This document originally came from the Journal of Mammalogy courtesy of Dr. Ronald Barry, a former editor of the journal.

How to Write and Publish a Research Paper for a Peer-Reviewed Journal

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  • Published: 30 April 2020
  • Volume 36 , pages 909–913, ( 2021 )

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  • Clara Busse   ORCID: orcid.org/0000-0002-0178-1000 1 &
  • Ella August   ORCID: orcid.org/0000-0001-5151-1036 1 , 2  

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Communicating research findings is an essential step in the research process. Often, peer-reviewed journals are the forum for such communication, yet many researchers are never taught how to write a publishable scientific paper. In this article, we explain the basic structure of a scientific paper and describe the information that should be included in each section. We also identify common pitfalls for each section and recommend strategies to avoid them. Further, we give advice about target journal selection and authorship. In the online resource 1 , we provide an example of a high-quality scientific paper, with annotations identifying the elements we describe in this article.

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Introduction

Writing a scientific paper is an important component of the research process, yet researchers often receive little formal training in scientific writing. This is especially true in low-resource settings. In this article, we explain why choosing a target journal is important, give advice about authorship, provide a basic structure for writing each section of a scientific paper, and describe common pitfalls and recommendations for each section. In the online resource 1 , we also include an annotated journal article that identifies the key elements and writing approaches that we detail here. Before you begin your research, make sure you have ethical clearance from all relevant ethical review boards.

Select a Target Journal Early in the Writing Process

We recommend that you select a “target journal” early in the writing process; a “target journal” is the journal to which you plan to submit your paper. Each journal has a set of core readers and you should tailor your writing to this readership. For example, if you plan to submit a manuscript about vaping during pregnancy to a pregnancy-focused journal, you will need to explain what vaping is because readers of this journal may not have a background in this topic. However, if you were to submit that same article to a tobacco journal, you would not need to provide as much background information about vaping.

Information about a journal’s core readership can be found on its website, usually in a section called “About this journal” or something similar. For example, the Journal of Cancer Education presents such information on the “Aims and Scope” page of its website, which can be found here: https://www.springer.com/journal/13187/aims-and-scope .

Peer reviewer guidelines from your target journal are an additional resource that can help you tailor your writing to the journal and provide additional advice about crafting an effective article [ 1 ]. These are not always available, but it is worth a quick web search to find out.

Identify Author Roles Early in the Process

Early in the writing process, identify authors, determine the order of authors, and discuss the responsibilities of each author. Standard author responsibilities have been identified by The International Committee of Medical Journal Editors (ICMJE) [ 2 ]. To set clear expectations about each team member’s responsibilities and prevent errors in communication, we also suggest outlining more detailed roles, such as who will draft each section of the manuscript, write the abstract, submit the paper electronically, serve as corresponding author, and write the cover letter. It is best to formalize this agreement in writing after discussing it, circulating the document to the author team for approval. We suggest creating a title page on which all authors are listed in the agreed-upon order. It may be necessary to adjust authorship roles and order during the development of the paper. If a new author order is agreed upon, be sure to update the title page in the manuscript draft.

In the case where multiple papers will result from a single study, authors should discuss who will author each paper. Additionally, authors should agree on a deadline for each paper and the lead author should take responsibility for producing an initial draft by this deadline.

Structure of the Introduction Section

The introduction section should be approximately three to five paragraphs in length. Look at examples from your target journal to decide the appropriate length. This section should include the elements shown in Fig.  1 . Begin with a general context, narrowing to the specific focus of the paper. Include five main elements: why your research is important, what is already known about the topic, the “gap” or what is not yet known about the topic, why it is important to learn the new information that your research adds, and the specific research aim(s) that your paper addresses. Your research aim should address the gap you identified. Be sure to add enough background information to enable readers to understand your study. Table 1 provides common introduction section pitfalls and recommendations for addressing them.

figure 1

The main elements of the introduction section of an original research article. Often, the elements overlap

Methods Section

The purpose of the methods section is twofold: to explain how the study was done in enough detail to enable its replication and to provide enough contextual detail to enable readers to understand and interpret the results. In general, the essential elements of a methods section are the following: a description of the setting and participants, the study design and timing, the recruitment and sampling, the data collection process, the dataset, the dependent and independent variables, the covariates, the analytic approach for each research objective, and the ethical approval. The hallmark of an exemplary methods section is the justification of why each method was used. Table 2 provides common methods section pitfalls and recommendations for addressing them.

Results Section

The focus of the results section should be associations, or lack thereof, rather than statistical tests. Two considerations should guide your writing here. First, the results should present answers to each part of the research aim. Second, return to the methods section to ensure that the analysis and variables for each result have been explained.

Begin the results section by describing the number of participants in the final sample and details such as the number who were approached to participate, the proportion who were eligible and who enrolled, and the number of participants who dropped out. The next part of the results should describe the participant characteristics. After that, you may organize your results by the aim or by putting the most exciting results first. Do not forget to report your non-significant associations. These are still findings.

Tables and figures capture the reader’s attention and efficiently communicate your main findings [ 3 ]. Each table and figure should have a clear message and should complement, rather than repeat, the text. Tables and figures should communicate all salient details necessary for a reader to understand the findings without consulting the text. Include information on comparisons and tests, as well as information about the sample and timing of the study in the title, legend, or in a footnote. Note that figures are often more visually interesting than tables, so if it is feasible to make a figure, make a figure. To avoid confusing the reader, either avoid abbreviations in tables and figures, or define them in a footnote. Note that there should not be citations in the results section and you should not interpret results here. Table 3 provides common results section pitfalls and recommendations for addressing them.

