6 EC
Semester 2, period 4, 5
5234CIID6Y
This course is aimed at 1st and 2nd year MSc students in the Biomedical/(Neuro)Biological Sciences with an interest in developmental biology. In this course the student will learn how to read, critically evaluate, present, discuss and review high-impact research articles in the fields of developmental biology and stem cell biology. The student will become familiar with current concepts and challenges in these fields and state of the art experimental techniques used to address these issues.
Whether you continue your career in scientific research or in any other field (business, politics, communication, teaching, entrepreneurship), you will continuously come into contact with new scientific discoveries. In this day and age, many of those are related to various aspects of developmental biology (think about aging research and regenerative medicine, for instance). Having been trained as a scientist, you will be expected to be able to critically evaluate the claims that you hear or read in the news. For this, it is crucial that you are able to go beyond the tweet, newspaper article or blogpost and back to the original source: the scientific publication.
Students will get the opportunity to broadly sample the recent (i.e. mostly published in the last 2 years) developmental biology literature. Papers will be discussed in a 'journal club' style setting. Class size will intentionally be kept small, to stimulate and interactive exchanges of ideas and opinions.
Articles will be provided by the coordinators, and will be made available for download on
Canvas if requested and/or if access is an issue.
By the time the course is completed, the student should be able to:
• discuss current concepts and challenges in developmental biology research and the state-of-the-art experimental approaches used to tackle these.
• analyze and interpret the primary literature.
• concisely present a paper in front of a peer group.
• discuss and critique a paper within a peer group.
• dissect the strength and weaknesses of a primary research article.
Weekly interactive group sessions ('journal club' style) under the guidance of dr. Renée van Amerongen and dr. Frank Jacobs. At least one guest speaker will be invited whose paper will be discussed in class. For more info: see ‘Assignments’.
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Activity |
Number of hours |
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Journal Club |
36 |
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Zelfstudie
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Total for zelfstudie: 132
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Total 6 EC x 28 hours |
168 |
The programme does not have requirements concerning attendance (OER-B).
Additional requirements for this course:
Students are expected to show up to class prepared, having read the paper to be discussed and to actively take part in the in class discussions. Attendance to all classes is highly recommended, but students are expected to attend at least 9 out of 12 lectures during the course.
| Item and weight | Details |
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Final grade | |
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15% Quality of the questions that are submitted by e-mail | |
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15% Own presentation and methodology/TA preparation | |
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20% Written Assignment 1: News & Views | |
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20% Written Assignment 2: Critical review report | |
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30% In class participation and discussion |
Preconditions to obtaining a final grade are a) the attendance of at least 9 out of 12 lectures b) completion of the written assignments and c) being the presenter once and methodology assistant twice.
A minimum overall final grade of 5.5 is sufficient to pass this course. A minimum of 5.0 should be obtained for each of the individual assignments.
Contact the course coordinator to make an appointment for inspection.
The students are expected to read and critically evaluate the article before it is presented by one of their fellow students on the day of the lecture. Prior to the lecture in which the article is discussed, each student is expected to send in 2-3 critical remarks or questions about the article, the quality of the data, or the interpretation and conclusions of the authors.
These remarks/questions are required to be emailed to both coordinators.
For each of the articles that will be presented, the coordinators will appoint one student as ‘Principal Presenter’ (the student that chose the article), as well as 2 ‘Methodology Assistants’ (Two students who will focus on the methods section to become familiar with the methodology that is used in the article).
The presenting student is required to use 1 or 2 introductory slides to present the context/background of the paper. This will set the stage before the paper is discussed in detail. Then each of the figures is presented in detail. At this point, the presenter can be assisted by the 2 Methodology assistants to clarify the technical aspects of each panel/figure.
After the figures are discussed, the student will present the ‘conclusions of the authors’ (not the student!). Finally, the presentation should end with 1-2 slides containing a critical evaluation of the paper, mainly focusing on the correctness of the authors’ interpretations, quality of the presented data, and the overall academic/societal impact of the work.
The students are expected to actively join in the group discussions. After each figure is presented, there will be time to critically evaluate the techniques used, the quality of the data and the author’s interpretation of the data. After the authors’ conclusions are presented, there will be time to critically evaluate the overall conclusions and interpretations, and to discuss the impact of the presented paper for the field. At this stage, the coordinators can fire-up the discussion by selecting good and critical questions from the 2-3 questions the students handed in beforehand.
The student will write a news and views article, focusing on the paper that the student presented. This News and Views article should take a “helicopter view” to highlight why this paper makes an important breakthrough in the field, while also incorporating the most critical points raised during the in class discussion. He/She should link this particular paper to the existing literature, highlighting the novelty. Think of this as a scientific advertisement that conveys your excitement for the paper. An example of such a ‘news and views’ article will be provided on Canvas.
