Abstract

Learning to write a scientific manuscript is one of the most important and rewarding scientific training experiences, yet most young scientists only embark on this experience relatively late in graduate school after gathering sufficient data in the lab. Familiarity with the process of writing a scientific manuscript and receiving peer reviews often leads to a more focused and driven experimental approach as well as a better understanding of the scientific literature. To jump-start this training, we developed a protocol for teaching manuscript writing and reviewing in a course, appropriate for new graduate or upper-level undergraduate students in biology. First, students are provided a cartoon data set. Students are instructed to use their creativity to convert evidence into argument and then to integrate their interpretations into a manuscript, including a mechanistic model figure. After student manuscripts are submitted, manuscripts are redacted and distributed to classmates for peer review. We present our cartoon data sets (based on animal development and interbacterial competition), homework instructions, and grading rubrics as a new resource for the scientific community. We also describe methods for developing new data sets so that instructors can adapt this activity to other disciplines. Our data-driven manuscript writing exercise as well as the formative and summative assessments resulting from the peer review process enable students to practice scientific skills and concepts. In addition, students practice scientific communication, arguing from evidence, developing and testing hypotheses, the unique conventions of scientific writing, and the joys of scientific story telling.

Primary Image: Manuscript 101 Workflow Schema. In this series of structured activities, students transform cartoon data sets into manuscripts that then undergo peer review.

Citation

Lesson Learning Goals

• Students will learn the structure of scientific manuscripts and conventions of scientific communication.
• Students will interpret scientific data and use evidence to form a model for the underlying biology.
• Students will assess how data can be interpreted in different ways.
• Students will apply the goals and conventions of peer review in their own reviews.
• Students will incorporate valuable, critical feedback resulting from peer review.
• Students may engage in collaborative problem solving.

Lesson Learning Objectives

• Students will be able to write a scientific manuscript.
• Students will be able to critically review manuscripts.
• Students will learn that the same data can be interpreted in different ways, leading to different scientific narratives.
• Students will discover how data collection translates to the communication of scientific discoveries.

Introduction

Manuscripts are one of the main products of academic scientific research. As students learn to critically read the scientific literature, it is useful for them to understand how manuscripts are constructed and what subjective decisions are made along the way. In addition, for graduate training, one major goal is to learn how to effectively package observations and interpretations into a compelling, logical, and mechanistic story. However, for most graduate students, lessons in manuscript writing become available relatively late in their training—after students have generated sufficient data. Arguably, an intimate knowledge of the manuscript-writing process should precede and drive the experimental approach. We propose that modeling the processes of writing and reviewing a manuscript in a course can accelerate the development of skills that are beneficial for undergraduate STEM training and are essential for independent laboratory study.

Recently, there has been an increasing push for a “writing to learn” framework as a strategy to cultivate collaboration in scientific inquiry (1, 2). In biology in particular, such writing exercises improve students’ abilities to form hypotheses and draw conclusions from evidence (3). As such, lessons have been developed to help students think through and explain biological mechanisms in writing (4), to craft effective results sections given initial data (5), and to have students participate in peer review of their scientific writing (1). Here, we describe a unique teaching approach that goes one step further, allowing students to integrate the full arc of thinking and writing skills necessary to transform a collection of experimental results into a fully realized scientific research paper. After students receive an initial set of cartoon data figures, they must interpret the data, craft a logical narrative, write a complete manuscript describing their findings, and participate in the peer review process as both writer and reviewer. We have used this lesson as an approach for undergraduates to deeply understand the scientific literature and to train student researchers in the skills they will need to publish their own research.

To address the need for early exposure to manuscript writing, we developed a multi-part homework assignment that enables beginning students to experience the process of writing and submitting a manuscript. For graduate students this activity takes place over two subsequent assignments. For undergraduates that are less familiar with primary literature, we have extended the exercise with additional intermediate assignments across 8–10 weeks.

