Sunday, September 28, 2008

The DNA Network

The DNA Network

What Post(s) Should I Submit to Open Lab? [evolgen]

Posted: 28 Sep 2008 08:00 PM CDT

Every year, the best science blog posts are collected in a book, the Open Laboratory (here are the 2006 and 2007 editions). Last year's edition included my cartoon, The Lab Fridge. It wasn't my best post of the year, but it filled one of the niche categories published in the book.

Bora has been soliciting submissions for this year's edition of Open Lab. I've dug through my archives and found a few posts that I think are worthy of submission. Unfortunately, I'm the worst judge of my own writing, so I need some help. I've provided links to the short list of my best blogging of 2008 (up 'til now). Go check them out and let me know which one you like best.

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HelixGene Foundation to Ensure Responsible Reporting of Genomic Medicine [Highlight HEALTH]

Posted: 28 Sep 2008 03:15 PM CDT

Traditional media (i.e. television, print) are the principal sources of science information for the public. This is changing however; adult home broadband users under the age of 30 report that the internet is the most popular source for science news and information [1]. Unfortunately, while the public is consuming science reporting today more than ever before, the media is doing a poorer job covering the field. This is particularly troublesome for genomic medicine and personal genetics, since many physicians who lack training in genomics and genetics frequently get their information from the same mainstream media sources as the public.

Genomic medicine is the use of information from the genome to guide the development of new therapeutics and directly influence patient care.
Personal genetics is the use of a person’s genetic makeup to predict health risks and provide ancestry information.

Moving knowledge from the world of scientists into the public arena, where there are limitations on both space and reader interest, can be a challenging task. Reporting on medical genomics and personal genetics requires a translation in both language and phrasing. A 2004 study addressed popular media’s coverage of genomics, tracing reports from their original source in a scientific journal through to media publication [2]. The researchers found a significant difference in content between the original research paper and the news report, demonstrating the failure of mainstream media to accurately translate and report genomics for the public. However, until today, no standards existed to hold journalists accountable for accurate reporting of genomic medicine.

The HelixGene Foundation for Genomics was created to address the issue of reporting accuracy in medical genomics. Developed in response to significant misinformation published in a recent New York Times article discussing Google co-founder Sergey Brin and risk of Parkinson Disease, the Foundation organizes the distributed efforts of academics. The HelixGene Foundation grades publications to hold the media accountable for honest and accurate reporting of medical genomics, acting as a liaison between researchers, doctors and journalists. Additionally, the HelixGene Foundation will publish press releases about mutations to help journalists better report medical genomics and produce media about medical genomics to educate others.

Genomic medicine is believed to be the future of healthcare. Indeed, it is poised to improve disease diagnosis, therapy and prevention. All physicians will soon need to have a fundamental grasp of genomic medicine; to understand the concept of genetic variability, its interactions with the environment and its implications for patient care [3]. For both public and physician education, medical genomics and personal genetics must be accurately reported by media. The HelixGene Foundation for Better Genomic Medicine will review media reports on genomic medicine, in essence providing a peer review for accuracy and honesty.

Additional information on Genetics and Genomics for patients and the public, as well as health professionals, can be found at the National Human Genome Research Institute website. A publicly accessible New England Journal of Medicine article from 2002, Genomic Medicine — A Primer, is also recommended [3].

Additional resources on genome-based medicine or personalized medicine can be found in the Personalized Medicine category of the Highlight HEALTH Web Directory.

The media isn’t doing its job educating the public about genomic medicine and personalized genetics. The HelixGene Foundation will thus provide a valuable resource to verify media reports and hold journalists accountable for the accurate reporting of genomic medicine.


  1. The Internet as a Resource for News and Information about Science. Pew Internet & American Life Project. 2006 Nov 20.
  2. Kua et al. Science in the news: a study of reporting genomics. Public Understand. Sci. 13: 309-322. 2004.
  3. Guttmacher and Collins. Genomic medicine–a primer. N Engl J Med. 2002 Nov 7;347(19):1512-20.
    View abstract
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This article was published on Highlight HEALTH.

Other Articles You May Like

Four Science Bloggers take over Seattle and celebrate one million comments [Discovering Biology in a Digital World]

Posted: 28 Sep 2008 11:25 AM CDT

Ozzie's will never be the same.

The sun shone so brightly yesterday afternoon that it left us with no choice. We had to go outdoors. Luckily, Ozzie's has a wonderful upper deck in full view of the daylight and well-equipped with chairs.

Photo footage below.

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The web as platform: We can do more [business|bytes|genes|molecules]

Posted: 28 Sep 2008 10:00 AM CDT

not only dropsImage by 5348 Franco via FlickrI have had my differences with Tim O’Reilly over the years on certain issues, but his keynote at Web 2.0 Expo resonated with me at many levels. I am writing this post several days later, so hopefully my notes suitably reflect my thoughts at the time. A lot of people have written about what he had to say, but hopefully this post provides a different perspective.

He spent a lot of time talking about a move towards doing something more meaningful and touched upon many themes. Here are some of the phrases that are worth mentioning

“Web meets world”
“Do stuff that needs to be done”
“Create more value than you capture”
Pascal’s wager
“We have to assume that the world is going to go to hell in a handbasket unless we do something about it”

The message once again placed an emphasis on tools and services that make our lives better, not just the next viral Facebook app. Something that many of us have been saying for a while, but Tim wields a bigger stick.

