Grants keep coming to Reed Biologists

As a new computational biologist at Reed College, I was excited about the prospect of continuing to do research while teaching innovative courses.  I’ve written about the research opportunities at Reed, and faculty across campus have received over two million dollars of grant funding in 2014/2015.

The Biology Department just secured two more research grants from the M.J. Murdock Charitable Trust to investigate neurogenesis in zebrafish (Dr. Kara Cerveny) and discover candidate driver genes in cancer (me!).

Small schools also have an opportunity to play a large role in undergraduate education programs.  Another NSF grant was recently awarded to Dr. Suzy Renn to organize a STEM workshop on undergraduate involvement in the NSF’s Brain Research through Advancing Innovative Neurotechnologies (BRAIN) Initiative.

All in all, 2016 seems like it will be another great research year.

Networks in Biology (it’s not what you think)

I am currently designing my upper-level undergraduate class I will teach next fall.  The proposed course description* begins with:

Computational Systems Biology

A survey of network models used to gain a systems-level understanding of biological processes.  Topics include computational models of gene regulation, signal transduction pathways, protein-protein interactions, and metabolic pathways…

As a result, I’ve been keeping my eye out for networks (or, mathematically-speaking, graphs) in biology.  I found a fascinating network in this recently-published paper:

Males Under-Estimate Academic Performance of Their Female Peers in Undergraduate Biology Classrooms
Grunspan DZ, Eddy SL, Brownell SE, Wiggins BL, Crowe AJ, et al. (2016) Males Under-Estimate Academic Performance of Their Female Peers in Undergraduate Biology Classrooms. PLoS ONE 11(2): e0148405. doi: 10.1371/journal.pone.0148405

I often see reports on gender bias in computer science, but I somehow thought that biology would be the least gender biased of the STEM disciplines.  I was surprised that this type of bias has been uncovered in biology, and in classes with more female students than male students.  The paper has already been highlighted on sources such as Science Daily, The Atlantic, and the Huffington Post, among others.  The wealth of information in the paper — from the experimental design to the study setting to the final results — warrants an important, broad discussion.

In this post, however, I’ll focus on the networks.

The authors conducted multiple surveys where students nominated the “best performers” in their introductory biology courses at a large American university.  These surveys were given at different parts of the course, and they were conducted across three different iterations of the same undergraduate biology class.  Figure 1 of the paper shows two networks displaying two surveys from the same class, six weeks apart.




Figure 1. Unequal distribution of peer perception of mastery of content among genders grows over the term.  Grunspan et al., PLOS ONE 2016.

These networks show the students (represented as nodes in the graph) in a particular class, and “votes” as directed edges from nominators to nominees.  Male students are shown in green, and female students are shown in orange.  The size of nodes indicates the number of nominations received by each student.  The structure of these networks is striking.  There are many students who do not nominate anyone and are not nominated by anyone, resulting in “singleton” nodes.  In both networks, there is a general cohort of students that receive nominations; however the distribution of these nominations are much more skewed in the second survey.

The intuitive trend that we see in these graphs is that “the green nodes tend to get bigger” corresponding to a larger proportion of nominations go to male students.  However we see female students also receive more nominations in the second survey compared to the first.  The authors quantify these aspects using exponential-family random graph models (ERGMs) to assign coefficients on model statistics relating to gender, outspokenness, and grade.  They found a specific gender bias, that male students tend to nominate other male students, after controlling for grade and outspokenness.  Female students, on the other hand, do not exhibit a gender bias toward nominating males (or females for that matter), after controlling for these factors.

There are many, many other factors that may contribute to these observations, and some are noted in the paper.  The courses were taught (and in some cases co-taught) by four male instructors and only one female instructor, the classes ranged in size from 196 to 760 students, one class employed “random call” lists rather than calling on raised hands.  Besides outspokenness, interactions in lab sections and outside class would undoubtedly affect students’ perceptions.  This paper opens a tremendously important conversation about implicit gender bias in the classroom, even in majors with more female students than male students.  As the paper concludes,

This gender biased pattern in celebrity was experienced by over 1,500 students in our analyses.  This number is striking, but less worrisome than the millions of students who attend college STEM classes that may perpetuate the same biases described here.

Grunspan et al., PLOS ONE 2016.

* Pending approval of various college committees – it may change

Quantifying the gender bias in federally-funded STEM research

We all know that there is a gender disparity in STEM fields.  Is it harder for women in these fields to obtain federal funding compared to their male colleagues?  In 2013, Helen Chen published an article in Nature summarizing women’s continual challenges in science.    The infographic below from the paper describes the gap in NIH-funded research grants.

from Inequality quantified: Mind the gender gap by Helen Chen, Nature Vol 595 Issue 7439 2013.

At first glance, the funding gap looks appalling – only 30% of the NIH’s grants are going to women!  However, there’s a missing ingredient here:  the fraction of NIH grant proposals submitted by women.  To get this information, let’s go back to 2008 for a minute.  Jennifer Pohlhaus and others at the NIH assessed the gender differences in application rates and success rates for 77% of the awards submitted in 2008, including training grants, midcareer grants, independent research grants (e.g., R01), and senior grants.  They found that the acceptance rates reflected the application rates for most NIH grants.  however, men had a higher success rate once they had received their first NIH grant and become NIH investigators.  So the funding gap in the infographic may not be tied to women having lower success rates in funding, but rather that fewer women are submitting grants.  A visualization of the data from the NIH is available on their webpage.

The Nature article (and many many other articles) point to the fact that women tend to leave science early in their education and careers.  In the 2008 NIH grant applications there were more female applicants than male applicants for three of the early career / training awards (F31, K01, K23), and two other early career awards (F30 and F32) showed no statistical difference between the number of male and female applicants.  However, male applicants significantly outnumbered female applicants in all midcareer, independent research, and senior career programs.

An evaluation of gender bias is currently underway for six other federal agencies: NSF, DOD, DOE, USDA, HHS, and NASA.  The audit, conducted by the Government Accountability Office (GAO), will first release a report that investigates whether the agencies evaluate proposals based on potentially biased measures.  The GAO will then release a second report identifying potential factors that lead to the disparity in funding between men and women.  Once out, it will be an interesting read…

Slaughter Announces GAO Audit on Gender Discrimination in Federal STEM Research Funding | Congresswoman Louise Slaughter.

If you go to UCLA, you can be a Big Bang Theory scholar

Jim Parsons and Mayim Bialik are two of the `The Big Bang Theory’ people funding the scholarship. Image from

STEM funding for undergraduates is cropping up from many unusual places, including Cards Against Humanity.  People from the show `The Big Bang Theory’ have done it for UCLA, raising over $4 million to endow a scholarship for students in STEM majors.

`The Big Bang Theory’ creates scholarship fund for STEM students at UCLA

Responses to the sexist review by PLOS One

There has recently been a lot of attention on the journal PLOS One and their handling of a heavily gender-biased review received by an evolutionary biologist on a manuscript about gender differences in the Ph.D. to Postdoc academic transition.  PLOS One has taken a few actions, including asking the academic editor who handled the manuscript to step down from the editorial board and removing the offending reviewer from their database.  Dr. Michael Eisen, one of the founders of PLOS, has provided interesting commentary on the subject.

What’s just as troubling is that the reviewer clearly used his personal assessment of not only the authors’ gender but also their “junior” academic status in his criticism.  A blog that focuses on manuscript retractions has another summary of the issue.  Dr. Fiona Ingleby, one of the authors of the manuscript, tells the authors,

Megan and Fiona are pretty unambiguous names when it comes to guessing gender.  But in fact, the reviewer acknowledged that they had looked up our websites prior to reading the MS (they said so in their review). They used the personal assessment they made from this throughout their review – not just gender, but also patronising comments throughout that suggested the reviewer considered us rather junior.  – Fiona Ingleby

This has raised some major issues about the peer-review process, including whether a reviewer’s identity should ever be revealed in a single-blind or double-blind review.  Dr. Eisen addresses this in his blog posted above.  Dr. Zuleyka Zevallos wrote about removing publishing bias in science, here in the form of sexism. In response to Dr. Eisen’s post, she explicitly addresses the accountability that institutions and publishers need to have in place.

It will be interesting to see how PLOS One and other publishers address this now-viral issue, especially by the changes to the peer-review process.  Some have noted that the PLOS One editor failed in his/her duty by returning this gender-biased review to the authors instead of disregarding it, and it wasn’t necessarily a problem with the procedures.  But more and more journals are moving to different review styles, including Nature’s experiment with double-blind peer review.  If the PLOS One review had been double-blind, the reviewer may have been able to guess the gender of the authors but would not have been able to verify that, and especially not verify their current academic positions.

Everyone’s a math person

I just read this article in WIRED in response to math to students majoring in elementary school education.

Quit Saying ‘I’m Just Not a Math Person’ | WIRED.

People end up doing math all the time, whether they realize it or not.  The author of the WIRED post, Rhett Allain, ends by saying that not only should math be taught in all grade levels, but programming should be taught at (nearly) all grade levels as well.  As we see a growing market for coding tutorials aimed at kids, I bet we’ll see programming become a meaningful part of elementary education.