Discussion Section

Opposite the introduction section, the discussion should take the form of a right-side-up triangle beginning with interpretation of your results and moving to general implications (Fig.  2 ). This section typically begins with a restatement of the main findings, which can usually be accomplished with a few carefully-crafted sentences.

figure 2

Major elements of the discussion section of an original research article. Often, the elements overlap

Next, interpret the meaning or explain the significance of your results, lifting the reader’s gaze from the study’s specific findings to more general applications. Then, compare these study findings with other research. Are these findings in agreement or disagreement with those from other studies? Does this study impart additional nuance to well-accepted theories? Situate your findings within the broader context of scientific literature, then explain the pathways or mechanisms that might give rise to, or explain, the results.

Journals vary in their approach to strengths and limitations sections: some are embedded paragraphs within the discussion section, while some mandate separate section headings. Keep in mind that every study has strengths and limitations. Candidly reporting yours helps readers to correctly interpret your research findings.

The next element of the discussion is a summary of the potential impacts and applications of the research. Should these results be used to optimally design an intervention? Does the work have implications for clinical protocols or public policy? These considerations will help the reader to further grasp the possible impacts of the presented work.

Finally, the discussion should conclude with specific suggestions for future work. Here, you have an opportunity to illuminate specific gaps in the literature that compel further study. Avoid the phrase “future research is necessary” because the recommendation is too general to be helpful to readers. Instead, provide substantive and specific recommendations for future studies. Table 4 provides common discussion section pitfalls and recommendations for addressing them.

Follow the Journal’s Author Guidelines

After you select a target journal, identify the journal’s author guidelines to guide the formatting of your manuscript and references. Author guidelines will often (but not always) include instructions for titles, cover letters, and other components of a manuscript submission. Read the guidelines carefully. If you do not follow the guidelines, your article will be sent back to you.

Finally, do not submit your paper to more than one journal at a time. Even if this is not explicitly stated in the author guidelines of your target journal, it is considered inappropriate and unprofessional.

Your title should invite readers to continue reading beyond the first page [ 4 , 5 ]. It should be informative and interesting. Consider describing the independent and dependent variables, the population and setting, the study design, the timing, and even the main result in your title. Because the focus of the paper can change as you write and revise, we recommend you wait until you have finished writing your paper before composing the title.

Be sure that the title is useful for potential readers searching for your topic. The keywords you select should complement those in your title to maximize the likelihood that a researcher will find your paper through a database search. Avoid using abbreviations in your title unless they are very well known, such as SNP, because it is more likely that someone will use a complete word rather than an abbreviation as a search term to help readers find your paper.

After you have written a complete draft, use the checklist (Fig. 3 ) below to guide your revisions and editing. Additional resources are available on writing the abstract and citing references [ 5 ]. When you feel that your work is ready, ask a trusted colleague or two to read the work and provide informal feedback. The box below provides a checklist that summarizes the key points offered in this article.

figure 3

Checklist for manuscript quality

Data Availability

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Vetto JT (2014) Short and sweet: a short course on concise medical writing. J Cancer Educ 29(1):194–195

Brett M, Kording K (2017) Ten simple rules for structuring papers. PLoS ComputBiol. https://doi.org/10.1371/journal.pcbi.1005619

Lang TA (2017) Writing a better research article. J Public Health Emerg. https://doi.org/10.21037/jphe.2017.11.06

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Acknowledgments

Ella August is grateful to the Sustainable Sciences Institute for mentoring her in training researchers on writing and publishing their research.

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Busse, C., August, E. How to Write and Publish a Research Paper for a Peer-Reviewed Journal. J Canc Educ 36 , 909–913 (2021). https://doi.org/10.1007/s13187-020-01751-z

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Scientific Writing: Structuring a scientific article

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How to Structure a Scientific Article

Many scientific articles include the following elements:

I. Abstract: The abstract should briefly summarize the contents of your article. Be sure to include a quick overview of the focus, results and conclusion of your study.

II. Introduction:  The introduction should include any relevant background information and articulate the idea that is being investigated. Why is this study unique? If others have performed research on the topic, include a literature review. 

III. Methods and Materials:  The methods and materials section should provide information on how the study was conducted and what materials were included. Other researchers should be able to reproduce your study based on the information found in this section. 

IV. Results:  The results sections includes the data produced by your study. It should reflect an unbiased account of the study's findings. 

V.  Discussion and Conclusion:  The discussion section provides information on what researches felt was significant and analyzes the data. You may also want to provide final thoughts and ideas for further research in the conclusion section. 

For more information, see How to Read a Scientific Paper.  

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  • By Rose Wolfe-Emery
  • July 21 st 2023

Academics normally learn how to write while on the job,  sugge s ts  Michael Hochberg. This usually starts with “the dissertation and interactions with their supervisor. Skills are honed and new ones acquired with each successive manuscript.” Writing continues to improve throughout a career, but that thought might bring little solace if you are staring at a blank document and wondering where to start. 

In this blog post, we share tips from editors and outline some ideas to bear in mind when drafting a journal article. Whether you are writing a journal article to share your research, contribute to your field, or progress your career, a well-written and structured article will increase the likelihood of acceptance and of your article making an impact after publication.

