Reflection

Today, a bit of a story ...

Kinsman Pond from ledges of North Kinsman

I stood near the edge of the clearing with the two scientists, straining my ears to hear the call of a Bicknell’s Thrush. They played the recording, and we listened. As I recall, it was a relatively cool summer evening, though it was often cool in the evening at Kinsman Pond campsite. It was 2002. I had just finished my third year of college, and I was working as a backcountry campsite caretaker for the Appalachian Mountain Club. I had been dreaming of having this job for at least two years at that point, and a few cold, rainy days aside, I was enjoying every moment of it. It was a stark contrast from the previous summer, when I worked at Brookhaven National Labs as a research assistant for one of my professors. That too was a great experience and important for my development as a scientist. But living in the woods, spending my days doing trail work, sleeping in a canvas tent, dealing with black flies ... that was the life!

On this particular evening, two scientists from the Vermont Institute of Natural Science came to my site, and were planning to spend the night so they could survey for Bicknell's Thrush both that evening and very early the next morning. We chatted for a while, and they told me that they were using known locations of this bird, along with environmental information from those locations, to build a model to predict where it might be observed. I had no knowledge of species distribution modeling, and honestly, probably only a vague notion of what a "species niche" was. What I did know was that I as a physics major, I knew what the word model meant. I knew that any such model would likely be constructed using some computer programming language. I naively thought you would probably code that up in C or C++, because hey, isn't that what most scientists were using? But most importantly, I thought "I could probably learn to do that". 

I've told this story many times over the last 7+ years, in part as a way of explaining to people how I went from physics to ecology. To be honest, the path from physics to ecology was not direct. I finished my degree, spent two more years working as a caretaker, and then spent two years working in a neuroscience research group. But this experience stuck with me, and eventually I got to "build ecological models". I was reflecting on this again recently and I finally went and looked to see if any publications resulted from this field work these scientists had been doing. Here's what I found:

Lambert et al. 2005. A practical model of Bicknell's Thrush distribution in the northeaster United States. The Wilson Bulletin 117(1): 1-12.

And here was the line I was looking for - "during 2000–2002 ... we recorded the presence or presumed absence of Bicknell’s Thrush on 130 mountains first sampled by Atwood et al. (1996) (New York: n = 30, Vermont: n = 56, New Hampshire: n = 26, Maine: n = 18)." I'm assuming that one of the 26 New Hampshire locations was Kinsman Pond.

Perhaps the best part of finding this paper is that since that meeting in 2002, I have acquired the knowledge necessary to understand what these researchers were working on. The species distribution model that they constructed is pretty uncommon compared to today's methods. It appears to be a mixture of quantile regression, which is reminiscent of some of the first distribution models used (e.g., Bioclim), and basic pattern observation. The model options for presence-absence data are quite numerous now, and it would be interesting to see how different the distribution predictions are using more modern techniques. 

It's nice to look back on this story and think "yeah, I did learn how to do that."

Completing my PhD (whilst working as a Post Doc)

Just over a week ago I defended my PhD. Almost 10 months ago I started my Post Doc. This shuffling of the order in which one "should" progress is not uncommon. I know at least a few other people who started their post doc, then went back to their PhD institution to defend. About four weeks ago, as I was finishing up my dissertation to send it off to my committee, I would say that I wasn't sure it was a good idea to take a post doc before you finish. The past 10 months have certainly been challenging. Going into it, I figured that I could probably work between 60 and 80 hours a week. After all, there are so many hours in the day. Start my post doc work at 7 AM, finish up around 4 PM, that still leaves me 6 to 7 hours of work time before I need to go to sleep. I quickly realized that was pretty naive. Perhaps some can work that hard for extended periods of time, but likely not many (as this post at Dynamic Ecology suggests http://bit.ly/1kD6KzG). This meant that it took me longer to complete my dissertation than I initially anticipated. But now, looking through the rose tinted glasses that come with a successful defense, it's easy to think, "oh yes, this was definitely a good idea". So, I thought I might list a few pros and cons, based on my experience.

Pros:
* My post doc is in a lab I had been following for some time, focusing on research that is incredibly interesting to me, with excellent colleagues - hard to beat that.
* I work close enough to home, in a flexible enough environment, to partially solve the two body problem. (My wife has a faculty position at a medical school on Long Island. We don't want to live separately and I would never ask her to leave her position so I can take a three year temporary position.)
* I am going to get to go to the Cape Floristic Region of South Africa! How cool is that?
* Working on my post doc gave me a wider view of the field of plant ecology, which helped me frame my PhD work as I was finishing up. In general, there was a great deal of reciprocal transfer of knowledge (in my own head) between my post doc project and my PhD work.

