Friday, December 23, 2005
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.
Tuesday, December 13, 2005
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?
Friday, December 02, 2005
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.
Thursday, December 01, 2005
Wednesday, November 23, 2005
I want to go back in time and be his graduate student!!!. If you have a time machine, let me know.
Thursday, October 27, 2005
Wednesday, October 26, 2005
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.
Monday, October 24, 2005
Thursday, October 20, 2005
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.
Wednesday, October 12, 2005
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.
Wednesday, September 21, 2005
Monday, September 19, 2005
1. Trip to Mexico.
2. Work update
3. Aleah and Emily pictures and update
4. Breeders tour
5. House repairs
6. SSRs etc.
Anyway. I am committed to taking work time for personal and blog related activities. Just kidding Dr. Stelly.
Really, I am kidding.
See you soon.
Wednesday, June 22, 2005
Saturday, June 18, 2005
Song et al. Figure of the comparative map. The black linkage group is from BC1F1 the right is from haploid/doubled haploid. Note inversion of markers bsd1122, jspr297,bsd1604 and lower larger inversion. Interesting that there are three groups, almost like three separate linkage groups in haploid line.
This article looked at two maps: BC1F1 TM-1(G. hirsutum) x [TM-1 x Hai7124 (G. barbadense)], and Vsg (G. barbadense) x [TM-1 x Hai7124]. Vsg is a virescent, a pale yellow-green, semigamous barbadense line. Semigamy is a mutation where the sperm and the egg nucleus do not fuse at fertilization and so depending on orientation of the spindles can produce progeny that are haploid, diploid, or with sectors of both. Haploids may be maternal or paternal. Sectors may be haploid or diploid. Diploid sectors are most vigorous and may overcome haploid regions.
The authors claim the maps are highly collinear. Discrepancies are noted as minor statistical errors or difficulty in ordering markers due to high number of double cross overs. I disagree with this claim. The differences are significant. I am posting an example linkage group. This may be due to using semigamous line or for comparing BC1s with different recurrent species. Was DNA extracted from whole plants? All lines tested in semigamous cross were haploid/doubled. How many were truly doubled? How many paternal/maternal haploids were produced? Maternal haploids would have no linkage information. Only paternally derived haploids would be beneficial since F1 was paternal. Were they chimaeric?
Maybe we should all do like in the Quadmap paper and bootstrap each linkage group to get a sense of how reliable the associations are.
Xianliang Song, Kai Wang, Wangzhen Guo, Jun Zhang, and Tianzhen Zhang. 2005. A comparison of genetic maps constructed from haploid and BC1 mapping populations from the same crossing between Gossypium hirsutum L. and Gossypium barbadense L. Genome 48: 378–390
Thursday, June 16, 2005
I wonder what Emily is going to say.
Wednesday, June 15, 2005
The cotton is now knee high. The first blooms are appearing. The F&B field will be ready for crossing in a week or two. The books are printed. The summer is fully here. When i am out chopping in the field. Chopping is our PC way of saying hoeing. Saying "I am going hoeing" or "I am a hoeer" or "I am going to find a hoe out in the field. " Hoe sounds too much like Ho. short for whore in case that little bit of Americana hadn't been up your way.
The only really troubling thing is my random-mating population for the mustelinum looks an awful lot like tomentosum. I am concerned that somehow it got mixed up between packaging the seed and planting. I hope not. If so i will have to random mate it by hand out at the bottoms where I have backup populations. I am glad that I do, just in case. I hate it when I make these kind of big mistakes, because then I have to admit it to Wayne, our technician, who already thinks I am incompetent.
Monday, May 16, 2005
How Emily came to the neighborhood.
It was a clear day. Word had spread through the sparrows, of course. They were terribly good gossips. They had seen her coming through the front gate and they flew to spread the word to everyone. Sparrows are like that. They are very excitable. They had told Mama Mouse, who has quite nervous about the whole affair, and had decided to keep the children in that day. One of the children mentioned it to a cricket, who sung about it to the lizards, and it was a lizard who told Frog. It was he that had decided to do something about it.
