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.

Data management and maturing as a scientist.

I attended an awesome workshop last week called Data Carpentry. I briefly mentioned my attendance at a Software Carpentry Bootcamp a few years back, and suffice it to say that I was really excited for another two days of computational bootcamping. I even made a quick little Storify of a few of my tweets if you'd care to take a gander at some highlights.

I've spent quite a bit of time in my professional life learning to manage, analyze, and interpret data. In the 10+ years I've been conducting scientific research, my thought processes about how I relate to data have changed markedly.

1. When I first started learning how to sequence data as an undergraduate, I thought the hardest part of science was collecting data, mostly because that's how I spent most of my time.
2. As I started graduate school, I thought the hardest part of science was getting started on a research project. No doubt this was due in part to my adventures trying to collect plants for my dissertation.
3. As I finished my PhD, I decided the hardest part of science was communicating scientific results to get them published, largely because I was being indoctrinated with publications demonstrating my value as a scientist.
4. During the first part of my postdoc, I thought the hardest part was analyzing data. This is also unsurprising, as my work now is entirely computational (no data collection).
5. The current iteration of my maturation as a scientist? I think the hardest part of science is keeping track of everything you've done and making it accessible to the rest of the community. It's a concept that encapsulates most of the previous "hardest parts," and while it doesn't often deliver tangible rewards like lines of code, pretty figures, or publications, it's satisfying and essential in its own way. Moreover, my career as a data vulture relies on the community's ability to maintain reproducible, open science.

Anyway, that's why I'm so excited about learning better ways to build/query databases, share code, and maintain data. 

Rich with science.

During my graduate studies, I shared the lab with a Chinese postdoc who was an expert at fluorescent in vitro hybridization (FISH). He spent hours at the lab bench and in front of the microscope, attempting to capture the perfect images of chromosomes with important portions of the genome highlighted in glowing dyes (you can see some of his beautiful pictures here). On productive days, he would report back to our advisor by saying "I am rich with chromosomes!" 

I wasn't alone in thinking that an odd turn of phrase, but it seemed such a beautiful way to think about science. Materials which allow accumulation of data and results are indeed worthy of excitement. Lately, as I traverse the boggy grounds of job applications, I find myself sinking down into uncertainty and dissatisfaction as my own scientific bean counting fails to match up to my peers: not enough papers, not enough grants, not enough "deliverables" to show my scientific prowess. 

Occasionally, I just take a deep breath, step back, and think about my favorite parts of my personal scientific process: kicking around wacky ideas about "big picture" science, thinking up ways to tackle interesting research questions, outlining papers before buckling down to write. Those times are my happiest at work, when I feel like I make real progress. 

In reality, I am very lucky and very intellectually "wealthy." I am rich with data. I am rich with ideas. I am rich in the currency of science that is most satisfying to me.

How to think about research much different from your own.

As a follow up to my post last week about the value in learning about a breadth of topics, I thought it apropos to briefly describe some of the most profound ways in which my scientific thinking has been altered because of talking about disparate research.

Here's a bit of context. I was trained as an undergrad in molecular systematics of plants. I knew a lot about plant evolution and a little about molecular genetics. What did I learn when I started grad school and had to attend seminars about cellular pathways in mice, or behavior in insects? Here are a few examples.