Activity Structure for Graduate Students

Manuscript 101 is a two-part homework assignment focused on preparation and peer review of scientific manuscripts (Figure 1). For Graduate Homework 1 (Table 1), each student is provided with the manuscript writing instructions as well as one of four sets of cartoon figures. The figures provided are cartoon data and are provided in an unsequenced order. Students are instructed to organize their figures in an order that tells the best story, to interpret the data, to draw a model figure illustrating their proposed molecular mechanism, and to write a manuscript using all of the figures. For the manuscript, students write Title, Abstract, Introduction, Results, and Discussion sections, according to the Homework 1 instructions. In the Discussion section, students are encouraged to provide alternative interpretations of their data and to propose experiments that would discriminate among possible interpretations. Students are also encouraged to state predictions of their model and to propose future experiments to test these predictions. Thus, Manuscript 101 exposes students to the structure and organization of a typical scientific manuscript but also provides students with a first-hand opportunity to experience the creative aspects of scientific story-telling and exploration.

Table 1. Graduate course lesson timeline for Homework 1: Writing the manuscript. This portion of the lesson can be delivered in one or two lecture periods.

The manuscripts are submitted to the instructor, who acts as journal editor in Graduate Homework 2 (Table 2) focused on manuscript review. For Homework 2, each student is asked to provide an anonymous review of a manuscript generated by a peer in Homework 1, according to the Homework 2 instructions. The instructor may also choose to provide a review of each submitted manuscript. Therefore, Homework 2 is both an assessment of the manuscript writing assignment as well as an experiential opportunity in critical evaluation of scientific manuscripts. At the end of Homework 2, each student will receive the review(s) of their manuscript as well as a formal assessment of both homework assignments from the instructor. Below, we provide the teaching tools and framework for implementing this practical exercise.

Table 2. Graduate course lesson timeline for Homework 2: Reviewing the manuscript. This portion of the lesson can be delivered in one lecture period, with the option to include a post-homework debriefing.

Intended Audience

First-year graduate students at research universities were engaged in this lesson.

Required Learning Time

Our lesson is focused around two homework assignments. Time lines for Homework 1 and Homework 2 are provided in Tables 1 and 2. Total learning time includes two lectures (50–85 minutes each), which explain the homework instructions and provide in-class group active learning opportunities. Students complete Homework 1 and Homework 2 outside of class time during two-week and one-week periods, respectively, for a total of two to three weeks. After the course, we encourage instructors to follow up with these graduate students longer term to compare their experiences in the Manuscript 101 lesson with their experiences writing their own first papers for publication.

Prerequisite Student Knowledge

It is helpful for students to have general knowledge about the structure of a scientific paper and the publication process (see Teaching Discussion and lecture slides). They should also have background knowledge specific to the topic of the cartoon data sets.

For example, for the Developmental Biology cartoon data set provided, students would benefit from prior knowledge of common molecular biology methods such as gel electrophoresis, immunofluorescence, and in situ hybridization. They would also benefit from familiarity with breeding strategies and forward and reverse genetic techniques for model organisms including frog, zebrafish, and mouse and common genomic techniques such as RNA-sequencing. For the Microbiology cartoon data set, students would benefit from prior knowledge about mechanisms of interbacterial competition (e.g., the type VI secretion system), mobile genetic elements, and common techniques in microbiology including bacterial competition assays, antibiotic selection, western blots, structural biology, PCR, and the ability to interpret the impacts of expressed mutant or fusion proteins. Some familiarity with bacterial gene organization and variation is also useful.

Prerequisite Teacher Knowledge

The teacher should have prior experience with writing and reviewing scientific manuscripts in any discipline along with the ability to draw new cartoon data or background in research pertaining to our cartoon data sets.

Activity Structure for Undergraduates

For undergraduates, the overall goal is the same as for graduate students: interpreting cartoon figures, writing a manuscript, and participating in peer review. However, because this could be a large and intensive process for undergraduates, the activity is divided across 7 Undergraduate Assignments (Table 3) with opportunities for peer and instructor feedback along the way.

Table 3. Undergraduate course lesson timeline.

