When Statistics slams into Science

In the near future my first scientific publications should be coming out. The first is on quantile regression applications for understanding cotton fiber length distributions. The others build on my PhD thesis. The problem is that according to this article the probability gods would say that my research findings are false. John Ioanniddis uses equations for calculating statistical error rates to show that most articles are wrong. His article reads like pilpul - in this case statistics of statistics, but it made me pause and think about the validity of the things I have written. I should confess that some of the claims I made in my masters thesis have already been debunked and it was a painful process.

Truth in scientific papers rests on "proving" that results are "statistically significant." This is not as simple as usually presented. First, statistically most tests are based on the probability of the data given a null hypothesis. This probability is called a p-value. Null hypotheses are usually the opposite of what you really hypothesize. They are usually assuming that the groups or treatments have no effect.

For example, suppose that you have been measuring lung cancer. Among the patients there are four groups: Chain smokers with asbestos sheets, smokers, non-smokers, and vegans from the garden of eden. Suppose the results of the study (Obviously I made this up) were that 100% of chain smokers with asbestos underwear had lung cancer, 20% smokers, 10% non smokers, and 0% of Utopian vegetarians. The null hypothesis would be that all four groups have the same cancer rate, which is on face value a ridiculous idea. We "know" that it is false, the significance of the findings are determined on how false it is. Now the p-value is the probability of a sample of people that match our results given the null hypothesis is TRUE.

This is a convoluted way of thinking, but is at the core of most science. We are assuming that the study is not of the entire population, just a sample, and that different samples might give different estimates of cancer rates depending on what people were included in the study. If we were to repeat this study a million times with a different random sample each time, most estimates of cancer rates would be close to the true value, but some would vary wildly, depending on the people picked to be included. Statistical tests find the sampling frequencies given a population value.

For example, say there were 1000 utopian vegetarians in the world total and 2 of them had lung cancer and only 1000 people are in the original study. So 1000 out of 6.6 billion people are utopian vegetarians and very few are likely to be included in the study. If say two are chosen each time randomly, then almost every time those two are not going to have lung cancer. But, there is a chance that both of the sick utopians would be picked and then the estimate of utopian cancer rate would not be close to 2/1000 but 100%. Now to prove significance of the research results of this made-up study we would set the population frequencies equal for all groups, our null hypothesis. The probability of getting a sample as divergent from that as we saw (100, 20, 5, 0) would be pretty low, assuming the true population values are equal (25, 25, 25, 25).

As pointed out by the Ioanniddis: the difficulty is that not all samples are done well; the biases of the researchers affect what the null hypothesis is; sample sizes may not be large enough; too often experiments aren't replicated; and statistical significance is easier to detect with large effects, not small subtle ones.

What he neglects is Likelihood. Which I only wish I could write a book about, luckily A.W.F. Edwards already did.

Colleen Renée Gardunia

We signed documents for a birth certificate and social security number so "girl" gardunia is now officially Colleen Renée.

Now that it is done I realize that there are a lot of e's in that name as well as the accent. Accent's don't work that great with Anglo keyboards, but can be written by holding the ALT key and pressing 0233. So Colleen's middle name is Ren[ALT-0233]e. She is like a Sci-fi robot.

Pictures of the baby

Well, I spoke too soon. Leila isn't sure about the name yet.

It's a baby Girl!!!

Trial: Let me know if it works.

The baby has landed!!!

Leila woke me up sometime between three and four in the morning and told me she was having contractions. I started to go back to sleep, contractions have come and gone all week, when I realized that she meant CONTRACTIONS! Luckily my Mom changed her flights and so didn't need to fly out of Chicago today so she drove Grandma to the airport and took care of the kids while Leila and I were at the hospital.

I won't describe any of the harrowing details of the process, but I will say thank goodness for Epidurals. Things went so much smoother after Leila wasn't completely overcome by pain.

The baby was born at 10:55 AM and weighed 7 lbs and 6 oz. She was bright eyed and awake, but quiet. It isn't 100% official yet, and I hope that I am not going out on a limb, but we are calling her Colleen Renée Gardunia.

Bowed Radio and "The Soloist"

I thought I would make a shameless plug for Bowed Radio. It is an odd mix of hard rock goth cello, bluegrass, modern orchestral, oriental/indian/iranian/egyptian classical music, and jazz violin music put together as a podcast each week.

Some of the music is downright wierd - like any of the goth cello stuff; one song was entitled "My mother was an opium smoker." I bet that didn't go over great at Mother's day brunch. But most of it is fresh and beautiful. I love the middle eastern music and the Indian/Chinese improvisations.

I don't know what the host, Mark Allender, does for a living. His group performs on one of the podcasts and he says they try to make as much noise as possible without pissing off the audience too much. Not exactly elevator music.

It has motivated me to expand my violin playing. I have just had the hardest time motivating myself to pick up scale books, etudes, and student concertos again. When I do practice, and it is not near often enough, I try to imitate some of the fiddle or eastern music I have been listening to. Since mom is here we all pulled out our instruments, even Emily. Mom played a song she learned in High School and we played it back and forth to each other. It was fun.

Violin music stopped being fun for me sometime ago. When I was at BYU I worked so hard at playing that first year and burned out on it completely. My teacher, Wolfgang TsouTsouris, pushed me so hard and instead of getting better, I just got so tense. I couldn't seem to get in tune. I would play the same part over and over again hours a day and it was never right. When I performed it was worse. It was like watching a puppet play and I could only make gross changes to force my distant fingers to adjust to the music as it crescendoed out of control.

I ran into a book called "The Soloist" by Mark Salzman that captured that feeling so exactly that I had to buy it. I reread it regularly. The main character was a child progeny that broke down and is unable to perform any more. In the beginning of the book, he is a mediocre musical teacher at a Californian university, until he gets a child prodigy as a student, is put on a jury for a murder trial, and finally gets a cat.

Like the main character, I have my violin ritual that has replaced much of my practice time. I now get out my violin and improv on something that I have listened to or I try to learn some fiddle songs. I think about how to teach my violin student and I let myself have fun while I play. When it stops being fun, I put it away.

Before . . . After

On Thursday we went to the Nefs' house for violin lessons/horseback riding lessons and to celebrate the 24th of July. I teach violin lessons to one of their boys in exchange for Emily taking riding lessons. She is becoming a proficient horsewoman. She runs around with their kids and plays on the horses like a natural.

Since we were having a barbecue and playing around Trent let me ride around on Paycheck. I am not a good horserider though. I was doing pretty well, ie I hadn't fallen off or gotten tangled in the stirrups yet, but then Leila needed diapers from the car that were in a white plastic sack. I rode Paycheck over there and got them and started back. I should have realized that the horse was a little on edge when he didn't turn right when we were heading back from the car and was skittish, but wanting to show that I could handle it I cued him to go into a trot. He instead started to lope and then run as fast as he could towards the fence. I was trying to hold onto the reins and the bag of diapers and wetwipes and couldn't get control. I dropped the bag to try and get a hold of the reins and get him to slow down. The second the bag dropped past his vision he started to kick, buck and really run! I remember thinking that I was going to jump off, but before I could formulate a plan for how to do that without getting hurt, I was flying through the air. I landed on my chest and leg. I couldn't breathe and everything ached but I was fine. Actually I hurt more today than I did then because I got up, tried to take a breath for some very long seconds and then got back on the horse.

Trent showed me what I was doing wrong - mostly everything, especially the panicking. The other thing he told me is that Paycheck freaks out about plastic bags. The sound they make sets him on edge and when I dropped it and he saw this white fluttery thing out of the corner of his eye he panicked. We rode around for a few minutes and I was happy not to break anything. My ribs are tender on one side and hurt if I breathe too hard or lift my left hand, and I will have some good bruises on my legs. I am just glad I didn't get hurt.

Normal Stuff

My sister Anna informed me that I write about weird stuff. She wanted to know when I would return to normalcy. I had no idea that was possible. Well, she did tell me that same thing years ago but it was that I did weird stuff and why couldn't I be normal, but we were teenagers then.

The horses have done a superb job of cleaning up the barnyard and the side pasture. We keep finding junk hidden by the grass and weeds - bits of metal, a rusty water pump, an 8 foot round tank, a cement pad with wood stacked on it. So far the horses have been a joy to have too. They drink a lot so filling up their water takes a while every day, but otherwise they are pretty low key.

