Pre-prints as a speedup to scientific communication

Tomorrow, I’ll sit on a panel about Open Data and Open Science as part of Reed’s Digital Scholarship Week.  I am somewhat familiar with these topics in computer science, but I decided to read up on the progress with Open Access in Biology.

As a junior professor trying to get a foothold in a research program, I’ll admit that I haven’t spent a lot of time thinking about Open Science.  In fact, the first thing I did was look up what it meant:

Open science is the movement to make scientific research, data and dissemination accessible to all levels of an inquiring society.                       – Foster Project Website

Ok, this seems obvious,  especially since so much research is funded by taxpayer dollars.  Surprisingly, Open Science is not yet a reality.  In this post, I’ll focus on the speed of dissemination – the idea that once you have a scientific finding, you want to communicate it to the community in a timely manner.

Biology findings are often shared in the form of peer-reviewed journal publications, where experts in the field comment on drafts before they are deemed acceptable for publication.  Peer-review may be controversial and even compromised (just read a few RetractionWatch posts), but in theory it’s a good idea for others to rigorously “check” your work.  However, the peer-review process can be slow. Painfully slow.  Findings are often published months to even years after the fact.

In computer science, my “home” research discipline, it’s a different story.  Computer science research is communicated largely through conferences, which often includes paper deadlines, quick peer-review turnaround times, and a chance to explain your research to colleagues.  Manuscripts that haven’t undergone peer-review yet may be posted to arXiv.org, a server dedicated to over one million papers in physics, mathematics, and other quantitative fields.  Manuscripts submitted to arXiv are freely available to anyone with an internet connection, targeting “all levels of an inquiring society.”

A biology version of the site, BioRxiv.org, was created in 2013 — more than 20 years after arXiv was established.   It only contains about three thousand manuscripts.  What is the discrepancy here?  Why is the field reluctant to change?

Last February, a meeting was held at the Howard Hughes Medical Institute (HHMI) Headquarters to discuss the state of publishing in the biological sciences. The meeting, Accelerating Science and Publication in Biology (appropriately shortened to ASAPbio), considered how “pre-prints” may accelerate and improve research.  Pre-prints are manuscript drafts that have not yet been peer-reviewed but are freely available to the scientific community.  ASAPBio posted a great video overview about pre-prints, for those unfamiliar with the idea.  While the general consensus was that publishing needs to change, there are still some major factors that make biologists reluctant to post pre-prints (see the infographic below).

This is an excellent time to talk open science in Biology.  It has become a hot topic in the last few months (though some in the field have been pushing for open science for years). The New York Times recently wrote about the Nobel Laureates who are posting pre-prints, and The Economist picked up a story about Zika virus experiment results that were released in real time in an effort to help stop the Zika epidemic.

Open Science has the potential to lead to more scientific impact than any journal or conference publication.  The obstacles are now determining what pre-prints mean to an academic’s career – in publishing the manuscripts, determining priority of discovery (meaning “I found this first”), and obtaining grants.  I rely on freely-available data and findings in my own research, yet I’ve never published a pre-print.  After writing this post, I think  I may start doing so.

preprint-opinions-graphicAdditional Sources:

Mick Watson’s 2/22/2016 post about generational change on his blog Opiniomics.

Michael Eisen’s  2/18/2016 post about pre-print posting on his blog it is NOT junk.

Handful of Biologists Went Rogue and Published Directly to Internet, New York Times, 3/15/2016.

Taking the online medicine, The Economist, 3/19/2016.

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.

Spotted in the Lab

Portland is known for being a rainy city, and this winter was no exception.  Last week had the first truly sunny and warm day, hinting at spring’s arrival.

Today I hung out in my computer lab as dozens of high school students toured the Physics, Chemistry, and Biology Departments during the Junior Visit Day. As I readied the lab for the rounds of visitors, I noticed a new drawing on the whiteboard.

the-sun

I could not agree more.

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.

 

 

journal.pone.0148405.g001

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

My Dream Job, Part 4

As of August, I am an Assistant Professor of Biology at Reed College.  In this series of blog posts, I will explain why I chose this environment as my academic landing pad (or launching pad).

