Spring Chicken

Spring is here with planting, grass to mow, weeds to hoe, and work to be done. I don't think I will ever get ahead.

My first week here in Indiana my brother Marc and I talked on the phone and he asked me what my hobbies were going to be now that I was not in school. At the time I was a bit flummoxed because my previous hobbies included odd statistical techniques, going to school, and my family. Not much time was left.

So I was left with the prospect of having time to develop cool new hobbies. I started teaching violin lessons to a family in our ward in exchange for riding lessons for Emily. Then I was made ward clerk. Then we decided to buy our house in the country. Now I have chickens to feed, cats to feed, fence to mend, gutters to fix, barns to clean, yard to mow, garden to put in, garden to water, things to paint, clean, organize, Oh and large ants have been invading my kitchen in the last few weeks. So an ant extermination crusade is in order. The time putting kids to bed at night hasn't gotten any shorter and dishes still need to be done and bathrooms to clean. I guess work is my new hobby, it is a break from home work. I have finished a paper though on quantile regression and fiber length distribution analysis if any one is interested in that hobby.

I have included a link to an album of pictures of events at our place, just click on the picture that follows:

Spring chicken

My house is full of Chicks!

Th temperatures dropped down into the 20s the last few nights and so I have moved the chicks into the basement. We have old heating ducts that allow air movement between the basement and the rest of the house that consist of a grate with a hole. (Ah, technology) So you can look down the grate and see into the basement. We put the chicks beneath the kitchen grate and you can spy on the chicks down below without disturbing them.

It is more entertaining than reality TV. The cats sit in the kitchen and watch them for hours. I caught National down with them two times. She was sitting under the heating lamp while the chicks pecked around her. Fox was down once on the prowl, but luckily the chicks freeze and don't make a sound when they are scared. If they had ran, Fox would have chased them just for fun.

The other news I have is that Leila is pregnant, I don't know if I mentioned that before. She is going to have another baby girl in August. We are excited. She is feeling a lot better now, but is already starting to look pregnant and can feel the baby do acrobatics when she is trying to sleep.

Google April Fools

Google had a April Fools joke that just about made me about fall out of my chair. One of my professors should definitely subscribe to this service. I helped clean out his office and loaded box after box with notebooks full of all of his emails. All were in order by date. Ah the age of the paperless office. I think that cheap printers and email just have made the office more paperfull.


They had another about a new Google telecenter.

Ok, I just found one more. Google's proposed kit for upgrading internet service. At least I would be able to read email on the can.

Odd violin on ebay

I saw this odd violin on ebay and had to restrain myself from bidding on it. It has an unusual shape and is a 5 string. I have no idea what its tone quality is, but I wanted it. If I hadn't just pluncked down money for a new lawn tractor, chicken supplies, and fencing materials I would have bought it. I didn't get it obviously, but for some reason it appealed to me. Violins have not changed for probably around 500 years. Bows have updated but violins themselves have not. I think that maybe a little innovation is due.

What body types could be tried? What different woods would work? (Say that ten times fast with a woodchuck) What changes to violin music and performance could be achieved by different strings/bow/violin designs? Electric fiddles are neat, but to me rather unappealing. Guitars have evolved through time, but violin design is remarkably static. Maybe that is because they cannot be improved, but I would be interested in seeing the attempts.

Trial with Picassa web albums

We will see if this works. I loaded our winter pictures onto a google web Album page. I am not sure if I like it so these links may not last forever. But check out our deep snow - all pictures taken by Emily our budding photographer, the cats and their mice, Emily and Aleah. Leila is not in any of these. I will try and rectify that.

Click on the picture below to see the album. Let me know if you like it and I will try and load similar albums more often. It seems pretty nice.

feb 2007

Popcorn from Argentina.

Funny things Aleah has said

In a bid to engage Aleah in scriptures last week I decided to skip reading the Isaiah chapter from 2 Nephi that was planned and tell the story of Daniel and the Lions Den. I was good. Both kids were quiet with wide eyes. They were sad when Daniel was thrown down with the Lions but jubilant when he was saved. Afterward I asked Aleah to say her prayers before bedtime.

She looked at me and said, "Won't."

"Won't, what Aleah", I said, hoping it was something unrelated, like "Won't eat junk food." or "Won't play with sharp knives."

But, no.

Aleah responded, "Won't, Lions no eat me. " She had learned her moral from Daniel and the Lions Den: If you pray, lions may eat you.

Ay, Ay, Ay

Another.

The other day I came home and Aleah came up and asked, "Daddy, boy?"

I said, " Yes, Daddy is a boy."

Aleah: "Mommy, boy?"

Me: "No, mommy is a girl"

Aleah, relieved sound in her voice: "Oh, Aleah Boy!"

We have talked and talked about all of the people we know and who are boys and girls and some of the time I can convince Aleah she is a girl, but most of the time she ends up sure that she is a boy.

