Activities

Introduction to Activities

The activity templates provided below are merely examples and prompts to help spur the development of assignments suited to the CURE you are implementing. Each of them should be customized to your audience, course structure, grading scheme, time frame, etc. Throughout the activity prompts below, [text in square brackets] denotes text that will need to be edited with the appropriate information for your course. Additional edits may be required depending on the structure of your course. For each activity, a link to a Word version of the file that can easily be edited is provided next to the activity title.

Activity 1: Learning Goals – Activity 1

Notes to instructor:

• The recommendation would be to use the specific CURE goals developed in section E2 for the list presented to students in question 1 of the activity.
• Depending on the size of the class and the instructor resources, it might be valuable to pair this activity with a beginning of the CURE conference with each student to discuss question 5.

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Purpose of this assignment: Develop a list of personal goals and concerns for the entire project.

How does it fit within the entire project? You should be coming back to this document several times throughout the project as you reflect upon your experience with this research project. We will formally evaluate our personal learning goal progresses at the end of the semester.

Tasks required:

• Identify learning goals of interest within a list
• Write personal learning goals
• Express your concerns with the project

Deliverable: A completed version of this handout uploaded on [LMS] by deadline.

Estimated time: Less than 30 minutes

Group work or individual work? Individual work

Step-by-step:

1. Identify which of the goals presented on the first page of the [Document introducing the CURE to students] repeated below are most important to you. Select three or four.

• [Analyze multivariate morphological data
• Summarize (including graphically) your results
• Engage with the primary literature
• Synthesize information
• Tackle the study of novel data
• Manage a semester-long project
• Think like a scientist and
• Help move forward a scientific line of inquiry]

2. Explain for each of the goals selected WHY they are important to you.

3. Articulate in a short bullet-point list what your personalized learning goals for the projects are. This does not mean repeating any of the learning goals above but rather writing out something that I did not. You should write three goals that are specific to you.

4. Write out what your three biggest concerns for the project are. Be specific. The more specific you are, the easier the next question will be.

5. How will you try to mitigate these concerns? For each concern above, explain what steps you will take. These might involve particular scheduling, specific approaches to interacting with students or myself, resources you will seek, help you will ask me for, etc. Think about what has helped you before. Feel free to talk to classmates, friends, or myself to fill out this table.

Activity 2: Narrowing a Research Question – Activity 2

Notes to instructor:

• This activity was modified from an activity developed by Jane Hammons.
• Provide students with a sample research question—this should be a complex question (perhaps multi-part) that would require a lengthy publication or even a set of publications to adequately answer.
• This activity was designed to take place in class.

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Purpose of this assignment: The goal of this activity is to lead you to understand the constraints inherent to research and the importance of defining a specific question as part of the research process. You will learn to determine an appropriate scope of investigation and deal with complex research by breaking it into simple questions, limiting the scope of investigation.

How does it fit within the entire project? This activity will help you learn to focus your research question by taking a broad, complex question and breaking it down into a more manageable question.

Tasks required: Complete the activity below.

Deliverable: Completed version of this handout uploaded to [LMS] by [deadline] (one per person).

Estimated time: [to determine based on the initial question provided to the students]

Group work or individual work? Group work.

1. On your own, consider the research question presented to you. Break it down into less complex questions that would be appropriate. You have 10 minutes to brainstorm as many sub-questions as you can think of related to the main question. It may help you to think about the following ways to narrow a broad research question [these should be edited based on the initial question]:

• specific population or group
• more limited date range
• geographical area
• specific events

2. Consider the limitations of time, access to data and equipment, and other constraints on research undertaken as part of this class. Associate appropriate levels of concerns with each of your sub-questions.

3. Share your more focused research questions with your group members. Together, narrow down your list of combined questions to three or four you find particularly interesting. Make sure to associate with each their list of concerns. Write the list of questions on the whiteboard [or shared document].

4. Turn your attention to the list of questions of another group. Discuss which of the questions would be manageable, given the requirements of the course. Rank the questions from most (1) to least (4) interesting.

Activity 3: Researching Research in the Discipline – Activity 3

Notes to instructor:

• This activity was modified from an activity originally developed by Jane Hammons.

• Provide students with different articles that give students an illustration of the types of research that scholars in the field might undertake. Depending on the number of articles you select, students could discuss all of the articles, or each individual student or group could be assigned one article to review.

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Purpose of this assignment: The goal of this activity is to help you identify what “research” in the field means and how it is conducted.

How does it fit within the entire project? This activity will help you approach the research process recognizing the need to consider research as open-ended exploration and engagement with information and the importance of using various research methods, based on need, circumstance, and type of inquiry.

Tasks required: Complete the activity below.

Deliverable: Completed version of this handout uploaded to [LMS] by [deadline] (one per person).

Estimated time: [to determine based on the depth of the reflection, the number of source provided to the students, etc.]

Group work or individual work? Individual work [can be also used for group work].

1. Write a short reflection describing your understanding of research. Consider the following questions:
   • What does it mean to do research?
   • What is the purpose of research [in field of the CURE]? Why do people research?
     • To gain knowledge?
     • To share knowledge?
     • To answer questions?
     • To solve problems?
   • What are the actions that someone takes when they are researching?
2. Look at the articles you were provided and answer the following questions for each publication:
   • What is the purpose of the research? What was the author hoping to do or find?
   • What actions did the authors take? What constituted their research process?
   • What specific research methods did the authors use? Why did they select that method?
3. What are the differences and similarities across publications?
4. Write a synthetic summary addressing the following questions:
   • Why do scholars research?
   • What are the different steps of the research process in [the field of the CURE]?
5. Review your answer to question 1. What is your understanding of research now? How does your previous view match with your answer to question 4? Did your view of the purpose and process of research change?

Activity 4: Mind-mapping – Activity 4

Notes to instructor:

• This activity can be undertaken on paper or in a graphics software like Microsoft Paint. One can also use VUE (https://vue.tufts.edu/) or Google Jamboard (https://jamboard.google.com/) to create concept maps that can easily be edited. Directions for the download, installation, and use of the software program should be added to the step-by-step guide below.
• This activity was developed for a CURE in which students were given the opportunity to select from a series of defined projects consisting of one main question.
• Each project was provided two recent papers from the primary literature that represented model papers that investigated similar questions in different study systems.
• Students had already completed an in-class activity on reading and analyzing the primary literature [Activity 2].

Purpose of this assignment: The purpose of this assignment is to help you think about the questions and issues associated with your project, the existing literature, and necessary data for the analyses you are planning.

How does it fit within the entire project? This exercise will help you jumpstart your reflection on the analytical framework of your project, the basis of your work.

Tasks required: Read the two papers associated with your project following the approach we went over in class and complete this activity

Deliverable: PDF of your completed mind map

Estimated time: Less than two hours

Group work or individual work? Individual work

 Step-by-step:

1. Start your mind map by entering the title/question of your project from the syllabus/class presentation.
2. Identify the three keywords/expressions of your project title. Create independent bubbles stemming from the title for each of them. Do not count the study system as one of the keywords; fo
   cus on concepts.
3. Away from the existing bubbles, create a new bubble and name it after one of the two example papers associated with your topic.
4. Do the same thing for the second paper.
5. For each of the two papers, create two new bubbles. One should be titled “Question”, the other “Hypothesis”.
6. Can you identify the question and hypothesis for each of the two papers associated to your project? Add them to your mind map.
7. Using the two papers and the data from the initial project presentation to the whole class, can you develop your own question(s) and hypothesis(-es) for your project?
8. Create bubbles for the three keywords/expressions you identified for your project but for the two example papers (as appropriate).
9. What other keywords and concepts come to your mind from reading the papers that are associated to each of the three keywords/expressions? Complete the bubbles for the two example papers. Use as many bubbles as necessary and selectively reread the papers as necessary.
10. Use the bubbles from the two example papers to expand the bubbles for your own project. Ask yourself questions like:

• “What data do I need to represent the variables associated to my project?”
• “How is this variable commonly measured in published analyses?”
• “What analyses have already been undertaken in the literature? What do we already know about the question and the study system?”
• Do you have any other question?

Activity 5: The Scholarly Conversation—True or False? – Activity 5

Notes to instructor:

• This activity was modified from an activity originally developed by Jane Hammons.
• Divide students into pairs or small groups.
• You should customize the list of statements for your discipline/CURE.
• This activity is intended as an in-class activity including a class-wide synthesis and discussion after students have completed question 2.

Purpose of this assignment: The goal of this activity is to introduce you to the concept of the scholarly conversation and help you develop a greater understanding of who is involved and what their roles are. This activity will help you describe the concept of the “scholarly conversation”, recognize that you are often entering into an ongoing conversation and not a finished one, recognize that scholarly conversations take place in various venues, and start to see yourself as potential contributors to scholarly conversations rather than merely a consumer.

How does it fit within the entire project? As a researcher yourself, you will be consuming scholarship (through your readings), will have to learn to be critical to it, and will be contributing to it with the product of your research. You should learn how to navigate scholarship, learn the codes of the conversation, and make your place in it.

Tasks required: Complete the activity below.

Deliverable: Completed version of this handout uploaded to [LMS] by [deadline] (one per group).

Estimated time: [to determine based on the number of statements given to the students]

Group work or individual work? Group work.

Step-by-step:

Consider the list of statements below:

• Scholars engage in ongoing debates or discussions through their work
• Each source you use in a research paper represents a “voice” in a scholarly conversation
• For most scholarly topics, there is one clear, right answer
• As a student, you are not allowed to insert your own voice into the scholarly conversations in your field
• Providing citations is a requirement of engaging in the scholarly conversations in your field
• Reading recent journal articles can help you to track the scholarly conversations in your field

1. ON YOUR OWN first, consider each of the statements above. Which one(s) do you agree with? Articulate in a single sentence your reasoning/justification.

2. Review and discuss the statements as a group. Consider the following follow-up questions as you prepare a series of short statements summarizing the group consensus on each of the statements above. You should be ready to present your work to the whole class.
   • How do you see your role in the scholarly conversations on your topic?
   • How else might you learn about the conversations that are taking place in the field?
   • What role do citations play as part of the conversations? How does this compare from your own view of why citations are necessary?

3. ON YOUR OWN, write a definition of the concept of the “scholarly conversation.”

4. Compare your conversation with your teammate(s). What would the group consider to be your definition of a “scholarly conversation.”

Activity 6: Scholarship as Conversation—Minute thesis – Activity 6

Notes to instructor:

• This activity was modified from an activity developed by Jane Hammons, itself originally derived from the Minute Thesis activity described by James Lang in Small Teaching: Everyday Lessons from the Science of Learning (2016), pp. 106-108.
• You should customize the list of concepts and actions for your discipline/CURE.
• You may wish to select only one or two of the three videos provided below.
• This activity is intended as an in-class assignment associated with a class-wide conversation after question three.

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Purpose of this assignment: The goal of this activity is to be able to describe the concept of Scholarship as Conversation and explain how key activities that are part of the research process connect to the concept of Scholarship as Conversation.

How does it fit within the entire project? This activity will help you make connections between Scholarship as Conversation and actions that you complete as part of the research you are undertaking in this class, such as reviewing the literature and providing citations

Tasks required: Complete the activity below.

