Friday, October 3, 2008

The DNA Network

The DNA Network

It's not just Wall Street that can't regulate itself... [adaptivecomplexity's column]

Posted: 03 Oct 2008 02:35 PM CDT

These people do much more harm than good for science:

"Top Psychiatrist Failed to Report Drug Income"


Genetic test was an investment in myself [deCODE You]

Posted: 03 Oct 2008 01:33 PM CDT

Jack Doughery says deCODEme genetic test was an investment

Jack Doughery says deCODEme genetic test was an investment

Jack Doughery feels great and wants everyone to know it.

"I almost feel evangelical about my health," says the 62-year-old businessman from Spokane, Washington. "I'm so excited about what can happen if you do the right things and have the right tools."

Jack started doing the right things once he began what he calls his journey, which kicked off one day after waking up at three in the morning craving a cigarette.

"When you're waking up at three in the morning, coughing and spluttering, and the only way to calm down is by smoking a cigarette, you don't have to be too smart to know this might not be the way to go. It got my attention," he remembers.

One of Jack's first stops along his grand trip was at Spokane's Heart Attack and Stroke Prevention Clinic, run by nurse practitioner Amy Doneen. It was Doneen and Dr. Bradley Bale who put Jack on the path to prevention, helping Jack to reshape his life using diagnostic testing, nutrition and exercise.

Recently, Amy Doneen began using a new test to help alter Jack's journey—deCODEme, a genetic test that scans a patient's genome for markers relating to 30 various diseases. The deCODEme genetic test gauges a patient's average and lifetime risk of developing diseases such as Alzheimer's, heart attack, prostate cancer, and most recently bladder cancer.

"I'm no doctor," Jack says. "But in laymen's terms, the tool is another arrow in Dr. Bale's quiver to help me do the right things."

Jack hasn't always done the right things. In addition to his a two-pack-a-day habit, he often drank copious amounts of alcohol. He was, in his own words, in "bad shape." Even the death of his father at the early age of 62 didn't alter the trajectory of his unhealthy lifestyle.

"Back then, I thought 62 was old. Now that I'm 62, I've changed my mind."

deCODEme genetic test customer Jack Doughery

deCODEme genetic test customer Jack Doughery

Children often pick up their parents' habits, and so it was for Jack. One of those habits was a breakfast straight from the heart-attack diet.

"We ate bacon, sausage, eggs, all fried and cooked in lard. We had biscuits, gravy and maybe some peach or cherry cobbler," he says, and then to make sure he's understood, he emphasizes: "I'm still talking about breakfast. I haven't moved on."

Pulling no punches, this eat-everything diet made Jack—"fat."

"I was one large unit," he remembers. "I weighed 197 pounds in the eighth grade. I had to breathe hard just trying to walk."

That changed when Jack discovered girls. Realizing that most girls weren't interested in boys that looked like him, he began eating nothing but cottage cheese and lost 60 pounds in 90 days.

"I think I was the first person to invent the Atkins diet," Jack says with a laugh, referring to the popular diet consisting of high protein and low carbohydrates.

But the weight loss was only temporary. Jack continued to smoke and drink and the pounds piled back on. Jack says that he didn't really take control of his health until he started a family. It was then he realized that he wanted to be around to see his grandchildren. So he quit smoking and drinking all in one day and began an exercise program. This, he recalls, was his first investment in his own health.

"I weighed over 200 pounds. Now I weigh 166 pounds. I wanted to make sure when I was older I was living a quality life rather than just trying to make it."

Helping Jack live a quality life are Dr. Bradley Bald and Amy Doneen, who discovered that Jack was loaded up with arterial plaque. When Jack was only 52, his vein age was 70. Today, after they helped Jack remake his lifestyle, Jack's vein age is 49. Dr. Bale and Doneen helped improve Jack's health by putting Jack on an exercise and nutrition program and by prescribing medication that reduced his cholesterol levels.

"Dr. Bale totally turned my life around."

