Archive | November, 2014

Five computational evolution meetings in a row with just one female speaker

28 Nov

Annoyed by the announcement of yet another mostly male meeting, and inspired by Jonathan Eisen’s recent posts about male-biased meetings, I decided to look at the series of meetings in France on Mathematical and Computational Evolutionary Biology of which the recently announced meeting is a part. Mathematical and computational evolutionary biology is exactly my field and the meetings take place in lovely places in the south of France, so initially, I was interested. But then I looked at the lists of invited speakers and found that in the last five instances of the meeting, there was exactly one female speaker each year. Wow. How sad!

Here are a few suggestions for the organizers to invite more women. This list is obviously far from complete, just women PIs who I happen to know and who came to my mind immediately: Sally Otto, Katia Koelle, Hanna Kokko, Doris Bachtrog, Katrina Lythgoe, Emilia Huerta, Sarah Cobey, Melissa Wilson-Sayres, Joanna Masel, Anna-Sophie Fiston-Lavier, Mercedes Pascual, Pardis Sabeti, Kate Hertweck, Amy Williams, Sohini Ramachandran, Angela McLean, Lindi Wahl, Maria Servidio, Hua Tang, Sally Blower. This list doesn’t include the many female postdocs in the field. Also doesn’t include the women who were invited by the MCEB organizers.

[Also Florence Débarre, Deborah Charlesworth, Maria Orive, Paulien Hogeweg, Charlotte Hemelrijk.]

Anyways, here are the data:

MCEB 2015 1 woman, 6 men (14%)

[Note added: the announcement says that this list is preliminary]

David Bryant (University of Otago, NZ)
Jukka Corander (Bayesian Statistics Group, University of Helsinki, FI)
Asger Hobolth (Bioinformatics Research Center (BiRC), Aarhus University, DK)
Philippe Lemey (Rega Institute, Clinical and Epidemiological Virology, BE)
Bernard Moret (Laboratory for Computational Biology and Bioinformatics, EPFL, CH)
Ludovic Orlando (Center for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK)
Molly Przeworski (Columbia University, New york, USA)

MCEB 2014 1 woman, 7 men (13%)

Rampal Etienne (University of Groningen, NL)
Daniel Huson (Center for Bioinformatics (ZBIT), Department of Computer Science, Tuebingen University, DE)
Nicolas Lartillot (Laboratoire de Biologie et Biométrie Évolutive, Lyon, FR)
Arne Mooers (Simon Fraser University, CA)
Hélène Morlon (Ecole polytechnique, FR)
Rasmus Nielsen (University of California, Berkeley, US)
Adam Siepel (University of California, Santa Cruz, US)
Mike Steel (University of Canterbury, NZ)

MCEB 2013 1 woman, 9 men (10%)

Sebastian Bonhoeffer (ETH Zürich, CH).
Bastien Boussau (University of California, Berkeley, US).
Alexei Drummond (University of Auckland, NZ).
Ian Holmes (University of California, Berkeley, US).
Steven Kelk (Maastricht University, NL).
Darren Martin (University of Cape Town, SA).
Erick Matsen (Fred Hutchinson Cancer Research Center, Seattle, US).
Tanja Stadler (ETH Zürich, CH).
Niko Beerenwinkel (ETH Zürich, CH).
Gil McVean (University of Oxford, UK).

MCEB 2012 1 woman, 10 men (9%)

Cécile Ané (University of Wisconsin, US).
Michael Blum (CNRS – TIMC, FR).
Oliver Eulenstein (Iowa State University, US).
Arnaud Estoup (INRA – CBGP, FR).
Asger Hobolth (Aarhus University, DK).
Vincent Moulton (University of East Anglia, UK).
Noah Rosenberg (University of Michigan, US).
Alexandros Stamatakis (Heidelberg, DE).
Mike Steel (University of Canterbury, NZ).
Edward Susko (Dalhousie University, CA).
Asger Hobolth (Aarhus University, DK).

(2010 meeting link is broken)

2008 1 woman, 15 men (6%)

Elisabeth Allman: University of Alaska, US.
Vincent Berry: CNRS, FR.
David Bryant: University of Auckland, NZ.
Frantz Depaulis: CNRS, FR.
Laurent Duret: CNRS, FR.
Nicolas Galtier: CNRS, FR.
Olivier Gascuel: CNRS, FR, chair.
Junhyong Kim: University of Pennsylvania, US.
Mike Hendy: Massey University, NZ.
Daniel Huson: University of Tübingen, DE.
Vincent Moulton: University of East Anglia, UK.
David Posada: Universidad de Vigo, ES.
Allen Rodrigo: University of Auckland, NZ, co-chair.
Noah Rosenberg: University of Michigan, US.
Charles Semple: University of Canterbury, NZ.
Mike Steel: University of Canterbury, NZ.

2005 3 women, 12 men (20%)

Walter FITCH, University of California at Irvine, USA.
Anne BERGERON, Université du Québec, Montréal, Canada.
David BRYANT, Mc Gill University, Montréal, Canada.
Nicolas GALTIER, CNRS-Université Montpellier II, France.
Ziheng YANG, University College London, UK.
Susan HOLMES, Stanford University, USA.
Mark PAGEL, University of Reading, UK.
David SANKOFF, Université de Montréal, Canada.
Li-San WANG, Austin University, USA.
Nadia EL-MABROUK, Université de Montréal.
Bernard MORET, University of New Mexico, USA.
Mike HENDY, Massey University, New-Zealand.
Vincent MOULTON, The Linnaeus Centre for Bioinformatics, Uppsala University .
Mike STEEL, University of Canterbury, New-Zealand.

2003 4 women, 17 men (19%)

Hugues Roest Crollius, Ecole Normale Supérieure de Paris
Laurent Excoffier, University of Bern
Allen Rodrigo, University of Auckland
Joe Felsenstein, University of Washington
Rose Hoberman, Carnegie Mellon University
Matthew Spencer, Dalhousie University
Nicolas Salamin, University of Washington
Elizabeth Allman, University of Southern Maine
Vincent Daubin, Université de Lyon
Mike Steel, University of Christchurch
Carolin Kosiol, European Bioinformatics Institute
Vivek Gowri-Shankar, University of Manchester
Emmanuel Douzery, Université de Montpellier
Arne Mooers, Simon Fraser University
Bret Larget, University of Wisconsin
Dan Gusfield, University of California Davis
Cecile Ané, University of Wisconsin
Michaël Blum, Centre Nationale de la Recherche Scientifique, Grenoble
Eric Bapteste, Dalhousie University
Charles Semple, University of Christchurch
Daniel Huson, University of Tuebingen

Come to the GRC and GRS on microbial populations!

12 Nov

In 2013 I went to the Microbial Population Biology GRC for the first time. GRC stands for Gordon Research Conference. GRCs are weeklong meetings, with around 150 participants, which typically repeat every other year. The GRC on Microbial Population Biology has been running since 1985!

The GRS: a pre-meeting for young scientists

Attached to the GRC is a GRS. GRS stands for Gordon Research Seminar. A Gordon Research Seminar is basically a mini-meeting for young scientists that takes place in the weekend before the GRC. At the GRS there are only students and postdocs, and this meeting is much smaller. I really liked the GRS because it was very easy to get to know people there. It was also nice to see postdocs and graduate students give talks, which is quite rare during the GRC. When the GRC started, I already knew quite a few faces and names.

This year (well, 2015) I am the chair of the GRS that is attached to the Micro Pop Bio GRC. Elizabeth Jerison, Lena Mendes-Soares and Krishna Swamy are co-organizers.

You should apply!

If you are a graduate student or postdoc in the field of microbial population biology, I want to encourage you to apply for the GRC and the GRS. Both meetings will fill up, so it is better to apply early (long before the official deadline). If you are unsure whether you can afford to come, apply anyways. Funds may become available. If you are from one of these countries: China, Russia, Ukraine, India, Africa, Central America, or South America, OR if you are a member of an underrepresented minority OR if you work at a primarily undergraduate institution, it is more likely that we could help you pay for participation.


One of the things I enjoyed most about the GRC in 2013 is how diverse the participants and speakers were. I don’t think I’ve ever been to a meeting where there were so many women and people of color. And I am not entirely sure why, but it felt very nice. It felt like this is a community that I’d want to be part of.