Garrison Keillor - "Homegrown Democrat"

While I was on my trip I bought Homegrown Democrat, by Garrison Keillor. He is the rambling personality behind A Prairie Home Companion, a weekly radio variety show detailing the times of the fictional town of Lake Woebegone, along with music, and NPR humor. His writing feels like he dictated the entire book after staying up all night downing capuccinos and arguing over politics. The sentances are long and can be cumbersome, but full of passion.

The wonder of the book, even though it rambles in and out anecdotes about growing up, attending the University of Wisconsin and the death of JFK, is that it mirrors many of the reasons why I also am a Democrat. I am a Mormon from Idaho who works with a popcorn seed company in rural Indiana, which means that my peers at church and work, my family, and most of my friends are dyed in the wool Republicans.

To most of which, my choice to abandon the Republican party is approaching apostacy, because the Democratic party is percieved to consist of socialists, abortionists, supporters of gay marriage, and unreasonable vegetarian environmentalists. The Republicans see themselves as supporters of Christian values of temperance, low taxes, traditional marriage, moral values, the American Dream, and the City on a Hill.

When I look at the Republican party I see whited sepulchres that advertise Christian values, the American Dream, the City on a Hill in bright letters on the outside, but behind the boardroom doors are happy to make deals with tobacco companies, the logging industry, the military industrial complex, the oil industry or who ever else holds the purse strings. I see the war in Iraq. I see Iran-contra. I see Abu Ghraib, Guantanamo bay, illegal detentions and nightime raids on Muslim American homes. I see oil wells in the Alaskan wildlife refuge, the loss of wilderness and public lands, high national debts, tax breaks for the rich, Jack Abramoff, and empty words to pacify the religous conservatists about flag burning, school prayer, and constitutional marriage amendments.

Garrison Keillor argues that the Democratic party, the ideal one he believes in, supports a social contract. This social contract argues that the government exists for our good and should do good. The government should support public works, public transportation, public schools, public welfare, public lands. The constitution and the bill of rights are the framework for this contract. Civil rights spring out of this contract, as well as responsibility to support public schools and services.

Unfortunately, these may not be the pillars of the actual Democratic party, but they should be. That is a moral standard I can grab on to and defend. It expands the morals of the party beyond gay marriage and abortion, as it should because the government does so many things besides marriages and abortions.

Back from Argentina

I spent the last two weeks in Argentina and Brazil, visiting the popcorn production there and walking through the research plots. Argentina had a disturbing resemblance to Illinois or Indiana and so I took very few pictures of the countryside. The towns and cities were not though. They had a vibrant feeling that rural United states has lost somehow. We went through the home town of Evita with her picture painted on the walls bearing only a vague resemblance to Madonna.

This is a park in downtown Buenos Aires. I don't know how many millions live there, but downtown and residential areas are indistinguishable. Apartments rise next to office towers and restaurants for rich and tourists sit next to small grocers and choripan (like a bratwurst) venders. The streets were clean and the food great. We saw one slum that reminded me of Nicaragua as we were entering Buenos Aires. It had house after house built of castoff corrugated tin and uneven wood slabs. It zipped by quickly and it is hard to believe that it existed when walking down the parisian shopping district or the well to do downtown.

Brazil felt tropical in comparison with rolling hills, palm trees, monkeys screeching in the distance and flocks of parrots overhead. The gauchos of Argentina have cousins in Brazil that run cattle there between the trees. Both drink mate out of wooden cups and metal straws. Both groups are contending with increasing cultivation of soybeans and corn. But one thing that was the same was the vibrancy of the agricultural economies. Agriculture was important enough that news about corn prices were on the front pages of the newspapers. People were as excited about the new Case tractors as we might be about new cars and the tractor dealerships had glassed in showrooms with the newest combines on turnstiles. Majoring in agronomy at the university was a sought after major and to be a Inginero Agronomo was highly sought after. Here in the heart of the midwest, the small towns feel empty, and agriculture is almost a four letter word. It is something that our grandparents did, but we are happy to leave behind.

While I was gone in the tropics, the temperature here at home plummetted and there was a blizzard. The night time temperatures were well below zero and our pumphouse froze again and left Leila and the girls without power. Matt and Todd from work came and thawed it out for them though and my neighbors came with their snowplows and dug Leila out. We had 17 inches of snow, but the drifts are 4 feet deep in places. The schools were closed all week due to the cold and then to the blizzard. Emily has been in heaven since she has been able to shovel snow and play outside in her snow clothes. She has been making snow tunnels for the cats. They run in and out of them trying to catch each other, jumping on top of each other and rolling in the snow and then begging to come inside once they are wet and cold.

It is good to be home.

