Category Archives: Reflection

Useful things: free-writing on your research project or dissertation


Author: Brianna

I have two similarly slender books on my desk that are both virtually guaranteed to give me a little motivation boost on any given day: How to Write a Lot, by Paul Silvia, and Writing Your Dissertation in Fifteen Minutes a Day, by Joan Bolker. These books are concise and have plenty of concrete advice that can actually get you writing more, so they’re worth a read.

A major decree from both books is that you must write, at least a little, every (work)day.

I haven’t written much over the last year or two (not just on this blog!), mainly because I’ve been amassing a pile of dissertation data that’s involved many museum trips, measuring hundreds of fossils, lots of pictures, more CT scans than you should shake a stick at, and several memorable weeks collecting gait data on the friendly tapirs at our local zoo.

A few weeks ago, as I tried to gather my thoughts and my PowerPoint slides before heading to the ICVM meeting, I was browsing through the Bolker book when I came across her suggestion to begin each day with ten minutes of free-writing. This can take the form of whiny stream-of-consciousness (“I don’t have any ideas. Why do I never have any ideas…?”), posing a series of questions to yourself (about the project in general, or a particular area you’re stuck on), exploring your thoughts and line of reasoning for something, or even just writing out sentences/paragraphs that might go into a paper.

I’m quite familiar with the creative-writing practices of beginning with free-writing, or shitty first drafts (link is to a PDF file), or starting the day with morning pages. I know it’s useful in that context; I spent a year in an intensive creative writing course at the University of Oregon where at one point we were turning in new short stories every couple weeks, and the only option was to write your tired little fingers off. Also, the license to whine or navel-gaze as part of the free-writing is useful for a fairly high-strung person like me so I can get the cluttered, gnawing thoughts out of my head and onto the page.

But for my research?

Once I thought about it, though, it makes a lot of sense. A recurring concept in books like these, whether about creative writing or scientific writing, is that we should write so that we can think—not think so that we can write.

After spending so much time collecting, processing, and analyzing data, I was feeling a distinct lack of big-picture thinking about the broader arc of my dissertation. Also, I’m nearing my favorite time: paper-writing time. One or two of my dissertation projects are very nearly ready to write up as papers, but that means I need to be in a writing frame of mind again!

Enter dissertation free-writing. Most resources on free-writing (/shitty first drafts/morning pages) recommend using a notebook and pen, but I’m lazy and I like things I can search or copy/paste, so I made a Word document. Do whatever works for you.

Let me tell you, it was the best idea I’ve had in awhile.

I started with all the questions I have, or want to answer, or am trying to answer. I wrote out ideas about how I am doing that, and how I might do that in the future. I noted down snags and doubts and areas where I feel like my logic or argument is fuzzy. I brought up papers I’ve read (or need to read) that relate to certain areas. I pondered follow-up projects. I sketched out some plans for my ICVM talk. I made a list of the last bits of data I need to get before writing up a paper. I sketched out the main ideas of each of the next few papers I’ll write. I whined (a little). I spent some time thinking about the Big Ideas that get me excited as a scientist, and how I might pursue those in the long run.

Naturally my overall thinking has been boosted by feedback and conversations at this conference, but even before I got here, I began to feel a nice sense of clarity – like I could actually wrap my brain around the project again instead of being lost in the weeds.

Time will tell how much this pays off in terms of actual writing productivity. I’ve begun writing snippets of actual…well, writing….in my free-write document, the kinds of sentences that might go into a paper. I tend to think pretty hierarchically, so before long I’ll begin working from an actual outline for these manuscripts. We’ll see how much of the material generated in these sessions translates to the draft itself, but I am already convinced of the utility of daily(ish) free-writing to boost productivity on a specific research project.

Thoughts on motivation

Author: Brianna

Sometimes motivation is hard to come by and that is okay.

For me, the trick is in being calm when motivation is gone; in being a grownup about keeping up my responsibilities even when I don’t have it; in finding it when it is hidden; in knowing and trying to learn more causes of its ebb and flow; in making choices that will nurture it in the long and short term; in spending time around and talking to interesting people; and in consciously aiming for more intense productivity when it is close at hand.

This all involves paying close attention to what excites me. The good news: my dissertation plans excite me! Right now, though, I am working on remembering my excitement for a few papers that need to get finished and out the door. It was there once, and I can still kind of feel it, but we’re in that last 10% of the publication process that always takes up about as much time and energy as the first 90% did. I will be pleased when these papers are off my plate. They are good projects and I like them.