Four tips for writing well

Stuart West and Lindsay Turnbull  suggest  four general principles to bear in mind when writing journal articles:

  • Keep it simple:  “Simple, clear writing is fundamental to this task. Instead of trying to sound […] clever, you should be clear and concise.”
  • Assume nothing:  “When writing a paper, it’s best to assume that your reader is [subject] literate, but has very little expert knowledge. Your paper is more likely to fail because you assumed too much, than because you dumbed it down too much.”
  • Keep to essentials:  “If you focus on the main message, and remove all distractions, then the reader will come away with the message that you want them to have.”
  • Tell your story : “Good […] writing tells a story. It tells the reader why the topic you have chosen is important, what you found out, and why that matters. For the story to flow smoothly, the different parts need to link clearly to each other. In creative writing this is called ‘narrative flow’.”

“A paper is well-written if a reader who is not involved in the work can understand every single sentence in the paper,”  argues  Nancy Dixon. But understanding is the bare minimum that you should aim for—ideally, you want to  engage  your audience, so they keep reading. 

As  West and Turnbull say , frankly: “Your potential reader is someone time-limited, stressed, and easily bored. They have a million other things to do and will take any excuse to give up on reading your paper.”

A complete guide to preparing a journal article for submission

Consider your research topic.

Before you begin to draft your article, consider the following questions:

  • What key message(s) do you want to convey?
  • Can you identify a significant advance that will arise from your article?
  • How could your argument, results, or findings change the way that people think or advance understanding in the field?

As  Nancy Dixon  says: “[A journal] editor wants to publish papers that interest and excite the journal’s readers, that are important to advancing knowledge in the field and that spark new ideas for work in the field.”

Think about the journal that you want to submit to

Research the journals in your field and create a shortlist of “target” journals  before  writing your article, so that you can adapt your writing to the journal’s audience and style. Journals sometimes have an official style guide but reading published articles can also help you to familiarise yourself with the format and tone of articles in your target journals. Journals often publish articles of varying lengths and structures, so consider what article type would best suit your argument or results. 

Check your target journals’ editorial policies and ethical requirements. As a minimum, all reputable journals require submissions to be original and previously unpublished. The  ThinkCheckSubmit  checklist can help you to assess whether a journal is suitable for your research.

Now that you’ve decided on your research topic and chosen the journal you plan on submitting to, what do you need to consider when drafting each section of your article?

Create an outline

Firstly, it’s worth creating an outline for your journal article, broken down by section. Seth J. Schwartz  explains  this as follows:

Writing an outline is like creating a map before you set out on a road trip. You know which roads to take, and where to turn or get off the highway. You can even decide on places to stop during your trip. When you create a map like this, the trip is planned and you don’t have to worry whether you are going in the correct direction. It has already been mapped out for you.

The typical structure of a journal article

  • Make it concise, accurate, and catchy
  • Avoid including abbreviations or formulae
  • Choose 5-7 keywords that you’d like your journal article to appear in the search results for
  • Summarize the findings of your journal article in a succinct, “punchy”, and relevant way
  • Keep it brief (200 words for the letter, and 250 words for the main journal)
  • Do not include references

Introduction

  • Introduce your argument or outline the problem
  • Describe your approach
  • Identify existing solutions and limitations, or provide the existing context for your discussion
  • Define abbreviations

Methods 

For STEM and some social sciences articles

  • Describe how the work was done and include plenty of detail to allow for reproduction
  • Identify equipment and software programs

Results 

For STEM and some social science articles

  • Decide on the data to present and how to present it (clearly and concisely)
  • Summarise the key results of the article
  • Do not repeat results or introduce new discussion points

 Acknowledgements

  • Include funding, contributors who are not listed as authors, facilities and equipment, referees (if they’ve been helpful; even though anonymous)
  • Do not include non-research contributors (parents, friends, or pets!)
  • Cite articles that have been influential in your research—these should be well-balanced and relevant
  • Follow your chosen journal’s reference style, such as Harvard or Chicago
  • List all citations in the text alphabetically at end of the article

Sharing data

Many journals now encourage authors to make all data on which the conclusions of their article rely available to readers. This data can be presented in the main manuscript, in additional supporting files, or placed in a public repository.

Journals also tend to support the Force 11 Data Citation Principles that require all publicly available datasets be fully referenced in the reference list with an accession number or unique identifier such as a digital object identifier (DOI).

Permissions

Permission to reproduce copyright material, for online publication without a time limit, must also be cleared and, if necessary, paid for by the author. Evidence in writing that such permissions have been secured from the rights-holder are usually required to be made available to the editors.

Learning from experience

Publishing a journal article is very competitive, so don’t lose hope if your article isn’t accepted to your first-choice journal the first-time round. If your article makes it to the peer-review stage, be sure to take note of what the reviewers have said, as their comments can be very helpful. As well as continuing to write, there are other things you can do to improve your writing skills, including peer review and editing.

Christopher, Marek, and Zebel note  that “there is no secret formula for success”, arguing that: 

The lack of a specific recipe for acceptances reflects, in part, the variety of factors that may influence publication decisions, such as the perceived novelty of the manuscript topic, how the manuscript topic relates to other manuscripts submitted at a similar time, and the targeted journal. Thus, beyond actively pursuing options for any one particular manuscript, begin or continue work on others. In fact, one approach to boosting writing productivity is to have a variety of ongoing projects at different stages of completion. After all, considering that “100 percent of the shots you do not take will not go in,” you can increase your chances of publication by taking multiple shots.

