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 (http://www.usanpn.org/participate/observe): 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).