Wednesday, December 15, 2010

In which we take a break

Greetings to all from Los Angeles!

I apologize for the very long break between the last post I wrote and this current one. Finals week impeded any progress that would have been made and diverted a substantial amount of my brainpower towards viewing and reviewing my several hundred sheets of printed notes (don't worry, I chose the most eco-friendly of options and printed front and back whenever I could).

Before finals week though, I had lunch with Lizzie, where she presented me with a challenge of coming up with my own ideas of how I could use data on pollination mode and flowering time to test ideas about niches. Despite the fact that Lizzie told me it was supposed to be a somewhat fun and light-hearted question to think about, I ended up racking my brain to find some all-encompassing idea that would tie these factors together.

In my not-so-coherent thought process, I based my ideas around temperature, and a few other factors that I've learned this quarter. Since it is generally concluded that plants would flower around the times of their preferred mode of pollination, I feel that it is safe to say that perhaps during the months of mid-March onwards, plants are more frequently animal pollinated as opposed to wind pollinated since temperatures begin to warm around then. On the other hand, the earlier months (January-March) would consist more of wind pollinated species, mostly those that are forbs/herbs (I had the picture of the graph we got from running R on the Gates' phenology data in my head while I was writing this). From what I've also learned this quarter is that the degree of latitude and altitude at which plants are observed at can play a role into phenology. The fact is that as climate becomes increasingly warmer earlier in the year, plants and animal species tend to migrate towards the poles and upwards in latitude to find locations more suited for their growth and reproduction. In terms of niches, this would mean that plants that flower later in the year are likely to be more specialized since there would be more competition for limiting resources (light, water, nutrients, etc), and vice versa.

With this in mind, Lizzie said we may be able to test some of these ideas on a smaller scale next quarter (or maybe the quarter after, but that's TBD). But for now, I'll be enjoying the comforts and festivities of home before heading back to San Diego and the last chapters of my undergraduate career!

Have a safe and happy holidays everyone! =D

Tuesday, November 23, 2010

The new queen of pollination modes (get it? bees, queens, pollination!)

While Winny tries to catch up on all the life (and bioinformatics work) missed while she was grounded by computer woes I am blogging to wish you all a Happy American Thanksgiving. Happy American Thanksgiving all.

One of the main things Winny missed while hanging out with the computing help staff was my ebullient emails to her about her progress. After weeks of reading old books on pollination modes, new papers suggesting we know nothing about pollination and visiting many websites, transcribing many, many (I repeat, many) pollination modes, Winny had 2,228 known pollination modes (at the species, genus or family level)! I ran this through a list of 16,659 species I was hoping we could get pollination mode data for and we have it for 77% of them -- or 14,490 species. I think Winny's known modes tab is probably the most complete directory of pollination modes anywhere.

So in summary, Winny -- the best and brightest new plant traits informatician I know - you rock!

That's Winny entering data buried in the Principles of Pollination Ecology. Back in the day when things with her computer were swell.

Winny will be back with an exciting end-of-term blog in the next week or so, so stay tuned for the final chapter of our current plant traits journey. Then I will round out the year with news from a trip to Santa Barbara for work and a visit to the Entomological Society of America, to be held right here in the happening hotel circle neighborhood of San Diego (I jest, about the 'happening,' the meeting really is in San Diego).

Holiday season started this week in San Diego: The beach-ball tree at Ocean Beach and lights up el Prado at Balboa Park. I admit we're a little Christian-centric here (it's a military town!) so apologies on the uni-denomination theme.

Tuesday, November 16, 2010

I've been grounded!

..or at least, benched, for the past 5 days due to hard drive failure. On Sunday night, at around 1:30am, I was finally able to do a clean reinstall of Windows 7 and Ubuntu. However, I also lost many of my documents that I haven't backed up in the past month, which is very aggravating to say the least. I thought that my troubles were at an end when I received multiple notifications from my computer that I need a new hard drive. So finally, I received my hard drive today and am currently re-reinstalling Windows 7. Oh PCs, how you aggravate me so.

I've also lost some nifty graphs that I saved from the R-script code that Lizzie wrote and went through with me on Tuesday. Though the scripting language still seems daunting, I can't deny that it looks very useful and helpful for sorting out a great multitude of data. Hopefully, once I am able to reinstall R and the VPN, I will be able to reconnect back to the server and run through the script again myself so I can update this post with some graphs (edit: Lizzie was awesome enough to help me upload the graphs from the R script that she wrote!).
Each color represents one species listed on Gates' records. The snazzy features of R allowed it to run the data in the excel sheet and colorfully map it out.
In the meantime, I've been reading the book that Lizzie uploaded onto the server, called R in a Nutshell, to gain a better understanding of this esoteric language. Fortunately, the author has an easygoing writing style that I like, which is similar to the books in the Dummies series. I like how it has a very nice, tutorial in the beginning accompanied by examples of the explanations and later on, provides more advanced material for readers that would like more in depth knowledge of R (in short, this book does not make me feel like such a n00b, so to speak).

