulic system that enhances water purity and regulates flow for practical uses and vital needs. Among the possible uses, our analysis shows that this sediment-free water could be used to build the pyramid by a hydraulic elevator system. By its scale and level of engineering, this work is so significant that it seems beyond just building the Step Pyramid. The architects’ geographical choices reflect their foresight in meeting various civil needs, making the Saqqara site suitable for settling down and engaging in sedentary activities, such as agriculture, with access to water resources and shelter from extreme weather conditions. This included ensuring adequate water quality and quantity for both consumption and irrigation purposes and for transportation, navigation, or construction. Additionally, after its construction, the moat may have represented a major defensive asset, particularly if filled with water, ensuring the security of the Saqqara complex [ 115 ]. The hydraulic lift mechanism seems to be revolutionary for building stone structures and finds no parallel in our civilization. This technology showcases excellent energy management and efficient logistics, which may have provided significant construction opportunities while reducing the need for human labor. Furthermore, it raises the question of whether the other Old Kingdom pyramids, besides the Step Pyramid, were constructed using similar, potentially upgraded processes, a point deserving further investigation. Overall, the hydraulic lift could have been a complementary construction technique to those in the literature for the Old Kingdom [ 8 , 10 ]. Indeed, it is unlikely that a single, exclusive building technique was used by the ancient architects but that a variety of methods were employed in order to adapt to the various constraints or unforeseen circumstances of a civil engineering site, such as a dry spell. Therefore, the beginning of the pyramid building was most probably performed using ramps prolonging the path from the local quarry. According to petrographic studies [ 47 ], the main limestone quarry of the Saqqara site could correspond to the Dry Moat that encircles the Djoser Complex, providing access on the four sides of the pyramid for the extracted blocks and reducing the average length of the ramps. An advanced technical and technological levelBy their technical level and sheer scale, the Saqqara engineering projects are truly impressive. When considering the technical implications of constructing a dam, water treatment facility, and lift, it is clear that such work results from a long-standing technical tradition. Beyond the technical aspects, it reflects modernity through the interactions between various professions and expertise. Even though basic knowledge in the hydraulics field existed during the early Dynastic period, this work seems to exceed the technical accomplishments mentioned in the literature of that time, like the Foggaras or smaller dams. Moreover, the designs of these technologies, such as the Gisr el-Mudir check-dam, indicate that well-considered choices were made in anticipation of their construction. They suggest that the ancient architects had some empirical and theoretical understanding of the phenomena occurring within these structures. …questioning the historical lineThe level of technological advancement displayed in Saqqara also raises questions about its place in history. When these structures were built remains the priority question to answer . Were all the observed technologies developed during the time of Djoser, or were they present even earlier? Without absolute dating of these works, it is essential to approach their attribution and construction period with caution. Because of the significant range of techniques used to build the Gisr el-Mudir, Reader estimates [ 70 ] that the enclosure may have been a long-term project developed and maintained over several subsequent reigns, a point also supported by the current authors. The water treatment facility follows a similar pattern, with the neatly cut stones being covered and filled with rougher later masonry. Finally, the Djoser Step Pyramid also presents a superposition of perfectly cut stones, sometimes arranged without joints with great precision and covered by other rougher and angular stones [ 3 ]. Some of these elements led some authors [ 6 , 100 ] to claim that Djoser’s pyramid had reused a pre-existing structure. Some remaining questionsThe Deep Trench was intentionally sealed off at some point in history, as evidenced by the pipe blockage between Compartment-0 and Compartment-1. The reasons are unknown and speculative, ranging from a desire to construct buildings (such as the Khenut, Nebet, or Kairer mastabas) above the trench to a technical malfunction or shutdown due to a water shortage. This sealing might also have been done for other cultural or religious purposes. The current topography of the land around the Djoser complex, although uncertain given the natural or anthropogenic changes that have occurred over the last five millennia, does not support the existence of a trench to the east side. Therefore, our observations join those of Welc et al. [ 61 ] and some of the first explorers [ 63 ], reasonably attributing only three sections to the Dry Moat. 6 Materials and methods
7. Concluding remarks and perspectivesThis article discloses several discoveries related to the construction of the Djoser complex, never reported before:
Graphical conclusionNorth Saqqara map showing the relation between the Abusir water course and the Step Pyramid construction process (Inset). The arrows figuring the flow directions are approximate and given for illustrative purposes based on the Franco-Egyptian SFS/IGN survey [ 52 ]. Satellite image: Airbus Pléiades, 2021-07-02, reprinted from Airbus D&S SAS library under a CC BY license, with permission from Michael Chemouny, original copyright 2021. https://doi.org/10.1371/journal.pone.0306690.g015 Supporting informationhttps://doi.org/10.1371/journal.pone.0306690.s001 https://doi.org/10.1371/journal.pone.0306690.s002 https://doi.org/10.1371/journal.pone.0306690.s003 How to cite ChatGPT![]() Use discount code STYLEBLOG15 for 15% off APA Style print products with free shipping in the United States. We, the APA Style team, are not robots. We can all pass a CAPTCHA test , and we know our roles in a Turing test . And, like so many nonrobot human beings this year, we’ve spent a fair amount of time reading, learning, and thinking about issues related to large language models, artificial intelligence (AI), AI-generated text, and specifically ChatGPT . We’ve also been gathering opinions and feedback about the use and citation of ChatGPT. Thank you to everyone who has contributed and shared ideas, opinions, research, and feedback. In this post, I discuss situations where students and researchers use ChatGPT to create text and to facilitate their research, not to write the full text of their paper or manuscript. We know instructors have differing opinions about how or even whether students should use ChatGPT, and we’ll be continuing to collect feedback about instructor and student questions. As always, defer to instructor guidelines when writing student papers. For more about guidelines and policies about student and author use of ChatGPT, see the last section of this post. Quoting or reproducing the text created by ChatGPT in your paperIf you’ve used ChatGPT or other AI tools in your research, describe how you used the tool in your Method section or in a comparable section of your paper. For literature reviews or other types of essays or response or reaction papers, you might describe how you used the tool in your introduction. In your text, provide the prompt you used and then any portion of the relevant text that was generated in response. Unfortunately, the results of a ChatGPT “chat” are not retrievable by other readers, and although nonretrievable data or quotations in APA Style papers are usually cited as personal communications , with ChatGPT-generated text there is no person communicating. Quoting ChatGPT’s text from a chat session is therefore more like sharing an algorithm’s output; thus, credit the author of the algorithm with a reference list entry and the corresponding in-text citation. When prompted with “Is the left brain right brain divide real or a metaphor?” the ChatGPT-generated text indicated that although the two brain hemispheres are somewhat specialized, “the notation that people can be characterized as ‘left-brained’ or ‘right-brained’ is considered to be an oversimplification and a popular myth” (OpenAI, 2023). OpenAI. (2023). ChatGPT (Mar 14 version) [Large language model]. https://chat.openai.com/chat You may also put the full text of long responses from ChatGPT in an appendix of your paper or in online supplemental materials, so readers have access to the exact text that was generated. It is particularly important to document the exact text created because ChatGPT will generate a unique response in each chat session, even if given the same prompt. If you create appendices or supplemental materials, remember that each should be called out at least once in the body of your APA Style paper. When given a follow-up prompt of “What is a more accurate representation?” the ChatGPT-generated text indicated that “different brain regions work together to support various cognitive processes” and “the functional specialization of different regions can change in response to experience and environmental factors” (OpenAI, 2023; see Appendix A for the full transcript). Creating a reference to ChatGPT or other AI models and softwareThe in-text citations and references above are adapted from the reference template for software in Section 10.10 of the Publication Manual (American Psychological Association, 2020, Chapter 10). Although here we focus on ChatGPT, because these guidelines are based on the software template, they can be adapted to note the use of other large language models (e.g., Bard), algorithms, and similar software. The reference and in-text citations for ChatGPT are formatted as follows:
Let’s break that reference down and look at the four elements (author, date, title, and source): Author: The author of the model is OpenAI. Date: The date is the year of the version you used. Following the template in Section 10.10, you need to include only the year, not the exact date. The version number provides the specific date information a reader might need. Title: The name of the model is “ChatGPT,” so that serves as the title and is italicized in your reference, as shown in the template. Although OpenAI labels unique iterations (i.e., ChatGPT-3, ChatGPT-4), they are using “ChatGPT” as the general name of the model, with updates identified with version numbers. The version number is included after the title in parentheses. The format for the version number in ChatGPT references includes the date because that is how OpenAI is labeling the versions. Different large language models or software might use different version numbering; use the version number in the format the author or publisher provides, which may be a numbering system (e.g., Version 2.0) or other methods. Bracketed text is used in references for additional descriptions when they are needed to help a reader understand what’s being cited. References for a number of common sources, such as journal articles and books, do not include bracketed descriptions, but things outside of the typical peer-reviewed system often do. In the case of a reference for ChatGPT, provide the descriptor “Large language model” in square brackets. OpenAI describes ChatGPT-4 as a “large multimodal model,” so that description may be provided instead if you are using ChatGPT-4. Later versions and software or models from other companies may need different descriptions, based on how the publishers describe the model. The goal of the