Cons:
* No free time, or almost none. I turned down a lot of invitations from family and friends over the past ten months, and always felt guilty when I didn't.
* As I said above, the time to completion for my PhD was extended. This was perhaps the greatest challenge.
* Hours wise, I'm pretty confident that I was fulfilling my post doc obligations, but I wasn't as efficient or as productive as I wanted to be. In part I think this was because my intellectual energy was split,
* I did not publish my chapters as I completed them, leaving me with three unpublished dissertation chapters (but perhaps it will be nice to have manuscripts almost ready to submit over the next year.)

Where to now? I'm excited to devote most of my energy to my post doc work (I have to reserve some to wrap up side projects that I let languish), and I'm optimistic about what I can accomplish in the next year and a half. I wouldn't be in this position if I had waited until I was finished to take a post doc. With that said, I have every intention on giving my future students a realistic portrayal of what this decision can feel like. And given the number of finishing PhD students who start their post docs early, I assume they too will do what they think is best for them at that time, just like I did.

What Strunk and White has come to mean to me.

Recently I was offered an excellent post doc position in the lab of Prof. John Silander at the University of Connecticut. This is big for me - it means my years as a grad student (6 so far) are coming to a close, I'll be working in a lab whose research I've been following for many years now, I'll continue to work in plant systems, I'll be applying and greatly expanding my analysis and programing skill set, and on a practical level, I can work in this lab and continue to live on Long Island, where my wife has a good job as an Assistant Professor at Hofstra Medical School. The logistics of my position are bit complicated, but all setup. Those are some of the good things. The challenge has been wrapping up my thesis. You would think that after 6 years my manuscripts would be mostly complete, but reflecting back on my experience, I have begun to realize how little time I spent on my thesis compared to all the other things I've done in grad school. Having not taken any biology since high school, I spent a lot of time taking classes. I also took a lot of classes focusing on math and statistics in ecology. I've done a lot of departmental service related things, which has led me to believe that receiving a Departmental Service Award is both a good and bad sign. And I've been involved in, and continue to be involved in, side projects. Add in TAing, peer reviews for journals, etc., etc., - you get my point. This all adds up to the last few months and next few weeks as being a crunch time for writing, and through this time I've been keeping my copy of William Strunk and E.B. White's The Elements of Style close at hand.

Why the Elements of Style? It is not the book that was used in my college writing class (that was The Bedford Handbook). It's not about scientific writing. For all I know, it may not even be what my writing friends would recommend. But it is highly recommended by many professors in my department,  which is why I picked it up in the first place. Regardless of why I began using this book, it has become quite important to me as a writer. In particular, it has two meanings for me. One, contained within its short descriptions of the rules of writing is the promise that I can become a better writer. I read one of the 'Principles of composition' and think, 'Yeah, that does sound better. I can do that in my writing.' Or I can look at the one of the 'Elementary rules of usage', and then go back to my manuscript, search for instances in which I break a rule, and fix it. I can make my writing cleaner, clearer, and more concise. The second meaning is a bit more symbolic. I like to read a bit from this book before I start writing for the day. I don't necessarily set out to apply what I read, I just find that it puts me in a writing mood. So at the end of a long day of grading problem sets or writing R code, if I look at my copy of Strunk and White, and I know that I didn't crack it open that day, I know I probably didn't do any writing. Sure, this is followed by a pang of guilt, but it also comes with an increased motivation to get some text down the next day, which is ultimately going to get me through writing my PhD.

And that's what Strunk and White has come to mean to me.

Fieldwork, ESA, and Moving

The last few weeks have been filled with fieldwork in New Hampshire, travel to Portland, OR for the annual Ecological Society of America (ESA) meeting, and moving from our home out near Stony Brook to a new place in Nassau County (closer to NYC and to my wife's new job) - hence the lack of posts.  Here's a brief post concerning my experiences at the recent ESA meeting.

While in Portland I participated in some audiocasts with a group of friends and colleagues, during which we discussed some conference highlights.  At the end of each day (the meeting was four full days) we gathered and talked about one standout presentation we saw that day.  Give a listen to these audiocasts if you're curious a) what ecologists think and say about each others presentations, b) if you're curious what I thought were a few standout talks, and c) if you want a bit more than an hours worth of entertainment.  The audiocasts can be downloaded from my friend Gabe Yospin's website for our Monday, Wednesday, and (coming soon) Thursday sessions.  Gabe also did solo sessions on Sunday and Tuesday that are worth listening to.

This was my first ESA meeting and I must say, I was impressed.  ESA is a (relatively) large meeting, approximately 4,500 people this year.  There are more than twenty concurrent sessions at a time! Which means during any session there was usually more than one talk I wanted to see.  Also, the conference center was so large that if back-to-back sessions were on opposite ends of the center, it was almost impossible to see both talks in their entirety (had to leave one early and still showed up at the other late).    But these problems aside, I was definitely impressed and inspired by the science reported at this meeting.