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.

Emily wants to be a veterinarian, because it is an important job because she is helping animals. She informs me that my job, in cotton breeding and genetics, is a GOOD job, but not IMPORTANT, because I don't help animals or people.  

Christmas lights from the Christmas tree. Looks like electric fire 

Leila helped her sister with her senior project of sewing bags for the breast cancer center. 

Disaster for gingerbread land. Leila made a gingerbread house for Christmas. The Royal icing was stronger than cement though and we had to use a sledgehammer to break in.  

Leila's Mom got us a digital camera for Christmas and so we have lot's of pictures. They may not be good, but we have a lot of them. Here is Aleah up close and personal. 

Chronicles of Narnia: The Lion, The Witch and The Wardrobe

Leila and I went to go to a movie yesterday, since we are in Seattle and we have free babysitting from Nana, Grandad, Anna, or Blake at any time. It has been nice. It is almost like dating again, except I am not sleeping out on the couch by myself. Now all four of us are sharing twin beds along the back of the pit. We can touch heads at night and all talk.

When I saw the opening credits and saw the distributor, Disney, I felt nervous and worried that somehow this would be so disneyfied like Pocahontas or something. For once, they left the beauty of the original story alone. The few modifications do not detract, nor do they change the spirit of the tale. In one case, with Edmund in prison meeting Mr. Tumnus as the witch informs Mr. Tumnus of Edmunds betrayal, it adds to the weight of his actions. Aslan and the rest are magical, but the special effects do not come at the cost of the story or meaning. The makers of this movie loved the books.

I think this is the best movie of the year. I hope everyone goes to see it so that they will make Prince Caspian, The Dawn Treader, and The Silver Chair while Edmund and Lucy are still young. The Horse and His Boy could be made later as well as The Magician's Aprentice.

C. S. Lewis had an insight into Christianity as well as children. That period in England after World War II was a magical time for literature. It is hard to believe that J.R.R. Tolkein and him worked and wrote together in England. Maybe the combination of the trials and horror of the war along with the depression and the hope of the recovery was necessary. I really would like to study some more to see the effect on other writers. I wonder if our tragedies are enough to inspire such art.

Cover of the Life of Pi.  

The life of Pi

I just finished this book.

The plot is odd in itself. The main character is travelling across the ocean with his family and the animals from their zoo, when the boat sinks. The boy, Pi Patel, is thrown into a life boat along with a hyena, a zebra, an orangatang, and a bengal tiger. The boat quickly sinks and they are left the only survivors. The zebra's leg was broken in the fall and is already injured. As the only prey in a boat full of predators he is quickly attacked by the hyena. The hyena kills the zebra slowly and then tries to attack the orangatang. The orangatang holds its own for a while, but as the days go on and on without rescue, the hyena overcomes it and consumes it. The hyena is then eaten by the tiger. Leaving Pi alone in the boat with a full grown tiger.

He manages to establish himself as dominant by providing food and blowing fiercely on his whistle while rocking the boat enough to induce sea sickness in the tiger. Like a lion tamer in the ring, he tames the tiger enough to survive 227 days on the raft until he runs into Mexico. Meanwhile they run into a blind frenchman in a similar life raft, both blinded by the sun and poor nutritien. They also find a carnivorous island inhabited by thousands of meerkats and a very complex algae.

The problem is that I don't believe it. I don't believe any of it, and I don't think that the character does either. There is another version of events told in the end, but how true is that account. What does it all mean? What is the island? What symbology is he pulling from and why include it? The story at the end explains everything, almost, except the island. Which makes me think that it is as fabricated. But why? Why start the book by explaining that this is a story to make you believe in God? If anything it shows how in the face of necessity even the most civilized, Pi Patel is an ideal vegetarian religious example, will become as feral as a tiger. But I think I am missing something. Any ideas?

My dad, back in high school. I don't remember him like this at all. I haven't seen him for 15 years; he might be living in Hawaii. Last time I saw him he had a beard and put on a lot of weight. He also wore these darkish glasses. I was only 12 or 13 at the time and so my memory is not clear. 

Christmas photo outtakes.

Don't we look prettty

Christmas photos  

Aggie palm pilot

AGGIE Palm Pilot.

Aggies seem to care a lot about one thing. Beer. And bonfire, but some people died because, well, a huge tower of burning logs put together by Aggies . . . Not a good idea.  

Dr. Borlaug is my hero

Dr. Borlaug met with some of us graduate students to discuss his history in plant breeding and international agriculture. He won the Nobel Peace Prize for the "Green Revolution". He personally has changed the world agriculture forever. From development of improved semidwarf wheat lines to trade and economic policies he made it possible for farmers in India, Pakistan, Mexico and others to have access to fertilizer, credit, and fair prices. That coupled with his disease resistant, high yielding lines drastically increased yields around the world.

I want to go back in time and be his graduate student!!!. If you have a time machine, let me know.

Aggie clock

My boss, Dr. Stelly, sent me this forward regarding an aggie clock. I can't resist putting it up.

Emily says these are sweet smelling flowers and a butterfly to liven up your day. 

