Wednesday, September 17, 2008

The DNA Network

The DNA Network

The DNA Network

Marketing science in the public square [Tomorrow's Table]

Posted: 17 Sep 2008 06:45 PM CDT

This week, members of the National Association of Science Writers mailing list have been discussing the reduction in science overage in major newspapers.

Just this week, the Washington Post's Monday science "page" was reduced to a 1/2-page feature article, plus a 1/2-page ad. This science feature article will appear only every second week. In the alternate weeks, the science "page" will host the "Department of Human Behavior" column.

Matt Clark, who retired in 1989 as medicine editor of Newsweek, where he had worked for 27 years had this to say:

"When I became a science writer in the 1950s, a major objective of NASW was to advance science as a worthy objective for journalistic coverage, along with politics, sports, and the rest. Eventually, papers began to take science reporting more seriously and some of them instituted science pages and sections, and meanwhile, NASW's membership grew and grew. I should add that a lot of this new journalistic interest in science had to do with the Cold War, Sputnik and the National Security State that tangentially fostered interest in space exploration.

Some of this growth in science coverage was attributed to polls showing that readers hungered for news about science. But I don't think this was always true. If you ask the man on the street if he thinks science is an important subject for news coverage, he isn't going to say No. But he or she really doesn't think it's important unless you can address the kind of issue he or she might be facing at the moment--the right kind of running shoes, the best herbal remedies for whatever, the latest cancer cluster but not much else that would justify a papers devoting a whole section to science. The only thing that saved the NY Times Science Tuesday was the advent of PC advertising, I'm told. And when that source dried up, pharmaceutical ads magically came along and the Times merged it's Thursday health pages with the Tuesday science section. The only reason Jim Gleick's book "Chaos" was a bestseller, according to a science-writing friend as cynical as I am, is that people thought it was about Wall Street. (That would be doubly true today.)

And contributing to all this, is the shrinking news hole and news staff to fill it at paper after paper, as many of you have noted.

But frankly, I have been convinced for some time that people don't fundamentally give a damn about the real sciences of physics and mathematics, unless you can show some spectacular space pictures. They're into fitness without effort, herbs that heal and astrological prophecy just as they were a half-century ago."

I see this as a call for scientists to get active and start communicating, which of course is one of the reasons we blog.

John Gever, currently a Staff writer for the medical news website MedPage Today; formerly freelance science and non-science journalist, wrote:

"This is where blogs and other web formats may do a better job [than conventional science writing], at least in terms of attracting an audience. Their ability to specialize and follow subjects on a daily basis makes it possible for them to develop storylines. And with loyal audiences come advertising opportunities and a business model for blogging as a job rather than a hobby or marketing sideline."

Lest you bloggers begin to feel overly satisified with your efforts, James Hathaway, Research Communications Manager at the University of North Carolina at Charlotte, further points out that:

"Blogs are great, but they only reach narrow, special target audiences. Our real challenge is to reach the broader audiences and tell them the news they don't already know, which is why the death of science reporting and science sections at newspapers (and, for that matter, the death of newspapers in general) is so upsetting.

I've been feeling for some time that we really need to be thinking more
about marketing science in the public square (in the broader media venues) if we don't want scientific research to vanish from in public awareness -- and if still want to "cling" to our illusory belief that we can create a more scientifically literate public. Of course, the mere mention of the word "marketing" is likely to cause a great disturbance in the force on this list...

What I'm thinking about when I'm talking about "marketing" is that science writers should go beyond simply writing science news, but should be actively involved in trying to market the news once they have reported it -- the way, for example, some of us market books (or, more accurately, the way publishers market books)-- appearing on talk shows, sending copies to prominent columnists and commentators to try to get the subject widely discussed. Other than by people like Sagan, Gould, and perhaps people like Chris Mooney, this kind of science proselytizing really hasn't been done much. Public information officers (like myself) do this kind of work on behalf of the universities and labs we represent, but if we are going to get more science out to a broader public, everyone who has a stake in public science communication needs to be involved. The information marketplace is very competitive, and, like all markets, this one can crash."

So the question for you is how can we market science better on the public square? Clearly the public does cares about global warming (if somewhat belatedly), as well as numerous other issues such as feeding the world, finding cures for diseases and enivronmental degradation- all issues intimately associated with scientific research.

Off to Toronto [The Daily Transcript]

Posted: 17 Sep 2008 05:57 PM CDT

My posting frequency may go down as I will be off to Toronto for a little while. There I'll be meeting up with Larry Moran and checking out what it means to be a Torontonian.

(Larry, it looks like I'll win the bet, but we won't know for sure untill after Nov. 2nd.)

Read the comments on this post...

Amy Harmon, New York Times, on Open Access publishing [The Tree of Life]

Posted: 17 Sep 2008 05:16 PM CDT

Amy Harmon, who writes for the New York Times and has written some excellent recent pieces on evolution and genomics is answering some questions on the New York Times website

And one of them was about communicating science and Amy responded (with other comments):
Of course, the one way scientists do, theoretically, communicate with the public is by publishing their results. Since these papers are written for other scientists, they can be hard to understand. But even for people game to wade through them, they are often hard to obtain. The two leading scientific journals, Science and Nature, and many others, require people to pay for access to papers whose authors have been financed by taxpayers. "Open access" publishers like the Public Library of Science do not, so it would be nice to see scientists choosing — or being required — to publish in journals that are open to the public.
Nothing more for me to add.