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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.

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‘The situation has become appalling’: fake scientific papers push research credibility to crisis point

Last year, 10,000 sham papers had to be retracted by academic journals, but experts think this is just the tip of the iceberg

Tens of thousands of bogus research papers are being published in journals in an international scandal that is worsening every year, scientists have warned. Medical research is being compromised, drug development hindered and promising academic research jeopardised thanks to a global wave of sham science that is sweeping laboratories and universities.

Last year the annual number of papers retracted by research journals topped 10,000 for the first time. Most analysts believe the figure is only the tip of an iceberg of scientific fraud .

“The situation has become appalling,” said Professor Dorothy Bishop of Oxford University. “The level of publishing of fraudulent papers is creating serious problems for science. In many fields it is becoming difficult to build up a cumulative approach to a subject, because we lack a solid foundation of trustworthy findings. And it’s getting worse and worse.”

The startling rise in the publication of sham science papers has its roots in China, where young doctors and scientists seeking promotion were required to have published scientific papers. Shadow organisations – known as “paper mills” – began to supply fabricated work for publication in journals there.

The practice has since spread to India, Iran, Russia, former Soviet Union states and eastern Europe, with paper mills supplying ­fabricated studies to more and more journals as increasing numbers of young ­scientists try to boost their careers by claiming false research experience. In some cases, journal editors have been bribed to accept articles, while paper mills have managed to establish their own agents as guest editors who then allow reams of ­falsified work to be published.

Dr Dorothy Bishop sitting in a garden

“Editors are not fulfilling their roles properly, and peer reviewers are not doing their jobs. And some are being paid large sums of money,” said Professor Alison Avenell of Aberdeen University. “It is deeply worrying.”

The products of paper mills often look like regular articles but are based on templates in which names of genes or diseases are slotted in at random among fictitious tables and figures. Worryingly, these articles can then get incorporated into large databases used by those working on drug discovery.

Others are more bizarre and include research unrelated to a journal’s field, making it clear that no peer review has taken place in relation to that article. An example is a paper on Marxist ideology that appeared in the journal Computational and Mathematical Methods in Medicine . Others are distinctive because of the strange language they use, including references to “bosom peril” rather than breast cancer and “Parkinson’s ailment” rather Parkinson’s disease.

Watchdog groups – such as Retraction Watch – have tracked the problem and have noted retractions by journals that were forced to act on occasions when fabrications were uncovered. One study, by Nature , revealed that in 2013 there were just over 1,000 retractions. In 2022, the figure topped 4,000 before jumping to more than 10,000 last year.

Of this last total, more than 8,000 retracted papers had been published in journals owned by Hindawi, a subsidiary of the publisher Wiley, figures that have now forced the company to act. “We will be sunsetting the Hindawi brand and have begun to fully integrate the 200-plus Hindawi journals into Wiley’s ­portfolio,” a Wiley spokesperson told the Observer .

The spokesperson added that Wiley had now identified hundreds of fraudsters present in its portfolio of journals, as well as those who had held guest editorial roles. “We have removed them from our systems and will continue to take a proactive … approach in our efforts to clean up the scholarly record, strengthen our integrity processes and contribute to cross-industry solutions.”

But Wiley insisted it could not tackle the crisis on its own, a message echoed by other publishers, which say they are under siege from paper mills. Academics remain cautious, however. The problem is that in many countries, academics are paid according to the number of papers they have published.

“If you have growing numbers of researchers who are being strongly incentivised to publish just for the sake of publishing, while we have a growing number of journals making money from publishing the resulting articles, you have a perfect storm,” said Professor Marcus Munafo of Bristol University. “That is exactly what we have now.”

The harm done by publishing poor or fabricated research is demonstrated by the anti-parasite drug ivermectin. Early laboratory studies indicated it could be used to treat Covid-19 and it was hailed as a miracle drug. However, it was later found these studies showed clear evidence of fraud, and medical authorities have refused to back it as a treatment for Covid.

“The trouble was, ivermectin was used by anti-vaxxers to say: ‘We don’t need vaccination because we have this wonder drug,’” said Jack Wilkinson at Manchester University. “But many of the trials that underpinned those claims were not authentic.”

Wilkinson added that he and his colleagues were trying to develop protocols that researchers could apply to reveal the authenticity of studies that they might include in their own work. “Some great science came out during the pandemic, but there was an ocean of rubbish research too. We need ways to pinpoint poor data right from the start.”

The danger posed by the rise of the paper mill and fraudulent research papers was also stressed by Professor Malcolm MacLeod of Edinburgh University. “If, as a scientist, I want to check all the papers about a particular drug that might target cancers or stroke cases, it is very hard for me to avoid those that are fabricated. Scientific knowledge is being polluted by made-up material. We are facing a crisis.”

This point was backed by Bishop: “People are building careers on the back of this tidal wave of fraudulent science and could end up running scientific institutes and eventually be used by mainstream journals as reviewers and editors. Corruption is creeping into the system.”

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  • CAREER COLUMN
  • 05 February 2024

‘Obviously ChatGPT’ — how reviewers accused me of scientific fraud

  • E. M. Wolkovich 0

E. M. Wolkovich is an associate professor of forest and conservation sciences at the University of British Columbia in Vancouver, Canada.

