Geeking out about acorns on the local news.

My university has a pretty decent relationship with the local news. Reporters fairly frequently contact the public relations office, seeking out an authority (i.e., professor) on the topic of the story they're preparing. A few folks in my department appear in news stories on a semi-regular basis, mostly offering facts and opinions on issues tangentially related to their areas of expertise.

I wasn't entirely surprised, therefore, when I got a phone call from the public relations office a few days ago, asking if I'd be willing to talk to a reporter. I was initially apprehensive, as I'm still trying to get my bearings in my new home state and wasn't sure I wanted to be put on the spot if asked about something controversial. I had no need for fear, though: I'd been recommended as someone who could talk about why it was there seemed to be such a large acorn crop this year.

"Heck yeah!" I thought, and calmly agreed to meet with the reporter that afternoon. I spent a few minutes doing a quick literature search. As I suspected, there's a decent amount of literature on that very topic. I made a list of talking points, including a few general notes about plant biology/ecology:

1. Acorns are the fruit of the oak tree, created by the fertilization of a female flower by pollen from a male flower.
2. Multiple factors can affect the development of an acorn, including how many flowers of each type are produced, effectiveness of pollination, and whether the tree has resources to dedicate to developing lots of fruits.
3. The factors above are, in turn, dependent on temperature, amount of sunlight, and levels of precipitation.
4. Acorn production (masting) also varies temporally (through years), spatially (across geography), and by species (some oak species produce more/larger acorns).
5. This summer has been particularly cool and wet compared to the past (I checked average temperature and precipitation for the month of July for 2011-2014), so perhaps those conditions favor more acorn production.
6. Trees are large and can't move, so resource allocations from previous years can affect acorn production in subsequent years.

The interview took about 15 minutes. We went outside and stood near some conveniently located oaks near my building. Of course, the talking points I had planned were shuffled around and reframed depending on the questions he asked, but I think I covered everything listed above and more (acorns are food for wildlife, they do eventually grow into trees, etc). Then the reporter grabbed a totally awkward shot of me walking down a path looking at leaves.

It's totally cringe worthy, but I know at least my dad will want the link, so you can see how my talking points above translated into the final story here: KLTV News, Why so many acorns this fall?

Lessons learned: keep makeup and a blazer in my office, to prepare for next time. Be a more careful about preparing appropriate sound-bites. I was also surprised to learn how much trouble the reporter had getting someone to talk to him about this; a number of arborists in town completely blew him off. I thought it was super cool! That's probably a good thing, because the public relations representative said at the end of the interview, "Great! I can add you to the list to talk about plant stuff!"

Great, indeed. Let's call this "service to the university." 

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.

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.

A trip back to my ol' Kentucky (and Indiana) home.

Historic buildings on Franklin Street are framed by neon
lights for one week a year.

As promised in my semester preview, and as a follow up to my Missouri trip a few weeks back, I had the opportunity to head back home to southern Indiana and central Kentucky last week. The timing of my trip was fortuitous, as my hometown of Evansville, Indiana was celebrating a momentous yearly event: the West Side Nut Club Fall Festival. More than a street fair, the Fall Festival marked the official start of autumn during my childhood. It's been probably ten years since I last partook of the food and frivolities. However, I was born and bred on the west side of town (my high school is less than a mile from the festival's location), so I fell back into old celebratory patterns without much trouble.

My happy face at
Fall Festival food.

As a kid, I was pretty invested in the games and rides at the festival. As an adult, I didn't even step foot into those areas, instead preferring to walk along the 4+ blocks of food vendors (each booth is a fundraiser for a group in the community, including several of my old school groups). My mom was kind enough to accompany me on my meanderings, which makes for great food-grazing because we could share twice the number of different menu options. I could wax philosophical about the virtues of various chili and cheese covered, deep fried concoctions, or you could take a look at the index of foods from this year's Munchie Map. Some items, like brain sandwiches and burgoo, are regional specialties. Some booth attract patrons with weirder options, like pickle juice slushies. I stuck with more traditional choices, like turkey burgers, stromboli, and cobbler with ice cream.

Of course, watching people is my favorite pastime at these events. The best overheard comment this year was from a family that stood in a semi-circle sharing corn dogs. One woman remarked (ever so sagely and without accusation), "Well, if one of us has ebola, I guess all of us do now." Indeed.

A rather large gingko tree.

The purpose of my trip was to give a seminar for the Department of Biology at my alma mater, Western Kentucky University. Part of the reason I'm enjoying my new job at UTTyler is because, as a regional school, it feels familiar to WKU. Campus has grown since I left, and the science folks have some great new teaching facilities. Despite these renovations, I was pleased to see this fantastic old ginkgo tree still standing between buildings.

It was a pleasure to meet with both mentors from my undergraduate years as well as with other assistant professors. After my graduate education and postdoc work at R1 universities, it's refreshing to talk to folks who are making a real difference in under-served parts of the country, both by helping students conduct science research as well as teaching classes in evolution.

