Fixing science, one researcher at a time

A recent column in Nature caught my attention today.  The piece, No researcher is too junior to fix science by John Tregoning, talks about the problematic competitiveness of science.  Tregoning ends the column with an appeal to combat this current scientific culture.

Let’s strive instead to stand together. One science historian called last month’s science march unprecedented in its scale and breadth. That energy and optimism need not dissipate — it should be funnelled into making the system function better. The pay-off might not be immediate, but let’s play the long game so that all can win.

I couldn’t have put it better.

Field Trip! Computational Biology on the Road

A few weeks ago I took my students to the Association Computing Machinery Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB) in Seattle, WA.  It was a fantastic experience for everyone involved – the organizers did an excellent job running the conference.  I asked my students to reflect on the conference, and I figured I should do the same.

With such a large cohort of undergraduates at a scientific conference, my role shifted to encompass one of an educator as well as a researcher.  I honed in on the accessibility of the material in talks, feeling a bit of pride when the speakers showed an image or mentioned a topic I have taught in class.  I also had some moments of “wow, should have taught them that” when a speaker presented a fundamental concept we have not yet covered.  Many of my students came out of sessions excited about what they had just learned – they talked with the speakers, asked for their papers, and are now delving into this new material.  Graduate student attendees became mentors, fielding questions about why they went to graduate school and how they picked their research topic.

ACM-BCB was an ideal size – the conference had compelling talks and tutorials while being small enough to chat with the keynote speakers and conference organizers.  I caught up with existing colleagues and met some potential collaborators in the Pacific Northwest.  I also found myself in discussions with  graduate students about my position in a liberal arts environment.  Reed had a research presence, since three Reed students submitted posters to the poster session.  My students had garnered enough research experience — either through their thesis, summer research, or independent projects in class — to have engaging conversations with other attendees.

Finally, the trip to ACM-BCB as a class taught everyone (including me) the importance of logistics.  Some gems:

  1. Make sure the taxi to the train station can fit the entire group.
  2. Remember who you gave the posters to in your mad dash to find parking before your train departs (see #1).
  3. Make sure your PCard credit limit is set so it’s not declined at the hotel.
  4. Tell your students the correct time of the first keynote.

And the question of the day: is a (very detailed) receipt for a can of soda written on a napkin by a bartender reimbursable?

Ready, Set, Year Two

I have returned from summer break to begin teaching a new course this fall.  My break  included a hiatus in blog posts; now that classes have started up, I’m back to writing them.  Other lessons from my first true “summer break:”

  1. Yep, I still love research. Summer was a refreshing change of pace, where I was able to chip away at existing research projects and establish new collaborations here in Portland.
  2. Pacific Northwest summer weather is great.  No humidity + few bugs. I didn’t think that was possible.
  3. Feelings of preparedness are relative.  Despite having a year under my belt, there are enough new tasks and responsibilities that I still feel like a newbie.

Happy back-to-school for those who live by the academic calendar, and welcome to the Reed Class of 2020.

class-of-20

The Class of 2020 at Reed College’s Convocation.  Photo by Leah Nash.

 

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.

Tenure

A couple articles came across my news feed in the past week a few months ago related to tenure.  While they are not directly related to each other, I thought I’d mention them in the same post.

First, how many faculty in the United States are actually tenured?  I was surprised to find that, according to the American Association of University Professors (AAUP), over 50% of faculty hold adjunct (non tenure-track) positions.  AAUP calls these positions “contingent faculty” because, regardless of their full-time or part-time status, their school makes little to no long-term commitment in terms of job security.  The increasing reliance of institutions on adjunct faculty has an impact not only on the faculty but also on the students and the research at the institution.  An article from The Atlantic summarizes many of these points:

The Cost of an Adjunct | The Atlantic

Now, tenure itself may be a controversial topic – some say that the system encourages faculty to slack off after getting tenure, or to keep teaching outdated material long after they should have retired.  The tenure process is incredibly stressful, sometimes unclear, and notoriously unfair – and this is just scratching the surface.  But once tenure is obtained, faculty may end up doing more out-of-the-box, high-risk research and teaching that they wouldn’t have attempted otherwise.

Trying to Kill Tenure | Inside Higher Ed

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.