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A woman working on a laptop with the ChatGPT interface visible on the screen

Accusations of plagiarism, including alleged misuse of ChatGPT, should not be made lightly. Credit: Alexandre Rotenberg/Alamy

I have just been accused of scientific fraud. Not data fraud — no one accused me of fabricating or misleadingly manipulating data or results. This, I suppose, is a relief because my laboratory, which studies how global change reshapes ecological communities, works hard to ensure that data are transparent and sharable, and that our work is reproducible. Instead, I was accused of writing fraud: passing off ‘writing’ produced by artificial intelligence (AI) as my own. That hurts, because — like many people — I find writing a paper to be a somewhat painful process. I read books on how to write — both to be comforted by how much these books stress that writing is generally slow and difficult, and to find ways to improve. My current strategy involves willing myself to write and creating several outlines before the first draft, which is followed by writing and a lot of revising. I always suggest this approach to my students, although I know it is not easy, because I think it’s important that scientists try to communicate well.

how to write scientific journal article

Collection: ChatGPT’s impact on careers in science

Imagine my surprise when I received reviews on a submitted paper declaring that it was the work of ChatGPT. One reviewer wrote that it was “obviously ChatGPT”, and the handling editor vaguely agreed, saying that they found “the writing style unusual”. Surprise was just one emotion I experienced; I also felt shock, dismay and a flood of confusion and alarm. Given how much work I put into writing, it was a blow to be accused of being a chatbot — especially without any evidence.

In reality, I hadn’t written a word of the manuscript using ChatGPT. I quickly brainstormed how I might prove my case. Because I write in plain-text files (using the typesetting language LaTeX) that I track using the version-control system Git, I could show my text change history on GitHub (with commit messages including “finally writing!” and “Another 25 mins of writing progress!” that I never thought I would share). I could also try to compare the writing style of my pre-ChatGPT papers with that of my submission.

Maybe I could ask ChatGPT itself if it thought it had written my paper. But then I realized I would be spending my time trying to prove that I am not a chatbot — which seemed a bad outcome to the whole situation. What I really wanted to do was pick up my ball and march off of the playground in a fury. How dare they? But first, I decided to get some perspectives from researchers who work on data fraud, co-authors on the paper and other colleagues. Most agreed with my alarm. One put it most succinctly: “All scientific criticism is admissible, but this is a different matter.”

Existential crisis

These reviews captured something both inherently broken about the peer-review process and — more importantly to me — about how AI could corrupt science without even trying.

Portrait of Elizabeth Wolkovich

E. M. Wolkovich was accused of passing off text generated by ChatGPT as her own work. Credit: T. J. Davies

People worry about AI gaining control over humanity, its potential to supercharge misinformation and how it might help to perpetuate insidious bias and inequality. Some are trying to create safeguards to prevent this. But communities are also trying to create AI that helps where it should, and maybe that will include as a writing aid. But, as my experience shows, ChatGPT corrupted the whole process simply by its existential presence in the world. I was at once annoyed at being mistaken for a chatbot and horrified that reviewers and editors were so blasé about the idea that someone had submitted AI-generated text.

So much of science is built on trust and faith in the ethics and integrity of our colleagues. We mostly trust that others do not fabricate their data, and I trust that people do not (yet) write their papers or grants using large language models without disclosing it. I wouldn’t accuse someone of data fraud or statistical manipulation without evidence, but a reviewer apparently felt no such qualms when accusing me. Perhaps they didn’t intend this to be a harsh accusation, and the editor thought nothing of passing along and echoing their comments — but they had effectively accused me of lying by deliberately presenting AI-generated text as my own. They also felt confident that they could discern my writing from that of an AI tool — but they obviously couldn’t.

how to write scientific journal article

We need to be able to call out fraud and misconduct in science. In my view, the costs to people who call out data fraud are too high, and the consequences for committing fraud are too low. But I worry about a world in which a reviewer can casually level an accusation of fraud, and the editors and journal editor simply shuffle along the review and invite a resubmission. It suggests not only that reviewers and editors have no faith in the scientific integrity of the submitting authors, but also that ethics are negotiable. Such a world seems easy for ChatGPT to corrupt without even trying — unless we raise our standards.

Scientific societies can start by having conversations during their meetings and conferences with the goal of more explicit, community-generated standards about when and how AI can be used in the manuscript-writing process, and how that help should be acknowledged. Such standards could help editors to develop better processes for handling accusations of AI-generated text, ideally in a way that is less demoralizing for authors.

As for me, I now plan to use Git and GitHub for all my writing from day one, and to document changes every day. It’s not an ironclad system, but it has given me some peace of mind — not to mention, a paper trail that clearly shows a manuscript written slowly and painstakingly, and without ChatGPT.

doi: https://doi.org/10.1038/d41586-024-00349-5

This is an article from the Nature Careers Community, a place for Nature readers to share their professional experiences and advice. Guest posts are encouraged .

Competing Interests

The author declares no competing interests.

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Futurism

Scientific Article With Insane AI-Generated Images Somehow Passes Peer Review

T he questionable use of AI-generated content in academic journals poses a problem for the credibility of the scientific community. Some of the culprits are easier to weed out than others, but no one could expect an example as ridiculous as this latest case.