If you are not yet convinced, read what my fellow GRS organizers have to say:

REU07JerisonElizabethElizabeth Jerison: “everyone was really interested in each others’ science”

The 2013 GRS was a great experience. I particularly liked meeting fellow students and post docs in a smaller-group setting before the other conference participants arrived. This way, when the GRC began, I felt comfortable and knew several people. It was also fun and constructive to share my work, and hear about others’ research, in setting where everyone was really interested in each others’ science. Conversations that started at the GRS continued throughout the week at the GRC, as we discussed talks and posters. I think I got much more out of the Gordon Conference as a whole by attending the GRS.

lenaMendes-SoaresLena Mendes-Soares: “will lead to the development of more successful scientific careers”

While the Gordon Research Conference is considered the main Gordon scientific event for presenting research, at the Gordon Research Seminar, students and postdocs are given an added opportunity to showcase their research to an audience with varied scientific backgrounds, and receive valuable feedback on their work. In addition, the Gordon Research Seminar is an ideal venue for students and postdocs to informally share experiences characteristic of their stage in the research career. The chat about the renewals of grants, and editorial and administrative hardships experienced by senior researchers are replaced by chats about the submission of the first grant to NIH, the writing of the first lead-author paper, or the upcoming defense of the degree. Due to all this, the Gordon Research Seminars result in the establishment of collaborations between early career scientists with similar interests that will ultimately lead to the development of more successful scientific careers.

Student blogpost: on bad-small-things and small animals

11 Nov

Nicolas Cole (MSc student at SFSU) does a great job explaining the Hersft et al 2012 paper on airborne Influenza A in ferrets using only the 1000 most common words of the English language. Enjoy!  


Figure 2 from Herfst et al 2012 Science

There is a “bad-small-thing” that goes from one flying animal to another flying animal, causing death. It can also go from a flying animal to a human, if a human touches that flying animal while it is dead. This causes the human to get sick. Does this “bad-small-thing” go from human to human through the air? A group of doctors studied the “bad-small-thing” in “small animals” that do not fly. The “small animals” can also die because of the “bad-small-thing” being in their bodies.

First, the doctors changed the “bad-small-thing” in small ways that could make it go from “small animal” to “small animal” through the air. At first, the “bad-small-thing” and the “changed-bad-small-thing” did not move through the air from one “small animal” to the next.

Then they passed the “bad-small-thing” from one “small animal” to the next, to change it more. They did this ten times with both the “bad-small-thing” and the “changed-bad-small-thing”. They found that the “changed-bad-small-thing” grew easier and more often after passing from “small animal” to “small animal”.

Next, they wanted to see if the “passed-changed-bad-small-thing” could pass from “small animal” to another “small animal” through the air. The doctors put the “small animals” in boxes that did not let the “small animals” touch, but air could pass between them. They put small animals with the normal “bad-small-thing” next to boxes of not-sick “small animals” and they put the “small animals” with the “passed-changed-bad-small-thing” next to not-sick “small animals”.

So, if the “passed-changed-bad-small-thing” could be passed, it could not pass by touch but could pass by air. Sure enough, the doctors found that the “passed-changed-bad-small-thing” passed from sick “small animals” to not-sick “small animals” but the “normal-bad-small-thing” did not pass through the air. However, none of the not-sick “small animals” that became sick through the air died.

The doctors took a closer look at the “air-passed-changed-bad-small-thing” and the “changed-bad-small-thing” and found that the “bad-small-thing” only needs 5 changes to be able to pass through the air from “small animal” to “small animal”. The doctors also say that even though the “small animals” were able to get sick from the “air-passed-changed-bad-small-thing” through the air, this does not mean that humans can change the “bad-small-thing” in the same way as the “small animals” so that it could pass through the air.

Finally, the doctors studied “man-made-human-good-stuff” that is meant to stop “bad-small-thing” from passing from humans to humans. They put the “man-made-human-good-stuff” in the “small animals” that were sick from the “air-passed-changed-bad-small-thing”. The “man-made-human-good-stuff” was able to stop the “air-passed-changed-bad-small-thing”!!!!!!!!!!!!!!!!!!!! (because happy points are free).

For the first time doctors were able to show that a “bad-small-thing” can pass from animal to animal enough that it can become a “air-passed-changed-bad-small-thing” and that can be bad for humans.