National Institutes of Health to Congress: We Need Basic Research [adaptivecomplexity's column]

Posted: 17 Sep 2008 04:27 PM CDT

Two years back, the US Congress passed the NIH Reform Act of 2006 in an effort to get the NIH to adapt its structure to the new landscape of biomedical research, and to institute more transparency and accountability so that Congress can do its job. Last week, the NIH Director Dr. Elias Zerhouni went to Congress to report on how well his agency has done meeting the new demands of the law. He lays out the challenge in today's interdisciplinary world:


10 Things about GE crops to Scratch From Your Worry List [Tomorrow's Table]

Posted: 17 Sep 2008 02:40 PM CDT

As New York Times columnist John Tierney points out in a recent article, many consumers worry about things that are not actually a threat to human health or to the environment. This is especially true in the case of food, farming and genetic engineering. While there are plenty of issues to debate (how can we make the best seed available to farmers that need it; how can we conserve land, how can we have productive farms without harming the environment), there are some scientific facts that have not yet seeped into the public consciousness.

With September upon us, perhaps you're in the mood for a break, so I've rounded up a list of 10 things not to worry about this fall. You can make your own nominations on this blog.

1. GE crops require more pesticides

Two classes of pesticides are affected by GE crops: Herbicides that kill weeds and insecticides that kill insects.

There is now clear and ample evidence that BT crops have reduced the use of insecticides- here and abroad. In China, cotton farmers were able to eliminate 150 million pounds of insecticide in a single year by using GE varieties. For comparison, in California, we spray 190 million pounds each year. Although BT-cotton in China has been dramatically effective in reducing pesticide use, after 7 years some farmers started spraying again to control secondary insect pests that are not controlled by Bt. This points to the need to integrate GE crops into organic farming systems that also use crop rotation and beneficial insects to control secondary pests.

In India a huge proportion of the farming expenses are going to insecticides. Although GE seed are more expensive, the yields are 80% higher and the farmer saves on insecticide costs.

In the US, pesticide use on corn, soybeans, and cotton declined by about 2.5 million pounds in the United States since the introduction of GE crops in 1996 (Fernandez-Cornejo and Caswell 2006).

In the case of herbicides applications, usage per acre has declined since the advent of herbicide-resistant crops (Fernandez-Cornejo and Caswell 2006), and because glyphosate breaks down quickly in the environment, the overall net effect is a reduction in the toxicity of herbicides used. For example, conventional soybean growers used to apply the more toxic herbicide metolachlor to control weeds of soybeans despite the fact that metolachlor is a known groundwater contaminant and is included in a class of herbicides with suspected toxicological problems. Switching from metolachlor to glyphosate in soybean production has had huge environmental benefits not measured in pounds of active ingredient but in environmental impact (Fernandez-Cornejo and McBride 2002). Another agricultural benefit is that herbicide-resistant soybean has helped foster use of low-till and no-till agriculture, which leaves the fertile topsoil intact and protects it from being removed by wind or rain. Also, because tractor-tilling is minimized, less fuel is consumed and greenhouse gas emissions are reduced (Farrell et al. 2006).

2. Corporate control of GE seeds forces farmers to buy seed each year

Most conventional and organic farmers in California buy their seed. They are not contractually obligated to buy seed from the same company each year (this is the same for GE and conventional seed). Farmers choose to buy hybrid seed and other improved seed because they are higher yielding and/or have qualities preferred by consumers.

Although the US seed industry is dominated by large corporations, this was the case before GE came into play. In some less developed countries, such as Bangladesh, national breeding programs distribute seed (GE or conventional) freely to farmers who can then self their own seed. For example a flood-tolerant gene cloned in my lab and used to develop new varieties in collaboration with colleagues has been distributed to Bangladeshi farmers through national breeding programs. The farmers are now saving the seed to share with neighbors.

In China and India, there are burgeoning seed industries and an increasing fraction of the agricultural seed is purchased, not provided free by the government. For example, over half of the rice planted now in China is hybrid, therefore purchased annually, most of it produced by private companies. (Thanks to Kent Bradford for providing this information).

3. If we could just distribute the food available, impoverished people would not need GE seed.

Many rural poor in Africa and S. Asia cannot afford to buy food. They must grow their own. Rather than relying on shipments from abroad, they need help improving their own production practices. This includes access to improved seed, farming practices and sound government policies. Now that is something we do need to worry about.

In China, there are proven health benefits to families because of the reduction in pesticide use after the introduction of GE crops. A recent analysis predicts that the lives of thousands of children will be saved once golden rice is launched in 2011.

4. We don't need GE to improve seed, we can use marker-assisted breeding.

Marker assisted breeding is a hybrid of conventional breeding and GE that relies on modern genetic techniques to modify seed. Flood tolerant rice, developed through marker assisted breeding, has the potential assist 75 million farmers who live on less than a dollar a day in major flood zones in places like Myanmar, Bangladesh, and India.

There are other agricultural problems, however, that cannot be addressed using marker-assisted breeding. For example, in the 1990s, papaya orchards on the island of Hawaii were threatened by papaya ring spot virus. Dennis Gonsalves, a former plant virologist at Cornell who is now with the U.S. Department of Agriculture, developed a genetically engineered papaya variety that was completely resistant to the virus. The GE papaya yielded 20 times more than the conventional variety was was distributed freely to growers. It's a great example of genetic engineering benefiting local farmers. There was no other tool available to combat papaya ringspot virus, nor is there now.