Procrastination on writing a paper

I have officially graduated now. I got the diploma in the mail this week in a red cardboard tube declaring me the proud recipient of a PhD. But, somehow it doesn't feel done, really. I still have papers to write and now I am in Indiana, far from Texas and far from motivated.

I want to write a paper on quantile analysis of AFIS data, but I just can not seem to make myself write it. Right now I have the time, I have a half hour to go and to the end of the day though and have not written a word. Procrastination always brings out the blogger and internet surfer in me..

Moving, New House, and blogger update

I have not written for too long. Much has happened:

we moved
Gas leak
Pipes froze
Chicago meetings
Decided to grow a beard
Argued with old apartment management and stormed out
Mouse under bathtub
Cats
Bones in Barn
Christmas is coming


we have not reconnected our internet at home and so we feel cut off from the digital world.

Fall Fun

The leaves are just about all down now, but before they were Emily and Aleah pushed them and piled them and ran in them. Winter keeps threatening to come and then it backs off. It gets cold enough to snow and then the winds change and then for a few days it is warm and sunny.

Aleah is sick today and threw up last night every hour on the hour. Today I stayed home with her during church. She was so tired that she actually asked to go to bed and immediately fell asleep when I put her down. Right now she is feeling good and asking for "anya, Oh wawo, me, up, Oh daddy, Fidge?" Which translated means I want some candy(anya). If someone moved a chair(wawo) up next to the fridge(Fidge) I could get some candy down."

Tomorrow I am going to the Crop Science Society meetings in Indianapolis. I hope that they will be useful for my work. I was hoping that Leila and they kids will go with me, but now Aleah is sick so they will stay home. 

Our new house

As they say in Zaboomafoo, "We are going on an a big adventure and we don't know what's in store!" We are going to buy this farmhouse and a chunk of the farm. It is out in the middle of nowhere, but only 5 minutes from my work. We decided that we might want to try the farm life after we spent all of our Saturdays at Prophetstown state park, a living history farm north of Lafayette. So we are going to try it out for ourselves. The girls have been making a list of animals to get:

cat, to catch the mice, rats, moles, etc.

dog, to chase the cat, etc,

horse - actually may be a possibility, the Nefs, from church, have 11 horses and need somewhere to board a few,

chickens, of course,

goats, we are not so sure,

giraffes, elephants, hippos, all possible zoo animals.

Any suggestions? 

Sand Dunes in China

I was playing with google earth and found the sand dunes in the desert between China and Mongolia, somewhere north of India. I just couldn't get the picture out of my head. 

Aleah trying to play the violin

Aleah is fascinated by the violin, she is just too little right now. That doesn't seem to stop her too much. 

Emily harvesting corn at Prophetstown

 

New House

We made an offer on a house last week. It is a farmhouse ~ 5 miles from my work. We have agonized about where we wanted to live and what kind of house we were looking for. This was worsened by the huge housing market here. There was a big building boom in the 90's and housing prices have been stagnant since then. That means that there are lots of houses for sale, especially older homes that Leila and I liked for reasonable prices. We debated whether we want to be as Leila says "city mice" or "country mice." My work is about 10 miles south of town, so moving closer to work means further from town.

There are some nice little towns in the area. The closest is Romney at ~ 1 mile from work, but four houses were for sale (out of maybe 50 total). Three were on the highway, and one was two bedroom and like 300 sq feet. Linden, Attica, and Crawfordsville are further south, also quite nice. New Richmond is to the west; it is where Hoosiers was filmed. I was dissappointed to find out that the gym in the movie has since been torn down. It is quite picturesque. To the east are Clarks Hill and Stockton. Lots of the houses for sale in these areas were built in the early 1900s. These little towns are quite small with less than 500 people in most. Crawfordsville is larger.

The house we put an offer on is a farmhouse, built around 1920. It has a large pole barn and walnut trees around it. It has an attic bedroom with sloped ceilings and a gabled roof. The kitchen is smallish and needs a new stove and refrigerator. There are wood floors in the bedrooms and under the carpet in the living room. It only has one bath, but it has a nice cellar. The washer dryer hookups are down there as well as a root cellar and the furnace. This is the house that we saw, liked and wanted to see again after we had pre approval from the bank, but then someone else made an offer by then. We thought it was out of the picture till last week when our realtor told us it was available, the financing fell through for the other buyers, but we had to move fast. We made an offer, but we haven't been back to tour the inside. There are many details that we don't have because of that, but we feel good about it. There is room for an orchard and for us to get some animals for Emily to take care of.

The dissertation is finished

I have finally finished all of the details with my dissertation!!!

