Tag: open access

Marketplace piece on open access

Marketplace on NPR had a mini story on Open Access publishing. See Marketplace: Publicly funded research for a price. Hat tip to Aaron Gussman and Keith Bradnam for pointing this out. I did not listen to the piece but the text is online here. Here are some bits (does not seem to be a particularly well researched piece but it is still something)

KAI RYSSDAL: A lot of the scientific research that goes on in this country is really expensive. And, as it happens, a lot of it is publicly funded. But when taxpayers want to read a particular study that has been paid for with their money, they have to pay again to read about it in, say, The New England Journal of Medicine.
…

JANET BABIN: People who grew up with the Internet expect information to be free. That’s what 21-year-old Josh Sommer thought. In 2006 he was a typical college freshman. Studying environmental engineering, hanging out, making new friends. Suddenly, he started to get severe headaches. He had a series of routine tests.

JOSH SOMMER: End up having an MRI and being told that I have a mass right in the very center of my head, entwined with critical arteries, in one of the most difficult locations to operate on. The cancer Josh has is called Chordoma. It’s a rare disease with a low survival rate. Even doctors don’t know much about it. So Josh threw himself into Chordoma research. He Googled the disease to find out all he could about it, but kept hitting roadblocks.

SOMMER: I’d find an abstract, and I’d click on it. And oh, you have to pay $60 to read this article. Oh, you have to pay $40 to read this article. I mean, I have this disease, I want to know about it. Journal subscriptions — like the Journal of the American Medical Association — can cost thousands of dollars each year. With universities and libraries trimming budgets, they can’t afford all of them either. What Josh needed was free access to the research online. Last year, the National Institutes of Health unlocked the gates on a lot of research. Through its Web portal called PubMed Central, you can now search research papers for any disease scientists are studying with public funds. It’s an estimated 80,000 articles a year. Duke University law professor James Boyle says open access is only fair.

JAMES BOYLE: Why would you possibly say that when the taxpayers funded something, then the public can’t get to read it afterwards without paying again?

…
Then they quote Martin Frank from the American Physiological Society. saying something defending restricted access. They also quote rebuttal from Professor Boyle, at Duke:

BOYLE: The Web works great for porn or for shoes, or for flirting on social networks. But it doesn’t work really well for science. We haven’t done for science what we did on the rest of the Web, which is basically to have this open Web with everything linked together.

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Congrats to Phil Bourne who beat out me and some others to win the Ben Franklin Award.

Congrats to Phil Bourne for winning the “Ben Franklin Award.” (Bio-IT World) I was honored to be one of the nominees, but if I had had a vote, I would have voted for him. He has been relentless as an Open Access advocate as well as as a bioinformatician.

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Conyers, Eisen, the Huffington Post and Open Access

In case you are not aware, my brother (Michael Eisen) and Larry Lessig have been engaging in a public “debate” with John Conyers over Conyers’ sponsorship of a bill to revoke the NIH policy on Open Access to publications. First the elder Eisen and Lessig wrote a posting:Is John Conyers Shilling for Special Interests? which they then followed up with John Conyers, It’s Time to Speak Up. Now Conyers has written a reply: A Reply to Larry Lessig (which I note should have been titled A Reply to Eisen and Lessig, but that is for another day). Anyway it is worth reading them all and if I had not been sick for the last like 3-4 weeks I would write more but I have a million things to catch up on now that I have mostly gotten rid of nasty microbe #3.

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Finally, PDFs of my papers from my home page starting to show up in Google Scholar.

Well, it has finally happened.  And not sure how.  But PDFs of all my papers, which I have posted on my MAC.COM (or now known as ME.COM) homepage are finally showing  up on Google Scholar.  If you go to Google Scholar and type Eisen JA into the window and then look for PDFs for each of the papers some of the files on my .MAC site show up.

When I originally discovered a few months ago that none of my PDFs from this site where showing up on Google Scholar I dug around and discovered in Google’s Faqs that it helps to have links to the PDFs of papers.  This seemed strange since I had links from my blog and that is run by Google now so it was weird that those did not help.  But I added some more links here and there and presto, now the links to the PDFs are showing up inside Google Scholar results.
Mind you, not all of the PDFs have shown up yet and I have no clue why some did and some did not, but this is part of my continuing effort to free up my past publications.  Good start.  Not done yet, but getting there.
——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Open Access Notes: Harold Varmus on the Daily Show tonight (3/2/09)

Just a quick note here.  For anyone interested in Open Access and science policy in general, Harold Varmus, Nobel Laureate and CoFounder of PLoS, will be on the Daily Show tonight to promote his new book The Art and Politics of Science.  Now when are they going to have my brother on the show?  He was a CoFounder of PLoS.  So what if he does not have a Nobel and never ran NIH.  He has won some cool awards here and there, is an HHMI Investigator, and more importantly, he has a blog and Varmus does not.  Doesn’t that count for something?  

