Thursday, November 20, 2008

The DNA Network

The DNA Network

Small changes equal impressive weight loss [The Navigator - Navigenics Blog]

Posted: 20 Nov 2008 09:20 PM CST

Michael Nierenberg, M.D.

imageI call it the "nickel and dime" approach to losing weight. 

As anyone who has ever looked under their couch cushions for loose coins knows, small change can add up. And when it comes to losing weight, small changes can also make a big difference. In fact slow and steady is the best way to sustain weight loss.

Thing is, many dieters unsuccessfully attempt a major makeover of their eating habits, giving up all pleasurable foods or starving themselves to reduce their calorie intake – and their waistline. Those strategies, however, are generally not ones people are able to stick with for a long time. So more often than not, the diet ends and the weight slowly (or not so slowly) comes back on, and the health benefits gained from weight loss slip away.

My "radical" suggestion is to consider something not at all radical: Making small, simple changes for life. Not only are they the easiest to attempt, they are also often the most successful.

"All proponents of organic agriculture, especially the noisier ones such as Prince Charles, should read Tomorrow's Table."- Review in Science magazine [Tomorrow's Table]

Posted: 20 Nov 2008 07:12 PM CST

Science 21 November 2008:
Vol. 322. no. 5905, pp. 1190 - 1191
DOI: 10.1126/science.1165961

Organic and GM—Why Not?
Mark Tester*

Tomorrow's Table
Organic Farming, Genetics, and the Future of Food
by Pamela C. Ronald and Raoul W. Adamchak
Oxford University Press, New York, 2008. 226 pp. $29.95, £17.99. ISBN 9780195301755. The organic movement's opposition to genetically modified (GM) crops is causing it to miss an opportunity. Like agriculture across the planet, organic farming needs all the technological help it can get to be both sustainable and high-yielding. As with many recent innovations, GM technologies provide myriad possibilities for reducing the impacts of agriculture on the environment and the need for chemical inputs to maintain yield. But from the start, the organic movement rejected the use of GM crops. Genetic engineering is a technology, and like so many technologies, its benefits, costs, and risks depend on how it is used. A comparison with nuclear technology is not unfair: most of us benefit from medical applications of nuclear technologies, while many of us have major concerns with the large stockpiles of nuclear weapons that still threaten the planet. So, the risks of GM depend on the genes being put into the plants, not on the technology per se. Yet the numerous potential applications of GM to reduce chemical inputs to agriculture are flatly rejected by most organic farmers.

In Tomorrow's Table, we now have the positive aspects of both organic and GM approaches discussed logically and clearly. The delightfully constructive book was written by a talented wife-and-husband team: Pamela Ronald, a very successful plant geneticist at the University of California, Davis, and Raoul Adamchak, an organic farmer who teaches at the same university. The authors are eminently qualified to present authoritative descriptions of their respective disciplines, which they do in a readable and accurate manner. But the noteworthy aspect of the book is the way they then marry their separate fields to argue logically for the use of GM technologies to improve organic agriculture. As Gordon Conway (a former president of the Rockefeller Foundation) comments in his foreword, "The marriage is long overdue."

Figure 1 To increase harvests and efficiency. The authors propose that combining genetic engineering with organic farming offers the best path to sustainable food production.


The authors describe the possibilities for GM to assist organic agriculture with examples drawn from their own and others' research. Pest control is a particular focus. Ronald was centrally involved in the genetic engineering of flooding tolerance in rice (1). She describes lucidly how this would enable farmers to flood a paddy field in which the rice has been established, thus killing the weeds that inevitably afflict the crop but not the rice itself. When the water is subsequently lowered, the rice has a head start on any weeds that eventually emerge, which provides a simple, cheap, and clearly organic method for weed control. How can the organic movement turn its back on such opportunities?