It was gratifying to see a lecture room near full to bursting with students for my seminar that afternoon. I'm sure it was due in part to extra credit being offered for classes, but I hope a few of them gleaned some sort of benefit from my discussion linking the evolution of organisms to that of genomes and transposons (the powerpoint is available on Slideshare if you'd care to take a gander). After all, I graduated with my bachelor's degree from WKU less than ten years ago; if I were to believe the words of several folks I've encountered lately, I'm a shining example of a "success story."

Historic letterpress prints from Hatch Show Print

Why do I feel the need to qualify my "success" with quotation marks? For now, suffice it to say that I'm way too excited about developing classes and proposing new research to feel like I've accomplished anything more than the promise of more work! As my undergrad advisor, Larry Alice, reminded me when I saw him last week, I also need to enjoy myself. Recalling my previous obsession with mosses, he remarked: "Don't forget to stop and smell the bryophytes." In the spirit of following his advice, I allowed myself to make my travel back to Texas a little less miserable by sipping a caramel latte and perusing the Hatch Show Print display of historic letterpress designs in the Nashville Airport. Mmm...whole hog sausage.

Failure, storytelling, and science.

It's been quiet around here at Princess Tradescantia lately, but I'm excited to report back with a few of my recent adventures!

In January I had an opportunity to participate in a storytelling event co-sponsored by some fantastic folks: The Monti, UNC's Morehead Planetarium, and Scientists with Stories (SwS). The event was called #ScienceFail, and each storyteller shared an experience regarding failure and our careers in science. If you're so inclined, watch this video to learn a bit more about the event and SwS's associated research.

The story I told was from my graduate career; I wrote a bit about it a few years back (I bleed for my thesis: Part I).  I met with Jeff Polish from The Monti several times to craft the details of the narrative, and found the process to be both amusing and intense. The quick version of the story is that I wrecked my truck while doing fieldwork. A longer version of the story can be heard below. The longest version of the story is one I'm still developing, as the repercussions of the events I describe still affect how I pursue my career and think about science. I could write numerous posts about how stories and science reciprocally inform each other, and I'm very grateful to have been afforded the opportunity to participate.

You can also head over to the SoundCloud page to hear the rest of the stories told that night.

On science writing: The reader's perspective

I have a good excuse for this most recent unplanned, unannounced blog break. During the month of September, I attended a writing workshop from George Gopen (Writing from the Reader's Perspective) and discovered that I still have much to learn about the process of writing. A brief overview of Gopen's premise can be found in a succinct article from American Scientist, but here are a few interesting points I noted:

1. Contemporary teaching for improving writing is often focused on the unimportant parts of communication and narration.
2. Preoccupation with good grammar and punctuation hides more effective ways to improve writing and enforces inequality.
3. First person can be useful in scientific writing but is often imprecise ("We" didn't all hold hands and perform PCR) and can sound ridiculous.
4. Passive voice is perfectly fine when used in the appropriate context.
5. Just because something "sounds" good doesn't mean readers will be able to appropriately interpret your meaning (I'm especially bad about this; I read things aloud to determine clarity).

As per Gopen's recommendations at the end of the course, I selected an old blog post and checked the writing sample for several of his identified "reader expectations" (explained in the article mentioned above). My biggest problem is misplacement of old and new information, which is a very common problem among science writers.

Knowing one or more errors may be lurking in my writing has danced on the periphery of my perception for weeks, stifling my urges to put pen to paper and making me acutely aware of my failings as a professional. While this assessment may seem a bit melodramatic, I am in the midst of sending off applications for jobs, and the requisite cover letters, research statements, and teaching philosophies I've been including now appear to be suboptimal. I've begun the tedious process of revising these documents. While perfect application of my newly learned skills is impossible, I'm hoping for marked improvement...or at least the ability to write without hearing Gopen's voice chastising me.

Spring Fling!

Today is the day everyone at NESCent talks for three minutes and we get to throw things at them if the go over time (see pic). So exciting!

Discussion role call!

I spent prolific amounts of time as a student participating in competitive speech and debate. One of the categories of high school speech in Indiana was Discussion. This aptly named group placed students in a room together where they were expected to talk about a pre-assigned issue. Such a set-up, however, begs the question: how do you rank participants, given it is a competitive event? Even more fundamentally: what makes someone better than another at talking about stuff?

Such was my first introduction to the importance of the variety of roles in a group discussion setting. Here's a description of different types of discussion roles from a non-profit group; I selected this particular link over myriad others because of the breakdown into "task" and "maintenance" roles. These same principles are applied in many contexts, including education. Often, teaching resources recommend students are assigned a single role for a class period or task. In the afore mentioned competitive sense, a successful participant was one who effectively filled multiple roles during the course of the conversation.

This digression to memories from high school is brought to you by reflections on the catalysis meeting in which I participated a few weeks back. As previously discussed, catalysis meetings present interesting dynamics. Scientists at different career stages are better suited to some types of discussion roles. Everyone can make contributions, albeit in different ways. In a broader sense, I find myself tallying my own (and others') fulfillment of these roles in other settings, such as during journal club (we meet once a week here at NESCent to talk about a recently published scientific article). My observations are based partly in a desire to study communication, but mostly in an effort to enrich my interactions with professional colleagues and expand my thinking.