What he had heard was that there was a something in the neighborhood that looked exactly like one of the big people that lived in the house, except she was only three and a half inches tall. According to the lizard it was definitely not an animal, but must have been some new minute variety of people. So frog went to investigate.
He watched as she came around by the flowers looking at each of the flowers looking at each one in turn as if she was some strange relative of the bees. He doubted that due to her lack of wings, long hair, and brightly colored clothes. Frog had never seen a bee wear clothes. Also she was walking rolling a penny with a stick and as she would roll she would hum a little tune and give the penny a little tap with the stick to keep it on track. Sometimes it would get off track and roll in a little circle flat on the ground. The itsy bitsy girl would get her knees and pry with all of her strength because the penny was nigh up to her waist. Well, not quite but it was still quite large for such an itsy bitsy girl. She also seemed quite young, which was contrary to one of the reports that he had heard that she was one of the big people, who were dangerous. She didn’t look at all dangerous to him rolling a penny down the road, humming a little tune and looking at flowers.
It was then that he decided and so with a leap and a ribbit he came out of his hiding place. The girl was so surprised that she gave her penny a huge tap and it rolled out of control into the jungle of grass, never to be seen again. As he landed, the little girl said, “ Oh, you startled me.”
Frog replied, “Ribbit.” Which is frog for hello, good bye, and many other things including “I love you.” It was a very useful phrase. The girl was startled, but introduced herself as Emily and explained that she was in need of help. She informed him that she was looking to move into the neighborhood. Her previous neighborhood had been destroyed due to landscaping. Frog shivered because he knew the dangers of landscaping. Landscaping was when the large people in the house decided to get busy with shovels, machines that whirred and made noise. This forced animals out of their homes and destroyed weedy sources of food. Luckily, the people in this house only landscaped sporadically. Being understanding of the problem, he told her he would help her find a new place to live and that she could call him “Frog.” Then he asked her what kind of place she would like.
She thought and then responded, “Maybe someplace warm with lots of flowers because I enjoy nectar to eat.”
“What else does something like you eat?” Frog asked.
“Sometimes nectar, sometimes seeds, sometimes vegetables or fruit.” Emily said
“Not usually flies.” she said.
Frog decided that due to her eating habits she would fit in best with the mice or maybe the bumblebees, although he was pretty sure that the bumblebees didn’t want a roommate.
So Emily and Frog ran to the mice’s burrow to see if they were willing to put up boarders. Papa mouse had left some time ago on an expedition and had not yet returned. This left Mama Mouse with a burrow full of young mice to care for by herself. Frog was pretty sure that Emily could help out around the house in exchange for a place to stay.
When they got to the entrance, Frog called out to them, “Hello in there,” and he gave a loud “Rribbbitt” to let them know who it was.
From inside he heard a tiny squeak that said “No one is home.”
Emily turned to frog and said “Did you hear that?”
Frog said, “I afraid of this. They are home; they are just timid. They are just worried about you.”
“Why would they be worried about me, I am just itsy bitsy.” Emily said. She thought that she heard very mouse-like giggles at that, but no matter what they did, even when they banged on the door and called out in loud voices, could they get anyone in the Mouse’s house to come out. Except, they did see the reflection of many young mice eyes and one young mouse was brave enough to peek out at them through the window of the door.
So they decided if some of the other animals in the neighborhood would be interested in an “extra help,” As Frog said. First, they went to the sparrows. They chitter-chattered that they didn’t have any room for a boarder. Then, they went to the robins, who told them that they were busy collecting stuff and they were about to have a brood of their own children and showed Emily and Frog their handsome blue eggs.
