Mwahahaha!
We just paid off one of Adria's student loans (or will when the check clears and such). It was a small one but it is progress, and progress is good!

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Programming and Alternative Medicine
Most non-programmers won't get this, but for those of you that do...


*rotflmao*

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California Supreme Court Rules For Marriage Equality
Some great news!

We therefore conclude that in view of the substance and significance of the fundamental constitutional right to form a family relationship, the California Constitution properly must be interpreted to guarantee this basic civil right to all Californians, whether gay or heterosexual, and to same-sex couples as well as to opposite-sex couples.

Culturally this may matter much more than previous gay marriage rulings. This clears the way for Hollywood celebrities to get married. Given our cultures celebrity obsession expect to hear about gay marriages in the news more frequently. As the experience of Massachusetts has shown, once gays are getting married and the sky isn't falling, the opposition to marriage equality starts to crumble.

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Join me for E.Coli?
Carl Zimmer is one of my favorite science writers. He will be giving a lecture promoting his new book Microcosm: E. coli and the New Science of Life at the Harvard Book Store, 1256 Massachusetts Avenue, this Friday, May 16th at 7:00pm. I haven't read the new book yet but publisher's weekly describes it thusly.

When most readers hear the words E. coli, they think tainted hamburger or toxic spinach. Noted science writer Zimmer says there are in fact many different strains of E. coli, some coexisting quite happily with us in our digestive tracts. These rod-shaped bacteria were among the first organisms to have their genome mapped, and today they are the toolbox of the genetic engineering industry and even of high school scientists. Zimmer (Evolution: The Triumph of an Idea) explains that by scrutinizing the bacteria's genome, scientists have discovered that genes can jump from one species to another and how virus DNA has become tightly intertwined with the genes of living creatures all the way up the tree of life to humans. Studying starving E. coli has taught us about how our own cells age. Advocates of intelligent design often produce the E. coli flagellum as Exhibit A, but the author shows how new research has shed light on the possible evolutionary arc of the flagellum. Zimmer devotes a chapter to the ethical debates surrounding genetic engineering. Written in elegant, even poetic prose, Zimmer's well-crafted exploration should be required reading for all well-educated readers.

Anyone interested in joining me for sciencey goodness?

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Cancer, how it works
The earliest records of cancer diagnosis come to us from the ancient Egyptians, but there are no records what they think caused it. The word comes to us from the Greeks who believed cancer was cause by an excess of "black bile." Traditional Chinese medicine still believes it is caused by "stagnant blood and a blockage or accumulation of qi." Scientific medicine has only recently begun to understand the real mechanism of cancer.

Early research focused on finding correlations between cancer and those who had it. They found both genetic factors (cancer is more common in some families) and environmental factors (smokers get lung cancer more than non-smokers). The experiment that showed the way was when a researcher transplanted the chromosomes from a cancer cell into a non-cancer cell. When this is done the non-cancerous cell becomes a cancer cell.

Cancer in a basic sense is when cells start multiplying out of control. To understand how this happens, it is useful to start by understanding my healthy cells don't. Cell activity is controlled by genes on the chromosomes. Those genes are made of DNA. But genes don't act as a central processor making "decision." Instead genes produce proteins and the ratios of those proteins in the cell determine how the cell behaves.

One gene that is critical to the process of cell division is the proto-oncogene gene. When signaled the proto-oncogene produces a protein that signals the cell to divide. If the DNA in the proto-oncogene is damage it can become an oncogene. An oncogene will produce more of the proteins that signal cell division. It might no longer require a signal to produce the cell division protein. It might stop responding to signals to stop producing the protein, or it my produce a modified protein that doesn't break down and thus last longer in the cell. Any of these mutations will lead to more proteins trying to signal cell division.

On the other side of the equation we have the tumor suppressor genes. In a healthy cell while proto-oncogene are producing proteins that signal cell division, tumor suppressor genes are producing proteins that tell the cell not to divide yet. If the tumor suppressor genes are damaged they may stop or slow production of proteins that signal not to divide the cell yet.

One tumor suppressor gene of particular interest is the tp53 gene which is located on the 17th chromosome in humans. This gene can do three things to stop a potentially cancerous cell. If damage to the DNA is detected, it can activate DNA repair proteins to fix damage thus preventing mutations (including cancerous ones). It can also hold up the cell division process, which can give the DNA repair proteins time to work. Finally if things are really bad it can code proteins to cause the cell to die, thus no more cancer cells.

There other mutations that can lead to cancer. But oncogene and defective tumor suppressor genes are among the more common culprits.

With this knowledge we now have a clearer understanding of both why cancer runs in families and why environmental factors are tied to it as well. Tumor suppressor genes often come in pairs, one on each pair of the chromosome, but only one working copy is need for most tumor suppressor genes to work. So someone can inherit on defective copy of this gene and still be perfectly healthy. However, this means that it takes only one gene mutation to knock out tumor suppressor gene instead of two. Thus they are at greater risk for cancer. The environmental causes are also easy to understand. Those are factors that can lead to cell mutation.

