Even in Kyoto

Several years ago in a conversation with someone who has a corporate engineering job, this person turned to me and asked, "So with that kind of work schedule, do you get to sit at home in your jammies while you grade papers?", implying the tiresome questioning about whether academic work constitutes "real" work.

I think about that, and about people wishing "a nice break" while I spend every available hour on a Sunday grading student final papers. This week our college's campus is closed, but I am here because I need to:

-Finish an overdue MS review
-Write a grant report
-Convert my CV to a PDR
-Read and give feedback on a coauthored manuscript
-Help my research students finalize poster presentations for an early-January conference

And that says nothing of my need to gear up for teaching Animal Physiology this spring.

Some break!

Not that any of this is new. Just that the assumptions about academic work can start to grate on a person, after a while.

I'm reminded of a tweet-machine thread from 1-2 weeks ago, too. Someone was so bold as to suggest that people who write for a profession should be turning out ____ number of words every day. Some of the replies were heartening.

This window between the fall and spring semesters is also so narrow that I am not happy about how much of it I am going to wind up spending on airplanes and in airports.

I woke up this morning at around 4:30, most likely due to a combination of the cat randomly meowing (just 1 meow / hour at ~ 4:30, 5:30, 6:30) and the overwhelming to-do list. The overwhelming to-do list is tipping me over the peak of the stress-performance curve and into Anxiety Land.

But I managed to get most of the critical things done today. Just in time for bed. Nothing like a nice, relaxing weekend of grading papers and exams, and writing lectures and quizzes.

My General Biology students didn't do as well on their third exam as I would have liked. Hard to see that and not know what we can all do to improve their progress. (no, the answer isn't to "dumb down" the material, or to offer extra credit!!)

I haven't yet touched the full paper drafts from my Scientific Writing students. I have 20 of them to grade before Monday, December 2. My experiences grading the students' Results sections suggest that I'd better spread out the grading across as many days as possible if I hope to retain any sanity at all. Students turned in their drafts on Friday, so now two whole days have passed and I haven't yet graded a single full draft. Yikes.

As mentioned in my previous post, I spent a lot of time over the past week with I, a new graduate student. Interacting with her is reminding me of a number of little things that I have learned over my time as a scientist. A lot of those little things are obvious, in retrospect, but I always have to wonder if I would have spent less time flailing around if I'd known about or thought about many of them earlier in my career. A few examples:

1. Enter in your data as you collect it. (this is what I'm working on today, which is what made me think about this entry)

2. Along those same lines: Clean up as you go along.

3. While writing manuscripts, keep a text file with a "to do next" list. Actually, this should be started even before you start writing a manuscript. For me, it has been the simplest way to put down a project and then be able to pick it back up with minimal fuss.

4. When meeting with other people, put as much as you can into writing, but keep it simple. To have a focused meeting, have a goal for the meeting and put that at the top. Do you want feedback on a specific piece of writing? Do you want help with the experimental design? Do you want help figuring out the holes in your logic? Are you trying to figure out who to put on your committee or who to include in the project? The sooner you can get concrete specifics in writing, the easier it will be for others to help you make progress.

5. Have a plan for analyzing your data *before* you collect the data. You might change your mind later on, but this will save you many potential massive headaches. This means having a thorough outline of your experiment and its dependent variables. Is it frequency data? Continuous data? How many treatments are you comparing? How many figures in a paper will this translate into?

6. Consider keeping annotated bibliographies for projects. I don't know about you, but my brain and memory are small, and the amount of literature I need to be familiar with is large, and covers a wide range of themes. Annotated bibliographies are a shortcut for organizing your thoughts about the literature, and for staying on task with #3. I just keep mine in text files. No need to get fancy.

7. There are a lot of other useful sources of information that might be helpful. Don't skip over them. Read them in the evening before bed. This book comes highly recommended (although I haven't read it, I suspect if I read it I would do a lot of nodding). For academic writers in all walks of writing, I've found How to Write a Lot helpful, too.

8. For keeping the different parts of a research project organized, here's an idea of how I structure my files. I'll come up with a short name for the project and will make a directory (folder) for it. Within the directory, I'll have subdirectories for: datasheets, raw data (as it is entered in to the spreadsheet), figures, R scripts, and the manuscript. I'm not good at throwing things away, so whenever I generate new files, I make a directory within a folder, label it "Old," and stick the previous version in there.