5. GE crops harm human health.

There is virtually universal scientific consensus that GE crops currently on the market are safe to eat. After over 10 years of consumption there has not been a single validated report of negative health effects from any GE crop. In contrast every year there are thousands of reported pesticide poisonings (ca. 1200 each year in California alone). The latest report comes from the Joint Research Centre, The European Union's scientific and technical research laboratory and an integral part of the European Commission. A copy of the executive summary of the report is downloadable here.

Every new GE crop must be evaluated on a case-by-case basis. Lets direct our efforts to generating new crop varieties that will benefit the maximum number of people.

6. GE crops harm the environment

GE crops themselves have had no negative environmental effects after over 1 billion acres have been planted.

The rising problem of herbicide resistant weeds and its consequences, for example, are a significant environmental (and practical) problem. But this is a problem anytime an herbicide is used extensively and is not an environmental consequence of the GE crop itself. The same result would occur if the crop is GE or non-GE (and many such herbicide tolerant non-GE crops have been generated).

Like non-GE crops, GE crops produce pollen. Thus pollen flow from GE crops poses essentially the same risks as non-GE crops. There is no example of a domesticated crops escaping into the wild and wreaking environmental harm. This is because they are highly domesticated and need a farmers care to survive. As Freeman Dyson once said, "Have you seen any wild poodles lately?"

A positive spin off of the whole GE debate is that now there is more attention being placed on the ecological effects of pollen flow from domesticated crops to wild populations.

7. GE crops reduce biological diversity

Bt has had some real benefits in reducing chemical insecticide use and in enhancing insect biodiversity. The recent analysis by Cattaneo et al (2005) clearly shows that there is similar biodiversity (ants and beetles) in GE cotton fields vs non-GE cotton fields. In contrast, broad-spectrum insecticides (which are used on the vast majority of non-GE cotton fields throughout the world) significantly reduces ant and beetle species richness.

If we hadn't genetically modified our crops by conventional methods over the last 50 years, we would be using twice as much of the Earth's surface to grow the same amount of food. In the future, if we don't increase yields, we'll need to use double the amount of land to produce the same amount of food. Sparing land from becoming farmland, is the greatest benefit to biodiversity. For this reason, some ecologists see the application of GE as a way to spare even more land from destruction by enhancing yields (Qaim and Zilberman 2003; Snow et al. 2005).

8. The regulation of GE crops is lax.

GE crops are more stringently regulated than other crops. That is, other crops are not regulated at all. Hundreds of thousands of children are dying each year because of vitamin A deficiency, thousands more are poisoned with pesticides, more land is being put into production every year, which negatively affects global warming. In contrast there has not been a single case of harm from GE crops to human health or the environment, even after over 1 billion acres grown. Their is broad scientific consensus that the GE crops currently on the market are safe for human health and the environment.

9. Organic agriculture has solved all agricultural problems. We don't need GE.

Organic farming seeks to maximize the health of the environment, the farmer, and the consumer. Organic farming came about as a response to the environmental and health problems associated with overuse of chemicals on conventional farms. Genetic engineering has contributed to this goal by reducing pesticide use (see #1). There are certain environmental or disease problems with no organic or conventional solution. There's nothing to make plants resistant to certain viruses, for example. Flood, drought, frost and salt tolerance have also been developed through GE and are now being tested.

10. We have already seen what is scientifically possible and it is not impressive.

Every time a GE crop has been approved, farmers have embraced it and the GE acreage for each crop has quickly grown to 50 to 90 percent of the total acreage.
To date most of the GE production is soybeans, corn, and cotton carrying two traits (herbicide tolerance and insect resistance). With unprecedented discoveries in genetics, many more traits are in the pipeline.

Online Reputation: Tips and Tricks [ScienceRoll]

Posted: 17 Sep 2008 01:50 PM CDT

The Independent Urologist just came up with some great tips about how to protect your online reputation. I thought I should add my suggestions to the useful list:

  • Blog and blog often.

Be patient. I had 15 readers a day in December, 2006. Now I have 1-1500 visitors a day. It takes time and effort (I wrote almost 1000 posts in 2 years).

  • Have your own website, even if you are part of a group.

Create a LinkedIn profile and manage your blog properly (e.g. construct a nice about me page).

  • Link your blog and website.

Google loves self-linkage… Build your page rank professionally.

  • Publish articles, such as review articles, in medical journals and periodicals.

Summerize your ideas in Google Docs and collect your favourite links on so it will be much easier to write a proper review later on a specific subject.

  • Post comments on other peoples blogs and allow them to post on yours.

Be fair and open to new ideas. Join respected groups like the DNA Network or contribute to blog carnivals.

  • Get your name in the media via interviews (see blogging and blogging often).

See my Behind The Scenes of Medical Bloggers series. Publish your slideshows and ideas so people will certainly find you.

  • Google yourself on a regular basis.

Or use Google Alert to receive automated alerts about who and why mentions your name on the web.

  • Contact content providers that allow subscribers to post malicious writings about you and request that that they remove the comments.
  • Have a lawyer contact the content services or the offenders themselves with threats of litigation.