Part 4:  Being in a Biology Department changes my perspective.

With one semester under my belt, I took some time this break to reflect on my position at Reed.*  As I begin teaching another round of Introduction to Computational Biology, I will try to articulate why I find my position so exciting.

The students who are taking my classes have had a mixture of backgrounds, but most of them major in the natural sciences.  Up to this point, I have been surrounded by people with strong backgrounds in math and computer science.  As a result, students ask questions that have a completely different underlying motivation than the questions I’ve received in talks and research meetings.  I walk a fine line between oversimplifying the biology in order to describe a problem in computational terms and oversimplifying an algorithm in order to describe how it is applied to a biological concept.  In some ways, this makes teaching class hard.  Talk about inviting the imposter syndrome to step in when you have to answer “I don’t know” in class more than once.  Yet it also makes class engaging, unexpected, and fun.  Add to that an occasional power pose, and teaching is very satisfying.

so-try-that-power-pose

Screenshot from Amy Cuddy’s TED Talk (provided from a blog post by Amy Neuzil)

I am currently one of two tenure-track computer scientists at Reed.  We are at the cusp of establishing a computer science program: students are excited, funds have been acquired, and an active search is underway. I feel like much of the incredibly hard work has been done, and I get to show up for the fun part.**  This momentum has trickled over to the Biology Department through the students I advise and teach.

The other computer scientists at Reed are affiliated with the Math Department.  One might think that being in a different department from the faculty who are “most like me” may make my research life isolating.  Instead, I may just have the best of both worlds.  I get to sit in the same department as my biological collaborators, while networking with faculty in the Math Department to establish computational research collaborations.  Put simply, I love being interdisciplinary.  I deeply appreciate the flexibility that Reed offers in designing my courses to be hybrids of two fields.

My professional identity is quickly becoming steeped in teaching interdisciplinary courses and conducting research across departments.  Over the next few years, my research will undoubtedly become more applications-focused as I co-advise more student projects with Biology faculty. Yet there is enough interest at Reed, from both faculty and students, for me to continue algorithmic research.

*It’s been a while since I posted. Consider it a Spring semester resolution to start posting more.

**This might be naive, but hey, I’m an optimist.

My dream job, part 3

As of August, I am an Assistant Professor of Biology at Reed College.  In this series of blog posts, I will explain why I chose this environment as my academic landing pad (or launching pad).

Part 3: Reed is designed for conducting research in a liberal arts environment.

A friend and Reed alumnus once described her experience at Reed as “mini grad school.”  One of the main reasons for this is the long-standing tradition of the senior thesis.  The thesis, which must be approved by a committee of readers, is part of the requirements for graduation.  It is also engrained in the student culture — the end of thesis writing is celebrated by ritualistically burning of a copy of the document. All theses are placed in the Library’s “thesis tower” for perusal by the public, becoming a permanent item in the Reed community.

Thesis Parade [photo posted by Reed College on Facebook]

reedhisttxt-library-thesis-tower-1992

Library thesis tower, 1992. Image from the Reed College Hauser Library Special Collections and Archives, Reed College Library.

As Reed faculty, we advise students on this year-long thesis writing endeavor.  Part of our responsibility, as educators, is to think about new problems in our field that become thesis topics.  In some departments, providing students with research experiences and opportunities goes hand-in-hand with academic scholarship.  For example, in the Biology Department, student theses may fit into the professor’s larger vision of their research.  I think this is echoed in the success of faculty all over campus at securing external funding – over $2.2 million in 2014/2015, a ten year historical record.

Conducting high-quality research is not an anomaly at liberal arts schools.  Granted, it may take more time than at larger institutions, since training and teaching undergraduates is a much larger piece of the work.  But the quality does not have to diminish.  Recently, Biology professor Todd Schlenke published a paper in Science with Shelly Skolfield (class of 2014) and others.  The work was a continuation of the senior thesis Shelly did with Todd in 2014.

I intend to continue my research projects with the help of Reed students – in fact, it is one of the reasons why I took the job.  Advising senior theses will be a great way to kick off my research program.