The DNA Network

At least they aren't raising expectations too high. [T Ryan Gregory's column]

Posted: 23 Jun 2008 06:15 PM CDT

I hesitate to scoop Jonathan Eisen by commenting on a news item verging on "Genomics by Press Release

Posted: 23 Jun 2008 11:37 AM CDT

When a member of the PGP-10 and an investor in 23andMe writes about curating one's online, personal data, a lot of people listen. Unfortunately, Esther Dyson (writing in MIT's Technology Review) does not mention the decision to share medical information or how she plans to curate her own genomic data online. Dyson rightly notes that "current website 'privacy' policies don't suffice. They're full of abstractions, euphemisms, and generalities, such as, 'We may, at any point in time, provide certain Specified Information to selected Marketing Partners ... .'" She appears to favor a complex, itemized consent policy, one that would allow users to opt in or out of sharing specific categories of information (user name, address, credit history, etc.) with a list of potential users (advertisers and other companies).

Imagine a similar consent for medical records sharing. For example, could someone like Esther consent to share her genome with a 23andMe social network, but not with researchers in this network? Or, perhaps, Esther could chose to share some of her genomic information, but not all of it. Then, again, maybe Esther would be willing to share her prescription history with an academic researcher, but not with pharmaceutical companies. The options could go on and on, resulting in an increasing complex array of choices.

Esther Dyson is obviously a very sophisticated information agent, but (as the opportunity to share medical information online increases) will the average user and patient be prepared to make informed decisions about the risks and benefits of participating? - J.O.

Fruit flies to study behavioral genetics [Yann Klimentidis' Weblog]

Posted: 23 Jun 2008 10:29 AM CDT

Researchers have been maintaining different inbred lines of fruit flies, They then focus in on behavioral differences between lines to study the genetic correlates (gene expression profiles) of those differences. This is very similar to what could and is being done among domestic dogs - except that the dog lines are not quite as inbred.
In this news piece in Science, Elizabeth Pennisi explains how this research started and describes some of the projects.
How they established the inbred lines:

The project began a decade ago. Twice, in 1999 and 2002, Mackay's NCSU collaborator Richard Lyman showed up at Raleigh's farmers' market and picked off the fruit flies that emerged as crates of freshly harvested peaches were opened. Individual females were placed in vials, and each fly that reproduced became the progenitor of a single line of flies. Their offspring were allowed to mate only with each other, resulting, after several generations, in a line of genetically identical individuals that display consistent behavior. Each line is genetically--and behaviorally--different from all the others. The overall goal is to capture the genetic variation in the North Carolina wild fruit fly population in these wild-derived inbred lines.

Two of the studies that they mention look at expression patterns related to sleeping patterns and alcohol sensitivity.

UC Davis Bodega Marine Lab getting some props [The Tree of Life]

Posted: 23 Jun 2008 09:50 AM CDT

Now, I have written here before about the spectacular site for UC Davis' Bodega Marina Lab in Bodega Bay). And lest anyone not believe me, Bodega Bay and the Marine Lab has been written up in the San Francisco Chronicle in an article entitled: Marine lab a spectacular spot on Bodega Bay.

The article lead in is all you really need to know:

Mention Bodega Bay, and the first thing that comes to mind - even now, 45 years later - is Tippi Hedren getting her head pecked by a gaggle of sociopathic seagulls. The town's visitor center hands out 8,000 maps a year pinpointing where Alfred Hitchcock filmed the most memorable scenes of the 1963 classic "The Birds."

But each year, 10,000 to 12,000 people travel to a spectacular spot west of town to visit a less-famous site, the Bodega Marine Laboratory, a UC Davis outpost where about 100 graduate students and scientists study underwater life along the Northern California coast.

Each Friday afternoon, from 2 to 4, docents lead free, hourlong tours that wind through parts of the sprawling complex. It soon becomes clear that visiting a marine lab isn't anything like visiting for-profit aquariums, with their polished tanks and fancy signs. Here, the only live exhibits are a tide pool and three small aquariums.