9. I like Zotero as an open-source browser plugin for keeping track of references. I still download pdfs of references into a big (separate) folder, and label them with the authornames, year, and a few keywords. Note that this is completely separate from my annotated bibliographies.

I suspect I'll think of ten more pointers somewhere further down the line, but this should be a good starting list.

What work-organization insights have you wished you'd had at an earlier stage?

A conversation with bluepapercup is deserving of a wider conversation. She was hoping to finish her master's degree this spring, but recently had to decide to postpone her defense until the fall. So much of the process has been out of her control, such that it's inspiring to see her determination to finish.

In the midst of it, I'm thinking about some of the things I wish I'd known more about back in the day when I started graduate school. I also wonder how many people actually finish their academic work "on time." My guess is, not many, and those who do often miss out on other important life experiences. What does it mean to be "on time," anyway, when it comes to high-quality scholarly contributions?

A lot of people apply to graduate programs and then start them without asking certain critical questions of the program:

1. What's the average time-to-graduation for participants? Departments generally won't share this information with you unless you pry it out of them, because the numbers usually aren't as zippy as they'd like. I talked to a Biology faculty member about this at some point in the midst of earning my degree - she said the TRUE national average for time-to-completion for biology Ph.D.s was 8 years. This pegs it closer to 7 years, but still. It still makes me scratch my head over the overly optimistic paperwork I received upon arriving in grad school, which had me scheduled to graduate in 5 years. If only they had told the ants about that.

2. Related - what's the attrition rate for the program, and why? Specifically, is it because they don't give anybody any money, or enough money?

3. What careers do people from the program pursue after they graduate?

What questions would you add to the list?

That whole bicycle expedition down to Tucson and back went pretty well overall, I must say. I was especially grateful for the fine company of DM and CG on the ride back to Phoenix - we were able to maintain a comfortable pace, neither too fast nor too slow, and enjoyed the scenery. The ride out was a little too jock-ish for my tastes, I've decided - the riders who ended up riding with me were kind of concerned about how slow they were going or how out of shape or how manly they were, and the pace was just a touch too fast to be comfortable to maintain. Interestingly, I don't think the return pace was significantly slower, overall. It was just less...combative, one could say. No one was trying to win anything or prove any point. DM, CG, and I all decided that the person in the lead would be decided by how we individually felt about being in front or being behind, without too many regimented expectations about drafting or pacelining. So rather than having the person in the lead "pull" the paceline for, say, 30 seconds, before cycling to the back, the person in the lead would fly along, enjoying the fresh, cool air and sunshine and scenery, while the people behind relaxed a bit. It probably helped that the return ride was more-or-less downhill, with a bit of tailwind as well.

Regardless, it was a good ride, overall. I am most pleased by the fact that my butt isn't extraordinarily sore, or chafed, or covered with saddle sores. I'm also pleased by the fact that I feel tired, but not exhausted, and I feel like my body is resting and recovering well. I have some numbness in the ring and pinky fingers in my right hand, from handlebar palsy, but that should clear up as long as I don't aggravate it too much. So altogether, I feel like I'll be in reasonably good shape for the 300-km ride in 2 weeks.

Other than that, let me just say, boy. Mondays are going to be busy, here. It took DP and myself a solid five hours to get things done for the Final Experiment. Basically, on Fridays, we prep for Mondays by mixing up four different batches of polenta (nothing like cooking almost-food in a beaker on a hot plate), and then we spread them into pans to dry over the weekend. On Mondays, we remove last week's feeding trays from the colonies and weigh the leftovers ("Is Mildred eating right this week?"). We also count all of the ants, and take photographs of their fungus gardens.

Then we grind up the dried-out polenta into a coarse powder, weigh it out, and give it to the colonies. The bottom line is that there's a lot of weighing of finicky materials. Last week, I tried using a coffee grinder (blade grinder) to grind up the polenta, with pretty poor results. By the end, the grinder's whack-blade was crumpled like an airplane propeller that lost a battle with a goose. So I ordered a corn grinder, which came in over the weekend, and used it yesterday. The difference was night-and-day, thank goodness.