After my defense, there were a bunch of comments from my professors that I had to incorporate into the final draft. Some were minor, like whether upland cotton was capitalized (But, we spent 20 minutes in my defense arguing about it and then it came up again and again in the last month), but others were major and required new analysis, new figures or tables, and inclusion of a summary chapter. I turned in a pdf copy to the thesis department 3 weeks ago and then they reviewed it and sent me 58 corrections to make. Most were technical details like placement of page numbers on landscape pages or wording of the abstract. But some involved changing the way I referenced tables and figures throughout the entire text. Minor, but tedious since I have 48 tables. I made those changes and then sent it back and they sent back 10 more requested changes. I have made those and now it is done.

I just have to pay my diploma fee and my dissertation review fee and I will be Dr. Gardunia.

Texas A&M is fee crazy. I had to register for one credit this semester that cost 470 dollars. The fees for that one credit upped the bill to over a 1000 dollars. Then, I have to pay a diploma fee, a graduation processing fee, and a dissertation processing fee. And there are no options, unless I didn't want to graduate, but there is probably a fee for that too.

Einstein

I have been reading Essays in Science by Albert Einstein. That he is a genius is already established, and so I won't go on too much about it. He does a good job explaining his cutting edge physics in ways that at least I think I understand. That is the worst of it. It feels like being blind and listening to an art lover lecture on the brush techniques of the masters. The words he uses are mostly familiar, and the math he mentions seems to call up names I heard in my calculus classes years ago: LaPlace, Fourier, Etc. But, I can't see what he sees. It must be like having another sense to have intuition and perception of the world tied in to mathematics.

It is a joy to read and I recommend it. I read his other essays on Zionism and politics in highschool and he is a persuasive writer, even when he does not talk about his world of physics.

We are doing well here in Indiana. We have not yet decided on a house. We found a place that we wanted, a little farmhouse with a few acres, near my work, but someone else bought it before we put an offer. Then we found another farmhouse with a few acres far from my work, but it is apparently gutted with no electrical or mechanical or drywall? We will see today to see how badly gutted it is. There are a lot of houses for sale and that is part of our problem. There are nice houses in town and there are houses in the country. There are some right near my work, but there hasn't been one that is just right I guess. I will try to put links up to some that we are looking at or some pictures this weekend.

Battleground, Indiana

We went to Prophetstown state park this last weekend. It is the site where Tecumseh had his city and ultimately his defeat by the US army. On the site is a working farm with 1920 equipment, varieties, house, etc. Leila and I love this kind of stuff, but Emily says that "it was a disappointment." I can't see how since the farmer let Emily pet the newborn calves, all of the cats, the sheep, and shell corn. We are going back this weekend for the 1920's county fair.

Bolivian jail

The BBC has a photo tour of a large Bolivian jail where the inmates can buy good cells or rent them out. They have food venders and a futbol field. Children live there with their fathers and attend local schools. Such an odd arrangement. It is like a country unto itself. The inmates are expected to manage local affairs and there is apparently an internal government that deals out justice for violence, etc. It used to allow tourists, but apparently the cocaine there is the best in the country and so many visitors came to buy drugs.

It is a surreal story that is hard to believe, except there was a smaller version of this jail in Viacha where we lived. It was small, but venders and people came and went. Prisoners, we were told, were expected to have their own food and medicine. It certainly cuts costs, but it just seems unreal.

Things are good here in Indiana. I will put up some pictures when I get home and write more.

Indiana, Defense, and Popcorn

There is so much to write. These last few weeks have not given me that much time and I have neglected writing here.

1. Monday, July 24th I practiced my defense presentation
2. Wednesday, July 26th we closed on the house.
   
3. Thursday, July 27 I defended my dissertation.
   
4. Friday, July 28th we left Bryan, TX for Aunt Sandra's.
   
5. Sunday, July 30th we started driving North and made it as far as Anna, Illinois.
6. Monday, July 31st, we arrived here in Indiana.
7. Tuesday, August 1st. I started work

So things have been a bit hectic. I worked on my presentation all weekend and then on Monday I gave it to the lab. Tuesday the movers were supposed to come at 8:00 AM, but did not come until after 11:00. I had promised Stelly and the lab that I would go to lunch with them as a farewell that day and the two movers took forever to finish loading everying, not that I mind that; they seemed to be careful. Leila let me go about 1:00 to go to the end, but noone had ordered, they were waiting for me. I worked on getting everything in order with my seed and office that day and also Monday. I had four boxes of stuff from my offices as well as one box that I wanted to take in the car with lab notebooks, etc. It just felt so unreal that the end was coming.

Wednesday I worked on my presentation and then we went to the title company for closing, which took quite a while since there are 10-20 lbs of paperwork. There are so many fees. We paid 8-9000 dollars in fees and so did the buyers. We were starving. Tuesday night we stayed in the La Salle Hotel in downtown Bryan. It was very nice, but the girls had a horrible time falling asleep.