This knowledge is also leading us to improved cancer treatments. But this post is getting long, so it will have to wait for another time.

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Funny things you read on the internet
It is so funny until you realize people actually believe it.

we've known about for years but couln't prove. Listen to your alternative healthcare practitioners!

Listening to alternative health care folks for advice on vaccines and whooping cough doesn't always turn out so well.

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I must be losing my bearings
A few days ago Barack Obama said that John McCain was "losing his bearings" for repeatedly suggesting terrorists want Obama to win. Personally I think Obama was being kind. The correct way to describe McCain isn't someone who has "lost his bearings" but someone who is a lying asshole. However, the McCain camp decided to whine about the charge[1]. McCain is claiming that Obama is making fun of McCain's age (McCain is 71, will be 72 in August). Several other out there have repeated this claim and stated that "losing his bearing" means "old and nutty".

I always thought "losing your bearings" meant being confused. Such as "I always lose my bearings when coming up out of the subway." I looked on line for definitions. Dictionary.com says:

To lose one's bearings, to become bewildered.

Ask.com says:

Awareness of one's position or situation relative to one's surroundings. Often used in the plural: lost my bearings after taking the wrong exit.

So are the internet dictionaries out of date, or is McCain making things up and getting the media to repeat his lies without bothering checking a dictionary?

[1] In the McCain universe calling someone the terrorist candidate is a reasonable thing to say. But suggesting your opponent is confused is beyond the pale. Don't ask me. It is very easy to lose ones bearings when contemplating conservative ethics. When you stare into the abyss and all...

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Bwahahah
Like magic, if reincarnation is real, I see no reason why regulating reincarnation would be wrong.

On August 3, 2007, [China's] State Administration for Religious Affairs (SARA) issued a set of regulations, effective September 1, 2007, that require all Tibetan lamas wishing to reincarnate to obtain prior government approval through the submission of a “reincarnation application.” In a statement accompanying the regulations, SARA called the step “an important move to institutionalize management on reincarnation of living Buddhas.”

Of course it isn't real, so the whole thing just shines a light on the silliness of it all.

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Torchwood on the Large Hadron Collider
I don't usually expect much from media celebrities. So I was happily surprised to discover John Barrowman (Captain Jack from Torchwood) is a generally smart guy. He ask both good and amusing questions while getting a tour of the Large Hadron Collider.

http://www.cernpodcast.com/?p=7

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National Prayer Day
Today is national prayer day. It is sponsored by the federal government and its local coordinators are required to sign a statement of faith saying:

I believe that the Holy Bible is the inerrant Word of The Living God. I believe that Jesus Christ is the Son of God and the only One by which I can obtain salvation and have an ongoing relationship with God. I believe in the deity of our Lord Jesus Christ, his virgin birth, his sinless life, his miracles, the atoning work of his shed blood, his resurrection and ascension, his intercession and his coming return to power and glory. I believe that those who follow Jesus are family and there should be unity among all who claim his name. I agree that these statements are true in my life.

So for any of my readers who are Jewish, Pagan, or just think that some Bible passages might not be literally true, you aren't really invited. Except perhaps as potential converts to the one true way.

Anyhow I figured I'd use this opportunity to update an earlier post about a case study of the efficacy of prayer. The parents who choose to treat their 11 year old diabetic daughter with prayer instead of evidence based medicine will be charged with second-degree reckless homicide.

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What Hydrogen Atoms Do
Brian Cox: As one of my heroes Carl Sagan said, "These are the things . . . Saturn 5 rockets, Sputnik, DNA, literature and science, these are the things that hydrogen atoms do when given 13.7 billion years."

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I guess I have been busy
I started this job in the middle of January. We recently switched to a new source control (TFS), it is Microsoft's replacement for Visual Source Safe. I haven't used it enough to give a full report but so far it is much more full featured than VSS and MUCH easier to setup and use than CVS or *shudders* ClearCase.

Anyhow, I'm currently moving projects into the new system. In the 3 1/2 months I've been here I have created 8 separate web applications. That doesn't include the 4 utility libraries I've built along the way.

I've also got to add several new and improved technologies to my resume. I now now SharePoint, TFS, MS SQL 2005, and Visual Studio 2008 .NET 3.5. I also still like this job which is always a good thing.

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Pets, Vets, Terror, and Relief
Several months back, our cat Peach died. It was not entirely unexpected. I dropped her off at the vet for a biopsy of something we through was cancer. So I knew she was sick and didn't have much hope for long term survival. But when I called the vet to see when I could pick her up I didn't expect to be told she died.

Last weekend I took Sebastian to the vet for a regular check up. As he is getting to be a middle aged dog they recommended a basic blood test to just make sure everything was alright. The vet just called. It is odd how my heart just dropped when the vet said "we have Sebastian's results." The blood test came back normal and I was relieved. But my gut reaction to the preface to that information was unexpected.

