Life as a falconer, insect systematist, and double Masters Student (or a look into the mind of someone who is questionably sane).

25 February 2012

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...

17 February 2012

A week's worth of data

9 ii 2012
0632- sleeping
1002- getting my motorcycle loaded
1521- driving
2000- driving

Random Fact- when tying down a bike, you want the front shocks compressed about 1/3 the way down- enough when it bounces there isn't slack, but not so much you screw your bike up.
Lunch/dinner- tortillas and bluebell 

Markus and I met up shortly before 10 and got my bike loaded and strapped down.  Checked my email and found out I needed to be back by 1125, not 1500... I ran a couple of errands and headed north.  I left a bit before noon, and by the time I got to Tyler found out Mikey was leaving Austin today also.  The weather was great, no rain and some sun.  About 1900 I got a text from Mikey saying he missed his plane so we coordinated to meet up in St. Louis about 0100 Friday.

10 ii 2012
0847- sleeping
1233- at Bird Lab
1410- waiting for Drew to get done talking to the admissions committee
1724- at the PEEC mixer

Random Fact- Carotenoids cannot be synthesized by animals, so are thought to be an honest marker where as animals can produce melanin so its possible for them to "cheat" and be more attractive then they really are.

Lunch- pizza  at Bird Lab
Dinner- shiner and random finger foods at the mixer  then nachos at Murphys

Today was incredibly long- I picked Mikey up, and then we took turns driving the rest of the way to Urbana, finally getting in a bit after 0500.  Unloaded and got a few hours of sleep before I had to walk a prospective student between meetings on campus.  The afternoon got complicated as recruit schedules kept changing but the recruit I was helping with was pretty cool so it worked out ok.  The highlight of the recruiting things today though was the free Shiner at the mixer (I wasn't excited about mixing so only talked to people I knew).  I also found out Chris took my data comment to heart- while we were talking about my DDIG he made a comment about the fact I'm only interested in the data.

11 ii 2012
0505- sleeping
0747- sleeping
1904- home playing WoW
2220- playing WoW

Random Fact- Male three spined sticklebacks provide all parental care including fanning the eggs to provide fresh oxygenated water and guarding the eggs and young.

Lunch- McDonalds 
Dinner- pizza (sausage, peperoni, extra cheese, and tomatoes) and beer (ordered an Anchor Steam, but mikey didn’t like his beer so we traded casue I'm nice like that) at Jupiter's  

As part of the recruiting weekend there is a research symposium where grad students present their work and then a mixer afterwards.  As usual, I didn't present anything so enjoyed sleeping until almost 11 at which time I figured I should attend.  Caught a couple presentations then met up with Mikey and Massimo for lunch after giving up waiting for the recruiting people to get their act together.  After lunch I sat through another 3 hrs of presentations, then to the mixer/poster session.  I was way over my limit on crowds, talking to people, and socialization in general so when KJ told me I looked bored I took that as a sign it was time to go home.

12 ii 2012
0433- sleeping
0743- sleeping
1917- Skyping with Eddie trying to fix my Nexus conversion program

2138- playing WoW

Random Fact- Unix and dos use different protocols for dealing with the ends of lines.  My brother and I spent 3 hours trying to make something work before realizing that was the problem...

Lunch- eggs at IHOP 
Dinner- fish sticks  

I had big plans of PCRing today, but instead spent a big part of the day skying with Eddie trying to get a program he wrote for me to work.  Taxonomy programs all want slightly different files, so he made me something to convert files from the alignment program I use to the nexus files.  It worked fine for him, but wasn't working for me.  After 3+ hours he realized it was the conversion issue mentioned above so that problem was solved.  Now I get to actually do the data analysis on the sequences I got last week.

13 ii 2012
0043- playing online
0720- sleeping
1641- reading the paper for biogeography discussion
2318- home playing WoW

Random Fact- Excluding captive bred animals, 2008 was the first time in over 200 years a Tuatara successfully bred on mainland New Zealand.
Lunch- corned beef 
Dinner- lingcod and rice  

Ran a bunch of PCRs today, and did some purification.  Assuming everything goes well I can submit my plate tomorrow- mostly 28s, but some 12s and Histone too. I added a bunch of outgroups from Jamie's extractions, so hopefully this will help with the kinda weird trees I've been getting.  I also sent Chris a new copy of my DDIG- not sure if it was better or worse than the old one but it was different (he said it was better).  The highlight though was free hot chocolate- my reward for keeping the recruit from getting too lost on Friday.