bracketed text is to briefly describe the kind of model to your reader. Source: When the publisher name and the author name are the same, do not repeat the publisher name in the source element of the reference, and move directly to the URL. This is the case for ChatGPT. The URL for ChatGPT is https://chat.openai.com/chat . For other models or products for which you may create a reference, use the URL that links as directly as possible to the source (i.e., the page where you can access the model, not the publisher’s homepage). Other questions about citing ChatGPTYou may have noticed the confidence with which ChatGPT described the ideas of brain lateralization and how the brain operates, without citing any sources. I asked for a list of sources to support those claims and ChatGPT provided five references—four of which I was able to find online. The fifth does not seem to be a real article; the digital object identifier given for that reference belongs to a different article, and I was not able to find any article with the authors, date, title, and source details that ChatGPT provided. Authors using ChatGPT or similar AI tools for research should consider making this scrutiny of the primary sources a standard process. If the sources are real, accurate, and relevant, it may be better to read those original sources to learn from that research and paraphrase or quote from those articles, as applicable, than to use the model’s interpretation of them. We’ve also received a number of other questions about ChatGPT. Should students be allowed to use it? What guidelines should instructors create for students using AI? Does using AI-generated text constitute plagiarism? Should authors who use ChatGPT credit ChatGPT or OpenAI in their byline? What are the copyright implications ? On these questions, researchers, editors, instructors, and others are actively debating and creating parameters and guidelines. Many of you have sent us feedback, and we encourage you to continue to do so in the comments below. We will also study the policies and procedures being established by instructors, publishers, and academic institutions, with a goal of creating guidelines that reflect the many real-world applications of AI-generated text. For questions about manuscript byline credit, plagiarism, and related ChatGPT and AI topics, the APA Style team is seeking the recommendations of APA Journals editors. APA Style guidelines based on those recommendations will be posted on this blog and on the APA Style site later this year. Update: APA Journals has published policies on the use of generative AI in scholarly materials . We, the APA Style team humans, appreciate your patience as we navigate these unique challenges and new ways of thinking about how authors, researchers, and students learn, write, and work with new technologies. American Psychological Association. (2020). Publication manual of the American Psychological Association (7th ed.). https://doi.org/10.1037/0000165-000 Related and recentComments are disabled due to your privacy settings. To re-enable, please adjust your cookie preferences. APA Style MonthlySubscribe to the APA Style Monthly newsletter to get tips, updates, and resources delivered directly to your inbox. Welcome! Thank you for subscribing. APA Style GuidelinesBrowse APA Style writing guidelines by category
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Van Way, C.W. (2007) Writing a Scientific Paper. Nutrition in Clinical Practice. 22: 663-40. PubMed ID: 1804295. Usually includes 4 sections: (corresponds with each of the paper sections) Methods: Briefly explain the type of study, sample/population size and description, the design, and any particular techniques for data collection and analysis.
Different sections are needed in different types of scientific papers (lab reports, literature reviews, systematic reviews, methods papers, research papers, etc.). Projects that overlap with the social sciences or humanities may have different requirements. Generally, however, you'll need to include:
The introduction section of a paper provides the background information necessary to understand why the described experiment was conducted. The introduction should describe previous research on the topic that has led to the unanswered questions being addressed by the experiment and should cite important previous papers that form the background for the experiment.
A scientific paper is the formal lasting record of a research process. It is meant to document research protocols, methods, results and conclusions derived from an initial working hypothesis. ... The following section will briefly review the structure of the different sections of a manuscript and describe their purpose. ... For clinical ...
Not all academic papers include a roadmap, but many do. Usually following the thesis, a roadmap is a narrative table of contents that summarizes the flow of the rest of the paper. Below, see an example roadmap in which Cuevas (2019) succinctly outlines her argument. You may also see roadmaps that list
The guide addresses four major aspects of writing journal-style scientific papers: (1) Fundamental style considerations; (2) a suggested strategy for efficiently writing up research results; (3) the nuts and bolts of format and content of each section of a paper (part of learning to
Abstract: "Structured abstract" has become the standard for research papers (introduction, objective, methods, results and conclusions), while reviews, case reports and other articles have non-structured abstracts. The abstract should be a summary/synopsis of the paper. III. Introduction: The "why did you do the study"; setting the ...
Delivered to your inbox every two weeks, the Writing Toolbox features practical advice and tools you can use to prepare a research manuscript for submission success and build your scientific writing skillset. Discover how to navigate the peer review and publishing process, beyond writing your article.
