Friday, November 27, 2009

A Twig on the Evolutionary Tree

Over Thanksgiving daughter Michelle showed me a different, (and new to me) evolutionary tree. We have all seen evolutionary trees. There is one in Darwin's notebooks from 1834.

Some of us are familiar with using DNA to determine parentage of domesticated plants, animals, or indeed children, for example finding the parents of prized wine grapes by sequencing them.

Classic evolutionary trees were drawn by Haechel, and there are several on Wikipedia.

I was surprised to see how different a quantitative tree like the one at right is from a qualitative one or the traditional one from grade school.

The quantitative tree comes from analysis of the 16s rDNA which is an important ribosome enzyme. Its function has been preserved since before the latest common ancestor of all existing plants and animals, and deviations in it provide a measure of evolution.

On this chart one change per base pair is about 8 centimeters along the line.  This is from "Tree of Life" published by Norm Pace in 1997. See this site. Pace is at U of Colorado where Michelle studies.

People are covered under homo as in homo sapiens and are on the bottom hook near the left. We are right next to coprinus, which is a kind of mushroom, and zea which is a family of grasses that includes corn (maize). Other mammal species are going to be even more closely related.

The implication is that a great deal of evolution occurred prior to the differentiation between plants, animals and fungus.

Cynical biologists assert that yeast or oak trees are just as evolved as people, but simply for different things. I say, why not put people on top of the tree? Something has to be on top, and most everyone is going to try to find homo sapiens -- put them on top to make it easy.

The second point is that mammals and "higher" plants are getting a lot of differentiated performance out of some fairly similar genes.

This makes me wonder about saving rain forests for genetic diversity.  There is probably more genetic diversity in pond scum than in a forest of trees.

Tuesday, November 24, 2009

Flower Based Medicines such as Bach's Rescue Remedy

Our vet is a "holistic vet," so when we asked for something to calm down our cats for a drive, she recommended Rescue Remedy. I would rather have had a real medicine, but too late.

England's Bach Flower Remedies makes Rescue Remedy. it contains heliathemum nummularium, clematis vitalba, impatiens glandulifera, prunus cerasifera, ornithogalum umbellatum in 80% glycerine and 20% water.  Generally these are common plants that look good in the garden. I had a hard time finding any of them that cause drowsiness. Most are harmless, but one is a mutagen, with a wide range of medicinal uses.

Heliathemum nummularium is the common rock rose which is native to Europe. It does not especially have any medicinal uses.

Clematis vitalba: I can't find medicinal uses except in Rescue Remedy itself. I used to grow clematis in the garden, and it is a nice enough flower. One site regards clematis vitalba as an invasive weed.

Impatiens grandulifera is another common garden flower. It causes indigestion, and it should not be eaten in large quantities because it has a high mineral content and may cause kidney stones et al. It is most commonly used topically for poison ivy or bee sting, not internally.

Prunus cerasifera or the cherry plum is a tree. One site says when dissolved in water it gives off hydrocyanic acid, which is poisonous. I could find no mention that it causes sleepiness.

 Ornithogalum umbellatum, or Sleepy  Dick, is the biggest problem.  It is thought to be a mutagen and poison. No animal eats it in the wild. It probably should not be given to animals. Herbalists use it for everything from depression, to ulcers, to flatulence.

The glycerine is the carrier, and it is sweet to taste. It is used in some medicine as a soothing agent, but not a medicine.

All in all,  I am pretty worried about this witch's brew of herbal extracts. Unless this is used in homeopathic quantities, it is probably more harm than good. The label mentions homeopathy, so perhaps it is more of a placebo for the pet owners.

Supporting the homeopathy idea are the label dose instructions for 4 drops for each animal, and this product is recommended for lots of animals including HORSES and BIRDS. The idea that a horse could take the same amount of medicine as a parakeet is pretty funny. Only an ineffective & harmless medicine could make that claim.

Friday, November 20, 2009

Happiness and Artificial Intelligence: Sci-Fi Part 2

In my first post on happiness and artificial intelligence, I tried to be fact-based and talked about artificial intelligence programing. In this post, I want to about artificial intelligence in "literature," (which sounds so much more substantive than in "Science Fiction".)

I became interested in this topic because I am reading the 1992 book  Mostly Harmless, by Douglas Adams, where hero Ford Prefect hotwires a security robot so that it is always happy. The happy robot is so content that it stops chasing him and cheerfully cooperates.  This got me thinking that even if people could build a self-aware robot, why would it want to do anything?

The epitome of bored science fiction AI is Marvin the Robot from Hitchhickers Guide to the Galaxy. He is so smart that everything that happens bores him, and he has lived so long that he has seen it all before. [At left is Marvin from the 2005 movie.]

 Ray Kerzwell considers that societies advanced enough to venture to earth might not be motivated to do so.

"this thinking might explain why we haven't found extraterrestrial life yet: intelligences on the cusp of achieving interstellar travel might be prone to thinking that with the galaxies boiling away in just 10^19 years, it might be better just to stay home and watch TV".

He introduces a future dystopia called  "A "societal fixed point" [that] might be defined as a state that self-reinforces, remaining in the status quo--which could in principle be peaceful and self-sustaining, but could also be extremely boring--say, involving lots of people plugged into the Internet watching videos forever."

Kerzwell's society has reached a high state of material prosperity, citizens don't really need to do anything productive.

You are probably are familiar with "Problem of Evil." Why does a good God allow suffering in the world? One of the answers is that pain serves a purpose, for example painful swelling helps a wound cure or a painful burn helps children to avoid touching the stove again.  Similarly sadness, anxiety, paranoia, need and desire, like hunger and lust get people up off the couch and doing things.

This shows up in The Matrix where Agent Smith says:

Agent Smith: Did you know that the first Matrix was designed to be a perfect human world? Where none suffered, where everyone would be happy. It was a disaster. No one would accept the program. Entire crops were lost. Some believed we lacked the programming language to describe your perfect world. But I believe that, as a species, human beings define their reality through suffering and misery. Which is why the Matrix was redesigned to this: the peak of your civilization.

Many people have observed that happiness is temporary, with stories like  "I thought the new red sports car/new boat/new house/new wife would make me happy but after a few weeks/months, I got bored and wanted something more."

Wednesday, November 18, 2009

The Federal Budget is Worse Than You Think

I came across this figure from the US Treasury via scottgrannis's blog that shows how imbalanced the Federal Budget is. The budget was having a problem in the mid 2000's, and now the recession and the Wars have knocked it again. Spending is up and tax revenue is down.

I have to point out that Scott made the y-axis logarithmic, so the true state of affairs is worse than it appears.

Monday, November 16, 2009

Happiness and Artificial Intelligence: Part I

Designing an artificial intelligence gives insight into the way people think, and creating an AI that feels happiness seems a long way off. AI's are not motivated by a desire to be happy, at least not yet. There does not seem to be many people working on motivation.
AI designers of video games give "agents" in the games fairly simple motivations by coding it in, and in fancier agents, the motivations can change. For example, a character can get hungry and look for food. In my mind, these game motivations are not real emotions or motivations, Just like a chess program that is trained to take an opponent's rook is not feeling emotions.

Other AI programs create motivational algorithms that can be fairly complicated, and the planned actions of the "agent" are subject to evaluation by an elaborate goal function, and its actions are determined finding an optimum outcome, perhaps using a Monte Carlo approach.

Artificial intelligence works can make machines that simulate emotions, and game makers can create programs that fictionally kill people or conquer the world, but these program simply act out programming, and don't have any reason or need to do these things. Animals from earthworms to people are built to eat when they are hungry, and have a will to survive.

An interesting AI program would be self-aware enough to want to understand and justify its internal valuation function. Simply coding it makes a soldier than can follow rules, not a general to lead them.

I recall the old Star Trek robot villain Roc  said, "Survival cancels programming! That! is the equation." Before he goes bezerk and starts bashing heads. Meaning that survival caused him to set aside his motivational algorithm, and go bezerk.  [Somebody help me find which episode this is. Leave a comment.]

Sunday, November 15, 2009

IGS Energy - I Signed Up

IGS Energy is an Ohio Gas utility that contracts to supply gas to other utilities. I put a post up about whether it is a scam or not, and that is one of my most popular posts. I also got an interesting reply from the company.

At the time, I was worried about some kind of Enron-style scam where a sleazy fly-by-night company promises bargains, but actually ends up charging far more. Well, time has passed, and it seems this IGS Energies is a regular company that can help me.

Anyway, I signed up for their latest offer. It is a 13.5% discount on natural gas from $0.798 per cubic foot of gas to $0.69. My regular utility is DTE Energy.   It is important to remember that this only applies to the gas portion of the charge, and I still need to pay DTE Energy to get the gas to me. This should save me about 10% on my total gas usage this winter. Maybe $40-50.

I signed up on the website, and it took about 3 minutes. It has taken longer than that to write this post on it.

I will let everyone know how this experiment in capitalism goes.

Saturday, November 14, 2009

Maps of Life Expectancy

The third in my series on global health has maps on life expectancy. [First post] [Second post]  I found this data while looking up the previous stuff, and it is interesting on its own.

The first map is first because it is the flashiest. It also shows the US only, and is a good place to start. Basically life expectancy is lowest in the south and highest in the midwest. It is nineteen years old data though. It is hard to find similar data on the county level. There is a four year old map at the state level here. It shows that we all should move to Minnesota, and South continues to lag.