Mind you, Bodega Bay itself is not the most happening town in the world. But it has a few stores, restaurants and cafes (which they review some of in the Chronicle article). The lab is also the site for the "Workshop in Applied Phylogenetics." One cool thing about this workshop is that the organizers have begun building a Wiki to gather information on phylogenetic methods and tools and this wiki is open to everyone to use and contribute to. So if you are interested in phylogenetics you might want to check out the wiki and start adding to it. And you might want to keep an eye out for announcements for next years course.

Low tide at Puget Sound [Discovering Biology in a Digital World]

Posted: 23 Jun 2008 09:01 AM CDT

It was a -1 tide on Sunday and great entertainment for people and birds.

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Going for a Sweep in Game 3 [evolgen]

Posted: 23 Jun 2008 09:00 AM CDT

Dak at Fire Joe Morgan asks:

I've been watching a fair amount of SportsCenter / BBTN today, and every two minutes someone mentions that there are "seven teams going for a sweep in an interleague series!", as if this is some sort of big deal. There are fourteen interleague series this weekend. If every match were a coin-flip, wouldn't we expect exactly seven teams to be going for sweeps in the third game of a series?

We'll start by assuming each team has an equal probability of winning each game, and the results of each game are independent. After one game, you're guaranteed that one team will have a 1-0 advantage. There is a 50% chance that the team that won the first game will win the second, meaning that there is a 50% chance the series will be 2-0 after two games. Therefore, dak is correct, you would expect half of the series to be on the verge of a sweep.

Why did the media make a big deal out of this -- and, I can confirm dak's observation: this was a big deal on SportsCenter and Baseball Tonight -- if it's actually expected? Because they don't understand basic probability. In fact, they are overtly antagonistic toward understanding simple logic and math. That's why websites like Fire Joe Morgan are so much fun to read. Media stupidity is such an easy target, and, even when their stupidity is pointed out them, they show no interest in correcting their errors or remedying the problem. It's like dealing with creationists.

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Giving Obesity the CHOP [Sciencebase Science Blog]

Posted: 23 Jun 2008 07:00 AM CDT

Obesity news I am once again drawn to research from a team at the University of Westminster, a renowned institution that doles out so-called science degrees in homeopathy. This time the paper in question, published in the inaugural issue of the International Journal of Food Safety, Nutrition and Public Health (2008, vol 1, issue 1, pp 16-32) is on that perennial favourite: what to do about the obesity epidemic.

Ihab Tewfik, a senior lecturer in the School of Biosciences, at Westminster, reports that “the prevalence and severity of people suffering from obesity has increased markedly worldwide,” and adds that “The WHO declared obesity a ‘crisis of epidemic proportion’.” Nothing of which I can be too critical in those statements, except for one small point.

While obesity and the diseases and disorders for which it is purportedly a risk factor - type II diabetes, hypertension, hyperlipidemia, atherosclerosis, cardiovascular disease, stroke, and heart attack - are almost certainly on the increase in North America, Western Europe, and pockets of the Pacific Rim, the use of the term “worldwide” is rather ironic. This is especially true given that the WHO and other international organizations consistently report massive cases of disease, malnourishment and poor water supply across great tracts of the earth’s surface from Africa and South America to Asia and the former Soviet Union.

Anyway, Tewfik and colleagues have proposed a conceptual framework for a three-year intervention programme that could be adapted to the prevention of childhood obesity, which is a growing problem in many parts of the world, if not quite worldwide.

Ironically, they have named the framework, with one of those shoehorned acronyms, as CHOP, for Childhood Obesity Prevention and explain their approach as follows:

The approach is based on a behaviour modification model without giving foods. Family, school and children are essential counterparts to achieve meaningful improvement. Advocated by policies makers and embraced with favourite environmental factors, CHOP programme could be the conceptual framework for nutrition intervention that can be effectively integrated within the national health framework to attain public health goals.

