Wednesday, October 22, 2008

The DNA Network

The DNA Network

I wanted to do this!! - Eating behavior at Chinese buffets [Yann Klimentidis' Weblog]

Posted: 22 Oct 2008 05:42 PM CDT

Dang!!, I've always wanted to do a study like this, but these researchers beat me to the punch. The things they look at here are pretty interesting (and frankly, pretty funny), but they could have looked at the types of foods people were eating (ex: meat vs. other), SES, ethnicity etc.... Of course that would entail more complicated data collection... This reminds me of this great study.

Eating behavior and obesity at Chinese buffets.
Wansink B, Payne CR.
Obesity 2008 Aug;16(8):1957-60.
Abstract: The aim of this study was to investigate whether the eating behaviors of people at all-you-can-eat Chinese buffets differs depending upon their body mass. The resulting findings could confirm or disconfirm previous laboratory research that has been criticized for being artificial. METHODS AND PROCEDURES: Trained observers recorded the height, weight, sex, age, and behavior of 213 patrons at Chinese all-you-can-eat restaurants. Various seating, serving, and eating behaviors were then compared across BMI levels. RESULTS: Patrons with higher levels of BMI were more likely to be associated with using larger plates vs. smaller plates (OR 1.16, P less than 0.01) and facing the buffet vs. side or back (OR 1.10, P less than 0.001). Patrons with higher levels of BMI were less likely to be associated with using chopsticks vs. forks (OR 0.90,P less than 0.05), browsing the buffet before eating vs. serving themselves immediately (OR 0.92, P less than 0.001), and having a napkin on their lap vs. not having a napkin on their lap (OR 0.92, P less than 0.01). Patrons with lower BMIs left more food on their plates (10.6% vs. 6.0%, P less than 0.05) and chewed more per bite of food (14.8 vs. 11.9, P less than 0.001). DISCUSSION: These observational findings of real-world behavior provide support for laboratory studies that have otherwise been dismissed as artificial.

Deep coverage []

Posted: 22 Oct 2008 04:52 PM CDT

Jason has a comprehensive roundup of press coverage of Monday’s festivities. Closer to home, the Duke Today website attempts to cure insomnia by linking to this blog. If you go there and scroll down, you can take a poll on whether making one’s genome public is a good idea.

Evolution: Education and Outreach special issue -- evolution of eyes. [Genomicron]

Posted: 22 Oct 2008 03:55 PM CDT

I was planning to wait until the issue was actually in print, or at least until all the articles were available in preprint, but there is already some buzz starting so here it is. The upcoming issue of Evolution: Education and Outreach, of which I was editor, is a special issue dedicated to eye evolution. The table of contents:

Evolution: Education and Outreach
Volume 1 Issue 4
The evolution of eyes
Edited by T. Ryan Gregory


1. Introduction by T. Ryan Gregory

2. Casting an Eye on Complexity by Niles Eldredge

Original science / evolution reviews

3. The Evolution of Complex Organs by T. Ryan Gregory

4. Opening the "black box": the genetic and biochemical basis of eye evolution by Todd H. Oakley and M. Sabrina Pankey (coming soon)

5. A Genetic Perspective on Eye Evolution: Gene Sharing, Convergence and Parallelism by Joram Piatigorsky

6. The Origin of the Vertebrate Eye by Trevor D. Lamb, Edward N. Pugh, Jr., and Shaun P. Collin

7. Early Evolution of the Vertebrate Eye—Fossil Evidence by Gavin C. Young

8. Charting Evolution's Trajectory: Using Molluscan Eye Diversity to Understand Parallel and Convergent Evolution by Jeanne M. Serb and Douglas J. Eernisse

9. Evolution of Insect Eyes: Tales of Ancient Heritage, Deconstruction, Reconstruction, Remodeling, and Recycling by Elke Buschbeck and Markus Friedrich

10. Exceptional Variation on a Common Theme: The Evolution of Crustacean Compound Eyes by Thomas W. Cronin and Megan L. Porter

11. The Causes and Consequences of Color Vision by Ellen J. Gerl and Molly R. Morris

12. The Evolution of Extraordinary Eyes: The Cases of Flatfishes and Stalk-eyed Flies by Carl Zimmer

13. Suboptimal optics: vision problems as scars of evolutionary history by Steven Novella (coming soon)

Curriculum articles

14. Losing sight of regressive evolution by Monika Espinasa and Luis Espinasa (coming soon)

15. Misconceptions About the Evolution of Complexity by Andrew J. Petto and Louise S. Mead

16. Bringing Homologies Into Focus by Anastasia Thanukos

Book reviews

17. Jay Hosler, An Evolutionary Novelty: Optical Allusions by Todd H. Oakley

Blogger’s Choice Awards 2008 [ScienceRoll]

Posted: 22 Oct 2008 02:22 PM CDT

Last year, Scienceroll won the Best Health Blog category in Blogger's Choice Awards. Now, Scienceroll had almost twice as many votes as last year, but I have to be satisfied with the Bronze medal. Thank you so much for your votes. It feels good to be read and appreciated.