I wasn't there because I had went home to finish working on the bathroom sinks. We had committed to stopping the drips in the sinks, thinking it would be a simple job. Unfortunately, the inside of the faucets were all rusted out and taking the handles off to replace washers was impossible. The only thing to do was to replace the faucets. I tried replacing pipes and shutoff valves first because the faucets were fused by rust and crustiness to the sink. The plastic deals that held it in place were stuck and even with the tool that the Smiths loaned me I could not get them off. The only thing left to try was drilling holes in the plastic thingamagigs and the faucets with AJ's, our neighbor who had us over to dinner that night, drill. I fixed them both, but as the son of a plumber it was not as easy as it should have been.

Wednesday and Thursday I spent preparing for my presentation. I didn't finish until lunch time on thursday. I prepared three presentations: one overview, one on methods, and one on stuff I didn't have time to talk about in the other. I only used the overview . I will try to atleast get a screenshot of the title page up. The slides looked pretty good, I will toot my own horn about them. My presentation was at 2:00 so I went to lunch with Kelly and then walked to the HEEP center to set up.

Things started out badly when we realized that I had not arranged for a substitute for Dr. Monica Menz, nor had I taken her off of my committee. She and her husband, Dr. Javier Betran, who is also on my committee, moved to France. Dr. Betran was there finishing up his corn harvest, she was not. Dr. Stelly scoured the halls for unoccupied professors. Dr. Dirk Hayes came by to get coffee so he became my new committee member. I started at about 20 after two and finished about 3:15.

Stelly made the audience ask questions. Leila asked about what my results says about the utility of random mating for breeding. That was a tough question that carried over into the next part where the audience leaves and I am left with the committee. Dr. Smith asked about whether upland should be capitalized or not. He also asked about which generations should be used for making assertions about random mating. I had to admit that my choice of generations was not right. The best would be to compare the F2 derived rm families. I think that there should be intensive study of that generation anyway to look at interspecific barriers. My BC1F2 etc were not well suited for that either. Too many other things going on. He also asked about my use of the term hybrid breakdown. This comes from good F1 yields, but disasterously low F2 yields. This to me is breakdown of the hybrid in later generations. To him, hybrid breakdown would be low fertility of the F1 generation. Dr. Betran pointed out that I had analyzed heritability wrongly since I had used the combined set of populations which are genetically different and so confounds heritability calculations. The Parent-Offspring regression also is wrong, since the slope needs to be adjusted by the covariance of the BC1F1 to the BC1F2 and BC1rm1 generation. I was a bit taken back by this since he had helped me set up the analysis, but they are things I can fix. Stelly asked me about day length sensitivity and breeding questions. There were more questions that I don't remember clearly, but at 5:45 it was over and they all shook my hand and gave me hugs. I had passed. It was over.

We went to dinner with Kelly and Bonita at Oxford square and had steak dinner. We spent that night with Bonita and then that afternoon set off for Sandra's. I had some things to take care of at work. I had forgotten to fix the gin and the seed room needed to be cleaned and organized one last time. I also went through the DNA lists, etc. After that I said goodbye and we were on the road.

Emily's Birthday

Emily went for pictures today. She is turning 6 tomorrow. It is dumbfounding that I could be her parent. She is growing so fast.

She has started reading on her own more and more. We were in the car the other day and Leila and I were discussing what to get her for her birthday with important words spelled out loud. Emily in the back seat started spelling things back to us. From now on we are going to have to speak in Spanish or French to discuss things around her since she is learning to read.

She is having a party tomorrow with her friends from school. Since we cook together often, Emily has started making up her own recipes. Often they have sprinkles as a major ingredient. She asked to make one of her recipes instead of a birthday cake for her party. We figured, why not? So Emily is making Jello with marshmellows and whip cream. I think it has sprinkles on the top and they are going to have pink cookies that Emily picked out from the store.

Happy Birthday!!!

Emily 

Brian's Brain

I had another "seizure-like episode" two weeks ago and so my doctor ordered a bunch of tests. The prognosis is not in, but I did get a copy of the MRI results to look through. I wish I knew what I was looking for. I can tell which is my brain, but what is normal? The ones on the right have a dye that they injected in my arm, the ones on the left do not. 

Gypsies by Robert Charles Wilson

This is a little known science fiction book from the 1980's, that I bought when I was in highschool at my favorite store, Redux - Used Junk. It was wedged between a comic book-sci fi store and someplace that bought used jeans on Broadway, near Garfield school, in Boise, ID. I used to stop in there and talk to the owners on my way home from school and if I had any money I bought a paperback for a dollar or two. I was was drawn in by the eclectic shop and its bohemian owners that made their living as waiters to pay the bills while running the store in between trips to South America in their VW bus.