Also, it is good to be home for a little while. I missed Oregon and my animals.

Communing with McKinna before my first ride in about 6 months.

Dealing with the first year of grad school, Part 1: the general sense

Author: Brianna

It occurs to me, as I sit in a cozy chair in a sunny lounge overlooking some pleasantly evergreen trees, that I am currently ‘dealing’ with graduate school. As in, things are going pretty well. I’ve published a paper, submitted another, drafted a couple more, given some presentations, taken some classes, made good friends, found a good first-year project. I haven’t written much lately, in part because I am not always sure what I (we) want this blog to be. Also, blogging is not always high on the priority list.

But I think this blog can be a place for advice. I like giving advice, but I am also “just” a first-year graduate student. (This is why we have an “Unsolicited Advice” category.) I still have some sensible ideas about getting work done, though. At the very least I have my own experience working my way through this first year and ostensibly the years after that. I think that might be a useful and/or interesting thing to people. Especially if you’re, say, a senior-ish undergrad looking to go to grad school. Or a first year grad. Something like that.

So this is the first in a several-part series, which I’ve just now decided will be a loosely organized collection detailing exactly what you’d think from the title: how I am dealing with the first year of graduate school.

For the first post, here’s some things I do to keep myself healthy and relatively happy and chugging along. Maybe in the next one I’ll go into some specifics of the first year, like learning to use a bike to commute (even in a terrifying place like Cambridge/Boston!) and being scared of meetings with your adviser.

I have been spending a lot of time around my fellow first-year grads, or G1s as the parlance here goes. Turns out they are a bunch of brilliant, kind, interesting and interested people. Our new-grad seminar, where we meet professors or work on professional development and do lots of talking, is a highlight every week. As a cohort we’ve been tight-knit socially but also academically, for lack of a better word – there are always several people willing to proofread a paper or grant application, give feedback on a presentation, or sit in the conference room eating lunch while you sketch out your lab meeting talk on the whiteboard. You can’t force cohesion, but you can seek out this contact. The first year is easier when you have some buddies to panic with you. (Same goes for the rest of the grad students in the department, of course. But I think making strong connections with your cohort is important, if you can.)

I have been paying close attention to what works for me and what doesn’t. The things that work for me have fluctuated a lot over the 8 months or so I’ve been here so far, which surprised me quite a bit. I talked about this more in the post on flux, but I’m still surprised just how adaptable I’ve needed to be. I need to remember that when I’m stagnating, I should probably go for a walk or go work somewhere else, like I did just a bit ago by relocating to this lounge. When the usual trick of goal-setting and bouncing ideas around really wasn’t helping me get out of a motivation slump, I accepted it eventually. I slept in a lot (for me, around 9 or 10am). I worked in coffee shops to enjoy the anonymous rumble of cheery conversation flowing around me. I read a lot of non-science books. I went from occasionally doing a few hours of work on weekends to never working weekends. You know what? The world didn’t end. I kept up with my classwork, and I made a little progress on my research each week even if it wasn’t mind-blowing giant steps. And then the sun came out, and it stopped snowing (mostly), and gradually I walked myself back up the hill to the place where I once again get excited by all the things I want to do.

But at the time, it felt a little like everything was ruined forever. It’s okay to feel like that.

When I’m getting overwhelmed by the short-term deadlines, I take a deep breath and remember the long timeline of this PhD. It’s oddly comforting that just about everyone in the program seems to say they didn’t get much of anything directly “useful” (i.e., that went into their dissertations) until their second or sometimes third year. This lets me be content with indirect usefulness.

When I’m getting overwhelmed by the long timeline of this PhD, I take a deep breath and focus on the short-term deadlines.

I lift a lot of weights. It’s satisfying, it makes you ready for bed at the end of the day, and it’s a good chance to chat with a friend if you talk one of them into being your lifting buddy. Also it is really good for you. If I had to pick one thing that helped me pull through the end-of-winter slump, it is starting up with a regular lifting schedule again. (Okay, two things: sleep too.)

I make a conscious effort to stop my stress, or at least mellow it, about things I can’t control.

I don’t go for as many walks as I should, but whenever I do it makes a world of difference to my mental state. I come back calmer, happier, and clearer of mind. Bonus points if you spend some time on your walk coming up with things to be grateful about. I usually start with the healthy legs that are obligingly carrying me around, particularly since I’ve spent enough time in the past with a broken ankle to know a taste of the alternatives.

