Thursday, October 21, 2010

Welcome to not-so-sunny San Diego

Rain has arrived! October. I have to say, I still find the weather strange. It was only a few weeks ago that temperatures soared up into the 110+ degrees Fahrenheit, but now it's the complete opposite with storm clouds dominating every part of the sky. The weather just doesn't seem to be making up its mind as to what it wants to do, which somewhat makes me sad.
I was told to look happy, but I was mostly laughing at the situation this picture was taken in.

Lizzie is sad too. Actually, she's mostly sad over the fact that one of the weather blogs she followed is no longer posting ( I can't tell you whether or not the blog was a good one (especially since I didn't know that weather blogs existed), but I am taking it on Lizzie's word that it was the best weather blog to be created. Personally, I thought that a weather blog was somewhat strange and kept by bloggers who weren't sure of what else they should be observing or commenting on besides the weather, to which I think is fine since everyone has their own idiosyncracies. (Note from Lizzie: This weatherblog was fantastic, especially as a grad student who was based 3.5K miles from my field sites in San Diego most of the year, and whenever you thought, ‘boy, is it oddly wet’ you could check it and it would say ‘this is the wettest March since . . . . ‘ And it did a complete review of all ENSO predictions.)

Anyway, the other big issue with the rain is that it’s putting a crimp in field work plans. Doing phenology work on first leaf means getting the jump on the season. But scheduling that work also means having some guesses at the seasons. Lizzie and I were hoping to collect some coastal sage scrub high-resolution phenology data – in the winter (the winter being when things usually start growing). Now we’re going to re-assess.

To take my sadness and slight displeasure to the rain, I have written an open letter to the weather, to which I will not have any responses.

Open letter to the storm clouds:

Hello, how are you? Fantastic. I've noticed that you've arrived somewhat early this year, and though normally I would be glad to see you, I'm tired of you quite frankly. This year was the first summer that I spent in San Diego, and I had expected San Diego to live up to its amazingly beautiful and sunny reputation. You, however, have dashed my hopes of San Diego ever being sunny again. Don't take this personally, storm clouds, I do like you...just not at this moment.

Fortunately, the temperature is still warm enough that your cold raindrops do not give me chills when I bike downhill heading home after a day on campus. At times, I even enjoy the rain that you bring down upon me, but I'm not here to tell you how I enjoy some of the benefits of your arrival. No, I'm writing to tell you that I am displeased, that you make places much less convenient to get to. If only you weren't so finicky as to when you decide to rain.

And curses to you too, not-so-accurate You have not lived up to your services either, especially your 'hourly' tab, where you think you are so accurate as to what the chance of precipitation is and its time of arrival. I am starting to wonder whether or not you are working together with these weather forecast services, storm clouds.

I hope you will be able to find some time to respond to me and retreat for a while, just so the days are actually days instead of a seamless evening. I do really miss the sun. Also, my tomato seedlings need sunlight too. I hope to not see you anytime soon in the next few days.



Computers, dogs and field work

Doing bioinformatics work seems to mean I am always sitting in front of a computer. The good news is that also means that while other people need to go out to their field sites I am around to hang out with the dogs left behind. So today, my officemate Claire and I have Willy for companionship.

Nice work Claire with the tidy desk,  apple and mug--looks very scholarly.

Tuesday, October 19, 2010

How computer-savvy do ecologists need to be?

Greetings from monsoonal San Diego! I am going to post every now and then as we get this blog started and in lull periods.

While waiting for the bus in the pouring rain to go from campus in La Jolla to my sopping wet bike in Hillcrest (smart move of the day #1 was leaving my bike helmet attached to my bike) I read a recent article by Aaron Ellison and Brian Dennis ( suggesting that all ecologists have two terms of college-level calculus, a touch of linear algebra and several probability courses. That’s a daunting list for a good number of ecologists (and I don’t exactly measure up—though I did sit in on linear algebra in my final year of grad school—clearly the perfect time to absorb new info), with some who far exceed it and many who dreadfully avoid differential equations.