I also had to submit another postdoc application yesterday. I'll be curious to see what my final tally is, for number of applications submitted. There are all kinds of alternate scenarios for how things could go this spring and summer. The only thing I'm at all certain about is that I will probably end up moving out of the Farmer House in May when our lease is up. That will be a good time to get my belongings all in order for whatever adventure happens next. The ideal, for me, would be to take some time over the summer to reward myself for finishing my dissertation (assuming that I complete it). But if my livelihood continues to depend on the biology of the ants, I may be out of luck. All I can do is wait and see.

Today was a busy day. Mostly busy for my brain. After breakfast this morning, I went out into the backyard to hang up some laundry and water the plants. The fig tree was not looking too good (not sure if it was the cold, or seasonal changes, or what), so I went back to water it. While I was there, I decided to jump on the old stick pile, which by now, is absolutely covered in grass. I hope that means that it is actually breaking down. I can't remember how old it is by this point, but it has been there for at least a year.

Anyway, while I was jumping on it, I glanced over and noticed a cozy little hole. SOMEBODY (or some chicken) had created a nice little nest, outside of the coop and outside of our purview. There were TEN eggs in it! She (or they) had been busy doing this, for quite a while. So I sent the chickens back into their coop for the day. This afternoon, I could hear them making that sad, chicken-moaning sound a bit. Silly birds.

Other than that, I've continued to work on Diss Chap 1. By last night, I got to feeling like I had a good idea of how I needed to outline the discussion. Today, after reading somewhere between 12 and 20 million and four additional papers, I was finally able to sit down and bang it out. Boy did that take a lot of mental effort. I think I'm starting to do a good job of situating my research within the body of related research, though, which is a really, really good stage to reach. I first had to remind myself that in dissertation-writing, I'm becoming an expert in a subject matter where no one else is an expert, so I can't depend on anybody else to provide the appropriate context for my work. I have to do that work, myself. It's a good, useful mental exercise, but it's also exhausting. I also just remembered something from completing my comps - I felt like I went in circles quite a lot with coming up with my research proposal, up until I had a solid first draft of the proposal written. THEN there was something for me to talk about with my advisor and committee members. I suspect the dissertation chapters will be similar. Fortunately, for the remaining dissertation chapters, I already have a solid idea of where my starting point is. That wasn't as true for the first chapter, but it's more true now.

So, now it's time to balance out the mental effort with some physical effort, aka the Holiday Challenge. Off to the erg I go.

Sometimes, this whole dissertation-writing thing makes me a stressbucket, as S has witnessed perhaps all too often recently. It requires tuning out distractions, focusing, and thinking. Yesterday wasn't a good day for it, although the day wasn't a complete wash. At this very moment, it consists of five major activities:

1. Trying to wrap up the Manuscript of Doom II: The Sequel. I meet with my advisor once a week to work on it. From those meetings, we generate about 6 hours of independent work for me. I think it's turning into the project I work on on weekends. All that I really care about is being able to work on it and then set it aside so I can work on more important things.

2. Working on writing up my first chapter. Most of the other work is done; the data were collected five years ago, a mathematician has helped to construct a model of the system, and the data are mostly analyzed. That last item was a bear to figure out, as I had to teach myself to use R before I could analyze the data, and even after I attempted multiple statistical approaches I still wasn't sure if they were correct. Fortunately, an incredibly helpful faculty member took a look and offered a useful suggestion. Unfortunately, his suggestion could only go so far in resolving the issue. The writing is the hardest part, though, because the subject and approach are quite novel, and I can't always see the logic that I need to clearly lay out on my own, without any help. If it were derivative work, it would be simpler, of course, but less interesting and rewarding in the long run. At least, that's what I'm trying to tell myself. I've rewritten the first paragraph about 6 times already. On Tuesday, after taking a nap, I was finally able to get it to a point where I wasn't absolutely and completely embarrassed to show it to my advisor. Only a little embarrassed. We meet to go over it on Thursdays. After today's meeting, I have a fresh set of concrete changes to make. I think I can make it. It will work out in the end. She thinks the study system and approach are novel enough to make a sizeable impact in the field. It's just a matter of constructing the writing to convince reviewers that we're correct about that. From there, perhaps it will influence the way other people think about the world around them. We hope. After all, that should be the goal of important theoretical scientific work.

