Category Archives: Research

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

tangle

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.

Interesting ways we can talk ourselves into productivity

Author: Brianna

This morning I’m working in pajamas, waiting for the utility company folks to send a person to look at the gas meter or whatever it is that they have to do that requires you to be home for a 4-hour window. The subject of my work is a manuscript that I’m rather fond of, one that I and my coauthors are aiming to get submitted next week.

But you know how the end of writing a paper goes: last 2% of the paper, what feels like 50% of the total work.

 

And yet, yesterday I wound up putting in quite a bit of revision and tidying. All this shortly after I’d pretty much written the afternoon off, because I was sleepy and we had lab meeting focused on a really challenging paper that more or less fried my brain for more complicated thinking. So what got me going?

A little task on my Google Calendar that said “Add references for R packages to PC horses paper.”

Because, hey, adding references for R packages is pretty easy and doesn’t require a lot of effort! And my time-tracking app was showing me that I wasn’t putting on much of a good show yesterday. (This is why I have one: to keep me honest.) So I decided I’d rack up a few more points minutes with an easy task.

Well, you know where the rest of this story goes. I added a short paragraph citing the R packages after tracking them all down and adding them to Zotero. I corrected some numbers on the manuscript that had changed a bit when I fixed a mistake in the code. I wrote a new caption for a figure that had changed considerably and then changed the main paper text to reflect the new figure. I found a couple places to improve our phrasing. Then I wandered over to the Discussion section that needed a little more love and found myself revising, and then adding new text…

All that from a Very Easy Item on a to-do list that I happened to see when I was checking my calendar.

I’m not sure what the unsolicited suggestion is here. Perhaps it is: keep in mind what small fiddly tasks you might be able to do as a way to ease into more challenging tasks on the same project.

Priorities in research doings (or: knitr, mammalogy labs, and motivation)

Author: Brianna

One of the nicest things about graduate school, for me, is the control over my schedule. I had that in undergrad too, but more constraints because of more classes. Also I was still riding horses almost every day, which cut out most evenings. Why is control over my schedule so great? Because I am obnoxious about my work habits and I think I can get better work out of myself when I follow my nose.

I drafted this post a few weeks ago in a fit of inspired work time. (I’m still just as excited about knitr, by the way. And the paper I mention is getting submitted in the next week or two, with full data and the code formatted all pleasantly thanks to knitr.)


You guys know the way I think about work habits all the time: I have detailed writing strategies, I enjoy settling into routines and then semi-frequently breaking them, I spend time thinking about nature of motivation. About the only thing that stays really constant is that I’m a morning person, so I don’t really do work past 7pm except in dire circumstances or…moments of pressing inspiration.

Which is to say: yesterday I was working on R code for a really neat project on horses from the Paisley Caves of Oregon, and as I was working I was pondering its eventual inclusion with the paper itself. So I was trying to be thorough, you know, including code to save the plots and commenting things nicely and such. And then I thought, what the hell, learning to use knitr and rmarkdown to make nice outputs has been on my to-do list for awhile, let’s learn it.

Which is more or less why I wound up working last night until about 8, when the grumbling of my stomach became too much to ignore. (You’ll note that the other half of Fossilosophy would snicker at this, as Kelsey sometimes doesn’t even warm up until around that time in the evening.)

Because I was having fun. So much fun. Do you guys REALIZE how cool knitr is??

Right, about priorities: yesterday I tasked myself with working on writing mammalogy labs. That is also a cool project that gets me really excited about science and teaching, because I get to design an entire semester’s worth of labs. And also I am feeling internal pressure to make forward progress on it because it has slipped down on the priorities list thanks to preparing two posters for SVP.

But I was really excited about knitr!

So you know what? I worked on my code and knitr. Because damned if I’m going to waste the kind of excitement that helps me learn important tools I’ll use in just about every research project ever, while also moving forward the project that is probably closest to submission of all my projects.

This is the glory of having few to no hard deadlines this semester, a luxury that I recognize is rare and thus will milk for all it is worth. I will still write all the mammalogy labs; a day or two will make zero difference. How silly it would have been to let the internal guilt meter decide what to work on when I was truly excited and motivated about something else that also offers me long-term research benefits.


Extra credit links:
A Beginner’s Tutorial for knitr
Knitr with R Markdown
Getting Started with R Markdown, knitr, and Rstudio 0.96
Drifting towards deadwood, or not: learning to use R (interesting thoughts on putting in the time to learn big new skills; same thought process I use to make myself put in the time to learn things like knitr)

Posts I have found useful that are about getting into and going to grad school

Author: Brianna

I had excellent mentoring as an undergraduate. Among the many wonderful things about being in the HopkinsDavis lab was their attention, when the time came, to giving us good and detailed advice throughout the graduate school application/admissions process. Potential labs to apply to, yes you really do need to apply for that NSF GRFP (thanks Sam!), feedback on essay structure, sympathy + a kick of motivation when all the deadlines collided, a sounding board for the Actual Decision About Where To Go For Grad School needed to be made, and more.

Anyway, there’s a new crop of undergrads at the UO pondering grad school, and I promised to write up a collection of blog posts I’d found useful. They’re mostly focused on Biology-type or at least science programs, because that’s what I do. I post the list and my comments here in hopes that it may be useful to other readers too! Feel free to add your own suggestions, particularly more recent posts, in the comments.

Preparation/Misc

Dynamic Ecology (a great blog to read in general!) with some thoughts on what to do before and while applying to graduate school.

Clear and concise advice on the whole thing (with a math/comp sci focus) from Matt Might, including book recommendations, what he looks for in grad students, what to do if you’re rejected, and lots more. Actually, his many posts on grad school/research/academia are well worth taking some time to read as a current or future grad student; you could start with the ‘related posts’ down at the bottom of that one.

Contacting professors

Writing to me” (about graduate school) from Female Science Professor. Discussion of levels of quality, and her likelihood of responding, from form letter to very well-considered.

Advice on choosing and applying, including emphasis on finding a potential advisor, in geology. From Mountain Beltway. (Listen to his advice about file-naming for your CV.)

More specific advice on contacting potential advisors, including some direct examples of emails, from Neurotypical?.

My general advice: be polite (use Dr. or Professor in the salutation, check that you haven’t left any copy/paste errors if you’re reusing parts of an email, don’t go on for paragraphs, show that you’ve done your homework), ask questions, definitely contact current students, try as hard as you can to actually meet professors of interest before applying to work with them, ask friends and colleagues for labs they know of that might be a good fit, and Google is your friend for finding potential labs you might not have otherwise heard of.

Applications

My grad school application essay” from Female Science Professor, including rules on not talking about how you have wanted to do X since you were 5 years old. And a really amusing shot at the Platonic ideal of a bad applications essay.

Things you should do and not do in your personal statement, from Prof-Like Substance.

Excellent advice on asking for letters of recommendation from Arthropod Ecology. (You know it’s a good post if I’m actually linking to a website THAT USES PICTURES OF SPIDERS IN ITS HEADER.)

Another note from me: start early. Submitting things at the last minute = mistakes, and almost certainly means you haven’t had enough people read and give thorough feedback on your application materials. Having good, critical editing is invaluable for the personal statement and research essays. Ask research mentors! Ask current grad students! This can be tough if you’re still taking classes, so plan ahead. (You will probably still end up scrambling at the last minute. If you do, try to take the brunt of the suffering yourself; don’t, for example, ask for a letter of rec with 3 days’ notice.)

Interviews

Good questions to ask current (biomedical) grad students.

It’s not an interview,” pay attention to cost of living, and other advice on grad school interviews from Not the Lab.

If you’re wondering what to wear (which I certainly did), I’d say it’s about comparable to what grad students wear at conferences. Which doesn’t solve the problem if you haven’t been to conferences. Happily advice on conference-wear for my general area of science is much easier to find than on interview-wear. In short, something you’re comfortable in, and that is less casual than jeans but more casual than a suit, is probably fine (though I saw both jeans and suits when I interviewed). Be prepared for weather: cold places are cold, especially during interview season. When I interviewed at Harvard we got ~3ft of snow overnight and it took extra days to get home. Fun! If you want more detailed recommendations than that, here are a few more takes on the idea (mostly aimed at women): How to dress for a conference like a fashionable lady scientist, Women’s attire at AGU (geology meeting!), and a beautifully bitter/rebellious/uplifting “What can I wear to this conference?” poem from the kickass Meaghan at Mary Anning’s Revenge.

Choosing a program

Dr. Isis on two really important features to ponder: funding and placement.

Brief advice on several questions about choosing a program, from advisor choice to geographic preference to teaching opportunities, from Sociobiology.

Note that there are many differing opinions on going for a Masters degree before jumping into a PhD program. For example, this Dynamic Ecology post on choosing a program argues why doing a Masters can be a very good idea (and has other good advice besides). For what it’s worth, both halves of Fossilosophy came out of the same undergrad lab, and one of us is doing a MS first while the other went straight to PhD. We are both happy with our respective choices.

I will note that making the final decision was really tough for me. I think I could have been quite happy and successful in any of the three graduate programs that accepted me; in some ways that made the choice easier because it was probably hard to truly screw it up, but in other ways it made the choice very difficult indeed. Talk to people about it — I had many discussions with my undergrad advisors, my friends and labmates, and my family while mulling the choices over. There are many variables to consider and it’s a deeply personal decision. Don’t forget that, if you have more questions at this stage, you can still be in contact with your potential advisor and/or labmates to ask about more things you want to know.

That seems like a sufficient amount of material for now. Happy reading!

Google Glass and paleontology collections: keeping a level head

Author: Kelsey

Today we continue on our Google Glass adventure! Check in here and here to see what we’re doing and why.

Confession time: At this point in time I know only a rudimentary amount of programming. This only becomes a problem when I get a brilliant idea (my Morse Code App will exist… one day) or Google Glass doesn’t do something I want it to do. Well, short of taking a crash course in shoddy programming, I decided to create a “physical app” to address my predicament.

The quandary: To take a picture with Glass, you say “Ok, Glass, take a picture”. The computer then beeps happily to you as it takes a ‘screen grab’ of your life. Now, our version of glass did not get the update to aim Glass’ camera before a picture is taken (this is a common complaint among those wandering Google Explorers). So, every time I took a picture, I found I that I tilt my head about 30 degrees to the right.

DrawerLean

Either that or we have a serious problem with our drawers

I’m not sure if this is because all the weight of Glass is on the right, or I naturally incline my head about 30 degrees, but I needed a way to keep my head level as I took pictures. When I was a kid, I used to play with my dad’s level, assessing the stability of my Barbie house and bunk bed (yep, I had a bunk bed/fort/space ship… on reflection I’ve significantly downgraded since then). So I decided to create a device to hold a small level in front of my left eye.

After a quick trip to JoAnne’s, I acquired a teeny level my kid-self would be jealous of. I raided the NPL supply closet and came away with tongue depressors, B-52 (an adhesive), and twisty ties. One hour later, it lived!

PatentedDesign1

Behold! Our product shot

Notice how far out the level is compared to the glass. That’s because Glass uses refraction to make the image appear farther away than it actually is. The level uses good old-fashioned corneal focusing. That day I achieved two goals: I provided the entertainment for the day by strutting around and I also managed to take level pictures.

20140815_113107_357

This represents a beautiful moment in my life

In the end, the device is more of a training tool than a permanent addition. Once I had the feel for what “level” was, I was able to remove the device and still take even shots with Glass. Then again, why would I want to take off such a classy addition?

 Level2

NPL: they tolerate me so well

Special thanks to Angie and Cissy for the photoshoot.

Questions? Comments? Leave them below.

Google Glass and paleontology collections: what we learned, Part II

Author: Kelsey

Recap: One of my projects this summer was testing Google Glass for the Nonvertebrate Paleontology Laboratory (NPL) here at the University of Texas Jackson School of Geosciences. We are interested in testing curation potential. After many rather artistic drawer shots and some casual photograph comparisons, I decided to suit up and get systematic. If you’re just joining us, check out Part I here!

Goals: My primary interest is in data preservation, so I’ll be focusing on the object and text resolution, including degree of pixelation, lighting conditions, and glare. I decided to compare Glass against another small, mobile device: the iPhone5.

IMG_2194

Setting: The set of drawers I decided to photograph houses a set of preserved insects (sadly, no DNA here). The external dimensions of the bottom cabinet are 59.5 x 71.2 x 121 cm (w x l x h). The average drawer width and length is 54 x 66 cm. The only light sources are overhead fluorescent bulbs. The temperature was around 85 degrees F (29.5 C) with a humidity around 60%.

GlassComp_iPhone_05

Not shown: cabinet of extra undergrads

 

Parameters: I am testing the “hands off” potential for Glass, so I only used voice commands and the touchpad when I had to. None of the pictures needed to be “shared,” just saved on the device, so no wi-fi or Bluetooth connection was necessary. I wore the glasses lanyard to prevent slippage (discussed in Part I). For comparison, I used the NPL’s iPhone5. Both tests weretimed and any label I removed from a bag to photograph for one trial, I would have to for the others as well. Both the outside (“Out”) and inside (“In”) were photographed.

Scoring System: The recording device with the the greatest object resolution and text resolution would be tallied for each drawer image. If there was no appreciable difference or both could work just as well, both were tallied for that picture.

TestComparison

 

Results:

Time: Glass 15 minutes 32 seconds, iPhone5 21 minutes 15 seconds

Table

Discussion

There you have it! Both the iPhone and Google Glass have good resolution to record object data (i.e. the fossils are recognizable). The iPhone outperforms Google Glass in text resolution, but Glass only takes about 75% of the time. This is only a pilot study with one trial (I know, but n = 1 sounds like a better and better plan as the temperature rises in the cages!), but it is very important in determining our next step. Mainly, we need a higher-resolution camera in Glass. At this point more information is lost to resolution, lighting, and glare than is made up for by the hands-free Glass experience…for now, anyway.

The pace of not only technology innovation, but technology adoption, is increasing. We could fear change and criticize the hiccups, or we can work to understand these emerging technologies and use them in novel ways no one ever thought possible. Personally, I love a bit of constructive criticism (it’s the only way I stopped being the “know-it-all” kid in high school), but too much negativity only highlights technology’s Orwellian uses. We expect Glass and similar devices will catch up with smartphones in no time. At that point we (NPL) plan to acquire a second Glass.

Our future projects include training volunteers, testing the screen projection capabilities, tagging images, linking images, app programming, and virtual field trips. Living on the bleeding edge definitely has its drawbacks, but this summer has been a fascinating experience and I can’t wait to see what is next.

Stay tuned for the next post in this series: how to deal with the dang drawer tilt.

Questions? Comments? Leave them below.

Google Glass and paleontology collections: what we learned, Part I

PFL16A_Glass

Author: Kelsey

Part I in the Google Glass series. Other posts: Part II.

The Lowdown: Google Glass has remarkable potential as a curation and documentation tool, but what it gains in efficiency it loses in picture resolution and lack of updates. Before we acquire our next one, we will wait for a newer version with a better camera, but we are stoked by this new piece of technology.

Background: This summer the Nonvertebrate Paleontology Laboratory (NPL) acquired Google Glass, version 2 of the explorer edition. NPL is part of the University of Texas Jackson School of Geosciences, where I go to grad school and study Australian agamid lizards in all their cranial kinetic glory. Full disclosure: I was working at NPL and had suggested to Ann (Curator and Collections Manager) earlier in the year that we try out this new technology. The idea of augmented reality or forehead cameras is not a new one—sci-fi writers have been heralding their coming for over half-a-century—but here was a chance to test a tangible piece of the future.

We had one “simple” goal at the beginning of our adventure: test the camera and video for curation potential. Ten to twenty thousand fossils are added to NPL every year. Only 1/8th of these are digitally recorded in our database. Inventory is a careful balance of speed and detail. Whole drawer contents and individual specimens are often recorded. Our fleet of staff and volunteers have begun using cameras, ipads, smart phones, and now Google Glass. In science (and, I suspect, academic institutions in general) simple goals often turn into reticulating fractals of fascinating sub-tests, sub-questions, and side studies. Fortunately, that’s why I got into this business.

Requirements: We are interested in devices that reliably and repeatedly capture images with a high enough resolution that all text in the field of view is readable and the fossils are individually recognizable. These photos would then be saved in our database for future research and inventory reviews

Stats: The Google Glass Explorer Edition comes with a 5MP fixed-focus CMOS camera capable of taking 2560 x 1888 resolution images. The fixed focus means the glass is set to capture as great a depth of field as possible and will not adjust, automatically or otherwise. Glass will tune the ISO (shutter and aperture controls) from as low as 60 to a high of at least 960. Videos are shot in 720p only. The aperture size of about f/2.5 with a focal length of 2.7 mm.

Start: I found taking pictures with glass is like switching from a go-cart to a normal car, you have to get used no longer aiming for the middle of the road. When you are wearing glass, the screen is above your right eye (NOT in front of it), and the camera lens is to the right of that, so you will have to aim your head at left side of the drawer while taking the picture. The camera app for our edition does not have an aiming feature, so getting the correct angle and resolution takes practice, patience, and intuition.

Observations: Hands-free is great! When I used the iphone to take pictures (more about that in a part II), I had to constantly put down the phone to move drawers or reposition specimen labels. It was incredibly handy to have both my hands free. Additionally, glass really is comfortable to wear.

OkGlassOk Glass, point the laser at…

However, I found I was never truly hands free. For every single picture you have to backtrack (the “swipe down” action) to the glass home screen (above) and ask it to take a picture. Glass saves all pictures, but immediately prompts you to share an image immediately after you capture it. This could be solved with a simple picture app that bypasses the social media features. Once I get my mad programming skills up to snuff, this is one of the first projects I’d like to tackle.

Pictures: I found the large depth of field meant I often underestimated how much of the drawer was in view, or I’d overcompensate and get WAY too close and personal with the fossils, which just resulted in close up shots of fuzzy fossils. Most of these can be solved with practice and the addition of aiming software.

AimingTroubles

Aiming Troubles

The camera is very sensitive to light levels and has no internal regulatory mechanism. Even a slight adjustment in head angle can make the difference between a dim or overexposed picture. Wearing a baseball hat or wide-brimmed hat does not help, only squishes the glass down to uncomfortable angles.

 TooBrightTooDim

This analysis? Just right.

I also had a problem tilting my head to the right. I suspect most people to not hold their heads perfectly upright, which results in a tilt to the picture. More on how I dealt with this problem in an upcoming blog post, “Keeping Level-Headed.”

Looking down to photographs low drawers caused the glass to slip, so I added a lanyard in the back. This was easy for one side, but the battery on the right necessitated a duct tape solution. The addition does not compromise comfort too much and helps really secure the glass to my head. Fashion may also be compromised to a certain degree.

GlassLanyard2

Google Glass: Nerd Edition

Overheating was also an issue. Our collections spaces (“the cages”) are, for the most part, not climate controlled and summertime Texas heat and humidity are high even early in the morning. However, even in the climate controlled areas, continuous use causes glass to flash a warning message after about 15 to 20 minutes. This is an oft-cited problem in the glass community, and comes as a consequence of clashing optimal operating temperatures.

Is the text readable? Sometimes. The smaller the text and the worse the lighting conditions, the more likely it is to lose data. Also, it’s impossible to check the pictures until they are loaded onto a larger screen. On the other hand, when I had to leave a project half-way through and wanted to pick up where I left off, I could simply review the most recent pictures or videos and quickly start where I left off.

 DocumentComparison

 If I never see this label again…

So, is NPL a victim of the Gartner Cycle  or are we pushing the boundaries of museum science? Once I had a handle on the initial pros and cons (hands free, trouble aiming, trouble with light balance, overheating, and resolution) we decided to conduct a more formal study comparing the iPhone 5 to Google Glass. See “What we learned: Part II” for results and my preliminary conclusions!

Questions? Comments? Leave your reflections below.

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.

Conference Wrapup: SVP 2013, Los Angeles

Authors: Brianna and Kelsey

We’ve just returned from our third time at the Society of Vertebrate Paleontology Annual Meeting, and our first as graduate students. What a wonderful, exhausting, exciting experience! SVP is always a great meeting, and it gets more fun every year. The first year or two were much more stressful because we didn’t know many people (more thoughts on conference-going as an undergrad in a future post), so it was nice to relax a little more. This was also the first time we really looked forward to reconnecting with our undergrad friends and mentors, the UO Paleontology crew. It was a bit like an early, very scientific Thanksgiving.

Instead of trying to sum up the whole conference, we’re planning to share a few highlights: our favorite talks and posters, how our presentations went, things we really enjoyed about this year’s venue, and a few bits we think could be improved in the future.

Favorite talks
Brianna: It’s tough to choose. One that really impressed me was Paul Koch’s investigation of network structure in Pleistocene megafaunal extinctions. He argued that extinctions have two main components- external factors, which trigger extinction, and internal factors, which are system properties that allow the effects of those triggers to operate. This second component is often overlooked, so he (and coauthors Pires and Guimaraes) set about investigating whether Pleistocene assemblages were in some intrinsic way more likely to collapse. They compared megafaunas from modern Africa and Pleistocene North and South America, looking at networks of relationships between animals. They modeled the probability of two animals interacting as a function of predator-prey body mass ratios. Essentially, the model specified that every time a large predator runs into a prey animal, it’s going to be bad for the prey; every time an animal runs into a conspecific, it’s going to be bad (because intraspecific competition); every time a smaller predator runs into a prey animal larger than itself, nothing happens, and so on.

They then examined the stability of these community matrices and found that modern Africa is no less susceptible to perturbation than the fossil assemblages. However, they did find that the probability of stability decreased with predator richness and increased with the average body mass of the prey. Koch suggested that large predators have a wide diet breadth, increasing connectivity in the web, whereas large prey are more controlled by bottom-up effects (temperature, food availability, etc) and thus decrease connectivity. In a tightly connected web with strong interactions, effects propagate faster, like motion that comes from hitting a tightly stretched sheet of fabric as opposed to a loosely draped one. Pleistocene North America had many large predators (sabertooth cats, cave lions, dire wolves, regular wolves, bears of several sorts…), so perhaps this contributed to the demise of our megafauna. A complex talk with much more nuance in methods and conclusions than I’ve described here, but very cool.

Other talks I really enjoyed: Tseng on skull morphology convergence both within and between bone-crackers and bamboo-eaters, Miller’s investigation of how well a death assemblage captures community ecology of the living assemblage, and Holroyd’s eye-opening talk on identification bias in collections, where she pointed out that specimens can only get studied and published if they are identified. She also quantified the probability of “losing” a specimen via lack of identification.

Kelsey: There were too many mind-expanding talks to cover here, but some of the ones that bent my world a bit (in a good way) were the ones that looked at the historical and identification biases of data sets. Pat Holroyd’s talk was nicely complimented by Matt Mihlbachler’s look at Cope’s rule as a product of historical collection bias. Specifically, brontotheres initially appeared to consistently increase in size throughout the Cenozoic. Matt pointed out that this conclusion was reasonable during Cope’s era, because this is what the available data were saying. However, greater sampling has shown there are multiple lineages that dwarf or just never increase in size over time. Compound this with the multiple migration events between the Americas and Eurasia and you’re looking at a much more complicated, nuanced relationship between the evolution of body size in lineages and time.

This is the vibe I got from many of the phylogenetic and systematic talks as well. It’s as if we are realizing that many of the “ground rules” of paleontology are not as solid as we thought. Now we are looking through the cracks and finding some very interesting mysteries. Perhaps it has always been this way and it’s my own assumptions that are beginning to crack.

Favorite posters
Brianna: I think my favorite was Poster #1 on the very first day, by Sadleir and colleagues. It was a reconstruction of body mass and related characteristics in an ornithischian dinosaur where the analysis drew on information from a gastrolith that stayed with the fossil through preservation. From a new CT-scanning algorithm originally designed for distinguishing metal-metal surfaces (led to much clearer imaging of the rock-rock bits, as fossils are!) to an interesting argument for massive tail muscles in this particular dino (perhaps needed to counterbalance gastrolith position, and supported by tail vertebral morphology). Had a great discussion with the author and am really interested to see where that project goes.

I also had a great time getting the poster-talks from current undergrad students in the UO Paleontology group. They were just revving their research engines as Kelsey and I left, and it reminds me of the fun and anxious times we had at our first conference. Plus, they are doing really cool work and I enjoyed hearing detail about their projects for the first time. Warm fuzzies all around.

Kelsey: I’m a sucker for bone histology, so I found myself discussing bone growth and function a great deal. This is a nice connection for me to the dinosaur world. There is an unfortunate schism between the “Mammal People” and “Dino People” (with neoaves falling somewhere in the middle and fish people partying on the side), and it’s easy to stay with your own crew. Hopefully I can find more connections in the future.

I also enjoyed the less-finished project posters, where I could really talk to the presenters about the structure of their future projects and why the label on the y-axis of their graph was missing. We’ve all been there…

Our presentations
Brianna: I gave a talk titled, “Identifying isolated postcrania using discriminant analysis.” In plainer language, that’s: “How to use some pretty simple data analysis to figure out what kind of horse/camel/whatever those ankle/toe/hand/foot bones belong to.” You know, the ones that are sitting all unloved in drawers in your museum. This was my first big conference talk, so while I usually do well with public speaking, I was a bit of an adrenaline-rushed mess for the two hours before I spoke. Happily, my nerves settled as soon as I started presenting and the whole thing went very well. My time slot was in the morning session on the first day of the conference and it was great to get the stress out of the way. I got some excellent feedback and ideas after the talk, including some fun new collaborations.

I’m really fond of this work. One bit of it will come out soon as a paper in Palaeo Electronica with my former advisor Edward Davis; I’m currently writing the second paper, which deals more specifically with the stuff I talked about at SVP. Both will get the blog post treatment when finished, but if you’re interested, shoot me an email (bmchorse at fas dot harvard dot edu) and I will happily explain how you, too, can get IDs on your postcranial fossils.

Kelsey: This was year #2 for presenting a poster on osteopathology in Rhinocerotidae, and never have I been more grateful to present an updated study. I’ve been looking at population-level osteopathology in rhinos from 50 mya to the present, a project that has motivated me to learn the intricacies of pathology, bone growth, large mammal evolution, and systematics. Being able to display my constellation of data and questions led to at least six firework moments (what some would call eureka moments) during my two hour poster session. This year I also kept a notepad and pen nearby so I could write every suggestion down. Paper, here I come!

Good things about the meeting!
The welcome reception at the Natural History Museum of Los Angeles County was really, really lovely. Everyone got to wander around the exhibits before eating some impressively tasty food. The dueling T. rex and Triceratops in the main atrium are beautiful, the brand new Dinosaur Hall is spectacular, and Brianna particularly enjoyed some very skeptical looking mammals:

Skeptical zebra and tiger at the NHM Los Angeles
Skeptical striped mammals are not impressed.

What else did the Society do well this year?

They added a family room for the first time, which is an important step in making the meeting more friendly to those of its members traveling with children.

The awards ceremony was quite enjoyable as well, particularly because it came complete with a tour through several films portraying paleontologists (including The Ghost of Slumber Mountain, The Lost World, Creature from the Black Lagoon, Bringing Up Baby, Lost Horizon, Lake Placid, and, of course, Jurassic Park ).  The food was also wonderful, though the vegetarian option ordered by our labmate was literally just white rice with steamed vegetables. That needs some definite work, though props for the gluten-free option, which Kelsey reports was delicious.

The costume contest at the student round table was also amazing (did you all get to see the two-man Quetzalcoatlus costume?) and we almost wish it could happen every year.

Finally, the coffee quality and tea selection in the mornings leveled-up from last year. These are important details for scientists with varying severity of jet lag and sleep deprivation.

Things the meeting could improve…
Speaking of all those things the meeting did nicely, we have suggestions for even more improvement on a few of them. We’ll do this in a nice numbered list.

  1. Offer childcare. Yes, it’s probably a pain to deal with; yes, liability and stuff; we get it. But not having available childcare (it doesn’t even have to be free!) can be a problem for many would-be participants. This is not something we have personal experience with, because neither of us has reproduced, but you can read more about it in many other places. Plenty of other conferences do it (e.g., Society for Molecular Biology and Evolution, American Political Science Association , American Geophysical Union, Geological Society of America, Society for Integrative and Comparative Biology…), and SVP should too.
  2. Free wifi for conference attendees. People have been begging SVP for this for years, and still nothing! Heard much unhappiness about this, verbally and online, during the conference this year.  We’re pretty sure that offering free wifi would drastically increase the number of people live-blogging and live-tweeting the conference, thus increasing visibility for the Society itself. 3G was only an option for a few people who are from the US, have smartphones, and weren’t worried about a data cap; it’s not good enough. This post has many curated links about live-tweeting and conferences, if you’re interested.
  3. Can you keep the coffee out all morning, please? Remember what we said earlier about sleepy scientists? You already bring it out at 7:30am and again at 10am – just leave it out til lunchtime. Or better yet, leave it out until the poster session starts at 4:15. It’s one of those keep everyone happy, keep everyone awake things. We are such sad pandas when we straggle down at 8:30 and the coffee/tea has been whisked away.

    Might as well have two cups, it's disappearing soon...from flickr user chichacha

  4. Give some serious consideration to venue with respect to pricing. We acknowledge there are probably many, many interests to balance when selecting a conference hotel, but please add this one. SVP 2013 was in the middle of the financial district in Los Angeles, meaning a very expensive hotel and limited (+ expensive) dining nearby. This is hard on students! And postdocs! And anyone without a lot of extra cash!
    Consider, for example, booking two smaller hotels together next time (maybe even with some cheaper hotels available nearby – the Raleigh meeting last year had lots of nearby, inexpensive choices). This would let you put it in a friendlier place, with affordable options for everyone. You can still have all the sessions in one hotel; it’s not like walking across the street is that much different than trying to navigate the Halo-level-like maze of the Westin Bonaventure in LA.
  5. On the expensive note: you know you’ll make more money at the bar in poster sessions and whatnot if we don’t have to pay an arm and a leg for the alcohol, right? We don’t know if the pricing was SVP or the hotel, but man, it was bad enough we didn’t even want to bully our coauthors into buying us a drink.

Criticisms aside (which we hope are constructive – and yes, we’ll be sending an email to relevant committees, as soon as we figure out who they are), this was a well-run conference that we enjoyed. As we said, SVP is an excellent time every year and it’s well worth going.

We really enjoyed live-tweeting some talks and posters this year, thanks to our phones. There weren’t many people doing so – again, see wifi situation – so we got to feel useful! Getting to experience little bites via tweet of talks we weren’t attending was really nice, so we hope we were able to provide a similar function to others for the sessions we attended. It’s a bit difficult sometimes because in the really interesting and complex ones, you want to take notes, but you can’t take notes if you’re tweeting. We tried to strike a balance. Meeting a bunch of people at the tweetup was great, too.

In all it was a most excellent conference (not least because the two halves of fossilosophy were reunited for five days!), and we are looking forward to the next one. We’ll both be at SICB in January, Kelsey will be at NAPC in Febuary, and we are definitely looking forward to SVP 2014 in Berlin, Germany!

Thoughts on the stretch point

Author: Brianna

I recently returned from a week-long bioinformatics training workshop put on by the wonderful people at VertNet. Soon I will write directly about what I learned there (plenty of useful, thought-provoking, and just plain awesome stuff) but first I want to consider something else. Between sleep and tea sipping on the flight back, I found myself reflecting on the particular mental state I drop into when I am trying very, very hard to learn something new and difficult. I think of it as the stretch point.

https://i0.wp.com/www.small-scale.net/yearofmud/wp-content/uploads//2012/12/hobbithouse01.jpg
Hobbit comfort zone

What is the stretch point? It’s a particular mental space beyond your comfort zone, and it’s not exactly fun. In fact, it’s kind of painful and frustrating. If someone else’s knowledge is a creek flowing by, I feel like I’m trying to carry it in my cupped hands to the little bucket of my brain twenty feet away: I get there, slowly, but no matter how tightly I hold or how quickly I move, much of it still runs through my fingers. Still, this repetitious suffering is oddly satisfying, a mental workout that is close cousin to lifting really heavy weights.

I’ve found ways to push through this stage faster (and more thoroughly and mindfully). Efficiency hinges on finding people who don’t mind question after persistent question and requests to wait, stop, say that last thing again. The questions serve to check my understanding: so if A is true, then is B also true? What about A under these different circumstances? How exactly do you test that? How does that relate to this other thing? I’m trying to extrapolate, to find ways to break the system in my mind so I find holes in my mental concept.

You see the need for a patient teacher.

It’s the immediate feedback, I think, that connects neurons faster than just staring at the information alone. When you’re getting more of it right and making more of the connections, you know because the other people tell you. When you run up against a mistake in your understanding, you know because they tell you. When neither of you knows the answer, you know, because you wind up staring blankly at each other.

The VertNet workshop provides a good example. I spent a great deal of time at the stretch point that week – part of why I was so wiped out when I finished! New concepts abounded, from playing with GIS programs for the first time to chewing over new four-dimensional research problems1. Luckily, feedback was also plentiful. Much of our material was cleverly organized into tutorials, so we followed along and were allowed to blunder off the path (they warned us so many times to make sure our clipped layers were the same extent for niche modeling…!), and then we were dragged gently back onto it when we discovered that our next step wouldn’t work. Sometimes that meant solving the mistake ourselves, with judicious use of swearing at the computer screen. Sometimes that meant calling in the workshop leaders for targeted troubleshooting.

Your head asplode!
Artist’s reconstruction of the learning process

I find myself spending time at the stretch point whenever I begin a new project or attempt a new skill. Maybe this is an extension of my career stage: every research project I start is new in a way that underscores just how little time I have under my belt working in this field. I have to find the most relevant literature, understand the open questions, figure out new methods or how to apply familiar methods to new data. I have to figure out where the project is going, and what questions we’re answering, and why those questions matter, and how to answer them using best practices.

Spending all my time in this place would become exhausting too quickly – there’s only so much information you can shove into your brain before your brain is done. I do think the limits of my capacity have been slowly growing, though. It’s nice to balance the stretch point with calmer times: writing, for example, or reading, or kicking around ideas with colleagues.  But sometimes it is important to seek out the stretch point. It’s a useful and interesting place to be in when the mind is ready and I seek it out when I am in knowledge-gaining mode. I kind of enjoy the familiar pain of stretching my mind, the same way I complain on my way to the gym but pick up the heavy weights anyway.

This is how we get better – by pushing. Muscle soreness, after all, is just the collection of microtraumas that will ultimately make you stronger.

Brianna conquering the wood pile
Artist’s reconstruction of Brianna actually conquering something (photo & magical fairy wand credit: Kelsey)

1 That is, considering both space (3 dimensions) and time (the 4th).