Deliverable: Completed version of this handout uploaded to [LMS] by [deadline] (one per person).

Estimated time: [to determine based on the number of videos and the number of concepts and actions given to the students]

Group work or individual work? Individual work [can be also used for group work].

1. Watch the following video [pick one of the videos or more]:
   1. Scholarship as Conversation
   2. How Library Stuff Works: Scholarship as Conversation
   3. Research is a Conversation
2. Consider the following list of concepts:
   1. Citations
   2. Developing a Research Question
   3. Literature Review
   4. Peer Review

Select two of the items on the list [depending on your goals, you could have students select the concepts themselves, or divide students into groups or pairs and assign concepts. You can also adjust the number of concepts students work with.].

3. For each concept you selected, write for one minute [or two or three] explaining how the concept connects to the broader concept of Scholarship as Conversation. How, for example, does providing citations part of engaging in the scholarly conversation? You should be prepared to present your work to the classroom.

Activity 7: Reading and Analyzing the primary literature – Activity 7

Notes to instructor:

• The key to this activity is to choose a well-written model paper from the published literature on a topic related to the one discussed in the CURE.
• The template below should be completed with the relevant sections from the chosen publication.
• Depending on the structure of the publication read, some adjustments to the prompt will be necessary, but the activity should make sure to match the critical elements of a publication identified in the introduction to the activity with the elements showed to students.
• The handout should be designed such that students do not look ahead while completing the activity (use explicit guidelines such as “Do not look below the line” or “Do not turn the page yet”).

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Purpose of this assignment: Learning the structure of [scientific] papers and an effective approach to reading the primary literature

How does it fit within the entire project? This activity will help you prepare for your literature review and help set the stage for the structure of the entire project by highlighting the different sections of an article from the primary literature.

Tasks required: Complete the handout below.

Deliverable: Completed version of this handout.

Estimated time: About one hour

Group work or individual work? Individual work and group discussion during class.

(1) the title gives you the main topic or point of the paper, sometimes even the punchline.

(2) the abstract is essentially a summary of the paper and should introduce the questions or hypotheses investigated, the main results and conclusions of the study.

(3) the figures and tables are critical because they present the data, results and sometimes interpretations

(4) the introduction and conclusion (or end of the discussion) may sometimes be useful

If you cannot get the key points of the study from these sections of the paper, it is not your fault. The paper was not well written. Let’s practice on the paper below published recently in [XXXXXXXXX], a journal where some of the projects of this class could be published.

[Full reference for the article formatted according to the guidelines the students will have to follow in their main written deliverable, if applicable, or a standard/classic publication outlet in the field]

Exercise: Answer the questions below based on the information presented to you up to that question in the handout. Do not jump ahead, you will spoil the fun!

 [Insert here the title, author information, abstract of the publication, and introduction omitting the approach adopted by the authors]

1. Based on the title and abstract above as well as the introduction , what was the question the authors sought to answer in this study? Use your own words. Do not quote the paper.
2. What was/were the hypothesis(es) the authors were testing? It may not be stated explicitly.
3. What is the [scientific] significance (i.e. importance/meaning) of this study that is articulated by the authors? Highlight the relevant sections in the text.
4. I have purposefully truncated the last paragraph of the introduction in which the authors describe their methodology. Do not peak at the following pages of this handout. Can you devise an analysis of your own to investigate the same questions as the authors? You do not have to know the technical terms, use your own words to describe your approach.

[Insert here the last paragraph of the introduction in which the authors describe their approach]

5. Use a schematic to draw expected results if the hypothesis tested by the authors is verified. Also include an alternative schematic in case the hypothesis is not supported. Use a different diagram to represent each of the hypotheses tested in the study.

[Insert here any figure or table associated with the material and methods section of the paper]

6. What data were collected by the authors based only on figures and tables? What other critical piece of information about the material and methods is not presented in the form of a table or figure in this article?

[Insert here any figure or table associated with the results section of the paper]

7. Based on the figures and tables, what tests did the authors of this paper actually perform?
8. Can you summarize the results (not interpretations) of the authors?
9. What conclusion can YOU draw from the results? (This is the time for interpretations).

[Insert here excerpts from the discussion section focusing on the conclusions drawn by the authors. Includes any associated summary figure(s)]

10. What are the conclusions of the paper according to the authors?
11. Do you think their conclusions are supported? What is a strength of this study? A weakness?
12. What would be the next step in this field of study in your mind? What follow-up study would you carry? Any lingering question?

Activity 8: Annotated Bibliography – Activity 8

Note to instructor:

• Also include guidelines from the library services of your institution on how to incorporate direct access to articles in Google Scholar as well as how to find articles not directly accessible via Google Scholar.

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Purpose of this assignment: The goal of this assignment is to identify relevant papers from the published literature to help you develop your project.

How does it fit within the entire project? The publications you will find and analyze will help you identify the dialogue around your research topics, develop analyses, compare your results to previous findings, and place them in a broader context.

Tasks required: Read five articles following the methods demonstrated in class and complete the activity below.

Deliverable: A completed copy of this handout uploaded on [LMS] by [due date] AND a PDF copy of each paper you are summarizing uploaded to the [online shared folder] for your project.

Estimated time: About two hours and a half

Group work or individual work? Individual work requiring group coordination.

1. Use your answers to the mind mapping activity to identify below keywords associated to your project:

2. Go to https://scholar.google.com/. Use the keywords you identified to search for relevant papers.

3. Click on the link to the papers that have cited the most relevant publications to find additional papers (“Cited by …”):

4. Consider also clicking on the “related articles” link for other suggestions:

5. Enter the title of each of the papers provided to you at the start of the semester. Search for papers that have cited these publications and related research.

6. Look at the authors of the paper you find. Are there authors that have published multiple papers on a topic of interest to you? Look at their other publications. Some authors have a Google Scholar profile (their name is underlined), for those who do not, consider searching by authors in Google Scholar or search for their website.

7. Search the literature cited/references of the papers you find to get older papers. Use the search function of Adobe Acrobat Reader and keywords to find other references cited in the papers you have found. You can apply these techniques to the papers I provided you at the start of the semester.

8. Use this tool: https://www.connectedpapers.com/. Enter the title of a paper to explore related papers and find papers central to the conversations.

9. You should coordinate with your teammates to avoid overlaps in publications among you. Your literature review should only be based on research publications (peer-reviewed articles, university press books/book chapters). If you are unsure whether or not a publication is appropriate, feel free to check with me. For a minimum of five publications, you should provide:

• Full reference (title, authors, journal, etc.) formatted as in [the Journal of Morphology] (see https://tinyurl.com/ycm7u9r8)
• Summary of the paper (<100 words)
• Why it is important to your research (i.e. what you will gain from it) in <100 words

Very important notes from the Library system:

[If you do not see OhioLink hyperlinks in your results, you must do the following:

Go to Google Scholar (http://scholar.google.com)

Click on the hamburger button.

Click on “Settings” near the gear.

Click on “Library Links” on the left side

Type OhioLINK in the text box and hit enter

OhioLINK-Find it with OhioLINK will now appear below that text box

Be sure the check box next to it IS checked

Click on “Save” at the top or bottom

Search with the OhioLINK connection!

If you are off-campus, you must ALSO do the following:

Open a new tab in your browser

Go to this address: https://auth.ohiolink.edu/DS/

Select Ohio State University

Select OARDC campus (this is the other Wooster campus)

Log in with your name.#

You will see a page for OhioLINK databases; leave this tab open while searching Google Scholar with the OhioLINK connection!]

[Use these Ohio State Libraries’ services if you do not find free full text through Google Scholar:

• Research Databases List: search or browse by database name or browse by subject. Many database have full text or use Find It! to locate available full text provided by the Ohio State Libraries or OhioLINK.
• Online catalog: search by journal title or book title.
• Online Journals List: search or browse by journal title.
• Request a copy via the Ohio State Libraries’ Interlibrary Services.]

Activity 9: Tracing the Scholarly Conversation – Activity 9

Notes to instructor:

• This activity was developed by Jane Hammons.
• Provide students with a source that is a few years old (it should be old enough that other researchers will have had time to cite it in their own published works). Or, have them locate a source relevant to their topic that is a few years old.

Purpose of this assignment: The goal of this activity is to help you learn how to trace the scholarly conversation on a topic, using references and “cited by” tools to find previous and more recent works related to a specific source.

How does it fit within the entire project? The review of the existing literature on a topic is critical to assessing the knowns and unknowns of the topic, the context for the scholarly conversation on this topic, the important actors of this conversation, and identify the contribution that particular articles, books, and other scholarly pieces make to knowledge on the topic.

Tasks required: Complete the activity below.

Deliverable: Completed version of this handout uploaded to [LMS] by [deadline] (one per person).

Estimated time: [to determine based on the depth of the reflection, the number of source from the citation list to study, etc.]

Group work or individual work? Individual work [can be also used for group work].

Tracing the Conversation Backward

1. Look at the source provided to you. Review and summarize briefly the source.
2. Answer the following questions:
   • Do you think this researcher(s) was the first to explore this topic?
   • How would you use this source to find previous research on this topic?
3. Review the citations/Literature cited for the article. Answer the following questions:
   • What is the oldest source that you can find listed?
   • Are there any journals that you see that are cited more than once?
   • Are there any authors that are cited more than once?
   • Which sources do you see that look as if they would be the most relevant to the specific research question?
4. Select [one] source from the citation list. Locate that source and compare it to the original source—what is the relationship between the two sources?
5. Repeat steps 3 and 4 for this second publication.

Tracing the Conversation Forward

6. Return to the original article. Answer the following questions:
   • Do you think this was the final word on the topic?
   • How could you use this source to find more recent sources on the topic or research question?
7. Locate the original source on “Google Scholar”. Review the citations for the article by clicking on “Cited by …”. Identify at least one source that cites the original source.
8. Compare the original and the more recent source. How would you describe the connections between the two sources?
9. Continue to trace the conversation forward, by finding a source that cite the newer publication.

Reflection

10. Write a short reflection on what the activity taught you. Answer the following questions:
    • What did you learn in this activity about the importance of citations (or how scholars use citations)?
    • What did you learn about the scholarly conversation on the topic?
    • How do you plan to apply what you learned to your own research practices?

Activity 10: Visualizing the Scholarly Conversation – Activity 10

Notes to instructor:

• This activity was developed by Jane Hammons.
• Provide students with a focused research question relevant to the CURE. You can also work with a student-generated question.
• Provide students with several articles or scholarly works on the topic. Depending on how much time you want students to take on the activity, you may want to provide them with summaries of the source. Be sure to include the citation information for each source, as well as the reference list.
• This activity can be undertaken on paper or in a graphics software like Microsoft Paint. One can also use VUE (https://vue.tufts.edu/) or Google Jamboard (https://jamboard.google.com/) to create concept maps that can easily be edited. Directions for the download, installation, and use of the software program should be added to the step-by-step guide below.

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Purpose of this assignment: The goal of this activity is to help you come to better understand the concept of the scholarly conversation by creating a visual representation of (a small part) of the scholarly conversation on a specific topic or research question.

