Trees and characters and common ancestors, oh my!

My teaching experience has taken a big step forward this month. I gave my first of two guest lectures to a large undergrad intro bio class (they clapped when I was done; I don't know what's wrong with them!), and am piloting a new module in lab this week. Both of these teaching endeavors are focused on the same topic: phylogenetics. Given that describing evolutionary relationships is one of my specialties, I was both excited and apprehensive to put these teaching materials together.

I've done outreach activities using phylogenetics before, and I've taught classes on computational phylogenetics. I was a teaching assistant in grad school for a semester-long class on plant systematics, which heavily featured phylogenetics. Striking the right balance for a single lecture and lab for an undergrad intro bio class was tricky. I skipped most of the tedious definitions and history of cladistics, as well as in-depth discussions of the attributes of various tree reconstruction methods. I did spent time talking about the practical applications of trees, and possible implementations of these techniques they might find interesting.

Why take that approach? Well, I operated under the assumption that most students wouldn't ever really build trees again, but they might perhaps need to interpret them. I also couched my discussion in the strength of comparative biology: what if we want to breed a better crop? What if we need to know how data about a gene in mouse transfers to a gene family in humans? What can a phylogeny tell us about how traits evolve? In that context, it's way more effective to spend time talking about interpreting phylogenies and deciding how much confidence you should have in them.

At the end of the day, phylogenetics is one of those areas which some students will just understand intuitively without much extra explanation necessary. Other students will struggle, ask questions, and it will take a long time to identify and then break through their misconceptions. The former students will get bored, think my lab is dumb and conclude it to be a waste of time. The latter students will get frustrated, think the lab is dumb and conclude it to be a waste of time.

OK, maybe I hope a few students will like it...and hopefully a few of the other teaching assistants learned something, too.

Writing a paper is like making a sandwich.

I'm putting the finishing touches on some figures for a manuscript right now, and I was discussing with my boyfriend how it was coming together. As I related my attempt to balance depth of discussion with length, he paused for a moment and then noted, "It's like making a sandwich."

Yowza, he really hit the nail on the head with that observation! You need the right ingredients, or bits of data and background, combined in an appropriate ratio, and constructed in such a way that it maintains structural integrity and coherence.

Pardon me, it's time to assemble my culinary masterpiece.

Don't make eye contact! Or perhaps maybe you should...

I've written briefly about the flipped classroom format being implemented in the intro bio class I'm helping to teach this semester. I get really jazzed about the increased amount of interaction I have with students. Even though there are twice as many students this semester as last, I still feel like I have more in-depth, meaningful conversations with more students, without an appreciable increase in face time. I've had time to think about how to facilitate interactions with students, and here's what I've found:

1. This is a tip I picked up years ago in education classes at my alma mater, MU. Ever been in front of a class, ask a question, and hear crickets instead of answers? That just means you need to wait longer for an answer. Students will respond eventually if you wait, and chances are, the next time you wait, it won't be as long.
2. Ask students how they are doing. It's shocking how many have questions they won't ask until prompted.
3. Make eye contact with students who are looking around while thinking. It's a less invasive than the previous tip, and easier to do in a large classroom.

I feel almost silly by posting these, given how simple they are. It makes a huge difference in personalizing yourself to students, though, and making them feel more comfortable coming to you for help. 

On science writing and boredom.

I'm trying to finish up revisions for a manuscript and I'm kind of bored.

The research I'm writing up is a pet project from my dissertation. It's a molecular phylogeny of a group of plants which I particularly fancy, and I enjoyed the background on pollinators and inflorescence structure I learned while finishing up the project. For all intents and purposes, I should be eager to finish it.

The problem, it seems, is that I'm stuck in a writing rut. I write frequently, for various personal and professional purposes, and feel very comfortable expressing myself in a written format. I completed minors in history and communication studies, and in the process, finely honed my tone and ability to express arguments. My writing errs on the side of informality, sometimes even to the chagrin of my colleagues, but I enjoy and embrace it.

Writing academic scientific articles, however, leaves me feeling lackluster at best. I started the introductory writing for this paper over five years ago, during the early years of my dissertation, and I find myself wholly sick of it now. I struggle to find balance between clarity necessary for academic publication and the verbosity to which I've grown accustomed for other types of writing. I want to edit the paragraphs that are plaguing my revisions so that they actually sound like me. However, I'm also eager to be rid of the damn thing for awhile, so I may move on to fresher projects, and I fear putting off reviewers with my modified tone.

So I wallow in writerly despair, blogging and whining. Perhaps it's time to suck it up and be a big adult scientist...boredom be damned.

Welcome back to myself!

It's been longer than I intended since my last post, but research and teaching deadlines left me drained. Never fear, loyal readers...I've many things to report!