Students are first divided into groups, each provided with a set of cartoon figures. After discussion in class, each student is asked to decide on a figure order, draw a model figure, and write a model figure legend for Undergraduate Assignment 1. Instructors give feedback on the model figure design and content. This is a useful formative assessment to gauge student comprehension and provide guidance. For Undergraduate Assignments 2, 3, and 4, students draft one or more sections of the manuscript. In class, students exchange their assignments with a peer who received a different cartoon data set for informal feedback on scientific logic and writing clarity. Assignment 2 includes the results section, Assignment 3 includes the introduction and discussion, and Assignment 4 includes the title and abstract. Finally, for Undergraduate Assignment 5, students submit a complete draft of their manuscript (equivalent to Homework 1 in the graduate student structure) along with a cover letter briefly describing the topic and highlights of their paper.

Once manuscripts are submitted, students serve as anonymous reviewers during a round of peer review, organized by the instructor. Their submitted reviews are graded as Undergraduate Assignment 6 (equivalent to Graduate Homework 2 described above). Following Assignment 6, students receive reviews of their manuscript from their instructor and anonymous peer reviewer. For their final goal in Undergraduate Assignment 7, students undergo a round of manuscript revision and resubmission. Students improve their manuscript based on the reviews, while also submitting a second cover letter that responds to the reviewer comments. The resubmitted manuscript is evaluated for a final grade, which assesses both the manuscript itself and how well students addressed the reviews. This structure allows for students to use the input from peer review to improve their own work and to see how the peer review process can alter the final scientific manuscript product.

Intended Audience

Third- and fourth-year undergraduate students at research universities were engaged in this lesson. As part of the class, all students received separate instruction outside this activity about how to read and interpret scientific papers.

Required Learning Time

Assignments 1 through 7 are completed as homework outside of class across 8–10 weeks. Total in-class learning time includes 10–15 minutes of instructions preceding each assignment, 40–50 min of group discussion of the data sets before Assignment 1, and 20–40 min of reading and informal peer feedback on sections of the manuscript following Assignments 2, 3, and 4. Additional class periods may be used for discussions of manuscript structure, scientific writing conventions, or to examine published papers as examples. Timelines for these assignments are provided in Table 3.

Prerequisite Student Knowledge

It is helpful for students to have general knowledge about the structure of a scientific paper and the publication process (see Teaching Discussion and lecture slides). They should also have background knowledge specific to the topic of the cartoon data sets, similar to the knowledge described for graduate students in the prior section.

Prerequisite Teacher Knowledge

The teacher should have prior experience with writing and reviewing scientific manuscripts in any discipline along with the ability to draw new cartoon data or background in research pertaining to our cartoon data sets.

Scientific Teaching Themes

The Manuscript 101 Lesson will incorporate multiple teaching/learning strategies.

Active Learning

The lesson engages active learning approaches both inside and outside of the classroom. Inside the classroom, students will participate in discussion to assess and formulate their understanding of the structure of a scientific manuscript, elements of scientific writing, and the goals and process of manuscript peer review. Students also have the opportunity to collaboratively interpret the results from their data sets in a think-pair-share and group discussion process, either in class or in an optional meeting outside of class. Finally, students actively engage in formal and informal peer critique, which contributes to active leaning and assessment approaches. The addition of a revision and resubmission step provides an additional opportunity for students to reflect on their writing and scientific interpretations while they improve their work.

Assessment

This activity framework provides multiple opportunities for feedback and student self-evaluation. Group discussions of data sets at the beginning provide an opportunity for collaborative problem solving. By creating a model figure and writing the full manuscript, students must articulate their understanding of the data and the scientific finding, allowing for metacognition and self-reflection. If instructors choose to evaluate the model figures as in the undergraduate structure, this allows for an early formative assessment of how well students have understood their data sets before they begin writing. In both formal peer review and informal peer feedback, students receive specific advice on how to improve. They also benefit from seeing approaches for writing or manuscript structure that their classmates have used to tackle the same assignment. Instructors evaluate the manuscripts and students’ reviews with quantitative rubrics and by providing written feedback on the quality of the finished assignments.