1. Researchers trained in particular fields approach the narratives of science from different perspectives. The way we ask scientific questions, design experiments, and convey our results differs widely depending on the biological scale and phenomena we're addressing. For example, my tendency towards thinking about organismal evolution is strikingly different from a reductionist view of molecular developmental pathways. These ways of thinking are not mutually exclusive, but sometimes it seems we get stuck in thinking about science the same way. One of my current officemates was trained as a physicist, which results in some pretty eye-opening revelations about biological complexity and uncertainty.
2. You can do really cool science by applying methods from one theoretical background to a novel question from another field. There are some obvious examples of the success of these mash-ups. The modern synthesis, evolutionary development, and systems biology are all examples of uniting previously disparate fields of research. My personal favorite is the application of ecological principles to genomics (some examples are here, here and here).
3. Cross-talk assists in uniting themes in biology that are exclusive of model system. A great example of this point comes from journal club last week. Metagenomic methods borrow largely from those developed by ecologists to evaluate how diversity and abundance of organisms differs between ecosystems. It's pretty obvious to ecologists who work on macro-organisms that the average size of species can factor heavily into their influence on an ecosystem. The same argument can apply for microbes that differ widely in average size, yet biomass is rarely considered in microbial studies. Talking about vastly different study systems helps remove model-system specific bias.

Of course, those are just a few of my favorite vignettes to validate the time I spend thinking about research that isn't directly related to my own. Dare I also say that such thought experiments are also simply fun? Basically, I refuse to let myself be impatient about attending seminars or meeting with visiting scientists if their work is very different from my own. I had a great one-on-one meeting with Darwin historian Alistair Sponsel  a few weeks back when he visited NESCent. We only spoke for half an hour, but the time was constructively spent talking about visualization of different types of data as conveyed across a time scale: certainly important insight for both historians and biologists.

My last point is that understanding a breadth of research helps make your own research deliverables more appealing to a broader audience. Some practical applications are obvious: how to communicate in a seminar to a broad audience, how to convince a panel of experts your grant is worth funding. I'll continue this thought in a few days, focusing on one particular part of our job: peer review.

Bladderwort: tiny plant, tiny genome, weird name. So what?

My dad emailed me a link this morning. Then a NESCent coworker passed along another. Then my boyfriend tagged me in a post linking a similar article on Facebook.

All those news articles refer to a recent paper (Ibarra-Laclette et al., 2013, Nature) which reports on a newly sequenced plant genome (Utricularia gibba). YAWN, we all say, it's a silly little plant and we can't even eat! What makes it news worthy?

Turns out there are a few reasons why. First, it's called badderwort, and that's just funny. Second, bladderworts are a wickedly awesome type of carnivorous plant which capture prey by rapidly sucking them into bladder-like traps (complete with a trapdoor!).

Then there are a whole slew of other (more "publishable-in-Nature") type reasons to care about bladderworts. This species has a remarkably small genome but still possesses the same number of genes as other plants surveyed. Most of the news articles linked above talk about the implications of the research for our understanding of "junk DNA," or portions of the genome which do not code for protein sequences. It's admittedly a hot topic in science news right now, following heavy on the heels of research in human genomics suggesting that a large portion of the human genome is junk (EDIT: but still functional). The repercussions of the bladderwort genome research is that junk DNA isn't really necessary for "healthy organisms," as we now have an example of one species which has managed to "throw out" junk DNA.

I find the bladderwort research interesting for a few reasons. First, my professional research interests revolve around junk DNA and how changes in genome size affect organisms. The main focus of my research here at NESCent is comparative genomics of a group of plants called Asparagales (includes agave, onion, iris, orchid, asparagus). Species in Asparagales have genomes which range from very small (i.e., a few times larger than bladderwort) to ginormous (200,000 times larger); the variation in genome size is like due at least in part to junk DNA. The conclusions from the bladderwort news articles are kind of no-brainers: OF COURSE plants can persist quite happily without tons of junk DNA. There are fungal species which entirely lack junk DNA, too.

I'm also pretty tired of the semantics surrounding the "Is junk DNA important?" argument, which has been very well described elsewhere (and there's concomitant throwback from the creationist community as well, but that's for another day). To me, junk DNA is just another source of mutation. In the context of evolutionary biology, junk DNA provides more opportunity for evolutionary innovation. That's a hypothesis which is better tested with a broad sampling of species' genomes to infer changes over time. A snapshot of a single genome at a single point in time can't tell you as much as broad comparisons. Asking about the relevance of junk DNA to an organism living today is like asking whether money is required for humans to survive. In a strict sense, currency ISN'T required for humans to persist. It IS a means to an end, though, and a mechanism through which contemporary humans purchase food, shelter, and other resources required to survive. That might be a crappy analogy.

