07 November 2014

How did I get here? Learning to love research.

I grew up in southern Indiana, in an area stuck mid-way between small town and big city (Evansville). I thought biology and music were both pretty cool in high school. I applied to colleges in a haphazard way, auditioning on flute for some schools, and checking out biology programs at others. I eventually ended up at Western Kentucky University, mostly because of the generous academic scholarship they offered me and the WKU Forensics (Speech and Debate) team. I had competed in high school, and had lots of friends who were also on the team, so it seemed like fun thing to do. After spending so much time my first semester practicing, traveling, and competing for speech, I declared my major in my second semester as something like "corporate and organizational communications," although I really lacked an understanding of what a job in such a field would entail. I stuck with a minor in biology, since I'd already taken a semester of introductory classes. My reasoning for this adjustment was that, although biology was interesting, I didn't want to be a doctor. Moreover, I literally couldn't imagine spending years of my life working on the same biological research question. 

That spring, I went to a departmental seminar for biology because I thought it sounded interesting. My professor for introductory biology, Larry Alice, saw me there and suggested I start working for him doing research. Not one to balk at offered opportunities, I relented and started learning how to sequence DNA to determine the evolutionary relationships among species of grass. It only took a semester of actually performing research to realize how gratifying it can be. I switched my major to biology within a few months, this time keeping communications (and also history) as minors.

05 November 2014

Casting a wide net.

I was fortunate as a post-doc at NESCent to have a huge community of like-minded scholars to help me develop intellectually. I'm still very fortunate to be surrounded by folks doing awesome research, but I was hired specifically to fill a missing niche (bioinformatics) in the department. That means I need to work extra hard to find ways to connect with my new students and colleagues. While my skills are definitely desired and I have lots to contribute, many things I'm doing simply haven't been done here before, so I'm thinking creatively about how to fit in on campus. I'm doing my best to think broadly (cast a wide net), while at the same time focusing my time and energy on tasks that will have an impact (and hopefully catch a few big fish).

The benefit of working as a bioinformaticist is that I can work with anyone who has data (hint: that means pretty much everyone). My specialty as a genomicist also makes me well suited for the emerging interests of other folks on campus. I've been sitting down to talk to lots of folks about opportunities for collaboration on such projects. It's incredibly interesting to learn about different model systems, and gratifying to know that I can contribute to such a breadth of projects. At the very least, I can save folks time by providing a bit of information in current genome assembly methods, for instance.

It's easy enough to work with folks in other science departments, but I've been casting an even wider net. I was delighted when a friend from the history department came over for a chat about filtering data. He had a large digital dataset of documents and was looking through them for a particular type of data. Luckily, that type of data was always described with a particular string of text. Three lines of bash scripting later, and we managed to save him days of work. I've long been interested in these broad approaches to academia, and even attended a THATCamp meeting at NCState several months back. My brain works best when building connections between seemingly disparate ideas, so a little bit of my time in pursuing small projects like that helps keep me happy.

The unexpected returns are also nice: getting to know folks over in nursing, for example, let me know about better ways to teach in ways for which they are distinguished: applied methods (for which bioinformatics certainly applies) as well as online classes. At the risk of extending the metaphor too far, casting a wide net is making the fishing expedition of research and academia more appealing to me.

27 October 2014

Value judgements and scientific results.

As scientists, we like to think that we are objective in the interpretation of data. As humans, our personal value-based judgments creep into these assessments far more than we might realize. I often think of these biases in my career, both as a researcher (when writing papers or reviewing manuscripts) but also as an educator.

I mentioned at the beginning of the semester that I'm obligated to watch student presentations for a class on science communication. As the semester progresses, I'm getting a better handle on how students (at least in our department) are starting to think about scientific arguments. A few students have made what are, at least to me, surprising statements about the strengths and weaknesses of the primary literature they discuss: they relate that failure of results to support a hypothesis is a weakness of the paper (also vice versa, that "supporting the hypothesis" is a strength).

One of the first lessons I learned while doing scientific research is that (more often than not) unexpected results and questions can emerge from our experiments. You can learn something from any experiment, even if it's simply a better way to perform the experiment in the future. Unfortunately, research on science research (I know, so meta) indicates that results which fail to support the hypothesis are often discarded by researchers as "useless" or "no good" (you can read more about this phenomenon in association with the formation of the Journal of Negative Results in Biomedicine here). Albeit unfortunate, this behavior makes sense in the face of the competitive realm of science research, where a nice, concise story can make the difference between publishing or wallowing in academic purgatory.