I try to focus on the parts of my research that I love (planning, data analysis usually, writing, exciting projects) and be a grownup and just matter-of-factly accomplish the parts that I love less (some types of data collection, cleaning up mistakes in data, doing a bunch of revisions after reviews, less exciting projects). Same goes for life: more enjoying things like cooking or rock climbing or thinking about the power tools I’m going to get this fall, less procrastinating on things like taxes or cleaning the bathroom. Just do it and move on.

I go to as many job seminars, departmental seminars, and dissertation defenses as I have the time and energy for. Sometimes I have other priorities or I can’t bear the thought of sitting in a dim room for an hour and a half. Those times I generally don’t feel guilty about.

Good food is important! We get a CSA (community supported agriculture) box with fresh fruit and veggies in it every week, which is nice when you learn to cook new delicious things and annoying when it’s the fifth straight week of way too many dandelion greens.  It helps that I like to cook. It’s easier when you live in a house with roommates who like to cook, too; we all go through cycles where sometimes you’re cooking giant meals all the time and sometimes you have no desire or available time to cook. It’s nice to have hot meals even on evenings when you come home hungry and grouchy at 8pm. I suppose my advice here is to get good roommates! Failing that, learn to make some simple, fairly healthy things that you like to eat. Make them in quantities and freeze some for the busy times.

That’s enough for now. The SVP abstract deadline is coming up, and I have things to finish!

Why I love paleontology field work

Author: Brianna

Lately I’ve been thinking about summer paleontology field work. (Field work? Fieldwork? I never know which to use.) The endless Boston winter has called up this nostalgia, because I am tired of the cold and slush. I want to be back out in Oregon’s high desert in the summer, taking painstaking field notes in little yellow Rite in the Rain notebooks, shivering in the cold morning while staring at the pot of water on the camp stove willing it to boil faster dammit I need my tea, hiking through sagebrush or climbing dry riverbeds up the valley, scrambling up crumbly slopes to measure section, holding in my hand an actual fossil that I just found….these are thoughts to get a person through.

I love paleontology field work because it connects me to my research in the most basic way: I am crawling around in the dirt, sometimes with my nose inches off the ground, and finding fossils that no one has ever found before. And they’re fossils that contribute directly to research. The first paleontology project I finished was completely digital: we did some stats on some data that came from other papers and a database. We found some neat things, and I got hooked on how awesome it is to find out something that nobody else knows. But it was pretty far removed from any physical specimens, for me. So the first time I went out in the field, when I got to find real fossils and take notes on them and bring them back with us to go in the museum…that drove home the connection. It brought a very nice sense of continuity to my grasp of paleontology.

I love paleontology field work because I get to go camp and hike with fellow scientists for a week or two, many of whom are my close friends. Better yet we’re in the desert, where my hatred of thermoregulating in the cold is offset by my complete and utter happiness in unreasonable heat. It never fails to amuse me that the hot, dry air sucks the sweat from your skin before you even realize you’re sweating, until you take off your backpack or knee pads and everywhere underneath is soaked. I like feeling badass when, at the end of a long day of work, I hike back to the truck carrying a big sandbag full of matrix from a microfossil site. I like sleeping in a tent. I like cooking dinner on a camp stove and eating for lunch whatever bizarre combination of fruit, nuts, salami, cheese, and tuna-in-a-packet I happen to have packed that day.

I do not love spiders in the pit toilets. I do love my rock hammer.

I love paleontology field work because, I’ll admit it: I really like long car rides. I know that’s a bit weird. But some of my favorite activities are napping, thinking about stuff, reading, and having long conversations with people…all valid choices for long, dusty car rides between field sites, which for us are spread out across much of Oregon.

I love paleontology field work because it’s a major change from the usual computer-centric work I do. Sometimes it’s hard to feel satisfaction and a sense of accomplishment when you’ve been hammering away at the keyboard all day, you know? But there’s no denying that you’ve done a good day’s work when you hike out there and find a bunch of new specimens or track down an old locality, flip a plaster jacket from yesterday’s work, or maybe measure a bunch of stratigraphy and bring back samples from each layer. Bonus points if you’re taking field camp for credit and stay up til 1am lovingly finishing your strat column, cough. Oh, the howls of despair when you mess up one of the lines with your Micron pen…

If summer scheduling allows, I’ll be out doing all these things (except making strat columns in the wee hours!) this July. For now, I suppose there’s nothing to do but glare at the snow-fluff coming down outside my office window and get back to work.

Routine and flux in my academic life (or: if what you’re doing isn’t working, change what you’re doing)

Author: Brianna

The title of this post reflects one of the most basic approaches I take to my work patterns. Not to the science itself, mind; troubleshooting there is a different beast entirely and giving up too quickly is bad. I am talking about how, when, and where I work. If my current approaches aren’t doing it for me – especially if things that WERE working previously begin to STOP working – I pay attention. Often I will change my working style in response. This willingness to change helps me stay attuned to patterns and styles that keep me happy and productive. (There’s also an implied inverse: if what you’re doing is working, keep doing it.) As a result, I wind up with an interesting balance of routine and flux. It works for me, and I thought some people might find it interesting.

Part 1: Routine

First, it’s important to note that I am a creature of habit. I like to go to bed at around the same time and get up at around the same time every day. I like to make myself a giant cup of black tea with whole milk and sugar and drink it slowly. I love adding structure to unstructured time (more on that later). I like standing appointments with friends for a meal or coffee or rock climbing. I like to cook, but I’m also happy eating a few more or less unchanging meals for long periods of time.

For me, routine is a powerful tool against the squishiness inherent in academic work. If you fuss around not doing any work until 4pm but then hammer out a beautiful discussion and conclusion section for your paper over the next few hours, is it still a bad work day? If you fight with your R code all day with a short lunch break and at the end of the day you finally figure out what you were doing wrong, is it a productive day or a wasted one? If you spend all day in meetings and responding to emails and filling out paperwork, should you feel accomplished or frustrated?

Yeah. It’s complicated, and routine gives me some structure to work with. It also helps with decision fatigue, I think.

I usually set a rough schedule for the week, blocking off a couple hours at a time. First I fill in classes and other unmoving commitments like meetings with my advisor and lab meeting. Then I start assigning time to reading, writing, working on writing up projects from undergrad, data analysis, classwork, and so on. I try not to use blocks smaller than about an hour for any academic work. I know from experience that my focus is best from around 8am until I stop for lunch (somewhere between 11am and 1pm), so I usually concentrate writing and reading earlier in the day. In a future post, I’ll go into detail about my daily/weekly schedule, how I choose it, and especially how I handle my to-do list. I really, really love lists.

A few things I keep consistent: I roll into the office around 8am. I work until I am too hungry to ignore my food calling to me from the fridge. I work some more or go to class. I go home around 5pm and often head over to the climbing gym shortly thereafter. I read papers on couches or in chairs or coffee shops, not at my desk. I brainstorm with a pen and paper – always in the same notebook – and write at my desk (with external monitor + keyboard) unless I’m feeling stuck.

Earlier in the semester, I wrote a post about a few new habits I aimed to establish for grad school. New post soon evaluating last semester and laying out next semester’s goals, but the short answer is that I pretty much stuck with those habits. Especially biking. I love my bike and ride it everywhere, and I actually really missed it when I was home for break.

You may now adore my beautiful bike.
You may now adore my beautiful bike.

Who shaped my thinking?
Most of my ideas about routine have been inspired by a few sources. When I was just a wee freshman in undergrad, I learned a lot about building an effective routine for classwork from this Study Hacks post. In recent years, similar posts have expanded the idea of a fixed schedule and how to arrange that time. Most terms in undergrad, I’d go through three or four iterations of a schedule, with each weekday blocked out in hours. I would try to follow the schedule, note where I failed, then tweak and rearrange things until it worked for me and my rhythms. I do the same in graduate school and I’m grateful for all the practice I got as an undergrad. Like I said above, more detailed post on that soon.
Another source that went into my ruminations awhile ago was this 2011 blog post from a novelist: How I Went From Writing 2,000 Words a Day to 10,000 Words a Day. Though I’m not writing fiction in my daily work, I am writing an awful lot, including sometimes on big nebulous projects that have many parallels to big nebulous novels. The author used three main techniques to seriously boost her word count: mastering knowledge, time, and enthusiasm.
Finally, recently I’ve seen some press for a book on the routines of various famous writers, painters, and other artists. It’s called “Daily Rituals: How Artists Work,” by Mason Currey. I don’t know how strictly useful it is in terms of copying patterns – many of their sleeping schedules sound positively awful to me – but it’s nice to muse on other peoples’ methods and/or neuroses, and perhaps pick up an idea or two.