How does it fit within the entire project? This activity will help you approach the research process including your literature review as well as the discussion of your findings by encouraging you to suspend judgement on a particular piece of scholarship until the larger context for the scholarly conversation is better understood, recognize that a given work may not represent the only or even the majority perspective on a topic, understand the context for the scholarly conversation on your topic of research, the important actors of this conversation, and what each element of the conversation has contributed.

Tasks required: Complete the activity below.

Deliverable: Completed version of this handout uploaded to [LMS] by [deadline] (one per person).

Estimated time: [to determine based on the depth of the reflection, the number of source provided to the students, etc.]

Group work or individual work? Individual work [can be also used for group work].

1. Create a visual representation that demonstrates the connections between the sources and the contribution that each has made to the conversation on the topic. You may wish to follow the model of a concept map (examples).
2. Consider the following questions:
   • Does it appear that the sources can be grouped or divided in any way? For example, are there any sources that provide a similar perspective on the topic, or come to similar conclusions?
   • Are there any sources that provide a perspective or conclusion that is radically different from the others?
   • Are there other similarities between the sources in terms of research methods?
   • Are there any of the sources that appear to have influenced the other sources? For example, are there sources that are cited by the majority of the other sources?
   • Are there sources that appear disconnected from the conversation? Are not cited by any of the other authors?
3. Write a summary of the conversation based on the sources provided.

Activity 11: Identifying Commonly Cited Sources – Activity 11

Notes to instructor:

• This activity was modified from a set of activities originally developed by Jane Hammons.
• Have each student locate a set of academic journal articles relevant to the course or field a part of the exercise or provide students with a list of articles relevant to the CURE and assign different students or groups of students to work with specific subsets of articles from the list.

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Purpose of this assignment: The goal of this activity is to help you understand the types of sources that are most commonly cited in research in the field and lead you to identify disciplinary authorities and recognize that authority is constructed and contextual.

How does it fit within the entire project? This activity will help you recognize the books, journals, databases, and scholars that are generally considered more authoritative than others and identify the types of sources that are most commonly cited by scholars in the field.

Tasks required: Complete the activity below.

Deliverable: Completed version of this handout uploaded to [LMS] by [deadline] (one per person) and participation on the discussion board of the [LMS] by [deadline].

Estimated time: [to determine based on the number of source provided to the students]

Group work or individual work? Individual work [can be also used for group work].

1. For each of your selected [or assigned] articles, you should review the citations AND the literature cited. Answer the following questions:
   • Rank the following source categories in order from most often cited to least often cited: academic journal articles, books, government reports, news and magazine articles, [insert other source types relevant to the CURE].
   • What other types of sources are cited?
   • Identify any scholar(s) whose work is cited multiple times by multiple authors across all sources.
   • Identify any journals that are cited multiple times. Are there journals that are cited more often than others? Which ones? Identify the top five.
   • Is there a specific source (e.g., an academic journal article) that is cited by a majority of other sources available to you?
2. Share your results on the [discussion board] by [deadline].
3. Between [date] and [date], review the combined results. Answer the following questions:
   • What types of sources seem to be most commonly cited by scholars in the field?
   • Are there any types of sources that rarely seem to be cited in the field?
   • Whose voices may be missing from these sources?
   • What did you learn in this activity that may be relevant to you as a future scholar in this field?

Activity 12A: Peer-Review (Model A) – Activity 12A

• Try to provide every student/group of students with two or three peer-reviews.
• The framework presented here can be truncated to enable peer-reviews at earlier stages of the CURE.
• Iterative reviews can be associated with additional peer-review elements such as: “Did the revisions incorporate your feedback? If not, what are they yet to implement?”
• Consider sharing with students examples of constructive and respectful peer-reviews (of your own work or other students’ work following ethical guidelines) that can act as models for the work they are expected to produce.

Purpose of this assignment: The goals of this assignment are (1) to provide your peer(s) with constructive feedback on their writing that will help them improve their papers and (2) to encourage you to reflect on your own writing.

How does it fit within the entire project? The process of scholarly publication involves peer-reviews. As such, the peer-review you are performing here is akin to the work asked of professional academics. The peer-review process is critical to assessing the quality of the research work, the modifications necessary to it, and the advancement of the scholarly dialogue. The peer-reviews you receive will directly enable you to improve your paper and those you provide will help you reflect on your own writing, thus indirectly leading to improvements in your paper.

Tasks required:

• Critically read the [paper] of your [classmate].
• Answer the questions below with complete sentences. Do not simply write yes or no. Explain every “no” answer and support your argument. Provide information on how each element of the paper could yet be improved when answering “yes”
• Remember to be constructive and acknowledge positive points.

Deliverable: Completed copy of this handout uploaded on [LMS] by [due date].

Estimated time: About [xxxx]

Group work or individual work? Individual work.

1. Please summarize the paper (less than 200 words): In other words, write an abstract for it
2. Highlight here three things that were done well in this paper
3. Highlight here three things that need to be revised for the final version of this paper
4. Answer the questions below in the table provided.
   

   General issues

   Is the writing appropriate for an academic paper?

   Is the paper appropriately formatted?

   Are the paper and its different sections of appropriate length?

   Are the paper and its different sections clearly organized following the structure of [scientific] publications?

   Is the paper free of writing, spelling, and grammatical errors that impact its understanding?

   Material and Methods

   Are the methods appropriate, given the research question?

   Are the data used appropriate (including sample size, variables measured, sampling across categories, etc.)?

   Are predictions derived from the hypothesis (-es) laid out?

   Are all analyses undertaken described with sufficient detail to enable another researcher to repeat the work?

   Does the paper repeat standard procedures that all scholars know how to do?

   Results

   Are the results thoroughly presented?

   Does the text reference the figures and tables?

   Is the interpretation clearly excluded from the results section?

   Discussion

   Does the paper skillfully interpret the results? Is the data interpretation appropriate, accurate, and unbiased?

   Does the paper provide a thoughtful and thorough discussion of possible future studies or alternative approaches?

   Does the paper provide an insightful explanation of the reasons underlying the pattern in the data?

   Is there a compelling discussion of the implications of findings?

   Does the paper explicitly interpret the results in relation to the hypothesis (-es)?

   Does the paper discuss inconsistencies, uncertainties, or limitations of the results?

   Are the findings compared to those published in prior research or put into contest (as appropriate)?

   References

   Are the citations presented consistently and professionally throughout the text and in the list of works cited?

   Figures and Tables

   Are the tables and figures clear, effective, appropriate, and informative?

   Are the figures and tables accompanied by brief but adequate captions?

   Do the figures and tables each have adequate labels (including legends and axes’ labels)?

   Are the figures and tables numbered and cited within the text?

   Are the tables properly formatted with no vertical lines and no unnecessary formatting?

   Is the text on the figures large enough to be read?

   Is the format of the graphics appropriate for the data represented?

   Are the figures informative and relevant to the paper?

   Do all captions start with the appropriate figure number?

   Is the caption informative?

   Are all elements of the figure appropriately explained?

   Are all abbreviations used in the image provided in the caption?

   Does each caption follow the required format?

5. Write below a bullet point list including six elements of your paper you will revise in light of your reading of your classmate(s) paper. For each of them, provide details about the change you will make and the rationale for that change.

Activity 12B: Peer-Review (Model B) – Activity 12B

Notes to instructor:

• This activity was modified from an activity originally developed by Ryan Norris.
• This activity is based upon the peer-review template of a discipline -specific journal (here the Journal of Mammalogy). The activity should be adapted to fit an appropriate model journal for the discipline of the CURE.
• Examples provided throughout the document should also be edited to reflect the disciplinary focus of the CURE.

Purpose of this assignment: The goals of this assignment are (1) to provide your peer(s) with constructive feedback on their writing that will help them improve their papers and (2) to encourage you to reflect upon the process of scholarly publishing.

How does it fit within the entire project? The process of scholarly publication involves peer-reviews. As such, the peer-review you are performing here is akin to the work asked of professional academics. The peer-review process is critical to assessing the quality of the research work, the modifications necessary to it, and the advancement of the scholarly dialogue. The peer-reviews you receive will directly enable you to improve your paper and those you provide will help you reflect on your own writing, thus indirectly leading to improvements in your paper.

Tasks required: Complete a review of a peer’s paper following the guidelines provided in this prompt.

Deliverable: Completed copy of this handout uploaded on [LMS] by [due date].

Estimated time: About [xxxx]

Group work or individual work? Individual work.

Regardless of your final profession, you will be influenced by the peer-review process. It is foundational to modern science and allows for science’s gold standard, the peer-reviewed publication. The process is similar whether it involves a publication in mammalogy, medicine, or astrophysics. You have read many peer-reviewed papers, but I’m hoping to de-mystify how they came to be what they are, and, hopefully, why we hold them in high regard. You and your classmates have written papers that involve novel data that allow for you to address questions in a way that is unique relative to what’s come before. Some of you have drawn exciting conclusions or refuted established ideas.

There are numerous online sources suggesting how to write a good review; I might suggest this one: http://www.indiana.edu/~halllab/grad_resources/Benos_2003_HowToReviewAPaper.pdf I will provide a short set of explanations below, but bear in mind two primary goals. You are reviewing this paper: 1) to help the editor assess the quality of the paper and its conclusions 2) with the goal of helping the authors make it as good as can be. As with more senior scientists, you should not go into a review with the intent to help your friends or to thwart your competitors. The process is often anonymous to aid in that purpose.

Your review has two components: “Confidential comments to the editor” and “Comments for the author”. Please clearly divide your review into these two sections.

Confidential comments to the editor

These comments will not be shared with the author(s).

1. Begin with your final recommendation. Your four options are “Accept”, “Accept pending minor revision”, “Reject but encourage resubmission following major revision”, and “Reject”. If you would like, you may use a shorthand of Accept, Minor revision, Major revision, or Reject. The [model journal] has an online form for the upload. It involves a button indicating your decision and two simple plain text boxes. You will just be including this recommendation in your email to me. Some journals have an “Accept pending major revision” decision, but these are rarely used and we are copying [model journal], which does not use this.

I generally think of minor revision as restricted to situations where there are a few problems, but no new analyses are needed and the conclusions are soundly supported by the data. As soon as you start to require a new analysis, you open up the possibility that the conclusions will no longer be supported and it becomes major revision. Reject involves situations where it is not appropriate for the journal, the core conclusion of the paper cannot be justified, or the paper is in such bad shape that you don’t anticipate it can be made acceptable without overwhelming changes.

The reason your recommendation is not shared with the author is because the final decision rests with the editor after receiving all reviews. You may have overlooked a fatal flaw in the manuscript or you may have been much harder on the authors than other reviewers. The editor may decide after reading your review that you may be too close to the author or topic, that your recommendation is completely at odds with your review, or that you may not have adequate knowledge about an important component.

2. Beyond the recommendation, you may have nothing else you need to say to only the editor. That is fine. You may, however, want to share information exclusively with the editor. For example, if you are really unhappy about some aspect of the paper, this is the place to tell the editor you’re your concerns are and why you think these preclude the publication of the paper. You might also be wary to note something in the comments to author that may expose your identity. Mostly, however, this section is used to clearly explain your recommendation. For example, you might wish you were given an option for “moderate revision”. Let the editor know that. The bulk (or all) of your review, however, should be available to the author.