As spotted by a user on X-formerly-Twitter , a new study published this week in the journal Frontiers in Cell and Developmental Biology  — which is supposedly peer-reviewed , mind you — heavily features figures and diagrams that are obviously AI-generated. And, how should we put this? They're insane-looking nonsense.

Take a look, for example, at this diagram of an extremely well endowed mouse. The morphology is so grotesque and comical it defies any explanation, flaunting what appears to be a dissected view of testicles as nearly as large as the mouse itself. They're also protruding from its stomach and just sort of hanging out there in the open, tethered to some unknown upper anatomy out of the frame.

Note the emphasis on "appears to be," because the labels on the diagram are made up gobbledygook like "testtomcels," "retat," and "dck." But it did get a few things right though, like this helpful line pointing to the middle of the creature labeled "Rat."

To the researchers' credit, they weren't being deceptive, disclosing that the "images in this article were generated by Midjourney." Yet they appear to have made little or no effort to edit them, which ends up undermining their credibility anyway. Moral of the story: double check your AI-hallucinated stuff.

Speaking of double-checking, some members in the scientific community warn that Frontiers is what's known as a " predatory journal ," a type of publication that misleadingly claims to peer-review submissions while taking advantage of scientists desperate to get a paper published. If true, that might help explain why these absolutely confounding images didn't raise any alarms; no one, it seems, is doing any real checking.

It's worth noting, however, that not everyone agrees with that characterization of Frontiers,  as what journals are considered "predatory" remains a heated topic in the community. Addressing this most recent controversy, the publisher acknowledged that it's seen the "scrutiny" blowing up on social media.

"We thank the readers for their scrutiny of our articles: when we get it wrong, the crowdsourcing dynamic of open science means that community feedback helps us to quickly correct the record,"  Frontiers wrote on X .

Regardless of the publication, it's undeniable that generative AI has made worrying inroads into academia. Some papers have been more upfront by listing ChatGPT as a co-author . Others made no such disclosure, but managed to slip through peer review anyway .

The ones that do get caught often make careless mistakes , like forgetting to delete telltale AI phrases such as "regenerate response." In any case, the content an AI generates is usually filled with factual errors . That's a no-go for any kind of published material, but especially the scientific kind, which relies on highly technical knowledge that a general-purpose chatbot won't use correctly.

More on AI: OpenAI Hiring Detective to Find Who's Leaking Its Precious Info

The post Scientific Article With Insane AI-Generated Images Somehow Passes Peer Review appeared first on Futurism .

Among its series of baffling AI-generated images is a mislabeled figure of a mouse with grotesquely large testicles.

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Ten Simple Rules for Writing a Literature Review

Marco pautasso.

1 Centre for Functional and Evolutionary Ecology (CEFE), CNRS, Montpellier, France

2 Centre for Biodiversity Synthesis and Analysis (CESAB), FRB, Aix-en-Provence, France

Literature reviews are in great demand in most scientific fields. Their need stems from the ever-increasing output of scientific publications [1] . For example, compared to 1991, in 2008 three, eight, and forty times more papers were indexed in Web of Science on malaria, obesity, and biodiversity, respectively [2] . Given such mountains of papers, scientists cannot be expected to examine in detail every single new paper relevant to their interests [3] . Thus, it is both advantageous and necessary to rely on regular summaries of the recent literature. Although recognition for scientists mainly comes from primary research, timely literature reviews can lead to new synthetic insights and are often widely read [4] . For such summaries to be useful, however, they need to be compiled in a professional way [5] .

When starting from scratch, reviewing the literature can require a titanic amount of work. That is why researchers who have spent their career working on a certain research issue are in a perfect position to review that literature. Some graduate schools are now offering courses in reviewing the literature, given that most research students start their project by producing an overview of what has already been done on their research issue [6] . However, it is likely that most scientists have not thought in detail about how to approach and carry out a literature review.

Reviewing the literature requires the ability to juggle multiple tasks, from finding and evaluating relevant material to synthesising information from various sources, from critical thinking to paraphrasing, evaluating, and citation skills [7] . In this contribution, I share ten simple rules I learned working on about 25 literature reviews as a PhD and postdoctoral student. Ideas and insights also come from discussions with coauthors and colleagues, as well as feedback from reviewers and editors.

Rule 1: Define a Topic and Audience

How to choose which topic to review? There are so many issues in contemporary science that you could spend a lifetime of attending conferences and reading the literature just pondering what to review. On the one hand, if you take several years to choose, several other people may have had the same idea in the meantime. On the other hand, only a well-considered topic is likely to lead to a brilliant literature review [8] . The topic must at least be:

  • interesting to you (ideally, you should have come across a series of recent papers related to your line of work that call for a critical summary),
  • an important aspect of the field (so that many readers will be interested in the review and there will be enough material to write it), and
  • a well-defined issue (otherwise you could potentially include thousands of publications, which would make the review unhelpful).

Ideas for potential reviews may come from papers providing lists of key research questions to be answered [9] , but also from serendipitous moments during desultory reading and discussions. In addition to choosing your topic, you should also select a target audience. In many cases, the topic (e.g., web services in computational biology) will automatically define an audience (e.g., computational biologists), but that same topic may also be of interest to neighbouring fields (e.g., computer science, biology, etc.).

Rule 2: Search and Re-search the Literature

After having chosen your topic and audience, start by checking the literature and downloading relevant papers. Five pieces of advice here:

  • keep track of the search items you use (so that your search can be replicated [10] ),
  • keep a list of papers whose pdfs you cannot access immediately (so as to retrieve them later with alternative strategies),
  • use a paper management system (e.g., Mendeley, Papers, Qiqqa, Sente),
  • define early in the process some criteria for exclusion of irrelevant papers (these criteria can then be described in the review to help define its scope), and
  • do not just look for research papers in the area you wish to review, but also seek previous reviews.

The chances are high that someone will already have published a literature review ( Figure 1 ), if not exactly on the issue you are planning to tackle, at least on a related topic. If there are already a few or several reviews of the literature on your issue, my advice is not to give up, but to carry on with your own literature review,

An external file that holds a picture, illustration, etc.
Object name is pcbi.1003149.g001.jpg

The bottom-right situation (many literature reviews but few research papers) is not just a theoretical situation; it applies, for example, to the study of the impacts of climate change on plant diseases, where there appear to be more literature reviews than research studies [33] .

  • discussing in your review the approaches, limitations, and conclusions of past reviews,
  • trying to find a new angle that has not been covered adequately in the previous reviews, and
  • incorporating new material that has inevitably accumulated since their appearance.

When searching the literature for pertinent papers and reviews, the usual rules apply:

  • be thorough,
  • use different keywords and database sources (e.g., DBLP, Google Scholar, ISI Proceedings, JSTOR Search, Medline, Scopus, Web of Science), and
  • look at who has cited past relevant papers and book chapters.

Rule 3: Take Notes While Reading

If you read the papers first, and only afterwards start writing the review, you will need a very good memory to remember who wrote what, and what your impressions and associations were while reading each single paper. My advice is, while reading, to start writing down interesting pieces of information, insights about how to organize the review, and thoughts on what to write. This way, by the time you have read the literature you selected, you will already have a rough draft of the review.

Of course, this draft will still need much rewriting, restructuring, and rethinking to obtain a text with a coherent argument [11] , but you will have avoided the danger posed by staring at a blank document. Be careful when taking notes to use quotation marks if you are provisionally copying verbatim from the literature. It is advisable then to reformulate such quotes with your own words in the final draft. It is important to be careful in noting the references already at this stage, so as to avoid misattributions. Using referencing software from the very beginning of your endeavour will save you time.

Rule 4: Choose the Type of Review You Wish to Write

After having taken notes while reading the literature, you will have a rough idea of the amount of material available for the review. This is probably a good time to decide whether to go for a mini- or a full review. Some journals are now favouring the publication of rather short reviews focusing on the last few years, with a limit on the number of words and citations. A mini-review is not necessarily a minor review: it may well attract more attention from busy readers, although it will inevitably simplify some issues and leave out some relevant material due to space limitations. A full review will have the advantage of more freedom to cover in detail the complexities of a particular scientific development, but may then be left in the pile of the very important papers “to be read” by readers with little time to spare for major monographs.

There is probably a continuum between mini- and full reviews. The same point applies to the dichotomy of descriptive vs. integrative reviews. While descriptive reviews focus on the methodology, findings, and interpretation of each reviewed study, integrative reviews attempt to find common ideas and concepts from the reviewed material [12] . A similar distinction exists between narrative and systematic reviews: while narrative reviews are qualitative, systematic reviews attempt to test a hypothesis based on the published evidence, which is gathered using a predefined protocol to reduce bias [13] , [14] . When systematic reviews analyse quantitative results in a quantitative way, they become meta-analyses. The choice between different review types will have to be made on a case-by-case basis, depending not just on the nature of the material found and the preferences of the target journal(s), but also on the time available to write the review and the number of coauthors [15] .

Rule 5: Keep the Review Focused, but Make It of Broad Interest

Whether your plan is to write a mini- or a full review, it is good advice to keep it focused 16 , 17 . Including material just for the sake of it can easily lead to reviews that are trying to do too many things at once. The need to keep a review focused can be problematic for interdisciplinary reviews, where the aim is to bridge the gap between fields [18] . If you are writing a review on, for example, how epidemiological approaches are used in modelling the spread of ideas, you may be inclined to include material from both parent fields, epidemiology and the study of cultural diffusion. This may be necessary to some extent, but in this case a focused review would only deal in detail with those studies at the interface between epidemiology and the spread of ideas.

While focus is an important feature of a successful review, this requirement has to be balanced with the need to make the review relevant to a broad audience. This square may be circled by discussing the wider implications of the reviewed topic for other disciplines.

Rule 6: Be Critical and Consistent

Reviewing the literature is not stamp collecting. A good review does not just summarize the literature, but discusses it critically, identifies methodological problems, and points out research gaps [19] . After having read a review of the literature, a reader should have a rough idea of:

  • the major achievements in the reviewed field,
  • the main areas of debate, and
  • the outstanding research questions.

It is challenging to achieve a successful review on all these fronts. A solution can be to involve a set of complementary coauthors: some people are excellent at mapping what has been achieved, some others are very good at identifying dark clouds on the horizon, and some have instead a knack at predicting where solutions are going to come from. If your journal club has exactly this sort of team, then you should definitely write a review of the literature! In addition to critical thinking, a literature review needs consistency, for example in the choice of passive vs. active voice and present vs. past tense.