We have the chickens in one side of the small barn. This barn is divided into two rooms with an open breezeway in the middle. The horses hang out in the breezeway where it is shaded throughout the day. The chickens pick through and break up any manure left there and keep the flies down. It really is a good system.

The donkey on the other hand is a trouble maker. The donkey I think feels this need to be in a stall and had been coveting the chicken coop. Emily opens the door for them in the morning and she would put a brick in front of the door and a brick behind the door so the chickens could come and go, but the horses could not get in. The donkey had no problem though pushing through the door. When I would get home I would find him holed up in the back, snacking on the chicken food. I decided that enough was enough and put a gate across the door that was about waist high. But, the donkey jumped the gate and came in anyway. The gate must have been the last straw because he decided to break everything in the chicken coop - feed cans, watering buckets, pallets set up for roosts, and he ate ALL of the chicken feed. So after I cleaned up his mess I put up a hotwire around the chicken coop so he can't get in any more. Now he is trying to get into the other barn. But he is very likeable. He is like a rebellious kid that everyone likes even though he keeps getting into trouble.

One good thing about the donkey is that he will not tolerate raccoons, cats, dogs, coyotes, or foxes in the barnyard. He has been gentle with the girls, but if another animal enters his area he becomes a heehawing terror.

Fingerprint in flood of Wikipedia

I have admired Wikipedia without contributing to it for some time. I love the idea of a grass roots encyclopedia of knowledge. I have used it almost as much as google in recent internet searches. Just the other day I was wondering if possums and opossums were the same thing and if they were really marsupials. Wikipedia had the answer. No they aren't the same. Yes they are both marsupials.

I have now joined up in the wikisociety by writing my first two articles. My first was on botanical keys, used to identify plant species. It has since been completely rewritten, merged with general identification keys and vastly improved. My second was on diallel mating schemes for quantitative genetics experiments. I am pretty sure it will have the same fate as my first post - evolving into something completely different than it started as. This is a powerful thing. Evolution meets knowledge.

Zombies, vampires and resurrection

Almost every day I watch movie trailers during my breaks on the internet. At A&M Kelly and I used to watch them together as we ate lunch and now I am a movie trailer addict. There is a lot you can tell about a movie from its short 2 minute summary, usually they show almost the entire plot in those two minutes. If so, then it really is not worth it to sit through the entire feature. Sometimes they even show the end of the movie. You know in the end of two minutes who the heroes were, what their struggles are, and what happens..

The other thing about watching all of the movie trailers is that you get a good idea of trends. One trend I see is the increase in horror movies, especially zombie, vampire, and undead monster movies (Rise, 28 weeks later, fido, I am legend) and the blood and guts torture movies. The torture movie seemed to have started with Saw and consists of "normal" people that become vicious and cruel and torture their fellow beings to death (Saw 1, Saw 2, Saw3, Hostel, Vacancy, The hills have eyes - even the trailers for these do not deserve to be watched. I think the horrors of Abu Ghraib and Guantanamo don't need to be flaunted as entertainment.). That millions of people will pay to see it is a horrifying confirmation that their diagnosis of human nature may be correct. Zombie/vampire movies say that human nature can do such horrible things after being transformed through some reverse resurrection.

Resurrection, as I see it, is raising up a mortal body to an eternal, exalted one. This is really a foundation of Christian theology. Zombie/vampire resurrection takes a mortal body strips it of its soul and drops it into a damned state for eternity. In christian theology resurrection is only possible because of the sacrifice of Christ and is given as a gift, a reward to everyone. In horror movies this godless resurrection is caught like a parasite or disease. It is like AIDS mated with alzheimers and rabies. This damned state usually requires continual feeding and destruction of mortal beings. Instead of being freed from mortal desires and weaknesses, this false resurrection leaves eternal, mindless hunger, without redemption or hope of exaltation. The plot for any zombie movie, except maybe Fido, consists of some normal mortal running/shooting/killing through the attacks of the zombie/vampire while fighting to stay alive. The shocks are when the undead jump out or break in, but the horror is the false resurrection.

This is one trend that I hope fades away. If Connie Willis is right about fads they reach a point where they outgrow their possible support and pop like an overblown balloon. I hope that is the case with both of these horror genres.

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.