Sometimes professors just don't listen

I have had this idea to use quantile-quantile comparisons to analyze AFIS distribution data. AFIS is a machine that takes a cotton sample runs it through a wheel with little combs and separates the fibers. The individual fibers are blown into an airstream in a narrow tube. In the middle of the tube is an optical sensor that registers when a fiber passes, its length, and thickness. It can tell the difference between tangled and single fibers as well as trash. It then classifies the fibers into length, fineness, and maturity categories, while keeping count on trash and tangles, called neps. The distribution of fibers of different lengths makes a big difference on spinning quality. So people want to select for the best distribution of fibers, not just the best mean length or upper quartile length.

Quantiles divide the distribution into regular divisions like the median is the 50% quantile. The mean is not a quantile. It is not a rank. Anyway, the distribution, if continuous, can be divided into as many quantiles as one could want. A box plot is a representation of the 25% quantile, 50% quantile, and 75% quantile making the box. The whiskers are usually the 5% quantile and 95 or 97.5% quantile. The length values for the same quantiles for different distributions can be compared. If they are the same then the distributions are identical. If different the pattern of differences is how the distributions differ.

Anyway, to make a short story even longer and more boring, I went to a Statistics professor to talk about my idea. He thought it was great, but he never has actually got around to hearing how I want to do it. He has lectured me for two visits on the details of quantiles and distributions. Not that it hasn't been helpful, but he doesn't realize that I already know what he is trying to teach me.

I want to know if what he is calling a p-p plot, or a sample quantile-quantile graphical approach can be extended to more than one comparison kinda like covariance analysis. The y would be the quantiles of the check cultivar. The x's the quantiles of the experimental cultivar. The equation would be y = B1*[Year]*[X] + B2*[Replication]*[X] + B3*[Genotype]*[X] + [error variance], where [] notes matrix. The test would be to see if the slopes for genotype, replication, and years are equal, as well as the intercepts. If this is not right, then the other test I thought of would be to look at the deviations from x=y for each distribution. He did tell me about graphing the quantiles as y-x = x so that it is around 0 instead of a slope of 1, then the area under the curve can be calculated, deviations again. This number can be treated like a Wilcoxon type statistic. I just need to read up on Wilcoxon statistics I vaguely remember them in terms of nonparametric statistics.

I will put pictures up for the steps in the next few days.


Well if that isn't boring enough for you I don't know what is. I think with a few more posts like this I can cut my readership back to 0. I need to include a few references to swimsuits or hot chicks or cute girls or something in order to get someone to read the site. Statistics just isn't sexy enough.

My species, again. Stelly needs the picture. 

Harvest is DONE, uh, well, kinda . . .

Ok we are not really done. We have 7 rows left and I haven't finished measuring heights or counting nodes. Augh.

The weather has been beautiful since our rain last week. The temperature is down to 90 and the mornings are a brisk 70 degrees. Nothing like Texas Fall weather. Employers really should interview candidates in Fall or Spring. Summer is just too oppressive here.

My field has three hawks that circle around waiting for us to scare vermin out of the brush. The other day one was sitting on the row ahead of us. The cotton plants were bent over under the weight and there was a rattling of bolls and breaking of limbs when he decided to take off.

Yesterday the cranes were out in the recently plowed field next door. The humingbirds are gone though and I haven't seen a monarch butterfly for a week. The black irridescent ones still hang around the morning glory vines. The vultures have stayed near the river or the road.

This year I haven't seen any snakes, lizards or turtles. Last year we had a large turtle that I took in the truck back to the pond near the lab. When I found it the turtle hissed at me, but did not run away or try to bite me. I put it in a box and drove back to lab. Just as I turned into the parking lot he managed to lunge out of the box and land in my lap. He tried to bite me as I was trying to turn the corner, so I batted at him and knocked him onto the floor, where he decided to hole up under the seat of the truck. I managed to get him out without getting bit and release him near the pond. He didn't seem grateful though. Kinda bitter if you ask me for a refugie turtle. I guess he didn't realize that the field was going to be plowed under.

Aleah at the party with Sheetal.  

Cotton harvest

Rita did not even come close to detroying us. It veered to the east on the last day and destroyed Beaumont and Port Arthur. But, now it is raining and my cotton is half picked and still in the field.

The problem is that with every rain the bolls hang lower and lower and then the cotton falls out onto the ground. The seeds absorb the moisture in the wet lint and then germinate. The little cotyledons in the boll die as soon as the sun dries everything out. The seeds die and the husks of seed coats get pulled through the gin and into the lint that I have to send in for testing. The fiber also gets weaker and weaker with rain and sun as well as accumulating dirt and trash from the wind and rain. All and all, not so good.

But, what can I do? I can't change the weather. If anyone knows how, please let me know, although with my luck it would have side effects and cause tornados instead of raining. Or worse stay insanely hot. Can you believe that it was over a 100 degrees just over a week ago?

We have a new student here in the lab, Stella from Greece. She is very nice. She is just discovering how difficult it is working here where no one is checking up on you or helping you to design good experiments.

I haven't written about Sheng Mei yet either. In part because this is a shared computer that I use and my blog is often up. I will change the settings so that a login is required after screen saver so that I can write about her. she is a different sort of person. To get to know her very well, one simply has to go to catforum, a sad site dedicated to people devoted entirely to cats. She posts on it 10-15 times a day and tells all the mundane, but strange parts of her life.

All I am going to say is that she tastes the cat food before she will give it to her 5 cats. So they only eat cat food that tastes good?

Anyway. I should not gossip.

Who knows. Maybe cat food is good. I should ask my little brother. We dared him to eat it when we were kids and he did. Maybe he liked it.