3. Working on writing up my second chapter. For a little while, there, I thought it would be part of the first chapter. It's becoming clear that it will be a distinct entity, directed towards a completely different field than the first chapter. This one is a fun project, at the moment, mostly because I'm in the midst of some relatively straightforward data analysis. Plus, it has provided me with an excuse to wrap up some data collection from three summers ago that I've wanted to work on for ages, but haven't had the time to work on. Too many other obligations were getting in the way. Yesterday's efforts were kind of hilarious. I reached a point where I discovered that I needed to collect some additional data that would allow me to calculate an ant's dried weight from her fresh (wet) weight. So I went from sitting in front of the computer to collecting up and weighing 250 ants (50 each from five colonies). And that's where the rest of that afternoon went. Unlike Chapter 1, the writing for Chapter 2 is kind of effortless at the moment. I sat down at the computer this morning and wrote two pages and constructed a diagram to go with the pages. I hope we can find a good target journal for this chapter. I'm excited to develop it to the point where I can discuss it with a couple of my committee members, as I think they'll be interested in it and excited about it, too.

4. Getting things finalized for my last experiment. I think, at the moment, I'm mostly just waiting for ants to hatch for this one. I also have to do a couple of hours worth of calculations, to figure out exact dosages of carbon, nitrogen, and phosphorus to add to supplement the polenta I'll give to the colonies. But that's not really a big deal, just hours of work to complete. Data collection is really the easiest stage of experimental work.

5. Working on figuring out what I'll do next year. I spoke to my brother about this, briefly, on the phone yesterday. "Oh yes," he said, "That's the phase where you basically run around doing little courtship dances to different professors until you find one that will accept you." Exactly, C, exactly. Such an ornithologically-oriented behavioral biologist, that one. I've seen his courtship dances - he did one at his wedding, in fact. But it worked for him, so I should take at least some comfort from that.

And there's one project on hold at the moment - analyzing the data from the experiment I conducted last summer. Again, it's one I'm looking forward to working on, because it should be relatively straightforward. Relatively. I bring it up because once I get underway with it, I know I'm well on my way to completing my dissertation.

My biggest comforts, in all of this, are knowing that my advisor will work with me to bring this work to life in the best way possible, and knowing that if I get this all done, it will be a pretty kick-ass dissertation. A career-starter. If I get it all done. Nose to the grindstone.

This is going to be a crazy summer.

Well, it basically already is summer, and basically, a month of it has passed already.

That's just about what I mean.

Insofar as school goes, I'm still scrambling to finalize the protocol for my final experiment. Ideally, I'd like to finish some old data analyses so I have a better idea about some of the measurements I'll make for my final experiment. It's generally a terrible idea to go into an experiment completely blind, that is, having no idea of how the experiment will turn out.

That leads into the next chain of events. The software package that worked so nicely for some initial data analyses is not set up well to let me do just exactly the procedures I want to do. So I decided it would be a good time to switch software packages and work with the open-source software package R (yes, the software package of pirates!). The new software package is command-line driven, which is to say it sits and waits with a little prompt while the user tries to figure out how to talk to it without making it angry. Not nearly as simple as figuring out how to navigate through an unfamiliar, (inevitably) clunky GUI.

I started out by trying to decipher the somewhat cryptic standard introductory manual. It's reasonably well-written, but does not exactly explain how to use R for particular statistical purposes. So then I ordered a book on just that, how to use R for statistical analyses. It's much, much more straightforward and organized according to the things I want to do. But it still takes a lot of effort to read it and retain what I'm learning from it. I have finally resorted to note-taking and feel like I'm almost ready to start using R now.

Once I've learned how this dragon works, I'll harness it to finish up those analyses, plus another set of analyses. Meanwhile, I'll keep working on other aspects of summer experiments.

My summer employment situation has also finally been resolved, or so I hope. At first, I was assigned to TA introductory Plant Biology for non-majors, which sounded reasonably interesting. Not interesting enough to the undergraduate population, unfortunately; it was canceled due to low enrollment. I only found out at the last possible minute.