Comments for the author

3. Both the author(s) and editor will be reading this section. There are many ways to construct a review. It’s one of those writing tasks with no formally correct methodology. I do, however, tend to think that effective reviews contain 4 main components: summary, positive statements, major concerns (if present), and minor concerns. I will make recommendations along those lines.

Summary. Start by summarizing the paper and your thoughts about the paper. This isn’t exactly an abstract; your focus should relate to the major conclusions in plain language and how well they are supported. By summarizing the paper, you establish your understanding of what you read and can often explain that to the editor in less technical language than the authors are able to use.

Positive statements. It is important to acknowledge the positive in your colleague’s (or classmate’s) work. Acknowledging the good in a work has several other benefits. If your editor is not knowledgeable about the topic, they may need you to tell them that what is presented here is important or valuable. You not only need to justify why you failed to suggest a paper be accepted, but also why you failed to suggest a paper be rejected.

Major concerns. What are the main points that represent the focus of your review? If you did not recommend accept or minor revision, why? (Hint: it’s not because they mixed up “their” and “there” on page 14). Do you think they need to conduct a different analysis? Repeat the one they conducted using different parameters? Did they misinterpret their statistical test? Are they trying to draw bigger conclusions than their data justify? Did they overlook an important paper?

I tend to number these major concerns and devote at least a paragraph to each. This gives the authors a clear set of bullet points in their response. Note that the authors do not have to accept everything you say (and even the editor may tone it down in his/her decision letter), but if they disagree with you, they will need to justify it. You may disagree with the conclusions the authors present, but your main job is to decide whether their conclusions are justifiable. Throughout the review, refer to the paragraph or sentences in question using the line numbers. For example: “I disagree with the statement (line 76) that Myodes is clearly monophyletic. Kohli et al. (2014) clearly demonstrated that several Alticola species are part of the Myodes clade.”

I tend to end my major revisions section by stating something along the lines “Minor concerns follow.”

Minor concerns. This is where I place changes that, absent the major concerns noted above, might only warrant a “minor revision” decision. These may require a paragraph for explanation, a sentence, or just a few words. This may involve good science (e.g. “Line 56: Report your standard deviation in addition to your mean.” Or “Lines 19-24: Explain the settings of your BEAST analysis”), clarity (“Fig 3: Your gray icon on white background is not visible. Try black.”), or spelling/grammar (“Line 78: “their” should be “there”).

I will often use a shorthand that looks like this but you are not required to use this.

Minor suggestions follow:

Line 5: their -> there

L7 Italicize Myodes.

L10-11 This sentence is unclear

L17-19. Have you looked at Kohli et al. (2014)?

L27 “2010), the next” -> “2010); the next”

Note that your review is usually converted to plain text. If you want to refer to italics, for example, you should say so and not rely on something you wrote being italicized.

4. Finally, you probably cited literature in your review. If the papers you cite are already in the manuscript’s Literature Cited section, you don’t need to add the full citation in the review. If not, however, add a Literature Cited section at the end of your review. Formatting rules are looser here, but generally follow the journal’s approach.

Activity 13: In-Class Group Meetings – Activity 13

Notes to instructor:

• The example provided here is for the material and methods. Similar meeting structures can be developed for other elements of the CURE.
• This activity is designed for groups of four students. Adjust accordingly.
• The dates in the last table are the dates between the day of the group meeting and the due date of the deliverable. The number of rows should be adjusted accordingly.

Purpose of this assignment: The goal of the meeting today is to help you prepare the [material and methods] section of your paper.

How does it fit within the entire project? [Explain here the purpose of the relevant section of the deliverable. Here is an example for the material and methods: The material and methods present to your readers all of the information necessary to explain how you obtained your results and how these analyses might be replicated. It mentions the nature and origin of the data studied (the material), how they were analyzed (the methods). This is a critical element of every research publication.]

Tasks required: Complete the activity below.

Deliverable: Completed version of this handout uploaded to [LMS] by [deadline] (one per group).

Estimated time: [to determine based on the number of group members, number of questions, etc.]

Group work or individual work? Group work.

1. Within your group, you will all, in turn assume the following roles:

• Recorder: Takes notes of the conversation taking place.
• Presenter: Presents their findings.
• Encourager: Pushes back on specific statements or too quick a consensus . Encourages the consideration of a number of options or viewpoints, focuses on potentially rich areas of disagreement.
• Facilitator: Ensures the group stays on task and on time. Additionally, the facilitator will enforce speaking opportunities (see below).

Fill out table below with your names. Notice that you will change roles throughout the conversation:

2. The structure of the conversation is the following. Please read the list in its entirety before to start the conversations:
   • The facilitator will remind everyone of their roles for the conversation that is about to take place.
   • The facilitator will yield the floor to the presenter who will go over their answers to the following questions from the agenda activity associated with this meeting.
     • Are there elements of your material and methods outline that need to be edited or added based on comparisons with the two template papers?
     • What other papers have you found to have helpful material and methods section?
     • Are there elements of your material and methods outline that need to be edited or added based on your readings beyond the two template papers? Mention specific elements.
   • The facilitator will (kindly) ask the person to stop their presentation after five minutes.
   • The facilitator will ask the encourager to ask questions and raise concerns or counterpoints for three minutes.
   • The facilitator will also raise concerns and ask questions for a maximum of two minute.
   • The presenter will reply to those for a maximum of two minutes.
   • The facilitator will check the clock and announce the time elapsed. The encourager should push for additional conversations drawing on points raised so far to get the time to approximately twelve minutes of conversation.
   • The recorder will take notes throughout the entire conversation and then provide a summary to the entire group in a maximum of two minutes.
   • The group will submit corrections to the record as they wish for a maximum of one minute enforced by the facilitator.
   • All members of the group should make use of the board as necessary to show information or organize their thoughts.
   • Go to the next person and repeat until everyone has presented their answers and had a chance to (respectfully) debate the other group members.

3. Using the notes from the recording role you assumed earlier, complete the following questions as a group:
   • What is the final outline of your material and methods section?
   • For each of those, provide a one to three sentence summary of the information that will be included. Use the table below. Leave the second column of the table blank.

• • For each element of your material and methods above, add in the second column relevant and necessary references. Those would be the papers that you will cite in your writing.
  • Use different colors (use the highlight tool of Word) to assign each section of your material and methods to a member of the group.

In doing so, keep in mind the following:

• The length of the section/subsection assigned to each person
• The familiarity of each team member with the relevant references/sections/concepts
• The technical complexity of each section/subsection
• The number of references to read/skim/check/cite
• Your own commitments to other classes, job, life …

4. Use the end of this page to develop a timeline for the writing process. The draft is due on [due date]. Keep in mind that you will need to check the entire work for a sense of unity. It should be a single piece, not a collection of pieces put together. The different sections of the material and methods should work TOGETHER both in terms of writing and in terms of concepts/explanations/narrative.

Activity 14: Meeting Agendas – Activity 14

Notes to instructor:

• Select the appropriate information above depending on the specific group meeting.
• Select the appropriate set of questions below depending on the specific group meeting.

—

Purpose of this assignment: Develop an agenda for your [specific meeting] meeting during class

How does it fit within the entire project?

[Framework]: The framework of your project will guide the entire experience. The framework is the basis of the analytical thinking. It is critical that you come to class with a sense of where you are taking your project.

[Material and Methods]: This agenda will enable you to have a productive in-class meeting to develop your material and methods section and articulate your data collection and analysis process in details to your readers.

[Figures and Tables]: This agenda will enable you to have a productive in-class meeting to develop your figures and tables, which are central to the presentation of your findings to readers.’

[Results]: This agenda will enable you to have a productive in-class meeting to develop your results section, which will complete your work on the figures and tables.

[Discussion]: This agenda will enable you to have a productive in-class meeting to develop your discussion section, which is one of the most critical element of your manuscript because it summarizes your findings, places them in context (of prior results, the field, etc.), and explains the significance of your work.

[Introduction]: This agenda will enable you to have a productive in-class meeting to develop your introduction section, which is the sister section of the discussion because it presents the questions and hypotheses you are investigating, places your work in context (of prior results, the field of research, etc.), and explains the significance of your work.

Tasks required:

• Coordinate with your team members to fill out the worksheet below
• Upload complete agenda on the discussion board

Deliverable: Upload of agenda on discussion board of [LMS] by [deadline].

Estimated time: Less than [thirty] minutes

Group work or individual work? Individual and Group work

Step-by-step:

[Framework]:

1. Much of the meeting will be devoted to the sharing of the information you prepared as part of your workbook activity reflecting upon your readings and mind mapping activity. You should make sure to do the following prior to the meeting
   • Complete and bring your workbook questions for [Framework I].
   • Complete and bring your [mind mapping activity].
   • Read the [project framework meeting sheet].
2. Complete the questions below individually:
   • What are your biggest concerns about the project so far?
   • What resources do you need from me?
   • What terms from your readings do you not understand?
   • Do you have questions for me about specific components of your readings?
   • Are there aspects of the project that still confuse you (structure and/or subject)?
3. AS A GROUP, go over your answers to the questions above.
   • Can you answer some of your teammate’s questions?
   • Combine redundant questions as necessary.
   • Make a list of all remaining questions. This is the agenda for the meeting to upload (we will go over these questions in class).

[Materials and Methods]:

1. Much of the meeting will be devoted to the discussion of the outline of your material and methods and the development of this section of your paper. You should make sure to do the following prior to the meeting
   • Complete and bring your workbook questions for [Material and Methods II].
   • Complete and bring the [outline activity from the last class meeting].
   • Read the [material and methods meeting sheet].
2. Complete the questions below individually:
   • Write out below an outline for your material and methods section that includes all headers and subheaders.
   • Go back to the two template papers you were provided at the start of the semester. Write out below an outline for each paper’s material and methods section including headers and subheaders (note that they might not be explicit).

• • Are there elements of your outline that need to be edited or that you need to add based on a comparison with the two published template papers?
  • What other papers have you found to have helpful material and methods section? These might include papers that describe analyses you will be using, papers that address similar questions to the one you are working on in a different study system … For each of them, provide a full reference as you would cite them in your paper.

3. Do you have questions for me about specific components of your material and methods?
4. AS A GROUP, put together a complete list of all of the references you included in your answer to question 2d. Upload it on the discussion board. It is your agenda assignment for the meeting. Make sure that a PDF copy of every paper that will be useful to you is available in [a shared folder] for all team members to see and download.

[Figures and Tables]:

1. Much of the meeting will be devoted to the discussion of the choice of figures to include in your paper, their format, and their captions. You should make sure to do the following prior to the meeting
   • Complete and bring your workbook questions for [Figures and Tables II].
   • Complete and bring the [Graph Predictions activity].
   • Read the [Figures and Tables meeting sheet].
2. Complete the questions below individually:
   • List below all figures and tables you expect to include in your paper.
   • Go back to the two template papers you were provided at the start of the semester. Write out below for each paper a list of all figures and tables included in the main section of the paper. Make sure to provide a shortened title or description for each. Differentiate between figures and tables explicitly.
     