First, the retrospective pensiveness of the turnover into a new year made me realize how many steps I've taken to really act on my commitment to open science. Here's what has happened:

1. I started posting my presentations and posters on SlideShare. I'm still blown away that people actually view and even download these!
2. After following advice early in my graduate education to always review academic papers anonymously, I decided to start signing my reviews and offering to discuss my comments with authors.
3. I received my first signed review for a paper from a colleague, and was gratified with how much easier it was to interpret her comments knowing her background.
4. I attended a Software Carpentry bootcamp at University of North Carolina Chapel Hill at the end of November. I loved the pedagogical approach used for this class, and was glad to finally receive the catalyst needed to start adding my scripts to GitHub. 
5. My teaching responsibilities with Duke University this semester involve teaching an intro bio course. Mohammed Noor is integrating this class with a MOOC (massive open online course) offered through Coursera. My responsibilities involve assisting during the 450 student lecture sessions (these are flipped-classroom format, where students watch recorded lectures ahead of time and participate in class with active learning) as well as teaching my own lab session. I'll be doing some lecturing later in the semester, as well as piloting a new inquiry-based phylogenetics lab I'm developing.

As you can see, exciting things abound! This doesn't even start to cover the awesome things I have going on with particular research projects, which are shaping up to be a bit mind-blowing. Hooray for science!

Impostors in synthetic science

An interesting article about "impostor syndrome" popped up in my twitter timeline this afternoon. It took a few moments to realize the article wasn't talking about some sort of animal mimicry. Rather, it refers to a prevalent phenomenon in the sociology of academic scientists, where we hesitate to offer information or opinions for topics outside our highly specialized area of expertise.

This topic is of particular relevance to me, as my brain has always functioned at the level of "big picture." I recall an assignment from high school English for which my classmates were selecting research topics related to a specific book, while my topic encompassed "feminist literature from the twentieth century." Yup...broad patterns.

In my current position, I think often about the push for specialization in methods, techniques, theory, and research programs. NESCent focuses on synthetic science, which involves fusing sometimes seemingly disparate research areas to achieve novel conclusions or tackle innovative questions. Synthetic science, therefore, is full of "imposters," since we constantly broach new theoretical areas and incorporate methods/results in non-traditional ways.

I'm totally okay with this label. It was nice to read this article and think about other types of scientists that regularly face this issue of being "PhD generalists," not just once during a career (i.e., changing from animal to plant research), but on a daily basis. The thoughts from other self-described impostors at the bottom are also enlightening, highlighting not only the characteristics of such researchers but their value as scientists as well.

Learning about learning: Part 1

A friend talked me into taking an introductory philosophy class with her our second semester of college. I don't know why I thought this would be a good idea, as I was already taking 18 hours and it was a section which met at 8 am. I was a precocious little academic hellion, though, so I persevered despite my friend dropping the class a few weeks later.

I remember taking copious notes during class, studying diligently, and very much enjoying the subject matter. I was a little disappointed when my grade on the first exam was a B. Dissatisfied with my ability to improve my grade based on the comments written in the blue book I'd filled with essays, I met with the professor to chat.

As you might expect of an academic in his field, Prof Philosophy was ferocious in his arguments and maintained high standards of cerebral function. I began by asking him about the few comments he made on my exam, trying to sort out why those minor points warranted what I saw as a dissatisfying grade. He answered the first few questions but then became impatient.

"Look," he said. "There are some exams that are obviously A papers. Yours was not one of them."

I was a little surprised, and I'm sure I felt the sting of tears behind my eyelashes. I blinked them away, processed that thought for a moment, thanked him for his time and then left. I thought about his assertion frequently throughout the course of the semester, improved the depth of my thinking while listening to his lectures, and ended up with an A in the class. I thought about his comments even more often during graduate school.

A student from the lab section I'm instructing approached me awhile back to ask about a question from the exam. It was a multiple choice question that required inference of a phenomenon based on information provided. I explained to her the reasoning behind the correct answer, and she honed in on one minor bit of information that seemed ambiguously worded in the question. "You mean I would've gotten the question right if I had made that assumption?" she asked.

I explained to her that it was not that simple. If you are answering higher level questions and only have a cursory understanding of each concept included, you are compounding uncertainty by the time you reach an answer. Getting "close enough" to an answer doesn't mean much when you are trying to combine and synthesize information, because each little bit of inaccuracy takes you farther from the correct answer.

This is the challenge of learning and teaching in science, particularly biological systems. It is a balance of accuracy and precision of content recall bolstered by reasoning and critical thinking. Students' bean counting points to get a better grade in the class reinforces that parameterization of a problem down to individual units will yield better results. In fact, understanding how all parts-- of a semester, or of a biological process-- fit together leads to improved learning.