Get a HONcode (Health on the Net Foundation) accreditation.

  • Seek help from online reputation management experts (yes they exist).

Contact the members of the Healthcare Blogger Code of Ethics group or check the service of out.

And here is a slideshow I presented at the Medicine 2.0 Congress about building an online reputation.

Adult stem cells and stroke [Mary Meets Dolly]

Posted: 17 Sep 2008 12:54 PM CDT

Researchers have found that stem cells from bone marrow help in mitigating the damage of a stroke in mice, but not in the way they anticipated. It was always thought that stem cells would replace the damaged tissue. But now it has been found that the stem cells injected into the stroke damaged brains of mice prevented immune system damage and reduced inflammation. From
Scientific American:

Injecting stem cells into the brains of mice that recently suffered a stroke can reduce nerve cell (neuron) damage by up to 60 percent, according to new research.

But the stem cells do not simply replace damaged tissue as previously believed. Instead, the immature cells trigger adult brain cells to switch gears and block a stroke-induced immune response that causes nerve damage.

"It is a paradigm shift," says Sean Savitz, a neurologist at the University of Texas Medical School at Houston, who was not involved in the study. "The original idea is that you put cells in there and it would reconstruct the cells that died. … The beauty of this is there's not just one mechanism; they are acting in many different ways."

Over the past 10 years, he says, research has shown that stem cells have the potential to reduce inflammation, morph into new nerve cells, and stimulate production of fresh blood vessels (to nourish cells) and axons (the long fingerlike projections that neurons use to send information to neighboring cells).

Study co-author Darwin Prockop, director of the Texas A&M University Health Science Center's Institute for Regenerative Medicine, says that previous studies have shown that mesenchymal stromal cells (bone marrow stem cells) can reverse neurodegeneration in the brain caused by disorders such as Parkinson's disease. But scientists were not quite sure how.

"This is the first time really that the mechanisms were laid out," Prockop says.

The finding, published today in Proceedings of the National Academy of Sciences USA, not only promise to pave the way for new therapies but may also help physicians assess the success of these treatments.

Your Genome, Your Choice: A buyer’s checklist for genetic tests [deCODE You]

Posted: 17 Sep 2008 12:20 PM CDT

Scientists at deCODE genetics' Genetic Service Facility lab in Iceland

Scientists at deCODE genetics Genetic Service Facility lab in Iceland

The number of companies offering genetic tests to the public is large and growing. But there are vast and very real differences in the quality, purpose and price of testing services out there. So how do you tell the difference between them? And how do you decide which to use?

Knowing what you want

First and foremost, you need to think about what sort of information you hope to gain from your genome and how accurate you want the results to be. Are you taking the test only for fun, perhaps hoping to talk about your results on Facebook? Or are you interested in using it to protect or improve your health, perhaps working with a doctor? And do you want your information to be kept strictly private so that you are in full control of those with whom you share it, or are you comfortable with others being able to access it and use it?

At deCODE, we have studied the genomes of hundreds of thousands of people over the past twelve years. Our goal has been to discover what variations in the human genome give some people higher or lower than average likelihood of developing many of the most common diseases in our society. We use that information to develop products like genetic tests that can help people to stay as healthy as possible for as long as possible. From day one that's been our bread and butter – it's not an idea that occurred to us last week or even last year.

And with that experience, and having worked with so many people, there are a few basic things that we think you should look for in any genetic testing service. These are fundamental characteristics that we demand of ourselves in all of our discovery work, and we think you should settle for nothing less.

Buyer's checklist

In any field, in order to offer services to the public you have to be able to stand behind the quality of your product. In genetic testing, the basis of any test worth paying for is good science: large-scale studies that establish and then replicate in independent groups links between specific markers in the genome and specific traits, such as diseases. Making those links requires gathering large sets of very high quality, consistent data. It requires teams of doctors, geneticists and other scientists, as well as certified DNA analysis laboratories, statistical tools and computing power and software to accurately analyze the datasets. If you can do all this under the strictest data and privacy protection protocols in the world, you will reward the participation of your research subjects with peace of mind they deserve.

That's just for starters. In order to offer a test, you need to be give your customers the same certified quality of DNA analysis, as well as the ability to accurately interpret what the findings of large studies mean for disease risk. In short, you need all the same capabilities and expertise as for research, but focused on accurately and securely delivering results to individuals.

The gold standard

These are the standards that lie behind deCODEme and all our diagnostic tests. We offer the best science, usually our own, as our scientists lead the world in finding genetic risk factors for common diseases. Where we do use discoveries made by others, our scientists have validated the findings according to our own rigorous criteria. We have our own CLIA-certified DNA analysis laboratory, one of the largest of its kind in the world, and do our own quality control. We share your results with no one but those you specifically request. We offer our customers the ability to check whether they carry validated risk factors for dozens of diseases, and update their profiles rapidly and regularly as new discoveries are made. This isn't trivial stuff, and our prices reflect the quality of the products we offer.

Don't just take our word for it: the value of deCODE tests is reflected most clearly in the stories of customers like you. On this blog you can read about what they have to say about how they are using their results to better look after their own health.

Your genome, your choice

This is a high bar, and one that few others will pass. Can you find cheaper services out there? Yes. Are there dot-com storefronts that outsource the science and the analysis of your genome? Yes. That are focused less on quality and more on website bells-and-whistles for using your genome for social networking? Yes again.