No one in the neighborhood seemed to have room. Frog took her over to the lizards to talk to them. They didn’t have room either. They went by the ants. Fire ants don’t tend to be very talkative sorts. As one of their mottos stated, they usually stung first and asked questions later. Frog didn’t think there was much of a chance, he just wanted to be thorough. This particular day was an important day in the fire ant community because they had a new queen and the hive was ready to split into two. When an ant hive was to divide, all of the followers of the new queen swarm to the top of the nest accompanied by the new queen and her consorts, the winged ants. They fly or swarm to a new nest. This is one of the only times that the queen ever leaves the nest. The rest of the time she is deep inside the ant nest laying eggs and reproducing, taking care of the hive. The only ones that go out are the worker ants or the army ants. They tend to be very authoritarian-type figures and rather unsociable, if you ask anyone that knows them. At least, anyone who has stuck a shovel through their nest and has been bit and stung dozens of times.
And on this particular day, just as Frog and Emily were passing by, was when the new queen first emerged from her hole. As they were identifying themselves to the sentries and trying to maintain a safe distance, the queen called out. “ Hello there, come talk to me why don’t you,.”
Emily and frog were both surprised to find that the queen ant was not only amicable, but also very interested in hearing about their dilemma. She even offered to let Emily stay with them in the new hive. But since the new hive was a few feet underground and Emily would have to find an entrance big enough to fit herself in, Emily was pretty sure that she would have a hard time convincing the sentry ants that she was part of the hive. She declined but thanked the queen for the offer. The queen was disappointed because she was often lonely inside the hive. She longed to go outside and see the world. She wanted to have friends that were not ants and told Emily and Frog so.
Frog and Emily sat on a pebble with their head in their hands because they had not found anywhere for Emily to live. They were a bit discouraged. Now Frog had not yet offered to let her stay at his house, and he did have a wonderful little house. He had a spare bedroom that was high up and had a good view of the flowers that he was pretty sure she would like. He didn’t know exactly how to offer such a thing. He had never had a roommate or a child before, but Emily seemed like she would be a good person to stay with. She maybe could be a very good friend. He was not sure she would like to live with a frog like himself. Some people in the neighborhood thought him a bit stodgy since he read so much and his house was filled with papers and books from one end to the other.
The house was quite nice, especially for a frog. And so what he decided to do was invite her back to his house to look at a map of the surrounding neighborhoods to see whom they could come and discuss possible living arrangements for Emily. So Emily went to Frog’s house.
As soon as Emily came in he told her, “wait here, make yourself at home.”
She sat down, looking out the window at the flower bed. The house was situated just on the edge of the porch where it had light in the morning, and also where it was protected from the rain and from dangerous animals to frogs like dogs and cats and people that wished to pick him up.
When frog returned with the map there was Emily looking out the window. Now Emily, feeling very brave, needing somewhere to live, said “Frog, couldn’t I stay here with you.”
For looking down at his feet Frog said. “At least for now, I guess.”
And so it was decided that Emily would stay with Frog at least for the rest of the season, until Frog went down for his winter nap. That gave frog plenty of time to find her somewhere else to stay in the winter time. So that was how itsy bitsy Emily came to live with her friend Frog.
They were inseparable after that. Frog even let Emily ride on his back around the neighborhood. No one that thought they knew Frog could believe he would let a tiny person ride on his back as if he was a horse or something. Riding on a frog is great fun and if you ever get the chance you should take it. Some notable authors have compared it to flying, but it is much more bouncy that that, but still very enjoyable. This was the beginning of many adventures together.
Monday, May 02, 2005
Monday, April 25, 2005
Monday, April 18, 2005
I have too much to do. I will explain later. Right now I have to write it up for Cotton inc. They pay the bills.
Thursday, April 14, 2005
Monday, April 11, 2005
Emily painted this for us yesterday. She says she learned Chinese characters from Sagwa, a cartoon about chinese cats that write with their tales. I didn't believe her, but my Chinese math teacher says that they are just about right for the characters for rain. Just like she said
Friday, April 08, 2005
Wednesday, April 06, 2005
I am just monotone today. It is like a constant F flat in my head. There are moments where it fades and I feel ? ? ?