14 ii 2012
0555- sleeping
1027- purifying sequencing reactions
1411- tea time
2211- talking online

Random fact- In some species female parrotfish can become male if the male leading the harem dies.

Lunch- lingcod and rice 
Dinner- Mas Amigas  

Submitting a plate is never easy, pipetting 96 reactions is enough to fry anyone's brain.  Couple that with having to purify a bunch of reactions before you even start and it's no surprise I had a bruised hand by the time I was done.  It took so long we even had to push lab meeting back an hour so I could get the SEQ reaction started by 1400 (the cut off for submission to the Keck Center since they close at 1700).  Looks like I'll be getting a new office- I'm not sure where yet but there is going to be a bunch of shifting around in the NRB and our office is way to crowded with 3 people.  Hopefully I'll get the one on the 3rd floor, its got sloped ceiling and a nice view...

15 ii 2012
1024- sleeping
1559- PEEC seminar on grass vs corn decomposition
1714- back at the lab clearing specimens
2102- at home reading a paper

Tundra peregrines often won't molt primaries 8-10 until sometime in January, when they are on the wintering grounds. 

Lunch- salami 
Dinner- salami and honey nut Cheerios  

At my biogeography discussion group I think I traumatized some first year grad students by telling them primers don't always work even, in fact, even when they work for closely related things they still may not work.  Oh to be young and full of hope for easy sequencing...  I also got the comments fixed on my DDIG and sent it back, so hopefully this round will be the last (excluding the preliminary results since I'm waiting for the sequences from yesterday's plate still).  I tried convincing Chris to send me to Australia but then he started finding the leafhoppers I needed so there went that plan.  He claims I need to work in the lab sometime, life can't only be field work, although I disagree.  Speaking of field work apparently I didn't tell KJ I was going to the Philippines, so now he's jealous- its 4th on his list (they have endemic families of birds), yeah the life of a grad student is amazing.

16 ii 2012
0257- playing World of Warcraft
1726- getting extractions set up
2016- eatting dinner
2359- working on the alignments

Random Fact-  AIC favors overparameterization of models.

Lunch- salami 
Dinner- cheesy cheddar steak burger  

I almost had a heart attack today since the first group of sequences I looked at were not the right lengths for the genes they should have been.  After BLASTing to discover they were in fact leafhoppers I figured out they were the sequences from my old plate and redownloaded the data (correct this time).  Overall they look fine, although the alignments are a bit strange on the Caliscelidae.  Systematics Discussion group was pretty good (once we got in the room, no climbing through the ceiling required), with plenty of laughter and random arguments about models (that's not a model, that's reality).  I also started some extractions of 10 leafhoppers from Australia- the last of the continents I needed represented. 

09 February 2012

Published and more

5ii 2012
0116- playing WoW
0310- playing online
0444- sleeping
2036- watching the super bowl

Random Fact- The Giants set a record of having the poorest season record of any Superbowl champion

Lunch- rice and sausage 
Dinner-burgers and brownies 

Brad and I went to Lowes to buy the supplies we needed for our various bird encloses.  We had to race home at 2 so I could do the WoW study I had signed up for, only to discover it had been canceled due to technical difficulties.  So instead we cut the lumber and assembled the long sides and decided we could start a custom budget construction company if the whole academia thing didn't work out.  About 1730 we went over to Chris's to watch the Super Bowl and have dinner.  I was happy the Giant's won and thought it was a great game- its always fun when a game where you don't have strong feelings about who you want to win goes down to the wire like that...

6 ii 2012
0434- sleeping
1057- on my way to campus
2024- at Mad Hatters with Eric
2233- setting up a quick BEAST analysis

Random Fact- Newfoundland didn't become part of Canada until 1949

Lunch- Freebirds steak, cheese, and sour cream burito 
Dinner- rice and sausage  

Eric and I had decided to meet up and make Ira take us to lunch which worked out quite nicely.  I found out Eric is considered a faculty member, a fact I find frightening.  I managed to get a tray of Xyphon databased, I'm getting close to the end finally.  The only really exciting thing I did today was some basic BEAST analyses with the new data.  I split out the Hecalus and so far it looks like there are two clades of Hecalus- a New World and an Old World group. 

7 ii 2012
0317- sleeping
0454- sleeping
1420- driving around trying to trap hawks
1950- dinner with Eric

Random Fact- You have to be on the graduate faculty to be on graduate committees, just being a faculty member isn't enough.
Lunch- Sausage plate and potato salad at J Cody's 
Dinner- chunky steak at Pho John's  

Had an unsuccessful trapping trip- saw a bunch of birds but they were all either uninterested or interested enough to come down but not hungry enough to land on the trap- rather they would land next to it and foot it from the side.  It was a really pretty day out though, with the sun shining it was a typical Texas spring day.  The big news though was that The Wildlife Techniques book is officially published, can't wait to actually get my copy of it.  I had a momentary scary though at dinner- since Eric is a faculty member now maybe he could also be on graduate committees, so I texted Ira and found out luckily that he can't.  As Ira said, the world is still safe. 

8 ii 2012
0159- reading a Victoria Thompson book
0240- sleeping
1539- databasing leafhoppers- 1 more drawer left
1720- at home watching TV

Random Fact- DIVA tends to infer ancestral ranges to include all the daughter taxa ranges because it treats vicariance as the null model (with a 0 cost) while disbursal and extinction have costs of 1.

Dinner- a pastry with ground beef and potatoes that Kira made  

Today I led the systematics discussion group meeting on Bayes-DIVA.  It went pretty well, and the fact 1/3 of the paper was spent bashing one of the profs who was in the group made it pretty amusing.  I think the paper was a bit advanced for some of the students, but it went well overall.  Amazingly, I found out the Jen in the group was the same Jen I went to High School with- she recognized me when I came in and I had been wondering about it myself...  Other than that spent the evening playing worms with Brad and Kira and doing some work in the lab.

05 February 2012

Good to be back home

0149- on the internet
0952- getting ready to go into work
1446- tea time
1742- packing up the truck

Random Fact- the size of hybrid zones in birds varies widely- in the tropics some zones are only a mile or so wide while in the central US zone can be hundreds of miles wide.

Lunch- Cheesy Cheddar steak burger
Dinner- lots of salami

The best part of today was (as it always is) getting sequences back.  Even awesomer was the fact only 5 of the 86 reactions I did failed (less awesome was getting a parking ticket while waiting for sequencer to open the files).  I also had my Skype discussion today, which went well except for that when I asked a question my computer crashed and by the time I got it up and running again they had moved on to a different topic.  Luckily I had tea with Kevin right after so I got to ask him about avian hybrid zones.  Loading up the truck took forever- it seemed like my stuff was scattered more than usual but I eventually got on the road about 1930.  Since I don't have a real phone charger the drive was kinda lame- I couldn't talk on the phone or listen to an audio book, but I made it work.

0451- sleeping
0937- getting ready to head off again
1323- driving
1940- hanging out with Brad

Random Fact- Traveling to Hong Kong does not have the same visa requirements as China itself- as long as you stay on the island you can just pick up a tourist visa when you arrive.

Lunch- the rest of the salami
Dinner- Plate at Layne's

After sleeping at a truckstop in Little Rock I drove the rest of the way to CS arriving about 1630 after 100+ miles of rain.  It was amazing seeing some green grass and the lake levels starting to come up after the awful drought we've had the past year.  Brad and I got dinner at Layne's, and went to Best Buy so I could get a phone charger.  I almost lost the charger though because I dropped part of it in the store, luckily I checked before we drove off and I was able to relocate it.  Today's excitement though was finally getting my Philippines tickets purchased.  Now we just have to come up with the itinerary so I know what gear to bring.

0601- sleeping
0721- getting ready to head in to the lab
1131- at work
1944- at Sodalaks with Eric

Random Fact- The Schmidt Sting Pain Index rates the relative pain/sensations caused by hymenopteran stings.  The descriptions are rather amusing...

Lunch- Lamb Kebabs
Dinner- steak and potato salad at Sodalaks

We had an amazing thunderstorm this evening, it featured tornado warnings, hail, strong winds, and a couple inches of rain.  Eric and I met up for dinner at the new Sodalaks (the one in the hole, as everyone apparently identifies it) and when the hail started a waitress opened a door to see if it was hail or not (it was).  Only problem was the door got stuck open, she got soaked and ran away, and by the time they got the door closed again there was a pretty nice flood going on.  At this point they closed the restaurant (but we had already placed our orders) and the entertainment portion of the night started- 6 waitresses trying to push all the water back out the door.  Ironically the 12 year old helper had the right idea of using 1 squeegee perpendicular to the door while the others parallel, but the older waitresses didn't like the idea and went back to pushing 3/4 of the water into the walls with every swipe. 

0423- sleeping
0939- still sleeping
1052- starting to wake up
1706- playing WoW

Random fact- Midland, TX has gotten more snow than Chicago, IL this year.

Lunch/Dinner- chili and bread

Took the birds out about noon, but both of them were being kinda pissy, they're still a bit heavy from the trip, so nothing too exciting today in that regard.  After dropping them off back home I went over to Jim Cathey's so we could try and figure out why Betsy's hazard lights don't work.  We ruled out all the easy things, so now it's going to be a major challenge, unless I get really, really lucky and it turns out to be a missing relay (which doesn't appear to be located where the diagrams say it is).  I spent the rest of the day playing WoW and working on my sequences.  I got everything aligned, even the 12s wasn't too difficult to fit into place.  

01 February 2012

lots of updates

27 i 2012
0039- playing online
0702- sleeping
1956- at the rec
2226- playing with Boo

Random Fact- Today is the day the National Geographic Society was founded (in 1888)

lunch- Steak and Shake
dinner- shrimp and rice  

Worked all day- the morning was spent finishing the extractions and the afternoon was taken up with doing PCRs and running a gel.  It's always good to see things light up when you flip the UV light on.  Assuming all goes well I'll be able to submit a plate before I head to Texas.  Not a whole lot else going on, just sat around and watched some TV while drinking Amarula and then quested.  Not a bad way to spend the evening.

28 i 2012
0229- trying to sleep
0619- sleeping
1055- driving to Charleston to deposit a check
1851- running PCRs

Random Fact-on this day in 1922 the roof of the Knickerbocker Theater in Washington DC collapsed due to a massive blizzard, killing 98 people watching a silent movie.
lunch- roast and pizza with Massimo and Brendan
dinner- steak  

I had to drive down to Charleston today and deposit a check.  This in itself isn't too bad, its only 45 minutes away, but I missed my exit and had to drive an additional 15 miles, which was super lame.  When I got home though Massimo and lunch waiting- Roast and pizza both of which were quite good.  Then it was off to the lab where I spent the day running PCRs, such fun.  I came home about 2100 and quested for the rest of the night.  I don't know what I did for the last 6 months without WoW to play.

29 i 2012
0056- playing WoW
0947- sleeping
1329- eating lunch with Mikey and Massimo
1713- purifying PCRs

Random Fact- The Santa Fe Opera house burnt down in the 1960's.  According to Santa Fe lore they really wanted to build a new one and coincidentally all the costumes etc had been sent out for washing the day before...

lunch- enchiladas verdes
dinner- fish sticks  

Mikey came into town briefly today- he was suppose to catch a 700 flight, missed it and then missed the next one out so instead he got lunch with Massimo and I and then Massimo took him to the airport.  I spent most of the day in the molecular lab running gels- looks like I have enough for my plate.  I also coded some morphology while waiting for the gels to run, so I was quite productive.  Excluding work it was a pretty quiet day, went and played with Boo for a while and then came home and harassed my dog.  Eddie and I also got our plane tickets for Egypt- we're leaving 7 March and getting back on the 18th, I can't wait [HRE]

30 i 2012
0228- wishing I could sleep
0537- sleeping
1037- taking out Boo
2140- eating dinner and working on the puzzle with Massimo and Brendan

Random Fact- Giza is only 20km from Cairo

lunch- salami
dinner- halibut and potatoes  

I got a sequencing plate ready to go today- ended up having to do a few more purifications and then Jamie and I loaded up the plate.  The sequencing reaction finished a bit after 1700 so Jamie will take it in first thing in the morning (and figure out the new submission protocol).  Other highlights of the day included getting an assigned tea time (1345 or so), finding a bunch of interesting biogeography papers, and going through some more morphology with Chris.  However, as Chris pointed out at the rate we're going it'll take us 20 years to do all the genera we need to score.  Massimo, Brendan, and I made substantial progress on the puzzle- most of the sky is done, I guess now it's time to work on the snow.

31 i 2012
0331- actually sleeping for once
0530- sleeping
1727- meeting John for dinner
2129- hanging around with Massimo and Brendan

Random Fact- Red imported fire ant has been found on a number of Caribbean Islands over the last 10 years, although so far not Dominica

lunch- the rest of the halibut and potato from last night
dinner- fish and chips  

My big accomplishment for the day as reading a ton of pdfs about biogeography.  These were mostly papers looking at various biogeographic analysis techniques, but a few looking at historical vs. current environmental factors in species assemblages, and one really interesting paper comparing RIFA introduced vs. native (and predicted vs. actual) ranges.  I also got a bunch of images extracted from Paralimnini pdfs and Jamie submitted the plate that we'd been working on.  We also had our lab meeting where we decided to start working our way through the Auch. subfamilies and talked about creating a new lab website.  I capped off my super productive day with a trip to the Rec with Massimo and while I only walked a mile instead of run (I'd eaten to close to when we went) I did up my weight for most of the strength training stuff...