But your genome is yours, and we think you have a right to choose the best for yourself if that's what you want. At deCODE we are not offering cut-rate services, outsourcing the analysis of your genome, or cutting corners on privacy protection. We give you a portal into the best and latest in genetics, offering the highest quality services available for those who want to know how the latest breakthroughs in human genetics can be used to improve their health and healthcare. If that's you, we encourage you to check how other services stack up to deCODE – and we look forward to hearing from you!

ThinkGene Wars!!!! [The Gene Sherpa: Personalized Medicine and You]

Posted: 17 Sep 2008 07:53 AM CDT

Drew over at Think Gene (Which BTW is getting a heck of a lot of the media's attention. Including WSJ, NYT....etc) unleashes a heck of a post that I wanted to comment on. Drew and I got into a heated...

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Seattle celebrates the millionth comment! [Discovering Biology in a Digital World]

Posted: 17 Sep 2008 07:16 AM CDT

Okay, occasional readers, friends, and former students, the date is official. I walked over to Ozzie's, chatted with one of the waitresses (a Garfield grad, no less!), talked with a manager on the phone, and we're on for the party.

You can find us on Saturday, Sept. 27th at 4 pm in the upstairs mezzanine at Ozzie's.

Address: 105 W. Mercer St., Seattle, WA 98119

Dave Bacon will be there (I don't think he's related to Kevin, but here's your chance to ask, and we could start a new game! Six degrees of David Bacon!). Grrl Scientist will be signing autographs. And, we'll get a chance to ask Maria just what she's really doing in those really curious wedding pictures she posted on her blog. Call me conventional, but I've never seen someone in a wedding dress fooling around with liquid nitrogen before.

Anyway, I passed on renting the karaoke machine, but if we get enough people attending, we do get our own bartender. So, let me know in the comments if you plan to attend. I'm sure we're gonna have a good time.

Read the comments on this post...

Terrorism: The Animal Research War [Bitesize Bio]

Posted: 17 Sep 2008 05:30 AM CDT

After some of the blog posts that I’ve written on animal rights’ extremists and violence against animal researchers, there’s now a review of a most appropriate book on the topic available in Science - Scientists Under Siege.

Suppose you are a scientist and a finalist for the position of vice president for research at the University of South Florida (USF). Before leaving for your interview trip, you receive copies of letters sent to the university’s administration informing them of your “ignominy” and stating that you are unwelcome in the university’s town. Animal rights activists meet your plane and (because of an open meetings law) are present at most of your interviews. Activists outside the meeting room doors lobby attendees and distribute fliers that make false and preposterous claims about your research. Demonstrators wear T-shirts demanding that you not be hired. When you deny the accusations being hurled at you, a faculty member calls you a “son of a bitch” and a liar. At your hotel room, you receive threatening calls and knocks on your door in the middle of the night. Fortunately, the campus police provide you with protection. Arriving at the airport for your return trip, you are surrounded and harassed by demonstrators until airport security rescues you. At home, you find protesters standing not far from your house, shouting at you. And USF’s president now refuses to speak to you. You don’t get the job.

Medium ImageNow suppose that really happened.

This and more is the situation that animal rights’ extremists have placed many biomedical researchers into. I say “and more,” because P. Michael Conn didn’t actually have his house firebombed, his car blown up, or been physically assaulted.

As a result, Conn has his new book out - The Animal Research War. While I haven’t gotten the chance to read it, it purportedly aims to educate and inform the general public as to what actually happens with animal research.

As to what position to take on bioethical questions surrounding research, of course one should read available materials such as this book, guidelines addressing animal welfare concerns written by the National Academies of Science, and other resources. And then come to your own conclusions. If you disagree with the status quo, address them through appropriate channels, like bioethics committees.

But above all, arm yourself with the knowledge of the tactics of extremism and terrorism, so that you can work against such destructive elements and forge towards a better world.

Melamine in Milk [Sciencebase Science Blog]

Posted: 17 Sep 2008 02:14 AM CDT

melamine-structure-3DToday, we learn that several thousand babies in China are seriously ill, having suffered acute kidney failure, with several fatalities, among those given formula milk contaminated with the industrial chemical melamine. The toll is far higher than was previously admitted by the Chinese authorities, according to the BBC.

Manufacturer, Sanlu, part-owned by New Zealand’s Fonterra Cooperative, recalled all of its powdered milk products in China’s north-west province of Gansu. However, twenty-two brands, including China Mengniu Diary Co and Inner Mongolia Yili Industrial Group, of milk powder have so far been identified as containing melamine. “The majority of afflicted infants ingested Sanlu-brand milk powder over a long period of time, their clinical symptoms showed up three to six months after ingesting the problematic products,” Health Minister Chen Zhu told Bloomberg Asia.

Allegedly, the manufacturer(s) involved in the scandal add toxic melamine to the formula to artificially inflate the reading for protein levels. Formula milk was not until now tested for melamine, because regulators never before suspected that manufacturers would adulterate their products with such a compound.

So, what is melamine and how does it spoof the protein levels in baby formula milk?

melamine-structureMelamine is an organic compounds, a base with chemical formula C3H6N6. Officially it is 1,3,5-triazine-2,4,6-triamine in the IUPAC nomenclature system (CAS #108-78-1). It is has a molecular mass of just over 126, forms a white, crystalline powder, and is only slightly soluble in water. It is used as a fire retardant additive in polymer resins because its high nitrogen content is released as flame-stifling nitrogen gas when the compound is burned or charred.