But getting Jack back in shape required more than fixing his weight and reducing the accumulation of plaque in his blood vessels. Even after these changes, Amy Doneen recommended that Jack go even further and take the deCODEme genetic test. By that time, Jack had been working with The Heart Attack Prevention Clinic for years and was in great shape. He'd step on the treadmill, and raise the pace and incline, but Jack kept going. He'd ace the stress test every time.

"If you looked at me you'd say, wow, that guy is in great shape."

But the deCODEme test revealed something that had previously remained hidden. Jack had a significantly higher than average risk of developing diabetes. This was a louder alarm than the 3-am cigarette.

"Diabetes. That's what killed my dad," Jack laments.

While the result scared Jack, he says that he was quickly comforted by the fact that he knew his vulnerabilities and that enabled him to take extra preventative precautions. The test, he says, was well worth the $1000 he paid for his results.

But let's face it. The economy is tight. Gas prices are going through the roof. Food prices keep rising. Health insurance costs are out of control. Some potential patients look at the cost of the test and wonder if it's worth the money. After all, not everyone is a successful businessman and public speaker like Jack. But Jack has a simple answer for them.

"I was talking to my brother about this very thing. I told him, 'Is your life worth $1000?' Now that might not be something a doctor can say, but that's my opinion. I think people have to look at it in perspective. They wouldn't even blink at spending that much on a big-screen TV. And they'll even put it on a credit card and pay for it over 30 years. So what's the priority? I don't look at the test as spending money. The deCODEme test is an investment in yourself."

Jack takes the money out of the equation. His thoughts turn to his four grandchildren. He wants to watch them grow up. He understands deCODEme's genetic test is not a silver bullet, and won't enable him to avoid all illnesses. It's another tool, or as Jack repeats, another arrow in Doneen and Dr. Bale's quiver.

"It gives Dr. Bale another awesome tool to assist me on this awesome journey. And at 62 here I am. I feel fantastic."

Jack Doughery

Jack Doughery's genetic test showed that he had a significantly higher than average risk of developing diabetes.

Embryos and Eldery: the duty to die [Mary Meets Dolly]

Posted: 03 Oct 2008 12:54 PM CDT

I came across this post from Dr. Nuckols at and I had an epiphany. I have always known there was a link between embryo-destructive research and assisted suicide and euthanasia.

There is the obvious "sanctity of life" connection, but this passage from Dr. Nuckols really put it together for me:

According to the Daily Mail, [Lady Warnock] now supports a "duty to die."

Lady Warnock, 84, was the head of the committee which during the 1980s opened the way for legal research on human embryos.

Influential in education as well as in medical ethics, she became an open supporter of euthanasia after her ill husband was helped to die by his doctor in 1995.

She told the Church of Scotland's magazine Life and Work: 'I've just written an article called A Duty to Die? for a Norwegian periodical. I wrote it really suggesting that there is nothing wrong with feeling you ought to do so for the sake of others as well as yourself.'

She added: 'I am absolutely, fully in agreement with the argument that if pain is insufferable, then someone should be given help to die, but I feel there is a wider argument that if somebody absolutely, desperately wants to die because they are a burden to their family or the state, then I think they too should be allowed to die.'

Does it surprise me that someone who advocated for the destruction of human embryos for research would also advocate death for those that feel like a burden to their families? Absolutely not.

But what I realized is that Lady Warnock and others who share her opinions really think there are humans that have a "duty to die." Not just the sick or elderly who are a burden on their families, but also the "left-over" embryos from IVF.

This twisted logic says that "left-over" human embryos in the deep freeze have a "duty to die" to give the rest of us "cures." It is the frozen embryo's duty to be ripped open for the "betterment of society" just like it is the duty of the sick and eldery to get rid of themselves.

I shudder to think where this "duty to die" will end. Do the disabled have a duty to die? Do the mentally ill? Do the obese?

I am guessing that Lady Warnock thinks everyone has a duty to die as long as it is not her or anyone she loves.