It's gratifying the multitude of time I spent competing in speech and debate continue to reap benefits.

Inexpert advice aiding expert research.

I had some sudden flashes of brilliant SCIENCE while driving to a friend's house for dinner last night. Upon arrival, I spent a few moments jotting these thoughts down while he finished cooking. I started grumbling about a few things not making sense. He told me to talk him through it.

My friend is not a biologist, but he is knowledgable and clever, and interrupted me frequently as I talked to ask questions or make comments. Is that assumption valid? That train of logic makes sense. I didn't have all the answers I needed at the end of the process, but I certainly understood the problem better.

A few moments of an inexpert but willing brain was productive and interesting time spent. I was reminded of the time I spent in graduate school with a group of students who, although not researching the same topics, still frequently conversed about out research and pitched ideas for experiments. As scientists, we settle into our intellectual niche and sometimes find it difficult to break out of this very specific area of expertise. We can help each other by offering a bit of insight from a different perspective, and we can help ourselves by asking for this assistance.

We can't possible know the small, minute details of all areas of science. We can, however, use our training in critical thinking and logical reasoning to process even very disparate research topics. The process of scientific research is nuanced in different fields, but even these small variations can inform our own research. There is no shame in talking about problems that don't quite make sense. There should be no pretentiousness in our responses as well.

Choice in biological systems

While discussing my research with my committee as a graduate student, I made a reference to plants "seeking out more suitable habitat." A faculty member asked if said plants sprouted legs and walked to a different area before plunking down and setting roots. I was able to resolve this semantic issue because the plants in question are clonal, so they can literally send out a rhizome toward a new area. Her point was well taken, though, and issues related to verbiage in biology continue to intrigue me.

There are common issues in molecular biology wherein enzymes or other portions of biochemical pathways are anthropomorphized in language. These issues arise most often when interactions between molecules are communicated like we would talk about human behavior.

A related but slightly different issue arose in a NESCent seminar today. A discussion about sex allocation included some references to human sex ratios at birth. The ratio of males to females are thought to be altered by a variety of factors, including acute or chronic stress. Someone argued that in certain situations, females may "choose" to alter the sex of their offspring to better suit the demographics of the new environment (i.e., more males to replace those lost in battle).

We're all scientists here. We know that women don't consciously choose to have male or female babies, but someone took issue with the previously mentioned hypothesis because of the failure of that mechanism. In terms of evolutionary time, though, it makes sense. The tendency to produce male offspring when an overabundance of females comprise a population is potentially heritable, and would definitely be positively selected, especially if the male population is low.

I don't know how plausible the latter hypothesis is, or whether selection could mechanistically support it. The point is that "choice" in this instance refers to a trait over which selection occurs throughout evolutionary time. The woman's genetically encoded physiology as shaped by evolutionary time is actually doing the choosing. Such is the plight of evolution research, where misinterpretations of even seemingly innocuous words can yield misunderstandings...even among scientists.

Life in the Hertweck-Alexander household: A few words about communication

In the car riding to work this morning, Bill and I had a nice meta-level conversation about communication. Specifically, how we communicate with each other. His comment?

"Talking to you is like trench warfare."

Why, thank you, honey!

After a relationship of almost five years, we're still trying to figure out how to talk to one another. I like to think this is because we work so well together...I will never get bored. Bill likes to talk about random things, sometimes to the extent that I feel like he practices lectures on me that he'll later use for a class. Unfortunately, this often has the inadvertent side effect of making me feel like he thinks I'm dumb (which happens often enough in graduate education).

He definitely won't get bored, either, cause he always reminds me how I like to twist words around (Example. Bill: Do you want to eat a salad for dinner? Me: You think I'm FAT?!). He finds this quite infuriating, but seems proud of himself when he's able to do the same to me.

How much of these differences are due to gender? Are they artifacts of two academics hanging out too much? How much comes from subtle differences in life experience? After all, Bill spent his time in college hanging out at a fraternity, talking lots to other men. I spent a lot of time as an undergrad competing in speech and debate, learning to listen, interpret, and make strong arguments (although I never made people cry like some of my old teammates).

Why am I thinking so much about communication lately? I was a communication minor as an undergrad, but I never really took it seriously as an area of research in which I might be interested. I suppose I'm thinking about it a lot because I'm working on writing up results of my research, and preparing for an oral presentation at a conference this summer. When combined with my traveling over the last few months and the computer programming I'm learning (which seems like learning several new languages), differentiating between different types of media and languages is taking on new urgency.



Anyone out there with smaller feet than me (I wear a women's size 9-9.5)? I knit these socks and they are a bit too tight, but I like them too much to rip out. They're mostly wool with a bit of nylon, handwash cold. Let me know if you'd like for me to send them your way.