Thursday, November 4, 2010

Summer in November with numbers, tables, and rulers

90°F in La Jolla? Sweet... except that it's already November. Not that I mind, but it would have been nice to have this be the other way around, where summer was actually summer and now to be autumn. It's like we're in the southern hemisphere!

Looks like the Sungod statue is happy as well!
I know that many phenological records we have today are from long time observations of many individuals taking time to painstakingly write down information about the species they have observed. This is exemplified by the paper that Lizzie gave me on Tuesday to peruse, called Gates' Phenological Records of 132 Plants at Manhattan, Kansas as transcribed by Lloyd C. Hulbert. In it, Hulbert talks about how most of the records started in 1929 by Dr. Gates were “...of plants around his home or seen when walking between his home and Dickens Hall on the KSU campus, a distance of about three-fourths mile” and he continued to do so until his death in 1955. Due to Gates' dedication to recording the flowering times of the species he observed, Hulbert later writes that maybe the reader will also wish to record phenological data and in doing so, can contribute useful knowledge while enjoying oneself.

Also accompanying this paper is an index of all plant species that Gates encountered and recorded, along with tables of flowering dates in conjunction to the year it was observed. The following picture should be able to illustrate what are on the tables:

Handy-dandy ruler
What I have been doing with the tables are going through each individual species listed and writing down the corresponding month, day, and year in which the species first flowered. 7 complete tables and 1450 entries later, I have to say that this is slightly eyestraining work, mostly because the tick marks that indicate the date are small, along with the years that are written down. At times, I take breaks and move my eyes around to prevent them from becoming stuck (if that's possible). The good thing about this is that I can easily fall into a routine and finish at a fairly even and rapid pace, so pretty soon, we should be able to create graphs from the data input in the excel sheet.

Monday, November 1, 2010

Aberrant phenologies

This weekend I got bonked on the nose by a foam surfboard while paddling out over a crazy wave -- it was that 'thhwwwamp' part where, if you're lucky, you've slammed down on the other side of the wave with most of your body still on the board. If you're less lucky, like me, you're halfway off your board and scrambling back on before the next thwampy wave, and your poor friend has lost total control of her board and it's careening quietly towards your nose.

But of course the exciting part of my week was the previous 5 days which I spent in a conference room in Tucson. Working with the USA National Phenology Network, a couple folks and I were hammering out how plants respond to climate across sites and how constrained by evolution phenology may be. The short story is flowering time is ridiculously constrained by phylogeny and responses to climate are not -- we're working on that latter bit now. I am cleaning up code: it gets so messy written on the fly. On the way to these exciting findings we made predictions about latitudinal gradients and invented the new Whittaker plot for phenology (see picture).

The new Whittaker Biome Plot! It took three PhDs two hours or so to come up with this work of clear genius. We're obviously taking it up a notch by adding the Atacoma desert to the plot.

I also got out to see some aberrant phenology research in action! On Friday, Jake Weltzin, Director of the USA National Phenology network took one colleague and I out to see something other than the construction zone of Tucson (which seemed to be the part of Tucson our morning walk from hotel to office was based). 

Jake let us see some of the plants he's monitoring as part of the USA National Phenology Network's Nature's Notebook program ( a couple buffel grass (a non-native with a uncommon phenology), a barrel cactus and two totally freak saguaros: one was moving beyond some disease or such; I forget what he called it but it definitely should be 'headdress saguaro.' The other one has freak buds and is named by Jake 'baby saguaro.'

Jake explained the current phenological state of one of the 3 buffel grasses he's monitoring. His buffel grasses seem normal but check out the crazy saguaro behind him (upper left) -- I call it 'headdress saguaro,' and he's monitoring it too.

Of course when you're trying to use a network of people to get at mean phenological trends for different species observing the most aberrant individuals is a special approach. But you have to spice up life a little: I think that's why I like to thwamped by waves and Jake likes to monitor an adorable cactus that seems to be developing alien buds.
Jake with another saguaro he's monitoring. He calls this one 'baby saguaro' because of its freak buds (top).

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.