That’s where I think the sciences come in. Science needs to be done. The web needs to be brought to science, and not just by big research labs, or by larger companies, but by forward thinking people who “get it”. It’s why I think the value in scientific web apps lies not in the next social network to foster collaboration, especially when there are so many around, but in projects and efforts that really do something to further science. That could come from open source tools, things like SNPedia, or the kinds of efforts that Cameron and Jean-Claude are pushing.

The question Tim asked was “are we working on the right things?”. That’s a question we all need to ask. I am not saying we are not allowed to have silly fun, and utility can be found in the strangest of places (e.g. Twitter or Friendfeed), but if we believe in something, we can do something about it. We can’t wait for the system to change, and there is the reality of making a living, but some of us are in a position to make a difference and we should. Whether it is by building awareness, or even better, building tools and services that enable the community and others around us, we should do so.

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CLC Genomics video [Mailund on the Internet]

Posted: 28 Sep 2008 04:14 AM CDT

If you are into next generation sequencing, then you might want to check out this video where Roald Forsberg presents CLC Bio’s Genomics Workbench.

Trying out Zotero [Mailund on the Internet]

Posted: 28 Sep 2008 01:47 AM CDT

I just found out about Zotero when I read this blog post yesterday.

It’s a Firefox extension for managing your literature lists. I’ve been looking for a good tool for this for a bit. My trial period of Papers ran out this week, and I had pretty much decided to buy it, but it only runs on Mac and I (still) have a Linux laptop.

Now, before I decide, I’ll try out Zotero.  I will be able to use it both at work and at home (or when travelling). For Papers I’d have to buy a Mac laptop of some kind (but then, I am planning to do that anyway so it is not a major problem).

Zotero also has a nice feature (currently in beta) for synchronising literature lists. Sounds like just the thing I need.

There is plugins for Word and OpenOffice (but of course not the Word 2008 I have on my Mac), to manage references in documents. While I really prefer BibTeX, I guess this is a nice substitute when not working in LaTeX.

I don’t think Zotero exports to BibTeX, though, and that is a bit of a downer… but it is open source, so that could be fixed. There seem to be a plugin for BibTeX here, but it is marked as “invalid” whatever that means.

Anyway, I will try it out for a while, and who knows, it might be my choice instead of Papers.

If it isn’t sued out of existence, of course…

Industry watching: Tripos acquires Pharsight [business|bytes|genes|molecules]

Posted: 28 Sep 2008 12:38 AM CDT

One piece of news that caught me by surprise was Tripos’ acquisition of Pharsight.

Most of us know Tripos as a cheminformatics/molecular modeling focused company which has been through some tough times. Pharsight is best known for developing software for clinical development, primarily software for PK/PD modeling and trial simulation. My first reaction was a little along the lines of WTF!, but taking a deeper look, it’s not that huge a leap.

In general, a lot of companies have realized that there is not much money to be made selling commercial software into life science basic research. At least not in the modeling and informatics space. Good open source software, low barriers to entry and the resulting fragmentation have resulting in significant pressure on prices and low sales volumes. However, the value that companies put on software that is more downstream in nature is significantly higher. With translational approaches getting more popular and more informatics tools being applied in pre-clinical and clinical research and development companies historically selling into the research market are increasingly looking at other markets.

Some are getting into business intelligence, while others are refocusing their efforts. This move by Tripos seems to be in that general direction, combining their research oriented tools with the clinically focused tools for . With Tripos’ strong background in chemistry, it actually makes some sense. Definitely looks like the folks at Vector Capital have done their homework and given Pharsight’s stock price, they didn’t have to pay too much either

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$ 700 billion will buy a lot of taq, LB, submarines, and other things [The Tree of Life]

Posted: 27 Sep 2008 11:58 PM CDT

I know, my research tends to be expensive as I work on deep sea organisms and do genomics and such. But for $700 billion, a lot could get done in my work areas. Here are some things one could get for that amount of money that directly relate to my work (this was inspired by a conversation with Drew Endy Friday)
  • 1,400,000 Roche 454 Sequencing Machines (for $500,000 each). If you had money for reagents, that would get you a lot of sequencing.
  • 70 million bacterial genomes (at $10,000 each for the shotgun sequencing)
  • 280,000 liters (yes that is right, liters) of Taq polymerase (at 100$/40 ul)
  • 29.16 billion liters of sterilized LB broth (from Sigma at 12$/500 ml). That is one big vat of LB. It is also about 11,666 olympic swimmings pools worth of LB.
  • 7 billion copies of my Evolution textbook
  • 7 million people years of computational biologists to analyze data (at $100,000 per person year)
  • 538 million open access fees for publishing in PLoS One (at $1300 each)
  • 116.67 years of the National Science Foundation's Budget (at current costs of $6 billion per year)
  • A fleet of 32,407 Alvin submarine replacements (at 21.6 million a pop). Think of all of the deep sea work that could be done
  • Registration fees for 350 million people to go to the AGBT meeting in Marco Island
  • 28 million special guest appearances by Craig Venter (assuming he charges a 25,000 speaking fee, which is probably a bit high)
So it goes. I was always thinking of writing this type of blog about the money spent on the Iraq War. But this "bailout" $$$ got me thinking again.

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