Apparently, what this boils down to is giving children healthy foods, increasing physical activity and workout limits, limited TV and other screen times, implementing a non-food reward system, and allowing self-monitoring. As part of this approach schools will intervene in teaching children that they should eat five portions of fruit and vegetables each day, that they should cut the amount of fat they eat, limit their screen time and be active every day.

It all sounds like good, solid advice. Indeed, it’s the kind of advice the medical profession, nannyish governments, and even grandparents, have been offering for decades. Unfortunately, growing children
are
notoriously reluctant
to take advicegrowing children are notoriously reluctant to take advice, especially when it comes to avoiding sweets and crisps, eating their greens, and switching off the Playstation (other gaming consoles are available).

The Westminster researchers, however, suggest their CHOP system would be convenient once the appropriate team, policies and resources have been successfully assembled. One has to wonder at a cost to whom these resources might be assembled. They do concede that, “In some circumstances this conceptual framework may be regarded to be too ambitious to attempt de novo within three years especially in some developing countries, where lack of access to health care, to drinkable water, to food, to education and housing is prevalent.”

It’s probably not necessary to implement it in places where food is in limited supply, surely. But, even in apparently developed nations, I’d suggest that costs will be severely prohibitive while children will be reluctant to partake (what positive rewards will replace treats and screen time?). Moreover, by their own admission, obesity is on a rapid climb among adults too and one has to wonder how these resources will be applied to persuade parents and carers of increasingly obese children will themselves be persuaded to take part if they do not appreciate the potential benefits.

A post from David Bradley Science Writer

Giving Obesity the CHOP

Podcast: How Genomic Medicine Is Changing the Management of Breast & Ovarian Cancer [Think Gene]

Posted: 23 Jun 2008 07:00 AM CDT

Complete Podcast and Panelist Bios at Helix Health

What what is the future of genomic and personalized medicine? In this panel organized by Helix Health, five experts discuss what new developments in pmed advances in breast and ovarian cancer management, what they means for patients, doctors, and the health industry, and how these treads apply to all health care.

“This [genomics] revolution is akin to the discovery that bacteria cause disease.” begins Dr. Steven Murphy, an expert in genomic medicine. Yet, “how did medicine advance so technologically, yet fail to keep us informed? … I’m amazed how difficult it is to translate this wealth of technology into truly effective patient care.”

And “we are in the beginning of an enormous tsunami of new [genomic] information that’s just beginning to hit,” says author David Duncan, who has subjected himself to “The Experimental Man” project to take every test to learn what can be learned about one’s body. These tests are expensive today, the BRCA breast cancer gene test costs upwards of $2500, but like microchips “technology is making these tests cheaper and easier —even including full genome sequencing.”

But who in the medical community needs to learn this information? “Everyone, so everyone is liable.” says Gary Marchant, J.D. By the “loss of chance doctrine,” simply by not discussing all the new genomic information to patients, “today, it’s any doctor who is potentially liable, from the general physician to the family physician to any kind of specialist.”

Yet, “such a small amount of physicians who are genetically knowledgeable,” says Steve, “there are less than 100 trained adult genetics specialists.” And while genomic education is truly empowerment to practice better health, medical students experience what Steve dubs “genomic knowledge erosion:” students know less about genomics after medical school than before and even less after residency. Gary adds, “Most doctors practicing today probably didn’t have genetics in medical school. If you’re an older doctor practicing in some rural community, this issue is all foreign to you.”

“Those doctors should then retire,” rebukes patient advocate Jessica Quller. “Perhaps fear of litigation will force doctors on a national level to become educated in their field and force them to present these options to patients.” Jessica’s mother died of preventable ovarian cancer, prompting Jessica to take the BRCA breast cancer gene test. Testing positive, she underwent a prophylactic mastectomy and oophorectomy. “The year is now 2004: no doctor had ever mentioned that I should be tested, and my sister and I essentially lived in NYU hospital with my mom for two years during her illness… Only my high school friend mentioned the [BRCA test] to me.”