The false dichotomy that has been constructed between GM crops and organic farming can be illustrated with numerous similar examples. Another discussed by the authors is Bacillus thuringiensis (Bt) toxin, which has been successfully commercialized by Monsanto. These small insecticidal proteins, synthesized by widespread soil bacteria, can be applied in an almost unregulated way by organic farmers. This has been done for many decades. Yet when genetic engineering is used to place the gene encoding the Bt toxin in a plant's genome, the resulting GM plants are vilified by the very people willing to spray the product encoded by this same gene over otherwise similar plants. The organic movement's sustained rejection of this current application of GM appears increasingly illogical as evidence continues to accumulate that it does reduce pesticide use. In fact, this reduction is the principal reason farmers pay more for the biotech seeds--their lowered expenditures on pesticides are saving them money.

The authors marshal many additional examples to support their thesis that GM technologies and organic agriculture are quite compatible. Their discussion of these two topics exposes the complexity of the biological systems in which the issues surrounding them have to be addressed. This highlights the superficial nature of much of the GM debate, in which both sides make oversimplifications that support unnecessarily polarized standpoints. The biology is more complex. Unlike most protagonists, Ronald and Adamchak do not crudely lump together every GM crop as though they are all the same. That oversimplification blurs the issues (2, 3) to the detriment of fruitful consideration of topics that are increasingly important in a world in which we need to produce more food, fiber, and fuels in the face of global environmental change. In contrast, the authors calmly argue something that makes perfect sense to me, but their book will be controversial.

All proponents of organic agriculture, especially the noisier ones such as Prince Charles, should read Tomorrow's Table. Ronald and Adamchak's clear, rational approach is refreshing, and the balance they present is sorely needed in our increasingly polarized world. In addition, plant scientists--who have the privilege of greater knowledge than most in this area and who therefore have a responsibility to share their understanding with a wider audience--will find the book provides useful information and arguments to help them when doing their next "science in the pub" talk.


1. K. Xu et al., Nature 442, 705 (2006).
2. M. Tester, Nature 402, 575 (1999).
3. M. Tester, New Phytol. 149, 9 (2001).


The reviewer is at the Australian Centre for Plant Functional Genomics and University of Adelaide, Australia. E-mail:

Pac Bio Publishes Proof-of-Concept Paper on Single-Molecule Sequencing Technology []

Posted: 20 Nov 2008 05:45 PM CST

WOW!!! Pacific Biosciences published a proof-of-concept study at online today in Science. Below is detailed news from Genomeweb: And the article is linked below:

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Introducing GeneSifter [FinchTalk]

Posted: 20 Nov 2008 04:21 PM CST

Today, Geospiza announced the acquisition of the award-winning GeneSifter microarray data analysis product. This news has significant implications for Geospiza's current and new customers. With...

In a Jurassic Park’esque move, scientists reconstruct extinct Mammoth genome [Next Generation Sequencing]

Posted: 20 Nov 2008 03:36 PM CST

An international team of scientists has reconstructed about two-thirds of the genome of the woolly mammoth using DNA extracted from balls of hair, the first time this has been accomplished for an extinct species. Read more at Washington Post and in Nature’s Darwin special issue.

Oprah's Community against 23andMe [The Gene Sherpa: Personalized Medicine and You]

Posted: 20 Nov 2008 12:36 PM CST

When Public Relations Backfires

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DNA in the plot – Part II [Genome Blog]

Posted: 20 Nov 2008 12:30 PM CST

At this year’s ATA Science Council conference I talked about how often these days we are faced with both fact and fiction about DNA. I also talked about how things that were fiction back in the 1990’s are now reality less than 15 years later. I mentioned that movies such as Gattaca are great for generating discussion about the issues and societal impact. I’m faced with this conflicting juxtaposition of ideas as I write this blog. In my newspaper today….

National Family History Day and Genetics [DNA Testing Blog]

Posted: 20 Nov 2008 12:19 PM CST

The U.S. Surgeon General has set Thanksgiving Day as the “National Family History Day.” According to their website, Over the holiday or at other times when families gather, the Surgeon General encourages Americans to talk about, and to write down, the health problems that seem to run in their family. Learning about their family’s health history [...]

Genes provide Minimal Benefit!!!! Seriously Oprah! [The Gene Sherpa: Personalized Medicine and You]

Posted: 20 Nov 2008 12:17 PM CST

Genotype Score in Addition to Common Risk Factors for Prediction of Type 2 Diabetes...... That's right, the New England Journal of Medicine has 2 publications in the Journal this week. What's the...

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Family Tree DNA and MyHeritage Partner to Combine DNA With Family Trees [The Genetic Genealogist]

Posted: 20 Nov 2008 12:08 PM CST

As the Guardian reported today in “Genealogy website MyHeritage offers low-cost DNA tests“, Family Tree DNA and MyHeritage have formed a partnership to combine DNA testing with online family trees.  From the press release:

“With close to 220,000 records, FamilyTreeDNA is the largest database of genealogic DNA information in the world. This provides the perfect complement to MyHeritage’s current research tools, giving our members another way to learn about where they come from,” said Gilad Japhet, founder and CEO of MyHeritage. “We help people around the world discover, connect and communicate with their extended family network and easily research their family history. Now, by working with FamilyTreeDNA, we can offer a solution when the paper trail runs out.”

imageAs part of the partnership, Family Tree DNA is offering special pricing to MyHeritage members.  However, readers of TGG can click here to obtain the discount without being a member of MyHeritage.  The following prices are with the discount:

  • Y-DNA25 - a Y-chromosome test for males (US$129)
  • mtDNA - a mitochondrial DNA test for males and females (US$129)
  • Y-DNA25 + mtDNA - a combined Y-chromosome and mitochondrial DNA test for males (US$219)

Genes don't add much value for predictions of type 2 diabetes risk [Genetic Future]

Posted: 20 Nov 2008 11:15 AM CST

At Gene Expression, p-ter points to two studies in this week's New England Journal of Medicine examining the predictive value of known genetic markers for type 2 diabetes.

Both studies find the additional predictive power of the genetic markers beyond traditional predictors (like age, sex, family history, body-mass index, fasting glucose levels, systolic blood pressure, high-density lipoprotein cholesterol levels, and serum triglyceride levels) to be extremely small, to the point of complete clinical insignificance. Thus while massive genome-wide association studies for T2D have been informative in terms of uncovering the molecular pathways underlying the disease, they haven't yet yielded much of value in terms of individual risk prediction.

As p-ter notes, this result is quite unsurprising given the small fraction of the overall risk variance explained by these markers, but it's still important to quantitate the extent of the disappointment...

One small ray of hope: one of the articles notes that "[t]he discriminative power of genetic risk factors improved with an increasing duration of follow-up, whereas that of clinical risk factors decreased". In other words, genetic information increases in value relative to clinical predictors when there is a long time lag between testing and disease onset - again unsurprising given that clinical variables change over time while genetic risk factors are fixed, but still important to bear in mind. This suggests that genetic information will be most valuable to clinicians for predicting the risk of adult-onset diseases in children, or predicting the risk of late-onset diseases in adults.

Subscribe to Genetic Future.

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FDA interested in collaborating with personal genomics companies [Genetic Future]

Posted: 20 Nov 2008 05:40 AM CST

Pharmacogenomics Reporter (subscription required) describes an intriguing twist in the ongoing struggle between the nascent personal genomics industry and regulatory bodies: apparently the FDA is exploring the possibility of collaborating with consumer genomics providers to track adverse drug reactions:

Lawrence Lesko, director of FDA's Office of Clinical Pharmacology, said the agency has already begun preliminary discussions with some undisclosed personal genomics firms "to evaluate the feasibility" of forging such alliances.

In marketing ancestry and disease-predisposition genetic testing services directly to consumers, personal genomics companies are building large electronic databases of clinical and genomic information that the FDA believes can be useful in tracking adverse drug reactions in a post-marketing setting.

The major advantage of the databases accumulated by personal genomics providers, of course, is that you can immediately look for common genetic variants associated with variation in the risk for any newly identified adverse response:

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Presidential DNA: Don’t Ask, Don’t Tell? [The Personal Genome]

Posted: 19 Nov 2008 09:35 PM CST

Millions of individuals in the United States will know something about their own DNA by 2012. Whole genome sequencing will no longer be the exotic luxury item it is today. Genome scans like those available now for a few hundred dollars will be dirt cheap, if not free. By almost all accounts, genetic information will be more accessible to more people in 2012 than it is today.

The next presidential candidates will face an electorate that is radically more conversant in and curious about DNA than ever before. We should reasonably expect that the presidential election of 2012 will include, for the first time, requests for candidates to make their genetic information part of the public record.

Should the candidates heed these requests?

In an article published today in the New England Journal of Medicine, Robert Green and George Annas advocate for the next presidential candidates to honor a “Don’t Ask, Don’t Tell” policy for DNA. If genetic information is invoked by either candidate, the authors argue, the outcome will almost surely be one of exaggerated claims:

“…in the world of inflammatory accusations and smears that characterize presidential politics, it would be easy to engage in what might be called “genetic McCarthyism” by implying that an increased risk of disease is more substantial than it really is.”

The issue of presidential DNA and who gets access to it, is here to stay. 2012 presidential hopefuls have a few years to work out their talking points.

What would your talking points be? Would requests for disclosure of genetic information affect your decision to run for public office? Could you imagine scenarios where genetic information might influence your decision to vote for one candidate over another?

This week I’ll be interviewing Robert Green to learn more about his views on the future role, or absence, of genetics in political campaigns. Comments are open.

Green, Robert C., Annas, George J. The Genetic Privacy of Presidential Candidates. N Engl J Med 2008 359: 2192-2193.

Improving the science in science fiction. [Genomicron]

Posted: 19 Nov 2008 09:16 PM CST

There is an interesting story in New Scientist about The Science & Entertainment Exchange, a program initiated by the National Academy of Sciences to improve the science in movies and TV [New project aims to unite science and Hollywood]. It would be hard to make it worse, so this strikes me as a very positive development!

The project is described thus:
The Science & Entertainment Exchange is a program of the National Academy of Sciences that provides entertainment industry professionals with access to top scientists and engineers to help bring the reality of cutting-edge science to creative and engaging storylines.


The portrayal of science – its practitioners, its methods, its effects – has often posed a challenge to the entertainment community. Though it has inspired some of the most intelligent and compelling storylines, science's many complexities have confounded even the most talented writer, director, or producer, time and again pitting creative license against scientific authenticity and clarity.

Likewise, the scientific community has struggled to find an effective conduit through which it can communicate its story accurately and effectively. Though many of the world's biggest problems require scientific solutions, finding a way to translate and depict scientific findings so that reach a wide audience has required a sounding board that has often been missing.

The Science & Entertainment Exchange bridges this gap and addresses the mutual need of the two communities by providing the credibility and the verisimilitude upon which quality entertainment depends – and which audiences have come to expect. Drawing on the deep knowledge of the scientific community, we can collaborate on narrative and visual solutions to a variety of problems while contributing directly to the creativity of the content in fresh and unexpected ways.
Especially cool is this, from the report:
...the Exchange organised a symposium, sponsored in part by New Scientist, in which scientists and entertainers were to discuss hot topics in science like climate change and genomics.

Standards for personal genomics information apply to everything but the data [Discovering Biology in a Digital World]

Posted: 19 Nov 2008 12:10 PM CST

Genome Web's Daily Scan noted an interesting blog post today from John D. Halamka, one of the people to get his genome sequenced through the personal genome project.

I was interested to see his post since Genome Web wrote that he was discussing data standards and we have been writing quite a bit, ourselves, about data measurements for Next Gen sequencing (e.g. Next Gen-Omics) on our company blog, FinchTalk.

But Halamka didn't write about standards for data.

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The Seattle Times puts MRSA database on-line and gets results from the state [Discovering Biology in a Digital World]

Posted: 19 Nov 2008 10:33 AM CST

I'm sure everyone else thinks the big news today is the announcement by the Washington State Health department requiring hospitals to report MRSA cases to the state. I think the cool news is their on-line database. We'll get to that a bit later.

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