A better question to ask from the bladderwort research is what pathways allow for regulation of junk DNA and other mechanisms of genome downsizing. It's not just about the ability of the bladderwort genome to remove sequences already present. It's also about the ability of the genome to prevent other sequences from incorporating themselves into extant sequences, since some junk DNA is derived from viruses and the genome can be continually invaded. There is also evidence the bladderwort genome has undergone whole genome duplications at least three times, but has managed to remove most of the extra genetic material (including extra genes!) after each event. Now THAT'S some cool science.

Architecture and evolution of a minute plant genome, Ibarra-Laclette et al., Nature (2013) doi:10.1038/nature12132

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!

I bleed for my thesis: Part I

No, really. Throughout the course of research for my dissertation, I have endured a wide variety of physical maladies, ranging from mild to fairly serious, all directly related to teaching, field work, greenhouse maintenance, etc. As I can now see the light at the end of the tunnel for my dissertation, I'm going to record all of these events for posterity. Here I will begin with the first, and perhaps most notable, experience.

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My second field season turned out to be far more exciting than I intended. I had done some plant collecting in southern Missouri and was meandering around central Arkansas looking for spiderworts. I found and collected from an absolutely amazing population in the middle of nowhere and got back in my truck to head to a nearby campground. I was driving down a narrow rural highway, dropped a wheel off the side of the road, and it blew out. I spun all the way around in the road and turned over upside down in the ditch on the other side (better than the alternative, which was a fairly steep, long hill).

You know the theory about drunk people not getting hurt in an accident because they don't have fast enough reactions to tense up and cause skeletal damage? My incredulity at having caused such a horrible accident likely kept me from getting hurt in much the same way. I remember the truck spinning, my shoulder slamming against the door, and my world turning upside down. It was only

when I hung there, wondering why the airbags didn't deploy, that I realized the full extent of my predicament. The week old camper shell on the truck apparently saved my life, as the cab was barely compressed. I unbuckled my seatbelt and fell to the glass-littered bottom/ceiling of the cab. I crawled out of the passenger side window and emerged into the sunshine, feeling like I had been reborn.

The pickup following a half mile behind me pulled over to help. The family didn't quite believe I was alone in the truck; apparently my collection and camping gear was far too much for one person. I grabbed my purse out of the pile of glass at the bottom of the ditch and found my cell phone. Although I was assured no signal would be available, I managed to reach emergency services and they dispatched a state police officer and ambulance.

After several more attempts to connect, despite crappy cell coverage, I finally talked with my boyfriend at the time. Nearly 6 pm, and he was hungover and at work. All I told him is that I was in a car accident, and that he should get in his car and start driving to central Arkansas. I was in the process of attempting to contact a few additional friends and family when I realized I was standing in a fire ant nest. I extricated myself from that travesty, and started picking the glass out of my arms and legs a safe distance from the domiciles of any biting insects.

The emergency contacts took their sweet time getting there. I apparently should have specified more about the severity of the incident. I refused medical treatment, and supervised the tow truck as it pulled my vehicle and possessions out of the ditch. I stared dispassionately at the mess, and contemplated pitching a tent in the adjoining field to stash my gear. I glanced down and spotted a flash of purple amid the small chunks of glass. My mother had given me a chunk of amethyst to keep in my car "for protection," and it sparkled poetically amidst the wreckage of my vehicle. I plucked it up off the ground and pocketed it, not sure if it had done its job, but instead hoping to reclaim everything possible.

A nice woman who volunteered for emergency services and lived a mile up the highway came by and offered to transfer me and my belongings to a hotel in nearby Glenwood, Arkansas. At that point, I had collected nearly 50 live plants, each of which were ensconced in their own large ziplock bag and placed carefully in huge tupperware boxes. My new friend stared at the jumble of plants in the ditch and said, "You're gonna have to go back and pick all your pretty flowers again." Yes, indeed. We loaded up all non-plant materials in her car and placed the plant tubs in the back of the sadly crumbled truck.

We stopped off at my friend's house to feed her dog, a dachshund aptly named Pecker. She then dropped me at a hotel in town, where I spent the next few hours shaking all of my belongings free from glass and grass. I touched base with my mother, father, and a few of my best friends while I periodically directed my boyfriend to the speck of a town I inhabited. He made the eight hour drive in record time, ending up at the hotel in the wee hours of the morning.

We slept a few hours, stopped by the tow yard to claim the rest of my belongings, and made the drive back. The boyfriend humored me by stopping to collect some plants near Joplin, Missouri. I tallied the final damage when I got back home. Truck was totaled. My shoulder was bruised, and my pride even more so. I had to cancel a professional presentation about my research to a university along my collecting path, and the rest of my collection trip was delayed. My arms and knees had numerous small cuts, and my legs had fire ant bites. But none of my equipment, including my laptop, was damaged, and all of my plant collections were salvageable.

My mom helped me locate another pickup within a few days, and my insurance payout covered most of it. The camper shell salesman didn't even bat an eyelash when I was back only a few weeks later with a different truck and a request for another shell. As soon as I was able, I drove straight to Texas to finish collecting plants. My research persevered, and I emerged wiser. The repercussions were relatively mild, all things considered, but there were some interesting side effects in my personal life....but then again, that's a whole other story. Suffice it to say that this was the first time I literally bled for my research.

Cool research questions and applied research

As a graduate student of an advisor that likes to socialize and network, I often find myself meeting with various visiting scientists to chat about research. Over the past few weeks, I've met with three such scientists. All of them are incredibly intelligent and do interesting work on genomics and chromosomal evolution in plants.

I had lunch with the first scientist. Each student or post doc chatted a little about our research. When it was my turn, I described my work (genome evolution in an obscure monocot family, Commelinaceae). He said he was going to ask me a mean, perhaps unfair, question. I was game, said OK. After all....why did I spend so much time competing in speech and debate if it wasn't to field unfair questions? He asked why I worked on plants that didn't have an applied research angle. I provided my standard answer about comparative biology offering a unique and useful approach for understanding biological complexity in the realm of plants not altered by humans, blah blah blah. I felt I was pretty articulate for being ill and doped up on cold medicine. He waited a moment, then said he didn't buy it. Basically, no answer would have worked...he didn't think a plant was worth studying unless people could eat it.

The second meeting with a scientist went much the same. Lunch, talk about science. This scientist was just mystified as to why I would choose to work on an obscure group. He accepted the value of empirical research, but didn't seem to grasp the relevance of working on a non-model system.

I just had a meeting with yet another scientist. This was an individual meeting with no other folks present. I must admit I approached the meeting with a moderate amount of trepidation, as I wasn't really geared up on this lovely Monday morning to defend my research again.

I'm pleased to say I was pleasantly surprised. We had a quite excellent discussion about chromosomal evolution, molecular mechanisms of genome restructuring, and emerging areas for research as technology develops and our knowledge base grows. He had not only heard of my group of plants, but used it as a teaching tool when instructing students in cytogenetics and chromosomal evolution. He helped me develop my conceptual framework for chromosomal evolution and the context in which I place different types of chromosomal information and analysis. It was an inspiring, refreshing, and very nice way to spend 45 minutes this morning.

In light of my new-found enthusiasm for cytogenetics, here's a picture of some painted wheat chromosomes I took a few years ago when learning cytogenetic techniques. The blue blobs are wheat chromosomes. The red dots are centromeres, and the green dots are an unknown genome fragment I was testing. Now if I could only get some Commelinaceae cytogenetic pics this pretty...