I don't know quite how now. That F flat is playing today.
Do you listen to Philip Glass? There are a number of his songs that are repetitive to a point where you would think that the performers would throw down their instruments and scream out an aria in C sharp major just to mix it up a little. That is how I feel with my life. I just haven't got up the courage to throw down my fiddle and start screaming.
I went to BYU to resolve things with my professors there. It is like none of it ever happened. It is like a dream that felt like a lifetime and then you wake up to find that it is almost the same time as when you fell asleep. Before I left, I sent an email with a tentative itinerary, outlining what I wanted to do. I asked for comments and for suggestions. In return, nothing. silence. ambivalence. when I got there, I proceded to start doing what I said on my itinerary. Response: "Ok, sounds good." "Where have you been eating for the past three days." "Oh, were you here till midnight working again? " Nothing. silence. ambivalence.
I went through all of the sequences and found all possible ligation points, restriction digestion sites, and vector contamination. Then I annotated them and sorted them by primer design and problem. Then I tested all the primers for ones without problems to see if the size was the same. Results: 95% that amplified were OK. 5% were not. This is error rate in sequencing so might have missed ligation site. Response: OK. Nothing. silence. ambivalence. Then I tested ones designed from other species and a subset of possibly messed up ones. Response OK, give us the good ones.
Then I did GISH. In one day. This is not that short of a protocol. I didn't finish. Response: Oh OK. Did they read my report? No. Did the look over the lab notebook with raw data? NO. Did they look over the sequencing data? NO. Did they have any questions. No. and NO.
Nothing. SILENCE. AMBIVALENCE.
When I got back. I asked what they thought about my field plans here. Response: whatever you think is best.
Nothing. Silence. Ambivalence.
What a sweet melody of advice from my advisors on my graduate committees.
Wednesday, March 30, 2005
Good recipes. Great writing.
I am late and procrastinating getting on my bike and going home.
Planting has begun and so my fingers and back ache from standing pressing seeds into peat pellets all day. Nilesh's experiment is all planted and tomorrow we will plant mine and Waynes. Total: 12,000. Not bad. My experiments for the bottoms are almost ready. After planting tomorrow I need to pull seed for check rows and then decide how I want to randomize. I wanted to just plant it out in order, without randomization, because it was for selection only. Stelly now has changed his mind and wants to put it out randomized. I refuse to collect data on all 4 acres of cotton. It is just too much.
Monday, March 21, 2005
Saturday, March 12, 2005
Tuesday, March 08, 2005
Sunday, March 06, 2005
Monday, February 28, 2005
Saturday, February 26, 2005
Dr. Fairbanks has pretty much finished with his analysis of my sequences.
Here is the verdict:
14/20 have multiple inserts
That is a lot. That is way more than even I in my worst imaginings thought could go wrong. That means that probably none of my primers are amplifying what we thought they were.
What does that mean for 6 sequences used for phylogenetic analysis? Where they chimaeric?
If yes, then the analysis is bunk.
If no, Then maybe, assuming there isn't any other HUGE messups then the analysis is legitimate.
What does that mean for the minisatellite sequences?
There were thirty something of those. We need to check the area used in the alignment, only 80 bases. Pretty good chance those 80 bases are intact.
Solution: Submit the consensus sequence to Genbank.
What does that mean for the FISH data (Microscopy pictures)?
IF the clones used are not chimaeric then it too is OK, if not then it also needs to be redone.
What does this mean for the microsatellites?
14/20 are probably not reliably amplifying from one region.
That is a huge problem, especially considering the number of short repeat sequences.
1. So the key with those might be to pick the best of the repeats and go over the sequences to see if they have multiple inserts.
2. Keep the ones that are good and
3. test to see if sequence size is consistent in 'Real'.
4. Test for polymorphism in other entries in panel used by Shanna.
Two words. Mental breakdown