Archive | January, 2016

Why I write my NSF preproposal by hand and to a lay audience

18 Jan


Susan Holmes suggests (here) that it’s best to write your first draft of anything on paper, with an old fashioned pen, rather than on your computer. She believes
that the process of writing by hand helps us clear our thoughts. l think she has a point. So, I am writing this blog post on paper.

I would like to add my own piece of advice for better writing: l like to write my first draft as if I am writing to a friend or family member. For me, this strategy helps to remedy some anxiety I have thinking about the colleagues who may ultimately read my manuscript or proposal, and who may be harsh and skeptical. Writing with a lay person in mind also helps me to use simple words and to get to he point faster.

Years ago, l was struggling with the introduction chapter of my PhD thesis. The audience for this chapter would be my advisor and the other committee members. They were all well established and accomplished researchers in the field of population genetics. I was completely writer’s blocked. What could l write that they didn’t already know? l guess the only real information they were going to get from this chapter was whether I had mastered the material, but I had no motivation at all to write the chapter as a test of my knowledge.
l don’t remember who or what gave me the idea, but I decided to write the chapter as if it was meant for a lay audience. I actually didn’t think that my committee cared about the chapter much anyways, so I imagined an audience of friendly lay-people and students who were interested to enter the field., and I started to write for them.

This change of perspective made a huge difference to my writing. Suddenly, I was eager to write and I enjoyed the process. I had no more fear and a clear goal. (If you’re interested, you can download the introduction of my thesis here:  2007_Pennings_Pleuni_ThesisIntroduction).

This week, I am working on an NSF proposal. This is just as daunting and possibly nearly as futile as writing an intro chapter to my thesis (OK, not really). I therefore decided to try the same trick. I will write my first draft as if I’m writing to a friendly lay person, not the NSF committee that will ultimately read and judge my work. In addition to writing to a lay person, I will write my first draft on paper, following Susan Holmes’ advice. Clear thoughts and sentences, here I come!


Reading in the lab

11 Jan

The winter break is a great opportunity to spend time in the lab with my students. One of the things we do, is read papers. Last week, we spent a morning reading the following paper:

Triple-Antiretroviral Prophylaxis to Prevent Mother-To-Child HIV Transmission through Breastfeeding—The Kisumu Breastfeeding Study, Kenya: A Clinical Trial. PLoS Medicine, 2011. Thomas , Masaba, Borkowf, et al. 

The paper shows that antiretroviral drugs taken by an HIV-infected mother help prevent transmission to the baby through breastfeeding. The reported rates of HIV infection of the infants during breastfeeding were less than half the previously reported rates from untreated women.

After everyone read the paper, and we all discussed it together, two students worked together to write an abstract and three students worked together to draw an abstract. Here are the results:

Abstract (by Kadie and Melissa)

The Kisumu Breastfeeding Study was a single-arm trial conducted with 522 HIV–infected pregnant women who took a triple antiretroviral regimen from 34 weeks of pregnancy to 6 months after delivery. The triple-ARV regimen consisted of zidovudine and lamivudine and either nevirapine or the protease inhibitor nelfinavir. The purpose of the study was to investigate how various ARV regimens given to mother and/or their infants affect mother to child transmission of HIV.

Data collected showed that between 0 and 24 months, the cumulative HIV transmission rate rose from 2.5% to 7.0%. The cumulative HIV transmission or death rate was 15.7%. Three percent of babies born to mothers with a low viral load were HIV-positive compared to 8.7% of babies born to mothers with a high viral load. Similarly, 8.4% of babies born to mothers with low baseline CD4 cell counts were HIV positive compared to 4.1% of babies born to mothers with high baseline CD4 cell counts. Although these findings are limited by the single-arm design, this study supports the idea that a simple triple-ARV regimen given to HIV-positive pregnant women regardless of their baseline CD4 cell count can reduce MTCT during pregnancy and breastfeeding in a resource-limited setting.

Graphical abstract (by Olivia, Patricia and Dasha)

2016-01-07 12.40.27


Some recommended and not-recommended science-related books

6 Jan

Last year I read some really cool books that are somehow related to my work. I also read books that were so annoying, I didn’t even finish them. I wanted to share some of my thoughts here.

Jim Ottaviani, Maris Wicks: Primates

Lovely comic book about three women researchers who study primates (Jane Goodall, Dian Fossey, and Biruté Galdikas). Great gift idea! Link to book


Steven Strogatz, The joy of X.

Highly recommended! Great book with essays about fun math. Made me want to learn more. Link to book.

Jennine Capó Crucet: Make Your Home Among Strangers

I very much enjoyed this novel about a young cuban woman who is the first of her family to go to college. It’s an easy read, but it has some insights that may be useful for those of us who teach. Link to book.

Vanessa Woods: Bonobo handshake

Well written memoire by traveler, writer and bonobo researcher Woods, with a lot of background on Congo and neighboring countries. The descriptions of awful violence during the wars in Congo may be upsetting to some. Link to book.

Bill Nye: Undeniable

The topic of this book, evolution, is dear to my heart, but I didn’t manage to finish it. It is simply not well written / edited. Link to book

Frank Ryan: Virolution

This book was definitely worse than Bill Nye’s book! It is not well written and it is full of nonsense about evolution. Disappointing, because it would have been nice to have a good popular book on viruses and evolution. Here Carl Zimmer explains why the book is not recommended: link to book review.