Peer Review in the Life Sciences

Spring 2021 Syllabus:

Goal: As scientists, one of our primary responsibilities to our colleagues, to our community, and to the public is communication of our research findings. By far, the most widely accepted means of communication is through publishing papers in scientific journals. The process of peer review plays an important role in refining the body of work prior to final publication. Yet, peer review is rarely taught to students in a formal setting, and is largely dependent on individual labs and mentors, leading to variable standards of peer review. Reflecting the evolution of technology, society and scientific culture, preprints have gained popularity in the life sciences in recent years, resulting in a shift in how progress in the life sciences is communicated, and raising questions of how we, as a scientific community, may work towards optimizing the peer review process in the life sciences. This class will use preprint servers (for example, BioRxiv) as a platform for formally teaching students how to peer review manuscripts in a critical and constructive way.

This class will be capped at 12 students.

Course organizers: Gira Bhabha, Damian Ekiert, Liam Holt & Timothee Lionnet

Teaching Assistant: -

Course credits: 4 credits for 2021

Grades: letter grade based on oral presentations, 1-page critiques, peer review and prelight write-ups. Attendance of all classes is mandatory.

Meeting times: Mondays and Wednesdays 11:15am-12:45pm

Meeting location: -

Meeting dates: Mon. Feb 1 - Mon. April 26 [Note: Mon. Feb 15 is a holiday]

Course structure:

Following the first six introductory classes, the course will be divided into modules

Each two-week module will focus on a particular scientific topic and will be led by two experts in that field
Classes will be highly interactive, with minimal lecture components

The 4 classes of each two-week module will be structured as follows:

Class 1:

Assignment: Students will read reviews and/or watch videos assigned by faculty

In class: This day will lay the foundation for the next three classes, and will therefore cover important background for the subject. One faculty member will prepare a 20-30 minute lecture, after which a flipped-classroom approach will be used, in which the students will present and discuss the main aspects of the reviews assigned for reading, ending in a survey of the current state of the field as pertaining to chosen preprints for the following classes.

Class 2:

Assignment: Students will read an assigned preprint. All students write a one-page review, except for two students who prepare a presentation & lead the class

In class: All students participate in discussing the paper, two student presenters lead the discussion, faculty and TAs assist by engaging students based on their 1-page critiques, which the faculty members and TAs will have the opportunity to read prior to the class

Class 3:

Assignment: Students will read an assigned preprint. All students write a one-page review, except for two students who prepare a presentation & lead the class

Class 4:

The class will be split into two groups. One group will work to synthesize the discussion points for one paper into a coherent review of the preprint, while the other group will work to synthesize a Prelight of the other paper.

After approval by the faculty leading the module, reviews will either uploaded to the preprint server (eg. bioRxiv), or emailed directly to the authors. Prelights will be submitted to be made available online.

In this way, students will participate in peer review, will provide feedback in real time to authors, and will be engaged in thinking about, and directly shaping science communication as it evolves. Students and faculty will also have the opportunity to engage with journal editors and synthesize the role of preprints, peer review and journal articles. This class is designed to be as stimulating for the faculty and TAs as for the students, introducing a balance in which the whole group actively participates in issues that are at the core of scientific communication in the broader life sciences community. This class will evolve each year as our means of scientific communication also constantly change and evolve.

Syllabus & Dates

Mon. Feb 1: How to read a paper [Liam Holt]

This class will focus on strategies for reading and evaluating papers in the context of peer review, including what degree of criticism is expected.

Wed. Feb 3: What is Peer Review [Damian Ekiert]

In this class we will focus on the role of peer review in the scientific community and how it has evolved.

Mon. Feb. 8: The rise of preprints in the life sciences [Jessica Polka, ASAPbio]

In this class we will focus on the use of preprints in the life sciences over the past few years, and the advantages and challenges they have posed.

Wed. Feb. 10: How to format reviews and prelights [Tim Lionnet]

In this class we will focus on the structure of Reviews and Prelights, with examples.

Wed. Feb 17: Opening the black box of peer review, 2 papers. case study - paper discussion [Shruti Naik]

In this class a case study from Cell Stem Cell will be discussed, which Cell Press has made available. Students present papers, explain results, general evaluation.

Mon. Feb 22: Opening the black box of peer review, case study - peer review process [Shruti Naik and Jon Saxe]

In this class a case study from Cell Stem Cell will be discussed, which Cell Press has made available. Students report on initial study, reviews (and why they made this critique), and how the issues were resolved.

Wed. Feb 24: editor panel [Richard Sever, Beth Moorefield & Rita Strack; moderated by Gira Bhabha]

In this class we have invited a panel of journal editors and the co-founder of bioRxiv to speak to the students about peer review from their perspectives [Beth Moorefield, NSMB; Rita Strack, Nature Methods; Richard Sever, bioRxiv/CSHL]. The format will be a moderated discussion, with active participation from students. This class session is open to others in the community as well, and we encourage participation of anyone who is interested.

Module 1 - Neuroscience [Shane Liddelow and Niels Ringstad]:

Mon. March 1: Topic background

Wed. March 3: Preprint 1 discussion

Mon. March 8: Preprint 2 discussion

Wed. March 10: Group exercise - develop Prelight (Paper 1, Group 1) and Peer review comments (Paper 2, Group 2)

Module 2 - Structural biology and biochemistry [Gira Bhabha & Damian Ekiert]:

Mon. March 15: Topic background

Wed. March 17: Preprint 1 discussion

Mon. March 22: Preprint 2 discussion

Wed. March 24: Group exercise - develop Prelight (Paper 1, Group 1) and Peer review comments (Paper 2, Group 2)

Module 3 - Quantitative cell biology [Tim Lionnet and Liam Holt]:

Mon. March 29: Topic background

Wed. March 31: Preprint 1 discussion

Mon. April 5: Preprint 2 discussion

Wed. April 7: Group exercise - develop Prelight (Paper 1, Group 1) and Peer review comments (Paper 2, Group 2)

Module 4 - Microbiology & Immunology [Heran Darwin & Ken Cadwell]:

Mon. April 12: Topic background

Wed. April 14: Preprint 1 discussion

Mon. April 19: Preprint 2 discussion

Wed. April 21: Group exercise - develop Prelight (Paper 1, Group 1) and Peer review comments (Paper 2, Group 2)

Wrap up, feedback & discussion:

Mon. April 26th