“For 2004, I certainly would have hoped that in New York City, somebody would have talked to you about genetic testing in light of your mom’s illness.” exclaims Dr. Barbara Ward, a surgical oncologist. While “about 7% to 8% of [breast cancer] is inherited… we do believe that [the BRCA 1 & 2] genes reflect most of the inherited breast cancers… as high as 87% of women carrying the BRCA 1&2 gene will develop breast cancer. I look forward to the day that we’ll look back and we’ll say ‘can you actually believe we did prophylactic mastectomy for gene carriers?’ But at this point in time it’s the best we can offer.” But will insurance companies pay for tests like this including breast MRIs? “We definitely struggle… it’s VERY frustrating. Sitting in my desk right now I have a chart of a lady who’s HAD breast cancer, has had a mastectomy, and her insurance company is refusing to screen her with a breast MRI… So, it is frustrating to realize that there’s a test that’s available and realize that you may not be able to get it.”

Thank you to the panelists and Helix Health for conducting this excellent session about genomic medicine and breast cancer management.

Let's Just Say..... [The Gene Sherpa: Personalized Medicine and You]

Posted: 23 Jun 2008 06:10 AM CDT

I, Steven Murphy MD, am for Genomic Medicine, I am for patient empowerment, I am for the revolution known as patient centered genomic healthcare. I did not delight in the governmental actions, I did...

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Open Science Highlight -- JoVE: Journal of Visual Experiments [The Tree of Life]

Posted: 23 Jun 2008 05:49 AM CDT

I am starting to browse around at JoVE (the Journal of Visualized Experiments). This is an open journal dedicated to publishing biological research in a visual format. It is pretty cool. Some good videos include ones by Jared Ledbetter's group on studying microbes inside termites (see Layers of Symbiosis - Visualizing the Termite Hindgut Microbial Community

and Extracting DNA from the Gut Microbes of the Termite (Zootermopsis nevadensis)) for example. Others of interest to this blog include one by Ed Delong's group on Large-Scale Screens of Metagenomic Libraries.

Anyway - JoVE is definitely worth checking out ... visual presentations are probably the way of the future ...

In addition to experiments, JoVE also has some interviews. For example, I am embedding a nice video from JoVE with a talk by Ed Delong on microbial communities (Microbial communities in nature and laboratory - interview (Video Protocol). To view the embedded video click the play button below.

Doctors, webcams and online consultation [ScienceRoll]

Posted: 23 Jun 2008 03:51 AM CDT

The most interesting thing I read this week was about the new doctor-patient paradigm. Because there is a new one:

“The doctor-patient relationship has changed dramatically with the demise of ‘good ol’ doc’ and the explosion of medical technology,” says Paul M. Ross, an orthopedic surgeon in Pawlet, VT. “Today, patients are not only more knowledgeable, they’re more cynical. The increased use of physician extenders, hurried service, and overbooking have all contributed to the number of physician-patient relationships that are adversarial as opposed to collegial.”

Practicing medicine is changing rapidly these days. Patients have more resources to get more information about their medical conditions but they also have more tools to contact their doctors. American Well is only one example:

The company's big idea is more ambitious: A patient who wants an online doctor consult can log on and get something approaching a complete doctor visit, often without waiting. The doc can review the patient's record, make a diagnosis, write a prescription and make a referral, all online. Patients without a webcam can talk to the doctor on the phone.

Jay Parkinson’s Hello Health is another.

Patients can find medical experts with Online Doctor Consultation:

We´ll put you in touch with the world´s leading specialists and medical institutions, giving you fast and comprehensive service that´s easy to access, and personalized to your needs.

The procedure is simple. Just choose your options, and we do the rest. You can start by contacting us now for more information, click on Services to see what we offer, or go to Getting Started to start the ball rolling.

So of course, it’s hard to be a patient nowadays (you have plenty of things to choose from); and hard to be a doctor as well (you have to be the good old doc, but should be open to these new technologies).

And if you think the solution would be a healthcare reform, George Halvorson, CEO of Kaiser Permanente, tells you what to do: