26 July 2020

1341 trying to sleep but the juicer was too loud
1809 eating
1833 finishing dinner
2235 having cake

Food: bison burgers, salad, veggies for lunch

Fact: Kraak porcelain (the blue and white ceramic) was one of the first large scale exports to Europe from China.  There is debate about the quality of the porcelain- some scholars claim that the exported samples are the same quality as those produced for domestic use, while others say that the domestic varieties were much higher quality than what was exported.  Imitation porcelain was made world wide, including in the middle east, Latin America, the UK, and continental Europe.  Like China, the blue and white ceramics made in Mexico were created using a cobalt pigment, but in the Mexican variety the cobalt was applied much more thickly, resulting in very different looking designs.

Woke up to the sound of juicing.  The parentals were juicing citrus to make limeade and lemonade.  Still fighting with monophyly, but I think I found the problem (for real this time).  The sample that is causing the issue has very short average UCE length (like 100bp while the other toepads are in the 150+ range)  This doesnt sound like a big difference, but at the population level where the informative sites are outside of the probe itself 100bp doesnt get you into the informative areas- especially when you consider there is on average 1 informative site per uce.  This also explains why the mitocondiral phylogeny doesn't have this issue- the mt DNA has so many more informative sites that even missing portions of it you can still infer an accurate phylogeny.  We had lunch and then set up the sunroom for churching.  Talked to Eddie, Maria, and Kevin for a while before and after.  Then we hung around in the sitting room and had some Texas chocolate sheet cake.  Around 2330 mother took the puppies out and said the stars looked bright so we went outside and spent over an hour looking at the stars and taking pictures.  Mother and I saw a shooting star (father claims it was a glowing bat) and later mother saw another shooting star (she also saw a firefly she thought was a star lol).  We got some good pics of a bright star a little above the trees, and then we decided to get a picture of Jupiter.  However right as father got it all lined up the camera ran out of batteries so we will have to postpone that project.  Spent the rest of the evening working on the Accipiter stuff. 

25 July 2020

0621 getting ready to go to bed
0826 sleeping
0931 sleeping
2212 desert

Food: left over Taziki's for lunch, steak for dinner, fruit for dinner number 2

Fact: Alma Vilibalda Maximiliana Karlin was a Slovenian poet who wrote in both German and English  however, as the Nazis came to power she stopped writing in English as an act of protest.  Her works were burned in Germany.  Interestingly, although she grew up in a german speaking part of what is now Slovenia (but back then Austrio-Hungary) she thought of herself as Austrian. 

Woke up and checked on the various analyses I have running.  The gang decided we were going to Saudi Arabia tomorrow and I was in charge of bringing non-pork sausages for our dinner (one of the other guys was bringing the non-alcoholic beer) Then we had lunch, and i went to the beer store to pick up the beer I ordered. The owner is going to start letting me know any time they have new beers that she things I might like.  After that I put on the game and did worked on my computer.  Father and I grilled steaks and bison burgers then we had dinner.  We decided to have beer with dinner, and both had the Dragon's Milk reserve (with marshmallow and dark chocolate).  We both really liked it- the chocolate took the edge off that you usually notice with the normal dragons milk.  The game was pretty depressing and we lost pretty badly.  We watched a House Hunteers in Queretaro and the parentals recognized a lot of places they filmed.  Then they went to bed and I kept working on my projects while watching House Hunters (including one about an author who moved to Slovenia from the US).  I did take a short break to play some World of Warcraft, need to start running some raids so I can get more gold. 

24 July 2020

0309 trying to get the SNPs to run
1853 eating Mediterranean Food
2050 getting ready to drive out to look at the comet
2318 skyping with Eddie and Ania

Food: Take out from Taziki's- lamb, salad, potatoes, bread for lunch fruit for dinner

Fact: In the early 20th century the US tried cross breeding zebras with horses, donkeys, and burros to make a work animal that wouldn't get demolished by tsetse flies. The project started with Dan (USNM 221086), a zebra given to TR by the king of Abyssinia (now Ethiopia) in 1904.  As you would expect it was ultimately unsuccessful since the hybrids (and the zebras themselves) were not very easy to work with, and were pretty much only useful if harnessed with actual domestic animals to keep them under control.  After they gave up on that projet Dan was sent to live at the National Zoo until he died in 1919.

I ended up not going to bed until right around 0600.  I was trying to get the SNP calling pipeline running.  In typical Phyluce style the file names had to be very exact- uce-<number>.fasta.  The error "too many files open" wasn't exactly helpful for figuring that out.  Even before I ran into that problem getting all the files formatted into the random (and undocumented) structure was frustrating.  This is why biologists should consult with actual programmers lol.  Right as I was going to sleep my raxml tree finished and I discovered I had lost monophyly.  I decided just to call it a night and deal with it later.  When I woke up I started looking through alignments and started flagging ones where some samples (toepads) had high numbers of mismatches.   I also called REI and put a hang board on hold, and placed an order with the beer store.  Then I talked to Julie about some uce analysis ideas and also my gameplan for getting Accipiter finished.  Then we loaded up and headed to Huntsville. First stop was REI.  I saw they were having a deal where if you spent 100 bucks you got a 20 dollar gift card.  since the hang board was 80 i got a pair of socks and some chalk to get me up to 100.  Then I went to costco and did battle for our groceries.  Was mostly successful, other than blackberries and disinfecting wipes.  Once I finished we headed to the Mediterranean place and they brought our food out to the car and we drove home.  We quickly unloaded and then ate.  The food was amazing, and the balsamic dressing was so tasty.  Then we drove back out to the dam and took some more comet pictures.  Father has gotten the process down- he had the comet in view in the second picture he took.  He also took a movie and wants to try and stack the frames on top of eachother to get a crisper picture.  Mother wanted some moon pictures so we got a couple pictures for her both of the moon and the landscape.  Tonight I was able to see a bunch of Jupiters moons so that was pretty cool.  Then we headed home and skyped with Eddie and Ania.  After that the parentals went to bed and I kept working on the hawk stuff.

23 July 2020

0034 working on Accipiter
0422 working on Accipiter
0843 sleeping
2257 dessert

Food: tamales for lunch

Fact: Egyptian fruit bats communicate with conspecifics in roosts.  This communication isn't just generic but directed at specific individuals (unlike things like bird song which are broadcast to everything within listening range) and mostly concentrates on disagreements about food, space, or mating (https://doi.org/10.1038/srep39419)

Woke up and did some file editing so i can start analyzing the Accipiter data.  Then it was time to take Schubie to the vet.  Dr. True said she looked really good for a 15 year old dog.  The tech wasn't aware of her quirks and was really confused about the mint inside jokes.  She is on an anti inflamitory to see if that helps with her stiffness, if not puppy chiropractor time.  Once I got home we ate dinner, fed t

he puppies, and then drove out to the dam.  We first tried by the bank but decided we didn't want to sit in the parking lot looking sketchy waiting for the sun to set and so figured wed drive out to the dam and then come back.  But it turned out the dam wasn't very bright, and so we stayed out there instead since it was a perfect set up.  It was pretty cloudy, but an hour or so after sunset it started clearing out.  Father started just taking 30 second wide angle exposures in the general area, and after a few different spots actually got the comet in frame.  Then i was able to find it with the binos and showed mother while father took a series of zoomed in shots and different exposures.  The comet today was almost green, it was really cool looking.  The clouds gave it some cool depth also, although you could tell when we looked at the computer that the clouds really dimmed the comet.  The moon was also really pretty and i saw what father thinks was jupiter because it was super bright and had a visible moon.  Then we headed home (got stopped by a train with a bunch of hopper cars) and had dessert.  Looked at the pictures and then watched House Hunters while working on Catharus alignments.

22 July 2020

0317 working on Accipiter
0333 working on Accipiter
1758 working on Accipiter
1820 working on Accipiter

Food: burgers for lunch fruit for dinner

Fact:  After Haiti declared itself independent from France the French government required them to pay 150 million francs to France for the loss.  In fact the poverty, lack of access to education and heath care today can be directly traced to this.  Haiti didn't finish paying off the loans it had to take to pay this penalty until 1947.  Similarily, when slavery was finally outlawed in France and its overseas territories France paid the former slave owners for their loss.

Pretty uneventful day, spent basically the entire time working on the Accipiter alignments.  Since I have Julie's alignments now I got them all incorprated, realigned, and ready to concatenate.  Other than that we listened to the Yankees/Phillies game from yesterday.  Tomorrow is the opening day, we will see how that goes.  Then I watched some House Hunters International and called it a night.

21 July 2020

1439 working on Accipiter
1644 working on Accipiter
1952 taking Dumas for a walk
2059 looking for the comet

Food: tamales for lunch fruit for dinner

Fact:  Joe DiMaggio had bone spurs in his right heel and surgery didn't fix the problem.  He spent the first half of the 1949 season bedridden unable to even put weight on his foot.  Then one day he woke up and could walk on it.  He immediately went and and took BP.  His first series back (basically 2 days after getting out of bed) was at Fenway, where he his 5 homers and drove in 9 runs resulting in the Yankees sweeping the series (and eventually going on to win the pennant, after DiMaggio coming back for the final 2 games after being hospitalized with a 102 fever and loosing 18 pounds due to illness)

Yet again spent almost the entire day working on Accipiter.  The end is in sight luckily, but then I have to get started on the NAOC alignments.  It never ends.  Mother played a bit with fathers camera since last night we were trying to take a timer picture and couldn't get it to work.  She got some good pictures of the puppies and I, and also me and Matilda.  The tomatoes are really growing nicely and we should have a pretty good harvest by the end of the week.  I did take the puppies for walks.  The weather was really nice and after the rain it was a pretty amazing sunset.  We did try going to see the comet again, but were thwarted by clouds (and no lightening) yet again.  We came home and ate Texas Chocolate Sheet Cake which was taste as always. 

20 July 2020

0040 working on Accipiter
1459 working on Accipiter
1627 working on Accipiter
1829 working on Accipiter listening to Yankees/Mets

Food: tamales for lunch, fruit for dinner

Fact:Lyudmila Mikhailovna Pavlichenko (or Lady Death) was the most successful female sniper in history.  She was a Russian soldier who didn't want to be a nurse when she enlisted during WWII and eventually convinced the Russian Army to let her be in a combat unit due to her shooting experience.  She was one of about 2000 female snipers in the Russian army.  Her kill count was 309 confirmed kills.  Ironically, due to equipment shortages she was only issued an grenade, but when one of the other soldiers in her unit was dying he gave her his gun and she killed 2 enemies almost immediately.  She also was friends with Eleanore Roosevelt. 

Woke up and spent the entire day working on Accipiter alignments.  Julie also texted to say hers would be finished today so hopefully that is the case.  We listened to the Yankees/Mets exhibition game.  It was pretty amusing listening to John and Suzyn talk about how weird things are.  They are broadcasting from different booths, and apparently they will broadcast away games from Yankee Stadium watching video feeds.  At 2100 I had my draft.  It was a little annoying since most people autodrafted but the 4 of us that were drafting by hand were all in a row so it was really hard to predict how things would play out.  Luckily I put together a pretty decent team.  Garret Cole was my number 1 pick.  The parentals and I went out to the bridge again to see if we could see the comet, but it was too cloudy.  There was a pretty nice lighting storm in the distance so we watched that for a while and tried to take some pictures.  There mostly was just cloud lightening without any structure but there were a few really nice bolts.  We couldn't quite get the timing right so mostly just got pictures of glowing clouds.  After a while we decided we were getting too many mosquito bites and headed home.