Tag Archives: graphical abstract

A reading seminar where every student reads, writes and contributes to the discussion in class

16 Jan

I remember reading seminars as follows: one student spends the entire week preparing for a powerpoint presentation, which often turns out to be stressful for the student and somewhat boring and uninformative for the audience. The other students only glanced over the paper and so any discussion quickly falls flat. I therefore decided to have multiple short presentations without powerpoint (less preparation, more fun to listen to, plus repetition is good for learning a skill). I also decided to use short writing assignments as homework to make sure that all students were prepared to contribute to the discussion in class. At the same time, I wanted to keep things manageable for everyone.

1. Learning to present: every student does multiple short presentations without powerpoint.

No powerpoint: I didn’t want students to spend too much time preparing a presentation. I believe that often, when students spend a lot of time preparing presentations, they focus too much on making powerpoint slides and not enough on informing the audience and telling a story.

Short presentations: Doing an engaging 45 minute presentation is extremely difficult, and a skill that most postdoc don’t have, so why do we use 45 minute presentations in our graduate seminars? I decided in stead to let each student do three 10 minute presentations.

Feedback: After each presentation the presenters got feedback (from the other students and myself), so that they could improve their presentation skills during the semester.

Easy listening: An added benefit of 10 minute presentations is that it is much easier for the audience. Each week started with three student presentations, one on the background and main question of the paper, one on the data and the results of the paper, and one on the conclusion and implications of the paper.

2. Practice writing: every student does a different writing assignment every week.

Graded homework each week: A paper discussion can only work if people have read the paper. If students don’t read, they may spend most of their energy to try to hide that they didn’t read (I know I was in that situation!). So even though I understand that life and research get in the way of reading, I really wanted to make sure that the students were prepared for the seminar. To do that, I made every student do a written assignment every week that would count towards their grade (unless they were presenting that week).

A different assignment for each student: I had a long list of assignments so that each week, many different assignments were done AND so that over the course of the semester each student did many different assignments. This guaranteed that the students read the paper, but each with a different question in mind.

There were several types of written assignments. Descriptive: 1. Describe the background and main question of the paper, 2. describe the data and the results, 3. describe the conclusions, 4. describe which virus the paper is about. Critical: 5. What is your opinion of the paper? 6. What do you think the authors should have done differently? 7. Play the devil’s advocate: why should the paper not have been published? Summaries: 8. Summarize the paper in your own words, as if writing to a friend, 9. summarize the paper using only the most common 1000 words of the English language, 10. summarize the paper in a graphical abstract, 11. summarize the paper in a tweet. Meta: 12. Who are the authors of the paper? 13. How often is the paper cited, do you think it is influential?

Short! Each written assignment could not be more than 150 words, to keep the workload manageable for me and for the students.

Surprisingly hard: Some of the assignments were harder than the others. Summarizing the paper using only the 1000 most common words from the English language turned out to be very hard, but some of the students did a great job (see here and here). The graphical abstract was also hard for some students, but others liked it just because it was so different from their usual work (see here and here). The ”devil’s advocate” writing assignment was always very interesting to read.

Easy: Grading the written assignments was quite easy. I simply gave a plus or minus for 5 categories (answered the question, scientific accuracy, clarity, grammar and word count).

Revisions allowed: After a request from a student, I decided that the students could redo any assignment where they had gotten less than 100% because I believe that feedback is most useful when it can be applied to a revision.

3. Promoting equity: thanks to the written assignments, every student could contribute to every class.

Everyone contributes: One of the nice things about the homework schedule with different assignments for everyone is that in class, I could ask each student about their homework. This way, each student contributed to the class, promoting equity, and the brief discussions of the homework assignments always let to questions from other students. Even if I didn’t ask, some students would volunteer to share information they found while they researched for their homework. For example, I remember someone remarking at the end of a presentation: “In your presentation, you said this result may be very important, but I found that the paper hardly has any citations even though it was published ten years ago, so I think it may not have been picked up by anyone.”

Sharing homework: I also encouraged the students to share their written assignments on the online forum we had for the class, so that the other students (and not just me) could read them. Sometimes they led to interesting forum threads. I also published some of the written assignments on my blog, after asking the students for permission. This way even more people could enjoy them.

Doing my own homework

28 Sep

This week I decided to do some of my own homework. Just for fun.

It’s a graphical abstract of a classic paper we read in class.

Turns out, making a graphical abstract is no easy task! Next week, there’ll be students’ work here again.

What I found most surprising about this paper is that they had to sequence the chimps’ MtDNA to find out what subspecies they were. I would have expected that experts could simply look at a chimp and know what subspecies it is.

Origin of HIV-1 in the chimpanzee Pan troglodytes troglodytes.
Gao F, Bailes E, Robertson DL, Chen Y, Rodenburg CM, Michael SF, Cummins LB, Arthur LO, Peeters M, Shaw GM, Sharp PM, Hahn BH. Nature. 1999 Feb 4;397(6718):436-41.


Reading about using phylogenetics in court

5 Sep

In my new job at SFSU, I am teaching a seminar on the evolution of human viruses. We are reading one paper every week and every student gets a different assignment for each paper. We’ve done one week now and I am very happy with the results. The paper we read was Metzker et al (PNAS, 2002), it is about using phylogenetic methods in an HIV infection case that went to court (thanks to Graham Coop for suggesting the paper).

I asked the students if I could publish some of their work. Here we go:

Describe the context and main question of the paper

The Metzker et al. study details the first instance of the admission of phylogenetic analysis as forensic evidence in a criminal case. It sought to determine whether scientific support existed for the proposed viral transmission event between the suspect (via injection of blood from an HIV-positive patient) and the victim by inferring phylogenies of the patient, victim, and HIV-infected control strains from the same geographic region using two loci under different selective pressures. In trees generated from both loci, the isolates from the victim clustered with the patient’s, supporting a close relationship between victim and patient HIV strains. Phylogenetic analysis has previously been used in inferring HIV transmission events, notably in the “Florida dentist case”. Five individuals were inferred to have contracted HIV-1 from their dentist based on the distinct clustering of their strains with the dentist’s relative to geographically similar HIV-positive controls.

Roxanne Bantay

Who are the (main) authors of the paper?

Dr. Michael Metzker, the primary author of Molecular evidence of HIV-1 transmission in a criminal case (2012), is an associate professor at Baylor college of Medicine and Rice University where he teaches human genetics. Additionally, he is president & CEO at RedVault Biosciences, a technology company that aims to advance personalized genomic medicine. Metzker is also an active researcher in the field of bioinformatics and next-generation sequencing.

The last author of the preceding publication is Dr. David Hillis, who is a current evolutionary biology professor and former director of the biology and bioinformatics department at the University of Texas (Austin). Hillis’ research focuses on experimental laboratory evolution; he believes that by studying this process we can ultimately gain insight into the underlying mechanisms that drive evolution.

Eduardo Lujan

Explain the main results of the paper using only the 1000 most common English words

This paper is about a doctor who tried to kill his girlfriend by using blood from a sick person. The doctor got the blood from their work and stuck their girlfriend during a fight. The important part of this case is the way that they showed that it really was the doctor who made the woman sick. For this case, tiny changes that happened in the thing that made the woman sick were found. These changes can show which person made the other people sick and show the relationships between all of the sick people.   By looking at these changes and the relationships, they showed that the doctor was the one who was at fault for making the woman sick.

Bradley Bowser

(see http://splasho.com/upgoer5/)

Make a graphical abstract of the paper


Peter Manzo