New Reed CompBio Blog

As part of a recently-funded collaborative REU (generously supported by the CRA-W), my colleague Derek Applewhite and I are working with undergraduates to study machine learning methods to predict genes that regulate cell movement patterns in schizophrenia.  The team will post their work on new a Reed College blog, The Pathway Not Taken, and I may re-post selected pieces here.  The first post gives a general idea of the problem we will work on, and how biology and computer science are intertwined in the project.

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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?

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.

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.