It gives me pause, however, when students indicate such a value preference for results that support a hypothesis. In my mind, results aren't "good" or "bad," they simply...are. Is devaluation of negative results innate in our educational mindset? On the other hand, students vocalizing negative results as a weakness of the paper may be more semantic than scientific; for example, students aren't nuancing their argument to discuss particular experimental drawbacks, which is a completely justifiable concern. Alternatively, they might just be saying what they think we (the instructors) want to hear, and hoping we'll give them points for covering all the required topics listed on the rubric.

Regardless of the direct causes of such reasoning, I'm going to be keeping an eye (ear?) on such comments as I continue developing classes. When operating in isolation, these judgements about the value of results can be a starting point to some interesting discussions about epistemology and hypothesis testing. More often, though, these mindsets work in concert with other scientific misconceptions, which can result in huge problems for me as an educator. Fortunately, there are sections in my bioinformatics class that I'm explicitly developing so we can have discussions about whether the results we're obtaining are accurate and meaningful. I'm looking forward to embedding these higher-level reasoning skills into the regular content of the class.

24 October 2014

The art of asking in science.

I posted some love for Neil Gaiman's spoken words a few weeks back, so it only seems fitting that I follow up with inspiration from his partner, Amanda Palmer. She did a TED talk (the video is slightly NSFW at 10:49) last year that explored the relationship between artist and fan, emphasizing that we need to think less about how to make people pay for music and more about how to let them. She relates that asking people to help us is hard because it makes us feel vulnerable and shameful, but that asking for help can also create a profound connection with other people that allows a mutually beneficial transaction to occur. But watch the TED talk...she says it much better than I ever could.

I am not a professional artist or musician, but life in the ivory tower of academia does not shield me from the need to reach out to other people. I'm lucky that I don't have to ask people for financial help to pay my bills, but there are plenty of other circumstances in which my professional success rests on my ability to appeal to other people for assistance.

Learning to ask other people for help was a major stepping stone for me during graduate school, as I realized the need for assistance in troubleshooting lab techniques, designing experiments, and proofreading papers. As an assistant professor, asking for help is becoming even more of an art. I wouldn't be able to navigate the logistical issues of university bureaucracy without running to the office next door every few days. I belong to a small department, so connecting with other academic units on campus and at other schools is important to have access to resources for teaching and research. An important part of my job right now is applying for grants, which is really just another way of saying "asking for money to fund my research." Some scientists are taking an even more Amanda-style approach to paying for research by launching crowdfunding campaigns for particular projects. Moreover, my job as a bioinformaticist means I rely on other people for data, so asking for research opportunities is essential. I knew my job would require me to engage in asking, and even persuading, my peers to help me. I'm only starting to realize, however, what it means to ask students for help.

Am I really asking students to help me? That seems counter-intuitive to the stereotypical role of a professor, but indeed, we rely on students to take our classes and do research with us. As a newbie, I can't rely on my reputation to attract students to my class or lab. I have to ask students to consider it (hence my post from a few days ago: Student motivation, AKA please take my class). Sometimes that requires educating students about what I have to offer, like the ability to obtain marketable skills. Moreover, it makes me consider another question Amanda ponders: "Is this fair?" For my job, that means asking whether this student has the capacity to succeed, and whether it will be beneficial for them to spend the time, energy, and money to do so.

Framing my professional, scientific interactions as "asking for help" appeals to me on a fundamental level. It gives me the responsibility of finding the things I need. Moreover, it allows choice and freedom on the part of the audience, whether it's a student wanting to work with me or a funding agency deciding to award a grant. We pursue science because we think the work is interesting, but we're fooling ourselves if we think everyone will innately feel the same. Making an art of asking is a way of starting a conversation, and opens the door to persuade without being overbearing.

There is also a benefit in the act of asking a question. I wouldn't've ended up in graduate school if one of my professors hadn't asked me to consider it, and you certainly have to ask (i.e., apply) to receive a grant. I'm practicing asking questions as way to start a conversation about obtaining the things I need.

Can you fund my research?
Would you like to work on a project together?
Have you thought about going to graduate school?
Are you interested in taking my class?

22 October 2014

When a computational biologist yearns for the field/lab/greenhouse.

