Sunday, June 1, 2008

The DNA Network

The DNA Network

Medicine 2.0 Carnival: Web 2.0 technologies and the practice of medicine [Discovering Biology in a Digital World]

Posted: 01 Jun 2008 08:03 PM CDT

This month's edition of Medicine 2.0 focuses on connections. You'll learn how new technologies are empowering patients by connecting them with their own health records, connecting patients and paramedics with doctors, and connecting doctors with each other.

Nothing connects like Web 2.0.

Let's hit the Midway!

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The power of e-patients [ScienceRoll]

Posted: 01 Jun 2008 04:24 PM CDT


There is a whole blogosphere around the idea of transforming medicine into e-health. There are plenty of bloggers who often write about the IT opportunities of medicine and healthcare. But! What about patients? The consumers? Even if we have a Jay Parkinson, what can he do without patients who are ready to use his service?

They are called e-patients, and without them there will be no change in the future of medicine.

By taking advantage of new online health tools, e-patients and health professionals now have the ability to create equal partnerships that enable individuals to be equipped, enabled, empowered and engaged in their health and health care decisions. (The Health Care Blog)

A new book from Tom Ferguson, MD analyzes the power of e-patients:

Tom Ferguson was a strong proponent of developing an online system for medical living documents, where informed patients (e-Patients) could cooperatively improve upon the quality of the original documents. This wiki is dedicated to his vision and is the first example of the new system.

Putting a little science in your life [business|bytes|genes|molecules]

Posted: 01 Jun 2008 03:00 PM CDT

Brian Greene at the World Science Festival launch press conference

Science is a way of life. Science is a perspective. Science is the process that takes us from confusion to understanding in a manner that's precise, predictive and reliable — a transformation, for those lucky enough to experience it, that is empowering and emotional. To be able to think through and grasp explanations — for everything from why the sky is blue to how life formed on earth — not because they are declared dogma but rather because they reveal patterns confirmed by experiment and observation, is one of the most precious of human experiences.

Those lines come from a wonderful op-ed in the New York Times entitled Put a little science in your life by Prof. Brian Greene (found via a Tweet by Tim O’Reilly).

He touches upon subjects and ideas that I’ve been thinking about for a long time, albeit much less eloquently. In my interview with Jon Udell, I spoke about the disconnect between science and the general public, and the need for better communication, to bridge these gaps. Prof. Greene writes

It's striking that science is still widely viewed as merely a subject one studies in the classroom or an isolated body of largely esoteric knowledge that sometimes shows up in the "real" world in the form of technological or medical advances. In reality, science is a language of hope and inspiration, providing discoveries that fire the imagination and instill a sense of connection to our lives and our world.

The way I see it, science ends up in three buckets; scientists lock themselves up into their silos, e.g scientific conferences, publications, etc; or magazines like Wired sensationalizing the ultra-geeky, somewhat futuristic side of science; or the mainstream media either overhyping discoveries or usually being very negative about science. What is lost in all this? The beauty of science today, and where we are headed, not 50 years from now, but in the next 5-10. How many people out there really appreciate the advances possible because of PCR? How many people understand the beauty and challenges of complex organic synthesis? Does anyone what it’s like to solve the crystal structure of a protein? Or what kind of advanced biosimulation we are doing today? Do people know the limitations of these methods? To they understand the potential? My answer would be no to all of them. Even within the sciences, we tend to lock ourselves up into our shells (there are notable exceptions, systems biology and bioinformatics being poster children, which is why they appeal so much to me).

But I digress. The fact remains that we have lost something along the way. We’ve lost the beauty of science (rather we’ve stereotyped it as nerdy or uncool). I won’t write anymore. Just read the article. It’s one of the best I’ve ever read. I will end with one last snippet

Like a life without music, art or literature, a life without science is bereft of something that gives experience a rich and otherwise inaccessible dimension.

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Web as platform: Google Health Data API [business|bytes|genes|molecules]

Posted: 01 Jun 2008 11:41 AM CDT

Google Inc.Robert Scoble had a post about AWS and GAE, into which he snuck in some pretty significant news. Google has launched a Health Data API.

What can you do with the API? Among other things you can upload patient medical records and get patient medical data to provide additional, personalized, functionality. This is clearly targeted at developing an ecosystem around the Google Health system. Google Health supports CCR (or at least a subset), and in theory, companies can set up services that allow hospitals/health systems to communicate with Google Health, and hopefully some day, enable health data portability between health systems.

Will be interesting to see how the API gets used? How will any privacy concerns be overcome? Who will the early adopters be? We will have to wait and see.

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Federal R&D in the FY 2009 Budget - AAAS Analysis [The Daily Transcript]

Posted: 01 Jun 2008 11:11 AM CDT

I heard about the report on the the latest Science Mag Podcast.

Some general notes:
-NIH budget will see a 0% increase
-NSF budget will see a 15% increase
-There is a significant increase in funding to the Department of Energy (up 21%)
-Support of research (basic and applied) would fall 0.3%. According to AAAS:

In real terms, the federal research portfolio would fall for the fifth year in a row, down 9.1 percent from 2004.

But now things may be changing due to new legislation introduced in the Senate.

From the podcast, here's what Science Magazine's Deputy Editor Barbara Jasny had to say:

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What is a species? [T Ryan Gregory's column]

Posted: 01 Jun 2008 09:53 AM CDT

If you have a subscription to Scientific American, make sure you check out Carl Zimmer's discussion of the question "What is a species?".  It's a good introduction to a long-running conundrum in biology.  Don't expect an answer, however -- not because Carl doesn't know, but because one does not curre

HAP DAP. [T Ryan Gregory's column]

Posted: 01 Jun 2008 08:20 AM CDT

In one of my snarkier moments, I coined the term "Dog's Ass Plot" (DAP) in reference to

How to write good. [T Ryan Gregory's column]

Posted: 01 Jun 2008 08:03 AM CDT

Perhaps you struggle with crafting elegant and effective prose. Fear not, gentle reader! Some simple guidelines are available to assist you.

 

HOW TO WRITE GOOD

1. Avoid alliteration. Always.

2. Prepositions are not words to end sentences with.

3. Avoid clichés like the plague.

Religion survey. [T Ryan Gregory's column]

Posted: 01 Jun 2008 07:35 AM CDT

Over on Sandwalk, Larry Moran reports on a survey revealing that about 1/4 of Canadians do not believe in God, and that among those under 25 this figure is about 1/3. What he didn't mention was the actual population sampled:

Junk DNA and the Onion Test [T Ryan Gregory's column]

Posted: 01 Jun 2008 05:00 AM CDT

One copy of the human genome is more than 3 billion nucleotides in length, and weighs in at about 3.5 picograms (pg, or trillionths of a gram). Only about 1.5% of this is composed of our 20,000 or so protein-coding genes, though other data suggest that at least 5% has been conserved by natural selection, suggesting that a notable portion of the non-coding majority is also functional.

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Let’s Share 23andMe data! [Think Gene]

Posted: 31 May 2008 11:00 PM CDT

23andmeIf you have a 23andMe account, my user name is andrewyates. Send me an invite! (under account => My Profiles) I promise to only use your genetic information for tweaking clones, raising your health insurance premiums, and raising venture capital.

Yes, bask in the all encompassing Power of WE!

Anne Wojcicki:

“We're at the beginning of a revolution that combines genetics and the Internet. Wikipedia, YouTube and MySpace have all changed the world by empowering individuals to share information. We believe this same phenomenon can revolutionize healthcare.”

The press reads this and thinks that 23andMe (and by proxy, deCODEme) is “yet another social network.” It’s not. It could help collect more genomic samples for research, which would benefit everyone, but so far, that’s a stretch considering that phenotypes are self-reported. (update: report on 23andWe coming soon)

Mark Hopkins of social networking news site Mashable:

One of the ideas floated to them from the press, one that was warmly received by both Linda and Anne, was a social network available at 23andMe where social connections were made for you by DNA genotype similarity. It was described by the press member asking the question as "the ultimate in social networking," a sentiment that seemed to be echoed in tone by Linda and Anne.

I can't imagine the usefulness or entertainment value in such a system, but then I'm not much of a geneticist (perhaps someone out there with a bit more of a background in it can explain the inside joke I seem to be missing).

Is “the ultimate social network” some kind of tongue-in-cheek joke? Can middle-aged wives of billionaires be snarky about the Silicon Valley press echo chamber when Rupert Murdoch entertains your questions about your stinky piss internet quiz? If you were one degree away from valley’s most connected company, and the success of your startup was independent of sucking everyone who could write a check, would silicon-valley-buzz like “connect genetically with friends, family, and others across the globe” be a big in-house joke?

I’m just saying, if I was a bored 30-something billionaire…

Davis is indeed Friendly [The Tree of Life]

Posted: 31 May 2008 08:28 PM CDT

I do not normally cross-post stories that I put on my blog about life in Davis, CA but I could not resist this one. Davis has been picked as one of the 5 friendliest cities in the US.

Here is the video from the Today Show. I suppose the people doing this did not take off too much for bloggers like me ...

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