Part 2: Flux

The problem with any routine is that it, by definition, loses novelty. I stop truly appreciating the delicious combination of milk and sugar and black tea in the mornings. I get to the paper-reading time of day and it takes Herculean efforts of focus to make it through a single paper. I rearrange my books on the shelf and wash all the dishes and mop the floors because just about anything sounds better than sitting down to revise that discussion section.

My solution is to change something that doesn’t affect my ability to get work done, but shakes things up a little. Usually it has to do with where I work, because right now, the majority of my work can be done anywhere.

I’m set as long as I have a computer, notebook, pen, and maybe an internet connection. Preferably also music and a hot beverage. Over the fall semester, here are the places I accomplished large amounts of work:

  • Main office on campus: reading on the couch, LOTS of writing at my desk on many different papers.
  • Ernst Mayr library on campus: reading on the giant leather couch, one day of surprisingly productive writing on a class paper when I forgot my laptop power cord.
  • Field Station: basically like my other office, except I go for a nice walk outside when I get stuck on something. I’m not as good about that on the main campus.
  • Home: usually writing at the kitchen table and reading upstairs in the Papasan chair. I often work from home on Fridays.
  • Coffee shop halfway between my apartment and campus: mostly writing. And biscotti. Mmmm.
  • Rock climbing gym: they have a lounge, a big work area with couches and sitting tables and standing tables, and treadmill desks. It’s glorious, I’m telling you. Have done great big swaths of writing papers on that treadmill desk and a good bit of reading in the work area. Plus, built-in break time: go climb, work for a couple hours, go climb some more…

I think those are all my regular places from the fall semester. The key is that I tend to stick with one as my major workplace for awhile, occasionally dropping in to the other places, before I make a switch. The switch only happens when what I am doing isn’t working. For example, early in the semester I did virtually all of my work in my office. When I could barely get myself to sit down on the reading couch in November, I hauled myself up to the library with a big cup of tea and promptly cruised through a giant stack of papers.

I change other things, too. Early in the semester I hand-wrote notes for all the papers I read in my research notebook, then later transferred those into Zotero annotations. Later, I stopped appreciating the aesthetic experience of handwriting into a notebook and craved speed, so I typed directly into Zotero. For most of the semester, I used my iPad for paper reading. After I found myself continuously switching to Facebook on the iPad instead, I printed off a stack of papers and banished myself from electronic devices for awhile. Sometimes I sought out people to work with, sometimes solitude. I started drinking Good Earth Original spiced tea for awhile instad of plain old black tea, and then even switched to Constant Comment! WHAT WILL SHE DO NEXT?

You get the idea. If what you’re doing isn’t working, change what you’re doing. You will notice that none of my shifts were an easy way out or an elaborate way to procrastinate…they just changed the context in which I was working, which seems to give my brain just enough novelty to help me settle down and just get to work already. Laying out the changes all in a row makes it seem like I flit more or less steadily from one working style to another (phyletic gradualism?), but I can assure you that the experience is much more of a punctuated equilibrium.

Who shaped my thinking?
I think my approach to regular change has come mostly out of just observing my own work habits and paying attention to what improves productivity. Nevertheless, I’ve certainly pulled ideas from a few places over the years.
Not surprisingly, more in the way of the Study Hacks blog. I’m telling you, there’s some serious gold in there, especially for undergrads looking to establish good working patterns early on. Adventure studying/work emphasizes changing your physical location, and here’s a post on context that discusses beer, for those of you who are into that sort of thing.
If you haven’t read about the pomodoro technique (basically work in short timed bursts), it’s useful. I don’t use this when things are going well, but if I am having a hard time bringing my mind to the task at hand or am procastinating like a madwoman, this approach gets me back on track.

I should note that this is particular to the scheduling flexibilities I have now, as a PhD student. According the whining discussion I hear from my more senior friends, meetings and paperwork and other undesirable things soon begin to fragment one’s schedule. I could take this as an interestingly reversed “uphill both ways in the snow” situation (it’s just that instead of “back in the day,” it’s “just you wait…”), but mostly I pay attention because I believe them. I think it’s instructive and motivating. If I can’t manage my time effectively when I have close to 100% control over my schedule and few commitments, how will I survive later? Right. So my goal is always to optimize my working habits for the situation I am currently in, while recognizing that over time that situation will change.

I am looking forward to revisiting my old routines now that I am back in Cambridge. It’s been a lovely winter vacation: two weeks back home in Oregon soaking up the time with friends and family and my cats and dog and horse, then a couple weeks in Austin for the Society for Integrative and Comparative Biology meeting, plus more friends and family. I like my apartment and my own bed. Especially my own pillow. And, awesome bonus: we’re catsitting! That’s right, came home to two adorable fluffy felines prowling around. Very pleased.

I’ll be spending more time out at the field station this spring and possibly doing some Actual Data Collection. But other than that, I don’t expect my working habits to change much. Read, write, study, think. Happily those are some of my favorite things, and undoubtedly I’ll find one or two new places in which to do them when the routine needs a little flux again.

Science poetry, AKA there exists a poem about capybaras and it’s beautiful

Author: Brianna

I wrote some science poems awhile ago for a remarkably intense creative writing course I was taking as an undergraduate at the University of Oregon. Remarkably intense for a scientist, anyway; it was difficult to balance organic chemistry, physics, and the beginnings of my thesis research with the expectation of deeply reading stories, giving detailed feedback to classmates, and above all producing quality writing week after week. The mental spaces I had to occupy for each task were quite different and challenging to switch among. I was a little bitter about the workload and frustrated with hunting for things that felt just out of reach, despite loving writing. (I’ve still hardly written any stories since that class, which was a couple years ago. But that doesn’t mean I don’t still love it, or that I don’t really value the time I spent. More on that in some other future blog post.)

Anyway, some of our portfolio assignments included a few poems even though the class was focused on short stories. The poems I wrote reflected my bitterness a little and they were about science, because if I have to write more poems they’re going to be about science dammit. But they weren’t about the parts of science I was really drawn to. I’ve tried occasionally since then, but it turns out it’s actually really hard to articulate the things I love about my branch of science without slipping right into a maudlin, cliche-ridden mess. It’s like writing a love poem, but to science. And fieldwork. And fossils.

I am thinking about this because thanks to Twitter, I found a poem about measuring all things by comparison to capybaras. (h/t to to @evelynjlamb and @DNLee5)

It’s unexpectedly beautiful. It’s called “Unit of Measure,” by Sandra Beasley, and I want you to click on that link.

It begins,
“All can be measured by the standard of the capybara.
Everyone is lesser than or greater than the capybara.
Everything is taller or shorter than the capybara.
Everything is mistaken for a Brazilian dance craze
more or less frequently than the capybara.”

I started reading and I thought I knew where it was going. Funny poem, right? Cheeky poem. Endless comparisons to the capybara.

The soft, fluffy, adorable capybara, Hydrochoerus hydrochaeris.Image by Dori / CC-BY-SA-3.0 / Wikimedia Commons

Well, sort of. It may be those years I spent immersed in creative writing, but for me the rest of the poem goes deeper until by the last lines it has me, and now I want to print this poem off and tape it to my wall. Reading it makes me want to try writing about science and fieldwork and fossils again. It also makes me just a little sad that I am not, in fact, a capybara.

Go on, go read it.

What we are thinking about lately: Bayesian vs. frequentist approaches, R coding, and reading all the things

Authors: Brianna and Kelsey

What are we up to lately at Fossilosophy? Good question. Here’s what was on our minds last week.

Reading Habits

Guys, there are not very many things as satisfying as going on a paper-downloading spree for something related to your research. There is something to be said for deciding what you need to know, flailing around up to your eyeballs in the literature for awhile, and pulling something coherent out of the mess. Lately Brianna has done this for a few different areas, including the painfully general “(evolutionary) locomotor biomechanics and skeleton stuff!” and a much more specific hunt for statistical quirks in using discriminant analysis to classify fossils. Now, to read and/or skim those ~70 papers…

Kelsey, on the other hand, is probably printing about ten papers per week, and greatly enjoying that every single one of them is in color.

Data Analysis in R

Whenever it comes time to do some data analysis in R, you generally have three situations: 1) You have no idea at all where to begin. Time to start asking books, friends, and the internet, 2) You know all the things you want to do but don’t have all the proper tools, or 3) You know what you want to do and are perfectly capable of writing efficient, elegant code to do so.
If you answered situation 3, that’s very nice. (We haven’t run into that very often yet.) Situation1 happens more often than we would like to admit, but right now we have been thinking about situation 2. You can take one of two general approaches: using the tools you have to get the job done, and teaching yourself new tools. The first choice means doing many things stuff manually, repeating lots of code, resorting to programs like JMP for bits and pieces because it’s so much faster, and just doing things in whatever way you can to get the job done. Sometimes this is what you need, especially if you’re crunched for time because of a deadline. It’s the penny-wise and pound-foolish approach, if you will.

Lately the ladies of Fossilosophy have been aiming for the seond approach, where you go teach yourself the tools you need to do things the right way. It takes way longer and it’s frustrating, but it also builds character (and coding skills). Three cheers for doing things the hard, but proper, way.

Kelsey likes to think of coding as a set of nested dolls or a machine where every part has to be hand-made. Every “gear” is tested as you go, which generally cuts down on debugging later on. The overall operation (say, the regression part of a regression analysis) may be the very last bit of surrounding code you add, after all the parts are moving.

Also, we are fond of giving objects amusing names. This will help you remember all the variables and make readers of your shiny published code smile.

If anyone is interested in a very friendly, straightforward introduction to R book, we liked Getting Started with R: An introduction for biologists, by Andrew Beckerman and Owen Petchey. It is written with great clarity, has good examples to work through, and has just enough tongue-in-cheek humor to make the reading fun.

Bayesian vs. frequentist approaches

It’s a giant can of worms. Make that wormholes…a can of wormholes that, once opened, can send you huddling up under the table faster than trying to wrap your head around what exactly a genus or species is. Though Brianna has enough statistical background to understand the broad ideas behind what’s going on in the Bayesian/frequentist/pragmatist arguments, the whole debate is a little overwhelming and difficult to wrap her head around. (Latest round of mental crisis sparked by an older Oikos post on the matter. Good links and comment section there, too.)

More on this later, after we straighten out our thoughts a little more.

Other fleeting things occupying our attention: how awesome flow charts are, how difficult it is to estimate how long some academic/research task will take to complete, and how great it is being able to bounce ideas off of fellow grad students.


Author: Kelsey

Two(ish) weeks ago I started graduate school at the Jackson School of Geosciences (JSG) at the University of Texas at Austin (UT Austin). I am a paleontologist, which means I straddle the boundary of Geology and Biology (also known as 4D Biology; the three dimensions of space, plus time). During this time I have moved into my own apartment, signed up for everything from W4 forms to background checks, and acquired an impressive number of keys and codes.

I have also met many amazingly intelligent (and surprisingly nice) people, both in the JSG and the greater Austin area. Don’t get me wrong, it wasn’t that I was expecting stuffy professors and cut-throat grad students, but the level of compassion for my well-being could rival the hockey stick curve for global warming.

The last two weeks have changed me from a kid to an adult. Not just any adult…my version of an adult. This version is significantly more fun and enlightened than the average stereotype of adulthood, but still runs to Starbucks and pays bills on time.

What bothers me is that the general populace seems to conflate responsibility with banality. The only way to “have fun” or “let loose” is to break a rule or two, or perhaps push the bounds of social conduct. Not only is this incorrect, it reveals a potentially fatal flaw in American perception. Either you slog through the day and hope to make enough cash to be irresponsible on the weekends or you enjoy your work and make no money at all (ex: “the starving artist”). Also, your level of importance in society seems to be dependent upon a complex calculation of race, clothing, money, and twitter activity.

If we must have some method of measuring each other, why can’t it be respect? There are three actions related to this idea of respect that I have been doing in the last two weeks that have improved my life considerably:

(1)    Shake hands

(2)    Look people in the eye

(3)    Listen

The amount I have learned and grown from this simple sequence has provided content at least ten blog posts. Hopefully I have to the time in grad school to write all of it down!

On Road Trips to Graduate School

Author: Brianna

A road trip was the right choice, I think, to take me from Oregon to Boston. Literally cross-country: Pacific to Atlantic, Northwest to Northeast, and all the land in between. It’s 3100 miles as the Google Maps flies, but just shy of 4000 if you take a more Scenic Route. (Which we are.)

Right now I’m watching a mild thunderstorm play out over the hills of a Montana ranch. Two days ago we hiked the Highline Trail at Glacier National Park, which between the alpine meadows and the great sweeping vistas of the glacier-scoured valleys was as awe-inspiring as national parks ought to be. Before that we visited an old friend in Idaho, and before that I dragged my traveling companion to see the Painted Hills and the beautiful Thomas Condon Paleontology Center in the John Day Fossil Beds National Monument.

Sheep Rock
Sheep Rock in John Day
A lake at Glacier National Park

I miss my cats already, and my lab (my colleagues and the lab space, that is; I left a dog in Oregon and miss him too, but he’s only half-Lab). But it’s easier to handle these things when day after day presents me with incredible new places. I’ll let you know if I’m still feeling the awe when we’re driving through hundreds of miles of corn fields…

At five days in, I have some thoughts on road-tripping to grad school, or any place really. Shall I pack it into a convenient listicle? I shall.

Brianna’s Remarkably Useful Thoughts on Taking a Road Trip to Graduate School

1. Pre-trip check your car. Les Schwab will do it for free, if you want. At the very least check your fluids and tires; we had a low tire that turned out to have a nail.

2. Chuck a Camelbak full of water up behind one of the seats. Hooray, water has become easily accessible at a moment’s notice! While it may lead to more pit stops, hydrated people = happy people. Also food. Jerky, string cheese, trail mix, fruit, cold slices of ribeye steak, whatever floats your boat.

3. Audiobooks, podcasts, music. We’ve burned through Anthony Bourdain’s Kitchen Confidential and Neil Gaiman’s The Ocean at the End of the Lane already – both narrated excellently by their authors – and are a few chapters into Ender’s Game. I admit, I am kind of itching to get back on the road so we can keep listening.

4. Baby wipes are insanely useful things. See also: sunglasses, pocket knife, Ziploc bags, duct tape.

5. Do you have ANY idea how much stuff you can fit into a Subaru wagon? We don’t have too many worldly possessions, but we do have more than it seems ought to fit in there. The mind, it boggles.

6. Ship your books media mail. Flat-rate boxes up to 70lbs.

7. Hitting up friends and relatives to stay with on the way is a good thing. Real showers, real beds, real food, real places to do laundry; this balances the camping times. You also get to visit people you care about and maybe don’t see very frequently.

I never thought much about the choice to drive instead of fly. It seemed reasonable: traveling companion wanted his car in Boston, neither of us has all that much stuff to move, August was pretty empty schedule-wise, and there are many cool things to see between the oceans. One of those “obvious” choices that I will later be very grateful for, I suspect–and I can’t tell you the number of people who’ve told me they wish they could take a Big Road Trip like this. I agree that it may not often be a feasible vacation. Road trips can be inconvenient. Expensive. Takes a lot longer to get places because the getting is the point. They require a certain amount of comfort with boredom, or at least long stretches of thinking and staring out the window. I don’t mind those things too much, and the waiting is good for me. While I feel a bit like an excited puppy when I think about starting my program in less than a month, the road trip makes it happen mile by patient mile. The road trip leaves me time to watch thunderstorms roll swiftly in, and darken the sky, and – much later – meander grumbling away.

Thunderstorm coming in over the sunflowers

Coping Mechanisms, #1

Author: Brianna

Do you ever think about just how much information is in your head? Sometimes I do, if I’m feeling a little overwhelmed by all the knowledge I have yet to acquire.

It turns out I know a lot of stuff, and some of it’s even useful!


I’m familiar with which metal pointy bits (studs) to put on the bottom of your horse’s shoes for traction when galloping and jumping cross-country. Road studs, grass tips, small bullets, big bullets, hex roads, semi-square medium spike? Different studs on front shoes and back shoes? Different studs inside and outside on the same shoe?

I know  how many feet are in a mile, and also who the lead singer of The Cars is. (Thanks for always quizzing me on those two things, Dad!)

I have memorized all three poems from Meredith Ann Pierce’s The Darkangel trilogy. I’m not sure why.

I can use Photoshop like…a person who has been messing with Photoshop since she was about 8 years old, which is actually pretty well.

I can still write in the basic Japanese alphabet, understand most things that are said to me, and communicate (with a good accent!) when ordering food or asking directions. Alas, I have always been and continue to be terrible at kanji.

Fact: you can start a fire with ice, if you polish it into a good enough lens.

I can read music in treble clef.

I’m conversant in the theory and practice of clicker training (operant conditioning) animals, especially dogs and horses.

I remember an awful lot of Greek, Egyptian, and Norse mythology.

Also, you know, I’ve got couple bits of information and ideas about evolution and paleontology.


Thus, my coping mechanism/ inspiration for the day: surely if I can fit all that business in my brain, I’ll be able to squish in whatever else needs squishing.