Whenever I read Gypsies, I think of their store. When I see the characters in my head, I see the owners: the beautiful, but aging hippies. It is the tale of a family that has the ability to step between alternate realities. The spectrum of possibilities being infinite they are limited by their imaginations to the worlds they can find and explore. But, they have not really explored or even used their talents. The family consists of three children Karen the oldest and the responsible one, Laura the ex hippy, and Tim the rebellious angry youngest brother, now grownup. Their parents were killed gruesomely and they were raised by adoptive parents. Their adoptive father, Willis, saw their skills as evil and beat them violently whenever he caught them "making doors" or "windows." This because inevitably afterwards they would be pursued by "the grey man" that had murdered their parents. Willis wordlessly would move them to a new location, beat them all soundly, and it would all begin again.

The story begins with Karen's divorce and realization that her son Michael has their talent, and is pursued by the Grey Man. She runs to her sister, Laura, and together the three attempt to find out the truth about their family and their talents. In the process they have to confront Willis, their brother, Tim, the Gray Man, and even travel to Novus Ordu, an alternative America where magic is real, and their parents were created as part of a mystical military industrial complex.

What makes this one of my favorite books, is that the bulk of the story is about the family, about the consequences of what happened before they want to remember. The need to understand feelings and memories suppressed since childhood because of unravelling adult life is also very real, and grounds the fantastical premise of the book. The characters are mundane, normal, but that is a great strength in a genre where too often all the men are ruggedly handsome, miraculously resourceful, and the women beautiful, busty, but shallow and unimportant. It makes the incredible situations believable.

I also love the descriptions of the worlds, that feel real enough that they could be out there, if only we knew how to get there.

Leila

 

New job in Indiana

Pictures of Ag Alumni, my new job. I am trying to get the video shots from my camera to load. I don't think that they did here, but it is worth the try. We went to visit this last week and are excited to go. Leila liked the area; the schools seem good and the neighborhoods are nice.

 

We are selling our house.

We just got our house on the market, after my friend Jim decided not to buy our house. Here is a link to the realtor's site with a virtual tour of our house.

Evolutionary humanism

I was listening to NPR yesterday while I was driving. The show was New Dimensions, which is a New Agey show. They had on two self-professed evolutionary humanists. They discussed evolution and the meaning it gave to their lives. They kept using religious terms to discuss the role of evolution. At one point the woman said:

(paraphrasing)
'I was thinking about why people should do good, or be moral, in a world without God, and I realized that evolution had the answer. The story of the creation of the world and our evolution had sacred meaning and that our responsibility was to ritualize it so that people can internalize it. '

How evolution can give them this meaning, I don't understand. I am a plant breeder, officially so when I get my doctorate this summer. Plant breeding is basically applied evolutionary principles and genetics to improve crop yield, disease resistance, etc. Evolution is not the same as artificial selection in that it is not purposeful. As described by Darwin and later evolutionists, there is not a direction to natural selection. It just is. There is no drive in nature to create us, as described by evolution. There is no meaning in our evolution; the biology does not attempt to discover that, nor the motivation. There is no morality in evolution. The changes in gene frequency due to selection or population dynamics hold no clues to how I should treat my brother or wife or children. They just describe the flux in the natural world.

That meaning, to me, can only be described with religion. I am also Mormon and believe in the same time in a religious creation that was purposeful. I still believe in the scientific principles of evolution. At the same time, I detest scientific creationism because it's basic message is that spirituality and creation are scientifically as valid as evolution; that they are equal. This weakens the science because it must fit assumptions of Genesis. This weakens religion because then it can be disproved as easily as Lamarkian inheritance.

My problem with scientific creationism is that it implies that the things we don't understand are "God" and the things we do aren't. I like that there are things like the dinosaurs that aren't explained in the two chapters in Genesis. I like complicated world where given time and isolation new species can evolve. I don't understand how human evolution fits with the Adam and Eve, but I can't deny that the fossil evidence exists and is pretty good. To me these things give the world a beauty and I want to understand them. It does not take away from spirituality nor does it replace it. But at the same time it is a testimony to me that so many things do fit with the Genesis creation story.

Aleah, trying to do a gymnastics routine from her highchair, not her favorite place to be.  

One our few bluebonnets that grew this year. We keep meaning to take a family picture in the bluebonnets, and then we procrastinate and they are gone. So here is our bluebonnet picture for the year.  

Emily all grown up 

Help with SAS

When I run the analysis to calculate repeatability, I used the code:

PROC GLM data = work.gma_must_yield;
class gen env rep;
model seedcotton = gen env rep(env) gen*env/ solution;
random gen env rep(env) gen*env;
run;

This gives me a table at the end of
The GLM Procedure
Source Type III Expected Mean Square
gen Var(Error) + 80.225 Var(gen*env) + 240.67 Var(gen)
env Var(Error) + 47.117 Var(gen*env) + 126.58 Var(rep(env)) + 471.17 Var(env)

rep(env) Var(Error) + 249.89 Var(rep(env))
gen*env Var(Error) + 84.48 Var(gen*env)


If I understand correctly, the numbers preceding Var(comp) are the constants and solving for each V can be done my subtracting the correct MS, dividing by constant. Why are these constants outputted by SAS not equal to those predicted by multiplying the degrees of freedom not associated with Var(comp)?

I also tried using code:
PROC VARCOMP data = work.gma_must_yield method = reml;
class gen env rep;
model seedcotton = gen env rep(env) gen*env;
run;

and

PROC MIXED data = work.gma_must_yield method = type2 cl;
class gen env rep;
model seedcotton = ;
random gen env rep(env) gen*env;
run;

VARCOMP with reml, ml, type1, type 2 all give different estimates. REML and ML are the highest. Type 1 and Type2 are very similar and contain negative values. These match those I calculate by hand with the constants given with PROC GLM pretty close. Mixed analysis gives the same, as long as the methods are the same. What is PROC GLM using to calculate the constants? Why are they different for gen and env? Should I just ignore them and use results from PROC VARCOMP?

Why can't it all be simple?

Nesting time

I am sitting at my computer procrastinating writing my dissertation. The birds outside the window seem to hold my attention better then analyzing my cotton plant heights and yields for genetic effects.

There is an annual vine that seems to attract chickadees, sparrows, cardinals, grackles and mockingbirds. It has no fruit yet or flowers, but plenty of dead twigs from last years growth. They all take turns hopping up and down the main stems and tugging at the last year's growth until they can pull a branch free. Then triumphantly they take off. I assume that they are making nests.

It is that time of year. Even here, for me. We are getting the house ready to sell. Leila has cleaned out the flower beds. We've washed the cabinets in the kitchen, painted the living room, painted Emily's room and the office, put up crown molding, repaired the damaged drywall in the closet, and still there is a growing list of things to do.

The worst of them is replacing 4 tiles in the kitchen. They had bubbled up and in a feverish fit I tore them up, fearing water damage or an invasion of tile eating ants. Instead we found nothing. This was supposed to be easily fixed with matching tiles saved in the attic, but now I can't find them. Apparently we have unique tile. It is almond colored, smooth, and THIRTEEN inches x THIRTEEN inches. Who ever heard of 13 x 13" tile? We found matching 12" tile, but no luck on 13" tile. So if anyone has 13" uniformly almond color, no texture, no pattern, just smooth, tile please have pity on me. Send them to me!! I beg you.

The crew and I. That sounds like the title of a musical.  

Measuring the plants and taking notes. The biggest difference between the experiments here and there is that in Mexico there were no day length issues. The F1 yielded well. The BC1F1 did very well, but the G. mustelinum parent did not have any bolls yet. Apparently it has not only day length sensitivity but also a juvenile period. Not to mention that it grows slow. But, some of the random mated material did great. 

Dawn in Mexico with my plants and I.  

Don't tell my children

I have to confess something. As I lay awake listening to my youngest cry at 12:30 AM a few nights ago, I realized something. Crying works. It gets you what you want. I don't think that it would work for me, but for my children certainly. I have little to no resistance to it. It tugs at me. When I here that cry there is a compulsion to do whatever possible to make it better, to make it stop.

Aleah has not been sleeping through the night. She wakes up two or even three times, cries, gets fed, and then goes back to sleep. We have tried inconsistently to grit our teeth and try to get her to fall back to sleep by herself, but by 2:00 AM I am too tired to be tough. I just want to go back to sleep.

We have continually told Emily that tempertantrums are not the way to get what she wants, but that is not true. Of course it is the way. It isn't a good way, but sometimes the desired result is acheived. Crying and tempertantrums, most of the time work. The other thing she does that works is go boneless. She just collapses into an amoebal state. It helps to get out of practicing her violin.

One last picture from Emily. There are about 8 closeups of plastic cows.  

Another of Emily's photos. Actually pretty good pictures.  

Emily has found where the camera was hidden away and took a series of pictures of her toys and my shoes. 

Job decision and skin disease

I am going to be a popcorn breeder after graduation! Leila and I really agonized over the decision, well I have at least. Leila has felt good about this from the beginning. I have been unsure, mostly because the potentiality of the Bayer position was so good, but it just didn't look like it was coming to pass.

So last Thursday I called Ag Alumni and accepted the offer. Within the hour, my face and neck were burning and red. My eyes had been itching earlier, but now I looked like I had a sunburn across my face. Then in a few hours it had spread to my chest, arms, legs, feet, hands, etc with a burning itch like poison ivy complete with tiny blisters. I went home early and went to bed. The next day it was worse and I went to the doctor. He told me it was an allergy and probably not rubella, unless I had been exposed in the last 72 hours, and gave me antihistimines which made me very tired and ferociously grumpy.

