Wednesday, December 22, 2010


At this point, 3 of the 4 people I want as committee members are on board, but I'm still waiting for a response from #4. Sent an email on Friday (as I was advised that this can be a nice way of asking as it doesn't put profs on the spot), and had no response by mid-day today... Sent a super-polite reminder email to make sure email #1 hadn't gotten lost in this person's inbox. Still no word. It'd be so nice to put this to rest before I leave for Christmas! Oh well; I have a back-up plan just in case (but it would make my life more complicated, by potentially adding a committee member from a different institution/state).

All kinds of planning going on right now too, for traveling to a conference (in a warm place!) coming up in Feb, plus applying for a fellowship to spend some time in Scandinavia next year (where my advisors will be during a sabbatical). Busy busy busy!

R function currently blowing my mind: melt() and cast() in the reshape library (the built in use of aggregate is fabulous).

Thursday, December 16, 2010

Taking another step (committee!)

Lots going on in real life that I'm not going to write about now (what else is new).

Big news for the moment is that after months of procrastinating/agonizing, I finally just sent an email to a former professor asking them to be the first member of my graduate committee. This is a big step for me; I've been writing and re-writing the email all week. I really really really hope that this person answers with a big YES, because I think that their knowledge and experience would be invaluable to me, and in a number of ways their work is closer to what I want to do than my own advisor's. In general, I'm still skeptical of the value of committees, but I can totally see how this person would fit in. Part of my anxiety about it is that if the answer is no, I can't think of anyone else even at this huge institution who would be able to fill a comparable role. Mostly I'm filling my committee because the rules say I have to, but I'd really love to work with this person more.

Anyways, that's where I'm at. Cross your fingers for me.

With the holidays coming up, maybe I'll post more, including the list of favorite R functions I've been accumulating.

Theo out.

UPDATE: Success!! Big weight off my shoulders. Now I can ask other people on my list.

Tuesday, October 5, 2010

In search of great ideas

Not surprisingly, I'm still on the hunt for a great thesis topic. My advisor and I have been meeting weekly, and while he says that I've got a couple of established projects that could become solid PhD theses, it's early enough yet in my graduate experience that I can still spend time challenging myself in search of a super-shiny topic. So we've been putting a good bit of thought into what makes particular topics time appropriate, influential, etc, such that they result in classic, highly cited papers. Good things to think about, but not always entirely obvious.

The last week or so was dubbed ' 70's week ', and we've been hitting up a bunch of classic papers from the 70's. Some of them are terrible, some of them are pretty neat. Mostly what I've been struck by however, is the realization that a lot of the topics that turn up in weekly lab meetings and paper discussions and over lunch at the cafeteria - they're not really 'new' hot topics to the extent that I usually consider them. I've been surprised by just how much these 'old' papers are really discussing the same ideas that we still wrestle with today in ecology and evolution. Sure their discussions tend to be a little more qualitative and verbal than quantitative, and they aren't using all of the powerful new methods and resources that have been developed more recently. But a lot of the ideas are there.

Maybe I shouldn't be so surprised - lots of smart people have been (and are) ecologists. Wading into the literature though has been a good experience. I am both comforted and somewhat stymied by these realizations though - on the one hand, it's good to realize that even though a lot of the really foundational ideas in our discipline have been thought out and written about for decades, people are still making a living and doing good work to flesh out these ideas without having to come up with paradigm shaking new concepts. On the other hand, while I'm challenging myself to try to come up with a super shiny new idea, it's intimidating to realize how much has already been though out/discovered, and the extent to which most of what is done these days is 'just' filling in the blanks.

Ok, back to the late 70's....

Monday, September 27, 2010

Where do classics come from?

Quotes from R. McIntosh, "Citation Classics of Ecology"

"A less professional recognition was given to a Scottish landlady who fed J. H. Connell very economically, and stretched out his G. I. Bill funds. [...] Collateral stimuli were attributed by some authors to liquid refreshments ranging from soup to bitters and to the cup that cheers without inebriating, tea."

