101 questions with a bioinformatician #28: Jonathan Eisen

This post is part of a series that interviews some notable bioinformaticians to get their views on various aspects of bioinformatics research. Hopefully these answers will prove useful to others in the field, especially to those who are just starting their bioinformatics careers.

Jonathan Eisen is a man who almost needs no introduction. As a Professor at UC Davis, he holds appointments at the Genome Center and in the Departments of Medical Microbiology & Immunology and Evolution and Ecology. He also holds an adjunct scientist position at the Department of Energy Joint Genome Initiative. If you can't find Jonathan in any one these locations, you should also remember to try his 'other' office.

His research interests focus on the diversity of microbes and the role microbes play in the health of ecosystems. One of his many projects relating to this is the microbiology of the Built Environment network (microBEnet).

You might think that studying at Harvard, winning a Benjamin Franklin Award, being a extremely vocal advocate of open access publishing, and making your name as an evolutionary biologist working for the University of California in NorCal would be enough to uniquely identify anyone on this planet. However, these are all feats that that have been accomplished by Jonathan and his brother Michael.

This leads me to what I consider to be the real highlight of Jonathan's career. Forget about his many accomplishments as a scientist. Also, forget about his key role in popularizing and legitimizing the use of tools such as twitter as an important component of scientific outreach. And definitely forget about his tireless efforts to expose the horrible gender bias present at so many academic meetings. No, the real zenith of Jonathan's career is that he is leading the fight to rid the world of badomics words.

You can find out more about Jonathan by visiting his lab's website, reading his extremely popular Tree of Life blog, or by following him on twitter (@phylogenomics). And now, on to the 101 questions...



001. What's something that you enjoy about current bioinformatics research?

I really like the move to improve visualizations as part of bioinformatics workflows. For example see the work of Holly Bik and her work on the Phinch project.

I also really really like the move for more people to be discussing their work and the work of others on social media.



010. What's something that you don't enjoy about current bioinformatics research?

The challenge of long term funding for open source projects.



011. If you could go back in time and visit yourself as a 18 year old, what single piece of advice would you give yourself to help your future bioinformatics career?

A better understanding of ergonomics.



100. What's your all-time favorite piece of bioinformatics software, and why?

MacClade because it got me into informatics and evolution. The developers (the Maddison brothers) were TAs for a class I took as an undergrad (a course by Stephen Jay Gould)



101. IUPAC describes a set of 18 single-character nucleotide codes that can represent a DNA base: which one best reflects your personality, and why?

- KRB: this is a dash, one of two IUPAC characters that can be used to represent a gap.



DVD bonus materials


KRB: Because of the relative brevity of this interview, I thought that I would also share some answers Jonathan gave me to the questions I also include when asking people to do these interviews (this info sometimes helps me write my introductions):

0111. What is the correct way of describing your current position or title(s)

Guardian of Microbial Diversity.


1000. How long have you been in this role?

My whole life.


1001. In 1–2 sentences, describe what your role entails

I am a secret superhero trying to protect the microbes of the world.

You wait ages to see a tweet about gender bias in science, and then three come along at once!

I uploaded my last post about gender bias in genomics/bioinformatics to my blog late on Sunday night. When I checked my twitter feed on Monday morning I was pleasantly surprised to see how much traffic the post had already generated. I was also amused by the serendipitous nature of seeing the following tweets appear closely together in my timeline:

 
 

So well done to the Crick Institute regarding the news that they will have a perfectly equal mix of male and female group leaders. This figure of 50% females would put them top of my list of research institutes in this field.

In contrast, finding out that the new Barcelona Institute of Science and Technology has an all male roster (11 Professors, 18 staff in total) is kind of depressing. This result would put them bottom of my list.

What would be a suitable value for the absolute minimum proportion of female speakers at genomics/bioinformatics conferences?

Photo by ViktorCap/iStock / Getty Images
Photo by ViktorCap/iStock / Getty Images

Background

Hopefully, many people reading this will be aware of Jonathan Eisen's valiant efforts to highlight the Yet Another Mostly Male Meeting (YAMMM) problem; these are conferences where the gender bias is disproportionately skewed towards male speakers. You can see all of Jonathan's YAMMM posts on his blog, and in his latest post he highlights a particularly egregious case: a CSHL meeting on the Evolution of Sequencing where only 7.8% of speakers are women.

In my last ACGT post I looked at how this figure (7.8%) compared to the male/female ratio of senior researchers at 10 different genomics/bioinformatics institutes. Nine out of the ten places that I looked at had a much higher proportion of female scientists. I tried making the point that this suggests that conference organizers have no excuses for not doing a better job at recruiting more female speakers.

But it struck me that my analysis was a bit too shallow, especially as the numbers of researchers in each place differed quite a bit (from 10 to almost 60). So I went back and looked at many more academic institutions and kept track of the absolute numbers of men and women in senior research roles.

Dataset

In total, my updated dataset comprises details from 40 different academic institutes (or centers/departments) that specialize in genomics and/or bioinformatics. The vast majority (33/40) mention 'genome', 'genomics', or 'bioinformatics' in their title (the exceptions to this include the Broad Institute, Cold Spring Harbor Laboratory, and the Wellcome Trust Sanger Institute).

The 40 different institutes represent locations in North America, Europe, Asia, and Australia. In some cases, the named institute represents an umbrella organization connecting researchers in different locations across that country (e.g. the Swiss Institute of Bioinformatics). There is probably an element of selection bias towards research institutes that provided an English-language version of their staff/personnel page (not all non-English websites have translations of every page available).

I think that this dataset contains most of the widely known research institutes that have a dedicated focus on genomics and bioinformatics. The list could probably be further expanded if I targeted more University departments that have a specialization in these fields.

In total I logged the gender of 1,039 people in various 'senior' research roles (e.g. Faculty, 'Group leaders', 'Project leaders', etc.). In many cases I deduced gender from first names, but looked for images of researchers where this was not easy to do so.

I've uploaded the main table of data to Figshare so that others can look at all of the detailed numbers if they so desire.

Results

  1. The most equitable result for any one academic institute with at least 15 senior research scientists was the Duke Department of Biostatistics and Bioinformatics (40.4% female, N=52)
  2. Only two other institutes had figures of 40% or higher: the National Human Genome Research Institute (40% female, N=40) and the Functional Genomics group at the Russian Academy of Medical Sciences (50% female, N=6).
  3. Only 3 out of 40 institutes had a lower proportion of female scientists than at the aforementioned CSHL meeting with 7.8% female speakers.
  4. Discounting the bottom placed institute due to small sample size (0% female, N=4), the next worse place was NBIC, the Netherlands Bioinformatics Center with only one female Faculty member (4.8% female, N=21).
  5. The overall ratio of female scientists in senior research roles is 23.6% (N=1,039).

Conclusions

It is somewhat depressing to see such a systematic gender bias in my field, where female scientists only account for approximately a quarter of senior research positions. This figure is in line with UK data for the proportion of female professors all biological sciences (25.1%). The lack of equal gender representation is presumably due to bias and discrimination (conscious or otherwise). In 2014 I conducted a survey to look at gender bias in bioinformaticians across different career stages. This survey had 370 responses — from undergraduate level right through to Deans of academic schools — and showed that there is essentially no gender bias at all stages prior to the level of Faculty (or equivalent). This suggests that there is no shortage of talented women coming through the system, they just are hitting a barrier when it comes to attaining senior research positions…a situation clearly not helped by further discrimination at conferences.

Based on the figures that I show here, one might argue that the figure of approximately 25% could be seen as a minimum target for female participation at conferences. However, such a target would only be encouraging the current levels of discrimination. Far better would be a target that not only attempts to reduce discrimination, but which also better reflects the equal representation of female scientists in post-doc and graduate student positions.

For these reasons I feel that conference organizers — in the fields of genomics and bioinformatics — should be aiming for at least a third of all speakers to be female. Ideally, we want to be doing better than this which is why I suggest this as an absolute minimum target. Depressingly, even this low target is something which most (all?) of the YAMMM meetings described by Jonathan Eisen fail to meet. Of course, such a target should apply for male speakers too, though I'm doubtful that there has ever been a conference in this field where men accounted for less than a third of all speakers.

I don't attend many conferences, but from now on I won't be attending any if at least 33% of the talks are not by women.

Update 2015-06-30: Added link to data for percentage of female professors in UK biological sciences, and clarified that my suggested target figure should also apply to male speakers. I also added a caveat that my methods of choosing institutes is biased towards websites written in English (or with English translations available).