A darling little rose bush.
I'm a sucker for cute little plants on sale at the grocery store. I saw these delightful miniature rose bushes when I first started shopping, and waffled for the next 15 minutes as I circulated the store about whether to take one home with me. I ultimately relented, because I decided that it was a small price to pay to feel more connected to my new home city (Tyler has a thing for roses, including a pretty nice rose garden!).

My compulsion to surround myself with plants started during my undergraduate education after taking plant taxonomy and beginning to work in a molecular systematics of plants lab. I enjoyed working in the field, but realized during graduate school I was more suited to computational work. After three years as a NESCent postdoc, during which my work was exclusively computer-based, I found myself yearning to physically get my hands on some live organisms (hence the compulsive purchases of houseplants).

Happy Commelinaceae in the greenhouse.
The problem is that I've been hired as the resident bioinformatics/genomics person, which brings with it certain expectations about how I spend my time (mostly, analyzing data that other people collect). As a scientist, though, I think it's important to still maintain a connection to my study organisms. My plants a source of inspiration and wonder, as well as a resource for future research questions, and I'm loathe to permanently pigeonhole myself as a "computer person." How do I balance these opposing expectations?

My research mindset right now is one of nearly infinite possibility. I want (and need) to be productive as a scientist, but it's up to my discretion exactly how to make that happen. I work at a small, regional university, which means I may need to be creative (financially and with other resources) about how to set up research projects for my students in the future. I have some of my Commelinaceae living collection growing quite happily in the greenhouse here in town, and access to growth chambers on campus if I want to do hybridization or selection experiments.  Even though I don't have immediate research plans for my plant and DNA collections, I'll keep them as long as I can to keep my options open.

From a teaching perspective, I'm really excited about designing courses which capitalize on either computers or live organisms. I've already written about the bioinformatics course I'll be teaching next semester, and I'm considering offering a class on plants of Texas (taxonomy and systematics). I helped teach plant systematics as a graduate student, and find myself really excited at the prospect of getting back into the business of instructing students about the local flora.

Ultimately, I know trying to balance these opposing forces are making my life at least a little harder. It's more work to figure out effective pedagogy for classes based in the field and on computers. Oddly enough, my educational and work experience has set me up for precisely these tasks (see references to my experiences above), and there are quite a few other academics who successfully split responsibilities between different projects. What's the main reason that I remain committed to being a jack-of-(plant and computer)-trades? It makes me happy, of course.

21 October 2014

Student motivation, AKA Please take my class.

My current homework for Software Carpentry instructor training is to think about a time when I lost my motivation to learn. I posted my response to the SWC blog, where you can also poke around a see other folks' stories (click on the "Motivation" tag).

The other part of our homework is to work on a three-minute pitch to motivate students to learn a particular topic. The timing of this assignment is fortuitous, as I'm also promoting the bioinformatics class I'm teaching next spring as well as an undergraduate minor in bioinformatics and genomics. I took to twitter with my attempts at persuasion:

Disclaimer: I am not planning on physically harming students if they have a different shell preference than bash, and I don't particularly dislike perl. I'm really just rather fond of word games.

A few other folks chipped in with their own token words of wisdom:




It's not surprising that my motivation for getting students to take bioinformatics differs from their reasons for enrolling. I am personally passionate about teaching next semester because I think I can help students be better scientists and thinkers. I'm hoping to convince them that it will help them be more marketable (taking additional biology and computer science classes will certainly accomplish that). 

At times, these persuasive attempts seem like fighting a rather uphill battle. Convincing students to take extra classes that bridge boundaries between different types of knowledge is difficult, especially when students who might be interested are already quite overwhelmed by courses required for their major. I come across lots of folks who are intimidated by large datasets or using a command line interface. 

I spend a lot of time talking to folks about my experiences, and how I'm planning on teaching. 
Here are my talking points in encouraging folks to step up to the plate and learn some bioinformatics, from the perspective of a biology student who has little computation experience: 
  1. You can do this. Not too long ago, I was in your shoes. I didn't know a lot about computers, how they worked, or how I could use them to answer questions. I don't have a ton of formal training in computer science, and my degrees are all in biology. Writing computer scripts may seem really different from other things you've studied, but...
  2. Learning a little can be very powerful. Learning to work on the command line and write computer scripts will take work. You will be surprised, however, at how many tedious, mundane tasks you can accomplish much more quickly and efficiently with a little bit of shell scripting. Better yet...
  3. These skills are transferrable. You may not end up working in a job where you need to assemble genomes or build phylogenetic trees. It is possible, though, that you'll need to manage large numbers of files or answer questions about large data sets. You can apply these skills to lots of other practical tasks, but in addition...
  4. The topics are interesting. Technological advances are producing genomic and other large-scale biological datasets at an unprecedented rate. The applications of these data include empirical research, agriculture, and medicine. 
At the very least, I hope to convince students the first point is true. Nothing is more frustrating than hearing students declare, "I can't do that." A student saying "That's too hard" is a student who's hit a motivational brick wall, and can't even ask themselves whether it might be beneficial for them (or, heaven forbid, that they might enjoy it!). If they can do that, hopefully one of the last three points will be appealing.