"Several [Ecological Classics] were explicitly considerations or tests of theory, and some urged the utility of theory as a guide in their research. Paul Dayton, however, among others, had reservations. He commented, 'Ecology often seems dominated by theoretical bandwagons driven by charismatic mathematicians; lost to many is the realization that good ecology rests on a foundation of solid natural history...'"

Sunday, September 19, 2010

Grad students are people...

"Initial premise: Graduate Students are People.

Graduate students can be described by models identifying their many functional and structural roles in research labs, field projects, classrooms, and budgets. However, the most encompassing model of the nature of a graduate student is the humanistic model, encompassing submodels of both physical and psychological well-being. Given this premise, a long list of corollaries can be developed. [...] "

- D. Binkley, 1988. Some advice for graduate advisors. Bulletin of the Ecological Society of America, 69 (1): 10-13.

Tuesday, August 24, 2010


"A wonderful fact to reflect upon, that every human creature is constituted to be that profound secret and mystery to every other. A solemn consideration, when I enter a great city by night, that every one of those darkly clustered houses encloses its own secret; that every room in every one of them encloses its own secret; that every breathing heart in the hundreds of thousands of breasts there, is, in some of its imaginings, a secret to the heart nearest it! Something of the awfulness, even of Death itself, is referable to this. No more can I turn the leaves of this dear book that I loved, and vainly hope in time to read it all. No more can I look into the depths of this unfathomable water, wherein, as momentary lights glance into it, I have had glimpses of buried treasure and other things submerged. It was appointed that the book should shut with a spring, for ever and for ever, when I had read but a page. It was appointed that the water should be locked in an eternal frost when the light was playing on its surface, and I stood in ignorance on the shore. My friend is dead, my neighbour is dead, my love, the darling of my soul, is dead; it is the inexorable consolidation and perpetuation of the secret that was always that individuality, and which I shall carry in mind to my life's end. In any of the burial-places of this city through which I pass, is there a sleeper more inscrutable than its busy inhabitants are, in their innermost personality, to me, or than I am to them?"

- Charles Dickens, "A Tale of Two Cities"

Wednesday, August 11, 2010

Changing structure of scientific inquiry

At ESA the other week (this post got slowed down by my now traditional post ESA cold), I attended an intriguing symposium on Ecoinformatics that led my thoughts in an interesting direction. Ecoinformatics (short for Ecological informatics) is, broadly, concerned with solving the technological challenges of making the increasing wealth of ecological data broadly available, accessible, and analyzable (?). In the symposium, several presentations were given on different efforts to unite existing ecological databases (DataONE) and to create a system for authors to submit datasets related to their publications (Dryad - which currently focuses on evolutionary biology, not ecology specifically).

This second project I find particularly exciting. There are many challenges that need to be worked out to make it a reality, but I really just want to comment on a few of the things that I found especially cool:

1) Authors will be expected to submit properly formatted and annotated data related to their papers for archival at the time they submit papers for publication. If done well, with an appropriate system, this means lots of cool data available to the scientific community allowing many interesting synthesis and modeling projects, and potentially fostering many cool collaborations. (Obviously lots of interesting challenges involving appropriate citations, etc, embargoing sensitive data or allowing authors more time to publish follow up papers, infrastructure issues, funding, etc.)

2) I was amused thinking about how this would mark a further step in the Ford-ification of Science; already within big lab groups, PI's have Big Ideas and write grants and get funding that supports various post docs and grad students and technicians who experiment, collect data, and analyze it. Open access data sets could compartmentalize science even more, making it totally possible to do great science and synthesis without ever collecting data. Fascinating to think about. Specialization can bring rewards in terms of skill levels at particular tasks, and increased efficiency, along with new challenges, such as making sure that appropriate data are gathered, and that communication between roles is good.

Anyways; fun to think about.