2008 IgNobels [Bayblab]

Posted: 03 Oct 2008 12:18 PM CDT

My favorite time of the year, the IgNobel ceremony! You may be able to watch tomorow's (1PM) lectures in a video feed here. Here are the winners:

"NUTRITION PRIZE. Massimiliano Zampini of the University of Trento, Italy and Charles Spence of Oxford University, UK, for electronically modifying the sound of a potato chip to make the person chewing the chip believe it to be crisper and fresher than it really is.

REFERENCE: "The Role of Auditory Cues in Modulating the Perceived Crispness and Staleness of Potato Chips," Massimiliano Zampini and Charles Spence, Journal of Sensory Studies, vol. 19, October 2004, pp. 347-63.

PEACE PRIZE. The Swiss Federal Ethics Committee on Non-Human Biotechnology (ECNH) and the citizens of Switzerland for adopting the legal principle that plants have dignity.
REFERENCE: "The Dignity of Living Beings With Regard to Plants. Moral Consideration of Plants for Their Own Sake"

ARCHAEOLOGY PRIZE. Astolfo G. Mello Araujo and José Carlos Marcelino of Universidade de São Paulo, Brazil, for measuring how the course of history, or at least the contents of an archaeological dig site, can be scrambled by the actions of a live armadillo.
REFERENCE: "The Role of Armadillos in the Movement of Archaeological Materials: An Experimental Approach," Astolfo G. Mello Araujo and José Carlos Marcelino, Geoarchaeology, vol. 18, no. 4, April 2003, pp. 433-60.

BIOLOGY PRIZE. Marie-Christine Cadiergues, Christel Joubert,, and Michel Franc of Ecole Nationale Veterinaire de Toulouse, France for discovering that the fleas that live on a dog can jump higher than the fleas that live on a cat.
REFERENCE: "A Comparison of Jump Performances of the Dog Flea, Ctenocephalides canis (Curtis, 1826) and the Cat Flea, Ctenocephalides felis felis (Bouche, 1835)," M.C. Cadiergues, C. Joubert, and M. Franc, Veterinary Parasitology, vol. 92, no. 3, October 1, 2000, pp. 239-41.

MEDICINE PRIZE. Dan Ariely of Duke University, USA, for demonstrating that high-priced fake medicine is more effective than low-priced fake medicine.
REFERENCE: "Commercial Features of Placebo and Therapeutic Efficacy," Rebecca L. Waber; Baba Shiv; Ziv Carmon; Dan Ariely, Journal of the American Medical Association, March 5, 2008; 299: 1016-1017.

COGNITIVE SCIENCE PRIZE. Toshiyuki Nakagaki of Hokkaido University, Japan, Hiroyasu Yamada of Nagoya, Japan, Ryo Kobayashi of Hiroshima University, Atsushi Tero of Presto JST, Akio Ishiguro of Tohoku University, and Ágotá Tóth of the University of Szeged, Hungary, for discovering that slime molds can solve puzzles.
REFERENCE: "Intelligence: Maze-Solving by an Amoeboid Organism," Toshiyuki Nakagaki, Hiroyasu Yamada, and Ágota Tóth, Nature, vol. 407, September 2000, p. 470.

ECONOMICS PRIZE. Geoffrey Miller, Joshua Tybur and Brent Jordan of the University of New Mexico, USA, for discovering that a professional lap dancer's ovulatory cycle affects her tip earnings.
REFERENCE: "Ovulatory Cycle Effects on Tip Earnings by Lap Dancers: Economic Evidence for Human Estrus?" Geoffrey Miller, Joshua M. Tybur, Brent D. Jordan, Evolution and Human Behavior, vol. 28, 2007, pp. 375-81.

PHYSICS PRIZE. Dorian Raymer of the Ocean Observatories Initiative at Scripps Institution of Oceanography, USA, and Douglas Smith of the University of California, San Diego, USA, for proving mathematically that heaps of string or hair or almost anything else will inevitably tangle themselves up in knots.
REFERENCE: "Spontaneous Knotting of an Agitated String," Dorian M. Raymer and Douglas E. Smith, Proceedings of the National Academy of Sciences, vol. 104, no. 42, October 16, 2007, pp. 16432-7.