Introduction. The introduction of a scientific paper discusses the problem being studied and other theory that is relevant to understanding the findings. The hypothesis of the experiment and the motivation for the research are stated in this section. Write the introduction in your own words. Try not to copy from a lab manual or other guidelines.
Scientific papers are often structured chronologically, thus reflecting the progression of the research project. ... The Results and Discussion sections present and discuss the research results ...
Scientific papers based on experimentation typically include five predominant sections: Abstract, Introduction, Methods, Results, and Discussion.This structure is a widely accepted approach to writing a research paper, and has specific sections that parallel the scientific method.
We describe here the basic steps to follow in writing a scientific article. We outline the main sections that an average article should contain; the elements that should appear in these sections, and some pointers for making the overall result attractive and acceptable for publication. Previousarticlein issue. Nextarticlein issue.
However careful writing of this section is important because for your results to be of scientific merit they must be reproducible. Otherwise your paper does not represent good science. Goals: Describe equipment used and provide illustrations where relevant. "Methods Checklist" from: How to Write a Good Scientific Paper. Chris A. Mack. SPIE. 2018.
Formal Research Structure. These are the primary purposes for formal research: enter the discourse, or conversation, of other writers and scholars in your field. learn how others in your field use primary and secondary resources. find and understand raw data and information. For the formal academic research assignment, consider an ...
Conducting scientific and clinical research is only the beginning of the scholarship of discovery. ... The task of writing a scientific paper and submitting it to a journal for publication is a time‐consuming and often daunting task. 3,4 Barriers to effective ... How to write the methods section of a research paper. Respir Care. 2004; 49:1229 ...
Bem, Daryl J. Writing the Empirical Journal Article. Psychology Writing Center. University of Washington; Denscombe, Martyn. The Good Research Guide: For Small-Scale Social Research Projects. 5th edition.Buckingham, UK: Open University Press, 2014; Lunenburg, Frederick C. Writing a Successful Thesis or Dissertation: Tips and Strategies for Students in the Social and Behavioral Sciences.
The results section contains the data collected during experimention. The results section is the heart of a scientific paper. In this section, much of the important information may be in the form of tables or graphs. When reading this section, do not readily accept an author's statements about the results. Rather, carefully analyze the raw data ...
Methods section is a crucial part of a manuscript and emphasizes the reliability and validity of a research study. And knowing how to write the methods section of a research paper is the first step in mastering scientific writing. Read this article to understand the importance, purpose, and the best way to write the methods section of a research paper.
A final summary of the paper, including whether or not you were able to answer your original research question. References and Appendices: The reference page(s) is a list of all the sources you used to research and create your project/experiment, including everything cited in the literature review and methods sections.
We describe here the basic steps to follow in writing a scientific article. We outline the main sections that an average article should contain; the elements that should appear in these sections, and some pointers for making the overall result attractive and acceptable for publication.
What to include: Usually includes 4 sections: (corresponds with each of the paper sections) Background/Objectives: include the hypothesis; Methods: Briefly explain the type of study, sample/population size and description, the design, and any particular techniques for data collection and analysis
The discussion section is often considered the most important part of your research paper because it: Most effectively demonstrates your ability as a researcher to think critically about an issue, to develop creative solutions to problems based upon a logical synthesis of the findings, and to formulate a deeper, more profound understanding of the research problem under investigation;
The Results section of a scientific research paper represents the core findings of a study derived from the methods applied to gather and analyze information. It presents these findings in a logical sequence without bias or interpretation from the author, setting up the reader for later interpretation and evaluation in the Discussion section. ...
Indigenous science may be fundamentally different from non-Indigenous ('Western') science, based on relational accountability (Wilson, 2008), with research interconnected to the community and driven by relationships with the community (Reid et al., 2024). We hope this special issue will provide a pathway to educate non-Indigenous scientists ...
The paper is divided into three main sections that analyze the current scientific literature to address the following inquiries: (i) Was the plateau of Saqqara supplied with water? ... It is unique in that it aligns with the research results previously published in the scientific literature in several research areas: hydrology, geology ...
Research Paper. Numerical analysis of NO x reduction in large-scale MSW grate furnace through in-bed combustion optimization using multi-section fuel bed model with thermally thick treatment. Author links open overlay panel Ruizhi Zhang 1, ... The authors acknowledge the financial support from the National Natural Science Foundation of China ...
If you've used ChatGPT or other AI tools in your research, describe how you used the tool in your Method section or in a comparable section of your paper. For literature reviews or other types of essays or response or reaction papers, you might describe how you used the tool in your introduction.