In addition, the student will write a critical referee report. An example of such a referee report will be provided on Canvas. This report should be a point by point, nitty-gritty critical breakdown of the paper discussed in class. The student can take into account any or all of the remarks made during the presentation of the paper. Think of this as a critical assessment of the paper: where the news and views highlights the big picture novelty and promise of the paper, the critical referee reports discusses the details, gaps/holes and shortcomings of the paper (unless there are none, of course), with only a short part spent on putting the paper in perspective of how it fits in the field.
Deadlines:
- The 2-3 critical questions / remarks should be sent by email to the coordinators prior to the start of the lecture.
- The writing assignments should be send by email to the coordinators ultimately 7 days after the final lecture has taken place.
The 'Regulations governing fraud and plagiarism for UvA students' applies to this course. This will be monitored carefully. Upon suspicion of fraud or plagiarism the Examinations Board of the programme will be informed. For the 'Regulations governing fraud and plagiarism for UvA students' see: www.student.uva.nl
Week 1 and 2: Introduction & Article Assignments
In an introductory lecture the idea behind the course will be explained and all other relevant information will be provided. The topics on which research articles can be selected will also be discussed in the introduction lecture.
After the first introductory lecture (week 1), the student will be asked to choose three research articles from a list of titles (week 2), pre-selected by the coordinators (or to suggest their own paper). The articles should be published in either Nature, Cell or Science, or any of the daughter/sister journals (such as Molecular-Cell; Nature Neuroscience; Nature Genetics, etc), since these articles are expected to be aimed at a broad readership (unlike some of the society journals).
Deadline for handing in the selection of papers is Thursday of week two at 23:59.
The selection should be emailed to Frank Jacobs and Renee van Amerongen.
From these three articles, the coordinators will choose one article which the student will be presenting during one of the following lectures (lectures 4-12).
The pre-selected articles and the schedule of presentations will be made available to everyone on Canvas before week 3.
Week 3: Guest lecture
In week 3, an invited speaker will discuss his/her own high impact article. Alternatively, one of the coordinators may take the lead in presenting the first paper. The presentation by the invited lecturer will also be in ‘journal club’ style, similar to the format that we ask from the students’ presentations, so it will be an example for what we expect from the students in lectures 4-12.
Handing in critical questions/remarks (lectures 3-12)
The students are expected to read and critically evaluate the article before it is presented by one of their fellow students on the day of the lecture. Prior to the lecture in which the article is discussed, each student is expected to send in 2-3 critical remarks or questions about the article, the quality of the data, or the interpretation and conclusions of the authors.
These remarks/questions are required to be emailed to both coordinators.
Journal club presentations (once as presenter, twice as ‘technical assistant; lectures 4-12)
For each of the articles that will be presented, the coordinators will appoint one student as ‘Principal Presenter’ (the student that chose the article), as well as 2 ‘Methodology Assistants’ (Two students who will focus on the methods section to become familiar with the methodology that is used in the article).
The presenting student is required to use 1 or 2 introductory slides to present the context/background of the paper. This will set the stage before the paper is discussed in detail. Then each of the figures is presented in detail. At this point, the presenter can be assisted by the 2 Methodology assistants to clarify the technical aspects of each panel/figure.
After the figures are discussed, the student will present the ‘conclusions of the authors’ (not the student!). Finally, the presentation should end with 1-2 slides containing a critical evaluation of the paper, mainly focusing on the correctness of the authors’ interpretations, quality of the presented data, and the overall academic/societal impact of the work.
Article discussions (lectures 3-12)
The students are expected to actively join in the group discussions. After each figure is presented, there will be time to critically evaluate the techniques used, the quality of the data and the author’s interpretation of the data. After the authors’ conclusions are presented, there will be time to critically evaluate the overall conclusions and interpretations, and to discuss the impact of the presented paper for the field. At this stage, the coordinators can fire-up the discussion by selecting good and critical questions from the 2-3 questions the students handed in beforehand.
Written assignments (at choice, throughout lectures 4-12)
The writing assignments should be sent by email to the coordinators at most 7 days after the final lecture has taken place.
Writing assignment 1: News and Views
The student will write a news and views article, focusing on the paper that the student presented. This News and Views article should take a “helicopter view” to highlight why this paper makes an important breakthrough in the field, while also incorporating the most critical points raised during the in class discussion. He/She should link this particular paper to the existing literature, highlighting the novelty. Think of this as a scientific advertisement that conveys your excitement for the paper. An example of such a ‘news and views’ article will be provided on Canvas.
Writing assignment 2: The critical referee report
In addition, the student will write a critical referee report. An example of such a referee report will be provided on Canvas. This report should be a point by point, nitty-gritty critical breakdown of the paper discussed in class. The student can take into account any or all of the remarks made during the presentation of the paper. Think of this as a critical assessment of the paper: where the news and views highlights the big picture novelty and promise of the paper, the critical referee reports discusses the details, gaps/holes and shortcomings of the paper (unless there are none, of course), with only a short part spent on putting the paper in perspective of how it fits in the field.
The schedule for this course is published on DataNose.
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Grade expires @ end of the academic year, no resit |