CHEMISTRY PRIZE. Sharee A. Umpierre of the University of Puerto Rico, Joseph A. Hill of The Fertility Centers of New England (USA), Deborah J. Anderson of Boston University School of Medicine and Harvard Medical School (USA), for discovering that Coca-Cola is an effective spermicide, and to Chuang-Ye Hong of Taipei Medical University (Taiwan), C.C. Shieh, P. Wu, and B.N. Chiang (all of Taiwan) for discovering that it is not.
REFERENCE: "Effect of 'Coke' on Sperm Motility," Sharee A. Umpierre, Joseph A. Hill, and Deborah J. Anderson, New England Journal of Medicine, 1985, vol. 313, no. 21, p. 1351.
REFERENCE: "The Spermicidal Potency of Coca-Cola and Pepsi-Cola," C.Y. Hong, C.C. Shieh, P. Wu, and B.N. Chiang, Human Toxicology, vol. 6, no. 5, September 1987, pp. 395-6.

LITERATURE PRIZE. David Sims of Cass Business School. London, UK, for his lovingly written study "You Bastard: A Narrative Exploration of the Experience of Indignation within Organizations."
REFERENCE: "You Bastard: A Narrative Exploration of the Experience of Indignation within Organizations," David Sims, Organization Studies, vol. 26, no. 11, 2005, pp. 1625-40."

HPV vaccine required for girls applying for green cards [Mary Meets Dolly]

Posted: 03 Oct 2008 12:16 PM CDT

The human papilloma virus or HPV is the leading cause of cervical cancer. And you guessed it, HPV is a sexually transmitted virus. It is estimated that over 6 million people contract HPV and close to 10,000 women are diagnosed with cervical cancer every year in the U.S. The annual pap smear is the first line of defense against HPV and cervical cancer.

There has been a lot of debate about where the new vaccine against HPV is going to promote promiscuity. The vaccine is recommended for girls as young as 11. The argument is that the earlier that vaccination, the better the protection against HPV.

There are some Catholics who feels very strongly that the HPV vaccination is evil. I disagree and so does the Catholic Medical Association. Just because HPV is a sexually transmitted virus does not mean that prevention is unethical.

What is unethical is making the vaccine mandatory. HPV is not pertussis or polio or the measles or even the chicken pox. You do not "accidentally" get HPV. HPV can be prevented by responsible sexual behavior. Girls and their parents should have a choice whether or not vaccination for HPV is right for them.

That is why this story from USA Today makes me angry:

A new requirement that girls as young as 11 be vaccinated against a sexually transmitted virus before they can become legal U.S. residents is unfair, immigration advocates say.

The federal rule added Gardasil to the list of vaccinations that female immigrants ages 11 to 26 must get before they can obtain "green cards."

The series of three shots over six months protects against the strains of the human papillomavirus blamed for most cases of cervical cancer and genital warts. But the vaccine is one of the most expensive on the market and controversial.

"This is a huge economic, social and cultural barrier to immigrants who are coming into America," said Tuyet Duong, senior staff attorney for the Immigration and Immigrant Rights Program at the Asian American Justice Center.

At a cost of $400, Gardasil places an added burden on green card applicants already paying more than $1,000 in form fees and hundreds of dollars for mandatory medical exams, advocates say.

I am all for legal immigration. I am all for making sure the legal immigrants that come to the U.S. are healthy and get the same vaccines that are required for my children. But mandating that girls as young as 11 get vaccinated against HPV is downright wrong. Education? Yes. Give us your daughter so we can inject her with a vaccine that may or may not protect her from a sexually transmitted virus that is detectable with routine pap smears or else you cannot live here? Absolutely not!

I have to wonder how much the immigration official who made this insane decision is getting from the makers of the vaccine.

