Video Round-up: Esther Dyson on Charlie Rose, Spencer Wells on Colbert, and important video I can’t show you on genetic discrimination

Esther Dyson was interviewed on the Charlie Rose Show this past week. Charlie Rose ends the show by saying to Esther, “I can’t wait to see your genome”. I think this is the first time I’ve ever witnessed this expression being used like this — said with such endearment too! — but I’m sure it won’t be the last. (A google search for this phrase shows zero results at the time this post was written.)

The first twenty minutes of the show are mostly about Esther’s involvement in the Personal Genome Project (PGP) [disclosure: I work for the PGP]. The discussion doesn’t stop at genomes or health; the rest of the show ventures into the future of commercial space travel, the internet, cookie monsters, personalized search, AI and more. Esther never ceases to inform and inspire me, and challenge the way I think. I’m so glad she is among the folks that will be pioneering personal genomics for the rest of us via the PGP. Check it out:

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Can a personal genome sequence get a creative commons license?

The short answer is no. There is a long essay waiting to be written here. But for now, I can say that the reason it will not work is because there is no clear legal foundation to build a license on top of when it comes to sequence data. Creative Commons licenses have copyright to build on. Material Transfer Agreements (MTAs) have good old fashioned property law to build on (turns out important things still exist outside of the bitsphere). A personal genome sequence is, well, just bits. (Update: Or lifebits? I love the term)

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Richter Scale and Your Genomic Portfolio

The field of personal genomics needs a richter scale. This scale would provide a mechanism for giving each new genomic association a score, maybe from 1-10, based on some criteria such as penentrance, actionability, and validity. Existing genetic tests should be scored as well. Commercially available tests might have additional criteria, like whether there is an FDA-approved test or whether the test is reimbursed.

The higher the score the “better” the association or test. A low score might indicate that the association is very likely just “noise” regardless of the fact that it was all over your morning newspaper.

This scale will be very handy once you have a copy of your own genome. Let’s be honest, if you’re sipping on your morning cup of coffee, reading the paper, and see an article about a newly discovered “gene for alzheimer’s” or “snp for sudden stroke”…you’re going to be compelled to run over to your computer to see if your genome possesses that genetic variant. Without a good way to quickly judge the relevance of the news article, journalistic sensationalism may have you running over to your computer several times a day. That doesn’t sound like a very good use of time, does it?

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Access to Digital Research Literature

If you’re truly an information maven, you’ve probably assembled a toolbox of tactics to get access to journal articles containing the info you want to consume (without paying the often outrageous per article fees).  Kevin Kelley over at Cool Tools offers a description of another tool to add to your arsenal: the digital library card.

In most states, you can get a library card from a public library
outside of your county of residence — as long as you can prove state
residence (true for the San Francisco Public Library). Often you will
have to go the actual state library in person to pick up your card, but
once in hand, you can access the library from the web. Fanatical
researchers are known to have a wallet full of library cards from
numerous public library systems within their respective states. Some
states, Ohio and Michigan being two of the better known, have statewide
consortiums of private, corporate and public libraries, which allows
you access to the combined services and databases licensing power of
them all.

If your local library system does not provide free online access to
digital content databases, the cheapest way to get into these expensive
databases is to pay for a library card from the New York Public Library.

If you’ve never heard of Cool Tools, you should consider subscribing to the weekly digest — its a great and fun resource.

Getting access to scientific and medical literature can be a real pain
in the neck.  Luckily there are organizations like PLOS and folks like Peter
Suber over at Open Access News working to change this state of

Free Medical Books

Hey free medical books! The URL presupposes that these books are for doctors, but…

Hat tip

PLOS Genetics: Volume 1, Issue 1

The library of open-access PLoS journals is growing.  The inaugural issue of PLoS Genetics is now online

For more on Open Access, see Peter Suber’s extensive blog.  Another good open access resource is the Open Access Webliography

Genes VIII and Open Access

Benjamin Lewin’s newest addition of Genes VIII, a widely used textbook on molecular genetics, has adopted a policy of only citing articles that are reasonably easy for readers to access.  Here is the policy statement from Lewin’s book:

A word is in order about the choice of references. With widespread adoption of policies that allow free access to material after a reasonable delay, the advantages to the scientific community for transparency in access have been made abundantly clear. In these circumstances, I do not regard publications in journals that neither adopt this policy nor are widely available (often because they are unreasonably expensive) as legitimate contributions to the scientific literature. I see no point in citing publications to which many readers will not have access.

Even though this policy clearly targets readers who are university students or other scientists, it also benefits members of the lay public that research matters of their own health.  Please see the post at Peter Suber’s Open Access News blog for more information.

Warning: No Lifeguard on Duty

Publisher as lifeguard?  Informational poverty is good for health?  I’m not sure this is a winning argument:

But the most surprising comment came when publishers were asked how they intended to enfranchise those currently unable to access scientific research…[John] Jarvis [managing director of Wiley Europe] startled the audience by replying that it was dangerous to make medical information widely available to the public.  "This rather enticing statement that everybody should be able to see everything could lead to chaos," he said dramatically. "There is a lot of information in the world which most of us need help with [and] you could get yourself in a terrible mess if you go and read this kind of information."

Richard Poynder, The Inevitable and the Optimal, Information Today, April 1, 2004.

(Thanks to Open Access News for the pointer)

Microarrays at PLOS Biology Journal

In recognition of the inaugural issue of PLOS Biology, an open-access journal:

Greg Gibson, Microarray Analysis: Genome-scale hypothesis scanning. PLOS Biology 1(1). (FREE to read!)

Here is a nifty flash animation explaining how microarray’s work.

For daily updates on open access, please see Peter Suber’s extensive blog: Open Access News.