     Paper 1:	Paper 2:

     1. • Compare your answers to questions 3a and 3b. Are there figures you should add or delete from the main section of your paper? What about tables?
        • Consult the supplementary information for one of the papers you have read. Write out below in the format of the [Journal of Morphology] the reference for this paper.
        • What figures or tables are you planning on including in the supplementary information/appendices of YOUR paper that will not be in the paper but online (Accessible via a link)? Explain why these are necessary but will not be in the main paper.
3. Do you have questions for me about specific components of your figures and tables?
4. AS A GROUP, make a list of your answers to question 3 combining them as appropriate. Put together a complete list of all of the references you included in your answer to question 2d. Upload this information as a single file on the discussion board. It will be your agenda assignment for the meeting. Make sure that a PDF copy of every paper that will be useful to you is available in [a shared folder] for all team members to see and download.

[Results]:

1. Much of the meeting will be devoted to the discussion of the outline of your results sections. You should make sure to do the following prior to the meeting
   • Complete and bring your workbook questions for [Results I].
   • Complete and bring the [Writing a results paragraph activity].
   • Read the [Results meeting sheet].
2. Complete the questions below individually:
   • Repeat below the outline for your results section that includes all headers and subheaders (from your workbook).
   • What are the highlights of your findings? Summarize in no more than two sentences each the four main findings of your study.
   • Match these four elements to the outline you wrote in question 3a. Do they all fit? Do you need to revise your outline?
   • How does each figure and each table associated with your results section fit onto the outline from 2c? Do you need to revise your outline?
   • Write below a revised outline including two sentences per section/subsection summarizing the gist of the findings and associate all necessary figures and tables.
3. Do you have questions for me about specific components of your results section?
4. AS A GROUP, make a list of your answers to question 3 combining them as appropriate. Upload this information as a single file on the discussion board. It will be your agenda assignment for the meeting. Make sure that a PDF copy of every paper that will be useful to you is available in [a shared folder] for all team members to see and download.

[Discussion]:

1. Much of the meeting will be devoted to the discussion of the significance of your research and its inclusion in your discussion section. You should make sure to do the following prior to the meeting
   • Complete and bring your workbook questions for [Discussion I].
   • Complete and bring [the Writing a discussion paragraph activity].
   • Complete and bring [the Response to counterarguments activity].
   • Read the [Discussion meeting sheet].
2. Complete the questions below individually:
   • Repeat in the first column of the table on the next page all of the main findings of your research you have identified. Add rows as necessary.
   • For each of those findings, identify in one sentence why that result is important to the study of [insert here relevant topics and keywords of the CURE].
3. Go back to the literature and answer the following questions:
   • Does your work provide an answer to a long-standing question in the field?
   • Are you the first to provide evidence for a pattern that has been assumed for a long time?
   • Do you provide broad support for a pattern proposed before by studying a small sample (few specimens, few species …)?
   • Are you providing the first evidence of a particular pattern or the first line of evidence for a question never studied in this study system?
   • What element of your work is novel? Think about method, sample, and variables in particular.
     

     Finding	Significance

4. Do you have questions for me about specific components of your discussion section?
5. AS A GROUP, make a list of your answers to questions 2b and 3 as well as a list of your questions for me, combining them as appropriate. Upload this information as a single file onto Carmen. It will be your agenda assignment for the meeting

[Introduction]:

1. Much of the meeting will be devoted to outlining the introduction and developing a plan for the final version of the manuscript of your project.
2. You should make sure to do the following prior to the meeting
   • Complete and bring [your workbook questions for the Introduction].
   • Complete and bring [the Writing an Introduction activity].
   • Complete and bring [the Response to counterarguments activity].
   • Read the [Introduction meeting sheet].
3. On your own, use the answers to your workbook activity to organize the information from the activity on Writing an introduction. In other words, create a detailed outline of your introduction that includes all necessary elements (i.e. Background information, Problematic / Question(s), Hypothesis (-es), Motivation and significance of study, Setup of study).
4. Include all necessary references for each element of your outline.
5. Do you have questions for me about specific components of your discussion section?
6. AS A GROUP, make a list of your answers to questions 5, combining them as appropriate. Upload this information as a single file onto the discussion board. It will be your agenda assignment for the meeting.

Activity 15: Project Framework – Activity 15

Notes to instructor:

• In an effort to guide students, they are provided below with examples from a published paper. The publication chosen as a reference should be:
  • Recently published
  • Relevant to the topic of the CURE
  • If appropriate be authored or co-authored by an instructor of the course to enable (1) a personal connection with the research of students and (2) students to see their instructor as experts they can turn to. Consider featuring peer-assistants, graduate student instructors, or postdoctoral researchers involved in the course if relevant and possible.
• Similarly, the selection of articles presented as examples for the selection of titles should be selected carefully, although the direct relevance to the CURE is not as necessary.

Purpose of this assignment: The goal of this assignment is to help you develop the structure for your research project.

How does it fit within the entire project? The key to a successful research project lies in part in a well-structured study with a clear question, hypotheses, and data collection plan. These guide the project throughout its entirety, determine the scope and focus of the work, and serve as reminders of the intent of the research all the way to its completion.

Tasks required: Complete the activity below.

Deliverable: Upload of agenda on discussion board of [LMS] by [deadline].

Estimated time: about 1 hour

Group work or individual work? Combined individual and group work – use the discussion board

1. Identify a title for your paper. This does not have to be the final title of your manuscript. Rather, you should think of it as a guiding thread. There are many different ways to phrase a title. Below are a few examples from my own research:

• A narrow topic and the more general issue it relates to are mentioned together: [A new species of Ceratogaulus from Nebraska and the evolution of nasal horns in Mylagaulidae (Mammalia, Rodentia, Aplodontioidea) – Calede and Samuels 2020]
• The title is a simple statement of the topic of research: [Locomotory adaptations in entoptychine gophers (Rodentia: Geomyidae) and the mosaic evolution of fossoriality – Calede et al. 2019]
• The title gives away the main finding: [Geometric morphometric analyses of worn cheek teeth help identify extant and extinct gophers (Rodentia: Geomyidae) – Calede and Glusman 2017]
• A colon enables the specific scope or focus of the paper to be mentioned: [Skeletal morphology of Palaeocastor peninsulatus (Rodentia, Castoridae) from the Fort Logan Formation of Montana (Early Arikareean): ontogenetic and paleoecological interpretations – Calede 2014]

Your title should be different from the project topic I gave you.

2. Go back to your mind mapping activity as well as the notes from your framework meeting. What are the questions you are investigating in your project? Remember that a question ends with a question mark.

[For example, in the Calede and Samuels (2020) paper mentioned above and available on the shared box folder, the question we addressed was: “What was the pattern and process of the evolution of horns in mylagaulids?”]

3. Explicitly articulate the hypothesis or hypotheses you will be testing. A hypothesis is an affirmative or negative statement that can be tested. A hypothesis proposes a specific pattern, relationship, or explanation for a phenomenon. A hypothesis is not a theory. In research, a theory is a general explanation backed up by lots of data (e.g., the theory of evolution). A hypothesis may be a small-scale observation that is yet to be tested. Do you have a null hypothesis and an alternative hypothesis?

[For example, in the Calede and Samuels (2020) paper, the hypothesis was: “Mylagaulid horns were linked to defense and could have been subject to natural selection driven by their effectiveness in increasing survival”]

4. What data support your hypothesis / lead you to state your hypothesis as such? Reference the papers from the literature you have read as necessary. In other words, what is the context from the published literature for your hypothesis? Are you trying to test a long-standing assumption? Are you trying to test a pattern supported in one taxon in another? …?

[For example, in the Calede and Samuels (2020) paper, we based our hypothesis on body mass and locomotion data on rodents and horn data from lizards (and other more minor lines of evidence).]

5. What variables will you be analyzing? How will you treat your data (use of averages, use of subset of data, data normalization, etc.), what summary statistics you will be calculating (mean, median, centroid, standard deviation …), and any other variable you will include in your analyses (mention all control variables, explanatory variables, response variables).

[For example, in the Calede and Samuels (2020) paper, we used data on horn height in relation to body mass, data on body mass evolution, and data on the pattern of evolution of horns in mylagaulids. We log-transformed linear measurements and use phylogenetic comparative methods to account for the role of evolutionary history. The data are all based on adult unbroken fossils (no sex data) at the species level (means).]

6. What are the predictions you make for your variables if your hypothesis is supported? What about if it is not?

[For example, in the Calede and Samuels (2020) paper, we predicted (among other things) that we should see jumps in body size when horns evolved if the two are in fact associated. We also predicted that the horns should scale with positive allometry if they are indeed associated with defense.]

Activity 16: Deliverable Tutorials – Activity 16

• The purpose of the assignment is to help [students] understand what constitutes a good [section of deliverable (e.g., introduction)] section, how it is organized, and how to approach writing it.
• The task required always consists of completing the handout. The activity is usually done in class with frequent conversations with group members and the entire class, possibly in a thin-pair-share format.
• The example papers chosen should fit the topic of the CURE.
• The work involves the instructor sharing their writing from past or current projects. This assumes that the CURE is relevant to the research program of the instructor and therefore applies most directly to researcher-driven CUREs.
• By sharing their own writing, the instructor opens themselves to critique from students and actively engages them in the collaborative and constructive process of peer-review.
• Students should be introduced to best practices on the sharing and distribution (or lack thereof rather) of unpublished research prior to the activities.
• Select the appropriate set of questions for the section from the options provided below.

Step-by-step:

[For all section except the introduction]: Our work today will be divided into three steps:

1. Read and analyze the [section of deliverable (e.g., material and methods)] from a published study.
2. Draft the [section of deliverable (e.g., material and methods)] section for a project that [the instructor] is working on.
3. Compare the draft produced in class to the one written by [the instructor].

[For the introduction]: Our work today will be divided into three steps:

1. Read and analyze the introduction section of a published study.
2. Identify key elements of the introduction of your paper.

READING AND ANALYZING:

We will be first reading the material and methods section from the following article: [Full reference for the article formatted according to the guidelines the students will have to follow in their main written deliverable, if applicable, or a standard/classic publication outlet in the field]

1. First, read the abstract below so you are familiar with the research project as a whole: [Insert here the full abstract of the article].
2. The following pages show the [section of deliverable (e.g., introduction)] section of the [author(s) of the paper the students are reading] paper. Use it to answer the questions starting on page [number] of this handout.

Questions [for material and methods]:

1. Identify the different sections of the material and methods of this paper (hint: look at headers and subheaders).
2. Use a highlighter to identify key components of each of the sections you identified (no more than one or two sentences should be highlighted).
3. For each section you identified, use a bullet point list to summarize the key elements you highlighted. For example, if you highlighted the following: “… from one to six specimens from each of 34 species from the …”, this would be the sample size and distribution.
4. Compare your list with your classmates. Edit accordingly.
5. Make a note on your list of the information that is presented in the form of figures, tables, and appendices.
6. Be prepared to present your lists to the whole class.

