Lots of updates

1 34 watching TV
7 30 sleeping
10 0 sleeping
17 54 at Steak and Shake with Mikey

The majority (75%) of nocturnal nest predations on Golden Cheeked Warblers by snakes resulted in the adult female getting eaten also (Reidy et al. 2009).

Lunch- Salami
Dinner- Cheesy Cheddar Steak Burger

My little sister arrived this evening from Alabama bringing boxes of girl scout cookies and Texas Chocolate Sheet Cake.  Before she arrived however I met mikey for dinner at Steak and Shake since he was on his way to TN.  Other than that though I spent my day in the lab other than a brief excursion to the Bird Lab meeting (predicting changes in nest predation by snakes with climate change).  Apparently bird lab really should be snake lab since most of the discussion was about designing experiments to test snake hunting skills (captive snakes become bad hunters even after a few months of captivity was one take home message).  Guess bird people really are all herp people at heart...

18 ii 2012
0356- sleeping
0910- sleeping
1421- picking up Eddie in a post apocolyptic wasteland
1756- vortexing

Random Fact- On 1 October 1908, Chicago Heights, IL installed telephones at 2 schools, some of the first in the nation.  Additionally, in 1912 tuition for non-resident students was $2 a month.

Lunch- bagel at Einsteins
Dinner- tacos at Chipolte

My little brother came to visit for the weekend, so we had to go pick him up at the train outside of Chicago.  Driving there was an adventure, we passed a place where parade floats go to die, a place where fair rides go to die, and a bunch of scrap places, all within a few miles of eachother.  Urban decay is so fascinating.  Once we got back down here we ate dinner and hung around the house while I did my WoW study session.  Then we ate cake, Texas Chocolate Sheet Cake rocks my world.

19 ii 2012
0019- watching TV with Maria and Eddie
0441- sleeping
0621- sleeping
1905- waiting for PCRs to be done and getting gels ready for said reactions

Random fact- Foldit is a computer game that allowed people to try and figure out the structure of various proteins and enzymes.  It took players just 3 weeks to solve an HIV protein structure problem after 15 years of research.

Lunch- lucky charms with chocolate ice cream
Dinner- burger and milkshake

Sadly my brother had to go back to Notre Dame today, Maria took him to Chicago by herself since I really needed to set up reactions.  Luckily she managed to safely deal with the post apocalyptic zombie wasteland without me.  We met up at Mass and then went back to the lab so I could pull my reactions.  I was hungry so rather than running the gels we decided to call it a night and left to get dinner.  For a college town everything sure closes down early here...

20 ii 2012
0251- watching TV
1727- eating Chinese
1948- setting up the sequencing reaction
2117- at Massimos eating Texas Chocolate Sheet Cake

Random Fact- Alcock's Arabian is thought to be the ancestor of all gray Thoroughbreds. 
Lunch/Dinner- Sweet and Sour Shrimp

My sister rocks at decorating cakes, and my mom rocks and pretty much everything.  My mom made a cake for Massimo's birthday and sent it up with Maria, along with cake decorating supplies.  So while I was setting up my sequencing reaction she drew a motorcycle and the stars and bars on it, then we all went to Massimos, sang happy birthday, and ate cake.  The best part though was watching Brendan go crazy when Massimo put Little Mermaid on the play piano, it was pretty intense.  Also of interest was getting 28s to work for a bunch of taxa I'd previously had no success with, hopefully the product is good enough for sequencing.

21 ii 2012
0223- watching TV with Maria
0649- sleeping
1629- at the lab
2220- Getting hot chocolate with Maria

Random Fact- Home Depot has a microwave that sells for over 1,000 dollars. 

Lunch/Dinner- leftover Sweet and Sour Shrimp

Maria and I spent the evening wandering around town, specifically the furniture store, Home Depot, and then a coffee shop in downtown  At Home Depot I found a desk top washer (maria claims it was a demo piece to show the high powered water jets) that I really wanted, and contractor packs of CFL bulbs (seriously, 12 for 7 bucks hell yeah).  At the furniture shop we identified a good couch for my dude room, and I found coffee tables that fold out into normal tables.  Before the fun though, I actually got some work done including submitting my plate first thing this morning and a multi hour long lab meeting.  We learned treehopper ID, but I think it can really be summarized as higher level treehopper taxonomy is a disaster, there are no good characters, and really you should just learn genera.

22 ii 2012
0508- watching TV with Maria
0926- sleeping
1211- eating some lucky charms before my biogeography discussion group
1817- at home with Maria watching Dr. G. medical examiner

Random Fact- When chicks from one species were moved into a nest (of the same species) but in a different region, ticks on the transplanted bird did poorly compared to the ticks on the bird in the region where it belonged.

Lunch- lucky charms
Dinner- pizza at Jupiter's with Maria

I managed to convince Maria to stay another day, she was feeling sickly, but we still managed to try a bakery and eat pizza.  At Jupiter's we discussed our most memorable beers- her's was at Lechner between finals while eating Antonio's and mine was probably in Argentina after carting these beers around for weeks (pulling them out at a light sheet earned me a "you'll be a good gradstudent" from Chris).  I also got the sequence data back this morning, I love waking up to sequences.  So far they look pretty good, even the 28s's with the faint bands seem to be golden.

23 ii 2012
0040- watching TV with Maria
1016- sleeping
1407- at systematics discussion group a KJ paper on phylogenomics from Illumina sequencing
2335- working with my sequences

Random Fact-  The Hawaiian Hawk is found on the island of Hawaii and as a vagrant to a couple of the other islands in the chain.  Unlike most other endemic Hawaiian avifauna, its population appears to be stable.

Lunch- left over pizza from Jupiter's
Dinner- pizza at Jupiter's with Massimo, Brendan, and a prospective student

Spent much of the day working with the sequence alignments from my most recent plate (my 10th one so far). I also got my abstract submitted for the ICE meeting (I think, the submission process was rather wierd), so now I can apply for yet another grant to help pay for the meeting.  I also discovered I either 1) learned more in genomics than I thought I did or 2) (and much more likely I think) KJ can explain next generation sequencing simply enough anyone can understand it.  I love the idea of millions of reads to play with, not so much the multiple months it takes to get sequence data back from the biotech center.  I think the highlight though was looking up hazmat placards that Maria saw on her drive home- the most exciting was 1859, SILICON TETRAFLUORIDE, which shall we say is bad, bad news.

24 ii 2012
0152- Working on the 12s alignment
0250- Getting my nexus file ready to run
0643- sleeping
1453- at the lab reading a paper

Random Fact- William Payne, a merchant in Massachusetts left 35 acres of seafront property to public school children in his will 351 years ago.  The trust that manages it is one of the oldest charitable trusts in the US.

Lunch- steak and shake
Dinner- Rockfish and lucky charms

I let the Hecalini analyses (both the straight concatenated and one with gappy regions removed) run overnight and woke up to find one was done and the other had 2 minutes left to run (talk about perfect timing).  I got the distributions coded and loaded it and the trees into RASP then did a Bayesian MCMC analysis.  The results were a bit different then the last time, but overall the relationships between groups and biogeographic history were not in conflict with the last run.  I also started some extractions and helped Brendan since he's going to learn how to do molecular work.  Now I'm waiting for the DEL+PARA analysis to finish... 17 more hours...