Congratulations to the winners:


The best medicine: On graffiti [ScienceRoll]

Posted: 22 Oct 2008 02:11 PM CDT

A great video from


What’s on the web? (22 October 2008): SocialVibe and MedHelp [ScienceRoll]

Posted: 22 Oct 2008 02:08 PM CDT

Only 4 days left before my final neurology exam, but now I will share some posts with you in record time…

  • Medhelp: The MedHelp site connects people with the leading medical experts and others who have similar experiences. Today, MedHelp empowers over 5.5 million people each month to take control over their health and find answers to their medical questions.

  • Unlearning: Incomplete musings on the game of life and the illusions that keep us playing. A useful book from Alex R. Jadad that you can download now for free.
  • SocialVibe’s Members Speak Out Against Breast Cancer: How to use the tools of web 2.0 against breast cancer?


Blogging as an Extreme Sport [adaptivecomplexity's blog]

Posted: 22 Oct 2008 01:58 PM CDT

Andrew Sullivan on the extreme sport of blogging:

A columnist can ignore or duck a subject less noticeably than a blogger committing thoughts to pixels several times a day. A reporter can wait—must wait—until every source has confirmed. A novelist can spend months or years before committing words to the world. For bloggers, the deadline is always now. Blogging is therefore to writing what extreme sports are to athletics: more free-form, more accident-prone, less formal, more alive. It is, in many ways, writing out loud.

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Eye Evolution Smorgasborg [adaptivecomplexity's blog]

Posted: 22 Oct 2008 12:14 PM CDT

The journal Evolution: Education and Outreach is coming out with an issue devoted to the evolution of the eye, and some of the articles are already online.

This journal is non-technical, aimed at both teachers and interested science readers, so you don't have to be a biologist to make sense of these articles.

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Another cat that glows in the dark [Discovering Biology in a Digital World]

Posted: 22 Oct 2008 11:50 AM CDT

I've heard that all cats are grey in the dark, but I guess that's no longer true in New Orleans. Scientists at the Audubon Center for Research of Endangered Species have made a cloned kitty that glows lime green.

Some of you already know my fascination with glowing fish, fluorescent cats, and cloned puppies. This New Orleans cat is interesting too, partly, because it's the first transgenic cat made in this country, and partly because of the work that ACRE has been doing to try and rescue endangered species.

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2020 Vision [Genome Blog]

Posted: 22 Oct 2008 09:30 AM CDT

I'm guessing that the title for this week's Genome Canada International Conference is both a play on the acuity of normal vision and a suggestion that the conference will be looking well into the future. Considering the pace of change that might be a pretty grand ambition for the conference but I'm here in Vancouver to attend the conference for a variety of reasons. First off we had a meeting of all the communicators from the various Genome Centres across the country. I'm part of a panel tonight at a Public Forum called "The Genetic Test Results Are In .... Now What?", and then of course there is the conference itself and its great line-up of speakers.

Proposition 1 [The Daily Transcript]

Posted: 22 Oct 2008 08:59 AM CDT

If you live in Massachusetts, one of the most important votes you'll be casting is for or against proposition 1.

What is proposition 1? It's the right-wing libertarian delusion that the best government is no government. Written by that societal piranha, Grover Norquist, proposition 1 would cut the state income tax by half next year and eliminate it by the following year.
Now let's get this straight, no one likes paying taxes, but running a state costs money. And in this financial climate where the state can expect less revenue from property taxes, sales taxes and income taxes, and when joblessness and homelessness and other societal problems are likely to rise, the proper functioning of the government is even more crucial. Eliminating the income tax can either lead to a decrease in government spending, or an increase in sales and property tax.

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Genetic Genealogy Tidbits [The Genetic Genealogist]

Posted: 22 Oct 2008 07:09 AM CDT

Image created by Abizar Lakdawalla - fair use.

Image via Wikipedia

This week I was quoted in the November issue of Wired Magazine about the use of autosomal DNA for genetic genealogy testing.