I'm not sure what the physiological cause of the "heart drop" sensation. I don't think it was purely emotional there is a clear physical sensation, but 2 minutes on Google didn't find an answer. My first guess is lower blood pressure, but I would stress it is just a guess. I wonder if there is a good place to ask such questions on the internet?

Anyhow, I'm relieved to hear my dog is still healthy. We also just got a new kitten last night. We will have some vet appointments in his near future too. I wonder if I'll have the same reaction if the vet calls me for him too.

We haven't named our new cat yet. He is a smoky grey color, and Adria has insisted he not be called smoky. I was thinking Gof (fog spelled backwards) but that was vetoed. Adria has countered with Nietzsche. We shall see as his personality develops.

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Apocalypse Watch, the end of the world as we know it...
Astronomy Cast begins their series on The end of the Univers.

We wanted you to know that we're positive, happy people with enthusiasm for astronomy and the future. It's time for some sadness. It's time for a grim look to see what the future holds for the Universe. This week we stay close to home and consider the end of humanity, the Earth, the Sun, and the entire Solar System.

Don't panic yet, the time scales they talk about are mostly of the order of 500,000 years or more.

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Our choice
Decide what kind of people we want be. Ask yourself what would that person do in my circumstances. Do it.

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Science Shorts
When I was a high school kid I had the not unusual fascination with magic and the occult. I scoured the libraries and book stores looking for the magic spell that would give me special powers. I never found them. Magic can't move objects at a distance, call lightning, or cast fireballs. Scientists on the other hand, have now learned how to call lightning using laser beams!

The US Defense Department announced the creation of the Armed Forces Institute of Regenerative Medicine which hopes to "harness stem cell research and technology in finding innovative ways to use a patient’s natural cellular structure to reconstruct new skin, muscles and tendons, and even ears, noses and fingers." They plan to spend $250 million on this over the next five years. That is slightly more than the US Defense Department spends on Iraq each day.

Scientist may have figured out the secret to growing plants on the moon. While water and air would still need to be shipped up from earth, adding certain bacteria to moon rocks appears make a good soil at least for marigolds.

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Ominous?
Work has been keeping me very busy which has limited my time to both read and post. As my "sample size" of the media falls I'm more prone to seeing patterns that aren't there. So I'm not actually worried, but having read these articles recently it is certainly tempting to predict doom and gloom.

Falling U.S. home prices and a lack of available credit may result in foreclosures on 6.5 million loans by the end of 2012 ...

The foreclosures could put 12.7 percent of all residential borrowers out of their homes.

---

Rye flour stocks have been depleted in the United States, and by June or July there will be no more U.S. rye flour to purchase, said Lee Sanders, senior vice president for government relations and public affairs at the American Bakers Association. . . .Grain prices have been soaring worldwide while stocks have been dwindling, causing riots in some poor countries. . . . In the past the market has typically had a three-month surplus of wheat stocks to serve as a cushion against supply interruptions, but now the surplus is down to less than 27 days worth of wheat, Sanders said.

---

The two biggest U.S. warehouse retail chains are limiting how much rice customers can buy because of what Sam's Club, a division of Wal-Mart Stores Inc., called on Wednesday "recent supply and demand trends." . . . The move comes as U.S. rice futures hit a record high amid global food inflation, although one rice expert said the warehouse chains may be reacting less to any shortages than to stockpiling by restaurants and small stores.

Anyhow I wish I wasn't so busy. I'd really like to say something about the whole Open Source Boob thing. But I'd like to have time to write real thoughts, not just cut and paste with 3 sentences of snark or commentary.

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Skeptics in the Pub!
WHEN
Monday, April 21 2008
7pm

WHO
Marc Abrahams!

WHAT
Improbable Research and the Ig Nobel Prizes

WHERE
The Asgard
(a few blocks toward MIT from the Central Square Red Line T stop)
350 Massachusetts Avenue
Cambridge, MA 02139

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Stork Theory


Very funny and work safe.

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Naturopathy, anti-Vaxors, and whooping cough, oh my
Back when you were a kid, do remember kids getting of whooping cough? I suspect few if anyone reads this blog does. There are two reason for that. First, a vaccine for whooping cough was discovered in at the beginning of the 20th century. Second, modern antibiotics became available in the middle of the 20th century.

But what happens in the 21st century when a child isn't vaccinated and and his mother tries to treat him with alternate medicine?

The baby was 9 months old, his birth weight was 8 lbs 5 ounces. At six months he weighed just shy of 20 pounds. Today he weighed 15 pounds - he was a skeleton and he was dying.

Mom had brought him in after treatment by his naturopath had failed. Constant coughing had made it impossible for him to take in adequate nutrition and starvation, coupled with a raging bacterial pneumonia were conspiring to shortly end his very short life.

We worked feverishly. Intubation, IV boluses, major antibiotics, vasopressors. All futile.

At 9:03 pm, after 30 minutes of cardiopulmonary resuscitation we pronounced him dead.

This boy had pertussis [whooping cough]. His mother choose not to vaccinate him.

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