Rule 7: Find a Logical Structure

Like a well-baked cake, a good review has a number of telling features: it is worth the reader's time, timely, systematic, well written, focused, and critical. It also needs a good structure. With reviews, the usual subdivision of research papers into introduction, methods, results, and discussion does not work or is rarely used. However, a general introduction of the context and, toward the end, a recapitulation of the main points covered and take-home messages make sense also in the case of reviews. For systematic reviews, there is a trend towards including information about how the literature was searched (database, keywords, time limits) [20] .

How can you organize the flow of the main body of the review so that the reader will be drawn into and guided through it? It is generally helpful to draw a conceptual scheme of the review, e.g., with mind-mapping techniques. Such diagrams can help recognize a logical way to order and link the various sections of a review [21] . This is the case not just at the writing stage, but also for readers if the diagram is included in the review as a figure. A careful selection of diagrams and figures relevant to the reviewed topic can be very helpful to structure the text too [22] .

Rule 8: Make Use of Feedback

Reviews of the literature are normally peer-reviewed in the same way as research papers, and rightly so [23] . As a rule, incorporating feedback from reviewers greatly helps improve a review draft. Having read the review with a fresh mind, reviewers may spot inaccuracies, inconsistencies, and ambiguities that had not been noticed by the writers due to rereading the typescript too many times. It is however advisable to reread the draft one more time before submission, as a last-minute correction of typos, leaps, and muddled sentences may enable the reviewers to focus on providing advice on the content rather than the form.

Feedback is vital to writing a good review, and should be sought from a variety of colleagues, so as to obtain a diversity of views on the draft. This may lead in some cases to conflicting views on the merits of the paper, and on how to improve it, but such a situation is better than the absence of feedback. A diversity of feedback perspectives on a literature review can help identify where the consensus view stands in the landscape of the current scientific understanding of an issue [24] .

Rule 9: Include Your Own Relevant Research, but Be Objective

In many cases, reviewers of the literature will have published studies relevant to the review they are writing. This could create a conflict of interest: how can reviewers report objectively on their own work [25] ? Some scientists may be overly enthusiastic about what they have published, and thus risk giving too much importance to their own findings in the review. However, bias could also occur in the other direction: some scientists may be unduly dismissive of their own achievements, so that they will tend to downplay their contribution (if any) to a field when reviewing it.

In general, a review of the literature should neither be a public relations brochure nor an exercise in competitive self-denial. If a reviewer is up to the job of producing a well-organized and methodical review, which flows well and provides a service to the readership, then it should be possible to be objective in reviewing one's own relevant findings. In reviews written by multiple authors, this may be achieved by assigning the review of the results of a coauthor to different coauthors.

Rule 10: Be Up-to-Date, but Do Not Forget Older Studies

Given the progressive acceleration in the publication of scientific papers, today's reviews of the literature need awareness not just of the overall direction and achievements of a field of inquiry, but also of the latest studies, so as not to become out-of-date before they have been published. Ideally, a literature review should not identify as a major research gap an issue that has just been addressed in a series of papers in press (the same applies, of course, to older, overlooked studies (“sleeping beauties” [26] )). This implies that literature reviewers would do well to keep an eye on electronic lists of papers in press, given that it can take months before these appear in scientific databases. Some reviews declare that they have scanned the literature up to a certain point in time, but given that peer review can be a rather lengthy process, a full search for newly appeared literature at the revision stage may be worthwhile. Assessing the contribution of papers that have just appeared is particularly challenging, because there is little perspective with which to gauge their significance and impact on further research and society.

Inevitably, new papers on the reviewed topic (including independently written literature reviews) will appear from all quarters after the review has been published, so that there may soon be the need for an updated review. But this is the nature of science [27] – [32] . I wish everybody good luck with writing a review of the literature.

Acknowledgments

Many thanks to M. Barbosa, K. Dehnen-Schmutz, T. Döring, D. Fontaneto, M. Garbelotto, O. Holdenrieder, M. Jeger, D. Lonsdale, A. MacLeod, P. Mills, M. Moslonka-Lefebvre, G. Stancanelli, P. Weisberg, and X. Xu for insights and discussions, and to P. Bourne, T. Matoni, and D. Smith for helpful comments on a previous draft.

Funding Statement

This work was funded by the French Foundation for Research on Biodiversity (FRB) through its Centre for Synthesis and Analysis of Biodiversity data (CESAB), as part of the NETSEED research project. The funders had no role in the preparation of the manuscript.

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    Introduction. The origins and development of the scientific and technical press can be traced back to 1665 when the first "modern" scientific papers appeared and were characterized by non standardised form and style 1.Subsequently, nearly 300 years ago 2, in an attempt to ensure that articles met the journal's standards of quality and scientific validity, the peer-reviewed process for ...

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    T he questionable use of AI-generated content in academic journals poses a problem for the credibility of the scientific community. Some of the culprits are easier to weed out than others, but no ...

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    Abstract. An article primarily includes the following sections: introduction, materials and methods, results, discussion, and conclusion. Before writing the introduction, the main steps, the heading and the familiarity level of the readers should be considered. Writing should begin when the experimental system and the equipment are available.

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    Literature reviews are in great demand in most scientific fields. Their need stems from the ever-increasing output of scientific publications .For example, compared to 1991, in 2008 three, eight, and forty times more papers were indexed in Web of Science on malaria, obesity, and biodiversity, respectively .Given such mountains of papers, scientists cannot be expected to examine in detail every ...