When I got up this morning and checked my e-mail, the department had come up with a scheme to pay me an hourly wage for the equivalent amount of work but for half the amount of money. Less than ideal. Later in the day, the department developed another scheme to transfer me into being a lecture TA for general Genetics. So that's what I'll be doing for two hours a day throughout June. It could be worse; I could stand to spend some time reviewing genetics concepts, and hey, I'll be earning enough of an income that I won't need to look for a second job.

For now, back to reading about R. ARRRRRRRRRRRRRRR.

I spent an hour yesterday afternoon talking to a professor about the nitty-gritty of postdoctoral research. Somehow, I hadn't realized he'd been to so many different places. I'm reaching the point in my graduate career where I need to go past the stage of contemplating postdoctoral research and into the stage of assessing my options and lining up opportunities. This stage of one's academic career involves a lot of planning; I have to identify who I would want to work with, what projects I'd want to work on, what skills I want to acquire, and how I'll get money to do what I want to do. In the grand scheme of things, this is a tooling-up stage, where I'll be filling out my skills and qualifications in preparation for applying for faculty jobs. That's a completely different ball of wax. Plus, there's the component of how all of that affects my personal life, and how it meshes with my life's philosophies. Somehow, in the last month or two, I've started coming to terms with the fact that I'll eventually be leaving Arizona behind.

So that's one set of plans. There are also plans for wrapping up my dissertation research. I have one more major experiment to complete this summer. I just got my teaching assignment for the summer as well. I won't be teaching a class that I've taught before; I'll be teaching introductory Plant Biology. That could be cool, but it could also be a tremendous amount of work. Probably both.

Along with the research, I need to get geared up to write my entire dissertation. I'm partway finished with the data analysis for my first chapter, and will start working on my second chapter towards the end of the summer. Hopefully I'll be able to get underway with my third chapter next spring.

I'll also be traveling; I'll be heading to Copenhagen and surroundings for a conference in August, and to California for my brother's wedding in July. I think I'm going to declare that that will be it for summer travel, other than Arizona-based trips and probably a trip to Colorado for some friends' wedding. I just cannot afford more travel than that.

And so, it is time to buckle down and get to work.

I am doing a lot of mulling things over at the moment, but am not ready to share any half-formed thoughts with the world just now. That's my excuse for not having a whole lot to say. But yesterday's list was useful enough that I'm inspired to write a new one for today (and to tell you what got done off of the old list). So, to did:

-Mail a package to trifold_flame
-Plant some eggplant seeds
-Prepare the side yard to plant some corn - Well, I got started on this by clearing out some of the greens growing in the spot and feeding them to the chickens. So I still need to do some more soil prep - pulling out the grass, and importing some of the delicious manure from the backyard. Hmm, a job for the yard trike!
-Make tostadas and they were delicious.
-Cook up some tepary beans and they went on the tostadas.
-Go on the Car Resistance Action Party Ride
-Spend time with scrottie I will miss him while he's traveling.
Muck out the chicken coop
Empty the litterbox - Okay, technically S did this, but it was on my list.

Plus:

-E-mail someone about some data analysis associated with my first dissertation chapter and I even heard back from her!
-Do some statistics for the Manuscript of Doom II: The Sequel and look up authorship info - hmm, nnot yet.
-Get my presentation materials together for the Social Insect EXPO! on Saturday, Feb 20 at the Desert Botanical Gardens - hmm, not yet
-Go through my To-Do punchlist for the conference we're hosting from Feb 18-20 (hmm, write poster, get catering stuff together, etc etc) - also hmmmmmmmm...this is looking like a bad trend
-Get an undergrad set up for our spring research project - phew, at least this got underway! Plus, DM is helping with the project, and she has already made a cool discovery.
-Tend to my teaching responsibilities (aka grade papers and prepare for next week) - I sort of got started on this...sort of...
-Finish up some writing responsibilities for the Phoenix Bike Guide - the plan for tonight!

So, how about an updated To Do list. The exclamation points make everything more exciting, and theoretically make me more likely to get things done.

-Data analysis for Diss Chap 1! (from now on, I'm going to call my dissertation The Neverending Story)
-Data analysis for MODII:TS!
-EXPO! Prep!
-Get lab geared up for Science with R!
-Read some book chapters!
-Punchlist review!
-Grade papers! Re-write assignments!
-Phoenix Bike Guide!