Cancer Carnival #14 is live! [Bayblab]

Posted: 03 Oct 2008 09:59 AM CDT

The 14th edition of the Cancer Research Blog Carnival is up at ScienceBase. It's jam-packed with all the sciencey goodness you've come to expect. Go check it out then head over the the carnival homepage to read past editions and sign up to host!

Nikon's Small World Competition [The Daily Transcript]

Posted: 03 Oct 2008 09:16 AM CDT

(Fresh water rotifer feeding among debris (200x). First prize 2001, Harold Taylor - Kensworth, UK)

Now in it's 35th year, Nikon's Small World Photomicrography Competition is one of the biggest events in the microscopy world. The finalists of this year's competition are up at You have until October 10th to vote for your favorite.

Read the comments on this post...

Web as platform: Wikified structure resources [business|bytes|genes|molecules]

Posted: 03 Oct 2008 09:12 AM CDT

topsanlogoThe bbgm wiki is run on Mindtouch Deki, which seems to be doing a pretty good job of making a business on top of their open source platform.

Earlier this year I had a chance to visit the New Communication Channels in Biology workshop in San Diego, where I found that Deki has quite a presence in the San Diego structural biology space, powering Topsan among other sites. The Mindtouch blog is carrying an interview with Srikrishna Subramanian, whom I had a chance to meet at Scifoo 2007. Definitely very curious about how the whole wiki-based approach to structural biology platform is going.

At the workshop I got the sense that they would like more crowdsourced involvement. Topsan does have an advantage, it’s related to the Protein Structure Initiative, and that’s where the early involvement should come. I think there needs to be a concerted effort (maybe there has been) to get everyone involved with the PSI to become active contributors, but that should only be the start. There are a whole bunch of people using PSI structures to generate structure-function information. They should get involved as well. I think if the structural biology community can start using Topsan as a key resource, then they’ll be in good shape. Perhaps it’s already there.

The interesting part for me will be to see how Topsan leverages Deki as more than just a wiki (which the interview alludes to). It’s a true web services platform and there could be some very innovative stuff done to make Topsan a true resource, not just another wiki, but a platform for structure-function information

Cancer Research Blog Carnival #14 [Sciencebase Science Blog]

Posted: 03 Oct 2008 07:00 AM CDT

cancer research blog carnivalI don’t know anyone who hasn’t got a cancer story to tell, whether it is personal experience, a relative or friend, or association with their patients or through their research.

Cancer has always been with us, but contrary to the popular image propagated by the mainstream media it is not a simple, nor single disease. In this month’s cancer research blog carnival hosted on the Sciencebase Science Blog, I present a few selected posts from fellow bloggers discussing various aspects of cancer research. Thanks to everyone who submitted a cancer research post.

First up is PalMD on the Denialism blog who explains that cancer is the second leading cause of death, in the US at least, and confirms the ubiquity of the disease as 4% of the population is directly affected (think six degrees of separation type networks to see how almost all of us can have a cancer story to tell). The post provides answers to some of the LAQs (least asked questions) and FAQs (frequently asked questions about cancer. A post from Stephan Grindley augments the cancer 101 with a straightforward commentary on breast cancer prevention and detection.

According to Charles Daney on Science & Reason, recent studies are making it increasingly apparent that cancer is really many different diseases and he explains how this means a new approach to understanding cancer at the molecular level.

More particularly covering cancer research, GrrlScientist offers an interesting take on the genetics of colour and cancer in Behold The Pale Horse and BayBlab discusses a recent publication in the journal Science on the subject of trans splicing and chromosomal translocations as well as the connection between chilis and cancer - preventative or protagonist?

HighlightHealth, meanwhile, discusses the implications of a large-scale, multi-dimensional analysis of the genomic characteristics of glioblastoma, the most common primary brain tumour in adults. On Hematopoiesis, we learn how travelling normal and malignant cells decide where to stay and on get linked up to five great talks from the experts.

Cancer vaccines are big news and none more so than the vaccine being offered to young girls to protect them from cervical cancer caused by HPV. Health blogger Grace Filby has posted on why this vaccination campaign is not a good idea given the lack of safety data currently available.

Orna Ross tells us about the good things she has gained from having cancer/ and points out that fighting cancer as if it were a battle is not the only approach to tackling the disease. Actorlicious meanwhile provides a star-studded perspective and how the famous and infamous are standing up to cancer.

A post from the University of Oxford science blog on exploiting the Achilles’ heel of cancer, describes how a new approach will lead to treatments with none of the common side effects of cancer therapy. And, Sally Church on the Pharma Strategy blog asks will Abiraterone impact survival in advanced prostate cancer?, the most common carcinoma in men. She also provides a fascinating insight into treating triple negative breast cancer.

Science Metropolis discusses how public health expert Dave Ozonoff hopes to use mathematics and chaos theory to explain paradoxical cancer frequencies, such as those seen in Cape Cod, where rates are 25% higher than the state average in Massachusetts.

Finally, one from the recent Sciencebase archives entitled (hopefully quite controversially) alcohol causes cancer.

Visit the Cancer Carnival site to read past carnivals, to get information on scheduled posts and to find out how to host your own cancer research blog carnival.

Cancer Research Blog Carnival #14

Around the Blogs [Bitesize Bio]

Posted: 03 Oct 2008 05:46 AM CDT

COME AND GET IT! Hot blog posts around the intertubes, served up from the feed reader.

More classroom science blogs: the collection continues
Calling all scientists and science-fans: you can help with science education by letting students know you’re interested. How? Go and comment on classroom blogs and wikis.

Emerging Model Organisms
A new book is coming out from Cold Spring Harbor Protocols, of the same title.

Author’s initial entry: Autism’s False Prophets
Finally, science pushes back against antivaccine lunacy.

Gaze into the crystal ball - Nobel Prize Predictions
Who do you think will win?

David Goldstein on the failure of genome-wide association studies

Varmus on “The Cure” for Cancer
Some of the Nobel Laureate’s thoughts on an oversimplification of cancer biology.

A bacterium’s-eye view of life
An informative post on E. coli’s major life challenge: living life at low Reynolds’ Number.

Whirlpool of scientific thought
Stream-of-consciousness whirlpools emerge from a grant-writing process.

CLC bio Partners with Illumina to Provide Next Generation Sequencing Analysis Technology [Next Generation Sequencing]

Posted: 03 Oct 2008 01:52 AM CDT

Following an overwhelming reception of CLC Genomics Workbench 1.0, CLC bio is happy to announce the release of its next major version of their flagship product: CLC Genomics Workbench 2.0. Additionally, CLC bio has taken another important step in leading next generation sequencing data analysis by becoming an Illumina Connect partner. Illumina Connect is [...]

Coworking and research [business|bytes|genes|molecules]

Posted: 03 Oct 2008 12:14 AM CDT

Bora writes about coworking and telecommuting. I’ve been wondering if coworking will ever catch on in the life sciences and what the models might be. It is one thing to do it as an informatician or software developer, but what about bench scientists. I can think of three models

1. Incubators which allow you to set up a small company and use lab space in a university or other research facility

2. A facility that specializes in a particular kind of research or expertise, e.g. you could have facilities that specialize in providing consumables and supporting infrastructure for Affymetrix arrays. You could then outsource other kinds of experiments and focus on your expertise, perhaps with a specific plan in mind (this is just one thought). You essentially reserve time on the instruments, and use the reagents and consumables and pay for what you use (or perhaps order your own and just pay for instrument time)

3. You could completely virtualize your research, outsourcing everything and just focusing on data analysis and experiment design. Can the Assay Depot model could be extended even further to support something like this?

Just some random thoughts. Would love to hear what others think

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1 comment:

johnsmith said...

The DNA Network of blogs about genetics, genomics, and DNA is growing arithmetically, if not exponentially. Today, we welcome our 27th member walter Jessen of highlight health. Our Facebook group is growing as well with some notable personalities from bloggers to genetics and healthcare professionals.


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