Questions for [results]:

1. Identify the information presented as text, figures, or tables.
2. How is the results section of this paper divided? (Hint: look at headers and subheaders).
3. Use a highlighter to identify key components of each of the sections you identified (no more than one or two sentences should be highlighted).
4. For each section you identified, use a bullet point list to summarize the key elements you highlighted. For example, if you highlighted [“… from one to six specimens from each of 34 species from the …”, this would be the sample size and distribution].
5. Compare your list with your classmates. Edit accordingly.

Questions for [discussion]:

1. How is the discussion of the paper organized? (Hint: look at headers and subheaders).
2. Choose a sub-section of the discussion: how is the information organized? Make sure to address the following elements: summary of the findings of the paper, putting them in the context of the literature, supporting those findings with other data, considering the limitations of the findings, and articulating their significance to the [scientific] community.
3. Answer the question above for a different section.
4. How is each of the elements of a discussion you discussed above communicated to readers? Once again, answer this question for two different subsections/topics of the discussion. Make sure to explicitly go over the structure of the text.
5. Compare your list with your classmates. Edit accordingly.

Questions for [introduction]:

1. Identify the following elements in the introduction you are reading. Note that they are not always presented in the same order as they are below.
   • Background information: This provides the reader with the context and knowledge necessary to understand the study system and the importance of this work by grounding in a big picture (for the study) issue.
   • Problematic / Question(s): This states explicitly what big question or issue the work sets out to explore.
   • Hypothesis (-es): The introduction states (best done explicitly) the hypothesis (-es) tested in the study.
   • Motivation and significance of study: It is important to explain the significance of the work for the [scientific] community at large including our understanding of the study system, big picture questions in [field of research], possible applications, relevant future applications to other systems, etc.
   • Setup of study: The introduction should preview the structure of the rest of the paper and set the stage for the reader by giving an overview of the work accomplished.
2. Compare your work to that of your teammates. Make necessary edits.
3. Answer the following questions:
   • How is the introduction of the paper organized? Are the elements described above in a particular order or are they woven together? Give details.
   • Are certain elements of the introduction provided to reader in the form of tables or figures? If so, which ones? If not, could some of the information have been provided in such formats? What info specifically?
   • Compare your answers to the questions above with your teammates. Edit accordingly.

DRAFTING:

For the [material and methods]: Below is some basic information on a research project that [the instructor] is working on. Use it to draft a mock material and methods section. Do NOT look at the rest of this handout. Note that I am having you focus on just a couple sections of the material and methods section. I am not asking you to understand the details of the research or provide any references (other than those given to you). I simply want you to create a narrative of the content (not a full-on material and methods section). I have somewhat organized the information so it would not be overwhelming.

For the [results]: A good results section will be written around high quality figures. The text should explain the entirety of the figure, highlighting the critical points, and provide associated statistical information. Below are two figures from a research project on [topic] that [the instructor] is working on. Use it to draft a mock results section. Do NOT look at the rest of this handout. Note that I am having you focus on just two figures and therefore only part of the entire results section for this paper.

 For the [discussion]: A good discussion section will summarize the findings of the paper, put them in the context of the literature, support those findings with additional data, consider the limitations of the findings, and articulate their significance to the scientific community. Below are the text and figures/tables associated with the results section of a paper published by [the instructor]. Use it to draft a mock discussion section. Do NOT look at the rest of this handout.

[For all section except the introduction]: COMPARING:

Below is a draft of (a portion of) the text that [the instructor] wrote for this paper. Read the text below and reread your own writing. Answer the following questions:

• What information was your [material and methods, results, or discussion] section lacking (besides details I had not provided you with the info for)?
• Are there any elements missing in the text of [the instructor]?
• What are the critical elements of a [material and methods, results, or discussion] section you can identify in the text below and the paper we looked at together earlier?
• What would you need to do to transform the text you wrote earlier into something like the text below?

[For the introduction]: REFLECTING:

1. Let’s start the process of writing the introduction for your paper. ON YOUR OWN, take NO MORE THAN 5 MINUTES and jot down a few bullet points for each of the elements of the introduction in the table below. This time limit will force you to focus on the essential elements.
   

   Background information
   Problematic / Question(s)
   Hypothesis (-es)
   Motivation and significance of study
   Setup of study

2. Compare your table with your teammates. Fill out the table below with the consensus of your group. It will likely be more thorough than the one above because of the time limit I imposed.
   

   Background information
   Problematic / Question(s)
   Hypothesis (-es)
   Motivation and significance of study
   Setup of study

3. ON YOUR OWN, focus on the Background information. Expand upon each of the bullet points, transforming each of them into two sentences that summarize the key point you want to make. For each set of sentences, provide at least one supporting reference to the literature.
4. ON YOUR OWN, focus on the Motivation and significance of the study. Expand upon each of the bullet points, transforming each of them into two sentences that summarize the key point you want to make. For each set of sentences, provide at least one supporting reference to the literature.
5. AS A GROUP, write below the most up-to-date version of your Problematic / Question(s).
6. AS A GROUP, write below the most up-to-date version of your Hypothesis (-es).
7. AS A GROUP, go over your answers to questions 3 and 4. Combine your answers into two sets of sentences (between 5 and 8 sentences each) and references (a minimum of 3).

Activity 17: Sequential Manuscript Drafts – Activity 17

• The purpose, fit, tasks, deadline, and time commitment of the assignment are provided to students as part of the handouts for the associated agendas, meetings, and tutorials.
• This assignment is iterative with students submitting several versions of the document throughout the CURE, incorporating feedback from peers and instructor(s) every time:
  • Material and Methods
  • Material and Methods and Figures and Tables
  • Material and Methods, Figures and Tables, and Results
  • Material and Methods, Figures and Tables, Results, and Discussion
  • Material and Methods, Figures and Tables, Results, Discussion, and Introduction
• The expectations are articulated in the rubric for the manuscript, which is presented as part of [Activity 6].
• The formatting should be adjusted to mimic the formatting of a suitable publication outlet.

• You should upload a doc or docx file.
• Your text should be formatted with a spacing of 1.5 lines with 0 additional spacing between lines.
• Your text should be in Calibri, font size 12 pts.
• Your document should have margins that are uniformly of 1 inch.
• All references to figures and tables you foresee including should be included in square brackets. Example: … cranial measurements (Fig. 1 [figure showing the cranial measurements measured]).
• All text should be aligned left.
• All primary headers should be all caps (e.g., INTRODUCTION) with no line skipped afterwards.
• All secondary headers should be in bold with title capitalization. (e.g., Hypotheses and Predictions)
• All tertiary headers should be underlined with sentence capitalization (e.g., Sampling)
• Do not indent paragraphs.
• All sections should end with two skipped lines.

Make sure to include all necessary references in a REFERENCES section at the end of the document. Those references should be formatted according to the requirements of the [relevant scholarly format]. See example below for an article and guidelines linked in the Bibliography assignment:
[Provide example here]

Activity 18: Group Contracts – Activity 18

Notes to instructor:

• This group contract is used at the very start of the CURE to set personalized rules for each research group (if the CURE is implemented in a group format).
• This group contract template was developed in part from resources at https://uwaterloo.ca/centre-for-teaching-excellence/teaching-resources/teaching-tips/developing-assignments/group-work/making-group-contracts where several examples of group contracts and templates are provided in addition to other helpful documents.

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Purpose of this assignment: This assignment help you develop rules for the work of your group throughout the semester.

How does it fit within the entire project? A well-designed and agreed-upon set of rules will facilitate your collaboration, prevent conflicts, and mitigate disagreements.

Tasks required:

• Decide on a team name.
• Complete the handout below by adding commitments to the table using the resources at the end of the document.
• Sign the document once agreed upon.

Deliverable: A completed version of this handout uploaded on [LMS] by the end of class.

Estimated time: Around 30 minutes

Group work or individual work? Group work

Team Name: ____________________________________________

Date: _______________________________

We share the goals, guidelines, and expectations set out above and agree to all of the policies, procedures, and consequences described.

You can pick rules from the options below, modify them, or develop your own:

PARTICIPATION:

• Participating fully (in spirit and actuality)
• Giving group members appropriate credit where due.
• Not giving credit where it isn’t due

COMMUNICATION:

• Every group member will check the discussion board for the group once a day.
• No “cross talking” is allowed. This means not interrupting when someone else is talking.
• We agree to share our phone numbers with one another to be able to communicate by texts and calls.
• We agree to share our Ohio State emails with one another to be able to communicate by emails.
• Every group member will check their Ohio State email address for project communication once a day.
• We will be setting up a Microsoft team board/Buckeye Box folder/Google Drive folder/… to share documents. Note that you should invite me to any folder you use to share documents.

OUT OF CLASS MEETINGS:

• All group members will be punctual. Meetings will start five minutes after the agreed start time, and everyone should be there and ready by then.
• We should turn up to all meetings unless it has been agreed beforehand or unless there are unavoidable events such as illness.
• Group members who are avoidably late must: [write out a consequence for being late.]
• All group members will remain in the meeting until (a) all tasks for that meeting are completed, or (b) there is unanimous adjournment.
• All group members will come to the meetings prepared by reading the assigned material and coming with ideas pertaining to the tasks and decisions to be made.
• Roles will be assigned prior to a meeting or, if this is not possible, at the beginning of a meeting. Roles will rotate each meeting.
• Roles will be assigned following the structure of the in-class meetings.

CONDUCT:

• There will be an assimilation period at the end of each meeting to evaluate group mechanics and ensure that all tasks have been completed adequately.
• Each member will take turns listening as well as talking, and active listening will be a strategy for all group discussions.
• Sexist and racist remarks are not acceptable.
• Aggressive and dominating behavior is not acceptable.
• Members agree to treat one another with respect. Respect includes no name-calling. If you don’t like an idea, address the idea, not the person (for example, “I don’t think that idea will work because…” not “That’s stupid”).
• The group will actively seek a consensus based on the opinions of every member.
• Participating professionally (i.e., civil discourse; abiding by the rules of academic honesty)
• Meeting responsibilities (i.e., completing assigned tasks on time and to the best of your ability).
• If a member submits plagiarized material and/or cheats, the group agrees to bring this to Jonathan’s attention immediately.
• Taking the consequences of not abiding by the group’s rules.

CONFLICT AND RESOLUTION:

• In the event that a group member treats someone inappropriately, she/he/they will [write a consequence].
• Each group member has the right to point out whether any of these rules are being broken.
• The group members will isolate areas of disagreement, and the group will come to a consensus. If no consensus is reached, the moderator of the meeting will decide the amount of time for discussion or arbitration before calling a vote. If the vote is a stalemate, the issue will be brought to Jonathan.

DEADLINES:

• Tasks that group members agree to undertake should be completed to the agreed deadline.
• If it looks as though there will be a problem meeting a deadline, the person concerned should seek help from other members of the team in time to avoid a delay.

DIVISION OF LABOR:

• The division of tasks between group members will be agreed upon by a vote.
• All tasks will be identified in writing on the discussion board.

Activity 19: Group Reviews – Activity 19

Notes to instructor:

• This group review framework can be used in association with different milestones of the CURE process. It can be truncated to enable group reviews at earlier stages of the CURE. This enables the instructor to catch and mitigate problems early on and regularly.
• Consider combining this activity with an informal review of the CURE by the student (and yourself) to engage your own work in the critique process.
• The tasks in the table can be customized to reflect the scope of the work covered by the CURE activities.

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Purpose of this assignment: This assignment enables you to reflect on your contribution to the project and behavior. It is also meant to enhance your group work and ensure that you work well together as a research team.

How does it fit within the entire project? This short group review gives me an opportunity to review the situation in your group, mitigate any problem, mediate conflicts, and help you achieve the best possible dynamic. Remember that a professional is often called upon to work with a diverse set of colleagues, including some difficult personalities. This is the nature of the workplace and research. Always remember to be respectful and treat others with dignity.

Tasks required: Complete the handout below.

Deliverable: A completed version of this handout uploaded on [LMS] by [due date].

Estimated time: Around 20 minutes

Group work or individual work? Individual work

1. Estimate the relative contribution as a percentage (e.g., half the work is 50%) of the work accomplished by yourself as well as your teammate so far. Start by putting the initials of each team member (including yourself) in the first row.

   Task
   Developing questions, hypotheses, predictions
   Reading the literature
   Developing the methods (data collection protocol and analyses)
   Implementing the analyses
   Writing the material and methods section of the paper
   Developing the table and figure captions
   Writing the results section
   Interpreting the data
   Writing the discussion section
   Writing the introduction section
   Writing the abstract
   Writing the reference section
   Other:

2. Please tell me how often you have met since the last group review outside of the class meetings to work on this project? What was the total number of hours?
3. How often would you say you communicate about the project outside of class (through emails, texts, calls, discussion board …)?
4. How many hours did YOU spend on this project since the last group review?
5. Please comment briefly on yourself with regards to the following criteria:
   • Did you come to class sessions or group meetings prepared?
   • How did you prepare?
   • What could you have done differently to be better prepared?
   • Did you complete all of the work you had committed to do?
   • Were you respectful of all of your teammates?
   • What have you done since the last group review to improve your interaction with other members of your team? Did you meet your own goals expressed in the last review (if applicable)
   • Did you give everyone the opportunity to speak, present arguments, and participate equally in the term project?
6. Please comment briefly on each of your term project partners with regards to the following criteria:
   • Did your classmates come to class sessions or group meetings prepared?
   • Did they do the work they had committed to do on their own?
   • Was your teammate respectful?
   • Did they give you the opportunity to speak, present arguments, and participate equally in the term project?
7. Do you have any violation of the group contract to report?
8. Has your group discussed amending the group contract? If so, provide details.
9. Do you have any other comment or concern you would like to share with me?

Activity 20: How to Analyze Data – Activity 20

Notes to instructor:

• This activity was developed for a CURE in which students were provided two recent papers from the primary literature that represented model papers that investigated similar questions in different study systems.
• Students had already completed two scaffolding activities prior to this one [Activities 4 and 8].

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Purpose of this assignment: Identifying the analyses you will need to test your hypothesis (-es).

How does it fit within the entire project? These analyses will be the test of your hypothesis. Settling on the right analyses will be critical to being able to draw conclusions from your dataset and to contributing meaningfully to research.

Tasks required: Critically read three papers from the primary literature and complete the handout below.

Deliverable: Completed version of this handout uploaded to [LMS] by [deadline].

Estimated time: less than an hour and a half

Group work or individual work? Individual work

Step-by-step: Recall that you have already done some of this work as part of your framework.

Fill out a table for each publication you were given at the start of the semester..

1.  Identify the hypothesis (-es) you will be testing in your study:
2. For each hypothesis above, identify the variables you will be using in your analyses:
3. In general terms, what will you need to do with these variables? In other worlds, identify the comparison you will be making. Examples: “We will be comparing variable x between males and females for all species in our sample”, “We will be comparing the variable x between all species in our sample”, …
4. What variables do you need to control for?
5. What analyses did the published articles provided to you at the start of the semester employ? Look at the material and methods as well as the figures. Replace [name] with the name of the analysis in the tables Paper 1 and Paper 2 below and complete the first row with the full reference for each of the two “model” papers associated with your project.
6. Identify a paper from the primary literature that has undertaken an analysis you are interested in running on your own data and complete the table for Paper 3 below. Think back to your bibliography activity for help.
7. How do your data differ from those published in the papers above?
8. How do your questions/hypotheses differ from those tested in the papers above?
9. Fill out the table just below for YOUR study. Note that the number of analyses is not fixed. You may have one, two, three, four … The research should dictate this. Add rows to the table as necessary.
   

   Analysis 1: [name]	Dependent variable(s):
   	Independent variable(s):
   	Control variable(s):
   	Goal of the analysis
   	Conclusion drawn from analysis:
   Analysis 2: [name]	Dependent variable(s):
   	Independent variable(s):
   	Control variable(s):
   	Goal of the analysis
   	Conclusion drawn from analysis:

10. How does your proposed analytical protocol differ from those previously used in the primary literature? Why?
11. What are some possible obstacles or challenges to the analyses you propose to run?

Activity 21: Condensing the Primary Literature – Activity 21

Note to instructor:

• This activity can be used to prepare students to write the discussion section of a manuscript.

Purpose of this assignment: The goal of this assignment is to help you summarize the current knowledge and arguments in the published literature.

How does it fit within the entire project? This activity will help you write your discussion section. It is important to put your work in the context of the existing literature in that part of the paper.

Tasks required: Complete the handout below.

Deliverable: Completed version of this handout uploaded to [LMS] by [deadline].

Estimated time: Less than two hours

Group work or individual work? Individual work with some group coordination.

1. Write below the most up-to-date hypotheses you are testing in your project. MAKE SURE to coordinate with your group members (I should see the same set of hypotheses from all group members):
2. List here a minimum of five papers that have explored one or more of these hypotheses in your study system. Think of “study system” broadly including [provide details here appropriate for the field of research and questions explored]. Think back to your bibliography and your framework assignments for help. Format the references according to the [journal format the students will follow for their deliverable].
3. For each of those five (or more) papers, identify in four sentences (no less, be thorough) the main conclusions of the paper with regards to the topic/hypothesis of interest to you.
   • Paper 1:
   • Paper 2:
   • Paper 3:
   • Paper 4:
   • Paper 5:
4. Bring together the information from those different papers. Write a paragraph that is twenty sentences long and summarizes the conclusions of all five papers. You should NOT merely copy-paste the sentences from the previous question but instead make sure that you are comparing and contrasting the different conclusions. Think about the following questions: Are different authors/datasets in agreement? On the contrary, are there differing findings? Are there particular patterns? Some exceptions/outliers? What is the strength of the relationships that have been recovered in prior analyses? Make sure that you cite the papers appropriately throughout your paragraph.
5. Condense this twenty-sentence paragraph to a paragraph that is only ten sentences long. Focus on the most important points. Get to the gist of the patterns. Make sure that you cite the papers appropriately throughout your paragraph.
6. Go back to your hypotheses. For each of them, provide a two-sentence summary of the position of the literature on the issue.
7. For each of your hypotheses, provide a two-sentence summary of YOUR relevant findings. MAKE SURE to coordinate with your group members (I should see the same set of conclusions from all group members).

Activity 22: Arguments and Counterarguments – Activity 22

 Note to instructor:

• The appropriate number of tables should be added to the template below

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Purpose of this assignment: The goal of this assignment is to help you build your discussion section with an eye towards contrasting your findings to those from the literature.

How does it fit within the entire project? This activity will help you write your discussion section. It is important to put your work in the context of the existing literature in that part of the paper.

Tasks required: Complete the handout below.

Deliverable: Completed version of this handout uploaded to [LMS] by [deadline].

Estimated time: About one hour

Group work or individual work? Group work.

1. List in the top left cell of each table on the next pages the main findings of your work. Place one finding per cell.
2. For each of those findings, identify the associated argument. This could be an explanation for the pattern, an implication of this pattern, an association between this pattern and another one of your findings or a prior finding.
3. Add to the table a co-argument. This is a supporting line of evidence for your argument. It could be a similar argument made in a different study system, a response to an obvious weakness of the argument, another finding of yours (or from the literature) that is consistent with your interpretation, etc.
4. Finally, add to the table at least one (could be more) counterargument. This is a skeptical response to your interpretation, a caveat, a “hole” in your reasoning, another line of evidence that does not support the explanation proposed, etc.
5. For each of those cells, make sure to identify the relevant sources to cite (a figure or table of yours, a statistical test result [e.g., regression, p value, AIC score, Akaike weight], a paper from the literature, etc.)

Activity 23: Responding to Counterarguments – Activity 23

Note to instructor:

• The appropriate number of tables should be added to the template below

Purpose of this assignment: The goal of this assignment is to help you build your discussion section with an eye towards building the argument of your discussion.

How does it fit within the entire project? This activity will help you write your discussion section. It is important to put your work in the context of the existing literature in that part of the paper.

Tasks required: Complete the handout below.

Deliverable: Completed version of this handout uploaded to [LMS] by [deadline].

Estimated time: About one hour

Group work or individual work? Individual work.

1. Go back to the “Arguments and Counterarguments” assignment you have already completed. Copy-paste into the tables on the next pages the information from the tables of that activity. In other words, replace the gray areas.
2. Write a response to the Counterargument in the bottom row for each table. Note that this is not necessarily a rejection of the counterargument. You may use this to revise your original interpretation. The statement you write in the last row of the table should be a statement supporting your argument AND explaining away the purported weakness/caveat/issue/… OR a statement supporting your argument AND incorporating/considering/explaining the weakness/caveat/issue/… OR a revised explanation that takes into account the counterargument.
3. Is there a counterargument to the response? Do you need to provide a new explanation for the new counterargument? Make sure to consider this for EVERY single one of your finding/argument/counterargument sets.

Activity 24: Closing – Activity 24

Note to instructor:

• The appropriate number of tables should be added to the template below

Purpose of this assignment: The goal of this assignment is to help you identify the next steps in the research avenue you have been exploring with this project.

How does it fit within the entire project? This activity will help you write your discussion section. It is important to explicitly articulate the next steps in the research, whether or not you will be investigating them yourself.

Tasks required: Complete the handout below.

Deliverable: Completed version of this handout uploaded to [LMS] by [deadline].

Estimated time: Less than two hours

Group work or individual work? Individual work with some group coordination.

1. Identify below the hypotheses you tested in your project (one per table) as well as the questions you set out to answer (go back to [your framework and associated assignments as necessary]). MAKE SURE to coordinate with your group members (I should see the same set of hypotheses and questions from all group members).
2. For each of them, answer the following questions:
   • What questions are still unanswered at the end of your research project?
   • Are there specific datasets/variables/etc. that should be studied to shed further light on the questions you explored?
   • Are there analyses you now wish you would have run?
   • Are there outliers that should be further analyzed?
   • Are there analyses or studies that your work enables?
   • Could your results be combined with some additional information to provide a new perspective?
   • Consider the application of your work to other study systems. What is the feasibility of such work and what can be gained from it? Do you have predictions?

Activity 25: Understanding and Designing Figures – Activity 25

Notes to instructor:

• The number of figures in the first part of the activity can easily be modified.
• One can also ask students to bring figures from their readings to share with others in the class for the first part of the activity.
• It is useful to present information for the datasets that is similar to the work the students are undertaking in the CURE themselves. Information/Associated figures can be drawn from the research of the instructor or published papers for the second and third parts of the activity.

Purpose of this assignment: The goal of this assignment is to help you develop an eye for the figures that will help represent your data and analyses the best.

How does it fit within the entire project? Figures are a critical component of a research paper. As you go through this activity you should consistently ask yourselves: Can my reader grasp the gist of my work by simply looking at my figures and tables?

Tasks required: Complete the activity below.

Deliverable: Completed version of this handout uploaded to [LMS] by [deadline].

Estimated time: about one hour and a half.

Group work or individual work? Individual work and group discussion during class.

• 1) Looking at and analyzing a selection of figures from published papers.
• 2) Designing a couple figures for some projects that [the instructor] is working on.
• 3) Compare your design to the figures developed by [the instructor].

ANALYZING PUBLISHED FIGURES:

We will be looking at figures from a selection of papers analyzing [topics of the CURE].

1. Look at the eight figures I have selected presented below. For each of them, categorize the figure or elements of the figure according to the following crude categories: [insert here a list of categories of graphical representations relevant to the CURE. Examples include bivariate regression plot, boxplot, dendrogram, structural formula, phylogenetic tree, photographs, network diagram, violin plot, Venn diagram, etc.]
2. For each graph, using YOUR OWN WORDS, describe the data represented. In other words, what does the graph show? [insert here the eight figures along with citations]

DESIGNING FIGURES:

Below is some basic information on a couple research projects that [the instructor] is working on. Use it to design a figure presenting the data. Do NOT look at the following pages of this handout. For each set of data, you should provide the following:

• The type of graph you would use
• The variables that would be graphed (what would be the labels on the axes, legends)
• A rough sketch of what the figure would look like
• A draft caption explaining the figure

[insert here the necessary information]

COMPARING FIGURES:

Below is a set of draft figures for manuscripts that [the instructor] and his students as well as collaborators are working on. Look at the figures and captions provided below. Look again at your own figure and caption designs above. Answer the following questions:

• How do your figure designs differ from the figures produced by [the instructor] and his colleagues?
• What are the characteristics of a good figure caption?

[insert here the figures and their captions]

Activity 26: Reflection workbook – Activity 26

Notes to instructor:

• Several of the questions used in this handout were derived from the framework provided by the Association of American College and Universities VALUE rubrics (https://www.aacu.org/value-rubrics).
• Others are taken or modified from the Framework for Information Literacy for Higher Education developed by the Association of College & Research Libraries: https://www.ala.org/acrl/standards/ilframework
• The exact structure of the workbook should be adapted to the structure of the whole CURE. Because it is meant to be discipline/topic-relevant, it should also be modified to better match the specific CURE implemented.

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Purpose of this assignment: The goal of this workbook is to help you reflect upon your writing and research process, help you self-correct, and most importantly help you develop metacognition: an understanding of your own thought processes. The work you put into this workbook will directly improve your research manuscript.

How does it fit within the entire project? This workbook is critical to helping you throughout the semester. It is critical that you complete it when prompted (see below) so that you can use the reflection to improve each section of your project and, eventually, your research manuscript.

Tasks required: Answer the questions below.

Estimated time: An average of 30 to 45 minutes per section.

Deliverable: Complete the different sections of this reflection workbook below according to the timeline provided. The workbook will be graded on the following dates: [dues dates]

Group work or individual work? Individual work

Framework I

Complete between [xxx] and [xxx]

Purpose: The goal of these questions is to help you develop the framework of your project and reflect on your mind mapping exercise.

Questions 1a and 1b: What do you already know about the topic? What do you need to explore further? Be specific.

Question 2: What is the scope of your research? Be specific.

Question 3: What is the existing knowledge or assumptions about your topic? List several specific elements.

Framework II

Complete between [xxx] and [xxx]

Purpose: The goal of these questions is to help you revise the framework you developed during your framework class meeting and articulate the significance of your work.

Question 1: What is the dialogue or debate surrounding your topic? Think about any disagreement and any outstanding question in particular.

Question 2: Have you sought a variety of perspectives? Have you consulted the [xxx], [xxx], and [xxx] literature?

Question 3: For whom is this project being developed? Provide details on the audience of your final manuscript. What stakeholders are likely to be interested in this work? How will your work be communicated to its audience? Think about format of the paper and its sections.

Question 4: What will your research enable (future analyses and investigations)? Be specific about possible follow up studies.

Material and Methods I

Complete between [xxx] and [xxx]

Purpose: The goal of these questions is to help you select your dataset, develop the approach you will take to analyzing those data, and reflect on your documented problem solutions exercise.

Question 1: Who else has done such analyses? Provide specific citations so you can consult them later.

Question 2: What analyses have published articles employed? Look at the material and methods as well as the figures. (Look at your Bibliography assignment for help)

Question 3: What other analyses would be helpful as follow-up analyses?

Data Collection I

Complete between [xxx] and [xxx]

Purpose: The goal of these questions is to help you plan your data collection.

Question 1: What data (that you need) already exist? Have any data already be published in the peer-reviewed literature? Make sure to check supplementary information files. What about as part of online databases? Insert below the references for all data sources and the details of the sample size / nature of the sample they include.

Question 2: Based on your reading of the literature, your questions/hypotheses, and your answer to question 1, what is the nature and size of the sample you need to collect yourself? Be as specific as possible in describing your data collection goals. Include the nature of the variables and their source.

Question 3: Describe the method by which you will be collecting these data. Essentially, write a DETAILED protocol for your data collection. Include all necessary supplies and equipment.

Data Collection II

Complete between [xxx] and [xxx]

Purpose: The goal of these questions is to help you plan your data collection.

Question 1: Collect data from a small subsample of your expected dataset. Make a note of the amount of time involved in the process. Based on this information, calculate the total amount of time that will be involved in the data collection process. Schedule this effort now to meet the deadline(s) of your project.

Question 2: Did you encounter any problem with data collection? Does the protocol you wrote for question 3 (Data Collection I) need to be revised based on your pilot data collection?

Data Analysis

Complete between [xxx] and [xxx]

Purpose: The goal of these questions is to help you reflect upon your data collection and initiate your data analysis.

Question 1: What is your final sample size? Are there data that could not be collected after all? Are all analyses that you had planned feasible given the actual data collected?

Question 2: What software programs or technological support will you need to analyze data? Which analyses will require technical assistance?

Question 3: Do your data need to be formatted in a particular way or a particular file format to be visualized/analyzed? Is any data manipulation necessary prior to analyses?

Question 4: List all analyses in the order that they are going to be undertaken associating the necessary data every time.

Material and Methods II

Complete between [xxx] and [xxx]

Purpose: The goal of these questions is to help you outline your material and methods section.

Question 1: What are the different subsections of a material and method section in similar studies? Make a bullet-point list for a few (two or three) different publications.

Question 2: Think about the following “classic” elements of a material and methods section. For each of them, provide a one sentence explanation of what you would include in your Material and Methods section to cover it.

Sampling (size/nature)

Data acquisition/sources

Data manipulation (standardization/normalization)

Analyses (software/nature/parameters)

Figures and Tables I

Complete between [xxx] and [xxx]

Purpose: The goal of these questions is to help you design the figures that will be part of your paper.

Question 1: What is the nature of the data you will be presenting to your readers? How many figures/tables will you need to represent these data? Make a numbered list of the figures/tables in your paper and the data they will represent.

Question 2: Based on the exercise we did in class and your readings, what broad category of figures would effectively represent these data?

Figures and Tables II

Complete between [xxx] and [xxx]

Purpose: The goal of these questions is to help you refine your figures for the paper.

Question 1: Pick a published article that published a similar analysis to the one you are proposing for your own paper. Observe carefully the corresponding figure and compare it to your proposed figure (in Graph Predictions activity). How do the two differ? Provide the complete reference for the paper selected as part of your answer and upload a PDF of it on the shared folder. You should do this for each figure included in your project. This may mean that you will have to select more than one published paper. Use the boxes below as appropriate.

Question 2a: As you read the results section of the published papers you selected for Question 1, what information is provided by the authors in the form of tables? Is all of this information provided in one of your tables? Make sure to check references to supplementary information/tables.

Question 2b: As you read the results section of the published papers you selected for Question 1, what information do you find yourself wondering about or do you wish was provided but is not? Is all of this information provided in one of your tables?

Results I

Complete between [xxx] and [xxx]

Purpose: The goal of these questions is to help you outline your results section.

Question 1: Choose two to three relevant papers from the primary literature. Make sure to provide the references for these papers and upload PDFs of them on the shared folder. How have they organized their results section? Did they go analysis by analysis? Question by question (lumping different analyses addressing the same question for example)? Any other structure?

Question 2: Based on your answers to the first question, outline your own results section. Make sure to include a justification for your decision.

Question 3: Look at the peer-reviews you have received and the comments from Jonathan. How have you modified your material and methods to address these comments? How would you modify the outline you sketched out above to preemptively address some of the structural and conceptual issues raised by reviewers on other sections of your paper?

Results II

Complete between [xxx] and [xxx]

Purpose: The goal of these questions is to help you reflect upon your results and how they shape your paper.

Question 1: How do your results differ from published data? What is novel about your results? Are they surprising or expected (i.e. matching predictions)? Make sure to cite each paper you reference and upload a PDF of that paper in the shard folder.

Question 2: Result sections must always reference relevant information including relevant statistical test results, tables of data, figures of the analyses, etc. List below every claim you make in your results section (in an abbreviated fashion) and next to it how you will demonstrate its validity to your reader.

Discussion I

Complete between [xxx] and [xxx]

Purpose: The goal of these questions is to help you bring to the forefront the most critical points of your research for the discussion section of your paper.

Question 1: What is the significance of your work in three bullet points? This is NOT a summary of your results but a suite of statements summarizing WHY those results are important (to research, the [scientific] community …)

Question 2: What point of view might be missing? This may be a point made from the literature that you are not addressing or an obvious alternative hypothesis you do not mention.

Discussion II

Complete between [xxx] and [xxx]

Purpose: The goal of these questions is to help you package your paper as an attractive narrative that guides your readers through the research.

Question 1: How do your findings contribute to your initial hypothesis? Write below your hypothesis and a sentence for your discussion section that explicitly addresses it.

Question 2: What is the next step in this line of inquiry? Do NOT think about simply increasing the sample size. Propose at least two new analyses, questions, or specific expansions of the framework of the project.

Introduction

Complete between [xxx] and [xxx]

Purpose: The goal of these questions is to help you develop the introduction section of your paper.

Question 1: Pick three papers from the primary literature. For each paper, provide the reference and upload a PDF on the shared folder. Detail below the structure of the introduction of each article including the different elements we discussed in class.

Question 2: How does the structure of the different papers differ? Note that I would like you to focus on the organization of the introduction specifically. Are those differences linked to the pitch/approach/structure/nature of the whole paper? Which of the three published studies is your work most similar to? Does your paper represent a hybrid approach instead?