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Boston University adopts Open Access policy

Just saw a nice story about BU adopting an Open Access policy.

See the BU Today article

Some detail with some nice quotes in support of OA:

Boston University took a giant step towards greater access to academic scholarship and research on February 11, when the University Council voted to support an open access system that would make scholarly work of the faculty and staff available online to anyone, for free, as long as the authors are credited and the scholarship is not used for profit.
…
“Open access will really highlight the tremendous productivity of our faculty,” says Millen. “Among the more important things needed to make it work is a collaboration between the libraries and our faculty to get their research onto the Web. It’s not an inconsequential task.”

….
“This vote sends a very strong message of support for open and free exchange of scholarly work,” says Hudson. “Open access means that the results of research and scholarship can be made open and freely accessible to anyone. It really has increased the potential to showcase the research and scholarship of the University in ways that have
not been evident to people.”

Hat tip to Tom Tullius …

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Please – bash my latest paper – for the benefit of humanity

My lab has a new paper that just came out on the sequencing and analysis of the genome of a pretty cool (or hot actually) bacterium, Thermomicrobium roseum, which was isolated from a Toadstool Spring, an alkaline siliceous hotspring in Yellowstone National Park. This paper is from a grant we had when I was at TIGR as part of the “Assembling the Tree of Life” program at NSF. Our grant was focused on generating genome sequences from phyla of bacteria for which no genomes were available.

At the time this species was a representative of a phylum that had no genomes. After we started sequencing, the phylum was dissolved, but never mind that for now. We report what I think are some very interesting things in the paper. Among them:
  • We report the first example of a plasmid that encodes all the genes needed for chemotaxis including all the genes for making a flagellum. Given that they are on a plasmid this suggests that motility could be easily transfered between species.
  • We report experimental work and genome analysis that helps understand the novel membrane and cell wall structure in this species.
  • This is the first thermophile known to oxidize carbon monoxide
But I am not writing per se about the things I like about our paper. I am instead asking people out there to find things wrong with our paper. Why am I doing this? Because this paper is part of a broader experiment in publishing in that it is in PLoS One. And one of the main benefits of PLoS One is the features that allows commenting on publications. I personally believe such features are part of the future of scientific publication. But it is currently unclear just how effectively such commenting features are used (note Euan Addie is doing a survey about comments on PLoS One papers here).

So I am offering up my paper as a case study. If you comment and ask questions or make critiques, I will try to respond. And if you think something in our paper is wrong or weird, please say so. If you think something in our paper is supported by other work we do not cite, please say this too. If you have anything useful to say, please make comments.

How do you do this?

  • Go to the paper at the PLoS One Web Site.
  • In the upper right click on “Login” if you have an account or “Create account” if you do not.
  • Return to the paper once you are logged in
  • Find some part of the text you want to comment on
  • Highlight that text and click over on the right “Add a note” or “Make a comment”
  • Fire away.
——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Harold Varmus on Science Friday

There was a very interesting interview on Science Friday last week.  The discussion was with Harold Varmus (see Science Friday Archives: Harold Varmus).
In the interview, Varmus discussed his new book, his role as an advisor to Obama, and some issues relating to Open Access.  I found his comments to be very interesting and insightful and it is worth listening to.  
——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Benefits of Open Access: enabling musical interpretations of human genomics …

Not this is one of the most creative uses of open access science publications I have seen in a while. The video is from a paper by Dan Falush and colleagues that was in PLoS Genetics. Listen/see how the music changes with the genetics/migration of humans.

So I guess given some of my recent posts, we must ask what should we call this? Musicomics (which has a following but most of the use of the term seems to refer to music and comics together, although I did find one site with a reference that is about genomics) or genomusic (most of which seems to refer to people named Geno making music). Maybe, maybe, we just should say it is “nameless” but nice.

Anyway — a nice use of open access — the material from the PLoS Genetics paper is under a broad Creative Commons license and thus this type of use is allowed (and the source is attributed in the YouTube notes). Not sure about the exact details of the origins of the music for the video, but Dan Falush has hinted to me that it was some spontaneous contribution by a band in LA.

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Genome Technology Runs the Table on Open Access …

Wow.  Again, wow.  Genome Technology Magazine has dedicated in essence an entire issue to Open Access and they have a whole series on interesting things to say about it.  In addition they are making the issue available under a Creative Commons License so everyone can check it out.  Among the articles are:

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–