On the other hand, I'm still trying to figure out effective ways to appeal to computer science students. The fourth point above definitely still applies, and they can arguably improve (or at least broaden) their job prospects by gaining some understanding of biology. More importantly, they can learn to answer hypothesis-driven questions, which seems to be less of a focus in their curriculum than in biology. 

As always, this is a work in progress. What am I missing? I'm planning a few mini-workshops on for students (graduate and undergraduate) on campus, which will certainly allow me more opportunity to pinpoint more effective pitches. These students are not motivated by the same factors that convinced me to pursue higher education, and bioinformatics for research. I need to find out what they need. However, I struggle with how much I should cater to student interests. That, however, is part of a broader discussion about the purview of higher education, and is perhaps left to another post.

15 October 2014

My office is a pit fall trap.

A real conversation starter.
If you couldn't tell from the entire post I wrote dedicated to my new office, I'm very committed to the space where I do the majority of my professional work. The items I choose to display in my office are used by students and colleagues, both consciously and subconsciously, to assess me as a person and scientist. Given that I'm trying to recruit students for research but also depend on other people for data, I'm invested in making sure visitors see my office as comfortable and welcoming (despite the dulcet tones of the toilet flushing next door, which are very audible at times).

To foster a sense of openness, I prefer to leave my office door open. I knew from the start that it would invite random visitors to drop in. What I didn't realize is how many such requests I would receive. I started keeping track of them: 


Most of the requests are innocuous (students looking for a particular classroom or office). I get pretty annoyed when students stop and ask for things like staplers, or for someplace ambiguous ("Advising?" For what department, pray tell?) as it's obviously a lack of foresight on their part. I was amused when a guy offered me a turtle that he found in the mechanical room (because OF COURSE a biologist would want a turtle, even if I don't actually have a lab yet or do wet lab work? I told him to take it outside to lake where DOZENS of other turtles live). 

While in the process of writing this post, a student stopped by and we had the following conversation:
Her: I know I don't have you for any classes, but you're a biologist, so can I ask you a question about inductive and deductive reasoning?
Me: Why me? It's just because I'm here? You have an exam today, don't you?
Her: Well, yeah... 
I've asked my colleagues, and I know they get far fewer questions like this. I sometimes wonder if students would interrupt my work so frequently if I were male, or 30 years older. But then I thought about how my office looks if you're walking down the hall:


That door is admittedly awkward, sticking out into the hallway. Then I realized how much my office looks like a pit fall trap, a commonly used method for capturing animals in the field:


As animals are wandering around, they hit the fence and walk along it until falling in the trap....just like what happens when someone is walking down the hallway, lost and confused. The location of my office is also partly to blame; I'm the first room inside the door to a confusing connection between buildings.

There aren't any easy solutions to alleviate my periodic irritation at having to answer random questions from strangers. I can open my door all the way to prevent the "drift fence" effect. I'm talking with campus facilities about putting up some signs to help direct folks to the appropriate building/department. I can remind students each time they interrupt me that they have the capacity to think ahead (i.e., look at the syllabus to find an instructor's office). 

Every once in awhile, though, I assist a student who is legitimately frustrated and I feel better for having alleviated their anxiety a little. Our university has a lots of first generation college students, and I empathize with folks who have little experience on which to base their interactions with folks working in higher education. As a result, there are a number of programs set up to help alleviate these issues and promote better students learning. It's easy for those of us from privileged backgrounds to view these efforts as hand-holding, but there is plenty of evidence on the efficacy of such programs in student retention and success.

If I challenge myself, I too admit the impact of a few individuals on my academic success, and how getting a simple question answered quickly makes a huge difference when juggling work, school, and family responsibilities. Besides...I wanted to work in academia because I like interacting with students! Ultimately, a handful of interruptions to my workday each week are a small price to pay for helping a student succeed.