That and a recent project re-synthesizing a >30 year dataset in plant phenology has got me wondering what the requirements should be for the more technical aspects of analyzing data. Lots of people say the future of ecology is synthesizing big datasets and asking questions on global scales, but that actually requires some key skills. I came out of grad school with a basic knowledge of R and thought I was ahead of the curve. Now that I am processing a number of long-term datasets I’m impressed by all the basics needed just to keep a decent pace, and also how much you can do with them.

For the 30-year dataset we needed to read in and manipulate hundreds of xls files into one nice, usable csv. Despite learning a couple new coding languages in the last year I can’t do that, but luckily Jim Regetz, a rare mix of ecologist and computer programmer can (in perl mixed with R). I play backup singer and help with post-processing in R. To do just that somewhat efficiently I have: a nice monitor (because monitors >24” but <30” increase productivity:, a version control system to keep track of the code Jim and I share, project management software which tallies all the project issues and their someday resolutions with key notes along the way, an editor I love (emacs) that I use for all my code, including R, where I do 95% of my data work and an irc chat so Jim and I can discuss what the word 'satlks' means (since he’s in sunny Santa Barbara and I apparently live in a puddle). And this is for just one of 29 datasets (though I admit the gnarliest).

My monitor today while working on one dataset (I highly recommend my new Dell Ultrasharp 27inch by the way, and I am not being paid to say that).

I am lucky to have an NCEAS working group that got the version control and project management stuff up and running but I am daunted by (well, first I am daunted that someday I need to set all these things up for myself, by myself) how much more we could get done in ecology if there were more people like Jim, slowly filtering the best resources to be productive and useful to labs and students. For most of grad school I used JMP and avoided scripting but I am no longer convinced it’s any harder to program my brain to remember to type a single word command than to remember which menu, submenu, right-click sequence to use to find the same command already pre-programmed for me. (And it’s of course immensely more useful for me to have all my code, crufty comments and all, to go back to, than to open JMP and a bunch of different, befuddled, saved file steps.)

Thursday, October 14, 2010

A Brief Introduction

How and why are these invasive species so successful?

While ecologists and land managers have been tackling this question for decades we’re going to give it another try, focusing here on phenology—the timing of seasonal life history events, such as flowering or losing leaves in the fall. We have four hypotheses to test. The first hypothesis is that there is a vacant temporal niche within the environment and the invasive species are able to utilize the resources available at unique times of the year compared to native communities. The second hypothesis is based on a first-come, first-serve idea, that the earlier a plant starts growing, the more resources it can sequester for its own use. Hypothesis three suggests that exotic species can do everything more and better (i.e. grow more leaves, have more flowers), while the last theory suggests that invasive plant species are earlier and faster responders to climate change because of their genotypic differences to native plants. With these four ideas in mind, we’ve set out to test whether phenology affects plant invasions and hopefully it will be able to help in predicting and managing invasive species.

We’re taking a bioinformatics approach, which means compiling lots of data to start. We have phenology data for a couple thousand species but we need some additional ‘trait’ data to help constrain our analyses. So the first step for me this fall to help answer the bigger question is to determine the different pollination modes of each species of plants. I’ll be in the library and online figuring out whether our species are wind, animal, or self-pollinated. For the current data set, I am looking at a list of plant species from Tucson, Arizona’s Sky Islands area. I have been able to go through a majority of the Poaceae family and label all subsequent genus as wind pollinated, which has slightly cut down the still daunting list. I hope that further investigation into the book, Principles of Pollination Ecology, which I am currently perusing, will help shorten the list by providing more information on the pollination modes of several plant families. I’ll then fill in the gaps with information from the Jepson online resources and USDA PLANTS database.

Stay tuned for progress on the work. We’ll post thoughts, fun updates and results here as we go. In the meantime, the design and layout of this blog will be continuously updated until Lizzie REALLY likes it.