Inclusive Teaching

The Manuscript 101 lesson is intended to promote inclusion in science and overall scientific literacy by providing explicit training in data interpretation, manuscript writing, and review, allowing senior undergraduates or beginning graduate students to gain these skills early in their careers.

For these early career students, learning to interpret and write in the language of scientific manuscripts can be intimidating. We therefore provide a structure for scaffolding student learning through regular instructor and peer-review feedback via small assignments spread across 8–10 weeks. This structure ensures students understand the data and assignment instructions well before they begin writing. It also provides early feedback to correct a student’s approach if they get off track. The peer review process additionally allows them to improve their writing and reasoning by seeing how other students have approached the assignment differently. The discussions of the data set and peer review feedback occur in small, informal groups, facilitating participation of both extroverted and introverted students. Through these steps, Manuscript 101 has the potential to level the playing field by delivering a structured lesson in manuscript writing and review and by providing students an opportunity to receive feedback on their own manuscripts and manuscript reviews.

Lesson Plan

1. In-Class Instruction

Because the Manuscript 101 activity takes place largely through a series of homework assignments, the main requirement in class is to give clear instructions and guidelines for the assignments. Optionally, instructors may choose to spend additional class time discussing how to read and interpret scientific papers or providing writing guidance on how to structure a manuscript (6). If instructors follow the undergraduate class structure described above, they will also provide time for group discussion of data sets and informal peer feedback.

Implementation

To begin, students receive an overview of the Manuscript 101 activity, including the instructions for all writing and peer review assignments (Supporting File S1). It is important that students receive instructions for the review phase at the same time that they receive the instructions for writing their manuscript because this will enable students to understand the assessment criteria for their manuscript. In addition, each student is assigned a cartoon data set. Student assignments and performance for each homework assignment can be recorded using the spreadsheet provided (Supporting File S2). Cartoon data sets should be emailed to each student (Supporting Files S3–S9). If desired, instructors can provide an imagined back story to the data, describing the initial project and questions used to motivate the experiments. This back story need not match the conclusions of the final data. Indeed, a mismatch between expectations and results may be best suited to simulating the scientific process. Finally, the instructor may want to emphasize that the order in which the data were collected does not have to match the order in which the data are presented in the manuscript.

The first lecture will explain manuscript writing instructions, manuscript structure, and scientific writing conventions. Lecture slides for the first lecture are provided (Supporting File S10), including an overview of the writing exercise as well as section-by-section manuscript guidelines to clarify content, format, and word limits. Depending on the class size, multiple students may receive the same data set. In this case, students are informed that they are permitted to work together to interpret their data but must acknowledge each other’s intellectual contributions as co-authors and must produce their own model figures and texts.

When all students have submitted their manuscripts, each document is assigned an anonymous identifier, redacted to protect student identity, and assigned to another student for formal peer review (Tables 2 and 3). Ideally, the data sets analyzed by author and peer reviewer should differ. We have kept track of assigned manuscript IDs and reviewer assignments using Supporting File S2. The goal of the peer review assignment is to provide students with a realistic peer-review experience from the perspective of the author and the reviewer. Peer review instructions include clear criteria for evaluating a manuscript (Supporting File S1). All of these instructions will be presented in the first lecture. Subsequent lectures will remind students of the homework instructions for each upcoming assignment. They will also assess student familiarity with the structure and style of a manuscript review and discuss the importance of tone in achieving constructive, critical peer review (Supporting File S10).

A final, optional lecture can be an excellent way to provide students with an overall evaluation of their performance and key lesson take-aways. We found it helpful to make note of recurring issues, problems, or themes and to highlight noteworthy examples while assessing each homework assignment. The final lecture is also an opportunity to compare and contrast the different interpretations and narratives that students come up with to explain the same cartoon data set.