A Controversy

At “Adoptees use DNA to find surname,” Larry Moran at Sandwalk comments on my recent articles (here, here, and here) regarding the use of genetic genealogy (or genetic sequencing in general) test results to find unknown biological parents.  Although Dr. Moran accuses me of being a “cheerleader” who is blind to any ethical concerns associated with using DNA to find biological parents, he obviously didn’t do his research!  Less than a month ago I wrote this on the blog:

“For most people, being able to identify your own ancestors based on your own DNA poses few if any ethical dilemmas. However, what if your neighbor or your stalker or even law enforcement wants to use a sample of your DNA to identify your ancestors? Additionally, what if your living ancestor doesn't wish to be identified? Does the ancestor have that right, or is possible identification through genetic genealogy just one of the consequences of parenting a child anonymously or simply having sex with another person?”

In response to a write-up at Genome Technology, Discovering Biology in a Digital World wrote “Hey sperm donors, could DNA testing be hazardous to your wealth?“.

Blending Genetic Genealogy and Personal Genomics

Often, articles that discuss both genetic genealogy and whole-genome scans (like those offered by deCODEme and 23andMe) blur the different services together and completely confuse the reader (usually because the author is confused!).  However, in “Will Technology Cure Health Care — Or Kill It?,” journalist Alistair Croll does a good job:

“Testing can get as low as $60, as Familybuilder recently showed. Founded in 2007, the company received a $1.5M Series A funding from DN Capital in February 2008. While the company only analyzes enough DNA to trace genealogy, it stores the raw samples for two years, so CEO Ilya Nikolayev hasn't ruled out the possibility of selling additional analysis to customers in future.”

Russ Altman, a scientific advisor for 23andMe, recently wrote a blog post about his first “post-genomic moment.”  After reading an article about the possible association between a SNP and muscle breakdown due to statins, Altman logged into his 23andMe account and examined his read at that SNP.  There’s also a post about Altman’s experience at The Spittoon, 23andMe’s corporate blog.

The Personal Genome Project

The “First 10,” the first 10 participants in the Personal Genome Project, met on Monday the 20th to review the results of their genetic sequencing.  For more information, see a blog post by participant Misha Angrist, and Jason Bobe has a great round-up of articles at “Press coverage on the Personal Genome Project's 2nd annual meeting at Harvard Medical School.”

Family Tree DNA Automates

Family Tree DNA is using new automated technology to manage their samples.  For more info, see “Family Tree DNA automates sample management” and “Geneology Testing Firm Adopts Tecan Sample-Management Systems” (but ignore the glaring spelling error!).

Rhodiola rosea [Sciencebase Science Blog]

Posted: 22 Oct 2008 07:00 AM CDT

rhodiola-roseaLive long and prosper with Rhodiola rosea? I very much doubt it. R rosea (aka golden root, roseroot, hóng jǐng tiān in TCM) is a member of the Crassulaceae family and grows across the Arctic, the mountains of Central Asia, the Rockies, the Alps, the Pyrenees, the Carpathian Mountains, Scandinavia, Iceland, Great Britain and Ireland. According to some herbalists it could be an elixir for life.

The Wiki entry for R rosea says it may be effective for improving mood and alleviating depression and early stage studies on people have shown some efficacy in improving physical and mental performance, alleviating fatigue, and reducing high-altitude sickness. A possible mode of action involves what the entry describes as, “optimizing serotonin and dopamine levels”. This apparently happens by inhibition of the enzyme monoamine oxidase, which supposedly ties in with an effect on endorphins, the body’s natural opiates. However, this is pure speculation rather than having basis in published scientific studies.

According to the latest press release I received today, R rosea is a remarkable story, the story of how a traditional herbal remedy from Sweden became the force behind Soviet Olympic athletes and cosmonauts. The Swedish Herbal Institute has even done what the email claims is “hard” research, unusually for a herbal product, in the form of double-blind, placebo-controlled, randomized clinical trials. The SHI holds a trademark on an extract of R rosea, referring to it as Arctic Root (SHR-5). So, their research is not without designs on the herbal remedies market. It is also sold in the US as ADAPT 232.

The press release highlights a previously published article by a science journalist and says that, “the roots appear to aid the brain by alertness and energy, without any trace of stimulants such as caffeine.” I find that phrase a little irritating. If the root has efficacy in stimulating the brain, then by definition it is a stimulant. It is irrelevant that it does not contain caffeine, why should it, there are dozens of natural products that act as stimulants that aren’t caffeine?

I asked the author of the press release, Linda Todten of publicity company TMC Communications, to explain exactly what the description was intended to convey, this is what she had to say:

As you know, the trend is for “energy drinks” that combine large amounts of caffeine, or caffeine containing plants such as Guarana, along with high amounts of carbs for a big “energy boost.” The studies that the Swedes and Russians have done over the years have shown how this category of plant, the Adaptogen, can actually bring the body back to its full energy level without being over stimulated as happens with caffeine. Plus, the extract SHR-5 has been shown to have a very solid mental acuity boost via double-blind, placebo controlled studies in students or night shift physicians and others.

So, this plant is an adaptogen, by definition “one that has no ill effects on the body at all - no interaction with pharmaceuticals - and yet which appear to have a normalizing influence on the body and brain.”

I’m afraid that sounds like wishful thinking to me. Previously, adaptogens were known as rejuvenating herbs, qi tonics, rasayanas, or restoratives, which sounds like a product of the Victorian sanitorium era or a dubious backstreet apothecary? Any product that has an apparently direct influence on brain enzymes, or enzymes anywhere else in the body for that matter, is not going to be without side-effects. Our bodies are far too complicated for that. It would be an incredible impossible coincidence that we could find a compound in nature that was perfectly adapted to improve our health but produce no byproducts and have no side effects. Life’s just not like that.

More to the point, the plant root contains a variety of natural products including rosavin, rosarin, rosin and salidroside (and sometimes p-tyrosol, rhodioniside, rhodiolin and rosiridin), which are claimed to be the active ingredients of R rosea. These compounds are polyphenols, they may have some antioxidant activity but have no proven health benefits in humans.

I realise, of course, that people can become desperate, especially when they or their loved ones are suffering, but simple herbs with
medicinal activity
are not a panacea
herbs with no medicinal activity are not a panacea. R rosea products are now being marketed in the USA and elsewhere. Todten had this suggestion: “Think about the fact that this one product (Arctic Root brand) has sold over 400 million doses. Not many dietary supplements can claim that. That says, to me, that people must like the way it works to reduce stress or energize,” she told me. “People are not sheep, and they wouldn’t make a product a best seller in Europe over ten years with hundreds of millions taken if it didn’t do something that they liked!”

Well, actually, that says to me that the herbal marketeers (do they call themselves adaptogenicists yet? Or Adaptopaths perhaps?) are very good at marketing and must be jumping for joy all the way to the bank as consumers unaware of the fundamentals of biochemistry lap up this abundant weed in the hope of boosting their brains, staying fit, and living longer.

Rhodiola rosea

Check out the new Genomicron 2.0 [Genomicron]

Posted: 22 Oct 2008 06:33 AM CDT

I am hoping to be back to blogging more regularly in November, but so far this semester has been very hectic. For now, why not head over to Genomicron 2.0 at Scientific Blogging and have a look at their new design? Looks great!

For the new stuff, see this summary.

Congrats to Hank and the other people there -- well done.

10 Reasons to Grow a Beard [Bayblab]

Posted: 22 Oct 2008 05:40 AM CDT

I've written about beards before, and I have an obvious bias, but this made me laugh. Put down your razor and check out The Bureau for Bigger, Better Beards.

The Times does tags [business|bytes|genes|molecules]

Posted: 21 Oct 2008 10:41 PM CDT

The New York Times continues to innovate. They have announced the TimesTags API. What is this?

The API returns official tags that match your search string. Even better, it ranks the results from most commonly used tags to least. That means you can quickly see what's making news, how a company's name has evolved, or which Baldwin brother currently has the biggest spotlight.

The Times has some powerful dictionaries underlying their data, which makes the metadata more powerful, e.g. it allows you to disambiguate tags like Turkey (the country vs. the bird). They also clearly have bigger fish to fry. As the blog post says

We see our tags as a contribution to existing metadata discussions and efforts, such as Freebase, Topic Maps, Fuzzzy and similar projects. If TimesTags can also spark a movement that advocates standardized tags for news sites, so much the better.

Please read this disclaimer

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Hey sperm donors, could DNA testing be hazardous to your wealth? [Discovering Biology in a Digital World]

Posted: 21 Oct 2008 10:07 PM CDT

Maybe you did it for the extra cash. Maybe you wanted to be part of the sperm cube public art project. Whatever the reason, it's possible, just possible, your sperm took on a life of it's own, once you left it.

And now that a genome is no longer an entirely personal bit of information, you may be in for a surprise meeting someday, with the end result.

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The future of simulation [business|bytes|genes|molecules]

Posted: 21 Oct 2008 09:52 PM CDT

Shirley picks up on a topic near and dear to my heart, physics-based simulation, specifically a couple of questions

  • What are high impact biomedical arenas that offer exciting challenges for physics-based simulation?
  • What are new areas of computational research in physics-based simulation that will have a major impact on biology?

The way I see it, our computational platforms will evolve, whether it be virtualized cloud infrastructures or GPUs as they always have. The real challenge is in methodology. I have fretted in the past about the lack of innovation in molecular simulation and lack of advances. Oh for sure, there is some innovation, not in the least from Shirley’s own institute. The key though, as pointed out, is in multiscale modeling. That’s an area I explored to quite a degree when I was at Accelrys, and there are approximations today, whether it be Elastic Network Models or QM/MM methods. People like Greg Voth have done some interesting work in this space as well. But we have a long way to go. The dream app, one that can perform systems level simulations at multiple scales, dynamically transferring information between scales as a system evolves, is still that, a dream. The complexity of biological systems makes it really really hard. Shirley alludes to just such an app in her post, so there is certainly the desire from a lot of people.

I have always felt that in the end we much be able to describe systems physically, even protein-protein interactions systems. On the flip side, our potentials and methods are far from doing so, which means there is a lot of exciting science to be done

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Press coverage on the Personal Genome Project’s 2nd annual meeting at Harvard Medical School [The Personal Genome]

Posted: 21 Oct 2008 09:20 PM CDT

The 2nd annual meeting of the Personal Genome Project was held at Harvard Medical School yesterday. Here is a round-up of articles thus far (updated 10/22/08):

Taking a Peek at the Experts’ Genetic Secrets” by Amy Harmon, The New York Times

Personal Genome Project Participants Get First Look at their DNA” by Carey Goldberg, Boston Globe

Subjects’ DNA Secrets to be Revealed” by Carey Goldberg, Boston Globe

Genome Fanatics to Post Own DNA Sequences on Web” by Denise Lavoie, Associated Press

Harvard Genome Volunteers Say They’ll Reveal Own DNA” by John Lauerman, Bloomberg News

Genomes on Display” by Emily Singer, Technology Review

Thousands Volunteer to Expose DNA Secrets to the World” by Ewen Callaway, New Scientist

Sharing Your Personal Genetic Map With the World” by Nancy Shute, U.S. News & World Report

A New Sort of Facebook: Posting Your Genes on the Web” by Sarah Rubenstein, Wall Street Journal blog entry

Genome Database Will Link Genes, Traits in Public View” by Ellen Nakashima, Washington Post

"10 Bay Staters to Post DNA Online" by Sacha Pfeiffer, WBUR (NPR's Boston affiliate)

"Meet my genome: 10 people release their DNA on the Web" by Susannah F. Locke, Scientific American online

"Personal genome sequences could herald a shift in research participation" by Erika Check Hayden, Nature News

"Genetic Privacy: An Outdated Concern?" by Emily Singer, Technology Review

"9 Volunteers in Harvard Study Agree to Post Their Personal Genomes Online" by David DeBolt, Chronicle of Higher Education

"For the greater good, ten pioneers will post their genomes on the Internet," Discover magazine blog post

"Volunteers unveil DNA, medical data in push for everyday gene sequencing" by Alvin Powell, Harvard News Office

I’ll post commentary over the next week. Articles are also slowly being posted on the PGP news page. If I’ve missed any articles, leave me a comment or drop me a line.

A Day of Discovery [Genome Blog]

Posted: 21 Oct 2008 09:00 PM CDT

Last week marked my 2nd visit to Discovery Days at the University of Calgary Health Sciences Centre and Medical School. The event is organized by the Canadian Medical Hall of Fame and has been running for 10 years in a variety of cities and academic institutions.
It is an opportunity for High School students to spend the day on campus and as the name implies, discover a bit about medicine and the health sciences. For many students it is an opportunity explore some career options and the general feeling from the organizers is that this year's crowd in Calgary was even more career oriented than in the past. These weren't just the science geeks out for a day away from class.

Invitrogen acquires single molecule startup Visigen! []

Posted: 21 Oct 2008 08:36 PM CDT

As part of their 3rd quarter 2008 earnings , Invitrogen noted that they have purchased early stage single molecule sequencing startup for $20 million. Visigen's centers on the use of a labeled polymerase and nucleotides which produce an intermolecular FRET fluorescence event during incorporation. They were recently granted what appears to be a in this area. Applied Biosystems had previously made an in Visigen.

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