Indeed, it is this high nitrogen level - 66% nitrogen by mass - in melamine that gives it the analytical characteristics of protein molecules. Melamine can also be described as a trimer of cyanamide, three cyanamide units joined in a ring. It is a rather harmful compound, according to its MSDS sheet: “Harmful if swallowed, inhaled or absorbed through the skin. Chronic exposure may cause cancer or reproductive damage. Eye, skin and respiratory irritant.” Not something you would want in your infant’s milk.

Previously, melamine was found in exported pet food last year and blamed for killing thousands of cats and dogs in the US. Bloomberg also reports that analysis of samples of ice cream produced by Yili have also revealed the presence of melamine. Regardless of crushing inflation and legislative pressure, there is no excuse for the adulteration of food in this way. Diluting a product, the previous approach by the manufacturers, is highly unethical and can lead to malnutrition, but straight poisoning is infanticide.

Melamine in Milk

CD/CV and Goldstein [Mailund on the Internet]

Posted: 17 Sep 2008 01:41 AM CDT

Everyone seems to be talking about this NY Times interview with David B. Goldstein (Gene Sherpas, biomarker-driven mental health, Adaptive Complexity, John Hawks …)

In the proud tradition of blogging, I will add my voice to the noise.

The common disease / common variant hypothesis

The arguments concern association mapping and the so-called Common Disease / Common Variant (CD/CV) hypothesis.  The CD/CV goes like this: a lot of common diseases are late-onset, so we do not expect selection to be strong against the genetic factors underlying them. This, combined with the recent expansion in the human population leads us to expect that a lot of common diseases to be caused by relatively common variants.

If the hypothesis is true, then we should be able to locate these common variants since we can tag all common variants in the genome with relatively few markers, and we can type these using SNP chips.

If the hypothesis is false, then we are screwed. We probably need complete re-sequencing and some heavy duty statistics to get anywhere.

Out of convenience more than anything, people chose to believe the CD/CV to be true, and started projects such as HapMap to map the common variation in the genome.  Based on this map, companies developed chips to tag all variation genome wide, and disease studies used these chips to do genome wide scans.

Goldstein argues:

It takes large, expensive trials with hundreds of patients in different countries to find even common variants behind a disease. Rare variants lie beyond present reach. "It's an astounding thing," Dr. Goldstein said, "that we have cracked open the human genome and can look at the entire complement of common genetic variants, and what do we find? Almost nothing. That is absolutely beyond belief."

If rare variants account for most of the genetic burden of disease, then the idea of decoding everyone's genome to see to what diseases they are vulnerable to will not work, at least not in the form envisaged. "I don't believe we should do more and more genomewide association studies for common diseases," Dr. Goldstein said. Instead, he suggested, the "missing heritability" might be tracked by thoroughly studying the genome of specific patients.

I would say the jury is still out on this one, but it is clear that the CD/CV isn’t as common as it was hyped to be.  We can only explain a small percentage of the heritability of diseases with the variants found so far.  Still, we have discovered more variants that we can replicate within the last year or two than in all the time up to genome wide scans, so writing off genome wide association studies completely is a bit extreme, in my view.

No, CD/CV is not the full story, but some common variants exist, cause we have found them!

The real question is, of course, how much heritability is explained by common variants and how much by rare variants.  Right now, we simply do not know.  The power to detect even common variants is limited, so there might be more out there to find.  On the other hand, it is hard to believe that the vast majority of the heritability is caused by common variants since we still can only explain very little of it, so some rare variants must be involved.

In the coming few years we will probably figure this out, and that is exciting indeed.

Common disease and selection

Now as for variants behind common diseases being selectively (near) neutral — part of why they can be common in the first place — that is an interesting question.

I personally think that selection is playing a larger part in the story of common diseases than we think, and I look forward to learning this story.

Are we seeing common variants because bottlenecks have reduced selection strength so rare variants — otherwise selected against –  have managed to increase in frequency by drift? Are we seeing common variants because they are selected for by some balancing selection? Are they hitch-hiking  on beneficial variants?

We are already hearing about interesting findings in here (Helgason et al. 2007, Blekhman et al. 2008) and we will learn much more in the future.

We live in interesting times indeed, and now is not the time to abandon genome wide association studies.

Health News in Second Life: New Classes and New Guidelines [ScienceRoll]

Posted: 17 Sep 2008 01:23 AM CDT

First, here is a review about virtual worlds published in the Journal of Medical Internet Research.

UIUC GSLIS and the Illinois Alliance Library System are pleased to offer a series of non-credit continuing education courses for librarians, educators, and others interested in libraries, learning, and teaching in virtual worlds such as Second Life.

Other psychologists instead propose Second life as a psychoanalytic tool, useful for understanding how the patient perceives as would be and act, what to see in the world and in others, taking control its output.

These Virtual Worlds Guidelines for IBM employees have been created to build upon those foundations and to address the some of the choices that individual IBMers may face in virtual worlds. These guidelines are not intended to address every situation you may encounter through use of a digital persona or personas.

Andrew Yates versus Dr. Steven Murphy [Think Gene]

Posted: 17 Sep 2008 12:08 AM CDT

On our “Why The Data Sale Story is Silly” story last week, Dr. Steven Murphy (the Gene Sherpa) of the genomics medical special practice Helix Health posted this video in the comments:


This is a must watch fellas…

“Google’s Master Plan

my response…


Steve, please don't, "The Master Plan" is well-polished crap. What is Google doing that this video claims is so bad? Oh no, the announcer said "don't be evil" with suggestive intonation? Oh no, they used currency symbols in the names of the founders? Oh no, let's sacrifice a goat and purge away this great evil!

So what if Google is getting into health care? Give me one concrete fact why Google in health would make my life objectively worse. Show me evidence of this impending Google malice that threatens me personally.

What, because of "privacy?" That's a nonsense word like "patriotism" or "democratic." Yes, it would be wrong if somebody didn't treat me for cancer because they knew I had cancer. But isn't that the fault of the health care establishment, you know, the system that doesn't treat what it knows about, and not the service that tries to learn what about me can be improved?

Just repeat that to yourself again: "Yes, it would be wrong if somebody didn't treat me for cancer because they knew I had cancer." Isn't that just insane? Yet, that's exactly how health care works today.

Give me one good reason why I should defend the status quo of health care. Because it's foolishly funded by risk ignorance, and its only impetus is health emergency? What crap. Instead of me paying to pumping crones full of drugs for two more years of semiconscious Jerry Springer, how about I get health care that improve the lives of young people like me who already seem healthy today? I can see Google providing services like that in exchange for referring my health profile to, for example, drug companies. Fine. Great.

And… this is bad… because I'm only supposed to buy health care that I don't think I'll use to fix diseases that I could prevent?

Yes, I find insipid marketing blather like "democratizing" insulting to my intelligence, but "annoying" isn't "wrong."

But, as far as I can tell, my life has only gotten much better thanks to Google and its satellite projects. Does that mean that Google as a company is rewarded, too? Yes… and? So? Good for them.

Dr. Steven Murphy responds: (edit: are you really accusing somebody of a federal crime using a Valleywag report, Steve?)

"So what if Google is getting into health care? Give me one concrete fact why Google in health would make my life objectively worse."

2 words Dean Ornish…..Dean is their medical advisor and what's his answer to better health? "More Love" Bullshit…here's an answer……pay freakin primary care doctors twice what they are getting paid now to see half as many patients….I don't see google doing that…

"Show me evidence of this impending Google malice that threatens me personally."
Not HIPAA compliant my friend…why does everyone think that sales of this information will be to the benign Pharma companies…..There are several F'in bigger fish that want that data

2.)The Hartford
3.)Any bank thinking of loaning you money

Give me a break Drew. This play has nothing to do with healthcare and everything to do with discrimination…..Think a FICO score is a big deal imagine your banker knowing you are predisposed to heart attacks when you try to take out that mortgage….Come on, you have to see that as a serious possibility, especially know that they have an algorithm to re-identify de-indentified DNA samples….

"But isn't that the fault of the health care establishment, you know, the system that doesn't treat what it knows about, and not the service that tries to learn what about me can be improved?"

I agree the system is broken, but tests that aren't evene scientifically or medically validated are not the way to fix this problem….How does a SNP scan give you better health Drew. I challenge you on that one. How will a SNP scan be used for better research without accompanying medical data like Coriell???

"Give me one good reason why I should defend the status quo of health care."

I never asked you too.

"it's foolishly funded by risk ignorance, and its only impetus is health emergency? What crap. Instead of me paying to pumping crones full of drugs for two more years of semiconscious Jerry Springer, how about I get health care that improve the lives of young people like me who already seem healthy today?"

I agree…we should stop treating people who have a negative life expectancy based on family history……And all patients should have to pay out of pocket for ICU care if they have a terminal illness….That will fix the system. NOT SNP scans and google searches….

"I can see Google providing services like that in exchange for referring my health profile to, for example, drug companies. Fine. Great."

It's not the drug companies I care about Drew….it is the financial institutions that set our credit rating and determine our borrowing capacity. You have to see that as a real possibility.

BTW, if you want to get people signing up for these scans all you have to do is give them Google stock for taking the test…..

"But, as far as I can tell, my life has only gotten much better thanks to Google and its satellite projects."

Ahhh yes…….they have done great things in IT, Advertising, Economics, Education. But, unless they want to spend their money on primary care doctors and preventative care delivery rather than collecting bullshit SNP data they will NEVER do anything great with healthcare…Sorry


I (Andrew) respond:

Steve: First and foremost, nothing said refutes my primary claim that the “Google’s Master Plan” video is all insinuation and no substance. You and I have created that substance, and credit for this discussion is ours —not this well-published but shallow propaganda internet video.

I have said that SNP data 23andMe sells now is mostly frivolous, and until it’s actionable medical information (which it is not yet), it will continue to be so. Partly, that’s because of the “gene patents” you lambasted today keep the most important tests out of SNP chips, and partly, that’s because doctors cannot professionally trust tests not that do not explicitly produce medical information. But mostly, it’s a new technology in the highly-regulated industry of medicine. It will improve, and patents will expire. It’s this idea of SNP scans I like: informatics to human biology.

And I have been one of the first to champion efforts like Coriell Personalized Medicine Collaborative. In fact, the findings released by studies like this will greatly benefit all genomic industry stakeholders, including 23andMe.