Optional: Scaffolding Student Writing Across Many Smaller Assignments and In-Class Discussions

For undergraduates or other students with less writing experience, instructors may choose to divide the Manuscript 101 lesson into smaller assignments distributed across a quarter or semester (see Table 3). When students first receive their data sets, instructors may provide them time to discuss their figures in small groups. Students are instructed to deduce what is happening in each figure so that they can each decide on the overall scientific narrative, model figure, and figure order for Undergraduate Assignment 1 (Table 3). In class, instructors should answer clarifying questions about terminology or abbreviations but should not interpret the figures themselves. Students are also encouraged to look up terms or methods independently.

Following Undergraduate Assignments 2, 3, and 4 (Table 3) where students draft different sections of the manuscript, instructors may provide class time for peer feedback. Students will be paired with a partner who received a different data set. These pairs are kept the same for all informal feedback discussions and, in the formal peer review phase, students are not assigned their partner’s manuscript. Students are instructed to trade drafts with their partner and are reminded of the guidelines for this manuscript section. They should provide suggestions for writing structure and clarity throughout the document while also evaluating it according to the grading rubric. Once they have finished reading and providing written comments, students meet again with their partner to return the draft and summarize their comments. This structure provides students with detailed peer feedback on each section before their manuscripts are evaluated by the instructor.

2. Homework Assessments

Following peer review, students will receive two assessments of the manuscript they have written: one from the instructor and one produced by a peer student during Graduate Homework 2 (Table 2) or Undergraduate Assignment 6 (Table 3). The instructor assesses student performance on manuscript writing using the rubric provided as part of Supporting File S2. Note that the provided rubric should be considered a starting point, on which instructors can expand, depending on how much detail and guidance their students will need. The instructor may also choose to provide feedback on the manuscript by annotating or editing each document. The amount of detail to be provided will depend on the instructor’s available effort. In the undergraduate structure, students undergo a round of revision and resubmission of their manuscript. The revised manuscript can be evaluated with the same rubric. Students are also evaluated on the quality of their work as a peer reviewer using the rubric provided as part of Supporting File S2. All rubrics should be provided to students at the outset of the Manuscript 101 assignment.

3. Designing Your Own Data Sets

We have included two types of sample data sets that were designed for very different classes: a graduate level course in vertebrate developmental genetics and an upper-level microbiology undergraduate seminar focused on interbacterial interactions. This breadth demonstrates the flexibility of the Manuscript 101 activity to include additional model organisms and biological processes by devising new cartoon data sets. Here, we describe our approach to creating new cartoon data sets.

To devise our sample data sets, we used four criteria, which are generalizable to multiple biological disciplines. Our first criterion was that the cartoon data set should focus on biological processes and methods that have been described in class. In this way, the manuscript writing and reviewing homework can synergize with prior lessons. The second criterion was that each data set should highlight techniques for creating genetic gain and loss of function in order to test hypotheses in specific organisms. For example, our data sets focused on various model organism-specific approaches for altering gene expression. In this way, the activity reinforces experimental approaches as well as concepts. The third criterion was that each data set should highlight standard approaches for evaluating experimental outcomes. For example, our data sets included data that would have been generated using growth assays, cryo-electron microscopy, light and fluorescent microscopy, PCR, quantitative PCR, RNA-sequencing, in situ hybridization, immunofluorescence, flow cytometry, and western blotting approaches. Thus, the manuscript writing and reviewing is an opportunity to expose students to multiple experimental approaches. The final criterion used in creating our data sets was that several of our cartoon results could be interpreted in multiple ways. For example, a band shift on a gel could be due to alternative mRNA splicing or to protein cleavage. In this way, students are challenged to consider multiple alternative interpretations of an experiment and to propose how they could discriminate between the possibilities in future experiments. New figures can be hand-drawn or prepared using any computer illustration software.

Instructors can create cartoon data sets from their imagination or they can take inspiration from published work. For the undergraduate class, the cartoon data sets were inspired by recent papers in the field of interbacterial competition (7–9) and fictionalized. If instructors base their data sets off published work, we recommend changing gene names, species names, and other easily searched-for terms so that students write their manuscripts independently, without relying on the structure or logic of the published work. Figures will also need to be modified for simplification.

Teaching Discussion

Manuscript 101 is designed to model some of the most important scholarly activities of working scientists so that students can experience these activities early in their training. An additional benefit of this activity is that it exposes students to the creativity intrinsic to experimental science as well as the elegant structure imposed by the scientific method and manuscript writing conventions. From the instructor’s perspective, it is fascinating to observe diverse models that arise from a singular set of figures and rewarding to coach beginning scientists through some of their first forays in science communication.

In the graduate classroom setting, student comments indicated that learning objectives were met by Manuscript 101. Additionally, some expressed frustration that they were unable to “solve” the mechanism underlying the cartoon data. Similarly, some students wanted to know if the mechanism that they had proposed based on the cartoon data was the “correct” one. This reaction presents additional opportunities to discuss the process of creating new scientific knowledge and to emphasize that there is no “answer key” for working scientists. Rather, successful application of the scientific method enables elucidation of some truths and some uncertainties.

The Manuscript 101 structure also was easily adapted to an undergraduate setting, with several modifications to ease students into scientific writing. For example, undergraduate students benefitted when the manuscript writing task was broken up into smaller assignments across 8–10 weeks. The extended schedule of assignments meant that students received instructor and/or peer feedback at many steps along the way, which ensured they understood the data and the assignment instructions. This activity was implemented as part of an undergraduate seminar that focused on skills for scientific reading, interpretation, and writing. It was therefore an ideal complement to a seminar-type discussion class of primary literature. The seminar familiarized students with the structure and writing conventions of scientific papers, while the Manuscript 101 activity allowed students to experience the process of interpreting data and creating a scientific narrative. As a result, students experienced first-hand how papers are made and which steps are open to interpretation, rather than interacting with the primary literature only as an official, finished document.

When designing cartoon figures, we recommend that instructors focus on techniques that the students have learned about earlier in the course or that they have been extensively exposed to in prior courses. One challenge of the undergraduate course design was that the seminar structure did not include much specific instruction in experimental techniques. As a result, while some of the cartoon data sets worked well, Microbiology Data Set C was much more difficult than anticipated for the students to interpret, as they required a degree of comfort in thinking about PCR and mobile genetic elements. This illustrates the importance of matching the cartoon data to students’ skill levels and backgrounds. Even so, those who received this difficult data set were highly motivated to understand it, voluntarily meeting up multiple times for extra brainstorming time outside of class. The instructor provided guidance but emphasized that this challenge of trying to make sense of the data is often a key part of scientific research!

In the undergraduate course structure, students benefitted greatly from the informal peer feedback following Undergraduate Assignments 2, 3, and 4 (Table 3). Beyond an opportunity to improve their writing, these feedback sessions helped them to see if they had misunderstood the assignment or if they were explaining in too much or too little detail and to see how others had structured their arguments. However, the workload varied substantially among the assignments, with Undergraduate Assignments 2 (Results section) and 3 (Intro & Discussion) being particularly large. We recommend moving the Discussion section to Undergraduate Assignment 4. Overall, the Manuscript 101 lesson was a highly effective set of activities for introducing students to the process of interpreting data, crafting a scientific narrative, and experiencing both sides of the peer review process.

Supporting Materials

All supporting files were produced by the authors.

• S1. Manuscript 101 – Sample Homework Instructions

• S2. Manuscript 101 – Sample Assessment Materials

• S3. Manuscript 101 – Development Data Set A

• S4. Manuscript 101 – Development Data Set B

• S5. Manuscript 101 – Development Data Set C

• S6. Manuscript 101 – Development Data Set D

• S7. Manuscript 101 – Microbiology Data Set A

• S8. Manuscript 101 – Microbiology Data Set B

• S9. Manuscript 101 – Microbiology Data Set C

• S10. Manuscript 101 – Sample Lecture Slides

Acknowledgments

Research in the Ralston Lab is supported by R35 GM131759 from the National Institutes of Health Research. Research in the Levin lab is supported by R00 AI139344 from the National Institutes of Health.

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