I think this is interesting, because when I go South, the only thing the restaurants have is fried food and the people are fatter too. I also wonder why sitting inside all winter makes people healthier, but it seems to.
University of California at Santa Cruz has a fascinating site where they show how life expectancy has changed over the last half century. I have put two of the maps here, but there are three more on their site. (I could have pasted all four of them here, but I thought that it was sleazy to swipe their whole page. The key is on next map.
You can see how life expectancy has advanced everywhere, but China has nearly jumped to first world standards and how Africa continues to lag.

Life expectancy has increased over time. Wikipedia says that ancient peoples may have had average life expectancy of about 18 or so. It seems that people who made it to adulthood often lived much longer to fifty or so.

The graph at right is for females, and it shows the oldest people that were found in the population, presumably by poking though graveyards. This is from the US National Institutes of Health.   These numbers are a little suspect since the curve is so smooth. It seems to show the world culture evolved uniformly.
There is a lot of analysis on the relationship of life expectancy and per capita GDP. The graph at right is from Oxfam.  Small increases in GDP really increase life expectancy, but then it stops mattering so much. Life is not good until one gets to $7000 per year or so.
Finally, since the H1N1 Swine flu is around, I thought I would put up this data on how the flu of 1918 reduced life expectancy. The info is from Nature Medicine 10, S82 - S87 (2004). The epidemic was more significant than either world war. This is pretty scary since it shows how serious an epidemic can be.

!See the other posts on global health:  [First post] [Second post]!

Friday, November 13, 2009

World Maps of Disease

Following up on the causes of death post, I found interesting graphics from Anna Barford and Danny Dorling from the Geography departmenr at the University of Sheffield. They made maps of the deaths in different regions where the areas are proportional to the occurrence of the disease. The maps make for some very distorted country profiles.

The top one is actually for poverty, and it shows a huge overage in India with the United States very small and Canada invisible.

Even more extreme is the map for childhood diseases which seems to occur primarily in Africa, India and Pakistan.

On the other hand, the map for lung cancer shows America far larger than Africa, which shrinks to insignificance. China and Japan have grown as well probably because so many people smoke.

See the next post in the global health series.

Thursday, November 12, 2009

Global Causes of Death

I was discussing with wife Jenny about how the number of suicides when I happened on this data on the causes of death in the world. I thought it was interesting so I graphed it out.  It is surprising that lung diseases (even not including lung cancer) equals heart disease.

The World Health Organization published the number of deaths by cause in 2001. I have combined some catagories and used common language. I did not change the strange spelling "diarrhoeal," but the label "diesease" is actually a mistake.

In developed countries causes of death are moving from acute diseases to chronic diseases like cancer and heart disease. In developing countries, infant deaths, malaria, tuberculosis and sadly measles are still big problems. This is illustrated in this graph from the University of California at Santa Cruz

I always thought that accidents were a bigger cause of death than they are. It would seem that buckling my seatbelt is not that important :-)

Saturday, November 7, 2009

Coldgear: For When It's Cold

I was at the sporting goods store, looking for sweatshirts and cold weather running stuff, and I came across this unintentionally funny slogan:

Coldgear - for when it's cold.

It is from the sportswear company Under Armour.

Under Armour had dumbed down their marketing pitch. "For When it's Cold" seems comic to me.  Do you suppose that people could figure out what Coldgear was for without the clever tag line? May be they could have used it for some thing better like  - comfort in the cold or something, but I suppose the Under Armour elite athletes are too tough to be comfortable.

This reminds me of the Levi "Nice Pants" campaign, where they included the tag line "Nice Pants" in all the ads so that their slower customers could figure out what they were advertising.

Thursday, November 5, 2009

Creepy Artificial Skin - Not Quite in Time for Halloween

Intercytex is a biotech company best known for the nobel effort to help bald men regrow hair -- hard for me to be against that.

They have branched out into the creepy trade of growing skin.  They are growing little bowls of skin that are later stitched onto burn victims.

The fake skin is more basic than regular skin, it only has two layers, and is grown from a skin cell concentrate spread over a matrix of non-woven fabric.

In contrast, the hair growth treatment involves injecting the patient's scalp with new hair follicle cells.

Despite their new fake skin, the company has hit hard times, and had to lay off workers earlier this year.

One would think with all the popularity of zombies, the market for fresh skin would be booming.

Sunday, November 1, 2009

Favre The Viking

Just watched Favre's triumphant return to Lambeau Field. The Vikings with former Packer star, Brett Favre, playing quarterback beat the Packers soundly on their home field. The Packer faithful felt betrayed. The full story about why Favre left Green Bay may never be known, but fans have already chosen sides.

Although I was born and raised as a Packer fan, I can't help but cheer for Farve and his boyish enthusiasm. After the last touchdown he was jumping up and down like it was high school homecoming.

The Vikings did not blow the Packers out, and if the Packers have fewer penalties it might have ended differently.

The saga of one man and his determination to win at his sport is a great football story, and just a great story.