Me: “So what if Google is getting into health care? Give me one concrete fact why Google in health would make my life objectively worse.”

Steve: “2 words Dean Ornish…..Dean is their medical adviser and what’s his answer to better health? “More Love” Bullshit…here’s an answer……pay freakin primary care doctors twice what they are getting paid now to see half as many patients….I don’t see google doing that…”

Statements like “Caffeine’s effect on the central nervous system interferes with the mind body connection and therefore meditation and relaxation…” does ping my bullshit meter. Does Dean mean, “caffeine is a stimulant, avoid it to relax?” Ok, avoid stimulants to relax. But, some MD newage froo-froo on some board does not make my life objectively worse in any obvious way in which I can readily discern. (and his message of “live healthier by not eating trash and exercise” is OK with me)

As for the futures of doctors, I have bad news, Steve. Health care is seen as much too expensive in the USA. Pretend we cut costs by 50% for the same standard of care. Where in that equation do doctors get paid twice as much to see half as many patients? WHO is going to pay doctors more? On average, for the foreseeable future, the median pay of doctors will only go down.

Steve: “How does SNP scan give you better health Drew?”

OK: Test X requested in your medical practice has been placed on a SNP scan with sufficient scientific confidence. Does do your services at Helix Health give me “better health?”

Steve: “How will a SNP scan be used for better research without accompanying medical data like Coriell?”

SNP scans will add the clinical verification and standards of best practice produced and vetted by Coriell with that accompanying medical data.

Steve: “But, unless they want to spend their money on primary care doctors and preventative care delivery…”

They are spending their money to create software that abstracts away the bureaucratic waste of the health care industry and the expertise of physicians. That is because software is Google’s expertise.

Steve: “This play has nothing to do with healthcare and everything to do with discrimination…..Think a FICO score is a big deal imagine your banker knowing you are predisposed to heart attacks”

I don’t see “we will share your information with banks” in Google Health’s user agreement, and why should I trust HIPAA and the US government more than Google? From what I read here, Google’s policy seems to be even more private than what’s required by HIPAA. My assumption is that Google decided that compliance with HIPAA would be expensive, unnecessarily pedantic, and an tool to be used against them by a potentially hostile regulatory establishment, so they gave the entire act a big “F-U” and wrote their own policy.

I don’t know what Dr. Murphy’s problem with Google/23andMe is other than some irrational fear about “being tracked like cattle” and “having your genome, which now belongs to 23andMe, can now sold to lenders, just wait until you try to get a mortgage, Drew.” 23andMe is Citizen Kane-esque adventure in business, and it’s pushing the genomic industry faster than what’s probably comfortable for the existing medical establishment. Take it for what it is.

Hey, when 23andMe posts a stock photo of some model wearing a stethoscope on their homepage and plays Internet Doctor, I will stomp them, too. But until then, I don’t understand why some company selling some expensive, hobbyist “Apple I of genomics” is of any significant concern to a professional medical specialist of genomics like Dr. Steven Murphy. Steve, let 23andMe have their “spit parties.” You are a medical professional. You don’t need to address their silliness.

Any Happy Navigenics Customers Yet? [Think Gene]

Posted: 16 Sep 2008 11:33 PM CDT

We here at Think Gene are still waiting for a report of least one person who will vouch as a satisfied Navigenics customer. To qualify:

  • You paid full price for the Navigenics service.
  • You are willing to vouch as a “satisfied” customer of Navigenics over the Internet using your full name and email address. (in lieu of a full name, we will accept a web domain)
  • You are not an employee of Navigenics nor have any affiliation with Navigenics or its employees.
  • You are not a member of the press. (blogs are OK)

There is no prize for identifying oneself as this happy Navigenics customer because we feel that the joy of being a happy customer of Navigenics would be its own reward.

A running tally of identified satisfied Navigenics customers will be kept below for your convenience:

Identified Satisfied Navigenics Customers: 0

Leave reports in the comments.

Worm therapy [Bayblab]

Posted: 16 Sep 2008 09:43 PM CDT

Leeches and maggots have a history of use in medicine - for blood-letting or wound cleaning, respectively (and both have FDA approval for modern medical use). Recent reports have suggested potential usefulness for another creepy-crawly.

Filarial nematode worms are particularly nasty mosquito-borne parasites that take up residence in the lymph nodes. The worm is endemic to many tropical and sub-tropical countries and causes elephantiasis - the enlargement of limbs and genitals (and for guys thinking this doesn't sound so bad, the genitals can get so big that they interfere with regular physical activity. Pictures here), as well as less obvious internal damage. However, areas with high rates of filarial worm infection tend to have lower rates of inflammatory bowel disease, arthritis and other inflammation-caused ailments. This is thought, in part, to be caused by ES-62 - a glycoprotein secreted by the worm that has anti-inflammatory properties.

Scientists in Glasgow are now looking for a way to develop ES-62 into a better, non-heart-attack-inducing, anti-inflammatory.

Don't worry though - I don't think they plan on treating with live worms.

1 comment:

james pandreson said...

The DNA Network is the only collection of blogs anywhere about genetics, genomics, and DNA. As of April 14, 2008, there are 52 members who work as scientists, journalists, students, doctors, and other genetics professionals and know genetics better than anyone.