My logical conclusion to this was that I was allergic to my new job and I had made the wrong choice. I stewed and worried, while trying not to scratch, for three days. Then, I decided, while lying in bed that I would turn back down the job, but I still needed to hurry and start to write. Deadlines are here and I have been anxious about writing my dissertation for a long time and it has been building like pressure inside of a geyser. At that moment, as I lay in bed thinking about what I needed to finish my proposal and get started on my first chapter, The rash spread like fire ants across my body and I could feel the blisters swell. The itching was tremendous.

So from that fun experiment, I decided that I had better get up and start writing. So I got out of bed, plastered myself with calamine lotion and headed for the computer. The closer I got to the computer, the worse the itching. By the time I sat down at the computer my hands and fingers were so swollen that I could barely type and couldn't concentrate. I gave up and went back to bed.

So either I am allergic to my new job or to writing my dissertation. It could also be the Cashew fruit I ate for dinner the previous night. I use to eat it in Nicaragua, mostly in Villa Venezuela, where I did break out in a nasty skin rash also come to think of it. OK, so I am either allergic to cashew fruit, popcorn breeding, or finishing my PhD. Let's hope it is cashew fruit since I can cut that out of my life with little pain or sacrifice.

I guess it all could be a psychosomatic anxiety attack. Some people hyperventilate, some people get dizzy, I break out in leparous rashes.

Emily with her violin. We don't have a clear practice program yet. Needless to say we need to work on it.  

So you have a Ph.D now what?

I am approaching the end of my Ph. D. and am looking for jobs. The good news is there are jobs. The bad news is I am not sure which I want. The sad thing is that I have been in school for almost 10 years and I am not sure what I want to be when I grow up.

There are really four kinds of positions available to someone with a Ph.D.:

1. Work for the government. For me that means USDA, usually in a plant geneticist or plant breeding position. Once and a while there is a germplasm curator position. More and more of these positions are molecular biologist positions. I think the reasoning is that molecular markers allow dissection of traits, etc. etc. but the long and short of it is that they publish more.

I don't think that I want to be a molecular geneticist, otherwise I think USDA positions are great because of steady research funds, job security, and good pay. I want to be actively involved in research, and I am not sure that I can sustainably work with markers. Currently, there is a Sudden Oak Death position in California and probably some postdoc positions.

2. Be a Professor. Teaching 1-3 classes a semester, advising graduate students, being on committees, writing grant proposals, publishing papers, trying to get tenure. Will the fun never end?

Life after tenure seems pretty good and pay ranges from 60,000 - 90,000 . Working with students is rewarding and there is a lot of lattitude for research and time. I have applied for three or four positions, including one here at A&M in cotton breeding. Too many professors seem to find better things to do than work at the bench or in the field.

3. Private industry. Make good money, see the world, sell your soul. Trade secrets and the bottom line make publishing in journals and presenting at conferences a very low priority. The good thing is that they also focus research into economically viable, and I guess that could mean important areas.

Seed companies are the main source of employment options for me such as in cotton: Bayer, DeltaPine, Phytogen, Monsanto, and a number of small companies. Outside cotton, the big players are Dupont which owns Pioneer, Seminis, DeRuiter, and many more depending on crop.
I have a job offer from Ag alumni seed, a small seed company in Indiana. They are looking for a popcorn breeder. There is also a possibility of a job with Bayer Crop Sciences as an experimental breeder. It is an interesting position because they seem to want someone that can pull together molecular as well as field data and start to integrate information that is coming out of genomics and mapping. They want to start interviewing candidates next couple of weeks and I would find out in the next month. I think that I would have a decent chance at it, but the popcorn company would like an answer before I would hear from Bayer.

The beauty of a private company is that there are no grants to apply for, no tenure to earn, no classes to teach and no graduate students to advise. The negative is that profitability drives promotion and retention. I have not worked in that environment and it is intimidating to jump in.

What to do? What would you choose? Is McDonalds hiring?

Timeline to graduation

There is so much to do between now and graduation. I feel like I have procrastinated so much. I am running markers right now in Dr. Menz's lab along with Stella and Nilesh. Things are working I just am frustrated with the politics of it all. That is all I dare say here, but if you want all the juicy details email me and I will give them all to you. I just wish we could all get along.

I got a JOB OFFER from Ag Alumni Seed!!!! They are a small popcorn breeding company owned by the alumni association of Purdue. They licence all of the wheat, soybean, and corn lines released by the Purdue breeders as well as their own popcorn lines. Their biggest competitors are ConAgra, a behemoth of a company, and Weaver, a local company. They are in Indiana, just outside of Lafayette, about an hour from Indianapolis. They are offering not bad pay with pretty good benefits. The town is nice, the company is small with good people working there. I feel like I could learn a lot from Max Robbins, the breeder. I think I could feel at home there. The negatives are that it is far from a temple about two and a half hours to Chicago, IL. It also doesn't involve teaching or will pay as much as some jobs, ie Bayer.

Well, back to work.